<title>Background</title> <p><italic>Phenylobacterium zucineum </italic>strain HLK1<sup>T </sup>is a facultative intracellular microbe recently identified by us [##REF##16908113##1##]. It is a rod-shaped Gram-negative bacterium 0.3–0.5 × 0.5–2 μm in size. It belongs to the genus <italic>Phenylobacterium </italic>[##UREF##0##2##], which presently comprises 5 species, <italic>P. lituiforme </italic>(FaiI3T) [##REF##15545448##3##], <italic>P. falsum </italic>(AC49T) [##REF##15997701##4##], <italic>P. immobile </italic>(ET) [##UREF##0##2##], <italic>P. koreense </italic>(Slu-01T) [##REF##16166702##5##], and <italic>P. zucineum </italic>(HLK1<sup>T</sup>) [##REF##16908113##1##]. They were isolated from subsurface aquifer, alkaline groundwater, soil, activated sludge from a wastewater treatment plant, and the human leukemia cell line K562, respectively. Except for <italic>P. zucineum</italic>, they are environmental bacteria, and there is no evidence that these microbes are associated with eukaryotic cells. The HLK1<sup>T </sup>strain, therefore, represents the only species so far in the genus <italic>Phenylobacterium </italic>that can infect and survive in human cells. Since most, if not all, of the known microbes that can invade human cells are pathogenic, we proposed that HLK1<sup>T </sup>may have pathogenic relevance to humans [##REF##16908113##1##]. Unlike the known intracellular pathogens that undergo a cycle involving invasion, overgrowth, and disruption of the host cells, and repeating the cycle by invading new cells, HLK1<sup>T </sup>is able to establish a stable parasitic association with its host, i.e., the strain does not overgrow intracellularly to kill the host, and the host cells carry them to their progeny. One cell line (SW480) infected with <italic>P. zucineum </italic>has been stably maintained for nearly three years in our lab (data not shown).</p> <p>In this report, we present the complete genome sequence of <italic>P. zucineum</italic>.</p>
<title>Methods</title> <title>Bacterial growth and genomic library construction</title> <p><italic>P. zucineum </italic>strain HLK1<sup>T</sup>was grown in LB (Luria-Bertani) broth at 37°C and then harvested for the preparation of genomic DNA[##REF##16908113##1##]. Genomic DNA was prepared using a bacterial genomic DNA purification kit (V-Gene Biotech., Hangzhou, China) according to the manufacturer's instructions. Sheared DNA samples were fractionated to construct three different genomic libraries, containing average insert sizes of 2.0–2.5 kb, 2.5–3.0 kb and 3.5–4.0 kb. The resulting pUC18-derived library plasmids were extracted using the alkaline lysis method and subjected to direct DNA sequencing with automated capillary DNA sequencers (ABI3730 or MegaBACE1000).</p> <title>Sequencing and finishing</title> <p>The genome of <italic>P. zucineum </italic>was sequenced by means of the whole genome shotgun method with the phred/phrap/consed software packages [##REF##9521922##24##, ####REF##9521921##25##, ##REF##9521923##26##, ##REF##7542800##27####7542800##27##]. Sequencing and subsequent gene identification was carried out as described in our earlier publications [##REF##11935017##28##, ####REF##17375201##29##, ##REF##11997336##30####11997336##30##]. Briefly, during the shotgun sequence phase, clones were picked randomly from three shotgun libraries and then sequenced from both ends. 44,667 successful sequence reads (&gt;100 bp at Phred value Q13), accounting for 5.47× sequence coverage of the genome, were assembled into 563 sequence contigs representing 60 scaffolds connected by end-pairing information.</p> <p>The finishing phase involved iterative cycles of laboratory work and computational analysis. To reduce the numbers of scaffolds, reads were added into initial contig assembly by using failed universal primers as primers and by using plasmid clones that extended outwards from the scaffolds as sequence reaction templates. To resolve the low-quality regions, resequencing of the involved reads in low quality regions with universal primers and primer walking the plasmid clones were the first choice, otherwise, resequencing with alternate temperature conditions resolved the remaining low-quality regions. New sequence reads obtained from the above laboratory work were assembled into existing contigs, which yielded new contigs and new scaffolds connected by end-pairing information. Then, consed interface helped us to do nest round of laboratory work based on new arisen contig assembly. After about four iterative cycles of the above "finish" procedures to close gaps and to resolve the low-quality regions, the PCR product obtained by using total genomic DNA as template was sequenced from both ends to close the last physical gap. In addition, the overall sequence quality of the genome was further improved by using the following criteria: (1) two independent high-quality reads as minimal coverage, and (2) Phred quality value = Q40 for each given base. Collectively, 3,542 successful reads were incorporated into initial assembles during the finishing phase. The final assembly was composed of two circular "contigs", of which a smaller one with a protein cluster (including <italic>repA</italic>, <italic>repB</italic>, <italic>parA </italic>and <italic>parB</italic>) related to plasmid replication was assigned as the plasmid, and the larger one was the chromosome.</p> <title>Annotation</title> <p>tRNA genes were predicted with tRNAscan-SE [##REF##9023104##31##]. Repetitive sequences were detected by REPuter [##REF##11713313##32##,##REF##10366664##33##], coupled with intensive manual alignment. We identified and annotated the protein profiles of chromosome and plasmid with the same workstream. For the chromosome, the first set of potential CDSs in the chromosome was established with Glimmer 2.0 trained with a set of ORFs longer than 500 bp from its genomic sequence at default settings [##REF##10556321##34##]. The resulting 5,029 predicted CDSs were BLAST searched against the NCBI non-redundant protein database to determine their homology [##REF##9254694##35##]. 1,174 annotated proteins without the word "hypothetical" or "unknown" in their function description, and without frameshifts or in-frame stop codons, were selected as the second training set. The resulting second set of 4,018 predicted CDSs (assigned as "predicted CDSs") were searched against the NCBI non-redundant protein database. Predicted CDSs that accorded with the following BLAST search criteria were considered "true proteins": (1) 80% of the query sequence was aligned and (2) E-value ≤ 1e<sup>-10</sup>. Then, the ORFs extracted from the chromosome region among "true proteins" were searched against the NCBI non-redundant protein database. The ORFs satisfying the same criteria as true proteins were considered "true ORFs". Overlapping proteins were manually inspected and resolved, according to the principle we described previously [##REF##11997336##30##]. The final version of the protein profile comprised three parts: true proteins, true ORFs, and predicted CDSs located in the rest of the genome. The translational start codon of each protein was identified by the widely used RBS script [##REF##11751220##36##] and then refined by comparison with homologous proteins [##REF##11997336##30##].</p> <p>To further investigate the function of each protein, we used InterProScan to search against the InterPro protein family database [##REF##12520011##37##]. The up-to-date KEGG pathway database was used for pathway analysis [##REF##16381885##38##]. All proteins were searched against the COG database which included 66 completed genomes [##REF##9381173##39##,##REF##12969510##40##]. The final annotation was manually inspected by comprehensively integrating the results from searching against the databases of nr, COG, KEGG, and InterPro.</p> <title>Phylogenetic tree construction</title> <p>16S rRNA genes were retrieved from 63 alphaproteobacteria, <italic>P. zucineum </italic>and <italic>Escherichia coli </italic>O157:H7 EDL933. A neighbor-joining tree with bootstrapping was built using MEGA [##REF##17488738##41##]. The gammaproteobacterium <italic>E. coli </italic>was used as the outgroup to root the tree. To illustrate the evolutionary history of heat shock related proteins (RpoH, DnaK and GrpE), neighbor-joining trees based on the 16S rRNA genes and the above three proteins of 5 representative alphaproteobacteria (<italic>Sinorhizobium meliloti </italic>1021, <italic>Brucella suis </italic>1330, <italic>C. crescentus </italic>CB15, <italic>Rickettsia conorii </italic>str. Malish 7, <italic>Gluconobacter oxydans </italic>621H), <italic>P. zucineum </italic>and <italic>E. coli </italic>O157:H7 EDL933 were constructed.</p> <title>Comparative genomics</title> <p>Sequence data for comparative analyses were obtained from the NCBI database <ext-link ext-link-type="ftp" xlink:href="ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria/"/>. The database has 520 completely sequenced bacterial genomes (sequences downloaded on 2007/06/05). All <italic>P. zucineum </italic>ORFs were searched against the ORFs from all other bacterial genomes with BLASTP. The number of <italic>P. zucineum </italic>ORFs matched to each genome with significance (E value = 1e<sup>-10</sup>) was calculated.</p> <p>To illustrate the contribution of transcriptional regulators and two-component signal transduction proteins to environmental adaptation, we compared the mean fraction of these two types of proteins in bacteria living in 6 different habitats, as described by Merav Parter [##REF##17888177##42##]. These are: (1) obligate bacteria that are necessarily associated with a host, (2) specialized bacteria that live in specific environments, such as marine thermal vents, (3) aquatic bacteria that live in fresh or seawater, (4) facultative bacteria, free-living bacteria that are often associated with a host, (5) multiple bacteria that live in many different environments, and (6) terrestrial bacteria that live in the soil. For bacteria with more than one sequenced strain, we chose only one strain for the comparative study. The numbers of bacterial species in each group were: 26 obligate, 5 specialized, 4 aquatic, 28 facultative, 27 multiple, and 3 terrestrial. We annotated the proteins of these 93 species with the same workflow used for <italic>P. zucineum </italic>and calculated the mean fraction of transcriptional regulators and two-component signal transduction proteins.</p> <p>In addition, we annotated the ORFs of 5 representative alphaproteobacteria with different habitats (multiple bacteria <italic>S. meliloti </italic>1021 and <italic>G. oxydan</italic>s 621H, facultative bacterium <italic>B. suis </italic>1330, aquatic bacterium <italic>C. crescentus </italic>CB15, and obligate bacterium <italic>R. conorii </italic>str. Malish 7) using the same workflow and computed the distributions of proteins involved in environmental adaptation.</p> <title>Ortholog identification</title> <p>All proteins encoded by one genome were BLASTP searched against a database of proteins encoded by another genome [##REF##9254694##35##], and <italic>vice versa</italic>. The threshold used in these comparisons was 1e<sup>-10</sup>. Orthology was identified if two proteins were each other's best BLASTP hit (best reciprocal match).</p> <title>Data accessibility</title> <p>The sequences reported in this paper have been deposited in the GenBank database. The accession numbers for chromosome and plasmid are <ext-link ext-link-type="gen" xlink:href="CP000747">CP000747</ext-link> and <ext-link ext-link-type="gen" xlink:href="CP000748">CP000748</ext-link>, respectively.</p>
<title>Results</title> <title>Genome anatomy</title> <p>The genome is composed of a circular chromosome (3,996,255 bp) and a circular plasmid (382,976 bp) (Figure ##FIG##0##1##; Table ##TAB##0##1##). The G + C contents of chromosome and plasmid are 71.35% and 68.5%, respectively. There are 3,861 putative protein-coding genes (3,534 in the chromosome and 327 in the plasmid), of which 3,180 have significant matches in the non-redundant protein database. Of the matches, 585 are conserved hypothetical proteins and 2,595 are proteins with known or predicted functions. Forty-two tRNA genes and one 16S-23S-5S rRNA operon were identified in the chromosome.</p> <p>There are 7 families of protein-coding repetitive sequences and a family of noncoding repeats in the genome (Table ##TAB##1##2##). Notably, identical copies of repeats 02–04 were found in both the chromosome and the plasmid, suggesting their potential involvement in homologous recombination.</p> <p>On the basis of COG (Cluster of Orthologous Groups) classification, the chromosome is enriched in genes for basic metabolism, such as categories E (amino acid transport and metabolism) and I (lipid transport and metabolism), accounting for 8.29% and 6.09% of the total genes in the chromosome, respectively. On the other hand, the plasmid is enriched for genes in categories O (posttranslational modification, protein turnover, chaperones) and T (signal transduction mechanisms), constituting 12.96% and 9.72% of the total genes in the plasmid, respectively.</p> <p>As to genes in the plasmid that cope with environmental stimuli, about half of the genes in category O are molecular chaperones (17/32), including 2 <italic>dnaJ</italic>-like molecular chaperones, 2 clusters of <italic>dnaK </italic>and its co-chaperonin <italic>grpE </italic>(PHZ_p0053-0054 and PHZ_p0121-122), a cluster of <italic>groEL </italic>and its co-chaperonin <italic>groES </italic>(PHZ_p0095-0096), and 9 heat shock proteins Hsp20. Of 23 genes in category T, there is one cluster (FixLJ, PHZ_p0187-0188), which is essential for the growth of <italic>C. crescentus </italic>under hypoxic conditions [##REF##15911751##6##].</p> <title>General metabolism</title> <p>The enzyme sets of glycolysis and the Entner-Doudoroff pathway are complete in the genome. All genes comprising the pentose phosphate pathway except gluconate kinase were identified, consistent with our previous experimental result that the strain cannot utilize gluconate [##REF##16908113##1##]. The genome lacks two enzymes (<italic>kdh</italic>, alpha ketoglutarate dehydrogenase and <italic>kgd</italic>, alpha ketoglutarate decarboxylase), making the oxidative and reductive branches of the tricarboxylic acid cycle operate separately. The genome has all the genes for the synthesis of fatty acids, 20 amino acids, and corresponding tRNAs. Although full sets of genes for the biosynthesis of purine and pyrimidine were identified, enzymes for the salvage pathways of purine (<italic>apt</italic>, adenine phosphoribosyltransferase; <italic>ade</italic>, adenine deaminase) and pyrimidine (<italic>cdd</italic>, cytidine deaminase; <italic>codA</italic>, cytosine deaminase; <italic>tdk</italic>, thymidine kinase; <italic>deoA</italic>, thymidine phosphorylase; <italic>upp</italic>, uracil phosphoribosyltransferase; <italic>udk</italic>, uridine kinase; and <italic>udp</italic>, uridine phosphorylase) were absent. The plasmid encodes some metabolic enzymes, such as those participating in glycolysis, the pentose phosphate pathway, and the citric acid cycle. However, it is worth noting that the plasmid has a gene (6-phosphogluconate dehydrogenase) that is the only copy in the genome (PHZ_p0183).</p> <p>Like most other species in the genus <italic>Phenylobacterium</italic>, the strain is able to use L-phenylalanine as a sole carbon source under aerobic conditions [##REF##16908113##1##]. A recent study revealed that phenylalanine can be completely degraded through the homogentisate pathway in <italic>Pseudomonas putida </italic>U [##REF##15262943##7##]. <italic>P. zucineum </italic>may use the same strategy to utilize phenylalanine, because all the enzymes for the conversion of phenylalanine through intermediate homogentisate to the final products fumarate and acetoacetate are present in the chromosome (Table ##TAB##2##3##).</p> <title>Functional elements responding to environmental transition</title> <p>HLK1<sup>T </sup>is able to survive intracellularly and extracellularly. Consistently, the genome contains the fundamental elements to support the life cycle in different environments. The genome contains abundant two-component signal transduction proteins, transcriptional regulators, and heat shock response proteins, enabling the strain to respond to extra- and intra-cellular stimuli at transcriptional and post-translational levels. Among the total of 102 two-component signal transduction proteins (91 in the chromosome and 11 in the plasmid), there are 36 histidine kinases, 48 response regulators, and 18 hybrid proteins fused with histidine kinase and response regulator. Sixteen pairs of histidine kinase and response regulator (1 in the plasmid) are adjacently aligned and may act as functional operons. These tightly linked modules make two-component signal transduction systems respond to environmental changes efficiently. The genome encodes 170 transcriptional regulators (16 in the plasmid) (Table ##TAB##3##4##). Notably, we annotated the proteins of 93 bacteria (see methods – comparative genomics) with the same annotation criteria used for <italic>P. zucineum </italic>and found that the fraction of two-component signal transduction proteins and transcriptional regulators was positively correlated with the capacity for environmental adaptation (Figure ##FIG##1##2##). The genome contains 17 extracytoplasmic function (ECF) sigma factors (3 in the plasmid) (Table ##TAB##4##5##). ECFs are suggested to play a role in environmental adaptation for <italic>Pseudomonas putida </italic>KT2440, whose genome contains 19 ECFs [##REF##12534467##8##]. <italic>P. zucineum </italic>has 3 heat shock sigma factors <italic>rpoH </italic>(2 in the plasmid) and 33 heat shock molecular chaperons (17 in the plasmid) (Table ##TAB##5##6##), which can cope with a variety of stresses, including cellular energy depletion, extreme concentrations of heavy metals, and various toxic substances. [##REF##9680198##9##].</p> <p>The genes for cell motility include 3 chemotaxis operons, 7 MCP (methyl-accepting chemotaxis) genes, 15 other genes related to chemotaxis (Table ##TAB##6##7##), and 43 genes for the biogenesis of the flagellum (Table ##TAB##7##8##).</p> <p>The genome contains sec-dependent, sec-independent, typical type II (Table ##TAB##8##9##) and IV secretion systems (Table ##TAB##9##10##), which are known to play important roles in adapting to diverse conditions [##REF##14572546##10##,##REF##16322447##11##].</p> <p>To better understand the roles of proteins responsible for environmental transition, we computed the distributions of those proteins in 5 representative alphaproteobacteria with typical habitats (see methods – comparative genomics). Like other multiple bacteria and facultative bacteria, which can survive in multiple niches, <italic>P. zucineum </italic>encodes a higher fraction of ECFs, transcriptional regulators and two-component signal transduction proteins than obligate bacteria (Table ##TAB##8##9##). Notably, <italic>P. zucineum </italic>has the largest number of heat shock related proteins (Table ##TAB##5##6##), in comparison to the 5 representative alphaproteobacteria and 93 bacteria (data not shown). Among the plasmid-encoded heat shock related proteins are 2 RpoH (PHZ_p0049 and PHZ_p0288) and 2 DnaK-GrpE clusters (PHZ_p0053-0054 and PHZ_p0121-0122). Further phylogenetic analysis suggested that the plasmid-encoded DnaK-GrpE clusters may have undergone a genus-specific gene duplication event (Figure ##FIG##2##3C## &amp;##FIG##2##3D##).</p> <title>Adaptation to an intracellular life cycle</title> <p>To survive intracellularly, <italic>P. zucineum </italic>must succeed in adhering to and subsequently invading the host cell [##REF##16497583##12##], defending against a hostile intracellular environment [##REF##15101970##13##, ####REF##8993856##14##, ##REF##12368447##15##, ##REF##10922044##16####10922044##16##], and capturing iron at very low concentration [##REF##11018148##17##].</p> <p>It is well known that the pilus takes part in adhering to and invading a host cell [##REF##16497583##12##]. We identified one pili biosynthesis gene (<italic>pilA</italic>) and 2 operons for pili biosynthesis (Table ##TAB##10##11##).</p> <p>The genes involved in defense against oxidative stress include superoxide dismutase (PHZ_c0927, PHZ_c1092), catalase (PHZ_c2899), peroxiredoxin (PHZ_c1548), hydroperoxide reductase (<italic>ahpF</italic>, alkyl hydroperoxide reductase, subunit f, PHZ_c2725, <italic>ahpC</italic>, alkyl hydroperoxide reductase, subunit c, PHZ_c2724), and the glutathione redox cycle system (glutathione reductase [PHZ_c1740, PHZ_c1981], glutathione synthetase [PHZ_c3479], and γ-glutamylcysteine synthetase [PHZ_c0446, PHZ_c0523]).</p> <p>Since intracellular free Fe is not sufficient to support the life of bacteria, to survive intracellularly, they must use protein-bound iron, such as heme and transferrin, via transporters and/or the siderophore system. The <italic>P. zucineum </italic>genome has one ABC type siderophore transporter system (PHZ_c1893-1895), one ABC type heme transporter system (PHZ_c0136, PHZ_c0139, PHZ_c0140), and 60 TonB-dependent receptors which may uptake the iron-siderophore complex (Table ##TAB##11##12##).</p> <title>Comparative genomics between <italic>P. zucineum </italic>and <italic>C. crescentus</italic></title> <p>Comparative genomic analysis demonstrated that <italic>P. zucineum </italic>is phylogenetically the closest to <italic>C. crescentus </italic>[##REF##11259647##18##] (Figure ##FIG##3##4##), consistent with the phylogenetic analysis based on 16S RNA gene sequences (Figure ##FIG##4##5##).</p> <p>Though the genome size and protein number of <italic>P. zucineum </italic>(4.37 Mb, 3,861 proteins) are similar to those of <italic>C. crescentus </italic>(4.01 Mb, 3,767 proteins), no large-scale synteny was found between the genomes. The largest synteny region is only about 30 kb that encodes 24 proteins. The conservation region with the largest number of proteins is the operon encoding 27 ribosomal proteins. In addition, the species share only 57.8% (2,231/3,861) of orthologous proteins. Categories J (translation, ribosomal structure and biogenesis), F (nucleotide transport and metabolism), and L (replication, recombination and repair) are the top 3 conservative COG categories between the species, sharing 88.01%, 81.67%, and 80.65% of the orthologs, respectively.</p> <title>Comparison of cell cycle genes between <italic>P. zucineum </italic>and <italic>C. crescentus</italic></title> <p>Since <italic>P. zucineum </italic>is phylogenetically closest to <italic>C. crescentus</italic>, and since the latter is a model organism for studies of the prokaryotic cell cycle [##REF##11930012##19##,##REF##15031731##20##], we compared the genes regulating the cell cycle between these species.</p> <p>The cell cycle of <italic>C. crescentus </italic>is controlled to a large extent by the master regulator CtrA, which controls the transcription of 95 genes involved in the cycle [##REF##11930012##19##,##REF##15031731##20##]. On the other hand, <italic>ctrA </italic>is regulated at the levels of transcription, phosphorylation, and proteolytic degradation by its target genes, e.g., DNA methyltransferase (CcrM) regulates the transcription of <italic>ctrA</italic>, histidine kinases (CckA, PleC, DivJ, DivL) regulate its activity, and ClpXP degrades it. These regulatory 'loops' enable CtrA to precisely control the progression of the cell cycle.</p> <p><italic>P. zucineum </italic>has most of the orthologs mentioned above (Table ##TAB##12##13##). Among the 95 CtrA-regulated genes in <italic>C. crescentus</italic>, 75 have orthologs in the <italic>P. zucineum </italic>genome (Additional file ##SUPPL##0##1##). The fraction of CtrA-regulated genes with orthologs in <italic>P. zucineum </italic>(76.9%, 73/95) is significantly greater than the mean level of the whole genome (57.8%, 2,231/3,861), indicating that the CtrA regulatory system is highly conserved. Genes participating in regulating central events of the cell cycle, such as CcrM (CC0378), Clp protease (CC1963) and 14 regulatory proteins, except for one response regulator (CC3286), are present in the <italic>P. zucineum </italic>genome. The genes without counterparts in <italic>P. zucineum </italic>are mostly for functionally unknown proteins.</p> <p>Notably, the sequence of CtrA is strikingly similar between <italic>P. zucineum </italic>and <italic>C. crescentus</italic>, with 93.07% identity of amino acid sequence and 89.88% identity of nucleotide sequence. In addition, they share identical promoters (p1 and p2) [##REF##10359766##21##] and the motif (GAnTC) recognized by DNA methyltransferase (CcrM) (Figure ##FIG##5##6##) [##REF##10464180##22##], suggesting that they probably share a similar regulatory loop of CtrA.</p> <p>Consistent with the results from <italic>in silico </italic>sequence analysis, the CtrA of <italic>P. zucineum </italic>can restore the growth of temperature-sensitive strain LC2195 (a CtrA mutant) of <italic>C. crescentus </italic>[##REF##8548829##23##] at 37°C, indicating that the CtrA of <italic>P. zucineum </italic>can functionally compliment that of <italic>C. crescentus </italic>in our experimental conditions (data not shown).</p> <p>Taken together, the comparative genomics of <italic>P. zucineum </italic>and <italic>C. crescentus </italic>suggests that the cell cycle of the former is likely to be regulated similarly to that of the latter.</p> <title>Presence of ESTs of the strain in human</title> <p>Since <italic>P. zucineum </italic>strain HLK1<sup>T </sup>can invade and persistently live in several human cell lines [##REF##16908113##1##], we were curious about whether this microbe can infect humans. By blasting against the human EST database (dbEST release 041307 with 7,974,440 human ESTs) with the whole genome sequence of <italic>P. zucineum</italic>, we found 9 matched ESTs (Table ##TAB##13##14##), of which 3 were from a library constructed from tissue adjacent to a breast cancer, and 6 were from a library constructed from a cell line of lymphatic origin. The preliminary data suggest that <italic>P. zucineum </italic>may invade humans.</p>
<title>Conclusion</title> <p>This work presents the first complete bacterial genome in the genus <italic>Phenylobacterium</italic>. Genome analysis reveals the fundamental basis for this strain to invade and persistently survive in human cells. <italic>P. zucineum </italic>is phylogenetically closest to <italic>C. crescentus </italic>based on comparative genome analysis.</p>
<p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0"/>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <title>Background</title> <p><italic>Phenylobacterium zucineum </italic>is a recently identified facultative intracellular species isolated from the human leukemia cell line K562. Unlike the known intracellular pathogens, <italic>P. zucineum </italic>maintains a stable association with its host cell without affecting the growth and morphology of the latter.</p> <title>Results</title> <p>Here, we report the whole genome sequence of the type strain HLK1<sup>T</sup>. The genome consists of a circular chromosome (3,996,255 bp) and a circular plasmid (382,976 bp). It encodes 3,861 putative proteins, 42 tRNAs, and a 16S-23S-5S rRNA operon. Comparative genomic analysis revealed that it is phylogenetically closest to <italic>Caulobacter crescentus</italic>, a model species for cell cycle research. Notably, <italic>P. zucineum </italic>has a gene that is strikingly similar, both structurally and functionally, to the cell cycle master regulator CtrA of <italic>C. crescentus</italic>, and most of the genes directly regulated by CtrA in the latter have orthologs in the former.</p> <title>Conclusion</title> <p>This work presents the first complete bacterial genome in the genus <italic>Phenylobacterium</italic>. Comparative genomic analysis indicated that the CtrA regulon is well conserved between <italic>C. crescentus </italic>and <italic>P. zucineum</italic>.</p>
<title>Abbreviations</title> <p>EST: Expressed Sequence Tag; KEGG: Kyoto Encyclopedia of Genes and Genomes.</p> <title>Authors' contributions</title> <p>XH and SH designed the project; YL, XX, ZD, ZL, ZY and JS performed the research; SH and BZ contributed new reagents\analytical tools; YL, XX, and ZD analyzed the data; and XH, YL, and SH wrote the paper. All authors read and approved the final manuscript.</p> <title>Supplementary Material</title>
<title>Acknowledgements</title> <p>This work was supported in part by the Cheung Kong Scholars Programme (National Ministry of Education, China, and the Li Ka Shing Foundation, Hong Kong) to XH, a Natural Science Foundation of China grant (30672382) to XH, and a Zhejiang Natural Science Foundation, China, grant (R204204) to XH. We thank Dr. Lucy Shapiro (Department of Developmental Biology, Stanford University) for the gifts of the <italic>C. crescentus </italic>temperature sensitive strain LC2195 and the plasmid pSAL14. We are grateful to Dr. Iain Bruce (Department of Physiology, Zhejiang University School of Medicine) for English editing.</p>
<fig position="float" id="F1"><label>Figure 1</label><caption><p><bold>Circular representation of the <italic>P. zucineum </italic>strain HLK1<sup>T </sup>chromosome and plasmid (smaller circle)</bold>. Circles indicate (from the outside): (1) Physical map scaled in megabases from base 1, the start of the putative replication origin. (2) Coding sequences transcribed in the clockwise direction are color-coded according to COG functional category. (3) Coding sequences transcribed in the counterclockwise direction are color-coded according to COG functional category. (4) Proteins involved in establishment of intracellular niche are TonB-dependent receptors (orange) and pilus genes (sienna). (5) Functional elements responsible for environmental transition are extracytoplasmic function sigma factors (royal blue), transcriptional regulators (violet red), two-component signal transduction proteins (deep sky blue), heat shock molecular chaperons (spring green), type IV secretion systems (plum), chemotaxis systems (green yellow) and flagellum proteins (gray). (6) G + C percent content (10-kb window and 1-kb incremental shift for chromosome; 300 bp window and 150 bp for incremental shift for plasmid); values larger than average (71.35% in chromosome and 68.5% in plasmid) are in red and smaller in medium blue. (7) GC skew (10-kb window and 1-kb incremental shift for chromosome; 300 bp window and 150 bp for incremental shift for plasmid); values greater than zero are in gold and smaller in purple. (8) Repeat families, repeats 01-08 are in dark salmon, dark red, wheat, tomato, light green, salmon, dark blue and gold, respectively.</p></caption></fig> <fig position="float" id="F2"><label>Figure 2</label><caption><p><bold>Comparative analysis of transcriptional regulators and two-component signal transduction proteins in 6 groups of bacteria classified according to their habitats</bold>. (A): The mean number of transcriptional regulators in each megabase pair of the genomes. (B): The mean number of two-component signal transduction proteins in each megabase pair of the genomes. The fraction of transcriptional regulators and two-component signal transduction proteins (solid black circle) of <italic>P. zucineum </italic>were 41.56 genes/Mb and 23.30 genes/Mb, respectively. Error bars represent standard errors. O: Obligate (26 species), S: Specialized (5 species), AQ: Aquatic (4 species), F: Facultative (28 species), M: Multiple (27 species), T: Terrestrial (3 species).</p></caption></fig> <fig position="float" id="F3"><label>Figure 3</label><caption><p><bold>Neighbor-joining trees of 5 representative alphaproteobacteria and <italic>P. zucineum</italic>, inferred from (A) 16S rRNA genes, (B) RpoH proteins, (C) DnaK proteins and (D) GrpE proteins</bold>. The node labels are bootstrap values (100 replicates). The plasmid-encoded DnaK and GrpE of <italic>P. zucineum </italic>may have undergone a genus-specific gene duplication event (C &amp;</p></caption></fig> <fig position="float" id="F4"><label>Figure 4</label><caption><p><bold>List of top 10 complete sequenced bacteria closest to <italic>P. zucineum</italic></bold>. All 10 are alphaproteobacteria. Among all the sequenced bacterial genomes, <italic>C. crescentus </italic>shares the greatest number of similar ORFs with <italic>P. zucineum</italic></p></caption></fig> <fig position="float" id="F5"><label>Figure 5</label><caption><p><bold>Neighbor-joining tree of the alphaproteobacteria, inferred from 16S rRNA genes</bold>. The node labels are bootstrap values (100 replicates). <italic>C. crescentus </italic>is phylogenetically the closest to <italic>P. zucineum</italic>.</p></caption></fig> <fig position="float" id="F6"><label>Figure 6</label><caption><p><bold>Nucleotide acid sequence alignment of the <italic>ctrA </italic>promoter regions (-200 to +21) of <italic>C. crescentus </italic>and <italic>P. zucineum</italic></bold>. Blue background: identical nucleotides; "-": gaps; red and black box: P1 and P2 promoter; black underline: motif recognized by CcrM; red underline: first 21 nucleotides starting with initial codon "ATG.".</p></caption></fig>
<table-wrap position="float" id="T1"><label>Table 1</label><caption><p>Genome summary of <italic>P. zucineum </italic>Strain <italic>HLK1</italic><sup>T</sup></p></caption><table frame="hsides" rules="groups"><thead><tr><td align="left">Genomic Element</td><td/><td align="center">Chromosome</td><td align="center">plasmid</td></tr></thead><tbody><tr><td align="left">Length (bp)</td><td/><td align="center">3,996,255</td><td align="center">382,976</td></tr><tr><td align="left">GC content (%)</td><td/><td align="center">71.35</td><td align="center">68.54</td></tr><tr><td align="left">Proteins</td><td/><td align="center">3, 534</td><td align="center">327</td></tr><tr><td/><td align="left">Coding region of genome (%)</td><td align="center">88.85%</td><td align="center">81.94%</td></tr><tr><td/><td align="left">Proteins with known or predicted function</td><td align="center">2,394(67.75%)</td><td align="center">201(61.47%)</td></tr><tr><td/><td align="left">Conserved hypothetical proteins</td><td align="center">560(15.84%)</td><td align="center">25(7.65%)</td></tr><tr><td/><td align="left">Hypothetical proteins</td><td align="center">580(16.41%)</td><td align="center">101(30.88%)</td></tr><tr><td align="left">rRNA operon</td><td/><td align="center">1</td><td align="center">0</td></tr><tr><td align="left">tRNAs</td><td/><td align="center">42</td><td align="center">0</td></tr><tr><td/><td/><td/><td/></tr><tr><td align="left">Proteins in each</td><td align="left">[J] Translation, ribosomal structure and biogenesis</td><td align="center">185 (5.24%)</td><td align="center">3 (1.21%)</td></tr><tr><td align="left">COG category</td><td align="left">[K] Transcription</td><td align="center">210 (5.94%)</td><td align="center">22 (8.91%)</td></tr><tr><td/><td align="left">[L] Replication, recombination and repair</td><td align="center">139 (3.93%)</td><td align="center">23 (9.31%)</td></tr><tr><td/><td align="left">[D] Cell cycle control, cell division, chromosome partitioning</td><td align="center">27 (0.76%)</td><td align="center">0</td></tr><tr><td/><td align="left">[V] Defense mechanisms</td><td align="center">51 (1.44%)</td><td align="center">3 (1.21%)</td></tr><tr><td/><td align="left">[T] Signal transduction mechanisms</td><td align="center">166 (4.7%)</td><td align="center">24 (9.72%)</td></tr><tr><td/><td align="left">[M] Cell wall/membrane/envelope biogenesis</td><td align="center">195 (5.52%)</td><td align="center">15 (6.07%)</td></tr><tr><td/><td align="left">[N] Cell motility</td><td align="center">62 (1.75%)</td><td align="center">4 (1.62%)</td></tr><tr><td/><td align="left">[U] Intracellular trafficking, secretion, and vesicular transport</td><td align="center">96 (2.72%)</td><td align="center">13 (5.26%)</td></tr><tr><td/><td align="left">[O] Posttranslational modification, protein turnover, chaperones</td><td align="center">151 (4.27%)</td><td align="center">32 (12.96%)</td></tr><tr><td/><td align="left">[C] Energy production and conversion</td><td align="center">188 (5.32%)</td><td align="center">16 (6.48%)</td></tr><tr><td/><td align="left">[G] Carbohydrate transport and metabolism</td><td align="center">161 (4.56%)</td><td align="center">15 (6.07%)</td></tr><tr><td/><td align="left">[E] Amino acid transport and metabolism</td><td align="center">293 (8.29%)</td><td align="center">5 (2.02%)</td></tr><tr><td/><td align="left">[F] Nucleotide transport and metabolism</td><td align="center">58 (1.64%)</td><td align="center">3 (1.21%)</td></tr><tr><td/><td align="left">[H] Coenzyme transport and metabolism</td><td align="center">116 (3.28%)</td><td align="center">3 (1.21%)</td></tr><tr><td/><td align="left">[I] Lipid transport and metabolism</td><td align="center">215 (6.09%)</td><td align="center">12 (4.86%)</td></tr><tr><td/><td align="left">[P] Inorganic ion transport and metabolism</td><td align="center">223 (6.31%)</td><td align="center">24 (9.72%)</td></tr><tr><td/><td align="left">[Q] Secondary metabolites biosynthesis, transport and catabolism</td><td align="center">152(4.3%)</td><td align="center">9 (3.64%)</td></tr><tr><td/><td align="left">[R] General function prediction only</td><td align="center">444 (12.57%)</td><td align="center">28 (11.34%)</td></tr><tr><td/><td align="left">[S] Function unknown</td><td align="center">307 (8.69%)</td><td align="center">20 (8.10%)</td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T2"><label>Table 2</label><caption><p>Repetitive elements in the <italic>P. zucineum </italic>genome</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="left">Repeat ID</td><td align="center">Length bp</td><td align="center">DR<sup>1</sup></td><td align="center" colspan="2">Number of copies</td><td align="center" colspan="2">Position of insertion</td><td align="left">Identity (%)</td><td align="left">Coding information</td></tr><tr><td/><td/><td/><td colspan="4"><hr/></td><td/><td/></tr><tr><td/><td/><td/><td align="center">Complete<sup>2</sup></td><td align="left">Partial</td><td align="center">Chromosome</td><td align="center">Plasmid</td><td/><td/></tr></thead><tbody><tr><td align="left">Repeat01<sup>3</sup></td><td align="center">2,587</td><td align="center">7</td><td align="center">3</td><td align="left">1</td><td align="center">0</td><td align="center">4</td><td align="left">&gt;99</td><td align="left">Transposase</td></tr><tr><td align="left">Repeat02<sup>4</sup></td><td align="center">1,262</td><td align="center">3</td><td align="center">3</td><td align="left">1</td><td align="center">2</td><td align="center">2</td><td align="left">100</td><td align="left">Transposase</td></tr><tr><td align="left">Repeat03<sup>5</sup></td><td align="center">1,392</td><td align="center">NA</td><td align="center">4</td><td align="left">2</td><td align="center">4</td><td align="center">2</td><td align="left">100</td><td align="left">Transposase</td></tr><tr><td align="left">Repeat04<sup>6</sup></td><td align="center">1,257</td><td align="center">NA</td><td align="center">10</td><td align="left">0</td><td align="center">7</td><td align="center">3</td><td align="left">100</td><td align="left">Transposase</td></tr><tr><td align="left">Repeat05</td><td align="center">1,554</td><td align="center">NA</td><td align="center">2</td><td align="left">0</td><td align="center">2</td><td align="center">0</td><td align="left">&gt;98</td><td align="left">Hypothetical protein</td></tr><tr><td align="left">Repeat06</td><td align="center">1,136</td><td align="center">NA</td><td align="center">2</td><td align="left">0</td><td align="center">2</td><td align="center">0</td><td align="left">&gt;90</td><td align="left">Isovaleryl-CoA dehydrogenase</td></tr><tr><td align="left">Repeat07</td><td align="center">1,077</td><td align="center">NA</td><td align="center">2</td><td align="left">0</td><td align="center">2</td><td align="center">0</td><td align="left">&gt;98</td><td align="left">2-nitropropane dioxygenase</td></tr><tr><td align="left">Repeat08</td><td align="center">≈130</td><td align="center">NA</td><td align="center">13</td><td align="left">0</td><td align="center">13</td><td align="center">0</td><td align="left">&gt;90</td><td align="left">Noncoding repeats</td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T3"><label>Table 3</label><caption><p>Phenylalanine-degrading enzymes in the <italic>P. zucineum </italic>genome</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="left">Gene</td><td align="left"><italic>P. zucineum </italic>Locus</td><td align="center" colspan="2">Length (bp)</td><td align="center" colspan="2">Alignment coverage (%)</td><td align="center">Score</td><td align="center">Amino acid Identity (%)</td><td align="left">Gene name</td></tr><tr><td/><td/><td colspan="4"><hr/></td><td/><td/><td/></tr><tr><td/><td/><td align="center"><italic>P. putida</italic></td><td align="center"><italic>P. zucineum</italic></td><td align="center"><italic>P. putida</italic></td><td align="center"><italic>P. zucineum</italic></td><td/><td/><td/></tr></thead><tbody><tr><td align="center"><italic>phhA</italic></td><td align="left">PHZ_c1409</td><td align="center">262</td><td align="center">308</td><td align="center">83.59</td><td align="center">71.75</td><td align="center">219</td><td align="center">48.65</td><td align="left">phenylalanine-4-hydroxylase</td></tr><tr><td align="center"><italic>phhB</italic></td><td align="left">PHZ_c0077</td><td align="center">118</td><td align="center">97</td><td align="center">79.66</td><td align="center">93.81</td><td align="center">38.5</td><td align="center">26.32</td><td align="left">carbinolamine dehydratase</td></tr><tr><td align="center"><italic>tryB</italic></td><td align="left">PHZ_c1644</td><td align="center">398</td><td align="center">406</td><td align="center">60.05</td><td align="center">57.39</td><td align="center">33.9</td><td align="center">21.86</td><td align="left">tyrosine aminotransferase</td></tr><tr><td align="center"><italic>hpd</italic></td><td align="left">PHZ_c2833</td><td align="center">358</td><td align="center">374</td><td align="center">98.32</td><td align="center">93.58</td><td align="center">398</td><td align="center">57.98</td><td align="left">4-hydroxyphenylpyruvate dioxygenase</td></tr><tr><td align="center"><italic>hmgA</italic></td><td align="left">PHZ_c2831</td><td align="center">433</td><td align="center">377</td><td align="center">60.28</td><td align="center">67.64</td><td align="center">53.5</td><td align="center">22.3</td><td align="left">homogentisate 1,2-dioxygenase</td></tr><tr><td align="center"><italic>hmgB</italic></td><td align="left">PHZ_c0313</td><td align="center">430</td><td align="center">226</td><td align="center">9.77</td><td align="center">18.14</td><td align="center">27.7</td><td align="center">39.53</td><td align="left">fumarylacetoacetate hydrolase</td></tr><tr><td align="center"><italic>hmgC</italic></td><td align="left">PHZ_c0314</td><td align="center">210</td><td align="center">212</td><td align="center">98.1</td><td align="center">98.11</td><td align="center">213</td><td align="center">51.67</td><td align="left">maleylacetoacetate isomerase</td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T4"><label>Table 4</label><caption><p>Transcriptional regulators in the <italic>P. zucineum </italic>genome</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="left">Family name</td><td align="left">Action type</td><td align="center">Chromosome</td><td align="center">Plasmid</td><td align="left">Proposed roles</td></tr></thead><tbody><tr><td align="left">AsnC family</td><td align="left">Activator/repressor</td><td align="center">8</td><td align="center">0</td><td align="left">Amino acid biosynthesis</td></tr><tr><td align="left">AraC family</td><td align="left">Activator</td><td align="center">10</td><td align="center">1</td><td align="left">Carbon metabolism, stress response and pathogenesis</td></tr><tr><td align="left">ArsR family</td><td align="left">Repressor</td><td align="center">8</td><td align="center">0</td><td align="left">Metal resistance</td></tr><tr><td align="left">BlaI family</td><td align="left">Repressor</td><td align="center">2</td><td align="center">0</td><td align="left">Penicillin resistance</td></tr><tr><td align="left">Cold shock family</td><td align="left">Activator</td><td align="center">6</td><td align="center">0</td><td align="left">Low-temperature resistance</td></tr><tr><td align="left">Cro/CI family</td><td align="left">Repressor</td><td align="center">9</td><td align="center">2</td><td align="left">Unknown<sup>2</sup></td></tr><tr><td align="left">Crp/Fnr family</td><td align="left">Activator/repressor</td><td align="center">7</td><td align="center">2</td><td align="left">Global responses, catabolite repression and anaerobiosis</td></tr><tr><td align="left">GntR family</td><td align="left">Repressor</td><td align="center">7</td><td align="center">0</td><td align="left">General metabolism</td></tr><tr><td align="left">LacI family</td><td align="left">Repressor</td><td align="center">4</td><td align="center">0</td><td align="left">Carbon source utilization</td></tr><tr><td align="left">LuxR family</td><td align="left">Activator</td><td align="center">5</td><td align="center">1</td><td align="left">Quorum sensing, biosynthesis and metabolism, etc.</td></tr><tr><td align="left">LysR family</td><td align="left">Activator/repressor</td><td align="center">15</td><td align="center">1</td><td align="left">Carbon and nitrogen metabolism</td></tr><tr><td align="left">MarR family</td><td align="left">Activator/repressor</td><td align="center">6</td><td align="center">0</td><td align="left">Multiple antibiotic resistance</td></tr><tr><td align="left">MerR family</td><td align="left">Repressor</td><td align="center">9</td><td align="center">2</td><td align="left">Resistance and detoxification</td></tr><tr><td align="left">TetR family</td><td align="left">Repressor</td><td align="center">22</td><td align="center">0</td><td align="left">Biosynthesis of antibiotics, efflux pumps, osmotic stress, etc.</td></tr><tr><td align="left">XRE family</td><td align="left">Repressor</td><td align="center">2</td><td align="center">2</td><td align="left">Unknown (initial function is lysogeny maintenance)</td></tr><tr><td align="left">Other types<sup>2</sup></td><td align="left">-</td><td align="center">34</td><td align="center">5</td><td align="left">-</td></tr><tr><td align="left">Total</td><td align="left">-</td><td align="center">154</td><td align="center">16</td><td align="left">-</td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T5"><label>Table 5</label><caption><p>Extracytoplasmic function (ECF) sigma factors in the <italic>P. zucineum </italic>genome</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="left">Locus</td><td align="center" colspan="3">Location of proteins</td><td align="center">COG category</td></tr><tr><td/><td colspan="3"><hr/></td><td/></tr><tr><td/><td align="center">Genomic element</td><td align="center">5'-end</td><td align="center">3'-end</td><td/></tr></thead><tbody><tr><td align="left">PHZ_p0151</td><td align="center">Plasmid</td><td align="center">171,032</td><td align="center">170,316</td><td align="center">COG1595<sup>1</sup></td></tr><tr><td align="left">PHZ_p0174</td><td align="center">Plasmid</td><td align="center">208,703</td><td align="center">208,053</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_p0192</td><td align="center">Plasmid</td><td align="center">229,133</td><td align="center">228,516</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c0249</td><td align="center">Chromosome</td><td align="center">249,840</td><td align="center">250,553</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c0301</td><td align="center">Chromosome</td><td align="center">296,299</td><td align="center">295,706</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c1475</td><td align="center">Chromosome</td><td align="center">1,676,920</td><td align="center">1,677,492</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c1529</td><td align="center">Chromosome</td><td align="center">1,730,783</td><td align="center">1,731,403</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c1531</td><td align="center">Chromosome</td><td align="center">1,732,219</td><td align="center">1,732,800</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c1907</td><td align="center">Chromosome</td><td align="center">2,134,971</td><td align="center">2,135,507</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c2171</td><td align="center">Chromosome</td><td align="center">2,447,581</td><td align="center">2,448,396</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c2233</td><td align="center">Chromosome</td><td align="center">2,526,836</td><td align="center">2,527,369</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c2394</td><td align="center">Chromosome</td><td align="center">2,724,759</td><td align="center">2,725,307</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c2577</td><td align="center">Chromosome</td><td align="center">2,965,250</td><td align="center">2,964,390</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c2585</td><td align="center">Chromosome</td><td align="center">2,970,368</td><td align="center">2,969,811</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c2684</td><td align="center">Chromosome</td><td align="center">3,077,272</td><td align="center">3,076,727</td><td align="center">COG1595</td></tr><tr><td align="left">PHZ_c0569</td><td align="center">Chromosome</td><td align="center">605,441</td><td align="center">604,233</td><td align="center">COG4941<sup>2</sup></td></tr><tr><td align="left">PHZ_c3154</td><td align="center">Chromosome</td><td align="center">3,582,010</td><td align="center">3,583,269</td><td align="center">COG4941</td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T6"><label>Table 6</label><caption><p>Distribution of heat shock related proteins in <italic>P. zucineum </italic>and representative alphaproteobacteria with different living habitats</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="center">Content\Species</td><td align="center"><italic>S. meliloti</italic></td><td align="center"><italic>B. suis</italic></td><td align="center"><italic>C. crescentus</italic></td><td align="center" colspan="2"><italic>P. zucineum</italic></td><td align="center"><italic>R. conorii</italic></td><td align="center"><italic>G. oxydans</italic></td></tr><tr><td/><td/><td/><td/><td colspan="2"><hr/></td><td/><td/></tr><tr><td/><td/><td/><td/><td align="center">Chromosome</td><td align="center">Plasmid</td><td/><td/></tr></thead><tbody><tr><td align="center"><italic>rpoH</italic>, heat shock sigma factor<sup>1</sup></td><td align="center">2</td><td align="center">2</td><td align="center">1</td><td align="center">1</td><td align="center">2</td><td align="center">1</td><td align="center">1</td></tr><tr><td align="center"><italic>dnaK</italic>, molecular chaperone<sup>2 </sup>(Hsp70)</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">2</td><td align="center">1</td><td align="center">1</td></tr><tr><td align="center"><italic>grpE</italic>, molecular chaperone (co-chaperonin of Hsp70)</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">2</td><td align="center">1</td><td align="center">1</td></tr><tr><td align="center">dnaK-like molecular chaperone</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">0</td><td align="center">1</td><td align="center">1</td></tr><tr><td align="center">dnaJ, molecular chaperone</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">0</td><td align="center">1</td><td align="center">1</td></tr><tr><td align="center">dnaJ-like molecular chaperone</td><td align="center">4</td><td align="center">3</td><td align="center">3</td><td align="center">6</td><td align="center">2</td><td align="center">1</td><td align="center">3</td></tr><tr><td align="center"><italic>groEL</italic>, molecular chaperone (hsp60)</td><td align="center">5</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td></tr><tr><td align="center"><italic>groES</italic>, molecular chaperone (Hsp10, co-chaperonin of Hsp60)</td><td align="center">3</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td></tr><tr><td align="center">molecular chaperone Hsp20</td><td align="center">5</td><td align="center">2</td><td align="center">2</td><td align="center">3</td><td align="center">9</td><td align="center">0</td><td align="center">3</td></tr><tr><td align="center">molecular chaperone Hsp33</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">1</td><td align="center">0</td><td align="center">0</td><td align="center">1</td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T7"><label>Table 7</label><caption><p>Chemotaxis proteins in the <italic>P. zucineum </italic>genome</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="left">Locus <italic>P. zucineum</italic></td><td align="center">5'-end</td><td align="center">3'-end</td><td align="left">Name</td><td align="center">Orthologs <italic>C. crescentus</italic></td><td align="center">Operon</td><td align="center">Best BLAST match</td></tr></thead><tbody><tr><td align="left">PHZ_c0690</td><td align="center">753,270</td><td align="center">753,812</td><td align="left">chemotaxis protein CheW</td><td align="center">-</td><td align="center">1</td><td align="center"><italic>M. magneticum AMB-1</italic></td></tr><tr><td align="left">PHZ_c0691</td><td align="center">753,812</td><td align="center">755,218</td><td align="left">chemotaxis protein methyltransferase CheR</td><td align="center">-</td><td align="center">1</td><td align="center"><italic>M. magnetotacticum MS-1</italic></td></tr><tr><td align="left">PHZ_c0692</td><td align="center">755,240</td><td align="center">755,836</td><td align="left">chemotaxis signal transduction protein</td><td align="center">-</td><td align="center">1</td><td align="center"><italic>Rhodospirillum centenum</italic></td></tr><tr><td align="left">PHZ_c0693</td><td align="center">755,836</td><td align="center">757,488</td><td align="left">methyl-accepting chemotaxis protein</td><td align="center">-</td><td align="center">1</td><td align="center"><italic>M. magneticum AMB-1</italic></td></tr><tr><td align="left">PHZ_c0694</td><td align="center">757,501</td><td align="center">759,642</td><td align="left">chemotaxis histidine kinase CheA</td><td align="center">-</td><td align="center">1</td><td align="center"><italic>M. magnetotacticum MS-1</italic></td></tr><tr><td align="left">PHZ_c0695</td><td align="center">759,642</td><td align="center">760,709</td><td align="left">chemotaxis response regulator CheB</td><td align="center">-</td><td align="center">1</td><td align="center"><italic>Rhodospirillum centenum</italic></td></tr><tr><td align="left">PHZ_c3230</td><td align="center">3,661,514</td><td align="center">3,661,050</td><td align="left">CheE protein</td><td align="center">-</td><td align="center">2</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c3231</td><td align="center">3,662,099</td><td align="center">3,661,527</td><td align="left">chemotaxis protein CheYIII</td><td align="center">CC0440</td><td align="center">2</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c3233</td><td align="center">3,662,860</td><td align="center">3,662,477</td><td align="left">chemotaxis protein CheYII</td><td align="center">CC0591</td><td align="center">2</td><td align="center"><italic>R. palustris CGA009</italic></td></tr><tr><td align="left">PHZ_c3234</td><td align="center">3,663,186</td><td align="center">3,666,188</td><td align="left">chemotaxis histidine kinase CheA</td><td align="center">CC0594</td><td align="center">2</td><td align="center"><italic>Azospirillum brasilense</italic></td></tr><tr><td align="left">PHZ_c3235</td><td align="center">3,666,188</td><td align="center">3,666,733</td><td align="left">chemotaxis protein CheW</td><td align="center">CC0595</td><td align="center">2</td><td align="center"><italic>Rhodospirillum centenum</italic></td></tr><tr><td align="left">PHZ_c3236</td><td align="center">3,666,786</td><td align="center">3,669,191</td><td align="left">methyl-accepting chemotaxis protein McpH</td><td align="center">CC3349</td><td align="center">2</td><td align="center"><italic>R. palustris CGA009</italic></td></tr><tr><td align="left">PHZ_c3237</td><td align="center">3,670,166</td><td align="center">3,669,336</td><td align="left">chemotaxis protein methyltransferase CheR</td><td align="center">CC0598</td><td align="center">2</td><td align="center"><italic>R. palustris HaA2</italic></td></tr><tr><td align="left">PHZ_c3238</td><td align="center">3,671,242</td><td align="center">3,670,166</td><td align="left">chemotaxis response regulator CheB</td><td align="center">CC0597</td><td align="center">2</td><td align="center"><italic>M. magneticum AMB-1</italic></td></tr><tr><td align="left">PHZ_c3371</td><td align="center">3,820,121</td><td align="center">3,819,669</td><td align="left">CheE protein</td><td align="center">CC0441</td><td align="center">3</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c3372</td><td align="center">3,820,729</td><td align="center">3,820,124</td><td align="left">chemotaxis protein CheYIII</td><td align="center">-</td><td align="center">3</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c3373</td><td align="center">3,821,034</td><td align="center">3,820,729</td><td align="left">CheU protein</td><td align="center">CC0439</td><td align="center">3</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c3374</td><td align="center">3,821,651</td><td align="center">3,821,082</td><td align="left">chemotaxis protein CheD</td><td align="center">CC0438</td><td align="center">3</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c3375</td><td align="center">3,822,037</td><td align="center">3,821,651</td><td align="left">chemotaxis protein CheYII</td><td align="center">CC0437</td><td align="center">3</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c3376</td><td align="center">3,823,068</td><td align="center">3,822,040</td><td align="left">chemotaxis response regulator CheB</td><td align="center">CC0436</td><td align="center">3</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c3377</td><td align="center">3,823,955</td><td align="center">3,823,068</td><td align="left">chemotaxis protein methyltransferase CheR</td><td align="center">CC0435</td><td align="center">3</td><td align="center"><italic>A. cryptum JF-5</italic></td></tr><tr><td align="left">PHZ_c3378</td><td align="center">3,824,410</td><td align="center">3,823,946</td><td align="left">chemotaxis protein CheW</td><td align="center">CC0434</td><td align="center">3</td><td align="center"><italic>Rhizobium etli CFN 42</italic></td></tr><tr><td align="left">PHZ_c3379</td><td align="center">3,826,614</td><td align="center">3,824,422</td><td align="left">chemotaxis histidine kinase CheA</td><td align="center">CC0433</td><td align="center">3</td><td align="center"><italic>A. cryptum JF-5</italic></td></tr><tr><td align="left">PHZ_c3380</td><td align="center">3,826,997</td><td align="center">3,826,635</td><td align="left">chemotaxis protein CheYI</td><td align="center">CC0432</td><td align="center">3</td><td align="center"><italic>Caulobacter vibrioides</italic></td></tr><tr><td align="left">PHZ_c3381</td><td align="center">3,827,299</td><td align="center">3,826,997</td><td align="left">CheX protein</td><td align="center">CC0431</td><td align="center">3</td><td align="center"><italic>Sinorhizobium meliloti</italic></td></tr><tr><td align="left">PHZ_c3382</td><td align="center">3,829,234</td><td align="center">3,827,306</td><td align="left">methyl-accepting chemotaxis protein McpA</td><td align="center">CC0430</td><td align="center">3</td><td align="center"><italic>A. cryptum JF-5</italic></td></tr><tr><td align="left">PHZ_c0101</td><td align="center">94,220</td><td align="center">93,750</td><td align="left">CheE protein</td><td align="center">-</td><td align="center">scatted</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c0102</td><td align="center">94,795</td><td align="center">94,220</td><td align="left">chemotaxis protein CheYIII</td><td align="center">-</td><td align="center">scatted</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c0297</td><td align="center">292,469</td><td align="center">292,864</td><td align="left">chemotaxis protein CheYIV</td><td align="center">CC3471</td><td align="center">scatted</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c0298</td><td align="center">292,867</td><td align="center">293,679</td><td align="left">chemotaxis protein methyltransferase CheR</td><td align="center">CC3472</td><td align="center">scatted</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c0732</td><td align="center">803,383</td><td align="center">804,876</td><td align="left">methyl-accepting chemotaxis protein McpB</td><td align="center">CC0428</td><td align="center">scatted</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c0961</td><td align="center">1,057,134</td><td align="center">1,058,720</td><td align="left">methyl-accepting chemotaxis protein McpI</td><td align="center">CC2847</td><td align="center">scatted</td><td align="center"><italic>R. palustris CGA009</italic></td></tr><tr><td align="left">PHZ_c1198</td><td align="center">1,380,883</td><td align="center">1,383,294</td><td align="left">methyl-accepting chemotaxis protein McpU</td><td align="center">-</td><td align="center">scatted</td><td align="center"><italic>A. cryptum JF-5</italic></td></tr><tr><td align="left">PHZ_c1199</td><td align="center">1,383,297</td><td align="center">1,383,758</td><td align="left">chemotaxis protein CheW1</td><td align="center">-</td><td align="center">scatted</td><td align="center"><italic>Sinorhizobium meliloti</italic></td></tr><tr><td align="left">PHZ_c1687</td><td align="center">1,890,274</td><td align="center">1,891,176</td><td align="left">chemotaxis MotB protein</td><td align="center">CC1573</td><td align="center">scatted</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c1936</td><td align="center">2,169,634</td><td align="center">2,169,939</td><td align="left">chemotactic signal response protein CheL</td><td align="center">CC2583</td><td align="center">scatted</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c2211</td><td align="center">2,499,744</td><td align="center">2,499,274</td><td align="left">chemotaxis protein CheYIII</td><td align="center">-</td><td align="center">scatted</td><td align="center"><italic>O. alexandrii HTCC2633</italic></td></tr><tr><td align="left">PHZ_c2392</td><td align="center">2,720,611</td><td align="center">2,720,144</td><td align="left">chemotaxis protein CheYIII</td><td align="center">-</td><td align="center">scatted</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c2741</td><td align="center">3,142,750</td><td align="center">3,143,238</td><td align="left">chemotaxis protein CheYIII</td><td align="center">CC3155</td><td align="center">scatted</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c3123</td><td align="center">3,549,150</td><td align="center">3,550,016</td><td align="left">chemotaxis MotA protein</td><td align="center">CC0750</td><td align="center">scatted</td><td align="center"><italic>C. crescentus CB15</italic></td></tr><tr><td align="left">PHZ_c3401</td><td align="center">3,848,811</td><td align="center">3,850,766</td><td align="left">methyl-accepting chemotaxis protein McpA</td><td align="center">-</td><td align="center">scatted</td><td align="center"><italic>C. vibrioides</italic></td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T8"><label>Table 8</label><caption><p>Flagella genes in the <italic>P. zucineum </italic>genome</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="left">Locus</td><td align="center">5'-end</td><td align="center">3'-end</td><td align="left">Name</td><td align="center">Gene symbol</td><td align="center">Proposed role</td></tr></thead><tbody><tr><td align="left">PHZ_c0080</td><td align="center">75,413</td><td align="center">76,462</td><td align="left">flagellin modification protein FlmA</td><td align="center"><italic>flmA</italic></td><td align="center">regulator</td></tr><tr><td align="left">PHZ_c0081</td><td align="center">76,467</td><td align="center">77,621</td><td align="left">flagellin modification protein FlmB</td><td align="center"><italic>flmB</italic></td><td align="center">regulator</td></tr><tr><td align="left">PHZ_c0745</td><td align="center">816,772</td><td align="center">818,034</td><td align="left">flagellar hook-length control protein FliK</td><td align="center"><italic>fliK</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0787</td><td align="center">868,051</td><td align="center">866,696</td><td align="left">flagellar hook protein FlgE</td><td align="center"><italic>flgE</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0788</td><td align="center">868,860</td><td align="center">868,171</td><td align="left">flagellar hook assembly protein FlgD</td><td align="center"><italic>flgD</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0789</td><td align="center">870,604</td><td align="center">868,865</td><td align="left">flagellar hook length determination protein</td><td align="center"><italic>flage</italic></td><td align="center">regulator</td></tr><tr><td align="left">PHZ_c0790</td><td align="center">870,819</td><td align="center">872,918</td><td align="left">flagellar hook-associated protein</td><td align="center"><italic>flaN</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0791</td><td align="center">872,933</td><td align="center">873,862</td><td align="left">flagellin and related hook-associated proteins</td><td align="center">-</td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0853</td><td align="center">945,008</td><td align="center">946,354</td><td align="left">flagellum-specific ATP synthase FliI</td><td align="center"><italic>fliI</italic></td><td align="center">protein export ATPase</td></tr><tr><td align="left">PHZ_c0854</td><td align="center">946,354</td><td align="center">946,758</td><td align="left">fliJ protein</td><td align="center"><italic>fliJ</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0857</td><td align="center">950,714</td><td align="center">948,621</td><td align="left">flagellar biosynthesis protein FlhA</td><td align="center"><italic>flhA</italic></td><td align="center">export apparatus</td></tr><tr><td align="left">PHZ_c0859</td><td align="center">952,470</td><td align="center">952,138</td><td align="left">flagellar motor switch protein FliN</td><td align="center"><italic>fliN</italic></td><td align="center">motor</td></tr><tr><td align="left">PHZ_c0860</td><td align="center">953,126</td><td align="center">952,479</td><td align="left">flbE protein</td><td align="center"><italic>flbE</italic></td><td align="center">regulator</td></tr><tr><td align="left">PHZ_c0861</td><td align="center">954,151</td><td align="center">953,126</td><td align="left">flagellar motor switch protein FliG</td><td align="center"><italic>fliG</italic></td><td align="center">motor</td></tr><tr><td align="left">PHZ_c0862</td><td align="center">955,794</td><td align="center">954,151</td><td align="left">flagellar M-ring protein FliF</td><td align="center"><italic>fliF</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0913</td><td align="center">1,007,753</td><td align="center">1,006,992</td><td align="left">flagellar L-ring protein FlgH</td><td align="center"><italic>flgH</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0914</td><td align="center">1,008,508</td><td align="center">1,007,753</td><td align="left">distal basal-body ring component protein FlaD</td><td align="center"><italic>flaD</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0915</td><td align="center">1,009,300</td><td align="center">1,008,515</td><td align="left">flagellar basal-body rod protein FlgG</td><td align="center"><italic>flgG</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0916</td><td align="center">1,010,052</td><td align="center">1,009,318</td><td align="left">flagellar basal-body rod protein FlgF</td><td align="center"><italic>flgF</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0917</td><td align="center">1,010,272</td><td align="center">1,010,874</td><td align="left">flagellar basal body-associated protein FliL</td><td align="center"><italic>fliL</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0918</td><td align="center">1,010,910</td><td align="center">1,011,983</td><td align="left">flagellar motor switch protein FliM</td><td align="center"><italic>fliM</italic></td><td align="center">motor</td></tr><tr><td align="left">PHZ_c0922</td><td align="center">1,017,085</td><td align="center">1,016,351</td><td align="left">flagellar biosynthesis protein FliP</td><td align="center"><italic>fliP</italic></td><td align="center">export apparatus</td></tr><tr><td align="left">PHZ_c0923</td><td align="center">1,017,420</td><td align="center">1,017,151</td><td align="left">flagellar protein FliO</td><td align="center"><italic>fliO</italic></td><td align="center">export apparatus</td></tr><tr><td align="left">PHZ_c0924</td><td align="center">1,017,502</td><td align="center">1,017,918</td><td align="left">flagellar basal-body rod protein FlgB</td><td align="center"><italic>flgB</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0925</td><td align="center">1,017,942</td><td align="center">1,018,355</td><td align="left">flagellar basal-body rod protein FlgC</td><td align="center"><italic>flgC</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0926</td><td align="center">1,018,370</td><td align="center">1,018,678</td><td align="left">flagellar hook-basal body complex protein FliE</td><td align="center"><italic>fliE</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c0930</td><td align="center">1,021,796</td><td align="center">1,022,056</td><td align="left">flagellar biosynthesis protein FliQ</td><td align="center"><italic>fliQ</italic></td><td align="center">export apparatus</td></tr><tr><td align="left">PHZ_c0931</td><td align="center">1,022,079</td><td align="center">1,022,837</td><td align="left">flagellar biosynthesis protein FliR</td><td align="center"><italic>fliR</italic></td><td align="center">export apparatus</td></tr><tr><td align="left">PHZ_c0932</td><td align="center">1,022,837</td><td align="center">1,023,913</td><td align="left">flagellar biosynthesis protein FlhB</td><td align="center"><italic>flhB</italic></td><td align="center">export apparatus</td></tr><tr><td align="left">PHZ_c1380</td><td align="center">1,563,281</td><td align="center">1,562,745</td><td align="left">putative flagella accessory protein FlaCE</td><td align="center"><italic>flaCE</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c1381</td><td align="center">1,565,145</td><td align="center">1,563,358</td><td align="left">flagellin modification protein FlmG</td><td align="center"><italic>flmG</italic></td><td align="center">regulator</td></tr><tr><td align="left">PHZ_c1382</td><td align="center">1,565,343</td><td align="center">1,565,765</td><td align="left">flagellar repressor protein FlbT</td><td align="center"><italic>flbT</italic></td><td align="center">regulator</td></tr><tr><td align="left">PHZ_c1383</td><td align="center">1,565,782</td><td align="center">1,566,093</td><td align="left">flagellar biosynthesis regulator FlaF</td><td align="center"><italic>flaF</italic></td><td align="center">regulator</td></tr><tr><td align="left">PHZ_c1384</td><td align="center">1,566,375</td><td align="center">1,567,202</td><td align="left">flagellin FljM</td><td align="center"><italic>fljM</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c1385</td><td align="center">1,567,469</td><td align="center">1,568,314</td><td align="left">flagellin FljM</td><td align="center"><italic>fljM</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c1386</td><td align="center">1,568,434</td><td align="center">1,568,724</td><td align="left">flagellin FlaG</td><td align="center"><italic>flaG</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c1387</td><td align="center">1,568,887</td><td align="center">1,569,720</td><td align="left">flagellin FljL</td><td align="center"><italic>fljL</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c1935</td><td align="center">2,168,522</td><td align="center">2,169,634</td><td align="left">flagellar P-ring protein FglI</td><td align="center"><italic>fglI</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c1937</td><td align="center">2,169,942</td><td align="center">2,170,382</td><td align="left">flagellar basal-body protein FlbY</td><td align="center"><italic>flbY</italic></td><td align="center">flagellar structure</td></tr><tr><td align="left">PHZ_c2595</td><td align="center">2,982,550</td><td align="center">2,983,593</td><td align="left">flagellin modification protein FlmD</td><td align="center"><italic>flmD</italic></td><td align="center">regulator</td></tr><tr><td align="left">PHZ_c2597</td><td align="center">2,984,874</td><td align="center">2,986,508</td><td align="left">flagellin modification protein FlmG</td><td align="center"><italic>flmG</italic></td><td align="center">regulator</td></tr><tr><td align="left">PHZ_c2599</td><td align="center">2,989,315</td><td align="center">2,989,974</td><td align="left">flmC; flagellin modification protein FlmC</td><td align="center"><italic>flmC</italic></td><td align="center">regulator</td></tr><tr><td align="left">PHZ_c2600</td><td align="center">2,990,549</td><td align="center">2,989,977</td><td align="left">flagellin modification protein FlmH</td><td align="center"><italic>flmH</italic></td><td align="center">regulator</td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T9"><label>Table 9</label><caption><p>Distributions of proteins involved in environmental adaptation in <italic>P. zucineum </italic>and representative alphaproteobacteria with different living habitats</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="center">Species</td><td align="center"><italic>S. meliloti</italic></td><td align="center"><italic>B. suis</italic></td><td align="center"><italic>C. crescentus</italic></td><td align="center"><italic>P. zucineum</italic></td><td align="center"><italic>R. conorii</italic></td><td align="center"><italic>G. oxydans</italic></td></tr></thead><tbody><tr><td align="center">Genome size (Mb)</td><td align="center">6.69</td><td align="center">3.32</td><td align="center">4.02</td><td align="center">4.38</td><td align="center">1.27</td><td align="center">2.92</td></tr><tr><td align="center">GC content (%)</td><td align="center">62.2</td><td align="center">57.3</td><td align="center">67.2</td><td align="center">71.1</td><td align="center">32.4</td><td align="center">60.8</td></tr><tr><td align="center">Habitat</td><td align="center">Multiple<sup>1</sup></td><td align="center">Facultative<sup>1</sup></td><td align="center">Aquatic<sup>1</sup></td><td align="center">Facultative<sup>2</sup></td><td align="center">Obligate<sup>1</sup></td><td align="center">Multiple<sup>3</sup></td></tr><tr><td align="center">ECF, extracytoplasmic function sigma factor (/Mb)</td><td align="center">11 (1.6)</td><td align="center">2 (0.6)</td><td align="center">15 (3.7)</td><td align="center">17 (3.9)</td><td align="center">0 (0)</td><td align="center">2 (0.7)</td></tr><tr><td align="center">Transcriptional regulator (/Mb)</td><td align="center">433 (64.7)</td><td align="center">149(44.9)</td><td align="center">183 (45.5)</td><td align="center">170 (38.8)</td><td align="center">11 (8.7)</td><td align="center">89 (30.1)</td></tr><tr><td align="center">Two-component signal transduction protein (/Mb)</td><td align="center">113 (16.9)</td><td align="center">44 (13.3)</td><td align="center">111 (27.6)</td><td align="center">102 (23.3)</td><td align="center">7 (5.5)</td><td align="center">41 (14.1)</td></tr><tr><td align="center">molecular chaperone</td><td align="center">23</td><td align="center">12</td><td align="center">14</td><td align="center">33</td><td align="center">8</td><td align="center">14</td></tr><tr><td align="center">Flagellar protein</td><td align="center">41</td><td align="center">37</td><td align="center">42</td><td align="center">43</td><td align="center">10</td><td align="center">40</td></tr><tr><td align="center">Chemotaxis protein</td><td align="center">42</td><td align="center">4</td><td align="center">48</td><td align="center">41</td><td align="center">0</td><td align="center">11</td></tr><tr><td align="center">Pilus protein</td><td align="center">13</td><td align="center">4</td><td align="center">9</td><td align="center">16</td><td align="center">2</td><td align="center">4</td></tr><tr><td align="center">Sec-dependent secretion system</td><td align="center">11</td><td align="center">11</td><td align="center">11</td><td align="center">11</td><td align="center">11</td><td align="center">12</td></tr><tr><td align="center">Sec-independent secretion system</td><td align="center">4</td><td align="center">4</td><td align="center">4</td><td align="center">4</td><td align="center">3</td><td align="center">4</td></tr><tr><td align="center">Type II secretory protein</td><td align="center">2</td><td align="center">0</td><td align="center">8</td><td align="center">13</td><td align="center">0</td><td align="center">3</td></tr><tr><td align="center">Type IV secretory protein</td><td align="center">9</td><td align="center">8</td><td align="center">9</td><td align="center">31</td><td align="center">15</td><td align="center">1</td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T10"><label>Table 10</label><caption><p>Type IV secretion systems in the <italic>P. zucineum </italic>genome</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="left">Locus</td><td align="center" colspan="3">Location of protein</td><td align="left">Name</td></tr><tr><td/><td colspan="3"><hr/></td><td/></tr><tr><td/><td align="center">Genomic element</td><td align="center">5'-end</td><td align="center">3'-end</td><td/></tr></thead><tbody><tr><td align="left">PHZ_p0007</td><td align="center">Plasmid</td><td align="center">6,786</td><td align="center">7,445</td><td align="left">type IV secretion protein, VirB1</td></tr><tr><td align="left">PHZ_p0008</td><td align="center">Plasmid</td><td align="center">7,483</td><td align="center">7,800</td><td align="left">type IV secretion protein, VirB2</td></tr><tr><td align="left">PHZ_p0009</td><td align="center">Plasmid</td><td align="center">7,816</td><td align="center">8,148</td><td align="left">type IV secretion protein, VirB3</td></tr><tr><td align="left">PHZ_p0010</td><td align="center">Plasmid</td><td align="center">8,144</td><td align="center">10,546</td><td align="left">type IV secretion protein, VirB4</td></tr><tr><td align="left">PHZ_p0011</td><td align="center">Plasmid</td><td align="center">10,546</td><td align="center">11,298</td><td align="left">type IV secretion protein, VirB5</td></tr><tr><td align="left">PHZ_p0012</td><td align="center">Plasmid</td><td align="center">11,553</td><td align="center">12,488</td><td align="left">type IV secretion protein, VirB6</td></tr><tr><td align="left">PHZ_p0013</td><td align="center">Plasmid</td><td align="center">12,816</td><td align="center">13,493</td><td align="left">type IV secretion protein, VirB8</td></tr><tr><td align="left">PHZ_p0014</td><td align="center">Plasmid</td><td align="center">13,493</td><td align="center">14,320</td><td align="left">type IV secretion protein, VirB9</td></tr><tr><td align="left">PHZ_p0015</td><td align="center">Plasmid</td><td align="center">14,320</td><td align="center">15,543</td><td align="left">type IV secretion protein, VirB10</td></tr><tr><td align="left">PHZ_p0016</td><td align="center">Plasmid</td><td align="center">15,543</td><td align="center">16,538</td><td align="left">type IV secretion protein, VirB11</td></tr><tr><td align="left">PHZ_c1506</td><td align="center">Chromosome</td><td align="center">1,709,481</td><td align="center">1,709,999</td><td align="left">type IV secretion protein, TraF</td></tr><tr><td align="left">PHZ_c1508</td><td align="center">Chromosome</td><td align="center">1,711,058</td><td align="center">1,712,773</td><td align="left">type IV secretion protein, VirD2</td></tr><tr><td align="left">PHZ_c1509</td><td align="center">Chromosome</td><td align="center">1,712,790</td><td align="center">1,714,763</td><td align="left">type IV secretion protein, VirD4</td></tr><tr><td align="left">PHZ_c1512</td><td align="center">Chromosome</td><td align="center">1,716,262</td><td align="center">1,717,242</td><td align="left">conjugal transfer protein, TrbB</td></tr><tr><td align="left">PHZ_c1513</td><td align="center">Chromosome</td><td align="center">1,717,242</td><td align="center">1,717,559</td><td align="left">conjugal transfer protein, TrbC</td></tr><tr><td align="left">PHZ_c1514</td><td align="center">Chromosome</td><td align="center">1,717,562</td><td align="center">1,717,828</td><td align="left">conjugal transfer protein, TrbD</td></tr><tr><td align="left">PHZ_c1515</td><td align="center">Chromosome</td><td align="center">1,717,836</td><td align="center">1,720,283</td><td align="left">conjugal transfer protein, TrbE</td></tr><tr><td align="left">PHZ_c1516</td><td align="center">Chromosome</td><td align="center">1,720,283</td><td align="center">1,721,014</td><td align="left">conjugal transfer protein, TrbJ</td></tr><tr><td align="left">PHZ_c1517</td><td align="center">Chromosome</td><td align="center">1,721,238</td><td align="center">1,722,398</td><td align="left">conjugal transfer protein, TrbL</td></tr><tr><td align="left">PHZ_c1518</td><td align="center">Chromosome</td><td align="center">1,722,401</td><td align="center">1,723,084</td><td align="left">conjugal transfer protein, TrbF</td></tr><tr><td align="left">PHZ_c1519</td><td align="center">Chromosome</td><td align="center">1,723,087</td><td align="center">1,724,064</td><td align="left">conjugal transfer protein, TrbG</td></tr><tr><td align="left">PHZ_c1520</td><td align="center">Chromosome</td><td align="center">1,724,070</td><td align="center">1,725,212</td><td align="left">conjugal transfer protein, TrbI</td></tr><tr><td align="left">PHZ_c2348</td><td align="center">Chromosome</td><td align="center">2,660,517</td><td align="center">2,660,813</td><td align="left">type IV secretion protein, VirB2</td></tr><tr><td align="left">PHZ_c2349</td><td align="center">Chromosome</td><td align="center">2,660,809</td><td align="center">2,661,144</td><td align="left">type IV secretion protein, VirB3</td></tr><tr><td align="left">PHZ_c2350</td><td align="center">Chromosome</td><td align="center">2,661,119</td><td align="center">2,663,497</td><td align="left">type IV secretion protein, VirB4</td></tr><tr><td align="left">PHZ_c2352</td><td align="center">Chromosome</td><td align="center">2,664,374</td><td align="center">2,665,309</td><td align="left">type IV secretion protein, VirB6</td></tr><tr><td align="left">PHZ_c2353</td><td align="center">Chromosome</td><td align="center">2,665,482</td><td align="center">2,666,159</td><td align="left">type IV secretion protein, VirB8</td></tr><tr><td align="left">PHZ_c2354</td><td align="center">Chromosome</td><td align="center">2,666,159</td><td align="center">2,667,004</td><td align="left">type IV secretion protein, VirB9</td></tr><tr><td align="left">PHZ_c2355</td><td align="center">Chromosome</td><td align="center">2,667,004</td><td align="center">2,668,041</td><td align="left">type IV secretion protein, VirB10</td></tr><tr><td align="left">PHZ_c2356</td><td align="center">Chromosome</td><td align="center">2,668,046</td><td align="center">2,669,035</td><td align="left">type IV secretion protein, VirB11</td></tr><tr><td align="left">PHZ_c2357</td><td align="center">Chromosome</td><td align="center">2,669,091</td><td align="center">2,670,872</td><td align="left">type IV secretion protein, VirD4</td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T11"><label>Table 11</label><caption><p>Pilus proteins in the <italic>P. zucineum </italic>genome</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="left">Locus</td><td align="center">5'-end</td><td align="center">3'-end</td><td align="left">Name</td><td align="center">Gene symbol</td></tr></thead><tbody><tr><td align="left">PHZ_c0356</td><td align="center">362,116</td><td align="center">362,289</td><td align="left">pilus subunit protein PilA</td><td align="center"><italic>pilA</italic></td></tr><tr><td align="left">PHZ_c2992</td><td align="center">3,412,800</td><td align="center">3,413,318</td><td align="left">Flp pilus assembly protein TadG</td><td align="center"><italic>tadG</italic></td></tr><tr><td align="left">PHZ_c2995</td><td align="center">3,415,220</td><td align="center">3,415,468</td><td align="left">Flp pilus assembly protein, pilin Flp</td><td align="center">-</td></tr><tr><td align="left">PHZ_c2996</td><td align="center">3,415,532</td><td align="center">3,416,023</td><td align="left">Flp pilus assembly protein, protease CpaA</td><td align="center"><italic>cpaA</italic></td></tr><tr><td align="left">PHZ_c2997</td><td align="center">3,416,039</td><td align="center">3,416,899</td><td align="left">pilus assembly protein CpaB</td><td align="center"><italic>cpaB</italic></td></tr><tr><td align="left">PHZ_c2998</td><td align="center">3,416,899</td><td align="center">3,418,350</td><td align="left">pilus assembly protein CpaC</td><td align="center"><italic>cpaC</italic></td></tr><tr><td align="left">PHZ_c2999</td><td align="center">3,418,355</td><td align="center">3,419,587</td><td align="left">pilus assembly protein CpaE</td><td align="center"><italic>cpaE</italic></td></tr><tr><td align="left">PHZ_c3000</td><td align="center">3,419,594</td><td align="center">3,420,991</td><td align="left">pilus assembly protein CpaF</td><td align="center"><italic>cpaF</italic></td></tr><tr><td align="left">PHZ_c3001</td><td align="center">3,421,030</td><td align="center">3,421,944</td><td align="left">Flp pilus assembly protein TadB</td><td align="center"><italic>tadB</italic></td></tr><tr><td align="left">PHZ_c3002</td><td align="center">3,421,944</td><td align="center">3,422,903</td><td align="left">Flp pilus assembly protein TadC</td><td align="center"><italic>tadC</italic></td></tr><tr><td align="left">PHZ_c3027</td><td align="center">3,451,637</td><td align="center">3,452,566</td><td align="left">Flp pilus assembly protein CpaB</td><td align="center"><italic>cpaB</italic></td></tr><tr><td align="left">PHZ_c3028</td><td align="center">3,452,580</td><td align="center">3,453,893</td><td align="left">Flp pilus assembly protein, secretin CpaC</td><td align="center"><italic>cpaC</italic></td></tr><tr><td align="left">PHZ_c3029</td><td align="center">3,453,893</td><td align="center">3,455,056</td><td align="left">Flp pilus assembly protein, ATPase CpaE</td><td align="center"><italic>cpaE</italic></td></tr><tr><td align="left">PHZ_c3030</td><td align="center">3,455,059</td><td align="center">3,456,489</td><td align="left">Flp pilus assembly protein ATPase CpaF</td><td align="center"><italic>cpaF</italic></td></tr><tr><td align="left">PHZ_c3031</td><td align="center">3,456,489</td><td align="center">3,457,445</td><td align="left">Flp pilus assembly protein TadB</td><td align="center"><italic>tadB</italic></td></tr><tr><td align="left">PHZ_c3032</td><td align="center">3,457,492</td><td align="center">3,458,391</td><td align="left">Flp pilus assembly protein TadC</td><td align="center"><italic>tadC</italic></td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T12"><label>Table 12</label><caption><p>TonB-dependent receptors in the <italic>P. zucineum </italic>genome</p></caption><table frame="hsides" rules="groups"><thead><tr><td align="left">Annotation</td><td align="center">Chromosome</td><td align="center">Plasmid</td><td align="center">COG category</td></tr></thead><tbody><tr><td align="left">TonB-dependent receptor</td><td align="center">51</td><td align="center">2</td><td align="center">COG1629<sup>1</sup></td></tr><tr><td align="left">TonB-dependent receptor vitamin B12</td><td align="center">3</td><td align="center">0</td><td align="center">COG4206<sup>2</sup></td></tr><tr><td align="left">TonB-dependent receptor</td><td align="center">4</td><td align="center">0</td><td align="center">COG4771<sup>3</sup></td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T13"><label>Table 13</label><caption><p>Comparison of the signal transduction pathways regulating CtrA between the <italic>P. zucineum </italic>and the <italic>C. crescentus</italic></p></caption><table frame="hsides" rules="groups"><thead><tr><td/><td align="left">Locus</td><td align="center" colspan="2">Length</td><td align="center">Amino acid Identity (%)</td><td align="center">Annotation</td></tr><tr><td align="center"><italic>C. crescentus</italic></td><td align="left"><italic>P. zucineum</italic></td><td align="center"><italic>C. crescentus</italic></td><td align="center"><italic>P. zucineum</italic></td><td/><td/></tr></thead><tbody><tr><td align="center">CC0378</td><td align="left">PHZ_c0577</td><td align="center">355</td><td align="center">359</td><td align="center">80.00</td><td align="center">modification methylase CcrM</td></tr><tr><td align="center">CC1078</td><td align="left">PHZ_c0933</td><td align="center">691</td><td align="center">663</td><td align="center">67.22</td><td align="center">cell cycle histidine kinase CckA</td></tr><tr><td align="center">CC2482</td><td align="left">PHZ_c2681</td><td align="center">842</td><td align="center">606</td><td align="center">63.78</td><td align="center">sensor histidine kinase PleC</td></tr><tr><td align="center">CC1063</td><td align="left">PHZ_c2712</td><td align="center">597</td><td align="center">504</td><td align="center">53.83</td><td align="center">sensor histidine kinase DivJ</td></tr><tr><td align="center">CC3484</td><td align="left">PHZ_c0218</td><td align="center">769</td><td align="center">769</td><td align="center">67.66</td><td align="center">tyrosine kinase DivL</td></tr><tr><td align="center">CC2463</td><td align="left">PHZ_c1309</td><td align="center">130</td><td align="center">121</td><td align="center">89.26</td><td align="center">polar differentiation response regulator DivK</td></tr><tr><td align="center">CC1963</td><td align="left">PHZ_c1817</td><td align="center">202</td><td align="center">205</td><td align="center">80.19</td><td align="center">ATP-dependent protease, ClpP subunit</td></tr><tr><td align="center">CC1961</td><td align="left">PHZ_c1814</td><td align="center">420</td><td align="center">420</td><td align="center">90.47</td><td align="center">ATP-dependent protease, ClpX subunit</td></tr></tbody></table></table-wrap> <table-wrap position="float" id="T14"><label>Table 14</label><caption><p>Human ESTs matching the genome sequences of <italic>P. zucineum</italic></p></caption><table frame="hsides" rules="groups"><thead><tr><td align="center">Query GI</td><td align="center">Sample origin</td><td align="center">Query Length</td><td align="center" colspan="2">Query Position</td><td align="center" colspan="2">Chromosome Position</td><td align="center">Score</td><td align="center">E Value</td><td align="center">Similarity (%)</td></tr><tr><td/><td/><td/><td colspan="4"><hr/></td><td/><td/><td/></tr><tr><td/><td/><td/><td align="center">Begin</td><td align="center">End</td><td align="center">Begin</td><td align="center">End</td><td/><td/><td/></tr></thead><tbody><tr><td align="center">14251638</td><td align="center">Breast tissue<sup>1</sup></td><td align="center">226</td><td align="center">41</td><td align="center">175</td><td align="center">1,276,914</td><td align="center">1,277,048</td><td align="center">204</td><td align="center">2.00E-53</td><td align="center">94.07</td></tr><tr><td align="center">8261474</td><td align="center">Breast tissue</td><td align="center">116</td><td align="center">1</td><td align="center">108</td><td align="center">1,277,042</td><td align="center">1,276,937</td><td align="center">167</td><td align="center">2.00E-42</td><td align="center">96.31</td></tr><tr><td align="center">14251634</td><td align="center">Breast tissue</td><td align="center">142</td><td align="center">19</td><td align="center">134</td><td align="center">1,277,054</td><td align="center">1,276,937</td><td align="center">204</td><td align="center">1.00E-53</td><td align="center">97.46</td></tr><tr><td align="center">33194938</td><td align="center">Lymphatic cell line<sup>2</sup></td><td align="center">441</td><td align="center">8</td><td align="center">441</td><td align="center">1,029,575</td><td align="center">1,029,142</td><td align="center">749</td><td align="center">0</td><td align="center">96.77</td></tr><tr><td align="center">33194696</td><td align="center">Lymphatic cell line</td><td align="center">652</td><td align="center">8</td><td align="center">652</td><td align="center">1,029,575</td><td align="center">1,028,931</td><td align="center">1,166</td><td align="center">0</td><td align="center">97.67</td></tr><tr><td align="center">33193754</td><td align="center">Lymphatic cell line</td><td align="center">654</td><td align="center">8</td><td align="center">654</td><td align="center">1,029,575</td><td align="center">1,028,929</td><td align="center">1,191</td><td align="center">0</td><td align="center">98.15</td></tr><tr><td align="center">7117824</td><td align="center">Lymphatic cell line</td><td align="center">405</td><td align="center">7</td><td align="center">405</td><td align="center">1,558,831</td><td align="center">1,558,433</td><td align="center">735</td><td align="center">0</td><td align="center">98.25</td></tr><tr><td align="center">33194587</td><td align="center">Lymphatic cell line</td><td align="center">638</td><td align="center">7</td><td align="center">638</td><td align="center">2,864,470</td><td align="center">2,863,838</td><td align="center">1,191</td><td align="center">0</td><td align="center">98.89</td></tr><tr><td align="center">7114909</td><td align="center">Lymphatic cell line</td><td align="center">347</td><td align="center">6</td><td align="center">347</td><td align="center">3,498,624</td><td align="center">3,498,283</td><td align="center">654</td><td align="center">0</td><td align="center">99.12</td></tr></tbody></table></table-wrap>
<supplementary-material content-type="local-data" id="S1"><caption><title>Additional file 1</title><p><bold>Supplemental Table 1 </bold>Comparison of genes directly regulated by CtrA between <italic>P. zucineum </italic>and <italic>C. crescentus</italic>.</p></caption></supplementary-material>
<table-wrap-foot><p><sup>1</sup>Size in base pairs of the consensus and the direct repeat (DR) generated by insertion into the genome target site.</p><p><sup>2</sup>A copy is complete if the length of the repeat is ≥ 90% of the consensus, otherwise, the copy is partial.</p><p><sup>3</sup>One complete copy which harbors a 7 bp direct repeat (TCCTAAC) that disrupts the VirD4.</p><p><sup>4</sup>The partial copy is located in the plasmid.</p><p><sup>5</sup>Two partial copies are located in the chromosome, of which a "partial" copy with full length is inserted by a copy of repeat04.</p><p><sup>6</sup>repeats 01–04 are IS elements</p></table-wrap-foot> <table-wrap-foot><p><sup>1</sup>Initial function is related to controlling the expression of phage gene</p><p><sup>2</sup>"Other types" include the transcriptional regulators with only one member in the <italic>P. zucineum </italic>genome or transcriptional regulators that could not be classified into any known family.</p></table-wrap-foot> <table-wrap-foot><p><sup>1</sup>COG1595, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog;</p><p><sup>2</sup>COG4941, predicted RNA polymerase sigma factor containing a TPR repeat domain</p></table-wrap-foot> <table-wrap-foot><p><sup>1</sup>rpoH may be responsible for the expression of some or all heat shock proteins</p><p><sup>2</sup>The function of molecular chaperones is to protect unfolded proteins induced by stress factors through renaturation or degradation in cooperation with protease.</p></table-wrap-foot> <table-wrap-foot><p><sup>1</sup>The habitats of <italic>S. meliloti, B. suis, and R. conorii </italic>were indicated in a recent publication [##REF##17888177##42##].</p><p><sup>2</sup>According to our recent publication [##REF##16908113##1##], <italic>P. zucineum </italic>was classified as "facultative". <sup>3</sup>Given that <italic>G. oxydans </italic>is often isolated from sugary niches (such as flowers and fruits) and associated soil (such as garden soil and baker's soil) [##REF##11361077##43##], we classified <italic>G. oxydans </italic>as "multiple".</p></table-wrap-foot> <table-wrap-foot><p><sup>1</sup>COG1629, Outer membrane receptor proteins, mostly Fe transport</p><p><sup>2</sup>COG4206, Outer membrane cobalamin receptor protein</p><p><sup>3</sup>COG4774, Outer membrane receptor for monomeric catechols</p></table-wrap-foot> <table-wrap-foot><p><sup>1</sup>All of three sequences come from the library BN0075 containing 182 ESTs; the original dataset was produced by a modification of the EST sequencing strategy ORESTES (open reading frame expressed sequences tags)[##REF##11593022##44##,##REF##10737800##45##]</p><p><sup>2</sup>All six sequences come from the library NIH_MGC_51 containing 2,381 ESTs; the original dataset was produced and released by the "Mammalian Gene Collection" project [##REF##15489334##46##].</p></table-wrap-foot>
<graphic xlink:href="1471-2164-9-386-1"/> <graphic xlink:href="1471-2164-9-386-2"/> <graphic xlink:href="1471-2164-9-386-3"/> <graphic xlink:href="1471-2164-9-386-4"/> <graphic xlink:href="1471-2164-9-386-5"/> <graphic xlink:href="1471-2164-9-386-6"/>
<media xlink:href="1471-2164-9-386-S1.xls" mimetype="application" mime-subtype="vnd.ms-excel"><caption><p>Click here for file</p></caption></media>
[{"surname": ["Lingens", "Blecher", "Blecher", "Blobel", "Eberspacher", "Frohner", "Gorisch", "Gorisch", "Layh"], "given-names": ["F", "R", "H", "F", "J", "C", "H", "H", "G"], "article-title": ["Phenylobacterium immobile gen. nov., sp. nov., a gram-negative bacterium that degrades the herbicide chloridazon"], "source": ["Int J Syst Bacteriol"], "year": ["1985"], "volume": ["35"], "fpage": ["26"], "lpage": ["39"]}]
BMC Genomics. 2008 Aug 13; 9:386