Listeria Monocytogenes La111 and Klebsiella Pneumoniae KCTC 2242: Shine-Dalgarno Sequences.

Listeria monocytogenes can cause serious infection and recently, relapse of listeriosis has been reported in leukemia and colorectal cancer, and the patients with Klebsiella pneumoniae are at increased risk of colorectal cancer. Translation initiation codon recognition is basically mediated by Shine-Dalgarno (SD) and the anti-SD sequences at the small ribosomal RNA (ssu rRNA). In this research, Shine-Dalgarno sequences prediction in Listeria monocytogenes La111 and Klebsiella pneumoniae KCTC 2242 was investigated. The whole genomic sequence of Listeria monocytogenes La111 and Klebsiella pneumoniae KCTC 2242 were retrieved from http://www.ncbi.nlm.nih.gov/ (Listeria monocytogenes La111 NCBI Reference sequence: NC_020557; Klebsiella pneumoniae KCTC 2242 NCBI Reference sequence: CP002910) in order to be analyzed with DAMBE software and BLAST. The results showed that the consensus sequence for Klebsiella pneumoniae KCTC 2242 was CCCCCCCUCCCCCUCCCCCUCCUCCUCCUUUUUAAAAAAGGGGAAAAACC and for Listeria monocytogenes La111 was CCCCCCCUCCCCCUUUCCCUCCUAUUCUUAUAAAAGGGGG-GGGGUUCAC. The PSD was higher in Listeria monocytogenes La111 compared to Klebsiella pneumoniae KCTC 2242 (0.9090> 0.8618). The results showed that Nm in Listeria monocytogenes La111 was higher than Klebsiella pneumoniae KCTC 2242 (4.5846> 4.4862). Accurate characterization of SD sequences may increase our knowledge on how an organism’s transcriptome is related to its cellular proteome.

E. coli and Klebsiella pneumoniae are especially prevalent in patients with gastrointestinal (GI) and lung cancers (6). Due to their abilities to cause basic cellular functional changes and attack host defense mechanisms, these bacteria have become a model for host pathogen interactions (7).
A molecular machine like ribosome translates the genetic code from messenger RNA into an amino acid sequence by RNA selection, peptide bond formation and translocation (8). Protein synthesis by ribosomes takes place on a linear substrate but at variable speeds. Transient pausing of ribosomes can impact a variety of cotranslational processes, including protein targeting and folding. These pauses are influenced by the sequence of the mRNA. Thus, redundancy in the genetic code allows the same protein to be translated at different rates (9). mRNA sequences contain many AUG. How does the translation machinery distinguish which one is the initiation codon? Initial positioning of the ribosome on mRNA involves the recognition of a purine rich sequence, known as the Shine Dalgarno (SD) sequence, located upstream of the AUG initiation codon on the mRNA (8).
In 1974, Shine and Dalgarno sequenced the 3' end of Escherichia coli's 16S ribosomal RNA (rRNA) and observed that part of the sequence, 5'-ACCUCC-3', was complementary to a motif, 5'-GGAGGU-3', located 5' of the initiation codons in several messenger RNAs (mRNAs) (9). They combined this observation with previously published experimental evidences and suggested that complementarity between the 3' tail of the 16S rRNA and the region 5' of the start codon on the mRNA was sufficient to create a stable, doublestranded structure that could position the ribosome correctly on the mRNA during translation initiation.
The motif on the mRNAs, 5'-GGAGGU-3', and variations on it that are also complementary to parts of the 3' 16S rRNA tail, have since been referred to as the Shine-Dalgarno (SD) sequence. Shine and Dalgarno's theory was bolstered by Steitz and Jakes in 1975 (10) and eventually experimentally verified in 1987, by Hui and de Boer (11) and Jacob et al. (12).The SD sequence has been established by experimental evidence that came from mutation studies. Unfortunately, experiments are tedious and only a few mutated SD sequences have been examined. Biopharmaceutical studies are highly interested in improving translation efficiency (13).
In the present study, we tried to find the best possible SD for translation in Listeria monocytogenes La111, and Klebsiella pneumoniae KCTC 2242 through DAMBE software and BLAST analyzes.  (14,15). PWM is computed as:

Materials and methods
(1) where i= 1, 2, 3 and 4 refer to A, C, G and U, respectively, and j is the site index, and p i is the background frequency of nucleotide i, and p ij is the site specific nucleotide frequency for nucleotide i at site j.

Discussion
This study was conducted in order to find SD    *First column is some of sequences name; second column is the number of matched sites (Nm) between the SD sequence and the 50mer, and the last column is the start of the match (Sm). *First column is some of sequences name; second column is the number of matched sites (Nm) between the SD sequence and the 50mer, and the last column is the start of the match (Sm). have not any short or even trace of a SD sequence and second, when SD sequences are present, their location is very often variable. The ribosomal protein S1 in gram negative bacteria helps to locate TIC or translation initiation codon by binding to AU-rich sequences located 15-30 nucleotides upstream of start codon (18). We called it as S1 hypothesis. For efficient translation initiation, Nm should be four or more and SD sequence may be defined as one with Nm ≥3 and 31 ≤Sm ≤45 (11,14). For mRNAs that have a weak or no SD sequence, the S1 protein is necessary to recognize the initiation codon and therefore, reduces the importance of a strong SD sequence and may allow the SD sequence to degrade. In grampositive bacteria, either they do not have the S1 protein, or have an "S1 protein" that is not conserved and probably is not used to recognize the initiation codon. This important fact suggests that in gram positive bacteria TIC localization may be more dependent on the SD sequence than in the gram negative bacteria (18). Therefore if an essential protein-coding gene in Listeria