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Taxonomic Reference Libraries for Environmental Barcoding: A Best Practice Example from Diatom Research

DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists) as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes) presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature.

Introduction
Diatoms are unicellular and usually photoautotroph micro algae which are responsible for about 25% of global CO 2 fixation [1][2][3] and contribute approximately 20% of the global net primary production [4].
Diatoms are important bioindicators for monitoring water quality because they are sensitive to changes in pollution, nutrient availability, acidity and salinity, e.g. [5,6]. They are the most ubiquitous group within the microscopic algae as they occur in all types of water bodies and play an important part in benthic and planktonic biocoenoses [7]. They are routinely used as bioindicators within the EU Water Framework Directive (WFD) as well as in water quality monitoring worldwide [8][9][10][11][12][13].
Each diatom cell is encased in two siliceous shells (frustules) that are connected by girdle bands [1][2][3]. Current identification of diatoms is based on a morphological and mostly descriptive species concept (Zimmermann et al. subm.) and relies exclusively on micro-characters of the frustule such as size, symmetry, shape, and sculpture which can be seen by light microscopy [14]; more detailed analyses of the siliceous structures lead to more and more refined differentiation of species, which is possible through the development of higher resolution techniques, e.g. electron microscopy.
Identification via microscopy is challenging and time consuming, especially for routine use [15], and relies on individual taxonomic expertise. Therefore different taxonomists could arrive at different conclusions, depending i.a. on the taxonomic concept, species with limited diagnostic morphological features, cryptic species, available reference floras and quality of microscopes used by each individual researcher [15] as well as unavailability of adequate descriptions.
The application of molecular markers for taxon identification -DNA barcoding -is an emerging method which has the potential to be faster, universally applicable and generate reliable identification. Furthermore, as it uses DNA sequences for identification, it is independent of pre-existing morphological species concepts and can be linked to any taxonomic concept [16]. However, correct identification relies fundamentally on the quality of the reference library the DNA barcodes are checked against. DNA barcoding is based on the assumption that sequences of a certain marker locus exhibit enough variation between species to be discriminative for unambiguous species discovery [17,18]. DNA barcoding is also a useful tool to access concealed diversity e.g. [19][20][21][22][23][24][25]. DNA barcoding in combination with next generation sequencing techniques also allows for the description of community compositions through the large numbers of sequences generated by this approach e.g. [26,27]. A schematic overview on environmental DNA barcoding of diatoms and the establishment of a reference library is given in Fig. 1.
The requirement for reliable taxon identification by DNA barcode(s) is an unambiguous link between the genotype and the phenotype (or morphotype) to which the name of the species is attached. This means that a reference library consisting of taxon names belonging to specimens that have been identified by experts as well as providing descriptions together with barcode sequences, which were derived from well documented strains (e.g. voucher deposition, sampling localities and collectors, basic environmental data, high-resolution LM pictures, morphometrics, taxonomy and nomenclature, maps, literature and references to databases where this data is deposited) for every single species is necessary. For unicellular diatoms, clone cultures (strains) need to be established which offer enough material for sequencing as well as for identification by light and electron microscopy. Once established and linked to a taxonomic reference library, the DNA barcoding method could offer a time and cost efficient alternative/extension to microscopic identification for routine applications by limiting morphological taxonomy to critical groups which feature a distinct genetic aberration to known and identified organisms in the library.
Recently, the CBOL Protist Working Group [28] has designated the 18S V4 rDNA marker region as first or pre-barcode for Protist organisms. In this paper, we follow the 18S V4 protocols designed for diatoms by Zimmermann et al. [19], and present 70 strains for which this pre-barcode (18S V4) as well as a second widely used barcode, rbcL [20,21,29], has been generated. The reference library includes these two DNA barcodes, the respective taxon name, images, morphometric and geographic data as well as vouchers for further reference. Further data and additional images also of living cells are available electronically through the AlgaTerra Information System [30]. We demonstrate the benefits of a well documented reference library for DNA barcoding for identification, taxonomy, phylogeny, and further scientific analyses on an exemplary group. This paper focuses on naviculoid diatom strains from Berlin waters since its diatom flora has been well studied for almost two centuries by light microscopy [31] and a recent diatom flora is available for water quality assessments [32].

Sampling
Benthic samples from which the 70 strains were established were collected at 11 sites in the catchment area of Berlin (Fig. 2); one additional sample was from the River Elbe, downstream of the Berlin Rivers Spree and Havel. Conductivity of Berlin water ranges mostly between 400 to 900 mS cm 21 , pH is frequently 6,5 to 9 (80% respectively 88% of about 300 measurements of Berlin water samples, Kusber unpubl. data). For samples, sites, dates, collectors of the samples and isolators of the strains see Table 1. No specific permissions were required for the sampled locations/ activities. The field studies did not involve endangered or protected species.

Cultivation
The diatom cells were isolated from environmental water samples observed under a stereo light microscope using capillary glass pipettes. The respective cell was then transferred to a 5 cm diameter plastic petri dish containing autoclaved habitat water and/or culture medium (WC [33], Chu [34], AlgaGrow, Plagron, Weert, Netherlands) of adequate salinity and pH. In order to remove unwanted particles, this treatment was repeated several times until microscopic inspection confirming that a culture derived from one cell, but not axenic had been established. The cultures were grown at a temperature between 18-22uC and a 12 h day/night cycle.

Preparation of frustules
By the time of harvesting the cultures, one fraction was used for obtaining DNA (see below) and the other part was cleaned with H 2 0 2 at 80uC and rinsed several times with H 2 0. A few drops of the resulting suspension of diatom frustules were dried on a cover slip and embedded as slides in Naphrax for study in LM or on stubs if for SEM. Vouchers of each strain were deposited in the Herbarium Berolinense (B) (see Table 2).

Light and electron microscopy
The LM pictures were acquired with a Zeiss Axio Imager.M2 with an implemented AxioCam HRc (Zeiss, Oberkochen, Germany). SEM pictures were produced with Philips SEM 515 operating at 30 KV (Philips, Eindhoven, The Netherlands), and Hitachi 8010 Field Emission Electron Microscope (Hitachi, Tokyo, Japan).

DNA isolation
The harvested cultures were transferred to 1.5 ml tubes. DNA was isolated using Dynal DynaBeads (Invitrogen Corporation; Carlsbad, CA, USA), NucleoSpin Plant II Mini Kit (Machery and Nagel, Düren, Germany) or Qiagen Dneasy Plant Mini Kit (Qiagen Inc.; Valencia, CA) following the respective product instructions. DNA concentrations were checked using gel electrophoresis (1.5% agarose gel) and Nanodrop (PeqLab Biotechnology LLC; Erlangen, Germany). DNA samples were stored at 220uC until further use. DNA material was deposited in the Berlin collection of the DNA bank network [39].

PCR amplification
The V4 region of the 18S locus was amplified in all strains with the primer pair M13F-D512 for 18S/M13F-D978rev 18S [19]. The rbcL locus was amplified in two overlapping parts using two different primer pairs; Diat-rbcL-F and Diat-rbcL-iR as well as Diat-rbcL-iF and Diat-rbcL-R [40] for all strains. The polymerase chain reaction (PCR) for the V4 region was conducted after Zimmermann et al. (2011) [19] and for rbcL carried out after Abarca et al. (2014) [40]. PCR products were visualised in a 1.5% agarose gel and cleaned with MSB Spin PCRapace (Invitek LLC; Berlin, Germany) following standard procedure. DNA content was measured using Nanodrop (PeqLab Biotechnology). The samples were normalised to a total DNA content .100 ng/ml using Nanodrop (PeqLab Biotechnology) for further sequencing.

Molecular analysis
The aligned sequences were compared to each other calculating uncorrected p distances in PAUP [45]. Then they were blasted against existing INSDC entries for the respective taxa (accessed July 2013). All INSDC accessions with references are given in Appendix S1. Base pair differences were counted in overlapping parts of the sequences in Mega 5 [46]. Results are summarised in Table 3.

Tree building
To identify molecular relations between the here presented strains, trees were calculated with Mega 5 using the Neighbour Joining algorithm with gamma distributed rates among sites followed by a statistical test of the tree topologies with 10 000 bootstrap replications. Trees for the individual alignments of 18S V4 and rbcL sets as well as a concatenated dataset were calculated.
Furthermore, we created 18S V4 as well as rbcL datasets including INSDC sequences for the genera Amphora, Mayamaea, Planothidium and Stauroneis to exemplarily test the taxonomic consistency of available sequences as well as the placement of our new taxa. Each of these eight datasets was analysed under the aforementioned conditions.

Nomenclature
The electronic version of this article in Portable Document Format (PDF) in a work with an ISSN or ISBN will represent a published work according to the International Code of Nomenclature for algae, fungi, and plants, and hence the new names contained in the electronic publication of a PLOS ONE article are effectively published under that Code from the electronic edition alone, so there is no longer any need to provide printed copies. The online version of this work is archived and available from the following digital repositories: PubMed Central, LOCKSS. http:// edocs.fu-berlin.de/docs/content/below/index.xml.

Morphological analyses
The morphological identification of the 70 strains resulted in 37 taxa (see Table 2 and Figs. 3 and 4). 21 taxa were identified by only one strain but 10 taxa were represented by two strains, three taxa by three strains, one taxon by four strains, one taxon by five strains and one taxon by 11 strains.

DNA sequence analyses
PCR and sequencing success for 18S V4 and rbcL was 100% for all strains, resulting in 140 reference sequences for 70 strains. We established 129 novel sequences (INSDC accession numbers KM084866-KM084994) and an additional 11 sequences that had been previously published in Abarca et al. [40] and Zimmermann et al. [19].
There was little molecular variation within the here generated sequence data -only up to 0.5% in 18S V4 (representing 2 bp) and 0.3% in rbcL (corresponding to 3 bp) -between the different strains representing one taxon (Appendix S2). The highest intaxon variation was found in e.g. Mayamaea terrestris 0.53% (18S V4), respectively Navicula cryptocephala e.g. 0.33% (rbcL). The uncorrected p distances for all genera and sequences are given in Appendix S2.
The results from sequence comparison with sequences published in the databases of the International Nucleotide Sequence Database Collaboration (INSDC, includes GenBank, EMBL and DDBJ) are shown in Table 3 and summarised in Fig. 5a, 5b. In the case of 18S V4, 22% of our taxa had entries with identical sequences in the INSDC whereas for rbcL this number was 21% (Fig. 5b). This was the case e.g. for Caloneis silicula and Navicula cryptotenella (Table 3). 22% (18S V4, Fig. 5a) respectively 25% (rbcL, Fig. 5b) of our taxa had no entry in the INSDC databases, e.g. Amphora ovalis and Luticola sparsipunctata (Table 3). For 15% of our taxa an identical 18S V4 sequence (Fig. 5a) with a different taxon name was found in the INSDC databases (e.g. Gomphonema parvulum); the number was considerably lower in rbcL with only 4% (Fig. 5b). The remaining taxa of which many showed sequence dissimilarities of over 15 bp were 41% for 18S V4 (Fig. 5a) and 50% for rbcL (Fig. 5b). The highest difference was found for Pinnularia viridiformis with 97 bp in 18S V4 ( Table 3).
The tree derived from the concatenated data set and calculated by the Neighbour Joining (NJ) algorithm, including only the here presented strains, is shown in Fig. 6; the trees of the individual analysis of both markers are given in the Appendix S2. The molecular clades are congruent between 18S V4 and rbcL, the tree topology is partly differing between both markers (Appendix S3, S4); however, the conflicting nodes have bootstrap values below 0.85 and are therefore neglected.
In the tree derived from the combined dataset, the sampled genera are monophyletic and well supported (.0.98 bootstrap support BS, Fig. 6), except for Caloneis, Craticula and Sellaphora.
Craticula buderi falls into a clade with the genera Stauroneis and Karayevia (0.48 BS; Fig. 6). Sellaphora falls into one group with Eolimna (0.98 BS; Fig. 6). The genus Caloneis is found in two distinct clades: Caloneis silicula is clustering with Pinnularia (0.61 BS; Fig. 6), Caloneis amphisbaena forms an independent clade on its own (1.00 BS; Fig. 6). The deeper bifurcations representing the relationship between the genera are generally not well supported by bootstrap values. All 37 subgeneric taxa included in this study are monophyletic (Fig. 6).
The trees for the genus Amphora including all available data from INSDC databases (this includes also accessions from the genus Halamphora) are shown in Fig. 7a (18S V4) and Fig. 7b (rbcL). The Amphora ovalis strains (Amph1, Amph4, Amph5, D45_003 and TeAm01) form a monophyletic clade, that is well supported in both 18S (0.99 BS) and rbcL (0.97 BS). The strain HSB02, identified as Amphora berolinensis appears to be rather isolated within the Amphora tree, except for an affiliation with the unidentified strain C10 (INSDC accession number FJ002132) in the rbcL tree (0.89 BS; Fig. 7b). All strains identified as Amphora pediculus cluster in one clade in 18S V4 (0.90 BS; Fig. 7a) and rbcL (Fig. 7b). This includes also the strain D54_002 named Amphora sp. aff. atomoides. The tree derived from rbcL sequences also includes the strain AT-21.206 (INSDC accession number AN502022) identified as Amphora cf. fogediana (Fig. 7b), which forms a branch with strain s0992 named Amphora copulata (INSDC accession number AB754831) in 18S V4 adjacent to the Amphora pediculus clade (Fig. 7a). In respect to the other strains available from the INSDC databases there is no topology consistent with the taxonomic identifications found in the trees (Fig. 7a, 7b). Several taxa, including the species Amphora coffeaeformis, Amphora normannii and Amphora montana were     recently transferred to the genus Halamphora [37]; these taxa and also the two INSDC accessions listed as Halamphora in the (numbers AB754832, AB754833;) are forming a loose cluster in the upper part of the 18S V4 tree (Fig. 7a). The rbcL data set supports an independent clade for the taxa of the genus Halamphora (Amphora coffeaeformis, Amphora normannii, Am-   Fig. 7b). However, within the Halamphora clade the strains identified as Amphora coffaeaformis are not monophyletic (Fig. 7b).

Nomenclatural and taxonomical consequences
Two new taxa were first discovered by morphological means namely Amphora berolinensis and Stauroneis schmidiae. The analysis of molecular data suggested the existence of two more previously undetected taxa that could later be also morphologi-cally confirmed (Mayamaea terrestris, Planothidium caputium). For yet another two taxa morphological data is incomplete (teratological outline, micro-morphological data missing) but the molecular data show that they both are different from an identified taxon in this genus; these strains are named sp. (Amphora sp. aff. atomoides); in one case we used the term cf. (Amphora cf. pediculus) to show that it is closely related to a known taxon.

Amphora cf. pediculus
The strains D03_063 & D03_082 are morphologically very similar to our Amphora pediculus D03_074 but have double areolae in each ventral stria and not only a single elongated areola like A. pediculus. The specimens of these strains have a similar valve outline as A. indistincta, but in SEM the differences are more distinct because in A. indistincta the width of the central and dorsal side is almost equal and the striae are composed of elongated areolae.

Amphora sp. aff. atomoides Levkov
The strain D54_002 has a valve semi elliptical with arched dorsal margin, concave ventral margin and narrowly rounded valve ends. Valve length is 10-12.4 mm, breadth 4.6-5 mm. The central area on dorsal side is a rectangular fascia almost extending to the dorsal margin; on the ventral side the much broader fascia is expanding towards the valve margin. Raphe branches linear, filiform. Proximal raphe endings straight, distal raphe endings ventrally deflected. Dorsal striae radiate throughout, 16 in 10 mm.
This species closely resembles A. atomoides but differences can be observed in the shape of the central area and valve breadth (7-11 mm in A. atomoides). In A. atomoides the central area on the dorsal side is small or absent not extending to the valve margin, contrary to our Amphora sp. aff. atomoides where the central area presents a rectangular fascia almost extending to the dorsal margin. D54_002 also resembles A. pediculus with respect to its valve shape and size. However D54_002 can be differentiated by the valve width (A. pediculus is narrower with 2.5-4 mm) the central area (A pediculus has a distal raphe dorsally deflected and a central area with a rectangular facia, extended to the dorsal valve margin) and the stria density (A. pediculus has more striae 18-24/ 10 mm). D54_002 can also be differentiated from A. minutissima by the shape of valve apices (ventrally bent in A. minutissima). Additional observations of more specimens by SEM would be necessary to establish the proper identity of this population from Heiligensee, Berlin.
Amphora berolinensis differs from A. copulata (Kützing) Schoeman & Archibald because the latter has bigger valves (19-42 mm length, 5-7.5 mm breadth). In SEM the differences are more distinct. Differences can be observed in the shape of the central area (bordered by striae close to the valve margin in A. copulata), the raphe (biarcuate in A. copulata) and the morphology of the dorsal striae (crossed by longitudinal bars in A. copulata). A. berolinense also differs from A. neglectiformis Levkov & Edlund by the larger valves of the later (18-53 mm length, 5-7 mm breadth) and the ventral striae which are composed of two areolae in A. neglictiformis near the valve ends.
The valves of Amphora berolinensis are semi-lanceolate to semielliptical, with smoothly arched dorsal margin and straight to slightly concave ventral margin, valve ends rounded. Valve length is 9.5-18.9 mm, breadth 4.7-5.2 mm. Axial area is narrow, slightly arched. The central area on the dorsal side has a rectangular fascia extending to the dorsal margin; on the ventral side the fascia is wider expanding towards the valve margin. Raphe is filiform and more or less straight, in some valves the proximal raphe endings are straight, in others they are dorsally bent and the distal raphe endings are straight and in some valves they are ventrally bent. Dorsal striae are coarsely punctated and radiate throughout, 12-14 in 10 mm. Ventrally striae are radiate, composed of one areola.
The valves of Mayamaea terrestris are narrow linear-elipical, ends obtusely rounded. Valve length is 7-8.7 mm, breadth 3-4.5 mm. Striae are radiate throughout, 22-24 (-26) in 10 mm with c. 50 areolae in 10 mm. Raphe is filiform, the two branches are gently arcuate with distinct central pores. Axial area is slightly broad, widening lanceolately towards the middle of the valve. Central raphe ends expanded by depressions around the central pores and deflected, while the ends of the terminal raphe fissures are deflected to the opposite side.
This new species lives in soil; this is signified by the epithet name.
10 further strains ( have only low sequence differences for 18S V4 and rbcL (Appendix S2) and form a clade clearly different from all the other available Mayamaea strains (Fig. 7c, 7d).
Morphologically, Planothidium caputium has a similar outline as Planothidium lanceolatum but differs from it by a hood over the depression on the rapheless valve as in P. frequentissimum. The difference to P. frequentissimum lies in the form and size of the hood; which is bigger, longer and wider in P. caputium than in P. frequentissimum and the hood has a wider opening; this results in a line-like instead of a horse shoe appearance when focusing through the hood. The uncorrected p-distances show that Planothidium caputium sequences differ at least 2.4% (18S V4) respectively 2% (rbcL) from Planothidium frequentissimum, and 6% (18S V4) respectively 4% (rbcL) from Planothidium lanceolatum (Appendix S2), this is also represented in the trees including all available Planothidium strains (Fig. 8a, 8b).
Valves are elliptical to elliptic-lanceolate, with rounded apices. Valve length is 20-22.9 mm, breadth 5.5-6.4 mm. The striae are radiate on both valves, becoming more radiate towards the apices, with 13-14 in 10 mm. Striae are multiseriate with three to five rows of areolae per stria. The axial area is narrow and linear to lanceolate in both valves. A weak central area on the raphe valve and a horseshoe-shaped collar on one side of the rapheless valve which by focusing in LM another line less arched can be recognized (see also Straub 1990 [49]).
Also strain D06_113 belongs to this species.
Morphologically, Stauroneis schmidiae differs from Stauroneis borrichii (Petersen) Lund, which has a similar valve outline but with protracted ends, because the latter is shorter and more slender and has more striae  Valves are linear-lanceolate with very slightly rounded nonprotracted ends. Valve length is 27-28.2 mm, breadth 5.5-6 mm.
Striae are radiate throughout the entire valve, 15-18 in 10 mm. Puncta of the striae are discernible in LM and are 24-28 in 10 mm. Pseudosepta present.
Also strain D28_002 belongs to this species. Figure 5. Chart giving classes of base pair (bp) differences for both markers (18S V4, rbcL) between here presented molecular data and corresponding data from INSDC databases. Inferred from data in Table 3 Compared to the other available Stauroneis strains Stauroneis schmidiae clusters independently for both markers (Fig. 8c, 8d).
This species is named in honor of Prof. Dr. AnnaMaria Schmid who was an inspiring diatom teacher to Regine Jahn.

Discussion
The 37 naviculoid diatom taxa, of which reference barcodes are published here, represent only about 7% of the total diatom flora which is 14% of the naviculoid taxa recorded for Berlin waters (539 taxa, see [31]). Nevertheless, it is a first milestone in characterising diatoms not only by morphological but also by molecular means, which represents the start of a taxonomic reference library for diatoms.
Identification via DNA sequences is an important tool, especially in microorganisms. Many of the large scale environmental DNA barcoding studies in protists so far rely on higher taxonomic levels of families and above; only rarely they reach a  resolution at genus level. In diatoms, assignment to genus level is unproblematic [51,52]. Even identification to the species level is possible, but strongly depends on the quality of the reference database [52][53][54][55][56][57][58]. We here tested the taxonomic consistency of naviculoid diatom taxa at the species level by comparing our identified sequences with the published sequences in the repositories of the INSDC. We found that the taxonomic assignment in INSDC is currently unsatisfying, because it is often erroneous. In the data of the two commonly used DNA barcoding markers for diatoms 18S V4 and rbcL we analysed, we found that for rbcL 26% for the sequences listed under the same name as our strains more than 15 bp sequence difference were recorded (Fig. 5b); for 18S V4 this was 12% (Fig. 5a). For the 800 bp long rbcL fragment 15 bp difference amounts to roughly 2% sequence difference, in the shorter (400 bp) 18S V4 fragment 15 bp difference correlates to even 4%. The relatively high percentage of differences in these short DNA fragments suggests that the sequences belong to a different taxon. This implies morphology-related misidentification, mislabelling or cross-contamination. There are an additional 16% (rbcL, Fig. 5b) respectively 5% (18S V4, Fig. 5a) of the sequences where sequences with the same taxon name showed differences between 6 and 15 bp, here it is unclear whether these strains belong to a different taxon of a closely related cryptic species or whether they reflect natural intraspecific variation. Furthermore, we found that in 4% (rbcL, Fig. 5b) respectively 15% (18S V4, Fig. 5a) of the cases, identical sequences in the repositories of the INSDC were annotated with a different taxon name than the strains of this study. These sequences therefore provide an erroneous identification. In summary, the unevaluated use of information deposited in the INSDC leads to wrong identifications in at least 30% of the cases; in only about 20% of our cases, the identifications coincided unambiguously.
Unfortunately, in most cases it is not possible to trace the DNA sequence to the specimen from which it originated and, because of lacking voucher specimens, taxonomic evaluation is not possible; hence there are no means to verify whether a faulty taxon assignment had occurred or an interesting biological phenomenon. Therefore such sequences are of no future use and valuable information is lost to science. Assessment of diatom community composition through environmental DNA barcoding could greatly benefit from better documented reference libraries, especially because biodiversity in general should be evaluated at least on the species level [59].
Furthermore, the linkage between historically and morphologically described taxa and molecular sequences is not very strong. A possible threat is that two independent data clouds might develop [60]: one including large amounts of molecular data from environmental sequencing, the other species specific data (e.g. paleontological and recent distribution, ecology, phylogeny) linked to morphological descriptions. For organism groups where next to no morphology based data exist (e.g. many groups of bacteria), there is little harm if the information in the two clouds cannot be correlated. However, in groups like diatoms, where two centuries of data collection linked to morphologically described species exists, it would be a waste of painfully acquired data not to link these two groups of data. At the moment, this link would be a reference sequence that is connected to a morphological voucher (and DNA sample) deposited in a natural history collection and therefore available for multiple testing and verification of results as well as for long-term studies.
We here define a taxonomic reference library as an entity combining molecular data -in our case DNA sequence data of two markers -with morphological documentation of important features as well as a valid name. Also environmental information on the collecting site should be provided in a standardised format.
Documentation should also include the deposition of DNA in a curated repository. To ensure traceability of a name/sequence back to the specimen it originated from, morphological details important for identification should be provided in an online photographic documentation, this includes high-resolution photographs giving an overview of the cell as well as details produced by electron microscopy or comparable techniques. Another special aspect for diatoms (and some other microorganism groups) is that many sequences derive from cultured clonal strains, especially if they are linked to morphological entities. Therefore, the strain number and other strain specifications are valuable information that should be presented along with the sequence.
Ideally, all the necessary information for traceable taxonomic classification should be available in a single data portal; however, at the moment there are several technological limitations to deposit and/or respectively retrieve all the information in and from one location. The Consortium for the Barcode of Life (CBOL) aims at compiling DNA barcode records in a public library (Barcoding of Life Database BOLD) [53] and even designed a Barcode Submission Tool for submitting sequences to the INSDC databases. However, this tool is limited to one marker, namely the mitochondrial cytochrome oxidase subunit I (COI) e.g. [17,[61][62][63][64][65]. For many groups, e.g. plants [66] but also diatoms, this barcoding marker is not routinely applicable [19,[21][22][23][24][25], albeit there are BOLD supported activities to implement alternative solutions for some organism groups e.g. [28]. On the other hand, the Barcode Submission Tool provides possibilities to at least upload a pherogram (output of sanger sequencing), but no pictures of the organisms can be stored. Therefore, this tool does not require a link to a morphological voucher (digital and physical), which would allow for subsequent taxonomic validation. Also a link to a herbarium specimen is only indirectly possible if the accession number of the specimen collection is given and the respective collection has their specimen picture online available. Although, it seems generally possible to deposit pictures and other data along with the DNA sequence in BOLD [53], unfortunately, the data deposited within BOLD is often not open access, depending on the rights given by the administrator. Also, we heard reports that data is not released to the public even if requested by the author. In conclusion it would be preferable if INSDC would extend their service, as they are the most commonly used platform to deposit sequence data [58].
Here we present our strategy on how documentation can be performed to build a comprehensive reference database for diatoms even with inconvenient IT possibilities. The here presented materials and data have been documented as follows: The physical vouchers (microscopic slides and SEM stubs) have been deposited in the Berlin Herbarium (B), the DNA in the DNA bank network of the Botanic Garden and Botanical Museum Berlin-Dahlem [39]. The data for both items are made available through The Global Genome Biodiversity Network (GGBN [67]) and The Global Biodiversity Information Facility (GBIF [68]). The sequences have been submitted to an INSDC database (EMBL) along with strain numbers, voucher number from the Berlin Herbarium (B) and DNA bank number. Also primer details and geo-references have been deposited there. Photographic documentation is online available from the AlgaTerra Information System [30], linked through INSDC accession number and accession number from the Berlin Herbarium. Morphological characters, cultivation details as well as sampling data of the collecting sites beyond the geo-references (e.g. ecological specifications) have also been deposited in the AlgaTerra Information System [30].
A carefully documented reference sequence could be considered as something similar to a molecular type of the name of a species. Biological taxon types should be documented with a maximum amount of data, which makes it possible for every researcher to determine whether a specific specimen belongs to the concept of the designated type. In the botanical [69] and zoological [70] codes of nomenclature the basis for species description is the deposition of physical specimen. A reference sequence or reference barcode should be similarly well documented.
Biological identification systems are in constant development, therefore a continuous process of confirmation, validation and updating in relation to alpha taxonomy is required to build a compressive and accurate reference library. Protocols for data curation and revision are indispensable for new species discovery as well as taxonomic revisions. Therefore, entries in a taxonomic reference library (e.g. in an extended INSDC like system) need to be curated and updated in order to be in line with current taxonomy. However, a huge impediment for data curation by the respective author -once it is submitted -is, that there is no reward system for researchers for curating their data [71]. It has been shown, that incentives for researchers for the publication of thoroughly documented datasets similar to the publication of the conclusions drawn from these could greatly increase the motivation to publish datasets [71]. Another approach would be that data curation would be carried out by professional personnel employed for this purpose or a combination of both approaches.
Not only DNA barcoding approaches would benefit from well documented and referenced molecular data but also taxonomic and phylogenetic studies of diatoms which could integrate published data more efficiently if better documentation linked to physical objects were available [72]. For example, the clusters found for the genus Mayamaea, based on available 18S V4 and rbcL sequences, show low taxonomic consistency (Fig. 7c, 7d). The INSDC data suggest that there are different groups of Mayamaea (atomus var.) permitis, and within the Mayamaea atomus (var. atomus) sequences is one sequence named Mayamaea fossalis var. fossalis (Fig. 7c, 7d, black and red). For two of the AT strains included in the Mayamaea analysis additional data is available from the AlgaTerra Information System [30] (Fig. 7c, 7d, green): (a) more taxonomic detail is given than deposited alongside the sequence in INSDC -strain AT-115Gel07 is identified as Mayamaea atomus var. atomus and AT-101Gel04 as Mayamaea atomus var. permitis -and (b) photographs with morphological details are provided. Therefore the identification of both strains could be checked and verified. Even though additional data for only two strains is available from the AlgaTerra Information System [30], this already aids in the interpretation of the trees given in Fig. 7c and 7d; especially for the tree based on 18S V4. There is a cluster of Mayamaea permitis (Syn. Mayamaea atomus var. permitis), incl. strain AT-101Gel04, and one strain (AT-115Gel07) belonging to Mayamaea atomus var. atomus (Fig. 7c,  green). As Mayamaea permitis (Syn. Mayamaea atomus var. permitis) has been raised to species rank due to morphological reasons (see above), this allows the interpretation that Mayamaea fossalis could be an independent taxon (Fig. 7c, green). For the tree based on rbcL, however, only an informed guess can be made: for two strains, namely (Wes2)f and AT-199Gel01, no additional data is available to check the identification (Fig. 7d). If it could be assumed that (Wes2)f was misidentified and AT-199Gel01 belongs to Mayamaea permitis, again four independent taxa could be assumed: Mayamaea atomus, Mayamaea fossalis, Mayamaea permitis and Mayamaea terrestris. This example, particularly the different interpretation possibilities between 18S V4 and rbcL trees, clearly shows how valuable additional data can be for the interpretation of sequence based analyses.
Due to the fact that species descriptions in diatoms are based on morphology derived from microscopic pictures (of variable quality) of single, or a limited number, of valves from a presumed population in mixed samples, it is often difficult to unambiguously identify a strain. Even within a single clonal culture, morphological variation sometimes fits in parts to different species circumscriptions [45]. In addition, size wise clonal cultures are often at the lower end of the morphometrics of a taxon description; if cultured for too long and if no auxosporulation has taken place, diatom valves tend to lose their typical morphological features because they get smaller with each cell division. This leads to the problem how to link sequences derived from cultures to a type specimen or at least to a current species concept. If a type specimen is designated, this can be achieved e.g. through epitypification as has been done for Cocconeis pediculus and C. placentula [73,74]. But in most cases, this will be done in the context of a taxonomic revision of a species group as e.g. for Gomphonema saprophilum [45] and needs to be done for the two unidentified Pinnularia species of this study. For the purpose of a reference library, if no unambiguous identification seems possible, the sequence could either be designated as belonging to a certain ''formenkreis'' (taxon group) marked as affine (e.g. Amphora sp. aff. atomoides), as not exactly fitting the original descriptions marked as confer (e.g. Amphora cf. pediculus) [http://bionomenclature-glossary.gbif. org/], or a new taxon has to be described formally along with providing the reference sequence (e.g. Amphora berolinense). The first two options are a practical way to make re-users of the data aware of an ''uncertainty level'' concerning the taxonomic identification; this is better than providing no guidance to the species group by giving just the genus name such as Amphora sp. As we documented in this study, the marine or halophilic species of Amphora sensu lato have been recently moved into the genus Halamphora; for a freshwater reference library, this is important ecological data. In addition, this information might become valuable for the interpretation of taxonomic discrepancies

Conclusions
As here shown exemplarily for some naviculoid diatoms, taxonomic reference libraries could serve as an online accessible and algorithmically searchable equivalent to commonly used printed identification literature. They are needed to link molecular based identification technologies with correct organism references. However, up to now searchable data bases often include large percentages of wrongly annotated sequencesand provide no possibility to trace the identification back to the respective specimen, leaving molecular based techniques often with identifications only to family or genus level. While for some studies this level of taxonomic depth seems to suffice (e.g. large scale biodiversity assessments), there are many studies that could profit from well documented molecular data (e.g. species inventories, monitoring, taxonomy, phylogeny). Therefore, it would be worth


extfieldsofstudy: Biology Medicine

s2fieldsofstudy: Biology Medicine

text:
Interactions of the Protein-tyrosine Phosphatase-α with the Focal Adhesion Targeting Domain of Focal Adhesion Kinase Are Involved in Interleukin-1 Signaling in Fibroblasts*

Background: Interleukin-1 signaling in fibroblasts is mediated through focal adhesions, which are enriched with tyrosine kinases and phosphatases. Results: The focal adhesion targeting domain of FAK interacts with protein-tyrosine phosphatase-α (PTPα) to restrict interleukin-induced Ca2+ release, ERK activation, and MMP-9 expression. Conclusion: Signaling through focal adhesions requires FAK and PTPα. Significance: FAK and PTPα cooperate to restrict IL-1 signaling. Interleukin-1 (IL-1) signaling in fibroblasts is mediated through focal adhesions, organelles that are enriched with adaptor and cytoskeletal proteins that regulate signal transduction. We examined interactions of the focal adhesion kinase (FAK) with protein-tyrosine phosphatase-α (PTP-α) in IL-1 signaling. In wild type and FAK knock-out mouse embryonic fibroblasts, we found by immunoblotting, immunoprecipitation, immunostaining, and gene silencing that FAK is required for IL-1-mediated sequestration of PTPα to focal adhesions. Immunoprecipitation and pulldown assays of purified proteins demonstrated a direct interaction between FAK and PTPα, which was dependent on the FAT domain of FAK and by an intact membrane-proximal phosphatase domain of PTPα. Recruitment of PTPα to focal adhesions, IL-1-induced Ca2+ release from the endoplasmic reticulum, ERK activation, and IL-6, MMP-3, and MMP-9 expression were all blocked in FAK knock-out fibroblasts. These processes were restored in FAK knock-out cells transfected with wild type FAK, FAT domain, and FRNK. Our data indicate that IL-1-induced signaling through focal adhesions involves interactions between the FAT domain of FAK and PTPα.

Interleukin-1 (IL-1) signaling in fibroblasts is mediated through focal adhesions, organelles that are enriched with adaptor and cytoskeletal proteins that regulate signal transduction. We examined interactions of the focal adhesion kinase (FAK) with protein-tyrosine phosphatase-␣ (PTP-␣) in IL-1 signaling.
In wild type and FAK knock-out mouse embryonic fibroblasts, we found by immunoblotting, immunoprecipitation, immunostaining, and gene silencing that FAK is required for IL-1-mediated sequestration of PTP␣ to focal adhesions. Immunoprecipitation and pulldown assays of purified proteins demonstrated a direct interaction between FAK and PTP␣, which was dependent on the FAT domain of FAK and by an intact membraneproximal phosphatase domain of PTP␣. Recruitment of PTP␣ to focal adhesions, IL-1-induced Ca 2؉ release from the endoplasmic reticulum, ERK activation, and IL-6, MMP-3, and MMP-9 expression were all blocked in FAK knock-out fibroblasts. These processes were restored in FAK knock-out cells transfected with wild type FAK, FAT domain, and FRNK. Our data indicate that IL-1-induced signaling through focal adhesions involves interactions between the FAT domain of FAK and PTP␣.
Interleukin-1 (IL-1) is a family of potent, pro-inflammatory cytokines that can induce multiple signaling cascades (1), which contribute to inflammatory tissue injury (2). IL-1 stimulates the expression of the early response genes c-fos and c-jun as well as multiple cytokines such as interleukin-6 (IL-6) (3) and inflam-matory factors that drive extracellular matrix degradation (4) via the up-regulation of various proteases, including members of the matrix metalloproteinase (MMP) 2 family such as MMP-9 in connective tissue cells (5). Enhanced expression of IL-6 (3), MMP-3 (6), and MMP-9 by IL-1 involves the activation of several interdependent signaling cascades that include the mitogen-activated protein kinase (MAPK) subfamily members, extracellular-signal regulated kinase (ERK), p38 MAPK, and stress-activated c-Jun N-terminal kinase (7). Although earlier studies have suggested a potential regulatory role of integrin receptors and the focal adhesion kinase (FAK) in MMP-9 expression (8), the mechanisms that coordinate the activation of these MAPK members in IL-6, MMP-3, and MMP-9 expression downstream of the IL-1 receptor are not well defined.
Focal adhesions (FAs) are mechanical linkages that connect the actin cytoskeleton to the extracellular matrix and serve as signaling platforms that concentrate numerous signaling and scaffolding proteins at regions of integrin receptor binding and clustering (9,10). Spatial co-localization of interacting signaling molecules provides a pivotal regulatory locus for signal transduction. In adherent cells such as fibroblasts, the formation of FAs is required for IL-1-induced signaling cascades leading to tyrosine phosphorylation and activation of the focal adhesion kinase (11), Ca 2ϩ release from the endoplasmic reticulum (ER) (12,13), and activation of ERK (14,15), which ultimately result in regulating the expression of MMPs (6,16).
FAK is a ubiquitously expressed, nonreceptor protein-tyrosine kinase that associates with integrin receptors and plays an integral role in integrin-mediated signaling (17,18). The N terminus of FAK contains the major autophosphorylation site, Tyr 397 , which binds the Src homology 2 domains of phospholipase C␥ (19), Shc (17), and Src family kinases (e.g. Src and Fyn) (20). Following binding, activated Src phosphorylates the C-terminal Tyr 925 residue on FAK, which consequently recruits Grb2 (21). Phospholipase C␥ catalyzes the hydrolysis of phosphatidylinositol 4,5-bisphosphate generating a secondary messenger, inositol 1,4,5-trisphosphate, which mobilizes Ca 2ϩ , whereas Shc and Grb2 serve as adaptors for signal transduction by the ERK pathway. These processes indicate that FAK may be important in coupling components of Ca 2ϩ and ERK signaling downstream of the IL-1 receptor by regulating tyrosine phosphorylation status of other signaling molecules and by interacting with other adaptor proteins.
The dynamic and reversible nature of tyrosine phosphorylation of focal adhesion proteins indicates an important role for protein-tyrosine kinases and phosphatases (PTPs) in focal adhesion-dependent signaling (22). Indeed, there are numerous PTPs in FAs. In particular, PTP␣ plays a prominent role in the regulation of FA remodeling and in cell adhesion and signaling (23). PTP␣ is a receptor-like PTP that activates Src family kinases (e.g. Src and Fyn) via dephosphorylation of an inhibitory C-terminal tyrosine residue (24 -29). Through its interactions with Src, we showed that PTP␣ controls IL-1-induced phosphorylation of the inositol 1,4,5-trisphosphate receptor1 (IP 3 R1) and consequently Ca 2ϩ release (30). Furthermore, PTP␣ regulates formation and maturation of FAs in response to mechanical force, reinforces connections between integrins and the cytoskeleton, and modulates cytoskeletal reorganization in response to integrin ligation (28,29). In the absence of PTP␣, fibroblasts show reduced spreading, increased numbers of abnormal FAs, decreased tyrosine phosphorylation of focal adhesion kinase and p130Cas, as well as attenuated ERK activation during adhesion and spreading (26).
Our previous studies have partially characterized the roles of PTP␣ in focal adhesion-dependent IL-1 signaling (6,23,30); however, it is not known whether PTP␣ and FAK collaborate to regulate IL-1 signaling through FAs. Furthermore, we do not understand how PTP␣ is spatially sequestered to FAs and whether it interacts with FAK to enable adhesion-restricted IL-1 signaling. Consequently, we examined the functional importance of FAK and three of its domains (band4.1-ezrinradixin-moesin (FERM) homology domain, kinase domain, and focal adhesion-targeting (FAT) domain) in influencing the interactions between FAK and PTP␣, as well as the impact on IL-1-induced signaling that leads to Ca 2ϩ release, ERK activation, and IL-6, MMP-3, and MMP-9 expression.
FAK Constructs and Transfection-pEGFP-FAK, pEGFP-FAK Y397F, pEGFP-FAK L1035S and pEGFP-FRNK constructs were provided by J. Thomas Parsons (Department of Microbiology and Cancer Center, University of Virginia, Charlottesville, VA). Transfections were performed with FuGENE HD (Promega, Madison, WI) according to the manufacturer's instructions. The siRNA transfections were conducted with DharmaFECT 1 (Thermo Fisher Scientific, Boulder, CO) according to the manufacturer's protocol.
FAK Expression Constructs-The cDNA templates of chicken wild type FAK, FAK Y397F, FAK L1035S, and FRNK (from J. Thomas Parsons) were amplified using corresponding primers that were designed according to the GenBank TM number provided on Table 1 and with Phusion HF DNA polymerase (New England Biolabs, Mississauga, Ontario, Canada), although PCR of FERM (amino acids 1-415), kinase (amino acids 416 -676), and FAT (amino acids 908 -1053) domains (32) of FAK (from J. Thomas Parsons) were carried out using Pfu DNA polymerase (Thermo Scientific Canada, Ontario, Canada). The resulting PCR products were either digested with BamHI and XhoI, as highlighted in the primer sequences, and cloned (T4 DNA ligase, New England Biolabs) into pGEX-4T-2 digested with the same enzymes, or ligated into BamHI-and XhoIlinearized pGEX-4T-2 directly using In-fusion HD enzyme premix (Clontech) after gel purification. The sequences of the inserts were confirmed (ACGT Corp., Toronto, Ontario, Canada), and constructs were transformed into BL21 (DE3) Escherichia coli (Agilent, Mississauga, Ontario, Canada) for protein expression and purification.
Isolation of FAs-Focal adhesion complexes were isolated from cells incubated with collagen-or BSA-coated magnetite beads after specific incubation time periods as described (30). In brief, cell-bead complexes were scraped into ice-cold cytoskeleton extraction buffer (CSKB: 0.5% Triton X-100, 50 mM NaCl, 300 mM sucrose, 3 mM MgCl 2 , 20 g/ml aprotinin, 1 g/ml leupeptin, 1 g/ml pepstatin, 1 mM phenylmethylsulfonyl fluoride, 10 mM PIPES, pH 6.8), and after washing the beads three times in CSKB using magnetic separation to remove nonspecific proteins, the remaining bead-associated focal adhesion proteins were eluted in Laemmli sample buffer by boiling for 10 min.
Subcellular Fractionation-Examination of ER fraction proteins was performed as described (33). Briefly, cells were resuspended in an isotonic buffer (10 mM Tris, pH 7.6, 100 mM CaCl 2 , 200 mM sucrose) and disrupted by Dounce homogenization using 20 strokes. The homogenate was centrifuged at 800 ϫ g for 10 min. The supernatant was further centrifuged for 10 min at 8,000 ϫ g, and the resulting supernatant was again centrifuged for 1.5 h at 28,000 ϫ g. The resulting pellet constituted the microsomal ER-enriched fraction. The authenticity of this putative ER fraction was confirmed by immunoblotting for the ER-specific protein calnexin.
Immunoblotting-Equal amounts of protein as determined by the Bradford assay (Bio-Rad) were resolved by SDS-PAGE and transferred onto nitrocellulose membranes. Immunoblotting was performed by blocking membranes with 5% milk or 2% BSA in Tris-buffered saline solution (TBS) for 1 h and then probing with primary antibodies overnight at 4°C in TBS with 0.1% Tween 20 and 5% milk or 2% BSA. The membranes were then incubated with HRP-conjugated secondary antibodies for 1 h in TBS with 0.1% Tween 20. All steps were done at room temperature, unless indicated otherwise. Labeled proteins were visualized by chemiluminescence using ECL reagent (Amersham Biosciences) according to the manufacturer's instructions.
Measurement of Ca 2ϩ in ER Stores-For estimating [Ca 2ϩ ] ER , cells were incubated with mag-fura-2/AM (4 M) for 150 min at 37°C in culture medium and measured by ratio fluorimetry as described (13). The nominally Ca 2ϩ -free buffer consisted of a bicarbonate-free medium containing 150 mM NaCl, 5 mM KCl, 10 mM D-glucose,1 mM MgSO 4 , 1 mM Na 2 HPO 4 , and 20 mM HEPES, pH 7.4, with an osmolarity of 291 mosM. For experiments requiring external Ca 2ϩ , 2 mM CaCl 2 was added to the buffer; for experiments requiring chelation of external Ca 2ϩ , 1 mM EGTA was added. Visual inspection of mag-fura-2-loaded cells showed fluorescent labeling of intracellular organelles. Mag fura-2 ratios were obtained with a C⅐Imaging System (Compix, Inc., Cranberry, PA) using excitation wavelengths of 340 and 380 nm and an emission wavelength of 520 nm.
Quantitative Real Time PCR-After IL-1 stimulation in low serum (1% FBS) DMEM, total RNA was extracted from FAK MEFs using an RNeasy mini kit (Qiagen, Mississauga, Ontario, Canada) according to the manufacturer's instructions. Total RNA samples (1 g; as determined with a NanoDrop 1000 spectrophotometer) were reverse-transcribed using the iScript TM cDNA synthesis kit (Bio-Rad) according to the man-

TABLE 1 Primer sequences used in the generation of GST fusion constructs
Fwd is forward, and Rev is reverse.
Experimental Design and Analysis-Data shown are representative of independent experiments conducted in triplicate. For numerical data, means Ϯ S.E. were calculated. When appropriate, Student's t test was used to compare two groups. For three or more groups, analysis of variance was used. Statistical significance was set at p Ͻ 0.05.

Accumulation of PTP␣ in FAs
Requires FAK-Focal adhesions are enriched with tyrosine phosphatases that may regulate signaling through FAs (34). PTP␣ is a critical adaptor in mediating functional links between FAs and the ER, a process that enables IL-1-induced Ca 2ϩ signaling and MMP-3 expression (6,30). To assess the fibroblasts used in the current experiments and to confirm key phenotypic features, we determined whether IL-1 affects the association of PTP␣ with FA-and ERassociated proteins in FAK ϩ/ϩ MEFs. After IL-1 treatment, the relative abundance of PTP␣ in focal adhesion preparations (which also contain plasma membrane constituents) and in ER fractions was increased by IL-1 treatment (Fig. 1A). By contrast, the relative abundance of the loading control proteins GAPDH (in whole cell lysates), ␣5␤1 integrin (in FA fractions), and calnexin (in ER fractions) was unchanged by IL-1 treatment.
We next determined whether the recruitment of PTP␣ to FAs in response to IL-1 was dependent on FAK. The relative abundance of FAK and PTP␣ in whole cell lysates or focal adhesion preparations was examined by immunoblotting lysates prepared from FAK wild type (FAK ϩ/ϩ ) and FAK knock-out (FAK Ϫ/Ϫ ) MEFs. IL-1 treatment enhanced the accumulation of PTP␣ and FAK in the FAs of FAK ϩ/ϩ cells but had a much smaller effect on the abundance of PTP␣ in the FAs of FAK Ϫ/Ϫ MEFs (Fig. 1B). We also found that IL-1 promoted the recruitment of FAK and PTP␣ to focal adhesion fractions prepared from FAK Ϫ/Ϫ MEFs that were transfected with wild type FAK (pEGFP-FAK) (Fig. 1C). The IL-1-enhanced accumulation of FAK and PTP␣ in focal adhesion fractions was strongly reduced in FAK ϩ/ϩ MEFs that had been transfected with FRNK (FAKrelated non-kinase), which strongly localizes to FAs but acts as a dominant negative inhibitor of FAK (Fig. 1D). Notably, the amount of calnexin and IP 3 R1 in the FAs of FAK Ϫ/Ϫ MEFs were also much lower than FAK ϩ/ϩ MEFs (Fig. 1B). Taken together, these data indicate that IL-1 signaling mediates associations of PTP␣ with FAs and with the ER that are dependent on FAK.
We examined the spatial association of FAK and PTP␣ in FAs using total internal reflection fluorescence microscopy of FAK ϩ/ϩ and FAK Ϫ/Ϫ MEFs. Cells were treated with vehicle or with IL-1 for 30 min and co-immunostained for paxillin and FAK ( Fig. 2A) or for paxillin and PTP␣ (Fig. 2B). The extent of co-localization of paxillin with FAK and the co-localization of paxillin with PTP␣ was quantified by calculating Pearson's correlation coefficient (35). These data showed that PTP␣ strongly co-localized with paxillin in FAK ϩ/ϩ MEFs but not in FAK Ϫ/Ϫ FIGURE 1. IL-1 induces recruitment of PTP␣ to FA and ER, and FAK is required for IL-1-induced PTP␣ accumulation in FAs. A, whole cell lysates (WCL), FA, and ER fractions were isolated as described under "Experimental Procedures" from FAK ϩ/ϩ MEFs treated with (ϩ) or without (Ϫ) IL-1 at 20 ng/ml for 30 min. Equivalent amounts of whole cell lysates, FA, and ER fractions were immunoblotted for PTP␣, GAPDH, ␣5␤1 integrin, and calnexin; the latter three were used as loading controls for WCL, FA, and ER fractions, respectively. B, WCL and FA proteins prepared from FAK ϩ/ϩ and FAK Ϫ/Ϫ MEFs treated with vehicle (Ϫ) or with (ϩ) IL-1 (20 ng/ml) for 30 min were immunoblotted for FAK and PTP␣. FA proteins were also immunoblotted for ␣5␤1 integrin, calnexin, and IP 3 R1. Same experiment as in B was done with C, FAK Ϫ/Ϫ MEFs transfected with pEGFP-control (pEGFP-C) and FAK wild type (pEGFP-FAK), as well as with D, FAK ϩ/ϩ MEFs were transfected with pEGFPcontrol (pEGFP-C) and FAK-related non-kinase (pEGFP-FRNK).
MEFs (p Ͻ 0.01). IL-1 treatment did not significantly change the extent of co-localization of PTP␣ with paxillin or with FAK in FAK ϩ/ϩ MEFs. These results indicate that FAK is required for accumulation of PTP␣ in FAs. Notably, the areas of FAs were much larger in FAK Ϫ/Ϫ than FAK ϩ/ϩ MEFs, consistent with previous reports indicating that FAK null fibroblasts have defective FA turnover mechanisms that result in highly adherent, large and stable FAs (36). Similarly, PTP␣ Ϫ/Ϫ MEFs exhibit large, super-mature FAs (23), indicating the importance of both of these proteins in FA remodeling.
FAK Is Required for IL-1-stimulated PTP␣-Tyr 789 Phosphorylation-Because the phosphorylation of Tyr 789 of PTP␣ regulates the localization of PTP␣ to FAs as well as integrininduced cell spreading (29), we examined whether FAK is required for IL-1-induced phosphorylation of PTP␣ at Tyr 789 . FAK ϩ/ϩ and FAK Ϫ/Ϫ MEFs were treated with vehicle or with IL-1, and PTP␣ immunoprecipitates were immunoblotted for PTP␣-Tyr(P) 789 . FAK Ϫ/Ϫ MEFs exhibited more prolonged and 4-fold lower PTP␣-Tyr 789 phosphorylation compared with FAK ϩ/ϩ MEFs after IL-1 stimulation (Fig. 3A, 30 min, p Ͻ 0.001). Transfection of FAK Ϫ/Ϫ MEFs with wild type FAK restored IL-1-induced PTP␣-Tyr 789 phosphorylation by 87% at 30 min (Fig. 3, A and B, p Ͻ 0.001). Although transfection of FAK Ϫ/Ϫ MEFs with a FAK-Y397F mutant did not significantly increase PTP␣-Tyr 789 phosphorylation in response to IL-1, expression of the FAK-L1035S mutant restored PTP␣-Tyr 789 phosphorylation levels comparable with that of wild type FAK. These data indicate that the Tyr 397 autophosphorylation site of FAK may play a role in PTP␣-Tyr 789 phosphorylation (Fig. 3B). Furthermore, we found that in FAK ϩ/ϩ MEFs transfected with FRNK, which strongly localizes to FAs and acts as a dominant negative inhibitor of endogenous FAK; the level of PTP␣- Tyr 789 phosphorylation in response to IL-1 was reduced by 91% (Fig. 3B, p Ͻ 0.001), thus underlining the importance of functional FAK in IL-1-induced PTP␣-Tyr 789 phosphorylation.
Src family kinase activation can be estimated from the phosphotyrosine levels of the inhibitory Tyr 527 in Src, a target site for dephosphorylation by PTP␣ (37,38). We examined the impact of FAK on IL-1-induced Src-Tyr 527 phosphorylation. FAK Ϫ/Ϫ MEFs that were transfected with wild type FAK showed very low levels of phosphorylation of Tyr 527 compared with control cells (Fig. 3C). Transfection of FAK Ϫ/Ϫ MEFs with PTP␣ Is Required for IL-1-stimulated FAK-Tyr 397 Phosphorylation-We determined whether autophosphorylation of FAK, which mediates its interaction with signaling molecules such as Src family kinases, is affected by PTP␣. We examined IL-1-induced FAK-Tyr 397 phosphorylation in cells with or without PTP␣. Compared with cells transfected with control siRNA, knockdown of PTP␣ reduced by 55% IL-1-induced FAK-Tyr 397 phosphorylation (30 min after IL-1 treatment; Fig.  4A, p Ͻ 0.01). Furthermore, there was a 75% reduction of IL-1induced FAK-Tyr 397 phosphorylation in PTP␣ Ϫ/Ϫ null cells compared with PTP␣ wild type cells 30 min after IL-1 stimulation (Fig. 4B, left panel, p Ͻ 0.001).
We examined whether the phosphorylation of FAK was dependent on the presence of catalytically active PTP␣. In cells that expressed phosphatase-inactive PTP␣ (i.e. NIH3T3 cells overexpressing a catalytically inert PTP␣ mutant C433S/ C723S, NIH3T3 CCSS ), IL-1-induced FAK-Tyr 397 phosphorylation was 62% lower than NIH3T3 fibroblasts expressing wild type PTP␣ (NIH3T3 PTP␣ ) (Fig. 4B, right panel, p Ͻ 0.01). In cells expressing the Y789F mutant (NIH3T3 Y789F ), FAK phosphorylation of Tyr 397 in response to IL-1 was comparable with wild type cells. These results indicate that the catalytic activity but not phosphorylation of Tyr 789 of PTP␣ is important for IL-1-induced FAK-Tyr 397 phosphorylation.
Associations between FAK and PTP␣-FAK and PTP␣ are both critical for focal adhesion-dependent cell adhesion through integrins (23,28,29,39). To understand how PTP␣ is spatially sequestered to FAs and how it interacts with FAK to enable adhesion-restricted IL-1 signaling, we verified whether PTP␣ associates with FAK in response to IL-1. Examination of FAK immunoprecipitates that were immunoblotted for PTP␣, or PTP␣ immunoprecipitates that were immunoblotted for FAK, showed a time-dependent enhancement of the association of FAK with PTP␣ that peaked ϳ40 min after IL-1 stimulation (Fig. 5A).
The phosphorylation of FAK at Tyr 397 is critical for its kinase activity (40). In addition, interaction of FAK with paxillin is impaired by a point mutation in the FAT domain (Leu 1035 to Ser), which disrupts paxillin binding. Accordingly, we examined the effect of expressing FAK Y397F and FAK L1035S mutants on the association of FAK with PTP␣. FAK Ϫ/Ϫ MEFs were transfected with pEGFP-FAK (FAK wild type), pEGFP-FAK Y397F (FAK Y397F), or pEGFP-FAK L1035S (FAK L1035S). FAK immunoprecipitates were prepared from whole cell lysates of vehicle or IL-1-treated cells and immunoblotted for PTP␣ and FAK (Fig. 5B, left panel). Expression of the Y397F and L1035S mutants did not affect IL-1-induced association between FAK and PTP␣, indicating that the Tyr 397 and Leu 1035 sites do not directly affect the association of FAK with PTP␣.
We also examined the requirements for the catalytic and adaptor functions of PTP␣ to enable associations between FAK and PTP␣ with the use of cells expressing the C433S/C723S or Y789F mutants, respectively. NIH3T3 fibroblasts expressing wild type PTP␣ (designated as NIH3T3 PTP␣ ), catalytically inert PTP␣ (C433S/C723S; designated as NIH3T3 CCSS ), and PTP␣ Y789F mutant (designated as NIH3T3 Y789F ) were treated with vehicle or IL-1. PTP␣ immunoprecipitates were prepared from whole cell lysates and immunoblotted for FAK and PTP␣. The association between FAK and PTP␣ was dependent on the integrity of the catalytic domain of PTP␣ because in NIH3T3 fibroblasts expressing the catalytically defective PTP␣ (C433S/ C723S mutant), there was ϳ85% reduction of FAK that co-precipitated with PTP␣ even after IL-1 treatment (Fig. 5B, right   panel, p Ͻ 0.001). The expression of the Y789F mutant did not affect the association between FAK and PTP␣. We suggest that the PTP␣-FAK interaction may precede interactions with other proteins like paxillin and Grb2 and phosphorylation events associated with these proteins, which in turn affect the catalytic activity of FAK and PTP␣.
We assessed whether FAK expression affects the association of PTP␣ with Src in cells treated with IL-1. FAK ϩ/ϩ and FAK Ϫ/Ϫ MEFs were treated with IL-1 or vehicle. PTP␣ immunoprecipitates were prepared from whole cell lysates and immunoblotted for Src. We found that PTP␣ associates with Src after IL-1. However, this association was partly dependent on the presence of FAK because in FAK-null cells, the IL-1induced association of PTP␣ with Src was decreased (Fig. 5C,  left panel). Furthermore, we found that after IL-1 stimulation, Src-Tyr 527 phosphorylation was abolished in NIH3T3 fibroblasts that expressed wild type PTP␣ (NIH3T3 PTP␣ ) compared with NIH3T3 fibroblasts expressing the catalytically defective PTP␣ (C433S/C723S mutant) (Fig. 5C, right panel), indicating that an intact catalytic phosphatase domain of PTP␣ is essential for Src-Tyr 527 dephosphorylation and thus activation. Collectively, the association of FAK with PTP␣ appears to be important for the association of PTP␣ with Src and Src-Tyr 527 dephosphorylation that is required for Src activation.
Interactions of FAK with PTP␣-Direct associations between FAK and PTP␣ were examined with pulldown assays using purified GST-tagged PTP␣ proteins. These bacterially expressed mutant proteins included either the entire cytosolic domain (GST-cPTP␣) or the catalytic domain D1 alone (GST-PTP␣ D1) or the D2 alone (GST-PTP␣ D2). Bead-bound proteins were incubated in a cell-free system with bacterially expressed FAK. GST-associated proteins and FAK were detected by immunoblotting (Fig. 6A). These data showed that purified FAK directly interacted with the whole cytosolic domain  of PTP␣ as well as the D1 catalytic domain but not with the catalytic domain D2.
FAK exhibits a domain structure consisting of a FERM, kinase, and focal adhesion-targeting (FAT) domain (40). We assessed which of these FAK domains binds to PTP␣. Wild type FAK, FERM, kinase, and FAT domains of FAK bound to GST were purified and incubated in a cell-free system with bacterially expressed cPTP␣. GST-associated proteins were immunoblotted for PTP␣. Equal protein loading was verified by immunoblotting for GST (Fig. 6B). These data showed that purified cPTP␣ interacted directly with wild type FAK as well as the FAT domain of FAK and FRNK, indicating that interactions between FAK and PTP␣ specifically require an intact FAT domain.

FAK Is Required for IL-1-induced PTP␣ Accumulation in ER-
For many complex regulatory systems, including IL-1, anchorage of signaling proteins to specific organellar membranes is required for effective signal transduction (41). We showed that PTP␣ co-localizes with ER-associated proteins (e.g. calnexin, IP 3 R1) in FAs, and this is further enhanced by IL-1 (30). In the current experiments, we observed that IL-1 treatment enhanced accumulation of PTP␣ in ER fractions of FAK ϩ/ϩ cells and in FAK Ϫ/Ϫ cells expressing wild type FAK (pEGFP-FAK) but not in FAK Ϫ/Ϫ MEFs (transfected with or without pEGFP-control (pEGFP-C)) (Fig. 7A). Furthermore, the ability of IL-1 to enhance the accumulation of FAK and PTP␣ in ER fractions was dramatically reduced in FAK ϩ/ϩ cells transfected with FRNK (an endogenous inhibitor of FAK), indicating that FA localization of FAK is required for IL-1-induced PTP␣ accumulation in ER fractions.
Immunoblot analysis of PTP␣ or FAK from FAK ϩ/ϩ or PTP␣ ϩ/ϩ MEFs showed that IL-1 treatment enhanced the amount of IP 3 R1 that co-precipitated with PTP␣ and with FAK in whole cell lysates prepared from these cells. There was very little IP 3 R1 that co-precipitated with PTP␣ in FAK Ϫ/Ϫ cells (Fig. 7B). Collectively, these results indicate that FAK binds to PTP␣, thereby facilitating IL-1-induced enrichment of PTP␣ in FAs and in proximal ER membranes and interaction with IP 3 R1.
Requirement for FAK in IL-1-induced Ca 2ϩ Signaling-IL-1 triggers FA-dependent Ca 2ϩ release from the ER (12,13). The experiments described above (Fig. 7B) demonstrated that IL-1 treatment enhanced co-precipitation of IP 3 R1 with FAK and PTP␣. Because previous studies showed that FAK is critical in regulating cell adhesion, contractility, migration, and signaling (42), we determined whether FAK regulates Ca 2ϩ signaling in response to IL-1. In FAK ϩ/ϩ MEFs, IL-1 treatment resulted in a transient release of Ca 2ϩ from the ER (Fig. 8A). By contrast, the amplitude of IL-1-induced ER Ca 2ϩ signals was reduced by Ͼ5-fold (p Ͻ 0.01) in FAK Ϫ/Ϫ MEFs. This defect could be reversed by transfecting FAK null cells with wild type FAK (Fig.  8B). Notably, there was a Ͼ3and 2-fold higher response (p Ͻ 0.01) in FAK Ϫ/Ϫ MEFs transfected with FAT domain or FRNK compared with FAK null cells (Fig. 8C). However, there was no change in FERM ϩ kinase domain transfections. Similarly, FAK wild type (FAK ϩ/ϩ ) cells expressing FRNK (Fig. 8D) exhibited a Ͼ3.5-fold (p Ͻ 0.01) lower ER Ca 2ϩ release compared with cells expressing the pEGFP-control (pEGFP-C). Taken together, these data indicate that the FAT domain of FAK is important for IL-1-induced Ca 2ϩ release from the ER.
FAK Restricts IL-1-induced ERK Phosphorylation-In many signaling systems, Ca 2ϩ release from the ER is required for ERK activation (43). Furthermore, FAK mediates activation of the ERK pathway in response to integrin ligation (17). Accordingly, we examined the role of FAK in IL-1-induced ERK activation in FAK ϩ/ϩ and FAK Ϫ/Ϫ MEFs (Fig. 9A). FAK ϩ/ϩ cells displayed a time-dependent increase in ERK phosphorylation in response to IL-1 treatment; by contrast, IL-1 did not induce ERK phosphorylation in FAK Ϫ/Ϫ MEFs As a control, when cells were plated on poly-L-lysine to prevent the formation of FAs, IL-1-in- duced ERK activation was not detectable in FAK ϩ/ϩ MEFs (Fig.  9A). These data indicate that formation of FAs, along with the expression of FAK, is crucial for IL-1-induced ERK activation.
To determine the role of FAK domains in ERK activation, we studied the effects of the FAT domain, FRNK, and the FERM ϩ kinase domains on IL-1-induced signaling using transfected FAK Ϫ/Ϫ and FAK ϩ/ϩ MEFs. In FAK Ϫ/Ϫ MEFs transfected with wild type FAK, the FAT domain, or FRNK, IL-1-induced ERK phosphorylation was increased. When FAK Ϫ/Ϫ MEFs were transfected with pEGFP-control or the FERM ϩ kinase domains, there was markedly reduced IL-1-induced ERK phosphorylation. Similarly, in FAK ϩ/ϩ cells transfected with pEGF-FRNK, IL-1-induced ERK phosphorylation was reduced (Fig.  9B). These data indicate that the FAT domain of FAK is required for IL-1 signaling to ERK.
FAK Regulates IL-1-induced IL-6, MMP-3, and MMP-9 Expression-IL-1 signaling leads to the expression of the early response gene c-fos and several cytokines and inflammatory factors that drive extracellular matrix remodeling via MMPs (4). Currently, it is not known whether FAK mediates IL-1induced expression of matrix-destructive genes. Hence, we examined the impact of FAK on IL-1-induced IL-6, MMP-3, and MMP-9 release into conditioned media of NIH3T3 fibroblasts. The cells were transfected with control siRNA or siRNA FAK and treated with IL-1 for 6 or 24 h. From ELISA analyses, FAK knockdown cells exhibited markedly reduced expression of MMP-3 in response to IL-1 at 6 and 24 h compared with control siRNA (Fig. 10A, p Ͻ 0.01). IL-1 also enhanced the secretion of MMP-9 and IL-6 at 6 and 24 h by NIH3T3 fibroblasts transfected with control siRNA and in FAK ϩ/ϩ MEFs (p Ͻ 0.01) but not in cells transfected with siRNA FAK or in FAK Ϫ/Ϫ MEFs (Fig. 10, B and C).
Notably, FAK has been implicated in matrix degradation leading to tumor cell metastasis (8) As MMP-9 is important for extracellular matrix remodeling and its expression is regulated by IL-1 (5, 7), we assessed the role of FAK in mediating MMP-9 FIGURE 10. FAK regulates IL-1-induced MMP-3, MMP-9, and IL-6 protein expression. A, NIH3T3 fibroblasts were transfected with siRNA control or siRNA FAK for 48 h, and then treated with vehicle (Ϫ) or with IL-1 (ϩ) (20 ng/ml) for 6 and 24 h. Culture medium was concentrated 5-10ϫ and MMP-3protein were quantified by ELISA (see "Experimental Procedures"). Lysates of siRNA control-and siRNA FAK-transfected cells were immunoblotted for FAK to confirm the knockdown of FAK. B, left panel, MMP-9 protein of above NIH3T3 cells in concentrated conditioned media was quantified by ELISA. Right panel, same experiment was repeated with FAK ϩ/ϩ and FAK Ϫ/Ϫ MEFs. C, left panel, IL-6 protein of above NIH3T3 cells in concentrated conditioned media was quantified by ELISA. Right panel, same experiment was repeated with FAK ϩ/ϩ and FAK Ϫ/Ϫ MEFs. Values are mean Ϯ S.E. from n ϭ three independent experiments. mRNA expression after IL-1 treatment of FAK ϩ/ϩ and FAK Ϫ/Ϫ MEFs (Fig. 11A). IL-1 enhanced production of MMP-9 mRNA at 6 and 24 h after IL-1 treatment in FAK ϩ/ϩ MEFs (p Ͻ 0.01) but not in FAK Ϫ/Ϫ MEFs. We then determined which domain of FAK was involved in IL-1-induced MMP-9 expression at transcriptional and translational levels. Expression of wild type FAK, FAT domain, and FRNK in FAK Ϫ/Ϫ cells strongly increased mRNA and protein levels of MMP-9 in response to IL-1 compared with the FAK Ϫ/Ϫ cells transfected with control plasmid (pEGFP-C) (Fig. 11, B and C, p Ͻ 0.01). However, expression of MMP-9 was slightly increased in cells transfected with the FERM ϩ kinase domains. When FAK ϩ/ϩ cells were transfected with pEGF-FRNK, IL-1-induced MMP-9 expres-sion was reduced Ͼ2-fold compared with FAK ϩ/ϩ cells (Fig. 11, B and C, p Ͻ 0.01). These data indicate that the FAT domain is essential for IL-1-induced MMP-9 expression.

DISCUSSION
Our principal finding is that IL-1-induced signaling in fibroblasts involves association of FAK with PTP␣. The interactions between FAK and PTP␣ require the FAT domain of FAK and the membrane-proximal domain of PTP␣. As shown here, FAK is critical for IL-1-induced Ca 2ϩ release from the ER and ERK activation and IL-6, MMP-3, and MMP-9 expression. Notably, in FAK-deficient fibroblasts, the structure and composition of FIGURE 11. FAK is required for IL-1-induced MMP-9 expression. A, FAK ϩ/ϩ and FAK Ϫ/Ϫ MEFs were treated with vehicle or with IL-1 (20 ng/ml) for 6 and 24 h. Total RNA was extracted, and MMP-9 mRNA levels were quantified by qRT-PCR analysis. B, MMP-9 mRNA levels were quantified in FAK Ϫ/Ϫ MEFs transfected with pEGFP-control (pEGFP-C), FAK wild type (FAK), pEGFP-FAT (FAT), pEGFP-FRNK (FRNK), and pEGFP-FERM ϩ kinase (FERMϩKinase) as well as FAK ϩ/ϩ MEFs transfected with pEGFP-control (pEGFP-C) and pEGFP-FRNK (FRNK) that were treated with vehicle or with IL-1 (20 ng/ml) for 6 h, respectively. C, transfected cells in B were treated with vehicle or with IL-1 (20 ng/ml) for 24 h, and MMP-9 protein in concentrated conditioned media was quantified by ELISA (see "Experimental Procedures"). Values are mean Ϯ S.E. from n ϭ 3 independent experiments.
FAs is altered (36), underscoring the importance of FAK in enabling IL-1 signaling through FAs.
FAs are signaling platforms enriched with molecules such as tyrosine kinases and phosphatases that regulate signaling through FAs (10,41). Our results show that PTP␣ and FAK were recruited into FAs in response to IL-1, which is consistent with our previous observations indicating that IL-1 increases the size and maturity of FAs (44). Indeed, we found fewer but larger FAs in cultured fibroblasts genetically deficient in FAK, which is in agreement with earlier data indicating that FAK is involved in the formation and turnover of these adhesive structures (36). Likewise, defective FA remodeling in PTP␣ Ϫ/Ϫ cells leads to the formation of "super-mature" adhesions in these cells (23). Hence, FAK and PTP␣ are critical for maintaining FA dynamics and the propagation of downstream signaling events.
Our data show that the role of FAK extends beyond IL-1 signaling through FAs because we also observed that association of the ER-associated protein calnexin and IP 3 R1 with FAs was substantially reduced in FAK Ϫ/Ϫ cells compared with wild type cells. These findings suggest that the local FA environment was changed by the absence of FAK, resulting in loss of functional connections between the ER and FAs. Conceivably, the proximity of FAs with the ER is important for IL-1-induced signaling that involves ER-Ca 2ϩ release and ERK activation (43).
Signaling platforms created by the spatial aggregation of interacting signaling molecules regulate the type and amplitude of signal transduction (34). The signaling events occurring immediately downstream of IL-1 that lead to the activation and interactions of FAK or PTP␣ are not defined. PTP␣ may provide a scaffolding function to promote PTP␣-mediated catalysis of Src family kinase activation by dephosphorylating the inhibitory C-terminal Tyr 527 residue of Src (45,46), which subsequently enables autophosphorylation of FAK at Tyr 397 . Furthermore, FAK is also an adaptor protein in many signaling processes, due to its ability to bind proteins such as Src family kinases (47). These previous findings are consistent with our data that PTP␣ and its catalytic domains are important for IL-1-induced phosphorylation of FAK on Tyr 397 . In addition, our data indicate that FAK and its Tyr 397 autophosphorylation site are necessary for IL-1-induced phosphorylation of PTP␣ on Tyr 789 . These findings suggest that PTP␣ phosphorylation may occur after the formation of the PTP␣-Src family kinase-FAK complex.
PTP␣ is a receptor-like PTP (48,49) that possesses an extracellular domain, a transmembrane domain, and a cytosolic domain containing two catalytic subdomains. Our data demonstrate that the accumulation of PTP␣ in FAs induced by IL-1 was strongly reduced in FAK Ϫ/Ϫ MEFs. These findings suggest that the enrichment of FAK in FAs may enable the recruitment of PTP␣ to FAs. We found that the FAT domain of FAK enhances interactions with PTP␣, which may provide essential focal adhesion-dependent anchorage motifs for PTP␣ that are important for IL-1 signaling through FAs. Notably, the phosphatase domains of PTP␣ are essential for phosphatase activity (6,23) and, as shown here, are important binding sites for FAK.
For many complex signaling systems, including IL-1, anchorage of signaling proteins to specific organellar membranes is required for effective signal transduction (34). In the context of signaling platforms in FAs, we found that PTP␣ and FAK are closely associated with the ER. We also found that the ER-associated proteins calnexin and IP 3 R1 co-localized with FAs in FAK ϩ/ϩ MEFs and that FAK is required for IL-1-induced PTP␣ accumulation in the ER. As FAK binds to PTP␣, these proteins may help to approximate FAs with the ER, thereby facilitating Ca 2ϩ release and downstream signaling to ERK activation and MMP expression.
Previous studies have shown that in substrate-dependent cells, FAs are essential for IL-1-induced Ca 2ϩ release and ERK activation (11)(12)(13)(14)(15) and that PTP␣ is a critical adaptor in mediating functional links between FAs and the ER to enable IL-1induced Ca 2ϩ signaling leading to ERK activation (6). This study demonstrates that only cells expressing intact FAK or FAT domain could respond to IL-1 stimulation by exhibiting Ca 2ϩ release from the ER, ERK phosphorylation, and IL-6, MMP-3, and MMP-9 expression.
Collectively these data indicate that FAK is required for the recruitment of specific proteins, such as PTP␣ to FAs, possibly as a result of the catalytic and/or regulatory activities that reside in these structural domains. These domains in turn may modulate IL-1 signaling that is transduced through FAs (34). The novelty of our report is that the FAT domain of FAK provides a docking site for PTPs like PTP␣, which then provide appropriate localization of other signaling proteins to FAs. These proteins in turn regulate downstream FA-restricted IL-1 signaling leading to IL-6, MMP-3, and MMP-9 expression.