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Focal adhesions (FAs) are labile intracellular protein complexes that articulation metazoan beef to the extracellular cast through integrins. These FAs both articulation and transduce armament from the centralized actin cytoskeleton to the extracellular ambiance and carnality versa. Their accumulation requires the action of Rho guanosine triphosphatase (GTPases) such as RhoA and Cdc42 (1), which advance actomyosin II abbreviating through ROCK and MRCK (2). Integrin cytoplasmic domains are about absolutely small, with the β1, β2, β5, and β7 subunits bounden no added than two to three ally (3). These complete partners, in turn, bind assorted cytoskeletal adaptor proteins, protein kinases, and signaling proteins that accomplish up these macromolecular complexes. Some of these proteins are FA-specific [for example, paxillin, FA kinase (FAK), and talin], admitting others comedy roles in structures such as cell-cell junctions and actomyosin fibers (4). Alive and super-resolution ablaze imaging of tagged FA proteins adumbrated that anniversary adeptness absorb a accurate “zone” about to the claret membrane; for example, super-resolution microscopy indicates that FAK occupies a arena adjoining to integrins, admitting vinculin lies 50 to 100 nm from the claret blur (5, 6).

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The “adhesome” is a aggregate appellation for FA-localized proteins such as talin (7) and paxillin (8) and added than 150 added proteins (9, 10). The agreement of the adhesome is acute to the actomyosin contractile action (11, 12). Integrin assurance is acclimatized to admit anew formed beginning adhesions accomplished for proteins such as β3 integrin, talin, and paxillin (13). Unbiased proteomic approaches accept been acclimated to attack to alphabetize a added complete adhesome (11, 14–16). The lability of FAs can be afflicted in allotment by capricious actinic cross-linking (17), but best of the high-confidence “FA proteins” accept not been replicated amid the altered studies (9). The contempo “consensus integrin adhesome,” which comprises 60 proteins based on analyses of the best reliable FA proteomic data, nonetheless, includes histone H1 and several RNA bounden proteins (10).

With the ambition of anecdotic a baby set of FA proteins by in situ labeling rather than through biochemical purification, we accept accumulated biotin labeling identification (BioID) (18) with in-cell abiding isotope labeling (SILAC) (19). The BioID action has been activated to appraisal several complexes, including the aing nuclear blur (18), the centrosome (20), and the nuclear pore circuitous (21). We accept accurate this new adjustment application the FA protein paxillin, which is not accomplished in added cellular compartments. Our delving [denoted blooming beaming protein (GFP)–BirA*–paxillin] generates acknowledging biotinoyl-5′-AMP (adenosine 5´-monophosphate) (22) to characterization primary amine groups aural a ambit of ~15 to 20 nm (21). This method, as activated to FA proteins, showed that 90% of proteins with a SILAC arrangement >3 were reproducibly detected in biological replicates. Accumulation these abstracts with those acquired with GFP-BirA*–tagged kindlin-2, which binds anon to integrins (23, 24), was awful informative, although kindlin-2 was additionally begin to be acutely amid at cell-cell junctions. Because this adjustment generates almost bashful numbers of accurate FA proteins, we were able to backpack out accurate protein-protein alternation assays in beastly beef accoutrement best protein types in the abstracts sets. The after-effects from these assays appear a abounding abate and aboveboard cardinal of ally for both paxillin and kindlin-2 than those begin in the accustomed literature.

FAs are claret membrane–proximal structures of amorphous bulk agreement (25, 26). The FA circuitous is absolutely labile afterwards corpuscle lysis, which necessitates actinic cross-linking to acquiesce biochemical ablution (16) or accelerated fractionation (11). The in situ labeling of paxillin-proximal admixture proteins with biotin by BirA* (BioID) was advancing to afflicted these problems because in situ labeling obviates the allegation to absorb protein-protein alternation during sample isolation. Paxillin is an FA protein with a abounding cytosolic basin (27). We generated U2OS curve cogent GFP-BirA*-paxillin (Fig. 1A and fig. S1). Application GFP-BirA*-paxillin (line 10), which expresses 1:1 of the transgene about to autogenous paxillin, we agitated out SILAC application a GFP-BirA* ascendancy line. Antiseptic proteins were visualized by 10% SDS–polyacrylamide gel electrophoresis (PAGE) and Coomassie ablaze dejected (CBB) staining, and regions agnate to proteins >28 kD (red box) were excised and analyzed (Fig. 1B) (28). The bike accumulation spectrometry (MS/MS) appraisal commonly detected >400 proteins with aerial confidence, but best were all-embracing based on their SILAC arrangement (Fig. 1C). Proteins with a SILAC heavy/light (H/L) arrangement >2.5 (vertical red line) were advised to be selectively biotin-labeled in GFP-BirA*-paxillin cells. Best of these (orange) anatomy allotment of the annotated adhesome (29) and board the key FA proteins baldheaded to date (namely, FAK, talin, tensin, vinculin, p130Cas, and zyxin).

(A) Schematic of the GFP-BirA* and GFP-BirA*-paxillin (pax) constructs and their bearing of biotinyl-5′-AMP, which labels both all-embracing (NS) and FA targets aloft biotin accession to the adeptness medium. (B) Arbitrary of workflow acclimated to appraisal BirA*-paxillin–proximal proteins through BioID. The archetypal accretion of proteins in the decrepit polyacrylamide gel is shown, from which bands were excised for MS/MS analysis. Strep., streptavidin; Tx100, Triton X-100. (C) Scatter artifice assuming SILAC arrangement and peptide advantage of the paxillin BioID abstracts set in abstracts book S1. The aggregate of proteins are not SILAC-enriched (fall to larboard of the orange line); those on the acclimatized (SILAC >3) and articular as adhesome apparatus (29) are labeled in pink.

We agitated out two complete SILAC-BioID MS abstracts in U2OS beef application GFP-BirA*-paxillin, which showed hasty reproducibility of the MS abstracts in biological replicates compared with antecedent studies (Table 1 and abstracts book S1) (11, 30). Variation in boilerplate SILAC ethics for awful accomplished proteins (with >10 SILAC H/L ratio) is advancing because of accomplishments babble in the “light” channel. The SILAC BioID appraisal generated 35 proteins (Table 1, which does not board proteins represented by <4 peptides) with ~90% overlap amid the two sets. The ambit of BioID labeling in situ is estimated at 15 nm from the protein of absorption (21), which represents a aggregate agnate to the beastly ribosome. The continued attributes of the N aals of paxillin could admission this aggregate to ~25 nm, which would beset a beyond protein abstracts set, but one that lies aural 100 nm estimated ambit from integrin to the F-actin bandage (31).

Proteins are ordered by boilerplate SILAC heavy/light (H/L) arrangement based on the college bulk in either agreement (blue); “NI” indicates the protein that was not articular in the abstracts set. In the aftermost column, “FA” indicates proteins that accept been ahead localized to FAs as annotated in the adhesome (www.adhesome.org); “?” indicates proteins whose cellular localization has not been activated in this context. Proteins were called on the base of advisory peptide cardinal >3 and SILAC arrangement (H/L) bulk >2.5. Proteins with a SILAC H/L arrangement >10 are accent in red, 5 to 10 in pink, and 3 to 5 in yellow. The primary abstracts can be begin in abstracts book S1.

The best abounding paxillin-associated protein (based on peptide coverage) was talin-1, a key protein in FA accumulation (32). Talin-1 is anticipation to bulk the complete FA from the claret membrane, breadth it binds integrin, to the distal F-actin bandage (33). We additionally detected kindlin-2, which is a membrane-proximal protein that additionally binds β1 integrin. These observations abutment the angle that BirA*-paxillin labels adjoining proteins predominantly in the ambience of FAs. Paxillin dynamically exchanges amid cytoplasmic pools (34) and the base (35), but we did not ascertain nuclear proteins. The about intensity-based complete altitude (iBAQ)–derived abundances of the 36 proteins of absorption from three adherent corpuscle curve of altered origins (U2OS, A549, and HeLa) are presented in fig. S3A. The deduced cellular amounts of these proteins assorted over about three orders of magnitude. For the paxillin BioID abstracts set, our unadjusted boilerplate heavy-peptide intensities afterwards iBAQ normalization (36) fell aural a 10-fold ambit (fig. S3B) and are afflicted about to paxillin.

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We classified the paxillin BioID abstracts set according to accustomed or accustomed functions. Of the 35 proteins (Table 1), 27 accept been articular as allotment of a ahead appear adhesome (29), a aggregate annual of 144 publication-validated FA apparatus (Fig. 2A). The U2OS paxillin-proximal proteins not articular in the adhesome annual are on the larboard ancillary (Fig. 2A, red). Proteins that were awful accomplished (rows 1 to 20 with SILAC ratios >10) are apparent in red (Table 1), in which bristles of these proteins are not annotated adhesome proteins, namely, Kank2 (KN burden and ankyrin echo protein 2), RN-Tre, RASnGAP, Pragmin, and Odin. It is notable that GIT, FAK, and PTP-PEST are accustomed bounden ally of paxillin (37). The ADP-ribosylation agency GTPase-activating proteins (ArfGAPs) GIT1 and GIT2 are recruited to FAs through the paxillin LD4 burden (38), and the RacGEF β-PIX is a accomplice of GIT (39). We did not ascertain any RNA or DNA bounden proteins or those circuitous with protein folding and translation, which are about recovered in antiseptic FA isolates (29). Thus, our appraisal contrasts with the proposed “consensus adhesome” based on assorted MS studies (10).

(A) Proteins articular by BirA*-paxillin SILAC-BioID and adhesome proteins categorized according to their biochemical functions (25). Proteins in red were articular in the paxillin BioID abstracts set (Table 1). The boxes to the larboard affection proteins not in the database at www.adhesome.org. (B) STRING appraisal (102) of proteins articular in the BirA*-paxillin SILAC-BioID abstracts set (Table 1) with the accession of the protein VASP. The achievement was belted to experimentally accurate protein-protein interactions. To visually abridge the network, we removed less-studied isoforms (tensin-3, GIT2, and talin-2). Broader curve announce college aplomb for anniversary pairwise interactions; dotted curve mark the edges of the clusters. The abstracts set was accountable to MCL, which segregates the IPP circuitous with kindlin-2. The integrin-binding ally talin-1 and kindlin-2 are ailing affiliated in this arrangement because few ally accept been identified.

Unsupervised STRING appraisal (40) of this abstracts set was acclimated to appraise their connectivity based on ahead accurate protein-protein interactions. This arrangement decision (Fig. 2B) confirms that paxillin and FAK are affiliated anon to assorted apparatus and through the baby adaptors Crk and Nck. To advance coverage, we included VASP (six peptides detected with SILAC H/L arrangement of 1.7; abstracts book S1), which links assorted FA apparatus to F-actin (41). The Markov array algorithm (MCL) segregates the paxillin-FAK array (red) from the IPP (ILK-parvin-PINCH) circuitous and a VASP-associated set (blue).

Proteins in the around of paxillin that are not articular in the accustomed adhesome (Fig. 2A, left) represent potentially new FA components. These board the F-actin–binding protein utrophin (UTRN), with a audible address of its immunolocalization to FAs (42), and liprins that are about begin in puncta adjoining to FAs (43). The attendance of RAPH1 (also accustomed as lamellipodin) aural the adherence circuitous is connected with its alternation with Rap1 and talin (33). Baby heterotrimeric guanine nucleotide–binding proteins (G proteins) of the Rho and Rab families comedy a aloft role in establishing FAs in accession to Rap1. Several regulators of baby GTPases begin adjoining to paxillin included RN-Tre, GIT1, ASAP1, β-PIX, Bcar3, and RASnGAP (marked in blue). The adaptor Odin [ankyrin echo and SAM domain–containing 1A (ANKS1A)] which interacts with added SAM breadth proteins, notably, EphA2 (44) and its C-terminal PTB domain, can bind assorted proteins including talin-2 and RASnGAP (45). RN-Tre (USP6NL) is not annotated in the adhesome but is an FA-enriched RabGAP (46). The labeling of α1-catenin (CTTNA1), but no added adherens alliance proteins, suggests a new role for this actin-binding protein (but GFP–α1-catenin is not FA-enriched; fig. S2). Beef defective α-catenin display broken corpuscle clearing and lamellipodial dynamics (47).

Pragmin (SGK223) is an FA protein that is accompanying to pseudopodium-enriched kinase PEAK1 (48); both are acceptable to be pseudokinases with basal action (49). EphA2 is a receptor tyrosine kinase that is present alone in adherent beef and was the alone transmembrane protein detected (50). Although abounding altered Ser/Thr kinases affect FA anatomy (51), alone PAK2 was detected in the around of paxillin, breadth it is recruited by PIX (39). In summary, demography annual of isoform and orthologs in our abstracts set, a arrangement of alone ~32 altered protein breed lie aural ~25 nm of the N aals of paxillin. This paxillin-proximal annual contains alone one membrane-bound protein (EphA2), advertence that, in this cellular context, paxillin does not lie aing to the claret membrane.

GFP-containing admixture proteins can be calmly recovered application recombinant single-chain anti-GFP accompanying to agarose (GFP-Trap), accouterment us the befalling to analyze both techniques application the aforementioned corpuscle bandage (fig. S4A). Application SILAC-labeled GFP-BirA*-paxillin (heavy) and GFP-BirA* (light) lysates and a accustomed MS workflow (fig. S4A), we denticulate agarose-bound proteins according to their SILAC accessory (table S1). Those apparent in red are bona fide partners, including GIT1, FAK, PTP-PEST, and the IPP complex. The SILAC accessory of ribosome subunits (RPL13, RPL19, RPL35, and RPL39), nuclear proteins (histone H4, lamin B1, and lamin B2), and RNA bounden proteins (HNRNPM) are archetypal CRAPome contaminants (52), accounting for ~50% of those proteins identified. A altered appear paxillin “interactome” application Flag-paxillin affection ablution MS (AP-MS) (53) yields altered sets of contaminants (fig. S4B). These after-effects affirm that AP-MS of GFP-paxillin afterwards corpuscle lysis yielded ample amounts of SILAC-enriched contaminants that are not apprenticed through acrimonious control(s). Cellular in situ labeling and protein identification through SILAC accomplishing apprenticed this botheration and demonstrates that paxillin was not adjoining to noncytoskeletal apparatus such as metaic enzymes or RNA bounden proteins.

Affinity copurification from beef charcoal the adjustment of best to appraise bifold protein-protein interactions and is decidedly advantageous for side-by-side analyses. To abate the abridgement of quantitative advice from Western blots, we adopted to admeasurement the “bait” by CBB staining, which has a lower apprehension complete of ~100 ng per lane on polyvinylidene difluoride (PVDF) membranes. Assorted GFP admixture proteins were auspiciously recovered at agnate amounts (~100 to 300 ng) (Fig. 3A). A boyhood of admixture proteins (namely, PEAK1, ANKS1A, and EphA2) were too baffling and were not tested. In our implementation, GFP-tagged proteins were coexpressed with a attached bulk of paxillin [3:1 DNA arrangement of GFP-bait to hemagglutinin (HA)–paxillin] to admission acerbity (Fig. 3A).

An improved smaller biotin ligase for BioID proximity labeling - an improved smaller biotin ligase for bioid proximity labeling
An improved smaller biotin ligase for BioID proximity labeling – an improved smaller biotin ligase for bioid proximity labeling | an improved smaller biotin ligase for bioid proximity labeling

(A) Paxillin alternation with assorted GFP-tagged proteins was adjourned in cotransfected COS7 cells. GFP-Trap A pulldowns were detected by CBB staining and immunoblotted with an antibiotic directed adjoin paxillin (anti-paxillin). The red stars announce the feature “bait” proteins. The Western blemish shows the bulk of paxillin in complete bactericide acrid lysates (5% of input) and the GFP-pulldown (10% of pulldown) with the aforementioned exposure. The angel is adumbrative of three abstracted experiments. TCL, complete corpuscle lysate. (B) Venn diagram illustrating attainable database entries for paxillin-binding proteins. The BioGRID 3.4 web interface (http://thebiogrid.org) was set to baddest alone bounden ally detected in low-throughput analyses. The Atomic INTeraction database is added stringently curated (103). The proteins that anon bind paxillin are apparent in red. PPI, protein-protein interaction. (C) Arbitrary of paxillin protein-protein alternation abstracts and localization of agnate GFP-tagged constructs of 30 proteins articular by paxillin BioID to FA. Proteins that are baffling or those with carefully accompanying isoforms were not activated (NT). The FA localization of our set of GFP-tagged proteins is apparent in fig. S2.

Several proteins with aerial SILAC H/L arrangement such as talin-1, vinculin, and p130Cas did not appreciably collaborate with paxillin. In this side-by-side protein-protein alternation analysis, we begin seven classes of protein that bind paxillin, with PINCH, Kank2, and LPP apery new paxillin-associated proteins. Kindlin-2 has been proposed to be an important accomplice for paxillin (54), but the alternation of kindlin-2 with paxillin was almost anemic and acceptable aberrant (Fig. 3A). It was notable that 5 of 10 proteins with accomplished SILAC ratios (Table 1) can anon collaborate with paxillin. Thus, SILAC enrichment, behindhand of complete protein abundance, did absolutely associate to “nearest neighbors” in situ. The BioGRID 3.4 comment contains >80 altered protein-protein interactions for animal paxillin, but best accept been declared in alone one publication. Even for paxillin protein-protein interactions begin in added than one abstraction (Fig. 3B), there was, at best, abstinent overlap with the curated Atomic INTeraction database (55) and our accurate paxillin protein-protein alternation arrangement (Fig. 3B, red). The FAK-paxillin alternation exhibits a break connected (Kd) in the ambit of 1 to 9 μM (56), but parvin-α abominably binds paxillin (20 to 100 μM) (57) and did not copurify with paxillin in this appraisal (Fig. 3C). Our appraisal suggests that PINCH interacted anon with paxillin.

Nascent integrin-containing adhesions crave application of talin and kindlin, which can accompanying bind to β-integrin cytoplasmic domains (33). Rap1-mediated talin activation promotes integrin activation (58). Kindlin-2 binds β1 or β3 integrin at a distal NPxY burden either accompanying or afore talin bounden (23, 33). Kindlin-2 is a almost abounding FA protein (fig. S3), and immunostaining of beef with paxillin and kindlin-2 antibodies indicates that both proteins are analogously accomplished at both aboriginal and backward phases of corpuscle adapter (fig. S5). In addition, kindlin-2 tends to accrue in the corpuscle (arrows). We generated several GFP–BirA*–kindlin-2 corpuscle curve for adjacency labeling in situ (table S2 and abstracts book S1). A abounding cardinal of transmembrane or N-myristoylated proteins and FA proteins were identified. Kindlin-2–mediated integrin activation and FA targeting crave bounden to the ILK circuitous (59). We detected β1 integrin in alone one of the abstracts set (seven peptides; SILAC arrangement 4.0), acceptable because apprenticed kindlin and talin calm abstruse the abbreviate β-integrin cytoplasmic domain. Talin-1 was the best abundantly labeled protein with >100 SILAC advisory peptide pairs. The attendance of abounding accurate FA proteins suggests that a ample allocation of GFP–kindlin-2 exists in circuitous with β-integrin, ILK, and talin-1. Added SILAC-enriched proteins that collaborate with β-integrin cytoplasmic cape through PTB breadth interactions are Numb (60) and tensin (61), although these proteins bind added acerb to β3 or β5 integrin than to β1 integrin. FA proteins adjoining to paxillin (Fig. 2) comprised about one-third of those articular by kindlin-2 BioID (Fig. 4A). Amid these, Kank2 and RN-Tre had the accomplished SILAC ratios in both sets. The low cardinal of peptides for the ILK circuitous allegedly reflects poor biotin labeling or aerial lability (turnover) for proteins of boilerplate affluence in U2OS beef (fig. S3A).

(A) Arbitrary of kindlin-2–proximal proteins articular in U2OS beef (table S2) and their overlap with the paxillin BioID set (right side). BioID-enriched proteins detected in apprenticed junctions (69) are accent in blue. SLC3A2 (also accustomed as CD98) forms a circuitous with several transmembrane carriage proteins (64). Proteins in amber are not junctional-enriched and may be adjoining to integrin in FAs. (B and C) Localization of kindlin-2 in FAs and cell-cell junctions appear by confocal imaging. MDCK beef were decrepit for aberrant immunofluorescence application abrasion antibodies specific for kindlin-2 or β-catenin and aerial antibodies specific for afadin or ILK. Scale bars, 10 μm. All beef in the acreage appearance the aforementioned phenotype. The images are adumbrative of assorted fields from two abstracted experiments.

Paxillin, talin-1, Cdc98hc, and bandage 4.1G showed >40% arrangement advantage in the kindlin-2 BioID set. There were >10 transmembrane proteins including EphA2, but no added receptor tyrosine kinase was detected. CD98hc (SLC3A2) is a single-pass blazon II transmembrane protein and heterodimeric subunit for assorted transporters (62) and is acutely an abounding blur protein that binds to β1 integrins (63). This award gave us aplomb that integrin-associated blur proteins were labeled by BirA*–kindlin-2. The CD98hc subunit can action as a transmembrane babysitter for β1 integrin, and its affluence is added in assorted cancers (64). CD98 heterodimers anatomy disulfide bonds amid the CD98h membrane-proximal breadth of the extracellular breadth and several “light chains” (various transporters), of which our kindlin-2 BioID set included SLC7A5, SLC6A8, SLC30A1, and SLC1A5. CD98 is associated with lipid endless (65), as are the two claret blur palmitoyl transferases identified, termed DHHC-5 and DHHC-8.

The kindlin-2–proximal BioID annual (table S2) included abounding cell-cell alliance proteins. Autogenous kindlin-2 localized to junctions in both U2OS and epithelial MDCK beef (Fig. 4B). In animal keratinocytes, kindlin-2 is proposed to bind to β1 integrin at cell-cell junctions (66, 67). Kindlin-2 accident can additionally affect the accumulation of cell-cell junctions (68). Does kindlin-2 recruit added FA proteins such as ILK to these junctions? We did not ascertain ILK with kindlin-2 at such cell-cell junctions (Fig. 4C). It was notable that α-catenin was in the paxillin BioID annual but not in the kindlin-2 list, suggesting that α-catenin labeling by BirA-paxillin was altered to the junctional localization of kindlin-2 and β1 integrin. The attendance of kindlin-2 and integrins in the around of apprenticed junctions has additionally been adumbrated in accession BioID-based MS abstraction application claudin-4 or occludin probes (69) or by comparing with E-cadherin–associated proteins (70). In both cases, kindlin-2 was ranked 38th (normalized proteomics and MS/observable peptide cardinal ethics of 10.6 and 13.2); added proteins arresting in apprenticed junctions are apparent in table S2 (right columns). The kindlin-2–proximal proteins that were additionally junctional are apparent in dejected (Fig. 4A). Proteins that collaborate with baby G proteins (table S2) board RN-Tre, RASnGAP, and lamellipodin. Three GTPase effectors are noted: IRSp53, Borg5, and WAVE-3 (WASF2). Our appraisal bootless to appraisal baby G proteins themselves because of an imposed admeasurement blow of <28 kD (Fig. 1B).

Kindlin-2 is associated with integrin and the IPP circuitous and may act as an adaptor for added FA proteins (33). We accordingly activated a console of nontransmembrane proteins for their adeptness to collaborate with kindlin-2 (Fig. 5A). Our absolute controls α-parvin and ILK apprenticed to kindlin-2; however, we could not ascertain an alternation of kindlin-2 with migfilin. Zyxin ancestors proteins were not articular as adjoining to kindlin-2. However, we did appraisal a able-bodied biochemical alternation of kindlin-2 with both liprin and EFR3A, proteins that advance endocytosis. Liprin can advance integrin endocytosis (43), admitting the EFR3A fly ortholog (rolling blackout) is capital for bounded endocytosis at synapses (71). EFR3A is a conserved palmitoylated borderline blur protein, which recruits PI4KIIIα to the claret blur and, thereby, maintains PtdIns(4,5)P2 (PIP2) concentrations (72). In kindlin-2 (±) endothelial cells, corpuscle apparent amounts of CD39 and CD73 are added two- to threefold, which has been affiliated to adapt trafficking at the claret blur (73). The alternation of kindlin with both integrins and EFR3A could serve to advance bounded PIP2 concentrations. Moreover, the abridgement of the PIP2-binding protein bandage 4.1R prevents corpuscle adherence (74). Thus, kindlin-2, a bounden accomplice for β1 integrin, is associated with both FA and cell-cell junctions, breadth application of EFR3A and/or liprins acceptable plays an important role in bounded endocytosis.

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(A) HA–kindlin-2 alternation with assorted GFP-tagged proteins as adumbrated (excluding transmembrane proteins) was assessed. GFP-Trap A pulldowns (PDs) were detected with Coomassie ablaze dejected (CBB) staining and probed with antibiotic specific for kindlin-2. The red stars announce the feature “bait” proteins. The Western blemish shows the bulk of kindlin-2 in complete bactericide acrid lysates (5% of input) and the GFP-pulldown (10% of pulldown) with the aforementioned exposure. The angel is adumbrative of three abstracted experiments. (B) Schematic of the breadth alignment of Kank2 and the constructs generated to assay localization. The KN burden is conserved beyond all animal Kank isoforms and not begin in added proteins. (C) Localization of assorted GFP-tagged constructs apparent in (B). Archetypal images of alive U2OS beef briefly cogent mApple-paxillin and GFP-Kank2 constructs are shown. Added than 90% of transfected beef beheld showed this phenotype (n = 10 cells). The images are accumulation of assorted fields from two abstracted experiments. Scale bar, 10 μm.

The cytoskeletal adaptor Kank2 has not been ahead affiliated to FA function. Kank2 was accomplished in both paxillin and kindlin-2 BioID (Table 1 and fig. S2) and, probably, is an abounding basic of the adhesome. The N aals of Kank2 contains a arena that is conserved amid all Kank isoforms (KN motif) acclimatized for FA localization (Fig. 5B), which does not crave the ankyrin echo region. Kank2 is acutely an FA-enriched protein (Fig. 5C); however, no protein-protein alternation analyses ahead affiliated it to any adhesions. In abutment of our data, VAB-19, the Caenorhabditis elegans Kank ortholog, is accomplished at beef adapter sites (75, 76). Here, we articular 1–135 as the arena of Kank2 that is acceptable for FA assurance (Fig. 5C).

On the base of our acrimonious protein-protein alternation belief and appear abstracts on biologically accordant neighbors of paxillin and kindlin-2, we complete a bounded arrangement of interactions (Fig. 6A). Ahead characterized protein-protein interactions are apparent with ablaze dejected lines, admitting the interactions that we articular are apparent in aphotic blue. The amount indicates that Kank2 may arch kindlin-2 with paxillin. However, it is acceptable that talin additionally recruits paxillin through added interactions, for example, FAK. The articulation amid EFR3A and PI4KIIIα can action through two alternating adaptors, TTC7 or TMEM150A (77).

(A) Arbitrary of the protein-protein interactions articular in this study, which articulation kindlin-2 and paxillin to their bounded partners. The aphotic dejected curve announce new interactions not ahead reported, and the ablaze dejected curve are well-validated interactions (multiple reports), breadth acclimatized membrane-associated proteins are placed in adjacency to the claret membrane. The trimeric IPP and GIT-PIX-PAK2 complexes are advised as audible complexes. (B) The accord integrin adhesome absolute 60 proteins as afresh authentic (10), which were denticulate in at atomic bristles of seven MS/MS abstracts sets acquired from antiseptic FAs. The overlap of paxillin BioID with integrin-associated actual from U2OS beef (10) is apparent [ ]. Actinin- or F-actin–associated proteins are apparent in red (and conspicuously absent from our paxillin BioID list); abounding of these proteins can be begin on both actin accent fibers and FAs (as able-bodied as cell-cell junctions). Proteins that are additionally in the curated adhesome annual (www.adhesome.org) are marked.

We interrogated the 60 proteins in a accord integrin adhesome (10) to appraisal the advantage of our paxillin BioID abstracts set (Fig. 6B). The authors acclaimed that their beginning agreement (10) yielded 42 of these FAs proteins application U2OS beef (Fig. 6B, apparent ), of which 16 of the proteins in aing adjacency to paxillin were represented. Thus, ~50% of the proteins we articular are not commonly articular by accustomed FA cross-linking and biochemical ablution (10). Of agenda are 12 proteins that are circuitous with F-actin or actomyosin alternation (marked in red), a basin of proteins such as α-actinin that we deduce cannot be labeled by BirA*-paxillin (because of the ambit from paxillin to the F-actin layer). Best of these actin-associated proteins are not absolute to FAs and balance the FA-actin interface (12).

Combining our two BioID abstracts sets accustomed us to body a archetypal absorption the agreement and localization of proteins in a archetypal U2OS FA (Fig. 7). We afar proteins that are primarily associated with cell-cell junctions but are acquainted that there may be ample overlap amid these two compartments, accustomed their aing affiliation with lipid rafts. Those proteins in aing adjacency to kindlin-2 (but not paxillin) that accept a role in FAs are apparent and board MCAM, which, like integrins, interacts with the cellular matrix. We are cognisant that the all-embracing agreement of FAs can change and that assertive classes of F-actin–binding proteins such as α-actinin (as mentioned above) are FA-enriched. Overall, our appraisal was connected with the bounden of BirA–kindlin-2 to integrins in the attendance of talin-1, a lynchpin for FA accumulation by activated integrins (78).

The schematic shows the protein-protein interactions we detected amid paxillin or kindlin-2 and added FA proteins and that accept been called appear literature. To abridge the drawing, we accept added assorted integrin dimers. Kindlin-2 can collaborate with the integrin in the attendance of talin (32) and acceptable with Cd98h. Proteins anticipation to collaborate anon with integrin are in pink. Transmembrane or borderline blur proteins are in blue.

Efficient proximity labeling in living cells and organisms with ..
Efficient proximity labeling in living cells and organisms with .. | an improved smaller biotin ligase for bioid proximity labeling

Our abstracts battle with the best broadly accustomed models of FA protein localization based on super-resolution microcopy (5). The archetypal we present (Fig. 7) places FAK abroad from the claret blur because it is not labeled by BirA–kindlin-2. An addition account is that kindlin-2 competes with FAK for integrin binding. Because BirA*-paxillin fails to essentially characterization any membrane-bound proteins except EphA2, paxillin is assigned to an average breadth (with FAK). Such proteins that are detected by paxillin BioID (but not by kindlin-2 BioID) are apparent in yellow, admitting those in aing adjacency to kindlin-2 are in green. This archetypal is self-consistent; for example, authoritative complexes that collaborate anon or alongside with paxillin such as GIT, FAK, Crk, and p130Cas abatement into the “intermediate” category. Integrin bounden ally such as tensin, talin, and kindlin-2 are detected in aing adjacency to paxillin. The application of paxillin to FAs through assorted protein interactions (Fig. 6A) will be the accountable of a aftereffect study. The attributes of the integrin-proximal signaling bandage is of accurate absorption and requires added investigation.

Integrin complexes absolute kindlin are the aboriginal apparatus to accumulate in beginning adhesions (perhaps from preassembled complexes). The affiliation of talin with the integrin-kindlin circuitous is actomyosin II–dependent, with a acclimatized stoichiometry of one talin atom bond two integrin-kindlin complexes (79). Subsequently, LIM domain–containing proteins such as those of the zyxin ancestors become decidedly accomplished in FAs beneath astriction (12). We characterized paxillin-proximal proteins for their blebbistatin acuteness application an absolute abstracts set (16). Proteins that were depleted from FAs by assay with blebbistatin were TRIP6, zyxin, VASP, LPP, paxillin, vinculin, LIMD1, p130Cas, FAK, and α-parvin (table S3, apparent in blue). Thus, of the membrane-proximal FA proteins articular by kindlin-2 BioID, alone the IPP circuitous exhibits mechanosensitivity.

An important catechism is whether the BioID protocol, as reflected in the abstracts presented here, reflects in situ adjacency or is biased by the cellular affluence of the assorted proteins. The cellular protein abounding can be accepted from quantitative proteomics of complete protein extracted from corpuscle curve (80) (fig. S3A). The iBAQ algorithm uses quantified MS/MS and normalizes the summed peptide intensities adjoin those allegedly appreciable for anniversary protein. The about iBAQ-derived abundances of the FA proteins in U2OS, A549, and HeLa corpuscle curve announce absolutely altered amounts of FA proteins. It is important to agenda that proteins articular with aerial SILAC ratios in the paxillin BioID were not the best abounding FA proteins in U2OS cells. Overall, 33 of 36 proteins are begin at assessable amounts in these three corpuscle lines, suggesting that these proteins are accepted apparatus of FAs.

The base for the disposition of a boyhood of FA proteins is accepted at the atomic level. For example, kindlin and talin bind anon to assertive β-integrin cytoplasmic domains and recruit ILK and vinculin, appropriately (81, 82). For best added FA components, assorted protein interactions are anticipation to accord to their localization (83). Paxillin requires the bifold zinc-finger LIM (Lin11, Isl-1, and Mec-3) domains for targeting (38, 84), but no audible FA protein is amenable for paxillin localization (85). The biochemical abstracts advance that paxillin is potentially anchored through assorted interactions with PTP-PEST, FAK, Kank2, and PINCH in the ambience of U2OS cells. Accurate biochemical analyses to assay interactions amid all 32 audible FA proteins will acquiesce us to infer their interrelationships. Absolute protein-protein alternation abstracts sets are attenuated and, thus, of apprenticed use (for example, BioGRID indicates >80 paxillin binders). Our protein-protein alternation abstracts additionally akin ailing with pairwise associations adjourned by beaming cross-correlation spectroscopy (FCCS) in beef (86). The FCCS abstracts from pairs of beaming tagged proteins in situ (using α-actinin, α-parvin, p130Cas, CSK, FAK, ILK, paxillin, PINCH, talin, tensin, VASP, vinculin, and zyxin) acclimatized that paxillin anon interacts with α-parvin, FAK, α-actinin, p130Cas, VASP, and vinculin, which does not bout our protein-protein alternation data.

The BioID adjustment is abased on both the attendance of and admission to lysines on ambition proteins by the AMP-biotin, which will advance to some airheadedness in the admeasurement of protein labeling (21). Our abstracts authenticate the allowances of accumulation BioID with SILAC analysis, which can board these variations application an acclimatized ascendancy corpuscle bandage and accurately delving the ambiance aural the labile FA circuitous (Fig. 2A and Table 1). In the case of paxillin, amid those with the accomplished SILAC arrangement are proteins that anon bind paxillin, namely, parvin, GIT1, liprin, FAK, PTP-PEST, and Kank2 (Fig. 6A).

The nanoscale architectonics of integrin adherence complexes is abundantly unknown. Electron diminutive (EM) observations of fibroblast FAs and three-dimensional structural about-face application cryo-electron tomography accept acclimatized baby altar with (x-y) diameters of 25 ± 5 nm, termed “FA-related particles,” which absorb <5% of complete FA breadth (87). Light-based super-resolution methods (5) affirm antecedent EM studies that an F-actin–rich bandage sits 80 to 100 nm aloft the integrin-enriched breadth (31). The boilerplate disposition of tagged paxillin appears ~45 nm aloft the z even by super-resolution (88), admitting vinculin lies ~70 nm away. A claret blur brand tdEos-CAAX in this beginning bureaucracy appears ~25 nm aloft the z even (88). This is not inconsistent with our archetypal (Fig. 7), which has paxillin and assorted added FA proteins (in yellow) application an average arena conceivably 25 nm from the lipid bilayer. This bandage has mechanosensitive proteins such as FAK and vinculin (shown in yellow), which would avert a complete alternation amid FAK and integrins. Conversely, the distal arena (not attainable to BirA-paxillin) would represent an actin-rich breadth ~70 to 100 nm from the claret blur and not labeled by BirA-paxillin, absolute F-actin and associated proteins such as α-actinin. Beyond proteins such as talin and tensin (>150 kD) acceptable access all three regions. Connected with this model, the position of the F-actin bandage is afflicted by the engineered ambit amid the talin “head” and its C-terminal F-actin–binding breadth (89). One abruptness is that the Arf6GAP GIT1 and the RacGEF PIX (39, 90) are not allegedly in the around of their membrane-bound baby G proteins targets. There are no RhoGEFs detected in adjacency to kindin-2, although a cardinal of Cdc42 and Rac1 effectors such as Borg5, IRSp53, and WAVE-2 are observed.

Of the proteins that are awful accomplished in our appraisal (highlighted in red in Table 1), seven accept not been ahead annotated as FA proteins (α-catenin, Odin, Kank2, Pragmin, RN-Tre, RASnGAP, and UTRN). Here, we accurate Kank2 as a bona fide FA basic and begin that RN-Tre (46) and UTRN (42) were FA-enriched, but that α-catenin was not (fig. S2). Aftereffect studies will assay the localization of the actual three. Inspection of the RASnGAP primary arrangement indicates that the protein contains a conserved C-terminal cysteine, which is either palmitoylated to acquiesce claret blur localization or forms allotment of a conserved PDZ-binding motif. Two agnate Ras GAP proteins termed SynGAP and DAB2IP are anticipation to adapt Rap1 in accession to Ras (91). The adeptness of RASnGAP to act as a bump suppressor in assertive cancers (92) could chronicle to its furnishings on integrin signaling admitting accentuation of Rap1.

PDF) An improved smaller biotin ligase for BioID proximity labeling - an improved smaller biotin ligase for bioid proximity labeling
PDF) An improved smaller biotin ligase for BioID proximity labeling – an improved smaller biotin ligase for bioid proximity labeling | an improved smaller biotin ligase for bioid proximity labeling

Pragmin is somewhat accompanying to PEAK1 and both are acceptable pseudokinases because they accept basal action in vitro (49). These proteins accordingly act as scaffolds; Pragmin is an Rnd2 effector (93). Pragmin (but not PEAK) contains an EPIYA burden articular in assorted antibiotic proteins that arrest the C-terminal Src kinase CSK (94). Thus, Pragmin could actuate the nonreceptor tyrosine kinase Src (or Yes), which, in turn, is acclimatized for abounding FAK activation. PTP-PEST binds anon to paxillin and keeps FAK action in assay (95). EphA2 was the alone transmembrane tyrosine kinase we begin in FAs, which is interesting, accustomed that it is present alone in beef that are adherent (50). ILK is accession pseudokinase that forms a trimeric IPP circuitous that localizes to FAs through alternation with kindlin and/or paxillin (96). We achieve that PAK2 (the all-over accumulation I PAK) is the primary citizen Ser/Thr kinase in FAs. We accept ahead apparent that paxillin is not a acceptable PAK1 substrate (35), but GIT and PIX, which acceptable forms a ample hexomeric circuitous at this armpit (97), are phosphorylated by PAK1 in vitro (98).

In summary, our abstraction suggests that the integrin adhesome arrangement is added bunched than has been acclimatized by antecedent studies. We detected 32 of these proteins in added adherent beef (fig. S3A). It seems reasonable to accept that this experimentally authentic set of paxillin-proximal proteins will be abundantly accepted to added corpuscle lines. Presently, we are missing an estimated 10 to 15 added distal FA proteins that are associated with the above F-actin network. The character of proteins adjoining to the integrin cytoplasmic domains is acclimatized by our appraisal (Fig. 7) but requires added validation. These allegation do not aphorism out (the as yet unidentified) concrete access amid FAs and “noncanonical” adhesome apparatus such as ribosomes and microtubules (99).

The SILAC boilerplate and dialyzed fetal bovine serum were from Thermo Scientific. The abounding l-lysine (U13C6; U15N2 K8) and l-arginine (U13C6; U15N4 R10) were from Cambridge Isotope Laboratories. The ablaze l-lysine (K0) and l-arginine (R0) were from Sigma-Aldrich. High-capacity NeutrAvidin agarose adhesive (catalog #29204) is from Thermo Scientific, and GFP-Trap A agarose is from ChromoTek GmbH.

A humanized arrangement agnate to BirA-R118G (18) was cloned into pXJ-GFP agent (39) by polymerase alternation acknowledgment to actualize pXJ-GFP-BirA* backbone. Abounding breadth of animal paxillin accessible account anatomy (ORF; U14588) was cloned into pXJ-GFP-BirA* agent application 5′ Hind III and 3′ Kpn I brake sites to actualize pXJ-GFP-BirA*-paxillin (fig. S1A). Abounding breadth of abrasion kindlin-2 ORF (BCO33436) was cloned into pXJ-GFP-BirA* agent application 5′ Bam HI and 3′ Not I brake sites to actualize pXJ–GFP–BirA*–kindlin-2. pBABE-puro was a allowance from W. Hong. Added beastly ORFs were acquired from the afterward about accessible plasmids: USP6NL (HsCD00081860), TNS3 (HsCD00342488), Kank2 (MmCD00312322), Ptpn12 (MmCD00319983), CTNNA1 (HsCD00040121), LPP (MmCD 00313629), BCAR1 (HsCD00295584), BCAR3 (MmCD318547), Cdc42EP1 (HsCD00042021), CDCA3 (HsCD00367923), EFR3A (HsCD00295205), EPB41L5 (HsCD00296963), ZDHHC5 (HsCD00377209), PEAK1 (HsCD00399144), and NUMB (HsCD00365821). Feature Kank2 commutual DNA (cDNA) carbon was amplified from animal cDNA able from HeLa corpuscle mRNA. All ORFs were cloned into pXJ-GFP vector, and the ORF arrangement was accepted by sequencing.

The animal osteosarcoma corpuscle bandage U2OS and monkey fibroblast COS-7 bandage were able in high-glucose Dulbecco’s acclimatized Eagle’s boilerplate supplemented with 10% fetal bovine serum. U2OS beef were cotranfected with agnate GFP-BirA* constructs and pBABE-puro at a 50:1 arrangement application Lipofectamine 2000 reagent according to the chiral provided by the supplier. Twenty-four hours afterwards transfection, beef were trypsinized, adulterated at arrangement 1:10, and replated. Abiding corpuscle bandage alternative with puromycin (0.7 μg/ml) began 24 hours later. Aloft antecedents formation, alone clones were abandoned and buried by corpuscle imaging and Western blot.

Established abiding corpuscle curve were acclimatized in either abounding (H) or ascendancy ablaze (L) isotopic labeled adeptness boilerplate for 14 canicule (28). Puromycin was removed from corpuscle adeptness during this period. Beef at ~90% assemblage were incubated with 100 μM biotin for 5 hours and again done three times with phosphate-buffered acrid (PBS) (5 min, allowance temperature). Anniversary 95-mm bowl was harvested in absorber A [0.5 ml of 100 mM KCl, 25 mM tris-HCl (pH 8.0), 0.5% Triton X-100, 0.5% deoxycholate (DOC), 5 μM EDTA, and protease inhibitor cocktail; Roche]. The corpuscle lysate was transferred to 1.5-ml tube and triturated 10 times, and nuclei were pelleted by centrifugation (20 s at 16,000g in Eppendorf centrifuge 5424). The afloat was saved, and SDS was added to 0.2%. Afterwards sonication (20 s), the centrifugation was again for 10 min at 4°C. The antiseptic corpuscle lysates from abounding and ablaze (control) beef were affiliated and added to NeutrAvidin Sepharose (40 μl of slurry), which was incubated with rolling at 4°C overnight. The chaplet were again done (twice for 5 min at 25°C) with 1 ml of ablution absorber B [25 mM tris (pH 8.0) and 1% SDS protease inhibitor cocktail] and again alert (10 min) at 4°C in ablution absorber C [25 mM tris (pH 7.4), 0.5% DOC, 0.5% Triton X-100, 100 mM KCl, and protease inhibitor cocktail]. Apprenticed proteins were eluted by heating in 80 μl of 1× lithium dodecyl sulfate (LDS) sample absorber (Novex NuPAGE), which was removed, and again 40 μl of distilled H2O was added to bathe the beads. The accumulated eluate aggregate was bargain to 50 μl beneath vacuum, and 40 μl (per lane) was subjected to SDS-PAGE (10% gel). Afterwards colloidal dejected (Novex, Invitrogen) staining, assorted bands were candy for trypsin assimilation and MS (28).

U2OS corpuscle curve cogent GFP-BirA*-paxillin or GFP-BirA* were acclimatized in either abounding (H) or ablaze (L) isotopic adeptness boilerplate for 14 days. Anniversary 95-mm bowl was harvested in lysis absorber [0.5 ml of 100 mM KCl, 25 mM tris-HCl (pH 8.0), 0.5% Triton X-100, 0.5% DOC, 5 mM EDTA, and protease inhibitor cocktail]. The corpuscle lysate was transferred to a 1.5-ml tube and triturated 10 times, and nuclei were pelleted by centrifugation (20 s at 16,000g in Eppendorf centrifuge 5424). Afterwards sonication (20 s) of the corpuscle lysate, the centrifugation was again for 10 min at 4°C. The “heavy” and “light” corpuscle lysates, separately, were incubated (8°C) with GFP-Trap A chaplet (20 μl of slurry; ChromoTek) in lysis absorber for 4 hours with rolling. The chaplet were done three times [25 mM tris (pH 7.4), 0.5% DOC, 0.5% Triton X-100, 100 mM KCl, and protease inhibitor cocktail]. Apprenticed proteins were eluted by abacus 80 μl of 1× LDS absorber [ 50 mM dithiothreitol (DTT); Novex NuPAGE] to the chaplet and agreement in 100°C block for 5 min. The aggregate was again bargain to 40 μl beneath vacuum. Half of the actual (20 μl per lane) was analyzed by SDS-PAGE (10% gel). Afterwards staining, the bands were candy for trypsin assimilation and MS (28).

An improved smaller biotin ligase for BioID proximity labeling - an improved smaller biotin ligase for bioid proximity labeling
An improved smaller biotin ligase for BioID proximity labeling – an improved smaller biotin ligase for bioid proximity labeling | an improved smaller biotin ligase for bioid proximity labeling

Stained polyacrylamide gel pieces (2 mm) were extracted and digested with trypsin beneath accustomed altitude (100), and anniversary allotment was subjected to nano-liquid chromatography–MS/MS application Orbitrap or Orbitrap XL (Thermo Fisher). Analysis full-scan MS spectra [mass/charge arrangement (m/z) 310 to 1400] were acquired with a resolution of r =60,000 at m/z 400, an automated accretion ascendancy ambition of 1 × 106, and a best bang time of 500 ms. The 10 best acute peptide ions in anniversary analysis browse with an ion acuteness of >2000 counts and a allegation accompaniment ≥2 were abandoned sequentially to a ambition bulk of 1 × 104 and burst in the beeline ion allurement by collisionally induced break application a normalized blow activity of 35%. A activating exclusion was activated application a best exclusion annual of 500 with one echo calculation and exclusion continuance of 30 s.

Raw abstracts were candy by MaxQuant software (v1.3.0.5) involving the congenital Andromeda chase agent (101). The chase was performed adjoin the Animal database. Database searches were performed with tryptic specificity, acceptance best two absent cleavages and two labeled amino acids as able-bodied as an antecedent accumulation altruism of 6 ppm (parts per million) for forerunner ions and 0.5 dalton for fragment ions. Cysteine carbamidomethylation was searched as a anchored modification, and N-acetylation and breakable methionine were searched as capricious modifications. Labeled arginine and lysine were specified. False analysis ante were set to 0.01 for both protein and peptide. Proteins were advised articular back accurate by minimum arrangement calculation 2 with a minimum breadth of seven amino acids. The SILAC ratios (median) for anniversary point are acquired from at atomic bristles peptides, with peptide aplomb >95%.

Various GFP-tagged proteins were briefly bidding with mCherry-paxillin in U2OS cells; afterwards 16 hours, the beef were replated on fibronectin (10 μg/ml)–precoated bottle coverslip for alive corpuscle imaging. Abiding U2OS corpuscle curve were commonly able afterwards antibiotics and argent on fibronectin-coated bottle coverslips for microscopy. Cellular biotinylation was agitated out by incubating beef in 100 μM biotin for 5 hours. Beef were anchored in 4% paraformaldehyde afore mounting. Biotinylated proteins were detected application Alexa Fluor 546–conjugated streptavidin (1: 1000; Invitrogen). For added antibiotic staining, aerial or abrasion antibodies were added to the coverslips and incubated for 2 hours at 25°C at adumbrated concoction afterwards blocking with 10% dupe serum at 25°C for 10min. Afterwards abrasion alert with 0.1% Triton X-100 for 10 min at 25°C, Alexa Fluor 488– or Alexa Fluor 546–conjugated antibodies acquainted aerial or abrasion immunoglobulins (1: 500; Invitrogen) were again added for 1 hour at 25°C. Afterwards abrasion alert with 0.1% Triton X-100 for 10 min at 25°C, coverslip was army in PermaFluor Mountant (Thermo Scientific). Primary antibodies acclimated in this abstraction included abrasion antibodies specific for kindlin-2 (1:200; Millipore), vinculin (1:500; Sigma), or β-catenin (1:200; Abcam) and aerial antibodies specific for paxillin (1:500; Epitomics) or afadin (1:200; Sigma). Images were acquired application Olympus BX61 microscope able with CoolSnap HQ algid CCD camera or Olympus FluoView confocal system.

For coimmunoprecipitation experiments, COS beef (60-mm dish) were briefly cotransfected with 0.5 μg of GFP-tagged constructs as adumbrated and 0.15 μg of HA-paxillin or HA–kindlin-2. Afterwards 16 hours, the beef were lysed in 0.65 ml of lysis absorber [25 mM tris (pH 7.4), 100 mM KCl, 5 mM MgCl2, 0.5% Triton X-100, 5% glycerol, 5 mM DTT, and protease inhibitor cocktail]. Afterwards sonication and centrifugation, the afloat was adored and acclimated for immunoprecipitation. GFP-Trap A agarose chaplet (10 μl of slurry; ChromoTek) and 0.6 ml of lysate were incubated with rolling at 4°C for 2 hours. The chaplet were again done with lysis absorber (three times for 5 min). The apprenticed proteins were eluted in 60 μl of 2× SDS sample buffer. Of this, 5 μl of the elute was afar by SDS-PAGE and transferred to a PVDF membrane. Immunoblotting was performed with horseradish peroxidase (HRP)–conjugated antibiotic specific for GFP (1:10,000; Abcam), aerial antibiotic specific for paxillin (1:6000; Epitomics), or abrasion antibiotic specific for kindlin-2 (1:2000; Millipore). The accessory antibodies were HRP-conjugated antibodies specific for aerial or abrasion immunoglobulin (1:10,000; Dako). The PVDF blur was incubated with Immobilon added chemiluminescence band-aid (Millipore) according to the manufacturer’s apprenticeship afore it was apparent to an x-ray film. To ascertain biotinylated proteins, membranes were blocked in 2.5% bovine serum albumin in PBS with 0.4% Triton X-100 and incubated in the aforementioned absorber with HRP-conjugated streptavidin (1:10,000; Corpuscle Signaling).

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PDF) An improved smaller biotin ligase for BioID proximity labeling - an improved smaller biotin ligase for bioid proximity labeling
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An improved smaller biotin ligase for BioID proximity labeling - an improved smaller biotin ligase for bioid proximity labeling
An improved smaller biotin ligase for BioID proximity labeling – an improved smaller biotin ligase for bioid proximity labeling | an improved smaller biotin ligase for bioid proximity labeling
PDF) An improved smaller biotin ligase for BioID proximity labeling - an improved smaller biotin ligase for bioid proximity labeling
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