Role for Escherichia coli YidD in Membrane Protein Insertion

Yu, Zhong; Lavèn, Mariëlle; Klepsch, Mirjam; Gier, Jan‐Willem de; Bitter, Wilbert; Ulsen, Peter van

doi:10.1128/jb.05429-11

Cited by 20 publications

(15 citation statements)

References 54 publications

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“…We generated a strain of E. coli in which both YidC and SecF can be depleted by placing chromosomal yidC and chromosomal secDF under the control of arabinose promoters. Immediately upstream of and cotranscribed with yidC is the small nonessential open reading frame yidD, which encodes a factor that participates in membrane protein insertion (33). Immediately upstream of and cotranscribed with secF are yajC and secD, which encode accessory proteins to the Sec translocon.…”

Section: Resultsmentioning

confidence: 99%

Identification of YidC Residues That Define Interactions with the Sec Apparatus

Boyd

Reindl

et al. 2013

Journal of Bacteriology

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In bacteria, a subset of membrane proteins insert into the membrane via the Sec apparatus with the assistance of the widely conserved essential membrane protein insertase YidC. After threading into the SecYEG translocon, transmembrane segments of nascent proteins are thought to exit the translocon via a lateral gate in SecY, where YidC facilitates their transfer into the lipid bilayer. Interactions between YidC and components of the Sec apparatus are critical to its function. The first periplasmic loop of YidC interacts directly with SecF. We sought to identify the regions or residues of YidC that interact with SecY or with additional components of the Sec apparatus other than SecDF. Using a synthetic lethal screen, we identified residues of YidC that, when mutated, led to dependence on SecDF for viability. Each residue identified is highly conserved among YidC homologs; most lie within transmembrane domains. Overexpression of SecY in the presence of two YidC mutants partially rescued viability in the absence of SecDF, suggesting that the corresponding wild-type YidC residues (G355 and M471) participate in interactions, direct or indirect, with SecY. Staphylococcus aureus YidC complemented depletion of YidC, but not of SecDF, in Escherichia coli. G355 of E. coli YidC is invariant in S. aureus YidC, suggesting that this highly conserved glycine serves a conserved function in interactions with SecY. This study demonstrates that transmembrane residues are critical in YidC interactions with the Sec apparatus and provides guidance on YidC residues of interest for future structure-function analyses.

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Section: Resultsmentioning

confidence: 99%

Identification of YidC Residues That Define Interactions with the Sec Apparatus

Boyd

Reindl

et al. 2013

Journal of Bacteriology

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“…Seq2Ref provided more information by detecting (e-value 8.0e-49; 90% identity; reciprocal best hit) the experimentally studied protein YidD from E. coli (gi|67476547), which is identical to the NCBI nr database representative protein (gi|16767126) from Salmonella enterica . This orthology is reinforced by the common conserved genomic context [23] (Additional file 2: Table S2) and the CLANS [24] protein similarity network, in which E. coli YidD and C. turicensis hlyA cluster tightly together among their homologs (Additional file 3: Figure S1). The reference [23] associated with E. coli YidD detected by our server suggests that YidD assists YidC, the protein insertase, in insertion of inner membrane proteins.…”

Section: Resultsmentioning

confidence: 99%

“…This orthology is reinforced by the common conserved genomic context [23] (Additional file 2: Table S2) and the CLANS [24] protein similarity network, in which E. coli YidD and C. turicensis hlyA cluster tightly together among their homologs (Additional file 3: Figure S1). The reference [23] associated with E. coli YidD detected by our server suggests that YidD assists YidC, the protein insertase, in insertion of inner membrane proteins. As a confident ortholog of E. coli YidD, the hlyA gene from C. turicensis very likely shares the same function.…”

Section: Resultsmentioning

confidence: 99%

Seq2Ref: a web server to facilitate functional interpretation

Cong

Kinch

et al. 2013

BMC Bioinformatics

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BackgroundThe size of the protein sequence database has been exponentially increasing due to advances in genome sequencing. However, experimentally characterized proteins only constitute a small portion of the database, such that the majority of sequences have been annotated by computational approaches. Current automatic annotation pipelines inevitably introduce errors, making the annotations unreliable. Instead of such error-prone automatic annotations, functional interpretation should rely on annotations of ‘reference proteins’ that have been experimentally characterized or manually curated.ResultsThe Seq2Ref server uses BLAST to detect proteins homologous to a query sequence and identifies the reference proteins among them. Seq2Ref then reports publications with experimental characterizations of the identified reference proteins that might be relevant to the query. Furthermore, a plurality-based rating system is developed to evaluate the homologous relationships and rank the reference proteins by their relevance to the query.ConclusionsThe reference proteins detected by our server will lend insight into proteins of unknown function and provide extensive information to develop in-depth understanding of uncharacterized proteins. Seq2Ref is available at: http://prodata.swmed.edu/seq2ref.

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“…It would be of interest to determine whether these proteins also interact physically to confirm experimentally the presumed role of YidC in membrane protein quality control. The overexpression of the regulators of the glutamate-dependent acid resistance system, GadX and GadY, in an E. coli YidC depletion strain restores the ability to generate a proton motive force and leads to an increased membrane sequestering of the chaperone GroEL (Yu et al , 2011b ). It was suggested that GroEL replaces YidC function and keeps newly synthesized membrane proteins in an insertion-competent conformation.…”

Section: Membrane Quality Controlmentioning

confidence: 99%

The YidC/Oxa1/Alb3 protein family: common principles and distinct features

Saller

Keyzer

et al. 2012

Biological Chemistry

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The members of the YidC/Oxa1/Alb3 protein family are evolutionary conserved in all three domains of life. They facilitate the insertion of membrane proteins into bacterial, mitochondrial, and thylakoid membranes and have been implicated in membrane protein folding and complex formation. The major classes of substrates are small hydrophobic subunits of large energy-transducing complexes involved in respiration and light capturing. All YidC-like proteins share a conserved membrane region, whereas the N- and C-terminal regions are diverse and fulfill accessory functions in protein targeting.

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Role for Escherichia coli YidD in Membrane Protein Insertion

Cited by 20 publications

References 54 publications

Identification of YidC Residues That Define Interactions with the Sec Apparatus

Identification of YidC Residues That Define Interactions with the Sec Apparatus

Seq2Ref: a web server to facilitate functional interpretation

The YidC/Oxa1/Alb3 protein family: common principles and distinct features

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