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Edge-strand of BepA interacts with immature LptD on the β-barrel assembly machine to direct it to on- and off-pathways

Miyazaki, Ryoji Watanabe, Tetsuro Yoshitani, Kohei Akiyama, Yoshinori 京都大学 DOI:10.7554/eLife.70541

2021

概要

The outer membrane (OM) of Gram-negative bacteria functions as a selective permeability barrier. Escherichia coli periplasmic Zn-metallopeptidase BepA contributes to the maintenance of OM integrity through its involvement in the biogenesis and degradation of LptD, a β-barrel protein component of the lipopolysaccharide translocon. BepA either promotes the maturation of LptD when it is on the normal assembly pathway (on-pathway) or degrades it when its assembly is compromised (off-pathway). BepA performs these functions probably on the β‐barrel assembly machinery (BAM) complex. However, how BepA recognizes and directs an immature LptD to different pathways remains unclear. Here, we explored the interactions among BepA, LptD, and the BAM complex. We found that the interaction of the BepA edge-strand located adjacent to the active site with LptD was crucial not only for proteolysis but also, unexpectedly, for assembly promotion of LptD. Site-directed crosslinking analyses indicated that the unstructured N-terminal half of the β-barrel-forming domain of an immature LptD contacts with the BepA edge-strand. Furthermore, the C-terminal region of the β-barrel-forming domain of the BepA-bound LptD intermediate interacted with a ‘seam’ strand of BamA, suggesting that BepA recognized LptD assembling on the BAM complex. Our findings provide important insights into the functional mechanism of BepA.

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Akiyama K, Mizuno S, Hizukuri Y, Mori H, Nogi T, Akiyama Y. 2015. Roles of the membrane-reentrant b-hairpinlike loop of RseP protease in selective substrate cleavage. eLife 4:e08928. DOI: https://doi.org/10.7554/eLife.

08928

Bakelar J, Buchanan SK, Noinaj N. 2016. The structure of the b-barrel assembly machinery complex. Science 351:

180–186. DOI: https://doi.org/10.1126/science.aad3460, PMID: 26744406

Bryant JA, Cadby IT, Chong ZS, Boelter G, Sevastsyanovich YR, Morris FC, Cunningham AF, Kritikos G, Meek

RW, Banzhaf M, Chng SS, Lovering AL, Henderson IR. 2020. Structure-Function characterization of the

conserved regulatory mechanism of the Escherichia coli M48 metalloprotease BepA. Journal of Bacteriology

203:e00434-20. DOI: https://doi.org/10.1128/JB.00434-20, PMID: 33106348

Chimalakonda G, Ruiz N, Chng SS, Garner RA, Kahne D, Silhavy TJ. 2011. Lipoprotein LptE is required for the

assembly of LptD by the beta-barrel assembly machine in the outer membrane of Escherichia coli. PNAS 108:

2492–2497. DOI: https://doi.org/10.1073/pnas.1019089108, PMID: 21257909

Chin JW, Schultz PG. 2002. In vivo photocrosslinking with unnatural amino acid mutagenesis. ChemBioChem 3:

1135–1137. DOI: https://doi.org/10.1002/1439-7633(20021104)3:11<1135::AID-CBIC1135>3.0.CO;2-M,

PMID: 12404640

Chng SS, Xue M, Garner RA, Kadokura H, Boyd D, Beckwith J, Kahne D. 2012. Disulfide rearrangement triggered

by translocon assembly controls lipopolysaccharide export. Science 337:1665–1668. DOI: https://doi.org/10.

1126/science.1227215, PMID: 22936569

Daimon Y, Iwama-Masui C, Tanaka Y, Shiota T, Suzuki T, Miyazaki R, Sakurada H, Lithgow T, Dohmae N, Mori H,

Tsukazaki T, Narita SI, Akiyama Y. 2017. The TPR domain of BepA is required for productive interaction with

substrate proteins and the b-barrel assembly machinery complex. Molecular Microbiology 106:760–776.

DOI: https://doi.org/10.1111/mmi.13844, PMID: 28960545

Daimon Y, Narita SI, Miyazaki R, Hizukuri Y, Mori H, Tanaka Y, Tsukazaki T, Akiyama Y. 2020. Reversible

autoinhibitory regulation of Escherichia coli metallopeptidase BepA for selective b-barrel protein degradation.

PNAS 117:27989–27996. DOI: https://doi.org/10.1073/pnas.2010301117, PMID: 33093205

Dong H, Xiang Q, Gu Y, Wang Z, Paterson NG, Stansfeld PJ, He C, Zhang Y, Wang W, Dong C. 2014. Structural

basis for outer membrane lipopolysaccharide insertion. Nature 511:52–56. DOI: https://doi.org/10.1038/

nature13464, PMID: 24990744

Miyazaki et al. eLife 2021;10:e70541. DOI: https://doi.org/10.7554/eLife.70541

19 of 21

A Self-archived copy in

Kyoto University Research Information Repository

https://repository.kulib.kyoto-u.ac.jp

Research article

Biochemistry and Chemical Biology Cell Biology

Gu Y, Li H, Dong H, Zeng Y, Zhang Z, Paterson NG, Stansfeld PJ, Wang Z, Zhang Y, Wang W, Dong C. 2016.

Structural basis of outer membrane protein insertion by the BAM complex. Nature 531:64–69. DOI: https://doi.

org/10.1038/nature17199, PMID: 26901871

Gunasinghe SD, Shiota T, Stubenrauch CJ, Schulze KE, Webb CT, Fulcher AJ, Dunstan RA, Hay ID, Naderer T,

Whelan DR, Bell TDM, Elgass KD, Strugnell RA, Lithgow T. 2018. The WD40 protein BamB mediates coupling

of BAM complexes into assembly precincts in the bacterial outer membrane. Cell Reports 23:2782–2794.

DOI: https://doi.org/10.1016/j.celrep.2018.04.093, PMID: 29847806

Han L, Zheng J, Wang Y, Yang X, Liu Y, Sun C, Cao B, Zhou H, Ni D, Lou J, Zhao Y, Huang Y. 2016. Structure of

the BAM complex and its implications for biogenesis of outer-membrane proteins. Nature Structural &

Molecular Biology 23:192–196. DOI: https://doi.org/10.1038/nsmb.3181, PMID: 26900875

Hart EM, Mitchell AM, Konovalova A, Grabowicz M, Sheng J, Han X, Rodriguez-Rivera FP, Schwaid AG,

Malinverni JC, Balibar CJ, Bodea S, Si Q, Wang H, Homsher MF, Painter RE, Ogawa AK, Sutterlin H, Roemer T,

Black TA, Rothman DM, et al. 2019. A small-molecule inhibitor of BamA impervious to efflux and the outer

membrane permeability barrier. PNAS 116:21748–21757. DOI: https://doi.org/10.1073/pnas.1912345116,

PMID: 31591200

Hart EM, Gupta M, Wu¨hr M, Silhavy TJ. 2020. The gain-of-function allele bamA E470K bypasses the essential

requirement for BamD in b-barrel outer membrane protein assembly. PNAS 117:18737–18743. DOI: https://

doi.org/10.1073/pnas.2007696117, PMID: 32675245

Hizukuri Y, Akiyama Y. 2012. PDZ domains of RseP are not essential for sequential cleavage of RseA or stressinduced s(E) activation in vivo. Molecular Microbiology 86:1232–1245. DOI: https://doi.org/10.1111/mmi.

12053, PMID: 23016873

Iadanza MG, Higgins AJ, Schiffrin B, Calabrese AN, Brockwell DJ, Ashcroft AE, Radford SE, Ranson NA. 2016.

Lateral opening in the intact b-barrel assembly machinery captured by cryo-EM. Nature Communications 7:

12865. DOI: https://doi.org/10.1038/ncomms12865, PMID: 27686148

Ieva R, Tian P, Peterson JH, Bernstein HD. 2011. Sequential and spatially restricted interactions of assembly

factors with an autotransporter beta domain. PNAS 108:E383–E391. DOI: https://doi.org/10.1073/pnas.

1103827108, PMID: 21646511

Kihara A, Akiyama Y, Ito K. 1995. FtsH is required for proteolytic elimination of uncomplexed forms of SecY, an

essential protein translocase subunit. PNAS 92:4532–4536. DOI: https://doi.org/10.1073/pnas.92.10.4532,

PMID: 7753838

Konovalova A, Kahne DE, Silhavy TJ. 2017. Outer membrane biogenesis. Annual Review of Microbiology 71:

539–556. DOI: https://doi.org/10.1146/annurev-micro-090816-093754, PMID: 28886680

Lee J, Xue M, Wzorek JS, Wu T, Grabowicz M, Gronenberg LS, Sutterlin HA, Davis RM, Ruiz N, Silhavy TJ, Kahne

DE. 2016. Characterization of a stalled complex on the b-barrel assembly machine. PNAS 113:8717–8722.

DOI: https://doi.org/10.1073/pnas.1604100113, PMID: 27439868

Lee J, Sutterlin HA, Wzorek JS, Mandler MD, Hagan CL, Grabowicz M, Tomasek D, May MD, Hart EM, Silhavy

TJ, Kahne D. 2018. Substrate binding to BamD triggers a conformational change in BamA to control membrane

insertion. PNAS 115:2359–2364. DOI: https://doi.org/10.1073/pnas.1711727115, PMID: 29463713

Lee J, Tomasek D, Santos TM, May MD, Meuskens I, Kahne D. 2019. Formation of a b-barrel membrane protein

is catalyzed by the interior surface of the assembly machine protein BamA. eLife 8:e49787. DOI: https://doi.

org/10.7554/eLife.49787, PMID: 31724945

Lo´pez-Pelegrı´n M, Cerda`-Costa N, Martı´nez-Jime´nez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom

MA, Lo´pez-Otı´n C, Arolas JL, Gomis-Ru¨th FX. 2013. A novel family of soluble minimal scaffolds provides

structural insight into the catalytic domains of integral membrane metallopeptidases. Journal of Biological

Chemistry 288:21279–21294. DOI: https://doi.org/10.1074/jbc.M113.476580

Miller JH. 1972. Experiments in Molecular Genetics. Cold Spring Harbor Laboratory Press.

Miyazaki R, Myougo N, Mori H, Akiyama Y. 2018. A photo-cross-linking approach to monitor folding and

assembly of newly synthesized proteins in a living cell. Journal of Biological Chemistry 293:677–686.

DOI: https://doi.org/10.1074/jbc.M117.817270

Miyazaki R, Akiyama Y, Mori H. 2020a. A photo-cross-linking approach to monitor protein dynamics in living

cells. Biochimica Et Biophysica Acta (BBA) - General Subjects 1864:129317. DOI: https://doi.org/10.1016/j.

bbagen.2019.03.003

Miyazaki R, Akiyama Y, Mori H. 2020b. Fine interaction profiling of VemP and mechanisms responsible for its

translocation-coupled arrest-cancelation. eLife 9:e62623. DOI: https://doi.org/10.7554/eLife.62623,

PMID: 33320090

Narita S, Masui C, Suzuki T, Dohmae N, Akiyama Y. 2013. Protease homolog BepA (YfgC) promotes assembly

and degradation of -barrel membrane proteins in Escherichia coli. PNAS 110:E3612–E3621. DOI: https://doi.

org/10.1073/pnas.1312012110, PMID: 24003122

Nichols BP, Shafiq O, Meiners V. 1998. Sequence analysis of Tn10 insertion sites in a collection of Escherichia coli

strains used for genetic mapping and strain construction. Journal of Bacteriology 180:6408–6411. DOI: https://

doi.org/10.1128/JB.180.23.6408-6411.1998, PMID: 9829956

Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M,

Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA. 2011. Phenotypic landscape of a bacterial cell. Cell 144:

143–156. DOI: https://doi.org/10.1016/j.cell.2010.11.052, PMID: 21185072

Nikaido H. 2003. Molecular basis of bacterial outer membrane permeability revisited. Microbiology and

Molecular Biology Reviews 67:593–656. DOI: https://doi.org/10.1128/MMBR.67.4.593-656.2003,

PMID: 14665678

Miyazaki et al. eLife 2021;10:e70541. DOI: https://doi.org/10.7554/eLife.70541

20 of 21

A Self-archived copy in

Kyoto University Research Information Repository

https://repository.kulib.kyoto-u.ac.jp

Research article

Biochemistry and Chemical Biology Cell Biology

Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman

JS, Bukau B. 2011. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in

vivo. Cell 147:1295–1308. DOI: https://doi.org/10.1016/j.cell.2011.10.044, PMID: 22153074

Plummer AM, Fleming KG. 2016. From chaperones to the membrane with a BAM!. Trends in Biochemical

Sciences 41:872–882. DOI: https://doi.org/10.1016/j.tibs.2016.06.005, PMID: 27450425

Qiao S, Luo Q, Zhao Y, Zhang XC, Huang Y. 2014. Structural basis for lipopolysaccharide insertion in the bacterial

outer membrane. Nature 511:108–111. DOI: https://doi.org/10.1038/nature13484, PMID: 24990751

Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. 2018. The MEROPS database of

proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER

database. Nucleic Acids Research 46:D624–D632. DOI: https://doi.org/10.1093/nar/gkx1134, PMID: 29145643

Ricci DP, Silhavy TJ. 2019. Outer membrane protein insertion by the b-barrel assembly machine. EcoSal Plus 8:1–

9. DOI: https://doi.org/10.1128/ecosalplus.ESP-0035-2018

Ruiz N, Falcone B, Kahne D, Silhavy TJ. 2005. Chemical conditionality: a genetic strategy to probe organelle

assembly. Cell 121:307–317. DOI: https://doi.org/10.1016/j.cell.2005.02.014, PMID: 15851036

Ruiz N, Chng SS, Hiniker A, Kahne D, Silhavy TJ. 2010. Nonconsecutive disulfide bond formation in an essential

integral outer membrane protein. PNAS 107:12245–12250. DOI: https://doi.org/10.1073/pnas.1007319107,

PMID: 20566849

Scha¨fer A, Tauch A, Ja¨ger W, Kalinowski J, Thierbach G, Pu¨hler A. 1994. Small mobilizable multi-purpose cloning

vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the

chromosome of Corynebacterium glutamicum. Gene 145:69–73. DOI: https://doi.org/10.1016/0378-1119(94)

90324-7, PMID: 8045426

Schwalm J, Mahoney TF, Soltes GR, Silhavy TJ. 2013. Role for skp in LptD assembly in Escherichia coli. Journal of

Bacteriology 195:3734–3742. DOI: https://doi.org/10.1128/JB.00431-13, PMID: 23772069

Shahrizal M, Daimon Y, Tanaka Y, Hayashi Y, Nakayama S, Iwaki S, Narita SI, Kamikubo H, Akiyama Y, Tsukazaki

T. 2019. Structural basis for the function of the b-Barrel Assembly-Enhancing protease BepA. Journal of

Molecular Biology 431:625–635. DOI: https://doi.org/10.1016/j.jmb.2018.11.024, PMID: 30521812

Soltes GR, Martin NR, Park E, Sutterlin HA, Silhavy TJ. 2017. Distinctive roles for periplasmic proteases in the

maintenance of essential outer membrane protein assembly. Journal of Bacteriology 199:e00418-17.

DOI: https://doi.org/10.1128/JB.00418-17, PMID: 28784813

Sperandeo P, Martorana AM, Polissi A. 2017. The lipopolysaccharide transport (Lpt) machinery: a

nonconventional transporter for lipopolysaccharide assembly at the outer membrane of Gram-negative

Bacteria. Journal of Biological Chemistry 292:17981–17990. DOI: https://doi.org/10.1074/jbc.R117.802512

Sto¨cker W, Bode W. 1995. Structural features of a superfamily of zinc-endopeptidases: the metzincins. Current

Opinion in Structural Biology 5:383–390. DOI: https://doi.org/10.1016/0959-440X(95)80101-4, PMID: 7583637

Tamae C, Liu A, Kim K, Sitz D, Hong J, Becket E, Bui A, Solaimani P, Tran KP, Yang H, Miller JH. 2008.

Determination of antibiotic hypersensitivity among 4,000 single-gene-knockout mutants of Escherichia coli.

Journal of Bacteriology 190:5981–5988. DOI: https://doi.org/10.1128/JB.01982-07, PMID: 18621901

Tomasek D, Rawson S, Lee J, Wzorek JS, Harrison SC, Li Z, Kahne D. 2020. Structure of a nascent membrane

protein as it folds on the BAM complex. Nature 583:473–478. DOI: https://doi.org/10.1038/s41586-020-23701, PMID: 32528179

Tomasek D, Kahne D. 2021. The assembly of b-barrel outer membrane proteins. Current Opinion in Microbiology

60:16–23. DOI: https://doi.org/10.1016/j.mib.2021.01.009, PMID: 33561734

Vertommen D, Ruiz N, Leverrier P, Silhavy TJ, Collet JF. 2009. Characterization of the role of the Escherichia coli

periplasmic chaperone SurA using differential proteomics. Proteomics 9:2432–2443. DOI: https://doi.org/10.

1002/pmic.200800794, PMID: 19343722

Wu T, McCandlish AC, Gronenberg LS, Chng SS, Silhavy TJ, Kahne D. 2006. Identification of a protein complex

that assembles lipopolysaccharide in the outer membrane of Escherichia coli. PNAS 103:11754–11759.

DOI: https://doi.org/10.1073/pnas.0604744103, PMID: 16861298

Young TS, Ahmad I, Yin JA, Schultz PG. 2010. An enhanced system for unnatural amino acid mutagenesis in E.

coli. Journal of Molecular Biology 395:361–374. DOI: https://doi.org/10.1016/j.jmb.2009.10.030, PMID: 19852

970

Yu D, Ellis HM, Lee EC, Jenkins NA, Copeland NG, Court DL. 2000. An efficient recombination system for

chromosome engineering in Escherichia coli. PNAS 97:5978–5983. DOI: https://doi.org/10.1073/pnas.

100127597, PMID: 10811905

Miyazaki et al. eLife 2021;10:e70541. DOI: https://doi.org/10.7554/eLife.70541

21 of 21

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