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
...