POTRA: a conserved domain in the FtsQ family and a class of β-barrel outer membrane proteins

doi:10.1016/j.tibs.2003.08.003

Trends in Biochemical Sciences

Volume 28, Issue 10, October 2003, Pages 523-526

https://doi.org/10.1016/j.tibs.2003.08.003 Get rights and content

Abstract

POTRA (for polypeptide-transport-associated domain) is a novel domain identified in proteins of the ShlB, Toc75, D15 and FtsQ/DivIB families. In most cases, the POTRA domain is associated with a β-barrel outer membrane domain and its function has been experimentally related to polypeptide transport in Toc75 (Tic–Toc protein import system in chloroplast) and ShlB families. In addition to potential key roles in protein transport across the outer membrane and in bacterial septation, the POTRA domain has attractive features for vaccine development in diseases such as cholera, meningitis, gonorrhoea and syphilis.

Section snippets

Characterization of the POTRA domain

For sequence searches, independent profiles were generated for the appearance of the domain in each family [10]. Searches with the corresponding global hidden Markov models (HMM; using hmmsearch of HMMer version 2.2 g; http://hmmer.wustl.edu/) produced statistically significant E-values that connected all POTRA-domain-containing families. Initial characterizations of the N-terminal region of the D15 family gave the following results: the HMM profile from repeat 1 detected repeat 5 with E-values

Putative role of the POTRA domain

The precise functional role of the POTRA domain remains to be elucidated. The lack of invariant residues in the multiple alignment renders a catalytic function improbable. However, interesting hypotheses can be formulated from the analysis of the experimentally characterized protein families bearing the POTRA domain.

FtsQ is one of the ten proteins known to be essential for cell division in the Gram-negative bacterium Escherichia coli [9]. FtsQ and DivIB (the FtsQ homolog in Bacillus subtilis)

Concluding remarks

The identification of the POTRA domain could help in the design of further experimental work to investigate its association with the transport-related process in Gram-negative bacteria (ShlB, OMP85 and YTMF families), chloroplast (Toc75 family) and eukaryotic (CGI51 family), and to analyze its precise role in bacterial cell division (FtsQ/DivIB family). The hypothesis that the POTRA domain could have a chaperone-like function creates an evolutionary picture in which an ubiquitous bacterial

Acknowledgements

We thank R. Roca, M. Tress (CNB-Spain), R. Rycroft and F. Davis (UCSF) for their helpful comments on the article.

References (25)

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F.L. Yang et al.
ShlB mutants of Serrantia marcescens allow uncoupling of activation and secretion of the ShlA hemolysin
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Identification and characterization of an in vivo regulated D15/Oma87 homologue in Shigella flexneri using differential display polymerase chain reaction
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U.W. Konninger

The haemolysin-secreting ShlB protein of the outer membrane of Serratia marcescens: determination of surface-exposed residues and formation of ion-permeable pores by ShlB mutants in artificial lipid bilayer membranes

Mol. Microbiol.

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The Omp85 protein of Neisseria meningitidis is required for lipid export to the outer membrane

EMBO J.

(2003)

Cited by (188)

Role of the small protein Mco6 in the mitochondrial sorting and assembly machinery
2024, Cell Reports
The majority of mitochondrial precursor proteins are imported through the Tom40 β-barrel channel of the translocase of the outer membrane (TOM). The sorting and assembly machinery (SAM) is essential for β-barrel membrane protein insertion into the outer membrane and thus required for the assembly of the TOM complex. Here, we demonstrate that the α-helical outer membrane protein Mco6 co-assembles with the mitochondrial distribution and morphology protein Mdm10 as part of the SAM machinery. MCO6 and MDM10 display a negative genetic interaction, and a mco6-mdm10 yeast double mutant displays reduced levels of the TOM complex. Cells lacking Mco6 affect the levels of Mdm10 and show assembly defects of the TOM complex. Thus, this work uncovers a role of the SAM^Mco6 complex for the biogenesis of the mitochondrial outer membrane.
Uncovering the membrane-integrated SecA<sup>N</sup> protein that plays a key role in translocating nascent outer membrane proteins
2023, Biochimica et Biophysica Acta - Proteins and Proteomics
A large number of nascent polypeptides have to get across a membrane in targeting to the proper subcellular locations. The SecYEG protein complex, a homolog of the Sec61 complex in eukaryotic cells, has been viewed as the common translocon at the inner membrane for targeting proteins to three extracytoplasmic locations in Gram-negative bacteria, despite the lack of direct verification in living cells. Here, via unnatural amino acid-mediated protein-protein interaction analyses in living cells, in combination with genetic studies, we unveiled a hitherto unreported SecA^N protein that seems to be directly involved in translocationg nascent outer membrane proteins across the plasma membrane; it consists of the N-terminal 375 residues of the SecA protein and exists as a membrane-integrated homooligomer. Our new findings place multiple previous observations related to bacterial protein targeting in proper biochemical and evolutionary contexts.
The structural dynamics of full-length divisome transmembrane proteins FtsQ, FtsB, and FtsL in FtsQBL complex formation
2022, Journal of Biological Chemistry
FtsQBL is a transmembrane protein complex in the divisome of Escherichia coli that plays a critical role in regulating cell division. Although extensive efforts have been made to investigate the interactions between the three involved proteins, FtsQ, FtsB, and FtsL, the detailed interaction mechanism is still poorly understood. In this study, we used hydrogen-deuterium exchange mass spectrometry to investigate these full-length proteins and their complexes. We also dissected the structural dynamic changes and the related binding interfaces within the complexes. Our data revealed that FtsB and FtsL interact at both the periplasmic and transmembrane regions to form a stable complex. Furthermore, the periplasmic region of FtsB underwent significant conformational changes. With the help of computational modeling, our results suggest that FtsBL complexation may bring the respective constriction control domains (CCDs) in close proximity. We show that when FtsBL adopts a coiled-coil structure, the CCDs are fixed at a vertical position relative to the membrane surface; thus, this conformational change may be essential for FtsBL’s interaction with other divisome proteins. In the FtsQBL complex, intriguingly, we show only FtsB interacts with FtsQ at its C-terminal region, which stiffens a large area of the β-domain of FtsQ. Consistent with this, we found the connection between the α- and β-domains in FtsQ is also strengthened in the complex. Overall, the present study provides important experimental evidence detailing the local interactions between the full-length FtsB, FtsL, and FtsQ protein, as well as valuable insights into the roles of FtsQBL complexation in regulating divisome activity.
Monitoring the antibiotic darobactin modulating the β-barrel assembly factor BamA
2022, Structure
The β-barrel assembly machinery (BAM) complex is an essential component of Escherichia coli that inserts and folds outer membrane proteins (OMPs). The natural antibiotic compound darobactin inhibits BamA, the central unit of BAM. Here, we employ dynamic single-molecule force spectroscopy (SMFS) to better understand the structure-function relationship of BamA and its inhibition by darobactin. The five N-terminal polypeptide transport (POTRA) domains show low mechanical, kinetic, and energetic stabilities. In contrast, the structural region linking the POTRA domains to the transmembrane β-barrel exposes the highest mechanical stiffness and lowest kinetic stability within BamA, thus indicating a mechano-functional role. Within the β-barrel, the four N-terminal β-hairpins H1–H4 expose the highest mechanical stabilities and stiffnesses, while the four C-terminal β-hairpins H5–H6 show lower stabilities and higher flexibilities. This asymmetry within the β-barrel suggests that substrates funneling into the lateral gate formed by β-hairpins H1 and H8 can force the flexible C-terminal β-hairpins to change conformations.
TtOmp85, a single Omp85 member protein functions as a β-barrel protein insertase and an autotransporter translocase without any accessory proteins
2021, Biochemical and Biophysical Research Communications
The biogenesis of outer membrane proteins requires the function of β-barrel assembly machinery (BAM), whose function is highly conserved while its composition is variable. The Escherichia coli BAM is composed of five subunits, while Thermus thermophilus seems to contain a single BAM protein, named TtOmp85. To search for the primitive form of a functional BAM, we investigated and compared the function of TtOmp85 and E. coli BAM by use of a reconstitution assay that examines the integration of OmpA and BamA from E. coli and TtoA from T. thermophilus, as well as the translocation of the E. coli Ag43. Our results show that a single TtOmp85 protein can substitute for the collective function of the five subunits constituting E. coli BAM.
Characterization of BamA reconstituted into a solid-supported lipid bilayer as a platform for measuring dynamics during substrate protein assembly into the membrane
2020, Biochimica et Biophysica Acta - Biomembranes
In Gram–negative bacteria, the multi-protein β-barrel assembly machine (BAM) complex is a nanomachine playing a vital role in the process of assembling β-barrel proteins into the outer membrane (OM). The core component of this multiprotein complex, BamA, is an evolutionarily conserved protein that carries five polypeptide-transport-associated (POTRA) domains that project from the outer membrane. BamA is essential for chaperoning the insertion of proteins into the OM surface of bacterial cells. In this work, we have reconstituted a membrane containing BamA on a gold substrate and characterized structure of each component and movement in different situation at the nanoscale level using quartz-crystal microbalance with dissipation and neutron reflectometry (NR). The purified BamA in n-dodecyl β-D-maltoside (DDM) was first engineered onto a nickel-NTA (Nα, Nα-bis-(carboxymethyl)-l-lysine) modified gold surface followed by DDM removal and bilayer assembly. The system was then used to monitor the binding and insertion of a substrate membrane protein. The data shows the total reach of BamA was 120 Å and the embedding of membrane had no effect on the BamA morphology. However, the addition of the substrate enabled the periplasmic POTRA domain of BamA to extend further away from the membrane surface. This dynamic behaviour of BamA POTRA domains is consistent with models invoking the gathering of transported substrates from the periplasmic space between the inner and outer membranes in bacterial cells. This study provides evidence that NR is a reliable tool for diverse investigations in the future, especially for applications in the field of membrane protein biogenesis.

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Trends in Biochemical Sciences

Abstract

Section snippets

Characterization of the POTRA domain

Putative role of the POTRA domain

Concluding remarks

Acknowledgements

References (25)

Toc, tic, and chloroplast protein import

Biochim. Biophys. Acta

ShlB mutants of Serrantia marcescens allow uncoupling of activation and secretion of the ShlA hemolysin

Int. J. Med. Microbiol.

Novel topological features of FhaC, the outer membrane transporter involved in the secretion of the Bordetella pertussis filamentous hemagglutinin

J. Biol. Chem.

The endosymbiotic origin of the protein import machinery of chloroplastic envelope membranes

Trends Plant Sci.

PHD: predicting one-dimensional protein structure by profile-based neural networks

Methods Enzymol.

The structure of bacterial outer membrane proteins

Biochim. Biophys. Acta

Omp85 proteins of Neisseria gonorrhoeae and Neisseria meningitidis are similar to Haemophilus influenzae D-15-Ag and Pasteurella multocida Oma87

Microb. Pathog.

Identification and characterization of an in vivo regulated D15/Oma87 homologue in Shigella flexneri using differential display polymerase chain reaction

Gene

Developing a nontypeable Haemophilus influenzae (NTHi) vaccine

Vaccine

T-Coffee: a novel method for fast and accurate multiple sequence alignment

J. Mol. Biol.

The haemolysin-secreting ShlB protein of the outer membrane of Serratia marcescens: determination of surface-exposed residues and formation of ion-permeable pores by ShlB mutants in artificial lipid bilayer membranes

Mol. Microbiol.

The Omp85 protein of Neisseria meningitidis is required for lipid export to the outer membrane

EMBO J.

Cited by (188)

Role of the small protein Mco6 in the mitochondrial sorting and assembly machinery

Uncovering the membrane-integrated SecA<sup>N</sup> protein that plays a key role in translocating nascent outer membrane proteins

The structural dynamics of full-length divisome transmembrane proteins FtsQ, FtsB, and FtsL in FtsQBL complex formation

Monitoring the antibiotic darobactin modulating the β-barrel assembly factor BamA

TtOmp85, a single Omp85 member protein functions as a β-barrel protein insertase and an autotransporter translocase without any accessory proteins

Characterization of BamA reconstituted into a solid-supported lipid bilayer as a platform for measuring dynamics during substrate protein assembly into the membrane

Trends in Biochemical Sciences

Protein Sequence MotifPOTRA: a conserved domain in the FtsQ family and a class of β-barrel outer membrane proteins

Abstract

Section snippets

Characterization of the POTRA domain

Putative role of the POTRA domain

Concluding remarks

Acknowledgements

Biochim. Biophys. Acta

Int. J. Med. Microbiol.

J. Biol. Chem.

Trends Plant Sci.

Methods Enzymol.

Biochim. Biophys. Acta

Microb. Pathog.

Gene

Vaccine

J. Mol. Biol.

The haemolysin-secreting ShlB protein of the outer membrane of Serratia marcescens: determination of surface-exposed residues and formation of ion-permeable pores by ShlB mutants in artificial lipid bilayer membranes

Mol. Microbiol.

The Omp85 protein of Neisseria meningitidis is required for lipid export to the outer membrane

EMBO J.

Protein Sequence Motif
POTRA: a conserved domain in the FtsQ family and a class of β-barrel outer membrane proteins