Evolution of the β-barrel assembly machinery

doi:10.1016/j.tim.2012.08.006

Trends in Microbiology

Volume 20, Issue 12, December 2012, Pages 612-620

https://doi.org/10.1016/j.tim.2012.08.006 Get rights and content

Proteins from the Omp85 family have roles in membrane biogenesis, and the archetypal protein of this family is the bacterial outer membrane protein BamA. Through evolution, BamA has acquired membrane protein partner subunits, but distinct partner subunits are evident in the various bacterial lineages. As a result, experimental work on several species of bacteria has revealed varietal forms of the β-barrel assembly machinery (BAM complex). This scenario extends even into mitochondria and plastids, organelles of eukaryotic cells that evolved from intracellular bacterial ancestors. In addition to the BAM complex, other molecular machines, namely the two-partner secretion system (TPS) and the translocation and assembly module (the TAM), probably evolved from gene duplication events involving BamA. We discuss what is known about the diverse composition of the BAM complex in various bacterial lineages, and how this diversity impacts on our understanding of the mechanism underlying the assembly of bacterial outer membranes.

Section snippets

An ancient protein family and a function essential to the first bacteria

Gram-negative bacteria are encased by two membranes, and proteins located in the outer membrane are crucial for transfer of substances (e.g., porins) and as the physical point of contact with the environment (e.g., adhesins and other cellular projections). The majority of integral outer membrane proteins are composed from β-strands, which, when stitched together, form a β-barrel structure, a membrane-embedded, cylinder-shaped protein that, in the case of porins, forms a channel for the passage

The three known classes of the Omp85 protein family in bacteria

The most architecturally simple protein transport system known, which has an Omp85 family protein as its core component, is the two-partner secretion system (TPSS), also referred to as the type Vb secretion system 10, 11. TPSSs have been characterized in just a few groups of proteobacteria, suggesting they are a relatively new evolutionary invention. Each TPSS is dedicated to secreting a unique virulence factor, some of which are characterized toxins and adhesins. The TPSS consists of an Omp85

Crystal structures and evolutionary insights

The complete architecture and subunit arrangement within the BAM complex are still to be deciphered, but recent characterization of the structures of BamB, BamC, BamD, and BamE from E. coli have contributed exciting new insights into their functional influences and their evolution (Figure 2). BamB exhibits a β-propeller fold that forms a ring-like structure 25, 26, 27. Genetic studies have demonstrated that BamB binds to the POTRA domains of BamA, an interaction supported by modeling studies

Evolution of protein translocases in organelles derived by endosymbiosis

There are two eukaryotic counterparts for BAM and these are found in plastids and mitochondria, organelles derived from bacterial endosymbionts.

Mitochondria evolved from Alphaproteobacteria and phylogenetics has shown that the mitochondrial outer membrane protein Sam50 evolved from the alphaproteobacterial BamA [59]. In addition, biochemical assays have demonstrated that Sam50 functions in the assembly of β-barrel proteins into the mitochondrial outer membrane 59, 60, 61. Despite the

Concluding remarks

The mechanism governing β-barrel protein assembly into a membrane remains elusive. Unlike transmembrane helices, which are inherently hydrophobic, β-barrels only adopt a hydrophobic surface once the β-strands interact and form their tertiary fold. Several studies have demonstrated that precursor β-barrel proteins can fold merely in the presence of a phospholipid bilayer [66]. In this way, integration into the membrane is directly associated with polypeptide folding. However, in a cellular

Acknowledgments

We thank Felicity Alcock, Khatira Anwari, Matthew Belousoff, Ian Gentle, and Tamas Hatfaludi for critical comments on the manuscript. Work in our laboratory is funded by a National Health & Medical Research Council (NHMRC) Program Grant (606788). C.T.W. is an NHMRC Postdoctoral Fellow and T.L. is an Australian Research Council Federation Fellow.

References (87)

I.C. Sutcliffe
A phylum level perspective on bacterial cell envelope architecture
Trends Microbiol.
(2010)
L. Sanchez-Pulido
POTRA: a conserved domain in the FtsQ family and a class of beta-barrel outer membrane proteins
Trends Biochem. Sci.
(2003)
S. Reumann et al.
The endosymbiotic origin of the protein import machinery of chloroplastic envelope membranes
Trends Plant Sci.
(1999)
D.P. Ricci et al.
The Bam machine: a molecular cooper
Biochim. Biophys. Acta
(2012)
T. Wu
Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli
Cell
(2005)
H. Hodak et al.
Current challenges in autotransport and two-partner protein secretion pathways
Res. Microbiol.
(2007)
J. Mazar et al.
New insight into the molecular mechanisms of two-partner secretion
Trends Microbiol.
(2007)
E. Fan
Two-partner secretion of Gram-negative bacteria: a single beta-barrel protein enables transport across the outer membrane
J. Biol. Chem.
(2012)
C. Webb
Dynamic association of BAM complex modules includes surface exposure of the lipoprotein BamC
J. Mol. Biol.
(2012)
R. Albrecht et al.
Structural basis of outer membrane protein biogenesis in bacteria
J. Biol. Chem.
(2011)

K.H. Kim et al.

Crystal structure of Escherichia coli BamB, a lipoprotein component of the beta-barrel assembly machinery complex

J. Mol. Biol.

(2011)

N. Noinaj

The crystal structure of BamB suggests interactions with BamA and its role within the BAM complex

J. Mol. Biol.

(2011)

C.K. Chen

The many blades of the β-propeller proteins: conserved but versatile

Trends Biochem. Sci.

(2011)

K.H. Kim

Crystal structure of beta-barrel assembly machinery BamCD protein complex

J. Biol. Chem.

(2011)

C. Dong

Structure of Escherichia coli BamD and its functional implications in outer membrane protein assembly

Acta Crystallogr. D: Biol. Crystallogr.

(2012)

C.M. Sandoval

Crystal structure of BamD: an essential component of the beta-barrel assembly machinery of Gram-negative bacteria

J. Mol. Biol.

(2011)

P.Z. Gatzeva-Topalova

Crystal structure of YaeT: conformational flexibility and substrate recognition

Structure

(2008)

T. Arnold

Omp85 from the thermophilic cyanobacterium Thermosynechococcus elongatus differs from proteobacterial Omp85 in structure and domain composition

J. Biol. Chem.

(2010)

P. Koenig

Conserved properties of polypeptide transport-associated (POTRA) domains derived from cyanobacterial Omp85

J. Biol. Chem.

(2010)

R. Bredemeier

Functional and phylogenetic properties of the pore-forming beta-barrel transporters of the Omp85 family

J. Biol. Chem.

(2007)

J. Tripp

Structure and conservation of the periplasmic targeting factor Tic22 from plants and cyanobacteria

J. Biol. Chem.

(2012)

V. Kozjak

An essential role of Sam50 in the protein sorting and assembly machinery of the mitochondrial outer membrane

J. Biol. Chem.

(2003)

J.H. Kleinschmidt

Folding kinetics of the outer membrane proteins OmpA and FomA into phospholipid bilayers

Chem. Phys. Lipids

(2006)

F. Ertel

The evolutionarily related beta-barrel polypeptide transporters from Pisum sativum and Nostoc PCC7120 contain two distinct functional domains

J. Biol. Chem.

(2005)

Y.C. Su

Immunization with the recombinant Burkholderia pseudomallei outer membrane protein Omp85 induces protective immunity in mice

Vaccine

(2010)

Y. Sun

Identification of an Edwardsiella tarda surface antigen and analysis of its immunoprotective potential as a purified recombinant subunit vaccine and a surface-anchored subunit vaccine expressed by a fish commensal strain

Vaccine

(2010)

T. Cavalier-Smith

Rooting the tree of life by transition analyses

Biol. Direct

(2006)

I.C. Sutcliffe

Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war

Environ. Microbiol.

(2011)

S. Genevrois

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

EMBO J.

(2003)

R. Voulhoux

Role of a highly conserved bacterial protein in outer membrane protein assembly

Science

(2003)

B. Clantin

Structure of the membrane protein FhaC: a member of the Omp85–TpsB transporter superfamily

Science

(2007)

J.F. Stegmeier

Characterisation of YtfM, a second member of the Omp85 family in Escherichia coli

Biol. Chem.

(2007)

J. Selkrig

Discovery of an archetypal protein transport system in bacterial outer membranes

Nat. Struct. Mol. Biol.

(2012)

R.R. Chaudhuri

Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042

PLoS ONE

(2010)

F. Jacob-Dubuisson

First structural insights into the TpsB/Omp85 superfamily

Biol. Chem.

(2009)

J. Selkrig

Discovery of an archetypal protein transport system in bacterial outer membranes

Nat. Struct. Mol. Biol.

(2012)

J.C. Malinverni

YfiO stabilizes the YaeT complex and is essential for outer membrane protein assembly in Escherichia coli

Mol. Microbiol.

(2006)

S. Okuda et al.

Lipoprotein sorting in bacteria

Annu. Rev. Microbiol.

(2011)

C.L. Hagan

Reconstitution of outer membrane protein assembly from purified components

Science

(2010)

S. Kim

Structure and function of an essential component of the outer membrane protein assembly machine

Science

(2007)

V. Robert

Assembly factor Omp85 recognizes its outer membrane protein substrates by a species-specific C-terminal motif

PLoS Biol.

(2006)

P. Vuong

Analysis of YfgL and YaeT interactions through bioinformatics, mutagenesis, and biochemistry

J. Bacteriol.

(2008)

R. Ieva

Sequential and spatially restricted interactions of assembly factors with an autotransporter beta domain

Proc. Natl. Acad. Sci. U. S. A.

(2011)

Cited by (116)

Categorization of Escherichia coli outer membrane proteins by dependence on accessory proteins of the β-barrel assembly machinery complex
2023, Journal of Biological Chemistry
The outer membrane (OM) of gram-negative bacteria is populated by various outer membrane proteins (OMPs) that fold into a unique β-barrel transmembrane domain. Most OMPs are assembled into the OM by the β-barrel assembly machinery (BAM) complex. In Escherichia coli, the BAM complex is composed of two essential proteins (BamA and BamD) and three nonessential accessory proteins (BamB, BamC, and BamE). The currently proposed molecular mechanisms of the BAM complex involve only essential subunits, with the function of the accessory proteins remaining largely unknown. Here, we compared the accessory protein requirements for the assembly of seven different OMPs, 8- to 22-stranded, by our in vitro reconstitution assay using an E. coli mid-density membrane. BamE was responsible for the full efficiency of the assembly of all tested OMPs, as it enhanced the stability of essential subunit binding. BamB increased the assembly efficiency of more than 16-stranded OMPs, whereas BamC was not required for the assembly of any tested OMPs. Our categorization of the requirements of BAM complex accessory proteins in the assembly of substrate OMPs enables us to identify potential targets for the development of new antibiotics.
Modeling intermediates of BamA folding an outer membrane protein
2022, Biophysical Journal
BamA, the core component of the β-barrel assembly machinery complex, is an integral outer-membrane protein (OMP) in Gram-negative bacteria that catalyzes the folding and insertion of OMPs. A key feature of BamA relevant to its function is a lateral gate between its first and last β-strands. Opening of this lateral gate is one of the first steps in the asymmetric-hybrid-barrel model of BamA function. In this study, multiple hybrid-barrel folding intermediates of BamA and a substrate OMP, EspP, were constructed and simulated to better understand the model’s physical consequences. The hybrid-barrel intermediates consisted of the BamA β-barrel and its POTRA5 domain and either one, two, three, four, five, or six β-hairpins of EspP. The simulation results support an asymmetric-hybrid-barrel model in which the BamA N-terminal β-strand forms stronger interactions with the substrate OMP than the C-terminal β-strand. A consistent “B”-shaped conformation of the final folding intermediate was observed, and the shape of the substrate β-barrel within the hybrid matched the shape of the fully folded substrate. Upon further investigation, inward-facing glycines were found at sharp bends within the hybrid and fully folded β-barrels. Together, the data suggest an influence of sequence on shape of the substrate barrel throughout the OMP folding process and of the fully folded OMP.
Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding
2022, Cell
Transmembrane β barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the β barrel assembly machinery (BAM) via a poorly understood process that occurs without known external energy sources. Here, we used single-particle cryo-EM to visualize the folding dynamics of a model β barrel protein (EspP) by BAM. We found that BAM binds the highly conserved “β signal” motif of EspP to correctly orient β strands in the OM during folding. We also found that the folding of EspP proceeds via “hybrid-barrel” intermediates in which membrane integrated β sheets are attached to the essential BAM subunit, BamA. The structures show an unprecedented deflection of the membrane surrounding the EspP intermediates and suggest that β sheets progressively fold toward BamA to form a β barrel. Along with in vivo experiments that tracked β barrel folding while the OM tension was modified, our results support a model in which BAM harnesses OM elasticity to accelerate β barrel folding.
Transmembrane β-barrel proteins of bacteria: From structure to function
2022, Advances in Protein Chemistry and Structural Biology
The outer membrane of Gram-negative bacteria is a specialized organelle conferring protection to the cell against various environmental stresses and resistance to many harmful compounds. The outer membrane has a number of unique features, including an asymmetric lipid bilayer, the presence of lipopolysaccharides and an individual proteome. The vast majority of the integral transmembrane proteins in the outer membrane belongs to the family of β-barrel proteins. These evolutionarily related proteins share a cylindrical, anti-parallel β-sheet core fold spanning the outer membrane. The loops and accessory domains attached to the β-barrel allow for a remarkable versatility in function for these proteins, ranging from diffusion pores and transporters to enzymes and adhesins. We summarize the current knowledge on β-barrel structure and folding and give an overview of their functions, evolution, and potential as drug targets.
Substrate-dependent arrangements of the subunits of the BAM complex determined by neutron reflectometry
2021, Biochimica et Biophysica Acta - Biomembranes
In Gram-negative bacteria, the β-barrel assembly machinery (BAM) complex catalyses the assembly of β-barrel proteins into the outer membrane, and is composed of five subunits: BamA, BamB, BamC, BamD and BamE. Once assembled, - β-barrel proteins can be involved in various functions including uptake of nutrients, export of toxins and mediating host-pathogen interactions, but the precise mechanism by which these ubiquitous and often essential β-barrel proteins are assembled is yet to be established. In order to determine the relative positions of BAM subunits in the membrane environment we reconstituted each subunit into a biomimetic membrane, characterizing their interaction and structural changes by Quartz Crystal Microbalance with Dissipation monitoring (QCM-D) and neutron reflectometry. Our results suggested that the binding of BamE, or a BamDE dimer, to BamA induced conformational changes in the polypeptide transported-associated (POTRA) domains of BamA, but that BamB or BamD alone did not promote any such changes. As monitored by neutron reflectometry, addition of an unfolded substrate protein extended the length of POTRA domains further away from the membrane interface as part of the mechanism whereby the substrate protein was folded into the membrane.
Building Better Barrels – β-barrel Biogenesis and Insertion in Bacteria and Mitochondria
2021, Journal of Molecular Biology
β-barrel proteins are folded and inserted into outer membranes by multi-subunit protein complexes that are conserved across different types of outer membranes. In Gram-negative bacteria this complex is the barrel-assembly machinery (BAM), in mitochondria it is the sorting and assembly machinery (SAM) complex, and in chloroplasts it is the outer envelope protein Oep80. Mitochondrial β-barrel precursor proteins are translocated from the cytoplasm to the intermembrane space by the translocase of the outer membrane (TOM) complex, and stabilized by molecular chaperones before interaction with the assembly machinery. Outer membrane bacterial BamA interacts with four periplasmic accessory proteins, whereas mitochondrial Sam50 interacts with two cytoplasmic accessory proteins. Despite these major architectural differences between BAM and SAM complexes, their core proteins, BamA and Sam50, seem to function the same way. Based on the new SAM complex structures, we propose that the mitochondrial β-barrel folding mechanism follows the budding model with barrel-switching aiding in the release of new barrels. We also built a new molecular model for Tom22 interacting with Sam37 to identify regions that could mediate TOM-SAM supercomplex formation.

View all citing articles on Scopus

^*: These authors contributed equally.

View full text

Trends in Microbiology

ReviewEvolution of the β-barrel assembly machinery

Section snippets

An ancient protein family and a function essential to the first bacteria

The three known classes of the Omp85 protein family in bacteria

Crystal structures and evolutionary insights

Evolution of protein translocases in organelles derived by endosymbiosis

Concluding remarks

Acknowledgments

Trends Microbiol.

Trends Biochem. Sci.

Trends Plant Sci.

Biochim. Biophys. Acta

Cell

Res. Microbiol.

Trends Microbiol.

J. Biol. Chem.

J. Mol. Biol.

J. Biol. Chem.

J. Mol. Biol.

J. Mol. Biol.

Trends Biochem. Sci.

J. Biol. Chem.

Acta Crystallogr. D: Biol. Crystallogr.

J. Mol. Biol.

Structure

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

Chem. Phys. Lipids

J. Biol. Chem.

Vaccine

Vaccine

Rooting the tree of life by transition analyses

Biol. Direct

Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war

Environ. Microbiol.

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

EMBO J.

Role of a highly conserved bacterial protein in outer membrane protein assembly

Science

Structure of the membrane protein FhaC: a member of the Omp85–TpsB transporter superfamily

Science

Characterisation of YtfM, a second member of the Omp85 family in Escherichia coli

Biol. Chem.

Discovery of an archetypal protein transport system in bacterial outer membranes

Nat. Struct. Mol. Biol.

Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042

PLoS ONE

First structural insights into the TpsB/Omp85 superfamily

Biol. Chem.

Discovery of an archetypal protein transport system in bacterial outer membranes

Nat. Struct. Mol. Biol.

YfiO stabilizes the YaeT complex and is essential for outer membrane protein assembly in Escherichia coli

Mol. Microbiol.

Lipoprotein sorting in bacteria

Annu. Rev. Microbiol.

Reconstitution of outer membrane protein assembly from purified components

Science

Structure and function of an essential component of the outer membrane protein assembly machine

Science

Assembly factor Omp85 recognizes its outer membrane protein substrates by a species-specific C-terminal motif

PLoS Biol.

Analysis of YfgL and YaeT interactions through bioinformatics, mutagenesis, and biochemistry

J. Bacteriol.

Sequential and spatially restricted interactions of assembly factors with an autotransporter beta domain

Proc. Natl. Acad. Sci. U. S. A.

Review
Evolution of the β-barrel assembly machinery