BBA - Molecular Cell Research (v.1694, #1-3)

Recent progress in the understanding of the nature of the extraordinary variety of protein translocation systems, mainly in Gram negative bacteria, is reviewed. This takes us from the insertion of proteins into the inner membrane via the sophisticated Sec apparatus, the lethal injection of Type III proteins into host cells and on to the beautiful machine that assembles the flagellum. Attempts are made to establish some order, some common principles that might explain the variety and the complexity of some systems. The fundamentals considered are the nature of different transport signals, the nature of translocons (a wide variety of inner membrane types, outer membrane translocons are more conserved), the process of docking to translocons, the role of chaperones and the folding of transported proteins, the energetics of translocation, and prospects for future advances.
Keywords: Bacterial protein; Translocation; Translocator system;

SRP-mediated protein targeting: structure and function revisited by Joen Luirink; Irmgard Sinning (17-35).
The signal recognition particle (SRP) and its membrane-bound receptor (SR) deliver membrane proteins and secretory proteins to the translocation channel in the plasma membrane (or the endoplasmic reticulum). The general outline of the SRP pathway is conserved in all three kingdoms of life. During the past decade, structure determination together with functional studies has brought our understanding of the SRP-mediated protein transport to an almost molecular level. An impressive amount of new information especially on the prokaryotic SRP is integrated into the current picture of the SRP pathway.
Keywords: SRP; SRP receptor; E. coli; Protein targeting; Ribosome; Trigger factor;

Sec-translocase mediated membrane protein biogenesis by Ross E. Dalbey; Minyong Chen (37-53).
α-Helical transmembrane proteins in bacteria are localized within the plasma membrane. The membrane assembly of these proteins requires protein devices for insertion into the lipid bilayer. In E. coli, membrane proteins require the SRP pathway components Ffh, 4.5S RNA and FtsY for membrane targeting and the SecYEGDF translocase and, in some cases, SecA, for translocation of hydrophilic domains. In addition, YidC, a recently discovered membrane protein, mediates the membrane integration and folding of hydrophobic domains of membrane proteins. In this review, we will describe the current status of the protein targeting and membrane integration pathways.
Keywords: SecYEG; Membrane protein insertion; Membrane protein assembly; Protein targeting; Membrane translocation;

Membrane integration of E. coli model membrane proteins by Sandra J. Facey; Andreas Kuhn (55-66).
The molecular events of membrane translocation and insertion have been investigated using a number of different model proteins. Each of these proteins has specific features that allow interaction with the membrane components which ensure that the proteins reach their specific local destination and final conformation. This review will give an overview on the best-characterized proteins studied in the bacterial system and emphasize the distinct aspects of the pathways.
Keywords: Membrane insertion; Sec translocon; YidC; Reconstitution; GES scale; Topology;

Structure and function of SecA, the preprotein translocase nanomotor by Eleftheria Vrontou; Anastassios Economou (67-80).
Most secretory proteins that are destined for the periplasm or the outer membrane are exported through the bacterial plasma membrane by the Sec translocase. Translocase is a complex nanomachine that moves processively along its aminoacyl polymeric substrates effectively pumping them to the periplasmic space. The salient features of this process are: (a) a membrane-embedded “clamp” formed by the trimeric SecYEG protein, (b) a “motor” provided by the dimeric SecA ATPase, (c) regulatory subunits that optimize catalysis and (d) both chemical and electrochemical metabolic energy. Significant recent strides have allowed structural, biochemical and biophysical dissection of the export reaction. A model incorporating stepwise strokes of the translocase nanomachine at work is discussed.
Keywords: Protein translocase; SecA; SecYEG; ATPase; Motor protein; Membrane transporter;

The protein-conducting channel SecYEG by Andreas K.J. Veenendaal; Chris van der Does; Arnold J.M. Driessen (81-95).
In bacteria, the translocase mediates the translocation of proteins into or across the cytosolic membrane. It consists of a membrane embedded protein-conducting channel and a peripherally associated motor domain, the ATPase SecA. The channel is formed by SecYEG, a multimeric protein complex that assembles into oligomeric forms. The structure and subunit composition of this protein-conducting channel is evolutionary conserved and a similar system is found in the endoplasmic reticulum of eukaryotes and the cytoplasmic membrane of archaea. The ribosome and other membrane proteins can associate with the protein-conducting channel complex and affect its activity or functionality.
Keywords: Protein-conducting channel; Translocase; SecYEG; Protein translocation; Secretion;

Phospholipids are essential building blocks of membranes and maintain the membrane permeability barrier of cells and organelles. They provide not only the bilayer matrix in which the functional membrane proteins reside, but they also can play direct roles in many essential cellular processes. In this review, we give an overview of the lipid involvement in protein translocation across and insertion into the Escherichia coli inner membrane. We describe the key and general roles that lipids play in these processes in conjunction with the protein components involved. We focus on the Sec-mediated insertion of leader peptidase. We describe as well the more direct roles that lipids play in insertion of the small coat proteins Pf3 and M13. Finally, we focus on the role of lipids in membrane assembly of oligomeric membrane proteins, using the potassium channel KcsA as model protein. In all cases, the anionic lipids and lipids with small headgroups play important roles in either determining the efficiency of the insertion and assembly process or contributing to the directionality of the insertion process.
Keywords: Lipid–protein interaction; Protein secretion; Protein insertion; Membrane protein assembly; Membrane phospholipid;

Disulfide bond formation is a catalyzed process in vivo. In prokaryotes, the oxidation of cysteine pairs is achieved by the transfer of disulfides from the highly oxidizing DsbA/DsbB catalytic machinery to substrate proteins. The oxidizing power utilized by this system comes from the membrane-embedded electron transport system, which utilizes molecular oxygen as a final oxidant. Proofreading of disulfide bond formation is performed by the DsbC/DsbD system, which has the ability to rearrange non-native disulfides to their native configuration. These disulfide isomerization reactions are sustained by a constant supply of reducing power provided by the cytoplasmic thioredoxin system, utilizing NADPH as the ultimate electron source.
Keywords: Disulfide bond; DsbA; DsbB; DsbC; DsbD; Escherichia coli;

Quality control in the bacterial periplasm by Amy R. Duguay; Thomas J. Silhavy (121-134).
Studies of the mechanisms that Gram-negative bacteria use to sense and respond to stress have led to a greater understanding of protein folding in both cytoplasmic and extracytoplasmic locations. In response to stressful conditions, bacteria induce a variety of stress response systems, examples of which are the σE and Cpx systems in Escherichia coli. Induction of these stress response systems results in upregulation of several gene targets that have been shown to be important for protein folding under normal conditions. Here we review the identification of stress response systems and their corresponding gene targets in E. coli. In addition, we discuss the apparent redundancy of the folding factors in the periplasm, and we consider the potential importance of the functional overlap that exists.
Keywords: Sigma-E; Cpx; Protein folding; Chaperone;

Tat-dependent protein targeting in prokaryotes and chloroplasts by Colin Robinson; Albert Bolhuis (135-147).
The twin-arginine translocation (Tat) system operates in the chloroplast thylakoid and the plasma membranes of a wide range of bacteria. It recognizes substrates bearing cleavable signal peptides in which a twin-arginine motif almost invariably plays a key role in recognition by the translocation machinery. These signal peptides are surprisingly similar to those used to specify transport by Sec-type systems, but the Tat pathway differs in fundamental respects from Sec-type and other protein translocases. Its key attribute is its ability to translocate large, fully folded (even oligomeric) proteins across tightly sealed membranes. To date, three key tat genes have been characterised and the first details of the Tat system are beginning to emerge. In this article we review the salient features of Tat systems, with an emphasis on the targeting signals involved, the substrate specificities of Tat systems, our current knowledge of Tat complex structures and the known mechanistic features. Although the article is focused primarily on bacterial systems, we incorporate relevant aspects of plant thylakoid Tat work and we discuss how the plant and bacterial systems may differ in some respects.
Keywords: Tat; Protein targeting; Prokaryote;

Type I secretion in gram-negative bacteria by P. Delepelaire (149-161).
In gram-negative bacteria, type I secretion is carried out by a translocator made up of three proteins that span the cell envelope. One of these proteins is a specific outer membrane protein (OMP) and the other two are cytoplasmic membrane proteins: an ATP-binding cassette (ABC) and the so-called membrane fusion or adaptor protein (MFP). Type I secretion is sec-independent and bypasses the periplasm. This widespread pathway allows the secretion of proteins of diverse sizes and functions via a C-terminal uncleaved secretion signal. This C-terminal secretion signal specifically recognizes the ABC protein, triggering the assembly of the functional trans-envelope complex. This report will mainly deal will recent data concerning the structure and assembly of the secretion complex as well as the effects and role of substrate folding on secretion by this pathway.
Keywords: Type I secretion; Gram-negative; Structure;

The cell envelope of Gram-negative bacteria is composed of two membranes, which are separated by the peptidoglycan-containing periplasm. Whereas the envelope forms an essential barrier against harmful substances, it is nevertheless a compartment of intense traffic for large proteins such as enzymes and toxins. Numerous studies dealing with the molecular mechanism of protein secretion have revealed that Gram-negative bacteria evolved different strategies to achieve this process. Among them, the type II secretion mechanism is part of a two-step process. Exoproteins following this pathway are synthesized as signal peptide-containing precursors. After cleavage of the signal peptide, the mature exoproteins are released into the periplasm, where they fold. The type II machinery, also known as the secreton, is responsible for the translocation of the periplasmic intermediates across the OM. The type II system is broadly conserved in Gram-negative bacteria and involves a set of 12–16 different proteins named GspC-M, GspAB, GspN, GspO, and GspS. The type II secretion system is highly reminiscent of the type IV piliation assembly system. Based on findings about the subcellular localisation of the Gsp components, protein–protein interactions between Gsps and their multimerisation status, structural data and electron microscopy observation, it could be proposed a working model that strikingly runs both systems in parallel.
Keywords: Type IV pilus; General Secretory Pathway or GSP; Secretin; Pseudopilin and pseudopilus; Traffic ATPase; Gram-negative bacteria;

Type III protein secretion mechanism in mammalian and plant pathogens by Sheng Yang He; Kinya Nomura; Thomas S. Whittam (181-206).
The type III protein secretion system (TTSS) is a complex organelle in the envelope of many Gram-negative bacteria; it delivers potentially hundreds of structurally diverse bacterial virulence proteins into plant and animal cells to modulate host cellular functions. Recent studies have revealed several basic features of this secretion system, including assembly of needle/pilus-like secretion structures, formation of putative translocation pores in the host membrane, recognition of N-terminal/5′ mRNA-based secretion signals, and requirement of small chaperone proteins for optimal delivery and/or expression of effector proteins. Although most of our knowledge about the TTSS is derived from studies of mammalian pathogenic bacteria, similar and unique features are learned from studies of plant pathogenic bacteria. Here, we summarize the most salient aspects of the TTSS, with special emphasis on recent findings.
Keywords: Flagellum; Disease resistance; Yersinia; Protein secretion; Immunity; Pseudomonas syringae;

Bacterial flagella, unlike eukaryotic flagella, are largely external to the cell and therefore many of their subunits have to be exported. Export is ATP-driven. In Salmonella, the bacterium on which this chapter largely focuses, the apparatus responsible for flagellar protein export consists of six membrane components, three soluble components and several substrate-specific chaperones. Other flagellated eubacteria have similar systems. The membrane components of the export apparatus are housed within the flagellar basal body and deliver their substrates into a channel or lumen in the nascent structure from which point they diffuse to the far end and assemble. Both on the basis of sequence similarities of several components and structural similarities, the flagellar protein export systems clearly belong to the type III superfamily, whose other members are responsible for secretion of virulence factors by many species of pathogenic bacteria.
Keywords: Bacterial flagellum; Type III protein export; FliI ATPase; Morphogenesis; Chaperone;

The translocation of DNA across biological membranes is an essential process for many living organisms. In bacteria, type IV secretion systems (T4SS) are used to deliver DNA as well as protein substrates from donor to target cells. The T4SS are structurally complex machines assembled from a dozen or more membrane proteins in response to environmental signals. In Gram-negative bacteria, the conjugation machines are composed of a cell envelope-spanning secretion channel and an extracellular pilus. These dynamic structures (i) direct formation of stable contacts—the mating junction—between donor and recipient cell membranes, (ii) transmit single-stranded DNA as a nucleoprotein particle, as well as protein substrates, across donor and recipient cell membranes, and (iii) mediate disassembly of the mating junction following substrate transfer. This review summarizes recent progress in our understanding of the mechanistic details of DNA trafficking with a focus on the paradigmatic Agrobacterium tumefaciens VirB/D4 T4SS and related conjugation systems.
Keywords: Conjugation; Type IV secretion; DNA transfer; Pathogenesis; Protein translocation; Pilus; Coupling protein;

Protein secretion through autotransporter and two-partner pathways by Françoise Jacob-Dubuisson; Rachel Fernandez; Loic Coutte (235-257).
Two distinct protein secretion pathways, the autotransporter (AT) and the two-partner secretion (TPS) pathways are characterized by their apparent simplicity. Both are devoted to the translocation across the outer membrane of mostly large proteins or protein domains. As implied by their name, AT proteins contain their own transporter domain, covalently attached to the C-terminal extremity of the secreted passenger domain, while TPS systems are composed of two separate proteins, with TpsA being the secreted protein and TpsB its specific transporter. In both pathways, the secreted proteins are exported in a Sec-dependent manner across the inner membrane, after which they cross the outer membrane with the help of their cognate transporters. The AT translocator domains and the TpsB proteins constitute distinct families of protein-translocating, outer membrane porins of Gram-negative bacteria. Both types of transporters insert into the outer membrane as β-barrel proteins possibly forming oligomeric pores in the case of AT and serve as conduits for their cognate secreted proteins or domains across the outer membrane. Translocation appears to be folding-sensitive in both pathways, indicating that AT passenger domains and TpsA proteins cross the periplasm and the outer membrane in non-native conformations and fold progressively at the cell surface.A major difference between AT and TPS pathways arises from the manner by which specificity is established between the secreted protein and its transporter. In AT, the covalent link between the passenger and the translocator domains ensures the translocation of the former without the need for a specific molecular recognition between the two modules. In contrast, the TPS pathway has solved the question of specific recognition between the TpsA proteins and their transporters by the addition to the TpsA proteins of an N-proximal module, the conserved TPS domain, which represents a hallmark of the TPS pathway.
Keywords: Protein secretion; Autotransporter; Two-partner secretion;

Fiber assembly by the chaperone–usher pathway by Frederic G. Sauer; Han Remaut; Scott J. Hultgren; Gabriel Waksman (259-267).
Bacterial pathogens utilize the chaperone–usher pathway to assemble extracellular multi-subunit fibers essential for virulence. The periplasmic chaperone facilitates the initial folding of fiber subunits but then traps them in activated folding transition states. Chaperone dissociation releases the folding energy that drives subunit incorporation into the fiber, which grows through a pore formed by the outer-membrane usher.
Keywords: Structural basis of fiber formation; Pilus assembly; Chaperone–usher pathway; Bacterial pathogenesis; Protein folding;

Protein sorting to the cell wall envelope of Gram-positive bacteria by Hung Ton-That; Luciano A. Marraffini; Olaf Schneewind (269-278).
The covalent anchoring of surface proteins to the cell wall envelope of Gram-positive bacteria occurs by a universal mechanism requiring sortases, extracellular transpeptidases that are positioned in the plasma membrane. Surface protein precursors are first initiated into the secretory pathway of Gram-positive bacteria via N-terminal signal peptides. C-terminal sorting signals of surface proteins, bearing an LPXTG motif or other recognition sequences, provide for sortase-mediated cleavage and acyl enzyme formation, a thioester linkage between the active site cysteine residue of sortase and the C-terminal carboxyl group of cleaved surface proteins. During cell wall anchoring, sortase acyl enzymes are resolved by the nucleophilic attack of peptidoglycan substrates, resulting in amide bond formation between the C-terminal end of surface proteins and peptidoglycan cross-bridges within the bacterial cell wall envelope. The genomes of Gram-positive bacteria encode multiple sortase genes. Recent evidence suggests that sortase enzymes catalyze protein anchoring reactions of multiple different substrate classes with different sorting signal motif sequences, protein linkage to unique cell wall anchor structures as well as protein polymerization leading to the formation of pili on the surface of Gram-positive bacteria.
Keywords: Surface protein; Sortase; Transpeptidation reaction; Pilus biogenesis; Heme-iron transport; Hyphae formation;

Type I signal peptidases of Gram-positive bacteria by Maarten L. van Roosmalen; Nick Geukens; Jan D.H. Jongbloed; Harold Tjalsma; Jean-Yves F. Dubois; Sierd Bron; Jan Maarten van Dijl; Jozef Anné (279-297).
Proteins that are exported from the cytoplasm to the periplasm and outer membrane of Gram-negative bacteria, or the cell wall and growth medium of Gram-positive bacteria, are generally synthesized as precursors with a cleavable signal peptide. During or shortly after pre-protein translocation across the cytoplasmic membrane, the signal peptide is removed by signal peptidases. Importantly, pre-protein processing by signal peptidases is essential for bacterial growth and viability. This review is focused on the signal peptidases of Gram-positive bacteria, Bacillus and Streptomyces species in particular. Evolutionary concepts, current knowledge of the catalytic mechanism, substrate specificity requirements and structural aspects are addressed. As major insights in signal peptidase function and structure have been obtained from studies on the signal peptidase LepB of Escherichia coli, similarities and differences between this enzyme and known Gram-positive signal peptidases are highlighted. Notably, while the incentive for previous research on Gram-positive signal peptidases was largely based on their role in the biotechnologically important process of protein secretion, present-day interest in these essential enzymes is primarily derived from the idea that they may serve as targets for novel anti-microbials.
Keywords: Bacillus; Leader peptidase; Protein secretion; Signal peptidase; Signal peptide; Streptomyces;

Bacillus subtilis is a rod-shaped, Gram-positive soil bacterium that secretes numerous enzymes to degrade a variety of substrates, enabling the bacterium to survive in a continuously changing environment. These enzymes are produced commercially and this production represents about 60% of the industrial-enzyme market. Unfortunately, the secretion of heterologous proteins, originating from Gram-negative bacteria or from eukaryotes, is often severely hampered. Several bottlenecks in the B. subtilis secretion pathway, such as poor targeting to the translocase, degradation of the secretory protein, and incorrect folding, have been revealed. Nevertheless, research into the mechanisms and control of the secretion pathways will lead to improved Bacillus protein secretion systems and broaden the applications as industrial production host. This review focuses on studies that aimed at optimizing B. subtilis as cell factory for commercially interesting heterologous proteins.
Keywords: Cell factory; Chaperone; Heterologous protein; Production; Protease; Secretion;

Post-translocational folding of secretory proteins in Gram-positive bacteria by Matti Sarvas; Colin R. Harwood; Sierd Bron; Jan Maarten van Dijl (311-327).
The transport of proteins from their site of synthesis in the cytoplasm to their functional location is an essential characteristic of all living cells. In Gram-positive bacteria the majority of proteins that are translocated across the cytoplasmic membrane are delivered to the membrane–cell wall interface in an essentially unfolded form. They must then be folded into their native configuration in an environment that is dominated by a high density of immobilised negative charge—in essence an ion exchange resin. It is essential to the viability of the cell that these proteins do not block the translocation machinery in the membrane, form illegitimate interactions with the cell wall or, through intermolecular interactions, form insoluble aggregates. Native Gram-positive proteins therefore have intrinsic folding characteristics that facilitate their rapid folding, and this is assisted by a variety of folding factors, including enzymes, peptides and metal ions. Despite these intrinsic and extrinsic factors, secretory proteins do misfold, particularly if the cell is subjected to certain types of stress. Consequently, Gram-positive bacteria such as Bacillus subtilis encode membrane- and cell wall-associated proteases that act as a quality control machine, clearing misfolded or otherwise aberrant proteins from the translocase and the cell wall.
Keywords: Cell wall; CssRS; PrsA; Secretion stress; Thiol-disulfide oxidoreductase;

Author Index (330-331).

Cumulative Contents (332-333).