Bacterial secretion system

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An illustration depicting diversity in the architecture of protein secretion systems found in diderm bacteria All secretion systems.jpg
An illustration depicting diversity in the architecture of protein secretion systems found in diderm bacteria

Bacterial secretion systems are protein complexes present on the cell membranes of bacteria for secretion of substances. Specifically, they are the cellular devices used by pathogenic bacteria to secrete their virulence factors (mainly of proteins) to invade the host cells. They can be classified into different types based on their specific structure, composition and activity. Generally, proteins can be secreted through two different processes. One process is a one-step mechanism in which proteins from the cytoplasm of bacteria are transported and delivered directly through the cell membrane into the host cell. Another involves a two-step activity in which the proteins are first transported out of the inner cell membrane, then deposited in the periplasm, and finally through the outer cell membrane into the host cell. [2]

Contents

These major differences can be distinguished between Gram-negative diderm bacteria and Gram-positive monoderm bacteria. But the classification is by no means clear and complete. There are at least eight types specific to Gram-negative bacteria, four to Gram-positive bacteria, while two are common to both. [3] In addition, there is appreciable difference between diderm bacteria with lipopolysaccharide on the outer membrane (diderm-LPS) and those with mycolic acid (diderm-mycolate). [4]

Export pathways

The export pathway is responsible for crossing the inner cell membrane in diderms, and the only cell membrane in monoderms. [4]

Sec system

The general secretion (Sec) involves secretion of unfolded proteins that first remain inside the cells. In Gram-negative bacteria, the secreted protein is sent to either the inner membrane or the periplasm. But in Gram-positive bacteria, the protein can stay in the cell or is mostly transported out of the bacteria using other secretion systems. Among Gram-negative bacteria, Escherichia coli , Vibrio cholerae , Klebsiella pneumoniae , and Yersinia enterocolitica use the Sec system. Staphylococcus aureus and Listeria monocytogenes are Gram-positive bacteria that use the Sec system. [5]

The Sec system utilises two different pathways for secretion: the SecA and signal recognition particle (SRP) pathways. SecA is an ATPase motor protein and has many related proteins including SecD, SecE, SecF, SegG, SecM, and SecY. SRP is a ribonucleoprotein (protein-RNA complex) that recognizes and targets specific proteins to the endoplasmic reticulum in eukaryotes and to the cell membrane in prokaryotes. The two pathways require different molecular chaperones and ultimately use a protein-transporting channel SecYEG for transporting the proteins across the inner cell membrane. [6] In the SecA pathway, SecB acts as a chaperone, helping protein transport to the periplasm after complete synthesis of the peptide chains. Whereas in the SRP pathway, YidC is the chaperone, and transport proteins to the cell membrane while they are still undergoing peptide synthesis. [7] In Escherichia coli, inner membrane proteins are mainly targeted by the SRP pathway and outer membrane or periplasmic proteins are targeted by the SecA pathway. [8] However, a recent selective ribosome profiling study suggest that inner membrane proteins with large periplasmic loops are targeted by the SecA pathway. [9]

SecA or post-translational pathway

Proteins are synthesised in ribosomes by a process of serially adding amino acids, called translation. In SecA pathway, a chaperone trigger factor (TF) first bind to the exposed N-terminal signal sequence of the peptide chain. As elongation of peptide chain continues, TF is replaced by SecB. SecB specifically maintains the peptide in an unfolded state, and aids in the binding of SecA. The complex can then bind to SecYEG, by which SecA is activated by binding with ATP. Driven by ATP energy, SecA pushes the protein through the secYEG channel. SecD/F complex also helps in the pulling of the protein from the other side of the cell membrane. [10]

In recent years, the SecA pathway has also been suggested to have a co-translational mechanism, meaning that the polypeptide would be targeted directly by SecA during its synthesis. [11]

SRP pathway

In this pathway, SRP competes with TF and binds to the N-terminal signal sequence. Proteins from inner membrane stops the process of chain elongation. The SRP then binds to a membrane receptor, FtsY. The peptide chain-SRP-FtsY complex is then transported to SecY, where peptide elongation resumes. [7]

Tat system

The twin-arginine translocation pathway (Tat pathway) is similar to Sec in the process of protein secretion, however, it sends proteins only in their folded (tertiary) state. It is used by all types of bacteria, as well as archaea, and chloroplasts and mitochondria of plants. [12] In bacteria, the Tat system exports proteins from the cytoplasm across the inner cell membrane; whereas in chloroplasts, it is present in the thylakoid membrane where it aids the import of proteins from the stroma. [13] Tat proteins are highly variable in different bacteria and are classified into three major types, namely TatA, TatB, and TatC. For example, while there are only two functional Tat proteins in Bacillus subtilis, [14] there can be over a hundred in Streptomyces coelicolor. [15] Signal peptides that can recognise the Tat proteins are characterised by a consensus motif Ser/Thr-Arg-Arg-X-Phe-Leu-Lys (where X can be any polar amino acid). It is the two successive arginines from which the name twin arginine translocation came from. Replacement of any of the arginine leads to slow down or failure of secretion. [16]

Wss/Esx pathway

The Wss/Esx (ESAT-6 system) pathway is sometimes called a type VII secretion system (T7SS) despite being an export pathway. [4] It is present in Gram-positive bacteria (as WSS) and Mycobacteria (as Esx in all diderm-mycolates) such as M. tuberculosis, M. bovis, Streptomyces coelicolor and S. aureus. It is also called T7b system in Bacillus subtilis and S. aureus. It is composed of two basic components: a membrane-bound hexameric ATPase that is member of the FtsK/SpoIIIE protein family, [17] and any one of the EsxA/EsxB-related protein such as EsaA, EsaD, EsxB, EsxD, as well as Ess system (EssA, EssB, and EsxC found in S. aureus). [18] EsxA and EsxB belong to a superfamily of WXG100 proteins that form dimeric helical hairpins.

In S. aureus, T7SS secretes a large toxin called EsaD, which is a member of nuclease enzymes. EsaD is made harmless (detoxified) during its biosynthesis with the help of its counterpart antitoxin EsaG. The EsaD-EsaG complex then binds with EsaE. The EsaE portion binds to EssC, which is an enzyme ATPase of the T7SS complex. During secretion, EsaG is left in the cytoplasm, and only EsaD and EsaE are secreted together. But in some strains of S. aureus, EsaD is not produced, but two copies of EsaG-like proteins are formed instead. This might explain the occurrence of T7SS in non-pathogenic species such as B. subtilis and S. coelicolor. [19]

Secretion systems

The secretion systems are responsible for crossing the outer cell membrane or both membranes in diderms. The current nomenclature applies to diderm-LPS only, as nothing is known about what diderm-mycolate bacteria use to cross their outer membrane. [4]

Type I

T1SS schematic T1SS.svg
T1SS schematic

Type I secretion system (T1SS or TOSS) is found in Gram-negative bacteria. It depends on chaperone activity using Hly and Tol proteins. The system activates as a signal sequence HlyA binds HlyB on the cell membrane. This signal sequence is an ABC transporter. The HlyAB complex activates HlyD which uncoils and moves to the outer cell membrane. The terminal signal is recognised by TolC in the inner membrane. The HlyA is secreted out of the outer membrane through a tunnel-like protein channel.

T1SS transports various molecules including ions, carbohydrates, drugs, proteins. The secreted molecules vary in size from the small Escherichia coli peptide colicin V, which is 10 kDa, to the Pseudomonas fluorescens cell adhesion protein LapA, which is 520 kDa. [20] Among the most well known molecules are RTX toxins and lipase enzymes.

Type II

T2SS schematic T2SS.svg
T2SS schematic

Type II (T2SS) secretion system depends on the Sec or Tat system for initial secretion inside the bacterial cell. From the periplasm, proteins are secreted out of the outer membrane secretins. Secretins are multimeric (12–14 subunits) complex of pore-forming proteins. Secretin is supported by 10–15 other inner and outer membrane proteins to constitute the complete secretion apparatus. [21]

Type III

T3SS schematic T3SS.svg
T3SS schematic

Type III secretion system (T3SS or TTSS) is structurally similar and related to the basal body of bacterial flagella. Seen in some of the most virulent Gram-negative bacteria such as Salmonella , Shigella , Yersinia , Vibrio , it is used to inject toxic proteins into eukaryotic cells. The structure of T3SS is often described as an injectisome or needle/syringe-like apparatus. Discovered in Yersinia pestis , it was found that T3SS can inject toxins directly from the bacterial cytoplasm into the cytoplasm of its host's cells. [22]

Type IV

T4SS schematic T4SS.svg
T4SS schematic

Type IV secretion system (T4SS or TFSS) is related to bacterial conjugation system, by which different bacteria can exchange their DNAs. The participating bacteria can be of the same or different Gram-negative bacterial species. It can transport single proteins, as well as protein-protein and DNA-protein complexes. Secretion is transferred directly from the recipient cell through the cell membranes. Agrobacterium tumefaciens , from which it was originally discovered, uses this system to send the T-DNA portion of the Ti plasmid into plant cells, in which a crown gall (tumor) is produced as a result. Helicobacter pylori uses it for delivering CagA into gastric epithelial cells, to induce gastric cancer. [23] Bordetella pertussis , the causative bacterium of whooping cough, secretes its pertussis toxin partly through T4SS. Legionella pneumophila that causes legionellosis (Legionnaires' disease) has a T4SS called icm/dot (intracellular multiplication/defect in organelle trafficking genes) that transport many bacterial proteins into its eukaryotic host. [24] More recently, it has been shown that the phytopathogen Xanthomonas citri utilizes its T4SS to secrete effectors that are lethal to other bacterial species, thus placing this system as a major fitness determinant of interspecies bacterial competition. [25] [26] The prototypic Type IVA secretion system is the VirB complex of Agrobacterium tumefaciens . [27]

Type V

T5SS schematic T5SS.svg
T5SS schematic

Type V secretion systems (T5SS) are different from other secretion systems in that they secrete themselves and only involves the outer cell membrane. For secreted protein to pass through the inner cell membrane, T5SS depends on Sec system. They have a β-barrel domain, which inserts into the outer cell membrane and forms a channel that can transport secreted protein along with it. For this activity, they are also called the autotransporter systems. [28] When the secreted proteins are exposed outside, the autotransporters are cut off (cleaved), releasing the protein from the β-barrel domain. An example of autotransporter is the Trimeric Autotransporter Adhesins. [29]

Type VI

Type VI secretion systems (T6SS) were discovered by the team of John Mekalanos at the Harvard Medical School in 2006 from Vibrio cholerae and Pseudomonas aeruginosa . [30] [31] They were recognised when mutations in the Vibrio CholeraeHcp and VrgG genes caused diminished virulence and pathogenicity. [32] [33] In addition to their classic role as the pathogenicity factor, T6SS are also involved in defense against simple eukaryotic predators and in inter-bacteria interactions. [34] [35] The gene for T6SS form a gene cluster that consists of more than 15 genes. Hcp and VgrG genes are the most universal genes. Structural similarity of T6SS with the tail spike of the T4 phage suggest that the process of infection is similar to that of the phage. [36]

Type VII

ESX-5: type VII secretion system, Mycobacterium xenopi 7b9s.jpg
ESX-5: type VII secretion system, Mycobacterium xenopi

The T7SS of diderm-LPS bacteria is the chaperone-usher pathway. [4]

In diderm-mycolate bacteria this secretion system is the ESAT-6. [4]

Type VIII

The T8SS of diderm-LPS bacteria is the extracellular nucleation-precipitation pathway. [4] [37]

Type IX secretion system schematic diagram T9ss.jpg
Type IX secretion system schematic diagram

Type IX

Type IX secretion systems (T9SS) are found regularly in the Fibrobacteres-Chlorobi-Bacteroidetes lineage of bacteria, where member species include an outer membrane. The system is involved variably in one type of gliding motility, in the proper targeting of certain virulence factors to the cell surface, and the degradation of complex of biopolymers. [39] T9SS has also been known as Por (porphyrin accumulation on the cell surface) secretion, [4] after the oral pathogen Porphyromonas gingivalis. At least sixteen structural components of the system have been described, including PorU, a protein-sorting transpeptidase that removes the C-terminal sorting signal from cargo proteins and mediates their attachment instead to lipopolysaccharide.

Related Research Articles

<span class="mw-page-title-main">Gram-positive bacteria</span> Bacteria that give a positive result in the Gram stain test

In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.

<span class="mw-page-title-main">Gram-negative bacteria</span> Group of bacteria that do not retain the Gram stain used in bacterial differentiation

Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is their cell envelope, which consists of a thin peptidoglycan cell wall sandwiched between an inner (cytoplasmic) membrane and an outer membrane. These bacteria are found in all environments that support life on Earth.

Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations within or outside the cell. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, the plasma membrane, or to the exterior of the cell via secretion. Information contained in the protein itself directs this delivery process. Correct sorting is crucial for the cell; errors or dysfunction in sorting have been linked to multiple diseases.

Peptidoglycan or murein is a unique large macromolecule, a polysaccharide, consisting of sugars and amino acids that forms a mesh-like layer (sacculus) that surrounds the bacterial cytoplasmic membrane. The sugar component consists of alternating residues of β-(1,4) linked N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). Attached to the N-acetylmuramic acid is an oligopeptide chain made of three to five amino acids. The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a structural role in the bacterial cell wall, giving structural strength, as well as counteracting the osmotic pressure of the cytoplasm. This repetitive linking results in a dense peptidoglycan layer which is critical for maintaining cell form and withstanding high osmotic pressures, and it is regularly replaced by peptidoglycan production. Peptidoglycan hydrolysis and synthesis are two processes that must occur in order for cells to grow and multiply, a technique carried out in three stages: clipping of current material, insertion of new material, and re-crosslinking of existing material to new material.

A signal peptide is a short peptide present at the N-terminus of most newly synthesized proteins that are destined toward the secretory pathway. These proteins include those that reside either inside certain organelles, secreted from the cell, or inserted into most cellular membranes. Although most type I membrane-bound proteins have signal peptides, most type II and multi-spanning membrane-bound proteins are targeted to the secretory pathway by their first transmembrane domain, which biochemically resembles a signal sequence except that it is not cleaved. They are a kind of target peptide.

The translocon is a complex of proteins associated with the translocation of polypeptides across membranes. In eukaryotes the term translocon most commonly refers to the complex that transports nascent polypeptides with a targeting signal sequence into the interior space of the endoplasmic reticulum (ER) from the cytosol. This translocation process requires the protein to cross a hydrophobic lipid bilayer. The same complex is also used to integrate nascent proteins into the membrane itself. In prokaryotes, a similar protein complex transports polypeptides across the (inner) plasma membrane or integrates membrane proteins. In either case, the protein complex are formed from Sec proteins, with the heterotrimeric Sec61 being the channel. In prokaryotes, the homologous channel complex is known as SecYEG.

<span class="mw-page-title-main">Secretion</span> Controlled release of substances by cells or tissues

Secretion is the movement of material from one point to another, such as a secreted chemical substance from a cell or gland. In contrast, excretion is the removal of certain substances or waste products from a cell or organism. The classical mechanism of cell secretion is via secretory portals at the plasma membrane called porosomes. Porosomes are permanent cup-shaped lipoprotein structures embedded in the cell membrane, where secretory vesicles transiently dock and fuse to release intra-vesicular contents from the cell.

The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the periplasmic space in Gram-negative bacteria. Using cryo-electron microscopy it has been found that a much smaller periplasmic space is also present in Gram-positive bacteria, between cell wall and the plasma membrane. The periplasm may constitute up to 40% of the total cell volume of gram-negative bacteria, but is a much smaller percentage in gram-positive bacteria.

Virulence factors are cellular structures, molecules and regulatory systems that enable microbial pathogens to achieve the following:

The twin-arginine translocation pathway is a protein export, or secretion pathway found in plants, bacteria, and archaea. In contrast to the Sec pathway which transports proteins in an unfolded manner, the Tat pathway serves to actively translocate folded proteins across a lipid membrane bilayer. In plants, the Tat translocase is located in the thylakoid membrane of the chloroplast, where it acts to export proteins into the thylakoid lumen. In bacteria, the Tat translocase is found in the cytoplasmic membrane and serves to export proteins to the cell envelope, or to the extracellular space. The existence of a Tat translocase in plant mitochondria is also proposed.

<span class="mw-page-title-main">Type III secretion system</span> Bacterial virulence factor

The type III secretion system is one of the bacterial secretion systems used by bacteria to secrete their effector proteins into the host's cells to promote virulence and colonisation. While the type III secretion system has been widely regarded as equivalent to the injectisome, many argue that the injectisome is only part of the type III secretion system, which also include structures like the flagellar export apparatus. The T3SS is a needle-like protein complex found in several species of pathogenic gram-negative bacteria.

<span class="mw-page-title-main">Autotransporter family</span>

In molecular biology, an autotransporter domain is a structural domain found in some bacterial outer membrane proteins. The domain is always located at the C-terminal end of the protein and forms a beta-barrel structure. The barrel is oriented in the membrane such that the N-terminal portion of the protein, termed the passenger domain, is presented on the cell surface. These proteins are typically virulence factors, associated with infection or virulence in pathogenic bacteria.

<span class="mw-page-title-main">SecY protein</span>

The SecY protein is the main transmembrane subunit of the bacterial Sec export pathway and of a protein-secreting ATPase complex, also known as a SecYEG translocon. Homologs of the SecYEG complex are found in eukaryotes and in archaea, where the subunit is known as Sec61α.

SecD and SecF are prokaryotic protein export membrane proteins. They are a part of the larger multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC. SecD and SecF are required to maintain a proton motive force.

<span class="mw-page-title-main">Trimeric autotransporter adhesin</span> Proteins found on the outer membrane of Gram-negative bacteria

In molecular biology, trimeric autotransporter adhesins (TAAs), are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion. TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. In essence, they are virulence factors, factors that make the bacteria harmful and infective to the host organism.

The type VI secretion system (T6SS) is molecular machine used by a wide range of Gram-negative bacterial species to transport effectors from the interior of a bacterial cell across the cellular envelope into an adjacent target cell. While often reported that the T6SS was discovered in 2006 by researchers studying the causative agent of cholera, Vibrio cholerae, the first study demonstrating that T6SS genes encode a protein export apparatus was actually published in 2004, in a study of protein secretion by the fish pathogen Edwardsiella tarda.

The type 2 secretion system is a type of protein secretion machinery found in various species of Gram-negative bacteria, including many human pathogens such as Pseudomonas aeruginosa and Vibrio cholerae. The type II secretion system is one of six protein secretory systems commonly found in Gram-negative bacteria, along with the type I, type III, and type IV secretion systems, as well as the chaperone/usher pathway, the autotransporter pathway/type V secretion system, and the type VI secretion system. Like these other systems, the type II secretion system enables the transport of cytoplasmic proteins across the lipid bilayers that make up the cell membranes of Gram-negative bacteria. Secretion of proteins and effector molecules out of the cell plays a critical role in signaling other cells and in the invasion and parasitism of host cells.

<span class="mw-page-title-main">Tracy Palmer</span> Professor of molecular microbiology

Tracy Palmer is a professor of microbiology in the Biosciences Institute at Newcastle University in Tyne & Wear, England. She is known for her work on the twin-arginine translocation (Tat) pathway.

Parvulin-like peptidyl-prolyl isomerase (PrsA), also referred to as putative proteinase maturation protein A (PpmA), functions as a molecular chaperone in Gram-positive bacteria, such as B. subtilis, S. aureus, L. monocytogenes and S. pyogenes. PrsA proteins contain a highly conserved parvulin domain that contains peptidyl-prolyl cis-trans isomerase (PPIase) activity capable of catalyzing the bond N-terminal to proline from cis to trans, or vice versa, which is a rate limiting step in protein folding. PrsA homologs also contain a foldase domain suspected to aid in the folding of proteins but, unlike the parvulin domain, is not highly conserved. PrsA proteins are capable of forming multimers in vivo and in vitro and, when dimerized, form a claw-like structure linked by the NC domains. Most Gram-positive bacteria contain only one PrsA-like protein, but some organisms such as L. monocytogenes, B. anthracis and S. pyogenes contain two PrsAs.

Type VII secretion systems are bacterial secretion systems first observed in the phyla Actinomycetota and Bacillota. Bacteria use such systems to transport, or secrete, proteins into the environment. The bacterial genus Mycobacterium uses type VII secretion systems (T7SS) to secrete proteins across their cell envelope. The first T7SS system discovered was the ESX-1 System.

References

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