Omptin

Last updated
Omptin
Identifiers
SymbolOmptin
Pfam PF01278
Pfam clan CL0193
PROSITE PDOC00657
MEROPS A26
SCOP2 1i78 / SCOPe / SUPFAM
OPM superfamily 27
OPM protein 2x55
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

Omptins (EC 3.4.23.49, protease VII, protease A, gene ompT proteins, ompT protease, protein a, Pla, OmpT) are a family of bacterial proteases. [1] They are aspartate proteases, which cleave peptides with the use of a water molecule. Found in the outer membrane of gram-negative enterobacteria such as Shigella flexneri , Yersinia pestis , Escherichia coli , and Salmonella enterica . Omptins consist of a widely conserved beta barrel spanning the membrane with 5 extracellular loops. These loops are responsible for the various substrate specificities. These proteases rely upon binding of lipopolysaccharide for activity. [2]

Contents

Omptins have been linked to bacterial pathogenesis. [1]

Background

Omptins, a group of membrane-bound proteins, are found in various organisms, including animals and plants, and particularly on the surface of certain bacteria, notably within the enterobacterial family. Known for their specificity in cleaving peptide bonds between adjacent basic amino acids, omptins serve dual functions as both proteases (enzymes that break down proteins) and adhesins (proteins that help cells stick together). [3] Omptin genes are also associated with plasmids or prophages, indicating a potential role of horizontal gene transfer in the dissemination of these genes. This means that omptin genes may be transferred between different bacterial cells or even between species through mechanisms like plasmid transfer or the integration of prophages into bacterial genomes. Omptin protease activity is triggered under conditions of low magnesium growth. This characteristic is named after the prototypical OmpT protein, which features a 10-stranded B-barrel structure. [4] The ability of genes to move horizontally between different organisms can contribute to the spread of advantageous traits, such as those involved in host-pathogen interactions or other cellular processes. In the case of omptins, understanding their genetic context and the mechanisms of horizontal gene transfer can provide insights into their evolution and the diversity of organisms that harbor these genes. [5]

Structure

Omptin proteins possess a structural composition featuring a B-barrel fold, an active site, catalytic residues, a lipopolysaccharide (LPS) binding site, and a multiplicity of elements. Despite their shared structural features, each individual omptin serves distinct functions. These proteins play a role in the lifestyle of bacteria and are associated with the mechanisms by which bacterial species cause disease. The structure of omptins is like a cylinder with four catalytic residues located on its outer surface. [3]  Initially classified as serine proteases, they were later recognized as aspartate proteases based on the crystal structure of OmpT. Omptins stand out because they exhibit characteristics of both serine and aspartate proteases. Members of this protein family share a significant sequence identity at the amino acid level, ranging from 40% to 80%. [5]  omptins like OmpT and Pla have very similar folding patterns.

Function

Omptins become active when they interact with a lipopolysaccharide molecule. [6]  They primarily cleave protein or peptide substrates between specific basic amino acid residues, serving as a defense against antimicrobial peptides that could disrupt the lipopolysaccharide network. These proteases target a variety of host substrates, and when lipopolysaccharide binds, it subtly alters the shape of the active site, activating the omptins. The expression of omptins is under the regulation of a factor called PhoP. [4]

Certain omptins, such as those cutting ArlC and CroP, exhibit high resistance to serum. Within the Enterobacteriaceae family, bacteria produce proteases that can target components of the host's innate immune system. [2] Omptin proteases function as a defense mechanism against antimicrobial peptides and are governed by PhoPQ. PhoP directly binds to specific gene sites, determining omptin activity. For omptins to be active in breaking down proteins, they need to bind to lipopolysaccharide as a cofactor.

Beyond their role in resisting antimicrobial peptides, omptins are involved in processing and secreting parts of bacterial auto transporters and breaking down host proteins. Pla, a specific omptin, can activate plasminogen through limited proteolysis. This activation is thought to assist the organism in escaping from a meshwork of fibrin, facilitating its spread through tissues outside blood vessels. Pla also possesses the capability to activate plasminogen through limited proteolysis. This function is believed to aid the organism in escaping from the fibrin meshwork, thereby facilitating its dissemination through extravascular tissues. [7]

Bacterial functions and locations

Outer Membrane of Gram Negative Bacteria Gram Negative Bacteria for Outer Membrane.jpg
Outer Membrane of Gram Negative Bacteria

Omptin outer membrane proteins are found in select Gram-negative bacteria, including members of the Enterobacteriaceae family like E. coli (OmpT), Yersinia pestis (Pla), Salmonella enterica (PgtE), Shigella flexneri (IcsP), and Citrobacter rodentium (CroP). [5] The Omptin family encompasses outer membrane proteases such as OmpT in E. coli and Ola in Salmonella. In E. coli, Omptin proteins like OmpT, OmpP, and ArlC can be identified, and all possess the ability to cleave antimicrobial peptides. [8] These Omptin proteases are commonly grouped into OmpT or Pla families, with Pla Omptins demonstrating higher efficacy in cleaving or activating plasminogen compared to OmpT. Omptins, such as Pla and PgtE, disrupt innate immunity by influencing various systems, including plasminogen/plasmin, complement, coagulation, fibrinolysis, and matrix metalloproteinase systems. They achieve this by inactivating antimicrobial peptides, resulting in an enhanced spread and multiplication of Pla and PgtE. On the other hand, OmpT functions as a housekeeping protease, playing a role in degrading cationic antimicrobial peptides and augmenting E. coli capabilities. [9] OmpT proteases are implicated in the cleavage of antimicrobial peptides, and an escalation in Omptin activity is closely linked to clinical UPEC strains isolated from individuals with urinary tract infections. The variability in activity is associated with diverse expressions of OmpT and ArlC in E. coli, with the presence of ArlC potentially accounting for the observed diversity in activity. This heightened Omptin activity is specifically identified with UPEC strains responsible for urinary tract infections [8]

Related Research Articles

<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.

<span class="mw-page-title-main">Lipopolysaccharide</span> Class of molecules found in the outer membrane of Gram-negative bacteria

Lipopolysaccharide, now more commonly known as Endotoxin, is a collective term for components of the outermost membrane of cell envelope of Gram-negative bacteria, such as E. coli and Salmonella. with a common structural architecture. Lipopolysaccharides (LPS) are large molecules consisting of 3 parts: an outer core polysaccharide termed the O-antigen, an inner core oligosaccharide and Lipid A, all covalently linked. In current terminology, the term endotoxin is often used synonymously with LPS, although there are a few endotoxins that are not related to LPS, such as the so-called delta endotoxin proteins produced by Bacillus thuringiensis.

<span class="mw-page-title-main">Polymyxin</span> Group of antibiotics

Polymyxins are antibiotics. Polymyxins B and E are used in the treatment of Gram-negative bacterial infections. They work mostly by breaking up the bacterial cell membrane. They are part of a broader class of molecules called nonribosomal peptides.

Braun's lipoprotein, found in some gram-negative cell walls, is one of the most abundant membrane proteins; its molecular weight is about 7.2 kDa. It is bound at its C-terminal end by a covalent bond to the peptidoglycan layer and is embedded in the outer membrane by its hydrophobic head. BLP tightly links the two layers and provides structural integrity to the outer membrane.

<span class="mw-page-title-main">Antimicrobial peptides</span> Class of peptides that have antimicrobial activity

Antimicrobial peptides (AMPs), also called host defence peptides (HDPs) are part of the innate immune response found among all classes of life. Fundamental differences exist between prokaryotic and eukaryotic cells that may represent targets for antimicrobial peptides. These peptides are potent, broad spectrum antimicrobials which demonstrate potential as novel therapeutic agents. Antimicrobial peptides have been demonstrated to kill Gram negative and Gram positive bacteria, enveloped viruses, fungi and even transformed or cancerous cells. Unlike the majority of conventional antibiotics it appears that antimicrobial peptides frequently destabilize biological membranes, can form transmembrane channels, and may also have the ability to enhance immunity by functioning as immunomodulators.

<span class="mw-page-title-main">Bacterial outer membrane</span> Plasma membrane found in gram-negative bacteria

The bacterial outer membrane is found in gram-negative bacteria. Gram-negative bacteria form two lipid bilayers in their cell envelopes - an inner membrane (IM) that encapsulates the cytoplasm, and an outer membrane (OM) that encapsulates the periplasm.

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

<span class="mw-page-title-main">MicF RNA</span> Gene found in bacteria

The micF RNA is a non-coding RNA stress response gene found in Escherichia coli and related bacteria that post-transcriptionally controls expression of the outer membrane porin gene ompF. The micF gene encodes a non-translated 93 nucleotide antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message. In addition, other factors, such as the RNA chaperone protein StpA also play a role in this regulatory system. The expression of micF is controlled by both environmental and internal stress factors. Four transcriptional regulators are known to bind the micF promoter region and activate micF expression.

<span class="mw-page-title-main">RybB RNA</span>

RybB is a small non-coding RNA was identified in a large scale screen of Escherichia coli. The function of this short RNA has been studied using a transcriptomic approach and kinetic analyses of target mRNA decay in vivo. RybB was identified as a factor that selectively accelerates the decay of multiple major omp mRNAs upon induction of the envelope stress response. This RNA has been shown to bind to the Hfq protein.

<span class="mw-page-title-main">MicA RNA</span>

The MicA RNA is a small non-coding RNA that was discovered in E. coli during a large scale screen. Expression of SraD is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well.

<span class="mw-page-title-main">OmpA-like transmembrane domain</span>

OmpA-like transmembrane domain is an evolutionarily conserved domain of bacterial outer membrane proteins. This domain consists of an eight-stranded beta barrel. OmpA is the predominant cell surface antigen in enterobacteria found in about 100,000 copies per cell. The expression of OmpA is tightly regulated by a variety of mechanisms. One mechanism by which OmpA expression is regulated in Vibrio species is by an antisense non-coding RNA called VrrA.

<span class="mw-page-title-main">Virulence-related outer membrane protein family</span>

Virulence-related outer membrane proteins, or outer surface proteins (Osp) in some contexts, are expressed in the outer membrane of gram-negative bacteria and are essential to bacterial survival within macrophages and for eukaryotic cell invasion.

<span class="mw-page-title-main">Vibrio regulatory RNA of OmpA</span>

VrrA is a non-coding RNA that is conserved across all Vibrio species of bacteria and acts as a repressor for the synthesis of the outer membrane protein OmpA. This non-coding RNA was initially identified from Tn5 transposon mutant libraries of Vibrio cholerae and its location within the bacterial genome was mapped to the intergenic region between genes VC1741 and VC1743 by RACE analysis.

<span class="mw-page-title-main">Yersiniabactin</span> Chemical compound

Yersiniabactin (Ybt) is a siderophore found in the pathogenic bacteria Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia enterocolitica, as well as several strains of enterobacteria including enteropathogenic Escherichia coli and Salmonella enterica. Siderophores, compounds of low molecular mass with high affinities for ferric iron, are important virulence factors in pathogenic bacteria. Iron—an essential element for life used for such cellular processes as respiration and DNA replication—is extensively chelated by host proteins like lactoferrin and ferritin; thus, the pathogen produces molecules with an even higher affinity for Fe3+ than these proteins in order to acquire sufficient iron for growth. As a part of such an iron-uptake system, yersiniabactin plays an important role in pathogenicity of Y. pestis, Y. pseudotuberculosis, and Y. entercolitica.

In molecular biology, the lipopolysaccharide kinase (Kdo/WaaP) family is a family of lipopolysaccharide kinases that includes lipopolysaccharide core heptose(I) kinase rfaP. Lipopolysaccharide core heptose(I) kinase rfaP is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that it is necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of Salmonella enterica. The family also includes 3-deoxy-D-manno-octulosonic acid kinase from Haemophilus influenzae, which phosphorylates Kdo-lipid IV(A), a lipopolysaccharide precursor, and is involved in virulence.

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

OmpT is an aspartyl protease found on the outer membrane of Escherichia coli. OmpT is a subtype of the family of omptin proteases, which are found on some gram-negative species of bacteria.

Plasminogen activator Pla is an enzyme. This enzyme catalyses the following chemical reaction

Bacterial effectors are proteins secreted by pathogenic bacteria into the cells of their host, usually using a type 3 secretion system (TTSS/T3SS), a type 4 secretion system (TFSS/T4SS) or a Type VI secretion system (T6SS). Some bacteria inject only a few effectors into their host’s cells while others may inject dozens or even hundreds. Effector proteins may have many different activities, but usually help the pathogen to invade host tissue, suppress its immune system, or otherwise help the pathogen to survive. Effector proteins are usually critical for virulence. For instance, in the causative agent of plague, the loss of the T3SS is sufficient to render the bacteria completely avirulent, even when they are directly introduced into the bloodstream. Gram negative microbes are also suspected to deploy bacterial outer membrane vesicles to translocate effector proteins and virulence factors via a membrane vesicle trafficking secretory pathway, in order to modify their environment or attack/invade target cells, for example, at the host-pathogen interface.

<span class="mw-page-title-main">Bacterial secretion system</span> Protein complexes present on the cell membranes of bacteria for secretion of substances

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 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.

<span class="mw-page-title-main">Virginia L. Miller</span> American microbiologist

Virginia L. Miller is a microbiologist known for her work on studying the factors leading to disease caused by bacteria. Miller is an elected fellow of the American Academy of Microbiology (2003) and a former Pew Charitable Trust Biomedical Scholar (1989).

References

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  2. 1 2 Kukkonen M, Korhonen TK (July 2004). "The omptin family of enterobacterial surface proteases/adhesins: from housekeeping in Escherichia coli to systemic spread of Yersinia pestis". International Journal of Medical Microbiology. 294 (1): 7–14. doi:10.1016/j.ijmm.2004.01.003. PMID   15293449.
  3. 1 2 Dufrisne MB, Petrou VI, Clarke OB, Mancia F (November 2017). "Structural basis for catalysis at the membrane-water interface". Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. Bacterial Lipids. 1862 (11): 1368–1385. doi:10.1016/j.bbalip.2016.11.011. PMC   5449265 . PMID   27913292.
  4. 1 2 Cho YH, Fadle Aziz MR, Malpass A, Sutradhar T, Bashal J, Cojocari V, McPhee JB (January 2023). Bäumler AJ (ed.). "Omptin Proteases of Enterobacterales Show Conserved Regulation by the PhoPQ Two-Component System but Exhibit Divergent Protection from Antimicrobial Host Peptides and Complement". Infection and Immunity. 91 (1): e0051822. doi:10.1128/iai.00518-22. PMC   9872669 . PMID   36533918.
  5. 1 2 3 Brannon JR, Burk DL, Leclerc JM, Thomassin JL, Portt A, Berghuis AM, et al. (June 2015). McCormick BA (ed.). "Inhibition of outer membrane proteases of the omptin family by aprotinin". Infection and Immunity. 83 (6): 2300–2311. doi:10.1128/IAI.00136-15. PMC   4432765 . PMID   25824836.
  6. Kum SL, Ho JC, Parikh AN, Liedberg B (February 2022). "Amphiphilic Membrane Environments Regulate Enzymatic Behaviors of Salmonella Outer Membrane Protease". ACS Bio & Med Chem Au. 2 (1): 73–83. doi:10.1021/acsbiomedchemau.1c00027. PMC   10114716 . PMID   37102179.
  7. "Bacterial Omptins Proteolytically Inactivate Tissue Factor Pathway Inhibitor (TFPI)". ashpublications.org. Retrieved 2023-11-27.
  8. 1 2 Desloges I, Taylor JA, Leclerc JM, Brannon JR, Portt A, Spencer JD, et al. (November 2019). "Identification and characterization of OmpT-like proteases in uropathogenic Escherichia coli clinical isolates". MicrobiologyOpen. 8 (11): e915. doi:10.1002/mbo3.915. PMC   6854850 . PMID   31496120.
  9. Haiko J, Suomalainen M, Ojala T, Lähteenmäki K, Korhonen TK (April 2009). "Invited review: Breaking barriers--attack on innate immune defences by omptin surface proteases of enterobacterial pathogens". Innate Immunity. 15 (2): 67–80. doi: 10.1177/1753425909102559 . PMID   19318417. S2CID   8540417.

Further reading