secretion#In gram-negative bacteria

File:Porosome for wiki-2.jpg

Eukaryotic cells, including human cells, have a highly evolved process of secretion. Proteins targeted for the outside are synthesized by ribosomes docked to the rough endoplasmic reticulum (ER). As they are synthesized, these proteins translocate into the ER lumen, where they are glycosylated and where molecular chaperones aid protein folding. Misfolded proteins are usually identified here and retrotranslocated by ER-associated degradation to the cytosol, where they are degraded by a proteasome. The vesicles containing the properly folded proteins then enter the Golgi apparatus.

In the Golgi apparatus, the glycosylation of the proteins is modified and further post-translational modifications, including cleavage and functionalization, may occur. The proteins are then moved into secretory vesicles which travel along the cytoskeleton to the edge of the cell. More modification can occur in the secretory vesicles (for example insulin is cleaved from proinsulin in the secretory vesicles).

Eventually, there is vesicle fusion with the cell membrane at porosomes, by a process called exocytosis, dumping its contents out of the cell's environment.{{cite journal | vauthors = Anderson LL | title = Discovery of the 'porosome'; the universal secretory machinery in cells | journal = Journal of Cellular and Molecular Medicine | volume = 10 | issue = 1 | pages = 126–31 | year = 2006 | pmid = 16563225 | pmc = 3933105 | doi = 10.1111/j.1582-4934.2006.tb00294.x }}

Strict biochemical control is maintained over this sequence by usage of a pH gradient: the pH of the cytosol is 7.4, the ER's pH is 7.0, and the cis-golgi has a pH of 6.5. Secretory vesicles have pHs ranging between 5.0 and 6.0; some secretory vesicles evolve into lysosomes, which have a pH of 4.8.

There are many proteins like FGF1 (aFGF), FGF2 (bFGF), interleukin-1 (IL1) etc. which do not have a signal sequence. They do not use the classical ER-Golgi pathway. These are secreted through various nonclassical pathways.

At least four nonclassical (unconventional) protein secretion pathways have been described.{{cite journal | vauthors = Nickel W, Seedorf M | title = Unconventional mechanisms of protein transport to the cell surface of eukaryotic cells | journal = Annual Review of Cell and Developmental Biology | volume = 24 | pages = 287–308 | year = 2008 | pmid = 18590485 | doi = 10.1146/annurev.cellbio.24.110707.175320 }} They include:

• direct protein translocation across the plasma membrane likely through membrane transport proteins
• blebbing
• lysosomal secretion
• release via exosomes derived from multivesicular bodies

In addition, proteins can be released from cells by mechanical or physiological wounding{{cite journal| vauthors = McNeil PL, Steinhardt RA | title = Plasma membrane disruption: repair, prevention, adaptation | journal = Annual Review of Cell and Developmental Biology | volume = 19 | pages = 697–731 | year = 2003 | pmid = 14570587 | doi = 10.1146/annurev.cellbio.19.111301.140101 }} and through non-lethal, transient oncotic pores in the plasma membrane induced by washing cells with serum-free media or buffers.{{cite journal | vauthors = Chirico WJ | title = Protein release through nonlethal oncotic pores as an alternative nonclassical secretory pathway | journal = BMC Cell Biology | volume = 12 | pages = 46 | date = October 2011 | pmid = 22008609 | pmc = 3217904 | doi = 10.1186/1471-2121-12-46 | doi-access = free }}

Many human cell types have the ability to be secretory cells. They have a well-developed endoplasmic reticulum, and Golgi apparatus to fulfill this function. Tissues that produce secretions include the gastrointestinal tract which secretes digestive enzymes and gastric acid, the lungs which secrete surfactants, and sebaceous glands which secrete sebum to lubricate the skin and hair. Meibomian glands in the eyelid secrete meibum to lubricate and protect the eye.

{{Main|Bacterial secretion system}}

Secretion is not unique to eukaryotes – it is also present in bacteria and archaea as well. ATP binding cassette (ABC) type transporters are common to the three domains of life. Some secreted proteins are translocated across the cytoplasmic membrane by the SecYEG translocon, one of two translocation systems, which requires the presence of an N-terminal signal peptide on the secreted protein. Others are translocated across the cytoplasmic membrane by the twin-arginine translocation pathway (Tat). Gram-negative bacteria have two membranes, thus making secretion topologically more complex. There are at least six specialized secretion systems in Gram-negative bacteria.{{cite book |editor1-last=Wooldridge |editor1-first=K |year=2009 |title=Bacterial Secreted Proteins: Secretory Mechanisms and Role in Pathogenesis |publisher=Caister Academic Press |isbn=978-1-904455-42-4}}{{page needed|date=February 2013}}

Image:T1SS.svg

Type I secretion is a chaperone dependent secretion system employing the Hly and Tol gene clusters. The process begins as a leader sequence on the protein to be secreted is recognized by HlyA and binds HlyB on the membrane. This signal sequence is extremely specific for the ABC transporter. The HlyAB complex stimulates HlyD which begins to uncoil and reaches the outer membrane where TolC recognizes a terminal molecule or signal on HlyD. HlyD recruits TolC to the inner membrane and HlyA is excreted outside of the outer membrane via a long-tunnel protein channel.

Type I secretion system transports various molecules, from ions, drugs, to proteins of various sizes (20 – 900 kDa). The molecules secreted vary in size from the small Escherichia coli peptide colicin V, (10 kDa) to the Pseudomonas fluorescens cell adhesion protein LapA of 520 kDa.{{cite journal | vauthors = Boyd CD, Smith TJ, El-Kirat-Chatel S, Newell PD, Dufrêne YF, O'Toole GA | title = Structural features of the Pseudomonas fluorescens biofilm adhesin LapA required for LapG-dependent cleavage, biofilm formation, and cell surface localization | journal = Journal of Bacteriology | volume = 196 | issue = 15 | pages = 2775–88 | date = August 2014 | pmid = 24837291 | pmc = 4135675 | doi = 10.1128/JB.01629-14 }} The best characterized are the RTX toxins and the lipases. Type I secretion is also involved in export of non-proteinaceous substrates like cyclic β-glucans and polysaccharides.

Image:T2SS.svg

{{Main|Type II secretion system}}

Proteins secreted through the type II system, or main terminal branch of the general secretory pathway, depend on the Sec or Tat system for initial transport into the periplasm. Once there, they pass through the outer membrane via a multimeric (12–14 subunits) complex of pore forming secretin proteins. In addition to the secretin protein, 10–15 other inner and outer membrane proteins compose the full secretion apparatus, many with as yet unknown function. Gram-negative type IV pili use a modified version of the type II system for their biogenesis, and in some cases certain proteins are shared between a pilus complex and type II system within a single bacterial species.

{{Main|Type III secretion system}}

Image:T3SS.svg

It is homologous to the basal body in bacterial flagella. It is like a molecular syringe through which a bacterium (e.g. certain types of Salmonella, Shigella, Yersinia, Vibrio) can inject proteins into eukaryotic cells. The low Ca²⁺ concentration in the cytosol opens the gate that regulates T3SS. One such mechanism to detect low calcium concentration has been illustrated by the lcrV (Low Calcium Response) antigen utilized by Yersinia pestis, which is used to detect low calcium concentrations and elicits T3SS attachment. The Hrp system in plant pathogens inject harpins and pathogen effector proteins through similar mechanisms into plants. This secretion system was first discovered in Yersinia pestis and showed that toxins could be injected directly from the bacterial cytoplasm into the cytoplasm of its host's cells rather than simply be secreted into the extracellular medium.Salyers, A. A. & Whitt, D. D. (2002). Bacterial Pathogenesis: A Molecular Approach, 2nd ed., Washington, D.C.: ASM Press. {{ISBN|1-55581-171-X}}{{page needed|date=February 2013}}

{{Infobox protein family

| Symbol = T4SS

| Name = T4SS

| image = Image:T4SS.svg

| width =

| caption = Type IV secretion system

| Pfam = PF07996

| Pfam_clan =

| InterPro = IPR012991

| SMART =

| PROSITE =

| MEROPS =

| SCOP = 1gl7

| TCDB = 3.A.7

| OPM family = 215

| OPM protein = 3jqo

| CAZy =

| CDD =

}}

{{Main|Type IV secretion system}}

It is homologous to conjugation machinery of bacteria, the conjugative pili. It is capable of transporting both DNA and proteins. It was discovered in Agrobacterium tumefaciens, which uses this system to introduce the T-DNA portion of the Ti plasmid into the plant host, which in turn causes the affected area to develop into a crown gall (tumor). Helicobacter pylori uses a type IV secretion system to deliver CagA into gastric epithelial cells, which is associated with gastric carcinogenesis.{{cite journal | vauthors = Hatakeyama M, Higashi H | title = Helicobacter pylori CagA: a new paradigm for bacterial carcinogenesis | journal = Cancer Science | volume = 96 | issue = 12 | pages = 835–43 | date = December 2005 | pmid = 16367902 | doi = 10.1111/j.1349-7006.2005.00130.x | s2cid = 5721063 | doi-access = free | pmc = 11159386 }} Bordetella pertussis, the causative agent of whooping cough, secretes the pertussis toxin partly through the type IV system. Legionella pneumophila, the causing agent of legionellosis (Legionnaires' disease) utilizes a type IVB secretion system, known as the icm/dot (intracellular multiplication / defect in organelle trafficking genes) system, to translocate numerous effector proteins into its eukaryotic host.{{cite journal | vauthors = Cascales E, Christie PJ | title = The versatile bacterial type IV secretion systems | journal = Nature Reviews. Microbiology | volume = 1 | issue = 2 | pages = 137–49 | date = November 2003 | pmid = 15035043 | pmc = 3873781 | doi = 10.1038/nrmicro753 }} The prototypic Type IVA secretion system is the VirB complex of Agrobacterium tumefaciens.{{cite journal | vauthors = Christie PJ, Atmakuri K, Krishnamoorthy V, Jakubowski S, Cascales E | title = Biogenesis, architecture, and function of bacterial type IV secretion systems | journal = Annual Review of Microbiology | volume = 59 | pages = 451–85 | year = 2005 | pmid = 16153176 | pmc = 3872966 | doi = 10.1146/annurev.micro.58.030603.123630 }}

Protein members of this family are components of the type IV secretion system. They mediate intracellular transfer of macromolecules via a mechanism ancestrally related to that of bacterial conjugation machineries.{{cite journal | vauthors = Christie PJ | title = Type IV secretion: the Agrobacterium VirB/D4 and related conjugation systems | journal = Biochimica et Biophysica Acta (BBA) - Molecular Cell Research | volume = 1694 | issue = 1–3 | pages = 219–34 | date = November 2004 | pmid = 15546668 | pmc = 4845649 | doi = 10.1016/j.bbamcr.2004.02.013 }}{{cite journal | vauthors = Yeo HJ, Yuan Q, Beck MR, Baron C, Waksman G | title = Structural and functional characterization of the VirB5 protein from the type IV secretion system encoded by the conjugative plasmid pKM101 | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 100 | issue = 26 | pages = 15947–52 | date = December 2003 | pmid = 14673074 | pmc = 307673 | doi = 10.1073/pnas.2535211100 | bibcode = 2003PNAS..10015947Y | jstor = 3149111 | doi-access = free }}

The Type IV secretion system (T4SS) is the general mechanism by which bacterial cells secrete or take up macromolecules. Their precise mechanism remains unknown. T4SS is encoded on Gram-negative conjugative elements in bacteria. T4SS are cell envelope-spanning complexes, or, in other words, 11–13 core proteins that form a channel through which DNA and proteins can travel from the cytoplasm of the donor cell to the cytoplasm of the recipient cell. T4SS also secrete virulence factor proteins directly into host cells as well as taking up DNA from the medium during natural transformation.{{cite journal | vauthors = Lawley TD, Klimke WA, Gubbins MJ, Frost LS | title = F factor conjugation is a true type IV secretion system | journal = FEMS Microbiology Letters | volume = 224 | issue = 1 | pages = 1–15 | date = July 2003 | pmid = 12855161 | doi = 10.1016/S0378-1097(03)00430-0 | doi-access = free }}

As shown in the above figure, TraC, in particular consists of a three helix bundle and a loose globular appendage.

T4SS has two effector proteins: firstly, ATS-1, which stands for Anaplasma translocated substrate 1, and secondly AnkA, which stands for ankyrin repeat domain-containing protein A. Additionally, T4SS coupling proteins are VirD4, which bind to VirE2.{{cite journal | vauthors = Rikihisa Y, Lin M, Niu H | title = Type IV secretion in the obligatory intracellular bacterium Anaplasma phagocytophilum | journal = Cellular Microbiology | volume = 12 | issue = 9 | pages = 1213–21 | date = September 2010 | pmid = 20670295 | pmc = 3598623 | doi = 10.1111/j.1462-5822.2010.01500.x }}

{{See also|Trimeric autotransporter adhesin#Type V secretion system (T5SS)}}

Image:T5SS.svg

Also called the autotransporter system,{{cite journal | vauthors = Thanassi DG, Stathopoulos C, Karkal A, Li H | title = Protein secretion in the absence of ATP: the autotransporter, two-partner secretion and chaperone/usher pathways of gram-negative bacteria (review) | journal = Molecular Membrane Biology | volume = 22 | issue = 1–2 | pages = 63–72 | year = 2005 | pmid = 16092525 | doi = 10.1080/09687860500063290 | s2cid = 2708575 }} type V secretion involves use of the Sec system for crossing the inner membrane. Proteins which use this pathway have the capability to form a beta-barrel with their C-terminus which inserts into the outer membrane, allowing the rest of the peptide (the passenger domain) to reach the outside of the cell. Often, autotransporters are cleaved, leaving the beta-barrel domain in the outer membrane and freeing the passenger domain. Some researchers believe remnants of the autotransporters gave rise to the porins which form similar beta-barrel structures.{{citation needed|date=October 2019}} A common example of an autotransporter that uses this secretion system is the Trimeric Autotransporter Adhesins.{{cite journal | vauthors = Gerlach RG, Hensel M | title = Protein secretion systems and adhesins: the molecular armory of Gram-negative pathogens | journal = International Journal of Medical Microbiology | volume = 297 | issue = 6 | pages = 401–15 | date = October 2007 | pmid = 17482513 | doi = 10.1016/j.ijmm.2007.03.017 }}

{{Main|Type VI secretion system}}

Type VI secretion systems were originally identified in 2006 by the group of John Mekalanos at the Harvard Medical School (Boston, USA) in two bacterial pathogens, Vibrio cholerae and Pseudomonas aeruginosa.{{cite journal | vauthors = Pukatzki S, Ma AT, Sturtevant D, Krastins B, Sarracino D, Nelson WC, Heidelberg JF, Mekalanos JJ | title = Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 5 | pages = 1528–33 | date = January 2006 | pmid = 16432199 | pmc = 1345711 | doi = 10.1073/pnas.0510322103 | bibcode = 2006PNAS..103.1528P | jstor = 30048406 | doi-access = free }}{{cite journal | vauthors = Mougous JD, Cuff ME, Raunser S, Shen A, Zhou M, Gifford CA, Goodman AL, Joachimiak G, Ordoñez CL, Lory S, Walz T, Joachimiak A, Mekalanos JJ | title = A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus | journal = Science | volume = 312 | issue = 5779 | pages = 1526–30 | date = June 2006 | pmid = 16763151 | pmc = 2800167 | doi = 10.1126/science.1128393 | bibcode = 2006Sci...312.1526M }} These were identified when mutations in the Hcp and VrgG genes in Vibrio cholerae led to decreased virulence and pathogenicity. Since then, Type VI secretion systems have been found in a quarter of all proteobacterial genomes, including animal, plant, human pathogens, as well as soil, environmental or marine bacteria.{{cite journal | vauthors = Bingle LE, Bailey CM, Pallen MJ | title = Type VI secretion: a beginner's guide | journal = Current Opinion in Microbiology | volume = 11 | issue = 1 | pages = 3–8 | date = February 2008 | pmid = 18289922 | doi = 10.1016/j.mib.2008.01.006 | url = http://sure.sunderland.ac.uk/id/eprint/3062/2/pallen_t6ss_2007_revised.pdf }}{{cite journal | vauthors = Cascales E | title = The type VI secretion toolkit | journal = EMBO Reports | volume = 9 | issue = 8 | pages = 735–41 | date = August 2008 | pmid = 18617888 | pmc = 2515208 | doi = 10.1038/embor.2008.131 }} While most of the early studies of Type VI secretion focused on its role in the pathogenesis of higher organisms, more recent studies suggested a broader physiological role in defense against simple eukaryotic predators and its role in inter-bacteria interactions.{{cite journal | vauthors = Schwarz S, Hood RD, Mougous JD | title = What is type VI secretion doing in all those bugs? | journal = Trends in Microbiology | volume = 18 | issue = 12 | pages = 531–7 | date = December 2010 | pmid = 20961764 | pmc = 2991376 | doi = 10.1016/j.tim.2010.09.001 }}{{cite journal | vauthors = Coulthurst SJ | title = The Type VI secretion system - a widespread and versatile cell targeting system | journal = Research in Microbiology | volume = 164 | issue = 6 | pages = 640–54 | year = 2013 | pmid = 23542428 | doi = 10.1016/j.resmic.2013.03.017 | doi-access = free }} The Type VI secretion system gene clusters contain from 15 to more than 20 genes, two of which, Hcp and VgrG, have been shown to be nearly universally secreted substrates of the system. Structural analysis of these and other proteins in this system bear a striking resemblance to the tail spike of the T4 phage, and the activity of the system is thought to functionally resemble phage infection.{{cite journal | vauthors = Silverman JM, Brunet YR, Cascales E, Mougous JD | title = Structure and regulation of the type VI secretion system | journal = Annual Review of Microbiology | volume = 66 | pages = 453–72 | year = 2012 | pmid = 22746332 | pmc = 3595004 | doi = 10.1146/annurev-micro-121809-151619 }}

{{Main|Type VII secretion system}}

{{Main|Type VIII secretion system}}

{{Main|Type IX secretion system}}

In addition to the use of the multiprotein complexes listed above, Gram-negative bacteria possess another method for release of material: the formation of bacterial outer membrane vesicles.{{cite journal | vauthors = Kuehn MJ, Kesty NC | title = Bacterial outer membrane vesicles and the host–pathogen interaction | journal = Genes & Development | volume = 19 | issue = 22 | pages = 2645–55 | date = November 2005 | pmid = 16291643 | doi = 10.1101/gad.1299905 | doi-access = free }} Portions of the outer membrane pinch off, forming nano-scale spherical structures made of a lipopolysaccharide-rich lipid bilayer enclosing periplasmic materials, and are deployed for membrane vesicle trafficking to manipulate environment or invade at host–pathogen interface. Vesicles from a number of bacterial species have been found to contain virulence factors, some have immunomodulatory effects, and some can directly adhere to and intoxicate host cells. release of vesicles has been demonstrated as a general response to stress conditions, the process of loading cargo proteins seems to be selective.{{cite journal | vauthors = McBroom AJ, Kuehn MJ | title = Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response | journal = Molecular Microbiology | volume = 63 | issue = 2 | pages = 545–58 | date = January 2007 | pmid = 17163978 | pmc = 1868505 | doi = 10.1111/j.1365-2958.2006.05522.x }}

{{Main|Bacterial secretion system}}

In some Staphylococcus and Streptococcus species, the accessory secretory system handles the export of highly repetitive adhesion glycoproteins.

• Bacterial effector protein
• Bacterial outer membrane vesicles
• Host–pathogen interaction
• Membrane vesicle trafficking
• Secretomics
• Secretory proteins
• Secretor status

Z. Esna Ashari, N. Dasgupta, K. Brayton & S. Broschat, “[https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197041#sec011 An optimal set of features for predicting type IV secretion system effector proteins for a subset of species based on a multi-level feature selection approach]”, PLOS ONE Journal, 2018, 13, e0197041. (doi.org/10.1371/journal.pone.0197041.)

{{Reflist|32em}}

{{refbegin}}

• {{cite book |chapter=Search: Secretion |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK21054/?term=secretion |editor-first=Bruce |editor-last=Alberts |editor2-first=Alexander |editor2-last=Johnson |editor3-first=Julian |editor3-last=Lewis |editor4-first=Martin |editor4-last=Raff |editor5-first=Keith |editor5-last=Roberts |editor6-first=Peter |editor6-last=Walter | name-list-style = vanc |title=Molecular Biology of the Cell |publisher=Garland Science |location=New York |year=2002 |isbn=978-0-8153-3218-3 |url=https://www.ncbi.nlm.nih.gov/books/NBK21054/ |edition=4th}}
• {{cite book |first=David |last=White | name-list-style = vanc |title=The Physiology and Biochemistry of Prokaryotes |url=https://archive.org/details/physiologybioche00whit |url-access=registration |year=2000 |publisher=Oxford University Press |isbn=978-0-19-512579-5 |edition=2nd}}
• {{cite web |first=David |last=Avon | name-list-style = vanc |title=Home page |work=Cells alive! |url=http://cellsalive.com/}}

{{refend}}

{{Wiktionary}}

• {{MeshName|Secretions}}
• T5SS / Autotransporter illustration at [https://www.uni-muenster.de/Chemie.pz/forschen/ag/jose/topicsofresearch.html Uni Münster]

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