Editing Helicobacter pylori (section)

==Microbiology==
''Helicobacter pylori'' is a species of [[gram-negative bacteria]] in the ''[[Helicobacter]]'' genus.<ref>{{cite journal |vauthors=Goodwin CS, Armstrong JA, Chilvers T, etal |title = Transfer of ''Campylobacter pylori'' and ''Campylobacter mustelae'' to ''Helicobacter'' gen. nov. as ''Helicobacter pylori'' comb. nov. and ''Helicobacter mustelae'' comb. nov., respectively|journal = Int. J. Syst. Bacteriol.|year = 1989 |volume = 39 |issue = 4 |pages = 397–405 |doi = 10.1099/00207713-39-4-397|doi-access = free}}</ref>
About half the world's population is infected with ''H. pylori'' but only a few strains are [[pathogenic]]. ''H pylori'' is a [[helical bacterium]] having a predominantly [[Helix|helical shape]], also often described as having a spiral or ''S'' shape.<ref name="Martínez2">{{cite journal |vauthors=Martínez LE, Hardcastle JM, Wang J, Pincus Z, Tsang J, Hoover TR, Bansil R, Salama NR |title=Helicobacter pylori strains vary cell shape and flagellum number to maintain robust motility in viscous environments |journal=Mol Microbiol |volume=99 |issue=1 |pages=88–110 |date=January 2016 |pmid=26365708 |pmc=4857613 |doi=10.1111/mmi.13218 |url=}}</ref><ref name="O'Rourke2">{{cite book |last1=O'Rourke |first1=Jani |last2=Bode |first2=Günter |title=Morphology and Ultrastructure |url=https://www.ncbi.nlm.nih.gov/books/NBK2452/ |publisher=ASM Press |date=2001|pmid=21290748 |isbn=978-1-55581-213-3 }}</ref> Its helical shape is better suited for progressing through the viscous [[gastric mucosa|mucosa lining of the stomach]], and is maintained by a number of [[protease|enzymes]] in the [[bacterial cell wall|cell wall's]] [[peptidoglycan]].<ref name="Martínez"/> The bacteria reach the less acidic mucosa by use of their [[Flagellum|flagella]].<ref name="Kao">{{cite journal |vauthors=Kao CY, Sheu BS, Wu JJ |title=Helicobacter pylori infection: An overview of bacterial virulence factors and pathogenesis |journal=Biomedical Journal |volume=39 |issue=1 |pages=14–23 |date=February 2016 |pmid=27105595 |pmc=6138426 |doi=10.1016/j.bj.2015.06.002 |url=}}</ref> Three strains studied showed a variation in length from 2.8 to 3.3&nbsp;μm but a fairly constant diameter of 0.55–0.58&nbsp;[[micrometre|μm]].<ref name="Martínez2" /> ''H. pylori'' can convert from a helical to an inactive [[coccus|coccoid]] form that can evade the immune system, and that may possibly become viable, known as [[viable but nonculturable]] (VBNC).<ref name="Ieradi">{{cite journal |vauthors=Ierardi E, Losurdo G, Mileti A, Paolillo R, Giorgio F, Principi M, Di Leo A |title=The Puzzle of Coccoid Forms of Helicobacter pylori: Beyond Basic Science |journal=Antibiotics |volume=9 |issue=6 |date=May 2020 |page=293 |pmid=32486473 |pmc=7345126 |doi=10.3390/antibiotics9060293 |doi-access=free |url=}}</ref><ref name="Luo">{{cite journal |vauthors=Luo Q, Liu N, Pu S, Zhuang Z, Gong H, Zhang D |title=A review on the research progress on non-pharmacological therapy of Helicobacter pylori |journal=Front Microbiol |volume=14 |issue= |pages=1134254 |date=2023 |pmid=37007498 |pmc=10063898 |doi=10.3389/fmicb.2023.1134254 |doi-access=free |url=}}</ref>

''Helicobacter pylori'' is [[microaerophilic]] – that is, it requires [[oxygen]], but at lower concentration than in the [[earth's atmosphere|atmosphere]]. It contains a [[hydrogenase]] that can produce energy by oxidizing molecular [[hydrogen]] (H<sub>2</sub>) made by [[Gut microbiota|intestinal bacteria]].<ref>{{cite journal | vauthors = Olson JW, Maier RJ | title = Molecular hydrogen as an energy source for Helicobacter pylori | journal = Science | volume = 298 | issue = 5599 | pages = 1788–90 | date = November 2002 | pmid = 12459589 | doi = 10.1126/science.1077123 | s2cid = 27205768 | bibcode = 2002Sci...298.1788O }}</ref>

''H.&nbsp;pylori'' can be demonstrated in tissue by [[Gram stain]], [[Giemsa stain]], [[H&E stain]], [[Warthin–Starry stain|Warthin-Starry silver stain]], [[Acridine orange|acridine orange stain]], and [[phase-contrast microscopy]]. It is capable of forming [[biofilm]]s. Biofilms help to hinder the action of antibiotics and can contribute to treatment failure.<ref name="Baj">{{cite journal |vauthors=Baj J, Forma A, Sitarz M, Portincasa P, Garruti G, Krasowska D, Maciejewski R |title=Helicobacter pylori Virulence Factors-Mechanisms of Bacterial Pathogenicity in the Gastric Microenvironment |journal=Cells |volume=10 |issue=1 |date=December 2020 |page=27 |pmid=33375694 |pmc=7824444 |doi=10.3390/cells10010027 |doi-access=free |url=}}</ref><ref name="Elshenawi2023">{{cite journal |vauthors=Elshenawi Y, Hu S, Hathroubi S |title=Biofilm of Helicobacter pylori: Life Cycle, Features, and Treatment Options |journal=Antibiotics |volume=12 |issue=8 |date=July 2023 |page=1260 |pmid=37627679 |pmc=10451559 |doi=10.3390/antibiotics12081260 |doi-access=free }}</ref>

To successfully colonize its host, ''H. pylori'' uses many different [[virulence factor]]s including [[oxidase]], [[catalase]], and [[urease]].<ref name="Kusters2006">{{cite journal | vauthors = Kusters JG, van Vliet AH, Kuipers EJ | title = Pathogenesis of Helicobacter pylori infection | journal = Clinical Microbiology Reviews | volume = 19 | issue = 3 | pages = 449–90 | date = July 2006 | pmid = 16847081 | pmc = 1539101 | doi = 10.1128/CMR.00054-05 }}</ref> Urease is the most abundant protein, its expression representing about 10% of the total protein weight.<ref name="Alzahrani">{{cite journal |vauthors=Alzahrani S, Lina TT, Gonzalez J, Pinchuk IV, Beswick EJ, Reyes VE |title=Effect of Helicobacter pylori on gastric epithelial cells |journal=World J Gastroenterol |volume=20 |issue=36 |pages=12767–80 |date=September 2014 |pmid=25278677 |pmc=4177462 |doi=10.3748/wjg.v20.i36.12767 |doi-access=free |url=}}</ref>

''H.&nbsp;pylori'' possesses five major [[outer membrane protein]] families.<ref name="Kusters2006"/> The largest family includes known and putative [[Bacterial adhesin|adhesins]]. The other four families are [[Porin (protein)|porin]]s, iron transporters, [[flagella|flagellum]]-associated proteins, and proteins of unknown function. Like other typical gram-negative bacteria, the outer membrane of ''H.&nbsp;pylori'' consists of [[phospholipids]] and [[lipopolysaccharide]] (LPS). The [[Lipopolysaccharide#O-antigen|O-antigen]] of LPS may be [[fucose|fucosylated]] and mimic [[Lewis antigen system|Lewis blood group antigens]] found on the gastric epithelium.<ref name="Kusters2006"/>

===Genome===
''Helicobacter pylori'' consists of a large diversity of strains, and hundreds of [[genome]]s have been completely [[sequencing|sequenced]].<ref>{{cite web |url=http://genolist.pasteur.fr/PyloriGene |title=Genome information for the ''H.&nbsp;pylori'' 26695 and J99 strains |publisher=Institut Pasteur |year=2002 |access-date=1 September 2008 |archive-date=26 November 2017 |archive-url=https://web.archive.org/web/20171126221437/http://genolist.pasteur.fr/PyloriGene/ |url-status=live }}</ref><ref>{{cite web |url=https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=139 |title=''Helicobacter pylori'' J99, complete genome |publisher=National Center for Biotechnology Information |access-date=1 September 2008 |archive-date=6 April 2011 |archive-url=https://web.archive.org/web/20110406134345/http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome |url-status=live }}</ref><ref name="Oh">{{cite journal | vauthors = Oh JD, Kling-Bäckhed H, Giannakis M, Xu J, Fulton RS, Fulton LA, Cordum HS, Wang C, Elliott G, Edwards J, Mardis ER, Engstrand LG, Gordon JI | title = The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 26 | pages = 9999–10004 | date = June 2006 | pmid = 16788065 | pmc = 1480403 | doi = 10.1073/pnas.0603784103 | bibcode = 2006PNAS..103.9999O | doi-access = free }}</ref> The genome of the strain ''26695'' consists of about 1.7&nbsp;million [[base pair]]s, with some 1,576&nbsp;genes.<ref name="NCBI">{{cite web |title=Helicobacter pylori 26695 genome assembly ASM30779v1 |url=https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000307795.1/ |website=NCBI |access-date=4 June 2024 |language=en}}</ref><ref name="Tomb 1997">{{cite journal | vauthors = Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC | title = The complete genome sequence of the gastric pathogen Helicobacter pylori | journal = Nature | volume = 388 | issue = 6642 | pages = 539–47 | date = August 1997 | pmid = 9252185 | doi = 10.1038/41483 | s2cid = 4411220 | bibcode = 1997Natur.388..539T | doi-access = free }}</ref> The [[pan-genome]], that is the combined set of 30&nbsp;sequenced strains, encodes 2,239&nbsp;protein families ([[Sequence homology#Orthology|orthologous groups]] OGs).<ref>{{cite journal | vauthors = van Vliet AH | title = Use of pan-genome analysis for the identification of lineage-specific genes of Helicobacter pylori | journal = FEMS Microbiology Letters | volume = 364 | issue = 2 | pages = fnw296 | date = January 2017 | pmid = 28011701 | doi = 10.1093/femsle/fnw296 | doi-access = free }}</ref> Among them, 1,248&nbsp;OGs are conserved in all the 30&nbsp;strains, and represent the [[Pan-genome#Core|universal core]]. The remaining 991&nbsp;OGs correspond to the [[Pan-genome#Cloud|accessory genome]] in which 277&nbsp;OGs are unique to one strain.<ref>{{cite journal | vauthors = Uchiyama I, Albritton J, Fukuyo M, Kojima KK, Yahara K, Kobayashi I | title = A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands | journal = PLOS ONE | volume = 11 | issue = 8 | pages = e0159419 | date = 9 August 2016 | pmid = 27504980 | pmc = 4978471 | doi = 10.1371/journal.pone.0159419 | bibcode = 2016PLoSO..1159419U | doi-access = free }}</ref>

There are eleven [[restriction modification system]]s in the genome of ''H. pylori''.<ref name="Tomb 1997" /> This is an unusually high number providing a [[DNA methylation#In bacteria|defence against bacteriophages]].<ref name="Tomb 1997" />

===Transcriptome===
[[Single-cell transcriptomics]] using [[Single-cell transcriptomics#Single-cell RNA-seq|single-cell RNA-Seq]] gave the complete [[transcriptome]] of ''H. pylori'' which was published in 2010. This analysis of its [[Bacterial transcription|transcription]] confirmed the known acid induction of major [[Virulence factor|virulence]] loci, including the urease (ure) operon and the Cag [[pathogenicity island]] (PAI).<ref name="Sharma2010">{{cite journal | vauthors = Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J | title = The primary transcriptome of the major human pathogen Helicobacter pylori | journal = Nature | volume = 464 | issue = 7286 | pages = 250–5 | date = March 2010 | pmid = 20164839 | doi = 10.1038/nature08756 | bibcode = 2010Natur.464..250S | s2cid = 205219639 }}</ref> A total of 1,907&nbsp;[[transcription start site]]s 337&nbsp;primary [[operon]]s, and 126&nbsp;additional suboperons, and 66&nbsp;mono[[cistron]]s were identified. Until 2010, only about 55&nbsp;transcription start sites (TSSs) were known in this species. 27% of the primary TSSs are also antisense TSSs, indicating that – similar to ''[[Escherichia coli|E.&nbsp;coli]]'' – [[Antisense RNA|antisense transcription]] occurs across the entire ''H.&nbsp;pylori'' genome. At least one antisense TSS is associated with about 46% of all [[open reading frame]]s, including many [[housekeeping gene]]s.<ref name="Sharma2010"/> About 50% of the [[Five prime untranslated region|5{{prime}} UTRs]] (leader sequences) are 20–40&nbsp;nucleotides (nt) in length and support the AAGGag motif located about 6&nbsp;nt (median distance) upstream of start codons as the consensus [[Shine-Dalgarno sequence|Shine–Dalgarno sequence]] in ''H.&nbsp;pylori''.<ref name="Sharma2010"/>

=== Proteome ===
The [[proteome]] of ''H. pylori'' has been systematically analyzed and more than 70% of its [[protein]]s have been detected by [[mass spectrometry]], and other methods. About 50% of the proteome has been quantified, informing of the number of protein copies in a typical cell.<ref>{{cite journal|date=2015-08-03|title=Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori|url=https://www.sciencedirect.com/science/article/abs/pii/S1874391915300099|journal=Journal of Proteomics|language=en|volume=126|pages=34–45|doi=10.1016/j.jprot.2015.05.011|issn=1874-3919|last1=Müller|first1=Stephan A.|last2=Pernitzsch|first2=Sandy R.|last3=Haange|first3=Sven-Bastiaan|last4=Uetz|first4=Peter|last5=von Bergen|first5=Martin|last6=Sharma|first6=Cynthia M.|last7=Kalkhof|first7=Stefan|pmid=25979772|s2cid=415255|access-date=26 July 2021|archive-date=27 July 2021|archive-url=https://web.archive.org/web/20210727071501/https://www.sciencedirect.com/science/article/abs/pii/S1874391915300099|url-status=live}}</ref>

Studies of the [[interactome]] have identified more than 3000 [[protein-protein interactions]]. This has provided information of how proteins interact with each other, either in stable [[protein complex]]es or in more dynamic, transient interactions, which can help to identify the functions of the protein. This in turn helps researchers to find out what the function of uncharacterized proteins is, e.g. when an uncharacterized protein interacts with several proteins of the [[ribosome]] (that is, it is likely also involved in ribosome function). About a third of all ~1,500 proteins in ''H. pylori'' remain uncharacterized and their function is largely unknown.<ref name="Wuchty">{{cite journal |vauthors=Wuchty S, Müller SA, Caufield JH, Häuser R, Aloy P, Kalkhof S, Uetz P |title=Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori |journal=Mol Cell Proteomics |volume=17 |issue=5 |pages=961–973 |date=May 2018 |pmid=29414760 |pmc=5930399 |doi=10.1074/mcp.RA117.000474 |doi-access=free |url=}}</ref>