Editing Treponema pallidum (section)

==Genome==
The genome of ''T. pallidum'' was first sequenced in 1998.<ref name="Fraser98">{{cite journal |display-authors=6 |vauthors=Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, Dodson R, Gwinn M, Hickey EK, Clayton R, Ketchum KA, Sodergren E, Hardham JM, McLeod MP, Salzberg S, Peterson J, Khalak H, Richardson D, Howell JK, Chidambaram M, Utterback T, McDonald L, Artiach P, Bowman C, Cotton MD, Fujii C, Garland S, Hatch B, Horst K, Roberts K, Sandusky M, Weidman J, Smith HO, Venter JC |date=July 1998 |title=Complete genome sequence of ''Treponema pallidum'', the syphilis spirochete |journal=Science |volume=281 |issue=5375 |pages=375–88 |bibcode=1998Sci...281..375F |doi=10.1126/science.281.5375.375 |pmid=9665876 |s2cid=8641048}}</ref> It is characterized by its helical, corkscrew-like shape.<ref>{{cite book |title=Brock Biology of Microorganisms |vauthors=Clark DP, Dunlap PV, Madigan JT, Martinko JM |publisher=Pearson |year=2009 |location=San Francisco |page=79}}</ref> ''T. pallidum'' is not obtainable in a pure culture, meaning that this sequencing played an important role in filling gaps of understanding regarding the microbes' functions. The DNA sequences of ''T. pallidum'' species are more than 99.7% identical, and PCR-based assays are effective at differentiating these species.<ref name="Smajs2018">{{cite journal |vauthors=Šmajs D, Strouhal M, Knauf S |date=July 2018 |title=Genetics of human and animal uncultivable treponemal pathogens |journal=Infection, Genetics and Evolution |volume=61 |pages=92–107 |bibcode=2018InfGE..61...92S |doi=10.1016/j.meegid.2018.03.015 |pmid=29578082 |s2cid=4826749}}</ref><ref name="linkinghub.elsevier.com">{{Cite journal |last1=Noda |first1=A.A. |last2=Grillová |first2=L. |last3=Lienhard |first3=R. |last4=Blanco |first4=O. |last5=Rodríguez |first5=I. |last6=Šmajs |first6=D. |date=November 2018 |title=Bejel in Cuba: molecular identification of Treponema pallidum subsp. endemicum in patients diagnosed with venereal syphilis |url=https://linkinghub.elsevier.com/retrieve/pii/S1198743X1830154X |journal=Clinical Microbiology and Infection |volume=24 |issue=11 |pages=1210.e1–1210.e5 |doi=10.1016/j.cmi.2018.02.006 |pmid=29454847 |issn=1198-743X}}</ref> About 92.9% of DNA was determined to be [[open reading frame]]s, 55% of which had predicted biological functions.<ref name="Norris-2001" /> ''T. pallidum'' was found to rely on its host for many molecules typically provided by biosynthetic pathways, and it is missing genes responsible for encoding key enzymes in oxidative phosphorylation and the tricarboxylic acid cycle.<ref>{{Cite book|title=Prescott's Microbiology |edition=11th |last=Willey|first=Joanne M.|publisher=McGraw-Hill Education|year=2020|isbn=978-1-260-21188-7|pages=436}}</ref> The ''T. pallidum'' group and its reduced genome is likely the result of various adaptations, such that it no longer contains the ability to synthesize fatty acids, nucleic acids, and amino acids, instead relying on its mammalian hosts for these materials.<ref name="ReferenceA" /> The recent sequencing of the genomes of several spirochetes permits a thorough analysis of the similarities and differences within this bacterial phylum and within the species.<ref>{{cite journal |vauthors=Zobaníková M, Mikolka P, Cejková D, Pospíšilová P, Chen L, Strouhal M, Qin X, Weinstock GM, Smajs D |title=Complete genome sequence of ''Treponema pallidum'' strain DAL-1 |journal=Standards in Genomic Sciences |volume=7 |issue=1 |pages=12–21 |date=October 2012 |pmid=23449808 |pmc=3570794 |doi=10.4056/sigs.2615838 |bibcode=2012SGenS...7...12Z }}</ref><ref>{{cite journal |vauthors=Tong ML, Zhao Q, Liu LL, Zhu XZ, Gao K, Zhang HL, Lin LR, Niu JJ, Ji ZL, Yang TC |title=Whole genome sequence of the ''Treponema pallidum'' subsp. pallidum strain Amoy: An Asian isolate highly similar to SS14 |journal=PLOS ONE |volume=12 |issue=8 |pages=e0182768 |date=2017 |pmid=28787460 |pmc=5546693 |doi=10.1371/journal.pone.0182768 |bibcode=2017PLoSO..1282768T |doi-access=free }}</ref><ref>{{cite journal |vauthors=Seshadri R, Myers GS, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, Ayodeji B, Shatsman S, McLeod MP, Smajs D, Howell JK, Pal S, Amin A, Vashisth P, McNeill TZ, Xiang Q, Sodergren E, Baca E, Weinstock GM, Norris SJ, Fraser CM, Paulsen IT |display-authors=6 |title=Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=101 |issue=15 |pages=5646–51 |date=April 2004 |pmid=15064399 |doi=10.1073/pnas.0307639101 |pmc=397461 |bibcode=2004PNAS..101.5646S|doi-access=free }}</ref> The chromosomes of the ''T. pallidum'' species are small, about 1.14 Mbp. It has one of the smallest bacterial genomes  and has limited metabolic capabilities, reflecting its adaptation through genome reduction to the rich environment of mammalian tissue. It conserves almost 99.8% of its small genome, and uses its constantly mutating protein TprK to avoid immune response from its host.<ref>{{Cite journal |last1=Pinto |first1=Miguel |last2=Borges |first2=Vítor |last3=Antelo |first3=Minia |last4=Pinheiro |first4=Miguel |last5=Nunes |first5=Alexandra |last6=Azevedo |first6=Jacinta |last7=Borrego |first7=Maria José |last8=Mendonça |first8=Joana |last9=Carpinteiro |first9=Dina |last10=Vieira |first10=Luís |last11=Gomes |first11=João Paulo |date=2016-10-17 |title=Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation |url=https://www.nature.com/articles/nmicrobiol2016190 |journal=Nature Microbiology |language=en |volume=2 |issue=1 |page=16190 |doi=10.1038/nmicrobiol.2016.190 |pmid=27748767 |issn=2058-5276}}</ref> To avoid antibodies attacking it, the cell has few proteins exposed on the outer membrane sheath.<ref>{{harvnb|Willey|2020|p=499}}</ref> Its chromosome is about 1000 kilobase pairs and is circular with a 52.8% G + C average.<ref name=Fraser98/> Sequencing has revealed a bundle of 12 proteins and some putative hemolysins are potential virulence factors of ''T. pallidum.''<ref name=Weinstock98>{{Cite journal |last1=Weinstock |first1=George M. |last2=Hardham |first2=John M. |last3=McLeod |first3=Michael P. |last4=Sodergren |first4=Erica J. |last5=Norris |first5=Steven J. |date=1 October 1998 |title=The genome of ''Treponema pallidum'': new light on the agent of syphilis |journal=FEMS Microbiology Reviews  |volume=22 |issue=4 |pages=323–332 |doi=10.1111/j.1574-6976.1998.tb00373.x |pmid=9862125 |doi-access=free }}</ref> These virulence factors are thought to contribute to the bacterium's ability to evade the immune system and cause disease.<ref name=Weinstock98/>