دورية أكاديمية
أعرض في EDS

Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China.

التفاصيل البيبلوغرافية
العنوان: Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China.
المؤلفون: Deng L; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China., Wang Q; Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China., Liu H; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China., Jiang Y; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China., Xu M; Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China., Xiang Y; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.; School of Public Health, University of South China, Hengyang, China., Yang T; Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China., Yang S; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.; School of Public Health, University of South China, Hengyang, China., Yan D; Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China., Li M; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China., Zhao L; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China., Zhao X; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China., Wan K; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China., He G; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China., Mijiti X; Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China., Li G; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
المصدر: Frontiers in microbiology [Front Microbiol] 2024 Apr 15; Vol. 15, pp. 1290227. Date of Electronic Publication: 2024 Apr 15 (Print Publication: 2024).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Frontiers Research Foundation Country of Publication: Switzerland NLM ID: 101548977 Publication Model: eCollection Cited Medium: Print ISSN: 1664-302X (Print) Linking ISSN: 1664302X NLM ISO Abbreviation: Front Microbiol Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: Lausanne : Frontiers Research Foundation
مستخلص: Background: Tuberculosis (TB), mainly caused by Mycobacterium tuberculosis ( Mtb ), remains a serious public health problem. Increasing evidence supports that selective evolution is an important force affecting genomic determinants of Mtb phenotypes. It is necessary to further understand the Mtb selective evolution and identify the positively selected genes that probably drive the phenotype of Mtb .
Methods: This study mainly focused on the positive selection of 807 Mtb strains from Southern Xinjiang of China using whole genome sequencing (WGS). PAML software was used for identifying the genes and sites under positive selection in 807 Mtb strains.
Results: Lineage 2 (62.70%) strains were the dominant strains in this area, followed by lineage 3 (19.45%) and lineage 4 (17.84%) strains. There were 239 codons in 47 genes under positive selection, and the genes were majorly associated with the functions of transcription, defense mechanisms, and cell wall/membrane/envelope biogenesis. There were 28 codons (43 mutations) in eight genes ( gyrA , rpoB , rpoC , katG , pncA , embB , gid , and cut1 ) under positive selection in multi-drug resistance (MDR) strains but not in drug-susceptible (DS) strains, in which 27 mutations were drug-resistant loci, 9 mutations were non-drug-resistant loci but were in drug-resistant genes, 2 mutations were compensatory mutations, and 5 mutations were in unknown drug-resistant gene of cut1 . There was a codon in Rv0336 under positive selection in L3 strains but not in L2 and L4 strains. The epitopes of T and B cells were both hyper-conserved, particularly in the T-cell epitopes.
Conclusion: This study revealed the ongoing selective evolution of Mtb . We found some special genes and sites under positive selection which may contribute to the advantage of MDR and L3 strains. It is necessary to further study these mutations to understand their impact on phenotypes for providing more useful information to develop new TB interventions.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2024 Deng, Wang, Liu, Jiang, Xu, Xiang, Yang, Yang, Yan, Li, Zhao, Zhao, Wan, He, Mijiti and Li.)
References: Nat Commun. 2021 Oct 20;12(1):6099. (PMID: 34671035)
PLoS One. 2012;7(4):e35847. (PMID: 22563409)
Front Med. 2020 Feb;14(1):51-59. (PMID: 31938981)
Nat Genet. 2013 Oct;45(10):1255-60. (PMID: 23995137)
Nat Commun. 2020 Jun 9;11(1):2917. (PMID: 32518235)
Bioinformatics. 2014 Aug 1;30(15):2114-20. (PMID: 24695404)
Gigascience. 2015 Feb 25;4:7. (PMID: 25722852)
Genome Med. 2020 Dec 14;12(1):114. (PMID: 33317631)
Tuberculosis (Edinb). 2011 Jan;91(1):1-7. (PMID: 20980199)
Biochem Biophys Res Commun. 2016 Jul 1;475(3):257-63. (PMID: 27207833)
Nucleic Acids Res. 2000 Jan 1;28(1):33-6. (PMID: 10592175)
mBio. 2013 Jul 30;4(4):. (PMID: 23900170)
Methods Mol Biol. 2021;2231:17-37. (PMID: 33289884)
BMC Infect Dis. 2022 Mar 30;22(1):312. (PMID: 35354436)
Nat Genet. 2013 Oct;45(10):1176-82. (PMID: 23995134)
Cell Host Microbe. 2015 Nov 11;18(5):538-48. (PMID: 26607161)
Infect Drug Resist. 2021 Aug 24;14:3379-3391. (PMID: 34466004)
J Mol Med (Berl). 2015 Jun;93(6):645-62. (PMID: 25586105)
Proc Natl Acad Sci U S A. 2022 Apr 26;119(17):e2113600119. (PMID: 35452305)
Mol Biol Evol. 2007 Aug;24(8):1586-91. (PMID: 17483113)
Front Microbiol. 2023 Oct 09;14:1244319. (PMID: 37876785)
Philos Trans R Soc Lond B Biol Sci. 2012 Mar 19;367(1590):850-9. (PMID: 22312052)
Gigascience. 2021 Feb 16;10(2):. (PMID: 33590861)
BMC Genomics. 2016 Feb 29;17:151. (PMID: 26923687)
Immunol Rev. 2015 Mar;264(1):6-24. (PMID: 25703549)
Trends Microbiol. 2008 Nov;16(11):528-34. (PMID: 18835713)
Nat Genet. 2016 Dec;48(12):1535-1543. (PMID: 27798628)
Nat Rev Microbiol. 2018 Apr;16(4):202-213. (PMID: 29456241)
Fly (Austin). 2012 Apr-Jun;6(2):80-92. (PMID: 22728672)
Immunol Rev. 2015 Mar;264(1):167-81. (PMID: 25703559)
Int J Mycobacteriol. 2020 Apr-Jun;9(2):121-137. (PMID: 32474533)
F1000Res. 2020 Apr 28;9:304. (PMID: 32489650)
Antimicrob Agents Chemother. 2015 Mar;59(3):1690-5. (PMID: 25583712)
Genome Res. 2001 May;11(5):863-74. (PMID: 11337480)
Mol Biol Evol. 2015 Jan;32(1):268-74. (PMID: 25371430)
Science. 2022 Dec 9;378(6624):1111-1118. (PMID: 36480634)
Cell Biosci. 2021 Aug 21;11(1):162. (PMID: 34419157)
Ann Transl Med. 2022 Jan;10(2):49. (PMID: 35282085)
Nat Genet. 2018 Jun;50(6):849-856. (PMID: 29785015)
Proc Natl Acad Sci U S A. 2021 Apr 27;118(17):. (PMID: 33879609)
Mol Biol Evol. 2013 Jun;30(6):1326-36. (PMID: 23449927)
Nat Genet. 2010 Jun;42(6):498-503. (PMID: 20495566)
Nat Genet. 2013 Oct;45(10):1183-9. (PMID: 23995135)
Genome Med. 2019 Jun 24;11(1):41. (PMID: 31234910)
BMC Infect Dis. 2016 Aug 09;16:385. (PMID: 27506391)
Appl Biochem Biotechnol. 2016 Apr;178(7):1377-89. (PMID: 26679705)
Microb Genom. 2021 Feb;7(2):. (PMID: 33555243)
Microbiologyopen. 2014 Dec;3(6):823-35. (PMID: 25238051)
Emerg Microbes Infect. 2022 Dec;11(1):2102-2111. (PMID: 35950916)
Front Microbiol. 2020 Jul 15;11:1444. (PMID: 32760357)
Microb Genom. 2021 Aug;7(8):. (PMID: 34431762)
فهرسة مساهمة: Keywords: China; Mycobacterium tuberculosis; positive selection; tuberculosis; whole genome sequencing (WGS)
تواريخ الأحداث: Date Created: 20240430 Latest Revision: 20240501
رمز التحديث: 20240501
مُعرف محوري في PubMed: PMC11056549
DOI: 10.3389/fmicb.2024.1290227
PMID: 38686109
قاعدة البيانات: MEDLINE
الوصف
تدمد:1664-302X
DOI:10.3389/fmicb.2024.1290227