دورية أكاديمية
Duplicate Gene Expression and Possible Mechanisms of Paralog Retention During Bacterial Genome Expansion.
العنوان: | Duplicate Gene Expression and Possible Mechanisms of Paralog Retention During Bacterial Genome Expansion. |
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المؤلفون: | Garber AI; Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA., Sano EB; Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA., Gallagher AL; Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA., Miller SR; Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA. |
المصدر: | Genome biology and evolution [Genome Biol Evol] 2024 May 02; Vol. 16 (5). |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. |
اللغة: | English |
بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 101509707 Publication Model: Print Cited Medium: Internet ISSN: 1759-6653 (Electronic) Linking ISSN: 17596653 NLM ISO Abbreviation: Genome Biol Evol Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: Oxford, UK : Oxford University Press |
مواضيع طبية MeSH: | Gene Duplication* , Genome, Bacterial* , Cyanobacteria*/genetics , Cyanobacteria*/metabolism , Evolution, Molecular*, Gene Dosage ; Gene Expression Regulation, Bacterial ; Genes, Duplicate |
مستخلص: | Gene duplication contributes to the evolution of expression and the origin of new genes, but the relative importance of different patterns of duplicate gene expression and mechanisms of retention remains debated and particularly poorly understood in bacteria. Here, we investigated gene expression patterns for two lab strains of the cyanobacterium Acaryochloris marina with expanding genomes that contain about 10-fold more gene duplicates compared with most bacteria. Strikingly, we observed a generally stoichiometric pattern of greater combined duplicate transcript dosage with increased gene copy number, in contrast to the prevalence of expression reduction reported for many eukaryotes. We conclude that increased transcript dosage is likely an important mechanism of initial duplicate retention in these bacteria and may persist over long periods of evolutionary time. However, we also observed that paralog expression can diverge rapidly, including possible functional partitioning, for which different copies were respectively more highly expressed in at least one condition. Divergence may be promoted by the physical separation of most Acaryochloris duplicates on different genetic elements. In addition, expression pattern for ancestrally shared duplicates could differ between strains, emphasizing that duplicate expression fate need not be deterministic. We further observed evidence for context-dependent transcript dosage, where the aggregate expression of duplicates was either greater or lower than their single-copy homolog depending on physiological state. Finally, we illustrate how these different expression patterns of duplicated genes impact Acaryochloris biology for the innovation of a novel light-harvesting apparatus and for the regulation of recA paralogs in response to environmental change. (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.) |
References: | J Bacteriol. 1974 Apr;118(1):242-9. (PMID: 4595200) Clin Sci (Lond). 2010 May 25;119(5):187-202. (PMID: 20522025) Annu Rev Genet. 2009;43:167-95. (PMID: 19686082) Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5932-7. (PMID: 24711408) J Bacteriol. 1993 Sep;175(17):5505-9. (PMID: 8366035) Mol Microbiol. 2003 Mar;47(5):1291-304. (PMID: 12603735) Sci Rep. 2015 Dec 01;5:17418. (PMID: 26621203) Nucleic Acids Res. 2004 Mar 19;32(5):1792-7. (PMID: 15034147) Genetics. 2010 Apr;184(4):1077-94. (PMID: 20083614) Mol Gen Genet. 1982;185(3):430-9. (PMID: 6212754) Science. 2000 Nov 10;290(5494):1151-5. (PMID: 11073452) Genetics. 1995 Dec;141(4):1245-52. (PMID: 8601470) J Mol Biol. 2011 Jan 7;405(1):201-13. (PMID: 21035460) Genome Biol. 2003;4(8):R48. (PMID: 12914657) Genome Biol Evol. 2018 Jun 1;10(6):1484-1492. (PMID: 29850825) Proc Biol Sci. 2012 Dec 22;279(1749):5048-57. (PMID: 22977152) Nat Med. 2009 Feb;15(2):211-4. (PMID: 19182798) Annu Rev Microbiol. 1977;31:473-505. (PMID: 334045) Mol Biol Evol. 2007 Aug;24(8):1586-91. (PMID: 17483113) FEMS Microbiol Lett. 1999 Dec 15;181(2):253-60. (PMID: 10585546) Annu Rev Genet. 1997;31:91-111. (PMID: 9442891) Biochim Biophys Acta Bioenerg. 2018 Jul;1859(7):544-553. (PMID: 29704497) Nature. 2000 Mar 2;404(6773):37-41. (PMID: 10716434) FEBS Lett. 2009 Aug 6;583(15):2535-9. (PMID: 19596002) Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):850-5. (PMID: 15637160) Nat Protoc. 2008;3(6):1101-8. (PMID: 18546601) Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12. (PMID: 16845082) J Struct Biol. 1998 Dec 15;124(2-3):311-34. (PMID: 10049814) Genetics. 1999 Apr;151(4):1531-45. (PMID: 10101175) Sci Rep. 2019 Jul 29;9(1):10912. (PMID: 31358794) Plant Cell. 2022 Jul 4;34(7):2466-2474. (PMID: 35253876) Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2005-10. (PMID: 18252824) Annu Rev Microbiol. 1990;44:365-94. (PMID: 2252387) Mol Microbiol. 2004 Jul;53(1):65-80. (PMID: 15225304) Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2512-7. (PMID: 24550276) Environ Microbiol. 2018 Feb;20(2):535-545. (PMID: 29052931) Nat Genet. 2006 Jun;38(6):636-43. (PMID: 16715097) Genome Biol Evol. 2011;3:601-13. (PMID: 21697100) Microorganisms. 2022 Mar 06;10(3):. (PMID: 35336144) Biochim Biophys Acta. 1999 Aug 4;1412(3):250-61. (PMID: 10482787) Nature. 2003 Jul 10;424(6945):194-7. (PMID: 12853957) Mol Biol Evol. 2015 Jan;32(1):268-74. (PMID: 25371430) Photosynth Res. 2005 Jun;84(1-3):269-73. (PMID: 16049785) BMC Microbiol. 2010 Jul 29;10:204. (PMID: 20670397) mBio. 2019 Apr 23;10(2):. (PMID: 31015331) Methods. 2001 Dec;25(4):402-8. (PMID: 11846609) Curr Biol. 2021 Apr 12;31(7):1539-1546.e4. (PMID: 33571437) G3 (Bethesda). 2017 Feb 9;7(2):517-532. (PMID: 27974439) Nat Genet. 2007 Apr;39(4):457-66. (PMID: 17334365) Science. 2016 May 20;352(6288):1009-13. (PMID: 27199432) Nat Rev Microbiol. 2009 Aug;7(8):578-88. (PMID: 19609259) Nat Methods. 2017 Jun;14(6):587-589. (PMID: 28481363) Genome Biol Evol. 2021 Nov 5;13(11):. (PMID: 34791212) Science. 2003 Nov 21;302(5649):1401-4. (PMID: 14631042) Microbiol Rev. 1984 Mar;48(1):1-23. (PMID: 6201704) Trends Genet. 2010 Oct;26(10):425-30. (PMID: 20708291) J Mol Evol. 2003 Jun;56(6):718-29. (PMID: 12911035) Plant Physiol. 2007 Jun;144(2):1200-10. (PMID: 17468217) |
معلومات مُعتمدة: | United States NASA NASA |
فهرسة مساهمة: | Keywords: bacteria; gene duplication; neofunctionalization; positive dosage |
تواريخ الأحداث: | Date Created: 20240426 Date Completed: 20240510 Latest Revision: 20240703 |
رمز التحديث: | 20240704 |
مُعرف محوري في PubMed: | PMC11086944 |
DOI: | 10.1093/gbe/evae089 |
PMID: | 38670115 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1759-6653 |
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DOI: | 10.1093/gbe/evae089 |