دورية أكاديمية
أعرض في EDS

Integrative Analysis of the Ethanol Tolerance of Saccharomyces cerevisiae .

التفاصيل البيبلوغرافية
العنوان: Integrative Analysis of the Ethanol Tolerance of Saccharomyces cerevisiae .
المؤلفون: Wolf IR; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil.; Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil., Marques LF; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil., de Almeida LF; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil.; Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil., Lázari LC; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil.; Department of Parasitology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo 05508-000, Brazil., de Moraes LN; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil., Cardoso LH; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil., Alves CCO; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil., Nakajima RT; Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil., Schnepper AP; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil., Golim MA; Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil., Cataldi TR; Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba 13418-900, Brazil., Nijland JG; Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands., Pinto CM; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil., Fioretto MN; Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil., Almeida RO; Instituto Federal de Educação, Ciência e Tecnologia do Sudeste de Minas Gerais-Campus Muriaé, Muriaé 36884-036, Brazil., Driessen AJM; Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands., Simōes RP; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil., Labate MV; Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba 13418-900, Brazil., Grotto RMT; Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu 18610-034, Brazil.; Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil., Labate CA; Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba 13418-900, Brazil., Fernandes Junior A; Laboratory of Bacteriology, Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil., Justulin LA; Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil., Coan RLB; Department of Biophysics and Pharmacology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil., Ramos É; Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil., Furtado FB; Laboratory of Applied Biotechnology, Clinical Hospital of the Medical School, São Paulo State University (UNESP), Botucatu 18618-970, Brazil., Martins C; Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil., Valente GT; Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany.
المصدر: International journal of molecular sciences [Int J Mol Sci] 2023 Mar 15; Vol. 24 (6). Date of Electronic Publication: 2023 Mar 15.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI, [2000-
مواضيع طبية MeSH: Saccharomyces cerevisiae*/genetics , Saccharomyces cerevisiae*/metabolism , RNA, Long Noncoding*/genetics, Ethanol/pharmacology ; Ethanol/metabolism
مستخلص: Ethanol (EtOH) alters many cellular processes in yeast. An integrated view of different EtOH-tolerant phenotypes and their long noncoding RNAs (lncRNAs) is not yet available. Here, large-scale data integration showed the core EtOH-responsive pathways, lncRNAs, and triggers of higher (HT) and lower (LT) EtOH-tolerant phenotypes. LncRNAs act in a strain-specific manner in the EtOH stress response. Network and omics analyses revealed that cells prepare for stress relief by favoring activation of life-essential systems. Therefore, longevity, peroxisomal, energy, lipid, and RNA/protein metabolisms are the core processes that drive EtOH tolerance. By integrating omics, network analysis, and several other experiments, we showed how the HT and LT phenotypes may arise: (1) the divergence occurs after cell signaling reaches the longevity and peroxisomal pathways, with CTA1 and ROS playing key roles; (2) signals reaching essential ribosomal and RNA pathways via SUI2 enhance the divergence; (3) specific lipid metabolism pathways also act on phenotype-specific profiles; (4) HTs take greater advantage of degradation and membraneless structures to cope with EtOH stress; and (5) our EtOH stress-buffering model suggests that diauxic shift drives EtOH buffering through an energy burst, mainly in HTs. Finally, critical genes, pathways, and the first models including lncRNAs to describe nuances of EtOH tolerance are reported here.
Competing Interests: The authors declare no conflict of interest.
References: Mol Cell. 2011 Sep 16;43(6):973-81. (PMID: 21925385)
Appl Microbiol Biotechnol. 2018 Sep;102(17):7319-7331. (PMID: 29974182)
J Appl Microbiol. 2010 Jul;109(1):13-24. (PMID: 20070446)
Sci Rep. 2020 Jan 14;10(1):233. (PMID: 31937829)
Adv Exp Med Biol. 2016;892:33-68. (PMID: 26721270)
Cold Spring Harb Perspect Biol. 2019 May 1;11(5):. (PMID: 30082464)
DNA Repair (Amst). 2018 Nov;71:23-32. (PMID: 30181040)
Biochim Biophys Acta. 2016 Jan;1859(1):147-54. (PMID: 26265144)
Science. 1999 Nov 5;286(5442):1166-71. (PMID: 10550056)
Brief Funct Genomics. 2019 Feb 14;18(1):58-82. (PMID: 30247501)
BMC Syst Biol. 2014 Aug 08;8:90. (PMID: 25103914)
Nat Rev Mol Cell Biol. 2007 Jan;8(1):9-22. (PMID: 17183357)
Bioessays. 2020 Dec;42(12):e2000027. (PMID: 33164244)
Oxid Med Cell Longev. 2016;2016:4010357. (PMID: 26682004)
PLoS Comput Biol. 2017 Oct 12;13(10):e1005598. (PMID: 29023449)
PLoS Comput Biol. 2022 May 19;18(5):e1010081. (PMID: 35587936)
FEMS Yeast Res. 2018 Sep 1;18(6):. (PMID: 29986027)
Front Genet. 2019 Feb 12;10:82. (PMID: 30809248)
Mol Cell. 2011 Sep 16;43(6):904-14. (PMID: 21925379)
RNA. 2017 Oct;23(10):1479-1492. (PMID: 28701522)
Nat Chem Biol. 2022 Dec;18(12):1380-1387. (PMID: 35970997)
Appl Microbiol Biotechnol. 2007 Jul;75(6):1343-51. (PMID: 17387467)
Mol Cell Biol. 2005 Mar;25(6):2138-46. (PMID: 15743812)
Nat Protoc. 2012 Mar 15;7(4):670-85. (PMID: 22422314)
Syst Med (New Rochelle). 2019 Mar 28;2(1):1-9. (PMID: 31119214)
J Biosci Bioeng. 2017 Aug;124(2):133-142. (PMID: 28427825)
World J Microbiol Biotechnol. 2017 Nov 3;33(11):206. (PMID: 29101531)
Nat Commun. 2020 Jan 3;11(1):102. (PMID: 31900386)
Biochim Biophys Acta. 2016 Jan;1859(1):139-46. (PMID: 26021608)
Proteomics. 2011 May;11(10):1857-67. (PMID: 21480527)
Biochem Biophys Res Commun. 1973 Apr 16;51(4):1034-41. (PMID: 4703549)
Brief Funct Genomics. 2012 Nov;11(6):420-33. (PMID: 22908211)
BMC Genomics. 2015 Feb 08;16:65. (PMID: 25759274)
Nat Cell Biol. 2018 Mar;20(3):233-242. (PMID: 29476151)
Int J Mol Sci. 2018 Mar 15;19(3):. (PMID: 29543708)
World J Microbiol Biotechnol. 2019 Mar 26;35(4):59. (PMID: 30915597)
Yeast. 2011 May;28(5):339-47. (PMID: 21341306)
Genetics. 2013 Jan;193(1):109-23. (PMID: 23105015)
J Cell Biol. 2008 Nov 3;183(3):441-55. (PMID: 18981231)
Wiley Interdiscip Rev RNA. 2017 Jan;8(1):. (PMID: 27436689)
Cell Death Dis. 2021 Jun 8;12(6):592. (PMID: 34103467)
J Proteome Res. 2021 Aug 6;20(8):3840-3852. (PMID: 34236875)
J Proteomics. 2017 Jan 16;151:114-121. (PMID: 27576599)
Wiley Interdiscip Rev RNA. 2012 Nov-Dec;3(6):779-96. (PMID: 22976942)
Eur J Cell Biol. 2010 Apr;89(4):339-48. (PMID: 19804918)
Trends Genet. 2018 Aug;34(8):612-626. (PMID: 29908710)
PLoS One. 2020 Nov 10;15(11):e0239528. (PMID: 33170850)
Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11901-6. (PMID: 8876235)
Elife. 2018 Jan 03;7:. (PMID: 29297464)
Yeast. 2022 Apr;39(4):247-261. (PMID: 34791685)
Trends Endocrinol Metab. 2014 Nov;25(11):558-66. (PMID: 25153840)
Genetics. 2010 Dec;186(4):1197-205. (PMID: 20855568)
Front Microbiol. 2016 Feb 18;7:189. (PMID: 26925053)
ACS Synth Biol. 2021 Jan 15;10(1):19-28. (PMID: 33356165)
J Biol Chem. 2003 May 30;278(22):20154-61. (PMID: 12654921)
Adv Exp Med Biol. 2013;768:23-43. (PMID: 23224963)
Metabolites. 2020 Apr 03;10(4):. (PMID: 32260275)
Mol Cell. 2019 May 2;74(3):521-533.e6. (PMID: 30952514)
PLoS Genet. 2021 Jan 25;17(1):e1008761. (PMID: 33493158)
Nat Cell Biol. 2009 Nov;11(11):1305-14. (PMID: 19801973)
FEMS Yeast Res. 2021 Jan 16;21(1):. (PMID: 33232441)
Traffic. 2019 Sep;20(9):623-638. (PMID: 31152627)
Mol Cell. 2019 Oct 17;76(2):286-294. (PMID: 31626750)
PLoS One. 2013;8(2):e55439. (PMID: 23408980)
Curr Genet. 2022 Apr;68(2):207-225. (PMID: 35220444)
Appl Microbiol Biotechnol. 2010 Sep;88(1):231-9. (PMID: 20661734)
Gigascience. 2019 Apr 1;8(4):. (PMID: 30715293)
J Proteomics. 2019 Jul 15;203:103377. (PMID: 31102756)
Microbiology (Reading). 2001 Aug;147(Pt 8):2037-2044. (PMID: 11495982)
J Cell Biol. 2005 Sep 12;170(6):913-24. (PMID: 16157702)
Adv Exp Med Biol. 2017;1008:119-132. (PMID: 28815538)
Genetics. 2014 Sep;198(1):369-82. (PMID: 24970865)
Yeast. 2001 Feb;18(3):273-82. (PMID: 11180460)
معلومات مُعتمدة: 2015/12090-9 São Paulo Research Foundation; 2017/08463-0 São Paulo Research Foundation; 2015/19211-7 São Paulo Research Foundation; 2017/14764-3 São Paulo Research Foundation; 401041/2016-6 National Council for Scientific and Technological Development; 12/2015-PROPe Programa Primeiros Projetos da UNESP
فهرسة مساهمة: Keywords: CRISPR–Cas9; data integration; lncRNAs; lncRNA–protein interactions; membraneless organelles; omics; systems biology
المشرفين على المادة: 0 (RNA, Long Noncoding)
3K9958V90M (Ethanol)
تواريخ الأحداث: Date Created: 20230329 Date Completed: 20230330 Latest Revision: 20230331
رمز التحديث: 20230331
مُعرف محوري في PubMed: PMC10051466
DOI: 10.3390/ijms24065646
PMID: 36982719
قاعدة البيانات: MEDLINE
الوصف
تدمد:1422-0067
DOI:10.3390/ijms24065646