High-quality RNA extraction and the regulation of genes encoding cellulosomes are correlated with growth stage in anaerobic fungi.
CAZymes
RNA
anaerobic
fungi
methanogens
Journal
Frontiers in fungal biology
ISSN: 2673-6128
Titre abrégé: Front Fungal Biol
Pays: Switzerland
ID NLM: 9918266300506676
Informations de publication
Date de publication:
2023
2023
Historique:
received:
21
02
2023
accepted:
02
06
2023
medline:
25
9
2023
pubmed:
25
9
2023
entrez:
25
9
2023
Statut:
epublish
Résumé
Anaerobic fungi produce biomass-degrading enzymes and natural products that are important to harness for several biotechnology applications. Although progress has been made in the development of methods for extracting nucleic acids for genomic and transcriptomic sequencing of these fungi, most studies are limited in that they do not sample multiple fungal growth phases in batch culture. In this study, we establish a method to harvest RNA from fungal monocultures and fungal-methanogen co-cultures, and also determine an optimal time frame for high-quality RNA extraction from anaerobic fungi. Based on RNA quality and quantity targets, the optimal time frame in which to harvest anaerobic fungal monocultures and fungal-methanogen co-cultures for RNA extraction was 2-5 days of growth post-inoculation. When grown on cellulose, the fungal strain
Identifiants
pubmed: 37746117
doi: 10.3389/ffunb.2023.1171100
pmc: PMC10512310
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1171100Subventions
Organisme : NIGMS NIH HHS
ID : T34 GM136466
Pays : United States
Informations de copyright
Copyright © 2023 Brown, Gierke, Butkovich, Swift, Singan, Daum, Barry, Grigoriev and O’Malley.
Déclaration de conflit d'intérêts
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.
Références
Fungal Genet Biol. 2010 Sep;47(9):736-41
pubmed: 20554054
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
Anaerobe. 2016 Apr;38:39-46
pubmed: 26620247
Nature. 2011 Jun 22;474(7352):S12-4
pubmed: 21697834
J Clin Microbiol. 2004 Jul;42(7):3159-63
pubmed: 15243076
Crit Rev Microbiol. 2010 May;36(2):146-67
pubmed: 20210692
Front Microbiol. 2017 Sep 25;8:1657
pubmed: 28993761
Database (Oxford). 2011 May 26;2011:bar020
pubmed: 21622642
Nat Genet. 2017 Jun;49(6):964-968
pubmed: 28481340
J Chromatogr A. 2013 Apr 5;1284:163-73
pubmed: 23484651
J Clin Microbiol. 2005 Oct;43(10):5122-8
pubmed: 16207973
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Science. 2016 Mar 11;351(6278):1192-5
pubmed: 26912365
Appl Environ Microbiol. 2013 Aug;79(15):4620-34
pubmed: 23709508
Genome Biol. 2014;15(12):550
pubmed: 25516281
Front Microbiol. 2019 Mar 06;10:435
pubmed: 30894845
J Gen Microbiol. 1991 Jun;137(6):1401-8
pubmed: 1919514
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
pubmed: 21593126
Biotechnol Bioeng. 2014 Aug;111(8):1471-82
pubmed: 24788404
J Ind Microbiol Biotechnol. 2019 Oct;46(9-10):1427-1433
pubmed: 31089985
Nat Genet. 2003 Jul;34(3):267-73
pubmed: 12808457
Nat Microbiol. 2017 May 30;2:17087
pubmed: 28555641
Biotechnol Biofuels. 2017 Dec 20;10:305
pubmed: 29270219
Nucleic Acids Res. 2014 Jan;42(Database issue):D699-704
pubmed: 24297253
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
ACS Synth Biol. 2019 Sep 20;8(9):2174-2185
pubmed: 31461261
Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419
pubmed: 33125078
J Neurosci Methods. 2007 Sep 30;165(2):198-209
pubmed: 17628689
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W187-91
pubmed: 24799436
Curr Opin Biotechnol. 2014 Aug;28:103-10
pubmed: 24503479
BMC Biol. 2014 May 30;12:42
pubmed: 24885439
J Gen Microbiol. 1977 Mar;99(1):215-8
pubmed: 864435
mSystems. 2021 Feb 16;6(1):
pubmed: 33594000
J Microbiol Methods. 2016 Aug;127:206-213
pubmed: 27288952
Genome Biol. 2015 Aug 06;16:157
pubmed: 26243257
Proc Natl Acad Sci U S A. 2021 May 4;118(18):
pubmed: 33906945
Science. 2007 Feb 9;315(5813):804-7
pubmed: 17289988
mBio. 2021 Aug 31;12(4):e0144221
pubmed: 34399620
Biotechnol Biofuels. 2021 Dec 10;14(1):234
pubmed: 34893091
Nucleic Acids Res. 2015 Jul 1;43(W1):W401-7
pubmed: 25969446
BMC Mol Biol. 2006 Jan 31;7:3
pubmed: 16448564