دورية أكاديمية
Epigenetic Response of Yarrowia lipolytica to Stress: Tracking Methylation Level and Search for Methylation Patterns via Whole-Genome Sequencing.
العنوان: | Epigenetic Response of Yarrowia lipolytica to Stress: Tracking Methylation Level and Search for Methylation Patterns via Whole-Genome Sequencing. |
---|---|
المؤلفون: | Kubiak-Szymendera M; Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland., Pryszcz LP; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain., Białas W; Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland., Celińska E; Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland. |
المصدر: | Microorganisms [Microorganisms] 2021 Aug 24; Vol. 9 (9). Date of Electronic Publication: 2021 Aug 24. |
نوع المنشور: | Journal Article |
اللغة: | English |
بيانات الدورية: | Publisher: MDPI AG Country of Publication: Switzerland NLM ID: 101625893 Publication Model: Electronic Cited Medium: Print ISSN: 2076-2607 (Print) Linking ISSN: 20762607 NLM ISO Abbreviation: Microorganisms Subsets: PubMed not MEDLINE |
أسماء مطبوعة: | Original Publication: Basel, Switzerland : MDPI AG, [2013]- |
مستخلص: | DNA methylation is a common, but not universal, epigenetic modification that plays an important role in multiple cellular processes. While definitely settled for numerous plant, mammalian, and bacterial species, the genome methylation in different fungal species, including widely studied and industrially-relevant yeast species, Yarrowia lipolytica , is still a matter of debate. In this paper, we report a differential DNA methylation level in the genome of Y. lipolytica subjected to sequential subculturing and to heat stress conditions. To this end, we adopted repeated batch bioreactor cultivations of Y. lipolytica subjected to thermal stress in specific time intervals. To analyze the variation in DNA methylation between stressed and control cultures, we (a) quantified the global DNA methylation status using an immuno-assay, and (b) studied DNA methylation patterns through whole-genome sequencing. Primarily, we demonstrated that 5 mC modification can be detected using a commercial immuno-assay, and that the modifications are present in Y. lipolytica 's genome at ~0.5% 5 mC frequency. On the other hand, we did not observe any changes in the epigenetic response of Y. lipolytica to heat shock (HS) treatment. Interestingly, we identified a general phenomenon of decreased 5 mC level in Y. lipolytica 's genome in the stationary phase of growth, when compared to a late-exponential epigenome. While this study provides an insight into the subculturing stress response and adaptation to the stress at epigenetic level by Y. lipolytica , it also leaves an open question of inability to detect any genomic DNA methylation level (either in CpG context or context-less) through whole-genome sequencing. The results of ONT sequencing, suggesting that 5 mC modification is either rare or non-existent in Y. lipolytica genome, are contradicted with the results of the immunoassay. |
References: | J Mass Spectrom. 2007 Nov;42(11):1453-62. (PMID: 17960580) Nucleic Acids Res. 2020 May 7;48(8):4081-4099. (PMID: 32187373) Mikrobiologiia. 2007 Mar-Apr;76(2):184-90. (PMID: 17583214) Biosci Rep. 2019 May 7;39(5):. (PMID: 30877183) Appl Microbiol Biotechnol. 2020 Nov;104(22):9785-9800. (PMID: 33025130) PLoS One. 2016 Sep 07;11(9):e0162363. (PMID: 27603307) Nat Genet. 2007 Apr;39(4):457-66. (PMID: 17334365) Mol Ecol. 2012 Jun;21(11):2602-16. (PMID: 22171717) Epigenomics. 2013;5(5):553-68. (PMID: 24059801) Cell. 2007 Feb 23;128(4):707-19. (PMID: 17320508) BMC Genomics. 2005 Oct 07;6:141. (PMID: 16209719) J Bacteriol. 1978 Sep;135(3):1156-7. (PMID: 99431) Mol Plant. 2010 May;3(3):594-602. (PMID: 20410255) J Biol Chem. 1984 Jul 10;259(13):8033-6. (PMID: 6330093) Nucleic Acids Res. 2018 Apr 6;46(6):3218-3231. (PMID: 29471350) Science. 2001 Aug 10;293(5532):1070-4. (PMID: 11498574) Mol Cell Biol. 1984 May;4(5):985-8. (PMID: 6374428) Appl Microbiol Biotechnol. 2017 Jan;101(1):351-366. (PMID: 27730339) ScientificWorldJournal. 2014 Mar 13;2014:476207. (PMID: 24715814) Appl Microbiol Biotechnol. 2020 Jul;104(13):5845-5859. (PMID: 32358762) Bioinformatics. 2021 Jul 22;:. (PMID: 34293115) Biochem Genet. 2013 Aug;51(7-8):554-63. (PMID: 23553491) Nat Rev Mol Cell Biol. 2019 Oct;20(10):590-607. (PMID: 31399642) Microbiol Mol Biol Rev. 2006 Sep;70(3):830-56. (PMID: 16959970) Sci Rep. 2015 Feb 24;5:8567. (PMID: 25708804) Hum Genomics. 2015 Jul 28;9:17. (PMID: 26216216) Nat Biotechnol. 2010 Oct;28(10):1057-68. (PMID: 20944598) Curr Opin Plant Biol. 2009 Apr;12(2):133-9. (PMID: 19179104) Microorganisms. 2020 Feb 20;8(2):. (PMID: 32093408) Genomics. 2020 Sep;112(5):3537-3548. (PMID: 32278023) FEMS Microbiol Lett. 2002 Jan 2;206(1):45-50. (PMID: 11786255) Mol Biol Rep. 2015 Dec;42(12):1615-21. (PMID: 26547851) J Clin Microbiol. 2002 Aug;40(8):3079-81. (PMID: 12149386) Nucleic Acids Res. 2014 Jan;42(Database issue):D699-704. (PMID: 24297253) PLoS Genet. 2018 Oct 1;14(10):e1007707. (PMID: 30273333) Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11965-70. (PMID: 21730141) mSphere. 2018 Dec 5;3(6):. (PMID: 30518677) Genome Biol. 2014 May 29;15(5):R73. (PMID: 24887635) Nat Rev Mol Cell Biol. 2018 Dec;19(12):774-790. (PMID: 30425324) Anal Chem. 2014 Apr 15;86(8):3697-702. (PMID: 24640988) Biotechnol Rep (Amst). 2021 Jun 11;31:e00646. (PMID: 34189064) Appl Microbiol Biotechnol. 2017 Oct;101(19):7317-7333. (PMID: 28879478) Elife. 2018 Dec 21;7:. (PMID: 30575519) J Microbiol Biotechnol. 2015 Jul;25(7):1056-69. (PMID: 25737116) Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28191-28200. (PMID: 33106417) Nucleic Acids Res. 2012 Dec;40(22):11648-58. (PMID: 23074192) Arch Microbiol. 2002 Dec;178(6):477-83. (PMID: 12420169) PLoS One. 2018 Oct 31;13(10):e0206667. (PMID: 30379964) Curr Microbiol. 2004 Feb;48(2):118-23. (PMID: 15057479) Bioprocess Biosyst Eng. 2003 Jul;25(6):371-5. (PMID: 13680341) J Appl Microbiol. 2011 Jun;110(6):1460-9. (PMID: 21395946) Mol Gen Genet. 1997 Feb 27;253(6):703-10. (PMID: 9079881) PLoS One. 2014 Aug 01;9(8):e103145. (PMID: 25084460) Biotechnol Rep (Amst). 2020 Aug 27;27:e00521. (PMID: 32923379) Anal Chem. 2012 Aug 21;84(16):7249-55. (PMID: 22852529) |
معلومات مُعتمدة: | DI2017 001047 Ministerstwo Edukacji i Nauki; 506.771.09.00 B Uniwersytet Przyrodniczy w Poznaniu; 754422 H2020 Marie Skłodowska-Curie Actions |
فهرسة مساهمة: | Keywords: Yarrowia lipolytica; epigenome; genomics; methylation level; next generation sequencing; stress response; yeast |
تواريخ الأحداث: | Date Created: 20210928 Latest Revision: 20211001 |
رمز التحديث: | 20221213 |
مُعرف محوري في PubMed: | PMC8471669 |
DOI: | 10.3390/microorganisms9091798 |
PMID: | 34576693 |
قاعدة البيانات: | MEDLINE |
تدمد: | 2076-2607 |
---|---|
DOI: | 10.3390/microorganisms9091798 |