Bioinformatics Analysis of the<i> NOT5</i> Gene in <i>Saccharomyces uvarum</i>

DING Shujin; YANG Yanping; DENG Ruyou; MA Fuxian; YIN Tuo; ZHANG Hanyao

doi:10.13386/j.issn1002-0306.2021120309

Volume 43 Issue 18

Sep. 2022

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Science and Technology of Food Industry > 2022 > 43(18): 145-151. > DOI: 10.13386/j.issn1002-0306.2021120309

DING Shujin, YANG Yanping, DENG Ruyou, et al. Bioinformatics Analysis of the NOT5 Gene in Saccharomyces uvarum[J]. Science and Technology of Food Industry, 2022, 43(18): 145−151. (in Chinese with English abstract). doi: 10.13386/j.issn1002-0306.2021120309.

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Bioinformatics Analysis of the NOT5 Gene in Saccharomyces uvarum

The Key Laboratory of Biodiversity Conservation of Southwest China State Forestry Administration, College of Forestry, Southwest Forestry University, Kunming 650224, China

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Received Date: December 28, 2021
Available Online: July 05, 2022

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Abstract

Abstract

Objective: In this paper, we obtained the NOT5 gene from Saccharomyces uvarum by transcriptome analysis. Analysis of its biological information can lay the foundation for the later study of the role of the gene. Methods: The primary structure, secondary structure, tertiary structure, and structural domains of the encoded protein were predicted using online analysis tools such as COILS Server, SOPMA, and Alpha Fold. Results: The length of the NOT5 gene was 1446 bp, encoding 481 amino acids, and it was located on chromosome XVI 690107~691789. The genetic relationship analysis showed that this gene was the closest to Saccharomyces eubayanus NOT5 like protein XP018219088.1, and had high homology. Its molecular formula was C_2493H3848N₆₅₄O₇₉₅S₁₉, and its molecular mass was 56311.02. It was an unstable hydrophilic protein. The protein encoded by this gene did not contain a signal peptide, had no transmembrane region, had a coiled helix region, and was subcellularly localized on the mitochondria in the cytoplasm. The secondary structure of the protein was dominated by random coils. Pfam Not3 and Pfam NOT2_3_5 domains were predicted. Yeast Not1-Not2-Not5 (4by6.1.C) was used as the template to construct the tertiary structure of NOT5 protein, and the sequence consistency between the two could reach 89.88%. Conclusion: The structure of the protein encoded by the NOT5 gene was unstable, and would interconnect translation and transcription in the cell.
- Saccharomyces uvarum,
- NOT5 gene,
- bioinformatics analysis,
- transcriptome,
- online analysis tools

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[1]	DEMUYTER C, LOLLIER M, LEGRAS J L, et al. Predominance of Saccharomyces uvarum during Spontaneous alcoholic fermentation, for three consecutive years, in an Alsatian winery[J]. Journal of Applied Microbiology,2004,97(6):1140−1148. doi: 10.1111/j.1365-2672.2004.02394.x
[2]	NAUMOV G I, Masneuf I, Naumova E S, et al. Association of Saccharomyces bayanus var. uvarum with some French wines: Genetic analysis of yeast populations[J]. Research in Microbiology,2000,151(8):683−691. doi: 10.1016/S0923-2508(00)90131-1
[3]	MORGAN S C, MCCARTHY G C, WATTERS B S, et al. Effect of sulfiteaddition and pied de cuve inoculation on the microbial communities and sensory profiles of Chardonnay wines: Dominance of indigenous Saccharomyces uvarum at a commercial winery[J]. FEMS Yeast Research,2019,19(5):foz049. doi: 10.1093/femsyr/foz049
[4]	ZHANG H, RICHARDS K D, WILSON S, et al. Genetic characterization of strains of Saccharomyces uvarum from New Zealand wineries[J]. Food Microbiology,2015,46:92−99. doi: 10.1016/j.fm.2014.07.016
[5]	COTON E, COTON M, LEVERT D, et al. Yeast ecology in French cider and black olive natural fermentations[J]. International Journal of Food Microbiology,2006,108(1):130−135. doi: 10.1016/j.ijfoodmicro.2005.10.016
[6]	ALLEN G E, PANASENKO O O, VILLANYI Z, et al. Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A[J]. Cell Reports,2021,36(9):109633. doi: 10.1016/j.celrep.2021.109633
[7]	ALLEN G E, PANASENKO O O, VILLANYI Z, et al. Switch from translation initiation to elongation needs Not4 and Not5 collaboration[J]. BioRxiv,2019:850859.
[8]	BUSCHAUER R, MATSUO Y, SUGIYAMA T, et al. The Ccr4-Not complex monitors the translating ribosome for codon optimality[J]. Science,2020,368(6488):eaay6912. doi: 10.1126/science.aay6912
[9]	SUAREZ V B, PANDO B R, FERNANDEZ T N, et al. Yeast species associated with the spontaneous fermentation of cider[J]. Food Microbiology,2007,24(1):25−31. doi: 10.1016/j.fm.2006.04.001
[10]	RODRIGUEZ M E, PEREZ T L, SANGORRIN M P, et al. Saccharomyces eubayanus and Saccharomyces uvarum associated with the fermentation of Araucaria araucana seeds in Patagonia[J]. FEMS Yeast Research,2014,14(6):948−65. doi: 10.1111/1567-1364.12183
[11]	ALHUSAINI N, COLLER J. The deadenylase components Not2p, Not3p, and Not5p promote mRNA decapping[J]. RNA,2016,22:709−721. doi: 10.1261/rna.054742.115
[12]	RODRIGUEZ M, PEREZ T L, SANGORRıN M, et al. Saccharomyces uvarum is responsible for the traditional fermentation of apple Chicha in Patagonia[J]. FEMS Yeast Research,2017,17(1):10.
[13]	DEED R C, FEDRIZZI B, GARDNER R C. Influence of fermentation temperature, yeast strain, and grape juice on the aroma chemistry and sensory profile of Sauvignon blanc wines[J]. Journal of Agricultural and Food Chemistry,2017,65(40):8902−8912. doi: 10.1021/acs.jafc.7b03229
[14]	张阳德. 生物信息学(1): 概论[J]. 外科理论与实践,2014(5):465−471. [ZHANG Y D. Bioinformatics (1): Introduction[J]. Surgical Theory and Practice,2014(5):465−471. ZHANG Y D. Bioinformatics (1): Introduction [J]. Surgical Theory and Practice, 2014(5): 465-471.
[15]	COLLART M A. The Ccr4-Not complex is a key regulator of eukaryotic gene expression[J]. Wiley Interdisciplinary Reviews RNA,2016,7(4):438−454. doi: 10.1002/wrna.1332
[16]	杨维恒. 分子生物学中核心概念的语义分析[D]. 太原: 山西大学, 2014 YANG W H. Semantic analysis of core concepts in molecular biology[D]. Taiyuan: Shanxi University, 2014.
[17]	COLLART M A. Global control of gene expression in yeast by the Ccr4-Not complex[J]. Gene,2003,313:1−16. doi: 10.1016/S0378-1119(03)00672-3
[18]	GUPTA I, VILLANYI Z, KASSEM S, et al. Translational capacity of a cell is determined during transcription elongation via the Ccr4-Not complex[J]. Cell Reports,2016,15(8):1782−1794. doi: 10.1016/j.celrep.2016.04.055
[19]	REED S I. The selection of S. cerevisiae mutants defective in the start event of cell division[J]. Genetics,1980,95(3):561−577. doi: 10.1093/genetics/95.3.561
[20]	PANASENKO O O, SOMASEKHARAN S P, VILLANYI Z, et al. Co-translational assembly of proteasome subunits in NOT1-containing assemblysomes[J]. Nature Structural & Molecular Biology,2019,26(2):110−120.
[21]	BASQUIN J, ROUDKO V V, RODE M, et al. Architecture of the nuclease module of the yeast Ccr4-not complex: The Not1-Caf1-Ccr4 interaction[J]. Molecular Cell,2012,48(2):207−218. doi: 10.1016/j.molcel.2012.08.014
[22]	SAKAI A, CHIBAZAKURA T, SHIMIZU Y, et al. Molecular analysis of POP2 gene, a gene required for glucose-derepression of gene expression in Saccharomyces cerevisiae[J]. Nucleic Acids Research,1992,20(23):6227−6233. doi: 10.1093/nar/20.23.6227
[23]	BHASKAR V, BASQUIN J, CONTI E. Architecture of the ubiquitylation module of the yeast Ccr4-Not complex[J]. Structure,2015,23(5):921−928. doi: 10.1016/j.str.2015.03.011
[24]	VILLANYI Z, RIBAUD V, KASSEM S, et al. The Not5 subunit of the ccr4-not complex connects transcription and translation[J]. PLoS Genetics,2014,10(10):e1004569. doi: 10.1371/journal.pgen.1004569
[25]	HSIN J P, MANLEY J L. The RNA polymerase II CTD coordinates transcription and RNA processing[J]. Genes & Development,2012,26(19):2119−2137.
[26]	AGUILERA A. Cotranscriptional mRNP assembly: From the DNA to the nuclear pore[J]. Current Opinion in Cell Biology,2005,17(3):242−250. doi: 10.1016/j.ceb.2005.03.001
[27]	ALMEIDA S F, CARMO F M. The CTD role in cotranscriptional RNA processing and surveillance[J]. FEBS Letters,2008,582(14):1971−1976. doi: 10.1016/j.febslet.2008.04.019
[28]	HAREL S L, ELDAD N, HAIMOVICH G, et al. RNA polymerase II subunits link transcription and mRNA decay to translation[J]. Cell,2010,143(4):552−563. doi: 10.1016/j.cell.2010.10.033
[29]	GOLER B V, SELITRENNIK M, BARKAI O, et al. Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes[J]. Genes & Development,2008,22(15):2022−2027.
[30]	WEBSTER M W, CHEN Y H, STOWELL J A, et al. mRNA deadenylation is coupled to translation rates by the differential activities of Ccr4-Not nucleases[J]. Molecular cell,2018,70(6):1089−1100.e8. doi: 10.1016/j.molcel.2018.05.033
[31]	COLLART M A, PANASENKO O. The Ccr4–Not complex[J]. Gene,2012,492(1):42−53. doi: 10.1016/j.gene.2011.09.033
[32]	LIU X Z, SANG M, ZHANG X A, et al. Enhancing expression of SSU1 genes in Saccharomyces uvarum leads to sulfite tolerance increase and transcriptome profiles change[J]. FEMS Yeast Research,2017,17(3):10.
[33]	ALBERT T K, HANZAWA H, LEGTENBERG Y I, et al. Identification of a ubiquitin-protein ligase subunit within the CCR4-NOT transcription repressor complex[J]. The EMBO Journal,2002,21(3):355−364. doi: 10.1093/emboj/21.3.355

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