基于转录组测序的异常汉逊酵母菌不同发酵时期差异表达基因功能分析
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摘要
异常汉逊酵母(Hansenula anomala)具有较强的发酵力和酯化力,并能积累色氨酸。为了进一步理解其发酵过程中的基因表达与代谢的关系,在转录组测序的基础上,利用生物信息学方法,分别对5个发酵时间点(0、24、48、72、96 h)的异常汉逊酵母菌的差异表达基因的功能进行了分析。结果表明,各发酵时间点与其相邻的上一个时间点相比,发酵24、48、72、96 h的上调表达的基因数量分别为585、487、154、615,下调表达的基因数量分别为1 112、725、5、245。差异表达基因功能的GO富集和KEGG通路富集结果表明,异常汉逊酵母菌的代谢强度在0～48 h下降,48～96 h上升,并且在96 h时,具有较强的代谢活动和遗传信息处理能力。产色氨酸通路的差异基因表达矩阵分析表明,异常汉逊酵母菌合成色氨酸的速率在0～24 h下降,随后上升;而色氨酸的分解速率从0～48 h上升,随后下降。这些结果可为异常汉逊酵母菌的分子育种及其代谢调控研究提供理论依据。
Hansenula anomala has outstanding performances on fermentation,esterification,and accumulating tryptophan. To illustrate the relationship between genes expression and metabolism of H. anomala during fermentation,differentially expressed genes( DEGs) at different fermentation points( 0,24,48,72,96 h) were analyzed by using transcriptomic sequencing and bioinformatic methods. The results showed that 585,487,154,and 615 genes were up-regulated at 24,48,72,96 h,respectively,while 1112,725,5,and 245 genes were down-regulated. The Gene Ontology( GO) and Kyoto Encyclopedia of Genes and Genomes( KEGG) pathway enrichment of DEGs indicated that the metabolic activity of H. anomala decreased from 0 h to 48 h,but increased from 48 h to 96 h. Additionally,H.anomala had strong metabolic activity and genetic information processing ability at 96 h. The differential gene expression matrix analysis of the tryptophan pathway showed that the synthesis rate of tryptophan in H. anomala decreased from 0 h to 24 h and increased thereafter,while the decomposition rate of tryptophan increased from 0 h to 48 h,and then decreased. In summary,these results provides a theoretical basis for molecular breeding and metabolic regulation of H. anomala.
Hansenula anomala has outstanding performances on fermentation,esterification,and accumulating tryptophan. To illustrate the relationship between genes expression and metabolism of H. anomala during fermentation,differentially expressed genes( DEGs) at different fermentation points( 0,24,48,72,96 h) were analyzed by using transcriptomic sequencing and bioinformatic methods. The results showed that 585,487,154,and 615 genes were up-regulated at 24,48,72,96 h,respectively,while 1112,725,5,and 245 genes were down-regulated. The Gene Ontology( GO) and Kyoto Encyclopedia of Genes and Genomes( KEGG) pathway enrichment of DEGs indicated that the metabolic activity of H. anomala decreased from 0 h to 48 h,but increased from 48 h to 96 h. Additionally,H.anomala had strong metabolic activity and genetic information processing ability at 96 h. The differential gene expression matrix analysis of the tryptophan pathway showed that the synthesis rate of tryptophan in H. anomala decreased from 0 h to 24 h and increased thereafter,while the decomposition rate of tryptophan increased from 0 h to 48 h,and then decreased. In summary,these results provides a theoretical basis for molecular breeding and metabolic regulation of H. anomala.
引文
[1]COMITINI F,GOBBI M,DOMIZIO P,et al.Selected non-Saccharomyces wine yeasts in controlled multistarter fermentations with Saccharomyces cerevisiae[J].Food Microbiology,2011,28(5):873-882.
[2]LEE P R,CHONG I S M,YU B,et al.Effects of sequentially inoculated Williopsis saturnus and Saccharomyces cerevisiae on volatile profiles of papaya wine[J].Food Research International,2012,45(1):177-183.
[3]刘景,王欣,辛红鸿,等.非酿酒酵母的筛选及其发酵低醇苹果汁的研究[J].中国食品学报,2017,17(1):134-140.
[4]EBIHARA Y,NIITSU N,TERUI G.Fermentative production of tryptophan from indole by Hansenula anomala[J].Ferment Technol,1969,47(12):733-738.
[5]WAKASA K,ISHIHARA A.Metabolic engineering of the tryptophan and phenylalanine biosynthetic pathways in rice[J].Plant Biotechnology,2009,26(5):523-533.
[6]毛培宏,吕杰.离子束重组酵母菌Ar_Han0458的RAPD与SSH的初步研究[J].基因组学与应用生物学,2015,34(3):449-453.
[7]LU Jie,JIN Xiang,MAO Pei-hong,et al.Transfer of Ephedra genomic DNA to yeasts by ion implantation[J].Appl Biochem Biotechnol,2009,158(3):571~581
[8]WANG Z,GERSTEIN M,SNYDER M.RNA-Seq:A revolutionary tool for transcriptomics[J].Nature reviews genetics,2009,10(1):57.
[9]BURKE D,DAWSON D,STEARNS T.Methods in yeast genetics:A cold spring harbor laboratory course manual[M].New York:Cold Spring Harbor Lab Press,2000:171-172.
[10]SAHRAEIAN S M E,MOHIYUDDIN M,SEBRA R,et al.Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis[J].Nature communications,2017,8(1):59.
[11]KIM D,LANGMEAD B,SALZBERG S L.HISAT:A fast spliced aligner with low memory requirements[J].Nature methods,2015,12(4):357.
[12]ANDERS S,PYL P T,HUBER W.HTSeq-a Python framework to work with high-throughput sequencing data[J].Bioinformatics,2015,31(2):166-169.
[13]GTZ S,ARNOLD R,SEBASTIN-LEN P,et al.B2G-FAR,a species-centered GO annotation repository[J].Bioinformatics,2011,27(7):919-924.
[14]MORIYA Y,ITOH M,OKUDA S,et al.KAAS:An automatic genome annotation and pathway reconstruction server[J].Nucleic acids research,2007,35:W182-W185.
[15]LOVE M I,HUBER W,ANDERS S.Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J].Genome biology,2014,15(12):550.
[16]YOUNG M D,WAKEFIELD M J,SMYTH G K,et al.Gene ontology analysis for RNA-seq:Accounting for selection bias[J].Genome biology,2010,11(2):R14.
[17]MALDONADO E N,LEMASTERS J J.ATP/ADP ratio,the missed connection between mitochondria and the Warburg effect[J].Mitochondrion,2014,19:78-84.
[18]WEI San-hua,LIN Fang,WANG Xi,et al.Prognostic significance of stathmin expression in correlation with metastasis and clinicopathological characteristics in human ovarian carcinoma[J].Acta Histochemica,2008,110(1):59-65.
[19]BRANDO I D S L,OLIVEIRA-MORAES H M D S,SOUZA M C M D,et al.Elastin increases biofilm and extracellular matrix production of Aspergillus fumigatus[J].Brazilian Journal of Microbiology,2018,49(3):675-682.
[20]李玲阁,唐任天,傅妙福,等.色氨酸发酵的初步研究[J].微生物学报,1975,15(3):212-216.
[2]LEE P R,CHONG I S M,YU B,et al.Effects of sequentially inoculated Williopsis saturnus and Saccharomyces cerevisiae on volatile profiles of papaya wine[J].Food Research International,2012,45(1):177-183.
[3]刘景,王欣,辛红鸿,等.非酿酒酵母的筛选及其发酵低醇苹果汁的研究[J].中国食品学报,2017,17(1):134-140.
[4]EBIHARA Y,NIITSU N,TERUI G.Fermentative production of tryptophan from indole by Hansenula anomala[J].Ferment Technol,1969,47(12):733-738.
[5]WAKASA K,ISHIHARA A.Metabolic engineering of the tryptophan and phenylalanine biosynthetic pathways in rice[J].Plant Biotechnology,2009,26(5):523-533.
[6]毛培宏,吕杰.离子束重组酵母菌Ar_Han0458的RAPD与SSH的初步研究[J].基因组学与应用生物学,2015,34(3):449-453.
[7]LU Jie,JIN Xiang,MAO Pei-hong,et al.Transfer of Ephedra genomic DNA to yeasts by ion implantation[J].Appl Biochem Biotechnol,2009,158(3):571~581
[8]WANG Z,GERSTEIN M,SNYDER M.RNA-Seq:A revolutionary tool for transcriptomics[J].Nature reviews genetics,2009,10(1):57.
[9]BURKE D,DAWSON D,STEARNS T.Methods in yeast genetics:A cold spring harbor laboratory course manual[M].New York:Cold Spring Harbor Lab Press,2000:171-172.
[10]SAHRAEIAN S M E,MOHIYUDDIN M,SEBRA R,et al.Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis[J].Nature communications,2017,8(1):59.
[11]KIM D,LANGMEAD B,SALZBERG S L.HISAT:A fast spliced aligner with low memory requirements[J].Nature methods,2015,12(4):357.
[12]ANDERS S,PYL P T,HUBER W.HTSeq-a Python framework to work with high-throughput sequencing data[J].Bioinformatics,2015,31(2):166-169.
[13]GTZ S,ARNOLD R,SEBASTIN-LEN P,et al.B2G-FAR,a species-centered GO annotation repository[J].Bioinformatics,2011,27(7):919-924.
[14]MORIYA Y,ITOH M,OKUDA S,et al.KAAS:An automatic genome annotation and pathway reconstruction server[J].Nucleic acids research,2007,35:W182-W185.
[15]LOVE M I,HUBER W,ANDERS S.Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J].Genome biology,2014,15(12):550.
[16]YOUNG M D,WAKEFIELD M J,SMYTH G K,et al.Gene ontology analysis for RNA-seq:Accounting for selection bias[J].Genome biology,2010,11(2):R14.
[17]MALDONADO E N,LEMASTERS J J.ATP/ADP ratio,the missed connection between mitochondria and the Warburg effect[J].Mitochondrion,2014,19:78-84.
[18]WEI San-hua,LIN Fang,WANG Xi,et al.Prognostic significance of stathmin expression in correlation with metastasis and clinicopathological characteristics in human ovarian carcinoma[J].Acta Histochemica,2008,110(1):59-65.
[19]BRANDO I D S L,OLIVEIRA-MORAES H M D S,SOUZA M C M D,et al.Elastin increases biofilm and extracellular matrix production of Aspergillus fumigatus[J].Brazilian Journal of Microbiology,2018,49(3):675-682.
[20]李玲阁,唐任天,傅妙福,等.色氨酸发酵的初步研究[J].微生物学报,1975,15(3):212-216.