Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1.
Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1.
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DOI：
10.1186/1471-2164-14-837
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发表时间：
2013-11-27
期刊：
影响因子：
4.4
通讯作者：
Skryabin KG
中科院分区：
文献类型：
--
作者：
Ravin NV;Eldarov MA;Kadnikov VV;Beletsky AV;Schneider J;Mardanova ES;Smekalova EM;Zvereva MI;Dontsova OA;Mardanov AV;Skryabin KG
多态汉逊酵母DL1是一种甲基营养酵母，广泛用于甲醇代谢、过氧化物酶的生物发生和功能的基础研究，也是生产重组蛋白和代谢工程的微生物细胞工厂，以实现高温乙醇生产的目标。我们已经测序了9 Mbp的多态H.Polya DL1基因组，并对从甲醇和葡萄糖生长的细胞中获得的H.Polya转录组进行了全基因组分析。RNA-seq分析揭示了在这两种研究条件下多态螺旋杆菌转录组的复杂和动态特征，在甲醇培养细胞中发现了40%的基因组的丰富和高度调控的表达，并揭示了不同的剪接事件。我们已经在H.Polyma中鉴定了具有亚端粒偏向的蛋白质家族，在七条H.Polya染色体的每条染色体中部的G+C贫乏染色体位点上都有LTR元件簇，并确定了H.Polyma DL1在一个独立的酵母分支中的进化地位，该分支与甲醇营养酵母Pichia Pasoris和非甲基营养酵母Dekkera Bruxellensis一起进化。基因组间的比较揭示了这三个酵母基因组之间广泛的基因顺序重新洗牌。系统发育分析使我们能够揭示酵母和丝状真菌中甲基营养的进化模式。我们的结果为深入了解多形杆菌生活史、生理和代谢以及甲醇营养酵母基因组进化的许多方面提供了新的机会，并可能导致多形杆菌DL-1作为微生物细胞工厂的应用的新改进。
Hansenula polymorpha DL1 is a methylotrophic yeast, widely used in fundamental studies of methanol metabolism, peroxisome biogenesis and function, and also as a microbial cell factory for production of recombinant proteins and metabolic engineering towards the goal of high temperature ethanol production. We have sequenced the 9 Mbp H. polymorpha DL1 genome and performed whole-genome analysis for the H. polymorpha transcriptome obtained from both methanol- and glucose-grown cells. RNA-seq analysis revealed the complex and dynamic character of the H. polymorpha transcriptome under the two studied conditions, identified abundant and highly unregulated expression of 40% of the genome in methanol grown cells, and revealed alternative splicing events. We have identified subtelomerically biased protein families in H. polymorpha, clusters of LTR elements at G + C-poor chromosomal loci in the middle of each of the seven H. polymorpha chromosomes, and established the evolutionary position of H. polymorpha DL1 within a separate yeast clade together with the methylotrophic yeast Pichia pastoris and the non-methylotrophic yeast Dekkera bruxellensis. Intergenome comparisons uncovered extensive gene order reshuffling between the three yeast genomes. Phylogenetic analyses enabled us to reveal patterns of evolution of methylotrophy in yeasts and filamentous fungi. Our results open new opportunities for in-depth understanding of many aspects of H. polymorpha life cycle, physiology and metabolism as well as genome evolution in methylotrophic yeasts and may lead to novel improvements toward the application of H. polymorpha DL-1 as a microbial cell factory.
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影响因子：
6
作者：
Bonekamp, Nina A.;Voelkl, Alfred;Schrader, Michael
通讯作者：
Schrader, Michael
DOI：
10.1073/pnas.0304170101
发表时间：
2004-02-10
影响因子：
11.1
作者：
Butler, G;Kenny, C;Wolfe, KH
通讯作者：
Wolfe, KH
影响因子：
3.5
作者：
GODECKE, S;ECKART, M;HOLLENBERG, CP
通讯作者：
HOLLENBERG, CP
使用orthomcl将蛋白质分配给Orthomcl-DB组或将蛋白质组群集分为新的直系同源组。
影响因子：
--
作者：
Fischer, Steve;Brunk, Brian P;Chen, Feng;Gao, Xin;Harb, Omar S;Iodice, John B;Shanmugam, Dhanasekaran;Roos, David S;Stoeckert, Christian J Jr
通讯作者：
Stoeckert, Christian J Jr
影响因子：
14.9
作者：
Besemer, J;Lomsadze, A;Borodovsky, M
通讯作者：
Borodovsky, M