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Gene function, metabolic pathways and comparative genomics in yeast

Q. Dong, Rama Balakrishnan, G. Binkley, K.R. Christie, M. Costanzo, K. Dolinski, S.S. Dwight, S. Engel, D.G. Fisk, J. Hirschman, E.L. Hong, R. Nash (+6 others)
Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003  
A second area of focus is on metabolic pathways. A new dataset of hand-curated information on metabolic pathways within budding yeast was released in May 2003.  ...  This resource also maps data from genome-wide expression analyses onto the pathway overview providing a visualization of the changes in gene expression in the context of cellular metabolism.  ...  The Pathways Tools facilitates the retrieval and visualization of biochemical pathways and genomic annotations based on information in a Pathway/Genome Database.  ... 
doi:10.1109/csb.2003.1227362 dblp:conf/csb/DongBBCCDDEFHHNISTWBC03 fatcat:vlw36rwb5bbivfmdbtp77ljfvy

The evolution of the GALactose utilization pathway in budding yeasts [article]

Marie-Claire Harrison, Abigail L. LaBella, Chris Todd Hittinger, Antonis Rokas
2021 arXiv   pre-print
More recently, the physical linkage of the structural genes GAL1, GAL7, and GAL10 in diverse budding yeast genomes has been used as a model for understanding the evolution of gene clustering.  ...  The Leloir galactose utilization or GAL pathway of budding yeasts, including that of the baker's yeast Saccharomyces cerevisiae and the opportunistic human pathogen Candida albicans, breaks down the sugar  ...  Recent studies have begun to identify similar types of adaptations in other budding yeast metabolic genes and pathways.  ... 
arXiv:2107.06823v1 fatcat:oh6lyhe53bfunf4bwe6whru4ce

Genomic and transcriptome analyses reveal that MAPK- and phosphatidylinositol-signaling pathways mediate tolerance to 5-hydroxymethyl-2-furaldehyde for industrial yeast Saccharomyces cerevisiae

Qian Zhou, Z. Lewis Liu, Kang Ning, Anhui Wang, Xiaowei Zeng, Jian Xu
2014 Scientific Reports  
Higher levels of sequence variations were also observed for genes involved in purine and pyrimidine metabolism pathways.  ...  Compared with the genome of laboratory model strain S288C, we identified more than 32,000 SNPs in Y-12632 with 23,000 missense and nonsense SNPs.  ...  , particularly in purine metabolism and pyrimidine metabolism pathways, each had 35 and 23 SNPs, respectively.  ... 
doi:10.1038/srep06556 pmid:25296911 pmcid:PMC4190571 fatcat:6eh3bqe6fzfvbg7hd2aa7s2kz4

Pathway swapping: Toward modular engineering of essential cellular processes

Niels G. A. Kuijpers, Daniel Solis-Escalante, Marijke A. H. Luttik, Markus M. M. Bisschops, Francine J. Boonekamp, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran, Pascale Daran-Lapujade
2016 Proceedings of the National Academy of Sciences of the United States of America  
Enzymes of central metabolism are encoded by hundreds of genes that, especially in eukaryotes, are scattered across microbial genomes.  ...  Recent developments in synthetic biology enable introduction of entire metabolic pathways and, thereby, new functionalities for product formation and substrate consumption, into microbial cells (1).  ...  Eladio Barrio for kindly providing S. kudriavzevii CR85 and for advice on selecting the genes to design S. kudriavzevii minimal glycolysis.  ... 
doi:10.1073/pnas.1606701113 pmid:27956602 pmcid:PMC5206561 fatcat:wfzdbrwpj5hxdc4rtttx5tf7uq

YeastWeb: a workset-centric web resource for gene family analysis in yeast

Yanhui Chu, Xiaohuan Yuan, Yanqin Guo, Yufei Zhang, Yan Wu, Haifeng Liu, Dan Wu, Haihua Bao, Lixin Guan, Xiudong Jin
2010 BMC Genomics  
/pathway databases, such as GO, COG and KEGG; 2) A well established userfriendly environment was created to allow users to retrieve the annotated genes and gene families using functional classification  ...  , structure and function of gene families.  ...  Acknowledgements This work was supported by funds from National Natural Science Foundation of China (30971086 and 30973897) and Heilongjiang Provincial Natural Science Foundation (D2007-99).  ... 
doi:10.1186/1471-2164-11-429 pmid:20624324 pmcid:PMC2996957 fatcat:qfb65yo6czgctaxsmb3bkny7cu

Genomic and transcriptomic analyses of the Chinese Maotai-flavored liquor yeast MT1 revealed its unique multi-carbon co-utilization

Xiaowei Lu, Qun Wu, Yan Zhang, Yan Xu
2015 BMC Genomics  
Genomic comparisons identified a distinct MT1 genome, 0.5 Mb smaller than that of S288c. There are 145 MT1-specific genes that are not in S288c, including MEL1, MAL63, KHR1, BIO1 and BIO6.  ...  Conclusions: Based on a functional genomics analysis, we revealed the genetic basis and evolutionary mechanisms underlying the traits of the Chinese Maotai-flavored yeast MT1.  ...  Nucleotide metabolism, translation, and cell growth and death were the responsive pathways that had a large number of down-regulated genes compared with in S288c (Table 2) .  ... 
doi:10.1186/s12864-015-2263-0 pmid:26666414 pmcid:PMC4678718 fatcat:xmac3bl43reatmfmbwdaoogp3i

Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1

Nikolai V Ravin, Michael A Eldarov, Vitaly V Kadnikov, Alexey V Beletsky, Jessica Schneider, Eugenia S Mardanova, Elena M Smekalova, Maria I Zvereva, Olga A Dontsova, Andrey V Mardanov, Konstantin G Skryabin
2013 BMC Genomics  
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  ...  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  ...  Jochen Blom from Bielefeld University for providing the access to the RAPYD, GenDB and EDGAR tools used in the course of functional gene annotation and comparative genomic analysis.  ... 
doi:10.1186/1471-2164-14-837 pmid:24279325 pmcid:PMC3866509 fatcat:6sozcv4dqffr3ixcl2mzciy26a

Conservation of gene co-regulation in prokaryotes and eukaryotes

Sarah A Teichmann, M.Madan Babu
2002 Trends in Biotechnology  
It has been shown previously that such genes have a strong tendency to belong to the same protein complex in prokaryotes, and we show by an analysis of the sequences and their expression in the yeast Saccharomyces  ...  If genes are consistently co-regulated across distantly related organisms, the genes have closely associated functions.  ...  Acknowledgements We are grateful to Martin Madera, Cyrus Chothia and Graeme Mitchison for comments on the manuscript.  ... 
doi:10.1016/s0167-7799(02)02032-2 pmid:12220896 fatcat:qkyppp4vnzbx5dljzpepik4iei

Comparative genomics of biotechnologically important yeasts

Robert Riley, Sajeet Haridas, Kenneth H. Wolfe, Mariana R. Lopes, Chris Todd Hittinger, Markus Göker, Asaf A. Salamov, Jennifer H. Wisecaver, Tanya M. Long, Christopher H. Calvey, Andrea L. Aerts, Kerrie W. Barry (+27 others)
2016 Proceedings of the National Academy of Sciences of the United States of America  
Gene clusters, with variable organization and distribution, encode many pathways of interest.  ...  We compared 29 yeast genomes with the goal of correlating genetics to useful traits.  ...  Kyoto Encyclopedia of Genes and Genomes pathways.  ... 
doi:10.1073/pnas.1603941113 pmid:27535936 pmcid:PMC5024638 fatcat:a7fte6ohoncbfjiqtbottcemim

Fifteen years of large scale metabolic modeling of yeast: Developments and impacts

Tobias Österlund, Intawat Nookaew, Jens Nielsen
2012 Biotechnology Advances  
different yeast genome-scale metabolic models.  ...  Here we review the historical development of large-scale mathematical modeling of yeast metabolism and the growing scope and impact of applications of these models in four different areas: as guide for  ...  Acknowledgment We acknowledge funding from the EU financed project SYSINBIO (contract no. 212766), European Research Council (project INSYSBIO), Chalmers Foundation and Knut and Alice Wallenberg Foundation  ... 
doi:10.1016/j.biotechadv.2011.07.021 pmid:21846501 fatcat:be5dsmdwqzahtobl3wabb7nurm

Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts

D. Sherman
2006 Nucleic Acids Research  
Consortium, to facilitate comparative genomic studies of hemiascomycetous yeasts.  ...  With their relatively small and compact genomes, yeasts offer a unique opportunity for exploring eukaryotic genome evolution.  ...  How are metabolic pathways conserved?  ... 
doi:10.1093/nar/gkj160 pmid:16381905 pmcid:PMC1347522 fatcat:uekt2trh4ffohmqmd62ygy5pju

From Endosymbiont to Host-Controlled Organelle: the Hijacking of Mitochondrial Protein Synthesis and Metabolism

Toni Gabaldón, Martijn A. Huynen
2005 PLoS Computational Biology  
More than half of what remains from the mitochondrial ancestor in modern mitochondria corresponds to translation, including post-translational modifications, and to metabolic pathways that are directly  ...  of the mitochondrion with the proteomes of alpha-proteobacteria as well as with the mitochondrial proteomes in yeast and man.  ...  TG and MAH conceived and designed the experiments and wrote the paper. TG performed the experiments and analyzed the data. Funding.  ... 
doi:10.1371/journal.pcbi.0030219.eor fatcat:kgdjaav57fairjb2ol2zzeolqa

From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism

Toni Gabaldón, Martijn A. Huynen
2007 PLoS Computational Biology  
More than half of what remains from the mitochondrial ancestor in modern mitochondria corresponds to translation, including post-translational modifications, and to metabolic pathways that are directly  ...  of the mitochondrion with the proteomes of alpha-proteobacteria as well as with the mitochondrial proteomes in yeast and man.  ...  TG and MAH conceived and designed the experiments and wrote the paper. TG performed the experiments and analyzed the data. Funding.  ... 
doi:10.1371/journal.pcbi.0030219 pmid:17983265 pmcid:PMC2062474 fatcat:vilewpte6nc5ne2r4rs6cczsfm

CYGD: the Comprehensive Yeast Genome Database

U. Guldener
2004 Nucleic Acids Research  
These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters.  ...  The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the  ...  (MNCDB) and the Government of the Brussels Region, Belgium, for the aMAZE project.  ... 
doi:10.1093/nar/gki053 pmid:15608217 pmcid:PMC540007 fatcat:nxst4ximuzau7gbukjpntb6d7u

Differential selection on gene translation efficiency between the filamentous fungus Ashbya gossypii and yeasts

Huifeng Jiang, Yue Zhang, Jun Sun, Wen Wang, Zhenglong Gu
2008 BMC Evolutionary Biology  
Functional enrichment and pathway analysis show that Group I genes are significantly enriched with cell cycle functions whereas Group II genes are biased toward metabolic functions.  ...  Codon usage patterns were compared to identify orthologous genes with different gene regulation between A. gossypii and nine closely related yeast species.  ...  This work was supported by a NSFC key grant (No. 30430400) and a 973 Program of China (No. 2007CB815703-5) to WW and startup funds from Cornell University awarded to ZG.  ... 
doi:10.1186/1471-2148-8-343 pmid:19111070 pmcid:PMC2632675 fatcat:afiwfqffczf73ony6ofxylb4nq
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