Cargando…

Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus

Kluyveromyces marxianus is a promising host for producing bioethanol and heterologous proteins. It displays many superior traits to a conventional industrial yeast species, Saccharomyces cerevisiae, including fast growth, thermotolerance and the capacity to assimilate a wider variety of sugars. Howe...

Descripción completa

Detalles Bibliográficos
Autores principales: Yu, Yao, Mo, Wenjuan, Ren, Haiyan, Yang, Xianmei, Lu, Wanlin, Luo, Tongyu, Zeng, Junyuan, Zhou, Jungang, Qi, Ji, Lu, Hong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953160/
https://www.ncbi.nlm.nih.gov/pubmed/33717000
http://dx.doi.org/10.3389/fmicb.2021.598060
_version_ 1783663866381598720
author Yu, Yao
Mo, Wenjuan
Ren, Haiyan
Yang, Xianmei
Lu, Wanlin
Luo, Tongyu
Zeng, Junyuan
Zhou, Jungang
Qi, Ji
Lu, Hong
author_facet Yu, Yao
Mo, Wenjuan
Ren, Haiyan
Yang, Xianmei
Lu, Wanlin
Luo, Tongyu
Zeng, Junyuan
Zhou, Jungang
Qi, Ji
Lu, Hong
author_sort Yu, Yao
collection PubMed
description Kluyveromyces marxianus is a promising host for producing bioethanol and heterologous proteins. It displays many superior traits to a conventional industrial yeast species, Saccharomyces cerevisiae, including fast growth, thermotolerance and the capacity to assimilate a wider variety of sugars. However, little is known about the mechanisms underlying the fast-growing feature of K. marxianus. In this study, we performed a comparative genomic analysis between K. marxianus and other Saccharomycetaceae species. Genes involved in flocculation, iron transport, and biotin biosynthesis have particularly high copies in K. marxianus. In addition, 60 K. marxianus specific genes were identified, 45% of which were upregulated during cultivation in rich medium and these genes may participate in glucose transport and mitochondrion related functions. Furthermore, the transcriptomic analysis revealed that under aerobic condition, normalized levels of genes participating in TCA cycles, respiration chain and ATP biosynthesis in the lag phase were higher in K. marxianus than those in S. cerevisiae. Levels of highly copied genes, genes involved in the respiratory chain and mitochondrion assembly, were upregulated in K. marxianus, but not in S. cerevisiae, in later time points during cultivation compared with those in the lag phase. Notably, during the fast-growing phase, genes involved in the respiratory chain, ATP synthesis and glucose transport were co-upregulated in K. marxianus. A few shared motifs in upstream sequences of relevant genes might result in the co-upregulation. Specific features in the co-regulations of gene expressions might contribute to the fast-growing phenotype of K. marxianus. Our study underscores the importance of genome-wide rewiring of the transcriptional network during evolution.
format Online
Article
Text
id pubmed-7953160
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-79531602021-03-13 Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus Yu, Yao Mo, Wenjuan Ren, Haiyan Yang, Xianmei Lu, Wanlin Luo, Tongyu Zeng, Junyuan Zhou, Jungang Qi, Ji Lu, Hong Front Microbiol Microbiology Kluyveromyces marxianus is a promising host for producing bioethanol and heterologous proteins. It displays many superior traits to a conventional industrial yeast species, Saccharomyces cerevisiae, including fast growth, thermotolerance and the capacity to assimilate a wider variety of sugars. However, little is known about the mechanisms underlying the fast-growing feature of K. marxianus. In this study, we performed a comparative genomic analysis between K. marxianus and other Saccharomycetaceae species. Genes involved in flocculation, iron transport, and biotin biosynthesis have particularly high copies in K. marxianus. In addition, 60 K. marxianus specific genes were identified, 45% of which were upregulated during cultivation in rich medium and these genes may participate in glucose transport and mitochondrion related functions. Furthermore, the transcriptomic analysis revealed that under aerobic condition, normalized levels of genes participating in TCA cycles, respiration chain and ATP biosynthesis in the lag phase were higher in K. marxianus than those in S. cerevisiae. Levels of highly copied genes, genes involved in the respiratory chain and mitochondrion assembly, were upregulated in K. marxianus, but not in S. cerevisiae, in later time points during cultivation compared with those in the lag phase. Notably, during the fast-growing phase, genes involved in the respiratory chain, ATP synthesis and glucose transport were co-upregulated in K. marxianus. A few shared motifs in upstream sequences of relevant genes might result in the co-upregulation. Specific features in the co-regulations of gene expressions might contribute to the fast-growing phenotype of K. marxianus. Our study underscores the importance of genome-wide rewiring of the transcriptional network during evolution. Frontiers Media S.A. 2021-02-26 /pmc/articles/PMC7953160/ /pubmed/33717000 http://dx.doi.org/10.3389/fmicb.2021.598060 Text en Copyright © 2021 Yu, Mo, Ren, Yang, Lu, Luo, Zeng, Zhou, Qi and Lu. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Yu, Yao
Mo, Wenjuan
Ren, Haiyan
Yang, Xianmei
Lu, Wanlin
Luo, Tongyu
Zeng, Junyuan
Zhou, Jungang
Qi, Ji
Lu, Hong
Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus
title Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus
title_full Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus
title_fullStr Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus
title_full_unstemmed Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus
title_short Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus
title_sort comparative genomic and transcriptomic analysis reveals specific features of gene regulation in kluyveromyces marxianus
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953160/
https://www.ncbi.nlm.nih.gov/pubmed/33717000
http://dx.doi.org/10.3389/fmicb.2021.598060
work_keys_str_mv AT yuyao comparativegenomicandtranscriptomicanalysisrevealsspecificfeaturesofgeneregulationinkluyveromycesmarxianus
AT mowenjuan comparativegenomicandtranscriptomicanalysisrevealsspecificfeaturesofgeneregulationinkluyveromycesmarxianus
AT renhaiyan comparativegenomicandtranscriptomicanalysisrevealsspecificfeaturesofgeneregulationinkluyveromycesmarxianus
AT yangxianmei comparativegenomicandtranscriptomicanalysisrevealsspecificfeaturesofgeneregulationinkluyveromycesmarxianus
AT luwanlin comparativegenomicandtranscriptomicanalysisrevealsspecificfeaturesofgeneregulationinkluyveromycesmarxianus
AT luotongyu comparativegenomicandtranscriptomicanalysisrevealsspecificfeaturesofgeneregulationinkluyveromycesmarxianus
AT zengjunyuan comparativegenomicandtranscriptomicanalysisrevealsspecificfeaturesofgeneregulationinkluyveromycesmarxianus
AT zhoujungang comparativegenomicandtranscriptomicanalysisrevealsspecificfeaturesofgeneregulationinkluyveromycesmarxianus
AT qiji comparativegenomicandtranscriptomicanalysisrevealsspecificfeaturesofgeneregulationinkluyveromycesmarxianus
AT luhong comparativegenomicandtranscriptomicanalysisrevealsspecificfeaturesofgeneregulationinkluyveromycesmarxianus