Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains

Dubinkina, Veronika; Bhogale, Shounak; Hsieh, Ping-Hung; Dibaeinia, Payam; Nambiar, Ananthan; Maslov, Sergei; Yoshikuni, Yasuo; Sinha, Saurabh

doi:10.13012/B2IDB-1336177_V1

Title: Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains

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Abstract

Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae. Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, tomore »« less

Authors:

; Bhogale, Shounak; Hsieh, Ping-Hung;

; Nambiar, Ananthan;

;

; Sinha, Saurabh

Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; The Gladstone Institute of Data Science and Biotechnology, San Francisco, California, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)
Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)
Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, California, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)
Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)
Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, California, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, Japan; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Biomedical Engineering at Georgia Tech and Emory University, Atlanta, Georgia, USA; Department of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)

Publication Date:: Wed Nov 29 00:00:00 UTC 2023

DOE Contract Number:: SC0018420

Research Org.:: Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States); University of Illinois Urbana-Champaign

Sponsoring Org.:: U.S. Department of Energy (DOE)

Subject:: Conversion; Transcriptomics

OSTI Identifier:: 3014696

DOI:: https://doi.org/10.13012/B2IDB-1336177_V1

Citation Formats


                    Dubinkina, Veronika, Bhogale, Shounak, Hsieh, Ping-Hung, Dibaeinia, Payam, Nambiar, Ananthan, Maslov, Sergei, Yoshikuni, Yasuo, and Sinha, Saurabh. Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains.  United States: N. p., 2023. 
        Web.  doi:10.13012/B2IDB-1336177_V1.

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                    Dubinkina, Veronika, Bhogale, Shounak, Hsieh, Ping-Hung, Dibaeinia, Payam, Nambiar, Ananthan, Maslov, Sergei, Yoshikuni, Yasuo, & Sinha, Saurabh. Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains.  United States.  doi:https://doi.org/10.13012/B2IDB-1336177_V1

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                    Dubinkina, Veronika, Bhogale, Shounak, Hsieh, Ping-Hung, Dibaeinia, Payam, Nambiar, Ananthan, Maslov, Sergei, Yoshikuni, Yasuo, and Sinha, Saurabh. 2023.  
"Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains".  United States.  doi:https://doi.org/10.13012/B2IDB-1336177_V1.  https://www.osti.gov/servlets/purl/3014696. Pub date:Wed Nov 29 00:00:00 UTC 2023

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@article{osti_3014696,

  title        = {Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains},

  author       = {Dubinkina, Veronika and Bhogale, Shounak and Hsieh, Ping-Hung and Dibaeinia, Payam and Nambiar, Ananthan and Maslov, Sergei and Yoshikuni, Yasuo and Sinha, Saurabh},

  abstractNote = {Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae. Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.},

  doi          = {10.13012/B2IDB-1336177_V1},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Wed Nov 29 00:00:00 UTC 2023},

  month        = {Wed Nov 29 00:00:00 UTC 2023}

}

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DOI: https://doi.org/10.13012/B2IDB-1336177_V1

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