A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains

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

doi:10.1128/spectrum.02536-23

A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains

Microbiol Spectr. 2024 Jan 11;12(1):e0253623. doi: 10.1128/spectrum.02536-23. Epub 2023 Nov 29.

Authors

Veronika Dubinkina^#^{1

2

3}, Shounak Bhogale^#⁴, Ping-Hung Hsieh^#^{5

6}, Payam Dibaeinia^{1

7}, Ananthan Nambiar^{1

2}, Sergei Maslov^{1

2

8}, Yasuo Yoshikuni^{5

6

9

10

11

12}, Saurabh Sinha^{1

4

7

13

14

15}

Affiliations

¹ Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign , Urbana, Illinois, USA.
² Department of Bioengineering, University of Illinois Urbana-Champaign , Urbana, Illinois, USA.
³ The Gladstone Institute of Data Science and Biotechnology , San Francisco, California, USA.
⁴ Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign , Urbana, Illinois, USA.
⁵ Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory , Berkeley, California, USA.
⁶ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory , Berkeley, California, USA.
⁷ Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, Illinois, USA.
⁸ Department of Physics, University of Illinois Urbana-Champaign , Urbana, Illinois, USA.
⁹ US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, California, USA.
¹⁰ Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley, California, USA.
¹¹ Global Institution for Collaborative Research and Education, Hokkaido University , Hokkaido, Japan.
¹² Institute of Global Innovation Research, Tokyo University of Agriculture and Technology , Tokyo, Japan.
¹³ Cancer Center at Illinois, University of Illinois Urbana-Champaign , Urbana, Illinois, USA.
¹⁴ Department of Biomedical Engineering at Georgia Tech and Emory University , Atlanta, Georgia, USA.
¹⁵ Department of Industrial and Systems Engineering, Georgia Institute of Technology , Atlanta, Georgia, USA.

^# Contributed equally.

Abstract

Issatchenkia orientalis is a promising industrial chassis to produce biofuels and bioproducts due to its high tolerance to multiple environmental stresses such as low pH, heat, and other chemicals otherwise toxic for the most widely used microbes. Yet, little is known about specific mechanisms of such tolerance in this organism, hindering our ability to engineer this species to produce valuable biochemicals. Here, we report a comprehensive study of the mechanisms of acidic tolerance in this species via transcriptome profiling across variable pH for 12 different strains with different phenotypes. We found multiple regulatory mechanisms involved in tolerance to low pH in different strains of I. orientalis, marking potential targets for future gene editing and perturbation experiments.

Keywords: Issatchenkia orientalis; acidic stress; gene regulation; low pH.

MeSH terms

Gene Expression Profiling
Hydrogen-Ion Concentration
Pichia*
Transcriptome*

Supplementary concepts

Pichia kudriavzevii

Grants and funding

R35 GM131819/GM/NIGMS NIH HHS/United States