title: RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH.
abstract: BACKGROUND
  The product yield and titers of biological processes involving the conversion of biomass to desirable chemicals can be limited by environmental stresses encountered by the microbial hosts used for the bioconversion. One of these main stresses is growth inhibition due to exposure to low pH conditions. In order to circumvent this problem, understanding the biological mechanisms involved in acid stress response and tolerance is essential. Characterisation of wild yeasts that have a natural ability to resist such harsh conditions will pave the way to understand the biological basis underlying acid stress resistance. Pichia anomala possesses a unique ability to adapt to and tolerate a number of environmental stresses particularly low pH stress giving it the advantage to outcompete other microorganisms under such conditions. However, the genetic basis of this resistance has not been previously studied.
  
  
  RESULTS
  To this end, we isolated an acid resistant strain of P. anomala, performed a gross phenotypic characterisation at low pH and also performed a whole genome and total RNA sequencing. By integrating the RNA-seq data with the genome sequencing data, we found that several genes associated with different biological processes including proton efflux, the electron transfer chain and oxidative phosphorylation were highly expressed in P. anomala cells grown in low pH media. We therefore present data supporting the notion that a high expression of proton pumps in the plasma membrane coupled with an increase in mitochondrial ATP production enables the high level of acid stress tolerance of P. anomala.
  
  
  CONCLUSIONS
  Our findings provide insight into the molecular and genetic basis of low pH tolerance in P. anomala which was previously unknown. Ultimately, this is a step towards developing non-conventional yeasts such as P. anomala for the production of industrially relevant chemicals under low pH conditions.
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden. eugenef@chalmers.se.|Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden. eugenef@chalmers.se.
authors.forename: Eugene
authors.initials: E
authors.lastname: Fletcher
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden. feizi@chalmers.se.|Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden. feizi@chalmers.se.
authors.forename: Amir
authors.initials: A
authors.lastname: Feizi
authors.affiliation: Samsung Advanced Institute of Technology, 130 Samsung-Ro YoungTong-Ku, Suwon, Kyunggi-do, South Korea. sskim227@gmail.com.|Biotech Research Team, Dongbu Farm Hannong Co., Ltd., Daejeon, 305-708, Republic of Korea. sskim227@gmail.com.
authors.forename: SungSoo
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden. siewers@chalmers.se.|Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden. siewers@chalmers.se.
authors.forename: Verena
authors.initials: V
authors.lastname: Siewers
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden. nielsenj@chalmers.se.|Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden. nielsenj@chalmers.se.|Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark. nielsenj@chalmers.se.
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D018533:Biomass; D004579:Electron Transport; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016681:Genome, Fungal; D006863:Hydrogen-Ion Concentration; D008928:Mitochondria / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010085:Oxidative Phosphorylation; D010843:Pichia / Q000235:genetics* / Q000502:physiology; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome
chemical_list: D005656:Fungal Proteins; D000255:Adenosine Triphosphate