title: Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters.
abstract: BACKGROUND
  Engineered cell factories that convert biomass into value-added compounds are emerging as a timely alternative to petroleum-based industries. Although often overlooked, integral membrane proteins such as solute transporters are pivotal for engineering efficient microbial chassis. Anaerobic gut fungi, adapted to degrade raw plant biomass in the intestines of herbivores, are a potential source of valuable transporters for biotechnology, yet very little is known about the membrane constituents of these non-conventional organisms. Here, we mined the transcriptome of three recently isolated strains of anaerobic fungi to identify membrane proteins responsible for sensing and transporting biomass hydrolysates within a competitive and rather extreme environment.
  
  
  RESULTS
  Using sequence analyses and homology, we identified membrane protein-coding sequences from assembled transcriptomes from three strains of anaerobic gut fungi: Neocallimastix californiae, Anaeromyces robustus, and Piromyces finnis. We identified nearly 2000 transporter components: about half of these are involved in the general secretory pathway and intracellular sorting of proteins; the rest are predicted to be small-solute transporters. Unexpectedly, we found a number of putative sugar binding proteins that are associated with prokaryotic uptake systems; and approximately 100 class C G-protein coupled receptors (GPCRs) with non-canonical putative sugar binding domains.
  
  
  CONCLUSIONS
  We report the first comprehensive characterization of the membrane protein machinery of biotechnologically relevant anaerobic gut fungi. Apart from identifying conserved machinery for protein sorting and secretion, we identify a large number of putative solute transporters that are of interest for biotechnological applications. Notably, our data suggests that the fungi display a plethora of carbohydrate binding domains at their surface, perhaps as a means to sense and sequester some of the sugars that their biomass degrading, extracellular enzymes produce.
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800, Kgs. Lyngby, Denmark.|Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.
authors.forename: Susanna
authors.initials: S
authors.lastname: Seppälä
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.|Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA.
authors.forename: Kevin V
authors.initials: KV
authors.lastname: Solomon
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.
authors.forename: Sean P
authors.initials: SP
authors.lastname: Gilmore
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.
authors.forename: John K
authors.initials: JK
authors.lastname: Henske
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA. momalley@engineering.ucsb.edu.
authors.forename: Michelle A
authors.initials: MA
authors.lastname: O'Malley
mesh_terms: D000693:Anaerobiosis; D000818:Animals; D002241:Carbohydrates; D005243:Feces / Q000382:microbiology; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D005658:Fungi / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods; D006041:Goats; D006736:Horses; D007422:Intestines / Q000382:microbiology*; D008031:Lignin / Q000378:metabolism; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism*; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism; D020085:Neocallimastigales / Q000235:genetics / Q000378:metabolism; D020089:Piromyces / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D020543:Proteome / Q000235:genetics / Q000378:metabolism*; D012756:Sheep; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics
chemical_list: D002241:Carbohydrates; D005656:Fungal Proteins; D008565:Membrane Proteins; D026901:Membrane Transport Proteins; D020543:Proteome; C036909:lignocellulose; D008031:Lignin
keywords: Anaerobic fungi; Carbohydrate binding proteins; Lignocellulose; Membrane proteins; Microbial engineering