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Title: Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters

Abstract

Here, 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. 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. In conclusion, we report the first comprehensive characterizationmore » 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.« less

Authors:
 [1];  [2];  [3];  [3];  [3]
  1. Technical Univ. of Denmark, Lyngby (Denmark); Univ. of California, Santa Barbara, CA (United States)
  2. Univ. of California, Santa Barbara, CA (United States); Purdue Univ., West Lafayette, IN (United States)
  3. Univ. of California, Santa Barbara, CA (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Univ. of California, Santa Barbara, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1373288
Alternate Identifier(s):
OSTI ID: 1485166
Grant/Contract Number:  
SC0010352; MCB-1553721; W911NF-09-0001; VKR023128
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Microbial Cell Factories
Additional Journal Information:
Journal Volume: 15; Journal Issue: 1; Journal ID: ISSN 1475-2859
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; microbial engineering; membrane proteins; anaerobic fungi; carbohydrate binding proteins; lignocellulose

Citation Formats

Seppala, Susanna, Solomon, Kevin V., Gilmore, Sean P., Henske, John K., and O’Malley, Michelle A. Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters. United States: N. p., 2016. Web. doi:10.1186/s12934-016-0611-7.
Seppala, Susanna, Solomon, Kevin V., Gilmore, Sean P., Henske, John K., & O’Malley, Michelle A. Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters. United States. doi:10.1186/s12934-016-0611-7.
Seppala, Susanna, Solomon, Kevin V., Gilmore, Sean P., Henske, John K., and O’Malley, Michelle A. Tue . "Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters". United States. doi:10.1186/s12934-016-0611-7. https://www.osti.gov/servlets/purl/1373288.
@article{osti_1373288,
title = {Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters},
author = {Seppala, Susanna and Solomon, Kevin V. and Gilmore, Sean P. and Henske, John K. and O’Malley, Michelle A.},
abstractNote = {Here, 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. 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. In conclusion, 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.},
doi = {10.1186/s12934-016-0611-7},
journal = {Microbial Cell Factories},
issn = {1475-2859},
number = 1,
volume = 15,
place = {United States},
year = {2016},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 3 works
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Figures / Tables:

Fig. 1 Fig. 1: Integral membrane proteins are identified from gut fungal transcriptomes using bioinformatics filtering. a Displays a quantitative ‘funneling process’, where the total transcriptome is reduced to the membrane protein component by filtering the predicted soluble proteins, antisense transcripts, and extracellularly secreted proteins. b Demonstrates the pipeline used for proteinmore » annotation. All possible ORFs are extracted from the assembled transcripts, and protein annotations, gene ontology (GO) terms, and enzyme commission (EC) numbers are obtained by aligning the ORFs to the NCBI database (E ≤10−3) with BLASTx and comparing the ORFs to the EMBL database with the InterProScan tool. InterProScan utilizes SignalP and TMHMM to predict ER targeting signal peptides and transmembrane domains. Finally, the ORFs are aligned to the TCDB database to identify possible transporters and predict transporter substrates« less

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      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.