1
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Affiliation(s)
- John K. Henske
- Dept. of Chemical Engineering University of California Santa Barbara CA, 93106
| | - Sean P. Gilmore
- Dept. of Chemical Engineering University of California Santa Barbara CA, 93106
| | - Charles H. Haitjema
- Dept. of Chemical Engineering University of California Santa Barbara CA, 93106
| | - Kevin V. Solomon
- Dept. of Chemical Engineering University of California Santa Barbara CA, 93106
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2
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Haitjema CH, Gilmore SP, Henske JK, Solomon KV, de Groot R, Kuo A, Mondo SJ, Salamov AA, LaButti K, Zhao Z, Chiniquy J, Barry K, Brewer HM, Purvine SO, Wright AT, Hainaut M, Boxma B, van Alen T, Hackstein JHP, Henrissat B, Baker SE, Grigoriev IV, O'Malley MA. A parts list for fungal cellulosomes revealed by comparative genomics. Nat Microbiol 2017; 2:17087. [PMID: 28555641 DOI: 10.1038/nmicrobiol.2017.87] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 04/25/2017] [Indexed: 12/16/2022]
Abstract
Cellulosomes are large, multiprotein complexes that tether plant biomass-degrading enzymes together for improved hydrolysis1. These complexes were first described in anaerobic bacteria, where species-specific dockerin domains mediate the assembly of enzymes onto cohesin motifs interspersed within protein scaffolds1. The versatile protein assembly mechanism conferred by the bacterial cohesin-dockerin interaction is now a standard design principle for synthetic biology2,3. For decades, analogous structures have been reported in anaerobic fungi, which are known to assemble by sequence-divergent non-catalytic dockerin domains (NCDDs)4. However, the components, modular assembly mechanism and functional role of fungal cellulosomes remain unknown5,6. Here, we describe a comprehensive set of proteins critical to fungal cellulosome assembly, including conserved scaffolding proteins unique to the Neocallimastigomycota. High-quality genomes of the anaerobic fungi Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis were assembled with long-read, single-molecule technology. Genomic analysis coupled with proteomic validation revealed an average of 312 NCDD-containing proteins per fungal strain, which were overwhelmingly carbohydrate active enzymes (CAZymes), with 95 large fungal scaffoldins identified across four genera that bind to NCDDs. Fungal dockerin and scaffoldin domains have no similarity to their bacterial counterparts, yet several catalytic domains originated via horizontal gene transfer with gut bacteria. However, the biocatalytic activity of anaerobic fungal cellulosomes is expanded by the inclusion of GH3, GH6 and GH45 enzymes. These findings suggest that the fungal cellulosome is an evolutionarily chimaeric structure-an independently evolved fungal complex that co-opted useful activities from bacterial neighbours within the gut microbiome.
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Affiliation(s)
- Charles H Haitjema
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Sean P Gilmore
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - John K Henske
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Kevin V Solomon
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Randall de Groot
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Asaf A Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Zhiying Zhao
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Jennifer Chiniquy
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Heather M Brewer
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Aaron T Wright
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288 Marseille, France.,INRA, USC 1408 AFMB, Marseille, France
| | - Brigitte Boxma
- Department of Evolutionary Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Theo van Alen
- Department of Evolutionary Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Johannes H P Hackstein
- Department of Evolutionary Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288 Marseille, France.,INRA, USC 1408 AFMB, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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3
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Natarajan A, Haitjema CH, Lee R, Boock JT, DeLisa MP. An Engineered Survival-Selection Assay for Extracellular Protein Expression Uncovers Hypersecretory Phenotypes in Escherichia coli. ACS Synth Biol 2017; 6:875-883. [PMID: 28182400 DOI: 10.1021/acssynbio.6b00366] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The extracellular expression of recombinant proteins using laboratory strains of Escherichia coli is now routinely achieved using naturally secreted substrates, such as YebF or the osmotically inducible protein Y (OsmY), as carrier molecules. However, secretion efficiency through these pathways needs to be improved for most synthetic biology and metabolic engineering applications. To address this challenge, we developed a generalizable survival-based selection strategy that effectively couples extracellular protein secretion to antibiotic resistance and enables facile isolation of rare mutants from very large populations (i.e., 1010-12 clones) based simply on cell growth. Using this strategy in the context of the YebF pathway, a comprehensive library of E. coli single-gene knockout mutants was screened and several gain-of-function mutations were isolated that increased the efficiency of extracellular expression without compromising the integrity of the outer membrane. We anticipate that this user-friendly strategy could be leveraged to better understand the YebF pathway and other secretory mechanisms-enabling the exploration of protein secretion in pathogenesis as well as the creation of designer E. coli strains with greatly expanded secretomes-all without the need for expensive exogenous reagents, assay instruments, or robotic automation.
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Affiliation(s)
- Aravind Natarajan
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Charles H. Haitjema
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Robert Lee
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jason T. Boock
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Matthew P. DeLisa
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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4
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Solomon KV, Haitjema CH, Henske JK, Gilmore SP, Borges-Rivera D, Lipzen A, Brewer HM, Purvine SO, Wright AT, Theodorou MK, Grigoriev IV, Regev A, Thompson DA, O'Malley MA. Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes. Science 2016; 351:1192-5. [PMID: 26912365 DOI: 10.1126/science.aad1431] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/09/2016] [Indexed: 01/22/2023]
Abstract
The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. We developed a systems-level approach that integrates transcriptomic sequencing, proteomics, phenotype, and biochemical studies of relatively unexplored basal fungi. Anaerobic gut fungi isolated from herbivores produce a large array of biomass-degrading enzymes that synergistically degrade crude, untreated plant biomass and are competitive with optimized commercial preparations from Aspergillus and Trichoderma. Compared to these model platforms, gut fungal enzymes are unbiased in substrate preference due to a wealth of xylan-degrading enzymes. These enzymes are universally catabolite-repressed and are further regulated by a rich landscape of noncoding regulatory RNAs. Additionally, we identified several promising sequence-divergent enzyme candidates for lignocellulosic bioprocessing.
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Affiliation(s)
- Kevin V Solomon
- Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA
| | - Charles H Haitjema
- Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA
| | - John K Henske
- Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA
| | - Sean P Gilmore
- Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA
| | | | - Anna Lipzen
- U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Heather M Brewer
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Samuel O Purvine
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Aaron T Wright
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Michael K Theodorou
- Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, Shropshire TF10 8NB, UK
| | - Igor V Grigoriev
- U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA
| | - Dawn A Thompson
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA.
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5
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Haitjema CH, Solomon KV, Henske JK, Theodorou MK, O'Malley MA. Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production. Biotechnol Bioeng 2014; 111:1471-82. [PMID: 24788404 DOI: 10.1002/bit.25264] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 12/12/2022]
Abstract
Anaerobic gut fungi are an early branching family of fungi that are commonly found in the digestive tract of ruminants and monogastric herbivores. It is becoming increasingly clear that they are the primary colonizers of ingested plant biomass, and that they significantly contribute to the decomposition of plant biomass into fermentable sugars. As such, anaerobic fungi harbor a rich reservoir of undiscovered cellulolytic enzymes and enzyme complexes that can potentially transform the conversion of lignocellulose into bioenergy products. Despite their unique evolutionary history and cellulolytic activity, few species have been isolated and studied in great detail. As a result, their life cycle, cellular physiology, genetics, and cellulolytic metabolism remain poorly understood compared to aerobic fungi. To help address this limitation, this review briefly summarizes the current body of knowledge pertaining to anaerobic fungal biology, and describes progress made in the isolation, cultivation, molecular characterization, and long-term preservation of these microbes. We also discuss recent cellulase- and cellulosome-discovery efforts from gut fungi, and how these interesting, non-model microbes could be further adapted for biotechnology applications.
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Affiliation(s)
- Charles H Haitjema
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106
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Haitjema CH, Boock JT, Natarajan A, Dominguez MA, Gardner JG, Keating DH, Withers ST, DeLisa MP. Universal genetic assay for engineering extracellular protein expression. ACS Synth Biol 2014; 3:74-82. [PMID: 24200127 DOI: 10.1021/sb400142b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A variety of strategies now exist for the extracellular expression of recombinant proteins using laboratory strains of Escherichia coli . However, secreted proteins often accumulate in the culture medium at levels that are too low to be practically useful for most synthetic biology and metabolic engineering applications. The situation is compounded by the lack of generalized screening tools for optimizing the secretion process. To address this challenge, we developed a genetic approach for studying and engineering protein-secretion pathways in E. coli . Using the YebF pathway as a model, we demonstrate that direct fluorescent labeling of tetracysteine-motif-tagged secretory proteins with the biarsenical compound FlAsH is possible in situ without the need to recover the cell-free supernatant. High-throughput screening of a bacterial strain library yielded superior YebF expression hosts capable of secreting higher titers of YebF and YebF-fusion proteins into the culture medium. We also show that the method can be easily extended to other secretory pathways, including type II and type III secretion, directly in E. coli . Thus, our FlAsH-tetracysteine-based genetic assay provides a convenient, high-throughput tool that can be applied generally to diverse secretory pathways. This platform should help to shed light on poorly understood aspects of these processes as well as to further assist in the construction of engineered E. coli strains for efficient secretory-protein production.
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Affiliation(s)
- Charles H. Haitjema
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Jason T. Boock
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Aravind Natarajan
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Miguel A. Dominguez
- Great
Lakes Bioenergy Research Center, Madison, Wisconsin 53706, United States
| | - Jeffrey G. Gardner
- Great
Lakes Bioenergy Research Center, Madison, Wisconsin 53706, United States
| | - David H. Keating
- Great
Lakes Bioenergy Research Center, Madison, Wisconsin 53706, United States
| | - Sydnor T. Withers
- Great
Lakes Bioenergy Research Center, Madison, Wisconsin 53706, United States
| | - Matthew P. DeLisa
- Department
of Microbiology, Cornell University, Ithaca, New York 14853, United States
- School
of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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