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Gardner JG. Microbe Profile: Cellvibrio japonicus: living the sweet life via biomass break-down. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001450. [PMID: 38568197 PMCID: PMC11084541 DOI: 10.1099/mic.0.001450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
Cellvibrio japonicus is a saprophytic bacterium proficient at environmental polysaccharide degradation for carbon and energy acquisition. Genetic, enzymatic, and structural characterization of C. japonicus carbohydrate active enzymes, specifically those that degrade plant and animal-derived polysaccharides, demonstrated that this bacterium is a carbohydrate-bioconversion specialist. Structural analyses of these enzymes identified highly specialized carbohydrate binding modules that facilitate activity. Steady progress has been made in developing genetic tools for C. japonicus to better understand the function and regulation of the polysaccharide-degrading enzymes it possesses, as well as to develop it as a biotechnology platform to produce renewable fuels and chemicals.
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Affiliation(s)
- Jeffrey G. Gardner
- Department of Biological Sciences, University of Maryland – Baltimore County Baltimore, Maryland, USA
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2
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Novak JK, Gardner JG. Galactomannan utilization by Cellvibrio japonicus relies on a single essential α-galactosidase encoded by the aga27A gene. Mol Microbiol 2023; 119:312-325. [PMID: 36604822 DOI: 10.1111/mmi.15024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023]
Abstract
Plant mannans are a component of lignocellulose that can have diverse compositions in terms of its backbone and side-chain substitutions. Consequently, the degradation of mannan substrates requires a cadre of enzymes for complete reduction to substituent monosaccharides that can include mannose, galactose, and/or glucose. One bacterium that possesses this suite of enzymes is the Gram-negative saprophyte Cellvibrio japonicus, which has 10 predicted mannanases from the Glycoside Hydrolase (GH) families 5, 26, and 27. Here we describe a systems biology approach to identify and characterize the essential mannan-degrading components in this bacterium. The transcriptomic analysis uncovered significant changes in gene expression for most mannanases, as well as many genes that encode carbohydrate active enzymes (CAZymes) when mannan was actively being degraded. A comprehensive mutational analysis characterized 54 CAZyme-encoding genes in the context of mannan utilization. Growth analysis of the mutant strains found that the man26C, aga27A, and man5D genes, which encode a mannobiohydrolase, α-galactosidase, and mannosidase, respectively, were important for the deconstruction of galactomannan, with Aga27A being essential. Our updated model of mannan degradation in C. japonicus proposes that the removal of galactose sidechains from substituted mannans constitutes a crucial step for the complete degradation of this hemicellulose.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
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3
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Al Makishah NH, Elfarash AE. Molecular characterization of cellulase genes in Pseudomonas stutzeri. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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4
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Liang Z, Lin X, Liao Y, Tang T. Characteristics and diversity of endophytic bacteria in Panax notoginseng under high temperature analysed using full-length 16S rRNA sequencing. Arch Microbiol 2022; 204:435. [PMID: 35763100 DOI: 10.1007/s00203-022-03043-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/27/2022] [Indexed: 11/02/2022]
Abstract
Panax notoginseng is a traditional Chinese medicinal herb with diverse properties that is cultivated in a narrow ecological range because of its sensitivity to high temperatures. Endophytic bacteria play a prominent role in plant response to climate warming. However, the endophytic bacterial structures in P. notoginseng at high temperatures are yet unclear. In the present study, the diversity and composition of the endophytic bacterial community, and their relationships with two P. notoginseng plants with different heat tolerance capacities were compared using the full-length 16S rRNA PacBio sequencing system. The results revealed that the diversity and richness of endophytic bacteria were negatively associated with the heat tolerance of P. notoginseng. Beneficial Cyanobacteria, Rhodanobacter and Sphingomonas may be recruited positively by heat-tolerant plants, while higher amounts of adverse Proteobacteria such as Cellvibrio fibrivorans derived from soil destructed the cellular protective barriers of heat-sensitive plants and caused influx of pathogenic bacteria Stenotrophomonas maltophilia. Harmonious and conflicting bacterial community was observed in heat-tolerant and heat-sensitive P. notoginseng, respectively, based on the co-occurrence network. Using functional gene prediction of metabolism, endophytic bacteria have been proposed to be symbiotic with host plants; the bacteria improved primary metabolic pathways and secondary metabolite production of plants, incorporated beneficial endophytes, and combated adverse endophytes to prompt the adaptation of P. notoginseng to a warming environment. These findings provided a new perspective on the function of endophytes in P. notoginseng adaptation to high temperatures, and could pave the way for expanding the cultivable range of P. notoginseng.
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Affiliation(s)
- Zhenting Liang
- School of Life and Health Sciences, Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal Polluted Soils, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Xianjing Lin
- School of Life and Health Sciences, Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal Polluted Soils, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Yiqun Liao
- School of Life and Health Sciences, Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal Polluted Soils, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Ting Tang
- School of Life and Health Sciences, Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal Polluted Soils, Hunan University of Science and Technology, Xiangtan, 411201, China.
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Shu F, Han J, Ndayambaje JP, Jia Q, Sarsaiya S, Jain A, Huang M, Liu M, Chen J. Transcriptomic analysis of Pinellia ternata (Thunb.) Breit T2 plus line provides insights in host responses resist Pectobacterium carotovorum infection. Bioengineered 2021; 12:1173-1188. [PMID: 33830860 PMCID: PMC8806331 DOI: 10.1080/21655979.2021.1905325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 10/25/2022] Open
Abstract
Transcriptome is used to determine the induction response of Pinellia ternata (Thunb.) Breit T2 plus line (abbreviated as PT2P line) infected with Pectobacterium carotovorum. The main objective of the study was to deal with the transcriptome database of PT2P line resistance to soft rot pathogens to provide a new perspective for identifying the resistance-related genes and understanding the molecular mechanism. Results indicated that water soaking and tissue collapse started at 20 h after PT2P line was infected by P. carotovorum. A total of 1360 and 5768 differentially expressed genes (DEGs) were identified at 0 h and 20 h, respectively. After 20 h of infection, growth and development-related pathways were inhibited. Meanwhile, DEGs were promoted the colonization of P. carotovorum pathogens in specific cell wall modification processes at the early infected stage. A shift to a defensive response was triggered at 0 h. A large number of DEGs were mainly up-controlled at 20 h and were substantially used in the pathogen recognition and the introduction of signal transformation cascades, secondary metabolites biosynthesis, pathogenic proteins activation, transcription aspects and numerous transporters. Furthermore, our data provided novel insights into the transcript reprogramming of PT2P line in response to P. carotovorum infestation.
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Affiliation(s)
- Fuxing Shu
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Jing Han
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Jean Pierre Ndayambaje
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Qi Jia
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
| | - Surendra Sarsaiya
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
| | - Archana Jain
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
| | - Minglei Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Minghong Liu
- Zunyi Branch of Guizhou Tobacco Company, Zunyi, China
| | - Jishuang Chen
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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Gardner JG, Schreier HJ. Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems. Appl Microbiol Biotechnol 2021; 105:8109-8127. [PMID: 34611726 DOI: 10.1007/s00253-021-11614-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/24/2022]
Abstract
Our current understanding of enzymatic polysaccharide degradation has come from a huge number of in vitro studies with purified enzymes. While this vast body of work has been invaluable in identifying and characterizing novel mechanisms of action and engineering desirable traits into these enzymes, a comprehensive picture of how these enzymes work as part of a native in vivo system is less clear. Recently, several model bacteria have emerged with genetic systems that allow for a more nuanced study of carbohydrate active enzymes (CAZymes) and how their activity affects bacterial carbon metabolism. With these bacterial model systems, it is now possible to not only study a single nutrient system in isolation (i.e., carbohydrate degradation and carbon metabolism), but also how multiple systems are integrated. Given that most environmental polysaccharides are carbon rich but nitrogen poor (e.g., lignocellulose), the interplay between carbon and nitrogen metabolism in polysaccharide-degrading bacteria can now be studied in a physiologically relevant manner. Therefore, in this review, we have summarized what has been experimentally determined for CAZyme regulation, production, and export in relation to nitrogen metabolism for two Gram-positive (Caldicellulosiruptor bescii and Clostridium thermocellum) and two Gram-negative (Bacteroides thetaiotaomicron and Cellvibrio japonicus) polysaccharide-degrading bacteria. By comparing and contrasting these four bacteria, we have highlighted the shared and unique features of each, with a focus on in vivo studies, in regard to carbon and nitrogen assimilation. We conclude with what we believe are two important questions that can act as guideposts for future work to better understand the integration of carbon and nitrogen metabolism in polysaccharide-degrading bacteria. KEY POINTS: • Regardless of CAZyme deployment system, the generation of a local pool of oligosaccharides is a common strategy among Gram-negative and Gram-positive polysaccharide degraders as a means to maximally recoup the energy expenditure of CAZyme production and export. • Due to the nitrogen deficiency of insoluble polysaccharide-containing substrates, Gram-negative and Gram-positive polysaccharide degraders have a diverse set of strategies for supplementation and assimilation. • Future work needs to precisely characterize the energetic expenditures of CAZyme deployment and bolster our understanding of how carbon and nitrogen metabolism are integrated in both Gram-negative and Gram-positive polysaccharide-degrading bacteria, as both of these will significantly influence a given bacterium's suitability for biotechnology applications.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.
| | - Harold J Schreier
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.,Department of Marine Biotechnology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD, USA
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7
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Garcia CA, Gardner JG. Development and evaluation of an agar capture system (ACS) for high-throughput screening of insoluble particulate substrates with bacterial growth and enzyme activity assays. J Microbiol Methods 2021; 190:106337. [PMID: 34571109 DOI: 10.1016/j.mimet.2021.106337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
We describe a method for containing insoluble particulates for use as substrates in either bacterial growth or enzyme assays. This method was designed for high-throughput screening of environmental or engineered bacteria. Benchmarking this method with several model bacteria uncovered phenotypes not observable with the particulate substrates alone.
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Affiliation(s)
- Cecelia A Garcia
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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8
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Trehalose Degradation by Cellvibrio japonicus Exhibits No Functional Redundancy and Is Solely Dependent on the Tre37A Enzyme. Appl Environ Microbiol 2020; 86:AEM.01639-20. [PMID: 32917758 DOI: 10.1128/aem.01639-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
The α-diglucoside trehalose has historically been known as a component of the bacterial stress response, though it more recently has been studied for its relevance in human gut health and biotechnology development. The utilization of trehalose as a nutrient source by bacteria relies on carbohydrate-active enzymes, specifically those of the glycoside hydrolase family 37 (GH37), to degrade the disaccharide into substituent glucose moieties for entry into metabolism. Environmental bacteria using oligosaccharides for nutrients often possess multiple carbohydrate-active enzymes predicted to have the same biochemical activity and therefore are thought to be functionally redundant. In this study, we characterized trehalose degradation by the biotechnologically important saprophytic bacterium Cellvibrio japonicus This bacterium possesses two predicted α-α-trehalase genes, tre37A and tre37B, and our investigation using mutational analysis found that only the former is essential for trehalose utilization by C. japonicus Heterologous expression experiments found that only the expression of the C. japonicus tre37A gene in an Escherichia coli treA mutant strain allowed for full utilization of trehalose. Biochemical characterization of C. japonicus GH37 activity determined that the tre37A gene product is solely responsible for cleaving trehalose and is an acidic α-α-trehalase. Bioinformatic and mutational analyses indicate that Tre37A directly cleaves trehalose to glucose in the periplasm, as C. japonicus does not possess a phosphotransferase system. This study facilitates the development of a comprehensive metabolic model for α-linked disaccharides in C. japonicus and more broadly expands our understanding of the strategies that saprophytic bacteria employ to capture diverse carbohydrates from the environment.IMPORTANCE The metabolism of trehalose is becoming increasingly important due to the inclusion of this α-diglucoside in a number of foods and its prevalence in the environment. Bacteria able to utilize trehalose in the human gut possess a competitive advantage, as do saprophytic microbes in terrestrial environments. While the biochemical mechanism of trehalose degradation is well understood, what is less clear is how bacteria acquire this metabolite from the environment. The significance of this report is that by using the model saprophyte Cellvibrio japonicus, we were able to functionally characterize the two predicted trehalase enzymes that the bacterium possesses and determined that the two enzymes are not equivalent and are not functionally redundant. The results and approaches used to understand the complex physiology of α-diglucoside metabolism from this study can be applied broadly to other polysaccharide-degrading bacteria.
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Monge EC, Tuveng TR, Vaaje-Kolstad G, Eijsink VGH, Gardner JG. Systems analysis of the glycoside hydrolase family 18 enzymes from Cellvibrio japonicus characterizes essential chitin degradation functions. J Biol Chem 2018; 293:3849-3859. [PMID: 29367339 DOI: 10.1074/jbc.ra117.000849] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/10/2018] [Indexed: 01/01/2023] Open
Abstract
Understanding the strategies used by bacteria to degrade polysaccharides constitutes an invaluable tool for biotechnological applications. Bacteria are major mediators of polysaccharide degradation in nature; however, the complex mechanisms used to detect, degrade, and consume these substrates are not well-understood, especially for recalcitrant polysaccharides such as chitin. It has been previously shown that the model bacterial saprophyte Cellvibrio japonicus is able to catabolize chitin, but little is known about the enzymatic machinery underlying this capability. Previous analyses of the C. japonicus genome and proteome indicated the presence of four glycoside hydrolase family 18 (GH18) enzymes, and studies of the proteome indicated that all are involved in chitin utilization. Using a combination of in vitro and in vivo approaches, we have studied the roles of these four chitinases in chitin bioconversion. Genetic analyses showed that only the chi18D gene product is essential for the degradation of chitin substrates. Biochemical characterization of the four enzymes showed functional differences and synergistic effects during chitin degradation, indicating non-redundant roles in the cell. Transcriptomic studies revealed complex regulation of the chitin degradation machinery of C. japonicus and confirmed the importance of CjChi18D and CjLPMO10A, a previously characterized chitin-active enzyme. With this systems biology approach, we deciphered the physiological relevance of the glycoside hydrolase family 18 enzymes for chitin degradation in C. japonicus, and the combination of in vitro and in vivo approaches provided a comprehensive understanding of the initial stages of chitin degradation by this bacterium.
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Affiliation(s)
- Estela C Monge
- From the Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250 and
| | - Tina R Tuveng
- the Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Gustav Vaaje-Kolstad
- the Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Vincent G H Eijsink
- the Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Jeffrey G Gardner
- From the Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250 and
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Blake AD, Beri NR, Guttman HS, Cheng R, Gardner JG. The complex physiology of
Cellvibrio japonicus
xylan degradation relies on a single cytoplasmic β‐xylosidase for xylo‐oligosaccharide utilization. Mol Microbiol 2018; 107:610-622. [DOI: 10.1111/mmi.13903] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Andrew D. Blake
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Nina R. Beri
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Hadassa S. Guttman
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Raymond Cheng
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Jeffrey G. Gardner
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
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Attia MA, Nelson CE, Offen WA, Jain N, Davies GJ, Gardner JG, Brumer H. In vitro and in vivo characterization of three Cellvibrio japonicus glycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:45. [PMID: 29467823 PMCID: PMC5816542 DOI: 10.1186/s13068-018-1039-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/01/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte Cellvibrio japonicus has emerged as a genetically tractable model system to study biomass saccharification, in part due to its innate capacity to utilize a wide range of plant polysaccharides for growth. Whereas the downstream debranching enzymes of the xyloglucan utilization system of C. japonicus have been functionally characterized, the requisite backbone-cleaving endo-xyloglucanases were unresolved. RESULTS Combined bioinformatic and transcriptomic analyses implicated three glycoside hydrolase family 5 subfamily 4 (GH5_4) members, with distinct modular organization, as potential keystone endo-xyloglucanases in C. japonicus. Detailed biochemical and enzymatic characterization of the GH5_4 modules of all three recombinant proteins confirmed particularly high specificities for the XyG polysaccharide versus a panel of other cell wall glycans, including mixed-linkage beta-glucan and cellulose. Moreover, product analysis demonstrated that all three enzymes generated XyG oligosaccharides required for subsequent saccharification by known exo-glycosidases. Crystallographic analysis of GH5D, which was the only GH5_4 member specifically and highly upregulated during growth on XyG, in free, product-complex, and active-site affinity-labelled forms revealed the molecular basis for the exquisite XyG specificity among these GH5_4 enzymes. Strikingly, exhaustive reverse-genetic analysis of all three GH5_4 members and a previously biochemically characterized GH74 member failed to reveal a growth defect, thereby indicating functional compensation in vivo, both among members of this cohort and by other, yet unidentified, xyloglucanases in C. japonicus. Our systems-based analysis indicates distinct substrate-sensing (GH74, GH5E, GH5F) and attack-mounting (GH5D) functions for the endo-xyloglucanases characterized here. CONCLUSIONS Through a multi-faceted, molecular systems-based approach, this study provides a new insight into the saccharification pathway of xyloglucan utilization system of C. japonicus. The detailed structural-functional characterization of three distinct GH5_4 endo-xyloglucanases will inform future bioinformatic predictions across species, and provides new CAZymes with defined specificity that may be harnessed in industrial and other biotechnological applications.
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Affiliation(s)
- Mohamed A. Attia
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
| | - Cassandra E. Nelson
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA
| | - Wendy A. Offen
- Department of Chemistry, University of York, Heslington, York, YO10 5DD UK
| | - Namrata Jain
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
| | - Gideon J. Davies
- Department of Chemistry, University of York, Heslington, York, YO10 5DD UK
| | - Jeffrey G. Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4 Canada
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12
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Nelson CE, Attia MA, Rogowski A, Morland C, Brumer H, Gardner JG. Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification. Environ Microbiol 2017; 19:5025-5039. [PMID: 29052930 DOI: 10.1111/1462-2920.13959] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/27/2017] [Accepted: 10/08/2017] [Indexed: 12/16/2022]
Abstract
Lignocellulose degradation is central to the carbon cycle and renewable biotechnologies. The xyloglucan (XyG), β(1→3)/β(1→4) mixed-linkage glucan (MLG) and β(1→3) glucan components of lignocellulose represent significant carbohydrate energy sources for saprophytic microorganisms. The bacterium Cellvibrio japonicus has a robust capacity for plant polysaccharide degradation, due to a genome encoding a large contingent of Carbohydrate-Active enZymes (CAZymes), many of whose specific functions remain unknown. Using a comprehensive genetic and biochemical approach, we have delineated the physiological roles of the four C. japonicus glycoside hydrolase family 3 (GH3) members on diverse β-glucans. Despite high protein sequence similarity and partially overlapping activity profiles on disaccharides, these β-glucosidases are not functionally equivalent. Bgl3A has a major role in MLG and sophorose utilization, and supports β(1→3) glucan utilization, while Bgl3B underpins cellulose utilization and supports MLG utilization. Bgl3C drives β(1→3) glucan utilization. Finally, Bgl3D is the crucial β-glucosidase for XyG utilization. This study not only sheds the light on the metabolic machinery of C. japonicus, but also expands the repertoire of characterized CAZymes for future deployment in biotechnological applications. In particular, the precise functional analysis provided here serves as a reference for informed bioinformatics on the genomes of other Cellvibrio and related species.
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Affiliation(s)
- Cassandra E Nelson
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, USA
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.,Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Carl Morland
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.,Department of Chemistry, University of British Columbia, Vancouver, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.,Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, USA
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13
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Nelson CE, Rogowski A, Morland C, Wilhide JA, Gilbert HJ, Gardner JG. Systems analysis in Cellvibrio japonicus resolves predicted redundancy of β-glucosidases and determines essential physiological functions. Mol Microbiol 2017; 104:294-305. [PMID: 28118504 DOI: 10.1111/mmi.13625] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2017] [Indexed: 12/29/2022]
Abstract
Degradation of polysaccharides forms an essential arc in the carbon cycle, provides a percentage of our daily caloric intake, and is a major driver in the renewable chemical industry. Microorganisms proficient at degrading insoluble polysaccharides possess large numbers of carbohydrate active enzymes (CAZymes), many of which have been categorized as functionally redundant. Here we present data that suggests that CAZymes that have overlapping enzymatic activities can have unique, non-overlapping biological functions in the cell. Our comprehensive study to understand cellodextrin utilization in the soil saprophyte Cellvibrio japonicus found that only one of four predicted β-glucosidases is required in a physiological context. Gene deletion analysis indicated that only the cel3B gene product is essential for efficient cellodextrin utilization in C. japonicus and is constitutively expressed at high levels. Interestingly, expression of individual β-glucosidases in Escherichia coli K-12 enabled this non-cellulolytic bacterium to be fully capable of using cellobiose as a sole carbon source. Furthermore, enzyme kinetic studies indicated that the Cel3A enzyme is significantly more active than the Cel3B enzyme on the oligosaccharides but not disaccharides. Our approach for parsing related CAZymes to determine actual physiological roles in the cell can be applied to other polysaccharide-degradation systems.
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Affiliation(s)
- Cassandra E Nelson
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Carl Morland
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Joshua A Wilhide
- Molecular Characterization and Analysis Complex, University of Maryland - Baltimore County, Maryland, USA
| | - Harry J Gilbert
- Molecular Characterization and Analysis Complex, University of Maryland - Baltimore County, Maryland, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
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14
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Nelson CE, Beri NR, Gardner JG. Custom fabrication of biomass containment devices using 3-D printing enables bacterial growth analyses with complex insoluble substrates. J Microbiol Methods 2016; 130:136-143. [DOI: 10.1016/j.mimet.2016.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/19/2016] [Accepted: 09/19/2016] [Indexed: 10/21/2022]
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15
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Attia M, Stepper J, Davies GJ, Brumer H. Functional and structural characterization of a potent GH74 endo-xyloglucanase from the soil saprophyte Cellvibrio japonicus unravels the first step of xyloglucan degradation. FEBS J 2016; 283:1701-19. [PMID: 26929175 DOI: 10.1111/febs.13696] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/09/2016] [Accepted: 02/25/2016] [Indexed: 11/27/2022]
Abstract
UNLABELLED The heteropolysaccharide xyloglucan (XyG) comprises up to one-quarter of the total carbohydrate content of terrestrial plant cell walls and, as such, represents a significant reservoir in the global carbon cycle. The complex composition of XyG requires a consortium of backbone-cleaving endo-xyloglucanases and side-chain cleaving exo-glycosidases for complete saccharification. The biochemical basis for XyG utilization by the model Gram-negative soil saprophytic bacterium Cellvibrio japonicus is incompletely understood, despite the recent characterization of associated side-chain cleaving exo-glycosidases. We present a detailed functional and structural characterization of a multimodular enzyme encoded by gene locus CJA_2477. The CJA_2477 gene product comprises an N-terminal glycoside hydrolase family 74 (GH74) endo-xyloglucanase module in train with two carbohydrate-binding modules (CBMs) from families 10 and 2 (CBM10 and CBM2). The GH74 catalytic domain generates Glc4 -based xylogluco-oligosaccharide (XyGO) substrates for downstream enzymes through an endo-dissociative mode of action. X-ray crystallography of the GH74 module, alone and in complex with XyGO products spanning the entire active site, revealed a broad substrate-binding cleft specifically adapted to XyG recognition, which is composed of two seven-bladed propeller domains characteristic of the GH74 family. The appended CBM10 and CBM2 members notably did not bind XyG, nor other soluble polysaccharides, and instead were specific cellulose-binding modules. Taken together, these data shed light on the first step of xyloglucan utilization by C. japonicus and expand the repertoire of GHs and CBMs for selective biomass analysis and utilization. DATABASE Structural data have been deposited in the RCSB protein database under the Protein Data Bank codes: 5FKR, 5FKS, 5FKT and 5FKQ.
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Affiliation(s)
- Mohamed Attia
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, Canada
| | | | | | - Harry Brumer
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, Canada
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16
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Forsberg Z, Nelson CE, Dalhus B, Mekasha S, Loose JSM, Crouch LI, Røhr ÅK, Gardner JG, Eijsink VGH, Vaaje-Kolstad G. Structural and Functional Analysis of a Lytic Polysaccharide Monooxygenase Important for Efficient Utilization of Chitin in Cellvibrio japonicus. J Biol Chem 2016; 291:7300-12. [PMID: 26858252 DOI: 10.1074/jbc.m115.700161] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Indexed: 01/11/2023] Open
Abstract
Cellvibrio japonicusis a Gram-negative soil bacterium that is primarily known for its ability to degrade plant cell wall polysaccharides through utilization of an extensive repertoire of carbohydrate-active enzymes. Several putative chitin-degrading enzymes are also found among these carbohydrate-active enzymes, such as chitinases, chitobiases, and lytic polysaccharide monooxygenases (LPMOs). In this study, we have characterized the chitin-active LPMO,CjLPMO10A, a tri-modular enzyme containing a catalytic family AA10 LPMO module, a family 5 chitin-binding module, and a C-terminal unclassified module of unknown function. Characterization of the latter module revealed tight and specific binding to chitin, thereby unraveling a new family of chitin-binding modules (classified as CBM73). X-ray crystallographic elucidation of theCjLPMO10A catalytic module revealed that the active site of the enzyme combines structural features previously only observed in either cellulose or chitin-active LPMO10s. Analysis of the copper-binding site by EPR showed a signal signature more similar to those observed for cellulose-cleaving LPMOs. The full-length LPMO shows no activity toward cellulose but is able to bind and cleave both α- and β-chitin. Removal of the chitin-binding modules reduced LPMO activity toward α-chitin compared with the full-length enzyme. Interestingly, the full-length enzyme and the individual catalytic LPMO module boosted the activity of an endochitinase equally well, also yielding similar amounts of oxidized products. Finally, gene deletion studies show thatCjLPMO10A is needed byC. japonicusto obtain efficient growth on both purified chitin and crab shell particles.
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Affiliation(s)
- Zarah Forsberg
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Cassandra E Nelson
- the Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, Maryland 21250
| | - Bjørn Dalhus
- the Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, P. O. Box 4950, Nydalen, N-0424 Oslo, Norway, the Department of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, Rikshospitalet, P. O. Box 4950, Nydalen, N-0424 Oslo, Norway, and
| | - Sophanit Mekasha
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Jennifer S M Loose
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Lucy I Crouch
- the Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Åsmund K Røhr
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Jeffrey G Gardner
- the Department of Biological Sciences, University of Maryland at Baltimore County, Baltimore, Maryland 21250
| | - Vincent G H Eijsink
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Gustav Vaaje-Kolstad
- From the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway,
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17
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In-Frame Deletions Allow Functional Characterization of Complex Cellulose Degradation Phenotypes in Cellvibrio japonicus. Appl Environ Microbiol 2015; 81:5968-75. [PMID: 26116676 DOI: 10.1128/aem.00847-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/16/2015] [Indexed: 12/31/2022] Open
Abstract
The depolymerization of the recalcitrant polysaccharides found in lignocellulose has become an area of intense interest due to the role of this process in global carbon cycling, human gut microbiome nutritional contributions, and bioenergy production. However, underdeveloped genetic tools have hampered study of bacterial lignocellulose degradation, especially outside model organisms. In this report, we describe an in-frame deletion strategy for the Gram-negative lignocellulose-degrading bacterium Cellvibrio japonicus. This method leverages optimized growth conditions for conjugation and sacB counterselection for the generation of markerless in-frame deletions. This method produces mutants in as few as 8 days and allows for the ability to make multiple gene deletions per strain. It is also possible to remove large sections of the genome, as shown in this report with the deletion of the nine-gene (9.4-kb) gsp operon in C. japonicus. We applied this system to study the complex phenotypes of cellulose degradation in C. japonicus. Our data indicated that a Δcel5B Δcel6A double mutant is crippled for cellulose utilization, more so than by either single mutation alone. Additionally, we deleted individual genes in the two-gene cbp2ED operon and showed that both genes contribute to cellulose degradation in C. japonicus. Overall, these described techniques substantially enhance the utility of C. japonicus as a model system to study lignocellulose degradation.
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Gardner JG, Crouch L, Labourel A, Forsberg Z, Bukhman YV, Vaaje-Kolstad G, Gilbert HJ, Keating DH. Systems biology defines the biological significance of redox-active proteins during cellulose degradation in an aerobic bacterium. Mol Microbiol 2014; 94:1121-1133. [PMID: 25294408 DOI: 10.1111/mmi.12821] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2014] [Indexed: 11/28/2022]
Abstract
Microbial depolymerization of plant cell walls contributes to global carbon balance and is a critical component of renewable energy. The genomes of lignocellulose degrading microorganisms encode diverse classes of carbohydrate modifying enzymes, although currently there is a paucity of knowledge on the role of these proteins in vivo. We report the comprehensive analysis of the cellulose degradation system in the saprophytic bacterium Cellvibrio japonicus. Gene expression profiling of C. japonicus demonstrated that three of the 12 predicted β-1,4 endoglucanases (cel5A, cel5B, and cel45A) and the sole predicted cellobiohydrolase (cel6A) showed elevated expression during growth on cellulose. Targeted gene disruptions of all 13 predicted cellulase genes showed that only cel5B and cel6A were required for optimal growth on cellulose. Our analysis also identified three additional genes required for cellulose degradation: lpmo10B encodes a lytic polysaccharide monooxygenase (LPMO), while cbp2D and cbp2E encode proteins containing carbohydrate binding modules and predicted cytochrome domains for electron transfer. CjLPMO10B oxidized cellulose and Cbp2D demonstrated spectral properties consistent with redox function. Collectively, this report provides insight into the biological role of LPMOs and redox proteins in cellulose utilization and suggests that C. japonicus utilizes a combination of hydrolytic and oxidative cleavage mechanisms to degrade cellulose.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, 324 Biological Sciences Building, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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Larsbrink J, Thompson AJ, Lundqvist M, Gardner JG, Davies GJ, Brumer H. A complex gene locus enables xyloglucan utilization in the model saprophyte Cellvibrio japonicus. Mol Microbiol 2014; 94:418-33. [PMID: 25171165 PMCID: PMC4285296 DOI: 10.1111/mmi.12776] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 12/17/2022]
Abstract
The degradation of plant biomass by saprophytes is an ecologically important part of the global carbon cycle, which has also inspired a vast diversity of industrial enzyme applications. The xyloglucans (XyGs) constitute a family of ubiquitous and abundant plant cell wall polysaccharides, yet the enzymology of XyG saccharification is poorly studied. Here, we present the identification and molecular characterization of a complex genetic locus that is required for xyloglucan utilization by the model saprophyte Cellvibrio japonicus. In harness, transcriptomics, reverse genetics, enzyme kinetics, and structural biology indicate that the encoded cohort of an α-xylosidase, a β-galactosidase, and an α-l-fucosidase is specifically adapted for efficient, concerted saccharification of dicot (fucogalacto)xyloglucan oligosaccharides following import into the periplasm via an associated TonB-dependent receptor. The data support a biological model of xyloglucan degradation by C. japonicus with striking similarities – and notable differences – to the complex polysaccharide utilization loci of the Bacteroidetes.
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Affiliation(s)
- Johan Larsbrink
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden
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Next generation biofuel engineering in prokaryotes. Curr Opin Chem Biol 2013; 17:462-71. [PMID: 23623045 DOI: 10.1016/j.cbpa.2013.03.037] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 02/23/2013] [Accepted: 03/28/2013] [Indexed: 12/15/2022]
Abstract
Next-generation biofuels must be compatible with current transportation infrastructure and be derived from environmentally sustainable resources that do not compete with food crops. Many bacterial species have unique properties advantageous to the production of such next-generation fuels. However, no single species possesses all characteristics necessary to make high quantities of fuels from plant waste or CO2. Species containing a subset of the desired characteristics are used as starting points for engineering organisms with all desired attributes. Metabolic engineering of model organisms has yielded high titer production of advanced fuels, including alcohols, isoprenoids, and fatty acid derivatives. Technical developments now allow engineering of native fuel producers, as well as lignocellulolytic and autotrophic bacteria, for the production of biofuels. Continued research on multiple fronts is required to engineer organisms for truly sustainable and economical biofuel production.
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