1
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Park MR, Gauttam R, Fong B, Chen Y, Lim HG, Feist AM, Mukhopadhyay A, Petzold CJ, Simmons BA, Singer SW. Revealing oxidative pentose metabolism in new Pseudomonas putida isolates. Environ Microbiol 2023; 25:493-504. [PMID: 36465038 PMCID: PMC10107873 DOI: 10.1111/1462-2920.16296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well-characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth-promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism (xylDXA) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism (araDXA). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.
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Affiliation(s)
- Mee-Rye Park
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rahul Gauttam
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Bonnie Fong
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hyun Gyu Lim
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Adam M Feist
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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2
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Liu L, Tao Y, Li Y, Deng X, Liu G, Yao Y, Chen X, Yang S, Tu M, Peng Q, Huang L, Xiang W, Rao Y. Isolation and characterization of bacteria that produce quorum sensing molecules during the fermentation and deterioration of pickles. Int J Food Microbiol 2022; 379:109869. [DOI: 10.1016/j.ijfoodmicro.2022.109869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 10/16/2022]
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3
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Borrero‐de Acuña JM, Poblete‐Castro I. Rational engineering of natural polyhydroxyalkanoates producing microorganisms for improved synthesis and recovery. Microb Biotechnol 2022; 16:262-285. [PMID: 35792877 PMCID: PMC9871526 DOI: 10.1111/1751-7915.14109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
Microbial production of biopolymers derived from renewable substrates and waste streams reduces our heavy reliance on petrochemical plastics. One of the most important biodegradable polymers is the family of polyhydroxyalkanoates (PHAs), naturally occurring intracellular polyoxoesters produced for decades by bacterial fermentation of sugars and fatty acids at the industrial scale. Despite the advances, PHA production still suffers from heavy costs associated with carbon substrates and downstream processing to recover the intracellular product, thus restricting market positioning. In recent years, model-aided metabolic engineering and novel synthetic biology approaches have spurred our understanding of carbon flux partitioning through competing pathways and cellular resource allocation during PHA synthesis, enabling the rational design of superior biopolymer producers and programmable cellular lytic systems. This review describes these attempts to rationally engineering the cellular operation of several microbes to elevate PHA production on specific substrates and waste products. We also delve into genome reduction, morphology, and redox cofactor engineering to boost PHA biosynthesis. Besides, we critically evaluate engineered bacterial strains in various fermentation modes in terms of PHA productivity and the period required for product recovery.
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Affiliation(s)
| | - Ignacio Poblete‐Castro
- Biosystems Engineering LaboratoryDepartment of Chemical and Bioprocess EngineeringUniversidad de Santiago de Chile (USACH)SantiagoChile
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4
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Padra JT, Loibman SO, Thorell K, Sundh H, Sundell K, Lindén SK. Atlantic Salmon Mucins Inhibit LuxS-Dependent A. Salmonicida AI-2 Quorum Sensing in an N-Acetylneuraminic Acid-Dependent Manner. Int J Mol Sci 2022; 23:ijms23084326. [PMID: 35457143 PMCID: PMC9026418 DOI: 10.3390/ijms23084326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
One of the most important bacterial diseases in salmonid aquaculture is furunculosis, caused by Aeromonas salmonicida. Bacterial communication through secreted autoinducer signals, quorum sensing, takes part in the regulation of gene expression in bacteria, influencing growth and virulence. The skin and mucosal surfaces, covered by a mucus layer, are the first point of contact between fish and bacteria. Mucins are highly glycosylated and are the main components of mucus. Here, we validate the Vibrio harveyi BB170 bioreporter assay for quantifying A. salmonicida quorum sensing and study the effects of Atlantic salmon mucins as well as mono- and disaccharides on the AI-2 levels of A. salmonicida. Atlantic salmon mucins from skin, pyloric ceca, proximal and distal intestine reduced A. salmonicida AI-2 levels. Among the saccharides abundant on mucins, fucose, N-acetylneuraminic acid and GlcNAcβ1-3Gal inhibited AI-2 A. salmonicida secretion. Removal of N-acetylneuraminic acid, which is the most abundant terminal residue on mucin glycans on Atlantic salmon mucins, attenuated the inhibitory effects on AI-2 levels of A. salmonicida. Deletion of A. salmonicida luxS abolished AI-2 production. In conclusion, Atlantic salmon mucins regulate A. salmonicida quorum sensing in a luxS and N-acetylneuraminic acid-dependent manner.
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Affiliation(s)
- János Tamás Padra
- Department of Medical Chemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden; (J.T.P.); (S.O.L.); (K.T.)
| | - Stefany Ojaimi Loibman
- Department of Medical Chemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden; (J.T.P.); (S.O.L.); (K.T.)
| | - Kaisa Thorell
- Department of Medical Chemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden; (J.T.P.); (S.O.L.); (K.T.)
| | - Henrik Sundh
- Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden; (H.S.); (K.S.)
| | - Kristina Sundell
- Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden; (H.S.); (K.S.)
| | - Sara K. Lindén
- Department of Medical Chemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden; (J.T.P.); (S.O.L.); (K.T.)
- Correspondence:
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5
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He Z, Jiang W, Jiang Y, Dong J, Song Z, Xu J, Zhou W. Anti-biofilm activities of coumarin as quorum sensing inhibitor for Porphyromonas gingivalis. J Oral Microbiol 2022; 14:2055523. [PMID: 35368854 PMCID: PMC8967191 DOI: 10.1080/20002297.2022.2055523] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Porphyromonas gingivalis is a keystone pathogen in periodontitis, a biofilm-mediated infection disease. This research aimed to investigate the effect of coumarin on P. gingivalis biofilm formation. We detected the antimicrobial effect on P. gingivalis planktonic growth, observed membrane structure and morphological change by TEM, and quantified membrane permeability by calcein-AM staining. The cell surface hydrophobicity, aggregation, and attachment were assessed. We also investigated different sub-MIC concentrations of coumarin on biofilm formation, and observed biofilm structureby confocal laser scanning microscopy. The biofilm-related gene expression was evaluated using real-time PCR. The results showed that coumarin inhibited P. gingivalis growth and damaged the cell morphology above 400 μM concentration. Coumarin did not affect cell surface hydrophobicity, aggregation, attachment, and the early stage of biofilm formation at sub-MIC concentrations. Still, it exhibited anti-biofilm effects for the late-stage and pre-formed biofilms dispersion. The biofilms after coumarin treatment became interspersed, and biofilm-related gene expression was downregulated. Coumarin also inhibited AI-2 activity and interacted with the HmuY protein by molecular docking analysis. Our research demonstrated that coumarin inhibited P. gingivalis biofilm formation through a quorum sensing system.
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Affiliation(s)
- Zhiyan He
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Wei Jiang
- Department of Endodontics and Operative Dentistry, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yiting Jiang
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiachen Dong
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Zhongchen Song
- Department of Periodontology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jianrong Xu
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine ; Shanghai, China.,Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Zhou
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, China
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6
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Keizers M, Dobrindt U, Berger M. A Simple Biosensor-Based Assay for Quantitative Autoinducer-2 Analysis. ACS Synth Biol 2022; 11:747-759. [PMID: 35090122 DOI: 10.1021/acssynbio.1c00459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteria produce and react to interspecies signaling molecules in order to control the expression of genes that are particularly beneficial when they are expressed by a bacterial community. In addition to intraspecies communication, the signaling molecule autoinducer-2 (AI-2) can also serve for interspecies communication between Gram-positive and Gram-negative bacteria and is therefore of particular interest. The analysis and quantification of AI-2 are essential for understanding population density-dependent changes in bacterial behavior and pathogenicity. However, currently available bioassays for AI-2 quantification are rather complex, have narrow detection ranges, and are very sensitive to trace components of, for example, growth media. To facilitate and improve the detection of AI-2, we have developed an Escherichia coli biosensor-based assay that is sensitive, cheap, fast, robust, and reliable in the quantification of biologically active AI-2. The bioassay is based on an lsr promoter-fluorescent reporter gene fusion cassette that we chromosomally integrated in a biosensor strain, but the cassette can also be used in a low-copy number plasmid for the application in other Gram-negative bacterial species. We show here that AI-2 quantification was possible in a concentration range from 400 nM to 100 μM and that a critical interpretation of the kinetics of the measurements can reveal sugar interference. With the help of our biosensor strain, coculture experiments were done to test the capability and kinetics of AI-2 secretion by various Gram-negative bacteria in real time. Finally, calibration curves were used to calculate the absolute AI-2 concentration in cell-free bacterial samples.
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Affiliation(s)
- Marla Keizers
- Institute of Hygiene, University of Münster, Münster 48149, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster 48149, Germany
| | - Michael Berger
- Institute of Hygiene, University of Münster, Münster 48149, Germany
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7
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Lin L. Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:14. [PMID: 35418100 PMCID: PMC8822760 DOI: 10.1186/s13068-022-02113-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/28/2022] [Indexed: 01/21/2023]
Abstract
Lignocellulose is the most abundant organic carbon polymer on the earth. Its decomposition and conversion greatly impact the global carbon cycle. Furthermore, it provides feedstock for sustainable fuel and other value-added products. However, it continues to be underutilized, due to its highly recalcitrant and heterogeneric structure. Microorganisms, which have evolved versatile pathways to convert lignocellulose, undoubtedly are at the heart of lignocellulose conversion. Numerous studies that have reported successful metabolic engineering of individual strains to improve biological lignin valorization. Meanwhile, the bottleneck of single strain modification is becoming increasingly urgent in the conversion of complex substrates. Alternatively, increased attention has been paid to microbial consortia, as they show advantages over pure cultures, e.g., high efficiency and robustness. Here, we first review recent developments in microbial communities for lignocellulose bioconversion. Furthermore, the emerging area of synthetic ecology, which is an integration of synthetic biology, ecology, and computational biology, provides an opportunity for the bottom-up construction of microbial consortia. Then, we review different modes of microbial interaction and their molecular mechanisms, and discuss considerations of how to employ these interactions to construct synthetic consortia via synthetic ecology, as well as highlight emerging trends in engineering microbial communities for lignocellulose bioconversion.
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Affiliation(s)
- Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
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8
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Zhang Y, Yu H, Xie Y, Guo Y, Cheng Y, Yao W. Quorum sensing inhibitory effect of hexanal on Autoinducer‐2 (AI‐2) and corresponding impacts on biofilm formation and enzyme activity in
Erwinia carotovora
and
Pseudomonas fluorescens
isolated from vegetables. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ying Zhang
- School of Health Science and Engineering University of Shanghai for Science and Technology Shanghai China
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
- School of Food Science and Technology Jiangnan University Wuxi China
| | - Hang Yu
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
- School of Food Science and Technology Jiangnan University Wuxi China
- Joint International Research Laboratory of Food Safety Jiangnan University Wuxi China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety Jiangnan University Wuxi China
| | - Yunfei Xie
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
- School of Food Science and Technology Jiangnan University Wuxi China
- Joint International Research Laboratory of Food Safety Jiangnan University Wuxi China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety Jiangnan University Wuxi China
| | - Yahui Guo
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
- School of Food Science and Technology Jiangnan University Wuxi China
- Joint International Research Laboratory of Food Safety Jiangnan University Wuxi China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety Jiangnan University Wuxi China
| | - Yuliang Cheng
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
- School of Food Science and Technology Jiangnan University Wuxi China
- Joint International Research Laboratory of Food Safety Jiangnan University Wuxi China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety Jiangnan University Wuxi China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology Jiangnan University Wuxi China
- School of Food Science and Technology Jiangnan University Wuxi China
- Joint International Research Laboratory of Food Safety Jiangnan University Wuxi China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety Jiangnan University Wuxi China
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9
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Atiwesh G, Parrish CC, Banoub J, Le TAT. Lignin degradation by microorganisms: A review. Biotechnol Prog 2021; 38:e3226. [PMID: 34854261 DOI: 10.1002/btpr.3226] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/19/2021] [Accepted: 11/28/2021] [Indexed: 11/09/2022]
Abstract
Lignin is an abundant plant-based biopolymer that has found applications in a variety of industries from construction to bioethanol production. This recalcitrant branched polymer is naturally degraded by many different species of microorganisms, including fungi and bacteria. These microbial lignin degradation mechanisms provide a host of possibilities to overcome the challenges of using harmful chemicals to degrade lignin biowaste in many industries. The classes and mechanisms of different microbial lignin degradation options available in nature form the primary focus of the present review. This review first discusses the chemical building blocks of lignin and the industrial sources and applications of this multifaceted polymer. The review further places emphasis on the degradation of lignin by natural means, discussing in detail the lignin degradation activities of various fungal and bacterial species. The lignin-degrading enzymes produced by various microbial species, specifically white-rot fungi, brown-rot fungi, and bacteria, are described. In the end, possible directions for future lignin biodegradation applications and research investigations have been provided.
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Affiliation(s)
- Ghada Atiwesh
- Environmental Science Program, Memorial University of Newfoundland. St. John's, St. John's, Newfoundland, Canada
| | - Christopher C Parrish
- Chemistry Department, Memorial University of Newfoundland St. John's, St. John's, Newfoundland, Canada.,Department of Ocean Sciences, Memorial University of Newfoundland St. John's, St. John's, Newfoundland, Canada
| | - Joseph Banoub
- Chemistry Department, Memorial University of Newfoundland St. John's, St. John's, Newfoundland, Canada.,Fisheries and Oceans Canada, Science Branch, Special Projects, St John's, Newfoundland, Canada
| | - Tuyet-Anh T Le
- School of Science and the Environment, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Environmental Policy Institute, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Forestry Economics Research Centre, Vietnamese Academy of Forest Sciences, Hanoi, Vietnam
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10
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Jing Y, Zuo J, Phouthapane V, Chen Z, Han X. An Optimized Method for Detecting AI-2 Signal Molecule by a Bioassay with Vibrio harveyi BB170. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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11
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Raj Rai S, Bhattacharyya C, Sarkar A, Chakraborty S, Sircar E, Dutta S, Sengupta R. Glutathione: Role in Oxidative/Nitrosative Stress, Antioxidant Defense, and Treatments. ChemistrySelect 2021. [DOI: 10.1002/slct.202100773] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sristi Raj Rai
- Amity Institute of Biotechnology Amity University Kolkata 700135, W.B. India
| | | | - Anwita Sarkar
- Amity Institute of Biotechnology Amity University Kolkata 700135, W.B. India
| | - Surupa Chakraborty
- Amity Institute of Biotechnology Amity University Kolkata 700135, W.B. India
| | - Esha Sircar
- Amity Institute of Biotechnology Amity University Kolkata 700135, W.B. India
| | - Sreejita Dutta
- Amity Institute of Biotechnology Amity University Kolkata 700135, W.B. India
| | - Rajib Sengupta
- Amity Institute of Biotechnology Amity University Kolkata 700135, W.B. India
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12
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Park MR, Chen Y, Thompson M, Benites VT, Fong B, Petzold CJ, Baidoo EEK, Gladden JM, Adams PD, Keasling JD, Simmons BA, Singer SW. Response of Pseudomonas putida to Complex, Aromatic-Rich Fractions from Biomass. CHEMSUSCHEM 2020; 13:4455-4467. [PMID: 32160408 DOI: 10.1002/cssc.202000268] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/11/2020] [Indexed: 06/10/2023]
Abstract
There is strong interest in the valorization of lignin to produce valuable products; however, its structural complexity has been a conversion bottleneck. Chemical pretreatment liberates lignin-derived soluble fractions that may be upgraded by bioconversion. Cholinium ionic liquid pretreatment of sorghum produced soluble, aromatic-rich fractions that were converted by Pseudomonas putida (P. putida), a promising host for aromatic bioconversion. Growth studies and mutational analysis demonstrated that P. putida growth on these fractions was dependent on aromatic monomers but unknown factors also contributed. Proteomic and metabolomic analyses indicated that these unknown factors were amino acids and residual ionic liquid; the oligomeric aromatic fraction derived from lignin was not converted. A cholinium catabolic pathway was identified, and the deletion of the pathway stopped the ability of P. putida to grow on cholinium ionic liquid. This work demonstrates that aromatic-rich fractions obtained through pretreatment contain multiple substrates; conversion strategies should account for this complexity.
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Affiliation(s)
- Mee-Rye Park
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mitchell Thompson
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Veronica T Benites
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bonnie Fong
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - John M Gladden
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, 94551, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technology, Shenzhen, China
| | - Blake A Simmons
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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13
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Singhvi M, Kim BS. Lignin valorization using biological approach. Biotechnol Appl Biochem 2020; 68:459-468. [PMID: 32725827 DOI: 10.1002/bab.1995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/27/2020] [Indexed: 11/06/2022]
Abstract
Due to the structural complexity and recalcitrance nature of lignin, its depolymerization into monomeric units becomes one of the biggest challenges in the bioconversion of lignin into value-added products. Depolymerization of lignin produces a blend of many compounds that are problematic for isolating components in a cost-effective way. Lignin valorization using a biological approach facilitates sustainable and commercially viable biorefineries. The use of microbes for the conversion of depolymerized lignin compounds into target products can be a solution to the heterogeneity issue. Several studies have been carried out to develop robust strains that can utilize all relevant lignin-derived compounds, but constructing these strains is difficult. As an alternative, designing multiple microbes to convert a mixture of various compounds into the desired product seems realistic. This review provides an overview of lignin bioconversion using various approaches such as metabolic engineering and synthetic biology. Ligninolytic strains have a broad enzymatic machine for depolymerization of lignin and its conversion into intermediates such as catechol or protocatechuate. These intermediates can be further converted to metabolite products such as polyhydroxyalkanoates and triacylglycerol. Synthetic biology offers encouraging methodologies to construct pathways for lignin conversion and to engineer ligninolytic microbes as prospective strains for lignin bioconversion.
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Affiliation(s)
- Mamata Singhvi
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Beom Soo Kim
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
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14
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Lin L, Wang X, Cao L, Xu M. Lignin catabolic pathways reveal unique characteristics of dye-decolorizing peroxidases in Pseudomonas putida. Environ Microbiol 2020; 21:1847-1863. [PMID: 30882973 DOI: 10.1111/1462-2920.14593] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 11/28/2022]
Abstract
Lignin is one of the largest carbon reservoirs in the environment, playing an important role in the global carbon cycle. However, lignin degradation in bacteria, especially non-model organisms, has not been well characterized either enzymatically or genetically. Here, a lignin-degrading bacterial strain, Pseudomonas putida A514, was used as the research model. Genomic and proteomic analyses suggested that two B subfamily dye-decolorizing peroxidases (DypBs) were prominent in lignin depolymerization, while the classic O2 -dependent ring cleavage strategy was utilized in central pathways to catabolize lignin-derived aromatic compounds that were funnelled by peripheral pathways. These enzymes, together with a range of transporters, sequential and expression-dose dependent regulation and stress response systems coordinated for lignin metabolism. Catalytic assays indicated these DypBs show unique Mn2+ independent lignin depolymerization activity, while Mn2+ oxidation activity is absent. Furthermore, a high synergy between DypB enzymes and A514 cells was observed to promote cell growth (5 × 1012 cfus/ml) and lignin degradation (27%). This suggested DypBs are competitive lignin biocatalysts and pinpointed limited extracellular secretion capacity as the rate-limiting factor in bacterial lignin degradation. DypB production was, therefore, optimized in recombinant strains and a 14,141-fold increase in DypB activity (56,565 U/l) was achieved, providing novel insights for lignin bioconversion.
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Affiliation(s)
- Lu Lin
- Institute of Marine Science and Technology, Shandong University, Jinan, China.,Ocean College, Zhejiang University, Hangzhou, China
| | | | - Lanfang Cao
- Ocean College, Zhejiang University, Hangzhou, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, China
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15
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Development of a CRISPR/Cas9n-based tool for metabolic engineering of Pseudomonas putida for ferulic acid-to-polyhydroxyalkanoate bioconversion. Commun Biol 2020; 3:98. [PMID: 32139868 PMCID: PMC7058019 DOI: 10.1038/s42003-020-0824-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/12/2020] [Indexed: 12/18/2022] Open
Abstract
Ferulic acid is a ubiquitous phenolic compound in lignocellulose, which is recognized for its role in the microbial carbon catabolism and industrial value. However, its recalcitrance and toxicity poses a challenge for ferulic acid-to-bioproducts bioconversion. Here, we develop a genome editing strategy for Pseudomonas putida KT2440 using an integrated CRISPR/Cas9n-λ-Red system with pyrF as a selection marker, which maintains cell viability and genetic stability, increases mutation efficiency, and simplifies genetic manipulation. Via this method, four functional modules, comprised of nine genes involved in ferulic acid catabolism and polyhydroxyalkanoate biosynthesis, were integrated into the genome, generating the KTc9n20 strain. After metabolic engineering and optimization of C/N ratio, polyhydroxyalkanoate production was increased to ~270 mg/L, coupled with ~20 mM ferulic acid consumption. This study not only establishes a simple and efficient genome editing strategy, but also offers an encouraging example of how to apply this method to improve microbial aromatic compound bioconversion. Yueyue Zhou et al. develop a genetic engineering method that increases the production of polyhydroxyalkanoate from ferulic acid, which is toxic at high concentrations. This study provides insight into the bioconversion of the aromatic compound in Pseudomonas.
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16
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Tourneroche A, Lami R, Hubas C, Blanchet E, Vallet M, Escoubeyrou K, Paris A, Prado S. Bacterial-Fungal Interactions in the Kelp Endomicrobiota Drive Autoinducer-2 Quorum Sensing. Front Microbiol 2019; 10:1693. [PMID: 31417510 PMCID: PMC6685064 DOI: 10.3389/fmicb.2019.01693] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022] Open
Abstract
Brown macroalgae are an essential component of temperate coastal ecosystems and a growing economic sector. They harbor diverse microbial communities that regulate algal development and health. This algal holobiont is dynamic and achieves equilibrium via a complex network of microbial and host interactions. We now report that bacterial and fungal endophytes associated with four brown algae (Ascophyllum nodosum, Pelvetia canaliculata, Laminaria digitata, and Saccharina latissima) produce metabolites that interfere with bacterial autoinducer-2 quorum sensing, a signaling system implicated in virulence and host colonization. Additionally, we performed co-culture experiments combined to a metabolomic approach and demonstrated that microbial interactions influence production of metabolites, including metabolites involved in quorum sensing. Collectively, the data highlight autoinducer-2 quorum sensing as a key metabolite in the complex network of interactions within the algal holobiont.
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Affiliation(s)
- Anne Tourneroche
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, Paris, France
| | - Raphaël Lami
- CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), USR3579, Observatoire Océanologique de Banyuls, Sorbonne Université, Banyuls-sur-Mer, France
| | - Cédric Hubas
- Muséum National d'Histoire Naturelle, UMR BOREA 7208 MNHN-Sorbonne Université-CNRS-UCN-UA-IRD, Station Marine de Concarneau, Paris, France
| | - Elodie Blanchet
- CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), USR3579, Observatoire Océanologique de Banyuls, Sorbonne Université, Banyuls-sur-Mer, France
| | - Marine Vallet
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, Paris, France
| | - Karine Escoubeyrou
- CNRS, Observatoire Océanologique de Banyuls, Sorbonne Université, FR3724, Banyuls-sur-Mer, France
| | - Alain Paris
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, Paris, France
| | - Soizic Prado
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, Paris, France
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17
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Xiao Y, Yaohari H, Zhou Z, Sze CC, Stuckey DC. Autoinducer-2-mediated quorum sensing partially regulates the toxic shock response of anaerobic digestion. WATER RESEARCH 2019; 158:94-105. [PMID: 31022531 DOI: 10.1016/j.watres.2019.04.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
This study discovered a strong correlation between the autoinducer-2 (AI-2)-mediated quorum sensing (QS) with the performance of a submerged anaerobic membrane bioreactor during its recovery from a pentachlorophenol (PCP) shock: a decrease in AI-2 levels coincided with a reduction in volatile fatty acid concentrations, and corresponded significantly to a decrease in the relative abundance of Firmicutes, and to an increase in the relative abundance of Bacteroidetes and Synergistetes. Further batch experiments with the addition of an AI-2-regulating Escherichia coli mutant culture showed that a reduction in AI-2 levels resulted in the highest biogas production rate during a PCP shock. In contrast, an increase in AI-2 levels via addition of the E. coli wild type strain or an AI-2 precursor showed no obvious effects on biogas production. These results suggest that the AI-2 level in anaerobic sludge was governed primarily by Firmicutes, and the AI-2-mediated QS partially regulates the toxic shock response of anaerobic sludge via tuning the activities of Firmicutes and Synergistetes. A decrease in the AI-2 level might reduce acetogenesis and favor hydrogenotrophic methanogenesis, thus resulting in less VFA accumulation and higher methane production during the PCP shock. This study is the first of this type that exploits the role of quorum sensing in the toxic shock response of anaerobic sludge; it demonstrates a novel approach to shortening the recovery period of anaerobic processes via manipulating the AI-2-mediated QS.
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Affiliation(s)
- Yeyuan Xiao
- Department of Civil and Environmental Engineering, Shantou University, 515063, China; Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Centre (NEWRI), Nanyang Technological University, 637141, Singapore
| | - Hazarki Yaohari
- Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Centre (NEWRI), Nanyang Technological University, 637141, Singapore
| | - Zhongbo Zhou
- Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Centre (NEWRI), Nanyang Technological University, 637141, Singapore
| | - Chun Chau Sze
- Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Centre (NEWRI), Nanyang Technological University, 637141, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - David C Stuckey
- Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Centre (NEWRI), Nanyang Technological University, 637141, Singapore; Department of Chemical Engineering, Imperial College London, SW7 2AZ, UK.
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18
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Li M, Eskridge K, Liu E, Wilkins M. Enhancement of polyhydroxybutyrate (PHB) production by 10-fold from alkaline pretreatment liquor with an oxidative enzyme-mediator-surfactant system under Plackett-Burman and central composite designs. BIORESOURCE TECHNOLOGY 2019; 281:99-106. [PMID: 30807996 DOI: 10.1016/j.biortech.2019.02.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
In this study, Plackett-Burman and central composite designs were applied to improve polyhydroxybutyrate (PHB) production from alkaline pretreatment liquor (APL) by Cupriavidus necator DSM 545 using a supplement system consisting of oxidative enzymes (laccase, aryl alcohol oxidase (AAO)), mediators (ABTS, HOBT), DMSO, silica nanoparticle Aerosol R816 and surfactant Tween 80. First, screening experiments under Plackett-Burman design showed R816, ABTS and Tween 80 could significantly enhance PHB production. Additional experiments showed that HOBT and DMSO could be removed, and laccase and AAO were needed to remain in the system. Second, a central composite design was applied to obtain the optimum supplemental levels of R816, ABTS and Tween 80. Under optimum conditions, theoretical maximum PHB production (1.9 g/L) was close to experimental PHB production (2.1 g/L). With the supplement system, a 10-fold increase was achieved compared to PHB production (0.2 g/L) without any supplements.
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Affiliation(s)
- Mengxing Li
- Department of Biological Systems Engineering, The University of Nebraska-Lincoln, Lincoln 68583, USA; Department of Statistics, The University of Nebraska-Lincoln, Lincoln 68583, USA
| | - Kent Eskridge
- Department of Statistics, The University of Nebraska-Lincoln, Lincoln 68583, USA
| | - Enshi Liu
- Department of Biological Systems Engineering, The University of Nebraska-Lincoln, Lincoln 68583, USA
| | - Mark Wilkins
- Department of Biological Systems Engineering, The University of Nebraska-Lincoln, Lincoln 68583, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588, USA; Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln 68583, USA.
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19
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Kumar P, Maharjan A, Jun H, Kim BS. Bioconversion of lignin and its derivatives into polyhydroxyalkanoates: Challenges and opportunities. Biotechnol Appl Biochem 2018; 66:153-162. [DOI: 10.1002/bab.1720] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/18/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Prasun Kumar
- Department of Chemical EngineeringChungbuk National University Chungbuk Republic of Korea
| | - Anoth Maharjan
- Department of Chemical EngineeringChungbuk National University Chungbuk Republic of Korea
| | - Hang‐Bae Jun
- Department of Environmental EngineeringChungbuk National University Chungbuk Republic of Korea
| | - Beom Soo Kim
- Department of Chemical EngineeringChungbuk National University Chungbuk Republic of Korea
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