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Caro-Astorga J, Meyerowitz JT, Stork DA, Nattermann U, Piszkiewicz S, Vimercati L, Schwendner P, Hocher A, Cockell C, DeBenedictis E. Polyextremophile engineering: a review of organisms that push the limits of life. Front Microbiol 2024; 15:1341701. [PMID: 38903795 PMCID: PMC11188471 DOI: 10.3389/fmicb.2024.1341701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/16/2024] [Indexed: 06/22/2024] Open
Abstract
Nature exhibits an enormous diversity of organisms that thrive in extreme environments. From snow algae that reproduce at sub-zero temperatures to radiotrophic fungi that thrive in nuclear radiation at Chernobyl, extreme organisms raise many questions about the limits of life. Is there any environment where life could not "find a way"? Although many individual extremophilic organisms have been identified and studied, there remain outstanding questions about the limits of life and the extent to which extreme properties can be enhanced, combined or transferred to new organisms. In this review, we compile the current knowledge on the bioengineering of extremophile microbes. We summarize what is known about the basic mechanisms of extreme adaptations, compile synthetic biology's efforts to engineer extremophile organisms beyond what is found in nature, and highlight which adaptations can be combined. The basic science of extremophiles can be applied to engineered organisms tailored to specific biomanufacturing needs, such as growth in high temperatures or in the presence of unusual solvents.
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Affiliation(s)
| | | | - Devon A. Stork
- Pioneer Research Laboratories, San Francisco, CA, United States
| | - Una Nattermann
- Pioneer Research Laboratories, San Francisco, CA, United States
| | | | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | | | - Antoine Hocher
- London Institute of Medical Sciences, London, United Kingdom
| | - Charles Cockell
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Erika DeBenedictis
- The Francis Crick Institute, London, United Kingdom
- Pioneer Research Laboratories, San Francisco, CA, United States
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2
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Yadav BNS, Sharma P, Maurya S, Yadav RK. Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil. 3 Biotech 2023; 13:423. [PMID: 38047037 PMCID: PMC10689336 DOI: 10.1007/s13205-023-03841-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.
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Affiliation(s)
- Bhupendra Narayan Singh Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Priyanka Sharma
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Shristy Maurya
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Rajiv Kumar Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
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3
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Gonzales JN, Treece TR, Mayfield SP, Simkovsky R, Atsumi S. Utilization of lignocellulosic hydrolysates for photomixotrophic chemical production in Synechococcus elongatus PCC 7942. Commun Biol 2023; 6:1022. [PMID: 37813969 PMCID: PMC10562401 DOI: 10.1038/s42003-023-05394-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023] Open
Abstract
To meet the need for environmentally friendly commodity chemicals, feedstocks for biological chemical production must be diversified. Lignocellulosic biomass are an carbon source with the potential for effective use in a large scale and cost-effective production systems. Although the use of lignocellulosic biomass lysates for heterotrophic chemical production has been advancing, there are challenges to overcome. Here we aim to investigate the obligate photoautotroph cyanobacterium Synechococcus elongatus PCC 7942 as a chassis organism for lignocellulosic chemical production. When modified to import monosaccharides, this cyanobacterium is an excellent candidate for lysates-based chemical production as it grows well at high lysate concentrations and can fix CO2 to enhance carbon efficiency. This study is an important step forward in enabling the simultaneous use of two sugars as well as lignocellulosic lysate. Incremental genetic modifications enable catabolism of both sugars concurrently without experiencing carbon catabolite repression. Production of 2,3-butanediol is demonstrated to characterize chemical production from the sugars in lignocellulosic hydrolysates. The engineered strain achieves a titer of 13.5 g L-1 of 2,3-butanediol over 12 days under shake-flask conditions. This study can be used as a foundation for industrial scale production of commodity chemicals from a combination of sunlight, CO2, and lignocellulosic sugars.
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Affiliation(s)
- Jake N Gonzales
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, 95616, USA
| | - Tanner R Treece
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Stephen P Mayfield
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shota Atsumi
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, 95616, USA.
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
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4
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Malla S, van der Helm E, Darbani B, Wieschalka S, Förster J, Borodina I, Sommer MOA. A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics. Front Microbiol 2022; 13:855736. [PMID: 35495724 PMCID: PMC9048822 DOI: 10.3389/fmicb.2022.855736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/23/2022] [Indexed: 12/14/2022] Open
Abstract
Lack of active export system often limits the industrial bio-based production processes accumulating the intracellular product and hence complexing the purification steps. L-lysine, an essential amino acid, is produced biologically in quantities exceeding two million tons per year; yet, L-lysine production is challenged by efficient export system at high titers during fermentation. To address this issue, new exporter candidates for efficient efflux of L-lysine are needed. Using metagenomic functional selection, we identified 58 genes encoded on 28 unique metagenomic fragments from cow gut microbiome library that improved L-lysine tolerance. These genes include a novel L-lysine transporter, belonging to a previously uncharacterized EamA superfamily, which is further in vivo characterized as L-lysine exporter using Xenopus oocyte expression system as well as Escherichia coli host. This novel exporter improved L-lysine tolerance in E. coli by 40% and enhanced yield, titer, and the specific production of L-lysine in an industrial Corynebacterium glutamicum strain by 7.8%, 9.5%, and 12%, respectively. Our approach allows the sequence-independent discovery of novel exporters and can be deployed to increase titers and productivity of toxicity-limited bioprocesses.
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Khan JA, Guss AM, Kao KC. Enhancing transcription in Escherichia coli and Pseudomonas putida using bacteriophage lambda anti-terminator protein Q. Biotechnol Lett 2021; 44:253-258. [PMID: 34792701 DOI: 10.1007/s10529-021-03206-x] [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: 07/08/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Functional characterization of metagenomic DNA often involves expressing heterologous DNA in genetically tractable microorganisms such as Escherichia coli. Functional expression of heterologous genes can suffer from limitations due to the lack of recognition of foreign promoters or presence of intrinsic terminators on foreign DNA between a vector-based promoter and the transcription start site. Anti-terminator proteins are a possible solution to overcome this limitation. When bacteriophage lambda infects E. coli, it relies on the host transcription machinery to transcribe and express phage DNA. Lambda anti-terminator protein Q (λQ) regulates the expression of late-genes of phage lambda. E. coli RNA polymerase recognizes the PR' promoter on the lambda genome and forms a complex with λQ, to overcome the terminator tR'. Here we show the use of λQ to efficiently transcribe a capsular polysaccharide cluster, cps3, from Lactobacillus plantarum containing intrinsic terminators in Escherichia coli. In addition, we expand the use of anti-terminator λQ in Pseudomonas putida. The results show ~ fivefold higher expression of a fluorescent reporter located ~ 12.5kbp downstream from the promoter, when the transcription is driven by PR' promoter in presence of λQ compared to a lac promoter. These results suggest that λQ could be used in metabolic engineering to enhance expression of heterologous DNA.
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Affiliation(s)
- Jibran A Khan
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6038, USA
| | - Katy C Kao
- Department of Chemical and Materials Engineering, San Jose State University, San José, CA, USA.
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Crofts TS, McFarland AG, Hartmann EM. Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries. mSystems 2021; 6:e0052421. [PMID: 34184912 PMCID: PMC8269240 DOI: 10.1128/msystems.00524-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
Functional metagenomic libraries, physical bacterial libraries which allow the high-throughput capture and expression of microbiome genes, have been instrumental in the sequence-naive and cultivation-independent exploration of metagenomes. However, preparation of these libraries is often limited by their high DNA input requirement and their low cloning efficiency. Here, we describe a new method, mosaic ends tagmentation (METa) assembly, for highly efficient functional metagenomic library preparation. We applied tagmentation to metagenomic DNA from soil and gut microbiomes to prepare DNA inserts for high-throughput cloning into functional metagenomic libraries. The presence of mosaic end sequences in the resulting DNA fragments synergized with homology-based assembly cloning to result in a 300-fold increase in cloning efficiency compared to traditional blunt-cloning-based protocols. We show that compared to published libraries prepared by state-of-the-art protocols, METa assembly is on average ca. 20- to 200-fold more efficient and can prepare gigabase-sized libraries with as little as 200 ng of input DNA. We show the usefulness of METa assembly first by using a normative 5-μg mass of soil metagenomic DNA to prepare a 700-Gb library that allowed us to discover novel nourseothricin resistance genes and a potentially new mode of resistance to this antibiotic and second by using only 300 ng of goose fecal metagenomic DNA to prepare a 27-Gb library that captured numerous tetracycline and colistin resistance genes. METa assembly provides a streamlined, flexible, and efficient method for preparing functional metagenomic libraries, enabling new avenues of genetic and biochemical research into low-biomass or scarce microbiomes. IMPORTANCE Medically and industrially important genes can be recovered from microbial communities by high-throughput sequencing, but precise annotation is often limited to characterized genes and their relatives. Cloning a metagenome en masse into an expression host to produce a functional metagenomic library, directly connecting genes to functions, is a sequence-naive and cultivation-independent method to discover novel genes. The process of preparing these libraries is DNA greedy and inefficient, however. Here, we describe a library preparation method that is an order of magnitude more efficient and less DNA greedy. This method is consistently efficient across libraries prepared from cultures, a soil microbiome, and a goose fecal microbiome and allowed us to discover new antibiotic resistance genes and mechanisms. This library preparation method will potentially allow the functional metagenomic exploration of microbiomes that were previously off limits due to their rarity or low microbial biomass, such as biomedical swabs or exotic samples.
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Affiliation(s)
- Terence S. Crofts
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Alexander G. McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
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Díaz-García L, Bugg TDH, Jiménez DJ. Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach. MICROBIAL ECOLOGY 2020; 80:885-896. [PMID: 32572536 DOI: 10.1007/s00248-020-01546-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/15/2020] [Indexed: 05/25/2023]
Abstract
An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.
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Affiliation(s)
- Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | | | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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Onyeabor M, Martinez R, Kurgan G, Wang X. Engineering transport systems for microbial production. ADVANCES IN APPLIED MICROBIOLOGY 2020; 111:33-87. [PMID: 32446412 DOI: 10.1016/bs.aambs.2020.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter highlights recent advancements in engineering microbial efflux systems to enhance cellular tolerance to industrially relevant chemical stress. Lastly, future directions to address current technological gaps are discussed.
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Affiliation(s)
- Moses Onyeabor
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Rodrigo Martinez
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Gavin Kurgan
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.
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9
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Forsberg KJ, Bhatt IV, Schmidtke DT, Javanmardi K, Dillard KE, Stoddard BL, Finkelstein IJ, Kaiser BK, Malik HS. Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome. eLife 2019; 8:e46540. [PMID: 31502535 PMCID: PMC6739867 DOI: 10.7554/elife.46540] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 08/09/2019] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas systems protect bacteria and archaea from phages and other mobile genetic elements, which use small anti-CRISPR (Acr) proteins to overcome CRISPR-Cas immunity. Because Acrs are challenging to identify, their natural diversity and impact on microbial ecosystems are underappreciated. To overcome this discovery bottleneck, we developed a high-throughput functional selection to isolate ten DNA fragments from human oral and fecal metagenomes that inhibit Streptococcus pyogenes Cas9 (SpyCas9) in Escherichia coli. The most potent Acr from this set, AcrIIA11, was recovered from a Lachnospiraceae phage. We found that AcrIIA11 inhibits SpyCas9 in bacteria and in human cells. AcrIIA11 homologs are distributed across diverse bacteria; many distantly-related homologs inhibit both SpyCas9 and a divergent Cas9 from Treponema denticola. We find that AcrIIA11 antagonizes SpyCas9 using a different mechanism than other previously characterized Type II-A Acrs. Our study highlights the power of functional selection to uncover widespread Cas9 inhibitors within diverse microbiomes.
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Affiliation(s)
- Kevin J Forsberg
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Ishan V Bhatt
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Danica T Schmidtke
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Kamyab Javanmardi
- Department of Molecular Biosciences and Institute of Cellular and Molecular BiologyUniversity of Texas at AustinAustinUnited States
| | - Kaylee E Dillard
- Department of Molecular Biosciences and Institute of Cellular and Molecular BiologyUniversity of Texas at AustinAustinUnited States
| | - Barry L Stoddard
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute of Cellular and Molecular BiologyUniversity of Texas at AustinAustinUnited States
- Center for Systems Biology and Synthetic BiologyUniversity of Texas at AustinAustinUnited States
| | - Brett K Kaiser
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
- Department of BiologySeattle UniversitySeattleUnited States
| | - Harmit S Malik
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research CenterSeattleUnited States
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Bioprospecting of Native Efflux Pumps To Enhance Furfural Tolerance in Ethanologenic Escherichia coli. Appl Environ Microbiol 2019; 85:AEM.02985-18. [PMID: 30635383 DOI: 10.1128/aem.02985-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/04/2019] [Indexed: 02/03/2023] Open
Abstract
Efficient microbial conversion of lignocellulose into valuable products is often hindered by the presence of furfural, a dehydration product of pentoses in hemicellulose sugar syrups derived from woody biomass. For a cost-effective lignocellulose microbial conversion, robust biocatalysts are needed that can tolerate toxic inhibitors while maintaining optimal metabolic activities. A comprehensive plasmid-based library encoding native multidrug resistance (MDR) efflux pumps, porins, and select exporters from Escherichia coli was screened for furfural tolerance in an ethanologenic E. coli strain. Small multidrug resistance (SMR) pumps, such as SugE and MdtJI, as well as a lactate/glycolate:H+ symporter, LldP, conferred furfural tolerance in liquid culture tests. Expression of the SMR pump potentially increased furfural efflux and cellular viability upon furfural assault, suggesting novel activities for SMR pumps as furfural efflux proteins. Furthermore, induced expression of mdtJI enhanced ethanol fermentative production of LY180 in the presence of furfural or 5-hydroxymethylfurfural, further demonstrating the applications of SMR pumps. This work describes an effective approach to identify useful efflux systems with desired activities for nonnative toxic chemicals and provides a platform to further enhance furfural efflux by protein engineering and mutagenesis.IMPORTANCE Lignocellulosic biomass, especially agricultural residues, represents an important potential feedstock for microbial production of renewable fuels and chemicals. During the deconstruction of hemicellulose by thermochemical processes, side products that inhibit cell growth and production, such as furan aldehydes, are generated, limiting cost-effective lignocellulose conversion. Here, we developed a new approach to increase cellular tolerance by expressing multidrug resistance (MDR) pumps with putative efflux activities for furan aldehydes. The developed plasmid library and screening methods may facilitate new discoveries of MDR pumps for diverse toxic chemicals important for microbial conversion.
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Mathews SL, Epps MJ, Blackburn RK, Goshe MB, Grunden AM, Dunn RR. Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste. ROYAL SOCIETY OPEN SCIENCE 2019; 6:180748. [PMID: 31031986 PMCID: PMC6458430 DOI: 10.1098/rsos.180748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 02/07/2019] [Indexed: 05/04/2023]
Abstract
A citizen science project found that the greenhouse camel cricket (Diestrammena asynamora) is common in North American homes. Public response was to wonder 'what good are they anyway?' and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle (Dermestes maculatus) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified that were capable of growth on lignocellulosic components, including lignin. Cedecea lapagei was selected for further study due to growth on most lignocellulose components. The C. lapagei secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms.
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Affiliation(s)
- Stephanie L. Mathews
- Department of Biological Sciences, Campbell University, Buies Creek, NC 27506, USA
| | - Mary Jane Epps
- Department of Biology, Mary Baldwin University, Staunton, VA 24401, USA
| | - R. Kevin Blackburn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Michael B. Goshe
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Amy M. Grunden
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
- Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen, 2100Denmark
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12
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The evolving interface between synthetic biology and functional metagenomics. Nat Chem Biol 2018; 14:752-759. [DOI: 10.1038/s41589-018-0100-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 06/13/2018] [Indexed: 12/15/2022]
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13
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Wang S, Sun X, Yuan Q. Strategies for enhancing microbial tolerance to inhibitors for biofuel production: A review. BIORESOURCE TECHNOLOGY 2018; 258:302-309. [PMID: 29567023 DOI: 10.1016/j.biortech.2018.03.064] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 05/05/2023]
Abstract
Using lignocellulosic biomass for the production of renewable biofuel provides a sustainable and promising solution to the crisis of energy and environment. However, the processes of biomass pretreatment and biofuel fermentation bring a variety of inhibitors to microbial strains. These inhibitors repress microbial growth, decrease biofuel yields and increase fermentation costs. The production of biofuels from renewable lignocellulosic biomass relies on the development of tolerant and robust microbial strains. In recent years, the advancement of tolerance engineering and evolutionary engineering provides powerful platform for obtaining host strains with desired tolerance for further metabolic engineering of biofuel pathways. In this review, we summarized the inhibitors derived from biomass pretreatment and biofuel fermentation, the mechanisms of inhibitor toxicity, and the strategies for enhancing microbial tolerance.
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Affiliation(s)
- Shizeng Wang
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China.
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14
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Jarboe LR. Improving the success and impact of the metabolic engineering design, build, test, learn cycle by addressing proteins of unknown function. Curr Opin Biotechnol 2018; 53:93-98. [PMID: 29306676 DOI: 10.1016/j.copbio.2017.12.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/12/2017] [Accepted: 12/17/2017] [Indexed: 12/20/2022]
Abstract
Rational, predictive metabolic engineering of organisms requires an ability to associate biological activity to the corresponding gene(s). Despite extensive advances in the 20 years since the Escherichia coli genome was published, there are still gaps in our knowledge of protein function. The substantial amount of data that has been published, such as: omics-level characterization in a myriad of conditions; genome-scale libraries; and evolution and genome sequencing, provide means of identifying and prioritizing proteins for characterization. This review describes the scale of this knowledge gap, demonstrates the benefit of addressing the knowledge gap, and demonstrates the availability of interesting candidates for characterization.
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Affiliation(s)
- Laura R Jarboe
- Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, United States; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, United States.
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Ceballos SJ, Yu C, Claypool JT, Singer SW, Simmons BA, Thelen MP, Simmons CW, VanderGheynst JS. Development and characterization of a thermophilic, lignin degrading microbiota. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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