1
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Boeck L. Pooled profiling of natural Mycobacterium tuberculosis diversity: linking genes, bacterial behaviours, and clinical outcomes. THE LANCET. MICROBE 2024; 5:e510-e511. [PMID: 38734027 DOI: 10.1016/s2666-5247(24)00070-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 05/13/2024]
Affiliation(s)
- Lucas Boeck
- Department of Biomedicine, University of Basel, Basel 4031, Switzerland.
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2
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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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3
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Voogdt CGP, Tripathi S, Bassler SO, McKeithen-Mead SA, Guiberson ER, Koumoutsi A, Bravo AM, Buie C, Zimmermann M, Sonnenburg JL, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics. Cell Rep 2024; 43:113519. [PMID: 38142398 DOI: 10.1016/j.celrep.2023.113519] [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: 07/17/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
The critical role of the intestinal microbiota in human health and disease is well recognized. Nevertheless, there are still large gaps in our understanding of the functions and mechanisms encoded in the genomes of most members of the gut microbiota. Genome-scale libraries of transposon mutants are a powerful tool to help us address this gap. Recent advances in barcoded transposon mutagenesis have dramatically lowered the cost of mutant fitness determination in hundreds of in vitro and in vivo experimental conditions. In an accompanying review, we discuss recent advances and caveats for the construction of pooled and arrayed barcoded transposon mutant libraries in human gut commensals. In this review, we discuss how these libraries can be used across a wide range of applications, the technical aspects involved, and expectations for such screens.
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Affiliation(s)
- Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Saria A McKeithen-Mead
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emma R Guiberson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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4
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Medin S, Dressel A, Specht DA, Sheppard TJ, Holycross ME, Reid MC, Gazel E, Wu M, Barstow B. Multiple Rounds of In Vivo Random Mutagenesis and Selection in Vibrio natriegens Result in Substantial Increases in REE Binding Capacity. ACS Synth Biol 2023; 12:3680-3694. [PMID: 38055772 PMCID: PMC10729037 DOI: 10.1021/acssynbio.3c00484] [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: 08/09/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023]
Abstract
Rare earth elements (REE) are essential ingredients in many modern technologies, yet their purification remains either environmentally harmful or economically unviable. Adsorption, or biosorption, of REE onto bacterial cell membranes offers a sustainable alternative to traditional solvent extraction methods. But in order for biosorption-based REE purification to compete economically, the capacity and specificity of biosorption sites must be enhanced. Although there have been some recent advances in characterizing the genetics of REE-biosorption, the variety and complexity of bacterial membrane surface sites make targeted genetic engineering difficult. Here, we propose using multiple rounds of in vivo random mutagenesis induced by the MP6 plasmid combined with plate-throughput REE-biosorption screening to improve a microbe's capacity and selectivity for biosorbing REE. We engineered a strain of Vibrio natriegens capable of biosorbing 210% more dysprosium compared to the wild-type and produced selectivity improvements of up to 50% between the lightest (lanthanum) and heaviest (lutetium) REE. We believe that mutations we observed in ABC transporters as well as a nonessential protein in the BAM outer membrane β-barrel protein insertion complex likely contribute to some─but almost certainly not all─of the biosorption changes we observed. Given the ease of finding significant biosorption mutants, these results highlight just how many genes likely contribute to biosorption as well as the power of random mutagenesis in identifying genes of interest and optimizing a biological system for a task.
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Affiliation(s)
- Sean Medin
- Department
of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Anastacia Dressel
- Department
of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - David A. Specht
- Department
of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Timothy J. Sheppard
- Department
of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Megan E. Holycross
- Department
of Earth and Atmospheric Sciences, Cornell
University, Ithaca, New York 14853, United States
| | - Matthew C. Reid
- School
of Civil and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Esteban Gazel
- Department
of Earth and Atmospheric Sciences, Cornell
University, Ithaca, New York 14853, United States
| | - Mingming Wu
- Department
of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Buz Barstow
- Department
of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
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5
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Medin S, Schmitz AM, Pian B, Mini K, Reid MC, Holycross M, Gazel E, Wu M, Barstow B. Genomic characterization of rare earth binding by Shewanella oneidensis. Sci Rep 2023; 13:15975. [PMID: 37749198 PMCID: PMC10520059 DOI: 10.1038/s41598-023-42742-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
Rare earth elements (REE) are essential ingredients of sustainable energy technologies, but separation of individual REE is one of the hardest problems in chemistry today. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for separation of rare earth elements (REE). The REE-biosorption capability of some microorganisms allows for REE separations that, under specialized conditions, are already competitive with solvent extractions, suggesting that genetic engineering could allow it to leapfrog existing technologies. To identify targets for genomic improvement we screened 3,373 mutants from the whole genome knockout collection of the known REE-biosorbing microorganism Shewanella oneidensis MR-1. We found 130 genes that increased biosorption of the middle REE europium, and 112 that reduced it. We verified biosorption changes from the screen for a mixed solution of three REE (La, Eu, Yb) using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) in solution conditions with a range of ionic strengths and REE concentrations. We identified 18 gene ontologies and 13 gene operons that make up key systems that affect biosorption. We found, among other things, that disruptions of a key regulatory component of the arc system (hptA), which regulates cellular response to anoxic environments and polysaccharide biosynthesis related genes (wbpQ, wbnJ, SO_3183) consistently increase biosorption across all our solution conditions. Our largest total biosorption change comes from our SO_4685, a capsular polysaccharide (CPS) synthesis gene, disruption of which results in an up to 79% increase in biosorption; and nusA, a transcriptional termination/anti-termination protein, disruption of which results in an up to 35% decrease in biosorption. Knockouts of glnA, pyrD, and SO_3183 produce small but significant increases (≈ 1%) in relative biosorption affinity for ytterbium over lanthanum in multiple solution conditions tested, while many other genes we explored have more complex binding affinity changes. Modeling suggests that while these changes to lanthanide biosorption selectivity are small, they could already reduce the length of repeated enrichment process by up to 27%. This broad exploratory study begins to elucidate how genetics affect REE-biosorption by S. oneidensis, suggests new areas of investigation for better mechanistic understanding of the membrane chemistry involved in REE binding, and offer potential targets for improving biosorption and separation of REE by genetic engineering.
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Affiliation(s)
- Sean Medin
- Department of Biological and Environmental Engineering, Cornell University, Cornell University, 228 Riley-Robb Hall, Ithaca, NY, 14853, USA
| | - Alexa M Schmitz
- Department of Biological and Environmental Engineering, Cornell University, Cornell University, 228 Riley-Robb Hall, Ithaca, NY, 14853, USA
| | - Brooke Pian
- Department of Biological and Environmental Engineering, Cornell University, Cornell University, 228 Riley-Robb Hall, Ithaca, NY, 14853, USA
| | - Kuunemuebari Mini
- Department of Sciences and Technology Studies, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew C Reid
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Megan Holycross
- Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Esteban Gazel
- Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Mingming Wu
- Department of Biological and Environmental Engineering, Cornell University, Cornell University, 228 Riley-Robb Hall, Ithaca, NY, 14853, USA
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Cornell University, 228 Riley-Robb Hall, Ithaca, NY, 14853, USA.
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6
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Willett JLE, Barnes AMT, Brunson DN, Lecomte A, Robertson EB, Dunny GM. Optimized Replication of Arrayed Bacterial Mutant Libraries Increases Access to Biological Resources. Microbiol Spectr 2023; 11:e0169323. [PMID: 37432110 PMCID: PMC10434011 DOI: 10.1128/spectrum.01693-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/19/2023] [Indexed: 07/12/2023] Open
Abstract
Biological collections, including arrayed libraries of single transposon (Tn) or deletion mutants, greatly accelerate the pace of bacterial genetic research. Despite the importance of these resources, few protocols exist for the replication and distribution of these materials. Here, we describe a protocol for creating multiple replicates of an arrayed bacterial Tn library consisting of approximately 6,800 mutants in 96-well plates (73 plates). Our protocol provides multiple checkpoints to guard against contamination and minimize genetic drift caused by freeze/thaw cycles. This approach can also be scaled for arrayed culture collections of various sizes. Overall, this protocol is a valuable resource for other researchers considering the construction and distribution of arrayed culture collection resources for the benefit of the greater scientific community. IMPORTANCE Arrayed mutant collections drive robust genetic screens, but few protocols exist for replication of these resources and subsequent quality control. Increasing the distribution of arrayed biological collections will increase the accessibility and use of these resources. Developing standardized techniques for replication of these resources is essential for ensuring their quality and usefulness to the scientific community.
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Affiliation(s)
- Julia L. E. Willett
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Aaron M. T. Barnes
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Debra N. Brunson
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Alexandre Lecomte
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Ethan B. Robertson
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Gary M. Dunny
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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7
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Winkler KR, Mizrahi V, Warner DF, De Wet TJ. High-throughput functional genomics: A (myco)bacterial perspective. Mol Microbiol 2023; 120:141-158. [PMID: 37278255 PMCID: PMC10953053 DOI: 10.1111/mmi.15103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/06/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023]
Abstract
Advances in sequencing technologies have enabled unprecedented insights into bacterial genome composition and dynamics. However, the disconnect between the rapid acquisition of genomic data and the (much slower) confirmation of inferred genetic function threatens to widen unless techniques for fast, high-throughput functional validation can be applied at scale. This applies equally to Mycobacterium tuberculosis, the leading infectious cause of death globally and a pathogen whose genome, despite being among the first to be sequenced two decades ago, still contains many genes of unknown function. Here, we summarize the evolution of bacterial high-throughput functional genomics, focusing primarily on transposon (Tn)-based mutagenesis and the construction of arrayed mutant libraries in diverse bacterial systems. We also consider the contributions of CRISPR interference as a transformative technique for probing bacterial gene function at scale. Throughout, we situate our analysis within the context of functional genomics of mycobacteria, focusing specifically on the potential to yield insights into M. tuberculosis pathogenicity and vulnerabilities for new drug and regimen development. Finally, we offer suggestions for future approaches that might be usefully applied in elucidating the complex cellular biology of this major human pathogen.
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Affiliation(s)
- Kristy R. Winkler
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
- Wellcome Centre for Infectious Diseases Research in AfricaUniversity of Cape TownRondeboschSouth Africa
| | - Digby F. Warner
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
- Wellcome Centre for Infectious Diseases Research in AfricaUniversity of Cape TownRondeboschSouth Africa
| | - Timothy J. De Wet
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
- Wellcome Centre for Infectious Diseases Research in AfricaUniversity of Cape TownRondeboschSouth Africa
- Department of Integrative Biomedical SciencesUniversity of Cape TownRondeboschSouth Africa
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8
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Müller J, Bollenbach T. Quantitative approaches to study phenotypic effects of large-scale genetic perturbations. Curr Opin Microbiol 2023; 74:102333. [PMID: 37276805 DOI: 10.1016/j.mib.2023.102333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/30/2023] [Accepted: 05/08/2023] [Indexed: 06/07/2023]
Abstract
How microbes interact with their environment and how the complex interplay of their genes enables them to survive and thrive under stress is a fundamental question in microbial system biology, which is also important from a public health perspective. Large-scale studies of gene-gene, gene-drug, and drug-drug interactions have proven to be powerful tools for elucidating gene function and functional modules in the cell. Approaches that systematically quantify phenotypes in libraries of microbial strains with genome-wide genetic perturbations are crucial for progress in this area. Here, we review recent advances in this field, and point out applications to the study of gene-drug interactions. We highlight newly developed techniques for the rapid generation of genome-wide mutant libraries and the high-throughput measurement of more complex phenotypes and other observables, such as cell morphology or thermal stability of the proteome.
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Affiliation(s)
- Janina Müller
- Institute for Biological Physics, University of Cologne, 50931 Cologne, Germany
| | - Tobias Bollenbach
- Institute for Biological Physics, University of Cologne, 50931 Cologne, Germany; Center for Data and Simulation Science, University of Cologne, 50931 Cologne, Germany.
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9
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Johnson MS, Venkataram S, Kryazhimskiy S. Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes. J Mol Evol 2023; 91:263-280. [PMID: 36651964 PMCID: PMC10276077 DOI: 10.1007/s00239-022-10083-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023]
Abstract
Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.
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Affiliation(s)
- Milo S Johnson
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Sandeep Venkataram
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093, USA.
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10
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Willett JLE, Barnes AMT, Brunson DN, Lecomte A, Robertson EB, Dunny GM. Optimized replication of arrayed bacterial mutant libraries increase access to biological resources. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.537918. [PMID: 37162974 PMCID: PMC10168237 DOI: 10.1101/2023.04.25.537918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Biological collections, including arrayed libraries of single transposon or deletion mutants, greatly accelerate the pace of bacterial genetics research. Despite the importance of these resources, few protocols exist for the replication and distribution of these materials. Here, we describe a protocol for creating multiple replicates of an arrayed bacterial Tn library consisting of approximately 6,800 mutants in 73 × 96-well plates. Our protocol provides multiple checkpoints to guard against contamination and minimize genetic drift caused by freeze/thaw cycles. This approach can also be scaled for arrayed culture collections of various sizes. Overall, this protocol is a valuable resource for other researchers considering the construction and distribution of arrayed culture collection resources for the benefit of the greater scientific community. Importance Arrayed mutant collections drive robust genetic screens, yet few protocols exist for replication of these resources and subsequent quality control. Increasing distribution of arrayed biological collections will increase accessibility to and use of these resources. Developing standardized techniques for replication of these resources is essential for ensuring their quality and usefulness to the scientific community.
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Affiliation(s)
- Julia L. E. Willett
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN USA
| | - Aaron M. T. Barnes
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN USA
- Present address: Minnesota Department of Health, MN, USA
| | - Debra N. Brunson
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL USA
| | - Alexandre Lecomte
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Ethan B. Robertson
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN USA
| | - Gary M. Dunny
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN USA
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11
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Mycobacterium tuberculosis Requires the Outer Membrane Lipid Phthiocerol Dimycocerosate for Starvation-Induced Antibiotic Tolerance. mSystems 2023; 8:e0069922. [PMID: 36598240 PMCID: PMC9948706 DOI: 10.1128/msystems.00699-22] [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] [Indexed: 01/05/2023] Open
Abstract
Tolerance of Mycobacterium tuberculosis to antibiotics contributes to the long duration of tuberculosis (TB) treatment and the emergence of drug-resistant strains. M. tuberculosis drug tolerance is induced by nutrient restriction, but the genetic determinants that promote antibiotic tolerance triggered by nutrient limitation have not been comprehensively identified. Here, we show that M. tuberculosis requires production of the outer membrane lipid phthiocerol dimycocerosate (PDIM) to tolerate antibiotics under nutrient-limited conditions. We developed an arrayed transposon (Tn) mutant library in M. tuberculosis Erdman and used orthogonal pooling and transposon sequencing (Tn-seq) to map the locations of individual mutants in the library. We screened a subset of the library (~1,000 mutants) by Tn-seq and identified 32 and 102 Tn mutants with altered tolerance to antibiotics under stationary-phase and phosphate-starved conditions, respectively. Two mutants recovered from the arrayed library, ppgK::Tn and clpS::Tn, showed increased susceptibility to two different drug combinations under both nutrient-limited conditions, but their phenotypes were not complemented by the Tn-disrupted gene. Whole-genome sequencing revealed single nucleotide polymorphisms in both the ppgK::Tn and clpS::Tn mutants that prevented PDIM production. Complementation of the clpS::Tn ppsD Q291* mutant with ppsD restored PDIM production and antibiotic tolerance, demonstrating that loss of PDIM sensitized M. tuberculosis to antibiotics. Our data suggest that drugs targeting production of PDIM, a critical M. tuberculosis virulence determinant, have the potential to enhance the efficacy of existing antibiotics, thereby shortening TB treatment and limiting development of drug resistance. IMPORTANCE Mycobacterium tuberculosis causes 10 million cases of active TB disease and over 1 million deaths worldwide each year. TB treatment is complex, requiring at least 6 months of therapy with a combination of antibiotics. One factor that contributes to the length of TB treatment is M. tuberculosis phenotypic antibiotic tolerance, which allows the bacteria to survive prolonged drug exposure even in the absence of genetic mutations causing drug resistance. Here, we report a genetic screen to identify M. tuberculosis genes that promote drug tolerance during nutrient starvation. Our study revealed the outer membrane lipid phthiocerol dimycocerosate (PDIM) as a key determinant of M. tuberculosis antibiotic tolerance triggered by nutrient starvation. Our study implicates PDIM synthesis as a potential target for development of new TB drugs that would sensitize M. tuberculosis to existing antibiotics to shorten TB treatment.
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12
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Venkataram S, Kuo HY, Hom EFY, Kryazhimskiy S. Mutualism-enhancing mutations dominate early adaptation in a two-species microbial community. Nat Ecol Evol 2023; 7:143-154. [PMID: 36593292 DOI: 10.1038/s41559-022-01923-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/03/2022] [Indexed: 01/03/2023]
Abstract
Species interactions drive evolution while evolution shapes these interactions. The resulting eco-evolutionary dynamics and their repeatability depend on how adaptive mutations available to community members affect fitness and ecologically relevant traits. However, the diversity of adaptive mutations is not well characterized, and we do not know how this diversity is affected by the ecological milieu. Here we use barcode lineage tracking to address this question in a community of yeast Saccharomyces cerevisiae and alga Chlamydomonas reinhardtii that have a net commensal relationship that results from a balance between competitive and mutualistic interactions. We find that yeast has access to many adaptive mutations with diverse ecological consequences, in particular those that increase and reduce the yields of both species. The presence of the alga does not change which mutations are adaptive in yeast (that is, there is no fitness trade-off for yeast between growing alone or with alga), but rather shifts selection to favour yeast mutants that increase the yields of both species and make the mutualism stronger. Thus, in the presence of the alga, adaptative mutations contending for fixation in yeast are more likely to enhance the mutualism, even though cooperativity is not directly favoured by natural selection in our system. Our results demonstrate that ecological interactions not only alter the trajectory of evolution but also dictate its repeatability; in particular, weak mutualisms can repeatably evolve to become stronger.
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Affiliation(s)
- Sandeep Venkataram
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, USA
| | - Huan-Yu Kuo
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, USA.,Department of Physics, University of California San Diego, La Jolla, CA, USA
| | - Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, USA.
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13
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Construction of an Ordered Transposon Library for Uropathogenic Proteus mirabilis HI4320. Microbiol Spectr 2022; 10:e0314222. [PMID: 36377916 PMCID: PMC9769666 DOI: 10.1128/spectrum.03142-22] [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] [Indexed: 11/16/2022] Open
Abstract
Ordered transposon libraries are a valuable resource for many bacterial species, especially those with difficult methods for generating targeted genetic mutations. Here, we present the construction of an ordered transposon library for the bacterial urinary tract pathogen Proteus mirabilis strain HI4320. This library will facilitate future studies into P. mirabilis biology. For large experimental screens, it may be used to overcome bottleneck constraints and avoid biased outcomes resulting from gene length. For smaller studies, the library allows sidestepping the laborious construction of single targeted mutants. This library, containing 18,432 wells, was condensed into a smaller library containing 1,728 mutants. Each selected mutant had a single transposon insertion in an open reading frame, covering 45% of predicted genes encoded by P. mirabilis HI4320. This coverage was lower than expected and was due both to library wells with no mapped insertions and a surprisingly high proportion of mixed clones and multiple transposon insertion events. We offer recommendations for improving future library construction and suggestions for how to use this P. mirabilis library resource. IMPORTANCE Ordered libraries facilitate large genetic screens by guaranteeing high genomic coverage with a minimal number of mutants, and they can save time and effort by reducing the need to construct targeted mutations. This resource is now available for P. mirabilis, a common and complicating agent of catheter-associated urinary tract infection. We also present obstacles encountered during library construction with the goal to aid others who would like to construct ordered transposon libraries in other species.
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14
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Arjes HA, Sun J, Liu H, Nguyen TH, Culver RN, Celis AI, Walton SJ, Vasquez KS, Yu FB, Xue KS, Newton D, Zermeno R, Weglarz M, Deutschbauer A, Huang KC, Shiver AL. Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron. BMC Biol 2022; 20:285. [PMID: 36527020 PMCID: PMC9758874 DOI: 10.1186/s12915-022-01481-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. RESULTS Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. CONCLUSION We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.
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Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taylor H Nguyen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rebecca N Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Arianna I Celis
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sophie Jean Walton
- Biophysics Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Katherine S Xue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel Newton
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ricardo Zermeno
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA, USA
| | - Meredith Weglarz
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Biophysics Training Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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15
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Long X, Zhang H, Cao X, Wang H, Shimokawa K, Chi H, Zhang C, Okamoto A, Li X. Biogenic Mn2O3 via the redox of Shewanella oneidensis MR-1 for peroxymonosulfate advanced oxidation. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.122144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Goodall ECA, Morris FC, McKeand SA, Sullivan R, Warner IA, Sheehan E, Boelter G, Icke C, Cunningham AF, Cole JA, Banzhaf M, Bryant JA, Henderson IR. LI-Detector: a Method for Curating Ordered Gene-Replacement Libraries. Microbiol Spectr 2022; 10:e0083322. [PMID: 35856675 PMCID: PMC9431181 DOI: 10.1128/spectrum.00833-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/01/2022] [Indexed: 12/04/2022] Open
Abstract
In recent years the availability of genome sequence information has grown logarithmically resulting in the identification of a plethora of uncharacterized genes. To address this gap in functional annotation, many high-throughput screens have been devised to uncover novel gene functions. Gene-replacement libraries are one such tool that can be screened in a high-throughput way to link genotype and phenotype and are key community resources. However, for a phenotype to be attributed to a specific gene, there needs to be confidence in the genotype. Construction of large libraries can be laborious and occasionally errors will arise. Here, we present a rapid and accurate method for the validation of any ordered library where a gene has been replaced or disrupted by a uniform linear insertion (LI). We applied our method (LI-detector) to the well-known Keio library of Escherichia coli gene-deletion mutants. Our method identified 3,718 constructed mutants out of a total of 3,728 confirmed isolates, with a success rate of 99.7% for identifying the correct kanamycin cassette position. This data set provides a benchmark for the purity of the Keio mutants and a screening method for mapping the position of any linear insertion, such as an antibiotic resistance cassette in any ordered library. IMPORTANCE The construction of ordered gene replacement libraries requires significant investment of time and resources to create a valuable community resource. During construction, technical errors may result in a limited number of incorrect mutants being made. Such mutants may confound the output of subsequent experiments. Here, using the remarkable E. coli Keio knockout library, we describe a method to rapidly validate the construction of every mutant.
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Affiliation(s)
- Emily C. A. Goodall
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Faye C. Morris
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Samantha A. McKeand
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Rudi Sullivan
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Isabel A. Warner
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Emma Sheehan
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Gabriela Boelter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Christopher Icke
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Adam F. Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Jeffrey A. Cole
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Jack A. Bryant
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Ian R. Henderson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
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17
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Sackett JD, Kamble N, Leach E, Schuelke T, Wilbanks E, Rowe AR. Genome-Scale Mutational Analysis of Cathode-Oxidizing Thioclava electrotropha ElOx9 T. Front Microbiol 2022; 13:909824. [PMID: 35756027 PMCID: PMC9226611 DOI: 10.3389/fmicb.2022.909824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular electron transfer (EET) – the process by which microorganisms transfer electrons across their membrane(s) to/from solid-phase materials – has implications for a wide range of biogeochemically important processes in marine environments. Though EET is thought to play an important role in the oxidation of inorganic minerals by lithotrophic organisms, the mechanisms involved in the oxidation of solid particles are poorly understood. To explore the genetic basis of oxidative EET, we utilized genomic analyses and transposon insertion mutagenesis screens (Tn-seq) in the metabolically flexible, lithotrophic Alphaproteobacterium Thioclava electrotropha ElOx9T. The finished genome of this strain is 4.3 MB, and consists of 4,139 predicted ORFs, 54 contain heme binding motifs, and 33 of those 54 are predicted to localize to the cell envelope or have unknown localizations. To begin to understand the genetic basis of oxidative EET in ElOx9T, we constructed a transposon mutant library in semi-rich media which was comprised of >91,000 individual mutants encompassing >69,000 unique TA dinucleotide insertion sites. The library was subjected to heterotrophic growth on minimal media with acetate and autotrophic oxidative EET conditions on indium tin oxide coated glass electrodes poised at –278 mV vs. SHE or un-poised in an open circuit condition. We identified 528 genes classified as essential under these growth conditions. With respect to electrochemical conditions, 25 genes were essential under oxidative EET conditions, and 29 genes were essential in both the open circuit control and oxidative EET conditions. Though many of the genes identified under electrochemical conditions are predicted to be localized in the cytoplasm and lack heme binding motifs and/or homology to known EET proteins, we identified several hypothetical proteins and poorly characterized oxidoreductases that implicate a novel mechanism(s) for EET that warrants further study. Our results provide a starting point to explore the genetic basis of novel oxidative EET in this marine sediment microbe.
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Affiliation(s)
- Joshua D Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Nitin Kamble
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Edmund Leach
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Taruna Schuelke
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Elizabeth Wilbanks
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
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18
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Aggeli D, Marad DA, Liu X, Buskirk SW, Levy SF, Lang GI. Overdominant and partially dominant mutations drive clonal adaptation in diploid Saccharomyces cerevisiae. Genetics 2022; 221:6569837. [PMID: 35435209 PMCID: PMC9157133 DOI: 10.1093/genetics/iyac061] [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] [Received: 12/12/2021] [Accepted: 04/06/2022] [Indexed: 11/14/2022] Open
Abstract
Identification of adaptive targets in experimental evolution typically relies on extensive replication and genetic reconstruction. An alternative approach is to directly assay all mutations in an evolved clone by generating pools of segregants that contain random combinations of evolved mutations. Here, we apply this method to six Saccharomyces cerevisiae clones isolated from four diploid populations that were clonally evolved for 2,000 generations in rich glucose medium. Each clone contains 17-26 mutations relative to the ancestor. We derived intermediate genotypes between the founder and the evolved clones by bulk mating sporulated cultures of the evolved clones to a barcoded haploid version of the ancestor. We competed the resulting barcoded diploids en masse and quantified fitness in the experimental and alternative environments by barcode sequencing. We estimated average fitness effects of evolved mutations using barcode-based fitness assays and whole genome sequencing for a subset of segregants. In contrast to our previous work with haploid evolved clones, we find that diploids carry fewer beneficial mutations, with modest fitness effects (up to 5.4%) in the environment in which they arose. In agreement with theoretical expectations, reconstruction experiments show that all mutations with a detectable fitness effect manifest some degree of dominance over the ancestral allele, and most are overdominant. Genotypes with lower fitness effects in alternative environments allowed us to identify conditions that drive adaptation in our system.
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Affiliation(s)
- Dimitra Aggeli
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015, USA
| | - Daniel A Marad
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015, USA
| | - Xianan Liu
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA94025, USA
| | - Sean W Buskirk
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015, USA.,Department of Biology, West Chester University, West Chester, PA19383, USA
| | - Sasha F Levy
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA94025, USA
| | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015, USA
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19
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Zhu TT, Cheng ZH, Yu SS, Li WW, Liu DF, Yu HQ. Unexpected role of electron-transfer hub in direct degradation of pollutants by exoelectrogenic bacteria. Environ Microbiol 2022; 24:1838-1848. [PMID: 35170205 DOI: 10.1111/1462-2920.15939] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 01/28/2022] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
Abstract
Exoelectrogenic bacteria (EEB) are capable of anaerobic respiration with diverse extracellular electron acceptors including insoluble minerals, electrodes and flavins, but the detailed electron transfer pathways and reaction mechanisms remain elusive. Here, we discover that CymA, which is usually considered to solely serve as an inner-membrane electron transfer hub in Shewanella oneidensis MR-1 (a model EEB), might also function as a reductase for direct reducing diverse nitroaromatic compounds (e.g., 2,4-dichloronitrobenzene) and azo dyes. Such a process can be accelerated by dosing anthraquinone-2,6-disulfonate. The CymA-based reduction pathways in S. oneidensis MR-1 for different contaminants could be functionally reconstructed and strengthened in Escherichia coli. The direct reduction of lowly polar contaminants by quinol oxidases like CymA homologs might be universal in diverse microbes. This work offers new insights into the pollutant reduction mechanisms of EEB and unveils a new function of CymA to act as a terminal reductase. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ting-Ting Zhu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhou-Hua Cheng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Sheng-Song Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.,University of Science and Technology of China-City University of Hong Kong Joint Advanced Research Center, Suzhou Institute for Advance Research of USTC, Suzhou, 215123, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.,Anhui Key Laboratory of Sewage Purification and Ecological Rehabilitation Materials, Hefei, 230601, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
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20
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de Bakker V, Liu X, Bravo AM, Veening JW. CRISPRi-seq for genome-wide fitness quantification in bacteria. Nat Protoc 2022; 17:252-281. [PMID: 34997243 DOI: 10.1038/s41596-021-00639-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 09/24/2021] [Indexed: 02/07/2023]
Abstract
CRISPR interference (CRISPRi) is a powerful tool to link essential and nonessential genes to specific phenotypes and to explore their functions. Here we describe a protocol for CRISPRi screenings to assess genome-wide gene fitness in a single sequencing step (CRISPRi-seq). We demonstrate the use of the protocol in Streptococcus pneumoniae, an important human pathogen; however, the protocol can easily be adapted for use in other organisms. The protocol includes a pipeline for single-guide RNA library design, workflows for pooled CRISPRi library construction, growth assays and sequencing steps, a read analysis tool (2FAST2Q) and instructions for fitness quantification. We describe how to make an IPTG-inducible system with small libraries that are easy to handle and cost-effective and overcome bottleneck issues, which can be a problem when using similar, transposon mutagenesis-based methods. Ultimately, the procedure yields a fitness score per single-guide RNA target for any given growth condition. A genome-wide screening can be finished in 1 week with a constructed library. Data analysis and follow-up confirmation experiments can be completed in another 2-3 weeks.
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Affiliation(s)
- Vincent de Bakker
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Xue Liu
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Pharmacology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Afonso M Bravo
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
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21
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Generation of a Gluconobacter oxydans knockout collection for improved extraction of rare earth elements. Nat Commun 2021; 12:6693. [PMID: 34795278 PMCID: PMC8602642 DOI: 10.1038/s41467-021-27047-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022] Open
Abstract
Bioleaching of rare earth elements (REEs), using microorganisms such as Gluconobacter oxydans, offers a sustainable alternative to environmentally harmful thermochemical extraction, but is currently not very efficient. Here, we generate a whole-genome knockout collection of single-gene transposon disruption mutants for G. oxydans B58, to identify genes affecting the efficacy of REE bioleaching. We find 304 genes whose disruption alters the production of acidic biolixiviant. Disruption of genes underlying synthesis of the cofactor pyrroloquinoline quinone (PQQ) and the PQQ-dependent membrane-bound glucose dehydrogenase nearly eliminates bioleaching. Disruption of phosphate-specific transport system genes enhances bioleaching by up to 18%. Our results provide a comprehensive roadmap for engineering the genome of G. oxydans to further increase its bioleaching efficiency.
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22
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Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation. Nat Commun 2021; 12:5193. [PMID: 34465770 PMCID: PMC8408183 DOI: 10.1038/s41467-021-25440-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/11/2021] [Indexed: 01/17/2023] Open
Abstract
Historical contingency and diminishing returns epistasis have been typically studied for relatively divergent genotypes and/or over long evolutionary timescales. Here, we use Saccharomyces cerevisiae to study the extent of diminishing returns and the changes in the adaptive mutational spectra following a single first adaptive mutational step. We further evolve three clones that arose under identical conditions from a common ancestor. We follow their evolutionary dynamics by lineage tracking and determine adaptive outcomes using fitness assays and whole genome sequencing. We find that diminishing returns manifests as smaller fitness gains during the 2nd step of adaptation compared to the 1st step, mainly due to a compressed distribution of fitness effects. We also find that the beneficial mutational spectra for the 2nd adaptive step are contingent on the 1st step, as we see both shared and diverging adaptive strategies. Finally, we find that adaptive loss-of-function mutations, such as nonsense and frameshift mutations, are less common in the second step of adaptation than in the first step. Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.
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23
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Rowe AR, Salimijazi F, Trutschel L, Sackett J, Adesina O, Anzai I, Kugelmass LH, Baym MH, Barstow B. Identification of a pathway for electron uptake in Shewanella oneidensis. Commun Biol 2021; 4:957. [PMID: 34381156 PMCID: PMC8357807 DOI: 10.1038/s42003-021-02454-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/14/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular electron transfer (EET) could enable electron uptake into microbial metabolism for the synthesis of complex, energy dense organic molecules from CO2 and renewable electricity1-6. Theoretically EET could do this with an efficiency comparable to H2-oxidation7,8 but without the need for a volatile intermediate and the problems it causes for scale up9. However, significant gaps remain in understanding the mechanism and genetics of electron uptake. For example, studies of electron uptake in electroactive microbes have shown a role for the Mtr EET complex in the electroactive microbe Shewanella oneidensis MR-110-14, though there is substantial variation in the magnitude of effect deletion of these genes has depending on the terminal electron acceptor used. This speaks to the potential for previously uncharacterized and/or differentially utilized genes involved in electron uptake. To address this, we screened gene disruption mutants for 3667 genes, representing ≈99% of all nonessential genes, from the S. oneidensis whole genome knockout collection using a redox dye oxidation assay. Confirmation of electron uptake using electrochemical testing allowed us to identify five genes from S. oneidensis that are indispensable for electron uptake from a cathode. Knockout of each gene eliminates extracellular electron uptake, yet in four of the five cases produces no significant defect in electron donation to an anode. This result highlights both distinct electron uptake components and an electronic connection between aerobic and anaerobic electron transport chains that allow electrons from the reversible EET machinery to be coupled to different respiratory processes in S. oneidensis. Homologs to these genes across many different genera suggesting that electron uptake by EET coupled to respiration could be widespread. These gene discoveries provide a foundation for: studying this phenotype in exotic metal-oxidizing microbes, genetic optimization of electron uptake in S. oneidensis; and genetically engineering electron uptake into a highly tractable host like E. coli to complement recent advances in synthetic CO2 fixation15.
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Affiliation(s)
- Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
| | - Farshid Salimijazi
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Leah Trutschel
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Joshua Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | | | - Isao Anzai
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Liat H Kugelmass
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Michael H Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA.
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24
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Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria. Nat Protoc 2021; 16:3049-3071. [PMID: 34021295 DOI: 10.1038/s41596-021-00531-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 02/16/2021] [Indexed: 02/07/2023]
Abstract
Commensal bacteria from the human intestinal microbiota play important roles in health and disease. Research into the mechanisms by which these bacteria exert their effects is hampered by the complexity of the microbiota, the strict growth requirements of the individual species and a lack of genetic tools and resources. The assembly of ordered transposon insertion libraries, in which nearly all nonessential genes have been disrupted and the strains stored as independent monocultures, would be a transformative resource for research into many microbiota members. However, assembly of these libraries must be fast and inexpensive in order to empower investigation of the large number of species that typically compose gut communities. The methods used to generate ordered libraries must also be adapted to the anaerobic growth requirements of most intestinal bacteria. We have developed a protocol to assemble ordered libraries of transposon insertion mutants that is fast, cheap and effective for even strict anaerobes. The protocol differs from currently available methods by making use of cell sorting to order the library and barcoded transposons to facilitate the localization of ordered mutations in the library. By tracking transposon insertions using barcode sequencing, our approach increases the accuracy and reduces the time and effort required to locate mutants in the library. Ordered libraries can be sorted and characterized over the course of 2 weeks using this approach. We expect this protocol will lower the barrier to generating comprehensive, ordered mutant libraries for many species in the human microbiota, allowing for new investigations into genotype-phenotype relationships within this important microbial ecosystem.
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Multiplexed Competition in a Synthetic Squid Light Organ Microbiome Using Barcode-Tagged Gene Deletions. mSystems 2020; 5:5/6/e00846-20. [PMID: 33323415 PMCID: PMC7771539 DOI: 10.1128/msystems.00846-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Beneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Beneficial symbioses between microbes and their eukaryotic hosts are ubiquitous and have widespread impacts on host health and development. The binary symbiosis between the bioluminescent bacterium Vibrio fischeri and its squid host Euprymna scolopes serves as a model system to study molecular mechanisms at the microbe-animal interface. To identify colonization factors in this system, our lab previously conducted a global transposon insertion sequencing (INSeq) screen and identified over 300 putative novel squid colonization factors in V. fischeri. To pursue mechanistic studies on these candidate genes, we present an approach to quickly generate barcode-tagged gene deletions and perform high-throughput squid competition experiments with detection of the proportion of each strain in the mixture by barcode sequencing (BarSeq). Our deletion approach improves on previous techniques based on splicing by overlap extension PCR (SOE-PCR) and tfoX-based natural transformation by incorporating a randomized barcode that results in unique DNA sequences within each deletion scar. Amplicon sequencing of the pool of barcoded strains before and after colonization faithfully reports on known colonization factors and provides increased sensitivity over colony counting methods. BarSeq enables rapid and sensitive characterization of the molecular factors involved in establishing the Vibrio-squid symbiosis and provides a valuable tool to interrogate the molecular dialogue at microbe-animal host interfaces. IMPORTANCE Beneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Model symbioses are therefore invaluable for studying the mechanisms of beneficial microbe-host interactions. Here, we present a combined barcode-tagged deletion and BarSeq approach to interrogate the molecular dialogue that ensures specific and reproducible colonization of the Hawaiian bobtail squid by Vibrio fischeri. The ability to precisely manipulate the bacterial genome, combined with multiplex colonization assays, will accelerate the use of this valuable model system for mechanistic studies of how environmental microbes—both beneficial and pathogenic—colonize specific animal hosts.
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Zhao B, Hu S, Liu X, Xiong H, Han X, Zhang Z, Li X, Wang L. A Novel Computational Approach for Identifying Essential Proteins From Multiplex Biological Networks. Front Genet 2020; 11:343. [PMID: 32373163 PMCID: PMC7186452 DOI: 10.3389/fgene.2020.00343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/23/2020] [Indexed: 11/13/2022] Open
Abstract
The identification of essential proteins can help in understanding the minimum requirements for cell survival and development. Ever-increasing amounts of high-throughput data provide us with opportunities to detect essential proteins from protein interaction networks (PINs). Existing network-based approaches are limited by the poor quality of the underlying PIN data, which exhibits high rates of false positive and false negative results. To overcome this problem, researchers have focused on the prediction of essential proteins by combining PINs with other biological data, which has led to the emergence of various interactions between proteins. It remains challenging, however, to use aggregated multiplex interactions within a single analysis framework to identify essential proteins. In this study, we created a multiplex biological network (MON) by initially integrating PINs, protein domains, and gene expression profiles. Next, we proposed a new approach to discover essential proteins by extending the random walk with restart algorithm to the tensor, which provides a data model representation of the MON. In contrast to existing approaches, the proposed MON approach considers for the importance of nodes and the different types of interactions between proteins during the iteration. MON was implemented to identify essential proteins within two yeast PINs. Our comprehensive experimental results demonstrated that MON outperformed 11 other state-of-the-art approaches in terms of precision-recall curve, jackknife curve, and other criteria.
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Affiliation(s)
- Bihai Zhao
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China.,Hunan Provincial Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, China.,Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Changsha University, Changsha, China
| | - Sai Hu
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China
| | - Xiner Liu
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China
| | - Huijun Xiong
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China
| | - Xiao Han
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China
| | - Zhihong Zhang
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China.,Hunan Provincial Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, China
| | - Xueyong Li
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China
| | - Lei Wang
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China.,Hunan Provincial Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, China
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Zhang Z, Luo Y, Hu S, Li X, Wang L, Zhao B. A novel method to predict essential proteins based on tensor and HITS algorithm. Hum Genomics 2020; 14:14. [PMID: 32252824 PMCID: PMC7137323 DOI: 10.1186/s40246-020-00263-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/05/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Essential proteins are an important part of the cell and closely related to the life activities of the cell. Hitherto, Protein-Protein Interaction (PPI) networks have been adopted by many computational methods to predict essential proteins. Most of the current approaches focus mainly on the topological structure of PPI networks. However, those methods relying solely on the PPI network have low detection accuracy for essential proteins. Therefore, it is necessary to integrate the PPI network with other biological information to identify essential proteins. RESULTS In this paper, we proposed a novel random walk method for identifying essential proteins, called HEPT. A three-dimensional tensor is constructed first by combining the PPI network of Saccharomyces cerevisiae with multiple biological data such as gene ontology annotations and protein domains. Then, based on the newly constructed tensor, we extended the Hyperlink-Induced Topic Search (HITS) algorithm from a two-dimensional to a three-dimensional tensor model that can be utilized to infer essential proteins. Different from existing state-of-the-art methods, the importance of proteins and the types of interactions will both contribute to the essential protein prediction. To evaluate the performance of our newly proposed HEPT method, proteins are ranked in the descending order based on their ranking scores computed by our method and other competitive methods. After that, a certain number of the ranked proteins are selected as candidates for essential proteins. According to the list of known essential proteins, the number of true essential proteins is used to judge the performance of each method. Experimental results show that our method can achieve better prediction performance in comparison with other nine state-of-the-art methods in identifying essential proteins. CONCLUSIONS Through analysis and experimental results, it is obvious that HEPT can be used to effectively improve the prediction accuracy of essential proteins by the use of HITS algorithm and the combination of network topology with gene ontology annotations and protein domains, which provides a new insight into multi-data source fusion.
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Affiliation(s)
- Zhihong Zhang
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022 China
| | - Yingchun Luo
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022 China
- Department of Ultrasound, Hunan Province Women and Children’s Hospital, Changsha, 410008 China
| | - Sai Hu
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022 China
| | - Xueyong Li
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022 China
| | - Lei Wang
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022 China
| | - Bihai Zhao
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022 China
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022 China
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Johnson MS, Martsul A, Kryazhimskiy S, Desai MM. Higher-fitness yeast genotypes are less robust to deleterious mutations. Science 2019; 366:490-493. [PMID: 31649199 PMCID: PMC7204892 DOI: 10.1126/science.aay4199] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022]
Abstract
Natural selection drives populations toward higher fitness, but second-order selection for adaptability and mutational robustness can also influence evolution. In many microbial systems, diminishing-returns epistasis contributes to a tendency for more-fit genotypes to be less adaptable, but no analogous patterns for robustness are known. To understand how robustness varies across genotypes, we measure the fitness effects of hundreds of individual insertion mutations in a panel of yeast strains. We find that more-fit strains are less robust: They have distributions of fitness effects with lower mean and higher variance. These differences arise because many mutations have more strongly deleterious effects in faster-growing strains. This negative correlation between fitness and robustness implies that second-order selection for robustness will tend to conflict with first-order selection for fitness.
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Affiliation(s)
- Milo S Johnson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alena Martsul
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergey Kryazhimskiy
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
- Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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29
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Nora LC, Westmann CA, Guazzaroni ME, Siddaiah C, Gupta VK, Silva-Rocha R. Recent advances in plasmid-based tools for establishing novel microbial chassis. Biotechnol Adv 2019; 37:107433. [PMID: 31437573 DOI: 10.1016/j.biotechadv.2019.107433] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 12/28/2022]
Abstract
A key challenge for domesticating alternative cultivable microorganisms with biotechnological potential lies in the development of innovative technologies. Within this framework, a myriad of genetic tools has flourished, allowing the design and manipulation of complex synthetic circuits and genomes to become the general rule in many laboratories rather than the exception. More recently, with the development of novel technologies such as DNA automated synthesis/sequencing and powerful computational tools, molecular biology has entered the synthetic biology era. In the beginning, most of these technologies were established in traditional microbial models (known as chassis in the synthetic biology framework) such as Escherichia coli and Saccharomyces cerevisiae, enabling fast advances in the field and the validation of fundamental proofs of concept. However, it soon became clear that these organisms, although extremely useful for prototyping many genetic tools, were not ideal for a wide range of biotechnological tasks due to intrinsic limitations in their molecular/physiological properties. Over the last decade, researchers have been facing the great challenge of shifting from these model systems to non-conventional chassis with endogenous capacities for dealing with specific tasks. The key to address these issues includes the generation of narrow and broad host plasmid-based molecular tools and the development of novel methods for engineering genomes through homologous recombination systems, CRISPR/Cas9 and other alternative methods. Here, we address the most recent advances in plasmid-based tools for the construction of novel cell factories, including a guide for helping with "build-your-own" microbial host.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | | | - Vijai Kumar Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil.
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Mevers E, Su L, Pishchany G, Baruch M, Cornejo J, Hobert E, Dimise E, Ajo-Franklin CM, Clardy J. An elusive electron shuttle from a facultative anaerobe. eLife 2019; 8:48054. [PMID: 31232690 PMCID: PMC6687433 DOI: 10.7554/elife.48054] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/24/2019] [Indexed: 01/06/2023] Open
Abstract
Some anaerobic bacteria use insoluble minerals as terminal electron acceptors and discovering the ways in which electrons move through the membrane barrier to the exterior acceptor forms an active field of research with implications for both bacterial physiology and bioenergy. A previous study suggested that Shewanella oneidensis MR-1 utilizes a small, polar, redox active molecule that serves as an electron shuttle between the bacteria and insoluble acceptors, but the shuttle itself has never been identified. Through isolation and synthesis, we identify it as ACNQ (2-amino-3-carboxy-1,4-naphthoquinone), a soluble analog of menaquinone. ACNQ is derived from DHNA (1,4-dihydroxy-2-naphthoic acid) in a non-enzymatic process that frustrated genetic approaches to identify the shuttle. Both ACNQ and DHNA restore reduction of AQDS under anaerobic growth in menaquinone-deficient mutants. Bioelectrochemistry analyses reveal that ACNQ (−0.32 VAg/AgCl) contributes to the extracellular electron transfer (EET) as an electron shuttle, without altering menaquinone generation or EET related cytochrome c expression. In order to survive, we break down food through a series of chemical reactions that release energy to power our cells. In these metabolic reactions, small electrically charged particles called electrons are removed from the food molecule, and transferred, via a series of reactions, to a terminal electron acceptor. For humans and many other organisms, oxygen is the terminal electron acceptor. Bacteria generate energy through a similar series of chemical reactions, but many species of bacteria live in environments where oxygen is absent. Some bacteria solve this problem by transferring the electrons released in their metabolic reactions to acceptor compounds in the external environment. These species must therefore employ a small molecule ‘shuttle’ to carry the electrons to the acceptor. Previous work has shown the bacterial strain Shewanella oneidensis MR-1 releases a small molecule into its surrounding environment, which serves as its electron shuttle. Despite identifying a mutant strain of MR-1 that cannot produce this shuttle, researchers have been unable to determine the exact chemical identity of this critical molecule. Now, Mevers, Su et al. have identified this elusive electron shuttle. This involved growing MR-1 and isolating the active molecule which restores the mutant bacteria’s ability to shuttle electrons. Further experiments characterizing the structure of this compound using techniques involving analytical and synthetic organic chemistry revealed it be a small molecule known as ACNQ. Mevers, Su et al. showed MR-1 produces this elusive electron shuttle by releasing a precursor structure into the environment where it spontaneously converts into ACNQ. As a result, there are no genes present in the genome of MR-1 or other bacterial strains that are required for the production of ACNQ. This genetic absence and low production levels of ACNQ has frustrated previous attempts to identify MR-1’s electron shuttle. Bacterial metabolism is studied for its applications in bioenergy (producing renewable energy using living organisms) and bioremediation (detoxification of substances using the reactions of bacterial metabolism). A better understanding of bacterial metabolism is thus essential for the continued development of these useful technologies.
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Affiliation(s)
- Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Lin Su
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, United States.,State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Gleb Pishchany
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.,Department of Microbiology, Harvard Medical School, Boston, United States
| | - Moshe Baruch
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, United States
| | - Jose Cornejo
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, United States
| | - Elissa Hobert
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Eric Dimise
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Caroline M Ajo-Franklin
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
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31
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Reaching full potential: bioelectrochemical systems for storing renewable energy in chemical bonds. Curr Opin Biotechnol 2019; 57:66-72. [DOI: 10.1016/j.copbio.2019.01.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/16/2018] [Accepted: 01/29/2019] [Indexed: 12/11/2022]
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Mayer M, Baeumner AJ. A Megatrend Challenging Analytical Chemistry: Biosensor and Chemosensor Concepts Ready for the Internet of Things. Chem Rev 2019; 119:7996-8027. [DOI: 10.1021/acs.chemrev.8b00719] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Mayer
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Antje J. Baeumner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
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33
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Hadjadj L, Baron SA, Diene SM, Rolain JM. How to discover new antibiotic resistance genes? Expert Rev Mol Diagn 2019; 19:349-362. [PMID: 30895843 DOI: 10.1080/14737159.2019.1592678] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Antibiotic resistance (AR) is a worldwide concern and the description of AR have been discovered mainly because of their implications in human medicine. Since the recent burden of whole-genome sequencing of microorganisms, the number of new AR genes (ARGs) have dramatically increased over the last decade. Areas covered: In this review, we will describe the different methods that could be used to characterize new ARGs using classic or innovative methods. First, we will focus on the biochemical methods, then we will develop on molecular methods, next-generation sequencing and bioinformatics approaches. The use of various methods, including cloning, mutagenesis, transposon mutagenesis, functional genomics, whole genome sequencing, metagenomic and functional metagenomics will be reviewed here, outlining the advantages and drawbacks of each method. Bioinformatics softwares used for resistome analysis and protein modeling will be also described. Expert opinion: Biological experiments and bioinformatics analysis are complementary. Nowadays, the ARGs described only account for the tip of the iceberg of all existing resistance mechanisms. The multiplication of the ecosystems studied allows us to find a large reservoir of AR mechanisms. Furthermore, the adaptation ability of bacteria facing new antibiotics promises a constant discovery of new AR mechanisms.
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Affiliation(s)
- Linda Hadjadj
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Sophie Alexandra Baron
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Seydina M Diene
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Jean-Marc Rolain
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France.,b IHU Méditerranée Infection , Marseille , France
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Conte E, Mende L, Grainge I, Colloms SD. A Mini-ISY100 Transposon Delivery System Effective in γ Proteobacteria. Front Microbiol 2019; 10:280. [PMID: 30873132 PMCID: PMC6400869 DOI: 10.3389/fmicb.2019.00280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/04/2019] [Indexed: 11/17/2022] Open
Abstract
Transposons are invaluable biological tools for the genetic manipulation of microorganisms. ISY100 from Synechocystis sp. PCC6803 is a member of the Tc1/mariner/IS630 superfamily, and is characterized by high transposition efficiency and a strong preference for TA target sequences. In this paper, we describe the design and application of a mini-ISY100 suicide vector for the in vivo creation of stable random transposon insertion libraries. The system was successfully applied in seven species belonging to four different orders of γ proteobacteria. In all cases, delivery using conjugation consistently showed the highest transposition efficiency compared to chemical transformation or electroporation. We determined the frequency of transposon insertions in all the species and proved the utility of the system by identifying genes involved in colony coloration in Shewanella oneidensis. The ease and the efficiency of the protocol developed here allow the creation of complete knock-out libraries in an extensive range of host microorganisms in less than a week with no requirement for preparatory modification.
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Affiliation(s)
- Emanuele Conte
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Linda Mende
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, NSW, Australia
| | - Ian Grainge
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, NSW, Australia
| | - Sean D Colloms
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
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Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF. mSystems 2018; 3:mSystems00062-18. [PMID: 30225373 PMCID: PMC6134198 DOI: 10.1128/msystems.00062-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/03/2018] [Indexed: 12/14/2022] Open
Abstract
The robust ability of Enterococcus faecalis to survive outside the host and to spread via oral-fecal transmission and its high degree of intrinsic and acquired antimicrobial resistance all complicate the treatment of hospital-acquired enterococcal infections. The conserved E. faecalis core genome serves as an important genetic scaffold for evolution of this bacterium in the modern health care setting and also provides interesting vaccine and drug targets. We used an innovative pooling/sequencing strategy to map a large collection of arrayed transposon insertions in E. faecalis OG1RF and generated an arrayed library of defined mutants covering approximately 70% of the OG1RF genome. Then, we performed high-throughput transposon sequencing experiments using this library to determine core genomic determinants of bile resistance in OG1RF. This collection is a valuable resource for comprehensive, functional enterococcal genomics using both traditional and high-throughput approaches and enables immediate recovery of mutants of interest. Enterococcus faecalis is a common commensal bacterium in animal gastrointestinal (GI) tracts and a leading cause of opportunistic infections of humans in the modern health care setting. E. faecalis OG1RF is a plasmid-free strain that contains few mobile elements yet retains the robust survival characteristics, intrinsic antibiotic resistance, and virulence traits characteristic of most E. faecalis genotypes. To facilitate interrogation of the core enterococcal genetic determinants for competitive fitness in the GI tract, biofilm formation, intrinsic antimicrobial resistance, and survival in the environment, we generated an arrayed, sequence-defined set of chromosomal transposon insertions in OG1RF. We used an orthogonal pooling strategy in conjunction with Illumina sequencing to identify a set of mutants with unique, single Himar-based transposon insertions. The mutants contained insertions in 1,926 of 2,651 (72.6%) annotated open reading frames and in the majority of hypothetical protein-encoding genes and intergenic regions greater than 100 bp in length, which could encode small RNAs. As proof of principle of the usefulness of this arrayed transposon library, we created a minimal input pool containing 6,829 mutants chosen for maximal genomic coverage and used an approach that we term SMarT (sequence-defined marinertechnology) transposon sequencing (TnSeq) to identify numerous genetic determinants of bile resistance in E. faecalis OG1RF. These included several genes previously associated with bile acid resistance as well as new loci. Our arrayed library allows functional screening of a large percentage of the genome with a relatively small number of mutants, reducing potential effects of bottlenecking, and enables immediate recovery of mutants following competitions. IMPORTANCE The robust ability of Enterococcus faecalis to survive outside the host and to spread via oral-fecal transmission and its high degree of intrinsic and acquired antimicrobial resistance all complicate the treatment of hospital-acquired enterococcal infections. The conserved E. faecalis core genome serves as an important genetic scaffold for evolution of this bacterium in the modern health care setting and also provides interesting vaccine and drug targets. We used an innovative pooling/sequencing strategy to map a large collection of arrayed transposon insertions in E. faecalis OG1RF and generated an arrayed library of defined mutants covering approximately 70% of the OG1RF genome. Then, we performed high-throughput transposon sequencing experiments using this library to determine core genomic determinants of bile resistance in OG1RF. This collection is a valuable resource for comprehensive, functional enterococcal genomics using both traditional and high-throughput approaches and enables immediate recovery of mutants of interest.
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36
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Rapidly moving new bacteria to model-organism status. Curr Opin Biotechnol 2018; 51:116-122. [DOI: 10.1016/j.copbio.2017.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/11/2017] [Indexed: 11/23/2022]
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37
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Anzai IA, Shaket L, Adesina O, Baym M, Barstow B. Rapid curation of gene disruption collections using Knockout Sudoku. Nat Protoc 2017; 12:2110-2137. [DOI: 10.1038/nprot.2017.073] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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38
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Abstract
Chemical-genetic approaches are based on measuring the cellular outcome of combining genetic and chemical perturbations in large-numbers in tandem. In these approaches the contribution of every gene to the fitness of an organism is measured upon exposure to different chemicals. Current technological advances enable the application of chemical genetics to almost any organism and at an unprecedented throughput. Here we review the underlying concepts behind chemical genetics, present its different vignettes and illustrate how such approaches can propel drug discovery.
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Affiliation(s)
- Elisabetta Cacace
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - George Kritikos
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
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Adesina O, Anzai IA, Avalos JL, Barstow B. Embracing Biological Solutions to the Sustainable Energy Challenge. Chem 2017. [DOI: 10.1016/j.chempr.2016.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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