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Rahiminejad S, De Sanctis B, Pevzner P, Mushegian A. Synthetic lethality and the minimal genome size problem. mSphere 2024; 9:e0013924. [PMID: 38904396 PMCID: PMC11288024 DOI: 10.1128/msphere.00139-24] [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: 02/19/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Gene knockout studies suggest that ~300 genes in a bacterial genome and ~1,100 genes in a yeast genome cannot be deleted without loss of viability. These single-gene knockout experiments do not account for negative genetic interactions, when two or more genes can each be deleted without effect, but their joint deletion is lethal. Thus, large-scale single-gene deletion studies underestimate the size of a minimal gene set compatible with cell survival. In yeast Saccharomyces cerevisiae, the viability of all possible deletions of gene pairs (2-tuples), and of some deletions of gene triplets (3-tuples), has been experimentally tested. To estimate the size of a yeast minimal genome from that data, we first established that finding the size of a minimal gene set is equivalent to finding the minimum vertex cover in the lethality (hyper)graph, where the vertices are genes and (hyper)edges connect k-tuples of genes whose joint deletion is lethal. Using the Lovász-Johnson-Chvatal greedy approximation algorithm, we computed the minimum vertex cover of the synthetic-lethal 2-tuples graph to be 1,723 genes. We next simulated the genetic interactions in 3-tuples, extrapolating from the existing triplet sample, and again estimated minimum vertex covers. The size of a minimal gene set in yeast rapidly approaches the size of the entire genome even when considering only synthetic lethalities in k-tuples with small k. In contrast, several studies reported successful experimental reductions of yeast and bacterial genomes by simultaneous deletions of hundreds of genes, without eliciting synthetic lethality. We discuss possible reasons for this apparent contradiction.IMPORTANCEHow can we estimate the smallest number of genes sufficient for a unicellular organism to survive on a rich medium? One approach is to remove genes one at a time and count how many of such deletion strains are unable to grow. However, the single-gene knockout data are insufficient, because joint gene deletions may result in negative genetic interactions, also known as synthetic lethality. We used a technique from graph theory to estimate the size of minimal yeast genome from partial data on synthetic lethality. The number of potential synthetic lethal interactions grows very fast when multiple genes are deleted, revealing a paradoxical contrast with the experimental reductions of yeast genome by ~100 genes, and of bacterial genomes by several hundreds of genes.
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Affiliation(s)
- Sara Rahiminejad
- Department of Bioengineering, University of California—San Diego, La Jolla, California, USA
| | - Bianca De Sanctis
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Ecology and Evolutionary Biology, University of California—Santa Cruz, Santa Cruz, California, USA
| | - Pavel Pevzner
- Department of Computer Science and Engineering, University of California—San Diego, La Jolla, California, USA
| | - Arcady Mushegian
- Molecular and Cellular Biosciences Division, National Science Foundation, Alexandria, Virginia, USA
- Clare Hall College, Cambridge, United Kingdom
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2
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Jana B, Liu X, Dénéréaz J, Park H, Leshchiner D, Liu B, Gallay C, Zhu J, Veening JW, van Opijnen T. CRISPRi-TnSeq maps genome-wide interactions between essential and non-essential genes in bacteria. Nat Microbiol 2024:10.1038/s41564-024-01759-x. [PMID: 39030344 DOI: 10.1038/s41564-024-01759-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/12/2024] [Indexed: 07/21/2024]
Abstract
Genetic interactions identify functional connections between genes and pathways, establishing gene functions or druggable targets. Here we use CRISPRi-TnSeq, CRISPRi-mediated knockdown of essential genes alongside TnSeq-mediated knockout of non-essential genes, to map genome-wide interactions between essential and non-essential genes in Streptococcus pneumoniae. Transposon-mutant libraries constructed in 13 CRISPRi strains enabled screening of ~24,000 gene pairs. This identified 1,334 genetic interactions, including 754 negative and 580 positive interactions. Network analyses show that 17 non-essential genes pleiotropically interact with more than half the essential genes tested. Validation experiments confirmed that a 7-gene subset protects against perturbations. Furthermore, we reveal hidden redundancies that compensate for essential gene loss, relationships between cell wall synthesis, integrity and cell division, and show that CRISPRi-TnSeq identifies synthetic and suppressor-type relationships between both functionally linked and disparate genes and pathways. Importantly, in species where CRISPRi and Tn-Seq are established, CRISPRi-TnSeq should be straightforward to implement.
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Affiliation(s)
- Bimal Jana
- Department of Biology, Boston College, Chestnut Hill, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Xue Liu
- Department of Pathogen Biology, Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Julien Dénéréaz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Hongshik Park
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | | | - Bruce Liu
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Clément Gallay
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Junhao Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA, USA.
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3
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Parkhill SL, Johnson EO. Integrating bacterial molecular genetics with chemical biology for renewed antibacterial drug discovery. Biochem J 2024; 481:839-864. [PMID: 38958473 DOI: 10.1042/bcj20220062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
The application of dyes to understanding the aetiology of infection inspired antimicrobial chemotherapy and the first wave of antibacterial drugs. The second wave of antibacterial drug discovery was driven by rapid discovery of natural products, now making up 69% of current antibacterial drugs. But now with the most prevalent natural products already discovered, ∼107 new soil-dwelling bacterial species must be screened to discover one new class of natural product. Therefore, instead of a third wave of antibacterial drug discovery, there is now a discovery bottleneck. Unlike natural products which are curated by billions of years of microbial antagonism, the vast synthetic chemical space still requires artificial curation through the therapeutics science of antibacterial drugs - a systematic understanding of how small molecules interact with bacterial physiology, effect desired phenotypes, and benefit the host. Bacterial molecular genetics can elucidate pathogen biology relevant to therapeutics development, but it can also be applied directly to understanding mechanisms and liabilities of new chemical agents with new mechanisms of action. Therefore, the next phase of antibacterial drug discovery could be enabled by integrating chemical expertise with systematic dissection of bacterial infection biology. Facing the ambitious endeavour to find new molecules from nature or new-to-nature which cure bacterial infections, the capabilities furnished by modern chemical biology and molecular genetics can be applied to prospecting for chemical modulators of new targets which circumvent prevalent resistance mechanisms.
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Affiliation(s)
- Susannah L Parkhill
- Systems Chemical Biology of Infection and Resistance Laboratory, The Francis Crick Institute, London, U.K
- Faculty of Life Sciences, University College London, London, U.K
| | - Eachan O Johnson
- Systems Chemical Biology of Infection and Resistance Laboratory, The Francis Crick Institute, London, U.K
- Faculty of Life Sciences, University College London, London, U.K
- Department of Chemistry, Imperial College, London, U.K
- Department of Chemistry, King's College London, London, U.K
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4
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Enright AL, Heelan WJ, Ward RD, Peters JM. CRISPRi functional genomics in bacteria and its application to medical and industrial research. Microbiol Mol Biol Rev 2024; 88:e0017022. [PMID: 38809084 DOI: 10.1128/mmbr.00170-22] [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] [Indexed: 05/30/2024] Open
Abstract
SUMMARYFunctional genomics is the use of systematic gene perturbation approaches to determine the contributions of genes under conditions of interest. Although functional genomic strategies have been used in bacteria for decades, recent studies have taken advantage of CRISPR (clustered regularly interspaced short palindromic repeats) technologies, such as CRISPRi (CRISPR interference), that are capable of precisely modulating expression of all genes in the genome. Here, we discuss and review the use of CRISPRi and related technologies for bacterial functional genomics. We discuss the strengths and weaknesses of CRISPRi as well as design considerations for CRISPRi genetic screens. We also review examples of how CRISPRi screens have defined relevant genetic targets for medical and industrial applications. Finally, we outline a few of the many possible directions that could be pursued using CRISPR-based functional genomics in bacteria. Our view is that the most exciting screens and discoveries are yet to come.
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Affiliation(s)
- Amy L Enright
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - William J Heelan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan D Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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5
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Green RA, Khaliullin RN, Zhao Z, Ochoa SD, Hendel JM, Chow TL, Moon H, Biggs RJ, Desai A, Oegema K. Automated profiling of gene function during embryonic development. Cell 2024; 187:3141-3160.e23. [PMID: 38759650 PMCID: PMC11166207 DOI: 10.1016/j.cell.2024.04.012] [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: 05/27/2023] [Revised: 02/10/2024] [Accepted: 04/12/2024] [Indexed: 05/19/2024]
Abstract
Systematic functional profiling of the gene set that directs embryonic development is an important challenge. To tackle this challenge, we used 4D imaging of C. elegans embryogenesis to capture the effects of 500 gene knockdowns and developed an automated approach to compare developmental phenotypes. The automated approach quantifies features-including germ layer cell numbers, tissue position, and tissue shape-to generate temporal curves whose parameterization yields numerical phenotypic signatures. In conjunction with a new similarity metric that operates across phenotypic space, these signatures enabled the generation of ranked lists of genes predicted to have similar functions, accessible in the PhenoBank web portal, for ∼25% of essential development genes. The approach identified new gene and pathway relationships in cell fate specification and morphogenesis and highlighted the utilization of specialized energy generation pathways during embryogenesis. Collectively, the effort establishes the foundation for comprehensive analysis of the gene set that builds a multicellular organism.
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Affiliation(s)
- Rebecca A Green
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | | | - Zhiling Zhao
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Stacy D Ochoa
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | | | | | - HongKee Moon
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Ronald J Biggs
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Arshad Desai
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karen Oegema
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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6
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Lo Presti L, Link H. Mobile CRISPRi moves through the complexity of bacterial genetics. CELL REPORTS METHODS 2024; 4:100697. [PMID: 38262347 PMCID: PMC10832260 DOI: 10.1016/j.crmeth.2024.100697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
In this issue of Cell Reports Methods, Rachwalski et al. describe a high-throughput method to screen genetic interactions in bacteria using a conjugative CRISPR interference (CRISPRi) plasmid. The method enables systematic studies of gene essentiality in diverse genomic and environmental contexts and is applicable to Escherichia coli as well as other bacteria.
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Affiliation(s)
- Libera Lo Presti
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections", University of Tübingen, 72076 Tübingen, Germany
| | - Hannes Link
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections", University of Tübingen, 72076 Tübingen, Germany; The M3 Research Center, Otfried-Müller-Straße 37, 72076 Tübingen, Germany.
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7
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Rachwalski K, Tu MM, Madden SJ, French S, Hansen DM, Brown ED. A mobile CRISPRi collection enables genetic interaction studies for the essential genes of Escherichia coli. CELL REPORTS METHODS 2024; 4:100693. [PMID: 38262349 PMCID: PMC10832289 DOI: 10.1016/j.crmeth.2023.100693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/27/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024]
Abstract
Advances in gene editing, in particular CRISPR interference (CRISPRi), have enabled depletion of essential cellular machinery to study the downstream effects on bacterial physiology. Here, we describe the construction of an ordered E. coli CRISPRi collection, designed to knock down the expression of 356 essential genes with the induction of a catalytically inactive Cas9, harbored on the conjugative plasmid pFD152. This mobile CRISPRi library can be conjugated into other ordered genetic libraries to assess combined effects of essential gene knockdowns with non-essential gene deletions. As proof of concept, we probed cell envelope synthesis with two complementary crosses: (1) an Lpp deletion into every CRISPRi knockdown strain and (2) the lolA knockdown plasmid into the Keio collection. These experiments revealed a number of notable genetic interactions for the essential phenotype probed and, in particular, showed suppressing interactions for the loci in question.
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Affiliation(s)
- Kenneth Rachwalski
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Megan M Tu
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Sean J Madden
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Shawn French
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Drew M Hansen
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Eric D Brown
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.
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8
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Yu Y, Gawlitt S, de Andrade E Sousa LB, Merdivan E, Piraud M, Beisel CL, Barquist L. Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration. Genome Biol 2024; 25:13. [PMID: 38200565 PMCID: PMC10782694 DOI: 10.1186/s13059-023-03153-y] [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: 06/19/2022] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
CRISPR interference (CRISPRi) is the leading technique to silence gene expression in bacteria; however, design rules remain poorly defined. We develop a best-in-class prediction algorithm for guide silencing efficiency by systematically investigating factors influencing guide depletion in genome-wide essentiality screens, with the surprising discovery that gene-specific features substantially impact prediction. We develop a mixed-effect random forest regression model that provides better estimates of guide efficiency. We further apply methods from explainable AI to extract interpretable design rules from the model. This study provides a blueprint for predictive models for CRISPR technologies where only indirect measurements of guide activity are available.
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Affiliation(s)
- Yanying Yu
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, 97080, Germany
| | - Sandra Gawlitt
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, 97080, Germany
| | | | - Erinc Merdivan
- Helmholtz AI, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Marie Piraud
- Helmholtz AI, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, 97080, Germany
- Medical Faculty, University of Würzburg, Würzburg, 97080, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, 97080, Germany.
- Medical Faculty, University of Würzburg, Würzburg, 97080, Germany.
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9
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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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10
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Zhu SB, Jiang QH, Chen ZG, Zhou X, Jin YT, Deng Z, Guo FB. Mslar: Microbial synthetic lethal and rescue database. PLoS Comput Biol 2023; 19:e1011218. [PMID: 37289843 DOI: 10.1371/journal.pcbi.1011218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Synthetic lethality (SL) occurs when mutations in two genes together lead to cell or organism death, while a single mutation in either gene does not have a significant impact. This concept can also be extended to three or more genes for SL. Computational and experimental methods have been developed to predict and verify SL gene pairs, especially for yeast and Escherichia coli. However, there is currently a lack of a specialized platform to collect microbial SL gene pairs. Therefore, we designed a synthetic interaction database for microbial genetics that collects 13,313 SL and 2,994 Synthetic Rescue (SR) gene pairs that are reported in the literature, as well as 86,981 putative SL pairs got through homologous transfer method in 281 bacterial genomes. Our database website provides multiple functions such as search, browse, visualization, and Blast. Based on the SL interaction data in the S. cerevisiae, we review the issue of duplications' essentiality and observed that the duplicated genes and singletons have a similar ratio of being essential when we consider both individual and SL. The Microbial Synthetic Lethal and Rescue Database (Mslar) is expected to be a useful reference resource for researchers interested in the SL and SR genes of microorganisms. Mslar is open freely to everyone and available on the web at http://guolab.whu.edu.cn/Mslar/.
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Affiliation(s)
- Sen-Bin Zhu
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Qian-Hu Jiang
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhi-Guo Chen
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiang Zhou
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan-Ting Jin
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Feng-Biao Guo
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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11
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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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12
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Jana B, Liu X, Dénéréaz J, Park H, Leshchiner D, Liu B, Gallay C, Veening JW, van Opijnen T. CRISPRi-TnSeq: A genome-wide high-throughput tool for bacterial essential-nonessential genetic interaction mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543074. [PMID: 37398100 PMCID: PMC10312587 DOI: 10.1101/2023.05.31.543074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Genetic interaction networks can help identify functional connections between genes and pathways, which can be leveraged to establish (new) gene function, drug targets, and fill pathway gaps. Since there is no optimal tool that can map genetic interactions across many different bacterial strains and species, we develop CRISPRi-TnSeq, a genome-wide tool that maps genetic interactions between essential genes and nonessential genes through the knockdown of a targeted essential gene (CRISPRi) and the simultaneous knockout of individual nonessential genes (Tn-Seq). CRISPRi-TnSeq thereby identifies, on a genome-wide scale, synthetic and suppressor-type relationships between essential and nonessential genes, enabling the construction of essential-nonessential genetic interaction networks. To develop and optimize CRISPRi-TnSeq, CRISPRi strains were obtained for 13 essential genes in Streptococcus pneumoniae, involved in different biological processes including metabolism, DNA replication, transcription, cell division and cell envelope synthesis. Transposon-mutant libraries were constructed in each strain enabling screening of ∼24,000 gene-gene pairs, which led to the identification of 1,334 genetic interactions, including 754 negative and 580 positive genetic interactions. Through extensive network analyses and validation experiments we identify a set of 17 pleiotropic genes, of which a subset tentatively functions as genetic capacitors, dampening phenotypic outcomes and protecting against perturbations. Furthermore, we focus on the relationships between cell wall synthesis, integrity and cell division and highlight: 1) how essential gene knockdown can be compensated by rerouting flux through nonessential genes in a pathway; 2) the existence of a delicate balance between Z-ring formation and localization, and septal and peripheral peptidoglycan (PG) synthesis to successfully accomplish cell division; 3) the control of c-di-AMP over intracellular K + and turgor, and thereby modulation of the cell wall synthesis machinery; 4) the dynamic nature of cell wall protein CozEb and its effect on PG synthesis, cell shape morphology and envelope integrity; 5) functional dependency between chromosome decatenation and segregation, and the critical link with cell division, and cell wall synthesis. Overall, we show that CRISPRi-TnSeq uncovers genetic interactions between closely functionally linked genes and pathways, as well as disparate genes and pathways, highlighting pathway dependencies and valuable leads for gene function. Importantly, since both CRISPRi and Tn-Seq are widely used tools, CRISPRi-TnSeq should be relatively easy to implement to construct genetic interaction networks across many different microbial strains and species.
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13
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Heigwer F, Scheeder C, Bageritz J, Yousefian S, Rauscher B, Laufer C, Beneyto-Calabuig S, Funk MC, Peters V, Boulougouri M, Bilanovic J, Miersch T, Schmitt B, Blass C, Port F, Boutros M. A global genetic interaction network by single-cell imaging and machine learning. Cell Syst 2023; 14:346-362.e6. [PMID: 37116498 DOI: 10.1016/j.cels.2023.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/17/2022] [Accepted: 03/17/2023] [Indexed: 04/30/2023]
Abstract
Cellular and organismal phenotypes are controlled by complex gene regulatory networks. However, reference maps of gene function are still scarce across different organisms. Here, we generated synthetic genetic interaction and cell morphology profiles of more than 6,800 genes in cultured Drosophila cells. The resulting map of genetic interactions was used for machine learning-based gene function discovery, assigning functions to genes in 47 modules. Furthermore, we devised Cytoclass as a method to dissect genetic interactions for discrete cell states at the single-cell resolution. This approach identified an interaction of Cdk2 and the Cop9 signalosome complex, triggering senescence-associated secretory phenotypes and immunogenic conversion in hemocytic cells. Together, our data constitute a genome-scale resource of functional gene profiles to uncover the mechanisms underlying genetic interactions and their plasticity at the single-cell level.
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Affiliation(s)
- Florian Heigwer
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany; Department of Life Sciences and Engineering, University of Applied Sciences Bingen, Bingen am Rhein, Germany
| | - Christian Scheeder
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Josephine Bageritz
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany; Center of Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Schayan Yousefian
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Benedikt Rauscher
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Christina Laufer
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Sergi Beneyto-Calabuig
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Maja Christina Funk
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Vera Peters
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Maria Boulougouri
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Jana Bilanovic
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Thilo Miersch
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Barbara Schmitt
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Claudia Blass
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Fillip Port
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.
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14
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Abstract
Escherichia coli is likely the most studied organism and was instrumental in developing many fundamental concepts in biology. But why E. coli? In the 1940s, E. coli was well suited for the biochemical and genetic research that blended to become the seminal field of biochemical genetics and led to the realization that processes already known to occur in complex organisms were conserved in bacteria. This now-obvious concept, combined with the advantages offered by its easy cultivation, ultimately drove many researchers to shift from the complexity of eukaryotic models to the simpler bacterial system, which eventually led to the development of molecular biology. As knowledge and experimental tools amassed, a positive-feedback loop fixed the central role of E. coli in research. However, given the vast diversity among bacteria and even among E. coli strains, it was by many fortuitous events that E. coli rose to the top as an experimental model. Here, we share how serendipity and its own biology selected E. coli as the flagship bacterium of molecular biology.
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15
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Past, Present, and Future of Genome Modification in Escherichia coli. Microorganisms 2022; 10:microorganisms10091835. [PMID: 36144436 PMCID: PMC9504249 DOI: 10.3390/microorganisms10091835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 12/04/2022] Open
Abstract
Escherichia coli K-12 is one of the most well-studied species of bacteria. This species, however, is much more difficult to modify by homologous recombination (HR) than other model microorganisms. Research on HR in E. coli has led to a better understanding of the molecular mechanisms of HR, resulting in technical improvements and rapid progress in genome research, and allowing whole-genome mutagenesis and large-scale genome modifications. Developments using λ Red (exo, bet, and gam) and CRISPR-Cas have made E. coli as amenable to genome modification as other model microorganisms, such as Saccharomyces cerevisiae and Bacillus subtilis. This review describes the history of recombination research in E. coli, as well as improvements in techniques for genome modification by HR. This review also describes the results of large-scale genome modification of E. coli using these technologies, including DNA synthesis and assembly. In addition, this article reviews recent advances in genome modification, considers future directions, and describes problems associated with the creation of cells by design.
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16
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Guo L, Dou Y, Xia D, Yin Z, Xiang Y, Luo L, Zhang Y, Wang J, Liang T. SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis. Database (Oxford) 2022; 2022:6677988. [PMID: 36029479 PMCID: PMC9419874 DOI: 10.1093/database/baac075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/27/2022] [Accepted: 08/20/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Synthetic lethality has been widely concerned because of its potential role in cancer treatment, which can be harnessed to selectively kill cancer cells via identifying inactive genes in a specific cancer type and further targeting the corresponding synthetic lethal partners. Herein, to obtain cancer-specific synthetic lethal interactions, we aimed to predict genetic interactions via a pan-cancer analysis from multiple molecular levels using random forest and then develop a user-friendly database. First, based on collected public gene pairs with synthetic lethal interactions, candidate gene pairs were analyzed via integrating multi-omics data, mainly including DNA mutation, copy number variation, methylation and mRNA expression data. Then, integrated features were used to predict cancer-specific synthetic lethal interactions using random forest. Finally, SLOAD (http://www.tmliang.cn/SLOAD) was constructed via integrating these findings, which was a user-friendly database for data searching, browsing, downloading and analyzing. These results can provide candidate cancer-specific synthetic lethal interactions, which will contribute to drug designing in cancer treatment that can promote therapy strategies based on the principle of synthetic lethality.
Database URL http://www.tmliang.cn/SLOAD/
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Affiliation(s)
- Li Guo
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications , No. 9, Wenyuan Road, Qixia District, Nanjing, Jiangsu 210023, China
| | - Yuyang Dou
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications , No. 9, Wenyuan Road, Qixia District, Nanjing, Jiangsu 210023, China
| | - Daoliang Xia
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications , No. 9, Wenyuan Road, Qixia District, Nanjing, Jiangsu 210023, China
| | - Zibo Yin
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications , No. 9, Wenyuan Road, Qixia District, Nanjing, Jiangsu 210023, China
| | - Yangyang Xiang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications , No. 9, Wenyuan Road, Qixia District, Nanjing, Jiangsu 210023, China
| | - Lulu Luo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University , No. 1, Wenyuan Road, Qixia District, Nanjing, Jiangsu 210023, China
| | - Yuting Zhang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications , No. 9, Wenyuan Road, Qixia District, Nanjing, Jiangsu 210023, China
| | - Jun Wang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications , No. 9, Wenyuan Road, Qixia District, Nanjing, Jiangsu 210023, China
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University , No. 1, Wenyuan Road, Qixia District, Nanjing, Jiangsu 210023, China
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17
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Synthetic Genetic Interactions Reveal a Dense and Cryptic Regulatory Network of Small Noncoding RNAs in Escherichia coli. mBio 2022; 13:e0122522. [PMID: 35920556 PMCID: PMC9426594 DOI: 10.1128/mbio.01225-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Over the past 20 years, we have learned that bacterial small noncoding RNAs (sRNAs) can rapidly effect changes in gene expression in response to stress. However, the broader role and impact of sRNA-mediated regulation in promoting bacterial survival has remained elusive. Indeed, there are few examples where disruption of sRNA-mediated gene regulation results in a discernible change in bacterial growth or survival. The lack of phenotypes attributable to loss of sRNA function suggests that either sRNAs are wholly dispensable or functional redundancies mask the impact of deleting a single sRNA. We investigated synthetic genetic interactions among sRNA genes in Escherichia coli by constructing pairwise deletions in 54 genes, including 52 sRNAs. Some 1,373 double deletion strains were studied for growth defects under 32 different nutrient stress conditions and revealed 1,131 genetic interactions. In one example, we identified a profound synthetic lethal interaction between ArcZ and CsrC when E. coli was grown on pyruvate, lactate, oxaloacetate, or d-/l-alanine, and we provide evidence that the expression of ppsA is dysregulated in the double deletion background, causing the conditionally lethal phenotype. This work employs a unique platform for studying sRNA-mediated gene regulation and sheds new light on the genetic network of sRNAs that underpins bacterial growth.
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18
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Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ. From systems to structure - using genetic data to model protein structures. Nat Rev Genet 2022; 23:342-354. [PMID: 35013567 PMCID: PMC8744059 DOI: 10.1038/s41576-021-00441-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/11/2022]
Abstract
Understanding the effects of genetic variation is a fundamental problem in biology that requires methods to analyse both physical and functional consequences of sequence changes at systems-wide and mechanistic scales. To achieve a systems view, protein interaction networks map which proteins physically interact, while genetic interaction networks inform on the phenotypic consequences of perturbing these protein interactions. Until recently, understanding the molecular mechanisms that underlie these interactions often required biophysical methods to determine the structures of the proteins involved. The past decade has seen the emergence of new approaches based on coevolution, deep mutational scanning and genome-scale genetic or chemical-genetic interaction mapping that enable modelling of the structures of individual proteins or protein complexes. Here, we review the emerging use of large-scale genetic datasets and deep learning approaches to model protein structures and their interactions, and discuss the integration of structural data from different sources.
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Affiliation(s)
- Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Robyn M Kaake
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | - Andrej Sali
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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19
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Hogan AM, Cardona ST. Gradients in gene essentiality reshape antibacterial research. FEMS Microbiol Rev 2022; 46:fuac005. [PMID: 35104846 PMCID: PMC9075587 DOI: 10.1093/femsre/fuac005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 02/03/2023] Open
Abstract
Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.
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Affiliation(s)
- Andrew M Hogan
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Silvia T Cardona
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
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20
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Muscato J, Morris HG, Mychack A, Rajagopal M, Baidin V, Hesser AR, Lee W, İnecik K, Wilson LJ, Kraml CM, Meredith TC, Walker S. Rapid Inhibitor Discovery by Exploiting Synthetic Lethality. J Am Chem Soc 2022; 144:3696-3705. [PMID: 35170959 PMCID: PMC9012225 DOI: 10.1021/jacs.1c12697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Synthetic lethality occurs when inactivation of two genes is lethal but inactivation of either single gene is not. This phenomenon provides an opportunity for efficient compound discovery. Using differential growth screens, one can identify biologically active compounds that selectively inhibit proteins within the synthetic lethal network of any inactivated gene. Here, based purely on synthetic lethalities, we identified two compounds as the only possible inhibitors of Staphylococcus aureus lipoteichoic acid (LTA) biosynthesis from a screen of ∼230,000 compounds. Both compounds proved to inhibit the glycosyltransferase UgtP, which assembles the LTA glycolipid anchor. UgtP is required for β-lactam resistance in methicillin-resistant S. aureus (MRSA), and the inhibitors restored sensitivity to oxacillin in a highly resistant S. aureus strain. As no other compounds were pursued as possible LTA glycolipid assembly inhibitors, this work demonstrates the extraordinary efficiency of screens that exploit synthetic lethality to discover compounds that target specified pathways. The general approach should be applicable not only to other bacteria but also to eukaryotic cells.
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Affiliation(s)
- Jacob
D. Muscato
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Heidi G. Morris
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Aaron Mychack
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mithila Rajagopal
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States,Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Vadim Baidin
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Anthony R. Hesser
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Wonsik Lee
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kemal İnecik
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Laura J. Wilson
- Lotus
Separations LLC, B20 Frick Chemistry Laboratory, Princeton, New Jersey 08544, United States
| | - Christina M. Kraml
- Lotus
Separations LLC, B20 Frick Chemistry Laboratory, Princeton, New Jersey 08544, United States
| | - Timothy C. Meredith
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Suzanne Walker
- Department
of Microbiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States,Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States,
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21
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Tan WB, Chng SS. Genetic interaction mapping highlights key roles of the Tol-Pal complex. Mol Microbiol 2022; 117:921-936. [PMID: 35066953 DOI: 10.1111/mmi.14882] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
The conserved Tol-Pal trans-envelope complex is important for outer membrane (OM) stability and cell division in Gram-negative bacteria. It is proposed to mediate OM constriction during cell division via cell wall tethering. Yet, recent studies suggest the complex has additional roles in OM lipid homeostasis and septal wall separation. How Tol-Pal facilitates all these processes is unclear. To gain insights into its function(s), we applied transposon-insertion sequencing, and report here a detailed network of genetic interactions with the tol-pal locus in Escherichia coli. We found one positive and >20 negative strong interactions based on fitness. Disruption osmoregulated-periplasmic glucan biosynthesis restores fitness and OM barrier function, but not proper division, in tol-pal mutants. In contrast, deleting genes involved in OM homeostasis and cell wall remodeling cause synthetic growth defects in strains lacking Tol-Pal, especially exacerbating OM barrier and/or division phenotypes. Notably, the ΔtolA mutant having additional defects in OM protein assembly (ΔbamB) exhibited severe division phenotypes, even when single mutants divided normally; this highlights the possibility for OM phenotypes to indirectly impact cell division. Overall, our work underscores the intricate nature of Tol-Pal function, and reinforces its key roles in cell wall-OM tethering, cell wall remodeling, and in particular, OM homeostasis.
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Affiliation(s)
- Wee Boon Tan
- Department of Chemistry, National University of Singapore, Singapore.,Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore.,Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore
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22
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Cho H. Transposon insertion site sequencing (TIS) of Pseudomonas aeruginosa. J Microbiol 2021; 59:1067-1074. [PMID: 34865196 DOI: 10.1007/s12275-021-1565-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 10/19/2022]
Abstract
Transposon insertion site sequencing (TIS) is a technique that determines the insertion profile of a transposon mutant library by massive parallel sequencing of transposon-genomic DNA junctions. Because the transposon insertion profile reflects the abundance of each mutant in the library, it provides information to assess the fitness contribution of each genetic locus of a bacterial genome in a specific growth condition or strain background. Although introduced only about a dozen years ago, TIS has become an important tool in bacterial genetics that provides clues to study biological functions and regulatory mechanisms. Here, I describe a protocol for generating high density transposon insertion mutant libraries and preparing Illumina sequencing samples for mapping the transposon junctions of the transposon mutant libraries using Pseudomonas aeruginosa as an example.
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Affiliation(s)
- Hongbaek Cho
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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23
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Silvis MR, Rajendram M, Shi H, Osadnik H, Gray AN, Cesar S, Peters JM, Hearne CC, Kumar P, Todor H, Huang KC, Gross CA. Morphological and Transcriptional Responses to CRISPRi Knockdown of Essential Genes in Escherichia coli. mBio 2021; 12:e0256121. [PMID: 34634934 PMCID: PMC8510551 DOI: 10.1128/mbio.02561-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 01/03/2023] Open
Abstract
CRISPR interference (CRISPRi) has facilitated the study of essential genes in diverse organisms using both high-throughput and targeted approaches. Despite the promise of this technique, no comprehensive arrayed CRISPRi library targeting essential genes exists for the model bacterium Escherichia coli, or for any Gram-negative species. Here, we built and characterized such a library. Each of the ∼500 strains in our E. coli library contains an inducible, chromosomally integrated single guide RNA (sgRNA) targeting an essential (or selected nonessential) gene and can be mated with a pseudo-Hfr donor strain carrying a dcas9 cassette to create a CRISPRi knockdown strain. Using this system, we built an arrayed library of CRISPRi strains and performed population and single-cell growth and morphology measurements as well as targeted follow-up experiments. These studies found that inhibiting translation causes an extended lag phase, identified new modulators of cell morphology, and revealed that the morphogene mreB is subject to transcriptional feedback regulation, which is critical for the maintenance of morphology. Our findings highlight canonical and noncanonical roles for essential genes in numerous aspects of cellular homeostasis. IMPORTANCE Essential genes make up only ∼5 to 10% of the genetic complement in most organisms but occupy much of their protein synthesis and account for almost all antibiotic targets. Despite the importance of essential genes, their intractability has, until recently, hampered efforts to study them. CRISPRi has facilitated the study of essential genes by allowing inducible and titratable depletion. However, all large-scale CRISPRi studies in Gram-negative bacteria thus far have used plasmids to express CRISPRi components and have been constructed in pools, limiting their utility for targeted assays and complicating the determination of antibiotic effects. Here, we use a modular method to construct an arrayed library of chromosomally integrated CRISPRi strains targeting the essential genes of the model bacterium Escherichia coli. This library enables targeted studies of essential gene depletions and high-throughput determination of antibiotic targets and facilitates studies targeting the outer membrane, an essential component that serves as the major barrier to antibiotics.
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Affiliation(s)
- Melanie R. Silvis
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Manohary Rajendram
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Handuo Shi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Hendrik Osadnik
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Andrew N. Gray
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Spencer Cesar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Cameron C. Hearne
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Parth Kumar
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Horia Todor
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Carol A. Gross
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
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24
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O'Meara CP, Guerri L, Lawir DF, Mateos F, Iconomou M, Iwanami N, Soza-Ried C, Sikora K, Siamishi I, Giorgetti O, Peter S, Schorpp M, Boehm T. Genetic landscape of T cells identifies synthetic lethality for T-ALL. Commun Biol 2021; 4:1201. [PMID: 34671088 PMCID: PMC8528931 DOI: 10.1038/s42003-021-02694-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/17/2021] [Indexed: 11/09/2022] Open
Abstract
To capture the global gene network regulating the differentiation of immature T cells in an unbiased manner, large-scale forward genetic screens in zebrafish were conducted and combined with genetic interaction analysis. After ENU mutagenesis, genetic lesions associated with failure of T cell development were identified by meiotic recombination mapping, positional cloning, and whole genome sequencing. Recessive genetic variants in 33 genes were identified and confirmed as causative by additional experiments. The mutations affected T cell development but did not perturb the development of an unrelated cell type, growth hormone-expressing somatotrophs, providing an important measure of cell-type specificity of the genetic variants. The structure of the genetic network encompassing the identified components was established by a subsequent genetic interaction analysis, which identified many instances of positive (alleviating) and negative (synthetic) genetic interactions. Several examples of synthetic lethality were subsequently phenocopied using combinations of small molecule inhibitors. These drugs not only interfered with normal T cell development, but also elicited remission in a model of T cell acute lymphoblastic leukaemia. Our findings illustrate how genetic interaction data obtained in the context of entire organisms can be exploited for targeted interference with specific cell types and their malignant derivatives.
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Affiliation(s)
- Connor P O'Meara
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Lucia Guerri
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism (NIAAA), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Divine-Fondzenyuy Lawir
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Zoology, Developmental Biology Unit, University of Cologne, Cologne, Germany
| | - Fernando Mateos
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Mary Iconomou
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Cristian Soza-Ried
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Fundacion Oncoloop & Center for Nuclear Medicine, Santiago, Chile
| | - Katarzyna Sikora
- Bioinformatics Unit, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Iliana Siamishi
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Orlando Giorgetti
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Sarah Peter
- Bioinformatics Unit, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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25
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Tsai NC, Hsu TS, Kuo SC, Kao CT, Hung TH, Lin DG, Yeh CS, Chu CC, Lin JS, Lin HH, Ko CY, Chang TH, Su JC, Lin YCJ. Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex. BMC Biol 2021; 19:214. [PMID: 34560855 PMCID: PMC8461970 DOI: 10.1186/s12915-021-01140-y] [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: 03/03/2021] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yeast one-hybrid (Y1H) is a common technique for identifying DNA-protein interactions, and robotic platforms have been developed for high-throughput analyses to unravel the gene regulatory networks in many organisms. Use of these high-throughput techniques has led to the generation of increasingly large datasets, and several software packages have been developed to analyze such data. We previously established the currently most efficient Y1H system, meiosis-directed Y1H; however, the available software tools were not designed for processing the additional parameters suggested by meiosis-directed Y1H to avoid false positives and required programming skills for operation. RESULTS We developed a new tool named GateMultiplex with high computing performance using C++. GateMultiplex incorporated a graphical user interface (GUI), which allows the operation without any programming skills. Flexible parameter options were designed for multiple experimental purposes to enable the application of GateMultiplex even beyond Y1H platforms. We further demonstrated the data analysis from other three fields using GateMultiplex, the identification of lead compounds in preclinical cancer drug discovery, the crop line selection in precision agriculture, and the ocean pollution detection from deep-sea fishery. CONCLUSIONS The user-friendly GUI, fast C++ computing speed, flexible parameter setting, and applicability of GateMultiplex facilitate the feasibility of large-scale data analysis in life science fields.
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Affiliation(s)
- Ni-Chiao Tsai
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Shu Hsu
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Shang-Che Kuo
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Chung-Ting Kao
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Huan Hung
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Da-Gin Lin
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Chen Chu
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsin-Hung Lin
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, 11114, Taiwan
| | - Chia-Ying Ko
- Department of Life Sciences and Institute of Fisheries Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tien-Hsien Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Jung-Chen Su
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| | - Ying-Chung Jimmy Lin
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
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26
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Halder V, McDonnell B, Uthayakumar D, Usher J, Shapiro RS. Genetic interaction analysis in microbial pathogens: unravelling networks of pathogenesis, antimicrobial susceptibility and host interactions. FEMS Microbiol Rev 2021; 45:fuaa055. [PMID: 33145589 DOI: 10.1093/femsre/fuaa055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022] Open
Abstract
Genetic interaction (GI) analysis is a powerful genetic strategy that analyzes the fitness and phenotypes of single- and double-gene mutant cells in order to dissect the epistatic interactions between genes, categorize genes into biological pathways, and characterize genes of unknown function. GI analysis has been extensively employed in model organisms for foundational, systems-level assessment of the epistatic interactions between genes. More recently, GI analysis has been applied to microbial pathogens and has been instrumental for the study of clinically important infectious organisms. Here, we review recent advances in systems-level GI analysis of diverse microbial pathogens, including bacterial and fungal species. We focus on important applications of GI analysis across pathogens, including GI analysis as a means to decipher complex genetic networks regulating microbial virulence, antimicrobial drug resistance and host-pathogen dynamics, and GI analysis as an approach to uncover novel targets for combination antimicrobial therapeutics. Together, this review bridges our understanding of GI analysis and complex genetic networks, with applications to diverse microbial pathogens, to further our understanding of virulence, the use of antimicrobial therapeutics and host-pathogen interactions. .
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Affiliation(s)
- Viola Halder
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Brianna McDonnell
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Jane Usher
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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27
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Farha MA, French S, Brown ED. Systems-Level Chemical Biology to Accelerate Antibiotic Drug Discovery. Acc Chem Res 2021; 54:1909-1920. [PMID: 33787225 DOI: 10.1021/acs.accounts.1c00011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Drug-resistant bacterial infections pose an imminent and growing threat to public health. The discovery and development of new antibiotics of novel chemical class and mode of action that are unsusceptible to existing resistance mechanisms is imperative for tackling this threat. Modern industrial drug discovery, however, has failed to provide new drugs of this description, as it is dependent largely on a reductionist genes-to-drugs research paradigm. We posit that the lack of success in new antibiotic drug discovery is due in part to a lack of understanding of the bacterial cell system as whole. A fundamental understanding of the architecture and function of bacterial systems has been elusive but is of critical importance to design strategies to tackle drug-resistant bacterial pathogens.Increasingly, systems-level approaches are rewriting our understanding of the cell, defining a dense network of redundant and interacting components that resist perturbations of all kinds, including by antibiotics. Understanding the network properties of bacterial cells requires integrative, systematic, and genome-scale approaches. These methods strive to understand how the phenotypic behavior of bacteria emerges from the many interactions of individual molecular components that constitute the system. With the ability to examine genomic, transcriptomic, proteomic, and metabolomic consequences of, for example, genetic or chemical perturbations, researchers are increasingly moving away from one-gene-at-a-time studies to consider the system-wide response of the cell. Such measurements are demonstrating promise as quantitative tools, powerful discovery engines, and robust hypothesis generators with great value to antibiotic drug discovery.In this Account, we describe our thinking and findings using systems-level studies aimed at understanding bacterial physiology broadly and in uncovering new antibacterial chemical matter of novel mechanism. We share our systems-level toolkit and detail recent technological developments that have enabled unprecedented acquisition of genome-wide interaction data. We focus on three types of interactions: gene-gene, chemical-gene, and chemical-chemical. We provide examples of their use in understanding cell networks and how these insights might be harnessed for new antibiotic discovery. By example, we show the application of these principles in mapping genetic networks that underpin phenotypes of interest, characterizing genes of unknown function, validating small-molecule screening platforms, uncovering novel chemical probes and antibacterial leads, and delineating the mode of action of antibacterial chemicals. We also discuss the importance of computation to these approaches and its probable dominance as a tool for systems approaches in the future. In all, we advocate for the use of systems-based approaches as discovery engines in antibacterial research, both as powerful tools and to stimulate innovation.
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Affiliation(s)
- Maya A. Farha
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Eric D. Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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28
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Judd JA, Canestrari J, Clark R, Joseph A, Lapierre P, Lasek-Nesselquist E, Mir M, Palumbo M, Smith C, Stone M, Upadhyay A, Wirth SE, Dedrick RM, Meier CG, Russell DA, Dills A, Dove E, Kester J, Wolf ID, Zhu J, Rubin ER, Fortune S, Hatfull GF, Gray TA, Wade JT, Derbyshire KM. A Mycobacterial Systems Resource for the Research Community. mBio 2021; 12:e02401-20. [PMID: 33653882 PMCID: PMC8092266 DOI: 10.1128/mbio.02401-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more difficult to grow and genetically manipulate than model systems such as Escherichia coli and Bacillus subtilis To facilitate functional characterization of mycobacterial proteins, we have established a Mycobacterial Systems Resource (MSR) using the model organism Mycobacterium smegmatis This resource focuses specifically on 1,153 highly conserved core genes that are common to many mycobacterial species, including Mycobacterium tuberculosis, in order to provide the most relevant information and resources for the mycobacterial research community. The MSR includes both biological and bioinformatic resources. The biological resource includes (i) an expression plasmid library of 1,116 genes fused to a fluorescent protein for determining protein localization; (ii) a library of 569 precise deletions of nonessential genes; and (iii) a set of 843 CRISPR-interference (CRISPRi) plasmids specifically targeted to silence expression of essential core genes and genes for which a precise deletion was not obtained. The bioinformatic resource includes information about individual genes and a detailed assessment of protein localization. We anticipate that integration of these initial functional analyses and the availability of the biological resource will facilitate studies of these core proteins in many Mycobacterium species, including the less experimentally tractable pathogens M. abscessus, M. avium, M. kansasii, M. leprae, M. marinum, M. tuberculosis, and M. ulceransIMPORTANCE Diseases caused by mycobacterial species result in millions of deaths per year globally, and present a substantial health and economic burden, especially in immunocompromised patients. Difficulties inherent in working with mycobacterial pathogens have hampered the development and application of high-throughput genetics that can inform genome annotations and subsequent functional assays. To facilitate mycobacterial research, we have created a biological and bioinformatic resource (https://msrdb.org/) using Mycobacterium smegmatis as a model organism. The resource focuses specifically on 1,153 proteins that are highly conserved across the mycobacterial genus and, therefore, likely perform conserved mycobacterial core functions. Thus, functional insights from the MSR will apply to all mycobacterial species. We believe that the availability of this mycobacterial systems resource will accelerate research throughout the mycobacterial research community.
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Affiliation(s)
- J A Judd
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - J Canestrari
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - R Clark
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - A Joseph
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - P Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - E Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - M Mir
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - M Palumbo
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - C Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - M Stone
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - A Upadhyay
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - S E Wirth
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - R M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - C G Meier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - D A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - A Dills
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - E Dove
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - J Kester
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - I D Wolf
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - J Zhu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - E R Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - S Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - G F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - T A Gray
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - J T Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - K M Derbyshire
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
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29
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Kryazhimskiy S. Emergence and propagation of epistasis in metabolic networks. eLife 2021; 10:e60200. [PMID: 33527897 PMCID: PMC7924954 DOI: 10.7554/elife.60200] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Epistasis is often used to probe functional relationships between genes, and it plays an important role in evolution. However, we lack theory to understand how functional relationships at the molecular level translate into epistasis at the level of whole-organism phenotypes, such as fitness. Here, I derive two rules for how epistasis between mutations with small effects propagates from lower- to higher-level phenotypes in a hierarchical metabolic network with first-order kinetics and how such epistasis depends on topology. Most importantly, weak epistasis at a lower level may be distorted as it propagates to higher levels. Computational analyses show that epistasis in more realistic models likely follows similar, albeit more complex, patterns. These results suggest that pairwise inter-gene epistasis should be common, and it should generically depend on the genetic background and environment. Furthermore, the epistasis coefficients measured for high-level phenotypes may not be sufficient to fully infer the underlying functional relationships.
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Affiliation(s)
- Sergey Kryazhimskiy
- Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
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30
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Jorgenson MA, Bryant JC. A genetic screen to identify factors affected by undecaprenyl phosphate recycling uncovers novel connections to morphogenesis in Escherichia coli. Mol Microbiol 2021; 115:191-207. [PMID: 32979869 PMCID: PMC10568968 DOI: 10.1111/mmi.14609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/11/2020] [Indexed: 01/30/2023]
Abstract
Undecaprenyl phosphate (Und-P) is an essential lipid carrier that ferries cell wall intermediates across the cytoplasmic membrane in bacteria. Und-P is generated by dephosphorylating undecaprenyl pyrophosphate (Und-PP). In Escherichia coli, BacA, PgpB, YbjG, and LpxT dephosphorylate Und-PP and are conditionally essential. To identify vulnerabilities that arise when Und-P metabolism is defective, we developed a genetic screen for synthetic interactions which, in combination with ΔybjG ΔlpxT ΔbacA, are lethal or reduce fitness. The screen uncovered novel connections to cell division, DNA replication/repair, signal transduction, and glutathione metabolism. Further analysis revealed several new morphogenes; loss of one of these, qseC, caused cells to enlarge and lyse. QseC is the sensor kinase component of the QseBC two-component system. Loss of QseC causes overactivation of the QseB response regulator by PmrB cross-phosphorylation. Here, we show that deleting qseB completely reverses the shape defect of ΔqseC cells, as does overexpressing rprA (a small RNA). Surprisingly, deleting pmrB only partially suppressed qseC-related shape defects. Thus, QseB is activated by multiple factors in QseC's absence and prior functions ascribed to QseBC may originate from cell wall defects. Altogether, our findings provide a framework for identifying new determinants of cell integrity that could be targeted in future therapies.
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Affiliation(s)
- Matthew A. Jorgenson
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Joseph C. Bryant
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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31
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Mathis AD, Otto RM, Reynolds KA. A simplified strategy for titrating gene expression reveals new relationships between genotype, environment, and bacterial growth. Nucleic Acids Res 2021; 49:e6. [PMID: 33221881 PMCID: PMC7797047 DOI: 10.1093/nar/gkaa1073] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/02/2020] [Accepted: 10/22/2020] [Indexed: 11/13/2022] Open
Abstract
A lack of high-throughput techniques for making titrated, gene-specific changes in expression limits our understanding of the relationship between gene expression and cell phenotype. Here, we present a generalizable approach for quantifying growth rate as a function of titrated changes in gene expression level. The approach works by performing CRISPRi with a series of mutated single guide RNAs (sgRNAs) that modulate gene expression. To evaluate sgRNA mutation strategies, we constructed a library of 5927 sgRNAs targeting 88 genes in Escherichia coli MG1655 and measured the effects on growth rate. We found that a compounding mutational strategy, through which mutations are incrementally added to the sgRNA, presented a straightforward way to generate a monotonic and gradated relationship between mutation number and growth rate effect. We also implemented molecular barcoding to detect and correct for mutations that 'escape' the CRISPRi targeting machinery; this strategy unmasked deleterious growth rate effects obscured by the standard approach of ignoring escapers. Finally, we performed controlled environmental variations and observed that many gene-by-environment interactions go completely undetected at the limit of maximum knockdown, but instead manifest at intermediate expression perturbation strengths. Overall, our work provides an experimental platform for quantifying the phenotypic response to gene expression variation.
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Affiliation(s)
- Andrew D Mathis
- The Green Center for Systems Biology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ryan M Otto
- The Green Center for Systems Biology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kimberly A Reynolds
- The Green Center for Systems Biology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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32
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Bryant JA, Morris FC, Knowles TJ, Maderbocus R, Heinz E, Boelter G, Alodaini D, Colyer A, Wotherspoon PJ, Staunton KA, Jeeves M, Browning DF, Sevastsyanovich YR, Wells TJ, Rossiter AE, Bavro VN, Sridhar P, Ward DG, Chong ZS, Goodall EC, Icke C, Teo AC, Chng SS, Roper DI, Lithgow T, Cunningham AF, Banzhaf M, Overduin M, Henderson IR. Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation. eLife 2020; 9:62614. [PMID: 33315009 PMCID: PMC7806268 DOI: 10.7554/elife.62614] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022] Open
Abstract
The Gram-negative outer-membrane envelops the bacterium and functions as a permeability barrier against antibiotics, detergents, and environmental stresses. Some virulence factors serve to maintain the integrity of the outer membrane, including DolP (formerly YraP) a protein of unresolved structure and function. Here, we reveal DolP is a lipoprotein functionally conserved amongst Gram-negative bacteria and that loss of DolP increases membrane fluidity. We present the NMR solution structure for Escherichia coli DolP, which is composed of two BON domains that form an interconnected opposing pair. The C-terminal BON domain binds anionic phospholipids through an extensive membrane:protein interface. This interaction is essential for DolP function and is required for sub-cellular localisation of the protein to the cell division site, providing evidence of subcellular localisation of these phospholipids within the outer membrane. The structure of DolP provides a new target for developing therapies that disrupt the integrity of the bacterial cell envelope.
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Affiliation(s)
- Jack Alfred Bryant
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Faye C Morris
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Timothy J Knowles
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Riyaz Maderbocus
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Eva Heinz
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Gabriela Boelter
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Dema Alodaini
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Adam Colyer
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Peter J Wotherspoon
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Kara A Staunton
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Mark Jeeves
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Douglas F Browning
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | | | - Timothy J Wells
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Amanda E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Vassiliy N Bavro
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Douglas G Ward
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Zhi-Soon Chong
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Emily Ca Goodall
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute for Molecular Bioscience, University of Queensland, St. Lucia, Australia
| | - Christopher Icke
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute for Molecular Bioscience, University of Queensland, St. Lucia, Australia
| | - Alvin Ck Teo
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore, Singapore.,School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - David I Roper
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Adam F Cunningham
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute of Inflammation and Immunotherapy, University of Birmingham, Edgbaston, United Kingdom
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Michael Overduin
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom.,Department of Biochemistry, University of Alberta, Edmonton, Canada
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Department of Chemistry, National University of Singapore, Singapore, Singapore
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Wytock TP, Zhang M, Jinich A, Fiebig A, Crosson S, Motter AE. Extreme Antagonism Arising from Gene-Environment Interactions. Biophys J 2020; 119:2074-2086. [PMID: 33068537 DOI: 10.1016/j.bpj.2020.09.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/27/2020] [Accepted: 09/21/2020] [Indexed: 01/06/2023] Open
Abstract
Antagonistic interactions in biological systems, which occur when one perturbation blunts the effect of another, are typically interpreted as evidence that the two perturbations impact the same cellular pathway or function. Yet, this interpretation ignores extreme antagonistic interactions wherein an otherwise deleterious perturbation compensates for the function lost because of a prior perturbation. Here, we report on gene-environment interactions involving genetic mutations that are deleterious in a permissive environment but beneficial in a specific environment that restricts growth. These extreme antagonistic interactions constitute gene-environment analogs of synthetic rescues previously observed for gene-gene interactions. Our approach uses two independent adaptive evolution steps to address the lack of experimental methods to systematically identify such extreme interactions. We apply the approach to Escherichia coli by successively adapting it to defined glucose media without and with the antibiotic rifampicin. The approach identified multiple mutations that are beneficial in the presence of rifampicin and deleterious in its absence. The analysis of transcription shows that the antagonistic adaptive mutations repress a stringent response-like transcriptional program, whereas nonantagonistic mutations have an opposite transcriptional profile. Our approach represents a step toward the systematic characterization of extreme antagonistic gene-drug interactions, which can be used to identify targets to select against antibiotic resistance.
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Affiliation(s)
- Thomas P Wytock
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois
| | - Manjing Zhang
- The Committee on Microbiology, University of Chicago, Chicago, Illinois
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Department of Medicine, Weill-Cornell Medical College, New York, New York
| | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Adilson E Motter
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois; Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois.
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34
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Suárez GA, Dugan KR, Renda BA, Leonard SP, Gangavarapu LS, Barrick JE. Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining. Nucleic Acids Res 2020; 48:4585-4600. [PMID: 32232367 PMCID: PMC7192602 DOI: 10.1093/nar/gkaa204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 03/15/2020] [Accepted: 03/18/2020] [Indexed: 01/10/2023] Open
Abstract
One goal of synthetic biology is to improve the efficiency and predictability of living cells by removing extraneous genes from their genomes. We demonstrate improved methods for engineering the genome of the metabolically versatile and naturally transformable bacterium Acinetobacter baylyi ADP1 and apply them to a genome streamlining project. In Golden Transformation, linear DNA fragments constructed by Golden Gate Assembly are directly added to cells to create targeted deletions, edits, or additions to the chromosome. We tested the dispensability of 55 regions of the ADP1 chromosome using Golden Transformation. The 18 successful multiple-gene deletions ranged in size from 21 to 183 kb and collectively accounted for 23.4% of its genome. The success of each multiple-gene deletion attempt could only be partially predicted on the basis of an existing collection of viable ADP1 single-gene deletion strains and a new transposon insertion sequencing (Tn-Seq) dataset that we generated. We further show that ADP1’s native CRISPR/Cas locus is active and can be retargeted using Golden Transformation. We reprogrammed it to create a CRISPR-Lock, which validates that a gene has been successfully removed from the chromosome and prevents it from being reacquired. These methods can be used together to implement combinatorial routes to further genome streamlining and for more rapid and assured metabolic engineering of this versatile chassis organism.
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Affiliation(s)
- Gabriel A Suárez
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kyle R Dugan
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brian A Renda
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sean P Leonard
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Lakshmi Suryateja Gangavarapu
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
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35
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Galili M, Tuller T. CSN: unsupervised approach for inferring biological networks based on the genome alone. BMC Bioinformatics 2020; 21:190. [PMID: 32414319 PMCID: PMC7227238 DOI: 10.1186/s12859-020-3479-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 03/31/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most organisms cannot be cultivated, as they live in unique ecological conditions that cannot be mimicked in the lab. Understanding the functionality of those organisms' genes and their interactions by performing large-scale measurements of transcription levels, protein-protein interactions or metabolism, is extremely difficult and, in some cases, impossible. Thus, efficient algorithms for deciphering genome functionality based only on the genomic sequences with no other experimental measurements are needed. RESULTS In this study, we describe a novel algorithm that infers gene networks that we name Common Substring Network (CSN). The algorithm enables inferring novel regulatory relations among genes based only on the genomic sequence of a given organism and partial homolog/ortholog-based functional annotation. It can specifically infer the functional annotation of genes with unknown homology. This approach is based on the assumption that related genes, not necessarily homologs, tend to share sub-sequences, which may be related to common regulatory mechanisms, similar functionality of encoded proteins, common evolutionary history, and more. We demonstrate that CSNs, which are based on S. cerevisiae and E. coli genomes, have properties similar to 'traditional' biological networks inferred from experiments. Highly expressed genes tend to have higher degree nodes in the CSN, genes with similar protein functionality tend to be closer, and the CSN graph exhibits a power-law degree distribution. Also, we show how the CSN can be used for predicting gene interactions and functions. CONCLUSIONS The reported results suggest that 'silent' code inside the transcript can help to predict central features of biological networks and gene function. This approach can help researchers to understand the genome of novel microorganisms, analyze metagenomic data, and can help to decipher new gene functions. AVAILABILITY Our MATLAB implementation of CSN is available at https://www.cs.tau.ac.il/~tamirtul/CSN-Autogen.
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Affiliation(s)
- Maya Galili
- Biomedical Engineering Department, Tel Aviv University, Tel-Aviv, Israel
- Department of Molecular Microbiology & Biotechnology, Tel Aviv University, Tel-Aviv, Israel
| | - Tamir Tuller
- Biomedical Engineering Department, Tel Aviv University, Tel-Aviv, Israel
- The Sagol School of Neuroscience, Tel Aviv University, Tel-Aviv, Israel
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36
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Klobucar K, French S, Côté JP, Howes JR, Brown ED. Genetic and Chemical-Genetic Interactions Map Biogenesis and Permeability Determinants of the Outer Membrane of Escherichia coli. mBio 2020; 11:e00161-20. [PMID: 32156814 PMCID: PMC7064757 DOI: 10.1128/mbio.00161-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 02/08/2023] Open
Abstract
Gram-negative bacteria are intrinsically resistant to many antibiotics due to their outer membrane barrier. Although the outer membrane has been studied for decades, there is much to uncover about the biology and permeability of this complex structure. Investigating synthetic genetic interactions can reveal a great deal of information about genetic function and pathway interconnectivity. Here, we performed synthetic genetic arrays (SGAs) in Escherichia coli by crossing a subset of gene deletion strains implicated in outer membrane permeability with nonessential gene and small RNA (sRNA) deletion collections. Some 155,400 double-deletion strains were grown on rich microbiological medium with and without subinhibitory concentrations of two antibiotics excluded by the outer membrane, vancomycin and rifampin, to probe both genetic interactions and permeability. The genetic interactions of interest were synthetic sick or lethal (SSL) gene deletions that were detrimental to the cell in combination but had a negligible impact on viability individually. On average, there were ∼30, ∼36, and ∼40 SSL interactions per gene under no-drug, rifampin, and vancomycin conditions, respectively; however, many of these involved frequent interactors. Our data sets have been compiled into an interactive database called the Outer Membrane Interaction (OMI) Explorer, where genetic interactions can be searched, visualized across the genome, compared between conditions, and enriched for gene ontology (GO) terms. A set of SSL interactions revealed connectivity and permeability links between enterobacterial common antigen (ECA) and lipopolysaccharide (LPS) of the outer membrane. This data set provides a novel platform to generate hypotheses about outer membrane biology and permeability.IMPORTANCE Gram-negative bacteria are a major concern for public health, particularly due to the rise of antibiotic resistance. It is important to understand the biology and permeability of the outer membrane of these bacteria in order to increase the efficacy of antibiotics that have difficulty penetrating this structure. Here, we studied the genetic interactions of a subset of outer membrane-related gene deletions in the model Gram-negative bacterium E. coli We systematically combined these mutants with 3,985 nonessential gene and small RNA deletion mutations in the genome. We examined the viability of these double-deletion strains and probed their permeability characteristics using two antibiotics that have difficulty crossing the outer membrane barrier. An understanding of the genetic basis for outer membrane integrity can assist in the development of new antibiotics with favorable permeability properties and the discovery of compounds capable of increasing outer membrane permeability to enhance the activity of existing antibiotics.
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Affiliation(s)
- Kristina Klobucar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jean-Philippe Côté
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - James R Howes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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37
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Adaptive walks on high-dimensional fitness landscapes and seascapes with distance-dependent statistics. Theor Popul Biol 2019; 130:13-49. [PMID: 31605706 DOI: 10.1016/j.tpb.2019.09.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 09/07/2019] [Accepted: 09/12/2019] [Indexed: 11/21/2022]
Abstract
The dynamics of evolution is intimately shaped by epistasis - interactions between genetic elements which cause the fitness-effect of combinations of mutations to be non-additive. Analyzing evolutionary dynamics that involves large numbers of epistatic mutations is intrinsically difficult. A crucial feature is that the fitness landscape in the vicinity of the current genome depends on the evolutionary history. A key step is thus developing models that enable study of the effects of past evolution on future evolution. In this work, we introduce a broad class of high-dimensional random fitness landscapes for which the correlations between fitnesses of genomes are a general function of genetic distance. Their Gaussian character allows for tractable computational as well as analytic understanding. We study the properties of these landscapes focusing on the simplest evolutionary process: random adaptive (uphill) walks. Conventional measures of "ruggedness" are shown to not much affect such adaptive walks. Instead, the long-distance statistics of epistasis cause all properties to be highly conditional on past evolution, determining the statistics of the local landscape (the distribution of fitness-effects of available mutations and combinations of these), as well as the global geometry of evolutionary trajectories. In order to further explore the effects of conditioning on past evolution, we model the effects of slowly changing environments. At long times, such fitness "seascapes" cause a statistical steady state with highly intermittent evolutionary dynamics: populations undergo bursts of rapid adaptation, interspersed with periods in which adaptive mutations are rare and the population waits for more new directions to be opened up by changes in the environment. Finally, we discuss prospects for studying more complex evolutionary dynamics and on broader classes of high-dimensional landscapes and seascapes.
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38
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Kumar A, Hosseinnia A, Gagarinova A, Phanse S, Kim S, Aly KA, Zilles S, Babu M. A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli. Bioinformatics 2019; 36:880-889. [PMID: 31504172 PMCID: PMC9883677 DOI: 10.1093/bioinformatics/btz673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/24/2019] [Accepted: 08/23/2019] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION A digenic genetic interaction (GI) is observed when mutations in two genes within the same organism yield a phenotype that is different from the expected, given each mutation's individual effects. While multiplicative scoring is widely applied to define GIs, revealing underlying gene functions, it remains unclear if it is the most suitable choice for scoring GIs in Escherichia coli. Here, we assess many different definitions, including the multiplicative model, for mapping functional links between genes and pathways in E.coli. RESULTS Using our published E.coli GI datasets, we show computationally that a machine learning Gaussian process (GP)-based definition better identifies functional associations among genes than a multiplicative model, which we have experimentally confirmed on a set of gene pairs. Overall, the GP definition improves the detection of GIs, biological reasoning of epistatic connectivity, as well as the quality of GI maps in E.coli, and, potentially, other microbes. AVAILABILITY AND IMPLEMENTATION The source code and parameters used to generate the machine learning models in WEKA software were provided in the Supplementary information. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ali Hosseinnia
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Alla Gagarinova
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sunyoung Kim
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Khaled A Aly
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | | | - Mohan Babu
- To whom correspondence should be addressed. or
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39
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Large-scale chemical-genetics yields new M. tuberculosis inhibitor classes. Nature 2019; 571:72-78. [PMID: 31217586 DOI: 10.1038/s41586-019-1315-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/21/2019] [Indexed: 01/07/2023]
Abstract
New antibiotics are needed to combat rising levels of resistance, with new Mycobacterium tuberculosis (Mtb) drugs having the highest priority. However, conventional whole-cell and biochemical antibiotic screens have failed. Here we develop a strategy termed PROSPECT (primary screening of strains to prioritize expanded chemistry and targets), in which we screen compounds against pools of strains depleted of essential bacterial targets. We engineered strains that target 474 essential Mtb genes and screened pools of 100-150 strains against activity-enriched and unbiased compound libraries, probing more than 8.5 million chemical-genetic interactions. Primary screens identified over tenfold more hits than screening wild-type Mtb alone, with chemical-genetic interactions providing immediate, direct target insights. We identified over 40 compounds that target DNA gyrase, the cell wall, tryptophan, folate biosynthesis and RNA polymerase, as well as inhibitors that target EfpA. Chemical optimization yielded EfpA inhibitors with potent wild-type activity, thus demonstrating the ability of PROSPECT to yield inhibitors against targets that would have eluded conventional drug discovery.
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40
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Yeh CS, Wang Z, Miao F, Ma H, Kao CT, Hsu TS, Yu JH, Hung ET, Lin CC, Kuan CY, Tsai NC, Zhou C, Qu GZ, Jiang J, Liu G, Wang JP, Li W, Chiang VL, Chang TH, Lin YCJ. A novel synthetic-genetic-array-based yeast one-hybrid system for high discovery rate and short processing time. Genome Res 2019; 29:1343-1351. [PMID: 31186303 PMCID: PMC6673709 DOI: 10.1101/gr.245951.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/06/2019] [Indexed: 12/18/2022]
Abstract
Eukaryotic gene expression is often tightly regulated by interactions between transcription factors (TFs) and their DNA cis targets. Yeast one-hybrid (Y1H) is one of the most extensively used methods to discover these interactions. We developed a high-throughput meiosis-directed yeast one-hybrid system using the Magic Markers of the synthetic genetic array analysis. The system has a transcription factor–DNA interaction discovery rate twice as high as the conventional diploid-mating approach and a processing time nearly one-tenth of the haploid-transformation method. The system also offers the highest accuracy in identifying TF–DNA interactions that can be authenticated in vivo by chromatin immunoprecipitation. With these unique features, this meiosis-directed Y1H system is particularly suited for constructing novel and comprehensive genome-scale gene regulatory networks for various organisms.
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Affiliation(s)
- Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Fang Miao
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chung-Ting Kao
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Shu Hsu
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Institute of Biomedical Informatics and Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Jhong-He Yu
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Er-Tsi Hung
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Chang Lin
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chen-Yu Kuan
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Ni-Chiao Tsai
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guan-Zheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
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41
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Suppressor Mutations in degS Overcome the Acute Temperature-Sensitive Phenotype of Δ degP and Δ degP Δ tol-pal Mutants of Escherichia coli. J Bacteriol 2019; 201:JB.00742-18. [PMID: 30858298 DOI: 10.1128/jb.00742-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/25/2019] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, the periplasmic protease DegP plays a critical role in degrading misfolded outer membrane proteins (OMPs). Consequently, mutants lacking DegP display a temperature-sensitive growth defect, presumably due to the toxic accumulation of misfolded OMPs. The Tol-Pal complex plays a poorly defined but an important role in envelope biogenesis, since mutants defective in this complex display a classical periplasmic leakage phenotype. Double mutants lacking DegP and an intact Tol-Pal complex display exaggerated temperature-sensitive growth defects and the leaky phenotype. Two revertants that overcome the temperature-sensitive growth phenotype carry missense mutations in the degS gene, resulting in D102V and D320A substitutions. D320 and E317 of the PDZ domain of DegS make salt bridges with R178 of DegS's protease domain to keep the protease in the inactive state. However, weakening of the tripartite interactions by D320A increases DegS's basal protease activity. Although the D102V substitution is as effective as D320A in suppressing the temperature-sensitive growth phenotype, the molecular mechanism behind its effect on DegS's protease activity is unclear. Our data suggest that the two DegS variants modestly activate RseA-controlled, σE-mediated envelope stress response pathway and elevate periplasmic protease activity to restore envelope homeostasis. Based on the release of a cytoplasmic enzyme in the culture supernatant, we conclude that the conditional lethal phenotype of ΔtolB ΔdegP mutants stems from a grossly destabilized envelope structure that causes excessive cell lysis. Together, the data point to a critical role for periplasmic proteases when the Tol-Pal complex-mediated envelope structure and/or functions are compromised.IMPORTANCE The Tol-Pal complex plays a poorly defined role in envelope biogenesis. The data presented here show that DegP's periplasmic protease activity becomes crucial in mutants lacking the intact Tol-Pal complex, but this requirement can be circumvented by suppressor mutations that activate the basal protease activity of a regulatory protease, DegS. These observations point to a critical role for periplasmic proteases when Tol-Pal-mediated envelope structure and/or functions are perturbed.
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42
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Costanzo M, Kuzmin E, van Leeuwen J, Mair B, Moffat J, Boone C, Andrews B. Global Genetic Networks and the Genotype-to-Phenotype Relationship. Cell 2019; 177:85-100. [PMID: 30901552 PMCID: PMC6817365 DOI: 10.1016/j.cell.2019.01.033] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/09/2019] [Accepted: 01/21/2019] [Indexed: 01/25/2023]
Abstract
Genetic interactions identify combinations of genetic variants that impinge on phenotype. With whole-genome sequence information available for thousands of individuals within a species, a major outstanding issue concerns the interpretation of allelic combinations of genes underlying inherited traits. In this Review, we discuss how large-scale analyses in model systems have illuminated the general principles and phenotypic impact of genetic interactions. We focus on studies in budding yeast, including the mapping of a global genetic network. We emphasize how information gained from work in yeast translates to other systems, and how a global genetic network not only annotates gene function but also provides new insights into the genotype-to-phenotype relationship.
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Affiliation(s)
- Michael Costanzo
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada.
| | - Elena Kuzmin
- Goodman Cancer Research Centre, McGill University, Montreal QC, Canada
| | | | - Barbara Mair
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada
| | - Jason Moffat
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada; Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto ON, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada; Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto ON, Canada.
| | - Brenda Andrews
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada; Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto ON, Canada.
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43
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Bu QT, Yu P, Wang J, Li ZY, Chen XA, Mao XM, Li YQ. Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approaches. Microb Cell Fact 2019; 18:16. [PMID: 30691531 PMCID: PMC6348691 DOI: 10.1186/s12934-019-1055-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/07/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptomyces chattanoogensis L10 is the industrial producer of natamycin and has been proved a highly efficient host for diverse natural products. It has an enormous potential to be developed as a versatile cell factory for production of heterologous secondary metabolites. Here we developed a genome-reduced industrial Streptomyces chassis by rational 'design-build-test' pipeline. RESULTS To identify candidate large non-essential genomic regions accurately and design large deletion rationally, we performed genome analyses of S. chattanoogensis L10 by multiple computational approaches, optimized Cre/loxP recombination system for high-efficient large deletion and constructed a series of universal suicide plasmids for rapid loxP or loxP mutant sites inserting into genome. Subsequently, two genome-streamlined mutants, designated S. chattanoogensis L320 and L321, were rationally constructed by depletion of 1.3 Mb and 0.7 Mb non-essential genomic regions, respectively. Furthermore, several biological performances like growth cycle, secondary metabolite profile, hyphae morphological engineering, intracellular energy (ATP) and reducing power (NADPH/NADP+) levels, transformation efficiency, genetic stability, productivity of heterologous proteins and secondary metabolite were systematically evaluated. Finally, our results revealed that L321 could serve as an efficient chassis for the production of polyketides. CONCLUSIONS Here we developed the combined strategy of multiple computational approaches and site-specific recombination system to rationally construct genome-reduced Streptomyces hosts with high efficiency. Moreover, a genome-reduced industrial Streptomyces chassis S. chattanoogensis L321 was rationally constructed by the strategy, and the chassis exhibited several emergent and excellent performances for heterologous expression of secondary metabolite. The strategy could be widely applied in other Streptomyces to generate miscellaneous and versatile chassis with minimized genome. These chassis can not only serve as cell factories for high-efficient production of valuable polyketides, but also will provide great support for the upgrade of microbial pharmaceutical industry and drug discovery.
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Affiliation(s)
- Qing-Ting Bu
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Pin Yu
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Jue Wang
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Zi-Yue Li
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China.
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China.
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44
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Klobucar K, Brown ED. Use of genetic and chemical synthetic lethality as probes of complexity in bacterial cell systems. FEMS Microbiol Rev 2018; 42:4563584. [PMID: 29069427 DOI: 10.1093/femsre/fux054] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/23/2017] [Indexed: 12/22/2022] Open
Abstract
Different conditions and genomic contexts are known to have an impact on gene essentiality and interactions. Synthetic lethal interactions occur when a combination of perturbations, either genetic or chemical, result in a more profound fitness defect than expected based on the effect of each perturbation alone. Synthetic lethality in bacterial systems has long been studied; however, during the past decade, the emerging fields of genomics and chemical genomics have led to an increase in the scale and throughput of these studies. Here, we review the concepts of genomics and chemical genomics in the context of synthetic lethality and their revolutionary roles in uncovering novel biology such as the characterization of genes of unknown function and in antibacterial drug discovery. We provide an overview of the methodologies, examples and challenges of both genetic and chemical synthetic lethal screening platforms. Finally, we discuss how to apply genetic and chemical synthetic lethal approaches to rationalize the synergies of drugs, screen for new and improved antibacterial therapies and predict drug mechanism of action.
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Affiliation(s)
- Kristina Klobucar
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St West, Hamilton, ON L8N 3Z5, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St West, Hamilton, ON L8N 3Z5, Canada
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45
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VanderSluis B, Costanzo M, Billmann M, Ward HN, Myers CL, Andrews BJ, Boone C. Integrating genetic and protein-protein interaction networks maps a functional wiring diagram of a cell. Curr Opin Microbiol 2018; 45:170-179. [PMID: 30059827 DOI: 10.1016/j.mib.2018.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 01/01/2023]
Abstract
Systematic experimental approaches have led to construction of comprehensive genetic and protein-protein interaction networks for the budding yeast, Saccharomyces cerevisiae. Genetic interactions capture functional relationships between genes using phenotypic readouts, while protein-protein interactions identify physical connections between gene products. These complementary, and largely non-overlapping, networks provide a global view of the functional architecture of a cell, revealing general organizing principles, many of which appear to be evolutionarily conserved. Here, we focus on insights derived from the integration of large-scale genetic and protein-protein interaction networks, highlighting principles that apply to both unicellular and more complex systems, including human cells. Network integration reveals fundamental connections involving key functional modules of eukaryotic cells, defining a core network of cellular function, which could be elaborated to explore cell-type specificity in metazoans.
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Affiliation(s)
- Benjamin VanderSluis
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Michael Costanzo
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Henry N Ward
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA.
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
| | - Charles Boone
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada; RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
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46
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Hussein NA, Cho SH, Laloux G, Siam R, Collet JF. Distinct domains of Escherichia coli IgaA connect envelope stress sensing and down-regulation of the Rcs phosphorelay across subcellular compartments. PLoS Genet 2018; 14:e1007398. [PMID: 29852010 PMCID: PMC5978795 DOI: 10.1371/journal.pgen.1007398] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/08/2018] [Indexed: 12/14/2022] Open
Abstract
In enterobacteria, the Rcs system (Regulator of capsule synthesis) monitors envelope integrity and induces a stress response when damages occur in the outer membrane or in the peptidoglycan layer. Built around a two-component system, Rcs controls gene expression via a cascade of phosphoryl transfer reactions. Being particularly complex, Rcs also involves the outer membrane lipoprotein RcsF and the inner membrane essential protein IgaA (Intracellular growth attenuator). RcsF and IgaA, which are located upstream of the phosphorelay, are required for normal Rcs functioning. Here, we establish the stress-dependent formation of a complex between RcsF and the periplasmic domain of IgaA as the molecular signal triggering Rcs. Moreover, molecular dissection of IgaA reveals that its negative regulatory role on Rcs is mostly carried by its first N-terminal cytoplasmic domain. Altogether, our results support a model in which IgaA regulates Rcs activation by playing a direct role in the transfer of signals from the cell envelope to the cytoplasm. This remarkable feature further distinguishes Rcs from other envelope stress response systems. A thorough understanding of the mechanisms that allow bacteria to thrive in various environments is crucial to the development of new antibiotics, an urgent endeavor to combat antimicrobial resistance. A landmark feature of Gram-negative bacteria is the presence of a multi-layered envelope. Because this structure is essential, its integrity is constantly monitored to detect and respond to potential breaches in a fast and adequate manner. Here, we describe how IgaA, an essential protein present in the cytoplasmic membrane of enterobacteria, participates in the transfer of stress signals from the envelope to the cytoplasm. We provide evidence that IgaA works in concert with RcsF, a lipoprotein that is posted as a sentinel in the outermost envelope layer, to detect envelope stress: under stress conditions, RcsF forms a complex with the C-terminal, periplasmic domain of IgaA. As a result, cells turn on the Rcs response. We also discovered that the N-terminal, cytoplasmic domain of IgaA plays an important role in inhibiting Rcs in the absence of stress. Together, these findings reveal that distinct IgaA domains coordinate stress sensing and Rcs activation across the cytoplasmic membrane. They enhance our understanding of Rcs regulation and open new avenues for the development of new antibacterials.
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Affiliation(s)
- Nahla A. Hussein
- WELBIO, Brussels, Belgium
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
- Biology Department, Biotechnology Graduate Program and YJ-Science and Technology Research Center, American University in Cairo, Cairo, Egypt
| | - Seung-Hyun Cho
- WELBIO, Brussels, Belgium
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Géraldine Laloux
- WELBIO, Brussels, Belgium
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Rania Siam
- Biology Department, Biotechnology Graduate Program and YJ-Science and Technology Research Center, American University in Cairo, Cairo, Egypt
| | - Jean-François Collet
- WELBIO, Brussels, Belgium
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
- * E-mail:
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47
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Sardi M, Gasch AP. Genetic background effects in quantitative genetics: gene-by-system interactions. Curr Genet 2018; 64:1173-1176. [PMID: 29644456 DOI: 10.1007/s00294-018-0835-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/18/2023]
Abstract
Proper cell function depends on networks of proteins that interact physically and functionally to carry out physiological processes. Thus, it seems logical that the impact of sequence variation in one protein could be significantly influenced by genetic variants at other loci in a genome. Nonetheless, the importance of such genetic interactions, known as epistasis, in explaining phenotypic variation remains a matter of debate in genetics. Recent work from our lab revealed that genes implicated from an association study of toxin tolerance in Saccharomyces cerevisiae show extensive interactions with the genetic background: most implicated genes, regardless of allele, are important for toxin tolerance in only one of two tested strains. The prevalence of background effects in our study adds to other reports of widespread genetic-background interactions in model organisms. We suggest that these effects represent many-way interactions with myriad features of the cellular system that vary across classes of individuals. Such gene-by-system interactions may influence diverse traits and require new modeling approaches to accurately represent genotype-phenotype relationships across individuals.
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Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Cargill, Incorporated, Minneapolis, MN, 55440, USA
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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48
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El Zahed SS, Brown ED. Chemical-Chemical Combinations Map Uncharted Interactions in Escherichia coli under Nutrient Stress. iScience 2018; 2:168-181. [PMID: 30428373 PMCID: PMC6136904 DOI: 10.1016/j.isci.2018.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/28/2018] [Accepted: 03/07/2018] [Indexed: 11/16/2022] Open
Abstract
Of the ∼4,400 genes that constitute Escherichia coli's genome, ∼300 genes are indispensable for its growth in nutrient-rich conditions. These encode housekeeping functions, including cell wall, DNA, RNA, and protein syntheses. Under conditions in which nutrients are limited to a carbon source, nitrogen source, essential phosphates, and salts, more than 100 additional genes become essential. These largely code for the synthesis of amino acids, vitamins, and nucleobases. Although much is known about this collection of ∼400 genes, their interactions under nutrient stress are uncharted. Using a chemical biology approach, we focused on 45 chemical probes targeting encoded proteins in this collection and mapped their interactions under nutrient-limited conditions. Encompassing 990 unique pairwise chemical combinations, we revealed a highly connected network of 186 interactions, of which 81 were synergistic and 105 were antagonistic. The network revealed signature interactions for each probe and highlighted new connectivity between housekeeping functions and those essential in nutrient stress. Chemical probes map a complex interaction network in E. coli under nutrient stress A total of 990 unique chemical combinations reveal a dense network of 186 interactions New connections between housekeeping functions and those in nutrient stress
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Affiliation(s)
- Sara S El Zahed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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49
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Wytock TP, Fiebig A, Willett JW, Herrou J, Fergin A, Motter AE, Crosson S. Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate. PLoS Genet 2018; 14:e1007284. [PMID: 29584733 PMCID: PMC5892946 DOI: 10.1371/journal.pgen.1007284] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 04/10/2018] [Accepted: 03/02/2018] [Indexed: 01/08/2023] Open
Abstract
Cell growth is determined by substrate availability and the cell’s metabolic capacity to assimilate substrates into building blocks. Metabolic genes that determine growth rate may interact synergistically or antagonistically, and can accelerate or slow growth, depending on genetic background and environmental conditions. We evolved a diverse set of Escherichia coli single-gene deletion mutants with a spectrum of growth rates and identified mutations that generally increase growth rate. Despite the metabolic differences between parent strains, mutations that enhanced growth largely mapped to core transcription machinery, including the β and β’ subunits of RNA polymerase (RNAP) and the transcription elongation factor, NusA. The structural segments of RNAP that determine enhanced growth have been previously implicated in antibiotic resistance and in the control of transcription elongation and pausing. We further developed a computational framework to characterize how the transcriptional changes that occur upon acquisition of these mutations affect growth rate across strains. Our experimental and computational results provide evidence for cases in which RNAP mutations shift the competitive balance between active transcription and gene silencing. This study demonstrates that mutations in specific regions of RNAP are a convergent adaptive solution that can enhance the growth rate of cells from distinct metabolic states. The loss of a metabolic function caused by gene deletion can be compensated, in certain cases, by the concurrent mutation of a second gene. Whether such gene pairs share a local chemical or regulatory relationship or interact via a non-local mechanism has implications for the co-evolution of genetic changes, development of alternatives to gene therapy, and the design of combination antimicrobial therapies that select against resistance. Yet, we lack a comprehensive knowledge of adaptive responses to metabolic mutations, and our understanding of the mechanisms underlying genetic rescue remains limited. We present results of a laboratory evolution approach that has the potential to address both challenges, showing that mutations in specific regions of RNA polymerase enhance growth rates of distinct mutant strains of Escherichia coli with a spectrum of growth defects. Several of these adaptive mutations are deleterious when engineered directly into the original wild-type strain under alternative cultivation conditions, and thus have epistatic rescue properties when paired with the corresponding primary metabolic gene deletions. Our combination of adaptive evolution, directed genetic engineering, and mathematical analysis of transcription and growth rate distinguishes between rescue interactions that are specific or non-specific to a particular deletion. Our study further supports a model for RNA polymerase as a locus of convergent adaptive evolution from different sub-optimal metabolic starting points.
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Affiliation(s)
- Thomas P. Wytock
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America
| | - Aretha Fiebig
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan W. Willett
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Julien Herrou
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Aleksandra Fergin
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Adilson E. Motter
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
- * E-mail: (AEM); (SC)
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (AEM); (SC)
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50
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Roguev A, Ryan CJ, Hartsuiker E, Krogan NJ. High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe. Cold Spring Harb Protoc 2018; 2018:pdb.top079905. [PMID: 28733404 DOI: 10.1101/pdb.top079905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Epistasis mapping, in which the phenotype that emerges from combining pairs of mutations is measured quantitatively, is a powerful tool for unbiased study of gene function. When performed at a large scale, this approach has been used to assign function to previously uncharacterized genes, define functional modules and pathways, and study their cross talk. These experiments rely heavily on methods for rapid sampling of binary combinations of mutant alleles by systematic generation of a series of double mutants. Epistasis mapping technologies now exist in various model systems. Here we provide an overview of different epistasis mapping technologies, including the pombe epistasis mapper (PEM) system designed for the collection of quantitative genetic interaction data in fission yeast Schizosaccharomyces pombe Comprising a series of high-throughput selection steps for generation and characterization of double mutants, the PEM system has provided insight into a wide range of biological processes as well as facilitated evolutionary analysis of genetic interactomes across different species.
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Affiliation(s)
- Assen Roguev
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94518
| | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Edgar Hartsuiker
- North West Cancer Research Institute, Bangor University, Bangor LL57 2UW, United Kingdom
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94518
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