1
|
Bae DW, Lee SH, Park JH, Son SY, Lin Y, Lee J, Jang BR, Lee KH, Lee YH, Lee H, Kang S, Kim B, Cha SS. An archaeal transcription factor EnfR with a novel 'eighth note' fold controls hydrogen production of a hyperthermophilic archaeon Thermococcus onnurineus NA1. Nucleic Acids Res 2023; 51:10026-10040. [PMID: 37650645 PMCID: PMC10570040 DOI: 10.1093/nar/gkad699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/13/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023] Open
Abstract
Thermococcus onnurineus NA1, a hyperthermophilic carboxydotrophic archaeon, produces H2 through CO oxidation catalyzed by proteins encoded in a carbon monoxide dehydrogenase (CODH) gene cluster. TON_1525 with a DNA-binding helix-turn-helix (HTH) motif is a putative repressor regulating the transcriptional expression of the codh gene cluster. The T55I mutation in TON_1525 led to enhanced H2 production accompanied by the increased expression of genes in the codh cluster. Here, TON_1525 was demonstrated to be a dimer. Monomeric TON_1525 adopts a novel 'eighth note' symbol-like fold (referred to as 'eighth note' fold regulator, EnfR), and the dimerization mode of EnfR is unique in that it has no resemblance to structures in the Protein Data Bank. According to footprinting and gel shift assays, dimeric EnfR binds to a 36-bp pseudo-palindromic inverted repeat in the promoter region of the codh gene cluster, which is supported by an in silico EnfR/DNA complex model and mutational studies revealing the implication of N-terminal loops as well as HTH motifs in DNA recognition. The DNA-binding affinity of the T55I mutant was lowered by ∼15-fold, for which the conformational change of N-terminal loops is responsible. In addition, transcriptome analysis suggested that EnfR could regulate diverse metabolic processes besides H2 production.
Collapse
Affiliation(s)
- Da-Woon Bae
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seong Hyuk Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea
| | - Ji Hye Park
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Se-Young Son
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Cheongju, Chungbuk 28119, Republic of Korea
| | - Jung Hyen Lee
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Bo-Ram Jang
- Department of Life Science, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul, South Korea
| | - Kyu-Ho Lee
- Department of Life Science, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul, South Korea
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Cheongju, Chungbuk 28119, Republic of Korea
- Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Republic of Korea
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Gyeonggi 17546, Republic of Korea
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea
- Department of Marine Biotechnology, KIOST School, University of Science and Technology, Daejeon, South Korea
| | - Sung Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea
- Department of Marine Biotechnology, KIOST School, University of Science and Technology, Daejeon, South Korea
| | - Byoung Sik Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| |
Collapse
|
2
|
Cho SY, Na HW, Oh H, Kwak YM, Song WS, Park S, Jeon WJ, Cho H, Oh BC, Park J, Kang S, Lee GS, Yoon SI. Structural basis of flagellar motility regulation by the MogR repressor and the GmaR antirepressor in Listeria monocytogenes. Nucleic Acids Res 2022; 50:11315-11330. [PMID: 36283692 PMCID: PMC9638930 DOI: 10.1093/nar/gkac815] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 08/01/2022] [Accepted: 09/11/2022] [Indexed: 08/27/2023] Open
Abstract
The pathogenic Listeria monocytogenes bacterium produces the flagellum as a locomotive organelle at or below 30°C outside the host, but it halts flagellar expression at 37°C inside the human host to evade the flagellum-induced immune response. Listeria monocytogenes GmaR is a thermosensor protein that coordinates flagellar expression by binding the master transcriptional repressor of flagellar genes (MogR) in a temperature-responsive manner. To understand the regulatory mechanism whereby GmaR exerts the antirepression activity on flagellar expression, we performed structural and mutational analyses of the GmaR-MogR system. At or below 30°C, GmaR exists as a functional monomer and forms a circularly enclosed multidomain structure via an interdomain interaction. GmaR in this conformation recognizes MogR using the C-terminal antirepressor domain in a unique dual binding mode and mediates the antirepressor function through direct competition and spatial restraint mechanisms. Surprisingly, at 37°C, GmaR rapidly forms autologous aggregates that are deficient in MogR neutralization capabilities.
Collapse
Affiliation(s)
- So Yeon Cho
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hye-won Na
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Han Byeol Oh
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yun Mi Kwak
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Wan Seok Song
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sun Cheol Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Wook-Jong Jeon
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hongbaek Cho
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Byung-Chul Oh
- Lee Gil Ya Cancer and Diabetes Institute, College of Medicine, Gachon University, Incheon 406-840, Republic of Korea
| | - Jeongho Park
- College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Seung Goo Kang
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Geun-Shik Lee
- College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sung-il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| |
Collapse
|
3
|
Miguel-Romero L, Alqasmi M, Bacarizo J, Tan JA, Cogdell RJ, Chen J, Byron O, Christie GE, Marina A, Penadés JR. Non-canonical Staphylococcus aureus pathogenicity island repression. Nucleic Acids Res 2022; 50:11109-11127. [PMID: 36200825 PMCID: PMC9638917 DOI: 10.1093/nar/gkac855] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 09/08/2022] [Accepted: 09/23/2022] [Indexed: 11/14/2022] Open
Abstract
Mobile genetic elements control their life cycles by the expression of a master repressor, whose function must be disabled to allow the spread of these elements in nature. Here, we describe an unprecedented repression-derepression mechanism involved in the transfer of Staphylococcus aureus pathogenicity islands (SaPIs). Contrary to the classical phage and SaPI repressors, which are dimers, the SaPI1 repressor StlSaPI1 presents a unique tetrameric conformation never seen before. Importantly, not just one but two tetramers are required for SaPI1 repression, which increases the novelty of the system. To derepress SaPI1, the phage-encoded protein Sri binds to and induces a conformational change in the DNA binding domains of StlSaPI1, preventing the binding of the repressor to its cognate StlSaPI1 sites. Finally, our findings demonstrate that this system is not exclusive to SaPI1 but widespread in nature. Overall, our results characterize a novel repression-induction system involved in the transfer of MGE-encoded virulence factors in nature.
Collapse
Affiliation(s)
- Laura Miguel-Romero
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Mohammed Alqasmi
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- College of Applied Medical Sciences, Shaqra University, Shaqra City 15572, Saudi Arabia
| | - Julio Bacarizo
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ, UK
- Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46113 Moncada, Spain
| | - Jason A Tan
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | | | - John Chen
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore
| | - Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ,UK
| | - Gail E Christie
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - José R Penadés
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ, UK
| |
Collapse
|
4
|
Azulay G, Pasechnek A, Stadnyuk O, Ran-Sapir S, Fleisacher AM, Borovok I, Sigal N, Herskovits AA. A dual-function phage regulator controls the response of cohabiting phage elements via regulation of the bacterial SOS response. Cell Rep 2022; 39:110723. [PMID: 35443160 PMCID: PMC9043618 DOI: 10.1016/j.celrep.2022.110723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 02/09/2022] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Listeria monocytogenes strain 10403S harbors two phage elements in its chromosome; one produces infective virions and the other tailocins. It was previously demonstrated that induction of the two elements is coordinated, as they are regulated by the same anti-repressor. In this study, we identified AriS as another phage regulator that controls the two elements, bearing the capacity to inhibit their lytic induction under SOS conditions. AriS is a two-domain protein that possesses two distinct activities, one regulating the genes of its encoding phage and the other downregulating the bacterial SOS response. While the first activity associates with the AriS N-terminal AntA/AntB domain, the second associates with its C-terminal ANT/KilAC domain. The ANT/KilAC domain is conserved in many AriS-like proteins of listerial and non-listerial prophages, suggesting that temperate phages acquired such dual-function regulators to align their response with the other phage elements that cohabit the genome. Listeria monocytogenes strain 10403S harbors two phage elements in its chromosome The lytic response of the phage elements is synchronized under SOS conditions AriS, a dual-function phage regulator, fine-tunes the elements’ response under SOS Aris regulates both its encoding phage and the bacterial SOS response
Collapse
Affiliation(s)
- Gil Azulay
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Anna Pasechnek
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Olga Stadnyuk
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Shai Ran-Sapir
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Ana Mejia Fleisacher
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Ilya Borovok
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Nadejda Sigal
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Anat A Herskovits
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
| |
Collapse
|
5
|
Kumar P, Meghvansi MK, Kamboj DV. Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage. Sci Rep 2021; 11:22197. [PMID: 34772986 PMCID: PMC8590004 DOI: 10.1038/s41598-021-01419-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Shigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controlling Shigella infections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity against Shigella dysenteriae, Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticus and Enterococcus faecium. The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genus Hanrivervirus of subfamily Tempevirinae under the family Drexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members of Drexlerviridae taking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genus Hanrivervirus. The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.
Collapse
Affiliation(s)
- Prince Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- Regional Ayurveda Research Institute, Gwalior, Madhya Pradesh, 474009, India
| | - Mukesh K Meghvansi
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- Bioprocess Technology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - D V Kamboj
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India.
- Defence Research Laboratory, Tezpur, Assam, 784001, India.
| |
Collapse
|
6
|
de Groot A, Siponen MI, Magerand R, Eugénie N, Martin-Arevalillo R, Doloy J, Lemaire D, Brandelet G, Parcy F, Dumas R, Roche P, Servant P, Confalonieri F, Arnoux P, Pignol D, Blanchard L. Crystal structure of the transcriptional repressor DdrO: insight into the metalloprotease/repressor-controlled radiation response in Deinococcus. Nucleic Acids Res 2020; 47:11403-11417. [PMID: 31598697 PMCID: PMC6868357 DOI: 10.1093/nar/gkz883] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022] Open
Abstract
Exposure to harmful conditions such as radiation and desiccation induce oxidative stress and DNA damage. In radiation-resistant Deinococcus bacteria, the radiation/desiccation response is controlled by two proteins: the XRE family transcriptional repressor DdrO and the COG2856 metalloprotease IrrE. The latter cleaves and inactivates DdrO. Here, we report the biochemical characterization and crystal structure of DdrO, which is the first structure of a XRE protein targeted by a COG2856 protein. DdrO is composed of two domains that fold independently and are separated by a flexible linker. The N-terminal domain corresponds to the DNA-binding domain. The C-terminal domain, containing three alpha helices arranged in a novel fold, is required for DdrO dimerization. Cleavage by IrrE occurs in the loop between the last two helices of DdrO and abolishes dimerization and DNA binding. The cleavage site is hidden in the DdrO dimer structure, indicating that IrrE cleaves DdrO monomers or that the interaction with IrrE induces a structural change rendering accessible the cleavage site. Predicted COG2856/XRE regulatory protein pairs are found in many bacteria, and available data suggest two different molecular mechanisms for stress-induced gene expression: COG2856 protein-mediated cleavage or inhibition of oligomerization without cleavage of the XRE repressor.
Collapse
Affiliation(s)
- Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - Marina I Siponen
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - Romaric Magerand
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - Nicolas Eugénie
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette cedex, F-91198, France
| | | | - Jade Doloy
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - David Lemaire
- Aix Marseille Univ, CEA, CNRS, BIAM, Interaction Protein Metal Team, Saint Paul-Lez-Durance, F-13108, France
| | - Géraldine Brandelet
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - François Parcy
- Univ. Grenoble Alpes, CNRS, CEA, INRA, IRIG-DBSCI-LPCV, Grenoble, F-38000, France
| | - Renaud Dumas
- Univ. Grenoble Alpes, CNRS, CEA, INRA, IRIG-DBSCI-LPCV, Grenoble, F-38000, France
| | - Philippe Roche
- Aix Marseille Univ, CNRS, Inserm, Institut Paoli Calmettes, CRCM, Marseille CEDEX 09, F-13273, France
| | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette cedex, F-91198, France
| | - Fabrice Confalonieri
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette cedex, F-91198, France
| | - Pascal Arnoux
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - David Pignol
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| | - Laurence Blanchard
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13108, France
| |
Collapse
|
7
|
Hinkley TC, Garing S, Jain P, Williford J, Le Ny ALM, Nichols KP, Peters JE, Talbert JN, Nugen SR. A Syringe-Based Biosensor to Rapidly Detect Low Levels of Escherichia Coli (ECOR13) in Drinking Water Using Engineered Bacteriophages. SENSORS (BASEL, SWITZERLAND) 2020; 20:E1953. [PMID: 32244369 PMCID: PMC7181147 DOI: 10.3390/s20071953] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
A sanitized drinking water supply is an unconditional requirement for public health and the overall prosperity of humanity. Potential microbial and chemical contaminants of drinking water have been identified by a joint effort between the World Health Organization (WHO) and the United Nations Children's Fund (UNICEF), who together establish guidelines that define, in part, that the presence of Escherichia coli (E. coli) in drinking water is an indication of inadequate sanitation and a significant health risk. As E. coli is a nearly ubiquitous resident of mammalian gastrointestinal tracts, no detectable counts in 100 mL of drinking water is the standard used worldwide as an indicator of sanitation. The currently accepted EPA method relies on filtration, followed by growth on selective media, and requires 24-48 h from sample to results. In response, we developed a rapid bacteriophage-based detection assay with detection limit capabilities comparable to traditional methods in less than a quarter of the time. We coupled membrane filtration with selective enrichment using genetically engineered bacteriophages to identify less than 20 colony forming units (CFU) E. coli in 100 mL drinking water within 5 h. The combination of membrane filtration with phage infection produced a novel assay that demonstrated a rapid, selective, and sensitive detection of an indicator organism in large volumes of drinking water as recommended by the leading world regulatory authorities.
Collapse
Affiliation(s)
- Troy C. Hinkley
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Spencer Garing
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Paras Jain
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - John Williford
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Anne-Laure M. Le Ny
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Kevin P. Nichols
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Joseph E. Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA;
| | - Joey N. Talbert
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA;
| | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| |
Collapse
|
8
|
Silpe JE, Bridges AA, Huang X, Coronado DR, Duddy OP, Bassler BL. Separating Functions of the Phage-Encoded Quorum-Sensing-Activated Antirepressor Qtip. Cell Host Microbe 2020; 27:629-641.e4. [PMID: 32101705 DOI: 10.1016/j.chom.2020.01.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/21/2020] [Accepted: 01/28/2020] [Indexed: 01/21/2023]
Abstract
Quorum sensing is a process of chemical communication that bacteria use to track cell density and coordinate gene expression across a population. Bacteria-infecting viruses, called phages, can encode quorum-sensing components that enable them to integrate host cell density information into the lysis-lysogeny decision. Vibriophage VP882 is one such phage, and activation of its quorum-sensing pathway leads to the production of an antirepressor called Qtip. Qtip interferes with the prophage repressor (cIVP882), leading to host-cell lysis. Here, we show that Qtip interacts with the N terminus of cIVP882, inhibiting both cIVP882 DNA binding and cIVP882 autoproteolysis. Qtip also sequesters cIVP882, localizing it to the poles. Qtip can localize to the poles independently of cIVP882. Alanine-scanning mutagenesis of Qtip shows that its localization and interference with cIVP882 activities are separable. Comparison of Qtip to a canonical phage antirepressor reveals that despite both proteins interacting with their partner repressors, only Qtip drives polar localization.
Collapse
Affiliation(s)
- Justin E Silpe
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Andrew A Bridges
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xiuliang Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Daniela R Coronado
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Olivia P Duddy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| |
Collapse
|
9
|
The phage gene wmk is a candidate for male killing by a bacterial endosymbiont. PLoS Pathog 2019; 15:e1007936. [PMID: 31504075 PMCID: PMC6736233 DOI: 10.1371/journal.ppat.1007936] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 06/20/2019] [Indexed: 12/22/2022] Open
Abstract
Wolbachia are the most widespread maternally-transmitted bacteria in the animal kingdom. Their global spread in arthropods and varied impacts on animal physiology, evolution, and vector control are in part due to parasitic drive systems that enhance the fitness of infected females, the transmitting sex of Wolbachia. Male killing is one common drive mechanism wherein the sons of infected females are selectively killed. Despite decades of research, the gene(s) underlying Wolbachia-induced male killing remain unknown. Here using comparative genomic, transgenic, and cytological approaches in fruit flies, we identify a candidate gene in the eukaryotic association module of Wolbachia prophage WO, termed WO-mediated killing (wmk), which transgenically causes male-specific lethality during early embryogenesis and cytological defects typical of the pathology of male killing. The discovery of wmk establishes new hypotheses for the potential role of phage genes in sex-specific lethality, including the control of arthropod pests and vectors.
Collapse
|
10
|
Rasmussen KK, Varming AK, Schmidt SN, Frandsen KEH, Thulstrup PW, Jensen MR, Lo Leggio L. Structural basis of the bacteriophage TP901-1 CI repressor dimerization and interaction with DNA. FEBS Lett 2018; 592:1738-1750. [PMID: 29683476 DOI: 10.1002/1873-3468.13060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/12/2018] [Accepted: 04/12/2018] [Indexed: 12/31/2022]
Abstract
Temperate bacteriophages are known for their bistability, which in TP901-1 is controlled by two proteins, CI and MOR. Clear 1 repressor (CI) is hexameric and binds three palindromic operator sites via an N-terminal helix-turn-helix domain (NTD). A dimeric form, such as the truncated CI∆58 investigated here, is necessary for high-affinity binding to DNA. The crystal structure of the dimerization region (CTD1 ) is determined here, showing that it forms a pair of helical hooks. This newly determined structure is used together with the known crystal structure of the CI-NTD and small angle X-ray scattering data, to determine the solution structure of CI∆58 in complex with a palindromic operator site, showing that the two NTDs bind on opposing sides of the DNA helix.
Collapse
|
11
|
Tao J, Zhang XW, Jin J, Du XX, Lian T, Yang J, Zhou X, Jiang Z, Su XD. Nonspecific DNA Binding of cGAS N Terminus Promotes cGAS Activation. THE JOURNAL OF IMMUNOLOGY 2017; 198:3627-3636. [PMID: 28363908 DOI: 10.4049/jimmunol.1601909] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/22/2017] [Indexed: 01/07/2023]
Abstract
The cytosolic DNA sensor cyclic GMP-AMP synthase (cGAS) mediates innate immune responses against invading pathogens, or against self-dsDNA, which causes autoimmune disorders. Upon nonspecific binding of cytosolic B-form DNA, cGAS synthesizes the second messenger 2'3'-cGAMP and triggers STING-dependent signaling to produce type I IFNs. The cGAS comprises less-conserved N-terminal residues and highly conserved nucleotidyltransferase/Mab21 domains. The function and structure of the well-conserved domains have been extensively studied, whereas the physiological function of the N-terminal domain of cGAS is largely uncharacterized. In this study we used a single-molecule technique combined with traditional biochemical and cellular assays to demonstrate that binding of nonspecific dsDNA by the N-terminal domain of cGAS promotes its activation. We have observed that the N terminus of human cGAS (hcGAS-N160) undergoes secondary structural change upon dsDNA binding in solution. Furthermore, we showed that the hcGAS-N160 helps full length hcGAS to expand the binding range on λDNA and facilitates its binding efficiency to dsDNA compared with hcGAS without the 160 N-terminal residues (hcGAS-d160). More importantly, hcGAS-N160 endows full length hcGAS relatively higher enzyme activity and stronger activation of STING/IRF3-mediated cytosolic DNA signaling. These findings strongly indicate that the N-terminal domain of cGAS plays an important role in enhancing its function.
Collapse
Affiliation(s)
- Jianli Tao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, China; and
| | - Xiao-Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Biodynamic Optical Imaging Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jianshi Jin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Biodynamic Optical Imaging Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiao-Xia Du
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Biodynamic Optical Imaging Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Tengfei Lian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Biodynamic Optical Imaging Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jing Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, China; and
| | - Xiang Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, China; and
| | - Zhengfan Jiang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; .,Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, China; and
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; .,Biodynamic Optical Imaging Center, School of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|