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Mayo-Muñoz D, Pinilla-Redondo R, Camara-Wilpert S, Birkholz N, Fineran PC. Inhibitors of bacterial immune systems: discovery, mechanisms and applications. Nat Rev Genet 2024; 25:237-254. [PMID: 38291236 DOI: 10.1038/s41576-023-00676-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 02/01/2024]
Abstract
To contend with the diversity and ubiquity of bacteriophages and other mobile genetic elements, bacteria have developed an arsenal of immune defence mechanisms. Bacterial defences include CRISPR-Cas, restriction-modification and a growing list of mechanistically diverse systems, which constitute the bacterial 'immune system'. As a response, bacteriophages and mobile genetic elements have evolved direct and indirect mechanisms to circumvent or block bacterial defence pathways and ensure successful infection. Recent advances in methodological and computational approaches, as well as the increasing availability of genome sequences, have boosted the discovery of direct inhibitors of bacterial defence systems. In this Review, we discuss methods for the discovery of direct inhibitors, their diverse mechanisms of action and perspectives on their emerging applications in biotechnology and beyond.
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Affiliation(s)
- David Mayo-Muñoz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Rafael Pinilla-Redondo
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.
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2
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Hardies SC, Cho BC, Jang GI, Wang Z, Hwang CY. Identification of Structural and Morphogenesis Genes of Sulfitobacter Phage ΦGT1 and Placement within the Evolutionary History of the Podoviruses. Viruses 2023; 15:1475. [PMID: 37515163 PMCID: PMC10386132 DOI: 10.3390/v15071475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
ΦGT1 is a lytic podovirus of an alphaproteobacterial Sulfitobacter species, with few closely matching sequences among characterized phages, thus defying a useful description by simple sequence clustering methods. The history of the ΦGT1 core structure module was reconstructed using timetrees, including numerous related prospective prophages, to flesh out the evolutionary lineages spanning from the origin of the ejectosomal podovirus >3.2 Gya to the present genes of ΦGT1 and its closest relatives. A peculiarity of the ΦGT1 structural proteome is that it contains two paralogous tubular tail A (tubeA) proteins. The origin of the dual tubeA arrangement was traced to a recombination between two more ancient podoviral lineages occurring ~0.7 Gya in the alphaproteobacterial order Rhizobiales. Descendants of the ancestral dual A recombinant were tracked forward forming both temperate and lytic phage clusters and exhibiting both vertical transmission with patchy persistence and horizontal transfer with respect to host taxonomy. The two ancestral lineages were traced backward, making junctions with a major metagenomic podoviral family, the LUZ24-like gammaproteobacterial phages, and Myxococcal phage Mx8, and finally joining near the origin of podoviruses with P22. With these most conservative among phage genes, deviations from uncomplicated vertical and nonrecombinant descent are numerous but countable. The use of timetrees allowed conceptualization of the phage's evolution in the context of a sequence of ancestors spanning the time of life on Earth.
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Affiliation(s)
- Stephen C Hardies
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
- Saemangeum Environmental Research Center, Kunsan National University, Gunsan 54150, Republic of Korea
| | - Gwang Il Jang
- Aquatic Disease Control Division, National Fishery Products Quality Management Service, Busan 46083, Republic of Korea
| | - Zhiqing Wang
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Chung Yeon Hwang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
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3
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Laanto E, Oksanen HM. Three Phages from a Boreal Lake during Ice Cover Infecting Xylophilus, Caulobacter, and Polaromonas Species. Viruses 2023; 15:v15020307. [PMID: 36851521 PMCID: PMC9959647 DOI: 10.3390/v15020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Although the important role of microbes in freshwater is well understood, studies on phage-host systems in such environments during ice cover are completely lacking. Here, we describe the isolation and characterization of three new bacteriophages infecting Xylophilus sp., Caudobacter sp., and Polaromonas sp. from freshwater samples taken under the ice cover of Lake Konnevesi, Finland. Lumi, Kuura, and Tiera bacteriophages have tailed icosahedral virions and double-stranded DNA. Lumi is a siphophage with a genome of 80,496 bp, and Kuura and Tiera are podophages, and their genomes are 43,205 and 45,327 bp in length, resembling viruses in the class Caudoviricetes. Their host ranges were very limited among the winter-isolated bacterial strains from Konnevesi, each infecting only their own hosts. They can infect efficiently at 4 °C, showing that they are adapted to living in lake water under ice cover. Analysis of the viral genome sequences showed that a significant number of the gene products of each virus are unique, indicating that there is unexplored viral diversity in freshwaters. To our knowledge, Lumi and Tiera are the first phages isolated on the Xylophilus sp. and Polaromonas sp. strains, allowing their exploitation in further studies of freshwater bacterial-phage interactions.
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Affiliation(s)
- Elina Laanto
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: ; Tel.: +358-2941-59104
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4
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Zakrzewska M, Burmistrz M. Mechanisms regulating the CRISPR-Cas systems. Front Microbiol 2023; 14:1060337. [PMID: 36925473 PMCID: PMC10013973 DOI: 10.3389/fmicb.2023.1060337] [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: 10/07/2022] [Accepted: 02/10/2023] [Indexed: 03/08/2023] Open
Abstract
The CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR associated proteins) is a prokaryotic system that enables sequence specific recognition and cleavage of nucleic acids. This is possible due to cooperation between CRISPR array which contains short fragments of DNA called spacers that are complimentary to the targeted nucleic acid and Cas proteins, which take part in processes of: acquisition of new spacers, processing them into their functional form as well as recognition and cleavage of targeted nucleic acids. The primary role of CRISPR-Cas systems is to provide their host with an adaptive and hereditary immunity against exogenous nucleic acids. This system is present in many variants in both Bacteria and Archea. Due to its modular structure, and programmability CRISPR-Cas system become attractive tool for modern molecular biology. Since their discovery and implementation, the CRISPR-Cas systems revolutionized areas of gene editing and regulation of gene expression. Although our knowledge on how CRISPR-Cas systems work has increased rapidly in recent years, there is still little information on how these systems are controlled and how they interact with other cellular mechanisms. Such regulation can be the result of both auto-regulatory mechanisms as well as exogenous proteins of phage origin. Better understanding of these interaction networks would be beneficial for optimization of current and development of new CRISPR-Cas-based tools. In this review we summarize current knowledge on the various molecular mechanisms that affect activity of CRISPR-Cas systems.
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Affiliation(s)
- Marta Zakrzewska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland.,Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michal Burmistrz
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Warsaw, Poland
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5
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Klonowska A, Ardley J, Moulin L, Zandberg J, Patrel D, Gollagher M, Marinova D, Reddy TBK, Varghese N, Huntemann M, Woyke T, Seshadri R, Ivanova N, Kyrpides N, Reeve W. Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018. Front Microbiol 2023; 14:1082107. [PMID: 36925474 PMCID: PMC10011098 DOI: 10.3389/fmicb.2023.1082107] [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: 10/27/2022] [Accepted: 01/24/2023] [Indexed: 03/08/2023] Open
Abstract
Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod/nif/noeM gene clusters from C. taiwanensis LMG19424T and "Cupriavidus neocalidonicus" STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.
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Affiliation(s)
- Agnieszka Klonowska
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Julie Ardley
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Lionel Moulin
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Jaco Zandberg
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Delphine Patrel
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rekha Seshadri
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wayne Reeve
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
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6
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When bacteria are phage playgrounds: interactions between viruses, cells, and mobile genetic elements. Curr Opin Microbiol 2022; 70:102230. [PMID: 36335712 DOI: 10.1016/j.mib.2022.102230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/23/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Studies of viral adaptation have focused on the selective pressures imposed by hosts. However, there is increasing evidence that interactions between viruses, cells, and other mobile genetic elements are determinant to the success of infections. These interactions are often associated with antagonism and competition, but sometimes involve cooperation or parasitism. We describe two key types of interactions - defense systems and genetic regulation - that allow the partners of the interaction to destroy or control the others. These interactions evolve rapidly by genetic exchanges, including among competing partners. They are sometimes followed by functional diversification. Gene exchanges also facilitate the emergence of cross-talk between elements in the same bacterium. In the end, these processes produce multilayered networks of interactions that shape the outcome of viral infections.
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7
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Guan J, Oromí-Bosch A, Mendoza SD, Karambelkar S, Berry JD, Bondy-Denomy J. Bacteriophage genome engineering with CRISPR-Cas13a. Nat Microbiol 2022; 7:1956-1966. [PMID: 36316452 PMCID: PMC9722621 DOI: 10.1038/s41564-022-01243-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/02/2022] [Indexed: 12/05/2022]
Abstract
Jumbo phages such as Pseudomonas aeruginosa ФKZ have potential as antimicrobials and as a model for uncovering basic phage biology. Both pursuits are currently limited by a lack of genetic engineering tools due to a proteinaceous 'phage nucleus' structure that protects from DNA-targeting CRISPR-Cas tools. To provide reverse-genetics tools for DNA jumbo phages from this family, we combined homologous recombination with an RNA-targeting CRISPR-Cas13a enzyme and used an anti-CRISPR gene (acrVIA1) as a selectable marker. We showed that this process can insert foreign genes, delete genes and add fluorescent tags to genes in the ФKZ genome. Fluorescent tagging of endogenous gp93 revealed that it is ejected with the phage DNA while deletion of the tubulin-like protein PhuZ surprisingly had only a modest impact on phage burst size. Editing of two other phages that resist DNA-targeting CRISPR-Cas systems was also achieved. RNA-targeting Cas13a holds great promise for becoming a universal genetic editing tool for intractable phages, enabling the systematic study of phage genes of unknown function.
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Affiliation(s)
- Jingwen Guan
- Department of Microbiology & Immunology, University of California, San Francisco, CA, USA
| | | | - Senén D Mendoza
- Department of Microbiology & Immunology, University of California, San Francisco, CA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shweta Karambelkar
- Department of Microbiology & Immunology, University of California, San Francisco, CA, USA
| | - Joel D Berry
- Felix Biotechnology, Inc., San Francisco, CA, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology & Immunology, University of California, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
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8
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Guzmán NM, Esquerra-Ruvira B, Mojica FJM. Digging into the lesser-known aspects of CRISPR biology. Int Microbiol 2021; 24:473-498. [PMID: 34487299 PMCID: PMC8616872 DOI: 10.1007/s10123-021-00208-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
A long time has passed since regularly interspaced DNA repeats were discovered in prokaryotes. Today, those enigmatic repetitive elements termed clustered regularly interspaced short palindromic repeats (CRISPR) are acknowledged as an emblematic part of multicomponent CRISPR-Cas (CRISPR associated) systems. These systems are involved in a variety of roles in bacteria and archaea, notably, that of conferring protection against transmissible genetic elements through an adaptive immune-like response. This review summarises the present knowledge on the diversity, molecular mechanisms and biology of CRISPR-Cas. We pay special attention to the most recent findings related to the determinants and consequences of CRISPR-Cas activity. Research on the basic features of these systems illustrates how instrumental the study of prokaryotes is for understanding biology in general, ultimately providing valuable tools for diverse fields and fuelling research beyond the mainstream.
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Affiliation(s)
- Noemí M Guzmán
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Belén Esquerra-Ruvira
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Francisco J M Mojica
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain.
- Instituto Multidisciplinar para el Estudio del Medio, Universidad de Alicante, Alicante, Spain.
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Bdira FB, Erkelens AM, Qin L, Volkov AN, Lippa A, Bowring N, Boyle A, Ubbink M, Dove S, Dame R. Novel anti-repression mechanism of H-NS proteins by a phage protein. Nucleic Acids Res 2021; 49:10770-10784. [PMID: 34520554 PMCID: PMC8501957 DOI: 10.1093/nar/gkab793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
H-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene repression is directly dependent on the DNA binding modes of H-NS family proteins. These proteins form lateral protofilaments along DNA. Under specific environmental conditions they switch to bridging two DNA duplexes. This switching is a direct effect of environmental conditions on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of H-NS proteins. The Pseudomonas lytic phage LUZ24 encodes the protein gp4, which modulates the DNA binding and function of the H-NS family protein MvaT of Pseudomonas aeruginosa. However, the mechanism by which gp4 affects MvaT activity remains elusive. In this study, we show that gp4 specifically interferes with the formation and stability of the bridged MvaT-DNA complex. Structural investigations suggest that gp4 acts as an 'electrostatic zipper' between the oppositely charged domains of MvaT protomers, and stabilizes a structure resembling their 'half-open' conformation, resulting in relief of gene silencing and adverse effects on P. aeruginosa growth. The ability to control H-NS conformation and thereby its impact on global gene regulation and growth might open new avenues to fight Pseudomonas multidrug resistance.
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Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Amanda M Erkelens
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Liang Qin
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexander N Volkov
- VIB-VUB Structural Biology Research Center, Pleinlaan 2, 1050 Brussels, Belgium
- Jean Jeener NMR Centre, VUB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Andrew M Lippa
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas Bowring
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Aimee L Boyle
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Simon L Dove
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Remus T Dame
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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10
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Amemiya HM, Schroeder J, Freddolino PL. Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription 2021; 12:182-218. [PMID: 34499567 PMCID: PMC8632127 DOI: 10.1080/21541264.2021.1973865] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 01/21/2023] Open
Abstract
Genome architecture has proven to be critical in determining gene regulation across almost all domains of life. While many of the key components and mechanisms of eukaryotic genome organization have been described, the interplay between bacterial DNA organization and gene regulation is only now being fully appreciated. An increasing pool of evidence has demonstrated that the bacterial chromosome can reasonably be thought of as chromatin, and that bacterial chromosomes contain transcriptionally silent and transcriptionally active regions analogous to heterochromatin and euchromatin, respectively. The roles played by histones in eukaryotic systems appear to be shared across a range of nucleoid-associated proteins (NAPs) in bacteria, which function to compact, structure, and regulate large portions of bacterial chromosomes. The broad range of extant NAPs, and the extent to which they differ from species to species, has raised additional challenges in identifying and characterizing their roles in all but a handful of model bacteria. Here we review the regulatory roles played by NAPs in several well-studied bacteria and use the resulting state of knowledge to provide a working definition for NAPs, based on their function, binding pattern, and expression levels. We present a screening procedure which can be applied to any species for which transcriptomic data are available. Finally, we note that NAPs tend to play two major regulatory roles - xenogeneic silencers and developmental regulators - and that many unrecognized potential NAPs exist in each bacterial species examined.
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Affiliation(s)
- Haley M. Amemiya
- University of Michigan Medical School, Ann Arbor, MI, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jeremy Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter L. Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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11
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Zhou H, Chen P, Zhang M, Chen J, Fang J, Li X. Revealing the Viral Community in the Hadal Sediment of the New Britain Trench. Genes (Basel) 2021; 12:genes12070990. [PMID: 34209474 PMCID: PMC8306916 DOI: 10.3390/genes12070990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022] Open
Abstract
Marine viruses are widely distributed and influence matter and energy transformation in ecosystems by modulating hosts’ metabolism. The hadal trenches represent the deepest marine habitat on Earth, for which the viral communities and related biogeochemical functions are least explored and poorly understood. Here, using the sediment samples (8720 m below sea level) collected from the New Britain Trench (NBT), we investigated the viral community, diversity, and genetic potentials in the hadal sediment habitat for the first time by deep shotgun metagenomic sequencing. We found the NBT sediment viral community was dominated by Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, and Phycodnaviridae, which belong to the dsDNA viruses. However, the large majority of them remained uncharacterized. We found the hadal sediment virome had some common components by comparing the hadal sediment viruses with those of hadal aquatic habitats and those of bathypelagic and terrestrial habitats. It was also distinctive in community structure and had many novel viral clusters not associated with the other habitual virome included in our analyses. Further phylogenetic analysis on its Caudovirales showed novel diversities, including new clades specially evolved in the hadal sediment habitat. Annotation of the NBT sediment viruses indicated the viruses might influence microbial hydrocarbon biodegradation and carbon and sulfur cycling via metabolic augmentation through auxiliary metabolic genes (AMGs). Our study filled in the knowledge gaps on the virome of the hadal sediment habitats and provided insight into the evolution and the potential metabolic functions of the hadal sediment virome.
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Affiliation(s)
- Hui Zhou
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
| | - Mengjie Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawang Chen
- Ocean College, Zhejiang University, Zhoushan 316021, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
- Correspondence: (J.C.); (J.F.); (X.L.)
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (H.Z.); (P.C.); (M.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.C.); (J.F.); (X.L.)
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12
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Adler A, Holliger C. Multistability and Reversibility of Aerobic Granular Sludge Microbial Communities Upon Changes From Simple to Complex Synthetic Wastewater and Back. Front Microbiol 2020; 11:574361. [PMID: 33324361 PMCID: PMC7726351 DOI: 10.3389/fmicb.2020.574361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/12/2020] [Indexed: 01/31/2023] Open
Abstract
Aerobic granular sludge (AGS) is a promising alternative wastewater treatment to the conventional activated sludge system allowing space and energy saving. Basic understanding of AGS has mainly been obtained using simple wastewater containing acetate and propionate as carbon source. Yet, the aspect and performances of AGS grown in such model systems are different from those obtained in reactor treating real wastewater. The impact of fermentable and hydrolyzable compounds on already formed AGS was assessed separately by changing the composition of the influent from simple wastewater containing volatile fatty acids to complex monomeric wastewater containing amino acids and glucose, and then to complex polymeric wastewater containing also starch and peptone. The reversibility of the observed changes was assessed by changing the composition of the wastewater from complex monomeric back to simple. The introduction of fermentable compounds in the influent left the settling properties and nutrient removal performance unchanged, but had a significant impact on the bacterial community. The proportion of Gammaproteobacteria diminished to the benefit of Actinobacteria and the Saccharibateria phylum. On the other hand, the introduction of polymeric compounds altered the settling properties and denitrification efficiency, but induced smaller changes in the bacterial community. The changes induced by the wastewater transition were only partly reversed. Seven distinct stables states of the bacterial community were detected during the 921 days of experiment, four of them observed with the complex monomeric wastewater. The transitions between these states were not only caused by wastewater changes but also by operation failures and other incidences. However, the nutrient removal performance and settling properties of the AGS were globally maintained due to the functional redundancy of its bacterial community.
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Affiliation(s)
- Aline Adler
- Laboratory for Environmental Biotechnology, School for Architecture, Civil and Environmental Engineering, Environmental Engineering Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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13
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Jiao J, Tian CF. Ancestral zinc-finger bearing protein MucR in alpha-proteobacteria: A novel xenogeneic silencer? Comput Struct Biotechnol J 2020; 18:3623-3631. [PMID: 33304460 PMCID: PMC7710501 DOI: 10.1016/j.csbj.2020.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
The MucR/Ros family protein is conserved in alpha-proteobacteria and characterized by its zinc-finger motif that has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure evolved. In the past decades, accumulated evidences have revealed MucR as a pleiotropic transcriptional regulator that integrating multiple functions such as virulence, symbiosis, cell cycle and various physiological processes. Scattered reports indicate that MucR mainly acts as a repressor, through oligomerization and binding to multiple sites of AT-rich target promoters. The N-terminal region and zinc-finger bearing C-terminal region of MucR mediate oligomerization and DNA-binding, respectively. These features are convergent to those of xenogeneic silencers such as H-NS, MvaT, Lsr2 and Rok, which are mainly found in other lineages. Phylogenetic analysis of MucR homologs suggests an ancestral origin of MucR in alpha- and delta-proteobacteria. Multiple independent duplication and lateral gene transfer events contribute to the diversity and phyletic distribution of MucR. Finally, we posed questions which remain unexplored regarding the putative roles of MucR as a xenogeneic silencer and a general manager in balancing adaptation and regulatory integration in the pangenome context.
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Affiliation(s)
- Jian Jiao
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.,MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.,MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University, Beijing, China
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14
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Pinilla-Redondo R, Shehreen S, Marino ND, Fagerlund RD, Brown CM, Sørensen SJ, Fineran PC, Bondy-Denomy J. Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements. Nat Commun 2020; 11:5652. [PMID: 33159058 PMCID: PMC7648647 DOI: 10.1038/s41467-020-19415-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
Many prokaryotes employ CRISPR-Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have developed strategies to bypass immunity, including anti-CRISPR (Acr) proteins; yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we report the discovery of new Acrs by assaying candidate genes adjacent to a conserved Acr-associated (Aca) gene, aca5, against a panel of six type I systems: I-F (Pseudomonas, Pectobacterium, and Serratia), I-E (Pseudomonas and Serratia), and I-C (Pseudomonas). We uncover 11 type I-F and/or I-E anti-CRISPR genes encoded on chromosomal and extrachromosomal MGEs within Enterobacteriaceae and Pseudomonas, and an additional Aca (aca9). The acr genes not only associate with other acr genes, but also with genes encoding inhibitors of distinct bacterial defense systems. Thus, our findings highlight the potential exploitation of acr loci neighborhoods for the identification of previously undescribed anti-defense systems.
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Affiliation(s)
- Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- University College Copenhagen, Copenhagen, Denmark
| | - Saadlee Shehreen
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Nicole D Marino
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Bio-protection Research Centre, University of Otago, Dunedin, New Zealand.
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA.
- Quantitative Biosciences Institute, UCSF, San Francisco, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
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15
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A bacteriophage mimic of the bacterial nucleoid-associated protein Fis. Biochem J 2020; 477:1345-1362. [PMID: 32207815 PMCID: PMC7166090 DOI: 10.1042/bcj20200146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 11/17/2022]
Abstract
We report the identification and characterization of a bacteriophage λ-encoded protein, NinH. Sequence homology suggests similarity between NinH and Fis, a bacterial nucleoid-associated protein (NAP) involved in numerous DNA topology manipulations, including chromosome condensation, transcriptional regulation and phage site-specific recombination. We find that NinH functions as a homodimer and is able to bind and bend double-stranded DNA in vitro. Furthermore, NinH shows a preference for a 15 bp signature sequence related to the degenerate consensus favored by Fis. Structural studies reinforced the proposed similarity to Fis and supported the identification of residues involved in DNA binding which were demonstrated experimentally. Overexpression of NinH proved toxic and this correlated with its capacity to associate with DNA. NinH is the first example of a phage-encoded Fis-like NAP that likely influences phage excision-integration reactions or bacterial gene expression.
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16
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Conquering CRISPR: how phages overcome bacterial adaptive immunity. Curr Opin Biotechnol 2020; 68:30-36. [PMID: 33113496 DOI: 10.1016/j.copbio.2020.09.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022]
Abstract
The rise of antibiotic-resistant bacteria has led to renewed interest in the use of their natural enemies, phages, for the prevention and treatment of infections. However, phage therapy requires detailed knowledge of the interactions between these entities. Bacteria defend themselves against phage predation with a large repertoire of defences. Among these, CRISPR-Cas systems stand out due to their adaptive character, mechanistic complexity and diversity, and present a significant hurdle for phage infection. Here, we provide an overview of how phages can circumvent CRISPR-Cas defence, ranging from target sequence mutations and DNA modifications to anti-CRISPR proteins and nucleus-like protective structures. An in-depth understanding of these phage evasion strategies is crucial for the successful development of phage therapy applications.
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17
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Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands. Genes (Basel) 2020; 11:genes11020142. [PMID: 32013150 PMCID: PMC7074111 DOI: 10.3390/genes11020142] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023] Open
Abstract
Acquisition of mobile elements by horizontal gene transfer can play a major role in bacterial adaptation and genome evolution by providing traits that contribute to bacterial fitness. However, gaining foreign DNA can also impose significant fitness costs to the host bacteria and can even produce detrimental effects. The efficiency of horizontal acquisition of DNA is thought to be improved by the activity of xenogeneic silencers. These molecules are a functionally related group of proteins that possess affinity for the acquired DNA. Binding of xenogeneic silencers suppresses the otherwise uncontrolled expression of genes from the newly acquired nucleic acid, facilitating their integration to the bacterial regulatory networks. Even when the genes encoding for xenogeneic silencers are part of the core genome, homologs encoded by horizontally acquired elements have also been identified and studied. In this article, we discuss the current knowledge about horizontally acquired xenogeneic silencer homologs, focusing on those encoded by genomic islands, highlighting their distribution and the major traits that allow these proteins to become part of the host regulatory networks.
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18
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Pfeifer E, Hünnefeld M, Popa O, Frunzke J. Impact of Xenogeneic Silencing on Phage-Host Interactions. J Mol Biol 2019; 431:4670-4683. [PMID: 30796986 PMCID: PMC6925973 DOI: 10.1016/j.jmb.2019.02.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 01/21/2023]
Abstract
Phages, viruses that prey on bacteria, are the most abundant and diverse inhabitants of the Earth. Temperate bacteriophages can integrate into the host genome and, as so-called prophages, maintain a long-term association with their host. The close relationship between host and virus has significantly shaped microbial evolution and phage elements may benefit their host by providing new functions. Nevertheless, the strong activity of phage promoters and potentially toxic gene products may impose a severe fitness burden and must be tightly controlled. In this context, xenogeneic silencing (XS) proteins, which can recognize foreign DNA elements, play an important role in the acquisition of novel genetic information and facilitate the evolution of regulatory networks. Currently known XS proteins fall into four classes (H-NS, MvaT, Rok and Lsr2) and have been shown to follow a similar mode of action by binding to AT-rich DNA and forming an oligomeric nucleoprotein complex that silences gene expression. In this review, we focus on the role of XS proteins in phage-host interactions by highlighting the important function of XS proteins in maintaining the lysogenic state and by providing examples of how phages fight back by encoding inhibitory proteins that disrupt XS functions in the host. Sequence analysis of available phage genomes revealed the presence of genes encoding Lsr2-type proteins in the genomes of phages infecting Actinobacteria. These data provide an interesting perspective for future studies to elucidate the impact of phage-encoded XS homologs on the phage life cycle and phage-host interactions.
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Affiliation(s)
- Eugen Pfeifer
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany.
| | - Max Hünnefeld
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Ovidiu Popa
- Heinrich Heine Universität Düsseldorf, Institute for Quantitative and Theoretical Biology, 40223 Düsseldorf, Germany
| | - Julia Frunzke
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany.
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19
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Dorman CJ, Ní Bhriain N. CRISPR-Cas, DNA Supercoiling, and Nucleoid-Associated Proteins. Trends Microbiol 2019; 28:19-27. [PMID: 31519332 DOI: 10.1016/j.tim.2019.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/02/2019] [Accepted: 08/08/2019] [Indexed: 12/11/2022]
Abstract
In this opinion article we highlight links between the H-NS nucleoid-associated protein, variable DNA topology, the regulation of CRISPR-cas locus expression, CRISPR-Cas activity, and the recruitment of novel genetic information by the CRISPR array. We propose that the requirement that the invading mobile genetic element be negatively supercoiled limits effective CRISPR action to a window in the bacterial growth cycle when DNA topology is optimal, and that this same window is used for the efficient integration of new spacer sequences at the CRISPR array. H-NS silences CRISPR promoters, and we propose that antagonists of H-NS, such as the LeuO transcription factor, provide a basis for a stochastic genetic switch that acts at random in each cell in the bacterial population. In addition, we wish to propose a mechanism by which mobile genetic elements can suppress CRISPR-cas transcription using H-NS homologues. Although the individual components of this network are known, we propose a new model in which they are integrated and linked to the physiological state of the bacterium. The model provides a basis for cell-to-cell variation in the expression and performance of CRISPR systems in bacterial populations.
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Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Trinity College Dublin, Dublin 2, Ireland.
| | - Niamh Ní Bhriain
- Department of Microbiology, Trinity College Dublin, Dublin 2, Ireland
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20
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da Silva Xavier A, de Almeida JCF, de Melo AG, Rousseau GM, Tremblay DM, de Rezende RR, Moineau S, Alfenas‐Zerbini P. Characterization of CRISPR-Cas systems in the Ralstonia solanacearum species complex. MOLECULAR PLANT PATHOLOGY 2019; 20:223-239. [PMID: 30251378 PMCID: PMC6637880 DOI: 10.1111/mpp.12750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) are composed of an array of short DNA repeat sequences separated by unique spacer sequences that are flanked by associated (Cas) genes. CRISPR-Cas systems are found in the genomes of several microbes and can act as an adaptive immune mechanism against invading foreign nucleic acids, such as phage genomes. Here, we studied the CRISPR-Cas systems in plant-pathogenic bacteria of the Ralstonia solanacearum species complex (RSSC). A CRISPR-Cas system was found in 31% of RSSC genomes present in public databases. Specifically, CRISPR-Cas types I-E and II-C were found, with I-E being the most common. The presence of the same CRISPR-Cas types in distinct Ralstonia phylotypes and species suggests the acquisition of the system by a common ancestor before Ralstonia species segregation. In addition, a Cas1 phylogeny (I-E type) showed a perfect geographical segregation of phylotypes, supporting an ancient acquisition. Ralstoniasolanacearum strains CFBP2957 and K60T were challenged with a virulent phage, and the CRISPR arrays of bacteriophage-insensitive mutants (BIMs) were analysed. No new spacer acquisition was detected in the analysed BIMs. The functionality of the CRISPR-Cas interference step was also tested in R. solanacearum CFBP2957 using a spacer-protospacer adjacent motif (PAM) delivery system, and no resistance was observed against phage phiAP1. Our results show that the CRISPR-Cas system in R. solanacearum CFBP2957 is not its primary antiviral strategy.
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Affiliation(s)
- André da Silva Xavier
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
| | - Juliana Cristina Fraleon de Almeida
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
| | - Alessandra Gonçalves de Melo
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
| | - Geneviève M. Rousseau
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine DentaireUniversité LavalQuébec CityQCGIV0A6Canada
| | - Denise M. Tremblay
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine DentaireUniversité LavalQuébec CityQCGIV0A6Canada
| | - Rafael Reis de Rezende
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine DentaireUniversité LavalQuébec CityQCGIV0A6Canada
| | - Poliane Alfenas‐Zerbini
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
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21
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Medina-Aparicio L, Dávila S, Rebollar-Flores JE, Calva E, Hernández-Lucas I. The CRISPR-Cas system in Enterobacteriaceae. Pathog Dis 2018; 76:4794941. [PMID: 29325038 DOI: 10.1093/femspd/fty002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/08/2018] [Indexed: 12/20/2022] Open
Abstract
In nature, microorganisms are constantly exposed to multiple viral infections and thus have developed many strategies to survive phage attack and invasion by foreign DNA. One of such strategies is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) bacterial immunological system. This defense mechanism is widespread in prokaryotes including several families such as Enterobacteriaceae. Much knowledge about the CRISPR-Cas system has been generated, including its biological functions, transcriptional regulation, distribution, utility as a molecular marker and as a tool for specific genome editing. This review focuses on these aspects and describes the state of the art of the CRISPR-Cas system in the Enterobacteriaceae bacterial family.
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Affiliation(s)
- Liliana Medina-Aparicio
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Sonia Dávila
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Av. Universidad No. 1001, Cuernavaca, Morelos 62209, México
| | - Javier E Rebollar-Flores
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Edmundo Calva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Ismael Hernández-Lucas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
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22
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Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element. Sci Rep 2018; 8:5550. [PMID: 29615803 PMCID: PMC5882942 DOI: 10.1038/s41598-018-23858-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/21/2018] [Indexed: 12/27/2022] Open
Abstract
Integrative and conjugative elements (ICEs) comprise ubiquitous large mobile regions in prokaryotic chromosomes that transmit vertically to daughter cells and transfer horizontally to distantly related lineages. Their evolutionary success originates in maximized combined ICE-host fitness trade-offs, but how the ICE impacts on the host metabolism and physiology is poorly understood. Here we investigate global changes in the host genetic network and physiology of Pseudomonas putida with or without an integrated ICEclc, a model ICE widely distributed in proteobacterial genomes. Genome-wide gene expression differences were analyzed by RNA-seq using exponentially growing or stationary phase-restimulated cultures on 3-chlorobenzoate, an aromatic compound metabolizable thanks to specific ICEclc-located genes. We found that the presence of ICEclc imposes a variety of changes in global pathways such as cell cycle and amino acid metabolism, which were more numerous in stationary-restimulated than exponential phase cells. Unexpectedly, ICEclc stimulates cellular motility and leads to more rapid growth on 3-chlorobenzoate than cells carrying only the integrated clc genes. ICEclc also concomitantly activates the P. putida Pspu28-prophage, but this in itself did not provoke measurable fitness effects. ICEclc thus interferes in a number of cellular pathways, inducing both direct benefits as well as indirect costs in P. putida.
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23
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Johnson MC, Sena-Velez M, Washburn BK, Platt GN, Lu S, Brewer TE, Lynn JS, Stroupe ME, Jones KM. Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome. J Struct Biol 2017; 200:343-359. [DOI: 10.1016/j.jsb.2017.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/24/2017] [Accepted: 08/21/2017] [Indexed: 11/26/2022]
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24
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Patterson AG, Yevstigneyeva MS, Fineran PC. Regulation of CRISPR–Cas adaptive immune systems. Curr Opin Microbiol 2017; 37:1-7. [DOI: 10.1016/j.mib.2017.02.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/19/2017] [Accepted: 02/20/2017] [Indexed: 12/20/2022]
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25
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Genomic and Transcriptional Mapping of PaMx41, Archetype of a New Lineage of Bacteriophages Infecting Pseudomonas aeruginosa. Appl Environ Microbiol 2016; 82:6541-6547. [PMID: 27590812 DOI: 10.1128/aem.01415-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022] Open
Abstract
Previously, a collection of virulent phages infecting Pseudomonas aeruginosa was isolated from open water reservoirs and residual waters. Here, we described the comparative genomics of a set of five related phages from the collection, the physical structure of the genome, the structural proteomics of the virion, and the transcriptional program of archetypal phage PaMx41. The phage genomes were closely associated with each other and with those of two other P. aeruginosa phages, 119X and PaP2, which were previously filed in the databases. Overall, the genomes were approximately 43 kb, harboring 53 conserved open reading frames (ORFs) and three short ORFs in indel regions and containing 45% GC content. The genome of PaMx41 was further characterized as a linear, terminally redundant DNA molecule. A total of 16 ORFs were associated with putative functions, including nucleic acid metabolism, morphogenesis, and lysis, and eight virion proteins were identified through mass spectrometry. However, the coding sequences without assigned functions represent 70% of the ORFs. The PaMx41 transcription program was organized in early, middle, and late expressed genomic modules, which correlated with regions containing functionally related genes. The high genomic conservation among these distantly isolated phages suggests that these viruses undergo selective pressure to remain unchanged. The 119X lineage represents a unique set of phages that corresponds to a novel phage group. The features recognized in the genomes and the broad host range of clinical strains suggest that these phages are candidates for therapy applications. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogen that causes stubborn nosocomial infections that are frequently resistant to multiple antibiotics. Bacterial viruses (bacteriophages or phages) represent a natural mechanism for pathogenic bacterial control. Here, a group of virulent phages, previously shown to infect a broad range of clinical P. aeruginosa strains, was characterized at the genomic and molecular levels. These phages belong to a unique and tightly related group. In addition, we conducted a transcriptional study of an archetypal phage of this group to characterize the role of many unknown coding sequences based on expression temporalities. These results contribute to our knowledge of 119X-like phages and, in general, provide information concerning P. aeruginosa podophage diversity and lytic cycles.
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26
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Chen M, Xu J, Yao H, Lu C, Zhang W. Isolation, genome sequencing and functional analysis of two T7-like coliphages of avian pathogenic Escherichia coli. Gene 2016; 582:47-58. [PMID: 26828615 DOI: 10.1016/j.gene.2016.01.049] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 01/09/2016] [Accepted: 01/28/2016] [Indexed: 01/21/2023]
Abstract
Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. Due to the drug residues and increased antibiotic resistance caused by antibiotic use, bacteriophages and other alternative therapeutic agents are expected to control APEC infection in poultry. Two APEC phages, named P483 and P694, were isolated from the feces from the farmers market in China. We then studied their biological properties, and carried out high-throughput genome sequencing and homology analyses of these phages. Assembly results of high-throughput sequencing showed that the structures of both P483 and P694 genomes consist of linear and double-stranded DNA. Results of the electron microscopy and homology analysis revealed that both P483 and P694 belong to T7-like virus which is a member of the Podoviridae family of the Caudovirales order. Comparative genomic analysis showed that most of the predicted proteins of these two phages showed strongest sequence similarity to the Enterobacteria phages BA14 and 285P, Erwinia phage FE44, and Kluyvera phage Kvp1; however, some proteins such as gp0.6a, gp1.7 and gp17 showed lower similarity (<85%) with the homologs of other phages in the T7 subgroup. We also found some unique characteristics of P483 and P694, such as the two types of the genes of P694 and no lytic activity of P694 against its host bacteria in liquid medium. Our results serve to further our understanding of phage evolution of T7-like coliphages and provide the potential application of the phages as therapeutic agents for the treatment of diseases.
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Affiliation(s)
- Mianmian Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing City, Jiangsu Province, China
| | - Juntian Xu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing City, Jiangsu Province, China
| | - Huochun Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing City, Jiangsu Province, China
| | - Chengping Lu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing City, Jiangsu Province, China
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing City, Jiangsu Province, China.
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Dy RL, Richter C, Salmond GP, Fineran PC. Remarkable Mechanisms in Microbes to Resist Phage Infections. Annu Rev Virol 2014; 1:307-31. [DOI: 10.1146/annurev-virology-031413-085500] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ron L. Dy
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand;
| | - Corinna Richter
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand;
| | - George P.C. Salmond
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Peter C. Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand;
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Wietz M, Millán-Aguiñaga N, Jensen PR. CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography. BMC Genomics 2014; 15:936. [PMID: 25344663 PMCID: PMC4223832 DOI: 10.1186/1471-2164-15-936] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/29/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Prokaryotic CRISPR-Cas systems confer resistance to viral infection and thus mediate bacteria-phage interactions. However, the distribution and functional diversity of CRISPRs among environmental bacteria remains largely unknown. Here, comparative genomics of 75 Salinispora strains provided insight into the diversity and distribution of CRISPR-Cas systems in a cosmopolitan marine actinomycete genus. RESULTS CRISPRs were found in all Salinispora strains, with the majority containing multiple loci and different Cas array subtypes. Of the six subtypes identified, three have not been previously described. A lower prophage frequency in S. arenicola was associated with a higher fraction of spacers matching Salinispora prophages compared to S. tropica, suggesting differing defensive capacities between Salinispora species. The occurrence of related prophages in strains from distant locations, as well as spacers matching those prophages inserted throughout spacer arrays, indicate recurring encounters with widely distributed phages over time. Linkages of CRISPR features with Salinispora microdiversity pointed to subclade-specific contacts with mobile genetic elements (MGEs). This included lineage-specific spacer deletions or insertions, which may reflect weak selective pressures to maintain immunity or distinct temporal interactions with MGEs, respectively. Biogeographic patterns in spacer and prophage distributions support the concept that Salinispora spp. encounter localized MGEs. Moreover, the presence of spacers matching housekeeping genes suggests that CRISPRs may have functions outside of viral defense. CONCLUSIONS This study provides a comprehensive examination of CRISPR-Cas systems in a broadly distributed group of environmental bacteria. The ubiquity and diversity of CRISPRs in Salinispora suggests that CRISPR-mediated interactions with MGEs represent a major force in the ecology and evolution of this cosmopolitan marine actinomycete genus.
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Affiliation(s)
- Matthias Wietz
- />Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037 USA
- />Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
| | - Natalie Millán-Aguiñaga
- />Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037 USA
| | - Paul R Jensen
- />Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037 USA
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29
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Genome Sequences of Two Temperate Phages, ΦCB2047-A and ΦCB2047-C, Infecting Sulfitobacter sp. Strain 2047. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00108-14. [PMID: 24903862 PMCID: PMC4047441 DOI: 10.1128/genomea.00108-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We announce the complete genome sequences of two temperate Podoviridae, Sulfitobacter phages ΦCB2047-A and ΦCB2047-C, which infect Sulfitobacter sp. strain 2047, a member of the Roseobacter clade. This is the first report of temperate podophage infecting members of the Sulfitobacter genus of the Roseobacter clade.
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30
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Kuhn JH, Bekal S, Caì Y, Clawson AN, Domier LL, Herrel M, Jahrling PB, Kondo H, Lambert KN, Mihindukulasuriya KA, Nowotny N, Radoshitzky SR, Schneider U, Staeheli P, Suzuki N, Tesh RB, Wang D, Wang LF, Dietzgen RG. Nyamiviridae: proposal for a new family in the order Mononegavirales. Arch Virol 2013; 158:2209-26. [PMID: 23636404 PMCID: PMC3857105 DOI: 10.1007/s00705-013-1674-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 02/12/2013] [Indexed: 10/26/2022]
Abstract
Nyamanini virus (NYMV) and Midway virus (MIDWV) are unclassified tick-borne agents that infect land birds and seabirds, respectively. The recent molecular characterization of both viruses confirmed their already known close serological relationship and revealed them to be nonsegmented, single- and negative-stranded RNA viruses that are clearly related to, but quite distinct from, members of the order Mononegavirales (bornaviruses, filoviruses, paramyxoviruses, and rhabdoviruses). A third agent, soybean cyst nematode virus 1 (SbCNV-1, previously named soybean cyst nematode nyavirus), was recently found to be an additional member of this new virus group. Here, we review the current knowledge about all three viruses and propose classifying them as members of a new mononegaviral family, Nyamiviridae.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA,
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31
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Dy RL, Pitman AR, Fineran PC. Chromosomal targeting by CRISPR-Cas systems can contribute to genome plasticity in bacteria. Mob Genet Elements 2013; 3:e26831. [PMID: 24251073 PMCID: PMC3827097 DOI: 10.4161/mge.26831] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/10/2013] [Accepted: 10/15/2013] [Indexed: 12/11/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins form adaptive immune systems in bacteria to combat phage and other foreign genetic elements. Typically, short spacer sequences are acquired from the invader DNA and incorporated into CRISPR arrays in the bacterial genome. Small RNAs are generated that contain these spacer sequences and enable sequence-specific destruction of the foreign nucleic acids. Occasionally, spacers are acquired from the chromosome, which instead leads to targeting of the host genome. Chromosomal targeting is highly toxic to the bacterium, providing a strong selective pressure for a variety of evolutionary routes that enable host cell survival. Mutations that inactivate the CRISPR-Cas functionality, such as within the cas genes, CRISPR repeat, protospacer adjacent motifs (PAM), and target sequence, mediate escape from toxicity. This self-targeting might provide some explanation for the incomplete distribution of CRISPR-Cas systems in less than half of sequenced bacterial genomes. More importantly, self-genome targeting can cause large-scale genomic alterations, including remodeling or deletion of pathogenicity islands and other non-mobile chromosomal regions. While control of horizontal gene transfer is perceived as their main function, our recent work illuminates an alternative role of CRISPR-Cas systems in causing host genomic changes and influencing bacterial evolution.
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Affiliation(s)
- Ron L Dy
- Department of Microbiology and Immunology; University of Otago; Dunedin, New Zealand
| | - Andrew R Pitman
- The New Zealand Institute for Plant & Food Research Limited; Christchurch, New Zealand
- Bio-Protection Research Centre; Lincoln University; Canterbury, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology; University of Otago; Dunedin, New Zealand
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32
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Exploring the costs of horizontal gene transfer. Trends Ecol Evol 2013; 28:489-95. [DOI: 10.1016/j.tree.2013.04.002] [Citation(s) in RCA: 261] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/15/2013] [Accepted: 04/25/2013] [Indexed: 11/20/2022]
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33
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Flowers JJ, He S, Malfatti S, del Rio TG, Tringe SG, Hugenholtz P, McMahon KD. Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME JOURNAL 2013; 7:2301-14. [PMID: 23887171 DOI: 10.1038/ismej.2013.117] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 05/14/2013] [Accepted: 06/11/2013] [Indexed: 11/09/2022]
Abstract
Members of the genus Candidatus Accumulibacter are important in many wastewater treatment systems performing enhanced biological phosphorus removal (EBPR). The Accumulibacter lineage can be subdivided phylogenetically into multiple clades, and previous work showed that these clades are ecologically distinct. The complete genome of Candidatus Accumulibacter phosphatis strain UW-1, a member of Clade IIA, was previously sequenced. Here, we report a draft genome sequence of Candidatus Accumulibacter spp. strain UW-2, a member of Clade IA, assembled following shotgun metagenomic sequencing of laboratory-scale bioreactor sludge. We estimate the genome to be 80-90% complete. Although the two clades share 16S rRNA sequence identity of >98.0%, we observed a remarkable lack of synteny between the two genomes. We identified 2317 genes shared between the two genomes, with an average nucleotide identity (ANI) of 78.3%, and accounting for 49% of genes in the UW-1 genome. Unlike UW-1, the UW-2 genome seemed to lack genes for nitrogen fixation and carbon fixation. Despite these differences, metabolic genes essential for denitrification and EBPR, including carbon storage polymer and polyphosphate metabolism, were conserved in both genomes. The ANI from genes associated with EBPR was statistically higher than that from genes not associated with EBPR, indicating a high selective pressure in EBPR systems. Further, we identified genomic islands of foreign origins including a near-complete lysogenic phage in the Clade IA genome. Interestingly, Clade IA appeared to be more phage susceptible based on it containing only a single Clustered Regularly Interspaced Short Palindromic Repeats locus as compared with the two found in Clade IIA. Overall, the comparative analysis provided a genetic basis to understand physiological differences and ecological niches of Accumulibacter populations, and highlights the importance of diversity in maintaining system functional resilience.
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Affiliation(s)
- Jason J Flowers
- Departments of Civil and Environmental Engineering, and Bacteriology, University of Wisconsin at Madison, Madison, WI, USA
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34
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Mick E, Stern A, Sorek R. Holding a grudge: persisting anti-phage CRISPR immunity in multiple human gut microbiomes. RNA Biol 2013; 10:900-6. [PMID: 23439321 PMCID: PMC3737347 DOI: 10.4161/rna.23929] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/06/2013] [Accepted: 02/08/2013] [Indexed: 12/13/2022] Open
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) system of bacteria and archaea constitutes a mechanism of acquired adaptive immunity against phages, which is based on genome-encoded markers of previously infecting phage sequences ("spacers"). As a repository of phage sequences, these spacers make the system particularly suitable for elucidating phage-bacteria interactions in metagenomic studies. Recent metagenomic analyses of CRISPRs associated with the human microbiome intriguingly revealed conserved "memory spacers" shared by bacteria in multiple unrelated, geographically separated individuals. Here, we discuss possible avenues for explaining this phenomenon by integrating insights from CRISPR biology and phage-bacteria ecology, with a special focus on the human gut. We further explore the growing body of evidence for the role of CRISPR/Cas in regulating the interplay between bacteria and lysogenic phages, which may be intimately related to the presence of memory spacers and sheds new light on the multifaceted biological and ecological modes of action of CRISPR/Cas.
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Affiliation(s)
- Eran Mick
- Department of Systems Biology; Harvard Medical School; Boston, MA USA
| | - Adi Stern
- Department of Microbiology and Immunology; University of California; San Francisco, CA USA
- Department of Integrative Biology; University of California; Berkeley, CA USA
| | - Rotem Sorek
- Department of Molecular Genetics; Weizmann Institute of Science; Rehovot, Israel
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35
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Westra ER, Swarts DC, Staals RHJ, Jore MM, Brouns SJJ, van der Oost J. The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity. Annu Rev Genet 2013; 46:311-39. [PMID: 23145983 DOI: 10.1146/annurev-genet-110711-155447] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
All organisms need to continuously adapt to changes in their environment. Through horizontal gene transfer, bacteria and archaea can rapidly acquire new traits that may contribute to their survival. However, because new DNA may also cause damage, removal of imported DNA and protection against selfish invading DNA elements are also important. Hence, there should be a delicate balance between DNA uptake and DNA degradation. Here, we describe prokaryotic antiviral defense systems, such as receptor masking or mutagenesis, blocking of phage DNA injection, restriction/modification, and abortive infection. The main focus of this review is on CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated), a prokaryotic adaptive immune system. Since its recent discovery, our biochemical understanding of this defense system has made a major leap forward. Three highly diverse CRISPR/Cas types exist that display major structural and functional differences in their mode of generating resistance against invading nucleic acids. Because several excellent recent reviews cover all CRISPR subtypes, we mainly focus on a detailed description of the type I-E CRISPR/Cas system of the model bacterium Escherichia coli K12.
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Affiliation(s)
- Edze R Westra
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, The Netherlands.
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36
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Neelakanta G, Sultana H. The use of metagenomic approaches to analyze changes in microbial communities. Microbiol Insights 2013; 6:37-48. [PMID: 24826073 PMCID: PMC3987754 DOI: 10.4137/mbi.s10819] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microbes are the most abundant biological entities found in the biosphere. Identification and measurement of microorganisms (including viruses, bacteria, archaea, fungi, and protists) in the biosphere cannot be readily achieved due to limitations in culturing methods. A non-culture based approach, called “metagenomics”, was developed that enabled researchers to comprehensively analyse microbial communities in different ecosystems. In this study, we highlight recent advances in the field of metagenomics for analyzing microbial communities in different ecosystems ranging from oceans to the human microbiome. Developments in several bioinformatics approaches are also discussed in context of microbial metagenomics that include taxonomic systems, sequence databases, and sequence-alignment tools. In summary, we provide a snapshot for the recent advances in metagenomics approach for analyzing changes in the microbial communities in different ecosystems.
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Affiliation(s)
- Girish Neelakanta
- Center for Molecular Medicine, Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | - Hameeda Sultana
- Center for Molecular Medicine, Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
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37
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Reconstruction of novel cyanobacterial siphovirus genomes from Mediterranean metagenomic fosmids. Appl Environ Microbiol 2012; 79:688-95. [PMID: 23160125 DOI: 10.1128/aem.02742-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cellular metagenomes are primarily used for investigating microbial community structure and function. However, cloned fosmids from such metagenomes capture phage genome fragments that can be used as a source of phage genomes. We show that fosmid cloning from cellular metagenomes and sequencing at a high coverage is a credible alternative to constructing metaviriomes and allows capturing and assembling novel, complete phage genomes. It is likely that phages recovered from cellular metagenomes are those replicating within cells during sample collection and represent "active" phages, naturally amplifying their genomic DNA and increasing chances for cloning. We describe five sets of siphoviral contigs (MEDS1, MEDS2, MEDS3, MEDS4, and MEDS5), obtained by sequencing fosmids from the cellular metagenome of the deep chlorophyll maximum in the Mediterranean. Three of these represent complete siphoviral genomes and two represent partial ones. This is the first set of phage genomes assembled directly from cellular metagenomic fosmid libraries. They exhibit low sequence similarities to one another and to known siphoviruses but are remarkably similar in overall genome architecture. We present evidence suggesting they infect picocyanobacteria, likely Synechococcus. Four of these sets also define a novel branch in the phylogenetic tree of phage large subunit terminases. Moreover, some of these siphoviral groups are globally distributed and abundant in the oceans, comparable to some known myoviruses and podoviruses. This suggests that, as more siphoviral genomes become available, we will be better able to assess the abundance and influence of this diverse and polyphyletic group in the marine habitat.
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38
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Wong K, Fong TT, Bibby K, Molina M. Application of enteric viruses for fecal pollution source tracking in environmental waters. ENVIRONMENT INTERNATIONAL 2012; 45:151-64. [PMID: 22537583 DOI: 10.1016/j.envint.2012.02.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 05/22/2023]
Abstract
Microbial source tracking (MST) tools are used to identify sources of fecal pollution for accurately assessing public health risk and implementing best management practices (BMPs). This review focuses on the potential of enteric viruses for MST applications. Following host infection, enteric viruses replicate and are excreted in high numbers in the hosts' feces and urine. Due to the specificity in host infection, enteric viruses have been considered one of the most accurate library-independent culture-independent MST tools. In an assessment of molecular viral assays based on sensitivity, specificity and the density of the target virus in fecal-impacted samples, human adenovirus and human polyomavirus were found to be the most promising human-specific viral markers. However, more research is needed to identify promising viral markers for livestock because of cross-reactions that were observed among livestock species or the limited number of samples tested for specificity. Other viral indicators of fecal origin, F+ RNA coliphage and pepper mild mottle virus, have also been proposed as potential targets for developing MST markers. Enhancing the utility of enteric viruses for MST applications through next generation sequencing (NGS) and virus concentration technology is discussed in the latter part of this review. The massive sequence databases generated by shotgun and gene-targeted metagenomics enable more efficient and reliable design of MST assays. Finally, recent studies revealed that alternative virus concentration methodologies may be more cost-effective than standard technologies such as 1MDS; however, improvements in the recovery efficiency and consistency are still needed. Overall, developments in metagenomic information combined with efficient concentration methodologies, as well as high host-specificity, make enteric viruses a promising tool in MST applications.
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Affiliation(s)
- Kelvin Wong
- United States Environmental Protection Agency, Ecosystems Research Division, 960 College Station Road, Athens, GA, USA.
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39
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Deng L, Kenchappa CS, Peng X, She Q, Garrett RA. Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus. Nucleic Acids Res 2012; 40:2470-80. [PMID: 22139923 PMCID: PMC3315313 DOI: 10.1093/nar/gkr1111] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/04/2011] [Accepted: 11/06/2011] [Indexed: 11/29/2022] Open
Abstract
CRISPR loci are essential components of the adaptive immune system of archaea and bacteria. They consist of long arrays of repeats separated by DNA spacers encoding guide RNAs (crRNA), which target foreign genetic elements. Cbp1 (CRISPR DNA repeat binding protein) binds specifically to the multiple direct repeats of CRISPR loci of members of the acidothermophilic, crenarchaeal order Sulfolobales. cbp1 gene deletion from Sulfolobus islandicus REY15A produced a strong reduction in pre-crRNA yields from CRISPR loci but did not inhibit the foreign DNA targeting capacity of the CRISPR/Cas system. Conversely, overexpression of Cbp1 in S. islandicus generated an increase in pre-crRNA yields while the level of reverse strand transcripts from CRISPR loci remained unchanged. It is proposed that Cbp1 modulates production of longer pre-crRNA transcripts from CRISPR loci. A possible mechanism is that it minimizes interference from potential transcriptional signals carried on spacers deriving from A-T-rich genetic elements and, occasionally, on DNA repeats. Supporting evidence is provided by microarray and northern blotting analyses, and publicly available whole-transcriptome data for S. solfataricus P2.
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Affiliation(s)
| | | | | | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200N Copenhagen K, Denmark
| | - Roger A. Garrett
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200N Copenhagen K, Denmark
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40
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Barrangou R, Horvath P. CRISPR: new horizons in phage resistance and strain identification. Annu Rev Food Sci Technol 2011; 3:143-62. [PMID: 22224556 DOI: 10.1146/annurev-food-022811-101134] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria have been widely used as starter cultures in the food industry, notably for the fermentation of milk into dairy products such as cheese and yogurt. Lactic acid bacteria used in food manufacturing, such as lactobacilli, lactococci, streptococci, Leuconostoc, pediococci, and bifidobacteria, are selectively formulated based on functional characteristics that provide idiosyncratic flavor and texture attributes, as well as their ability to withstand processing and manufacturing conditions. Unfortunately, given frequent viral exposure in industrial environments, starter culture selection and development rely on defense systems that provide resistance against bacteriophage predation, including restriction-modification, abortive infection, and recently discovered CRISPRs (clustered regularly interspaced short palindromic repeats). CRISPRs, together with CRISPR-associated genes (cas), form the CRISPR/Cas immune system, which provides adaptive immunity against phages and invasive genetic elements. The immunization process is based on the incorporation of short DNA sequences from virulent phages into the CRISPR locus. Subsequently, CRISPR transcripts are processed into small interfering RNAs that guide a multifunctional protein complex to recognize and cleave matching foreign DNA. Hypervariable CRISPR loci provide insights into the phage and host population dynamics, and new avenues for enhanced phage resistance and genetic typing and tagging of industrial strains.
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41
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Garrett RA, Vestergaard G, Shah SA. Archaeal CRISPR-based immune systems: exchangeable functional modules. Trends Microbiol 2011; 19:549-56. [PMID: 21945420 DOI: 10.1016/j.tim.2011.08.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/05/2011] [Accepted: 08/15/2011] [Indexed: 12/26/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-based immune systems are essentially modular with three primary functions: the excision and integration of new spacers, the processing of CRISPR transcripts to yield mature CRISPR RNAs (crRNAs), and the targeting and cleavage of foreign nucleic acid. The primary target appears to be the DNA of foreign genetic elements, but the CRISPR/Cmr system that is widespread amongst archaea also specifically targets and cleaves RNA in vitro. The archaeal CRISPR systems tend to be both diverse and complex. Here we examine evidence for exchange of functional modules between archaeal systems that is likely to contribute to their diversity, particularly of their nucleic acid targeting and cleavage functions. The molecular constraints that limit such exchange are considered. We also summarize mechanisms underlying the dynamic nature of CRISPR loci and the evidence for intergenomic exchange of CRISPR systems.
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Affiliation(s)
- Roger A Garrett
- Archaea Centre, Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK2200 Copenhagen N, Denmark.
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42
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The 5.5 protein of phage T7 inhibits H-NS through interactions with the central oligomerization domain. J Bacteriol 2011; 193:4881-92. [PMID: 21764926 DOI: 10.1128/jb.05198-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The 5.5 protein (T7p32) of coliphage T7 (5.5(T7)) was shown to bind and inhibit gene silencing by the nucleoid-associated protein H-NS, but the mechanism by which it acts was not understood. The 5.5(T7) protein is insoluble when expressed in Escherichia coli, but we find that 5.5(T7) can be isolated in a soluble form when coexpressed with a truncated version of H-NS followed by subsequent disruption of the complex during anion-exchange chromatography. Association studies reveal that 5.5(T7) binds a region of H-NS (residues 60 to 80) recently found to contain a distinct domain necessary for higher-order H-NS oligomerization. Accordingly, we find that purified 5.5(T7) can disrupt higher-order H-NS-DNA complexes in vitro but does not abolish DNA binding by H-NS per se. Homologues of the 5.5(T7) protein are found exclusively among members of the Autographivirinae that infect enteric bacteria, and despite fairly low sequence conservation, the H-NS binding properties of these proteins are largely conserved. Unexpectedly, we find that the 5.5(T7) protein copurifies with heterogeneous low-molecular-weight RNA, likely tRNA, through several chromatography steps and that this interaction does not require the DNA binding domain of H-NS. The 5.5 proteins utilize a previously undescribed mechanism of H-NS antagonism that further highlights the critical importance that higher-order oligomerization plays in H-NS-mediated gene repression.
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43
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Rosario K, Breitbart M. Exploring the viral world through metagenomics. Curr Opin Virol 2011; 1:289-97. [PMID: 22440785 DOI: 10.1016/j.coviro.2011.06.004] [Citation(s) in RCA: 182] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 06/07/2011] [Indexed: 01/07/2023]
Abstract
Viral metagenomics, or shotgun sequencing of purified viral particles, has revolutionized the field of environmental virology by allowing the exploration of viral communities in a variety of sample types throughout the biosphere. The introduction of viral metagenomics has demonstrated that dominant viruses in environmental communities are not well-represented by the cultured viruses in existing sequence databases. Viral metagenomic studies have provided insights into viral ecology by elucidating the genetic potential, community structure, and biogeography of environmental viruses. In addition, viral metagenomics has expanded current knowledge of virus-host interactions by uncovering genes that may allow viruses to manipulate their hosts in unexpected ways. The intrinsic potential for virus discovery through viral metagenomics can help advance a wide array of disciplines including evolutionary biology, pathogen surveillance, and biotechnology.
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Affiliation(s)
- Karyna Rosario
- University of South Florida, College of Marine Science, 140 7th Avenue South, Saint Petersburg, FL 33701, USA
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