1
|
Heinrichs ME, Piedade GJ, Popa O, Sommers P, Trubl G, Weissenbach J, Rahlff J. Breaking the Ice: A Review of Phages in Polar Ecosystems. Methods Mol Biol 2024; 2738:31-71. [PMID: 37966591 DOI: 10.1007/978-1-0716-3549-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.
Collapse
Affiliation(s)
- Mara Elena Heinrichs
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Gonçalo J Piedade
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Ovidiu Popa
- Institute of Quantitative and Theoretical Biology Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | | | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Julia Weissenbach
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Janina Rahlff
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
- Aero-Aquatic Virus Research Group, Friedrich Schiller University Jena, Jena, Germany.
| |
Collapse
|
2
|
Zlatohurska M, Gorb T, Romaniuk L, Shenderovska N, Faidiuk Y, Zhuminska G, Hubar Y, Hubar O, Kropinski AM, Kushkina A, Tovkach F. Broad-host-range lytic Erwinia phage Key with exopolysaccharide degrading activity. Virus Res 2023; 329:199088. [PMID: 36907559 DOI: 10.1016/j.virusres.2023.199088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 02/18/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023]
Abstract
In this study, the genome of the lytic broad-host-range phage Key infecting Erwinia amylovora, Erwinia horticola, and Pantoea agglomerans strains was characterized. Key phage has a 115,651 bp long double-stranded DNA genome with the G + C ratio of 39.03%, encoding 182 proteins and 27 tRNA genes. The majority (69%) of predicted coding sequences (CDSs) encode proteins with unknown functions. The protein products of 57 annotated genes were found to have probable functions in nucleotide metabolism, DNA replication, recombination, repair, and packaging, virion morphogenesis, phage-host interaction and lysis. Furthermore, the product of gene 141 shared amino acid sequence similarity and conserved domain architecture with the exopolysaccharide (EPS) degrading proteins of Erwinia and Pantoea infecting phages as well as bacterial EPS biosynthesis proteins. Due to the genome synteny and similarity to the proteins of T5-related phages, phage Key, together with its closest relative, Pantoea phage AAS21, was suggested to represent a novel genus within the Demerecviridae family, for which we tentatively propose the name "Keyvirus".
Collapse
Affiliation(s)
- Maryna Zlatohurska
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine
| | - Tetiana Gorb
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine
| | - Liudmyla Romaniuk
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine
| | - Natalia Shenderovska
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine; Biotechnology products development lab, Scientific Center, Pharmaceutical Corporation YURiA-PHARM, Kyiv 03151, Ukraine
| | - Yuliia Faidiuk
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine; Educational and Scientific Center "Institute of Biology and Medicine", Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw 53-114, Poland
| | - Ganna Zhuminska
- Department of Microbiology, Virology and Biotechnology, Biological Faculty, Odesa National Mechnykov University, Odesa 65058, Ukraine
| | - Yuliia Hubar
- Preclinical and Clinical Trials Department, Pharmaceutical Corporation YURiA-PHARM, Kyiv 03151, Ukraine
| | - Oleksandr Hubar
- Biotechnology products development lab, Scientific Center, Pharmaceutical Corporation YURiA-PHARM, Kyiv 03151, Ukraine
| | - Andrew M Kropinski
- Departments of Food Science; and, Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alla Kushkina
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine
| | - Fedor Tovkach
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine
| |
Collapse
|
3
|
Šimoliūnienė M, Žukauskienė E, Truncaitė L, Cui L, Hutinet G, Kazlauskas D, Kaupinis A, Skapas M, de Crécy-Lagard V, Dedon PC, Valius M, Meškys R, Šimoliūnas E. Pantoea Bacteriophage vB_PagS_MED16-A Siphovirus Containing a 2'-Deoxy-7-amido-7-deazaguanosine-Modified DNA. Int J Mol Sci 2021; 22:7333. [PMID: 34298953 PMCID: PMC8306585 DOI: 10.3390/ijms22147333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC-MS/MS analysis indicates 2'-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.
Collapse
Affiliation(s)
- Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Emilija Žukauskienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; (L.C.); (P.C.D.)
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (G.H.); (V.d.C.-L.)
| | - Darius Kazlauskas
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Martynas Skapas
- Department of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (G.H.); (V.d.C.-L.)
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Peter C. Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; (L.C.); (P.C.D.)
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| |
Collapse
|
4
|
Žukauskienė E, Šimoliūnienė M, Truncaitė L, Skapas M, Kaupinis A, Valius M, Meškys R, Šimoliūnas E. Pantoea Bacteriophage vB_PagS_AAS23: A Singleton of the Genus Sauletekiovirus. Microorganisms 2021; 9:668. [PMID: 33807116 PMCID: PMC8004638 DOI: 10.3390/microorganisms9030668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed that 25 of all AAS23 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. Based on the phylogenetic analysis, AAS23 has no close relationship to other viruses publicly available to date and represents a single species of the genus Sauletekiovirus within the family Drexlerviridae. The phage is able to form plaques in bacterial lawns even at 4 °C and demonstrates a depolymerase activity. Thus, the data presented in this study not only provides the information on Pantoea-infecting bacteriophages, but also offers novel insights into the diversity of cold-adapted viruses and their potential to be used as biocontrol agents.
Collapse
Affiliation(s)
- Emilija Žukauskienė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Monika Šimoliūnienė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Lidija Truncaitė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Martynas Skapas
- Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Eugenijus Šimoliūnas
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| |
Collapse
|