<i>Pantoea</i> Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA

<i>Pantoea</i> Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA

A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using <i>Pantoea agglomerans</i> 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...

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Main Authors: Monika Šimoliūnienė, Emilija Žukauskienė, Lidija Truncaitė, Liang Cui, Geoffrey Hutinet, Darius Kazlauskas, Algirdas Kaupinis, Martynas Skapas, Valérie de Crécy-Lagard, Peter C. Dedon, Mindaugas Valius, Rolandas Meškys, Eugenijus Šimoliūnas
Format: Article
Language:English
Published: MDPI AG 2021-07-01
Series:International Journal of Molecular Sciences
Subjects:
<i>Pantoea</i> <i>agglomerans</i>
bacteriophage
vB_PagS_MED16
siphovirus
DNA modifications
DpdA
Online Access:https://www.mdpi.com/1422-0067/22/14/7333
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spelling doaj-d326d72ba5f94b01a77a507fe32f1b982021-07-23T13:45:27ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-07-01227333733310.3390/ijms22147333<i>Pantoea</i> Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNAMonika Šimoliūnienė0Emilija Žukauskienė1Lidija Truncaitė2Liang Cui3Geoffrey Hutinet4Darius Kazlauskas5Algirdas Kaupinis6Martynas Skapas7Valérie de Crécy-Lagard8Peter C. Dedon9Mindaugas Valius10Rolandas Meškys11Eugenijus Šimoliūnas12Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, LithuaniaDepartment of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, LithuaniaDepartment of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, LithuaniaSingapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, SingaporeDepartment of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USADepartment of Bioinformatics, Institute of Biotechnology, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, LithuaniaProteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, LithuaniaDepartment of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, LithuaniaDepartment of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USASingapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, SingaporeProteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, LithuaniaDepartment of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, LithuaniaDepartment of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, LithuaniaA novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using <i>Pantoea agglomerans</i> 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 preQ<sub>0</sub> 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 <i>Pantoea</i> phages. Thus, the data presented in this study provide new information on <i>Pantoea</i>-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.https://www.mdpi.com/1422-0067/22/14/7333<i>Pantoea</i> <i>agglomerans</i>bacteriophagevB_PagS_MED16siphovirusDNA modificationsDpdA
collection DOAJ
language English
format Article
sources DOAJ
author Monika Šimoliūnienė
Emilija Žukauskienė
Lidija Truncaitė
Liang Cui
Geoffrey Hutinet
Darius Kazlauskas
Algirdas Kaupinis
Martynas Skapas
Valérie de Crécy-Lagard
Peter C. Dedon
Mindaugas Valius
Rolandas Meškys
Eugenijus Šimoliūnas
spellingShingle Monika Šimoliūnienė
Emilija Žukauskienė
Lidija Truncaitė
Liang Cui
Geoffrey Hutinet
Darius Kazlauskas
Algirdas Kaupinis
Martynas Skapas
Valérie de Crécy-Lagard
Peter C. Dedon
Mindaugas Valius
Rolandas Meškys
Eugenijus Šimoliūnas
<i>Pantoea</i> Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA
International Journal of Molecular Sciences
<i>Pantoea</i> <i>agglomerans</i>
bacteriophage
vB_PagS_MED16
siphovirus
DNA modifications
DpdA
author_facet Monika Šimoliūnienė
Emilija Žukauskienė
Lidija Truncaitė
Liang Cui
Geoffrey Hutinet
Darius Kazlauskas
Algirdas Kaupinis
Martynas Skapas
Valérie de Crécy-Lagard
Peter C. Dedon
Mindaugas Valius
Rolandas Meškys
Eugenijus Šimoliūnas
author_sort Monika Šimoliūnienė
title <i>Pantoea</i> Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA
title_short <i>Pantoea</i> Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA
title_full <i>Pantoea</i> Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA
title_fullStr <i>Pantoea</i> Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA
title_full_unstemmed <i>Pantoea</i> Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA
title_sort <i>pantoea</i> bacteriophage vb_pags_med16—a siphovirus containing a 2′-deoxy-7-amido-7-deazaguanosine-modified dna
publisher MDPI AG
series International Journal of Molecular Sciences
issn 1661-6596
1422-0067
publishDate 2021-07-01
description A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using <i>Pantoea agglomerans</i> 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 preQ<sub>0</sub> 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 <i>Pantoea</i> phages. Thus, the data presented in this study provide new information on <i>Pantoea</i>-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.
topic <i>Pantoea</i> <i>agglomerans</i>
bacteriophage
vB_PagS_MED16
siphovirus
DNA modifications
DpdA
url https://www.mdpi.com/1422-0067/22/14/7333
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