Pantoea Bacteriophage vB_PagS_MED16-A Siphovirus Containing a 2'-Deoxy-7-amido-7-deazaguanosine-Modified DNA

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

doi:10.3390/ijms22147333

Pantoea Bacteriophage vB_PagS_MED16-A Siphovirus Containing a 2'-Deoxy-7-amido-7-deazaguanosine-Modified DNA

Int J Mol Sci. 2021 Jul 8;22(14):7333. doi: 10.3390/ijms22147333.

Authors

Affiliations

¹ Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
² Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore.
³ Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
⁴ Department of Bioinformatics, Institute of Biotechnology, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
⁵ Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
⁶ Department of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania.
⁷ Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
⁸ Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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.

Keywords: 2′-deoxy-7-amido-7-deazaguanosine (dADG); DNA modifications; DpdA; Pantoea agglomerans; bacteriophage; siphovirus; vB_PagS_MED16.

MeSH terms

DNA, Viral* / genetics
DNA, Viral* / metabolism
Genome, Viral*
Guanosine* / analogs & derivatives
Guanosine* / chemistry
Guanosine* / metabolism
Open Reading Frames*
Pantoea / virology*
Siphoviridae* / genetics
Siphoviridae* / metabolism
Viral Proteins* / genetics
Viral Proteins* / metabolism

Substances

DNA, Viral
Viral Proteins
Guanosine

Grants and funding

No. SIT-7/2015/Research Council of Lithuania