Sinorhizobium meliloti Phage ΦM9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid

Abstract

Relatively little is known about the phages that infect agriculturally important nitrogen-fixing rhizobial bacteria. Here we report the genome and cryo-electron microscopy structure of the Sinorhizobium meliloti-infecting T4 superfamily phage ΦM9. This phage and its close relative Rhizobium phage vB_RleM_P10VF define a new group of T4 superfamily phages. These phages are distinctly different from the recently characterized cyanophage-like S. meliloti phages of the ΦM12 group. Structurally, ΦM9 has a T=16 capsid formed from repeating units of an extended gp23-like subunit that assemble through interactions between one subunit and the adjacent E-loop insertion domain. Though genetically very distant from the cyanophages, the ΦM9 capsid closely resembles that of the T4 superfamily cyanophage Syn9. ΦM9 also has the same T=16 capsid architecture as the very distant phage SPO1 and the herpesviruses. Despite their overall lack of similarity at the genomic and structural levels, ΦM9 and S. meliloti phage ΦM12 have a small number of open reading frames in common that appear to encode structural proteins involved in interaction with the host and which may have been acquired by horizontal transfer. These proteins are predicted to encode tail baseplate proteins, tail fibers, tail fiber assembly proteins, and glycanases that cleave host exopolysaccharide.IMPORTANCE Despite recent advances in the phylogenetic and structural characterization of bacteriophages, only a small number of phages of plant-symbiotic nitrogen-fixing soil bacteria have been studied at the molecular level. The effects of phage predation upon beneficial bacteria that promote plant growth remain poorly characterized. First steps in understanding these soil bacterium-phage dynamics are genetic, molecular, and structural characterizations of these groups of phages. The T4 superfamily phages are among the most complex phages; they have large genomes packaged within an icosahedral head and a long, contractile tail through which the DNA is delivered to host cells. This phylogenetic and structural study of S. meliloti-infecting T4 superfamily phage ΦM9 provides new insight into the diversity of this family. The comparison of structure-related genes in both ΦM9 and S. meliloti-infecting T4 superfamily phage ΦM12, which comes from a completely different lineage of these phages, allows the identification of host infection-related factors.

Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome

“…In the next step, with the application of the Circoletto tool [ 35 ], local nucleotide similarities within the genomes of analyzed (pro)phages were found ( Figure S2 ). Although, all of the analyzed lytic phages were classified into T4 phage superfamily, the analysis confirmed previous findings showing that phages ΦN3, ΦM7, ΦM12, and ΦM19 create a separate group [not showing significant similarities with other sinorhizobial (pro)phages] and the ΦM9 was unique [ 12 , 53 ]. It is also worth mentioning that in 2016 phages ΦN3, ΦM7, ΦM12, and ΦM19 were clustered into a single genus called the M12-like viruses, and additionally phages ΦM12 and ΦM19 were considered as two strains of the same phage [ 53 ].…”

“…KP881232), and ΦN3 (GenBank accession No. KR052482)) [ 12 , 13 ], and three temperate viruses (Φ16-3 (GenBank accession No. DQ500118), ΦPBC5 (GenBank accession No.…”

Molecular Analysis of Arthrobacter Myovirus vB_ArtM-ArV1: We Blame It on the Tail

“…However, comparative phage genomics suggest that two proteins, the terminase large subunit and the portal protein, can be recognized by sequence/structure similarity to be encoded by most sequenced tailed phages (46)(47)(48), and they have often been used as markers in phylogenetic analysis (49)(50)(51). Another protein whose amino acid sequence alignment has often been used in phylogenetics is the major capsid/head protein (52,53).…”

In vitro studies of DNA condensation by bridging protein in a crowding environment

“…* 213 This allows for significant depletion of phages and protein complexes in the sample, although smaller proteins may remain in the gradient. 214 The main problem with this is related to sedimentation dynamics, as the higher density and viscosity further down in the centrifugation medium lowers the sedimentation speed according to Stokes' law (Eq. 1.3), prolonging the time needed for satisfactory separation.…”