The Sinorhizobium meliloti Essential Porin RopA1 Is a Target for Numerous Bacteriophages

Crook, Martin F.; Draper, Alicia L.; Guillory, R. Jordan; Griffitts, Joel S.

doi:10.1128/jb.00480-13

Cited by 18 publications

(13 citation statements)

References 46 publications

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“…Phages of the ΦM9 and ΦM12 groups interact with the S. meliloti host cell surface by different mechanisms. Phages of the ΦM9 group are dependent upon the presence of an outer membrane lipopolysaccharide containing a complete core oligosaccharide ( 59 , 60 ). In contrast, phages of the ΦM12 group are dependent upon the outer membrane protein encoded by ropA1 for infection of S. meliloti ( 60 ).…”

Section: Discussionmentioning

confidence: 99%

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

Johnson

Tatum

Lynn

et al. 2015

J Virol

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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.

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Section: Discussionmentioning

confidence: 99%

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

Johnson

Tatum

Lynn

et al. 2015

J Virol

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“…The function of these porins in rhizobia is largely undefined but it was determined that the RopA1, RopA2 and RopA3 proteins found in R. etli OMVs are not involved in copper transport like the plasmid-encoded RopAe (56), which was not present in the exoproteome. In Sinorhizobium meliloti RopA1 is a major phage binding site and, presumably due to other, yet undefined physiological roles, is essential for cell viability (57, 58). Some bacteria produce OMVs containing phage binding proteins as decoy targets for the virus (59, 60).…”

Section: Resultsmentioning

confidence: 99%

Proteins in the periplasmic space and outer membrane vesicles ofRhizobium etliCE3 grown in minimal medium are largely distinct and change with growth phase

Taboada

Meneses

Dunn

et al. 2018

Preprint

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3Rhizobium etli CE3 grown in succinate-ammonium minimal medium (MM) excreted 4 outer membrane vesicles (OMVs) with diameters of 40 to 100 nm. Proteins from the 5 OMVs and the periplasmic space were isolated from 6 and 24 h cultures and identified 6 by proteome analysis. A total 770 proteins were identified: 73.8 and 21.3 % of these 7 proteins occurred only in the periplasm and OMVs, respectively, and only 4.9 % were 8 found in both locations. The majority of proteins found in either location were present 9 only at 6 or 24 h: in the periplasm and OMVs, only 24 and 9 % of proteins, respectively,

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“…The phylogenetically more distant Coxiella OMPP P1 (CPP1) Family (1.B.43) consists of OMPPs of a size similar to those of the BRP Family with 8–12 predicted β-TMSs. Finally the most distant member of cluster XIV, the OMC Family (1.B.70) [ 117 ] is so poorly characterized that an OMPP function is not established. These putative β-barrel OMPPs may have about 16 β-TMSs.…”

Section: Resultsmentioning

confidence: 99%

Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins

Reddy

Saier

2016

PLoS ONE

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We here report statistical analyses of 76 families of integral outer membrane pore-forming proteins (OMPPs) found in bacteria and eukaryotic organelles. 47 of these families fall into one superfamily (SFI) which segregate into fifteen phylogenetic clusters. Families with members of the same protein size, topology and substrate specificities often cluster together. Virtually all OMPP families include only proteins that form transmembrane pores. Nine such families, all of which cluster together in the SFI phylogenetic tree, contain both α- and β-structures, are multi domain, multi subunit systems, and transport macromolecules. Most other SFI OMPPs transport small molecules. SFII and SFV homologues derive from Actinobacteria while SFIII and SFIV proteins derive from chloroplasts. Three families of actinobacterial OMPPs and two families of eukaryotic OMPPs apparently consist primarily of α-helices (α-TMSs). Of the 71 families of (putative) β-barrel OMPPs, only twenty could not be assigned to a superfamily, and these derived primarily from Actinobacteria (1), chloroplasts (1), spirochaetes (8), and proteobacteria (10). Proteins were identified in which two or three full length OMPPs are fused together. Family characteristic are described and evidence agrees with a previous proposal suggesting that many arose by adjacent β-hairpin structural unit duplications.

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The Sinorhizobium meliloti Essential Porin RopA1 Is a Target for Numerous Bacteriophages

Cited by 18 publications

References 46 publications

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

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

Proteins in the periplasmic space and outer membrane vesicles ofRhizobium etliCE3 grown in minimal medium are largely distinct and change with growth phase

Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins

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