Antirestriction protein ard (type C) encoded by IncW plasmid psa has a high similarity to the “protein transport” domain of TraC1 primase of promiscuous plasmid RP4 1 1Edited by M. Gottesman

Белогуров, А. А.; Delver, E. P.; Agafonova, O. V.; Belogurova, N. G.; Lee, Lan‐Ying; Kado, Clarence I.

doi:10.1006/jmbi.1999.3493

Cited by 57 publications

(61 citation statements)

References 27 publications

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“…Msi152 is a homologue of the incW plasmid pSa antirestriction protein ArdC (6). Homologues are also encoded on several Agrobacterium plasmids: pNGR234a, pNL1 from Sphingomonas aromaticivorans, and M. loti pMLa and pMLb (14,25,47,59).…”

Section: Resultsmentioning

confidence: 99%

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Comparative Sequence Analysis of the Symbiosis Island ofMesorhizobium lotiStrain R7A

et al. 2002

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The Mesorhizobium loti strain R7A symbiosis island is a 502-kb chromosomally integrated element which transfers to nonsymbiotic mesorhizobia in the environment, converting them to Lotus symbionts. It integrates into a phenylalanine tRNA gene in a process mediated by a P4-type integrase encoded at the left end of the element. We have determined the nucleotide sequence of the island and compared its deduced genetic complement with that reported for the 611-kb putative symbiosis island of M. loti strain MAFF303099. The two islands share 248 kb of DNA, with multiple deletions and insertions of up to 168 kb interrupting highly conserved colinear DNA regions in the two strains. The shared DNA regions contain all the genes likely to be required for Nod factor synthesis, nitrogen fixation, and island transfer. Transfer genes include a trb operon and a cluster of potential tra genes which are also present on the strain MAFF303099 plasmid pMLb. The island lacks plasmid replication genes, suggesting that it is a site-specific conjugative transposon. The R7A island encodes a type IV secretion system with strong similarity to the vir pilus from Agrobacterium tumefaciens that is deleted from MAFF303099, which in turn encodes a type III secretion system not found on the R7A island. The 414 genes on the R7A island also include putative regulatory genes, transport genes, and an array of metabolic genes. Most of the unique hypothetical genes on the R7A island are strain-specific and clustered, suggesting that they may represent other acquired genetic elements rather than symbiotically relevant DNA.The symbiosis between legumes and the root nodule bacteria collectively known as rhizobia is of critical agronomic and environmental importance, accounting for the majority of the nitrogen fixed through biological processes. Rhizobia are phylogenetically diverse, falling into five genera of ␣-proteobacteria (Rhizobium, Bradyrhizobium, Sinorhizobium, Azorhizobium, and Mesorhizobium) (64, 70) and at least two genera of ␤-proteobacteria (Burkholderia and Ralstonia) (35). It is thought that the rhizobial lineages diverged well before the evolution of legumes and that the genes required for the formation of the symbiosis were subsequently acquired by lateral transfer from undefined sources (8,33). Reflecting the accessory nature of the traits, several species of rhizobia contain the genes required for nodulation and nitrogen fixation on large plasmids that can be cured under laboratory conditions without affecting the survival of the bacteria (31). Exceptions in which the symbiosis genes are encoded on the chromosome include Bradyrhizobium species, in which the symbiosis genes are clustered but not known to be mobile (18), and at least one strain of Mesorhizobium loti, strain ICMP3153, in which the genes are located on a mobile symbiosis island (57).M. loti is the microsymbiont of several Lotus species, including Lotus corniculatus and L. japonicus. The symbiosis island of M. loti strain ICMP3153 was discovered through its ability to transfe...

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Section: Resultsmentioning

confidence: 99%

“…A complete copy of the RP4-type traC gene is not located on the island, Ti plasmids, or pNGR234a. ArdC and TraC1 are able to bind single-stranded DNA and escort plasmid DNA during conjugation (6), and so ArdC may play a role in the conjugative transfer of the island.…”

Section: Resultsmentioning

confidence: 99%

Comparative Sequence Analysis of the Symbiosis Island ofMesorhizobium lotiStrain R7A

et al. 2002

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“…The most likely mechanism of this benefit would be analogous to the proposed function of P1 DarB, wherein the mobile DNA is methylated during or shortly after transfer to a new cell in order to protect it from host restriction. If so, this would make these DarB-like proteins a novel class of widely distributed antirestriction proteins, similar in effect (if not in mechanism) to proteins such as ArdA, ArdB, and ArdC (4,5,13). The presence of these proteins in phages, plasmids, and IS elements also highlights the potential for horizontal genetic transfer, not only between phages (as has been well documented [26]) but also between phages and other bacterial genetic elements.…”

Section: Vol 193 2011mentioning

confidence: 88%

Genomes and Characterization of Phages Bcep22 and BcepIL02, Founders of a Novel Phage Type in Burkholderia cenocepacia

et al. 2011

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Within the Burkholderia cepacia complex, B. cenocepacia is the most common species associated with aggressive infections in the lungs of cystic fibrosis patients, causing disease that is often refractive to treatment by antibiotics. Phage therapy may be a potential alternative form of treatment for these infections. Here we describe the genome of the previously described therapeutic B. cenocepacia podophage BcepIL02 and its close relative, Bcep22. Phage Bcep22 was found to contain a circularly permuted genome of 63,882 bp containing 77 genes; BcepIL02 was found to be 62,714 bp and contains 76 predicted genes. Major virion-associated proteins were identified by proteomic analysis. We propose that these phages comprise the founding members of a novel podophage lineage, the Bcep22-like phages. Among the interesting features of these phages are a series of tandemly repeated putative tail fiber genes that are similar to each other and also to one or more such genes in the other phages. Both phages also contain an extremely large (ca. 4,600-amino-acid), virion-associated, multidomain protein that accounts for over 20% of the phages' coding capacity, is widely distributed among other bacterial and phage genomes, and may be involved in facilitating DNA entry in both phage and other mobile DNA elements. The phages, which were previously presumed to be virulent, show evidence of a temperate lifestyle but are apparently unable to form stable lysogens in their hosts. This ambiguity complicates determination of a phage lifestyle, a key consideration in the selection of therapeutic phages.

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“…This ORF forms a monophyletic clade with ArdC proteins from other a-proteobacterial plasmid, and is most closely related (74% AA identity) to ArdC from N. hamburgensis X14. The Ard proteins are thought to protect plasmid DNA from host restriction endonuclease activity during conjugal transfer (Belogurov et al, 2000).…”

Section: Conjugation and Gene Transfer Systemsmentioning

confidence: 99%

Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains

et al. 2008

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In silico, physiological and in planta analyses were used to characterize pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1, and assess its potential ecological function under free-living and symbiotic growth conditions. Sequence analysis revealed the presence of an uptake hydrogenase system, a repABC family plasmid replication module and open reading frames encoding type IV secretion system, TraI and TraR autoinducer proteins and several copper resistance-related proteins. Bradyrhizobium sp. BTAi1 was capable of growing in 200 mg l À1 CuCl 2 . In contrast, the closely related, plasmid-free Bradyrhizobium sp. strain ORS278 could not grow at copper concentrations exceeding 100 mg l À1 . The plasmid-localized hydrogenase genes were phylogenetically distinct from those typically found in other rhizobial species, and were most related to hup genes from Thiobacillus denitrificans. The induction of the plasmid-borne hydrogenase genes during symbiosis was significantly lower than the two chromosomal-borne hydrogenase clusters. CHEF-pulsed-field gel electrophoresis was used for a comprehensive analysis of the diversity, abundance and genetic composition of accessory plasmids in other Bradyrhizobium strains. Plasmids were detected in 11 of 46 (23.9%) geographically diverse Bradyrhizobium japonicum and Bradyrhizobium elkanii strains, isolated from the United States, China and Thailand. Plasmid size was heterogeneous, ranging from 75 to 330 kb, with only two strains (DASA01244 and DASA01265) harboring plasmids with identical (240 kb) size. None of the plasmids harbored nodulation or hydrogenase genes. Taken together, our results indicate that while plasmids having ecologically significant functions may be detected in Bradyrhizobium sp. strains, they lack genes necessary for symbioses with legumes.

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Antirestriction protein ard (type C) encoded by IncW plasmid psa has a high similarity to the “protein transport” domain of TraC1 primase of promiscuous plasmid RP4 1 1Edited by M. Gottesman

Cited by 57 publications

References 27 publications

Comparative Sequence Analysis of the Symbiosis Island ofMesorhizobium lotiStrain R7A

Comparative Sequence Analysis of the Symbiosis Island ofMesorhizobium lotiStrain R7A

Genomes and Characterization of Phages Bcep22 and BcepIL02, Founders of a Novel Phage Type in Burkholderia cenocepacia

Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains

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