Sequence Analysis of the 144-Kilobase Accessory Plasmid pSmeSM11a, Isolated from a DominantSinorhizobium melilotiStrain Identified during a Long-Term Field Release Experiment

Abstract

The genome of Sinorhizobium meliloti type strain Rm1021 consists of three replicons: the chromosome and two megaplasmids, pSymA and pSymB. Additionally, many indigenous S. meliloti strains possess one or more smaller plasmids, which represent the accessory genome of this species. Here we describe the complete nucleotide sequence of an accessory plasmid, designated pSmeSM11a, that was isolated from a dominant indigenous S. meliloti subpopulation in the context of a long-term field release experiment with genetically modified S. meliloti strains. Sequence analysis of plasmid pSmeSM11a revealed that it is 144,170 bp long and has a mean G؉C content of 59.5 mol%. Annotation of the sequence resulted in a total of 160 coding sequences. Functional predictions could be made for 43% of the genes, whereas 57% of the genes encode hypothetical or unknown gene products. Two plasmid replication modules, one belonging to the repABC replicon family and the other belonging to the plasmid type A replicator region family, were identified. Plasmid pSmeSM11a contains a mobilization (mob) module composed of the type IV secretion system-related genes traG and traA and a putative mobC gene. A large continuous region that is about 42 kb long is very similar to a corresponding region located on S. meliloti Rm1021 megaplasmid pSymA. Single-base-pair deletions in the homologous regions are responsible for frameshifts that result in nonparalogous coding sequences. Plasmid pSmeSM11a carries additional copies of the nodulation genes nodP and nodQ that are responsible for Nod factor sulfation. Furthermore, a tauD gene encoding a putative taurine dioxygenase was identified on pSmeSM11a. An acdS gene located on pSmeSM11a is the first example of such a gene in S. meliloti. The deduced acdS gene product is able to deaminate 1-aminocyclopropane-1-carboxylate and is proposed to be involved in reducing the phytohormone ethylene, thus influencing nodulation events. The presence of numerous insertion sequences suggests that these elements mediated acquisition of accessory plasmid modules.

Structural and functional genomics of plasmid pSinA of Sinorhizobium sp. M14 encoding genes for the arsenite oxidation and arsenic resistance

“…W54R). Thus, we hypothesize that this replication system can serve as an additional replication region, like those found in other repABC-type plasmids such as pSmeSM11a (Stiens et al, 2006) and pRmeGR4a (Burgos et al, 1996). It is also probable that pMSA5 does not encode a functional replication initiation protein, but contains only an origin of replication (oriV) that requires the activity of additional gene products encoded within the bacterial chromosome to function.…”

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

“…strains (Li and Farrand, 2000) and the second chromosome in the animal pathogen Brucella (Paulsen et al, 2002). The repABC genes also appear to be widely distributed on accessory plasmids in several rhizobial species (Cevallos et al, 2002;Stiens et al, 2006;Watson and Heys, 2006). Amino-acid sequence analysis revealed that two ORFs, BBta_p0014 and BBta_p0015, located downstream of the repABC replication module, were 42% and 35% identical to ParA-like ATPase and ParBlike partition protein from S. meliloti plasmid pMBA19a (accession number AY914874) and the Rhodobacter sphaeroides plasmid pRSPA04 (accession number NC_009432), respectively.…”

“…In addition to symbiotic plasmids, several rhizobial strains also contain one or more smaller, accessory plasmids, also termed non-symbiotic plasmids (Mercado-Blanco and Toro, 1996;Gonzalez et al, 2006;Stiens et al, 2006;Young et al, 2006). Some of these plasmids have been shown to transfer between populations of indigenous rhizobia (Mercado-Blanco and Toro, 1996).…”

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

“…The genome of S. medicae WSM 419 also includes a 219-kb plasmid called pSMED03. Although S. meliloti 1021 does not have any comparable plasmid, additional plasmids have also been observed in some other strains of this species Olivares, 1993, 1994;Stiens et al, 2006Stiens et al, , 2007Kuhn et al, 2008). Based on sequencing of several loci, S. medicae is less diverse than S. meliloti, especially at chromosomal loci (Bailly et al, 2006;van Berkum et al, 2006).…”

“…Novel genomic sequences have been described both from the cryptic plasmids of the strain SM11 (Stiens et al, 2006(Stiens et al, , 2007 and also from a representational difference analysis based on the strain ATCC 9930 (Guo et al, 2005). These new sequences occur with a wide range of frequencies in natural populations of S. meliloti (Guo et al, 2005;Kuhn et al, 2008).…”