Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid

Abstract

The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti contains three replicons: pSymA, pSymB, and the chromosome. We report here the complete 1,354,226-nt sequence of pSymA. In addition to a large fraction of the genes known to be specifically involved in symbiosis, pSymA contains genes likely to be involved in nitrogen and carbon metabolism, transport, stress, and resistance responses, and other functions that give S. meliloti an advantage in its specialized niche.

Figure 1

Map of pSymA. The position of the first nucleotide (denoted 1) was assigned adjacent to and clockwise from the repABC genes and putative origin of replication (6). Selected genes and regions mentioned in text are labeled. Locations of insertion sequence (IS) elements and IS fragments are marked with colored triangles. Additional information on IS elements is available in ref. and at the genome web site (http://sequence.toulouse.inra.fr/meliloti.html). Putative chemotaxis genes (che), pilus assembly genes (pil), and NADH–ubiquinone dehydrogenase genes (nuo) are discussed in a concurrent publication (6). Sites of infrequently cutting restriction enzymes (SwaI, PacI, and PmeI) are marked. SMA designations for regions shown on the map are: tRNA-sec, SMa0011; groESL3, SMA0124–125; pilQ, SMA0163; gdhA, SMA0228; gabD3, SMA0260; fdh, SMA0478; idn, SMA0512–514; nrt, SMA0581–585; fix-3, SMA0612–622; arcABC, SMA0693–697; groESL2, SMA0744–745; fix-2, SMA0760–769; gabD4, SMA0805; nif, SMA0825–831; nod, SMA0840–878; dnaE3, SMA0892; oriT, SMa4018; att, SMA0950–958; fixL-like, SMA1142; nos, SMA1179–1188; fix-1, SMA107–1229; nir, SMA1247–1250; nor, SMA1269–1279; vir, SMA1302–1321; nuo, SMA1516–1536; che/pil, SMA1552–1578; arcDA, SMA1667–1670; argI2, SMA1711; bet, SMA1726–1731; iron uptake, SMA1740–1747; argE, SMA1836; gabD5, SMA1848; sulfur metabolism, SMA2067–2103; glyA2, SMA2135; tRNA-met, SMa2168; opine metabolism, SMA2223–2225; and oriV, SMa4019.