Figure 3

Analysis of the neighborhood of FRE652 in the S. meliloti and S. medicae genomes. (a) Locally collinear block corresponding to a conserved segment containing FRE652 sequences identified by Mauve. Complete sequences of megaplasmid pSymA from S. meliloti strains AK83 and SM11, the cryptic plasmids pHRC017 and pRmeGR4b from S. meliloti strains CO17 and GR4, respectively, and that of megaplasmid pSMED02 from S. medicae strain WSM419 were aligned with the progressive Mauve algorithm, and locally collinear blocks were extracted with Geneious Pro software (Biomatters Ltd). The relevant ORFs (coding sequence (CDS)) are depicted (yellow). The authors of the original studies in the database annotated carbonate dehydratase as carbonic anhydrase (GR4 and pHRC017); diguanylate cyclase/phosphodiesterase as GGDEF domain/EAL domain protein (GR4), conserved hypothetical protein (SM11) and PAS/PAC sensor-containing diguanylate cyclase (GGDEF)/phosphodiesterase (EAL) (pHRC017); the putative transcriptional regulator as hypothetical protein (SM11), XRE family helix-turn-helix transcriptional regulator (pHRC017) and helix-turn-helix domain protein (AK83). Pink open arrows above some of the CDS indicate putative signal peptides and an S within some of the CDS correspond to annotated short hypothetical proteins. FRE652 annotations and annotations for a group II intron derivative have been introduced manually here. The consensus identity is shown above the block, and the green color reflects the regions of higher identity. Genomic positions, as shown from left to right, are: S. me GR4 pRmeGR4b (bases 69 345–74 866), S. md WSM419 pSMED02 (bases 1 066 557–1 060 009), S. me SM11 pSymA (bases 91 375–96 621), S. me C017 pHRC017 (bases 59 086–64 605), S. me AK83 pSymA copy 1 (bases 1 253 952 to 1 248 066) and S. me AK83 pSymA copy 2 (bases 326 826–332 352). (b) DNA target sites recognized by group II introns RmInt1 and Sr.md.I1, and the putative sequences recognized by the intron from which FRE652 was derived. 5′ Exon positions are indicated relative to the intron insertion site, and the EBS and IBS sequences are shown. The unpaired residues are highlighted in red. Note that for FRE652, the −1 residue of the 5′ exon is absent; as it was probably deleted as the first G residue of the intron (see Figure 1).