Analysis of pFQ12, a 22.4-kb Frankia plasmid

Frankia are gram-positive, filamentous bacteria capable of fixing atmospheric dinitrogen in symbiosis with a wide variety of woody plants and shrubs. Some isolates of Frankia harbor plasmids of 8.5 (pFQ11) and 22.4 kb (pFQ12) that have no known function but are transmitted through many generations in culture. We have sequenced the 22,437-bp pFQ12 plasmid that is present in isolates CpI1 and ArI3. This sequence, with 76% G+C, is almost totally unrelated to that of pFQ11 found in the same cells. However, four regions of identity, 40-90 bp each, are dispersed around the plasmids. The 22.4-kb plasmid has >50 open reading frames (ORFs) that encode putative proteins of more than 100 amino acids, with the largest being 2226 amino acids. Twenty of these ORFs are likely to encode proteins based on their codon bias as determined by two different algorithms. Transcripts from nine of these regions have been identified by reverse transcriptase-polymerase chain reaction (RT-PCR) or filter hybridization. The two Frankia plasmids each encode a protein similar to the korSA protein that regulates transmission of pSAM2 in Streptomyces. The origin of replication (ORI) region of pFQ12 was localized by intrastrand AT and GC equivalence switch. It includes a 40-bp, intergenic, A+T-rich region that has a strong identity in pFQ11.