Variation in 16S-23S rRNA Intergenic Spacer Regions in Photobacterium damselae: a Mosaic-Like Structure

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American Society for Microbiology

RESUMO

Phenotypically, Photobacterium damselae subsp. piscicida and P. damselae subsp. damselae are easily distinguished. However, their 16S rRNA gene sequences are identical, and attempts to discriminate these two subspecies by molecular tools are hampered by their high level of DNA-DNA similarity. The 16S-23S rRNA internal transcribed spacers (ITS) were sequenced in two strains of Photobacterium damselae subsp. piscicida and two strains of P. damselae subsp. damselae to determine the level of molecular diversity in this DNA region. A total of 17 different ITS variants, ranging from 803 to 296 bp were found, some of which were subspecies or strain specific. The largest ITS contained four tRNA genes (tDNAs) coding for tRNAGlu(UUC), tRNALys(UUU), tRNAVal(UAC), and tRNAAla(GGC). Five amplicons contained tRNAGlu(UUC) combined with two additional tRNA genes, including tRNALys(UUU), tRNAVal(UAC), or tRNAAla(UGC). Five amplicons contained tRNAIle(GAU) and tRNAAla(UGC). Two amplicons contained tRNAGlu(UUC) and tRNAAla(UGC). Two different isoacceptor tRNAAla genes (GGC and UGC anticodons) were found. The five smallest amplicons contained no tRNA genes. The tRNA-gene combinations tRNAGlu(UUC)-tRNAVal(UAC)-tRNAAla(UGC) and tRNAGlu(UUC)-tRNAAla(UGC) have not been previously reported in bacterial ITS regions. The number of copies of the ribosomal operon (rrn) in the P. damselae chromosome ranged from at least 9 to 12. For ITS variants coexisting in two strains of different subspecies or in strains of the same subspecies, nucleotide substitution percentages ranged from 0 to 2%. The main source of variation between ITS variants was due to different combinations of DNA sequence blocks, constituting a mosaic-like structure.

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