DISTRIBUTION AND CHARACTERIZATION OF PLASMID-RELATED SEQUENCES IN THECHROMOSOMAL DNA OF DIFFERENT THERMOPHILIC METHANOBACTERIUM STRAINS

The genomes of several thermophilic members of the genus Methanobacter ium were analyzed for homology to the related restriction-modification plasmids pFV1 and pFZ1 from M. thermoformicicum strains THF and Z-245 , respectively. Two plasmid regions, designated FR-I and FR-II, could be identified with chromosomal counterparts in six Methanobacterium st rains. Multiple copies of the pFV1-specific element FR-I were detected in the M. thermoformicicum strains CSM3, FF1, FF3 and M. thermoautotr ophicum AH. Sequence analysis showed that one FR-I element had been in tegrated in almost identical sequence contexts into the chromosomes of the strains CSM3 and AH. Comparison of the FR-I elements from these s trains with that from pFV1 revealed that they consisted of two subfrag ments, boxI (1118 bp) and boxII (383 bp), the order of which is variab le. Each subfragment was identical on the sequence level with the corr esponding plasmid-borne element and was flanked by terminal direct rep eats with the consensus sequence A(A/T)ATTT. These results suggest tha t FR-I represents a mobile element. FR-II was located on both plasmids pFV1 and pFZ1, and on the chromosome of M. thermoformicicum strains T HF, CSM3 and HN4. Comparison of the nucleotide sequences of the two pl asmid FR-II copies and that from the chromosome of strain CSM3 showed that the FR-II segments were approximately 2.5-3.0 kb in size and cont ained large open reading frames (ORFs) that may encode highly related proteins with an as yet unknown function.