RNA-seq of Bifidobacterium longum NCC2705

ABSTRACT: Bacterial promoters consist of core sequence motifs termed –35 and –10 boxes. The consensus motifs are TTGACA and TATAAT, respectively, which were identified from leading investigations on E. coli. However, the consensus sequences are not likely to fit genetically divergent bacteria. The sigma factor of the genus Bifidobacterium has a characteristic polar domain in the N-terminus, suggesting the possibility of specific promoter recognition. We reevaluated the structure of B. longum NCC2705 promoters and compared them to other bacteria. Transcriptional start sites (TSS) of the B. longum NCC2705 strain were identified using RNA-Seq analysis to extract promoter regions. Conserved motifs of a bifidobacterial promoter were determined using regions upstream of TSSs and a hidden Markov model. As a result, consensus motifs of the –35 and –10 boxes were TTGTGC and TACAAT, respectively. To assess each base of both motifs, we constructed thirty-seven plasmids based on pKO403-TPCTcon, including the hup promoter connected with a chloramphenicol acetyltransferase as a reporter gene. This reporter assay showed two optimal motifs of the –35 and –10 boxes, TTGNNN and TANNNT, respectively. We further analyzed spacer-lengths between the –35 and –10 boxes via a bioinformatics approach. The spacer-lengths predominant in bacteria have been generally reported to be approximately 17 bp. In contrast, the predominant spacer-lengths in the genus Bifidobacterium and related species were 11 bp, in addition to 17 bp. A reporter assay to assess the spacer-lengths indicated that the 11 bp spacer-length produced unusually high activity.

ORGANISM(S): Bifidobacterium longum NCC2705

PROVIDER: GSE143410 | GEO | 2020/01/26

REPOSITORIES: GEO