PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 1784830

From data banks to data bases.

A Danchin·C Médigue·O Gascuel·H Soldano·A Hénaut
View original source ↗Export metadata ↓

Abstract

The information collected in national and international libraries on nucleotide and protein sequences cannot be directly treated for proper handling by existing software. Therefore we evaluated the feasibility of constructing a data base for Escherichia coli using the data present in the banks. The knowhow thus acquired was applied to Bacillus subtilis. Specific examples of the general procedure are given.

Explore related subjects

Bacillus subtilisBase SequenceChromosomes, BacterialDNA, BacterialDatabase Management SystemsDatabases, BibliographicDatabases, FactualEscherichia coliIn Vitro TechniquesMolecular Sequence DataJournal ArticleReview

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

A Danchin, C Médigue, O Gascuel, H Soldano, A Hénaut. From data banks to data bases.. https://doi.org/10.1016/0923-2508(91)90073-j

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

Genome-informed qPCR tracking revealed preferential persistence of Bacillus subtilis BS9 in the broiler chicken gastrointestinal tract.

This study aimed to develop a strain-specific quantitative PCR (qPCR) assay for Bacillus subtilis BS9 and characterize its persistence and spatial distribution in the broiler chicken gastrointestinal tract. Whole-genome sequencing and comparative genomic analysis identified a unique 110-bp sequence within a strain-specific genomic island, which was used to design a highly specific qPCR assay with excellent efficiency and sensitivity. In a 14-day in vivo trial, broiler chicks receiving daily oral doses of BS9 were analyzed using both culture-based methods and the newly developed qPCR. The assay was applied qualitatively, presence or absence, to detect BS9 in intestinal samples. BS9 was detected exclusively in the duodenum, jejunum, and cecum, with no presence in the gizzard or ileum. These findings demonstrate that BS9 exhibits region-specific persistence in the gut, likely reflecting adaptation to distinct physiological niches, which may contribute to its probiotic mechanisms.IMPORTANCEThis work provides the first detailed account of B. subtilis BS9's spatial persistence in poultry, revealing preferential adherence to specific intestinal regions. The strain-specific qPCR assay developed here offers a precise, culture-independent tool for tracking BS9 in complex gut environments. These insights into the genetic basis and tissue tropism of BS9 persistence advance our understanding of probiotic-host interactions and establish a framework for characterizing novel probiotic strains.

Bacillus subtilis↗
PubMed2026

Long-range mRNA folding shapes expression and sequence of bacterial genes.

Bacterial gene expression is strongly influenced by local mRNA secondary structure, yet the impact of long-range folding remains poorly understood. Here, we show that sequences hundreds of nucleotides from the mRNA 5' end can act as potent repressors of gene expression through long-range base pairing to the ribosome binding site (RBS), subjecting anti-RBS sequences to negative selection. Using massively parallel reporter assays in Bacillus subtilis, we identify anti-RBS sequences as among the strongest determinants of reduced mRNA abundance across the transcript body. We demonstrate that distal anti-RBS elements engage in long-range folding with the Shine-Dalgarno sequence, blocking ribosome entry and promoting mRNA decay. Consistent with these repressive effects, anti-RBS-like sequences are depleted throughout diverse bacterial coding sequences but not from leaderless transcripts, and introducing distal anti-RBS to native genes reduces expression. Our findings establish that long-range mRNA folding is a conserved force shaping gene expression and constrains coding sequence evolution.

Bacillus subtilis↗