Complex formation of T 7 DNA with RNA polymerase from E . coli B/r WU‐36‐10‐11‐12 ( E . coli W 12) and its rifampicin‐resistant mutant rpoB409 was studied. The rpoB409 mutant possesses a highly pleiotropic effect due to alteration in the RNA polymerase β‐subunit structure. The two RNA polymerases have been previously shown to differ in gene selection during RNA synthesis on T 7 DNA. In this study it was found that the change in selective properties of the mutant RNA polymerase occurs during its interaction with DNA, the general ability of the enzyme to melt DNA being unaffected.
Until recently, no examples of the in-frame translation of several proteins from one gene in bacteria were known. The first one was the VirF transcription factor controlling pathogenicity development in Shigella flexneri and CobB sirtuin in Salmonella enterica. Recently, we observed synthesis of shortened protein products for YjjM (LgoR) and LeuO functioning as transcription factors in Escherichia coli. To determine the evolutionary factors that could lead to the appearance of alternative start codons, we performed phylogenetic analysis and showed that each protein had a unique phylogenetic history, and additional starting methionines appeared only in Enterobacteria. Using the Western-blot analysis of proteins synthesized from the Escherichia coli K-12 MG1655 chromosome with the his-tagged leuO gene two shortened variants of LeuO, corresponding to translation starting from Met34 and Met48 were detected. Synthesis of all three LeuO forms was inhibited in the absence of the yjjM gene, suggesting interplay of these transcription factors. The YjjM recognition motif revealed from the ChIP-seq data appeared to be very similar to that of LeuO, known previously. Taking this into account, we compared ChIP and SELEX data for LeuO and YjjM and found six common targets. At least five of them were confirmed to be under control of these regulators by qRT-PCR. Interestingly, the effects were more prominent during anaerobic growth at 37°C simulating conditions inside a host organism. Two genes, coding for the enterobactin transporter FepA, and a repressor of genes responsible for flagellar biosynthesis and virulence YjjQ, were repressed, mainly by YjjM, only in these conditions, while tsr coding for the chemotaxis receptor protein was more repressed under lower temperature and higher aeration.
Alignment-free approaches employing short k-mers as barcodes for individual genomes have created a new strategy for taxonomic analysis and paved a way for high-resolution phylogeny. Here, we introduce this strategy for the Lacticaseibacillus paracasei species as a taxon requiring barcoding support for precise systematics. Using this approach for phylotyping of L. paracasei VKM B-1144 at the genus level, we identified four L. paracasei phylogroups and found that L. casei 12A belongs to one of them, rather than to the L. casei clade. Therefore, we propose to change the specification of this strain. At the genus level we found only one relative of L. paracasei VKM B-1144 among 221 genomes, complete or available in contigs, and showed that the coding potential of the genome of this "rare" strain allows its consideration as a potential probiotic component. Four sets of published metagenomes were used to assess the dependence of L. paracasei presence in the human gut microbiome on chronic diseases, dietary changes and antibiotic treatment. Only antibiotics significantly affected their presence, and strain-specific barcoding allowed the identification of the main scenarios of the adaptive response. Thus, suggesting bacteria of this species for compensatory therapy, we also propose strain-specific barcoding for selecting optimal strains for target microbiomes.
Beneficial properties of lactic acid bacteria have been known long ago, but particular interest in probiotics has arisen in the last two decades due to the understanding of the important role of intestinal microflora in human life. Thus, the ability of probiotics to support healthy homeostasis of gut microbiomes has received particular attention. Here, we evaluated the effect of a probiotic consisting of Bifidobacterium longum and Lacticaseibacillus paracasei on the gut microbiome of male rats, assessed their persistence in the fecal biota, and compared probiotic-mediated changes in vitro and in vivo. As expected, microbiomes of two enterotypes were identified in the feces of 21 animals, and it turned out that even a single dose of the probiotic altered the microbial composition. Upon repeated administration, the E1 biota temporarily acquired properties of the E2 type. Being highly sensitive to the intervention of probiotic bacteria at the phylum and genus levels, the fecal microbiomes retained the identity of their enterotypes when transferred to a medium optimized for gut bacteria. For the E2 biota, even similarities between probiotic-mediated reactions in vitro and in vivo were detected. Therefore, fecal-derived microbial communities are proposed as model consortia to optimize the response of resident bacteria to various agents.
Аннотация.Функциональные свойства промоторных островков генома кишечной палочки, т.е.участков с аномально высокой плотностью сигналов транскрипции, сопоставлены со свойствами геномных областей, аномально обогащённых А/Т-парами.Установлено, что компьютерные выборки участков обоих типов по соответствующим критериям частично перекрываются, а их функциональные свойства во многом похожи
