Riboswitch-mediated regulation of riboflavin biosynthesis genes in prokaryotes

Mapping the IscR regulon sheds light on the regulation of iron homeostasis in Caulobacter

The role of the iron-sulfur [Fe-S] cluster transcriptional regulator IscR in maintaining [Fe-S] homeostasis in bacteria is still poorly characterized in many groups. Caulobacter crescentus and other Alphaproteobacteria have a single operon encoding [Fe-S] cluster biosynthesis enzymes. We showed that the expression of this operon increases in iron starvation, but not in oxidative stress, and is controlled mainly by IscR. Transcriptome analysis comparing an iscR null mutant strain with the wild-type (wt) strain identified 94 differentially expressed genes (DEGs), with 47 upregulated and 47 downregulated genes in the ΔiscR mutant. We determined the IscR binding sites in conditions of sufficient or scarce iron by Chromatin Immunoprecipitation followed by DNA sequencing (ChIP-seq), identifying two distinct putative DNA binding motifs. The estimated IscR regulon comprises 302 genes, and direct binding to several regulatory regions was shown by Electrophoresis Mobility Shift Assay (EMSA). The results showed that the IscR and Fur regulons partially overlap and that IscR represses the expression of the respiration regulator FixK, fine-tuning gene regulation in response to iron and redox balance.

Regulatory RNAs in Bacillus subtilis: A review on regulatory mechanism and applications in synthetic biology

Bacteria exhibit a rich repertoire of RNA molecules that intricately regulate gene expression at multiple hierarchical levels, including small RNAs (sRNAs), riboswitches, and antisense RNAs. Notably, the majority of these regulatory RNAs lack or have limited protein-coding capacity but play pivotal roles in orchestrating gene expression by modulating transcription, post-transcription or translation processes. Leveraging and redesigning these regulatory RNA elements have emerged as pivotal strategies in the domains of metabolic engineering and synthetic biology. While previous investigations predominantly focused on delineating the roles of regulatory RNA in Gram-negative bacterial models such as Escherichia coli and Salmonella enterica, this review aims to summarize the mechanisms and functionalities of endogenous regulatory RNAs inherent to typical Gram-positive bacteria, notably Bacillus subtilis. Furthermore, we explore the engineering and practical applications of these regulatory RNA elements in the arena of synthetic biology, employing B. subtilis as a foundational chassis.

Techno-Functional Assessment of Riboflavin-Enriched Yogurt-Based Fermented Milk Prepared by Supplementing Riboflavin-Producing Probiotic Strains of Lactiplantibacillus plantarum

Vitamin enrichment in fermented dairy products through the intervention of vitamin-producing probiotic strains during fermentation is a novel approach in the field of probioceuticals. In this study, riboflavin-enriched yogurt-based fermented milk was prepared by mixing 1% (v/v) riboflavin-producing strain [1.2 × 108 CFU/mL of Lactiplantibacillus plantarum MTCC 25432 or L. plantarum MTCC 25433 or L. plantarum MTCC 25434] with 2% (v/v) traditional yogurt cultures [Streptococcus thermophilus NCDC 295 and L. delbrueckii subsp. bulgaricus NCDC 293; each of 1.3 × 107 CFU/mL]. The yogurt-based fermented milk prepared with traditional yogurt cultures (2%, v/v) was served as a control. The prepared yogurt-based fermented milk samples were analyzed and compared for riboflavin content, antimicrobial activity, physicochemical, and functional properties. As a result, the yogurt-based fermented milk prepared with L. plantarum MTCC 25432 produced a significantly higher amount of riboflavin (2.49 mg/L) as compared with MTCC 25433 (2.33 mg/L), MTCC 25434 (2.14 mg/L), and control (1.70 mg/L). The probiotic supplementation to yogurt cultures maintained the pH and titratable acidity in the range of 4.1-4.4 and 1.0-1.05% (lactic acid/100 mL), as recommended by Indian yogurt standards. The rheological, texture, and antimicrobial properties of yogurt-based fermented milk were enhanced with the addition of riboflavin-producing probiotic strains. Moreover, all yogurt-based fermented milk samples prepared in this study were acceptable as per the sensory evolution scores. In conclusion, the use of riboflavin-producing L. plantarum strains along with standard yogurt cultures could be the best approach to enhancing riboflavin content in yogurt-based fermented milk and fulfilling the daily riboflavin requirement in humans.

Ribocentre-switch: a database of riboswitches

Riboswitches are regulatory elements found in the untranslated regions (UTRs) of certain mRNA molecules. They typically comprise two distinct domains: an aptamer domain that can bind to specific small molecules, and an expression platform that controls gene expression. Riboswitches work by undergoing a conformational change upon binding to their specific ligand, thus activating or repressing the genes downstream. This mechanism allows gene expression regulation in response to metabolites or small molecules. To systematically summarise riboswitch structures and their related ligand binding functions, we present Ribocentre-switch, a comprehensive database of riboswitches, including the information as follows: sequences, structures, functions, ligand binding pockets and biological applications. It encompasses 56 riboswitches and 26 orphan riboswitches from over 430 references, with a total of 89 591 sequences. It serves as a good resource for comparing different riboswitches and facilitating the identification of potential riboswitch candidates. Therefore, it may facilitate the understanding of RNA structural conformational changes in response to ligand signaling. The database is publicly available at https://riboswitch.ribocentre.org.