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Bacterial genes are typically grouped into operons defined as clusters of adjacent genes encoding for proteins that fill related roles and are transcribed into a single polycistronic mRNA molecule. This simple organization provides an efficient mechanism to coordinate the expression of neighboring genes and is at the basis of gene regulation in bacteria. Here, we report the existence of a higher level of organization in operon structure that we named noncontiguous operon and consists in an operon containing a gene(s) that is transcribed in the opposite direction to the rest of the operon. This transcriptional architecture is exemplified by the genes menE-menC-MW1733-ytkD-MW1731 involved in menaquinone synthesis in the major human pathogen Staphylococcus aureus. We show that menE-menC-ytkD-MW1731 genes are transcribed as a single transcription unit, whereas the MW1733 gene, located between menC and ytkD, is transcribed in the opposite direction. This genomic organization generates overlapping transcripts whose expression is mutually regulated by transcriptional interference and RNase III processing at the overlapping region. In light of our results, the canonical view of operon structure should be revisited by including this operon arrangement in which cotranscription and overlapping transcription are combined to coordinate functionally related gene expression. ; This work was supported by the Spanish Ministry of Economy and Competitiveness Grants BIO2014-53530-R and BIO2017-83035-R (Agencia Española de Investigacion/Fondo Europeo de Desarrollo Regional, European Union). A.T.-A. is supported by the European Research Council under the European Union's Horizon 2020 research and innovation programme Grant Agreement 646869.

One: Rearrangement of Prokaryotic Genetic Material and DNA Cloning Vectors -- 1 Genomic Structure and Evolution of Bacillus licheniformis ? and LP52 Phage Family -- 2 Expression of the Synthetic Proenkephalin Gene in E. coli -- 3 Cloning and Expression of Bacillus?-Glucanase Genes -- 4 Regulation of ?-Amylase Synthesis in Bacillus subtilis -- 5 New Variations on an Old Theme: Type I Restriction Enzymes and Their Recognition Sequences -- 6 The EcoDXX1 Restriction and Modification System of Escherichia coli ET7 -- 7 Biological Function of Type I Restriction Enzymes -- 8 The Fosfomycin Resistance Transposon Tn2921 -- 9 Transposition-like Events Mediated by Single-ended Derivatives of Transposon Tn21 -- 10 Cloning and Expression of Determinants Encoding Toxigenicity in Enterobacteria -- 11 Extrachromosomal Replicons in Streptomyces lavendulaegrasserius -- Two: DNA-Dependent RNA Polymerase in Prokaryotes: Structure and Function, Promoter Selection -- 1 Genetic Dissection of E. coli RNA Polymerase -- 2 Non-essential Sequences in the ? Subunit of E. coli RNA Polymerase -- 3 Sequence Analysis of the ? Gene of E. coli RNA Polymerase: Correlation with Structure-Function Studies -- 4 DNA-Dependent RNA Polymerase from Streptomyces granaticolor -- 5 Transcriptional and Translational Signals in Phages PZA and ø29 -- 6 Host-Vector System with the PR' Promoter of Phage Lambda -- 7 On the Difficulties of Defining and Measuring Promoter Strength1 The Case of the Promoters of Bacterial rRNA Genes -- Three: The Role of cAMP in Gene Expression -- 1 Cyclic AMP in Bacteria: Catabolite Repression and Related Effects -- 2 DNA Sequences Involved in Expression and Regulation of deoR-, cytR- and cAMP/CRP-Controlled Genes in Escherichia coli -- 3 Differential Cellular Distribution of Cyclic AMP-Dependent Protein Kinase during Development of Dictyostelium discoideum -- 4 Amplification of the Adenylate Cyclase Gene in Escherichia coli K12 -- 5 Factors Regulating the Activity of Escherichia coli Adenylate Cyclase -- 6 Regulation of Carbohydrate Metabolism by the Bacterial PEP:Sugar Phosphotransferase System -- 7 ATP-Dependent HPr Kinase Involved in Regulation of Carbohydrate Uptake in Gram-positive Bacteria: Inducer Exclusion and Inducer Expulsion -- 8 Regulation of cAMP Synthesis in Streptomyces granaticolor -- 9 Differences in Regulation of a Bacillus megaterium Metalloproteinase during Growth and Sporulation -- Four: Translational Control of Gene Expression -- 1 Ribosomal Protein Sl: "The Messenger RNA-Catching Arm" of Escherichia coli Ribosome -- 2 Initiation of Translation of Genetic Information in Streptomyces aureofaciens -- 3 Bacilli as Hosts for Protein Production -- 4 Structure and Expression of a Chloramphenicol Resistance Gene, cat-86, Cloned from Bacillus pumilus -- 5 An Approach to Controlled Removal of the 3? End of Ribosomal 16S RNA -- 6 Three Ribosomal tRNA-Binding Sites Involved in the Elongation Process -- 7 Structure, Function and Evolution of the 3? Ends of Small Ribosomal Subunit RNA -- 8 Amino Acid Residues In Elongation Factor Tu from Escherichia coli Near the Binding Site for the 3? Terminus of Aminoacyl-tRNA -- 9 Structural and Functional Alterations of Protein-Synthesis Elongation Factor Tu Purified from Streptomyces aureofaciens in an Aggregated State -- 10 Excessive Translational Accuracy Can Inhibit Growth -- 11 Particulate Protein-Synthesis Factors Associated with Translatable mRNA in Mammalian Cells.

Hypoxia inducible factor (HIF) up-regulates the transcription of a few hundred genes required for the adaptation to hypoxia. This restricted set of targets is in sharp contrast with the widespread distribution of the HIF binding motif throughout the genome. Here, we investigated the transcriptional response of GYS1 and RUVBL2 genes to hypoxia to understand the mechanisms that restrict HIF activity toward specific genes. GYS1 and RUVBL2 genes are encoded by opposite DNA strands and separated by a short intergenic region (∼1kb) that contains a functional hypoxia response element equidistant to both genes. However, hypoxia induced the expression of GYS1 gene only. Analysis of the transcriptional response of chimeric constructs derived from the intergenic region revealed an inhibitory sequence whose deletion allowed RUVBL2 induction by HIF. Enhancer blocking assays, performed in cell culture and transgenic zebrafish, confirmed the existence of an insulator element within this inhibitory region that could explain the differential regulation of GYS1 and RUVBL2 by hypoxia. Hence, in this model, the selective response to HIF is achieved with the aid of insulator elements. This is the first report suggesting a role for insulators in the regulation of differential gene expression in response to environmental signals ; The Ministerio de Ciencia e Innovación (Spanish Ministry of Science and Innovation, MICINN) grant numbers Nucleic Acids Research, 2012, Vol. 40, No. 5 1925 SAF2008-03147 (to L.del P.), BIO2009-1297 (to L.M.), BFU2010-14839 (to J.L.G.-S.), CSD2007-00008 (to J.L.G.-S.); Comunidad Autónoma de Madrid grant number S-SAL-0311_2006 (to L.del P.); the 7th Research Framework Programme of the European Union grant number METOXIA project ref. HEALTH-F2-2009-222741 (to L.del P.); Junta de Andalucía grant number CVI-3488 (to J.L.G.-S.); CIBERER (ISCIII) (to E.M.). Funding for open access charge: SAF2008-03147 (to L.del P.)

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License. ; Hypoxia inducible factor (HIF) up-regulates the transcription of a few hundred genes required for the adaptation to hypoxia. This restricted set of targets is in sharp contrast with the widespread distribution of the HIF binding motif throughout the genome. Here, we investigated the transcriptional response of GYS1 and RUVBL2 genes to hypoxia to understand the mechanisms that restrict HIF activity toward specific genes. GYS1 and RUVBL2 genes are encoded by opposite DNA strands and separated by a short intergenic region (~1 kb) that contains a functional hypoxia response element equidistant to both genes. However, hypoxia induced the expression of GYS1 gene only. Analysis of the transcriptional response of chimeric constructs derived from the intergenic region revealed an inhibitory sequence whose deletion allowed RUVBL2 induction by HIF. Enhancer blocking assays, performed in cell culture and transgenic zebrafish, confirmed the existence of an insulator element within this inhibitory region that could explain the differential regulation of GYS1 and RUVBL2 by hypoxia. Hence, in this model, the selective response to HIF is achieved with the aid of insulator elements. This is the first report suggesting a role for insulators in the regulation of differential gene expression in response to environmental signals. ; The Ministerio de Ciencia e Innovación (Spanish Ministry of Science and Innovation, MICINN) grant numbers SAF2008-03147 (to L.del P.), BIO2009-1297 (to L.M.), BFU2010-14839 (to J.L.G.-S.), CSD2007-00008 (to J.L.G.-S.); Comunidad Autónoma de Madrid grant number S-SAL-0311_2006 (to L.del P.); the 7th Research Framework Programme of the European Union grant number METOXIA project ref. HEALTH-F2-2009-222741 (to L.del P.); Junta de Andalucía grant number CVI-3488 (to J.L.G.-S.); CIBERER (ISCIII) (to E.M.). Funding for open access charge: SAF2008-03147 (to L.del P.). ; Peer reviewed

Bacterial physiology and adaptation are influenced by the exopolysaccharides (EPS) they produce. These polymers are indispensable for the assembly of the biofilm extracellular matrix in multiple bacterial species. In a previous study, we described the profound gene expression changes leading to biofilm assembly in B. cereus ATCC14579 (CECT148). We found that a genomic region putatively dedicated to the synthesis of a capsular polysaccharide (eps2) was overexpressed in a biofilm cell population compared to in a planktonic population, while we detected no change in the transcript abundance from another genomic region (eps1) also likely to be involved in polysaccharide production. Preliminary biofilm assays suggested a mild role for the products of the eps2 region in biofilm formation and no function for the products of the eps1 region. The aim of this work was to better define the roles of these two regions in B. cereus multicellularity. We demonstrate that the eps2 region is indeed involved in bacterial adhesion to surfaces, cell-to-cell interaction, cellular aggregation and biofilm formation, while the eps1 region appears to be involved in a kind of social bacterial motility. Consistent with these results, we further demonstrate using bacterial-host cell interaction experiments that the eps2 region is more relevant to the adhesion to human epithelial cells and the zebrafish intestine, suggesting that this region encodes a bacterial factor that may potentiate gut colonization and enhance pathogenicity against humans. ; This work was supported by grants [AGL2012-31968 and AGL2016-78662-R] from the Ministerio de Economía y Competitividad, the Spanish Government and the European Research Council Starting Grant under Grant [BacBio 637971]. ; Yes