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Accueil > Départements > Biologie des Génomes > Anciennes équipes du département > Nara FIGUEROA-BOSSI : Régulation génétique chez Salmonella et ses phages

Publications de l’équipe

2019


  • I. J. Silva, S. Barahona, A. Eyraud, D. Lalaouna, N. Figueroa-Bossi, E. Massé, et C. M. Arraiano, « SraL sRNA interaction regulates the terminator by preventing premature transcription termination of rho mRNA », Proceedings of the National Academy of Sciences of the United States of America, vol. 116, nᵒ 8, p. 3042-3051, févr. 2019.
    Résumé : Transcription termination is a critical step in the control of gene expression. One of the major termination mechanisms is mediated by Rho factor that dissociates the complex mRNA-DNA-RNA polymerase upon binding with RNA polymerase. Rho promotes termination at the end of operons, but it can also terminate transcription within leader regions, performing regulatory functions and avoiding pervasive transcription. Transcription of rho is autoregulated through a Rho-dependent attenuation in the leader region of the transcript. In this study, we have included an additional player in this pathway. By performing MS2-affinity purification coupled with RNA sequencing (MAPS), rho transcript was shown to directly interact with the small noncoding RNA SraL. Using bioinformatic in vivo and in vitro experimental analyses, SraL was shown to base pair with the 5'-UTR of rho mRNA upregulating its expression in several growth conditions. This base pairing was shown to prevent the action of Rho over its own message. Moreover, the results obtained indicate that both ProQ and Hfq are associated with this regulation. We propose a model that contemplates the action of Salmonella SraL sRNA in the protection of rho mRNA from premature transcription termination by Rho. Note that since the interaction region between both RNAs corresponds to a very-well-conserved sequence, it is plausible to admit that this regulation also occurs in other enterobacteria.
    Mots-clés : autogenous regulation, bacteria, DBG, escherichia-coli, expression, functional regulatory RNA, gene, hfq, identification, localization, posttranscriptional control, prediction, prokaryotes, RGSP, small noncoding RNA, transcription termination, translation.

2018


  • N. Figueroa-Bossi et L. Bossi, « Sponges and Predators in the Small RNA World », Microbiology Spectrum, vol. 6, nᵒ 4, juill. 2018.
    Résumé : Most noncoding small RNAs (sRNAs) that regulate gene expression do so by base-pairing with mRNAs, affecting their translation and/or stability. Regulators as evolutionarily distant as the trans-encoded sRNAs of bacteria and the microRNAs (miRNAs) of higher eukaryotes share the property of targeting short sequence segments that occur in multiple copies in bacterial and eukaryotic transcriptomes. This target promiscuity has major implications for sRNA function. On the one hand, it allows the sRNA to coordinately control several different targets and thus be at the center of regulatory networks. On the other hand, it allows the existence of target mimics or decoys that divert the sRNA/miRNA away from bona fide targets and thus serve as mechanisms to regulate the regulator. In addition, by competing for pairing with the same sRNA, bona fide targets establish a cross talk that can impact on each other's expression levels. Here we review evidence that target mimicry and competition are important components of the regulatory architecture of bacterial sRNA networks.
    Mots-clés : DBG, RGSP.

  • C. Nadiras, E. Eveno, A. Schwartz, N. Figueroa-Bossi, et M. Boudvillain, « A multivariate prediction model for Rho-dependent termination of transcription », Nucleic Acids Research, vol. 46, nᵒ 16, p. 8245-8260, sept. 2018.
    Résumé : Bacterial transcription termination proceeds via two main mechanisms triggered either by simple, well-conserved (intrinsic) nucleic acid motifs or by the motor protein Rho. Although bacterial genomes can harbor hundreds of termination signals of either type, only intrinsic terminators are reliably predicted. Computational tools to detect the more complex and diversiform Rho-dependent terminators are lacking. To tackle this issue, we devised a prediction method based on Orthogonal Projections to Latent Structures Discriminant Analysis [OPLS-DA] of a large set of in vitro termination data. Using previously uncharacterized genomic sequences for biochem(i)cal evaluation and OPLS-DA, we identified new Rho-dependent signals and quantitative sequence descriptors with significant predictive value. Most relevant descriptors specify features of transcript C>G skewness, secondary structure, and richness in regularly-spaced 5'CC/UC dinucleotides that are consistent with known principles for Rho-RNA interaction. Descriptors collectively warrant OPLS-DA predictions of Rho-dependent termination with a similar to 85% success rate. Scanning of the Escherichia coli genome with the OPLS-DA model identifies significantly more termination-competent regions than anticipated from transcriptomics and predicts that regions intrinsically refractory to Rho are primarily located in open reading frames. Altogether, this work delineates features important for Rho activity and describes the first method able to predict Rhodependent terminators in bacterial genomes.
    Mots-clés : antisense transcription, DBG, gene-regulation, mechanism, motif, motor-activity, polymerase, recognition, RGSP, rna-binding domain, structural basis, translocation.

2016


  • R. Balbontín, N. Villagra, M. Pardos de la Gándara, G. Mora, N. Figueroa-Bossi, et L. Bossi, « Expression of IroN, the salmochelin siderophore receptor, requires mRNA activation by RyhB small RNA homologues », Molecular Microbiology, vol. 100, nᵒ 1, p. 139-155, avr. 2016.
    Résumé : The iroN gene of Salmonella enterica and uropathogenic Escherichia coli encodes the outer membrane receptor of Fe(3+) -bound salmochelin, a siderophore tailored to evade capture by the host's immune system. The iroN gene is under negative control of the Fur repressor and transcribed under iron limiting conditions. We show here that transcriptional de-repression is not sufficient to allow iroN expression, as this also requires activation by either of two partially homologous small RNAs (sRNAs), RyhB1 and RyhB2. The two sRNAs target the same sequence segment approximately in the middle of the 94-nucleotide 5' untranslated region (UTR) of iroN mRNA. Several lines of evidence suggest that base pair interaction stimulates iroN mRNA translation. Activation does not result from the disruption of a secondary structure masking the ribosome binding site; rather it involves sequences at the 5' end of iroN 5' UTR. In vitro 'toeprint' assays revealed that this upstream site binds the 30S ribosomal subunit provided that RyhB1 is paired with the mRNA. Altogether, our data suggest that RyhB1, and to lesser extent RyhB2, activate iroN mRNA translation by promoting entry of the ribosome at an upstream 'standby' site. These findings add yet an additional nuance to the polychromatic landscape of sRNA-mediated regulation.
    Mots-clés : 5' Untranslated Regions, Bacterial Outer Membrane Proteins, Bacterial Proteins, Base Sequence, Binding Sites, Codon, Initiator, Conserved Sequence, DBG, Gene Expression Regulation, Bacterial, Nucleic Acid Conformation, Nucleotide Motifs, Protein Binding, Receptors, Cell Surface, RGSP, Ribosomes, RNA Stability, RNA, Bacterial, RNA, Messenger, RNA-Binding Proteins.

  • L. Bossi et N. Figueroa-Bossi, « Competing endogenous RNAs: a target-centric view of small RNA regulation in bacteria », Nature Reviews. Microbiology, vol. 14, nᵒ 12, p. 775-784, 2016.
    Résumé : Many bacterial regulatory small RNAs (sRNAs) have several mRNA targets, which places them at the centre of regulatory networks that help bacteria to adapt to environmental changes. However, different mRNA targets of any given sRNA compete with each other for binding to the sRNA; thus, depending on relative abundances and sRNA affinity, competition for regulatory sRNAs can mediate cross-regulation between bacterial mRNAs. This 'target-centric' perspective of sRNA regulation is reminiscent of the competing endogenous RNA (ceRNA) hypothesis, which posits that competition for a limited pool of microRNAs (miRNAs) in higher eukaryotes mediates cross-regulation of mRNAs. In this Opinion article, we discuss evidence that a similar network of RNA crosstalk operates in bacteria, and that this network also includes crosstalk between sRNAs and competition for RNA-binding proteins.
    Mots-clés : DBG, RGSP.

  • A. R. Gall, K. A. Datsenko, N. Figueroa-Bossi, L. Bossi, I. Masuda, Y. - M. Hou, et L. N. Csonka, « Mg2+ regulates transcription of mgtA in Salmonella Typhimurium via translation of proline codons during synthesis of the MgtL peptide », Proceedings of the National Academy of Sciences of the United States of America, vol. 113, nᵒ 52, p. 15096-15101, déc. 2016.
    Résumé : In Salmonella enterica serovar Typhimurium, Mg(2+) limitation induces transcription of the mgtA Mg(2+) transport gene, but the mechanism involved is unclear. The 5' leader of the mgtA mRNA contains a 17-codon, proline-rich ORF, mgtL, whose translation regulates the transcription of mgtA [Park S-Y et al. (2010) Cell 142:737-748]. Rapid translation of mgtL promotes formation of a secondary structure in the mgtA mRNA that permits termination of transcription by the Rho protein upstream of mgtA, whereas slow or incomplete translation of mgtL generates a different structure that blocks termination. We identified the following mutations that conferred high-level transcription of mgtA at high [Mg(2+)]: (i) a base-pair change that introduced an additional proline codon into mgtL, generating three consecutive proline codons; (ii) lesions in rpmA and rpmE, which encode ribosomal proteins L27 and L31, respectively; (iii) deletion of efp, which encodes elongation factor EF-P that assists the translation of proline codons; and (iv) a heat-sensitive mutation in trmD, whose product catalyzes the m(1)G37 methylation of tRNA(Pro) Furthermore, substitution of three of the four proline codons in mgtL rendered mgtA uninducible. We hypothesize that the proline codons present an impediment to the translation of mgtL, which can be alleviated by high [Mg(2+)] exerted on component(s) of the translation machinery, such as EF-P, TrmD, or a ribosomal factor. Inadequate [Mg(2+)] precludes this alleviation, making mgtL translation inefficient and thereby permitting mgtA transcription. These findings are a significant step toward defining the target of Mg(2+) in the regulation of mgtA transcription.
    Mots-clés : 50S ribosomal proteins, DBG, EF-P translation factor, MgtA Mg2+ transporter, MgtL leader peptide, RGSP, TrmD methyltransferase.

  • L. P. Nedialkova, M. Sidstedt, M. B. Koeppel, S. Spriewald, D. Ring, R. G. Gerlach, L. Bossi, et B. Stecher, « Temperate phages promote colicin-dependent fitness of Salmonella enterica serovar Typhimurium », Environmental Microbiology, vol. 18, nᵒ 5, p. 1591-1603, mai 2016.
    Résumé : Bacteria employ bacteriocins for interference competition in microbial ecosystems. Colicin Ib (ColIb), a pore-forming bacteriocin, confers a significant fitness benefit to Salmonella enterica serovar Typhimurium (S. Tm) in competition against commensal Escherichia coli in the gut. ColIb is released from S. Tm into the environment, where it kills susceptible competitors. However, colicin-specific release proteins, as they are known for other colicins, have not been identified in case of ColIb. Thus, its release mechanism has remained unclear. In the current study, we have established a new link between ColIb release and lysis activity of temperate, lambdoid phages. By the use of phage-cured S. Tm mutant strains, we show that the presence of temperate phages and their lysis genes is necessary and sufficient for release of active ColIb into the culture supernatant. Furthermore, phage-mediated lysis significantly enhanced S. Tm fitness in competition against a ColIb-susceptible competitor. Finally, transduction with the lambdoid phage 933W rescued the defect of E. coli strain MG1655 with respect to ColIb release. In conclusion, ColIb is released from bacteria in the course of phage lysis. Our data reveal a new mechanism for colicin release and point out a novel function of temperate phages in enhancing colicin-dependent bacterial fitness.
    Mots-clés : DBG, RGSP.

2015


  • N. Figueroa-Bossi et L. Bossi, « Recombineering applications for the mutational analysis of bacterial RNA-binding proteins and their sites of action », Methods in Molecular Biology (Clifton, N.J.), vol. 1259, p. 103-116, 2015.
    Résumé : Genetics remains a powerful tool to study structure-function relationships in proteins and RNA. Structural elements important for the biological activity of these molecules can be dissected through the isolation of mutations and analysis of their effects on the mechanism under study. In suitable model organisms, this approach can greatly benefit from the ability to introduce mutations directly in the chromosomal context in ways that do not perturb neighboring sequences. Methods for performing such "markerless" site-directed chromosomal mutagenesis in bacteria have been developed in recent years. One such technique, used routinely in our laboratory, is described here.
    Mots-clés : DBG, DNA Mutational Analysis, Mutation, RGSP, RNA, RNA-Binding Proteins.

  • T. Rochat, O. Delumeau, N. Figueroa-Bossi, P. Noirot, L. Bossi, E. Dervyn, et P. Bouloc, « Tracking the Elusive Function of Bacillus subtilis Hfq », PloS One, vol. 10, nᵒ 4, p. e0124977, 2015.
    Résumé : RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species including Escherichia coli, Salmonella enterica and Vibrio cholera. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive and somewhat controversial. In the present study, we have further addressed this point by comparing growth phenotypes and transcription profiles between wild-type and an hfq deletion mutant of the model Gram-positive bacterium, Bacillus subtilis. The absence of Hfq had no significant consequences on growth rates under nearly two thousand metabolic conditions and chemical treatments. The only phenotypic difference was a survival defect of B. subtilis hfq mutant in rich medium in stationary phase. Transcriptomic analysis correlated this phenotype with a change in the levels of nearly one hundred transcripts. Albeit a significant fraction of these RNAs (36%) encoded sporulation-related functions, analyses in a strain unable to sporulate ruled out sporulation per se as the basis of the hfq mutant's stationary phase fitness defect. When expressed in Salmonella, B. subtilis hfq complemented the sharp loss of viability of a degP hfq double mutant, attenuating the chronic σE-activated phenotype of this strain. However, B. subtilis hfq did not complement other regulatory deficiencies resulting from loss of Hfq-dependent small RNA activity in Salmonella indicating a limited functional overlap between Salmonella and B. subtilis Hfqs. Overall, this study confirmed that, despite structural similarities with other Hfq proteins, B. subtilis Hfq does not play a central role in post-transcriptional regulation but might have a more specialized function connected with stationary phase physiology. This would account for the high degree of conservation of Hfq proteins in all 17 B. subtilis strains whose genomes have been sequenced.
    Mots-clés : Bacillus subtilis, DBG, Host Factor 1 Protein, Phenotype, RGSP, SRRB, Transcriptome.
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Sélection de publications avant 2015

- Figueroa-Bossi N, Schwartz A, Guillemardet B, D’Heygère F, Bossi* L, Boudvillain* M (*co-corresponding authors) (2014) RNA remodeling by bacterial global regulator CsrA promotes Rho-dependent transcription termination. Genes Dev. 28:1239-1251
pubmed

- Plumbridge* J, Bossi L, Oberto J, Wade JT and Figueroa-Bossi* N (*co-corresponding authors). (2014) Interplay of transcriptional and small RNA-dependent control mechanisms regulates chitosugar uptake in Escherichia coli and Salmonella. Mol Microbiol 92:648-658. pubmed
Accompanying MicroCommentary : Göpel Y & Görke B (2014) Lies and deception in bacterial gene regulation : the roles of nuclei acid decoys. Mol Microbiol 92:641-647

- Yang Q, Figueroa-Bossi N, Bossi L* (2014). Translation Enhancing ACA Motifs and Their Silencing by a Bacterial Small Regulatory RNA. PLoS Genet 10(1):e1004026. doi:10.1371/journal.pgen.1004026
pubmed

- Boudvillain, M., Figueroa-Bossi, N. and Bossi, L*. (2013) Terminator still moving forward : expanding roles for Rho factor. Curr Opin Microbiol. (2013), doi.org/10.1016/j.mib.2012.12.003
pubmed

- Bossi. L., Schwartz, A., Guillemardet, B., Boudvillain, M., and Figueroa- Bossi, N.* (2012) A role for Rho-dependent polarity in gene regulation by a non-coding small RNA. Genes Dev 26 : 1864-1873.
pubmed

- Lemire, S., Figueroa-Bossi, N. and Bossi, L. (2011) "Bacteriophage Crosstalk : Coordination of Prophage Induction by Trans-Acting Antirepressors". PLoS Genet 7(6) : e1002149. doi:10.1371/journal.pgen.1002149
pubmed

- Balbontín, R., Fiorini, F., Figueroa-Bossi, N., Casadesús, J. and Bossi, L. (2010) "Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica". Mol Microbiol 78 : 380–394
pubmed

- Figueroa-Bossi, N., Valentini, M., Malleret, L., Fiorini, F. and Bossi, L. (2009) Caught at its own game : Regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes Dev 23 : 2004-2015.
pubmed

- Balbontín, R., Figueroa-Bossi, N., Casadesús., J. and Bossi, L. (2008) Insertion hotspot for horizontally acquired DNA within a bidirectional small RNA locus in Salmonella enterica. J Bacteriol 190 : 4075-4078.
pubmed

- Bossi, L. and Figueroa-Bossi, N*. (2007) MicA small RNA down-regulates LamB Maltoporin in Salmonella. Mol Microbiol 65 : 799–810.
pubmed

- Figueroa-Bossi, N., Lemire, S., Maloriol, D., Balbontin, R., Casadesus, J., and Bossi, L. (2006). Loss of Hfq activates the sigmaE-dependent envelope stress response in Salmonella enterica. Mol Microbiol 62 : 838-852.
pubmed

- Uzzau, S., Figueroa-Bossi, N., Rubino, S. and Bossi, L. (2001) Epitope Tagging of Chromosomal genes in Salmonella. Proc. Natl Acad.Sci. USA 98 : 15264-69.
pubmed

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