Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in
            <i>Bacillus subtilis</i>

Nicolas, Pierre; Mäder, Ulrike; Dervyn, Etienne; Rochat, Tatiana; Leduc, Aurélie; Pigeonneau, Nathalie; Bidnenko, Elena; Marchadier, Elodie; Hoebeke, Mark; Aymerich, Stéphane; Becher, Dörte; Bisicchia, Paola; Botella, Eric; Delumeau, Olivier; Doherty, Geoff; Denham, Emma L.; Fogg, Mark J.; Fromion, Vincent; Goelzer, Anne; Hansen, Annette G.; Härtig, Elisabeth; Harwood, Colin R.; Homuth, Georg; Jarmer, Hanne Østergaard; Jules, Matthieu; Klipp, Edda; Chat, Ludovic Le; Lecointe, François; Lewis, Peter J.; Liebermeister, Wolfram; March, Anika; Mars, Ruben A. T.; Nannapaneni, Priyanka; Noone, David; Pohl, Susanne; Rinn, Bernd; Rügheimer, Frank; Sappa, Praveen Kumar; Samson, Franck; Schaffer, Marc; Schwikowski, Benno; Steil, Leif; Stülke, Jörg; Wiegert, Thomas; Devine, Kevin M.; Wilkinson, Anthony J.; Dijl, Jan Maarten van; Hecker, Michael; Völker, Uwe; Bessières, Philippe; Naveilhan, Philippe

doi:10.1126/science.1206848

Cited by 834 publications

(1,486 citation statements)

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“…The link with cell wall metabolism is further reinforced by the correlation of expression of asnB with cell wall metabolism genes in approximately 200 different growth conditions (Nicolas et al ., 2012). All but two of the first twenty genes which are most correlated with asnB are involved in cell wall metabolism, which is not the case for asnH or asnO (http://genome.jouy.inra.fr/cgi-bin/seb/index.py).…”

Section: Resultsmentioning

confidence: 99%

Hydrolysis of peptidoglycan is modulated by amidation of meso‐diaminopimelic acid and Mg²⁺ in Bacillus subtilis

Dajkovic

Tesson

Chauhan

et al. 2017

Molecular Microbiology

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SummaryThe ability of excess Mg2+ to compensate the absence of cell wall related genes in Bacillus subtilis has been known for a long time, but the mechanism has remained obscure. Here, we show that the rigidity of wild‐type cells remains unaffected with excess Mg2+, but the proportion of amidated meso‐diaminopimelic (mDAP) acid in their peptidoglycan (PG) is significantly reduced. We identify the amidotransferase AsnB as responsible for mDAP amidation and show that the gene encoding it is essential without added Mg2+. Growth without excess Mg2+ causes ΔasnB mutant cells to deform and ultimately lyse. In cell regions with deformations, PG insertion is orderly and indistinguishable from the wild‐type. However, PG degradation is unevenly distributed along the sidewalls. Furthermore, ΔasnB mutant cells exhibit increased sensitivity to antibiotics targeting the cell wall. These results suggest that absence of amidated mDAP causes a lethal deregulation of PG hydrolysis that can be inhibited by increased levels of Mg2+. Consistently, we find that Mg2+ inhibits autolysis of wild‐type cells. We suggest that Mg2+ helps to maintain the balance between PG synthesis and hydrolysis in cell wall mutants where this balance is perturbed in favor of increased degradation.

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Section: Resultsmentioning

confidence: 99%

Hydrolysis of peptidoglycan is modulated by amidation of meso‐diaminopimelic acid and Mg²⁺ in Bacillus subtilis

Dajkovic

Tesson

Chauhan

et al. 2017

Molecular Microbiology

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“…Even spurious transcription elicited by rho inactivation is not necessarily catastrophic, as observed for B. subtilis (Nicolas et al, 2012), although condition-dependent or long-term effects may not be readily detected. For instance, genome instability may arise from uncontrolled encounters between transcription and replication machineries, since Rho inactivation should favour their codirectional collisions and the resultant formation of DNA double-strand breaks (Dutta et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

Phyletic distribution and conservation of the bacterial transcription termination factor Rho

2013

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Transcription termination factor Rho is a ring-shaped, ATP-dependent molecular motor that targets hundreds of transcription units in Escherichia coli. Interest in Rho was renewed recently on the realization that this essential factor is involved in multiple interactions and cellular processes that protect the E. coli genome and regulate its expression on a global scale. Yet it is currently unknown if (and how) Rho-dependent mechanisms are conserved throughout the bacterial kingdom. Here, we mined public databases to assess the distribution, expression and structural conservation of Rho across bacterial phyla. We found that rho is present in more than 90 % of sequenced bacterial genomes, although Cyanobacteria, Mollicutes and a fraction of Firmicutes are totally devoid of rho. Genomes lacking rho tend to be small and AT-rich and often belong to species with parasitic/symbiotic lifestyles (such as Mollicutes). By contrast, large GCrich genomes, such as those of Actinobacteria, often contain rho duplicates and/or encode Rho proteins that bear insertion domains of unknown function(s). Notwithstanding, most Rho sequences across taxa contain canonical RNA-binding and ATP hydrolysis signature motifs, a feature suggestive of largely conserved mechanism(s) of action. Mutations that impair binding of bicyclomycin are present in~5 % of rho sequences, implying that species from diverse ecosystems have developed resistance against this natural antibiotic. Altogether, these findings assert that Rho function is widespread among bacteria and suggest that it plays a particularly relevant role in the expression of complex genomes and/or bacterial adaptation to changing environments.

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“…FliW is the first known protein antagonist of CsrA, which we here show binds to CsrA at an allosteric site and noncompetitively inhibits RNA binding. We speculate that the noncompetitive mechanism of FliW antagonism may be necessary because it would be difficult for sRNA, or perhaps other mRNA targets should they exist, to regulate CsrA by competing with the highly abundant hag transcript (39,(42)(43)(44).…”

Section: Discussionmentioning

confidence: 99%

FliW antagonizes CsrA RNA binding by a noncompetitive allosteric mechanism

Mukherjee

Oshiro

Yakhnin

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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CsrA (carbon storage regulator A) is a widely distributed bacterial RNA binding protein that regulates translation initiation and mRNA stability of target transcripts. In γ-proteobacteria, CsrA activity is competitively antagonized by one or more small RNAs (sRNAs) containing multiple CsrA binding sites, but CsrA in bacteria outside the γ-proteobacteria is antagonized by a protein called FliW. Here we show that FliW of Bacillus subtilis does not bind to the same residues of CsrA required for RNA binding. Instead, CsrA mutants resistant to FliW antagonism (crw) altered residues of CsrA on an allosteric surface of previously unattributed function. Some crw mutants abolished CsrA–FliW binding, but others did not, suggesting that FliW and RNA interaction is not mutually exclusive. We conclude that FliW inhibits CsrA by a noncompetitive mechanism that differs dramatically from the well-established sRNA inhibitors. FliW is highly conserved with CsrA in bacteria, appears to be the ancestral form of CsrA regulation, and represents a widespread noncompetitive mechanism of CsrA control.

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Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

Cited by 834 publications

References 99 publications

Hydrolysis of peptidoglycan is modulated by amidation of meso‐diaminopimelic acid and Mg²⁺ in Bacillus subtilis

Hydrolysis of peptidoglycan is modulated by amidation of meso‐diaminopimelic acid and Mg²⁺ in Bacillus subtilis

Phyletic distribution and conservation of the bacterial transcription termination factor Rho

FliW antagonizes CsrA RNA binding by a noncompetitive allosteric mechanism

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Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

Cited by 834 publications

References 99 publications

Hydrolysis of peptidoglycan is modulated by amidation of meso‐diaminopimelic acid and Mg2+ in Bacillus subtilis

Hydrolysis of peptidoglycan is modulated by amidation of meso‐diaminopimelic acid and Mg2+ in Bacillus subtilis

Phyletic distribution and conservation of the bacterial transcription termination factor Rho

FliW antagonizes CsrA RNA binding by a noncompetitive allosteric mechanism

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Hydrolysis of peptidoglycan is modulated by amidation of meso‐diaminopimelic acid and Mg²⁺ in Bacillus subtilis

Hydrolysis of peptidoglycan is modulated by amidation of meso‐diaminopimelic acid and Mg²⁺ in Bacillus subtilis