I2CT

@article{pmid36846801,

title = { CspA stimulates translation in the cold of its own mRNA by promoting ribosome progression},

author = {Anna Maria Giuliodori and Riccardo Belardinelli and Melodie Duval and Raffaella Garofalo and Emma Schenckbecher and Vasili Hauryliuk and Eric Ennifar and Stefano Marzi},

doi = {10.3389/fmicb.2023.1118329},

issn = {1664-302X},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Front Microbiol},

volume = {14},

pages = {1118329},

abstract = { CspA is an RNA binding protein that accumulates during cold-shock and stimulates translation of several mRNAs-including its own. Translation in the cold of  mRNA involves a cis-acting thermosensor element, which enhances ribosome binding, and the trans-acting action of CspA. Using reconstituted translation systems and probing experiments we show that, at low temperature, CspA specifically promotes the translation of the  mRNA folded in the conformation less accessible to the ribosome, which is formed at 37°C but is retained upon cold shock. CspA interacts with its mRNA without inducing large structural rearrangements, but allowing the progression of the ribosomes during the transition from translation initiation to translation elongation. A similar structure-dependent mechanism may be responsible for the CspA-dependent translation stimulation observed with other probed mRNAs, for which the transition to the elongation phase is progressively facilitated during cold acclimation with the accumulation of CspA.},

keywords = {ENNIFAR, ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36846801b,

title = { CspA stimulates translation in the cold of its own mRNA by promoting ribosome progression},

author = {Anna Maria Giuliodori and Riccardo Belardinelli and Melodie Duval and Raffaella Garofalo and Emma Schenckbecher and Vasili Hauryliuk and Eric Ennifar and Stefano Marzi},

doi = {10.3389/fmicb.2023.1118329},

issn = {1664-302X},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Front Microbiol},

volume = {14},

pages = {1118329},

abstract = { CspA is an RNA binding protein that accumulates during cold-shock and stimulates translation of several mRNAs-including its own. Translation in the cold of  mRNA involves a cis-acting thermosensor element, which enhances ribosome binding, and the trans-acting action of CspA. Using reconstituted translation systems and probing experiments we show that, at low temperature, CspA specifically promotes the translation of the  mRNA folded in the conformation less accessible to the ribosome, which is formed at 37°C but is retained upon cold shock. CspA interacts with its mRNA without inducing large structural rearrangements, but allowing the progression of the ribosomes during the transition from translation initiation to translation elongation. A similar structure-dependent mechanism may be responsible for the CspA-dependent translation stimulation observed with other probed mRNAs, for which the transition to the elongation phase is progressively facilitated during cold acclimation with the accumulation of CspA.},

keywords = {ENNIFAR, ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36353712,

title = { 30S Ribosomal Subunit Purification and Its Biochemical and Cryo-EM Analysis},

author = {Margarita Belinite and Iskander Khusainov and Stefano Marzi},

doi = {10.21769/BioProtoc.4532},

issn = {2331-8325},

year  = {2022},

date = {2022-10-01},

urldate = {2022-10-01},

journal = {Bio Protoc},

volume = {12},

number = {20},

abstract = {The ribosome is a complex cellular machinery whose solved structure allowed for an incredible leap in structural biology research. Different ions bind to the ribosome, stabilizing inter-subunit interfaces and structurally linking rRNAs, proteins, and ligands. Besides cations such as K  and Mg  , polyamines are known to stabilize the folding of RNA and overall structure. The bacterial ribosome is composed of a small (30S) subunit containing the decoding center and a large (50S) subunit devoted to peptide bond formation. We have previously shown that the small ribosomal subunit of  is sensitive to changes in ionic conditions and polyamines concentration. In particular, its decoding center, where mRNA codons and tRNA anticodons interact, is prone to structural deformations in the absence of spermidine. Here, we report a detailed protocol for the purification of the intact and functional 30S, achieved through specific ionic conditions and the addition of spermidine. Using this protocol, we obtained the cryo-electron microscopy (cryo-EM) structure of the 30S-mRNA complex from  at 3.6 Å resolution. The 30S-mRNA complex formation was verified by a toeprinting assay. In this article, we also include a description of toeprinting and cryo-EM protocols. The described protocols can be further used to study the process of translation regulation. Graphical abstract.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36353712b,

title = { 30S Ribosomal Subunit Purification and Its Biochemical and Cryo-EM Analysis},

author = {Margarita Belinite and Iskander Khusainov and Stefano Marzi},

doi = {10.21769/BioProtoc.4532},

issn = {2331-8325},

year  = {2022},

date = {2022-10-01},

urldate = {2022-10-01},

journal = {Bio Protoc},

volume = {12},

number = {20},

abstract = {The ribosome is a complex cellular machinery whose solved structure allowed for an incredible leap in structural biology research. Different ions bind to the ribosome, stabilizing inter-subunit interfaces and structurally linking rRNAs, proteins, and ligands. Besides cations such as K  and Mg  , polyamines are known to stabilize the folding of RNA and overall structure. The bacterial ribosome is composed of a small (30S) subunit containing the decoding center and a large (50S) subunit devoted to peptide bond formation. We have previously shown that the small ribosomal subunit of  is sensitive to changes in ionic conditions and polyamines concentration. In particular, its decoding center, where mRNA codons and tRNA anticodons interact, is prone to structural deformations in the absence of spermidine. Here, we report a detailed protocol for the purification of the intact and functional 30S, achieved through specific ionic conditions and the addition of spermidine. Using this protocol, we obtained the cryo-electron microscopy (cryo-EM) structure of the 30S-mRNA complex from  at 3.6 Å resolution. The 30S-mRNA complex formation was verified by a toeprinting assay. In this article, we also include a description of toeprinting and cryo-EM protocols. The described protocols can be further used to study the process of translation regulation. Graphical abstract.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36108089,

title = {A tRNA-derived fragment present in E. coli OMVs regulates host cell gene expression and proliferation},

author = {Idrissa Diallo and Jeffrey Ho and Marine Lambert and Abderrahim Benmoussa and Zeinab Husseini and David Lalaouna and Eric Massé and Patrick Provost},

doi = {10.1371/journal.ppat.1010827},

issn = {1553-7374},

year  = {2022},

date = {2022-09-01},

urldate = {2022-09-01},

journal = {PLoS Pathog},

volume = {18},

number = {9},

pages = {e1010827},

abstract = {RNA-sequencing has led to a spectacular increase in the repertoire of bacterial sRNAs and improved our understanding of their biological functions. Bacterial sRNAs have also been found in outer membrane vesicles (OMVs), raising questions about their potential involvement in bacteria-host relationship, but few studies have documented this issue. Recent RNA-Sequencing analyses of bacterial RNA unveiled the existence of abundant very small RNAs (vsRNAs) shorter than 16 nt. These especially include tRNA fragments (tRFs) that are selectively loaded in OMVs and are predicted to target host mRNAs. Here, in Escherichia coli (E. coli), we report the existence of an abundant vsRNA, Ile-tRF-5X, which is selectively modulated by environmental stress, while remaining unaffected by inhibition of transcription or translation. Ile-tRF-5X is released through OMVs and can be transferred to human HCT116 cells, where it promoted MAP3K4 expression. Our findings provide a novel perspective and paradigm on the existing symbiosis between bacteria and human cells.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35732654,

title = {RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression},

author = {Stuart W McKellar and Ivayla Ivanova and Pedro Arede and Rachel L Zapf and Noémie Mercier and Liang-Cui Chu and Daniel G Mediati and Amy C Pickering and Paul Briaud and Robert G Foster and Grzegorz Kudla and J Ross Fitzgerald and Isabelle Caldelari and Ronan K Carroll and Jai J Tree and Sander Granneman},

doi = {10.1038/s41467-022-31173-y},

issn = {2041-1723},

year  = {2022},

date = {2022-06-01},

urldate = {2022-06-01},

journal = {Nat Commun},

volume = {13},

number = {1},

pages = {3560},

abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen responsible for significant human morbidity and mortality. Post-transcriptional regulation by small RNAs (sRNAs) has emerged as an important mechanism for controlling virulence. However, the functionality of the majority of sRNAs during infection is unknown. To address this, we performed UV cross-linking, ligation, and sequencing of hybrids (CLASH) in MRSA to identify sRNA-RNA interactions under conditions that mimic the host environment. Using a double-stranded endoribonuclease III as bait, we uncovered hundreds of novel sRNA-RNA pairs. Strikingly, our results suggest that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. Additionally, we also uncover an sRNA sponging interaction between RsaE and RsaI. Taken together, we present a comprehensive analysis of sRNA-target interactions in MRSA and provide details on how these contribute to the control of virulence in response to changes in metabolism.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {The 3'UTR-derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose-6-phosphate uptake in Staphylococcus aureus},

author = {E. Desgranges and L. Barrientos and L. Herrgott and S. Marzi and A. Toledo-Arana and K. Moreau and F. Vandenesch and P. Romby and I. Caldelari},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34783400},

doi = {10.1111/mmi.14845},

isbn = {34783400},

year  = {2022},

date = {2022-01-01},

urldate = {2021-01-01},

journal = {Mol Microbiol},

abstract = {Staphylococcus aureus RsaG is a 3' untranslated region (3'UTR) derived sRNA from the conserved uhpT gene encoding a glucose-6-phosphate (G6P) transporter expressed in response to extracellular G6P. The transcript uhpT-RsaG undergoes degradation from 5' to 3' end by the action of the exoribonucleases J1/J2, which are blocked by a stable hairpin structure at the 5' end of RsaG, leading to its accumulation. RsaG together with uhpT are induced when bacteria are internalized into host cells or in presence of mucus-secreting cells. Using MS2 affinity purification coupled with RNA sequencing, several RNAs were identified as targets including mRNAs encoding the transcriptional factors Rex, CcpA, SarA and the sRNA RsaI. Our data suggested that RsaG contributes to the control of redox homeostasis and adjusts metabolism to changing environmental conditions. RsaG uses different molecular mechanisms to stabilize, to degrade, or to repress translation of its mRNA targets. While RsaG is conserved only in closely related species, the uhpT 3'UTR of the ape pathogen S. simiae harbors a sRNA, whose sequence is highly different, and which does not respond to G6P levels. Our results hypothesized that the 3'UTRs from UhpT transporter encoding mRNAs could have rapidly evolved to enable adaptation to host niches.},

note = {1365-2958 (Electronic) 

0950-382X (Linking) 

Journal Article},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues},

author = {A. Laveilhe and S. Fochesato and D. Lalaouna and T. Heulin and W. Achouak},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35502577},

doi = {10.1111/1751-7915.14023},

isbn = {35502577},

year  = {2022},

date = {2022-01-01},

journal = {Microb Biotechnol},

abstract = {Pseudomonads play crucial roles in plant growth promotion and control of plant diseases. However, under natural conditions, other microorganisms competing for the same nutrient resources in the rhizosphere may exert negative control over their phytobeneficial characteristics. We assessed the expression of phytobeneficial genes involved in biocontrol, biostimulation and iron regulation such as, phlD, hcnA, acdS, and iron-small regulatory RNAs prrF1 and prrF2 in Pseudomonas brassicacearum co-cultivated with three phytopathogenic fungi, and two rhizobacteria in the presence or absence of Brassica napus, and in relation to iron availability. We found that the antifungal activity of P. brassicacearum depends mostly on the production of DAPG and not on HCN whose production is suppressed by fungi. We have also shown that the two-competing bacterial strains modulate the plant growth promotion activity of P. brassicacearum by modifying the expression of phlD, hcnA and acdS according to iron availability. Overall, it allows us to better understand the complexity of the multiple molecular dialogues that take place underground between microorganisms and between plants and its rhizosphere microbiota and to show that synergy in favour of phytobeneficial gene expression may exist between different bacterial species.},

note = {1751-7915 (Electronic) 

1751-7915 (Linking) 

Journal Article},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35865816,

title = {Battle for Metals: Regulatory RNAs at the Front Line},

author = {Mathilde Charbonnier and Gabriela González-Espinoza and Thomas E Kehl-Fie and David Lalaouna},

doi = {10.3389/fcimb.2022.952948},

issn = {2235-2988},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Front Cell Infect Microbiol},

volume = {12},

pages = {952948},

abstract = {Metal such as iron, zinc, manganese, and nickel are essential elements for bacteria. These nutrients are required in crucial structural and catalytic roles in biological processes, including precursor biosynthesis, DNA replication, transcription, respiration, and oxidative stress responses. While essential, in excess these nutrients can also be toxic. The immune system leverages both of these facets, to limit bacterial proliferation and combat invaders. Metal binding immune proteins reduce the bioavailability of metals at the infection sites starving intruders, while immune cells intoxicate pathogens by providing metals in excess leading to enzyme mismetallation and/or reactive oxygen species generation. In this dynamic metal environment, maintaining metal homeostasis is a critical process that must be precisely coordinated. To achieve this, bacteria utilize diverse metal uptake and efflux systems controlled by metalloregulatory proteins. Recently, small regulatory RNAs (sRNAs) have been revealed to be critical post-transcriptional regulators, working in conjunction with transcription factors to promote rapid adaptation and to fine-tune bacterial adaptation to metal abundance. In this mini review, we discuss the expanding role for sRNAs in iron homeostasis, but also in orchestrating adaptation to the availability of other metals like manganese and nickel. Furthermore, we describe the sRNA-mediated interdependency between metal homeostasis and oxidative stress responses, and how regulatory networks controlled by sRNAs contribute to survival and virulence.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments},

author = {D Lalaouna and S Fochesato and M Harir and P Ortet and P Schmitt-Kopplin and T Heulin and W Achouak},

url = {https://www.mdpi.com/2076-2607/9/2/250},

doi = {10.3390/microorganisms9020250},

year  = {2021},

date = {2021-01-01},

journal = {Microorganisms},

volume = {9},

number = {2},

pages = {250},

abstract = {In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.},

keywords = {GacA-dependent, nutritional stress, Pseudomonas brassicacearum, ROMBY, Rsm sRNAs, sRNAs stability, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{Mercier2021,

title = {MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria},

author = {N Mercier and K Prévost and E Massé and P Romby and I Caldelari and D Lalaouna},

url = {https://www.jove.com/t/61731/ms2-affinity-purification-coupled-with-rna-sequencing-gram-positive},

doi = {10.3791/61731},

year  = {2021},

date = {2021-01-01},

journal = {J Vis Exp},

pages = {e61731},

abstract = {Although small regulatory RNAs (sRNAs) are widespread among the bacterial domain of life, the functions of many of them remain poorly characterized notably due to the difficulty of identifying their mRNA targets. Here, we described a modified protocol of the MS2-Affinity Purification coupled with RNA Sequencing (MAPS) technology, aiming to reveal all RNA partners of a specific sRNA in vivo. Broadly, the MS2 aptamer is fused to the 5’ extremity of the sRNA of interest. This construct is then expressed in vivo, allowing the MS2-sRNA to interact with its cellular partners. After bacterial harvesting, cells are mechanically lysed. The crude extract is loaded into an amylose-based chromatography column previously coated with the MS2 protein fused to the maltose binding protein. This enables the specific capture of MS2-sRNA and interacting RNAs. After elution, co-purified RNAs are identified by high-throughput RNA sequencing and subsequent bioinformatic analysis. The following protocol has been implemented in the Gram-positive human pathogen Staphylococcus aureus and is, in principle, transposable to any Gram-positive bacteria. To sum up, MAPS technology constitutes an efficient method to deeply explore the regulatory network of a particular sRNA, offering a snapshot of its whole targetome. However, it is important to keep in mind that putative targets identified by MAPS still need to be validated by complementary experimental approaches.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{Catalan-Moreno2021,

title = {RNA thermoswitches modulate Staphylococcus aureus adaptation to ambient temperatures},

author = {A Catalan-Moreno and M Cela and P Menendez-Gil and N Irurzun and C J Caballero and I Caldelari and A Toledo-Arana},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33660769},

doi = {0.1093/nar/gkab117},

isbn = {33660769},

year  = {2021},

date = {2021-01-01},

journal = {Nucleic Acids Res},

pages = {on press},

abstract = {Thermoregulation of virulence genes in bacterial pathogens is essential for environment-to-host transition. However, the mechanisms governing cold adaptation when outside the host remain poorly understood. Here, we found that the production of cold shock proteins CspB and CspC from Staphylococcus aureus is controlled by two paralogous RNA thermoswitches. Through in silico prediction, enzymatic probing and site-directed mutagenesis, we demonstrated that cspB and cspC 5'UTRs adopt alternative RNA structures that shift from one another upon temperature shifts. The open (O) conformation that facilitates mRNA translation is favoured at ambient temperatures (22 degrees C). Conversely, the alternative locked (L) conformation, where the ribosome binding site (RBS) is sequestered in a double-stranded RNA structure, is folded at host-related temperatures (37 degrees C). These structural rearrangements depend on a long RNA hairpin found in the O conformation that sequesters the anti-RBS sequence. Notably, the remaining S. aureus CSP, CspA, may interact with a UUUGUUU motif located in the loop of this long hairpin and favour the folding of the L conformation. This folding represses CspB and CspC production at 37 degrees C. Simultaneous deletion of the cspB/cspC genes or their RNA thermoswitches significantly decreases S. aureus growth rate at ambient temperatures, highlighting the importance of CspB/CspC thermoregulation when S. aureus transitions from the host to the environment.},

note = {1362-4962 (Electronic) 

0305-1048 (Linking) 

Journal Article},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Evolutionary history expands the range of signaling interactions in hybrid multikinase networks},

author = {P Ortet and S Fochesato and A F Bitbol and D E Whitworth and D Lalaouna and C Santaella and T Heulin and W Achouak and M Barakat},

url = {https://pubmed.ncbi.nlm.nih.gov/34083699/},

doi = {10.1038/s41598-021-91260-w},

isbn = {34083699},

year  = {2021},

date = {2021-01-01},

journal = {Sci Rep},

volume = {11},

number = {1},

pages = {11763},

abstract = {Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein communicating via intramolecular phosphotransfer. Here, we report how evolutionary relationships between hybrid HKs can be used as predictors of potential intermolecular and intramolecular interactions ('phylogenetic promiscuity'). We used domain-swap genes chimeras to investigate the specificity of phosphotransfer within hybrid HKs of the GacS-GacA multikinase network of Pseudomonas brassicacearum. The receiver domain of GacS was replaced with those from nine donor hybrid HKs. Three chimeras with receivers from other hybrid HKs demonstrated correct functioning through complementation of a gacS mutant, which was dependent on strains having a functional gacA. Formation of functional chimeras was predictable on the basis of evolutionary heritage, and raises the possibility that HKs sharing a common ancestor with GacS might remain components of the contemporary GacS network. The results also demonstrate that understanding the evolutionary heritage of signaling domains in sophisticated networks allows their rational rewiring by simple domain transplantation, with implications for the creation of designer networks and inference of functional interactions.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Editorial: Interview With the Translational Apparatus: Stories of Intriguing Circuits and Mechanisms to Regulate Translation in Bacteria},

author = {A M Giuliodori and S Marzi},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34220790},

doi = {10.3389/fmicb.2021.707354},

isbn = {34220790},

year  = {2021},

date = {2021-01-01},

journal = {Front Microbiol},

volume = {12},

pages = {707354},

note = {1664-302X (Print) 

1664-302X (Linking) 

Editorial},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Assembling the Current Pieces: The Puzzle of RNA-Mediated Regulation in Staphylococcus aureus},

author = {L Barrientos and N Mercier and D Lalaouna and I Caldelari},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34367109},

doi = {10.3389/fmicb.2021.706690},

isbn = {34367109},

year  = {2021},

date = {2021-01-01},

journal = {Front Microbiol},

volume = {12},

pages = {706690},

abstract = {The success of the major opportunistic human Staphylococcus aureus relies on the production of numerous virulence factors, which allow rapid colonization and dissemination in any tissues. Indeed, regulation of its virulence is multifactorial, and based on the production of transcriptional factors, two-component systems (TCS) and small regulatory RNAs (sRNAs). Advances in high-throughput sequencing technologies have unveiled the existence of hundreds of potential RNAs with regulatory functions, but only a fraction of which have been validated in vivo. These discoveries have modified our thinking and understanding of bacterial physiology and virulence fitness by placing sRNAs, alongside transcriptional regulators, at the center of complex and intertwined regulatory networks that allow S. aureus to rapidly adapt to the environmental cues present at infection sites. In this review, we describe the recently acquired knowledge of characterized regulatory RNAs in S. aureus that are associated with metal starvation, nutrient availability, stress responses and virulence. These findings highlight the importance of sRNAs for the comprehension of S. aureus infection processes while raising questions about the interplay between these key regulators and the pathways they control.},

note = {1664-302X (Print) 

1664-302X (Linking) 

Journal Article 

Review},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Burning the Candle at Both Ends: Have Exoribonucleases Driven Divergence of Regulatory RNA Mechanisms in Bacteria?},

author = {D G Mediati and D Lalaouna and J J Tree},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34372700},

doi = {10.1128/mBio.01041-21},

isbn = {34372700},

year  = {2021},

date = {2021-01-01},

journal = {mBio},

pages = {e0104121},

abstract = {Regulatory RNAs have emerged as ubiquitous gene regulators in all bacterial species studied to date. The combination of sequence-specific RNA interactions and malleable RNA structure has allowed regulatory RNA to adopt different mechanisms of gene regulation in a diversity of genetic backgrounds. In the model Gammaproteobacteria Escherichia coli and Salmonella, the regulatory RNA chaperone Hfq appears to play a global role in gene regulation, directly controlling approximately 20 to 25% of the entire transcriptome. While the model Firmicutes Bacillus subtilis and Staphylococcus aureus encode a Hfq homologue, its role has been significantly depreciated. These bacteria also have marked differences in RNA turnover. E. coli and Salmonella degrade RNA through internal endonucleolytic and 3'-->5' exonucleolytic cleavage that appears to allow transient accumulation of mRNA 3' UTR cleavage fragments that contain stabilizing 3' structures. In contrast, B. subtilis and S. aureus are able to exonucleolytically attack internally cleaved RNA from both the 5' and 3' ends, efficiently degrading mRNA 3' UTR fragments. Here, we propose that the lack of 5'-->3' exoribonuclease activity in Gammaproteobacteria has allowed the accumulation of mRNA 3' UTR ends as the "default" setting. This in turn may have provided a larger pool of unconstrained RNA sequences that has fueled the expansion of Hfq function and small RNA (sRNA) regulation in E. coli and Salmonella. Conversely, the exoribonuclease RNase J may be a significant barrier to the evolution of 3' UTR sRNAs in B. subtilis and S. aureus that has limited the pool of RNA ligands available to Hfq and other sRNA chaperones, depreciating their function in these model Firmicutes.},

note = {2150-7511 (Electronic) 

Journal Article},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence},

author = {L Antoine and R Bahena-Ceron and H Devi Bunwaree and M Gobry and V Loegler and P Romby and S Marzi},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34440299},

doi = {10.3390/genes12081125},

isbn = {34440299},

year  = {2021},

date = {2021-01-01},

journal = {Genes (Basel)},

volume = {12},

number = {8},

abstract = {RNA modifications are involved in numerous biological processes and are present in all RNA classes. These modifications can be constitutive or modulated in response to adaptive processes. RNA modifications play multiple functions since they can impact RNA base-pairings, recognition by proteins, decoding, as well as RNA structure and stability. However, their roles in stress, environmental adaptation and during infections caused by pathogenic bacteria have just started to be appreciated. With the development of modern technologies in mass spectrometry and deep sequencing, recent examples of modifications regulating host-pathogen interactions have been demonstrated. They show how RNA modifications can regulate immune responses, antibiotic resistance, expression of virulence genes, and bacterial persistence. Here, we illustrate some of these findings, and highlight the strategies used to characterize RNA modifications, and their potential for new therapeutic applications.},

note = {2073-4425 (Electronic) 

2073-4425 (Linking) 

Journal Article 

Review},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli},

author = {D. Lalaouna and K. Prévost and S. Park and T. Chénard and M - P. Bouchard and M - P. Caron and C. K. Vanderpool and J. Fei and E. Massé},

url = {https://www.mdpi.com/2311-553X/7/4/64},

doi = {10.3390/ncrna7040064},

year  = {2021},

date = {2021-01-01},

journal = {Non-Coding RNA},

volume = {7},

number = {4},

pages = {64},

abstract = {Many RNA-RNA interactions depend on molecular chaperones to form and remain stable in living cells. A prime example is the RNA chaperone Hfq, which is a critical effector involved in regulatory interactions between small RNAs (sRNAs) and cognate target mRNAs in Enterobacteriaceae. While there is a great deal of in vitro biochemical evidence supporting the model that Hfq enhances rates or affinities of sRNA:mRNA interactions, there is little corroborating in vivo evidence. Here we used in vivo tools including reporter genes, co-purification assays, and super-resolution microscopy to analyze the role of Hfq in RyhB-mediated regulation, and we found that Hfq is often unnecessary for efficient RyhB:mRNA complex formation in vivo. Remarkably, our data suggest that a primary function of Hfq is to promote RyhB-induced cleavage of mRNA targets by RNase E. Moreover, our work indicates that Hfq plays a more limited role in dictating regulatory outcomes following sRNAs RybB and DsrA complex formation with specific target mRNAs. Our investigation helps evaluate the roles played by Hfq in some RNA-mediated regulation.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in Staphylococcus aureus},

author = {M. Belinite and I. Khusainov and H. Soufari and S. Marzi and P. Romby and M. Yusupov and Y. Hashem},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34869582},

doi = {10.3389/fmolb.2021.738752},

isbn = {34869582},

year  = {2021},

date = {2021-01-01},

journal = {Front Mol Biosci},

volume = {8},

pages = {738752},

abstract = {Cryo-electron microscopy is now used as a method of choice in structural biology for studying protein synthesis, a process mediated by the ribosome machinery. In order to achieve high-resolution structures using this approach, one needs to obtain homogeneous and stable samples, which requires optimization of ribosome purification in a species-dependent manner. This is especially critical for the bacterial small ribosomal subunit that tends to be unstable in the absence of ligands. Here, we report a protocol for purification of stable 30 S from the Gram-positive bacterium Staphylococcus aureus and its cryo-EM structures: in presence of spermidine at a resolution ranging between 3.4 and 3.6 A and in its absence at 5.3 A. Using biochemical characterization and cryo-EM, we demonstrate the importance of spermidine for stabilization of the 30 S via preserving favorable conformation of the helix 44.},

note = {2296-889X (Print) 

2296-889X (Linking) 

Journal Article},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{Lalouna2020,

title = {Manganese: the battle of the two armies},

author = {D Lalaouna and P Romby},

url = {https://univoak.eu/islandora/object/islandora:105630},

year  = {2020},

date = {2020-07-01},

journal = {Project Repository Journal},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Differential evolution in 3'UTRs leads to specific gene expression in Staphylococcus},

author = {P Menendez-Gil and C J Caballero and A Catalan-Moreno and N Irurzun and I Barrio-Hernandez and I Caldelari and A Toledo-Arana},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32016395},

doi = {10.1093/nar/gkaa047},

isbn = {32016395},

year  = {2020},

date = {2020-01-01},

journal = {Nucleic Acids Res},

volume = {48},

number = {5},

pages = {2544-2563},

abstract = {The evolution of gene expression regulation has contributed to species differentiation. The 3' untranslated regions (3'UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3'UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3'UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3'UTR of orthologous genes and demonstrated that 3'UTR sequence variations affect protein production. This suggested that species-specific functional 3'UTRs might be specifically selected during evolution. 3'UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3'UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3'UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3'UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs},

author = {J Georg and D Lalaouna and S Hou and S C Lott and I Caldelari and S Marzi and W R Hess and P Romby},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31705780},

doi = {10.1111/mmi.14420},

isbn = {31705780},

year  = {2020},

date = {2020-01-01},

journal = {Mol Microbiol},

volume = {113},

number = {3},

pages = {603-612},

abstract = {Trans-acting small regulatory RNAs (sRNAs) are key players in the regulation of gene expression in bacteria. There are hundreds of different sRNAs in a typical bacterium, which in contrast to eukaryotic miRNAs are more heterogeneous in length, sequence composition, and secondary structure. The vast majority of sRNAs function post-transcriptionally by binding to other RNAs (mRNAs, sRNAs) through rather short regions of imperfect sequence complementarity. Besides, every single sRNA may interact with dozens of different target RNAs and impact gene expression either negatively or positively. These facts contributed to the view that the entirety of the regulatory targets of a given sRNA, its targetome, is challenging to identify. However, recent developments show that a more comprehensive sRNA's targetome can be achieved through the combination of experimental and computational approaches. Here, we give a short introduction into these methods followed by a description of two sRNAs, RyhB and RsaA, to illustrate the particular strengths and weaknesses of these approaches in more detail. RyhB is an sRNA involved in iron homeostasis in Enterobacteriaceae, while RsaA is a modulator of virulence in Staphylococcus aureus. Using such a combined strategy, a better appreciation of the sRNA-dependent regulatory networks is now attainable.},

keywords = {ROMBY, Staphylococcus aureus CopraRNA MAPS post-transcriptional regulation sRNAs, Unité ARN},

pubstate = {published},

tppubtype = {article}

}