Team
RNARCHAEA
Team manager: Clouet-d’Orval Béatrice
Presentation
The team “RNA biology of Archaea” is identifying and characterising RNA metabolic pathways that are at the centre of gene expression regulation in Archaea, in close collaboration with local, national and international partners.
Archaea, as the third domain of living organisms, are captivating microorganisms, which are ubiquitous in all ecosystems. They have been model systems for understanding life in extreme conditions, and insightful for the evolution of both molecular genetic processes and central metabolic pathways. Our study models, Thermococcus barophilus and Pyrococcus abyssi, optimally grow in laboratory conditions at 85 and 90°C, respectively. They are deep-sea hyperthermophile Thermococcales, offering a unique opportunity to investigate RNA, DNA, and protein stability at temperatures that challenge the frontiers of life.
We develop interconnected, basic research projects to identify and characterize novel enzymes and machineries that mediate RNA quality control, RNA stability and RNA processing pathways. The team focuses in deciphering the functions of archaeal β-CASP RNases and associated RNA helicases and identifying RNA metabolic pathways at work in archaeal cells. Our long-term goal is to elucidate how the RNA quality control coordinates the fine-tuning of gene expression.
Project 1
Coherent pictures of mRNA decay and RNA quality control pathways that regulate gene expression at the post-transcriptional level are still missing in Archaea. Many questions remain open about the biological roles and structures of the RNA-degrading machines, the aRNase J /ASH-Ski2 RNA helicase complex and the RNA exosome machine, that trim RNA molecules by their 5’ or 3’ ends, respectively. How do they act, recognize their RNA targets and coordinate their actions? What are the molecular bases of the interplay between 5’-3’ and 3’-5’ RNA decay pathways? Is there a link between RNA decay pathways and the translation apparatus? We propose to tackle these critical questions by using molecular and structural biology, biochemistry, genetic, transcriptomic and proteomic approaches. In the RNARCH project (founded by ANR®) that benefit from the complementary expertise of the three partners: our team, “Oncorib” team lead by C. Plisson-Chastang (MCD, CBI, Toulouse) & “Translation mechanisms” team lead by E. Schmitt (BIOC, école Polytechnique, Palaiseau), we develop cutting-edge technological approaches and open new perspectives on the structure and function of RNA-degrading machines at work in Thermococcales. In addition, using long-read RNA-seq, we investigate transcriptomic landscapes to determine the impact of deleting RNA-degrading machines in collaboration with the team of Dina Grohmann (Institut of Microbiology & Archaea, University of Regensburg , Germany)
Project 2
RNA players in genome stability – The control of genome integrity and genome expression are linked and reciprocally impact each other in multiple ways. RNA-processing enzymes and RNA molecules are known to play critical roles in DNA repair. We identified nucleases and helicases that could linked these processes in Thermococcales: the nuclease DHHS1, the RNA helicase ASH-Ski2, and the RNA/DNA helicase aLhr2. We want to explore the roles of these RNA players in DNA replication and repair. Recent data suggested that these proteins could play a role in the regulation of structures that involve RNA strands (R-loops & G-quadruplexes). These structures are not characterized in archaea. We will map them on the genome and determine how RNA players impact their formation (MCD Xplore 2024). Finally, we will determine the interactome and the structure of the RNA processing machinery involved in these pathways to obtain a complete picture of these regulations. This project is in collaboration with Roxane Lestini (Ecole Polytechnique, Palaiseau)
Project 3
In their natural habitat, microbial populations, such as archaea, bacteria or yeast, rarely inhabit environments that support long-lasting exponential growth. Their cells enter a stationary state in response to different type of stresses (starvation, temperature, cell density or toxic byproducts), to be able to persist in adverse conditions for undefined periods of time. It requires the cells to re-program their gene expression, to switch their metabolism. Our aim is to explore the re-programming that occur in hyperthermophile archaeal cells upon entry into a stationary state, at the transcriptional and posttranscriptional levels. First, we will describe the processes that collectively prompt the cells to enter a stationary state. Then, we will investigate how RNA players influence the molecular processes that drive the cells to enter into a stationary state This project is in collaborations with Yann Moalic – ISEN, Yncréa, (Brest, France), Mohamed Jebbar & Remi Dulermo – (BEEP, Brest, France) et Anaïs Cario & Samuel Marre – (ICMCB, Bordeaux, France)
– Aktary Z., Cucchiarini A., Vesco G., Noury D., Jourdain T., Verga D., Mahou P., Olivier N., Valková N., Porubiaková O., Brázda V., Bouvier M., Kwapisz M., Clouet-d’Orval B., Allers T., Lestini R., Mergny JL., Guittat L. (2024) G-quadruplexes in Haloferax volcanii. bioRxiv 2024.01.16.575881; doi: https://doi.org/10.1101/2024.01.16.575881.
– Batista M, Langendijk-Genevaux P., Hajj M., Phung D.K., Plassart L., Canal I., Capeyrou R., Lefort G, Moisan A, Gaspin C., Kwapisz K., Flament D., Dulermo R., Laurent S., Fichant G., Bouvier M., & Clouet-d’Orval B. * (2024) Novel Insights into the functions of the Ski2-like helicase family in Archaea: Evolution, enzymatic activities and biological functions of euryarchaeal ASH-Ski2. NAR genomics & Informatics Mar 18;6(1)doi: 10.1093/nargab/lqae026.
– Hadjeras L, Bouvier M, Canal I, Poljak L, Morin-Ogier Q, Froment C, Burlet-Schlitz O, Hamouche L, Girbal L, Cocaign-Bousquet M, Carpousis A.J. Attachment of the RNA degradosome to the inner cytoplasmic membrane of Escherichia coli prevents wasteful degradation of rRNA intermediates in ribosome assembly. (2023) PLoS Biol. Jan 5;21(1):e3001942. doi: 10.1371/journal.pbio.3001942.
– Hogrel G, Marino-Puertas L, Laurent S, Ibrahim, Coves J, Girard E, Gabel F, Fenel D, Daugeron MC, Clouet-d’Orval, B, Basta T, Flament D, Franzetti B (2022) Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex Mol Microbiology DOI: 10.1111/mmi.14948
– * Hajj M., Langendijk-Genevaux P. , Batista M., Quentin Y., Laurent S. , Capeyrou R., Abdel-Razzak Z, Flament D., Chamieh H., Fichant G., Clouet-d’Orval B.* & Bouvier M (2021). Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase. Biomolecules, 11, 950. https://doi.org/10.3390/biom11070950
– Lesage E., Perez-Fernandez J., Queille S., Dez C., Gadal O. & Kwapisz M. (2021) Non-Coding, RNAPII-Dependent Transcription at the Promoters of rRNA Genes Regulates Their Chromatin State in S. cerevisiae. Non-Coding RNA, MDPI , 7 (3).
– * Phung DK, Etienne C., Batista M, Langendijk-Genevaux P., Moalic Y., Laurent S., Morales V., Jebbar M., Fichant G., Bouvier M., Flament D., & Clouet-d’Orval B.* (2020) RNA processing machineries in Archaea: the 5’-3’exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3’-5’exoribonucleolytic RNA exosome machinery. Nucleic Acids Res. Apr 17;48(7):3832-3847. doi: 10.1093/nar/gkaa052.
– Darrière T., Pilsl M., Sarthou MK., Chauvier A., Genty T., Audibert S., Dez C., Léger- Silvestre I., Normand C., Henras AK., Kwapisz M., Calvo O., Fernández-Tornero C., Tschochner H., Gadal O. (2019) Genetic analyses led to the discovery of a super-active mutant of the RNA polymerase I. PLoS Genet. May 28;15(5).
– Hadjeras L, Poljak L, Bouvier M, Morin-Ogier Q, Canal I, Cocaign-Bousquet M, Girbal L, Carpousis AJ. Detachment of the RNA degradosome from the inner membrane of Escherichia coli results in a global slowdown of mRNA degradation, proteolysis of RNase E and increased turnover of ribosome-free transcripts. (2019) Mol Microbiol. Jun;111(6):1715-1731. doi: 10.1111/mmi.14248
– Hogrel G., Lu Y., Laurent S., Henry E., Etienne C., Phung DK., Dulermo R., Bossé A., Pluchon PF., Clouet-d’Orval B., Flament D.# (2018) Physical and functional interplay between PCNA DNA clamp and Mre11–Rad50 complex from the archaeon Pyrococcus furiosus Nucleic Acids Research, vol 46 pp 5651-5663-doi: 10.1093/nar/gky322
Reviews & Book chapters & Methods
– Batista M, Clouet-d’Orval B , Bouvier M (2024) Les archées, micro-organismes du troisième domaine du vivant 2 : Chap 4 pp 81-118 Les classes d’ARN et leurs enzymes de maturation et de dégradation DOI : 10.51926/ISTE.9169.ch4
– Kwapisz M., Morillon A. (2020) Subtelomeric Transcription and its Regulation. Journal of Molecular Biology, Elsevier, 2020, 432 (15).
– Hajj M., El-Hamaoui, S. Batista M., Bouvier M., Abdel-Razzak, Z, Clouet-D’Orval, B., and Chamieh, H¶. (2019) Archaeal SF1 and SF2 helicases: Unwinding in the extreme Chap 1 pp 1-17 Helicases from all domains of life, edited by Dr. Tutejah, Acadamic Press Elsevier, ISBN: 978-0-12-814685-9,
– Clouet-d’Orval B *, Batista M., Bouvier M., Quentin Y., Fichant G., Marchfelder A. &. Maier L. (2018) Insights into RNA processing pathways and associated-RNA degrading enzymes in Archaea, FEMS Microbiology Reviews, 42(5):579-613. doi: 10.1093/femsre/fuy016
– Laguerre S, González I, Nouaille S, Moisan A, Villa-Vialaneix N, Gaspin C, Bouvier M, Carpousis AJ, Cocaign-Bousquet M, Girbal L. (2018) Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to Delay. Methods Enzymol.; 612:47-66. doi: 10.1016/bs.mie.2018.07.003.
Book Guest Editor
– Clouet-D’Orval, B – 2024 Guest Editor for ISTE Group- Encyclopédie Sciences “Les Archées, micro-organismes du troisième domaine du vivant” Vol1 Découverte, évolution et diversité des archées ISBN ebook : 9781789491685/ Vol 2 Biologie moléculaire des archées, de la maintenance des génomes à la régulation de l’expression des gènes ISBN ebook : 9781789491692
– Clouet-D’Orval, B – 2017 Guest Editor for NAMB-series Book “RNA metabolism and gene expression in Archaea” Nucleic Acids and Molecular Biology, 32( Springer International Publishing (A.W. Nicholson)- doi 10.1007/978-3-319-65795-0
Funding
Affiliation
