Sébastien Ferreira-Cerca

Verified @ur.de



                 

https://researchid.co/sebastienfc
23

Scopus Publications

1331

Scholar Citations

14

Scholar h-index

18

Scholar i10-index

Scopus Publications

  • RNase W, a conserved ribonuclease family with a novel active site
    Marlène Vayssières, Michael Jüttner, Karina Haas, Aurélie Ancelin, Anita Marchfelder, Nicolas Leulliot, Sébastien Ferreira-Cerca, and Magali Blaud
    Oxford University Press (OUP)
    Abstract Ribosome biogenesis is a complex process requiring multiple precursor ribosomal RNA (rRNA) cleavage steps. In archaea, the full set of ribonucleases (RNases) involved in rRNA processing remains to be discovered. A previous study suggested that FAU-1, a conserved protein containing an RNase G/E-like protein domain fused to a domain of unknown function (DUF402), acts as an RNase in archaea. However, the molecular basis of this activity remained so far elusive. Here, we report two X-ray crystallographic structures of RNase G/E-like–DUF402 hybrid proteins from Pyrococcus furiosus and Sulfolobus acidocaldarius, at 2.1 and 2.0 Å, respectively. The structures highlight a structural homology with the 5′ RNA recognition domain of Escherichia coli RNase E but no homology with other known catalytic nuclease domains. Surprisingly, we demonstrate that the C-terminal domain of this hybrid protein, annotated as a putative diphosphatase domain, harbors the RNase activity. Our functional analysis also supports a model by which the RNase G/E-like domain acts as a regulatory subunit of the RNase activity. Finally, in vivo experiments in Haloferax volcanii suggest that this RNase participates in the maturation of pre-16S rRNA. Together, our study defines a new RNase family, which we termed the RNase W family, as the first archaea-specific contributor to archaeal ribosome biogenesis.

  • Transcriptional and translational dynamics underlying heat shock response in the thermophilic crenarchaeon Sulfolobus acidocaldarius
    Rani Baes, Felix Grünberger, Sébastien Pyr dit Ruys, Mohea Couturier, Sarah De Keulenaer, Sonja Skevin, Filip Van Nieuwerburgh, Didier Vertommen, Dina Grohmann, Sébastien Ferreira-Cerca,et al.
    American Society for Microbiology
    ABSTRACT High-temperature stress is critical for all organisms and induces a profound cellular response. For Crenarchaeota, little information is available on how heat shock affects cellular processes and on how this response is regulated. We set out to study heat shock response in the thermoacidophilic model crenarchaeon Sulfolobus acidocaldarius, which thrives in volcanic hot springs and has an optimal growth temperature of 75°C. Pulse-labeling experiments demonstrated that a temperature shift to 86°C induces a drastic reduction of the transcriptional and translational activity, but that RNA and protein neosynthesis still occurs. By combining RNA sequencing and mass spectrometry, an integrated mapping of the transcriptome and proteome was performed. This revealed that heat shock causes an immediate change in the gene expression profile, with RNA levels of half of the genes being affected, followed by a more subtle reprogramming of the protein landscape. Functional enrichment analysis indicated that nearly all cellular processes are affected by heat shock. A limited correlation was observed in the differential expression on the RNA and protein level, suggesting a prevalence of post-transcriptional and post-translational regulation. Furthermore, promoter sequence analysis of heat shock regulon genes demonstrated the conservation of strong transcription initiation elements for highly induced genes, but an absence of a conserved protein-binding motif. It is, therefore, hypothesized that histone-lacking archaea such as Sulfolobales use an evolutionarily ancient regulatory mechanism that relies on temperature-responsive changes in DNA organization and compaction induced by the action of nucleoid-associated proteins, as well as on enhanced recruitment of initiation factors. IMPORTANCE Heat shock response is the ability to respond adequately to sudden temperature increases that could be harmful for cellular survival and fitness. It is crucial for microorganisms living in volcanic hot springs that are characterized by high temperatures and large temperature fluctuations. In this study, we investigated how S. acidocaldarius , which grows optimally at 75°C, responds to heat shock by altering its gene expression and protein production processes. We shed light on which cellular processes are affected by heat shock and propose a hypothesis on underlying regulatory mechanisms. This work is not only relevant for the organism’s lifestyle, but also with regard to its evolutionary status. Indeed, S. acidocaldarius belongs to the archaea, an ancient group of microbes that is more closely related to eukaryotes than to bacteria. Our study thus also contributes to a better understanding of the early evolution of heat shock response.

  • Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea
    Felix Grünberger, Michael Jüttner, Robert Knüppel, Sébastien Ferreira-Cerca, and Dina Grohmann
    Cold Spring Harbor Laboratory
    Ribosomal RNA (rRNA) maturation in archaea is a complex multistep process that requires well-defined endo- and exoribonuclease activities to generate fully mature linear rRNAs. However, technical challenges prevented detailed mapping of rRNA processing steps and a systematic analysis of rRNA maturation pathways across the tree of life. In this study, we used long-read (PCR)-cDNA and direct RNA nanopore-based sequencing to study rRNA maturation in three archaeal model organisms, namely the EuryarchaeaHaloferax volcaniiandPyrococcus furiosusand the CrenarchaeonSulfolobus acidocaldarius. Compared to standard short-read protocols, nanopore sequencing facilitates simultaneous readout of 5′- and 3′-positions, which is required for the classification of rRNA processing intermediates. More specifically, we (i) accurately detect and describe rRNA maturation stages by analysis of terminal read positions of cDNA reads and thereupon (ii) explore the stage-dependent installation of the KsgA-mediated dimethylations inH. volcaniiusing base-calling and signal characteristics of direct RNA reads. Due to the single-molecule sequencing capacity of nanopore sequencing, we could detect hitherto unknown intermediates with high confidence, revealing details about the maturation of archaea-specific circular rRNA intermediates. Taken together, our study delineates common principles and unique features of rRNA processing in euryarchaeal and crenarchaeal representatives, thereby significantly expanding our understanding of rRNA maturation pathways in archaea.

  • Ribosomenbiogenese in Archaeen
    Michael Jüttner and Sébastien Ferreira-Cerca
    Springer Science and Business Media LLC
    AbstractThe ribosome is a universally conserved macromolecular machine responsible for the translation of mRNAs into proteins. The synthesis of ribosomes is a crucial task that has been well characterized in bacteria and eukarya, but not in archaea. Here we summarize our current understanding of ribosome biogenesis in archaea and how it might help to further answer evolutionary questions.

  • Nanopore sequencing of RNA and cDNA molecules in Escherichia coli
    Felix Grünberger, Sébastien Ferreira-Cerca, and Dina Grohmann
    Cold Spring Harbor Laboratory
    High-throughput sequencing dramatically changed our view of transcriptome architectures and allowed for ground-breaking discoveries in RNA biology. Recently, sequencing of full-length transcripts based on the single-molecule sequencing platform from Oxford Nanopore Technologies (ONT) was introduced and is widely used to sequence eukaryotic and viral RNAs. However, experimental approaches implementing this technique for prokaryotic transcriptomes remain scarce. Here, we present an experimental and bioinformatic workflow for ONT RNA-seq in the bacterial model organism Escherichia coli, which can be applied to any microorganism. Our study highlights critical steps of library preparation and computational analysis and compares the results to gold standards in the field. Furthermore, we comprehensively evaluate the applicability and advantages of different ONT-based RNA sequencing protocols, including direct RNA, direct cDNA, and PCR-cDNA. We find that (PCR)-cDNA-seq offers improved yield and accuracy compared to direct RNA sequencing. Notably, (PCR)-cDNA-seq is suitable for quantitative measurements and can be readily used for simultaneous and accurate detection of transcript 5′ and 3′ boundaries, analysis of transcriptional units, and transcriptional heterogeneity. In summary, based on our comprehensive study, we show nanopore RNA-seq to be a ready-to-use tool allowing rapid, cost-effective, and accurate annotation of multiple transcriptomic features. Thereby nanopore RNA-seq holds the potential to become a valuable alternative method for RNA analysis in prokaryotes.

  • Preface


  • The dark side of the ribosome life cycle
    Sébastien Ferreira-Cerca
    Informa UK Limited
    ABSTRACT Thanks to genetics, biochemistry, and structural biology many features of the ribosome´s life cycles in models of bacteria, eukaryotes, and some organelles have been revealed to near-atomic details. Collectively, these studies have provided a very detailed understanding of what are now well-established prototypes for ribosome biogenesis and function as viewed from a ‘classical’ model organisms perspective. However, very important challenges remain ahead to explore the functional and structural diversity of both ribosome biogenesis and function across the biological diversity on earth. Particularly, the ‘third domain of life’, the archaea, and also many non-model bacterial and eukaryotic organisms have been comparatively neglected. Importantly, characterizing these additional biological systems will not only offer a yet untapped window to enlighten the evolution of ribosome biogenesis and function but will also help to unravel fundamental principles of molecular adaptation of these central cellular processes.

  • Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea
    Michael Kern and Sébastien Ferreira-Cerca
    Springer US
    AbstractThe study of protein production and degradation in a quantitative and time-dependent manner is a major challenge to better understand cellular physiological response. Among available technologies bioorthogonal noncanonical amino acid tagging (BONCAT) is an efficient approach allowing for time-dependent labeling of proteins through the incorporation of chemically reactive noncanonical amino acids like l-azidohomoalanine (L-AHA). The azide-containing amino-acid derivative enables a highly efficient and specific reaction termed click chemistry, whereby the azide group of the L-AHA reacts with a reactive alkyne derivate, like dibenzocyclooctyne (DBCO) derivatives, using strain-promoted alkyne–azide cycloaddition (SPAAC). Moreover, available DBCO containing reagents are versatile and can be coupled to fluorophore (e.g., Cy7) or affinity tag (e.g., biotin) derivatives, for easy visualization and affinity purification, respectively.Here, we describe a step-by-step BONCAT protocol optimized for the model archaeon Haloferax volcanii, but which is also suitable to harness other biological systems. Finally, we also describe examples of downstream visualization, affinity purification of L-AHA-labeled proteins and differential expression analysis.In conclusion, the following BONCAT protocol expands the available toolkit to explore proteostasis using time-resolved semiquantitative proteomic analysis in archaea.


  • Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil
    Christina Braun, Robert Knüppel, Jorge Perez-Fernandez, and Sébastien Ferreira-Cerca
    Springer US
    AbstractRNA molecules and their expression dynamics play essential roles in the establishment of complex cellular phenotypes and/or in the rapid cellular adaption to environmental changes. Accordingly, analyzing RNA expression remains an important step to understand the molecular basis controlling the formation of cellular phenotypes, cellular homeostasis or disease progression. Steady-state RNA levels in the cells are controlled by the sum of highly dynamic molecular processes contributing to RNA expression and can be classified in transcription, maturation and degradation. The main goal of analyzing RNA dynamics is to disentangle the individual contribution of these molecular processes to the life cycle of a given RNA under different physiological conditions. In the recent years, the use of nonradioactive nucleotide/nucleoside analogs and improved chemistry, in combination with time-dependent and high-throughput analysis, have greatly expanded our understanding of RNA metabolism across various cell types, organisms, and growth conditions.In this chapter, we describe a step-by-step protocol allowing pulse labeling of RNA with the nonradioactive nucleotide analog, 4-thiouracil, in the eukaryotic model organism Saccharomyces cerevisiae and the model archaeon Haloferax volcanii.

  • Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis
    Michael Jüttner and Sébastien Ferreira-Cerca
    Oxford University Press (OUP)
    Abstract Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fueled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, such as the origin of the eukaryotic lineage from the recently discovered archaeal Asgard superphylum, is debated. The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses. Using selected examples, such as the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.

  • Editorial: Archaeal Ribosomes: Biogenesis, Structure and Function
    Sébastien Ferreira-Cerca, Anna La Teana, and Paola Londei
    Frontiers Media SA
    1 Biochemistry III-Regensburg Center for Biochemistry, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany, Department of Life and Environmental Science, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy, Department Molecular Medicine, Policlinico Umberto I◦Viale Regina, University of Rome Sapienza, Rome, Italy

  • Ribosome Biogenesis in Archaea
    Paola Londei and Sébastien Ferreira-Cerca
    Frontiers Media SA
    Making ribosomes is a major cellular process essential for the maintenance of functional ribosome homeostasis and to ensure appropriate gene expression. Strikingly, although ribosomes are universally conserved ribonucleoprotein complexes decoding the genetic information contained in messenger RNAs into proteins, their biogenesis shows an intriguing degree of variability across the tree of life. In this review, we summarize our knowledge on the least understood ribosome biogenesis pathway: the archaeal one. Furthermore, we highlight some evolutionary conserved and divergent molecular features of making ribosomes across the tree of life.

  • Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea
    Robert Knüppel, Christian Trahan, Michael Kern, Alexander Wagner, Felix Grünberger, Winfried Hausner, Tessa E F Quax, Sonja-Verena Albers, Marlene Oeffinger, and Sébastien Ferreira-Cerca
    Oxford University Press (OUP)
    Abstract Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.

  • The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
    Stefan Schulze, Zachary Adams, Micaela Cerletti, Rosana De Castro, Sébastien Ferreira-Cerca, Christian Fufezan, María Inés Giménez, Michael Hippler, Zivojin Jevtic, Robert Knüppel,et al.
    Springer Science and Business Media LLC
    AbstractWhile many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii, we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.

  • Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea
    Thandi S. Schwarz, Sarah J. Berkemer, Stephan H. Bernhart, Matthias Weiß, Sébastien Ferreira-Cerca, Peter F. Stadler, and Anita Marchfelder
    Frontiers Media SA
    In all three domains of life, tRNA genes contain introns that must be removed to yield functional tRNA. In archaea and eukarya, the first step of this process is catalyzed by a splicing endonuclease. The consensus structure recognized by the splicing endonuclease is a bulge-helix-bulge (BHB) motif which is also found in rRNA precursors. So far, a systematic analysis to identify all biological substrates of the splicing endonuclease has not been carried out. In this study, we employed CRISPRi to repress expression of the splicing endonuclease in the archaeonHaloferax volcaniito identify all substrates of this enzyme. Expression of the splicing endonuclease was reduced to 1% of its normal level, resulting in a significant extension of lag phase inH. volcaniigrowth. In the repression strain, 41 genes were down-regulated and 102 were up-regulated. As an additional approach in identifying new substrates of the splicing endonuclease, we isolated and sequenced circular RNAs, which identified excised introns removed from tRNA and rRNA precursors as well as from the 5′ UTR of the gene HVO_1309.In vitroprocessing assays showed that the BHB sites in the 5′ UTR of HVO_1309 and in a 16S rRNA-like precursor are processed by the recombinant splicing endonuclease. The splicing endonuclease is therefore an important player in RNA maturation in archaea.

  • A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea
    Michael Jüttner, Matthias Weiß, Nina Ostheimer, Corinna Reglin, Michael Kern, Robert Knüppel, and Sébastien Ferreira-Cerca
    Oxford University Press (OUP)
    Abstract General molecular principles of ribosome biogenesis have been well explored in bacteria and eukaryotes. Collectively, these studies have revealed important functional differences and few similarities between these processes. Phylogenetic studies suggest that the information processing machineries from archaea and eukaryotes are evolutionary more closely related than their bacterial counterparts. These observations raise the question of how ribosome synthesis in archaea may proceed in vivo. In this study, we describe a versatile plasmid-based cis-acting reporter system allowing to analyze in vivo the consequences of ribosomal RNA mutations in the model archaeon Haloferax volcanii. Applying this system, we provide evidence that the bulge-helix-bulge motif enclosed within the ribosomal RNA processing stems is required for the formation of archaeal-specific circular-pre-rRNA intermediates and mature rRNAs. In addition, we have collected evidences suggesting functional coordination of the early steps of ribosome synthesis in H. volcanii. Together our investigation describes a versatile platform allowing to generate and functionally analyze the fate of diverse rRNA variants, thereby paving the way to better understand the cis-acting molecular determinants necessary for archaeal ribosome synthesis, maturation, stability and function.

  • In vivo RNA chemical footprinting analysis in archaea
    Robert Knüppel, Martin Fenk, Michael Jüttner, and Sébastien Ferreira-Cerca
    Springer US
    RNA structural conformation and dynamics govern the functional properties of all RNA/RNP. Accordingly, defining changes of RNA structure and dynamics in various conditions may provide detailed insight into how RNA structural properties regulate the function of RNA/RNP. Traditional chemical footprinting analysis using chemical modifiers allows to sample the dynamics and conformation landscape of diverse RNA/RNP. However, many chemical modifiers are limited in their capacity to provide unbiased information reflecting the in vivo RNA/RNP structural landscape. In the recent years, the development of selective-2'-hydroxyl acylation analyzed by primer extension (SHAPE) methodology that uses powerful new chemical modifiers has significantly improved in vitro and in vivo structural probing of secondary and tertiary interactions of diverse RNA species at the single nucleotide level.Although the original discovery of Archaea as an independent domain of life is intimately linked to the technological development of RNA analysis, our understanding of in vivo RNA structural conformation and dynamics in this domain of life remains scarce.This protocol describes the in vivo use of SHAPE chemistry in two evolutionary divergent model Archaea, Sulfolobus acidocaldarius and Haloferax volcanii.

  • Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism
    Valentin Mitterer, Ramtin Shayan, Sébastien Ferreira-Cerca, Guillaume Murat, Tanja Enne, Dana Rinaldi, Sarah Weigl, Hajrija Omanic, Pierre-Emmanuel Gleizes, Dieter Kressler,et al.
    Springer Science and Business Media LLC
    Eukaryotic ribosomes are synthesized in a hierarchical process driven by a plethora of assembly factors, but how maturation events at physically distant sites on pre-ribosomes are coordinated is poorly understood. Using functional analyses and cryo-EM, we show that ribosomal protein Rps20 orchestrates communication between two multi-step maturation events across the pre-40S subunit. Our study reveals that during pre-40S maturation, formation of essential contacts between Rps20 and Rps3 permits assembly factor Ltv1 to recruit the Hrr25 kinase, thereby promoting Ltv1 phosphorylation. In parallel, a deeply buried Rps20 loop reaches to the opposite pre-40S side, where it stimulates Rio2 ATPase activity. Both cascades converge to the final maturation steps releasing Rio2 and phosphorylated Ltv1. We propose that conformational proofreading exerted via Rps20 constitutes a checkpoint permitting assembly factor release and progression of pre-40S maturation only after completion of all earlier maturation steps.The biogenesis of eukaryotic ribosomes is a multi-step process involving the action of more than 200 different ribosome assembly factors. Here the authors show that Rps20 acts as a conduit to coordinate maturation steps across the head domain of the nascent small ribosomal subunit.

  • The Rio1 protein kinases/ATPases: conserved regulators of growth, division, and genomic stability
    Giovanna Berto, Sébastien Ferreira-Cerca, and Peter De Wulf
    Springer Science and Business Media LLC
    The atypical Rio1 protein kinases/ATPases, which exist in most archaea and eukaryotes, have been studied intensely to understand how they promote small ribosomal subunit (SSU) maturation. However, mutant and knockdown phenotypes in various organisms suggested roles in activities beyond SSU biogenesis, including the regulation of cell cycle progression (DNA transcription, replication, condensation, and segregation), cell division, metabolism, physiology, and development. Recent work with budding yeast, indeed, revealed that Rio1 (RIOK1 in metazoans) manages a large signaling network at the protein and gene levels via which it stimulates or restricts growth and division in response to nutrient availability. We examine how these findings translate to human cells and suggest that RIOK1 over-expression or mutations, as observed in primary cancer cells, may cause a mis-regulation of its network, contributing to cancer initiation and progression. We also reflect on how targeting RIOK1 might eradicate hitherto incurable tumors in the clinic.

  • Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors
    Jan Linnemann, Gisela Pöll, Steffen Jakob, Sébastien Ferreira-Cerca, Joachim Griesenbeck, Herbert Tschochner, and Philipp Milkereit
    Public Library of Science (PLoS)
    Many of the small ribosomal subunit proteins are required for the stabilisation of late small ribosomal subunit (SSU) precursors and for final SSU rRNA processing in S. cerevisiae. Among them are ribosomal proteins (r-proteins) which form a protein cluster around rpS0 (uS2) at the "neck" of the SSU (S0-cluster) and others forming a nearby protein cluster around rpS3 (uS3) at the SSU "beak". Here we applied semi-quantitative proteomics together with complementary biochemical approaches to study how incomplete assembly of these two r-protein clusters affects binding and release of SSU maturation factors and assembly of other r-proteins in late SSU precursors in S. cerevisiae. For each of the two clusters specific impairment of the local r-protein assembly state was observed in Rio2 associated SSU precursors. Besides, cluster-specific effects on the association of biogenesis factors were detected. These suggested a role of S0-cluster formation for the efficient release of the two nuclear export factors Rrp12 and Slx9 from SSU precursors and for the correct incorporation of the late acting biogenesis factor Rio2. Based on our and on previous results we propose the existence of at least two different r-protein assembly checkpoints during late SSU maturation in S. cerevisiae. We discuss in the light of recent SSU precursor structure models how r-protein assembly states might be sensed by biogenesis factors at the S0-cluster checkpoint.

  • Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae
    Maria G Iacovella, Michael Bremang, Omer Basha, Luciano Giacò, Walter Carotenuto, Cristina Golfieri, Barnabas Szakal, Marianna Dal Maschio, Valentina Infantino, Galina V Beznoussenko,et al.
    Oxford University Press (OUP)
    Abstract The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subunit biogenesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the protein, chromatin and RNA levels. Rio1 orchestrates growth and division depending on resource availability, in parallel to the nutrient-activated Tor1 kinase. To define the Rio1 network, we identified its physical interactors, profiled its target genes/transcripts, mapped its chromatin-binding sites and integrated our data with yeast’s protein–protein and protein–DNA interaction catalogs using network computation. We experimentally confirmed network components and localized Rio1 also to mitochondria and vacuoles. Via its network, Rio1 commands protein synthesis (ribosomal gene expression, assembly and activity) and turnover (26S proteasome expression), and impinges on metabolic, energy-production and cell-cycle programs. We find that Rio1 activity is conserved to humans and propose that pathological RIOK1 may fuel promiscuous transcription, ribosome production, chromosomal instability, unrestrained metabolism and proliferation; established contributors to cancer. Our study will advance the understanding of numerous processes, here revealed to depend on Rio1 activity.

  • Insights into the evolutionary conserved regulation of Rio ATPase activity
    Robert Knüppel, Regitse H Christensen, Fiona C Gray, Dominik Esser, Daniela Strauß, Jan Medenbach, Bettina Siebers, Stuart A MacNeill, Nicole LaRonde, and Sébastien Ferreira-Cerca
    Oxford University Press (OUP)
    Abstract Eukaryotic ribosome biogenesis is a complex dynamic process which requires the action of numerous ribosome assembly factors. Among them, the eukaryotic Rio protein family members (Rio1, Rio2 and Rio3) belong to an ancient conserved atypical protein kinase/ ATPase family required for the maturation of the small ribosomal subunit (SSU). Recent structure–function analyses suggested an ATPase-dependent role of the Rio proteins to regulate their dynamic association with the nascent pre-SSU. However, the evolutionary origin of this feature and the detailed molecular mechanism that allows controlled activation of the catalytic activity remained to be determined. In this work we provide functional evidence showing a conserved role of the archaeal Rio proteins for the synthesis of the SSU in archaea. Moreover, we unravel a conserved RNA-dependent regulation of the Rio ATPases, which in the case of Rio2 involves, at least, helix 30 of the SSU rRNA and the P-loop lysine within the shared RIO domain. Together, our study suggests a ribosomal RNA-mediated regulatory mechanism enabling the appropriate stimulation of Rio2 catalytic activity and subsequent release of Rio2 from the nascent pre-40S particle. Based on our findings we propose a unified release mechanism for the Rio proteins.

  • Toward time-resolved analysis of RNA metabolism in archaea using 4-thiouracil
    Robert Knüppel, Corinna Kuttenberger, and Sébastien Ferreira-Cerca
    Frontiers Media SA
    Archaea are widespread organisms colonizing almost every habitat on Earth. However, the molecular biology of archaea still remains relatively uncharacterized. RNA metabolism is a central cellular process, which has been extensively analyzed in both bacteria and eukarya. In contrast, analysis of RNA metabolism dynamic in archaea has been limited to date. To facilitate analysis of the RNA metabolism dynamic at a system-wide scale in archaea, we have established non-radioactive pulse labeling of RNA, using the nucleotide analog 4-thiouracil (4TU) in two commonly used model archaea: the halophile Euryarchaeota Haloferax volcanii, and the thermo-acidophile Crenarchaeota Sulfolobus acidocaldarius. In this work, we show that 4TU pulse labeling can be efficiently performed in these two organisms in a dose- and time-dependent manner. In addition, our results suggest that uracil prototrophy had no critical impact on the overall 4TU incorporation in RNA molecules. Accordingly, our work suggests that 4TU incorporation can be widely performed in archaea, thereby expanding the molecular toolkit to analyze archaeal gene expression network dynamic in unprecedented detail.

  • Rio1 promotes rDNA stability and downregulates RNA polymerase I to ensure rDNA segregation
    Maria G. Iacovella, Cristina Golfieri, Lucia F. Massari, Sara Busnelli, Cinzia Pagliuca, Marianna Dal Maschio, Valentina Infantino, Rosella Visintin, Karl Mechtler, Sébastien Ferreira-Cerca,et al.
    Springer Science and Business Media LLC
    The conserved protein kinase Rio1 localizes to the cytoplasm and nucleus of eukaryotic cells. While the roles of Rio1 in the cytoplasm are well characterized, its nuclear function remains unknown. Here we show that nuclear Rio1 promotes rDNA array stability and segregation in Saccharomyces cerevisiae. During rDNA replication in S phase, Rio1 downregulates RNA polymerase I (PolI) and recruits the histone deacetylase Sir2. Both interventions ensure rDNA copy-number homeostasis and prevent the formation of extrachromosomal rDNA circles, which are linked to accelerated ageing in yeast. During anaphase, Rio1 downregulates PolI by targeting its subunit Rpa43, causing PolI to dissociate from the rDNA. By stimulating the processing of PolI-generated transcripts at the rDNA, Rio1 allows for rDNA condensation and segregation in late anaphase. These events finalize the genome transmission process. We identify Rio1 as an essential nucleolar housekeeper that integrates rDNA replication and segregation with ribosome biogenesis.

RECENT SCHOLAR PUBLICATIONS

  • RNase W, a conserved ribonuclease family with a novel active site
    M Vayssires, M Jttner, K Haas, A Ancelin, A Marchfelder, N Leulliot, ...
    Nucleic Acids Research 52 (21), 13386-13401 2024

  • Biogense des ribosomes et des ARN de transfert
    T Basta, S Ferreira-Cerca
    Les arches, micro-organismes du troisime domaine du vivant 2, 119-175 2024

  • Transcriptional and translational dynamics underlying heat shock response in the thermophilic crenarchaeon Sulfolobus acidocaldarius
    R Baes, F Grnberger, S Pyr dit Ruys, M Couturier, S De Keulenaer, ...
    MBio 14 (5), e03593-22 2023

  • Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea
    F Grnberger, M Jttner, R Knppel, S Ferreira-Cerca, D Grohmann
    RNA 29 (8), 1255-1273 2023

  • The dark side of the ribosome life cycle
    S Ferreira-Cerca
    RNA biology 19 (1), 1045-1049 2022

  • Ribosomenbiogenese in Archaeen
    M Jttner, S Ferreira-Cerca
    BIOspektrum 28 (5), 478-480 2022

  • Post-transcriptional regulation of the heat shock response in the thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius
    R Baes, F Grnberger, SP dit Ruys, M Couturier, S De Keulenaer, ...
    EMBO: Molecular Biology of Archaea 2022 2022

  • A comparative perspective on ribosome biogenesis: unity and diversity across the tree of life
    M Jttner, S Ferreira-Cerca
    Ribosome Biogenesis: Methods and Protocols, 3-22 2022

  • Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil
    C Braun, R Knppel, J Perez-Fernandez, S Ferreira-Cerca
    Ribosome Biogenesis: Methods and Protocols, 199-213 2022

  • Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea
    M Kern, S Ferreira-Cerca
    Ribosome Biogenesis: Methods and Protocols, 229-246 2022

  • Looking through the lens of the ribosome biogenesis evolutionary history: possible implications for archaeal phylogeny and eukaryogenesis
    M Jttner, S Ferreira-Cerca
    Molecular Biology and Evolution 39 (4), msac054 2022

  • A General Microbiology
    R Baes, SP dit Ruys, S De Keulenaer, S Skevin, F Van, DV Nieuwerburgh, ...
    Annual symposium 2022 Future Challenges in Microbiology, 49 2022

  • Nanopore sequencing of RNA and cDNA molecules in Escherichia coli
    F Grnberger, S Ferreira-Cerca, D Grohmann
    Rna 28 (3), 400-417 2022

  • Archaea
    S Ferreira-Cerca
    Springer US 2022

  • A system-level perspective on heat shock response in Sulfolobus acidocaldarius
    R Baes, F Grnberger, SP dit Ruys, M Couturier, S De Keulenaer, ...
    Extremophiles 2022: 13th International Congress on Extremophiles 2022

  • Archaeal Ribosomes: Biogenesis, Structure and Function
    S Ferreira-Cerca, A La Teana, P Londei
    Frontiers in Microbiology 12, 800052 2021

  • Ribosome biogenesis in archaea
    P Londei, S Ferreira-Cerca
    Frontiers in Microbiology 12, 686977 2021

  • Insights into rRNA processing and modification mapping in Archaea using Nanopore-based RNA sequencing
    F Grnberger, M Jttner, R Knppel, S Ferreira-Cerca, D Grohmann
    bioRxiv, 2021.06. 14.448286 2021

  • Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea
    R Knppel, C Trahan, M Kern, A Wagner, F Grnberger, W Hausner, ...
    Nucleic Acids Research 49 (3), 1662-1687 2021

  • Nanopore sequencing of RNA and cDNA molecules expands the transcriptomic toolbox in prokaryotes
    F Grnberger, S Ferreira-Cerca, D Grohmann
    bioRxiv 2021

MOST CITED SCHOLAR PUBLICATIONS

  • Roles of eukaryotic ribosomal proteins in maturation and transport of pre-18S rRNA and ribosome function
    S Ferreira-Cerca, G Pll, PE Gleizes, H Tschochner, P Milkereit
    Molecular cell 20 (2), 263-275 2005
    Citations: 381

  • Eukaryotic ribosome biogenesis at a glance
    E Thomson, S Ferreira-Cerca, E Hurt
    Journal of cell science 126 (21), 4815-4821 2013
    Citations: 366

  • Analysis of the in vivo assembly pathway of eukaryotic 40S ribosomal proteins
    S Ferreira-Cerca, G Pll, H Khn, A Neueder, S Jakob, H Tschochner, ...
    Molecular cell 28 (3), 446-457 2007
    Citations: 198

  • ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit
    S Ferreira-Cerca, V Sagar, T Schfer, M Diop, AM Wesseling, H Lu, ...
    Nature structural & molecular biology 19 (12), 1316-1323 2012
    Citations: 137

  • The ribosomal protein Rps15p is required for nuclear exit of the 40S subunit precursors in yeast
    I Lger‐Silvestre, P Milkereit, S Ferreira‐Cerca, C Saveanu, JC Rousselle, ...
    The EMBO journal 23 (12), 2336-2347 2004
    Citations: 133

  • Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes
    S Ferreira-Cerca, I Kiburu, E Thomson, N LaRonde, E Hurt
    Nucleic acids research 42 (13), 8635-8647 2014
    Citations: 90

  • Nanopore sequencing of RNA and cDNA molecules in Escherichia coli
    F Grnberger, S Ferreira-Cerca, D Grohmann
    Rna 28 (3), 400-417 2022
    Citations: 73

  • Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism
    V Mitterer, R Shayan, S Ferreira-Cerca, G Murat, T Enne, D Rinaldi, ...
    Nature communications 10 (1), 2754 2019
    Citations: 43

  • The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
    S Schulze, Z Adams, M Cerletti, R De Castro, S Ferreira-Cerca, C Fufezan, ...
    Nature Communications 11 (1), 3145 2020
    Citations: 41

  • Insights into the evolutionary conserved regulation of Rio ATPase activity
    R Knppel, RH Christensen, FC Gray, D Esser, D Strau, J Medenbach, ...
    Nucleic Acids Research 46 (3), 1441-1456 2018
    Citations: 38

  • Ribosome biogenesis in archaea
    P Londei, S Ferreira-Cerca
    Frontiers in Microbiology 12, 686977 2021
    Citations: 37

  • Rio1 promotes rDNA stability and downregulates RNA polymerase I to ensure rDNA segregation
    MG Iacovella, C Golfieri, LF Massari, S Busnelli, C Pagliuca, ...
    Nature communications 6 (1), 6643 2015
    Citations: 32

  • Arrest by ribosome
    S Ferreira-Cerca, E Hurt
    Nature 459 (7243), 46-47 2009
    Citations: 27

  • Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing
    F Grnberger, R Knppel, M Jttner, M Fenk, A Borst, R Reichelt, ...
    BioRxiv 10 (2019.12), 18.880849 2020
    Citations: 26

  • A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea
    M Jttner, M Wei, N Ostheimer, C Reglin, M Kern, R Knppel, ...
    Nucleic Acids Research 48 (4), 2073-2090 2020
    Citations: 25

  • Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea
    R Knppel, C Trahan, M Kern, A Wagner, F Grnberger, W Hausner, ...
    Nucleic Acids Research 49 (3), 1662-1687 2021
    Citations: 23

  • Toward time-resolved analysis of RNA metabolism in archaea using 4-thiouracil
    R Knppel, C Kuttenberger, S Ferreira-Cerca
    Frontiers in microbiology 8, 286 2017
    Citations: 21

  • Life and death of ribosomes in archaea
    S Ferreira-Cerca
    RNA metabolism and gene expression in archaea, 129-158 2017
    Citations: 21

  • A General Microbiology
    R Baes, SP dit Ruys, S De Keulenaer, S Skevin, F Van, DV Nieuwerburgh, ...
    Annual symposium 2022 Future Challenges in Microbiology, 49 2022
    Citations: 20

  • The Rio1 protein kinases/ATPases: conserved regulators of growth, division, and genomic stability
    G Berto, S Ferreira-Cerca, P De Wulf
    Current Genetics 65 (2), 457-466 2019
    Citations: 20