Sébastien Ferreira-Cerca

@ur.de

University of Regensburg

Sébastien Ferreira-Cerca


                  Download Compact PDF  
https://researchid.co/sebastienfc
35

Scopus Publications

2189

Scholar Citations

23

Scholar h-index

28

Scholar i10-index

Scopus Publications

  • Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome
    Miguel A. Garcia-Campos, Joe Georgeson, Ronit Nir, Robert Reichelt, Kristin A. Fluke, et al.
    Cell, 2025
  • Circular RNAs in Archaea
    Hubert F. Becker, Sébastien Ferreira-Cerca
    Advances in Experimental Medicine and Biology, 2025
  • Ribosome and Transfer RNA Biogenesis
    Tamara BASTA, Sébastien FERREIRA‐CERCA
    Biology of Archaea 2 Molecular Biology of Archaea from Genome Maintenance to the Regulation of Gene Expression, 2025
  • RNase W, a conserved ribonuclease family with a novel active site
    Marlène Vayssières, Michael Jüttner, Karina Haas, Aurélie Ancelin, Anita Marchfelder, et al.
    Nucleic Acids Research, 2024
    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, et al.
    Mbio, 2023
    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, Dina Grohmann
    RNA, 2023
    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.
  • Ribosome biogenesis in archaea
    Michael Jüttner, Sébastien Ferreira-Cerca
    Biospektrum, 2022
    The 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, Dina Grohmann
    RNA, 2022
    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.
  • The dark side of the ribosome life cycle
    Sébastien Ferreira-Cerca
    RNA Biology, 2022
    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.
  • Preface
    Methods in Molecular Biology, 2022
  • Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea
    Michael Kern, Sébastien Ferreira-Cerca
    Methods in Molecular Biology, 2022
  • A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life
    Michael Jüttner, Sébastien Ferreira-Cerca
    Methods in Molecular Biology, 2022
  • Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis
    Michael Jüttner, Sébastien Ferreira-Cerca
    Molecular Biology and Evolution, 2022
  • Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil
    Christina Braun, Robert Knüppel, Jorge Perez-Fernandez, Sébastien Ferreira-Cerca
    Methods in Molecular Biology, 2022
  • Editorial: Archaeal Ribosomes: Biogenesis, Structure and Function
    Sébastien Ferreira-Cerca, Anna La Teana, Paola Londei
    Frontiers in Microbiology, 2021
  • Ribosome Biogenesis in Archaea
    Paola Londei, Sébastien Ferreira-Cerca
    Frontiers in Microbiology, 2021
  • Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea
    Robert Knüppel, Christian Trahan, Michael Kern, Alexander Wagner, Felix Grünberger, et al.
    Nucleic Acids Research, 2021
  • 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, et al.
    Nature Communications, 2020
  • 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, et al.
    Frontiers in Microbiology, 2020
  • 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, et al.
    Nucleic Acids Research, 2020
  • In vivo RNA chemical footprinting analysis in archaea
    Robert Knüppel, Martin Fenk, Michael Jüttner, Sébastien Ferreira-Cerca
    Methods in Molecular Biology, 2020
  • 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, et al.
    Nature Communications, 2019
  • The Rio1 protein kinases/ATPases: conserved regulators of growth, division, and genomic stability
    Giovanna Berto, Sébastien Ferreira-Cerca, Peter De Wulf
    Current Genetics, 2019
  • 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, et al.
    Plos One, 2019
  • Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae
    Maria G Iacovella, Michael Bremang, Omer Basha, Luciano Giacò, Walter Carotenuto, et al.
    Nucleic Acids Research, 2018

RECENT SCHOLAR PUBLICATIONS

  • Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome
    MA Garcia-Campos, J Georgeson, R Nir, R Reichelt, KA Fluke, D Matzov, ...
    Cell 188 (24), 6825-6844. e28 , 2025
    2025
    Citations: 5
  • Circular RNAs in Archaea
    HF Becker, S Ferreira-Cerca
    Advances in Circular RNAs: The Basis and Disease Relevance, 451-464 , 2025
    2025
    Citations: 1
  • RNA Biogenesis
    T BASTA¹, S FERREIRA-CERCA
    Biology of Archaea 2: Molecular Biology of Archaea, From Genome Maintenance … , 2025
    2025
  • Ribosome and Transfer RNA Biogenesis
    T Basta-Le Berre, S Ferreira-Cerca
    Biology of Archaea 2: Molecular Biology of Archaea, From Genome Maintenance … , 2025
    2025
  • Ribosome and Transfer RNA Biogenesis
    T BASTA, S FERREIRA‐CERCA
    Biology of Archaea 2: Molecular Biology of Archaea, From Genome Maintenance … , 2025
    2025
  • RNase W, a conserved ribonuclease family with a novel active site
    M Vayssières, M Jüttner, K Haas, A Ancelin, A Marchfelder, N Leulliot, ...
    Nucleic Acids Research 52 (21), 13386-13401 , 2024
    2024
    Citations: 4
  • Chapitre 5-Biogenèse des ribosomes et des ARN de transfert
    T BASTA, S FERREIRA-CERCA
    ISTE Group , 2024
    2024
  • Biogenèse des ribosomes et des ARN de transfert
    T Basta, S Ferreira-Cerca
    Les archées, micro-organismes du troisième domaine du vivant 2, 119-175 , 2024
    2024
  • Transcriptional and translational dynamics underlying heat shock response in the thermophilic crenarchaeon Sulfolobus acidocaldarius
    R Baes, F Grünberger, S Pyr dit Ruys, M Couturier, S De Keulenaer, ...
    MBio 14 (5), e03593-22 , 2023
    2023
    Citations: 18
  • Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea
    F Grünberger, M Jüttner, R Knüppel, S Ferreira-Cerca, D Grohmann
    Rna 29 (8), 1255-1273 , 2023
    2023
    Citations: 26
  • The dark side of the ribosome life cycle
    S Ferreira-Cerca
    RNA biology 19 (1), 1045-1049 , 2022
    2022
    Citations: 5
  • Ribosomenbiogenese in Archaeen
    M Jüttner, S Ferreira-Cerca
    BIOspektrum 28 (5), 478-480 , 2022
    2022
  • Post-transcriptional regulation of the heat shock response in the thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius
    R Baes, F Grünberger, SP dit Ruys, M Couturier, S De Keulenaer, ...
    EMBO: Molecular Biology of Archaea 2022 , 2022
    2022
  • A comparative perspective on ribosome biogenesis: unity and diversity across the tree of life
    M Jüttner, S Ferreira-Cerca
    Ribosome Biogenesis: Methods and Protocols, 3-22 , 2022
    2022
    Citations: 25
  • Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil
    C Braun, R Knüppel, J Perez-Fernandez, S Ferreira-Cerca
    Ribosome Biogenesis: Methods and Protocols, 199-213 , 2022
    2022
    Citations: 1
  • 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
    2022
    Citations: 5
  • Looking through the lens of the ribosome biogenesis evolutionary history: possible implications for archaeal phylogeny and eukaryogenesis
    M Jüttner, S Ferreira-Cerca
    Molecular Biology and Evolution 39 (4), msac054 , 2022
    2022
    Citations: 25
  • 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
    2022
    Citations: 19
  • Nanopore sequencing of RNA and cDNA molecules in Escherichia coli
    F Grünberger, S Ferreira-Cerca, D Grohmann
    Rna 28 (3), 400-417 , 2022
    2022
    Citations: 106
  • Archaea
    S Ferreira-Cerca
    Springer US , 2022
    2022
    Citations: 12

MOST CITED SCHOLAR PUBLICATIONS

  • Eukaryotic ribosome biogenesis at a glance
    E Thomson, S Ferreira-Cerca, E Hurt
    Journal of cell science 126 (21), 4815-4821 , 2013
    2013
    Citations: 412
  • Roles of eukaryotic ribosomal proteins in maturation and transport of pre-18S rRNA and ribosome function
    S Ferreira-Cerca, G Pöll, PE Gleizes, H Tschochner, P Milkereit
    Molecular cell 20 (2), 263-275 , 2005
    2005
    Citations: 404
  • Analysis of the in vivo assembly pathway of eukaryotic 40S ribosomal proteins
    S Ferreira-Cerca, G Pöll, H Kühn, A Neueder, S Jakob, H Tschochner, ...
    Molecular cell 28 (3), 446-457 , 2007
    2007
    Citations: 210
  • ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit
    S Ferreira-Cerca, V Sagar, T Schäfer, M Diop, AM Wesseling, H Lu, ...
    Nature structural & molecular biology 19 (12), 1316-1323 , 2012
    2012
    Citations: 151
  • The ribosomal protein Rps15p is required for nuclear exit of the 40S subunit precursors in yeast
    I Léger‐Silvestre, P Milkereit, S Ferreira‐Cerca, C Saveanu, JC Rousselle, ...
    The EMBO journal 23 (12), 2336-2347 , 2004
    2004
    Citations: 138
  • Nanopore sequencing of RNA and cDNA molecules in Escherichia coli
    F Grünberger, S Ferreira-Cerca, D Grohmann
    Rna 28 (3), 400-417 , 2022
    2022
    Citations: 106
  • 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
    2014
    Citations: 100
  • 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
    2020
    Citations: 57
  • Ribosome biogenesis in archaea
    P Londei, S Ferreira-Cerca
    Frontiers in Microbiology 12, 686977 , 2021
    2021
    Citations: 52
  • 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
    2019
    Citations: 52
  • Insights into the evolutionary conserved regulation of Rio ATPase activity
    R Knüppel, RH Christensen, FC Gray, D Esser, D Strauß, J Medenbach, ...
    Nucleic Acids Research 46 (3), 1441-1456 , 2018
    2018
    Citations: 49
  • Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing
    F Grünberger, R Knüppel, M Jüttner, M Fenk, A Borst, R Reichelt, ...
    BioRxiv 10 (2019.12), 18.880849 , 2020
    2020
    Citations: 36
  • 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
    2015
    Citations: 36
  • Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea
    R Knüppel, C Trahan, M Kern, A Wagner, F Grünberger, W Hausner, ...
    Nucleic Acids Research 49 (3), 1662-1687 , 2021
    2021
    Citations: 30
  • A versatile cis -acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea
    M Jüttner, M Weiß, N Ostheimer, C Reglin, M Kern, R Knüppel, ...
    Nucleic Acids Research 48 (4), 2073-2090 , 2020
    2020
    Citations: 30
  • Arrest by ribosome
    S Ferreira-Cerca, E Hurt
    Nature 459 (7243), 46-47 , 2009
    2009
    Citations: 29
  • Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea
    F Grünberger, M Jüttner, R Knüppel, S Ferreira-Cerca, D Grohmann
    Rna 29 (8), 1255-1273 , 2023
    2023
    Citations: 26
  • Splicing endonuclease is an important player in rRNA and tRNA maturation in archaea
    TS Schwarz, SJ Berkemer, SH Bernhart, M Weiß, S Ferreira-Cerca, ...
    Frontiers in microbiology 11, 594838 , 2020
    2020
    Citations: 26
  • A comparative perspective on ribosome biogenesis: unity and diversity across the tree of life
    M Jüttner, S Ferreira-Cerca
    Ribosome Biogenesis: Methods and Protocols, 3-22 , 2022
    2022
    Citations: 25
  • Looking through the lens of the ribosome biogenesis evolutionary history: possible implications for archaeal phylogeny and eukaryogenesis
    M Jüttner, S Ferreira-Cerca
    Molecular Biology and Evolution 39 (4), msac054 , 2022
    2022
    Citations: 25