1
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Rathnayaka-Mudiyanselage IW, Nandana V, Schrader JM. Proteomic composition of eukaryotic and bacterial RNA decay condensates suggests convergent evolution. Curr Opin Microbiol 2024; 79:102467. [PMID: 38569418 PMCID: PMC11162941 DOI: 10.1016/j.mib.2024.102467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024]
Abstract
Bacterial cells have a unique challenge to organize their cytoplasm without the use of membrane-bound organelles. Biomolecular condensates (henceforth BMCs) are a class of nonmembrane-bound organelles, which, through the physical process of phase separation, can form liquid-like droplets with proteins/nucleic acids. BMCs have been broadly characterized in eukaryotic cells, and BMCs have been recently identified in bacteria, with the first and best studied example being bacterial ribonucleoprotein bodies (BR-bodies). BR-bodies contain the RNA decay machinery and show functional parallels to eukaryotic P-bodies (PBs) and stress granules (SGs). Due to the finding that mRNA decay machinery is compartmentalized in BR-bodies and in eukaryotic PBs/SGs, we will explore the functional similarities in the proteins, which are known to enrich in these structures based on recent proteomic studies. Interestingly, despite the use of different mRNA decay and post-transcriptional regulatory machinery, this analysis has revealed evolutionary convergence in the classes of enriched enzymes in these structures.
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Affiliation(s)
- I W Rathnayaka-Mudiyanselage
- Wayne State University, Department of Biological Sciences, Detroit, MI, USA; Wayne State University, Department of Chemistry, Detroit, MI, USA
| | - V Nandana
- Wayne State University, Department of Biological Sciences, Detroit, MI, USA
| | - J M Schrader
- Wayne State University, Department of Biological Sciences, Detroit, MI, USA.
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2
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Batista M, Langendijk-Genevaux P, Kwapisz M, Canal I, Phung DK, Plassart L, Capeyrou R, Moalic Y, Jebbar M, Flament D, Fichant G, Bouvier M, Clouet-d'Orval B. Evolutionary and functional insights into the Ski2-like helicase family in Archaea: a comparison of Thermococcales ASH-Ski2 and Hel308 activities. NAR Genom Bioinform 2024; 6:lqae026. [PMID: 38500564 PMCID: PMC10946056 DOI: 10.1093/nargab/lqae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. Here, by studying the phylogenetic diversity of Ski2-like helicases among archaeal genomes and the enzymatic activities of those in Thermococcales, we provide further evidence of the function of this protein family in archaeal metabolism of nucleic acids. We show that, in the course of evolution, ASH-Ski2 and Hel308-Ski2, the two main groups of Ski2-like proteins, have diverged in their biological functions. Whereas Hel308 has been shown to mainly act on DNA, we show that ASH-Ski2, previously described to be associated with the 5'-3' aRNase J exonuclease, acts on RNA by supporting an efficient annealing activity, but also an RNA unwinding with a 3'-5' polarity. To gain insights into the function of Ski2, we also analyse the transcriptome of Thermococcus barophilus ΔASH-Ski2 mutant strain and provide evidence of the importance of ASH-Ski2 in cellular metabolism pathways related to translation.
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Affiliation(s)
- Manon Batista
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | | | - Marta Kwapisz
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Isabelle Canal
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Duy Khanh Phung
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Laura Plassart
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Régine Capeyrou
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Yann Moalic
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Mohamed Jebbar
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Didier Flament
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Gwennaele Fichant
- LMGM, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Marie Bouvier
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Béatrice Clouet-d'Orval
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
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3
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Baum B, Spang A. On the origin of the nucleus: a hypothesis. Microbiol Mol Biol Rev 2023; 87:e0018621. [PMID: 38018971 PMCID: PMC10732040 DOI: 10.1128/mmbr.00186-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.
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Affiliation(s)
- Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
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4
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Altae-Tran H, Kannan S, Suberski AJ, Mears KS, Demircioglu FE, Moeller L, Kocalar S, Oshiro R, Makarova KS, Macrae RK, Koonin EV, Zhang F. Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering. Science 2023; 382:eadi1910. [PMID: 37995242 PMCID: PMC10910872 DOI: 10.1126/science.adi1910] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/28/2023] [Indexed: 11/25/2023]
Abstract
Microbial systems underpin many biotechnologies, including CRISPR, but the exponential growth of sequence databases makes it difficult to find previously unidentified systems. In this work, we develop the fast locality-sensitive hashing-based clustering (FLSHclust) algorithm, which performs deep clustering on massive datasets in linearithmic time. We incorporated FLSHclust into a CRISPR discovery pipeline and identified 188 previously unreported CRISPR-linked gene modules, revealing many additional biochemical functions coupled to adaptive immunity. We experimentally characterized three HNH nuclease-containing CRISPR systems, including the first type IV system with a specified interference mechanism, and engineered them for genome editing. We also identified and characterized a candidate type VII system, which we show acts on RNA. This work opens new avenues for harnessing CRISPR and for the broader exploration of the vast functional diversity of microbial proteins.
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Affiliation(s)
- Han Altae-Tran
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Soumya Kannan
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Anthony J. Suberski
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Kepler S. Mears
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - F. Esra Demircioglu
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Lukas Moeller
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Selin Kocalar
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Rachel Oshiro
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD 20894, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD 20894, USA
| | - Feng Zhang
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
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5
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Reichelt R, Rothmeier T, Grünberger F, Willkomm S, Bruckmann A, Hausner W, Grohmann D. The archaeal Lsm protein from Pyrococcus furiosus binds co-transcriptionally to poly(U)-rich target RNAs. Biol Chem 2023; 404:1085-1100. [PMID: 37709673 DOI: 10.1515/hsz-2023-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Posttranscriptional processes in Bacteria include the association of small regulatory RNAs (sRNA) with a target mRNA. The sRNA/mRNA annealing process is often mediated by an RNA chaperone called Hfq. The functional role of bacterial and eukaryotic Lsm proteins is partially understood, whereas knowledge about archaeal Lsm proteins is scarce. Here, we used the genetically tractable archaeal hyperthermophile Pyrococcus furiosus to identify the protein interaction partners of the archaeal Sm-like proteins (PfuSmAP1) using mass spectrometry and performed a transcriptome-wide binding site analysis of PfuSmAP1. Most of the protein interaction partners we found are part of the RNA homoeostasis network in Archaea including ribosomal proteins, the exosome, RNA-modifying enzymes, but also RNA polymerase subunits, and transcription factors. We show that PfuSmAP1 preferentially binds messenger RNAs and antisense RNAs recognizing a gapped poly(U) sequence with high affinity. Furthermore, we found that SmAP1 co-transcriptionally associates with target RNAs. Our study reveals that in contrast to bacterial Hfq, PfuSmAP1 does not affect the transcriptional activity or the pausing behaviour of archaeal RNA polymerases. We propose that PfuSmAP1 recruits antisense RNAs to target mRNAs and thereby executes its putative regulatory function on the posttranscriptional level.
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Affiliation(s)
- Robert Reichelt
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Tamara Rothmeier
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Sarah Willkomm
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology (Biochemistry I), Protein Mass Spectrometry Laboratory, University of Regensburg, D-93053 Regensburg, Germany
| | - Winfried Hausner
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, D-93053 Regensburg, Germany
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6
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Jia H, Dantuluri S, Margulies S, Smith V, Lever R, Allers T, Koh J, Chen S, Maupin-Furlow JA. RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii. mBio 2023; 14:e0085223. [PMID: 37458473 PMCID: PMC10470531 DOI: 10.1128/mbio.00852-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
Nucleases are strictly regulated and often localized in the cell to avoid the uncontrolled degradation of DNA and RNA. Here, a new type of nuclease complex, composed of RecJ3, RecJ4, and aRNase J, was identified through its ATP-dependent association with the ubiquitin-like SAMP1 and AAA-ATPase Cdc48a. The complex was discovered in Haloferax volcanii, an archaeon lacking an RNA exosome. Genetic analysis revealed aRNase J to be essential and RecJ3, RecJ4, and Cdc48a to function in the recovery from DNA damage including genotoxic agents that generate double-strand breaks. The RecJ3:RecJ4:aRNase J complex (isolated in 2:2:1 stoichiometry) functioned primarily as a 3'-5' exonuclease in hydrolyzing RNA and ssDNA, with the mechanism non-processive for ssDNA. aRNase J could also be purified as a homodimer that catalyzed endoribonuclease activity and, thus, was not restricted to the 5'-3' exonuclease activity typical of aRNase J homologs. Moreover, RecJ3 and RecJ4 could be purified as a 560-kDa subcomplex in equimolar subunit ratio with nuclease activities mirroring the full RecJ3/4-aRNase J complex. These findings prompted reconstitution assays that suggested RecJ3/4 could suppress, alter, and/or outcompete the nuclease activities of aRNase J. Based on the phenotypic results, this control mechanism of aRNase J by RecJ3/4 is not necessary for cell growth but instead appears important for DNA repair. IMPORTANCE Nucleases are critical for various cellular processes including DNA replication and repair. Here, a dynamic type of nuclease complex is newly identified in the archaeon Haloferax volcanii, which is missing the canonical RNA exosome. The complex, composed of RecJ3, RecJ4, and aRNase J, functions primarily as a 3'-5' exonuclease and was discovered through its ATP-dependent association with the ubiquitin-like SAMP1 and Cdc48a. aRNase J alone forms a homodimer that has endonuclease function and, thus, is not restricted to 5'-3' exonuclease activity typical of other aRNase J enzymes. RecJ3/4 appears to suppress, alter, and/or outcompete the nuclease activities of aRNase J. While aRNase J is essential for growth, RecJ3/4, Cdc48a, and SAMPs are important for recovery against DNA damage. These biological distinctions may correlate with the regulated nuclease activity of aRNase J in the RecJ3/4-aRNaseJ complex.
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Affiliation(s)
- Huiyong Jia
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Swathi Dantuluri
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Shae Margulies
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rebecca Lever
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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7
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Marshall CJ, Qayyum MZ, Walker JE, Murakami KS, Santangelo TJ. The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex. Proc Natl Acad Sci U S A 2022; 119:e2207581119. [PMID: 35917344 PMCID: PMC9371683 DOI: 10.1073/pnas.2207581119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Transcription must be properly regulated to ensure dynamic gene expression underlying growth, development, and response to environmental cues. Regulation is imposed throughout the transcription cycle, and while many efforts have detailed the regulation of transcription initiation and early elongation, the termination phase of transcription also plays critical roles in regulating gene expression. Transcription termination can be driven by only a few proteins in each domain of life. Detailing the mechanism(s) employed provides insight into the vulnerabilities of transcription elongation complexes (TECs) that permit regulated termination to control expression of many genes and operons. Here, we describe the biochemical activities and crystal structure of the superfamily 2 helicase Eta, one of two known factors capable of disrupting archaeal transcription elongation complexes. Eta retains a twin-translocase core domain common to all superfamily 2 helicases and a well-conserved C terminus wherein individual amino acid substitutions can critically abrogate termination activities. Eta variants that perturb ATPase, helicase, single-stranded DNA and double-stranded DNA translocase and termination activities identify key regions of the C terminus of Eta that, when combined with modeling Eta-TEC interactions, provide a structural model of Eta-mediated termination guided in part by structures of Mfd and the bacterial TEC. The susceptibility of TECs to disruption by termination factors that target the upstream surface of RNA polymerase and potentially drive termination through forward translocation and allosteric mechanisms that favor opening of the clamp to release the encapsulated nucleic acids emerges as a common feature of transcription termination mechanisms.
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Affiliation(s)
- Craig J. Marshall
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523
| | - M. Zuhaib Qayyum
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Julie E. Walker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523
| | - Katsuhiko S. Murakami
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523
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8
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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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9
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Hogrel G, Marino-Puertas L, Laurent S, Ibrahim Z, Covès J, Girard E, Gabel F, Fenel D, Daugeron MC, Clouet-d'Orval B, Basta T, Flament D, Franzetti B. Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex. Mol Microbiol 2022; 118:16-29. [PMID: 35615908 PMCID: PMC9540759 DOI: 10.1111/mmi.14948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/27/2022]
Abstract
The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterised a small orphan protein, Q9UZY3 (Uniprot ID) conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (PAN) as bait. X-ray crystallography and SAXS experiments revealed that the protein is monomeric and adopts a β-barrel core structure with an Oligonucleotide/oligosaccharide-Binding (OB) fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays tRNA binding properties. Pull-downs, co-immunoprecipitation and ITC studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi cellular extracts. The protein was therefore named Pbp11, for Proteasome Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery.
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Affiliation(s)
- Gaëlle Hogrel
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.,University of St Andrews, St Andrews, UK
| | | | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Ziad Ibrahim
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.,University of Leicester, Leicester, UK
| | - Jacques Covès
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Eric Girard
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Frank Gabel
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Daphna Fenel
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Marie-Claire Daugeron
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Tamara Basta
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
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10
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The Redox Active [2Fe-2S] Clusters: Key-Components of a Plethora of Enzymatic Reactions—Part I: Archaea. INORGANICS 2022. [DOI: 10.3390/inorganics10010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The earliest forms of life (i.e., Archaea, Bacteria, and Eukarya) appeared on our planet about ten billion years after its formation. Although Archaea do not seem to possess the multiprotein machinery constituted by the NIF (Nitrogen Fixation), ISC (Iron Sulfur Cluster), SUF (sulfur mobilization) enzymes, typical of Bacteria and Eukarya, some of them are able to encode Fe-S proteins. Here we discussed the multiple enzymatic reactions triggered by the up-to-date structurally characterized members of the archaeal family that require the crucial presence of structurally characterized [2Fe-2S] assemblies, focusing on their biological functions and, when available, on their electrochemical behavior.
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Birikmen M, Bohnsack KE, Tran V, Somayaji S, Bohnsack MT, Ebersberger I. Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity. Front Microbiol 2021; 12:739000. [PMID: 34603269 PMCID: PMC8481954 DOI: 10.3389/fmicb.2021.739000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/17/2021] [Indexed: 01/23/2023] Open
Abstract
Ribosome assembly is an essential and carefully choreographed cellular process. In eukaryotes, several 100 proteins, distributed across the nucleolus, nucleus, and cytoplasm, co-ordinate the step-wise assembly of four ribosomal RNAs (rRNAs) and approximately 80 ribosomal proteins (RPs) into the mature ribosomal subunits. Due to the inherent complexity of the assembly process, functional studies identifying ribosome biogenesis factors and, more importantly, their precise functions and interplay are confined to a few and very well-established model organisms. Although best characterized in yeast (Saccharomyces cerevisiae), emerging links to disease and the discovery of additional layers of regulation have recently encouraged deeper analysis of the pathway in human cells. In archaea, ribosome biogenesis is less well-understood. However, their simpler sub-cellular structure should allow a less elaborated assembly procedure, potentially providing insights into the functional essentials of ribosome biogenesis that evolved long before the diversification of archaea and eukaryotes. Here, we use a comprehensive phylogenetic profiling setup, integrating targeted ortholog searches with automated scoring of protein domain architecture similarities and an assessment of when search sensitivity becomes limiting, to trace 301 curated eukaryotic ribosome biogenesis factors across 982 taxa spanning the tree of life and including 727 archaea. We show that both factor loss and lineage-specific modifications of factor function modulate ribosome biogenesis, and we highlight that limited sensitivity of the ortholog search can confound evolutionary conclusions. Projecting into the archaeal domain, we find that only few factors are consistently present across the analyzed taxa, and lineage-specific loss is common. While members of the Asgard group are not special with respect to their inventory of ribosome biogenesis factors (RBFs), they unite the highest number of orthologs to eukaryotic RBFs in one taxon. Using large ribosomal subunit maturation as an example, we demonstrate that archaea pursue a simplified version of the corresponding steps in eukaryotes. Much of the complexity of this process evolved on the eukaryotic lineage by the duplication of ribosomal proteins and their subsequent functional diversification into ribosome biogenesis factors. This highlights that studying ribosome biogenesis in archaea provides fundamental information also for understanding the process in eukaryotes.
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Affiliation(s)
- Mehmet Birikmen
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Vinh Tran
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Sharvari Somayaji
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Center (S-BIK-F), Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
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Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase. Biomolecules 2021; 11:biom11070950. [PMID: 34206878 PMCID: PMC8301817 DOI: 10.3390/biom11070950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
Helicase proteins are known to use the energy of ATP to unwind nucleic acids and to remodel protein-nucleic acid complexes. They are involved in almost every aspect of DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be DNA helicases that act in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In Thermococcales, a protein annotated as an Lhr2 protein was found in the network of proteins involved in RNA metabolism. To investigate this, we performed in-depth phylogenomic analyses to report the classification and taxonomic distribution of Lhr-type proteins in Archaea, and to better understand their relationship with bacterial Lhr. Furthermore, with the goal of envisioning the role(s) of aLhr2 in Thermococcales cells, we deciphered the enzymatic activities of aLhr2 from Thermococcus barophilus (Tbar). We showed that Tbar-aLhr2 is a DNA/RNA helicase with a significant annealing activity that is involved in processes dependent on DNA and RNA transactions.
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Bathke J, Gauernack AS, Rupp O, Weber L, Preusser C, Lechner M, Rossbach O, Goesmann A, Evguenieva-Hackenberg E, Klug G. iCLIP analysis of RNA substrates of the archaeal exosome. BMC Genomics 2020; 21:797. [PMID: 33198623 PMCID: PMC7667871 DOI: 10.1186/s12864-020-07200-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/27/2020] [Indexed: 12/25/2022] Open
Abstract
Background The archaeal exosome is an exoribonucleolytic multiprotein complex, which degrades single-stranded RNA in 3′ to 5′ direction phosphorolytically. In a reverse reaction, it can add A-rich tails to the 3′-end of RNA. The catalytic center of the exosome is in the aRrp41 subunit of its hexameric core. Its RNA-binding subunits aRrp4 and aDnaG confer poly(A) preference to the complex. The archaeal exosome was intensely characterized in vitro, but still little is known about its interaction with natural substrates in the cell, particularly because analysis of the transcriptome-wide interaction of an exoribonuclease with RNA is challenging. Results To determine binding sites of the exosome to RNA on a global scale, we performed individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) analysis with antibodies directed against aRrp4 and aRrp41 of the chrenarchaeon Sulfolobus solfataricus. A relatively high proportion (17–19%) of the obtained cDNA reads could not be mapped to the genome. Instead, they corresponded to adenine-rich RNA tails, which are post-transcriptionally synthesized by the exosome, and to circular RNAs (circRNAs). We identified novel circRNAs corresponding to 5′ parts of two homologous, transposase-related mRNAs. To detect preferred substrates of the exosome, the iCLIP reads were compared to the transcript abundance using RNA-Seq data. Among the strongly enriched exosome substrates were RNAs antisense to tRNAs, overlapping 3′-UTRs and RNAs containing poly(A) stretches. The majority of the read counts and crosslink sites mapped in mRNAs. Furthermore, unexpected crosslink sites clustering at 5′-ends of RNAs was detected. Conclusions In this study, RNA targets of an exoribonuclease were analyzed by iCLIP. The data documents the role of the archaeal exosome as an exoribonuclease and RNA-tailing enzyme interacting with all RNA classes, and underlines its role in mRNA turnover, which is important for adaptation of prokaryotic cells to changing environmental conditions. The clustering of crosslink sites near 5′-ends of genes suggests simultaneous binding of both RNA ends by the S. solfataricus exosome. This may serve to prevent translation of mRNAs dedicated to degradation in 3′-5′ direction. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07200-x.
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Affiliation(s)
- Jochen Bathke
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, 35392, Giessen, Germany.,Institute of Bioinformatics and Systems Biology, Justus-Liebig-University, 35392, Giessen, Germany
| | - A Susann Gauernack
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, 35392, Giessen, Germany
| | - Oliver Rupp
- Institute of Bioinformatics and Systems Biology, Justus-Liebig-University, 35392, Giessen, Germany
| | - Lennart Weber
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, 35392, Giessen, Germany
| | - Christian Preusser
- Institute of Biochemistry, Justus-Liebig-University, 35392, Giessen, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology & Department of Pharmaceutical Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Justus-Liebig-University, 35392, Giessen, Germany
| | - Alexander Goesmann
- Institute of Bioinformatics and Systems Biology, Justus-Liebig-University, 35392, Giessen, Germany
| | | | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, 35392, Giessen, Germany
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Marshall CJ, Santangelo TJ. Archaeal DNA Repair Mechanisms. Biomolecules 2020; 10:E1472. [PMID: 33113933 PMCID: PMC7690668 DOI: 10.3390/biom10111472] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/29/2022] Open
Abstract
Archaea often thrive in environmental extremes, enduring levels of heat, pressure, salinity, pH, and radiation that prove intolerable to most life. Many environmental extremes raise the propensity for DNA damaging events and thus, impact DNA stability, placing greater reliance on molecular mechanisms that recognize DNA damage and initiate accurate repair. Archaea can presumably prosper in harsh and DNA-damaging environments in part due to robust DNA repair pathways but surprisingly, no DNA repair pathways unique to Archaea have been described. Here, we review the most recent advances in our understanding of archaeal DNA repair. We summarize DNA damage types and their consequences, their recognition by host enzymes, and how the collective activities of many DNA repair pathways maintain archaeal genomic integrity.
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Affiliation(s)
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA;
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Wenck BR, Santangelo TJ. Archaeal transcription. Transcription 2020; 11:199-210. [PMID: 33112729 PMCID: PMC7714419 DOI: 10.1080/21541264.2020.1838865] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
Increasingly sophisticated biochemical and genetic techniques are unraveling the regulatory factors and mechanisms that control gene expression in the Archaea. While some similarities in regulatory strategies are universal, archaeal-specific regulatory strategies are emerging to complement a complex patchwork of shared archaeal-bacterial and archaeal-eukaryotic regulatory mechanisms employed in the archaeal domain. The prokaryotic archaea encode core transcription components with homology to the eukaryotic transcription apparatus and also share a simplified eukaryotic-like initiation mechanism, but also deploy tactics common to bacterial systems to regulate promoter usage and influence elongation-termination decisions. We review the recently established complete archaeal transcription cycle, highlight recent findings of the archaeal transcription community and detail the expanding post-initiation regulation imposed on archaeal transcription.
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Affiliation(s)
- Breanna R. Wenck
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
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