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Gastineau R, Harðardóttir S, Guilmette C, Lemieux C, Turmel M, Otis C, Boyle B, Levesque RC, Gauthier J, Potvin M, Lovejoy C. Mitochondrial genome sequence of the protist Ancyromonas sigmoides Kent, 1881 (Ancyromonadida) from the Sugluk Inlet, Hudson Strait, Nunavik, Québec. Front Microbiol 2023; 14:1275665. [PMID: 38143861 PMCID: PMC10749196 DOI: 10.3389/fmicb.2023.1275665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/09/2023] [Indexed: 12/26/2023] Open
Abstract
Introduction There is little information on evolutionarily ancient eukaryotes, which are often referred to as basal eukaryotes, in Arctic waters. Despite earlier studies being conducted in the Russian White Sea, only few have been reported. Methods Following a shotgun sequence survey of diatom cultures from Sugluk Inlet off the Hudson Strait in Northern Québec, we obtained the complete mitochondrial genome and the operon of nuclear ribosomal RNA genes from a strain that matches that of Ancyromonas sigmoides (Kent, 1881). Results The sequence of the mitogenome retrieved was 41,889 bp in length and encoded 38 protein-coding genes, 5 non-conserved open-reading frames, and 2 rRNA and 24 tRNA genes. The mitogenome has retained sdh2 and sdh3, two genes of the succinate dehydrogenase complex, which are sometimes found among basal eukaryotes but seemingly missing among the Malawimonadidae, a lineage sister to Ancyromonadida in some phylogenies. The phylogeny inferred from the 18S rRNA gene associated A. sigmoides from Sugluk Inlet with several other strains originating from the Arctic. The study also unveiled the presence of a metagenomic sequence ascribed to bacteria in GenBank, but it was clearly a mitochondrial genome with a gene content highly similar to that of A. sigmoides, including the non-conserved open-reading frames. Discussion After re-annotation, a phylogeny was inferred from mitochondrial protein sequences, and it strongly associated A. sigmoides with the misidentified organism, with the two being possibly conspecific or sibling species as they are more similar to one another than to species of the genus Malawimonas. Overall our phylogeny showed that the ice associated ancryomonads were clearly distinct from more southerly strains.
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Affiliation(s)
- Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Sara Harðardóttir
- Geological Survey of Denmark and Greenland, København K, Denmark
- Biology Department, Takuvik International Research Laboratory (IRL 3376), Université Laval – CNRS, Québec City, QC, Canada
- The Marine and Freshwater Research Institute in Iceland, Hafnarfjörður, Iceland
| | - Caroline Guilmette
- Biology Department, Takuvik International Research Laboratory (IRL 3376), Université Laval – CNRS, Québec City, QC, Canada
| | - Claude Lemieux
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
- Département de biochimie, de microbiologie et de bio-Informatique, Université Laval, Québec City, QC, Canada
| | - Monique Turmel
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
- Département de biochimie, de microbiologie et de bio-Informatique, Université Laval, Québec City, QC, Canada
| | - Christian Otis
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
- Plateforme d’Analyse génomique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
- Plateforme d’Analyse génomique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Roger C. Levesque
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Jeff Gauthier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Marianne Potvin
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
- Département de biochimie, de microbiologie et de bio-Informatique, Université Laval, Québec City, QC, Canada
| | - Connie Lovejoy
- Biology Department, Takuvik International Research Laboratory (IRL 3376), Université Laval – CNRS, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
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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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Lechner M, Rossmanith W, Hartmann RK, Thölken C, Gutmann B, Giegé P, Gobert A. Distribution of Ribonucleoprotein and Protein-Only RNase P in Eukarya. Mol Biol Evol 2015; 32:3186-93. [PMID: 26341299 DOI: 10.1093/molbev/msv187] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
RNase P is the endonuclease that removes 5' leader sequences from tRNA precursors. In Eukarya, separate RNase P activities exist in the nucleus and mitochondria/plastids. Although all RNase P enzymes catalyze the same reaction, the different architectures found in Eukarya range from ribonucleoprotein (RNP) enzymes with a catalytic RNA and up to 10 protein subunits to single-subunit protein-only RNase P (PRORP) enzymes. Here, analysis of the phylogenetic distribution of RNP and PRORP enzymes in Eukarya revealed 1) a wealth of novel P RNAs in previously unexplored phylogenetic branches and 2) that PRORP enzymes are more widespread than previously appreciated, found in four of the five eukaryal supergroups, in the nuclei and/or organelles. Intriguingly, the occurrence of RNP RNase P and PRORP seems mutually exclusive in genetic compartments of modern Eukarya. Our comparative analysis provides a global picture of the evolution and diversification of RNase P throughout Eukarya.
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Affiliation(s)
- Marcus Lechner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Walter Rossmanith
- Zentrum für Anatomie & Zellbiologie, Medizinische Universität Wien, Wien, Austria
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Clemens Thölken
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Bernard Gutmann
- Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg, France
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg, France
| | - Anthony Gobert
- Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg, France
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Borriello R, Bianciotto V, Orgiazzi A, Lumini E, Bergero R. Sequencing and comparison of the mitochondrial COI gene from isolates of Arbuscular Mycorrhizal Fungi belonging to Gigasporaceae and Glomeraceae families. Mol Phylogenet Evol 2014; 75:1-10. [PMID: 24569015 DOI: 10.1016/j.ympev.2014.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 12/16/2022]
Abstract
Arbuscular Mycorrhizal Fungi (AMF) are well known for their ecological importance and their positive influence on plants. The genetics and phylogeny of this group of fungi have long been debated. Nuclear markers are the main tools used for phylogenetic analyses, but they have sometimes proved difficult to use because of their extreme variability. Therefore, the attention of researchers has been moving towards other genomic markers, in particular those from the mitochondrial DNA. In this study, 46 sequences of different AMF isolates belonging to two main clades Gigasporaceae and Glomeraceae have been obtained from the mitochondrial gene coding for the Cytochrome c Oxidase I (COI), representing the largest dataset to date of AMF COI sequences. A very low level of divergence was recorded in the COI sequences from the Gigasporaceae, which could reflect either a slow rate of evolution or a more recent evolutionary divergence of this group. On the other hand, the COI sequence divergence between Gigasporaceae and Glomeraceae was high, with synonymous divergence reaching saturated levels. This work also showed the difficulty in developing valuable mitochondrial markers able to effectively distinguish all Glomeromycota species, especially those belonging to Gigasporaceae, yet it represents a first step towards the development of a full mtDNA-based dataset which can be used for further phylogenetic investigations of this fungal phylum.
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Affiliation(s)
- Roberto Borriello
- Plant Protection Institute (IPP)-Turin UOS, National Research Council (CNR), c/o Department of Life Science and Systems Biology, University of Turin, Viale P.A. Mattioli 25, Turin 10125, Italy
| | - Valeria Bianciotto
- Plant Protection Institute (IPP)-Turin UOS, National Research Council (CNR), c/o Department of Life Science and Systems Biology, University of Turin, Viale P.A. Mattioli 25, Turin 10125, Italy
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre, Institute for Environment and Sustainability, Via E. Fermi, 2749, Ispra, VA I-21027, Italy
| | - Erica Lumini
- Plant Protection Institute (IPP)-Turin UOS, National Research Council (CNR), c/o Department of Life Science and Systems Biology, University of Turin, Viale P.A. Mattioli 25, Turin 10125, Italy.
| | - Roberta Bergero
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom.
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Burger G, Gray MW, Forget L, Lang BF. Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists. Genome Biol Evol 2013; 5:418-38. [PMID: 23335123 PMCID: PMC3590771 DOI: 10.1093/gbe/evt008] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The most bacteria-like mitochondrial genome known is that of the jakobid flagellate Reclinomonas americana NZ. This genome also encodes the largest known gene set among mitochondrial DNAs (mtDNAs), including the RNA subunit of RNase P (transfer RNA processing), a reduced form of transfer-messenger RNA (translational control), and a four-subunit bacteria-like RNA polymerase, which in other eukaryotes is substituted by a nucleus-encoded, single-subunit, phage-like enzyme. Further, protein-coding genes are preceded by potential Shine-Dalgarno translation initiation motifs. Whether similarly ancestral mitochondrial characters also exist in relatives of R. americana NZ is unknown. Here, we report a comparative analysis of nine mtDNAs from five distant jakobid genera: Andalucia, Histiona, Jakoba, Reclinomonas, and Seculamonas. We find that Andalucia godoyi has an even larger mtDNA gene complement than R. americana NZ. The extra genes are rpl35 (a large subunit mitoribosomal protein) and cox15 (involved in cytochrome oxidase assembly), which are nucleus encoded throughout other eukaryotes. Andalucia cox15 is strikingly similar to its homolog in the free-living α-proteobacterium Tistrella mobilis. Similarly, a long, highly conserved gene cluster in jakobid mtDNAs, which is a clear vestige of prokaryotic operons, displays a gene order more closely resembling that in free-living α-proteobacteria than in Rickettsiales species. Although jakobid mtDNAs, overall, are characterized by bacteria-like features, they also display a few remarkably divergent characters, such as 3'-tRNA editing in Seculamonas ecuadoriensis and genome linearization in Jakoba libera. Phylogenetic analysis with mtDNA-encoded proteins strongly supports monophyly of jakobids with Andalucia as the deepest divergence. However, it remains unclear which α-proteobacterial group is the closest mitochondrial relative.
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Affiliation(s)
- Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada.
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Pinker F, Bonnard G, Gobert A, Gutmann B, Hammani K, Sauter C, Gegenheimer PA, Giegé P. PPR proteins shed a new light on RNase P biology. RNA Biol 2013; 10:1457-68. [PMID: 23925311 PMCID: PMC3858429 DOI: 10.4161/rna.25273] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A fast growing number of studies identify pentatricopeptide repeat (PPR) proteins as major players in gene expression processes. Among them, a subset of PPR proteins called PRORP possesses RNase P activity in several eukaryotes, both in nuclei and organelles. RNase P is the endonucleolytic activity that removes 5′ leader sequences from tRNA precursors and is thus essential for translation. Before the characterization of PRORP, RNase P enzymes were thought to occur universally as ribonucleoproteins, although some evidence implied that some eukaryotes or cellular compartments did not use RNA for RNase P activity. The characterization of PRORP reveals a two-domain enzyme, with an N-terminal domain containing multiple PPR motifs and assumed to achieve target specificity and a C-terminal domain holding catalytic activity. The nature of PRORP interactions with tRNAs suggests that ribonucleoprotein and protein-only RNase P enzymes share a similar substrate binding process.
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Affiliation(s)
- Franziska Pinker
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France; Institut de Biologie Moléculaire et Cellulaire du CNRS; Architecture et Réactivité de l'ARN; Université de Strasbourg; Strasbourg, France
| | - Géraldine Bonnard
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Anthony Gobert
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Bernard Gutmann
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Kamel Hammani
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Claude Sauter
- Institut de Biologie Moléculaire et Cellulaire du CNRS; Architecture et Réactivité de l'ARN; Université de Strasbourg; Strasbourg, France
| | | | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
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7
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Nadimi M, Beaudet D, Forget L, Hijri M, Lang BF. Group I intron-mediated trans-splicing in mitochondria of Gigaspora rosea and a robust phylogenetic affiliation of arbuscular mycorrhizal fungi with Mortierellales. Mol Biol Evol 2012; 29:2199-210. [PMID: 22411852 DOI: 10.1093/molbev/mss088] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Gigaspora rosea is a member of the arbuscular mycorrhizal fungi (AMF; Glomeromycota) and a distant relative of Glomus species that are beneficial to plant growth. To allow for a better understanding of Glomeromycota, we have sequenced the mitochondrial DNA of G. rosea. A comparison with Glomus mitochondrial genomes reveals that Glomeromycota undergo insertion and loss of mitochondrial plasmid-related sequences and exhibit considerable variation in introns. The gene order between the two species is almost completely reshuffled. Furthermore, Gigaspora has fragmented cox1 and rns genes, and an unorthodox initiator tRNA that is tailored to decoding frequent UUG initiation codons. For the fragmented cox1 gene, we provide evidence that its RNA is joined via group I-mediated trans-splicing, whereas rns RNA remains in pieces. According to our model, the two cox1 precursor RNA pieces are brought together by flanking cox1 exon sequences that form a group I intron structure, potentially in conjunction with the nad5 intron 3 sequence. Finally, we present analyses that address the controversial phylogenetic association of Glomeromycota within fungi. According to our results, Glomeromycota are not a separate group of paraphyletic zygomycetes but branch together with Mortierellales, potentially also Harpellales.
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Affiliation(s)
- Maryam Nadimi
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
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8
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Rossmanith W. Of P and Z: mitochondrial tRNA processing enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:1017-26. [PMID: 22137969 PMCID: PMC3790967 DOI: 10.1016/j.bbagrm.2011.11.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/11/2011] [Accepted: 11/15/2011] [Indexed: 12/18/2022]
Abstract
Mitochondrial tRNAs are generally synthesized as part of polycistronic transcripts. Release of tRNAs from these precursors is thus not only required to produce functional adaptors for translation, but also responsible for the maturation of other mitochondrial RNA species. Cleavage of mitochondrial tRNAs appears to be exclusively accomplished by endonucleases. 5'-end maturation in the mitochondria of different Eukarya is achieved by various kinds of RNase P, representing the full range of diversity found in this enzyme family. While ribonucleoprotein enzymes with RNA components of bacterial-like appearance are found in a few unrelated protists, algae, and fungi, highly degenerate RNAs of dramatic size variability are found in the mitochondria of many fungi. The majority of mitochondrial RNase P enzymes, however, appear to be pure protein enzymes. Human mitochondrial RNase P, the first to be identified and possibly the prototype of all animal mitochondrial RNases P, is composed of three proteins. Homologs of its nuclease subunit MRPP3/PRORP, are also found in plants, algae and several protists, where they are apparently responsible for RNase P activity in mitochondria (and beyond) without the help of extra subunits. The diversity of RNase P enzymes is contrasted by the uniformity of mitochondrial RNases Z, which are responsible for 3'-end processing. Only the long form of RNase Z, which is restricted to eukarya, is found in mitochondria, even when an additional short form is present in the same organism. Mitochondrial tRNA processing thus appears dominated by new, eukaryal inventions rather than bacterial heritage. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Austria.
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9
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Chen WY, Pulukkunat DK, Cho IM, Tsai HY, Gopalan V. Dissecting functional cooperation among protein subunits in archaeal RNase P, a catalytic ribonucleoprotein complex. Nucleic Acids Res 2010; 38:8316-27. [PMID: 20705647 PMCID: PMC3001054 DOI: 10.1093/nar/gkq668] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
RNase P catalyzes the Mg2+-dependent 5′-maturation of precursor tRNAs. Biochemical studies on the bacterial holoenzyme, composed of one catalytic RNase P RNA (RPR) and one RNase P protein (RPP), have helped understand the pleiotropic roles (including substrate/Mg2+ binding) by which a protein could facilitate RNA catalysis. As a model for uncovering the functional coordination among multiple proteins that aid an RNA catalyst, we use archaeal RNase P, which comprises one catalytic RPR and at least four RPPs. Exploiting our previous finding that these archaeal RPPs function as two binary RPP complexes (POP5•RPP30 and RPP21•RPP29), we prepared recombinant RPP pairs from three archaea and established interchangeability of subunits through homologous/heterologous assemblies. Our finding that archaeal POP5•RPP30 reconstituted with bacterial and organellar RPRs suggests functional overlap of this binary complex with the bacterial RPP and highlights their shared recognition of a phylogenetically-conserved RPR catalytic core, whose minimal attributes we further defined through deletion mutagenesis. Moreover, single-turnover kinetic studies revealed that while POP5•RPP30 is solely responsible for enhancing the RPR’s rate of precursor tRNA cleavage (by 60-fold), RPP21•RPP29 contributes to increased substrate affinity (by 16-fold). Collectively, these studies provide new perspectives on the functioning and evolution of an ancient, catalytic ribonucleoprotein.
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Affiliation(s)
- Wen-Yi Chen
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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Hartmann RK, Gössringer M, Späth B, Fischer S, Marchfelder A. The making of tRNAs and more - RNase P and tRNase Z. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:319-68. [PMID: 19215776 DOI: 10.1016/s0079-6603(08)00808-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transfer-RNA (tRNA) molecules are essential players in protein biosynthesis. They are transcribed as precursors, which have to be extensively processed at both ends to become functional adaptors in protein synthesis. Two endonucleases that directly interact with the tRNA moiety, RNase P and tRNase Z, remove extraneous nucleotides on the molecule's 5'- and 3'-side, respectively. The ribonucleoprotein enzyme RNase P was identified almost 40 years ago and is considered a vestige from the "RNA world". Here, we present the state of affairs on prokaryotic RNase P, with a focus on recent findings on its role in RNA metabolism. tRNase Z was only identified 6 years ago, and we do not yet have a comprehensive understanding of its function. The current knowledge on prokaryotic tRNase Z in tRNA 3'-processing is reviewed here. A second, tRNase Z-independent pathway of tRNA 3'-end maturation involving 3'-exonucleases will also be discussed.
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Affiliation(s)
- Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany
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Franz Lang B, Hijri M. The complete Glomus intraradices mitochondrial genome sequence--a milestone in mycorrhizal research. THE NEW PHYTOLOGIST 2009; 183:3-6. [PMID: 19555368 DOI: 10.1111/j.1469-8137.2009.02885.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- B Franz Lang
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, 2900 Boulevard Edouard Montpetit, Montréal (Québec), Canada H3C 3J7
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal (Québec), Canada H1X 2B2
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12
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Pulukkunat DK, Gopalan V. Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis. Nucleic Acids Res 2008; 36:4172-80. [PMID: 18558617 PMCID: PMC2475606 DOI: 10.1093/nar/gkn360] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Ribonuclease P (RNase P), a ribonucleoprotein (RNP) complex required for tRNA maturation, comprises one essential RNA (RPR) and protein subunits (RPPs) numbering one in bacteria, and at least four in archaea and nine in eukarya. While the bacterial RPR is catalytically active in vitro, only select euryarchaeal and eukaryal RPRs are weakly active despite secondary structure similarity and conservation of nucleotide identity in their putative catalytic core. Such a decreased archaeal/eukaryal RPR function might imply that their cognate RPPs provide the functional groups that make up the active site. However, substrate-binding defects might mask the ability of some of these RPRs, such as that from the archaeon Methanocaldococcus jannaschii (Mja), to catalyze precursor tRNA (ptRNA) processing. To test this hypothesis, we constructed a ptRNA-Mja RPR conjugate and found that indeed it self-cleaves efficiently (k(obs), 0.15 min(-1) at pH 5.5 and 55 degrees C). Moreover, one pair of Mja RPPs (POP5-RPP30) enhanced k(obs) for the RPR-catalyzed self-processing by approximately 100-fold while the other pair (RPP21-RPP29) had no effect; both binary RPP complexes significantly reduced the monovalent and divalent ionic requirement. Our results suggest a common RNA-mediated catalytic mechanism in all RNase P and help uncover parallels in RNase P catalysis hidden by plurality in its subunit make-up.
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Affiliation(s)
- Dileep K Pulukkunat
- Ohio State Biochemistry Program and Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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Seif E, Altman S. RNase P cleaves the adenine riboswitch and stabilizes pbuE mRNA in Bacillus subtilis. RNA (NEW YORK, N.Y.) 2008; 14:1237-43. [PMID: 18441052 PMCID: PMC2390808 DOI: 10.1261/rna.833408] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Accepted: 03/13/2008] [Indexed: 05/23/2023]
Abstract
RNase P from Bacillus subtilis cleaves in vitro the adenine riboswitch upstream of pbuE, which codes for an adenine efflux pump. The guanine riboswitch, encoded upstream of xpt-pbuX operon, is not cleaved. The cleavage sites do not occur at any predicted structures that should be recognized by RNase P in the theoretical model of the adenine riboswitch. However, it is possible to draw alternative secondary structure models that match the apparent requirements for RNase P substrates at these cleavage sites. Support for these models is provided by appropriate mutagenesis experiments. Adenine showed no effect on the cleavage in vitro of the pbuE adenine riboswitch by RNase P holoenzyme from B. subtilis. The results of genetic experiments performed in B. subtilis support the cleavage of adenine riboswitch by RNase P in vivo and suggest that it induces the stabilization of pbuE mRNA under normal conditions.
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Affiliation(s)
- Elias Seif
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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Li D, Willkomm DK, Schön A, Hartmann RK. RNase P of the Cyanophora paradoxa cyanelle: A plastid ribozyme. Biochimie 2007; 89:1528-38. [PMID: 17881113 DOI: 10.1016/j.biochi.2007.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 08/04/2007] [Indexed: 11/23/2022]
Abstract
Ribonuclease P (RNase P) is a ribonucleoprotein enzyme that generates the mature 5' ends of tRNAs. Ubiquitous across all three kingdoms of life, the composition and functional contributions of the RNA and protein components of RNase P differ between the kingdoms. RNA-alone catalytic activity has been reported throughout bacteria, but only for some archaea, and only as trace activity for eukarya. Available information for RNase P from photosynthetic organelles points to large differences to bacterial as well as to eukaryotic RNase P: for spinach chloroplasts, protein-alone activity has been discussed; for RNase P from the cyanelle of the glaucophyte Cyanophora paradoxa, a type of organelle sharing properties of both cyanobacteria and chloroplasts, the proportion of protein was found to be around 80% rather than the usual 10% in bacteria. Furthermore, the latter RNase P was previously found catalytically inactive in the absence of protein under a variety of conditions; however, the RNA could be activated by a cyanobacterial protein, but not by the bacterial RNase P protein from Escherichia coli. Here we demonstrate that, under very high enzyme concentrations, the RNase P RNA from the cyanelle of C. paradoxa displays RNA-alone activity well above the detection level. Moreover, the RNA can be complemented to a functional holoenzyme by the E. coli RNase P protein, further supporting its overall bacterial-like architecture. Mutational analysis and domain swaps revealed that this A,U-rich cyanelle RNase P RNA is globally optimized but conformationally unstable, since changes as little as a single point mutation or a base pair identity switch at positions that are not part of the universally conserved catalytic core led to a complete loss of RNA-alone activity. Likely related to this low robustness, extensive structural changes towards an E. coli-type P5-7/P15-17 subdomain as a canonical interaction site for tRNA 3'-CCA termini could not be coaxed into increased ribozyme activity.
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MESH Headings
- Base Sequence
- Cyanobacteria/enzymology
- Enzyme Activation
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Holoenzymes/genetics
- Holoenzymes/metabolism
- Kinetics
- Nucleic Acid Conformation
- Organelles/enzymology
- Plasmids
- Plastids/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Catalytic/chemistry
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Recombinant Proteins/metabolism
- Ribonuclease P/genetics
- Ribonuclease P/metabolism
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
- Dan Li
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35037 Marburg, Germany
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Rodríguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H, Lang BF. Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans. Curr Biol 2007; 17:1420-5. [PMID: 17689961 DOI: 10.1016/j.cub.2007.07.036] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2006] [Revised: 07/10/2007] [Accepted: 07/17/2007] [Indexed: 11/18/2022]
Abstract
Resolving the global phylogeny of eukaryotes has proven to be challenging. Among the eukaryotic groups of uncertain phylogenetic position are jakobids, a group of bacterivorous flagellates that possess the most bacteria-like mitochondrial genomes known. Jakobids share several ultrastructural features with malawimonads and an assemblage of anaerobic protists (e.g., diplomonads and oxymonads). These lineages together with Euglenozoa and Heterolobosea have collectively been designated "excavates". However, published molecular phylogenies based on the sequences of nuclear rRNAs and up to six nucleus-encoded proteins do not provide convincing support for the monophyly of excavates, nor do they uncover their relationship to other major eukaryotic groups. Here, we report the first large-scale eukaryotic phylogeny, inferred from 143 nucleus-encoded proteins comprising 31,604 amino acid positions, that includes jakobids, malawimonads and cercozoans. We obtain compelling support for the monophyly of jakobids, Euglenozoa plus Heterolobosea (JEH group), and for the association of cercozoans with stramenopiles plus alveolates. Furthermore, we observe a sister-group relationship between the JEH group and malawimonads after removing fast-evolving species from the dataset. We discuss the implications of these results for the concept of "excavates" and for the elucidation of eukaryotic phylogeny in general.
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Affiliation(s)
- Naiara Rodríguez-Ezpeleta
- Centre Robert Cedergren, Département de Biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec H3T 1J4, Canada
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