1
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Gumińska N, Hałakuc P, Zakryś B, Milanowski R. Circular extrachromosomal DNA in Euglena gracilis under normal and stress conditions. Protist 2024; 175:126033. [PMID: 38574508 DOI: 10.1016/j.protis.2024.126033] [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: 11/30/2023] [Revised: 03/10/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
Extrachromosomal circular DNA (eccDNA) enhances genomic plasticity, augmenting its coding and regulatory potential. Advances in high-throughput sequencing have enabled the investigation of these structural variants. Although eccDNAs have been investigated in numerous taxa, they remained understudied in euglenids. Therefore, we examined eccDNAs predicted from Illumina sequencing data of Euglena gracilis Z SAG 1224-5/25, grown under optimal photoperiod and exposed to UV irradiation. We identified approximately 1000 unique eccDNA candidates, about 20% of which were shared across conditions. We also observed a significant enrichment of mitochondrially encoded eccDNA in the UV-irradiated sample. Furthermore, we found that the heterogeneity of eccDNA was reduced in UV-exposed samples compared to cells that were grown in optimal conditions. Hence, eccDNA appears to play a role in the response to oxidative stress in Euglena, as it does in other studied organisms. In addition to contributing to the understanding of Euglena genomes, our results contribute to the validation of bioinformatics pipelines on a large, non-model genome.
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Affiliation(s)
- Natalia Gumińska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland; Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland.
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland
| | - Bożena Zakryś
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland
| | - Rafał Milanowski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland.
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2
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Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun 2023; 14:3363. [PMID: 37291154 PMCID: PMC10250338 DOI: 10.1038/s41467-023-39084-2] [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: 12/14/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
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Affiliation(s)
- Yongsung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
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3
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Guerra-Slompo E, Cesaro G, Guimarães B, Zanchin N. Dissecting Trypanosoma brucei RRP44 function in the maturation of segmented ribosomal RNA using a regulated genetic complementation system. Nucleic Acids Res 2023; 51:396-419. [PMID: 36610751 PMCID: PMC9841430 DOI: 10.1093/nar/gkac1217] [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: 02/14/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Trypanosoma brucei belongs to a group of protozoans presenting fragmented large subunit rRNA. Its LSU rRNA equivalent to the 25S/28S rRNA of other eukaryotes is split into six fragments, requiring additional processing for removal of the extra spacer sequences. We have used a genetic complementation strategy to further investigate the T. brucei RRP44 nuclease in pre-rRNA maturation. TbRRP44 contains both a PIN and a RNB domain whose homologues are found in association with the exosome complex. We found that the exonucleolytic activity of the RNB domain as well as the physical presence of the PIN domain are essential for TbRRP44 function, while a catalytic site mutation in the PIN domain has no detectable effect on cell growth. A new endonucleolytic cleavage site in ITS1 was identified. In addition to the 5.8S rRNA 3'-end maturation, TbRRP44 is required for degradation of the excised 5'-ETS and for removal of part of ITS1 during maturation of the 18S rRNA 3'-end. TbRRP44 deficiency leads to accumulation of many LSU intermediate precursors, most of them not detected in control cells. TbRRP44 is also required for U3 snoRNA and spliced leader processing, indicating that TbRRP44 may have a wide role in RNA processing in T. brucei.
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Affiliation(s)
- Eloise Pavão Guerra-Slompo
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ, R. Prof. Algacyr Munhoz Mader 3775, 81350-010, Curitiba-PR, Brazil
| | - Giovanna Cesaro
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ, R. Prof. Algacyr Munhoz Mader 3775, 81350-010, Curitiba-PR, Brazil,Biochemistry Postgraduate Program, Federal University of Paraná, Curitiba-PR, Brazil
| | - Beatriz Gomes Guimarães
- Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ, R. Prof. Algacyr Munhoz Mader 3775, 81350-010, Curitiba-PR, Brazil,Biochemistry Postgraduate Program, Federal University of Paraná, Curitiba-PR, Brazil
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4
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Cordoba J, Perez E, Van Vlierberghe M, Bertrand AR, Lupo V, Cardol P, Baurain D. De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis. Genes (Basel) 2021; 12:842. [PMID: 34072576 PMCID: PMC8227486 DOI: 10.3390/genes12060842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023] Open
Abstract
Euglena gracilis is a well-known photosynthetic microeukaryote considered as the product of a secondary endosymbiosis between a green alga and a phagotrophic unicellular belonging to the same eukaryotic phylum as the parasitic trypanosomatids. As its nuclear genome has proven difficult to sequence, reliable transcriptomes are important for functional studies. In this work, we assembled a new consensus transcriptome by combining sequencing reads from five independent studies. Based on a detailed comparison with two previously released transcriptomes, our consensus transcriptome appears to be the most complete so far. Remapping the reads on it allowed us to compare the expression of the transcripts across multiple culture conditions at once and to infer a functionally annotated network of co-expressed genes. Although the emergence of meaningful gene clusters indicates that some biological signal lies in gene expression levels, our analyses confirm that gene regulation in euglenozoans is not primarily controlled at the transcriptional level. Regarding the origin of E. gracilis, we observe a heavily mixed gene ancestry, as previously reported, and rule out sequence contamination as a possible explanation for these observations. Instead, they indicate that this complex alga has evolved through a convoluted process involving much more than two partners.
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Affiliation(s)
- Javier Cordoba
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
| | - Emilie Perez
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Mick Van Vlierberghe
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Amandine R. Bertrand
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Valérian Lupo
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Pierre Cardol
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
| | - Denis Baurain
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
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Záhonová K, Lax G, Sinha SD, Leonard G, Richards TA, Lukeš J, Wideman JG. Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans. BMC Biol 2021; 19:103. [PMID: 34001130 PMCID: PMC8130358 DOI: 10.1186/s12915-021-01035-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/22/2021] [Indexed: 12/28/2022] Open
Abstract
Background The supergroup Euglenozoa unites heterotrophic flagellates from three major clades, kinetoplastids, diplonemids, and euglenids, each of which exhibits extremely divergent mitochondrial characteristics. Mitochondrial genomes (mtDNAs) of euglenids comprise multiple linear chromosomes carrying single genes, whereas mitochondrial chromosomes are circular non-catenated in diplonemids, but circular and catenated in kinetoplastids. In diplonemids and kinetoplastids, mitochondrial mRNAs require extensive and diverse editing and/or trans-splicing to produce mature transcripts. All known euglenozoan mtDNAs exhibit extremely short mitochondrial small (rns) and large (rnl) subunit rRNA genes, and absence of tRNA genes. How these features evolved from an ancestral bacteria-like circular mitochondrial genome remains unanswered. Results We sequenced and assembled 20 euglenozoan single-cell amplified genomes (SAGs). In our phylogenetic and phylogenomic analyses, three SAGs were placed within kinetoplastids, 14 within diplonemids, one (EU2) within euglenids, and two SAGs with nearly identical small subunit rRNA gene (18S) sequences (EU17/18) branched as either a basal lineage of euglenids, or as a sister to all euglenozoans. Near-complete mitochondrial genomes were identified in EU2 and EU17/18. Surprisingly, both EU2 and EU17/18 mitochondrial contigs contained multiple genes and one tRNA gene. Furthermore, EU17/18 mtDNA possessed several features unique among euglenozoans including full-length rns and rnl genes, six mitoribosomal genes, and nad11, all likely on a single chromosome. Conclusions Our data strongly suggest that EU17/18 is an early-branching euglenozoan with numerous ancestral mitochondrial features. Collectively these data contribute to untangling the early evolution of euglenozoan mitochondria. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01035-y.
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Affiliation(s)
- Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Savar D Sinha
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, USA
| | - Guy Leonard
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
| | - Jeremy G Wideman
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, USA.
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6
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Harada R, Inagaki Y. Phage Origin of Mitochondrion-Localized Family A DNA Polymerases in Kinetoplastids and Diplonemids. Genome Biol Evol 2021; 13:6081025. [PMID: 33432342 PMCID: PMC7883662 DOI: 10.1093/gbe/evab003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2021] [Indexed: 01/18/2023] Open
Abstract
Mitochondria retain their own genomes as other bacterial endosymbiont-derived organelles. Nevertheless, no protein for DNA replication and repair is encoded in any mitochondrial genomes (mtDNAs) assessed to date, suggesting that the nucleus primarily governs the maintenance of mtDNA. As the proteins of diverse evolutionary origins occupy a large proportion of the current mitochondrial proteomes, we anticipate finding the same evolutionary trend in the nucleus-encoded machinery for mtDNA maintenance. Indeed, none of the DNA polymerases (DNAPs) in the mitochondrial endosymbiont, a putative α-proteobacterium, seemingly had been inherited by their descendants (mitochondria), as none of the known types of mitochondrion-localized DNAP showed a specific affinity to the α-proteobacterial DNAPs. Nevertheless, we currently have no concrete idea of how and when the known types of mitochondrion-localized DNAPs emerged. We here explored the origins of mitochondrion-localized DNAPs after the improvement of the samplings of DNAPs from bacteria and phages/viruses. Past studies have revealed that a set of mitochondrion-localized DNAPs in kinetoplastids and diplonemids, namely PolIB, PolIC, PolID, PolI-Perk1/2, and PolI-dipl (henceforth designated collectively as “PolIBCD+”) have emerged from a single DNAP. In this study, we recovered an intimate connection between PolIBCD+ and the DNAPs found in a particular group of phages. Thus, the common ancestor of kinetoplastids and diplonemids most likely converted a laterally acquired phage DNAP into a mitochondrion-localized DNAP that was ancestral to PolIBCD+. The phage origin of PolIBCD+ hints at a potentially large contribution of proteins acquired via nonvertical processes to the machinery for mtDNA maintenance in kinetoplastids and diplonemids.
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Affiliation(s)
- Ryo Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan.,Center for Computational Sciences, University of Tsukuba, Japan
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7
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Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa. Pathogens 2020; 9:pathogens9040257. [PMID: 32244644 PMCID: PMC7238167 DOI: 10.3390/pathogens9040257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/29/2020] [Accepted: 03/30/2020] [Indexed: 11/17/2022] Open
Abstract
The order Trypanosomatida has been well studied due to its pathogenicity and the unique biology of the mitochondrion. In Trypanosoma brucei, four DNA polymerases, namely PolIA, PolIB, PolIC, and PolID, related to bacterial DNA polymerase I (PolI), were shown to be localized in mitochondria experimentally. These mitochondrion-localized DNA polymerases are phylogenetically distinct from other family A DNA polymerases, such as bacterial PolI, DNA polymerase gamma (Polγ) in human and yeasts, “plant and protist organellar DNA polymerase (POP)” in diverse eukaryotes. However, the diversity of mitochondrion-localized DNA polymerases in Euglenozoa other than Trypanosomatida is poorly understood. In this study, we discovered putative mitochondrion-localized DNA polymerases in broad members of three major classes of Euglenozoa—Kinetoplastea, Diplonemea, and Euglenida—to explore the origin and evolution of trypanosomatid PolIA-D. We unveiled distinct inventories of mitochondrion-localized DNA polymerases in the three classes: (1) PolIA is ubiquitous across the three euglenozoan classes, (2) PolIB, C, and D are restricted in kinetoplastids, (3) new types of mitochondrion-localized DNA polymerases were identified in a prokinetoplastid and diplonemids, and (4) evolutionarily distinct types of POP were found in euglenids. We finally propose scenarios to explain the inventories of mitochondrion-localized DNA polymerases in Kinetoplastea, Diplonemea, and Euglenida.
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Abstract
The ribosome and RNase P are cellular ribonucleoprotein complexes that perform peptide bond synthesis and phosphodiester bond cleavage, respectively. Both are ancient biological assemblies that were already present in the last universal common ancestor of all life. The large subunit rRNA in the ribosome and the RNA subunit of RNase P are the ribozyme components required for catalysis. Here, we explore the idea that these two large ribozymes may have begun their evolutionary odyssey as an assemblage of RNA "fragments" smaller than the contemporary full-length versions and that they transitioned through distinct stages along a pathway that may also be relevant for the evolution of other non-coding RNAs.
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Affiliation(s)
- Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210.
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9
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Vesteg M, Hadariová L, Horváth A, Estraño CE, Schwartzbach SD, Krajčovič J. Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa. Biol Rev Camb Philos Soc 2019; 94:1701-1721. [PMID: 31095885 DOI: 10.1111/brv.12523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 01/23/2023]
Abstract
Parasitic trypanosomatids and phototrophic euglenids are among the most extensively studied euglenozoans. The phototrophic euglenid lineage arose relatively recently through secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga that evolved into the euglenid secondary chloroplast. The parasitic trypanosomatids (i.e. Trypanosoma spp. and Leishmania spp.) and the freshwater phototrophic euglenids (i.e. Euglena gracilis) are the most evolutionary distant lineages in the Euglenozoa phylogenetic tree. The molecular and cell biological traits they share can thus be considered as ancestral traits originating in the common euglenozoan ancestor. These euglenozoan ancestral traits include common mitochondrial presequence motifs, respiratory chain complexes containing various unique subunits, a unique ATP synthase structure, the absence of mitochondria-encoded transfer RNAs (tRNAs), a nucleus with a centrally positioned nucleolus, closed mitosis without dissolution of the nuclear membrane and nucleoli, a nuclear genome containing the unusual 'J' base (β-D-glucosyl-hydroxymethyluracil), processing of nucleus-encoded precursor messenger RNAs (pre-mRNAs) via spliced-leader RNA (SL-RNA) trans-splicing, post-transcriptional gene silencing by the RNA interference (RNAi) pathway and the absence of transcriptional regulation of nuclear gene expression. Mitochondrial uridine insertion/deletion RNA editing directed by guide RNAs (gRNAs) evolved in the ancestor of the kinetoplastid lineage. The evolutionary origin of other molecular features known to be present only in either kinetoplastids (i.e. polycistronic transcripts, compaction of nuclear genomes) or euglenids (i.e. monocistronic transcripts, huge genomes, many nuclear cis-spliced introns, polyproteins) is unclear.
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Affiliation(s)
- Matej Vesteg
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Lucia Hadariová
- Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV), 252 50, Vestec, Czech Republic.,Department of Parasitology, Faculty of Science, Charles University in Prague, 128 44, Prague, Czech Republic
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia
| | - Carlos E Estraño
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152-3560, USA
| | - Steven D Schwartzbach
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152-3560, USA
| | - Juraj Krajčovič
- Department of Biology, Faculty of Natural Sciences, University of ss. Cyril and Methodius, 917 01, Trnava, Slovakia
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10
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Burger G, Valach M. Perfection of eccentricity: Mitochondrial genomes of diplonemids. IUBMB Life 2018; 70:1197-1206. [PMID: 30304578 DOI: 10.1002/iub.1927] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 01/14/2023]
Abstract
Mitochondria are the sandbox of evolution as exemplified most particularly by the diplonemids, a group of marine microeukaryotes. These protists are uniquely characterized by their highly multipartite mitochondrial genome and systematically fragmented genes whose pieces are spread out over several dozens of chromosomes. The type species Diplonema papillatum was the first member of this group in which the expression of fragmented mitochondrial genes was investigated experimentally. We now know that gene expression involves separate transcription of gene pieces (modules), RNA editing of module transcripts, and module joining to mature mRNAs and rRNAs. The mechanism of cognate module recognition and ligation is distinct from known intron splicing and remains to be uncovered. Here, we review the current status of research on mitochondrial genome architecture, as well as gene complement, structure, and expression modes in diplonemids. Further, we discuss the potential molecular mechanisms of posttranscriptional processing, and finally reflect on the evolutionary trajectories and trends of mtDNA evolution as seen in this protist group. © 2018 IUBMB Life, 70(12):1197-1206, 2018.
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Affiliation(s)
- Gertraud Burger
- Département de Biochimie, Robert Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Québec, Canada
| | - Matus Valach
- Département de Biochimie, Robert Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, Québec, Canada
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11
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Faktorová D, Valach M, Kaur B, Burger G, Lukeš J. Mitochondrial RNA Editing and Processing in Diplonemid Protists. RNA METABOLISM IN MITOCHONDRIA 2018. [DOI: 10.1007/978-3-319-78190-7_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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12
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Zimorski V, Rauch C, van Hellemond JJ, Tielens AGM, Martin WF. The Mitochondrion of Euglena gracilis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 979:19-37. [PMID: 28429315 DOI: 10.1007/978-3-319-54910-1_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the presence of oxygen, Euglena gracilis mitochondria function much like mammalian mitochondria. Under anaerobiosis, E. gracilis mitochondria perform a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. Some components (enzymes and cofactors) of Euglena's anaerobic energy metabolism are found among the anaerobic mitochondria of invertebrates, others are found among hydrogenosomes, the H2-producing anaerobic mitochondria of protists.
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Affiliation(s)
- Verena Zimorski
- Institute of Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Cessa Rauch
- Institute of Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jaap J van Hellemond
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Aloysius G M Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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13
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Yang J, Harding T, Kamikawa R, Simpson AGB, Roger AJ. Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids. Genome Biol Evol 2017; 9:1161-1174. [PMID: 28453770 PMCID: PMC5421314 DOI: 10.1093/gbe/evx086] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 12/20/2022] Open
Abstract
Discoba (Excavata) is an evolutionarily important group of eukaryotes that includes Jakobida, with the most bacterial-like mitochondrial genomes known, and Euglenozoa, many of which have extensively fragmented mitochondrial genomes. However, little is known about the mitochondrial genomes of Heterolobosea, the third main group of Discoba. Here, we studied two heteroloboseids—an undescribed amoeba “BB2” and Pharyngomonas kirbyi. Phylogenomic analysis revealed that they form a clade that is a sister group to all other Heterolobosea. We characterized the mitochondrial genomes of BB2 and P. kirbyi, which encoded 44 and 48 putative protein-coding genes respectively. Their gene contents were similar to that of Naegleria. In BB2, mitochondrially encoded RNAs were heavily edited, with ∼500 mononucleotide insertion events, mostly guanosines. These insertions always have the same identity as an adjacent nucleotide. Editing occurs in all ribosomal RNAs and protein-coding transcripts except one, and half of the transfer RNAs. Analysis of Illumina deep-sequencing data suggested that this RNA editing is very accurate and efficient, and most likely co-transcriptional. The dissimilarity of this editing process to other RNA editing phenomena in discobids, as well as its apparent absence in P. kirbyi, suggest that this remarkably extensive system of insertional editing evolved independently in the BB2 lineage, after its divergence from the P. kirbyi lineage.
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Affiliation(s)
- Jiwon Yang
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Tommy Harding
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Graduate School of Global Environmental Studies, Kyoto University, Japan
| | - Alastair G B Simpson
- Centre for Comparative Genomics and Evolutionary Bioinformatics and Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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14
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Ebenezer TE, Carrington M, Lebert M, Kelly S, Field MC. Euglena gracilis Genome and Transcriptome: Organelles, Nuclear Genome Assembly Strategies and Initial Features. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 979:125-140. [PMID: 28429320 DOI: 10.1007/978-3-319-54910-1_7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain. Earlier studies suggested an extensive nuclear DNA content, with likely a high degree of repetitive sequence, together with significant extrachromosomal elements. To produce a list of coding sequences we have combined transcriptome data from both published and new sources, as well as embarked on de novo sequencing using a combination of 454, Illumina paired end libraries and long PacBio reads. Preliminary analysis suggests a surprisingly large genome approaching 2 Gbp, with a highly fragmented architecture and extensive repeat composition. Over 80% of the RNAseq reads from E. gracilis maps to the assembled genome sequence, which is comparable with the well assembled genomes of T. brucei and T. cruzi. In order to achieve this level of assembly we employed multiple informatics pipelines, which are discussed here. Finally, as a preliminary view of the genome architecture, we discuss the tubulin and calmodulin genes, which highlight potential novel splicing mechanisms.
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Affiliation(s)
- ThankGod Echezona Ebenezer
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.,School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Michael Lebert
- Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, Staudtstraβe 5, Erlangen, 91058, Germany
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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15
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Burger G, Moreira S, Valach M. Genes in Hiding. Trends Genet 2016; 32:553-565. [PMID: 27460648 DOI: 10.1016/j.tig.2016.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 12/25/2022]
Abstract
Unrecognizable genes are an unsettling problem in genomics. Here, we survey the various types of cryptic genes and the corresponding deciphering strategies employed by cells. Encryption that renders genes substantially different from homologs in other species includes sequence substitution, insertion, deletion, fragmentation plus scrambling, and invasion by mobile genetic elements. Cells decode cryptic genes at the DNA, RNA or protein level. We will focus on a recently discovered case of unparalleled encryption involving massive gene fragmentation and nucleotide deletions and substitutions, occurring in the mitochondrial genome of a poorly understood protist group, the diplonemids. This example illustrates that comprehensive gene detection requires not only auxiliary sequence information - transcriptome and proteome data - but also knowledge about a cell's deciphering arsenal.
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Affiliation(s)
- Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada.
| | - Sandrine Moreira
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
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16
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Smith DR, Keeling PJ. Protists and the Wild, Wild West of Gene Expression: New Frontiers, Lawlessness, and Misfits. Annu Rev Microbiol 2016; 70:161-78. [PMID: 27359218 DOI: 10.1146/annurev-micro-102215-095448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The DNA double helix has been called one of life's most elegant structures, largely because of its universality, simplicity, and symmetry. The expression of information encoded within DNA, however, can be far from simple or symmetric and is sometimes surprisingly variable, convoluted, and wantonly inefficient. Although exceptions to the rules exist in certain model systems, the true extent to which life has stretched the limits of gene expression is made clear by nonmodel systems, particularly protists (microbial eukaryotes). The nuclear and organelle genomes of protists are subject to the most tangled forms of gene expression yet identified. The complicated and extravagant picture of the underlying genetics of eukaryotic microbial life changes how we think about the flow of genetic information and the evolutionary processes shaping it. Here, we discuss the origins, diversity, and growing interest in noncanonical protist gene expression and its relationship to genomic architecture.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada N6A 5B7;
| | - Patrick J Keeling
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4;
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17
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Faktorová D, Dobáková E, Peña-Diaz P, Lukeš J. From simple to supercomplex: mitochondrial genomes of euglenozoan protists. F1000Res 2016. [PMID: 27018240 DOI: 10.12688/f1000research.8040.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitochondria are double membrane organelles of endosymbiotic origin, best known for constituting the centre of energetics of a eukaryotic cell. They contain their own mitochondrial genome, which as a consequence of gradual reduction during evolution typically contains less than two dozens of genes. In this review, we highlight the extremely diverse architecture of mitochondrial genomes and mechanisms of gene expression between the three sister groups constituting the phylum Euglenozoa - Euglenida, Diplonemea and Kinetoplastea. The earliest diverging euglenids possess a simplified mitochondrial genome and a conventional gene expression, whereas both are highly complex in the two other groups. The expression of their mitochondrial-encoded proteins requires extensive post-transcriptional modifications guided by complex protein machineries and multiple small RNA molecules. Moreover, the least studied diplonemids, which have been recently discovered as a highly abundant component of the world ocean plankton, possess one of the most complicated mitochondrial genome organisations known to date.
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Affiliation(s)
- Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Departments of Biochemistry and Genetics, Faculty of Natural Sciences, Comenius Universtity, Bratislava, Slovakia
| | - Priscila Peña-Diaz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Canadian Institute for Adavanced Research, Toronto, Ontario, Canada
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18
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Faktorová D, Dobáková E, Peña-Diaz P, Lukeš J. From simple to supercomplex: mitochondrial genomes of euglenozoan protists. F1000Res 2016; 5. [PMID: 27018240 PMCID: PMC4806707 DOI: 10.12688/f1000research.8040.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2016] [Indexed: 01/06/2023] Open
Abstract
Mitochondria are double membrane organelles of endosymbiotic origin, best known for constituting the centre of energetics of a eukaryotic cell. They contain their own mitochondrial genome, which as a consequence of gradual reduction during evolution typically contains less than two dozens of genes. In this review, we highlight the extremely diverse architecture of mitochondrial genomes and mechanisms of gene expression between the three sister groups constituting the phylum Euglenozoa - Euglenida, Diplonemea and Kinetoplastea. The earliest diverging euglenids possess a simplified mitochondrial genome and a conventional gene expression, whereas both are highly complex in the two other groups. The expression of their mitochondrial-encoded proteins requires extensive post-transcriptional modifications guided by complex protein machineries and multiple small RNA molecules. Moreover, the least studied diplonemids, which have been recently discovered as a highly abundant component of the world ocean plankton, possess one of the most complicated mitochondrial genome organisations known to date.
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Affiliation(s)
- Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Departments of Biochemistry and Genetics, Faculty of Natural Sciences, Comenius Universtity, Bratislava, Slovakia
| | - Priscila Peña-Diaz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Canadian Institute for Adavanced Research, Toronto, Ontario, Canada
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19
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Moreira S, Valach M, Aoulad-Aissa M, Otto C, Burger G. Novel modes of RNA editing in mitochondria. Nucleic Acids Res 2016; 44:4907-19. [PMID: 27001515 PMCID: PMC4889940 DOI: 10.1093/nar/gkw188] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/10/2016] [Indexed: 11/20/2022] Open
Abstract
Gene structure and expression in diplonemid mitochondria are unparalleled. Genes are fragmented in pieces (modules) that are separately transcribed, followed by the joining of module transcripts to contiguous RNAs. Some instances of unique uridine insertion RNA editing at module boundaries were noted, but the extent and potential occurrence of other editing types remained unknown. Comparative analysis of deep transcriptome and genome data from Diplonema papillatum mitochondria reveals ∼220 post-transcriptional insertions of uridines, but no insertions of other nucleotides nor deletions. In addition, we detect in total 114 substitutions of cytosine by uridine and adenosine by inosine, amassed into unusually compact clusters. Inosines in transcripts were confirmed experimentally. This is the first report of adenosine-to-inosine editing of mRNAs and ribosomal RNAs in mitochondria. In mRNAs, editing causes mostly amino-acid additions and non-synonymous substitutions; in ribosomal RNAs, it permits formation of canonical secondary structures. Two extensively edited transcripts were compared across four diplonemids. The pattern of uridine-insertion editing is strictly conserved, whereas substitution editing has diverged dramatically, but still rendering diplonemid proteins more similar to other eukaryotic orthologs. We posit that RNA editing not only compensates but also sustains, or even accelerates, ultra-rapid evolution of genome structure and sequence in diplonemid mitochondria.
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Affiliation(s)
- Sandrine Moreira
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada
| | - Mohamed Aoulad-Aissa
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada
| | - Christian Otto
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, D-04109, Germany
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada
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20
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Bicudo CEDM, Menezes M. Phylogeny and Classification of Euglenophyceae: A Brief Review. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Zíková A, Hampl V, Paris Z, Týč J, Lukeš J. Aerobic mitochondria of parasitic protists: Diverse genomes and complex functions. Mol Biochem Parasitol 2016; 209:46-57. [PMID: 26906976 DOI: 10.1016/j.molbiopara.2016.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 02/08/2023]
Abstract
In this review the main features of the mitochondria of aerobic parasitic protists are discussed. While the best characterized organelles are by far those of kinetoplastid flagellates and Plasmodium, we also consider amoebae Naegleria and Acanthamoeba, a ciliate Ichthyophthirius and related lineages. The simplistic view of the mitochondrion as just a power house of the cell has already been abandoned in multicellular organisms and available data indicate that this also does not apply for protists. We discuss in more details the following mitochondrial features: genomes, post-transcriptional processing, translation, biogenesis of iron-sulfur complexes, heme metabolism and the electron transport chain. Substantial differences in all these core mitochondrial features between lineages are compatible with the view that aerobic protists harbor organelles that are more complex and flexible than previously appreciated.
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Affiliation(s)
- Alena Zíková
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice (Budweis), Czech Republic.
| | - Vladimír Hampl
- Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice (Budweis), Czech Republic; Canadian Institute for Advanced Research, Toronto, Canada.
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22
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O’Neill EC, Trick M, Henrissat B, Field RA. Euglena in time: Evolution, control of central metabolic processes and multi-domain proteins in carbohydrate and natural product biochemistry. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.pisc.2015.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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23
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Dobáková E, Flegontov P, Skalický T, Lukeš J. Unexpectedly Streamlined Mitochondrial Genome of the Euglenozoan Euglena gracilis. Genome Biol Evol 2015; 7:3358-67. [PMID: 26590215 PMCID: PMC4700960 DOI: 10.1093/gbe/evv229] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2015] [Indexed: 11/29/2022] Open
Abstract
In this study, we describe the mitochondrial genome of the excavate flagellate Euglena gracilis. Its gene complement is reduced as compared with the well-studied sister groups Diplonemea and Kinetoplastea. We have identified seven protein-coding genes: Three subunits of respiratory complex I (nad1, nad4, and nad5), one subunit of complex III (cob), and three subunits of complex IV (cox1, cox2, and a highly divergent cox3). Moreover, fragments of ribosomal RNA genes have also been identified. Genes encoding subunits of complex V, ribosomal proteins and tRNAs were missing, and are likely located in the nuclear genome. Although mitochondrial genomes of diplonemids and kinetoplastids possess the most complex RNA processing machineries known, including trans-splicing and editing of the uridine insertion/deletion type, respectively, our transcriptomic data suggest their total absence in E. gracilis. This finding supports a scenario in which the complex mitochondrial processing machineries of both sister groups evolved relatively late in evolution from a streamlined genome and transcriptome of their common predecessor.
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Affiliation(s)
- Eva Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic Departments of Biochemistry and Genetics, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Tomáš Skalický
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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24
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Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes. Proc Natl Acad Sci U S A 2015; 112:10177-84. [PMID: 25814499 DOI: 10.1073/pnas.1422049112] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial and plastid genomes show a wide array of architectures, varying immensely in size, structure, and content. Some organelle DNAs have even developed elaborate eccentricities, such as scrambled coding regions, nonstandard genetic codes, and convoluted modes of posttranscriptional modification and editing. Here, we compare and contrast the breadth of genomic complexity between mitochondrial and plastid chromosomes. Both organelle genomes have independently evolved many of the same features and taken on similar genomic embellishments, often within the same species or lineage. This trend is most likely because the nuclear-encoded proteins mediating these processes eventually leak from one organelle into the other, leading to a high likelihood of processes appearing in both compartments in parallel. However, the complexity and intensity of genomic embellishments are consistently more pronounced for mitochondria than for plastids, even when they are found in both compartments. We explore the evolutionary forces responsible for these patterns and argue that organelle DNA repair processes, mutation rates, and population genetic landscapes are all important factors leading to the observed convergence and divergence in organelle genome architecture.
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25
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How amino acids and peptides shaped the RNA world. Life (Basel) 2015; 5:230-46. [PMID: 25607813 PMCID: PMC4390850 DOI: 10.3390/life5010230] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 12/16/2014] [Accepted: 01/14/2015] [Indexed: 11/17/2022] Open
Abstract
The “RNA world” hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis. However, this view is incomplete at best. The modern protein-RNA ribosome most probably is not a distorted form of a “pure RNA ribosome” evolution started out with. Though the oldest center of the ribosome seems “RNA only”, we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides. Very small RNAs (versatile and stable due to basepairing) and amino acids, as well as dipeptides, coevolved. Remember, it is the amino group of aminoacylated tRNA that attacks peptidyl-tRNA, destroying the bond between peptide and tRNA. This activity of the amino acid part of aminoacyl-tRNA illustrates the centrality of amino acids in life. With the rise of the “RNA world” view of early life, the pendulum seems to have swung too much towards the ribozymatic part of early biochemistry. The necessary presence and activity of amino acids and peptides is in need of highlighting. In this article, we try to bring the role of the peptide component of early life back into focus. We argue that an RNA world completely independent of amino acids never existed.
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26
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Kamikawa R, Kolisko M, Nishimura Y, Yabuki A, Brown MW, Ishikawa SA, Ishida KI, Roger AJ, Hashimoto T, Inagaki Y. Gene content evolution in Discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa. Genome Biol Evol 2015; 6:306-15. [PMID: 24448982 PMCID: PMC3942025 DOI: 10.1093/gbe/evu015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The unicellular eukaryotic assemblage Discoba (Excavata) comprises four lineages: the Heterolobosea, Euglenozoa, Jakobida, and Tsukubamonadida. Discoba has been considered as a key assemblage for understanding the early evolution of mitochondrial (mt) genomes, as jakobids retain the most gene-rich (i.e., primitive) genomes compared with any other eukaryotes determined to date. However, to date, mt genome sequences have been completed for only a few groups within Discoba, including jakobids, two closely related heteroloboseans, and kinetoplastid euglenozoans. The Tsukubamonadida is the least studied lineage, as the order was only recently established with the description of a sole representative species, Tsukubamonas globosa. The evolutionary relationship between T. globosa and other discobids has yet to be resolved, and no mt genome data are available for this particular organism. Here, we use a “phylogenomic” approach to resolve the relationship between T. globosa, heteroloboseans, euglenozoans, and jakobids. In addition, we have characterized the mt genome of T. globosa (48,463 bp in length), which encodes 52 putative protein-coding and 29 RNA genes. By mapping the gene repertoires of discobid mt genomes onto the well-resolved Discoba tree, we model gene loss events during the evolution of discobid mt genomes.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Global Environmental Studies and Graduate School of Human and Environmental Studies, Kyoto University, Japan
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27
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Abstract
I am honored to have been asked to contribute to this memorial issue, although I cannot claim to have known Carl Woese well. Carl's insights and the discoveries that his research group made over the years certainly stimulated my own research program, and at several points early on, interactions with him were pivotal in my career. Here I comment on these personal dealings with Carl and emphasize his influence in two areas of long-standing interest in my lab: organelle evolution and rRNA evolution.
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Affiliation(s)
- Michael W Gray
- Centre for Comparative Genomics and Evolutionary Bioinformatics; Department of Biochemistry and Molecular Biology; Dalhousie University; Halifax, NS Canada
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28
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Valach M, Moreira S, Kiethega GN, Burger G. Trans-splicing and RNA editing of LSU rRNA in Diplonema mitochondria. Nucleic Acids Res 2013; 42:2660-72. [PMID: 24259427 PMCID: PMC3936708 DOI: 10.1093/nar/gkt1152] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Mitochondrial ribosomal RNAs (rRNAs) often display reduced size and deviant secondary structure, and sometimes are fragmented, as are their corresponding genes. Here we report a mitochondrial large subunit rRNA (mt-LSU rRNA) with unprecedented features. In the protist Diplonema, the rnl gene is split into two pieces (modules 1 and 2, 534- and 352-nt long) that are encoded by distinct mitochondrial chromosomes, yet the rRNA is continuous. To reconstruct the post-transcriptional maturation pathway of this rRNA, we have catalogued transcript intermediates by deep RNA sequencing and RT-PCR. Gene modules are transcribed separately. Subsequently, transcripts are end-processed, the module-1 transcript is polyuridylated and the module-2 transcript is polyadenylated. The two modules are joined via trans-splicing that retains at the junction ∼26 uridines, resulting in an extent of insertion RNA editing not observed before in any system. The A-tail of trans-spliced molecules is shorter than that of mono-module 2, and completely absent from mitoribosome-associated mt-LSU rRNA. We also characterize putative antisense transcripts. Antisense-mono-modules corroborate bi-directional transcription of chromosomes. Antisense-mt-LSU rRNA, if functional, has the potential of guiding concomitantly trans-splicing and editing of this rRNA. Together, these findings open a window on the investigation of complex regulatory networks that orchestrate multiple and biochemically diverse post-transcriptional events.
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Affiliation(s)
- Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics; Université de Montréal, Montreal, H3C 3J7, Canada
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29
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Fuhrmann G, Swart E, Nowacki M, Lipps HJ. RNA-dependent genome processing during nuclear differentiation: the model systems of stichotrichous ciliates. Epigenomics 2013; 5:229-36. [PMID: 23566098 DOI: 10.2217/epi.13.15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We introduce ciliated protozoa, and more specifically the stichotrichous ciliates Oxytricha and Stylonychia, as biological model systems for the analysis of programmed DNA-reorganization processes during nuclear differentiation. These include DNA excision, DNA elimination, reordering of gene segments and specific gene amplification. We show that small nuclear RNAs specify DNA sequences to be excised or retained, but also discuss the need for a RNA template molecule derived from the parental nucleus for these processes. This RNA template guides reordering of gene segments to become functional genes and determines gene copy number in the differentiated nucleus. Since the template is derived from the parental macronucleus, gene reordering and DNA amplification are inherited in a non-Mendelian epigenetic manner.
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Affiliation(s)
- Gloria Fuhrmann
- Institute of Cell Biology, Centre for Biomedical Research & Education (ZBAF), Stockumer Str. 10, 58453 Witten, Germany
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30
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Kolesnikov AA, Gerasimov ES. Diversity of mitochondrial genome organization. BIOCHEMISTRY (MOSCOW) 2013; 77:1424-35. [PMID: 23379519 DOI: 10.1134/s0006297912130020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this review, we discuss types of mitochondrial genome structural organization (architecture), which includes the following characteristic features: size and the shape of DNA molecule, number of encoded genes, presence of cryptogenes, and editing of primary transcripts.
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Affiliation(s)
- A A Kolesnikov
- Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russia.
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Euglena gracilis and Trypanosomatids Possess Common Patterns in Predicted Mitochondrial Targeting Presequences. J Mol Evol 2012; 75:119-29. [DOI: 10.1007/s00239-012-9523-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 09/24/2012] [Indexed: 10/27/2022]
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Pelin A, Pombert JF, Salvioli A, Bonen L, Bonfante P, Corradi N. The mitochondrial genome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals two unsuspected trans-splicing events of group I introns. THE NEW PHYTOLOGIST 2012; 194:836-845. [PMID: 22320438 DOI: 10.1111/j.1469-8137.2012.04072.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
• Arbuscular mycorrhizal fungi (AMF) are ubiquitous organisms that benefit ecosystems through the establishment of an association with the roots of most plants: the mycorrhizal symbiosis. Despite their ecological importance, however, these fungi have been poorly studied at the genome level. • In this study, total DNA from the AMF Gigaspora margarita was subjected to a combination of 454 and Illumina sequencing, and the resulting reads were used to assemble its mitochondrial genome de novo. This genome was annotated and compared with those of other relatives to better comprehend the evolution of the AMF lineage. • The mitochondrial genome of G. margarita is unique in many ways, exhibiting a large size (97 kbp) and elevated GC content (45%). This genome also harbors molecular events that were previously unknown to occur in fungal mitochondrial genomes, including trans-splicing of group I introns from two different genes coding for the first subunit of the cytochrome oxidase and for the small subunit of the rRNA. • This study reports the second published genome from an AMF organelle, resulting in relevant DNA sequence information from this poorly studied fungal group, and providing new insights into the frequency, origin and evolution of trans-spliced group I introns found across the mitochondrial genomes of distantly related organisms.
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Affiliation(s)
- Adrian Pelin
- Department of Biology, University of Ottawa, Ottawa, K1N 6N5, ON, Canada
| | - Jean-François Pombert
- Department of Botany, University of British Columbia; Vancouver, V6T 1Z4, BC, Canada
| | - Alessandra Salvioli
- Dipartimento di Biologia Vegetale, Università di Torino, Torino, I-10125, Italy
| | - Linda Bonen
- Department of Biology, University of Ottawa, Ottawa, K1N 6N5, ON, Canada
| | - Paola Bonfante
- Dipartimento di Biologia Vegetale, Università di Torino, Torino, I-10125, Italy
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, K1N 6N5, ON, Canada
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Moreira S, Breton S, Burger G. Unscrambling genetic information at the RNA level. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:213-28. [PMID: 22275292 DOI: 10.1002/wrna.1106] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Genomics aims at unraveling the blueprint of life; however, DNA sequence alone does not always reveal the proteins and structural RNAs encoded by the genome. The reason is that genetic information is often encrypted. Recognizing the logic of encryption, and understanding how living cells decode hidden information--at the level of DNA, RNA or protein--is challenging. RNA-level decryption includes topical RNA editing and more 'macroscopic' transcript rearrangements. The latter events involve the four types of introns recognized to date, notably spliceosomal, group I, group II, and archaeal/tRNA splicing. Intricate variants, such as alternative splicing and trans-splicing, have been reported for each intron type, but the biological significance has not always been confirmed. Novel RNA-level unscrambling processes were recently discovered in mitochondria of dinoflagellates and diplonemids, and potentially euglenids. These processes seem not to rely on known introns, and the corresponding molecular mechanisms remain to be elucidated.
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Affiliation(s)
- Sandrine Moreira
- Robert-Cedergren Centre for Bioinformatics and Genomics, Department of Biochemistry, Université de Montréal, Montreal, Quebec, Canada
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Lukeš J, Archibald JM, Keeling PJ, Doolittle WF, Gray MW. How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 2012; 63:528-37. [PMID: 21698757 DOI: 10.1002/iub.489] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Complex cellular machines and processes are commonly believed to be products of selection, and it is typically understood to be the job of evolutionary biologists to show how selective advantage can account for each step in their origin and subsequent growth in complexity. Here, we describe how complex machines might instead evolve in the absence of positive selection through a process of "presuppression," first termed constructive neutral evolution (CNE) more than a decade ago. If an autonomously functioning cellular component acquires mutations that make it dependent for function on another, pre-existing component or process, and if there are multiple ways in which such dependence may arise, then dependence inevitably will arise and reversal to independence is unlikely. Thus, CNE is a unidirectional evolutionary ratchet leading to complexity, if complexity is equated with the number of components or steps necessary to carry out a cellular process. CNE can explain "functions" that seem to make little sense in terms of cellular economy, like RNA editing or splicing, but it may also contribute to the complexity of machines with clear benefit to the cell, like the ribosome, and to organismal complexity overall. We suggest that CNE-based evolutionary scenarios are in these and other cases less forced than the selectionist or adaptationist narratives that are generally told.
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Affiliation(s)
- Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, České Budĕjovice (Budweis), Czech Republic
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Jackson CJ, Gornik SG, Waller RF. The mitochondrial genome and transcriptome of the basal dinoflagellate Hematodinium sp.: character evolution within the highly derived mitochondrial genomes of dinoflagellates. Genome Biol Evol 2011; 4:59-72. [PMID: 22113794 PMCID: PMC3268668 DOI: 10.1093/gbe/evr122] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The sister phyla dinoflagellates and apicomplexans inherited a drastically reduced mitochondrial genome (mitochondrial DNA, mtDNA) containing only three protein-coding (cob, cox1, and cox3) genes and two ribosomal RNA (rRNA) genes. In apicomplexans, single copies of these genes are encoded on the smallest known mtDNA chromosome (6 kb). In dinoflagellates, however, the genome has undergone further substantial modifications, including massive genome amplification and recombination resulting in multiple copies of each gene and gene fragments linked in numerous combinations. Furthermore, protein-encoding genes have lost standard stop codons, trans-splicing of messenger RNAs (mRNAs) is required to generate complete cox3 transcripts, and extensive RNA editing recodes most genes. From taxa investigated to date, it is unclear when many of these unusual dinoflagellate mtDNA characters evolved. To address this question, we investigated the mitochondrial genome and transcriptome character states of the deep branching dinoflagellate Hematodinium sp. Genomic data show that like later-branching dinoflagellates Hematodinium sp. also contains an inflated, heavily recombined genome of multicopy genes and gene fragments. Although stop codons are also lacking for cox1 and cob, cox3 still encodes a conventional stop codon. Extensive editing of mRNAs also occurs in Hematodinium sp. The mtDNA of basal dinoflagellate Hematodinium sp. indicates that much of the mtDNA modification in dinoflagellates occurred early in this lineage, including genome amplification and recombination, and decreased use of standard stop codons. Trans-splicing, on the other hand, occurred after Hematodinium sp. diverged. Only RNA editing presents a nonlinear pattern of evolution in dinoflagellates as this process occurs in Hematodinium sp. but is absent in some later-branching taxa indicating that this process was either lost in some lineages or developed more than once during the evolution of the highly unusual dinoflagellate mtDNA.
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Affiliation(s)
- C J Jackson
- School of Botany, University of Melbourne, Australia
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Nowacki M, Shetty K, Landweber LF. RNA-Mediated Epigenetic Programming of Genome Rearrangements. Annu Rev Genomics Hum Genet 2011; 12:367-89. [PMID: 21801022 DOI: 10.1146/annurev-genom-082410-101420] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
RNA, normally thought of as a conduit in gene expression, has a novel mode of action in ciliated protozoa. Maternal RNA templates provide both an organizing guide for DNA rearrangements and a template that can transport somatic mutations to the next generation. This opportunity for RNA-mediated genome rearrangement and DNA repair is profound in the ciliate Oxytricha, which deletes 95% of its germline genome during development in a process that severely fragments its chromosomes and then sorts and reorders the hundreds of thousands of pieces remaining. Oxytricha's somatic nuclear genome is therefore an epigenome formed through RNA templates and signals arising from the previous generation. Furthermore, this mechanism of RNA-mediated epigenetic inheritance can function across multiple generations, and the discovery of maternal template RNA molecules has revealed new biological roles for RNA and has hinted at the power of RNA molecules to sculpt genomic information in cells.
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Affiliation(s)
- Mariusz Nowacki
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland.
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Flegontov P, Gray MW, Burger G, Lukeš J. Gene fragmentation: a key to mitochondrial genome evolution in Euglenozoa? Curr Genet 2011; 57:225-32. [PMID: 21544620 DOI: 10.1007/s00294-011-0340-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 04/08/2011] [Indexed: 11/30/2022]
Abstract
Phylum Euglenozoa comprises three groups of eukaryotic microbes (kinetoplastids, diplonemids, and euglenids), the mitochondrial (mt) genomes of which exhibit radically different modes of organization and expression. Gene fragmentation is a striking feature of both euglenid and diplonemid mtDNAs. To rationalize the emergence of these highly divergent mtDNA types and the existence of insertion/deletion RNA editing (in kinetoplastids) and trans-splicing (in diplonemids), we propose that in the mitochondrion of the common evolutionary ancestor of Euglenozoa, small expressed gene fragments promoted a rampant neutral evolutionary pathway. Interactions between small antisense transcripts of these gene fragments and full-length transcripts, assisted by RNA-processing enzymes, permitted the emergence of RNA editing and/or trans-splicing activities, allowing the system to tolerate indel mutations and further gene fragmentation, respectively, and leading to accumulation of additional mutations. In this way, dramatically different mitochondrial genome structures and RNA-processing machineries were able to evolve. The paradigm of constructive neutral evolution acting on the widely different mitochondrial genetic systems in Euglenozoa posits the accretion of initially neutral molecular interactions by genetic drift, leading inevitably to the observed 'irremediable complexity'.
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Affiliation(s)
- Pavel Flegontov
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 37005, České Budĕjovice, Czech Republic
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Kiethega GN, Turcotte M, Burger G. Evolutionarily conserved cox1 trans-splicing without cis-motifs. Mol Biol Evol 2011; 28:2425-8. [PMID: 21436119 DOI: 10.1093/molbev/msr075] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In the protist Diplonema papillatum (Diplonemea, Euglenozoa), mitochondrial genes are systematically fragmented with each nonoverlapping piece (module) encoded individually on a distinct circular chromosome. Gene modules are transcribed separately, and precursor transcripts are assembled to mature mRNA by a trans-splicing process of yet unknown mechanism. Expression of the cox1 gene that consists of nine modules, also involves RNA editing by which six uridines are added between Modules 4 and 5. Here, we investigate whether the unusual features of cox1 are shared by all Diplonemea and what the mechanism of trans-splicing might be. We examine three additional species representing both Diplonemea genera, namely D. papillatum described before, and D. ambulator, Diplonema sp.2, and Rhynchopus euleeides and discover that in all Diplonemea, the cox1 gene is discontinuous and split up into nine modules that each reside on a distinct chromosome. Positions of gene breakpoints vary by up to two nucleotides. Further, all taxa have six nonencoded uridines inserted in cox1 mRNA at exactly the same position as D. papillatum. In silico searches do not detect signatures of introns known to engage in trans-splicing, in particular Group I, Group II, spliceosomal, and transfer RNA introns. Nor did we find statistically significant reverse-complementary motifs between adjacent modules and their flanking regions, or residues conserved within or across species. This provides compelling evidence that trans-splicing in Diplonemea mitochondria does not rely on sequence elements in cis but rather proceeds by a mechanism employing matchmaking trans factors, such as RNAs or proteins.
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