1
|
Harada R, Hirakawa Y, Yabuki A, Kim E, Yazaki E, Kamikawa R, Nakano K, Eliáš M, Inagaki Y. Encyclopedia of Family A DNA Polymerases Localized in Organelles: Evolutionary Contribution of Bacteria Including the Proto-Mitochondrion. Mol Biol Evol 2024; 41:msae014. [PMID: 38271287 PMCID: PMC10877234 DOI: 10.1093/molbev/msae014] [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: 08/29/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
DNA polymerases synthesize DNA from deoxyribonucleotides in a semiconservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are 2 genome-containing organelles, mitochondria, and plastids, which were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNA polymerases that localize and work in them to maintain their genomes. The evolution of organellar DNA polymerases has yet to be fully understood because of 2 unsettled issues. First, the diversity of organellar DNA polymerases has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNA polymerases that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNA polymerases known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNA polymerase sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNA polymerases were further examined experimentally. The results presented here suggest that the diversity of organellar DNA polymerases has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed 2 mitochondrial DNA polymerases, POP, and a candidate of the direct descendant of the proto-mitochondrial DNA polymerase I, rdxPolA, identified in this study.
Collapse
Affiliation(s)
- Ryo Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akinori Yabuki
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Eunsoo Kim
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Euki Yazaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Japan
- Interdisciplinary Theoretical and Mathematical Sciences program (iTHEMS), RIKEN, Wako, Saitama, Japan
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kentaro Nakano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| |
Collapse
|
2
|
Harada R, Inagaki Y. Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data. Protist 2023; 174:125997. [PMID: 38039844 DOI: 10.1016/j.protis.2023.125997] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Multiple genes encoding family A DNA polymerases (famA DNAPs), which are evolutionary relatives of DNA polymerase I (PolI) in bacteria and phages, have been found in eukaryotic genomes, and many of these proteins are used mainly in organelles. Among members of the phylum Euglenozoa, distinct types of famA DNAP, PolIA, PolIBCD+, POP, and eugPolA, have been found. It is intriguing how the suite of famA DNAPs had been established during the evolution of Euglenozoa, but the DNAP data have not been sampled from the taxa that sufficiently represent the diversity of this phylum. In particular, little sequence data were available for basal branching species in Euglenozoa until recently. Thanks to the single-cell transcriptome data from symbiontids and phagotrophic euglenids, we have an opportunity to cover the "hole" in the repertory of famA DNAPs in the deep branches in Euglenozoa. The current study identified 16 new famA DNAP sequences in the transcriptome data from 33 phagotrophic euglenids and two symbiontids, respectively. Based on the new famA DNAP sequences, the updated diversity and evolution of famA DNAPs in Euglenozoa are discussed.
Collapse
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.
| |
Collapse
|
3
|
Delzell S, Nelson SW, Frost MP, Klingbeil MM. Trypanosoma brucei Mitochondrial DNA Polymerase POLIB Contains a Novel Polymerase Domain Insertion That Confers Dominant Exonuclease Activity. Biochemistry 2022; 61:2751-2765. [PMID: 36399653 PMCID: PMC9731263 DOI: 10.1021/acs.biochem.2c00392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/31/2022] [Indexed: 11/19/2022]
Abstract
Trypanosoma brucei and related parasites contain an unusual catenated mitochondrial genome known as kinetoplast DNA (kDNA) composed of maxicircles and minicircles. The kDNA structure and replication mechanism are divergent and essential for parasite survival. POLIB is one of three Family A DNA polymerases independently essential to maintain the kDNA network. However, the division of labor among the paralogs, particularly which might be a replicative, proofreading enzyme, remains enigmatic. De novo modeling of POLIB suggested a structure that is divergent from all other Family A polymerases, in which the thumb subdomain contains a 369 amino acid insertion with homology to DEDDh DnaQ family 3'-5' exonucleases. Here we demonstrate recombinant POLIB 3'-5' exonuclease prefers DNA vs RNA substrates and degrades single- and double-stranded DNA nonprocessively. Exonuclease activity prevails over polymerase activity on DNA substrates at pH 8.0, while DNA primer extension is favored at pH 6.0. Mutations that ablate POLIB polymerase activity slow the exonuclease rate suggesting crosstalk between the domains. We show that POLIB extends an RNA primer more efficiently than a DNA primer in the presence of dNTPs but does not incorporate rNTPs efficiently using either primer. Immunoprecipitation of Pol I-like paralogs from T. brucei corroborates the pH selectivity and RNA primer preferences of POLIB and revealed that the other paralogs efficiently extend a DNA primer. The enzymatic properties of POLIB suggest this paralog is not a replicative kDNA polymerase, and the noncanonical polymerase domain provides another example of exquisite diversity among DNA polymerases for specialized function.
Collapse
Affiliation(s)
- Stephanie
B. Delzell
- Department
of Microbiology, University of Massachusetts, Amherst, Massachusetts01003, United States
| | - Scott W. Nelson
- Roy
J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa50011, United States
| | - Matthew P. Frost
- Department
of Microbiology, University of Massachusetts, Amherst, Massachusetts01003, United States
| | - Michele M. Klingbeil
- Department
of Microbiology, University of Massachusetts, Amherst, Massachusetts01003, United States
- The
Institute for Applied Life Sciences, University
of Massachusetts, Amherst, Massachusetts01003, United States
| |
Collapse
|
4
|
Kaszecki E, Kennedy V, Shah M, Maciszewski K, Karnkowska A, Linton E, Ginger ML, Farrow S, Ebenezer TE. Meeting Report: Euglenids in the Age of Symbiogenesis: Origins, Innovations, and Prospects, November 8-11, 2021. Protist 2022; 173:125894. [PMID: 35772300 DOI: 10.1016/j.protis.2022.125894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 10/18/2022]
Affiliation(s)
- Emma Kaszecki
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Victoria Kennedy
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Mahfuzur Shah
- Department of Cell Biology, Metabolism and Systems Biology, Noblegen Inc., 2140 East Bank Dr, Peterborough, ON, Canada
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Eric Linton
- Central Michigan University, Department of Biology, Mount Pleasant, MI 48859, USA
| | - Michael L Ginger
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Scott Farrow
- Department of Cell Biology, Metabolism and Systems Biology, Noblegen Inc., 2140 East Bank Dr, Peterborough, ON, Canada
| | - ThankGod Echezona Ebenezer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK
| |
Collapse
|
5
|
Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology. Sci Rep 2021; 11:13070. [PMID: 34158556 PMCID: PMC8219788 DOI: 10.1038/s41598-021-92174-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting genomic and transcriptomic drafts of a primary osmotroph, Rhabdomonas costata. The current genomic assembly length of 100 Mbp is 14× smaller than that of E. gracilis. Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns, including several candidates for nonconventional types. A set of 39,456 putative R. costata proteins was predicted from the transcriptome. Annotation of the mitochondrial core metabolism provides the first data on the facultatively anaerobic mitochondrion of R. costata, which in most respects resembles the mitochondrion of E. gracilis with a certain level of streamlining. R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis. The low percentage of green algae-affiliated genes supports the ancestrally osmotrophic status of this species.
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Butenko A, Hammond M, Field MC, Ginger ML, Yurchenko V, Lukeš J. Reductionist Pathways for Parasitism in Euglenozoans? Expanded Datasets Provide New Insights. Trends Parasitol 2020; 37:100-116. [PMID: 33127331 DOI: 10.1016/j.pt.2020.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/21/2022]
Abstract
The unicellular trypanosomatids belong to the phylum Euglenozoa and all known species are obligate parasites. Distinct lineages infect plants, invertebrates, and vertebrates, including humans. Genome data for marine diplonemids, together with freshwater euglenids and free-living kinetoplastids, the closest known nonparasitic relatives to trypanosomatids, recently became available. Robust phylogenetic reconstructions across Euglenozoa are now possible and place the results of parasite-focused studies into an evolutionary context. Here we discuss recent advances in identifying the factors shaping the evolution of Euglenozoa, focusing on ancestral features generally considered parasite-specific. Remarkably, most of these predate the transition(s) to parasitism, suggesting that the presence of certain preconditions makes a significant lifestyle change more likely.
Collapse
Affiliation(s)
- Anzhelika Butenko
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
| | - Michael Hammond
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Mark C Field
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael L Ginger
- School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Vyacheslav Yurchenko
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic; Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
| |
Collapse
|
8
|
Poveda A, Méndez MÁ, Armijos-Jaramillo V. Analysis of DNA Polymerases Reveals Specific Genes Expansion in Leishmania and Trypanosoma spp. Front Cell Infect Microbiol 2020; 10:570493. [PMID: 33117729 PMCID: PMC7576959 DOI: 10.3389/fcimb.2020.570493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/02/2020] [Indexed: 01/01/2023] Open
Abstract
Leishmaniasis and trypanosomiasis are largely neglected diseases prevailing in tropical and subtropical conditions. These are an arthropod-borne zoonosis that affects humans and some animals and is caused by infection with protozoan of the genera Leishmania and Trypanosoma, respectively. These parasites present high genomic plasticity and are able to adapt themselves to adverse conditions like the attack of host cells or toxicity induced by drug exposure. Different mechanisms allow these adapting responses induced by stress, such as mutation, chromosomal rearrangements, establishment of mosaic ploidies, and gene expansion. Here we describe how a subset of genes encoding for DNA polymerases implied in repairing/translesion (TLS) synthesis are duplicated in some pathogenic species of the Trypanosomatida order and a free-living species from the Bodonida order. These enzymes are both able to repair DNA, but are also error-prone under certain situations. We discuss about the possibility that these enzymes can act as a source of genomic variation promoting adaptation in trypanosomatids.
Collapse
Affiliation(s)
- Ana Poveda
- DNA Replication and Genome Instability Unit, Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Salud Pública y Zoonosis-CIZ, Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito, Ecuador.,Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Burjassot, Spain
| | - Miguel Ángel Méndez
- Grupo de Química Computacional y Teórica, Universidad San Francisco de Quito, Quito, Ecuador
| | - Vinicio Armijos-Jaramillo
- Grupo de Bio-Quimioinformática, Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| |
Collapse
|