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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.
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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
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2
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Park SI, Cho CH, Ciniglia C, Huang TY, Liu SL, Bustamante DE, Calderon MS, Mansilla A, McDermott T, Andersen RA, Yoon HS. Revised classification of the Cyanidiophyceae based on plastid genome data with descriptions of the Cavernulicolales ord. nov. and Galdieriales ord. nov. (Rhodophyta). JOURNAL OF PHYCOLOGY 2023; 59:444-466. [PMID: 36792488 DOI: 10.1111/jpy.13322] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/06/2023] [Accepted: 01/21/2023] [Indexed: 06/15/2023]
Abstract
The Cyanidiophyceae, an extremophilic red algal class, is distributed worldwide in extreme environments. Species grow either in acidic hot environments or in dim light conditions (e.g., "cave Cyanidium"). The taxonomy and classification systems are currently based on morphological, eco-physiological, and molecular phylogenetic characters; however, previous phylogenetic results showed hidden diversity of the Cyanidiophyceae and suggested a revision of the classification system. To clarify phylogenetic relationships within this red algal class, we employ a phylogenomic approach based on 15 plastomes (10 new) and 15 mitogenomes (seven new). Our phylogenies show consistent relationships among four lineages (Galdieria, "cave Cyanidium", Cyanidium, and Cyanidioschyzon lineages). Each lineage is distinguished by organellar genome characteristics. The "cave Cyanidium" lineage is a distinct clade that diverged after the Galdieria clade but within a larger monophyletic clade that included the Cyanidium and Cyanidioschyzon lineages. Because the "cave Cyanidium" lineage is a mesophilic lineage that differs substantially from the other three thermoacidophilic lineages, we describe it as a new order (Cavernulicolales). Based on this evidence, we reclassified the Cyanidiophyceae into four orders: Cyanidiales, Cyanidioschyzonales, Cavernulicolales ord. nov., and Galdieriales ord. nov. The genetic distance among these four orders is comparable to, or greater than, the distances found between other red algal orders and subclasses. Three new genera (Cavernulicola, Gronococcus, Sciadococcus), five new species (Galdieria javensis, Galdieria phlegrea, Galdieria yellowstonensis, Gronococcus sybilensis, Sciadococcus taiwanensis), and a new nomenclatural combination (Cavernulicola chilensis) are proposed.
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Affiliation(s)
- Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Claudia Ciniglia
- Department of Environmental, Biological and Pharmaceutical Science and Technologies, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Tzu-Yen Huang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Shao-Lun Liu
- Department of Life Science & Center for Ecology and Environment, Tunghai University, Taichung, Taiwan
| | - Danilo E Bustamante
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Amazonas, Peru
- Cape Horn International Center (CHIC), Chile
| | - Martha S Calderon
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Amazonas, Peru
- Cape Horn International Center (CHIC), Chile
| | - Andres Mansilla
- Cape Horn International Center (CHIC), Chile
- Laboratorio de Macroalgas Antárticas y Subantárticas, Universidad de Magallanes, Punta Arenas, Chile
| | - Timothy McDermott
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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Van Etten J, Benites LF, Stephens TG, Yoon HS, Bhattacharya D. Algae obscura: The potential of rare species as model systems. JOURNAL OF PHYCOLOGY 2023; 59:293-300. [PMID: 36764681 DOI: 10.1111/jpy.13321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 05/28/2023]
Abstract
Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Luiz Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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Christian R, Labbancz J, Usadel B, Dhingra A. Understanding protein import in diverse non-green plastids. Front Genet 2023; 14:969931. [PMID: 37007964 PMCID: PMC10063809 DOI: 10.3389/fgene.2023.969931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/24/2023] [Indexed: 03/19/2023] Open
Abstract
The spectacular diversity of plastids in non-green organs such as flowers, fruits, roots, tubers, and senescing leaves represents a Universe of metabolic processes in higher plants that remain to be completely characterized. The endosymbiosis of the plastid and the subsequent export of the ancestral cyanobacterial genome to the nuclear genome, and adaptation of the plants to all types of environments has resulted in the emergence of diverse and a highly orchestrated metabolism across the plant kingdom that is entirely reliant on a complex protein import and translocation system. The TOC and TIC translocons, critical for importing nuclear-encoded proteins into the plastid stroma, remain poorly resolved, especially in the case of TIC. From the stroma, three core pathways (cpTat, cpSec, and cpSRP) may localize imported proteins to the thylakoid. Non-canonical routes only utilizing TOC also exist for the insertion of many inner and outer membrane proteins, or in the case of some modified proteins, a vesicular import route. Understanding this complex protein import system is further compounded by the highly heterogeneous nature of transit peptides, and the varying transit peptide specificity of plastids depending on species and the developmental and trophic stage of the plant organs. Computational tools provide an increasingly sophisticated means of predicting protein import into highly diverse non-green plastids across higher plants, which need to be validated using proteomics and metabolic approaches. The myriad plastid functions enable higher plants to interact and respond to all kinds of environments. Unraveling the diversity of non-green plastid functions across the higher plants has the potential to provide knowledge that will help in developing climate resilient crops.
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Affiliation(s)
- Ryan Christian
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - June Labbancz
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | | | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Amit Dhingra,
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5
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Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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6
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Casey A, Dolan L. Genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with herbicide resistance evolved before the origin of land plants. PLoS One 2023; 18:e0273594. [PMID: 36800395 PMCID: PMC9937507 DOI: 10.1371/journal.pone.0273594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Cytochrome P450 (CYP) monooxygenases and glutathione S-transferases (GST) are enzymes that catalyse chemical modifications of a range of organic compounds. Herbicide resistance has been associated with higher levels of CYP and GST gene expression in some herbicide-resistant weed populations compared to sensitive populations of the same species. By comparing the protein sequences of 9 representative species of the Archaeplastida-the lineage which includes red algae, glaucophyte algae, chlorophyte algae, and streptophytes-and generating phylogenetic trees, we identified the CYP and GST proteins that existed in the common ancestor of the Archaeplastida. All CYP clans and all but one land plant GST classes present in land plants evolved before the divergence of streptophyte algae and land plants from their last common ancestor. We also demonstrate that there are more genes encoding CYP and GST proteins in land plants than in algae. The larger numbers of genes among land plants largely results from gene duplications in CYP clans 71, 72, and 85 and in the GST phi and tau classes [1,2]. Enzymes that either metabolise herbicides or confer herbicide resistance belong to CYP clans 71 and 72 and the GST phi and tau classes. Most CYP proteins that have been shown to confer herbicide resistance are members of the CYP81 family from clan 71. These results demonstrate that the clan and class diversity in extant plant CYP and GST proteins had evolved before the divergence of land plants and streptophyte algae from a last common ancestor estimated to be between 515 and 474 million years ago. Then, early in embryophyte evolution during the Palaeozoic, gene duplication in four of the twelve CYP clans, and in two of the fourteen GST classes, led to the large numbers of CYP and GST proteins found in extant land plants. It is among the genes of CYP clans 71 and 72 and GST classes phi and tau that alleles conferring herbicide resistance evolved in the last fifty years.
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Affiliation(s)
- Alexandra Casey
- Gregor Mendel Institute, Vienna, Austria
- Department of Plant Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Liam Dolan
- Gregor Mendel Institute, Vienna, Austria
- Department of Plant Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
- * E-mail:
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Phycobilisomes and Phycobiliproteins in the Pigment Apparatus of Oxygenic Photosynthetics: From Cyanobacteria to Tertiary Endosymbiosis. Int J Mol Sci 2023; 24:ijms24032290. [PMID: 36768613 PMCID: PMC9916406 DOI: 10.3390/ijms24032290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/15/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Eukaryotic photosynthesis originated in the course of evolution as a result of the uptake of some unstored cyanobacterium and its transformation to chloroplasts by an ancestral heterotrophic eukaryotic cell. The pigment apparatus of Archaeplastida and other algal phyla that emerged later turned out to be arranged in the same way. Pigment-protein complexes of photosystem I (PS I) and photosystem II (PS II) are characterized by uniform structures, while the light-harvesting antennae have undergone a series of changes. The phycobilisome (PBS) antenna present in cyanobacteria was replaced by Chl a/b- or Chl a/c-containing pigment-protein complexes in most groups of photosynthetics. In the form of PBS or phycobiliprotein aggregates, it was inherited by members of Cyanophyta, Cryptophyta, red algae, and photosynthetic amoebae. Supramolecular organization and architectural modifications of phycobiliprotein antennae in various algal phyla in line with the endosymbiotic theory of chloroplast origin are the subject of this review.
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8
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Bhattacharya D, Etten JV, Benites LF, Stephens TG. Endosymbiotic ratchet accelerates divergence after organelle origin: The Paulinella model for plastid evolution: The Paulinella model for plastid evolution. Bioessays 2023; 45:e2200165. [PMID: 36328783 DOI: 10.1002/bies.202200165] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
We hypothesize that as one of the most consequential events in evolution, primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet. Our proposal is supported by recent work on the photosynthetic amoeba, Paulinella, that underwent primary plastid endosymbiosis about 124 Mya. This amoeba model allows us to explore the early impacts of photosynthetic organelle (plastid) origin on the host lineage. The current data point to a central role for effective population size (Ne ) in accelerating divergence post-endosymbiosis due to limits to dispersal and reproductive isolation that reduce Ne , leading to local adaptation. We posit that isolated populations exploit different strategies and behaviors and assort themselves in non-overlapping niches to minimize competition during the early, rapid evolutionary phase of organelle integration. The endosymbiotic ratchet provides a general framework for interpreting post-endosymbiosis lineage evolution that is driven by disruptive selection and demographic and population shifts. Also see the video abstract here: https://youtu.be/gYXrFM6Zz6Q.
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Affiliation(s)
- Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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9
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Cavalier-Smith T. Ciliary transition zone evolution and the root of the eukaryote tree: implications for opisthokont origin and classification of kingdoms Protozoa, Plantae, and Fungi. PROTOPLASMA 2022; 259:487-593. [PMID: 34940909 PMCID: PMC9010356 DOI: 10.1007/s00709-021-01665-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/03/2021] [Indexed: 05/19/2023]
Abstract
I thoroughly discuss ciliary transition zone (TZ) evolution, highlighting many overlooked evolutionarily significant ultrastructural details. I establish fundamental principles of TZ ultrastructure and evolution throughout eukaryotes, inferring unrecognised ancestral TZ patterns for Fungi, opisthokonts, and Corticata (i.e., kingdoms Plantae and Chromista). Typical TZs have a dense transitional plate (TP), with a previously overlooked complex lattice as skeleton. I show most eukaryotes have centriole/TZ junction acorn-V filaments (whose ancestral function was arguably supporting central pair microtubule-nucleating sites; I discuss their role in centriole growth). Uniquely simple malawimonad TZs (without TP, simpler acorn) pinpoint the eukaryote tree's root between them and TP-bearers, highlighting novel superclades. I integrate TZ/ciliary evolution with the best multiprotein trees, naming newly recognised major eukaryote clades and revise megaclassification of basal kingdom Protozoa. Recent discovery of non-photosynthetic phagotrophic flagellates with genome-free plastids (Rhodelphis), the sister group to phylum Rhodophyta (red algae), illuminates plant and chromist early evolution. I show previously overlooked marked similarities in cell ultrastructure between Rhodelphis and Picomonas, formerly considered an early diverging chromist. In both a nonagonal tube lies between their TP and an annular septum surrounding their 9+2 ciliary axoneme. Mitochondrial dense condensations and mitochondrion-linked smooth endomembrane cytoplasmic partitioning cisternae further support grouping Picomonadea and Rhodelphea as new plant phylum Pararhoda. As Pararhoda/Rhodophyta form a robust clade on site-heterogeneous multiprotein trees, I group Pararhoda and Rhodophyta as new infrakingdom Rhodaria of Plantae within subkingdom Biliphyta, which also includes Glaucophyta with fundamentally similar TZ, uniquely in eukaryotes. I explain how biliphyte TZs generated viridiplant stellate-structures.
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Yang T, Sahu SK, Yang L, Liu Y, Mu W, Liu X, Strube ML, Liu H, Zhong B. Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:808156. [PMID: 35498716 PMCID: PMC9038950 DOI: 10.3389/fpls.2022.808156] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/07/2022] [Indexed: 05/03/2023]
Abstract
The plastid organelle is essential for many vital cellular processes and the growth and development of plants. The availability of a large number of complete plastid genomes could be effectively utilized to understand the evolution of the plastid genomes and phylogenetic relationships among plants. We comprehensively analyzed the plastid genomes of Viridiplantae comprising 3,654 taxa from 298 families and 111 orders and compared the genomic organizations in their plastid genomic DNA among major clades, which include gene gain/loss, gene copy number, GC content, and gene blocks. We discovered that some important genes that exhibit similar functions likely formed gene blocks, such as the psb family presumably showing co-occurrence and forming gene blocks in Viridiplantae. The inverted repeats (IRs) in plastid genomes have doubled in size across land plants, and their GC content is substantially higher than non-IR genes. By employing three different data sets [all nucleotide positions (nt123), only the first and second codon positions (nt12), and amino acids (AA)], our phylogenomic analyses revealed Chlorokybales + Mesostigmatales as the earliest-branching lineage of streptophytes. Hornworts, mosses, and liverworts forming a monophylum were identified as the sister lineage of tracheophytes. Based on nt12 and AA data sets, monocots, Chloranthales and magnoliids are successive sister lineages to the eudicots + Ceratophyllales clade. The comprehensive taxon sampling and analysis of different data sets from plastid genomes recovered well-supported relationships of green plants, thereby contributing to resolving some long-standing uncertainties in the plant phylogeny.
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Affiliation(s)
- Ting Yang
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sunil Kumar Sahu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- *Correspondence: Sunil Kumar Sahu,
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yang Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Weixue Mu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Xin Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Huan Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Bojian Zhong,
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11
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Russell S, Jackson C, Reyes-Prieto A. High Sequence Divergence but Limited Architectural Rearrangements in Organelle Genomes of Cyanophora (Glaucophyta) Species. J Eukaryot Microbiol 2020; 68:e12831. [PMID: 33142007 DOI: 10.1111/jeu.12831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/16/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022]
Abstract
Cyanophora is the glaucophyte model taxon. Following the sequencing of the nuclear genome of C. paradoxa, studies based on single organelle and nuclear molecular markers revealed previously unrecognized species diversity within this glaucophyte genus. Here, we present the complete plastid (ptDNA) and mitochondrial (mtDNA) genomes of C. kugrensii, C. sudae, and C. biloba. The respective sizes and coding capacities of both ptDNAs and mtDNAs are conserved among Cyanophora species with only minor differences due to specific gene duplications. Organelle phylogenomic analyses consistently recover the species C. kugrensii and C. paradoxa as a clade and C. sudae and C. biloba as a separate group. The phylogenetic affiliations of the four Cyanophora species are consistent with architectural similarities shared at the organelle genomic level. Genetic distance estimations from both organelle sequences are also consistent with phylogenetic and architecture evidence. Comparative analyses confirm that the Cyanophora mitochondrial genes accumulate substitutions at 3-fold higher rates than plastid counterparts, suggesting that mtDNA markers are more appropriate to investigate glaucophyte diversity and evolutionary events that occur at a population level. The study of complete organelle genomes is becoming the standard for species delimitation and is particularly relevant to study cryptic diversity in microbial groups.
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Affiliation(s)
- Sarah Russell
- Department of Biology, University of New Brunswick, 10 Bailey Drive, Fredericton, NB, E3B 5A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christopher Jackson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Royal Botanic Gardens Victoria, Melbourne, Vic., Australia
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, 10 Bailey Drive, Fredericton, NB, E3B 5A3, Canada
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Khan AK, Kausar H, Jaferi SS, Drouet S, Hano C, Abbasi BH, Anjum S. An Insight into the Algal Evolution and Genomics. Biomolecules 2020; 10:E1524. [PMID: 33172219 PMCID: PMC7694994 DOI: 10.3390/biom10111524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 01/06/2023] Open
Abstract
With the increase in biotechnological, environmental, and nutraceutical importance of algae, about 100 whole genomic sequences of algae have been published, and this figure is expected to double in the coming years. The phenotypic and ecological diversity among algae hints at the range of functional capabilities encoded by algal genomes. In order to explore the biodiversity of algae and fully exploit their commercial potential, understanding their evolutionary, structural, functional, and developmental aspects at genomic level is a pre-requisite. So forth, the algal genomic analysis revealed us that algae evolved through endosymbiotic gene transfer, giving rise to around eight phyla. Amongst the diverse algal species, the unicellular green algae Chlamydomonas reinhardtii has attained the status of model organism as it is an ideal organism to elucidate the biological processes critical to plants and animals, as well as commercialized to produce range of bio-products. For this review, an overview of evolutionary process of algae through endosymbiosis in the light of genomics, as well as the phylogenomic, studies supporting the evolutionary process of algae was reviewed. Algal genomics not only helped us to understand the evolutionary history of algae but also may have an impact on our future by helping to create algae-based products and future biotechnological approaches.
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Affiliation(s)
- Amna Komal Khan
- Department of Biotechnology, Kinnaird College for Women, Lahore 54000, Pakistan; (A.K.K.); (H.K.); (S.S.J.)
| | - Humera Kausar
- Department of Biotechnology, Kinnaird College for Women, Lahore 54000, Pakistan; (A.K.K.); (H.K.); (S.S.J.)
| | - Syyada Samra Jaferi
- Department of Biotechnology, Kinnaird College for Women, Lahore 54000, Pakistan; (A.K.K.); (H.K.); (S.S.J.)
| | - Samantha Drouet
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAE USC1328, Université d’Orléans, 28000 Chartres, France; (S.D.); (C.H.)
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAE USC1328, Université d’Orléans, 28000 Chartres, France; (S.D.); (C.H.)
| | - Bilal Haider Abbasi
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Sumaira Anjum
- Department of Biotechnology, Kinnaird College for Women, Lahore 54000, Pakistan; (A.K.K.); (H.K.); (S.S.J.)
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Gray MW, Burger G, Derelle R, Klimeš V, Leger MM, Sarrasin M, Vlček Č, Roger AJ, Eliáš M, Lang BF. The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome. BMC Biol 2020; 18:22. [PMID: 32122349 PMCID: PMC7050145 DOI: 10.1186/s12915-020-0741-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/21/2020] [Indexed: 01/02/2023] Open
Abstract
Background Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date. Results In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids. Conclusions As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.
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Affiliation(s)
- Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Gertraud Burger
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| | - Romain Derelle
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Michelle M Leger
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada.,Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Matt Sarrasin
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| | - Čestmír Vlček
- Current address: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - B Franz Lang
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
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Finkenwirth F, Eitinger T. ECF-type ABC transporters for uptake of vitamins and transition metal ions into prokaryotic cells. Res Microbiol 2019; 170:358-365. [PMID: 31283960 DOI: 10.1016/j.resmic.2019.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/15/2022]
Abstract
Energy-coupling factor (ECF) transporters mediate the uptake of micronutrients in prokaryotes. They consist of two ATP-binding-cassette family ATPases, a transmembrane coupling protein (T component) and a substrate-binding membrane protein (S component). ECF transporters for Co2+ and Ni2+ ions have one or two additional proteins with extracytoplasmic regions but poorly understood function. Homologs of T components with a predicted localization in plastids are widespread in plants but their physiological role is unclear. S components in eukaryotes are very rare and restricted to biotin-specific variants. Apart from a potential contribution to the export of flavins to serve the assembly of extracytoplasmic electron transfer chains, ECF transporters function as importers.
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Affiliation(s)
- Friedrich Finkenwirth
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Thomas Eitinger
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany.
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