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Goldman AD, Becerra A. A New View of the Last Universal Common Ancestor. J Mol Evol 2024:10.1007/s00239-024-10193-w. [PMID: 39122826 DOI: 10.1007/s00239-024-10193-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024]
Affiliation(s)
- Aaron D Goldman
- Department of Biology, Oberlin College, Oberlin, OH, USA.
- Blue Marble Space Institute of Science, Seattle, WA, USA.
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2
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Moody ERR, Álvarez-Carretero S, Mahendrarajah TA, Clark JW, Betts HC, Dombrowski N, Szánthó LL, Boyle RA, Daines S, Chen X, Lane N, Yang Z, Shields GA, Szöllősi GJ, Spang A, Pisani D, Williams TA, Lenton TM, Donoghue PCJ. The nature of the last universal common ancestor and its impact on the early Earth system. Nat Ecol Evol 2024:10.1038/s41559-024-02461-1. [PMID: 38997462 DOI: 10.1038/s41559-024-02461-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/04/2024] [Indexed: 07/14/2024]
Abstract
The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA's metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09-4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49-2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.
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Affiliation(s)
- Edmund R R Moody
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
| | | | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - James W Clark
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Holly C Betts
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Lénárd L Szánthó
- Department of Biological Physics, Eötvös University, Budapest, Hungary
- MTA-ELTE 'Lendulet' Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, HUN-REN Center for Ecological Research, Budapest, Hungary
| | | | - Stuart Daines
- Global Systems Institute, University of Exeter, Exeter, UK
| | - Xi Chen
- Department of Earth Sciences, University College London, London, UK
| | - Nick Lane
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Graham A Shields
- Department of Earth Sciences, University College London, London, UK
| | - Gergely J Szöllősi
- MTA-ELTE 'Lendulet' Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, HUN-REN Center for Ecological Research, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK.
| | | | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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3
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Yu Y, Li YP, Ren K, Hao X, Fru EC, Rønn R, Rivera WL, Becker K, Feng R, Yang J, Rensing C. A brief history of metal recruitment in protozoan predation. Trends Microbiol 2024; 32:465-476. [PMID: 38103995 DOI: 10.1016/j.tim.2023.11.008] [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: 02/08/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
Metals and metalloids are used as weapons for predatory feeding by unicellular eukaryotes on prokaryotes. This review emphasizes the role of metal(loid) bioavailability over the course of Earth's history, coupled with eukaryogenesis and the evolution of the mitochondrion to trace the emergence and use of the metal(loid) prey-killing phagosome as a feeding strategy. Members of the genera Acanthamoeba and Dictyostelium use metals such as zinc (Zn) and copper (Cu), and possibly metalloids, to kill their bacterial prey after phagocytosis. We provide a potential timeline on when these capacities first evolved and how they correlate with perceived changes in metal(loid) bioavailability through Earth's history. The origin of phagotrophic eukaryotes must have postdated the Great Oxidation Event (GOE) in agreement with redox-dependent modification of metal(loid) bioavailability for phagotrophic poisoning. However, this predatory mechanism is predicted to have evolved much later - closer to the origin of the multicellular metazoans and the evolutionary development of the immune systems.
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Affiliation(s)
- Yanshuang Yu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuan-Ping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Kexin Ren
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiuli Hao
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Ernest Chi Fru
- Centre for Geobiology and Geochemistry, School of Earth and Ocean Sciences, Cardiff University, CF10 3AT Cardiff, UK
| | - Regin Rønn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Karsten Becker
- Friedrich Loeffler-Institute for Medical Microbiology, University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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Belato FA, Mello B, Coates CJ, Halanych KM, Brown FD, Morandini AC, de Moraes Leme J, Trindade RIF, Costa-Paiva EM. Divergence time estimates for the hypoxia-inducible factor-1 alpha (HIF1α) reveal an ancient emergence of animals in low-oxygen environments. GEOBIOLOGY 2024; 22:e12577. [PMID: 37750460 DOI: 10.1111/gbi.12577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 07/13/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023]
Abstract
Unveiling the tempo and mode of animal evolution is necessary to understand the links between environmental changes and biological innovation. Although the earliest unambiguous metazoan fossils date to the late Ediacaran period, molecular clock estimates agree that the last common ancestor (LCA) of all extant animals emerged ~850 Ma, in the Tonian period, before the oldest evidence for widespread ocean oxygenation at ~635-560 Ma in the Ediacaran period. Metazoans are aerobic organisms, that is, they are dependent on oxygen to survive. In low-oxygen conditions, most animals have an evolutionarily conserved pathway for maintaining oxygen homeostasis that triggers physiological changes in gene expression via the hypoxia-inducible factor (HIFa). However, here we confirm the absence of the characteristic HIFa protein domain responsible for the oxygen sensing of HIFa in sponges and ctenophores, indicating the LCA of metazoans lacked the functional protein domain as well, and so could have maintained their transcription levels unaltered under the very low-oxygen concentrations of their environments. Using Bayesian relaxed molecular clock dating, we inferred that the ancestral gene lineage responsible for HIFa arose in the Mesoproterozoic Era, ~1273 Ma (Credibility Interval 957-1621 Ma), consistent with the idea that important genetic machinery associated with animals evolved much earlier than the LCA of animals. Our data suggest at least two duplication events in the evolutionary history of HIFa, which generated three vertebrate paralogs, products of the two successive whole-genome duplications that occurred in the vertebrate LCA. Overall, our results support the hypothesis of a pre-Tonian emergence of metazoans under low-oxygen conditions, and an increase in oxygen response elements during animal evolution.
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Affiliation(s)
- Flavia A Belato
- Institute of Biosciences, Department of Zoology, University of Sao Paulo, São Paulo - SP, Brazil
| | - Beatriz Mello
- Biology Institute, Genetics Department, Federal University of Rio de Janeiro, Rio de Janeiro - RJ, Brazil
| | - Christopher J Coates
- Zoology, Ryan Institute, School of Natural Sciences, University of Galway, Galway, Ireland
| | - Kenneth M Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Federico D Brown
- Institute of Biosciences, Department of Zoology, University of Sao Paulo, São Paulo - SP, Brazil
| | - André C Morandini
- Institute of Biosciences, Department of Zoology, University of Sao Paulo, São Paulo - SP, Brazil
| | | | - Ricardo I F Trindade
- Institute of Astronomy, Geophysics and Atmospheric Sciences, University of Sao Paulo, São Paulo - SP, Brazil
| | - Elisa Maria Costa-Paiva
- Institute of Biosciences, Department of Zoology, University of Sao Paulo, São Paulo - SP, Brazil
- Institute of Astronomy, Geophysics and Atmospheric Sciences, University of Sao Paulo, São Paulo - SP, Brazil
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Mahendrarajah TA, Moody ERR, Schrempf D, Szánthó LL, Dombrowski N, Davín AA, Pisani D, Donoghue PCJ, Szöllősi GJ, Williams TA, Spang A. ATP synthase evolution on a cross-braced dated tree of life. Nat Commun 2023; 14:7456. [PMID: 37978174 PMCID: PMC10656485 DOI: 10.1038/s41467-023-42924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
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Affiliation(s)
- Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Dominik Schrempf
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Lénárd L Szánthó
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Karolina ut 29, H-1113, Budapest, Hungary
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Adrián A Davín
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Gergely J Szöllősi
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK.
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands.
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
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Donoghue PCJ, Kay C, Spang A, Szöllősi G, Nenarokova A, Moody ERR, Pisani D, Williams TA. Defining eukaryotes to dissect eukaryogenesis. Curr Biol 2023; 33:R919-R929. [PMID: 37699353 DOI: 10.1016/j.cub.2023.07.048] [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] [Indexed: 09/14/2023]
Abstract
The origin of eukaryotes is among the most contentious debates in evolutionary biology, attracting multiple seemingly incompatible theories seeking to explain the sequence in which eukaryotic characteristics were acquired. Much of the controversy arises from differing views on the defining characteristics of eukaryotes. We argue that eukaryotes should be defined phylogenetically, and that doing so clarifies where competing hypotheses of eukaryogenesis agree and how we may test among aspects of disagreement. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes and are distinguishable on that basis. However, other hypotheses differ only in the order of key evolutionary steps, like mitochondrial endosymbiosis and nuclear assembly, which cannot currently be distinguished phylogenetically. Stages within eukaryogenesis may be made identifiable through the absolute dating of gene duplicates that map to eukaryotic traits, such as in genes of host or mitochondrial origin that duplicated and diverged functionally prior to emergence of the last eukaryotic common ancestor. In this way, it may finally be possible to distinguish heat from light in the debate over eukaryogenesis.
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Affiliation(s)
- Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | - Chris Kay
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg 1790 AB, The Netherlands
| | - Gergely Szöllősi
- Department of Biological Physics, Eötvös Lorand University, H-1117 Budapest, Hungary; MTA-ELTE "Lendü let" Evolutionary Genomics Research Group, H-1117 Budapest, Hungary; Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Hungary
| | - Anna Nenarokova
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK; Bristol Palaeobiology Group, School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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Craig JM, Kumar S, Hedges SB. The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen. FRONTIERS IN BIOINFORMATICS 2023; 3:1233281. [PMID: 37727796 PMCID: PMC10505794 DOI: 10.3389/fbinf.2023.1233281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/07/2023] [Indexed: 09/21/2023] Open
Abstract
The origin of eukaryotes was among the most important events in the history of life, spawning a new evolutionary lineage that led to all complex multicellular organisms. However, the timing of this event, crucial for understanding its environmental context, has been difficult to establish. The fossil and biomarker records are sparse and molecular clocks have thus far not reached a consensus, with dates spanning 2.1-0.91 billion years ago (Ga) for critical nodes. Notably, molecular time estimates for the last common ancestor of eukaryotes are typically hundreds of millions of years younger than the Great Oxidation Event (GOE, 2.43-2.22 Ga), leading researchers to question the presumptive link between eukaryotes and oxygen. We obtained a new time estimate for the origin of eukaryotes using genetic data of both archaeal and bacterial origin, the latter rarely used in past studies. We also avoided potential calibration biases that may have affected earlier studies. We obtained a conservative interval of 2.2-1.5 Ga, with an even narrower core interval of 2.0-1.8 Ga, for the origin of eukaryotes, a period closely aligned with the rise in oxygen. We further reconstructed the history of biological complexity across the tree of life using three universal measures: cell types, genes, and genome size. We found that the rise in complexity was temporally consistent with and followed a pattern similar to the rise in oxygen. This suggests a causal relationship stemming from the increased energy needs of complex life fulfilled by oxygen.
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Affiliation(s)
- Jack M. Craig
- Center for Biodiversity, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Sudhir Kumar
- Center for Biodiversity, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - S. Blair Hedges
- Center for Biodiversity, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
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Duan Y, Li Y, Zhang J, Song Y, Jiang Y, Tong X, Bi Y, Wang S, Wang S. Genome Survey and Chromosome-Level Draft Genome Assembly of Glycine max var. Dongfudou 3: Insights into Genome Characteristics and Protein Deficiencies. PLANTS (BASEL, SWITZERLAND) 2023; 12:2994. [PMID: 37631204 PMCID: PMC10459189 DOI: 10.3390/plants12162994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/11/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Dongfudou 3 is a highly sought-after soybean variety due to its lack of beany flavor. To support molecular breeding efforts, we conducted a genomic survey using next-generation sequencing. We determined the genome size, complexity, and characteristics of Dongfudou 3. Furthermore, we constructed a chromosome-level draft genome and speculated on the molecular basis of protein deficiency in GmLOX1, GmLOX2, and GmLOX3. These findings set the stage for high-quality genome analysis using third-generation sequencing. The estimated genome size is approximately 1.07 Gb, with repetitive sequences accounting for 72.50%. The genome is homozygous and devoid of microbial contamination. The draft genome consists of 916.00 Mb anchored onto 20 chromosomes, with annotations of 46,446 genes and 77,391 transcripts, achieving Benchmarking Single-Copy Orthologue (BUSCO) completeness of 99.5% for genome completeness and 99.1% for annotation. Deletions and substitutions were identified in the three GmLox genes, and they also lack corresponding active proteins. Our proposed approach, involving k-mer analysis after filtering out organellar DNA sequences, is applicable to genome surveys of all plant species, allowing for accurate assessments of size and complexity. Moreover, the process of constructing chromosome-level draft genomes using closely related reference genomes offers cost-effective access to valuable information, maximizing data utilization.
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Affiliation(s)
- Yajuan Duan
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, China; (Y.D.); (Y.L.)
| | - Yue Li
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, China; (Y.D.); (Y.L.)
| | - Jing Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, China; (Y.D.); (Y.L.)
| | - Yongze Song
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, China; (Y.D.); (Y.L.)
| | - Yan Jiang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, China; (Y.D.); (Y.L.)
| | - Xiaohong Tong
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, China; (Y.D.); (Y.L.)
| | - Yingdong Bi
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China
| | - Shaodong Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, China; (Y.D.); (Y.L.)
| | - Sui Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, 600 Changjiang Road, Harbin 150030, China; (Y.D.); (Y.L.)
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Battistuzzi M, Cocola L, Liistro E, Claudi R, Poletto L, La Rocca N. Growth and Photosynthetic Efficiency of Microalgae and Plants with Different Levels of Complexity Exposed to a Simulated M-Dwarf Starlight. Life (Basel) 2023; 13:1641. [PMID: 37629498 PMCID: PMC10455698 DOI: 10.3390/life13081641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/16/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Oxygenic photosynthetic organisms (OPOs) are primary producers on Earth and generate surface and atmospheric biosignatures, making them ideal targets to search for life from remote on Earth-like exoplanets orbiting stars different from the Sun, such as M-dwarfs. These stars emit very low light in the visible and most light in the far-red, an issue for OPOs, which mostly utilize visible light to photosynthesize and grow. After successfully testing procaryotic OPOs (cyanobacteria) under a simulated M-dwarf star spectrum (M7, 365-850 nm) generated through a custom-made lamp, we tested several eukaryotic OPOs: microalgae (Dixoniella giordanoi, Microchloropsis gaditana, Chromera velia, Chlorella vulgaris), a non-vascular plant (Physcomitrium patens), and a vascular plant (Arabidopsis thaliana). We assessed their growth and photosynthetic efficiency under three light conditions: M7, solar (SOL) simulated spectra, and far-red light (FR). Microalgae grew similarly in SOL and M7, while the moss P. patens showed slower growth in M7 with respect to SOL. A. thaliana grew similarly in SOL and M7, showing traits typical of shade-avoidance syndrome. Overall, the synergistic effect of visible and far-red light, also known as the Emerson enhancing effect, could explain the growth in M7 for all organisms. These results lead to reconsidering the possibility and capability of the growth of OPOs and are promising for finding biosignatures on exoplanets orbiting the habitable zone of distant stars.
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Affiliation(s)
- Mariano Battistuzzi
- National Council of Research of Italy, Institute for Photonics and Nanotechnologies (CNR-IFN), 35131 Padua, Italy; (L.C.)
- Department of Biology, University of Padua, 35121 Padua, Italy (N.L.R.)
- Center for Space Studies and Activities (CISAS), University of Padua, 35131 Padua, Italy
| | - Lorenzo Cocola
- National Council of Research of Italy, Institute for Photonics and Nanotechnologies (CNR-IFN), 35131 Padua, Italy; (L.C.)
| | | | - Riccardo Claudi
- National Institute for Astrophysics (INAF), Astronomical Observatory of Padua, 35122 Padua, Italy
- Department of Mathematics and Physics, University Roma Tre, 00146 Rome, Italy
| | - Luca Poletto
- National Council of Research of Italy, Institute for Photonics and Nanotechnologies (CNR-IFN), 35131 Padua, Italy; (L.C.)
| | - Nicoletta La Rocca
- Department of Biology, University of Padua, 35121 Padua, Italy (N.L.R.)
- Center for Space Studies and Activities (CISAS), University of Padua, 35131 Padua, Italy
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10
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Rockwell NC, Lagarias JC. GUN4 appeared early in cyanobacterial evolution. PNAS NEXUS 2023; 2:pgad131. [PMID: 37152672 PMCID: PMC10156173 DOI: 10.1093/pnasnexus/pgad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/15/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023]
Abstract
Photosynthesis relies on chlorophylls, which are synthesized via a common tetrapyrrole trunk pathway also leading to heme, vitamin B12, and other pigmented cofactors. The first committed step for chlorophyll biosynthesis is insertion of magnesium into protoporphyrin IX by magnesium chelatase. Magnesium chelatase is composed of H-, I-, and D-subunits, with the tetrapyrrole substrate binding to the H-subunit. This subunit is rapidly inactivated in the presence of substrate, light, and oxygen, so oxygenic photosynthetic organisms require mechanisms to protect magnesium chelatase from similar loss of function. An additional protein, GUN4, binds to the H-subunit and to tetrapyrroles. GUN4 has been proposed to serve this protective role via its ability to bind linear tetrapyrroles (bilins). In the current work, we probe the origins of bilin binding by GUN4 via comparative phylogenetic analysis and biochemical validation of a conserved bilin-binding motif. Based on our results, we propose that bilin-binding GUN4 proteins arose early in cyanobacterial evolution and that this early acquisition represents an ancient adaptation for maintaining chlorophyll biosynthesis in the presence of light and oxygen.
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11
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Leterme S, Bastien O, Aiese Cigliano R, Amato A, Michaud M. Phylogenetic and Structural Analyses of VPS13 Proteins in Archaeplastida Reveal Their Complex Evolutionary History in Viridiplantae. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231211976. [PMID: 38033810 PMCID: PMC10683392 DOI: 10.1177/25152564231211976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
VPS13 is a lipid transfer protein family conserved among Eukaryotes and playing roles in fundamental processes involving vesicular transport and membrane expansion including autophagy and organelle biogenesis. VPS13 folds into a long hydrophobic tunnel, allowing lipid transport, decorated by distinct domains involved in protein localization and regulation. Whereas VPS13 organization and function have been extensively studied in yeast and mammals, information in organisms originating from primary endosymbiosis is scarce. In the higher plant Arabidopsis thaliana, four paralogs, AtVPS13S, X, M1, and M2, were identified, AtVPS13S playing a role in the regulation of root growth, cell patterning, and reproduction. In this work, we performed phylogenetic, as well as domain and structural modeling of VPS13 proteins in Archaeplastida in order to understand their general organization and evolutionary history. We confirmed the presence of human VPS13B orthologues in some phyla and described two new VPS13 families presenting a particular domain arrangement: VPS13R in Rhodophytes and VPS13Y in Chlorophytes and Streptophytes. By focusing on Viridiplantae, we were able to draw the evolutionary history of these proteins made by multiple gene gains and duplications as well as domain rearrangements. We showed that some Chlorophytes have only three (AtVPS13M, S, Y) whereas some Charophytes have up to six VPS13 paralogs (AtVPS13M1, M2, S, Y, X, B). We also highlighted specific structural features of VPS13M and X paralogs. This study reveals the complex evolution of VPS13 family and opens important perspectives for their functional characterization in photosynthetic organisms.
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Affiliation(s)
- Sébastien Leterme
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Olivier Bastien
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | | | - Alberto Amato
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Morgane Michaud
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
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12
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Ward LM, Shih PM. Phototrophy and carbon fixation in Chlorobi postdate the rise of oxygen. PLoS One 2022; 17:e0270187. [PMID: 35913911 PMCID: PMC9342728 DOI: 10.1371/journal.pone.0270187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 06/07/2022] [Indexed: 11/28/2022] Open
Abstract
While most productivity on the surface of the Earth today is fueled by oxygenic photosynthesis, for much of Earth history it is thought that anoxygenic photosynthesis-using compounds like ferrous iron or sulfide as electron donors-drove most global carbon fixation. Anoxygenic photosynthesis is still performed by diverse bacteria in niche environments today. Of these, the Chlorobi (formerly green sulfur bacteria) are often interpreted as being particularly ancient and are frequently proposed to have fueled the biosphere during late Archean and early Paleoproterozoic time before the rise of oxygenic photosynthesis. Here, we perform comparative genomic, phylogenetic, and molecular clock analyses to determine the antiquity of the Chlorobi and their characteristic phenotypes. We show that contrary to common assumptions, the Chlorobi clade is relatively young, with anoxygenic phototrophy, carbon fixation via the rTCA pathway, and iron oxidation all significantly postdating the rise of oxygen ~2.3 billion years ago. The Chlorobi therefore could not have fueled the Archean biosphere, but instead represent a relatively young radiation of organisms which likely acquired the capacity for anoxygenic photosynthesis and other traits via horizontal gene transfer sometime after the evolution of oxygenic Cyanobacteria.
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Affiliation(s)
- L. M. Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Geosciences, Smith College, Northampton, Massachusetts, United States of America
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, United States of America
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13
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Tomasello S, Oberprieler C. Reticulate Evolution in the Western Mediterranean Mountain Ranges: The Case of the Leucanthemopsis Polyploid Complex. FRONTIERS IN PLANT SCIENCE 2022; 13:842842. [PMID: 35783934 PMCID: PMC9247603 DOI: 10.3389/fpls.2022.842842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Polyploidization is one of the most common speciation mechanisms in plants. This is particularly relevant in high mountain environments and/or in areas heavily affected by climatic oscillations. Although the role of polyploidy and the temporal and geographical frameworks of polyploidization have been intensively investigated in the alpine regions of the temperate and arctic biomes, fewer studies are available with a specific focus on the Mediterranean region. Leucanthemopsis (Asteraceae) consists of six to ten species with several infraspecific entities, mainly distributed in the western Mediterranean Basin. It is a polyploid complex including montane, subalpine, and strictly alpine lineages, which are locally distributed in different mountain ranges of Western Europe and North Africa. We used a mixed approach including Sanger sequencing and (Roche-454) high throughput sequencing of amplicons to gather information from single-copy nuclear markers and plastid regions. Nuclear regions were carefully tested for recombinants/PCR artifacts and for paralogy. Coalescent-based methods were used to infer the number of polyploidization events and the age of formation of polyploid lineages, and to reconstruct the reticulate evolution of the genus. Whereas the polyploids within the widespread Leucanthemopsis alpina are autopolyploids, the situation is more complex among the taxa endemic to the western Mediterranean. While the hexaploid, L. longipectinata, confined to the northern Moroccan mountain ranges (north-west Africa), is an autopolyploid, the Iberian polyploids are clearly of allopolyploid origins. At least two different polyploidization events gave rise to L. spathulifolia and to all other tetraploid Iberian taxa, respectively. The formation of the Iberian allopolyploids took place in the early Pleistocene and was probably caused by latitudinal and elevational range shifts that brought into contact previously isolated Leucanthemopsis lineages. Our study thus highlights the importance of the Pleistocene climatic oscillations and connected polyploidization events for the high plant diversity in the Mediterranean Basin.
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Affiliation(s)
- Salvatore Tomasello
- Department of Systematics, Biodiversity and Evolution of Plants (With Herbarium), University of Göttingen, Göttingen, Germany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
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14
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Gabr A, Stephens TG, Bhattacharya D. Hypothesis: Trans-splicing Generates Evolutionary Novelty in the Photosynthetic Amoeba Paulinella. JOURNAL OF PHYCOLOGY 2022; 58:392-405. [PMID: 35255163 PMCID: PMC9311404 DOI: 10.1111/jpy.13247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 05/19/2023]
Abstract
Plastid primary endosymbiosis has occurred twice, once in the Archaeplastida ancestor and once in the Paulinella (Rhizaria) lineage. Both events precipitated massive evolutionary changes, including the recruitment and activation of genes that are horizontally acquired (HGT) and the redeployment of existing genes and pathways in novel contexts. Here we address the latter aspect in Paulinella micropora KR01 (hereafter, KR01) that has independently evolved spliced leader (SL) trans-splicing (SLTS) of nuclear-derived transcripts. We investigated the role of this process in gene regulation, novel gene origination, and endosymbiont integration. Our analysis shows that 20% of KR01 genes give rise to transcripts with at least one (but in some cases, multiple) sites of SL addition. This process, which often occurs at canonical cis-splicing acceptor sites (internal introns), results in shorter transcripts that may produce 5'-truncated proteins with novel functions. SL-truncated transcripts fall into four categories that may show: (i) altered protein localization, (ii) altered protein function, structure, or regulation, (iii) loss of valid alternative start codons, preventing translation, or (iv) multiple SL addition sites at the 5'-terminus. The SL RNA genes required for SLTS are putatively absent in the heterotrophic sister lineage of photosynthetic Paulinella species. Moreover, a high proportion of transcripts derived from genes of endosymbiotic gene transfer (EGT) and HGT origin contain SL sequences. We hypothesize that truncation of transcripts by SL addition may facilitate the generation and expression of novel gene variants and that SLTS may have enhanced the activation and fixation of foreign genes in the host genome of the photosynthetic lineages, playing a key role in primary endosymbiont integration.
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Affiliation(s)
- Arwa Gabr
- Graduate Program in Molecular Bioscience and Program in Microbiology and Molecular GeneticsRutgers UniversityNew BrunswickNew Jersey08901USA
| | - Timothy G. Stephens
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNew Jersey08901USA
| | - Debashish Bhattacharya
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNew Jersey08901USA
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15
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Maria Costa-Paiva E, Mello B, Santos Bezerra B, Coates CJ, Halanych KM, Brown F, de Moraes Leme J, Trindade RIF. Molecular dating of the blood pigment hemocyanin provides new insight into the origin of animals. GEOBIOLOGY 2022; 20:333-345. [PMID: 34766436 DOI: 10.1111/gbi.12481] [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: 12/23/2020] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
The Neoproterozoic included changes in oceanic redox conditions, the configuration of continents and climate, extreme ice ages (Sturtian and Marinoan), and the rise of complex life forms. A much-debated topic in geobiology concerns the influence of atmospheric oxygenation on Earth and the origin and diversification of animal lineages, with the most widely popularized hypotheses relying on causal links between oxygen levels and the rise of animals. The vast majority of extant animals use aerobic metabolism for growth and homeostasis; hence, the binding and transportation of oxygen represent a vital physiological task. Considering the blood pigment hemocyanin (Hc) is present in sponges and ctenophores, and likely to be present in the common ancestor of animals, we investigated the evolution and date of Hc emergence using bioinformatics approaches on both transcriptomic and genomic data. Bayesian molecular dating suggested that the ancestral animal Hc gene arose approximately 881 Ma during the Tonian Period (1000-720 Ma), prior to the extreme glaciation events of the Cryogenian Period (720-635 Ma). This result is corroborated by a recently discovered fossil of a putative sponge ~890 Ma and modern molecular dating for the origin of metazoans of ~1,000-650 Ma (but does contradict previous inferences regarding the origin of Hc ~700-600 Ma). Our data reveal that crown-group animals already possessed hemocyanin-like blood pigments, which may have enhanced the oxygen-carrying capacity of these animals in hypoxic environments at that time or acted in the transport of hormones, detoxification of heavy metals, and immunity pathways.
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Affiliation(s)
- Elisa Maria Costa-Paiva
- Zoology Department, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
- Geophysics and Atmospheric Sciences, Institute of Astronomy, University of Sao Paulo, Sao Paulo, Brazil
| | - Beatriz Mello
- Genetics Department, Biology Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Santos Bezerra
- Zoology Department, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Christopher J Coates
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Swansea, UK
| | - Kenneth M Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Federico Brown
- Zoology Department, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Ricardo I F Trindade
- Geophysics and Atmospheric Sciences, Institute of Astronomy, University of Sao Paulo, Sao Paulo, Brazil
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16
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Gabr A, Zournas A, Stephens TG, Dismukes GC, Bhattacharya D. Evidence for a robust photosystem II in the photosynthetic amoeba Paulinella. THE NEW PHYTOLOGIST 2022; 234:934-945. [PMID: 35211975 DOI: 10.1111/nph.18052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
Paulinella represents the only known case of an independent primary plastid endosymbiosis, outside Archaeplastida, that occurred c. 120 (million years ago) Ma. These photoautotrophs grow very slowly in replete culture medium with a doubling time of 6-7 d at optimal low light, and are highly sensitive to photodamage under moderate light levels. We used genomic and biophysical methods to investigate the extreme slow growth rate and light sensitivity of Paulinella, which are key to photosymbiont integration. All photosystem II (PSII) genes except psb28-2 and all cytochrome b6 f complex genes except petM and petL are present in Paulinella micropora KR01 (hereafter, KR01). Biophysical measurements of the water oxidation complex, variable chlorophyll fluorescence, and photosynthesis-irradiance curves show no obvious evidence of PSII impairment. Analysis of photoacclimation under high-light suggests that although KR01 can perform charge separation, it lacks photoprotection mechanisms present in cyanobacteria. We hypothesize that Paulinella species are restricted to low light environments because they are deficient in mitigating the formation of reactive oxygen species formed within the photosystems under peak solar intensities. The finding that many photoprotection genes have been lost or transferred to the host-genome during endosymbiont genome reduction, and may lack light-regulation, is consistent with this hypothesis.
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Affiliation(s)
- Arwa Gabr
- Graduate Program in Molecular Bioscience and Program in Microbiology and Molecular Genetics, Rutgers University, Nelson Lab-604 Allison Road, Piscataway, NJ, 08854, USA
| | - Apostolos Zournas
- Graduate Program in Chemical and Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ, 08854, USA
- The Waksman Institute, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, Lipman Drive, New Brunswick, NJ, 08901, USA
| | - G Charles Dismukes
- The Waksman Institute, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, Lipman Drive, New Brunswick, NJ, 08901, USA
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17
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Eukaryogenesis and oxygen in Earth history. Nat Ecol Evol 2022; 6:520-532. [PMID: 35449457 DOI: 10.1038/s41559-022-01733-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/15/2022] [Indexed: 02/07/2023]
Abstract
The endosymbiotic origin of mitochondria during eukaryogenesis has long been viewed as an adaptive response to the oxygenation of Earth's surface environment, presuming a fundamentally aerobic lifestyle for the free-living bacterial ancestors of mitochondria. This oxygen-centric view has been robustly challenged by recent advances in the Earth and life sciences. While the permanent oxygenation of the atmosphere above trace concentrations is now thought to have occurred 2.2 billion years ago, large parts of the deep ocean remained anoxic until less than 0.5 billion years ago. Neither fossils nor molecular clocks correlate the origin of mitochondria, or eukaryogenesis more broadly, to either of these planetary redox transitions. Instead, mitochondria-bearing eukaryotes are consistently dated to between these two oxygenation events, during an interval of pervasive deep-sea anoxia and variable surface-water oxygenation. The discovery and cultivation of the Asgard archaea has reinforced metabolic evidence that eukaryogenesis was initially mediated by syntrophic H2 exchange between an archaeal host and an α-proteobacterial symbiont living under anoxia. Together, these results temporally, spatially and metabolically decouple the earliest stages of eukaryogenesis from the oxygen content of the surface ocean and atmosphere. Rather than reflecting the ancestral metabolic state, obligate aerobiosis in eukaryotes is most probably derived, having only become globally widespread over the past 1 billion years as atmospheric oxygen approached modern levels.
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18
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Azuma T, Pánek T, Tice AK, Kayama M, Kobayashi M, Miyashita H, Suzaki T, Yabuki A, Brown MW, Kamikawa R. An enigmatic stramenopile sheds light on early evolution in Ochrophyta plastid organellogenesis. Mol Biol Evol 2022; 39:6555011. [PMID: 35348760 PMCID: PMC9004409 DOI: 10.1093/molbev/msac065] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary producers. However, early evolution of the plastid organelle in Ochrophyta is not fully understood. In this study, we provide a well-supported tree of the Stramenopiles inferred by the large-scale phylogenomic analysis that unveils the eukaryvorous (nonphotosynthetic) protist Actinophrys sol (Actinophryidae) is closely related to Ochrophyta. We used genomic and transcriptomic data generated from A. sol to detect molecular traits of its plastid and we found no evidence of plastid genome and plastid-mediated biosynthesis, consistent with previous ultrastructural studies that did not identify any plastids in Actinophryidae. Moreover, our phylogenetic analyses of particular biosynthetic pathways provide no evidence of a current and past plastid in A. sol. However, we found more than a dozen organellar aminoacyl-tRNA synthases (aaRSs) that are of algal origin. Close relationships between aaRS from A. sol and their ochrophyte homologs document gene transfer of algal genes that happened before the divergence of Actinophryidae and Ochrophyta lineages. We further showed experimentally that organellar aaRSs of A. sol are targeted exclusively to mitochondria, although organellar aaRSs in Ochrophyta are dually targeted to mitochondria and plastids. Together, our findings suggested that the last common ancestor of Actinophryidae and Ochrophyta had not yet completed the establishment of host–plastid partnership as seen in the current Ochrophyta species, but acquired at least certain nuclear-encoded genes for the plastid functions.
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Affiliation(s)
- Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida nihonmatsu cho, Sakyo ku, Kyoto, Kyoto, Japan
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida nihonmatsu cho, Sakyo ku, Kyoto, Kyoto, Japan
| | | | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida nihonmatsu cho, Sakyo ku, Kyoto, Kyoto, Japan
| | | | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology, Japan
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa oiwake cho, Sakyo ku, Kyoto, Kyoto, Japan
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19
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Vigneau J, Borg M. The epigenetic origin of life history transitions in plants and algae. PLANT REPRODUCTION 2021; 34:267-285. [PMID: 34236522 PMCID: PMC8566409 DOI: 10.1007/s00497-021-00422-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Plants and algae have a complex life history that transitions between distinct life forms called the sporophyte and the gametophyte. This phenomenon-called the alternation of generations-has fascinated botanists and phycologists for over 170 years. Despite the mesmerizing array of life histories described in plants and algae, we are only now beginning to learn about the molecular mechanisms controlling them and how they evolved. Epigenetic silencing plays an essential role in regulating gene expression during multicellular development in eukaryotes, raising questions about its impact on the life history strategy of plants and algae. Here, we trace the origin and function of epigenetic mechanisms across the plant kingdom, from unicellular green algae through to angiosperms, and attempt to reconstruct the evolutionary steps that influenced life history transitions during plant evolution. Central to this evolutionary scenario is the adaption of epigenetic silencing from a mechanism of genome defense to the repression and control of alternating generations. We extend our discussion beyond the green lineage and highlight the peculiar case of the brown algae. Unlike their unicellular diatom relatives, brown algae lack epigenetic silencing pathways common to animals and plants yet display complex life histories, hinting at the emergence of novel life history controls during stramenopile evolution.
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Affiliation(s)
- Jérômine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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20
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Fournier GP, Moore KR, Rangel LT, Payette JG, Momper L, Bosak T. The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages. Proc Biol Sci 2021; 288:20210675. [PMID: 34583585 PMCID: PMC8479356 DOI: 10.1098/rspb.2021.0675] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/06/2021] [Indexed: 12/21/2022] Open
Abstract
The record of the coevolution of oxygenic phototrophs and the environment is preserved in three forms: genomes of modern organisms, diverse geochemical signals of surface oxidation and diagnostic Proterozoic microfossils. When calibrated by fossils, genomic data form the basis of molecular clock analyses. However, different interpretations of the geochemical record, fossil calibrations and evolutionary models produce a wide range of age estimates that are often conflicting. Here, we show that multiple interpretations of the cyanobacterial fossil record are consistent with an Archean origin of crown-group Cyanobacteria. We further show that incorporating relative dating information from horizontal gene transfers greatly improves the precision of these age estimates, by both providing a novel empirical criterion for selecting evolutionary models, and increasing the stringency of sampling of posterior age estimates. Independent of any geochemical evidence or hypotheses, these results support oxygenic photosynthesis evolving at least several hundred million years before the Great Oxygenation Event (GOE), a rapid diversification of major cyanobacterial lineages around the time of the GOE, and a post-Cryogenian origin of extant marine picocyanobacterial diversity.
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Affiliation(s)
- G. P. Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - K. R. Moore
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Planetary Science Section, NASA Jet Propulsion Laboratory, Pasadena, CA, USA
| | - L. T. Rangel
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J. G. Payette
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - L. Momper
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Exponent, Inc., Pasadena, CA, USA
| | - T. Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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21
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Abstract
The origin of plastids (chloroplasts) by endosymbiosis stands as one of the most important events in the history of eukaryotic life. The genetic, biochemical, and cell biological integration of a cyanobacterial endosymbiont into a heterotrophic host eukaryote approximately a billion years ago paved the way for the evolution of diverse algal groups in a wide range of aquatic and, eventually, terrestrial environments. Plastids have on multiple occasions also moved horizontally from eukaryote to eukaryote by secondary and tertiary endosymbiotic events. The overall picture of extant photosynthetic diversity can best be described as “patchy”: Plastid-bearing lineages are spread far and wide across the eukaryotic tree of life, nested within heterotrophic groups. The algae do not constitute a monophyletic entity, and understanding how, and how often, plastids have moved from branch to branch on the eukaryotic tree remains one of the most fundamental unsolved problems in the field of cell evolution. In this review, we provide an overview of recent advances in our understanding of the origin and spread of plastids from the perspective of comparative genomics. Recent years have seen significant improvements in genomic sampling from photosynthetic and nonphotosynthetic lineages, both of which have added important pieces to the puzzle of plastid evolution. Comparative genomics has also allowed us to better understand how endosymbionts become organelles.
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Affiliation(s)
- Shannon J Sibbald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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22
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Kaur J, Sharma J. Orchid Root Associated Bacteria: Linchpins or Accessories? FRONTIERS IN PLANT SCIENCE 2021; 12:661966. [PMID: 34249034 PMCID: PMC8264303 DOI: 10.3389/fpls.2021.661966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/19/2021] [Indexed: 05/28/2023]
Abstract
Besides the plant-fungus symbiosis in arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) plants, many endorhizal and rhizosphere bacteria (Root Associated Bacteria, or RAB) also enhance plant fitness, diversity, and coexistence among plants via bi- or tripartite interactions with plant hosts and mycorrhizal fungi. Assuming that bacterial associations are just as important for the obligate mycorrhizal plant family Orchidaceae, surprisingly little is known about the RAB associated with orchids. Herein, we first present the current, underwhelming state of RAB research including their interactions with fungi and the influence of holobionts on plant fitness. We then delineate the need for novel investigations specifically in orchid RAB ecology, and sketch out questions and hypotheses which, when addressed, will advance plant-microbial ecology. We specifically discuss the potential effects of beneficial RAB on orchids as: (1) Plant Growth Promoting Rhizobacteria (PGPR), (2) Mycorrhization Helper Bacteria (MHB), and (3) constituents of an orchid holobiont. We further posit that a hologenomic view should be considered as a framework for addressing co-evolution of the plant host, their obligate Orchid Mycorrhizal Fungi (OMF), and orchid RAB. We conclude by discussing implications of the suggested research for conservation of orchids, their microbial partners, and their collective habitats.
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Affiliation(s)
- Jaspreet Kaur
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
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Cai C, Gu K, Zhao H, Steinhagen S, He P, Wichard T. Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea. PLoS One 2021; 16:e0250968. [PMID: 34061855 PMCID: PMC8168861 DOI: 10.1371/journal.pone.0250968] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/18/2021] [Indexed: 11/18/2022] Open
Abstract
Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.
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Affiliation(s)
- Chuner Cai
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Kai Gu
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Hui Zhao
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Sophie Steinhagen
- Department of Marine Sciences-Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
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Matzke NJ, Lin A, Stone M, Baker MAB. Flagellar export apparatus and ATP synthetase: Homology evidenced by synteny predating the Last Universal Common Ancestor. Bioessays 2021; 43:e2100004. [PMID: 33998015 DOI: 10.1002/bies.202100004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 11/07/2022]
Abstract
We report evidence further supporting homology between proteins in the F1 FO -ATP synthetase and the bacterial flagellar motor (BFM). BFM proteins FliH, FliI, and FliJ have been hypothesized to be homologous to FO -b + F1 -δ, F1 -α/β, and F1 -γ, with similar structure and interactions. We conduct a further test by constructing a gene order dataset, examining the order of fliH, fliI, and fliJ genes across the phylogenetic breadth of flagellar and nonflagellar type 3 secretion systems, and comparing this to published surveys of gene order in the F1 FO -ATP synthetase, its N-ATPase relatives, and the bacterial/archaeal V- and A-type ATPases. Strikingly, the fliHIJ gene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F-ATPase gene order atpFHAG, coding for subunits b-δ-α-γ. The V/A-type ATPases have a similar conserved gene order. Our results confirm homology between these systems, and suggest a rare case of synteny conserved over billions of years, predating the Last Universal Common Ancestor (LUCA).
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Affiliation(s)
- Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Micaella Stone
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew A B Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
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25
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Caspari OD, Lafontaine I. The role of antimicrobial peptides in the evolution of endosymbiotic protein import. PLoS Pathog 2021; 17:e1009466. [PMID: 33857255 PMCID: PMC8049325 DOI: 10.1371/journal.ppat.1009466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Oliver D. Caspari
- UMR7141, Institut de Biologie Physico-Chimique (CNRS/Sorbonne Université), Paris, France
- * E-mail: (ODC); (IL)
| | - Ingrid Lafontaine
- UMR7141, Institut de Biologie Physico-Chimique (CNRS/Sorbonne Université), Paris, France
- * E-mail: (ODC); (IL)
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26
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Ward LM, Shih PM. Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer. PLoS One 2021; 16:e0239248. [PMID: 33507911 PMCID: PMC7842958 DOI: 10.1371/journal.pone.0239248] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/29/2020] [Indexed: 11/19/2022] Open
Abstract
Photosynthesis-both oxygenic and more ancient anoxygenic forms-has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic "Granick hypothesis" for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.
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Affiliation(s)
- Lewis M. Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| | - Patrick M. Shih
- Department of Plant Biology, University of California, Davis, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Genome Center, University of California, Davis, California, United States of America
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27
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Ward LM, Johnston DT, Shih PM. Phanerozoic radiation of ammonia oxidizing bacteria. Sci Rep 2021; 11:2070. [PMID: 33483596 PMCID: PMC7822890 DOI: 10.1038/s41598-021-81718-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
The modern nitrogen cycle consists of a web of microbially mediated redox transformations. Among the most crucial reactions in this cycle is the oxidation of ammonia to nitrite, an obligately aerobic process performed by a limited number of lineages of bacteria (AOB) and archaea (AOA). As this process has an absolute requirement for O2, the timing of its evolution-especially as it relates to the Great Oxygenation Event ~ 2.3 billion years ago-remains contested and is pivotal to our understanding of nutrient cycles. To estimate the antiquity of bacterial ammonia oxidation, we performed phylogenetic and molecular clock analyses of AOB. Surprisingly, bacterial ammonia oxidation appears quite young, with crown group clades having originated during Neoproterozoic time (or later) with major radiations occurring during Paleozoic time. These results place the evolution of AOB broadly coincident with the pervasive oxygenation of the deep ocean. The late evolution AOB challenges earlier interpretations of the ancient nitrogen isotope record, predicts a more substantial role for AOA during Precambrian time, and may have implications for understanding of the size and structure of the biogeochemical nitrogen cycle through geologic time.
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Affiliation(s)
- L M Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA.
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.
| | - D T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
| | - P M Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Department of Energy, Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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28
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The origin, evolution and diversification of multiple isoforms of light-dependent protochlorophyllide oxidoreductase (LPOR): focus on angiosperms. Biochem J 2020; 477:2221-2236. [PMID: 32568402 DOI: 10.1042/bcj20200323] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
Light-dependent protochlorophyllide oxidoreductase (LPOR) catalyzes the reduction of protochlorophyllide to chlorophyllide, which is a key reaction for angiosperm development. Dark operative light-independent protochlorophyllide oxidoreductase (DPOR) is the other enzyme able to catalyze this reaction, however, it is not present in angiosperms. LPOR, which evolved later than DPOR, requires light to trigger the reaction. The ancestors of angiosperms lost DPOR genes and duplicated the LPORs, however, the LPOR evolution in angiosperms has not been yet investigated. In the present study, we built a phylogenetic tree using 557 nucleotide sequences of LPORs from both bacteria and plants to uncover the evolution of LPOR. The tree revealed that all modern sequences of LPOR diverged from a single sequence ∼1.36 billion years ago. The LPOR gene was then duplicated at least 10 times in angiosperms, leading to the formation of two or even more LPOR isoforms in multiple species. In the case of Arabidopsis thaliana, AtPORA and AtPORB originated in one duplication event, in contrary to the isoform AtPORC, which diverged first. We performed biochemical characterization of these isoforms in vitro, revealing differences in the lipid-driven properties. The results prone us to hypothesize that duplication events of LPOR gave rise to the isoforms having different lipid-driven activity, which may predispose them for functioning in different locations in plastids. Moreover, we showed that LPOR from Synechocystis operated in the lipid-independent manner, revealing differences between bacterial and plant LPORs. Based on the presented results, we propose a novel classification of LPOR enzymes based on their biochemical properties and phylogenetic relationships.
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29
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Islam MI, Lin A, Lai YW, Matzke NJ, Baker MAB. Ancestral Sequence Reconstructions of MotB Are Proton-Motile and Require MotA for Motility. Front Microbiol 2020; 11:625837. [PMID: 33424826 PMCID: PMC7787011 DOI: 10.3389/fmicb.2020.625837] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/27/2020] [Indexed: 12/23/2022] Open
Abstract
The bacterial flagellar motor (BFM) is a nanomachine that rotates the flagellum to propel many known bacteria. The BFM is powered by ion transit across the cell membrane through the stator complex, a membrane protein. Different bacteria use various ions to run their BFM, but the majority of BFMs are powered by either proton (H+) or sodium (Na+) ions. The transmembrane (TM) domain of the B-subunit of the stator complex is crucial for ion selectivity, as it forms the ion channel in complex with TM3 and TM4 of the A-subunit. In this study, we reconstructed and engineered thirteen ancestral sequences of the stator B-subunit to evaluate the functional properties and ionic power source of the stator proteins at reconstruction nodes to evaluate the potential of ancestral sequence reconstruction (ASR) methods for stator engineering and to test specific motifs previously hypothesized to be involved in ion-selectivity. We found that all thirteen of our reconstructed ancient B-subunit proteins could assemble into functional stator complexes in combination with the contemporary Escherichia coli MotA-subunit to restore motility in stator deleted E. coli strains. The flagellar rotation of the thirteen ancestral MotBs was found to be Na+ independent which suggested that the F30/Y30 residue was not significantly correlated with sodium/proton phenotype, in contrast to what we had reported previously. Additionally, four among the thirteen reconstructed B-subunits were compatible with the A-subunit of Aquifex aeolicus and able to function in a sodium-independent manner. Overall, this work demonstrates the use of ancestral reconstruction to generate novel stators and quantify which residues are correlated with which ionic power source.
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Affiliation(s)
- Md Imtiazul Islam
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Yu-Wen Lai
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Nicholas J. Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
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30
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Agafonov VA, Negrobov VV, Igamberdiev AU. Symbiogenesis as a driving force of evolution: The legacy of Boris Kozo-Polyansky. Biosystems 2020; 199:104302. [PMID: 33227379 DOI: 10.1016/j.biosystems.2020.104302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023]
Abstract
We analyze evolutionary views of Boris Kozo-Polyansky (1890-1957) who was the first who formulated the symbiotic theory of evolution as a concept in his book, Symbiogenesis: A New Principle of Evolution (1924). Later, starting from 1967, Lynn Margulis independently formulated and further developed the concept of symbiogenesis. Although the ideas on the symbiotic origin of chloroplasts and mitochondria appeared earlier, the book of Kozo-Polyansky presented symbiogenesis as the main factor of complexification in the course of evolution, not only in relation to the origin of eukaryotic cell. Kozo-Polyansky incorporated the ideas of symbiogenesis into a broader paradigm that anticipated the important concepts of the modern Extended Evolutionary Synthesis such as the idea of net of life, the evolutionary role of apoptosis, the ideas of punctuated equilibrium, and the concept of metasystem transition.
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Affiliation(s)
- Vladimir A Agafonov
- Department of Botany and Mycology, Voronezh State University, Voronezh, 394006, Russia.
| | - Vladimir V Negrobov
- Department of Botany and Mycology, Voronezh State University, Voronezh, 394006, Russia.
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.
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31
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The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress. Int J Mol Sci 2020; 21:ijms21176082. [PMID: 32846932 PMCID: PMC7503970 DOI: 10.3390/ijms21176082] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/16/2022] Open
Abstract
Chloroplasts are plant organelles that carry out photosynthesis, produce various metabolites, and sense changes in the external environment. Given their endosymbiotic origin, chloroplasts have retained independent genomes and gene-expression machinery. Most genes from the prokaryotic ancestors of chloroplasts were transferred into the nucleus over the course of evolution. However, the importance of chloroplast gene expression in environmental stress responses have recently become more apparent. Here, we discuss the emerging roles of the distinct chloroplast gene expression processes in plant responses to environmental stresses. For example, the transcription and translation of psbA play an important role in high-light stress responses. A better understanding of the connection between chloroplast gene expression and environmental stress responses is crucial for breeding stress-tolerant crops better able to cope with the rapidly changing environment.
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32
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Porter SM. Insights into eukaryogenesis from the fossil record. Interface Focus 2020; 10:20190105. [PMID: 32642050 PMCID: PMC7333905 DOI: 10.1098/rsfs.2019.0105] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 12/17/2022] Open
Abstract
Eukaryogenesis-the process by which the eukaryotic cell emerged-has long puzzled scientists. It has been assumed that the fossil record has little to say about this process, in part because important characters such as the nucleus and mitochondria are rarely preserved, and in part because the prevailing model of early eukaryotes implies that eukaryogenesis occurred before the appearance of the first eukaryotes recognized in the fossil record. Here, I propose a different scenario for early eukaryote evolution than is widely assumed. Rather than crown group eukaryotes originating in the late Paleoproterozoic and remaining ecologically minor components for more than half a billion years in a prokaryote-dominated world, I argue for a late Mesoproterozoic origin of the eukaryotic crown group, implying that eukaryogenesis can be studied using the fossil record. I review the proxy records of four crown group characters: the capacity to form cysts as evidenced by the presence of excystment structures; a complex cytoskeleton as evidenced by spines or pylomes; sterol synthesis as evidenced by steranes; and aerobic respiration-and therefore mitochondria-as evidenced by eukaryotes living in oxic environments, and argue that it might be possible to use these proxy records to infer the order in which these characters evolved. The records indicate that both cyst formation and a complex cytoskeleton appeared by late Paleoproterozoic time, and sterol synthesis appeared in the late Mesoproterozioc or early Neoproterozoic. The origin of aerobic respiration cannot as easily be pinned down, but current evidence permits the possibility that it evolved sometime in the Mesoproterozoic.
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Affiliation(s)
- Susannah M. Porter
- Department of Earth Science, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
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33
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Gabr A, Grossman AR, Bhattacharya D. Paulinella, a model for understanding plastid primary endosymbiosis. JOURNAL OF PHYCOLOGY 2020; 56:837-843. [PMID: 32289879 PMCID: PMC7734844 DOI: 10.1111/jpy.13003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/25/2020] [Indexed: 05/07/2023]
Abstract
The uptake and conversion of a free-living cyanobacterium into a photosynthetic organelle by the single-celled Archaeplastida ancestor helped transform the biosphere from low to high oxygen. There are two documented, independent cases of plastid primary endosymbiosis. The first is the well-studied instance in Archaeplastida that occurred ca. 1.6 billion years ago, whereas the second occurred 90-140 million years ago, establishing a permanent photosynthetic compartment (the chromatophore) in amoebae in the genus Paulinella. Here, we briefly summarize knowledge about plastid origin in the Archaeplastida and then focus on Paulinella. In particular, we describe features of the Paulinella chromatophore that make it a model for examining earlier events in the evolution of photosynthetic organelles. Our review stresses recently gained insights into the evolution of chromatophore and nuclear encoded DNA sequences in Paulinella, metabolic connectivity between the endosymbiont and cytoplasm, and systems that target proteins into the chromatophore. We also describe future work with Paulinella, and the potential rewards and challenges associated with developing further this model system.
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Affiliation(s)
- Arwa Gabr
- School of Graduate Studies, Graduate Program in Molecular Bioscience and Program in Microbiology and Molecular Genetics, Rutgers University, New Brunswick, New Jersey 08901, USA
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, California 94305, USA
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Falciatore A, Jaubert M, Bouly JP, Bailleul B, Mock T. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity. THE PLANT CELL 2020; 32:547-572. [PMID: 31852772 PMCID: PMC7054031 DOI: 10.1105/tpc.19.00158] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/18/2019] [Accepted: 12/13/2019] [Indexed: 05/08/2023]
Abstract
Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ∼20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.
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Affiliation(s)
- Angela Falciatore
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Marianne Jaubert
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Jean-Pierre Bouly
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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35
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Waterworth SC, Flórez LV, Rees ER, Hertweck C, Kaltenpoth M, Kwan JC. Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome. mBio 2020; 11:e02430-19. [PMID: 32098813 PMCID: PMC7042692 DOI: 10.1128/mbio.02430-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/13/2020] [Indexed: 12/20/2022] Open
Abstract
Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont's genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation-bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation.
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Affiliation(s)
- Samantha C Waterworth
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Laura V Flórez
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenburg University, Mainz, Germany
| | - Evan R Rees
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, Jena, Germany
- Department of Natural Product Chemistry, Friedrich Schiller University, Jena, Germany
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenburg University, Mainz, Germany
| | - Jason C Kwan
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
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36
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Tang Q, Pang K, Yuan X, Xiao S. A one-billion-year-old multicellular chlorophyte. Nat Ecol Evol 2020; 4:543-549. [PMID: 32094536 PMCID: PMC8668152 DOI: 10.1038/s41559-020-1122-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/20/2020] [Indexed: 11/09/2022]
Abstract
Chlorophytes (representing a clade within the Viridiplantae and a sister group of the Streptophyta) probably dominated marine export bioproductivity and played a key role in facilitating ecosystem complexity before the Mesozoic diversification of phototrophic eukaryotes such as diatoms, coccolithophorans and dinoflagellates. Molecular clock and biomarker data indicate that chlorophytes diverged in the Mesoproterozoic or early Neoproterozoic, followed by their subsequent phylogenetic diversification, multicellular evolution and ecological expansion in the late Neoproterozoic and Palaeozoic. This model, however, has not been rigorously tested with palaeontological data because of the scarcity of Proterozoic chlorophyte fossils. Here we report abundant millimetre-sized, multicellular and morphologically differentiated macrofossils from rocks approximately 1,000 million years ago. These fossils are described as Proterocladus antiquus new species and are interpreted as benthic siphonocladalean chlorophytes, suggesting that chlorophytes acquired macroscopic size, multicellularity and cellular differentiation nearly a billion years ago, much earlier than previously thought.
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Affiliation(s)
- Qing Tang
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA.
| | - Ke Pang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xunlai Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA.
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Larkum AWD, Grossman AR, Raven JA. Recent Advances in the Photosynthesis of Cyanobacteria and Eukaryotic Algae. PHOTOSYNTHESIS IN ALGAE: BIOCHEMICAL AND PHYSIOLOGICAL MECHANISMS 2020. [DOI: 10.1007/978-3-030-33397-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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38
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Lawrence TJ, Amrine KCH, Swingley WD, Ardell DH. tRNA functional signatures classify plastids as late-branching cyanobacteria. BMC Evol Biol 2019; 19:224. [PMID: 31818253 PMCID: PMC6902448 DOI: 10.1186/s12862-019-1552-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/29/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Eukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data. RESULTS Using Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies ("phyloclassifies") cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data. CONCLUSIONS Phylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies.
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Affiliation(s)
- Travis J Lawrence
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831 USA
- Quantitative and Systems Biology Program, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
| | - Katherine CH Amrine
- Quantitative and Systems Biology Program, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
- Insight Data Science, 500 3rd St., San Francisco, CA, 94107 USA
| | - Wesley D Swingley
- Department of Biological Sciences, Northern Illinois University, 1425 Lincoln Hwy., DeKalb, IL, 60115 USA
| | - David H Ardell
- Quantitative and Systems Biology Program, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
- Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
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Gavelis GS, Gile GH. How did cyanobacteria first embark on the path to becoming plastids?: lessons from protist symbioses. FEMS Microbiol Lett 2019; 365:5079637. [PMID: 30165400 DOI: 10.1093/femsle/fny209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/23/2018] [Indexed: 12/13/2022] Open
Abstract
Symbioses between phototrophs and heterotrophs (a.k.a 'photosymbioses') are extremely common, and range from loose and temporary associations to obligate and highly specialized forms. In the history of life, the most transformative was the 'primary endosymbiosis,' wherein a cyanobacterium was engulfed by a eukaryote and became genetically integrated as a heritable photosynthetic organelle, or plastid. By allowing the rise of algae and plants, this event dramatically altered the biosphere, but its remote origin over one billion years ago has obscured the sequence of events leading to its establishment. Here, we review the genetic, physiological and developmental hurdles involved in early primary endosymbiosis. Since we cannot travel back in time to witness these evolutionary junctures, we will draw on examples of unicellular eukaryotes (protists) spanning diverse modes of photosymbiosis. We also review experimental approaches that could be used to recreate aspects of early primary endosymbiosis on a human timescale.
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Affiliation(s)
- Gregory S Gavelis
- School of Life Sciences, Arizona State University, Room 611, Life Science Tower E, 427 E, Tyler Mall, Tempe, AZ 85287, USA
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, Room 611, Life Science Tower E, 427 E, Tyler Mall, Tempe, AZ 85287, USA
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40
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Ward LM, Shih PM. The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time. Free Radic Biol Med 2019; 140:188-199. [PMID: 30790657 DOI: 10.1016/j.freeradbiomed.2019.01.049] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/12/2019] [Accepted: 01/31/2019] [Indexed: 12/25/2022]
Abstract
The fixation of inorganic carbon species like CO2 to more reduced organic forms is one of the most fundamental processes of life as we know it. Although several carbon fixation pathways are known to exist, on Earth today nearly all global carbon fixation is driven by the Calvin cycle in oxygenic photosynthetic plants, algae, and Cyanobacteria. At other times in Earth history, other organisms utilizing different carbon fixation pathways may have played relatively larger roles, with this balance shifting over geological time as the environmental context of life has changed and evolutionary innovations accumulated. Among the most dramatic changes that our planet and the biosphere have undergone are those surrounding the rise of O2 in our atmosphere-first during the Great Oxygenation Event at ∼2.3 Ga, and perhaps again during Neoproterozoic or Paleozoic time. These oxygenation events likely represent major step changes in the tempo and mode of biological productivity as a result of the increased productivity of oxygenic photosynthesis and the introduction of O2 into geochemical and biological systems, and likely involved shifts in the relative contribution of different carbon fixation pathways. Here, we review what is known from both the rock record and comparative biology about the evolution of carbon fixation pathways, their contributions to primary productivity through time, and their relationship to the evolving oxygenation state of the fluid Earth following the evolution and expansion of oxygenic photosynthesis.
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Affiliation(s)
- Lewis M Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States.
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, United States; Department of Energy, Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, United States; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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41
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Demoulin CF, Lara YJ, Cornet L, François C, Baurain D, Wilmotte A, Javaux EJ. Cyanobacteria evolution: Insight from the fossil record. Free Radic Biol Med 2019; 140:206-223. [PMID: 31078731 PMCID: PMC6880289 DOI: 10.1016/j.freeradbiomed.2019.05.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/13/2019] [Accepted: 05/05/2019] [Indexed: 11/07/2022]
Abstract
Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis.
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Affiliation(s)
- Catherine F Demoulin
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium.
| | - Yannick J Lara
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium
| | - Luc Cornet
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium; Eukaryotic Phylogenomics, InBioS-PhytoSYSTEMS, University of Liège, Liège, Belgium
| | - Camille François
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium
| | - Denis Baurain
- Eukaryotic Phylogenomics, InBioS-PhytoSYSTEMS, University of Liège, Liège, Belgium
| | - Annick Wilmotte
- BCCM/ULC Cyanobacteria Collection, InBioS-CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution - Astrobiology, UR ASTROBIOLOGY, Geology Department, University of Liège, Liège, Belgium
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42
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Braakman R. Evolution of cellular metabolism and the rise of a globally productive biosphere. Free Radic Biol Med 2019; 140:172-187. [PMID: 31082508 DOI: 10.1016/j.freeradbiomed.2019.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 02/28/2019] [Accepted: 05/02/2019] [Indexed: 01/14/2023]
Abstract
Metabolic processes in cells and chemical processes in the environment are fundamentally intertwined and have evolved in concert for most of Earth's existence. Here I argue that intrinsic properties of cellular metabolism imposed central constraints on the historical trajectories of biopsheric productivity and atmospheric oxygenation. Photosynthesis depends on iron, but iron is highly insoluble under the aerobic conditions produced by oxygenic photosynthesis. These counteracting constraints led to two major stages of Earth oxygenation. After a cyanobacteria-driven biospheric expansion near the Archean-Proterozoic boundary, productivity remained largely restricted to continental boundaries and shallow aquatic environments where weathering inputs made iron more accessible. The anoxic deep open ocean was rich in free iron during the Proterozoic, but this iron was largely inaccessible, partly because an otherwise nutrient-poor ocean was limiting to photosynthesis, but also because a photosynthetic expansion would have quenched its own iron supply. Near the Proterozoic-Phanerozoic boundary, bioenergetics innovations allowed eukaryotic photosynthesis to overcome these interconnected negative feedbacks and begin expanding into the deep open oceans and onto the continents, where nutrients are inherently harder to come by. Key insights into what drove the ecological rise of eukaryotic photosynthesis emerge from analyses of marine Synechococcus and Prochlorococcus, abundant marine picocyanobacteria whose ancestors colonized the oceans in the Neoproterozoic. The reconstructed evolution of this group reveals a sequence of innovations that ultimately produced a form of photosynthesis in Prochlorococcus that is more like that of green plant cells than other cyanobacteria. Innovations increased the energy flux of cells, thereby enhancing their ability to acquire sparse nutrients, and as by-product also increased the production of organic carbon waste. Some of these organic waste products had the ability to chelate iron and make it bioavailable, thereby indirectly pushing the oceans through a transition from an anoxic state rich in free iron to an oxygenated state with organic carbon-bound iron. Resulting conditions (and parallel processes on the continents) in turn led to a series of positive feedbacks that increased the availability of other nutrients, thereby promoting the rise of a globally productive biosphere. In addition to the occurrence of major biospheric expansions, the several hundred million-year periods around the Archean-Proterozoic and Proterozoic-Phanerozoic boundaries share a number of other parallels. Both epochs have also been linked to major carbon cycle perturbations and global glaciations, as well as changes in the nature of plate tectonics and increases in continental exposure and weathering. This suggests the dynamics of life and Earth are intimately intertwined across many levels and that general principles governed transitions in these coupled dynamics at both times in Earth history.
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Affiliation(s)
- Rogier Braakman
- Department of Civil & Environmental Engineering, Massachusetts Institute of Technology, USA; Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, USA.
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43
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Oborník M. Endosymbiotic Evolution of Algae, Secondary Heterotrophy and Parasitism. Biomolecules 2019; 9:E266. [PMID: 31288476 PMCID: PMC6681372 DOI: 10.3390/biom9070266] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/01/2019] [Accepted: 07/05/2019] [Indexed: 12/15/2022] Open
Abstract
Photosynthesis is a biochemical process essential for life, serving as the ultimate source of chemical energy for phototrophic and heterotrophic life forms. Since the machinery of the photosynthetic electron transport chain is quite complex and is unlikely to have evolved multiple independent times, it is believed that this machinery has been transferred to diverse eukaryotic organisms by endosymbiotic events involving a eukaryotic host and a phototrophic endosymbiont. Thus, photoautotrophy, as a benefit, is transmitted through the evolution of plastids. However, many eukaryotes became secondarily heterotrophic, reverting to hetero-osmotrophy, phagotrophy, or parasitism. Here, I briefly review the constructive evolution of plastid endosymbioses and the consequential switch to reductive evolution involving losses of photosynthesis and plastids and the evolution of parasitism from a photosynthetic ancestor.
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Affiliation(s)
- Miroslav Oborník
- Institute of Parasitology, Biology Centre CAS, 37005 České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic.
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Abstract
Metabolism drives life; thus, understanding how and when various branches of metabolism evolved provides a critical piece to understanding how life has integrated itself into the geochemical cycles of our planet over billions of years. Although the most transformative metabolisms that have significantly altered the trajectory of Earth are inherently linked to primary metabolism, natural products that stem from specialized metabolic pathways are also key components to many auxiliary facets of life. Cyanobacteria are primarily known as the original inventors of oxygenic photosynthesis, using sunlight to split water to create our dioxygen-filled atmosphere; however, many of them also have evolved to produce small molecules that function as sunscreens to protect themselves from ultraviolet radiation. Determining when cyanobacteria first evolved the ability to biosynthesize such compounds is an important piece to understanding the rise of oxygen and the eventual success of the phylum.
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45
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Ishida T, Ito R, Clark J, Matzke NJ, Sowa Y, Baker MAB. Sodium‐powered stators of the bacterial flagellar motor can generate torque in the presence of phenamil with mutations near the peptidoglycan‐binding region. Mol Microbiol 2019; 111:1689-1699. [DOI: 10.1111/mmi.14246] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Tsubasa Ishida
- Department of Frontier Bioscience Hosei University Tokyo Japan
| | - Rie Ito
- Department of Frontier Bioscience Hosei University Tokyo Japan
| | - Jessica Clark
- School of Biotechnology and Biomolecular Science University of New South Wales Kensington NSW Australia
| | - Nicholas J. Matzke
- School of Biological Sciences University of Auckland Auckland New Zealand
| | - Yoshiyuki Sowa
- Department of Frontier Bioscience Hosei University Tokyo Japan
- Research Center for Micro‐Nano Technology Hosei University Tokyo Japan
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Science University of New South Wales Kensington NSW Australia
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46
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Cardona T, Sánchez‐Baracaldo P, Rutherford AW, Larkum AW. Early Archean origin of Photosystem II. GEOBIOLOGY 2019; 17:127-150. [PMID: 30411862 PMCID: PMC6492235 DOI: 10.1111/gbi.12322] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/03/2018] [Accepted: 10/11/2018] [Indexed: 05/09/2023]
Abstract
Photosystem II is a photochemical reaction center that catalyzes the light-driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale, we hypothesize that this early Archean photosystem was capable of water oxidation to oxygen and had already evolved protection mechanisms against the formation of reactive oxygen species. This would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.
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Affiliation(s)
- Tanai Cardona
- Department of Life SciencesImperial College LondonLondonUK
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47
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Figueroa-Martinez F, Jackson C, Reyes-Prieto A. Plastid Genomes from Diverse Glaucophyte Genera Reveal a Largely Conserved Gene Content and Limited Architectural Diversity. Genome Biol Evol 2019; 11:174-188. [PMID: 30534986 PMCID: PMC6330054 DOI: 10.1093/gbe/evy268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 12/30/2022] Open
Abstract
Plastid genome (ptDNA) data of Glaucophyta have been limited for many years to the genus Cyanophora. Here, we sequenced the ptDNAs of Gloeochaete wittrockiana, Cyanoptyche gloeocystis, Glaucocystis incrassata, and Glaucocystis sp. BBH. The reported sequences are the first genome-scale plastid data available for these three poorly studied glaucophyte genera. Although the Glaucophyta plastids appear morphologically “ancestral,” they actually bear derived genomes not radically different from those of red algae or viridiplants. The glaucophyte plastid coding capacity is highly conserved (112 genes shared) and the architecture of the plastid chromosomes is relatively simple. Phylogenomic analyses recovered Glaucophyta as the earliest diverging Archaeplastida lineage, but the position of viridiplants as the first branching group was not rejected by the approximately unbiased test. Pairwise distances estimated from 19 different plastid genes revealed that the highest sequence divergence between glaucophyte genera is frequently higher than distances between species of different classes within red algae or viridiplants. Gene synteny and sequence similarity in the ptDNAs of the two Glaucocystis species analyzed is conserved. However, the ptDNA of Gla. incrassata contains a 7.9-kb insertion not detected in Glaucocystis sp. BBH. The insertion contains ten open reading frames that include four coding regions similar to bacterial serine recombinases (two open reading frames), DNA primases, and peptidoglycan aminohydrolases. These three enzymes, often encoded in bacterial plasmids and bacteriophage genomes, are known to participate in the mobilization and replication of DNA mobile elements. It is therefore plausible that the insertion in Gla. incrassata ptDNA is derived from a DNA mobile element.
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Affiliation(s)
- Francisco Figueroa-Martinez
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,CONACyT-Universidad Autónoma Metropolitana Iztapalapa, Biotechnology Department, Mexico City, Mexico
| | - Christopher Jackson
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,School of Biosciences, University of Melbourne, Melbourne, Australia
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
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Mccann J, Jang TS, Macas J, Schneeweiss GM, Matzke NJ, Novák P, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H. Dating the Species Network: Allopolyploidy and Repetitive DNA Evolution in American Daisies (Melampodium sect. Melampodium, Asteraceae). Syst Biol 2018; 67:1010-1024. [PMID: 29562303 PMCID: PMC6193527 DOI: 10.1093/sysbio/syy024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 02/17/2018] [Accepted: 03/15/2018] [Indexed: 12/04/2022] Open
Abstract
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid. Whereas parentage is typically inferred from cytogenetic and phylogenetic data, age inference is hampered by the reticulate nature of the phylogenetic relationships. Treating subgenomes of allopolyploids as if they belonged to different species (i.e., no recombination among subgenomes) and applying cross-bracing (i.e., putting a constraint on the age difference of nodes pertaining to the same event), we can infer the age of allopolyploids within the framework of the multispecies coalescent within BEAST2. Together with a comprehensive characterization of the repetitive DNA fraction using the RepeatExplorer pipeline, we apply the dating approach in a group of closely related allopolyploids and their progenitor species in the plant genus Melampodium (Asteraceae). We dated the origin of both the allotetraploid, Melampodium strigosum, and its two allohexaploid derivatives, Melampodium pringlei and Melampodium sericeum, which share both parentage and the direction of the cross, to the Pleistocene ($<$1.4 Ma). Thus, Pleistocene climatic fluctuations may have triggered formation of allopolyploids possibly in short intervals, contributing to difficulties in inferring the precise temporal order of allopolyploid species divergence of M. sericeum and M. pringlei. The relatively recent origin of the allopolyploids likely played a role in the near-absence of major changes in the repetitive fraction of the polyploids' genomes. The repetitive elements most affected by the postpolyploidization changes represented retrotransposons of the Ty1-copia lineage Maximus and, to a lesser extent, also Athila elements of Ty3-gypsy family.
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Affiliation(s)
- Jamie Mccann
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Jiři Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Nicholas J Matzke
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Tod F Stuessy
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- Herbarium and Department of Evolution, Ecology and Organismal Biology, 1315 Kinnear Road, The Ohio State University, Columbus, Ohio, USA
| | - José L Villaseñor
- Department of Botany, UNAM, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, MX-04510 México, D.F., México
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
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49
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Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin. Nat Ecol Evol 2018; 2:1556-1562. [PMID: 30127539 PMCID: PMC6152910 DOI: 10.1038/s41559-018-0644-x] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/13/2018] [Indexed: 11/08/2022]
Abstract
Establishing a unified timescale for the early evolution of Earth and life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it and dispute over the deepest branching relationships in the tree of life. Surprisingly, it remains perhaps the only episode in the history of life where literal interpretations of the fossil record hold sway, revised with every new discovery and reinterpretation. We derive a timescale of life, combining a reappraisal of the fossil material with new molecular clock analyses. We find the last universal common ancestor of cellular life to have predated the end of late heavy bombardment (>3.9 billion years ago (Ga)). The crown clades of the two primary divisions of life, Eubacteria and Archaebacteria, emerged much later (<3.4 Ga), relegating the oldest fossil evidence for life to their stem lineages. The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that oxygenic photosynthesis evolved within the cyanobacterial stem lineage. Modern eukaryotes do not constitute a primary lineage of life and emerged late in Earth's history (<1.84 Ga), falsifying the hypothesis that the Great Oxidation Event facilitated their radiation. The symbiotic origin of mitochondria at 2.053-1.21 Ga reflects a late origin of the total-group Alphaproteobacteria to which the free living ancestor of mitochondria belonged.
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50
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Nowack ECM, Weber APM. Genomics-Informed Insights into Endosymbiotic Organelle Evolution in Photosynthetic Eukaryotes. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:51-84. [PMID: 29489396 DOI: 10.1146/annurev-arplant-042817-040209] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The conversion of free-living cyanobacteria to photosynthetic organelles of eukaryotic cells through endosymbiosis transformed the biosphere and eventually provided the basis for life on land. Despite the presumable advantage conferred by the acquisition of photoautotrophy through endosymbiosis, only two independent cases of primary endosymbiosis have been documented: one that gave rise to the Archaeplastida, and the other to photosynthetic species of the thecate, filose amoeba Paulinella. Here, we review recent genomics-informed insights into the primary endosymbiotic origins of cyanobacteria-derived organelles. Furthermore, we discuss the preconditions for the evolution of nitrogen-fixing organelles. Recent genomic data on previously undersampled cyanobacterial and protist taxa provide new clues to the origins of the host cell and endosymbiont, and proteomic approaches allow insights into the rearrangement of the endosymbiont proteome during organellogenesis. We conclude that in addition to endosymbiotic gene transfers, horizontal gene acquisitions from a broad variety of prokaryotic taxa were crucial to organelle evolution.
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Affiliation(s)
- Eva C M Nowack
- Microbial Symbiosis and Organelle Evolution Group, Biology Department, Heinrich Heine University, 40225 Düsseldorf, Germany;
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany;
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