1
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Boden JS, Zhong J, Anderson RE, Stüeken EE. Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics. Nat Commun 2024; 15:3703. [PMID: 38697988 PMCID: PMC11066067 DOI: 10.1038/s41467-024-47914-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 04/11/2024] [Indexed: 05/05/2024] Open
Abstract
Phosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations in the Precambrian ocean, during life's origin and early evolution, vary over several orders of magnitude. While reduced phosphorus species may have served as alternative substrates to phosphate, their bioavailability on the early Earth remains unknown. Here, we reconstruct the phylogenomic record of life on Earth and find that phosphate transporting genes (pnas) evolved in the Paleoarchean (ca. 3.6-3.2 Ga) and are consistent with phosphate concentrations above modern levels ( > 3 µM). The first gene optimized for low phosphate levels (pstS; <1 µM) appeared around the same time or in the Mesoarchean depending on the reconstruction method. Most enzymatic pathways for metabolising reduced phosphorus emerged and expanded across the tree of life later. This includes phosphonate-catabolising CP-lyases, phosphite-oxidising pathways and hypophosphite-oxidising pathways. CP-lyases are particularly abundant in dissolved phosphate concentrations below 0.1 µM. Our results thus indicate at least local regions of declining phosphate levels through the Archean, possibly linked to phosphate-scavenging Fe(III), which may have limited productivity. However, reduced phosphorus species did not become widely used until after the Paleoproterozoic Great Oxidation Event (2.3 Ga), possibly linked to expansion of the biosphere at that time.
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Affiliation(s)
- Joanne S Boden
- School of Earth and Environmental Sciences, University of St. Andrews, Bute Building, Queen's terrace, St. Andrews, Fife, United Kingdom.
| | - Juntao Zhong
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Rika E Anderson
- Department of Biology, Carleton College, Northfield, MN, USA
| | - Eva E Stüeken
- School of Earth and Environmental Sciences, University of St. Andrews, Bute Building, Queen's terrace, St. Andrews, Fife, United Kingdom
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2
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Coale TH, Loconte V, Turk-Kubo KA, Vanslembrouck B, Mak WKE, Cheung S, Ekman A, Chen JH, Hagino K, Takano Y, Nishimura T, Adachi M, Le Gros M, Larabell C, Zehr JP. Nitrogen-fixing organelle in a marine alga. Science 2024; 384:217-222. [PMID: 38603509 DOI: 10.1126/science.adk1075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Symbiotic interactions were key to the evolution of chloroplast and mitochondria organelles, which mediate carbon and energy metabolism in eukaryotes. Biological nitrogen fixation, the reduction of abundant atmospheric nitrogen gas (N2) to biologically available ammonia, is a key metabolic process performed exclusively by prokaryotes. Candidatus Atelocyanobacterium thalassa, or UCYN-A, is a metabolically streamlined N2-fixing cyanobacterium previously reported to be an endosymbiont of a marine unicellular alga. Here we show that UCYN-A has been tightly integrated into algal cell architecture and organellar division and that it imports proteins encoded by the algal genome. These are characteristics of organelles and show that UCYN-A has evolved beyond endosymbiosis and functions as an early evolutionary stage N2-fixing organelle, or "nitroplast."
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Affiliation(s)
- Tyler H Coale
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
| | - Valentina Loconte
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
| | - Bieke Vanslembrouck
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Shunyan Cheung
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Axel Ekman
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
| | - Jian-Hua Chen
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kyoko Hagino
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
| | - Yoshihito Takano
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
| | - Tomohiro Nishimura
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Hatsukaichi, Hiroshima, Japan
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Mark Le Gros
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carolyn Larabell
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, CA, USA
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3
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Lindsey CR, Knoll AH, Herron MD, Rosenzweig F. Fossil-calibrated molecular clock data enable reconstruction of steps leading to differentiated multicellularity and anisogamy in the Volvocine algae. BMC Biol 2024; 22:79. [PMID: 38600528 PMCID: PMC11007952 DOI: 10.1186/s12915-024-01878-1] [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: 10/30/2023] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred. RESULTS Our ancestral-state reconstructions, show that multicellularity arose independently twice in the volvocine algae. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae. CONCLUSIONS Large molecular datasets and robust phylogenetic methods are bringing the evolutionary history of the volvocine algae more sharply into focus. Mounting evidence suggests that extant species in this group are the result of two independent origins of multicellularity and multiple independent origins of cell differentiation. Also, the origin of the Tetrabaenaceae-Goniaceae-Volvocaceae clade may be much older than previously thought. Finally, the possibility of cryptic species in the Tetrabaenaceae provides an exciting opportunity to study the recent divergence of lineages adapted to live in very different thermal environments.
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Affiliation(s)
- Charles Ross Lindsey
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
| | - Matthew D Herron
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Frank Rosenzweig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Atlanta, GA, 30332, USA.
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4
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Liu M, Yu J, Yang M, Cao L, Chen C. Adaptive evolution of chloroplast division mechanisms during plant terrestrialization. Cell Rep 2024; 43:113950. [PMID: 38489264 DOI: 10.1016/j.celrep.2024.113950] [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: 10/16/2023] [Revised: 01/12/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Despite extensive research, the origin and evolution of the chloroplast division machinery remain unclear. Here, we employ recently sequenced genomes and transcriptomes of Archaeplastida clades to identify the core components of chloroplast division and reconstruct their evolutionary histories, respectively. Our findings show that complete division ring structures emerged in Charophytes. We find that Glaucophytes experienced strong selection pressure, generating diverse variants adapted to the changing terrestrial environments. By integrating the functions of chloroplast division genes (CDGs) annotated in a workflow developed using large-scale multi-omics data, we further show that dispersed duplications acquire more species-specific functions under stronger selection pressures. Notably, PARC6, a dispersed duplicate CDG, regulates leaf color and plant growth in Solanum lycopersicum, demonstrating neofunctionalization. Our findings provide an integrated perspective on the functional evolution of chloroplast division machinery and highlight the potential of dispersed duplicate genes as the primary source of adaptive evolution of chloroplast division.
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Affiliation(s)
- Moyang Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Yu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming Yang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingyan Cao
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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5
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Demoulin CF, Sforna MC, Lara YJ, Cornet Y, Somogyi A, Medjoubi K, Grolimund D, Sanchez DF, Tachoueres RT, Addad A, Fadel A, Compère P, Javaux EJ. Polysphaeroides filiformis, a proterozoic cyanobacterial microfossil and implications for cyanobacteria evolution. iScience 2024; 27:108865. [PMID: 38313056 PMCID: PMC10837632 DOI: 10.1016/j.isci.2024.108865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/29/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Deciphering the fossil record of cyanobacteria is crucial to understand their role in the chemical and biological evolution of the early Earth. They profoundly modified the redox conditions of early ecosystems more than 2.4 Ga ago, the age of the Great Oxidation Event (GOE), and provided the ancestor of the chloroplast by endosymbiosis, leading the diversification of photosynthetic eukaryotes. Here, we analyze the morphology, ultrastructure, chemical composition, and metals distribution of Polysphaeroides filiformis from the 1040-1006 Ma Mbuji-Mayi Supergroup (DR Congo). We evidence trilaminar and bilayered ultrastructures for the sheath and the cell wall, respectively, and the preservation of Ni-tetrapyrrole moieties derived from chlorophyll in intracellular inclusions. This approach allows an unambiguous interpretation of P. filiformis as a branched and multiseriate photosynthetic cyanobacterium belonging to the family of Stigonemataceae. It also provides a possible minimum age for the emergence of multiseriate true branching nitrogen-fixing and probably heterocytous cyanobacteria.
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Affiliation(s)
- Catherine F Demoulin
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | - Marie Catherine Sforna
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
- Centre de Biophysique Moléculaire, (UPR CNRS 4301), 45071 Orléans, France
| | - Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | - Yohan Cornet
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
| | | | | | - Daniel Grolimund
- Paul Scherrer Institut, Swiss Light Source, 5232 Villigen PSI, Switzerland
| | | | | | - Ahmed Addad
- Unité Matériaux et Transformations (UMR CNRS 8207), Université Lille 1 - Sciences et Technologies, 59650 Villeneuve d'Ascq, France
| | - Alexandre Fadel
- Unité Matériaux et Transformations (UMR CNRS 8207), Université Lille 1 - Sciences et Technologies, 59650 Villeneuve d'Ascq, France
| | - Philippe Compère
- Functional and Evolutive Morphology, UR FOCUS, and Center for Applied Research and Education in Microscopy (CAREM-ULiege), University of Liège, 4000 Liège, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, 4000 Liège, Belgium
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6
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Feng H, Tan J, Deng Z. Decoding plant adaptation: deubiquitinating enzymes UBP12 and UBP13 in hormone signaling, light response, and developmental processes. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:721-732. [PMID: 37904584 DOI: 10.1093/jxb/erad429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/26/2023] [Indexed: 11/01/2023]
Abstract
Ubiquitination, a vital post-translational modification in plants, plays a significant role in regulating protein activity, localization, and stability. This process occurs through a complex enzyme cascade that involves E1, E2, and E3 enzymes, leading to the covalent attachment of ubiquitin molecules to substrate proteins. Conversely, deubiquitinating enzymes (DUBs) work in opposition to this process by removing ubiquitin moieties. Despite extensive research on ubiquitination in plants, our understanding of the function of DUBs is still emerging. UBP12 and UBP13, two plant DUBs, have received much attention recently and are shown to play pivotal roles in hormone signaling, light perception, photoperiod responses, leaf development, senescence, and epigenetic transcriptional regulation. This review summarizes current knowledge of these two enzymes, highlighting the central role of deubiquitination in regulating the abundance and activity of critical regulators such as receptor kinases and transcription factors during phytohormone and developmental signaling.
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Affiliation(s)
- Hanqian Feng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Jinjuan Tan
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
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7
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Bowles AMC, Williamson CJ, Williams TA, Donoghue PCJ. Cryogenian Origins of Multicellularity in Archaeplastida. Genome Biol Evol 2024; 16:evae026. [PMID: 38333966 PMCID: PMC10883732 DOI: 10.1093/gbe/evae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution.
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
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8
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Miao L, Yin Z, Knoll AH, Qu Y, Zhu M. 1.63-billion-year-old multicellular eukaryotes from the Chuanlinggou Formation in North China. SCIENCE ADVANCES 2024; 10:eadk3208. [PMID: 38266082 PMCID: PMC10807817 DOI: 10.1126/sciadv.adk3208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
Multicellularity is key to the functional and ecological success of the Eukarya, underpinning much of their modern diversity in both terrestrial and marine ecosystems. Despite the widespread occurrence of simple multicellular organisms among eukaryotes, when this innovation arose remains an open question. Here, we report cellularly preserved multicellular microfossils (Qingshania magnifica) from the ~1635-million-year-old Chuanlinggou Formation, North China. The fossils consist of large uniseriate, unbranched filaments with cell diameters up to 190 micrometers; spheroidal structures, possibly spores, occur within some cells. In combination with spectroscopic characteristics, the large size and morphological complexity of these fossils support their interpretation as eukaryotes, likely photosynthetic, based on comparisons with extant organisms. The occurrence of multicellular eukaryotes in Paleoproterozoic rocks not much younger than those containing the oldest unambiguous evidence of eukaryotes as a whole supports the hypothesis that simple multicellularity arose early in eukaryotic history, as much as a billion years before complex multicellular organisms diversified in the oceans.
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Affiliation(s)
- Lanyun Miao
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Andrew H. Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yuangao Qu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Miyagishima SY. Taming the perils of photosynthesis by eukaryotes: constraints on endosymbiotic evolution in aquatic ecosystems. Commun Biol 2023; 6:1150. [PMID: 37952050 PMCID: PMC10640588 DOI: 10.1038/s42003-023-05544-0] [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: 07/06/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023] Open
Abstract
An ancestral eukaryote acquired photosynthesis by genetically integrating a cyanobacterial endosymbiont as the chloroplast. The chloroplast was then further integrated into many other eukaryotic lineages through secondary endosymbiotic events of unicellular eukaryotic algae. While photosynthesis enables autotrophy, it also generates reactive oxygen species that can cause oxidative stress. To mitigate the stress, photosynthetic eukaryotes employ various mechanisms, including regulating chloroplast light absorption and repairing or removing damaged chloroplasts by sensing light and photosynthetic status. Recent studies have shown that, besides algae and plants with innate chloroplasts, several lineages of numerous unicellular eukaryotes engage in acquired phototrophy by hosting algal endosymbionts or by transiently utilizing chloroplasts sequestrated from algal prey in aquatic ecosystems. In addition, it has become evident that unicellular organisms engaged in acquired phototrophy, as well as those that feed on algae, have also developed mechanisms to cope with photosynthetic oxidative stress. These mechanisms are limited but similar to those employed by algae and plants. Thus, there appear to be constraints on the evolution of those mechanisms, which likely began by incorporating photosynthetic cells before the establishment of chloroplasts by extending preexisting mechanisms to cope with oxidative stress originating from mitochondrial respiration and acquiring new mechanisms.
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Affiliation(s)
- Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
- The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
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10
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Harvey THP. Colonial green algae in the Cambrian plankton. Proc Biol Sci 2023; 290:20231882. [PMID: 37876191 PMCID: PMC10598416 DOI: 10.1098/rspb.2023.1882] [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: 08/20/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023] Open
Abstract
The fossil record indicates a major turnover in marine phytoplankton across the Ediacaran-Cambrian transition, coincident with the rise of animal-rich ecosystems. However, the diversity, affinities and ecologies of Cambrian phytoplankton are poorly understood, leaving unclear the role of animal interactions and the drivers of diversification. New exceptionally preserved acritarchs (problematic organic-walled microfossils) from the late early Cambrian (around 510 Ma) reveal colonial organization characterized by rings and plates of interconnected, geometrically arranged cells. The assemblage exhibits a wide but gradational variation in cell size, ornamentation and intercell connection, interpreted as representing one or more species with determinate (coenobial) colony formation via cell division, aggregation and growth by cell expansion. An equivalent strategy is known only among green algae, specifically chlorophycean chlorophytes. The fossils differ in detail from modern freshwater examples and apparently represent an earlier convergent radiation in marine settings. Known trade-offs between sinking risk and predator avoidance in colonial phytoplankton point to adaptations triggered by intensifying grazing pressure during a Cambrian metazoan invasion of the water column. The new fossils reveal that not all small acritarchs are unicellular resting cysts, and support an early Palaeozoic prominence of green algal phytoplankton as predicted by molecular biomarkers.
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Affiliation(s)
- Thomas H. P. Harvey
- Centre for Palaeobiology and Biosphere Evolution, School of Geography, Geology and the Environment, University of Leicester, University Road, Leicester LE1 7RH, UK
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11
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Díez Menéndez C, Poczai P, Williams B, Myllys L, Amiryousefi A. IRplus: An Augmented Tool to Detect Inverted Repeats in Plastid Genomes. Genome Biol Evol 2023; 15:evad177. [PMID: 37793175 PMCID: PMC10581538 DOI: 10.1093/gbe/evad177] [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: 02/28/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023] Open
Abstract
High-throughput sequencing methods have increased the accessibility of plastid genomes, which are crucial for clarifying phylogenetic relationships. Current large sequencing efforts require software tools for routine display of their distinctive quadripartite structure, which is denoted by four junction sites. By concentrating on these junctions and their close vicinity, IRscope has emerged as the standard tool for detection of this structure and creating simplified comparative graphical maps of plastid genomes. Here, we provide an augmented version (IRplus) that encompasses a novel set of functions such as integrated error detection, flexible color schemes, and an upgraded method to detect inverted repeats in genomic sequences. Spanning across the plant tree of life, IRplus allows the quick visualization of various sets of plastid genomes and features, next to smooth interoperability with other widely used annotation file formats and platforms. The IRplus can be accessed at https://irscope.shinyapps.io/IRplus/, and source codes are freely available at https://github.com/AmiryousefiLab/IRplus.
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Affiliation(s)
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Museomics Research Group, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Bernardo Williams
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Leena Myllys
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Systems Oncology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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12
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Borg M, Krueger-Hadfield SA, Destombe C, Collén J, Lipinska A, Coelho SM. Red macroalgae in the genomic era. THE NEW PHYTOLOGIST 2023; 240:471-488. [PMID: 37649301 DOI: 10.1111/nph.19211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023]
Abstract
Rhodophyta (or red algae) are a diverse and species-rich group that forms one of three major lineages in the Archaeplastida, a eukaryotic supergroup whose plastids arose from a single primary endosymbiosis. Red algae are united by several features, such as relatively small intron-poor genomes and a lack of cytoskeletal structures associated with motility like flagella and centrioles, as well as a highly efficient photosynthetic capacity. Multicellular red algae (or macroalgae) are one of the earliest diverging eukaryotic lineages to have evolved complex multicellularity, yet despite their ecological, evolutionary, and commercial importance, they have remained a largely understudied group of organisms. Considering the increasing availability of red algal genome sequences, we present a broad overview of fundamental aspects of red macroalgal biology and posit on how this is expected to accelerate research in many domains of red algal biology in the coming years.
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Affiliation(s)
- Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Stacy A Krueger-Hadfield
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Virginia Institute of Marine Science Eastern Shore Laboratory, Wachapreague, VA, 23480, USA
| | - Christophe Destombe
- International Research Laboratory 3614 (IRL3614) - Evolutionary Biology and Ecology of Algae, Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, 29680, France
| | - Jonas Collén
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff, Sorbonne Université, Roscoff, 29680, France
| | - Agnieszka Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tübingen, Germany
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13
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Yang Z, Ma X, Wang Q, Tian X, Sun J, Zhang Z, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae. Nat Commun 2023; 14:5542. [PMID: 37696791 PMCID: PMC10495350 DOI: 10.1038/s41467-023-41137-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of these lineages, Prasinodermophyta, which is previously grouped with prasinophytes, has been identified as the sister lineage to both Chlorophyta and Streptophyta. Resolving the deep relationships among green plants is crucial for understanding the historical impact of green algal diversity on marine ecology and geochemistry, but has been proven difficult given the ancient timing of the diversification events. Through extensive taxon and gene sampling, we conduct large-scale phylogenomic analyses to resolve deep relationships and reveal the Prasinodermophyta as the lineage sister to Chlorophyta, raising questions about the necessity of classifying the Prasinodermophyta as a distinct phylum. We unveil that incomplete lineage sorting is the main cause of discordance regarding the placement of Prasinodermophyta. Molecular dating analyses suggest that crown-group green plants and crown-group Prasinodermophyta date back to the Paleoproterozoic-Mesoproterozoic. Our study establishes a plausible link between oxygen levels in the Paleoproterozoic-Mesoproterozoic and the origin of Viridiplantae.
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Affiliation(s)
- Zhiping Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolin Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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14
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Yao H, Li T, Ma Z, Wang X, Xu L, Zhang Y, Cai Y, Tang Z. Codon usage pattern of the ancestor of green plants revealed through Rhodophyta. BMC Genomics 2023; 24:538. [PMID: 37697255 PMCID: PMC10496412 DOI: 10.1186/s12864-023-09586-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/14/2023] [Indexed: 09/13/2023] Open
Abstract
Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that although there are some differences among species, high-bias genes in most red algae prefer codons ending with GC. Correlation analysis, Nc-GC3s plots, parity rule 2 plots, neutrality plot analysis, differential protein region analysis and comparison of the nucleotide content of introns and flanking sequences showed that the bias phenomenon is likely to be influenced by local mutation pressure and natural selection, the latter of which is the dominant factor in terms of translation accuracy and efficiency. It is worth noting that selection on translation accuracy could even be detected in the low-bias genes of individual species. In addition, we identified 15 common optimal codons in seven red algae except for G. sulphuraria for the first time, most of which were found to be complementary and bound to the tRNA genes with the highest copy number. Interestingly, tRNA modification was found for the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae, which indicates that highly biased genes tend to use modified tRNA in translation. Our research not only lays a foundation for exploring the characteristics of codon usage of the red algae as green plant ancestors, but will also facilitate the design and performance of transgenic work in some economic red algae in the future.
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Affiliation(s)
- Huipeng Yao
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China.
| | - Tingting Li
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Zheng Ma
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Xiyuan Wang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Lixiao Xu
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Yuxin Zhang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Yi Cai
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Zizhong Tang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
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15
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He S, Crans VL, Jonikas MC. The pyrenoid: the eukaryotic CO2-concentrating organelle. THE PLANT CELL 2023; 35:3236-3259. [PMID: 37279536 PMCID: PMC10473226 DOI: 10.1093/plcell/koad157] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023]
Abstract
The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.
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Affiliation(s)
- Shan He
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
| | - Victoria L Crans
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
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16
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Strullu-Derrien C, Fercoq F, Gèze M, Kenrick P, Martos F, Selosse MA, Benzerara K, Knoll AH. Hapalosiphonacean cyanobacteria (Nostocales) thrived amid emerging embryophytes in an early Devonian (407-million-year-old) landscape. iScience 2023; 26:107338. [PMID: 37520734 PMCID: PMC10382934 DOI: 10.1016/j.isci.2023.107338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/11/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Cyanobacteria have a long evolutionary history, well documented in marine rocks. They are also abundant and diverse in terrestrial environments; however, although phylogenies suggest that the group colonized land early in its history, paleontological documentation of this remains limited. The Rhynie chert (407 Ma), our best preserved record of early terrestrial ecosystems, provides an opportunity to illuminate aspects of cyanobacterial diversity and ecology as plants began to radiate across the land surface. We used light microscopy and super-resolution confocal laser scanning microscopy to study a new population of Rhynie cyanobacteria; we also reinvestigated previously described specimens that resemble the new fossils. Our study demonstrates that all are part of a single fossil species belonging to the Hapalosiphonaceae (Nostocales). Along with other Rhynie microfossils, these remains show that the accommodation of morphologically complex cyanobacteria to terrestrial ecosystems transformed by embryophytes was well underway more than 400 million years ago.
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Affiliation(s)
- Christine Strullu-Derrien
- Institut Systématique Évolution Biodiversité (UMR 7205), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, UA, 75005 Paris, France
- Science Group, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Frédéric Fercoq
- Unité Molécules de Communication et Adaptation des Micro-organismes (MCAM, UMR7245), Muséum national d’Histoire naturelle, CNRS, 75005 Paris, France
| | - Marc Gèze
- Unité Molécules de Communication et Adaptation des Micro-organismes (MCAM, UMR7245), Muséum national d’Histoire naturelle, CNRS, 75005 Paris, France
| | - Paul Kenrick
- Science Group, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Florent Martos
- Institut Systématique Évolution Biodiversité (UMR 7205), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, UA, 75005 Paris, France
| | - Marc-André Selosse
- Institut Systématique Évolution Biodiversité (UMR 7205), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, UA, 75005 Paris, France
- Institut Universitaire de France, 75005 Paris, France
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (UMR 7590), CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, 75005 Paris, France
| | - Andrew H. Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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17
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Flores Tinoco V, Herrera-Estrella L, Lopez-Arredondo D. Back to primary endosymbiosis: from plastids to artificial photosynthetic life-forms. TRENDS IN PLANT SCIENCE 2023; 28:743-745. [PMID: 37085412 DOI: 10.1016/j.tplants.2023.03.026] [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: 02/20/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
Throughout evolution, only two known primary photosynthetic endosymbiosis occurred, which originated the Archaeplastida and the Paulinella spp. Fundamental questions regarding primary endosymbiosis remain unsolved, but may now be addressed with the recent development of chimeric photosynthetic life-form. Cournoyer et al. could establish artificial photosynthetic endosymbiosis between yeast and cyanobacteria.
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Affiliation(s)
- Valeria Flores Tinoco
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA; Unidad de Genómica Avanzada/LANGEBIO, Centro de Investigación y de Estudios Avanzados, Irapuato, México
| | - Damar Lopez-Arredondo
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA.
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18
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López-García P, Moreira D. The symbiotic origin of the eukaryotic cell. C R Biol 2023; 346:55-73. [PMID: 37254790 DOI: 10.5802/crbiol.118] [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: 01/26/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 06/01/2023]
Abstract
Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.
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19
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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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20
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Van Etten J, Benites LF, Stephens TG, Yoon HS, Bhattacharya D. Algae obscura: The potential of rare species as model systems. JOURNAL OF PHYCOLOGY 2023; 59:293-300. [PMID: 36764681 DOI: 10.1111/jpy.13321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 05/28/2023]
Abstract
Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Luiz Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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21
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Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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22
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Li W, Guo J, Han X, Da X, Wang K, Zhao H, Huang ST, Li B, He H, Jiang R, Zhou S, Yan P, Chen T, He Y, Xu J, Liu Y, Wu Y, Shou H, Wu Z, Mao C, Mo X. A novel protein domain is important for photosystem II complex assembly and photoautotrophic growth in angiosperms. MOLECULAR PLANT 2023; 16:374-392. [PMID: 36566350 DOI: 10.1016/j.molp.2022.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/24/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Photosystem II (PSII) is a multi-subunit protein complex of the photosynthetic electron transport chain that is vital to photosynthesis. Although the structure, composition, and function of PSII have been extensively studied, its biogenesis mechanism remains less understood. Thylakoid rhodanese-like (TROL) provides an anchor for leaf-type ferredoxin:NADP+ oxidoreductase. Here, we report the chacterizaton of a second type of TROL protein, TROL2, encoded by seed plant genomes whose function has not previously been reported. We show that TROL2 is a PSII assembly cofactor with essential roles in the establishment of photoautotrophy. TROL2 contains a 45-amino-acid domain, termed the chlorotic lethal seedling (CLS) domain, that is both necessary and sufficient for TROL2 function in PSII assembly and photoautotrophic growth. Phylogenetic analyses suggest that TROL2 may have arisen from ancestral TROL1 via gene duplication before the emergence of seed plants and acquired the CLS domain via evolution of the sequence encoding its N-terminal portion. We further reveal that TROL2 (or CLS) forms an assembly cofactor complex with the intrinsic thylakoid membrane protein LOW PSII ACCUMULATION2 and interacts with small PSII subunits to facilitate PSII complex assembly. Collectively, our study not only shows that TROL2 (CLS) is essential for photoautotrophy in angiosperms but also reveals its mechanistic role in PSII complex assembly, shedding light on the molecular and evolutionary mechanisms of photosynthetic complex assemblyin angiosperms.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Jiangfan Guo
- College of Life Science, Shaanxi Normal University, Xi'an, Shaanxi Province 710062, PR China
| | - Xue Han
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Xiaowen Da
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Kai Wang
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Hongfei Zhao
- College of Urban Construction, Zhejiang Shuren University, Hangzhou 310015, PR China
| | - Shi-Tang Huang
- School of Life Sciences, Peking University, Beijing 100871, PR China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Hang He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Ruirui Jiang
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Shichen Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Peng Yan
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Tao Chen
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Yi He
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, PR China
| | - Jiming Xu
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Yu Liu
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Yunrong Wu
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Huixia Shou
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Zhongchang Wu
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Chuanzao Mao
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China
| | - Xiaorong Mo
- State Key Laboratory of Plant Environmental Resilience, College of Life Science, Zhejiang University, Hangzhou 310058, PR China.
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23
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [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: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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Gololobova MA, Belyakova GA. Position of Algae on the Tree of Life. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2022; 507:312-326. [PMID: 36781528 DOI: 10.1134/s0012496622060035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 02/15/2023]
Abstract
Issues related to evolution of algal chloroplasts are considered. The position of algae on the Tree of Life is discussed. Algae are now included in five of the monophyletic eukaryotic supergroups: Archaeplastida (Glaucocystophyta, Rhodophyta, Prasinodermophyta, Chlorophyta, and Charophyta), TSAR (Ochrophyta; Dinophyta; Chlorarachniophyta; and photosynthetic species of the genera Chromera, Vetrella, and Paulinella), Haptista (Prymnesiophyta and Rappemonads), Cryptista (Cryptophyta), and Discoba (Euglenophyta). The algal divisions and the respective supergroups are characterized in brief.
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Affiliation(s)
- M A Gololobova
- Biological Faculty, Moscow State University, Moscow, Russia.
| | - G A Belyakova
- Biological Faculty, Moscow State University, Moscow, Russia
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25
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Navvabi A, Homaei A, Pletschke BI, Navvabi N, Kim SK. Marine Cellulases and their Biotechnological Significance from Industrial Perspectives. Curr Pharm Des 2022; 28:3325-3336. [PMID: 35388747 DOI: 10.2174/1381612828666220406125132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/03/2021] [Accepted: 01/18/2022] [Indexed: 01/28/2023]
Abstract
Marine microorganisms represent virtually unlimited sources of novel biological compounds and can survive extreme conditions. Cellulases, a group of enzymes that are able to degrade cellulosic materials, are in high demand in various industrial and biotechnological applications, such as in the medical and pharmaceutical industries, food, fuel, agriculture, and single-cell protein, and as probiotics in aquaculture. The cellulosic biopolymer is a renewable resource and is a linearly arranged polysaccharide of glucose, with repeating units of disaccharide connected via β-1,4-glycosidic bonds, which are broken down by cellulase. A great deal of biodiversity resides in the ocean, and marine systems produce a wide range of distinct, new bioactive compounds that remain available but dormant for many years. The marine environment is filled with biomass from known and unknown vertebrates and invertebrate microorganisms, with much potential for use in medicine and biotechnology. Hence, complex polysaccharides derived from marine sources are a rich resource of microorganisms equipped with enzymes for polysaccharides degradation. Marine cellulases' extracts from the isolates are tested for their functional role in degrading seaweed and modifying wastes to low molecular fragments. They purify and renew environments by eliminating possible feedstocks of pollution. This review aims to examine the various types of marine cellulase producers and assess the ability of these microorganisms to produce these enzymes and their subsequent biotechnological applications.
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Affiliation(s)
- Azita Navvabi
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Brett I Pletschke
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Nazila Navvabi
- Department of Tumor Biology and Immunotherapy, Molecular Biology of Cancer, Institute of Experimental Medicine, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Prague, Czech Republic
| | - Se-Kwon Kim
- Department of Marine Sciences and Convergent Technology, Hanyang University, Ansan, Seoul 426-791, Republic of Korea
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Enzingmüller-Bleyl TC, Boden JS, Herrmann AJ, Ebel KW, Sánchez-Baracaldo P, Frankenberg-Dinkel N, Gehringer MM. On the trail of iron uptake in ancestral Cyanobacteria on early Earth. GEOBIOLOGY 2022; 20:776-789. [PMID: 35906866 DOI: 10.1111/gbi.12515] [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: 05/16/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria oxygenated Earth's atmosphere ~2.4 billion years ago, during the Great Oxygenation Event (GOE), through oxygenic photosynthesis. Their high iron requirement was presumably met by high levels of Fe(II) in the anoxic Archean environment. We found that many deeply branching Cyanobacteria, including two Gloeobacter and four Pseudanabaena spp., cannot synthesize the Fe(II) specific transporter, FeoB. Phylogenetic and relaxed molecular clock analyses find evidence that FeoB and the Fe(III) transporters, cFTR1 and FutB, were present in Proterozoic, but not earlier Archaean lineages of Cyanobacteria. Furthermore Pseudanabaena sp. PCC7367, an early diverging marine, benthic strain grown under simulated Archean conditions, constitutively expressed cftr1, even after the addition of Fe(II). Our genetic profiling suggests that, prior to the GOE, ancestral Cyanobacteria may have utilized alternative metal iron transporters such as ZIP, NRAMP, or FicI, and possibly also scavenged exogenous siderophore bound Fe(III), as they only acquired the necessary Fe(II) and Fe(III) transporters during the Proterozoic. Given that Cyanobacteria arose 3.3-3.6 billion years ago, it is possible that limitations in iron uptake may have contributed to the delay in their expansion during the Archean, and hence the oxygenation of the early Earth.
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Affiliation(s)
| | - Joanne S Boden
- School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, UK
- School of Earth and Environmental Sciences, University of St. Andrews, St. Andrews, UK
| | - Achim J Herrmann
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Katharina W Ebel
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | | | - Michelle M Gehringer
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
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27
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Kalwani P, Rath D, Ballal A. Loss of 2-Cys-Prx affects cellular ultrastructure, disturbs redox poise and impairs photosynthesis in cyanobacteria. PLANT, CELL & ENVIRONMENT 2022; 45:2972-2986. [PMID: 35909079 DOI: 10.1111/pce.14412] [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: 06/10/2022] [Revised: 07/19/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
In a striking similarity to plant chloroplasts, the cyanobacterium Anabaena displays very low catalase activity, but expresses several peroxiredoxins (Prxs), including the typical 2-Cys-Prx (annotated as Alr4641), that detoxify H2 O2 . Due to the presence of multiple Prxs, the precise contribution of Alr4641 to the oxidative stress response of Anabaena is not well-defined. To unambiguously assess its in vivo function, the Alr4641 protein was knocked down using the CRISPRi approach in Anabaena PCC 7120. The knockdown strain (An-KD4641), which showed over 85% decrease in the content of Alr4641, was viable, but grew slower than the control strain (An-dCas9). An-KD4641 showed elevated levels of reactive oxygen species and the expression of several redox-responsive genes was analogous to that of An-dCas9 subjected to oxidative stress. The knockdown strain displayed reduced filament size, altered thylakoid ultrastructure, a marked drop in the ratio of phycocyanin to chlorophyll a and decreased photosynthetic parameters compared to An-dCas9. In comparison to the control strain, exposure to H2 O2 had a more severe effect on the photosynthetic parameters or survival of An-KD4641. Thus, in the absence of adequate catalase activity, 2-Cys-Prx appears to be the principal Prx responsible for maintaining redox homoeostasis in diverse photosynthetic systems ranging from chloroplasts to cyanobacteria.
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Affiliation(s)
- Prakash Kalwani
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Devashish Rath
- Applied Genomics Section, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Anand Ballal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
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Jamy M, Biwer C, Vaulot D, Obiol A, Jing H, Peura S, Massana R, Burki F. Global patterns and rates of habitat transitions across the eukaryotic tree of life. Nat Ecol Evol 2022; 6:1458-1470. [PMID: 35927316 PMCID: PMC9525238 DOI: 10.1038/s41559-022-01838-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/23/2022] [Indexed: 12/30/2022]
Abstract
The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life.
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Affiliation(s)
- Mahwash Jamy
- Department of Organismal Biology (Systematic Biology), Uppsala University, Uppsala, Sweden
| | - Charlie Biwer
- Department of Organismal Biology (Systematic Biology), Uppsala University, Uppsala, Sweden
| | - Daniel Vaulot
- CNRS, UMR7144, Team ECOMAP, Station Biologique, Sorbonne Université, Roscoff, France
| | - Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Hongmei Jing
- CAS Key Lab for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Sari Peura
- Department of Ecology and Genetics (Limnology), Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Uppsala, Sweden.
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Hassler GW, Magee A, Zhang Z, Baele G, Lemey P, Ji X, Fourment M, Suchard MA. Data integration in Bayesian phylogenetics. ANNUAL REVIEW OF STATISTICS AND ITS APPLICATION 2022; 10:353-377. [PMID: 38774036 PMCID: PMC11108065 DOI: 10.1146/annurev-statistics-033021-112532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Researchers studying the evolution of viral pathogens and other organisms increasingly encounter and use large and complex data sets from multiple different sources. Statistical research in Bayesian phylogenetics has risen to this challenge. Researchers use phylogenetics not only to reconstruct the evolutionary history of a group of organisms, but also to understand the processes that guide its evolution and spread through space and time. To this end, it is now the norm to integrate numerous sources of data. For example, epidemiologists studying the spread of a virus through a region incorporate data including genetic sequences (e.g. DNA), time, location (both continuous and discrete) and environmental covariates (e.g. social connectivity between regions) into a coherent statistical model. Evolutionary biologists routinely do the same with genetic sequences, location, time, fossil and modern phenotypes, and ecological covariates. These complex, hierarchical models readily accommodate both discrete and continuous data and have enormous combined discrete/continuous parameter spaces including, at a minimum, phylogenetic tree topologies and branch lengths. The increased size and complexity of these statistical models have spurred advances in computational methods to make them tractable. We discuss both the modeling and computational advances below, as well as unsolved problems and areas of active research.
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Affiliation(s)
- Gabriel W Hassler
- Department of Computational Medicine, University of California, Los Angeles, USA, 90095
| | - Andrew Magee
- Department of Biostatistics, University of California, Los Angeles, USA, 90095
| | - Zhenyu Zhang
- Department of Biostatistics, University of California, Los Angeles, USA, 90095
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium, 3000
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium, 3000
| | - Xiang Ji
- Department of Mathematics, Tulane University, New Orleans, USA, 70118
| | - Mathieu Fourment
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo NSW, Australia, 2007
| | - Marc A Suchard
- Department of Computational Medicine, University of California, Los Angeles, USA, 90095
- Department of Biostatistics, University of California, Los Angeles, USA, 90095
- Department of Human Genetics, University of California, Los Angeles, USA, 90095
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Chai S, Aria C, Hua H. A stem group Codium alga from the latest Ediacaran of South China provides taxonomic insight into the early diversification of the plant kingdom. BMC Biol 2022; 20:199. [PMID: 36127662 PMCID: PMC9491005 DOI: 10.1186/s12915-022-01394-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/18/2022] [Indexed: 12/05/2022] Open
Abstract
Background In recent years, Precambrian lifeforms have generated an ever-increasing interest because they revealed a rich eukaryotic diversity prior to the Cambrian explosion of modern animals. Among them, macroalgae are known to be a conspicuous component of Neoproterozoic ecosystems, and chlorophytes in particular are already documented in the Tonian, when they were so far expected to originate. However, like for other major eukaryotic lineages, and despite predictions of molecular clock analyses placing roots of these lineages well into the Neoproterozoic, a taxonomic constraint on Precambrian green algae has remained difficult. Results Here, we present an exceptionally preserved spherical, coenocytic unicellular alga from the latest Ediacaran Dengying Formation of South China (> ca. 541 Ma), known from both external and internal morphology, fully tridimensional and in great detail. Tomographic X-ray and electronic microscopy revealed a characteristic medulla made of intertwined siphons and tightly packed peripheral utricles, suggesting these fossils belong to the Bryopsidales genus Codium. However, its distinctly smaller size compared to extant species leads us to create Protocodium sinense gen. et sp. nov. and a phylomorphospace investigation points to a possible stem group affinity. Conclusions Our finding has several important implications. First, Protocodium allows for a more precise calibration of Archaeplastida and directly confirms that a group as derived as Ulvophyceae was already well diversified in various ecosystems prior to the Cambrian explosion. Details of tridimensional morphology also invite a reassessment of the identification of other Ediacaran algae, such as Chuaria, to better discriminate mono-versus multicellularity, and suggest unicellular Codium-like morphotypes could be much older and widespread. More broadly, Protocodium provides insights into the early diversification of the plant kingdom, the composition of Precambrian ecosystems, and the extreme longevity of certain eukaryotic plans of organization. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01394-0.
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Affiliation(s)
- Shu Chai
- Shaanxi Key Laboratory of Early Life and Environments, Northwest University, Xi'an 710069, People's Republic of China
| | - Cédric Aria
- Shaanxi Key Laboratory of Early Life and Environments, Northwest University, Xi'an 710069, People's Republic of China. .,Present address: Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada. .,Present address: Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada.
| | - Hong Hua
- Shaanxi Key Laboratory of Early Life and Environments, Northwest University, Xi'an 710069, People's Republic of China.
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31
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Turudić A, Liber Z, Grdiša M, Jakše J, Varga F, Šatović Z. Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats. Int J Mol Sci 2022; 23:ijms231810804. [PMID: 36142721 PMCID: PMC9503105 DOI: 10.3390/ijms231810804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/01/2022] [Accepted: 09/13/2022] [Indexed: 12/31/2022] Open
Abstract
The development of next-generation sequencing technology and the increasing amount of sequencing data have brought the bioinformatic tools used in genome assembly into focus. The final step of the process is genome annotation, which works on assembled genome sequences to identify the location of genome features. In the case of organelle genomes, specialized annotation tools are used to identify organelle genes and structural features. Numerous annotation tools target chloroplast sequences. Most chloroplast DNA genomes have a quadripartite structure caused by two copies of a large inverted repeat. We investigated the strategies of six annotation tools (Chloë, Chloroplot, GeSeq, ORG.Annotate, PGA, Plann) for identifying inverted repeats and analyzed their success using publicly available complete chloroplast sequences of taxa belonging to the asterid and rosid clades. The annotation tools use two different approaches to identify inverted repeats, using existing general search tools or implementing stand-alone solutions. The chloroplast sequences studied show that there are different types of imperfections in the assembled data and that each tool performs better on some sequences than the others.
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Affiliation(s)
- Ante Turudić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-91-3141592
| | - Zlatko Liber
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia
| | - Martina Grdiša
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Jernej Jakše
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Filip Varga
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Zlatko Šatović
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
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32
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Richards SM, Li L, Breen J, Hovhannisyan N, Estrada O, Gasparyan B, Gilliham M, Smith A, Cooper A, Zhang H. Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia. Sci Rep 2022; 12:15164. [PMID: 36071150 PMCID: PMC9452526 DOI: 10.1038/s41598-022-17931-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Panicum miliaceum L. was domesticated in northern China at least 7000 years ago and was subsequentially adopted in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, where vast quantities archaeobotanical material were well preserved via desiccation. The rich botanical material found at Areni-1 includes P. miliaceum grains that were identified morphologically and14C dated to the medieval period (873 ± 36 CE and 1118 ± 35 CE). To investigate the demographic and evolutionary history of the Areni-1 millet, we used ancient DNA extraction, hybridization capture enrichment, and high throughput sequencing to assemble three chloroplast genomes from the medieval grains and then compared these sequences to 50 modern P. miliaceum chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity with domesticated accessions separated by a maximum of 5 SNPs and little inference on demography could be made. However, in phylogenies the chloroplast genomes separated into two clades, similar to what has been reported for nuclear DNA from P. miliaceum. The chloroplast genomes of two wild (undomesticated) accessions of P. miliaceum contained a relatively large number of variants, 11 SNPs, not found in the domesticated accessions. These results demonstrate that P. miliaceum grains from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.
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Affiliation(s)
- Stephen M Richards
- School of Biological Science, The University of Adelaide, Adelaide, Australia.
| | - Leiting Li
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - James Breen
- School of Biological Science, The University of Adelaide, Adelaide, Australia.,Telethon Kids Institute, Australian National University, Canberra, Australia
| | | | - Oscar Estrada
- School of Biological Science, The University of Adelaide, Adelaide, Australia.,Grupo de Agrobiotecnología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Matthew Gilliham
- Waite Research Institute and School of Agriculture, Food, and Wine, ARC Centre of Excellence in Plant Energy Biology, The University of Adelaide, Waite Campus, Glen Osmond, Australia
| | - Alexia Smith
- Department of Anthropology, University of Connecticut, Connecticut, USA
| | - Alan Cooper
- BlueSky Genetics, Ashton, SA, Australia.,South Australian Museum, Adelaide, SA, Australia
| | - Heng Zhang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
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33
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Liao T, Wang S, Stüeken EE, Luo H. Phylogenomic evidence for the Origin of Obligately Anaerobic Anammox Bacteria around the Great Oxidation Event. Mol Biol Evol 2022; 39:6653777. [PMID: 35920138 PMCID: PMC9387917 DOI: 10.1093/molbev/msac170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remain enigmatic. Here, we performed a comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which include implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32–2.5 Ga) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics, and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.
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Affiliation(s)
- Tianhua Liao
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Sishuo Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Eva E Stüeken
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, Bute Building, Queen's Terrace, KY16 9TS, UK
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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Wang Q, Smith SM, Huang J. Origins of strigolactone and karrikin signaling in plants. TRENDS IN PLANT SCIENCE 2022; 27:450-459. [PMID: 34876337 DOI: 10.1016/j.tplants.2021.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Strigolactones (SLs) and karrikins (KARs) are butenolides that influence multiple aspects of plant growth and development. D14 and KAI2 are members of the α/β-fold hydrolase superfamily and act as receptors of SLs and KARs, as well as of unidentified endogenous KAI2-ligands (KLs). Phylogenetic analyses suggest that plant KAI2 was derived from bacterial RsbQ via horizontal gene transfer (HGT) before the emergence of streptophytes. The D14/KAI2 and RsbQ proteins share conserved tertiary structures and functional features. In this opinion article, we suggest that the acquisition of RsbQ by plant cells was fundamental to the formation of butenolide sensing systems. Recruitment of additional signal transduction components and gene duplication subsequently led to versatile butenolide signaling systems throughout land plants.
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Affiliation(s)
- Qia Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Steven M Smith
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, School of Natural Sciences, University of Tasmania, Hobart 7001, Australia.
| | - Jinling Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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35
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Cournoyer JE, Altman SD, Gao YL, Wallace CL, Zhang D, Lo GH, Haskin NT, Mehta AP. Engineering artificial photosynthetic life-forms through endosymbiosis. Nat Commun 2022; 13:2254. [PMID: 35474066 PMCID: PMC9042829 DOI: 10.1038/s41467-022-29961-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/08/2022] [Indexed: 12/28/2022] Open
Abstract
The evolutionary origin of the photosynthetic eukaryotes drastically altered the evolution of complex lifeforms and impacted global ecology. The endosymbiotic theory suggests that photosynthetic eukaryotes evolved due to endosymbiosis between non-photosynthetic eukaryotic host cells and photosynthetic cyanobacterial or algal endosymbionts. The photosynthetic endosymbionts, propagating within the cytoplasm of the host cells, evolved, and eventually transformed into chloroplasts. Despite the fundamental importance of this evolutionary event, we have minimal understanding of this remarkable evolutionary transformation. Here, we design and engineer artificial, genetically tractable, photosynthetic endosymbiosis between photosynthetic cyanobacteria and budding yeasts. We engineer various mutants of model photosynthetic cyanobacteria as endosymbionts within yeast cells where, the engineered cyanobacteria perform bioenergetic functions to support the growth of yeast cells under defined photosynthetic conditions. We anticipate that these genetically tractable endosymbiotic platforms can be used for evolutionary studies, particularly related to organelle evolution, and also for synthetic biology applications. The endosymbiotic theory posits that chloroplasts in eukaryotes arise from bacterial endosymbionts. Here, the authors engineer the yeast/cyanobacteria chimeras and show that the engineered cyanobacteria perform chloroplast-like functions to support the growth of yeast cells under photosynthetic conditions.
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Affiliation(s)
- Jason E Cournoyer
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL, 61801, USA
| | - Sarah D Altman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL, 61801, USA
| | - Yang-le Gao
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL, 61801, USA
| | - Catherine L Wallace
- The Imaging Technology Group, Beckman Institute for Advanced Science & Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL, 61801, USA
| | - Dianwen Zhang
- The Imaging Technology Group, Beckman Institute for Advanced Science & Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL, 61801, USA
| | - Guo-Hsuen Lo
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL, 61801, USA
| | - Noah T Haskin
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL, 61801, USA
| | - Angad P Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL, 61801, USA.
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36
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Maloney KM, Schiffbauer JD, Halverson GP, Xiao S, Laflamme M. Preservation of early Tonian macroalgal fossils from the Dolores Creek Formation, Yukon. Sci Rep 2022; 12:6222. [PMID: 35418588 PMCID: PMC9007953 DOI: 10.1038/s41598-022-10223-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
The rise of eukaryotic macroalgae in the late Mesoproterozoic to early Neoproterozoic was a critical development in Earth’s history that triggered dramatic changes in biogeochemical cycles and benthic habitats, ultimately resulting in ecosystems habitable to animals. However, evidence of the diversification and expansion of macroalgae is limited by a biased fossil record. Non-mineralizing organisms are rarely preserved, occurring only in exceptional environments that favor fossilization. Investigating the taphonomy of well-preserved macroalgae will aid in identifying these target environments, allowing ecological trends to be disentangled from taphonomic overprints. Here we describe the taphonomy of macroalgal fossils from the Tonian Dolores Creek Formation (ca. 950 Ma) of northwestern Canada (Yukon Territory) that preserves cm-scale macroalgae. Analytical microscopy, including scanning electron microscopy and tomographic x-ray microscopy, was used to investigate fossil preservation, which was the result of a combination of pyritization and aluminosilicification, similar to accessory mineralization observed in Paleozoic Burgess Shale-type fossils. These new Neoproterozoic fossils help to bridge a gap in the fossil record of early algae, offer a link between the fossil and molecular record, and provide new insights into evolution during the Tonian Period, when many eukaryotic lineages are predicted to have diversified.
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Affiliation(s)
- Katie M Maloney
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.
| | - James D Schiffbauer
- Department of Geological Sciences, University of Missouri, Columbia, MO, 65211, USA.,X-Ray Microanalysis Core, University of Missouri, Columbia, MO, 65211, USA
| | - Galen P Halverson
- Department of Earth and Planetary Sciences/GEOTOP, McGill University, Montréal, QC, H3A 0E8, Canada
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Marc Laflamme
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
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37
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Román-Palacios C, Moraga-López D, Wiens JJ. The origins of global biodiversity on land, sea and freshwater. Ecol Lett 2022; 25:1376-1386. [PMID: 35334149 DOI: 10.1111/ele.13999] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/06/2022] [Accepted: 02/16/2022] [Indexed: 11/28/2022]
Abstract
Many biodiversity studies focus on explaining high tropical species richness, but an equally dramatic yet understudied pattern involves the divergent richness of land, sea and freshwater. Here, we reveal the origins of these richness differences among habitats across animals and plants. Most plant and animal species are terrestrial, although these habitats cover only ~28% of Earth's surface. Marine habitats have fewer species over a larger area (~70%). Freshwater habitats have relatively high richness and exceptional phylogenetic diversity given their tiny area (2%). The relative richness of habitats is related to variation in diversification rates. Based on ancestral reconstructions of habitat, we find that most marine species are descended from marine ancestors and most terrestrial species from freshwater ancestors. Yet, most extant animal richness in freshwater is derived from terrestrial ancestors. Overall, our results reveal the origins of fundamental but neglected biodiversity patterns, and highlight the conservation importance of freshwater habitats.
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Affiliation(s)
| | - Daniela Moraga-López
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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38
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Hou Z, Ma X, Shi X, Li X, Yang L, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomic insights into a Mesoproterozoic-Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae). Nat Commun 2022; 13:1610. [PMID: 35318329 PMCID: PMC8941102 DOI: 10.1038/s41467-022-29282-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/09/2022] [Indexed: 01/09/2023] Open
Abstract
The Ulvophyceae, a major group of green algae, is of particular evolutionary interest because of its remarkable morphological and ecological diversity. Its phylogenetic relationships and diversification timeline, however, are still not fully resolved. In this study, using an extensive nuclear gene dataset, we apply coalescent- and concatenation-based approaches to reconstruct the phylogeny of the Ulvophyceae and to explore the sources of conflict in previous phylogenomic studies. The Ulvophyceae is recovered as a paraphyletic group, with the Bryopsidales being a sister group to the Chlorophyceae, and the remaining taxa forming a clade (Ulvophyceae sensu stricto). Molecular clock analyses with different calibration strategies emphasize the large impact of fossil calibrations, and indicate a Meso-Neoproterozoic origin of the Ulvophyceae (sensu stricto), earlier than previous estimates. The results imply that ulvophyceans may have had a profound influence on oceanic redox structures and global biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition. “Ulvophyceae is a remarkably morphologically and ecologically diverse clade of green algae. Here, the authors reconstruct the Ulvophyceae phylogeny, showing that these algae originated earlier than expected and may have influenced biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition.”
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Affiliation(s)
- Zheng Hou
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xi Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Frederik Leliaert
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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39
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Stüeken EE, Viehmann S, Hohl SV. Contrasting nutrient availability between marine and brackish waters in the late Mesoproterozoic: Evidence from the Paranoá Group, Brazil. GEOBIOLOGY 2022; 20:159-174. [PMID: 34661335 DOI: 10.1111/gbi.12478] [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: 02/24/2021] [Revised: 10/02/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Understanding the delayed rise of eukaryotic life on Earth is one of the most fundamental questions about biological evolution. Numerous studies have presented evidence for oxygen and nutrient limitations in seawater during the Mesoproterozoic era, indicating that open marine settings may not have been able to sustain a eukaryotic biosphere with complex, multicellular organisms. However, many of these data sets represent restricted marine basins, which may bias our view of habitability. Furthermore, it remains untested whether rivers could have supplied significant nutrient fluxes to coastal habitats. To better characterize the sources of the major nutrients nitrogen and phosphorus, we turned to the late Mesoproterozoic Paranoá Group in Brazil (~1.1 Ga), which was deposited on a passive margin of the São Francisco craton. We present carbon, nitrogen and sulphur isotope data from an open shelf setting (Fazenda Funil) and from a brackish-water environment with significant riverine input (São Gabriel). Our results show that waters were well-oxygenated and nitrate was bioavailable in the open ocean setting at Fazenda Funil; the redoxcline appears to have been deeper and further offshore compared to restricted marine basins elsewhere in the Mesoproterozoic. In contrast, the brackish site at São Gabriel received only limited input of marine nitrate and sulphate. Nevertheless, previous reports of acritarchs reveal that this brackish-water setting was habitable to eukaryotic life. Paired with previously published cadmium isotope data, which can be used as a proxy for phosphorus cycling, our results suggest that complex organisms were perhaps not strictly dependent on marine nutrient supplies. Riverine influxes of P and possibly other nutrients likely rendered coastal waters perhaps equally habitable to the Mesoproterozoic open ocean. This conclusion supports the notion that eukaryotic organisms may have thrived in brackish or perhaps even freshwater environments.
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Affiliation(s)
- Eva E Stüeken
- School of Earth & Environmental Sciences, University of St Andrews, St Andrews, UK
| | - Sebastian Viehmann
- Department of Geology, University of Vienna, Vienna, Austria
- Department of Lithospheric Research, University of Vienna, Vienna, Austria
| | - Simon V Hohl
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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40
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Spang A, Mahendrarajah TA, Offre P, Stairs CW. Evolving perspective on the origin and diversification of cellular life and the virosphere. Genome Biol Evol 2022; 14:6537539. [PMID: 35218347 PMCID: PMC9169541 DOI: 10.1093/gbe/evac034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 11/14/2022] Open
Abstract
The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.
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Affiliation(s)
- Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, The Netherlands and 1790 AB Den Burg.,Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden SE-75123, Uppsala
| | - Tara A Mahendrarajah
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, The Netherlands and 1790 AB Den Burg
| | - Pierre Offre
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, The Netherlands and 1790 AB Den Burg
| | - Courtney W Stairs
- Department of Biology, Lund University, Sweden Sölvegatan 35, 223 62 Lund
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41
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Medina-Chávez NO, Travisano M. Archaeal Communities: The Microbial Phylogenomic Frontier. Front Genet 2022; 12:693193. [PMID: 35154237 PMCID: PMC8826477 DOI: 10.3389/fgene.2021.693193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Archaea are a unique system for investigating the diversity of life. There are the most diverse group of organisms with the longest evolutionary history of life on Earth. Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life. They exist in the harshest environments and benign conditions, providing a system to investigate the basis for living in extreme environments. They are frequently members of microbial communities, albeit generally rare. Archaea were central in the evolution of Eukaryotes and can be used as a proxy for studying life on other planets. Future advances will depend not only upon phylogenomic studies but also on a better understanding of isolation and cultivation techniques.
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Affiliation(s)
- Nahui Olin Medina-Chávez
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Michael Travisano
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN, United States
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42
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Lee WK, Ho CL. Ecological and evolutionary diversification of sulphated polysaccharides in diverse photosynthetic lineages: A review. Carbohydr Polym 2022; 277:118764. [PMID: 34893214 DOI: 10.1016/j.carbpol.2021.118764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/02/2022]
Abstract
Sulphated polysaccharides (SPs) are carbohydrate macromolecules with sulphate esters that are found among marine algae, seagrasses, mangroves and some terrestrial plants. The sulphate concentration in the ocean (28 mM) since ancient time could have driven the production of SPs in marine algae. SPs have a gelatinous property that can protect marine algae against desiccation and salinity stress. Agar and carrageenan are red algal SPs that are widely used as gelling agents in the food and pharmaceutical industries. The information on the SPs from freshwater and land plants are limited. In this review, we reviewed the taxonomic distribution and composition of SPs in different photosynthetic lineages, and explored the association of SP production in these diversified photosynthetic organisms with evolution history and environmental stresses. We also reviewed the genes/proteins involved in SP biosynthesis. Insights into SP biosynthetic machinery may shed light on the evolution that accompanied adaptation to life on earth.
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Affiliation(s)
- Wei-Kang Lee
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM-Serdang, Selangor, Malaysia; Codon Genomics Sdn Bhd, No. 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia.
| | - Chai-Ling Ho
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM-Serdang, Selangor, Malaysia.
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43
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Evolution of Phytoplankton in Relation to Their Physiological Traits. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10020194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Defining the physiological traits that characterise phytoplankton involves comparison with related organisms in benthic habitats. Comparison of survival time in darkness under natural conditions requires more information. Gas vesicles and flagella as mechanisms of upward movement relative to surrounding water, allowing periodic vertical migration, are not confined to plankton, although buoyancy changes related to compositional changes of a large central vacuole may be restricted to plankton. Benthic microalgae have the same range of photosynthetic pigments as phytoplankton; it is not clear if there are differences in the rate of regulation and acclimation of photosynthetic machinery to variations in irradiance for phytoplankton and for microphytobenthos. There are inadequate data to determine if responses to variations in frequency or magnitude of changes in the supply of inorganic carbon, nitrogen or phosphorus differ between phytoplankton and benthic microalgae. Phagophotomixotrophy and osmophotomixotrophy occur in both phytoplankton and benthic microalgae. Further progress in identifying physiological traits specific to phytoplankton requires more experimentation on benthic microalgae that are closely related to planktonic microalgae, with attention to whether the benthic algae examined have, as far as can be determined, never been planktonic during their evolution or are derived from planktonic ancestors.
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44
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Sforna MC, Loron CC, Demoulin CF, François C, Cornet Y, Lara YJ, Grolimund D, Ferreira Sanchez D, Medjoubi K, Somogyi A, Addad A, Fadel A, Compère P, Baudet D, Brocks JJ, Javaux EJ. Intracellular bound chlorophyll residues identify 1 Gyr-old fossils as eukaryotic algae. Nat Commun 2022; 13:146. [PMID: 35013306 PMCID: PMC8748435 DOI: 10.1038/s41467-021-27810-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 12/03/2021] [Indexed: 11/09/2022] Open
Abstract
The acquisition of photosynthesis is a fundamental step in the evolution of eukaryotes. However, few phototrophic organisms are unambiguously recognized in the Precambrian record. The in situ detection of metabolic byproducts in individual microfossils is the key for the direct identification of their metabolisms. Here, we report a new integrative methodology using synchrotron-based X-ray fluorescence and absorption. We evidence bound nickel-geoporphyrins moieties in low-grade metamorphic rocks, preserved in situ within cells of a ~1 Gyr-old multicellular eukaryote, Arctacellularia tetragonala. We identify these moieties as chlorophyll derivatives, indicating that A. tetragonala was a phototrophic eukaryote, one of the first unambiguous algae. This new approach, applicable to overmature rocks, creates a strong new proxy to understand the evolution of phototrophy and diversification of early ecosystems.
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Affiliation(s)
- Marie Catherine Sforna
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium.
| | - Corentin C Loron
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Catherine F Demoulin
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Camille François
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium.,Commission for the Geological Map of the World, Paris, France
| | - Yohan Cornet
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Daniel Grolimund
- Paul Scherrer Institut, Swiss Light Source, CH-5232, Villigen PSI, Switzerland
| | | | | | | | - Ahmed Addad
- Unité Matériaux et Transformations (UMR CNRS 8207), Université Lille 1 - Sciences et Technologies, Villeneuve d'Ascq, France
| | - Alexandre Fadel
- Unité Matériaux et Transformations (UMR CNRS 8207), Université Lille 1 - Sciences et Technologies, Villeneuve d'Ascq, France
| | - Philippe Compère
- Functional and Evolutive Morphology, Department of Biology, Ecology and Evolution, UR FOCUS, and Center for Applied Research and Education in Microscopy (CAREM-ULiege), University of Liège, Liège, Belgium
| | - Daniel Baudet
- Geodynamics & Mineral Resources Service, Royal Museum for Central Africa, Tervuren, Belgium
| | - Jochen J Brocks
- Research School of Earth Sciences, The Australian National University, Canberra ACT, Australia
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium.
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45
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Semchonok DA, Mondal J, Cooper CJ, Schlum K, Li M, Amin M, Sorzano CO, Ramírez-Aportela E, Kastritis PL, Boekema EJ, Guskov A, Bruce BD. Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium. PLANT COMMUNICATIONS 2022; 3:100248. [PMID: 35059628 PMCID: PMC8760143 DOI: 10.1016/j.xplc.2021.100248] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/03/2021] [Accepted: 10/08/2021] [Indexed: 05/19/2023]
Abstract
Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric form of PSI in plants and algae. The tetrameric organization raises questions about its structural, physiological, and evolutionary significance. Here we report the ∼3.72 Å resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic, unicellular cyanobacterium Chroococcidiopsis sp. TS-821. The structure resolves 44 subunits and 448 cofactor molecules. We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization. The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers. Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state. Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.
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Affiliation(s)
- Dmitry A. Semchonok
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jyotirmoy Mondal
- Biochemistry & Cellular and Molecular Biology Department, University of Tennessee, Knoxville, TN, USA
| | - Connor J. Cooper
- Program in Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Katrina Schlum
- Program in Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Meng Li
- Biochemistry & Cellular and Molecular Biology Department, University of Tennessee, Knoxville, TN, USA
- Bredesen Center for Interdisciplinary Research & Education, University of Tennessee, Knoxville, TN, USA
| | - Muhamed Amin
- Department of Sciences, University College Groningen, Groningen, the Netherlands
| | - Carlos O.S. Sorzano
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
- Universidad CEU San Pablo, Campus Urb. Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain
| | - Erney Ramírez-Aportela
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Panagiotis L. Kastritis
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Egbert J. Boekema
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Albert Guskov
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Barry D. Bruce
- Biochemistry & Cellular and Molecular Biology Department, University of Tennessee, Knoxville, TN, USA
- Program in Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
- Bredesen Center for Interdisciplinary Research & Education, University of Tennessee, Knoxville, TN, USA
- Microbiology Department, University of Tennessee, Knoxville, TN, USA
- Corresponding author
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46
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Zhang H, Wang S, Luo H. A Computational Protocol for Dating the Evolution of Cyanobacteria. Methods Mol Biol 2022; 2569:23-40. [PMID: 36083442 DOI: 10.1007/978-1-0716-2691-7_2] [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] [Indexed: 05/24/2023]
Abstract
Cyanobacteria are known to play important roles in driving biological and geochemical innovations in ancient Earth. The origin of Cyanobacteria is the key to understanding these evolutionary events and thus has gained much interest to biologists and geobiologists. Recent development of the molecular dating approaches provides us an opportunity to assess the timeline of Cyanobacteria evolution based on relaxed clock models. The implementation of Bayesian phylogenetic approaches accommodates the uncertainties from different sources, such as fossil calibrations and topological structure of the phylogenomic tree, and provides us converged estimates of posterior mean ages. In this chapter, by taking Cyanobacteria as an example, we introduce a refined strategy to perform molecular dating analysis, as well as a practical method to evaluate the precision of dating analysis.
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Affiliation(s)
- Hao Zhang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sishuo Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Haiwei Luo
- School of Life Sciences, Earth and Environmental Sciences Programme, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
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Fournier GP, Parsons CW, Cutts EM, Tamre E. Standard Candles for Dating Microbial Lineages. Methods Mol Biol 2022; 2569:41-74. [PMID: 36083443 DOI: 10.1007/978-1-0716-2691-7_3] [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] [Indexed: 05/24/2023]
Abstract
Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.
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Affiliation(s)
- Gregory P Fournier
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Chris W Parsons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elise M Cutts
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erik Tamre
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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Ye T, Wang B, Li C, Bian P, Chen L, Wang G. Exposure of cyanobacterium Nostoc sp. to the Mars-like stratosphere environment. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 224:112307. [PMID: 34649187 DOI: 10.1016/j.jphotobiol.2021.112307] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 01/19/2023]
Abstract
During the HH-19-2 flight mission of the Chinese Scientific Experimental System, dried Nostoc sp. cells were exposed to the stratosphere environment (32,508 m altitude) for 3 h and 22 min. The atmospheric pressure, temperature, relative humidity, and ionizing and non-ionizing radiation levels at that altitude are similar to those on the surface of Mars. Although analyses revealed decreased photosynthetic activity, a decline in autofluorescence, and damage to the cellular morphology in the flight-exposed sample, the death rate was low (28%). Physiological changes were not obvious after the exposure to the Mars-like vacuum conditions. The ground-exposed samples showed a similar trend to the flight-exposed samples, but the damage was relatively slight. RNA-sequencing data revealed a number of affected metabolic pathways: photosynthetic system and CO2 fixation function, activation of antioxidant systems, heat shock protein, DNA repair, and protein synthesis. Results suggest that Nostoc sp. has the potential to survive in a Mars-like environment and that it may be a suitable pioneer species to colonize Mars in the future in closed life-support systems (base) or in localities with relatively suitable conditions for life, such as localities with water available.
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Affiliation(s)
- Tong Ye
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caiyan Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Po Bian
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031, China
| | - Lanzhou Chen
- School of Resource & Environmental Sciences, Wuhan University, Wuhan 430079, PR China
| | - Gaohong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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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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Abstract
The ancestors of cyanobacteria generated Earth's first biogenic molecular oxygen, but how they dealt with oxidative stress remains unconstrained. Here we investigate when superoxide dismutase enzymes (SODs) capable of removing superoxide free radicals evolved and estimate when Cyanobacteria originated. Our Bayesian molecular clocks, calibrated with microfossils, predict that stem Cyanobacteria arose 3300-3600 million years ago. Shortly afterwards, we find phylogenetic evidence that ancestral cyanobacteria used SODs with copper and zinc cofactors (CuZnSOD) during the Archaean. By the Paleoproterozoic, they became genetically capable of using iron, nickel, and manganese as cofactors (FeSOD, NiSOD, and MnSOD respectively). The evolution of NiSOD is particularly intriguing because it corresponds with cyanobacteria's invasion of the open ocean. Our analyses of metalloenzymes dealing with reactive oxygen species (ROS) now demonstrate that marine geochemical records alone may not predict patterns of metal usage by phototrophs from freshwater and terrestrial habitats.
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