1
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Sundar Panja A. The systematic codon usage bias has an important effect on genetic adaption in native species. Gene 2024; 926:148627. [PMID: 38823656 DOI: 10.1016/j.gene.2024.148627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.
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Affiliation(s)
- Anindya Sundar Panja
- Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal 721102, India.
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2
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Zhang T, Liu D, Zhang Y, Chen L, Zhang W, Sun T. Biomedical engineering utilizing living photosynthetic cyanobacteria and microalgae: Current status and future prospects. Mater Today Bio 2024; 27:101154. [PMID: 39113912 PMCID: PMC11304071 DOI: 10.1016/j.mtbio.2024.101154] [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: 05/04/2024] [Revised: 06/24/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Cyanobacteria are the only prokaryotes capable of performing oxygenic photosynthesis on Earth. Besides their traditional roles serving as primary producers, cyanobacteria also synthesize abundant secondary metabolites including carotenoids, alkaloids, peptides, which have been reported to possess medicinal potentials. More importantly, the advancement of synthetic biology technology has further expanded their potential biomedical applications especially using living/engineered cyanobacteria, providing promising and attractive strategies for future disease treatments. To improve the understanding and to facilitate future applications, this review aims to discuss the current status and future prospects of cyanobacterial-based biomedical engineering. Firstly, specific properties of cyanobacteria related with biomedical applications like their natural products of bioactive compounds and heavy metal adsorption were concluded. Subsequently, based on these properties of cyanobacteria, we discussed the progress of their applications in various disease models like hypoxia microenvironment alleviation, wound healing, drug delivery, and so on. Finally, the future prospects including further exploration of cyanobacteria secondary metabolites, the integration of bioactive compounds synthesized by cyanobacteria in situ with medical diagnosis and treatment, and the optimization of in vivo application were critically presented. The review will promote the studies related with cyanobacteria-based biomedical engineering and its practical application in clinical trials in the future.
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Affiliation(s)
- Tong Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Dailin Liu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Yingying Zhang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China
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3
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Bhattacharya R, Brown JS, Gatenby RA, Ibrahim-Hashim A. A gene for all seasons: The evolutionary consequences of HIF-1 in carcinogenesis, tumor growth and metastasis. Semin Cancer Biol 2024; 102-103:17-24. [PMID: 38969311 DOI: 10.1016/j.semcancer.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/23/2024] [Accepted: 06/06/2024] [Indexed: 07/07/2024]
Abstract
Oxygen played a pivotal role in the evolution of multicellularity during the Cambrian Explosion. Not surprisingly, responses to fluctuating oxygen concentrations are integral to the evolution of cancer-a disease characterized by the breakdown of multicellularity. Poorly organized tumor vasculature results in chaotic patterns of blood flow characterized by large spatial and temporal variations in intra-tumoral oxygen concentrations. Hypoxia-inducible growth factor (HIF-1) plays a pivotal role in enabling cells to adapt, metabolize, and proliferate in low oxygen conditions. HIF-1 is often constitutively activated in cancers, underscoring its importance in cancer progression. Here, we argue that the phenotypic changes mediated by HIF-1, in addition to adapting the cancer cells to their local environment, also "pre-adapt" them for proliferation at distant, metastatic sites. HIF-1-mediated adaptations include a metabolic shift towards anaerobic respiration or glycolysis, activation of cell survival mechanisms like phenotypic plasticity and epigenetic reprogramming, and formation of tumor vasculature through angiogenesis. Hypoxia induced epigenetic reprogramming can trigger epithelial to mesenchymal transition in cancer cells-the first step in the metastatic cascade. Highly glycolytic cells facilitate local invasion by acidifying the tumor microenvironment. New blood vessels, formed due to angiogenesis, provide cancer cells a conduit to the circulatory system. Moreover, survival mechanisms acquired by cancer cells in the primary site allow them to remodel tissue at the metastatic site generating tumor promoting microenvironment. Thus, hypoxia in the primary tumor promoted adaptations conducive to all stages of the metastatic cascade from the initial escape entry into a blood vessel, intravascular survival, extravasation into distant tissues, and establishment of secondary tumors.
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Affiliation(s)
- Ranjini Bhattacharya
- Department of Cancer Biology, University of South Florida, United States; Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, United States
| | - Joel S Brown
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, United States; Department of Evolutionary Biology, University of Illinois, at Chicago, United States
| | - Robert A Gatenby
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, United States; Department of Radiology, H. Lee Moffitt Cancer Center, United States.
| | - Arig Ibrahim-Hashim
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center, United States.
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4
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Ostrander CM, Heard AW, Shu Y, Bekker A, Poulton SW, Olesen KP, Nielsen SG. Onset of coupled atmosphere-ocean oxygenation 2.3 billion years ago. Nature 2024; 631:335-339. [PMID: 38867053 DOI: 10.1038/s41586-024-07551-5] [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: 11/15/2023] [Accepted: 05/09/2024] [Indexed: 06/14/2024]
Abstract
The initial rise of molecular oxygen (O2) shortly after the Archaean-Proterozoic transition 2.5 billion years ago was more complex than the single step-change once envisioned. Sulfur mass-independent fractionation records suggest that the rise of atmospheric O2 was oscillatory, with multiple returns to an anoxic state until perhaps 2.2 billion years ago1-3. Yet few constraints exist for contemporaneous marine oxygenation dynamics, precluding a holistic understanding of planetary oxygenation. Here we report thallium (Tl) isotope ratio and redox-sensitive element data for marine shales from the Transvaal Supergroup, South Africa. Synchronous with sulfur isotope evidence of atmospheric oxygenation in the same shales3, we found lower authigenic 205Tl/203Tl ratios indicative of widespread manganese oxide burial on an oxygenated seafloor and higher redox-sensitive element abundances consistent with expanded oxygenated waters. Both signatures disappear when the sulfur isotope data indicate a brief return to an anoxic atmospheric state. Our data connect recently identified atmospheric O2 dynamics on early Earth with the marine realm, marking an important turning point in Earth's redox history away from heterogeneous and highly localized 'oasis'-style oxygenation.
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Affiliation(s)
- Chadlin M Ostrander
- Department of Geology & Geophysics, University of Utah, Salt Lake City, UT, USA.
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
- NIRVANA Laboratories, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Andy W Heard
- NIRVANA Laboratories, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Yunchao Shu
- NIRVANA Laboratories, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Andrey Bekker
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA
- Department of Geology, University of Johannesburg, Auckland Park, South Africa
| | - Simon W Poulton
- School of Earth and Environment, University of Leeds, Leeds, UK
| | - Kasper P Olesen
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Sune G Nielsen
- NIRVANA Laboratories, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- CRPG, CNRS, Université de Lorraine, Vandoeuvre lès Nancy, France
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5
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Motomura K, Bekker A, Ikehara M, Sano T, Lin Y, Kiyokawa S. Lateral redox variability in ca. 1.9 Ga marine environments indicated by organic carbon and nitrogen isotope compositions. GEOBIOLOGY 2024; 22:e12614. [PMID: 39129173 DOI: 10.1111/gbi.12614] [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: 03/14/2024] [Revised: 07/18/2024] [Accepted: 07/20/2024] [Indexed: 08/13/2024]
Abstract
The stepwise oxygenation of Earth's surficial environment is thought to have shaped the evolutionary history of life. Microfossil records and molecular clocks suggest eukaryotes appeared during the Paleoproterozoic, perhaps shortly after the Great Oxidation Episode at ca. 2.43 Ga. The mildly oxygenated atmosphere and surface oceans likely contributed to the early evolution of eukaryotes. However, the principal trigger for the eukaryote appearance and a potential factor for their delayed expansion (i.e., intermediate ocean redox conditions until the Neoproterozoic) remain poorly understood, largely owing to a lack of constraints on marine and terrestrial nutrient cycling. Here, we analyzed redox-sensitive element contents and organic carbon and nitrogen isotope compositions of relatively low metamorphic-grade (greenschist facies) black shales preserved in the Flin Flon Belt of central Canada to examine open-marine redox conditions and biological activity around the ca. 1.9 Ga Flin Flon oceanic island arc. The black shale samples were collected from the Reed Lake area in the eastern part of the Flin Flon Belt, and the depositional site was likely distal from the Archean cratons. The black shales have low Al/Ti ratios and are slightly depleted in light rare-earth elements relative to the post-Archean average shale, which is consistent with a limited contribution from felsic igneous rocks in Archean upper continental crust. Redox conditions have likely varied between suboxic and euxinic at the depositional site of the studied section, as suggested by variable U/Al and Mo/Al ratios. Organic carbon and nitrogen isotope compositions of the black shales are approximately -23‰ and +13.7‰, respectively, and these values are systematically higher than those of broadly coeval continental margin deposits (approximately -30‰ for δ13Corg and +5‰ for δ15Nbulk). These elevated values are indicative of high productivity that led to enhanced denitrification (i.e., a high denitrification rate relative to nitrogen influx at the depositional site). Similar geochemical patterns have also been observed in the modern Peruvian oxygen minimum zone where dissolved nitrogen compounds are actively lost from the reservoir via denitrification and anammox, but the large nitrate reservoir of the deep ocean prevents exhaustion of the surface nitrate pool. Nitrogen must have been widely bioavailable in the ca. 1.9 Ga oceans, and its supply to upwelling zones must have supported habitable environments for eukaryotes, even in the middle of oceans around island arcs.
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Affiliation(s)
- Kento Motomura
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
- Department of Earth and Planetary Sciences, Kyushu University, Fukuoka, Japan
| | - Andrey Bekker
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
| | - Minoru Ikehara
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
| | - Takashi Sano
- Department of Geology and Paleontology, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Ying Lin
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
| | - Shoichi Kiyokawa
- Department of Earth and Planetary Sciences, Kyushu University, Fukuoka, Japan
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
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6
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Banfalvi G. The Origin of RNA and the Formose-Ribose-RNA Pathway. Int J Mol Sci 2024; 25:6727. [PMID: 38928433 PMCID: PMC11203418 DOI: 10.3390/ijms25126727] [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: 05/10/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Prebiotic pre-Darwinian reactions continued throughout biochemical or Darwinian evolution. Early chemical processes could have occurred on Earth between 4.5 and 3.6 billion years ago when cellular life was about to come into being. Pre-Darwinian evolution assumes the development of hereditary elements but does not regard them as self-organizing processes. The presence of biochemical self-organization after the pre-Darwinian evolution did not justify distinguishing between different types of evolution. From the many possible solutions, evolution selected from among those stable reactions that led to catalytic networks, and under gradually changing external conditions produced a reproducible, yet constantly evolving and adaptable, living system. Major abiotic factors included sunlight, precipitation, air, minerals, soil and the Earth's atmosphere, hydrosphere and lithosphere. Abiotic sources of chemicals contributed to the formation of prebiotic RNA, the development of genetic RNA, the RNA World and the initial life forms on Earth and the transition of genRNA to the DNA Empire, and eventually to the multitude of life forms today. The transition from the RNA World to the DNA Empire generated new processes such as oxygenic photosynthesis and the hierarchical arrangement of processes involved in the transfer of genetic information. The objective of this work is to unite earlier work dealing with the formose, the origin and synthesis of ribose and RNA reactions that were published as a series of independent reactions. These reactions are now regarded as the first metabolic pathway.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, 4032 Debrecen, Hungary
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7
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Nishihara A, Tsukatani Y, Azai C, Nobu MK. Illuminating the coevolution of photosynthesis and Bacteria. Proc Natl Acad Sci U S A 2024; 121:e2322120121. [PMID: 38875151 PMCID: PMC11194577 DOI: 10.1073/pnas.2322120121] [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: 12/18/2023] [Accepted: 05/06/2024] [Indexed: 06/16/2024] Open
Abstract
Life harnessing light energy transformed the relationship between biology and Earth-bringing a massive flux of organic carbon and oxidants to Earth's surface that gave way to today's organotrophy- and respiration-dominated biosphere. However, our understanding of how life drove this transition has largely relied on the geological record; much remains unresolved due to the complexity and paucity of the genetic record tied to photosynthesis. Here, through holistic phylogenetic comparison of the bacterial domain and all photosynthetic machinery (totally spanning >10,000 genomes), we identify evolutionary congruence between three independent biological systems-bacteria, (bacterio)chlorophyll-mediated light metabolism (chlorophototrophy), and carbon fixation-and uncover their intertwined history. Our analyses uniformly mapped progenitors of extant light-metabolizing machinery (reaction centers, [bacterio]chlorophyll synthases, and magnesium-chelatases) and enzymes facilitating the Calvin-Benson-Bassham cycle (form I RuBisCO and phosphoribulokinase) to the same ancient Terrabacteria organism near the base of the bacterial domain. These phylogenies consistently showed that extant phototrophs ultimately derived light metabolism from this bacterium, the last phototroph common ancestor (LPCA). LPCA was a non-oxygen-generating (anoxygenic) phototroph that already possessed carbon fixation and two reaction centers, a type I analogous to extant forms and a primitive type II. Analyses also indicate chlorophototrophy originated before LPCA. We further reconstructed evolution of chlorophototrophs/chlorophototrophy post-LPCA, including vertical inheritance in Terrabacteria, the rise of oxygen-generating chlorophototrophy in one descendant branch near the Great Oxidation Event, and subsequent emergence of Cyanobacteria. These collectively unveil a detailed view of the coevolution of light metabolism and Bacteria having clear congruence with the geological record.
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Affiliation(s)
- Arisa Nishihara
- Department of Life Science and Biotechnology, The National Institute of Advanced Industrial Science and Technology, Ibaraki305-0817, Japan
| | - Yusuke Tsukatani
- Biogeochemistry Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa237-0061, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa237-0061, Japan
| | - Chihiro Azai
- College of Life Sciences, Ritsumeikan University, Shiga525-8577, Japan
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo112-8551, Japan
| | - Masaru K. Nobu
- Department of Life Science and Biotechnology, The National Institute of Advanced Industrial Science and Technology, Ibaraki305-0817, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa237-0061, Japan
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8
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Majhi BK, Melis A. Recombinant protein synthesis and isolation of human interferon alpha-2 in cyanobacteria. BIORESOURCE TECHNOLOGY 2024; 400:130664. [PMID: 38583672 DOI: 10.1016/j.biortech.2024.130664] [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: 01/24/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Synechocystis sp. PCC 6803 (Synechocystis) is a unicellular photosynthetic microorganism that has been used as a model for photo-biochemical research. It comprises a potential cell factory for the generation of valuable bioactive compounds, therapeutic proteins, and possibly biofuels. Fusion constructs of recombinant proteins with the CpcA α-subunit or CpcB β-subunit of phycocyanin in Synechocystis have enabled true over-expression of several isoprenoid pathway enzymes and biopharmaceutical proteins to levels of 10-20 % of the total cellular protein. The present work employed the human interferon α-2 protein, as a study case of over-expression and downstream processing. It advanced the state of the art in the fusion constructs for protein overexpression technology by developing the bioresource for target protein separation from the fusion construct and isolation in substantially enriched or pure form. The work brings the cyanobacterial cell factory concept closer to meaningful commercial application for the photosynthetic production of useful recombinant proteins.
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Affiliation(s)
- Bharat K Majhi
- Department of Plant and Microbial Biology, 111 Koshland Hall, MC-3102, University of California, Berkeley, CA 94720-3102, USA
| | - Anastasios Melis
- Department of Plant and Microbial Biology, 111 Koshland Hall, MC-3102, University of California, Berkeley, CA 94720-3102, USA.
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9
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Reimink JR, Smye AJ. Subaerial weathering drove stabilization of continents. Nature 2024; 629:609-615. [PMID: 38720084 PMCID: PMC11096103 DOI: 10.1038/s41586-024-07307-1] [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: 10/26/2023] [Accepted: 03/13/2024] [Indexed: 05/15/2024]
Abstract
Earth's silica-rich continental crust is unique among the terrestrial planets and is critical for planetary habitability. Cratons represent the most imperishable continental fragments and form about 50% of the continental crust of the Earth, yet the mechanisms responsible for craton stabilization remain enigmatic1. Large tracts of strongly differentiated crust formed between 3 and 2.5 billion years ago, during the late Mesoarchaean and Neoarchaean time periods2. This crust contains abundant granitoid rocks with elevated concentrations of U, Th and K; the formation of these igneous rocks represents the final stage of stabilization of the continental crust2,3. Here, we show that subaerial weathering, triggered by the emergence of continental landmasses above sea level, facilitated intracrustal melting and the generation of peraluminous granitoid magmas. This resulted in reorganization of the compositional architecture of continental crust in the Neoarchaean period. Subaerial weathering concentrated heat-producing elements into terrigenous sediments that were incorporated into the deep crust, where they drove crustal melting and the chemical stratification required to stabilize the cratonic lithosphere. The chain of causality between subaerial weathering and the final differentiation of Earth's crust implies that craton stabilization was an inevitable consequence of continental emergence. Generation of sedimentary rocks enriched in heat-producing elements, at a time in the history of the Earth when the rate of radiogenic heat production was on average twice the present-day rate, resolves a long-standing question of why many cratons were stabilized in the Neoarchaean period.
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Affiliation(s)
- Jesse R Reimink
- Department of Geosciences, Pennsylvania State University, University Park, PA, USA.
| | - Andrew J Smye
- Department of Geosciences, Pennsylvania State University, University Park, PA, USA
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10
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Michimori Y, Izaki R, Su Y, Fukuyama Y, Shimamura S, Nishimura K, Miwa Y, Hamakita S, Shimosaka T, Makino Y, Takeno R, Sato T, Beppu H, Cann I, Kanai T, Nunoura T, Atomi H. Removal of phosphoglycolate in hyperthermophilic archaea. Proc Natl Acad Sci U S A 2024; 121:e2311390121. [PMID: 38593075 PMCID: PMC11032457 DOI: 10.1073/pnas.2311390121] [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: 07/19/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
Many organisms that utilize the Calvin-Benson-Bassham (CBB) cycle for autotrophic growth harbor metabolic pathways to remove and/or salvage 2-phosphoglycolate, the product of the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). It has been presumed that the occurrence of 2-phosphoglycolate salvage is linked to the CBB cycle, and in particular, the C2 pathway to the CBB cycle and oxygenic photosynthesis. Here, we examined 2-phosphoglycolate salvage in the hyperthermophilic archaeon Thermococcus kodakarensis, an obligate anaerobe that harbors a Rubisco that functions in the pentose bisphosphate pathway. T. kodakarensis harbors enzymes that have the potential to convert 2-phosphoglycolate to glycine and serine, and their genes were identified by biochemical and/or genetic analyses. 2-phosphoglycolate phosphatase activity increased 1.6-fold when cells were grown under microaerobic conditions compared to anaerobic conditions. Among two candidates, TK1734 encoded a phosphatase specific for 2-phosphoglycolate, and the enzyme was responsible for 80% of the 2-phosphoglycolate phosphatase activity in T. kodakarensis cells. The TK1734 disruption strain displayed growth impairment under microaerobic conditions, which was relieved upon addition of sodium sulfide. In addition, glycolate was detected in the medium when T. kodakarensis was grown under microaerobic conditions. The results suggest that T. kodakarensis removes 2-phosphoglycolate via a phosphatase reaction followed by secretion of glycolate to the medium. As the Rubisco in T. kodakarensis functions in the pentose bisphosphate pathway and not in the CBB cycle, mechanisms to remove 2-phosphoglycolate in this archaeon emerged independent of the CBB cycle.
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Affiliation(s)
- Yuta Michimori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Top Global University Program, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Rikihisa Izaki
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Yu Su
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Yuto Fukuyama
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka237–0061, Japan
| | - Shigeru Shimamura
- Super-Cutting-Edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka237–0061, Japan
| | - Karin Nishimura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Yuya Miwa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Sotaro Hamakita
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Takahiro Shimosaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Top Global University Program, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Yuki Makino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Ryo Takeno
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Integrated Research Center for Carbon Negative Science, Institute of Advanced Energy, Kyoto University, Uji611-0011, Japan
| | - Haruki Beppu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Isaac Cann
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Top Global University Program, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Department of Animal Science, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka237–0061, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Top Global University Program, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Integrated Research Center for Carbon Negative Science, Institute of Advanced Energy, Kyoto University, Uji611-0011, Japan
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11
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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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12
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Fan L, Xu B, Chen S, Liu Y, Li F, Xie W, Prabhu A, Zou D, Wan R, Li H, Liu H, Liu Y, Kao SJ, Chen J, Zhu Y, Rinke C, Li M, Zhu M, Zhang C. Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth. PNAS NEXUS 2024; 3:pgae057. [PMID: 38380056 PMCID: PMC10877094 DOI: 10.1093/pnasnexus/pgae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024]
Abstract
Land-ocean interactions greatly impact the evolution of coastal life on earth. However, the ancient geological forces and genetic mechanisms that shaped evolutionary adaptations and allowed microorganisms to inhabit coastal brackish waters remain largely unexplored. In this study, we infer the evolutionary trajectory of the ubiquitous heterotrophic archaea Poseidoniales (Marine Group II archaea) presently occurring across global aquatic habitats. Our results show that their brackish subgroups had a single origination, dated to over 600 million years ago, through the inversion of the magnesium transport gene corA that conferred osmotic-stress tolerance. The subsequent loss and gain of corA were followed by genome-wide adjustment, characterized by a general two-step mode of selection in microbial speciation. The coastal family of Poseidoniales showed a rapid increase in the evolutionary rate during and in the aftermath of the Cryogenian Snowball Earth (∼700 million years ago), possibly in response to the enhanced phosphorus supply and the rise of algae. Our study highlights the close interplay between genetic changes and ecosystem evolution that boosted microbial diversification in the Neoproterozoic continental margins, where the Cambrian explosion of animals soon followed.
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Affiliation(s)
- Lu Fan
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Bu Xu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Fuyan Li
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI 96822, USA
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangdong 519082, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong 519082, China
| | - Apoorva Prabhu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Ru Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan 570228, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310012, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
| | - Hongliang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310012, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
| | - Haodong Liu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Yuhang Liu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan 570228, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310012, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai 200062, China
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Maoyan Zhu
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, China
- Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
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13
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Felix JD. Modern analogs for ammonia flux from terrestrial hydrothermal features to the Archean atmosphere. Sci Rep 2024; 14:1544. [PMID: 38233446 PMCID: PMC10794450 DOI: 10.1038/s41598-024-51537-2] [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: 07/08/2023] [Accepted: 01/06/2024] [Indexed: 01/19/2024] Open
Abstract
The isotopic composition of nitrogen in the rock record provides valuable evidence of reactive nitrogen sources and processing on early Earth, but the wide range of δ15N values (- 10.2 to + 50.4‰) leads to ambiguity in defining the early Precambrian nitrogen cycle. The high δ15N values have been explained by large fractionation associated with the onset of nitrification and/or fractionation produced by ammonia-ammonium equilibrium and water-air flux in alkaline paleolakes. Previous flux sensitivity studies in modern water bodies report alkaline pH is not a prerequisite and temperature can be the dominate parameter driving water-air flux. Here, I use the chemical and physical components of 1022 modern hydrothermal features to provide evidence that water-air NH3 flux produced a significant source of fixed nitrogen to early Earth's atmosphere and biosphere. With regard to the modeled average NH3 flux (2.1 kg N m-2 year-1) and outlier removed average flux (1.2 kg N m-2 year-1), the Archean Earth's surface would need to be 0.0092, and 0.017% terrestrial hydrothermal features, respectively, for the flux to match the annual amount of N produced by biogenic fixation on modern Earth. Water-air NH3 flux from terrestrial hydrothermal features may have played a significant role in supplying bioavailable nitrogen to early life.
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Affiliation(s)
- J David Felix
- Physical and Environmental Sciences Department, Center for Water Supply Studies, Texas A&M University - Corpus Christi, Corpus Christi, USA.
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14
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Xu X, Li C, Cao W, Yan L, Cao L, Han Q, Gao M, Chen Y, Shen Z, Jiang J, Chen C. Bacterial growth and environmental adaptation via thiamine biosynthesis and thiamine-mediated metabolic interactions. THE ISME JOURNAL 2024; 18:wrae157. [PMID: 39129674 PMCID: PMC11346370 DOI: 10.1093/ismejo/wrae157] [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: 03/19/2024] [Revised: 07/24/2024] [Accepted: 08/11/2024] [Indexed: 08/13/2024]
Abstract
Understanding the ancestral transition from anaerobic to aerobic lifestyles is essential for comprehending life's early evolution. However, the biological adaptations occurring during this crucial transition remain largely unexplored. Thiamine is an important cofactor involved in central carbon metabolism and aerobic respiration. Here, we explored the phylogenetic and global distribution of thiamine-auxotrophic and thiamine-prototrophic bacteria based on the thiamine biosynthetic pathway in 154 838 bacterial genomes. We observed strong coincidences of the origin of thiamine-synthetic bacteria with the "Great Oxygenation Event," indicating that thiamine biosynthesis in bacteria emerged as an adaptation to aerobic respiration. Furthermore, we demonstrated that thiamine-mediated metabolic interactions are fundamental factors influencing the assembly and diversity of bacterial communities by a global survey across 4245 soil samples. Through our newly established stable isotope probing-metabolic modeling method, we uncovered the active utilization of thiamine-mediated metabolic interactions by bacterial communities in response to changing environments, thus revealing an environmental adaptation strategy employed by bacteria at the community level. Our study demonstrates the widespread thiamine-mediated metabolic interactions in bacterial communities and their crucial roles in setting the stage for an evolutionary transition from anaerobic to aerobic lifestyles and subsequent environmental adaptation. These findings provide new insights into early bacterial evolution and their subsequent growth and adaptations to environments.
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Affiliation(s)
- Xihui Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Can Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weimiao Cao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lulu Yan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lulu Cao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qi Han
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Minling Gao
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
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15
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Martinez-Gutierrez CA, Uyeda JC, Aylward FO. A timeline of bacterial and archaeal diversification in the ocean. eLife 2023; 12:RP88268. [PMID: 38059790 DOI: 10.7554/elife.88268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.
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Affiliation(s)
| | - Josef C Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, United States
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16
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Zhi Y, Guo Q, Xie J, Hu J, Tian SX. Direct production of molecular oxygen from carbon dioxide and helium ion collisions. Commun Chem 2023; 6:267. [PMID: 38057399 DOI: 10.1038/s42004-023-01074-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023] Open
Abstract
The prebiotic mechanism to produce molecular oxygen (O2) in carbon dioxide (CO2)-rich planetary atmospheres is of great importance in understanding astrochemical reactions and is potentially relevant to the origin of life on Earth. Here, we demonstrate that, aside from the direct productions of O2 by photodissociation and dissociative electron attachment, the low-energy ion-molecule reaction between cationic helium in solar winds and molecular CO2 is a noticeable mechanism. Branching ratios of the reaction channels are determined, and their absolute cross-sections are estimated accordingly. The present findings represent a further, indispensable step towards fully understanding the origins of atmospheric O2.
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Affiliation(s)
- Yaya Zhi
- Department of Chemical Physics, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, 230026, Hefei, China
| | - Qiang Guo
- Department of Chemical Physics, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, 230026, Hefei, China
| | - Jingchen Xie
- Department of Chemical Physics, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, 230026, Hefei, China
| | - Jie Hu
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 230026, Hefei, China.
| | - Shan Xi Tian
- Department of Chemical Physics, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, 230026, Hefei, China.
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, 230026, Hefei, China.
- Hefei National Laboratory, University of Science and Technology of China, 230088, Hefei, China.
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17
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Huang B, Liu M, Kusky TM, Johnson TE, Wilde SA, Fu D, Deng H, Qian Q. Changes in orogenic style and surface environment recorded in Paleoproterozoic foreland successions. Nat Commun 2023; 14:7997. [PMID: 38042882 PMCID: PMC10693560 DOI: 10.1038/s41467-023-43893-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/23/2023] [Indexed: 12/04/2023] Open
Abstract
The Earth's interior and surficial systems underwent dramatic changes during the Paleoproterozoic, but the interaction between them remains poorly understood. Rocks deposited in orogenic foreland basins retain a record of the near surface to deep crustal processes that operate during subduction to collision and provide information on the interaction between plate tectonics and surface responses through time. Here, we document the depositional-to-deformational life cycle of a Paleoproterozoic foreland succession from the North China Craton. The succession was deposited in a foreland basin following ca. 2.50-2.47 Ga Altaid-style arc-microcontinent collision, and then converted to a fold-and-thrust belt at ca. 2.0-1.8 Ga due to Himalayan-style continent-continent collision. These two periods correspond to the assembly of supercratons in the late Archean and of the Paleoproterozoic supercontinent Columbia, respectively, which suggests that similar basins may have been common at the periphery of other cratons. The multiple stages of orogenesis and accompanying tectonic denudation and silicate weathering, as recorded by orogenic foreland basins, likely contributed to substantial changes in the hydrosphere, atmosphere, and biosphere known to have occurred during the Paleoproterozoic.
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Affiliation(s)
- Bo Huang
- Badong National Observation and Research Station of Geohazards, State Key Laboratory of Geological Processes and Mineral Resources, Center for Global Tectonics, School of Earth Sciences, China University of Geosciences, Wuhan, 430074, China.
| | - Man Liu
- Badong National Observation and Research Station of Geohazards, State Key Laboratory of Geological Processes and Mineral Resources, Center for Global Tectonics, School of Earth Sciences, China University of Geosciences, Wuhan, 430074, China
| | - Timothy M Kusky
- Badong National Observation and Research Station of Geohazards, State Key Laboratory of Geological Processes and Mineral Resources, Center for Global Tectonics, School of Earth Sciences, China University of Geosciences, Wuhan, 430074, China
| | - Tim E Johnson
- Badong National Observation and Research Station of Geohazards, State Key Laboratory of Geological Processes and Mineral Resources, Center for Global Tectonics, School of Earth Sciences, China University of Geosciences, Wuhan, 430074, China
- School of Earth and Planetary Sciences, the Institute for Geoscience Research, Timescales of Mineral Systems Group, Curtin University, Perth, WA, 6102, Australia
| | - Simon A Wilde
- School of Earth and Planetary Sciences, the Institute for Geoscience Research, Timescales of Mineral Systems Group, Curtin University, Perth, WA, 6102, Australia
| | - Dong Fu
- Badong National Observation and Research Station of Geohazards, State Key Laboratory of Geological Processes and Mineral Resources, Center for Global Tectonics, School of Earth Sciences, China University of Geosciences, Wuhan, 430074, China
| | - Hao Deng
- Badong National Observation and Research Station of Geohazards, State Key Laboratory of Geological Processes and Mineral Resources, Center for Global Tectonics, School of Earth Sciences, China University of Geosciences, Wuhan, 430074, China
| | - Qunye Qian
- Badong National Observation and Research Station of Geohazards, State Key Laboratory of Geological Processes and Mineral Resources, Center for Global Tectonics, School of Earth Sciences, China University of Geosciences, Wuhan, 430074, China
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18
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Lim L, Kang J, Song J. Extreme diversity of 12 cations in folding ALS-linked hSOD1 unveils novel hSOD1-dependent mechanisms for Fe 2+/Cu 2+-induced cytotoxicity. Sci Rep 2023; 13:19868. [PMID: 37964005 PMCID: PMC10645853 DOI: 10.1038/s41598-023-47338-8] [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: 09/04/2023] [Accepted: 11/12/2023] [Indexed: 11/16/2023] Open
Abstract
153-Residue copper-zinc superoxide dismutase 1 (hSOD1) is the first gene whose mutation was linked to FALS. To date, > 180 ALS-causing mutations have been identified within hSOD1, yet the underlying mechanism still remains mysterious. Mature hSOD1 is exceptionally stable constrained by a disulfide bridge to adopt a Greek-key β-barrel fold that accommodates copper/zinc cofactors. Conversely, nascent hSOD1 is unfolded and susceptible to aggregation and amyloid formation, requiring Zn2+ to initiate folding to a coexistence of folded and unfolded states. Recent studies demonstrate mutations that disrupt Zn2+-binding correlate with their ability to form toxic aggregates. Therefore, to decode the role of cations in hSOD1 folding provides not only mechanistic insights, but may bear therapeutic implications for hSOD1-linked ALS. Here by NMR, we visualized the effect of 12 cations: 8 essential for humans (Na+, K+, Ca2+, Zn2+, Mg2+, Mn2+, Cu2+, Fe2+), 3 mimicking zinc (Ni2+, Cd2+, Co2+), and environmentally abundant Al3+. Surprisingly, most cations, including Zn2+-mimics, showed negligible binding or induction for folding of nascent hSOD1. Cu2+ exhibited extensive binding to the unfolded state but led to severe aggregation. Unexpectedly, for the first time Fe2+ was deciphered to have Zn2+-like folding-inducing capacity. Zn2+ was unable to induce folding of H80S/D83S-hSOD1, while Fe2+ could. In contrast, Zn2+ could trigger folding of G93A-hSOD1, but Fe2+ failed. Notably, pre-existing Fe2+ disrupted the Zn2+-induced folding of G93A-hSOD1. Comparing with the ATP-induced folded state, our findings delineate that hSOD1 maturation requires: (1) intrinsic folding capacity encoded by the sequence; (2) specific Zn2+-coordination; (3) disulfide formation and Cu-load catalyzed by hCCS. This study unveils a previously-unknown interplay of cations in governing the initial folding of hSOD1, emphasizing the pivotal role of Zn2+ in hSOD1-related ALS and implying new hSOD1-dependent mechanisms for Cu2+/Fe2+-induced cytotoxicity, likely relevant to aging and other diseases.
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Affiliation(s)
- Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Republic of Singapore
| | - Jian Kang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Republic of Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Republic of Singapore.
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19
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Pan J, Zhang X, Xu W, Liu Y, Liu L, Luo Z, Li M. Wood-Ljungdahl pathway found in novel marine Korarchaeota groups illuminates their evolutionary history. mSystems 2023; 8:e0030523. [PMID: 37458475 PMCID: PMC10469681 DOI: 10.1128/msystems.00305-23] [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: 03/28/2023] [Accepted: 05/29/2023] [Indexed: 07/22/2023] Open
Abstract
Korarchaeota, due to its rarity in common environments, is one of the archaeal phyla that has received the least attention from researchers. It was previously thought to consist solely of strict thermophiles. However, our study provides genetic evidence for the presence of korarchaeal members in temperate subsurface seawater. Furthermore, a systematic reclassification of the Korarchaeota based on 16S rRNA genes and genomes has revealed three novel marine groups (Kor-6 to Kor-8) at the root of the Korarchaeota branch. Kor-6 contains microbes that are present in moderate temperatures. All three novel marine phyla possess genes for the Wood-Ljungdahl pathway, and Kor-7 and Kor-8 possess fewer genes encoding oxygen resistance traits than other korarchaeal groups, suggesting a distinct lifestyle for these novel phyla. Our results, together with estimations of Korarchaeota divergence times, suggest that oxygen availability may be one of the important factors that have influenced the evolution of Korarchaeota. IMPORTANCE Korarchaeota were previously thought to inhabit exclusively high-temperature environments. However, our study provides genetic evidence for their unexpected presence in temperate marine waters. Through analysis of publicly available korarchaeal reference data, we have systematically reclassified Korarchaeota and identified the existence of three previously unknown marine groups (Kor-6, Kor-7, and Kor-8) at the root of the Korarchaeota branch. Comparative analysis of their gene content revealed that these novel groups exhibit a lifestyle distinct from other Korarchaeota. Specifically, they have the ability to fix carbon exclusively via the Wood-Ljungdahl (WL) pathway, and the genomes within Kor-7 and Kor-8 contain few genes encoding antioxidant enzymes, indicating their strictly anaerobic lifestyle. Further studies suggest that the genes related to methane metabolism and the WL pathway may have been inherited from a common ancestor of the Korarchaeota and that oxygen availability may be one of the important evolutionary factors that shaped the diversification of this archaeal phylum.
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Affiliation(s)
- Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Xbiome Biotech Co. Ltd., Shenzhen, Guangdong, China
| | - Xinxu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
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20
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Cuéllar-Cruz M. New Insights on the Origin of Life: The Role of Silico-Carbonates of Ba (II) to Preserve DNA against Highly Intense UV Radiation. ACS OMEGA 2023; 8:29585-29594. [PMID: 37599928 PMCID: PMC10433334 DOI: 10.1021/acsomega.3c03516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/26/2023] [Indexed: 08/22/2023]
Abstract
Understanding the origin of life on our planet has generated diverse theories. Currently, the theory is that life has a single origin; however, its starting point has not been defined. As evidenced, it is indispensable to unify the different theories to reach a single theory that would also allow linking the different areas of knowledge to finally understand the mechanism by which life originated on Earth. In this regard, aiming at contributing to the unification of the diverse theories on the origin of life, in this work, the hypothesis based on the condition that silica-carbonates of alkaline earth metals, called biomorphs, are the ones that could unify all the proposed theories on the origin of life is proposed. Aimed at evaluating if this hypothesis is viable, this work assessed whether biomorphs are able to protect the DNA from continuous UV radiation under two conditions that emulate the habitats that could have co-existed in the Precambrian and, after the radiation, evaluated the time during which DNA remained inside the biomorphs. Our results showed that biomorphs can protect the DNA for months after continuous UV exposure. It was also determined that biomorphs protect the DNA from external factors in different habitats, like normal atmospheric conditions and in aqueous environments. The obtained data allowed me to infer that biomorphs may be the gap that unifies the diverse proposed theories on the origin of life in our Planet.
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Affiliation(s)
- Mayra Cuéllar-Cruz
- Departamento de Biología, División
de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta, Guanajuato, Guanajuato 36050, Mexico
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21
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Chang Y, Fu Y, Chen Z, Luo Z, Zhao Y, Li Z, Zhang W, Wu G, Fu B, Zhang DH, Ashfold MNR, Yang X, Yuan K. Vacuum ultraviolet photodissociation of sulfur dioxide and its implications for oxygen production in the early Earth's atmosphere. Chem Sci 2023; 14:8255-8261. [PMID: 37564413 PMCID: PMC10411858 DOI: 10.1039/d3sc03328g] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
The emergence of molecular oxygen (O2) in the Earth's primitive atmosphere is an issue of major interest. Although the biological processes leading to its accumulation in the Earth's atmosphere are well understood, its abiotic source is still not fully established. Here, we report a new direct dissociation channel yielding S(1D) + O2(a1Δg/X3Σg-) products from vacuum ultraviolet (VUV) photodissociation of SO2 in the wavelength range between 120 and 160 nm. Experimental results show O2 production to be an important channel from SO2 VUV photodissociation, with a branching ratio of 30 ± 5% at the H Lyman-α wavelength (121.6 nm). The relatively large amounts of SO2 emitted from volcanic eruptions in the Earth's late Archaean eon imply that VUV photodissociation of SO2 could have provided a crucial additional source term in the O2 budget in the Earth's primitive atmosphere. The results could also have implications for abiotic oxygen formation on other planets with atmospheres rich in volcanically outgassed SO2.
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Affiliation(s)
- Yao Chang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yanlin Fu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Zhichao Chen
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Zijie Luo
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- Marine Engineering College, Dalian Maritime University Liaoning 116026 China
| | - Yarui Zhao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Zhenxing Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Weiqing Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Guorong Wu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Bina Fu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Hefei National Laboratory Hefei 230088 China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- Hefei National Laboratory Hefei 230088 China
- Department of Chemistry, Center for Advanced Light Source Research, College of Science, Southern University of Science and Technology Shenzhen 518055 China
| | | | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- Hefei National Laboratory Hefei 230088 China
- Department of Chemistry, Center for Advanced Light Source Research, College of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Kaijun Yuan
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Coherent Light Source, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Hefei National Laboratory Hefei 230088 China
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22
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Mateos K, Chappell G, Klos A, Le B, Boden J, Stüeken E, Anderson R. The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth. SCIENCE ADVANCES 2023; 9:eade4847. [PMID: 37418533 PMCID: PMC10328410 DOI: 10.1126/sciadv.ade4847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 02/06/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
The biogeochemical sulfur cycle plays a central role in fueling microbial metabolisms, regulating the Earth's redox state, and affecting climate. However, geochemical reconstructions of the ancient sulfur cycle are confounded by ambiguous isotopic signals. We use phylogenetic reconciliation to ascertain the timing of ancient sulfur cycling gene events across the tree of life. Our results suggest that metabolisms using sulfide oxidation emerged in the Archean, but those involving thiosulfate emerged only after the Great Oxidation Event. Our data reveal that observed geochemical signatures resulted not from the expansion of a single type of organism but were instead associated with genomic innovation across the biosphere. Moreover, our results provide the first indication of organic sulfur cycling from the Mid-Proterozoic onwards, with implications for climate regulation and atmospheric biosignatures. Overall, our results provide insights into how the biological sulfur cycle evolved in tandem with the redox state of the early Earth.
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Affiliation(s)
- Katherine Mateos
- Carleton College, Northfield, MN, USA
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Garrett Chappell
- Carleton College, Northfield, MN, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aya Klos
- Carleton College, Northfield, MN, USA
| | - Bryan Le
- Carleton College, Northfield, MN, USA
| | - Joanne Boden
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Eva Stüeken
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Rika Anderson
- Carleton College, Northfield, MN, USA
- NASA NExSS Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
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23
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Pardo-De la Hoz CJ, Magain N, Piatkowski B, Cornet L, Dal Forno M, Carbone I, Miadlikowska J, Lutzoni F. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. Syst Biol 2023; 72:694-712. [PMID: 36827095 DOI: 10.1093/sysbio/syad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 02/12/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].
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Affiliation(s)
| | - Nicolas Magain
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Luc Cornet
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | | | - Ignazio Carbone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
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24
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Bernaola-Galván P, Carpena P, Gómez-Martín C, Oliver JL. Compositional Structure of the Genome: A Review. BIOLOGY 2023; 12:849. [PMID: 37372134 PMCID: PMC10295253 DOI: 10.3390/biology12060849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
As the genome carries the historical information of a species' biotic and environmental interactions, analyzing changes in genome structure over time by using powerful statistical physics methods (such as entropic segmentation algorithms, fluctuation analysis in DNA walks, or measures of compositional complexity) provides valuable insights into genome evolution. Nucleotide frequencies tend to vary along the DNA chain, resulting in a hierarchically patchy chromosome structure with heterogeneities at different length scales that range from a few nucleotides to tens of millions of them. Fluctuation analysis reveals that these compositional structures can be classified into three main categories: (1) short-range heterogeneities (below a few kilobase pairs (Kbp)) primarily attributed to the alternation of coding and noncoding regions, interspersed or tandem repeats densities, etc.; (2) isochores, spanning tens to hundreds of tens of Kbp; and (3) superstructures, reaching sizes of tens of megabase pairs (Mbp) or even larger. The obtained isochore and superstructure coordinates in the first complete T2T human sequence are now shared in a public database. In this way, interested researchers can use T2T isochore data, as well as the annotations for different genome elements, to check a specific hypothesis about genome structure. Similarly to other levels of biological organization, a hierarchical compositional structure is prevalent in the genome. Once the compositional structure of a genome is identified, various measures can be derived to quantify the heterogeneity of such structure. The distribution of segment G+C content has recently been proposed as a new genome signature that proves to be useful for comparing complete genomes. Another meaningful measure is the sequence compositional complexity (SCC), which has been used for genome structure comparisons. Lastly, we review the recent genome comparisons in species of the ancient phylum Cyanobacteria, conducted by phylogenetic regression of SCC against time, which have revealed positive trends towards higher genome complexity. These findings provide the first evidence for a driven progressive evolution of genome compositional structure.
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Affiliation(s)
- Pedro Bernaola-Galván
- Department of Applied Physics II and Institute Carlos I for Theoretical and Computational Physics, University of Málaga, 29071 Málaga, Spain; (P.B.-G.); (P.C.)
| | - Pedro Carpena
- Department of Applied Physics II and Institute Carlos I for Theoretical and Computational Physics, University of Málaga, 29071 Málaga, Spain; (P.B.-G.); (P.C.)
| | - Cristina Gómez-Martín
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
- Department of Genetics, Faculty of Sciences, 18071 and Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, University of Granada, 18100 Granada, Spain
| | - Jose L. Oliver
- Department of Genetics, Faculty of Sciences, 18071 and Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, University of Granada, 18100 Granada, Spain
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25
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Mallén-Ponce MJ, Gámez-Arcas S, Pérez-Pérez ME. Redox partner interactions in the ATG8 lipidation system in microalgae. Free Radic Biol Med 2023; 203:58-68. [PMID: 37028463 DOI: 10.1016/j.freeradbiomed.2023.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/09/2023]
Abstract
Autophagy is a catabolic pathway that functions as a degradative and recycling process to maintain cellular homeostasis in most eukaryotic cells, including photosynthetic organisms such as microalgae. This process involves the formation of double-membrane vesicles called autophagosomes, which engulf the material to be degraded and recycled in lytic compartments. Autophagy is mediated by a set of highly conserved autophagy-related (ATG) proteins that play a fundamental role in the formation of the autophagosome. The ATG8 ubiquitin-like system catalyzes the conjugation of ATG8 to the lipid phosphatidylethanolamine, an essential reaction in the autophagy process. Several studies identified the ATG8 system and other core ATG proteins in photosynthetic eukaryotes. However, how ATG8 lipidation is driven and regulated in these organisms is not fully understood yet. A detailed analysis of representative genomes from the entire microalgal lineage revealed a high conservation of ATG proteins in these organisms with the remarkable exception of red algae, which likely lost ATG genes before diversification. Here, we examine in silico the mechanisms and dynamic interactions between different components of the ATG8 lipidation system in plants and algae. Moreover, we also discuss the role of redox post-translational modifications in the regulation of ATG proteins and the activation of autophagy in these organisms by reactive oxygen species.
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Affiliation(s)
- Manuel J Mallén-Ponce
- Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 75005, Paris, France
| | - Samuel Gámez-Arcas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092, Sevilla, Spain
| | - María Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, 41092, Sevilla, Spain.
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26
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Saleem F, Jiang JL, Atrache R, Paschos A, Edge TA, Schellhorn HE. Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems. Microorganisms 2023; 11:851. [PMID: 37110273 PMCID: PMC10144707 DOI: 10.3390/microorganisms11040851] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Cyanobacteria (blue-green algae) can accumulate to form harmful algal blooms (HABs) on the surface of freshwater ecosystems under eutrophic conditions. Extensive HAB events can threaten local wildlife, public health, and the utilization of recreational waters. For the detection/quantification of cyanobacteria and cyanotoxins, both the United States Environmental Protection Agency (USEPA) and Health Canada increasingly indicate that molecular methods can be useful. However, each molecular detection method has specific advantages and limitations for monitoring HABs in recreational water ecosystems. Rapidly developing modern technologies, including satellite imaging, biosensors, and machine learning/artificial intelligence, can be integrated with standard/conventional methods to overcome the limitations associated with traditional cyanobacterial detection methodology. We examine advances in cyanobacterial cell lysis methodology and conventional/modern molecular detection methods, including imaging techniques, polymerase chain reaction (PCR)/DNA sequencing, enzyme-linked immunosorbent assays (ELISA), mass spectrometry, remote sensing, and machine learning/AI-based prediction models. This review focuses specifically on methodologies likely to be employed for recreational water ecosystems, especially in the Great Lakes region of North America.
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Affiliation(s)
| | | | | | | | | | - Herb E. Schellhorn
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
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27
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Development of the Anaerobic Microbiome in the Infant Gut. Pediatr Infect Dis J 2023:00006454-990000000-00384. [PMID: 36917032 DOI: 10.1097/inf.0000000000003905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Ninety-five percent of gut microbiota are anaerobes and vary according to age and diet. Complex carbohydrates in human milk enhance the growth of Bifidobacterium and Bacteroides in the first year. Complex carbohydrates in solid foods enhance the growth of Bacteroides and Clostridium in the second year. Short-chain fatty acids produced by Akkermansia and Faecalibacterium may reduce obesity, diabetes and IBD.
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28
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Ngugi DK, Salcher MM, Andrei AS, Ghai R, Klotz F, Chiriac MC, Ionescu D, Büsing P, Grossart HP, Xing P, Priscu JC, Alymkulov S, Pester M. Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes. SCIENCE ADVANCES 2023; 9:eadc9392. [PMID: 36724220 PMCID: PMC9891703 DOI: 10.1126/sciadv.adc9392] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.
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Affiliation(s)
- David Kamanda Ngugi
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
- Corresponding author.
| | - Michaela M. Salcher
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Adrian-Stefan Andrei
- Microbial Evogenomics Lab, Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Rohit Ghai
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Franziska Klotz
- Department of Biology, University of Konstanz, D-78457 Constance, Germany
| | - Maria-Cecilia Chiriac
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Danny Ionescu
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, D-12587 Stechlin, Germany
| | - Petra Büsing
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, D-12587 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, D-14469 Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Free University, D-14195 Berlin, Germany
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - John C. Priscu
- Department of Land Resources and Environmental Sciences, Montana State University, 334 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Salmor Alymkulov
- Institute of Physics, National Academy of Sciences of Kyrgyz Republic, Chui Avenue, 265-a, Bishkek 720071, Kyrgyzstan
| | - Michael Pester
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
- Institute of Microbiology, Technical University of Braunschweig, D-38108 Braunschweig, Germany
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29
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Van Etten J, Cho CH, Yoon HS, Bhattacharya D. Extremophilic red algae as models for understanding adaptation to hostile environments and the evolution of eukaryotic life on the early earth. Semin Cell Dev Biol 2023; 134:4-13. [PMID: 35339358 DOI: 10.1016/j.semcdb.2022.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/20/2022] [Accepted: 03/04/2022] [Indexed: 01/08/2023]
Abstract
Extremophiles have always garnered great interest because of their exotic lifestyles and ability to thrive at the physical limits of life. In hot springs environments, the Cyanidiophyceae red algae are the only photosynthetic eukaryotes able to live under extremely low pH (0-5) and relatively high temperature (35ºC to 63ºC). These extremophiles live as biofilms in the springs, inhabit acid soils near the hot springs, and form endolithic populations in the surrounding rocks. Cyanidiophyceae represent a remarkable source of knowledge about the evolution of extremophilic lifestyles and their genomes encode specialized enzymes that have applied uses. Here we review the evolutionary origin, taxonomy, genome biology, industrial applications, and use of Cyanidiophyceae as genetic models. Currently, Cyanidiophyceae comprise a single order (Cyanidiales), three families, four genera, and nine species, including the well-known Cyanidioschyzon merolae and Galdieria sulphuraria. These algae have small, gene-rich genomes that are analogous to those of prokaryotes they live and compete with. There are few spliceosomal introns and evidence exists for horizontal gene transfer as a driver of local adaptation to gain access to external fixed carbon and to extrude toxic metals. Cyanidiophyceae offer a variety of commercial opportunities such as phytoremediation to detoxify contaminated soils or waters and exploitation of their mixotrophic lifestyles to support the efficient production of bioproducts such as phycocyanin and floridosides. In terms of exobiology, Cyanidiophyceae are an ideal model system for understanding the evolutionary effects of foreign gene acquisition and the interactions between different organisms inhabiting the same harsh environment on the early Earth. Finally, we describe ongoing research with C. merolae genetics and summarize the unique insights they offer to the understanding of algal biology and evolution.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
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30
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Reconciling discrepant minor sulfur isotope records of the Great Oxidation Event. Nat Commun 2023; 14:279. [PMID: 36650167 PMCID: PMC9845385 DOI: 10.1038/s41467-023-35820-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Understanding the timing and trajectory of atmospheric oxygenation remains fundamental to deciphering its causes and consequences. Given its origin in oxygen-free photochemistry, mass-independent sulfur isotope fractionation (S-MIF) is widely accepted as a geochemical fingerprint of an anoxic atmosphere. Nevertheless, S-MIF recycling through oxidative sulfide weathering-commonly termed the crustal memory effect (CME)-potentially decouples the multiple sulfur isotope (MSI) record from coeval atmospheric chemistry. Herein, however, after accounting for unrecognised temporal and spatial biases within the Archaean-early-Palaeoproterozoic MSI record, we demonstrate that the global expression of the CME is barely resolvable; thereby validating S-MIF as a tracer of contemporaneous atmospheric chemistry during Earth's incipient oxygenation. Next, utilising statistical approaches, supported by new MSI data, we show that the reconciliation of adjacent, yet seemingly discrepant, South African MSI records requires that the rare instances of post-2.3-billion-year-old S-MIF are stratigraphically restricted. Accepting others' primary photochemical interpretation, our approach demands that these implied atmospheric dynamics were ephemeral, operating on sub-hundred-thousand-year timescales. Importantly, these apparent atmospheric relapses were fundamentally different from older putative oxygenation episodes, implicating an intermediate, and potentially uniquely feedback-sensitive, Earth system state in the wake of the Great Oxidation Event.
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31
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Lubitz W, Pantazis DA, Cox N. Water oxidation in oxygenic photosynthesis studied by magnetic resonance techniques. FEBS Lett 2023; 597:6-29. [PMID: 36409002 DOI: 10.1002/1873-3468.14543] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
The understanding of light-induced biological water oxidation in oxygenic photosynthesis is of great importance both for biology and (bio)technological applications. The chemically difficult multistep reaction takes place at a unique protein-bound tetra-manganese/calcium cluster in photosystem II whose structure has been elucidated by X-ray crystallography (Umena et al. Nature 2011, 473, 55). The cluster moves through several intermediate states in the catalytic cycle. A detailed understanding of these intermediates requires information about the spatial and electronic structure of the Mn4 Ca complex; the latter is only available from spectroscopic techniques. Here, the important role of Electron Paramagnetic Resonance (EPR) and related double resonance techniques (ENDOR, EDNMR), complemented by quantum chemical calculations, is described. This has led to the elucidation of the cluster's redox and protonation states, the valence and spin states of the manganese ions and the interactions between them, and contributed substantially to the understanding of the role of the protein surrounding, as well as the binding and processing of the substrate water molecules, the O-O bond formation and dioxygen release. Based on these data, models for the water oxidation cycle are developed.
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Affiliation(s)
- Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim/Ruhr, Germany
| | | | - Nicholas Cox
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
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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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Cuéllar-Cruz M, Islas SR, Ramírez-Ramírez N, Pedraza-Reyes M, Moreno A. Protection of the DNA from Selected Species of Five Kingdoms in Nature by Ba(II), Sr(II), and Ca(II) Silica-Carbonates: Implications about Biogenicity and Evolving from Prebiotic Chemistry to Biological Chemistry. ACS OMEGA 2022; 7:37410-37426. [PMID: 36312347 PMCID: PMC9609056 DOI: 10.1021/acsomega.2c04170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The origin of life on Earth is associated with the Precambrian era, in which the existence of a large diversity of microbial fossils has been demonstrated. Notwithstanding, despite existing evidence of the emergence of life many unsolved questions remain. The first question could be as follows: Which was the inorganic structure that allowed isolation and conservation of the first biomolecules in the existing reduced conditions of the primigenial era? Minerals have been postulated as the ones in charge of protecting theses biomolecules against the external environment. There are calcium, barium, or strontium silica-carbonates, called biomorphs, which we propose as being one of the first inorganic structures in which biomolecules were protected from the external medium. Biomorphs are structures with different biological morphologies that are not formed by cells, but by nanocrystals; some of their morphologies resemble the microfossils found in Precambrian cherts. Even though biomorphs are unknown structures in the geological registry, their similarity with some biological forms, including some Apex fossils, could suggest them as the first "inorganic scaffold" where the first biomolecules became concentrated, conserved, aligned, and duplicated to give rise to the pioneering cell. However, it has not been documented whether biomorphs could have been the primary structures that conserved biomolecules in the Precambrian era. To attain a better understanding on whether biomorphs could have been the inorganic scaffold that existed in the primigenial Earth, the aim of this contribution is to synthesize calcium, barium, and strontium biomorphs in the presence of genomic DNA from organisms of the five kingdoms in conditions emulating the atmosphere of the Precambrian era and that CO2 concentration in conditions emulating current atmospheric conditions. Our results showed, for the first time, the formation of the kerogen signal, which is a marker of biogenicity in fossils, in the biomorphs grown in the presence of DNA. We also found the DNA to be internalized into the structure of biomorphs.
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Affiliation(s)
- Mayra Cuéllar-Cruz
- Departamento
de Biología, División de Ciencias Naturales y Exactas,
Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta,
C.P. 36050, Guanajuato, Mexico
| | - Selene R. Islas
- Instituto
de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, México City, 04510 Mexico
| | - Norma Ramírez-Ramírez
- Departamento
de Biología, División de Ciencias Naturales y Exactas,
Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta,
C.P. 36050, Guanajuato, Mexico
| | - Mario Pedraza-Reyes
- Departamento
de Biología, División de Ciencias Naturales y Exactas,
Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta,
C.P. 36050, Guanajuato, Mexico
| | - Abel Moreno
- Instituto
de Química, Universidad Nacional
Autónoma de México, Av. Universidad 3000, Ciudad Universitaria, México City 04510. Mexico
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Song B, Modjewski LD, Kapust N, Mizrahi I, Martin WF. The origin and distribution of the main oxygen sensing mechanism across metazoans. Front Physiol 2022; 13:977391. [PMID: 36324306 PMCID: PMC9618697 DOI: 10.3389/fphys.2022.977391] [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: 06/24/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
Oxygen sensing mechanisms are essential for metazoans, their origin and evolution in the context of oxygen in Earth history are of interest. To trace the evolution of a main oxygen sensing mechanism among metazoans, the hypoxia induced factor, HIF, we investigated the phylogenetic distribution and phylogeny of 11 of its components across 566 eukaryote genomes. The HIF based oxygen sensing machinery in eukaryotes can be traced as far back as 800 million years (Ma) ago, likely to the last metazoan common ancestor (LMCA), and arose at a time when the atmospheric oxygen content corresponded roughly to the Pasteur point, or roughly 1% of present atmospheric level (PAL). By the time of the Cambrian explosion (541–485 Ma) as oxygen levels started to approach those of the modern atmosphere, the HIF system with its key components HIF1α, HIF1β, PHD1, PHD4, FIH and VHL was well established across metazoan lineages. HIF1α is more widely distributed and therefore may have evolved earlier than HIF2α and HIF3α, and HIF1β and is more widely distributed than HIF2β in invertebrates. PHD1, PHD4, FIH, and VHL appear in all 13 metazoan phyla. The O2 consuming enzymes of the pathway, PHDs and FIH, have a lower substrate affinity, Km, for O2 than terminal oxidases in the mitochondrial respiratory chain, in line with their function as an environmental signal to switch to anaerobic energy metabolic pathways. The ancient HIF system has been conserved and widespread during the period when metazoans evolved and diversified together with O2 during Earth history.
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Affiliation(s)
- Bing Song
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Luca David Modjewski
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Nils Kapust
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be’er-Sheva, Israel
| | - William F. Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- *Correspondence: William F. Martin,
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da Silva VS, Machado CR. Sex in protists: A new perspective on the reproduction mechanisms of trypanosomatids. Genet Mol Biol 2022; 45:e20220065. [PMID: 36218381 PMCID: PMC9552303 DOI: 10.1590/1678-4685-gmb-2022-0065] [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: 02/28/2022] [Accepted: 08/07/2022] [Indexed: 11/04/2022] Open
Abstract
The Protist kingdom individuals are the most ancestral representatives of eukaryotes. They have inhabited Earth since ancient times and are currently found in the most diverse environments presenting a great heterogeneity of life forms. The unicellular and multicellular algae, photosynthetic and heterotrophic organisms, as well as free-living and pathogenic protozoa represents the protist group. The evolution of sex is directly associated with the origin of eukaryotes being protists the earliest protagonists of sexual reproduction on earth. In eukaryotes, the recombination through genetic exchange is a ubiquitous mechanism that can be stimulated by DNA damage. Scientific evidences support the hypothesis that reactive oxygen species (ROS) induced DNA damage can promote sexual recombination in eukaryotes which might have been a decisive factor for the origin of sex. The fact that some recombination enzymes also participate in meiotic sex in modern eukaryotes reinforces the idea that sexual reproduction emerged as consequence of specific mechanisms to cope with mutations and alterations in genetic material. In this review we will discuss about origin of sex and different strategies of evolve sexual reproduction in some protists such that cause human diseases like malaria, toxoplasmosis, sleeping sickness, Chagas disease, and leishmaniasis.
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Affiliation(s)
- Verônica Santana da Silva
- Universidade Federal de Minas Gerais, Departamento de Genética,
Ecologia e Evolução, Belo Horizonte, MG, Brazil
| | - Carlos Renato Machado
- Universidade Federal de Minas Gerais, Departamento de Bioquímica e
Imunologia, Belo Horizonte, MG, Brazil
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Naz N, Liu D, Harandi BF, Kounaves SP. Microbial Growth in Martian Soil Simulants Under Terrestrial Conditions: Guiding the Search for Life on Mars. ASTROBIOLOGY 2022; 22:1210-1221. [PMID: 36000998 DOI: 10.1089/ast.2022.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The search for life elsewhere in the Universe goes together with the search for liquid water. Life as we know it requires water; however, it is possible for microbial life to exist under hyperarid conditions with a minimal amount of water. We report on the ability of two typical terrestrial bacteria (Escherichia coli B and Eucapsis sp) and two extremophiles (Gloeocapsa-20201027-1 sp and Planococcus halocryophilus) to grow and survive in three martian soil (regolith) simulants (Mohave Mars Simulant-1 [MMS-1] F, Mars Global Simulant-1 [MGS-1], and JSC Mars-1A [JSC]). Survival and growth were assessed over a 21-day period under terrestrial conditions and with water:soil (vol:wt) ratios that varied from 0.25:1 to 5:1. We found that Eucapsis and Gloeocapsa sp grew best in the simulants MMS and JSC, respectively, while P. halocryophilus growth rates were better in the JSC simulant. As expected, E. coli did not show significant growth. Our results indicate that these martian simulants and thus martian regolith, with minimal or no added nutrients or water, can support the growth of extremophiles such as P. halocryphilus and Gloeocapsa. Similar extremophiles on early Mars may have survived to the present in near-surface ecological niches analogous to those where these organisms exist on Earth.
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Affiliation(s)
- Neveda Naz
- Department of Chemistry, Tufts University, Medford, Massachusetts, USA
| | - Dongyu Liu
- Department of Chemistry, Tufts University, Medford, Massachusetts, USA
| | - Bijan F Harandi
- Department of Chemistry, Tufts University, Medford, Massachusetts, USA
| | - Samuel P Kounaves
- Department of Chemistry, Tufts University, Medford, Massachusetts, USA
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Moreira C, Matos A, Barreiro A, Gomes C, Vasconcelos V, Antunes A. Statistical Inferences Applying Non-Parametric Data on Cyanobacterial Investigations: Contributions to Water Quality and New Trends under Global Changes on Portuguese Freshwater Ecosystems. Toxins (Basel) 2022; 14:toxins14090638. [PMID: 36136576 PMCID: PMC9506200 DOI: 10.3390/toxins14090638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Cyanobacteria are a bloom-forming ancient group of photosynthetic prokaryotes. A rise in temperature is a major contributor to its massive proliferation, namely on freshwater ecosystems, with social and economic impacts. Thus, reliable and cost-effective tools can permit the fast surveillance and assessment of temperature effects on potentially toxic cyanobacteria distribution and impacts. The occurrence of three potentially toxic cyanobacteria species was assessed on seven sampling points across three sampling years. Moreover, the association between the occurrence of those cyanobacteria species with climate change events was addressed. Here, we combined molecular and statistical methods to study the impacts of temperature on the occurrence of three globally occurring cyanotoxin-producing cyanobacteria species—Microcystis aeruginosa (microcystins), Raphidiopsis raciborskii (cylindrospermopsins and saxitoxins) and Planktothrix agardhii (microcystins and saxitoxins). Samples were collected on seven European temperate freshwater systems located on the North and Centre regions of Portugal, across three distinct sampling years with distinct ranges of air temperature. Data support that M. aeruginosa is still a common inhabitant of Portuguese freshwater ecosystems and a new trend was found on R. raciborskii recent invasion and establishment on the colder north ecosystems of Portugal. Additionally, the highest frequency of detection of both cyanobacteria was associated with warmer years. P. agardhii also revealed a new trend, being reported for the first time on North and Centre Regions of Portugal, however with no statistical relation with air temperature, demonstrating a higher ecological fitness. Distinct profiles of the statistical analysis on the three tested cyanobacteria species contribute to deepen the studies on other species as well as of our analyzed species on a global level. This assessment may help to anticipate possible repercussions on water quality and public health due to most probable alterations on cyanotoxins profile given the ecological fitness established among air temperature and PCR detection of potentially toxic cyanobacteria.
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Affiliation(s)
- Cristiana Moreira
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
| | - Ana Matos
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Aldo Barreiro
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
| | - Cidália Gomes
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
| | - Vitor Vasconcelos
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: ; Tel.: +351-223401813
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Vujovic F, Hunter N, Farahani RM. Cellular self-organization: An overdrive in Cambrian diversity? Bioessays 2022; 44:e2200033. [PMID: 35900058 DOI: 10.1002/bies.202200033] [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: 02/05/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 11/10/2022]
Abstract
During the early Cambrian period metazoan life forms diverged at an accelerated rate to occupy multiple ecological niches on earth. A variety of explanations have been proposed to address this major evolutionary phenomenon termed the "Cambrian explosion." While most hypotheses address environmental, developmental, and ecological factors that facilitated evolutionary innovations, the biological basis for accelerated emergence of species diversity in the Cambrian period remains largely conjectural. Herein, we posit that morphogenesis by self-organization enables the uncoupling of genomic mutational landscape from phenotypic diversification. Evidence is provided for a two-tiered interpretation of genomic changes in metazoan animals wherein mutations not only impact upon function of individual cells, but also alter the self-organization outcome during developmental morphogenesis. We provide evidence that the morphological impacts of mutations on self-organization could remain repressed if associated with an unmet negative energetic cost. We posit that accelerated morphological diversification in transition to the Cambrian period has occurred by emergence of dormant (i.e., reserved) morphological novelties whose molecular underpinnings were seeded in the Precambrian period.
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Affiliation(s)
- Filip Vujovic
- IDR/Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Ramin M Farahani
- IDR/Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
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Competitive interaction of Mn(II) and Fe(II) cations with the high-affinity Mn-binding site of the photosystem II: evolutionary aspect. ORIGINS LIFE EVOL B 2022; 52:113-128. [PMID: 35796895 DOI: 10.1007/s11084-022-09625-8] [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: 04/24/2022] [Accepted: 06/16/2022] [Indexed: 10/17/2022]
Abstract
The evolutionary origin of the oxygen-evolving complex (OEC) in the photosystem II (PSII) is still unclear, as is the nature of electron source for the photosystem before the OEC had appeared. Johnson et al. (in PNAS 110:11238, 2013) speculated that Mn(II) cations were the source of electrons for transitional photosystems. However, Archean oceans also contained Fe(II) cations at concentrations comparable or higher than that of Mn(II). Fe(II) cations can bind to the high-affinity (НА) Mn-binding site in the OEC (Semin et al. in Biochemistry 41:5854, 2002). Now we have investigated the competitive interaction of Mn(II) and Fe(II) cations with the HA site in the Mn-depleted PSII membranes (PSII[-Mn]). Fe cations, oxidized under illumination, bind strongly to the HA site and, thus, prevent the interaction of Mn(II) with this site. If the Mn(II) and Fe(II) cations, at relatively equal concentration, are simultaneously present in the buffer, together with PSII(-Mn) membranes, there is competition between these two cations for the binding site, which manifests itself in partial inhibition of the Mn(II) oxidation and the blocking of the HA site by Fe(II) cations. If the concentration of Fe(II) cations is several times higher than the concentration of Mn(II), the HA site is completely blocked and the oxidation of Mn(II) cations is inhibited; under saturating light, the effectiveness of this inhibitory effect increases. This may be due to the generation of H2O2 on the acceptor side of the photosystem, which significantly accelerates the rate of the turnover reaction of Mn(II) on the HA site.
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The Evolution of Nitric Oxide Function: From Reactivity in the Prebiotic Earth to Examples of Biological Roles and Therapeutic Applications. Antioxidants (Basel) 2022; 11:antiox11071222. [PMID: 35883712 PMCID: PMC9311577 DOI: 10.3390/antiox11071222] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 12/01/2022] Open
Abstract
Nitric oxide was once considered to be of marginal interest to the biological sciences and medicine; however, there is now wide recognition, but not yet a comprehensive understanding, of its functions and effects. NO is a reactive, toxic free radical with numerous biological targets, especially metal ions. However, NO and its reaction products also play key roles as reductant and oxidant in biological redox processes, in signal transduction, immunity and infection, as well as other roles. Consequently, it can be sensed, metabolized and modified in biological systems. Here, we present a brief overview of the chemistry and biology of NO—in particular, its origins in geological time and in contemporary biology, its toxic consequences and its critical biological functions. Given that NO, with its intrinsic reactivity, appeared in the early Earth’s atmosphere before the evolution of complex lifeforms, we speculate that the potential for toxicity preceded biological function. To examine this hypothesis, we consider the nature of non-biological and biological targets of NO, the evolution of biological mechanisms for NO detoxification, and how living organisms generate this multifunctional gas.
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41
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Genome Sequence and Characterization of a Xanthorhodopsin-Containing, Aerobic Anoxygenic Phototrophic Rhodobacter Species, Isolated from Mesophilic Conditions at Yellowstone National Park. Microorganisms 2022; 10:microorganisms10061169. [PMID: 35744687 PMCID: PMC9231093 DOI: 10.3390/microorganisms10061169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 11/17/2022] Open
Abstract
The genus Rhodobacter consists of purple nonsulfur photosynthetic alphaproteobacteria known for their diverse metabolic capabilities. Here, we report the genome sequence and initial characterization of a novel Rhodobacter species, strain M37P, isolated from Mushroom hot spring runoff in Yellowstone National Park at 37 °C. Genome-based analyses and initial growth characteristics helped to define the differentiating characteristics of this species and identified it as an aerobic anoxygenic phototroph (AAP). This is the first AAP identified in the genus Rhodobacter. Strain M37P has a pinkish-red pigmentation that is present under aerobic dark conditions but disappears under light incubation. Whole genome-based analysis and average nucleotide identity (ANI) comparison indicate that strain M37P belongs to a specific clade of recently identified species that are genetically and physiologically unique from other representative Rhodobacter species. The genome encodes a unique xanthorhodopsin, not found in any other Rhodobacter species, which may be responsible for the pinkish-red pigmentation. These analyses indicates that strain M37P is a unique species that is well-adapted to optimized growth in the Yellowstone hot spring runoff, for which we propose the name Rhodobacter calidifons sp. nov.
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Ahmerkamp S, Jalaluddin FM, Cui Y, Brumley DR, Pacherres CO, Berg JS, Stocker R, Kuypers MM, Koren K, Behrendt L. Simultaneous visualization of flow fields and oxygen concentrations to unravel transport and metabolic processes in biological systems. CELL REPORTS METHODS 2022; 2:100216. [PMID: 35637907 PMCID: PMC9142687 DOI: 10.1016/j.crmeth.2022.100216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/05/2022] [Accepted: 04/20/2022] [Indexed: 10/26/2022]
Abstract
From individual cells to whole organisms, O2 transport unfolds across micrometer- to millimeter-length scales and can change within milliseconds in response to fluid flows and organismal behavior. The spatiotemporal complexity of these processes makes the accurate assessment of O2 dynamics via currently available methods difficult or unreliable. Here, we present "sensPIV," a method to simultaneously measure O2 concentrations and flow fields. By tracking O2-sensitive microparticles in flow using imaging technologies that allow for instantaneous referencing, we measured O2 transport within (1) microfluidic devices, (2) sinking model aggregates, and (3) complex colony-forming corals. Through the use of sensPIV, we find that corals use ciliary movement to link zones of photosynthetic O2 production to zones of O2 consumption. SensPIV can potentially be extendable to study flow-organism interactions across many life-science and engineering applications.
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Affiliation(s)
- Soeren Ahmerkamp
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | | | - Yuan Cui
- Science for Life Laboratory, Department of Organismal Biology, Uppsala University, Norbyvägen 18A, SE-752 36 Uppsala, Sweden
| | - Douglas R. Brumley
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Cesar O. Pacherres
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Jasmine S. Berg
- Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Klaus Koren
- Aarhus University Centre for Water Technology, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | - Lars Behrendt
- Science for Life Laboratory, Department of Organismal Biology, Uppsala University, Norbyvägen 18A, SE-752 36 Uppsala, Sweden
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Guéguen N, Maréchal E. Origin of cyanobacterial thylakoids via a non-vesicular glycolipid phase transition and their impact on the Great Oxygenation Event. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2721-2734. [PMID: 35560194 DOI: 10.1093/jxb/erab429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/16/2021] [Indexed: 06/15/2023]
Abstract
The appearance of oxygenic photosynthesis in cyanobacteria is a major event in evolution. It had an irreversible impact on the Earth, promoting the Great Oxygenation Event (GOE) ~2.4 billion years ago. Ancient cyanobacteria predating the GOE were Gloeobacter-type cells lacking thylakoids, which hosted photosystems in their cytoplasmic membrane. The driver of the GOE was proposed to be the transition from unicellular to filamentous cyanobacteria. However, the appearance of thylakoids expanded the photosynthetic surface to such an extent that it introduced a multiplier effect, which would be more coherent with an impact on the atmosphere. Primitive thylakoids self-organize as concentric parietal uninterrupted multilayers. There is no robust evidence for an origin of thylakoids via a vesicular-based scenario. This review reports studies supporting that hexagonal II-forming glucolipids and galactolipids at the periphery of the cytosolic membrane could be turned, within nanoseconds and without any external source of energy, into membrane multilayers. Comparison of lipid biosynthetic pathways shows that ancient cyanobacteria contained only one anionic lamellar-forming lipid, phosphatidylglycerol. The acquisition of sulfoquinovosyldiacylglycerol biosynthesis correlates with thylakoid emergence, possibly enabling sufficient provision of anionic lipids to trigger a hexagonal II-to-lamellar phase transition. With this non-vesicular lipid-phase transition, a framework is also available to re-examine the role of companion proteins in thylakoid biogenesis.
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Affiliation(s)
- Nolwenn Guéguen
- Laboratoire de Physiologie Cellulaire et Végétale; INRAE, CNRS, CEA, Université Grenoble Alpes; IRIG; CEA Grenoble, 17 rue des Martyrs, 38000 Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale; INRAE, CNRS, CEA, Université Grenoble Alpes; IRIG; CEA Grenoble, 17 rue des Martyrs, 38000 Grenoble, France
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Vinyard D, Yocum CF, Bricker TM. Preface: special issues on photosystem II. PHOTOSYNTHESIS RESEARCH 2022; 152:87-90. [PMID: 35761114 DOI: 10.1007/s11120-022-00930-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- David Vinyard
- Department of Biological Sciences, Biochemistry and Molecular Biology Section, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Charles F Yocum
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Terry M Bricker
- Department of Biological Sciences, Biochemistry and Molecular Biology Section, Louisiana State University, Baton Rouge, LA, 70803, USA.
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Soares F, Trovão J, Ahn AC, Wilmotte A, Cardoso SM, Tiago I, Portugal A. Introducing Petrachlorosaceae fam. nov., Petrachloros gen. nov. and Petrachloros mirabilis sp. nov. (Synechococcales, Cyanobacteria) Isolated from a Portuguese UNESCO monument. JOURNAL OF PHYCOLOGY 2022; 58:219-233. [PMID: 35133645 DOI: 10.1111/jpy.13241] [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: 09/23/2021] [Revised: 12/03/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
The Synechococcales is a large cyanobacterial order comprising both unicellular and filamentous forms, with parietal thylakoid arrangement. Previously, this order has been the subject of taxonomic revisions with new families being erected. During studies of the phototrophic communities on the limestone walls of the Old Cathedral of Coimbra (UNESCO monument), a coccoid Aphanocapsa-like cyanobacterium was isolated. It was characterized using a polyphasic approach, based on morphology, 16S rRNA phylogenetic and phylogenomic analyses, internal transcribed spacer (ITS) secondary structure, and ecology. The 16S rRNA phylogenetic analyses showed that this strain is placed in a separate and highly supported family-level clade, as part of a large group comprising the families Prochlorococcaceae and Prochlorotrichaceae, with Lagosinema as the closest (although quite distant) taxon. Additionally, the phylogenomic analysis also placed this strain in a separate lineage, situated distantly apart from the family Thermosynechococcaceae, but with strains assigned to Acaryochloris marina MBIC 11017 and Aphanocapsa montana BDHKU210001 as the closest taxa. Based on these data, as well as on the results from the secondary ITS structure, morphology, and ecology, we here propose the establishment of Petrachlorosaceae fam. nov., along with the description of Petrachloros gen. nov. and Petrachloros mirabilis sp. nov. We also address additional considerations regarding some cyanobacterial taxa within the order Synechococcales, which we believe deserve further revisions.
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Affiliation(s)
- Fabiana Soares
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, 3000-456, Portugal
| | - João Trovão
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, 3000-456, Portugal
| | - Anne-Catherine Ahn
- BCCM/ULC Culture Collection, InBios-Centre for Protein Engineering, University of Liège, Liège, B-4000, Belgium
| | - Annick Wilmotte
- BCCM/ULC Culture Collection, InBios-Centre for Protein Engineering, University of Liège, Liège, B-4000, Belgium
| | - Susana M Cardoso
- QOPNA &, LAQV-REQUIMTE, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Igor Tiago
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, 3000-456, Portugal
| | - António Portugal
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, 3000-456, Portugal
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46
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Bulk and grain-scale minor sulfur isotope data reveal complexities in the dynamics of Earth's oxygenation. Proc Natl Acad Sci U S A 2022; 119:e2025606119. [PMID: 35312361 PMCID: PMC9060445 DOI: 10.1073/pnas.2025606119] [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] [Indexed: 11/18/2022] Open
Abstract
The permanent disappearance of mass-independent sulfur isotope fractionation (S-MIF) from the sedimentary record has become a widely accepted proxy for atmospheric oxygenation. This framework, however, neglects inheritance from oxidative weathering of pre-existing S-MIF–bearing sedimentary sulfide minerals (i.e., crustal memory), which has recently been invoked to explain apparent discrepancies within the sulfur isotope record. Herein, we demonstrate that such a crustal memory effect does not confound the Carletonville S-isotope record; rather, the pronounced Δ33S values identified within the Rooihoogte Formation represent the youngest known unequivocal oxygen-free photochemical products. Previously observed 33S-enrichments within the succeeding Timeball Hill Formation, however, contrasts with our record, revealing kilometer-scale heterogeneities that highlight significant uncertainties in our understanding of the dynamics of Earth’s oxygenation. The disappearance of mass-independent sulfur isotope fractionation (S-MIF) within the c. 2.3-billion-year-old (Ga) Rooihoogte Formation has been heralded as a chemostratigraphic marker of permanent atmospheric oxygenation. Reports of younger S-MIF, however, question this narrative, leaving significant uncertainties surrounding the timing, tempo, and trajectory of Earth’s oxygenation. Leveraging a new bulk quadruple S-isotope record, we return to the South African Transvaal Basin in search of support for supposed oscillations in atmospheric oxygen beyond 2.3 Ga. Here, as expected, within the Rooihoogte Formation, our data capture a collapse in Δ3×S values and a shift from Archean-like Δ36S/Δ33S slopes to their mass-dependent counterparts. Importantly, the interrogation of a Δ33S-exotic grain reveals extreme spatial variability, whereby atypically large Δ33S values are separated from more typical Paleoproterozoic values by a subtle grain-housed siderophile-enriched band. This isotopic juxtaposition signals the coexistence of two sulfur pools that were able to escape diagenetic homogenization. These large Δ33S values require an active photochemical sulfur source, fingerprinting atmospheric S-MIF production after its documented cessation elsewhere at ∼2.4 Ga. By contrast, the Δ33S monotony observed in overlying Timeball Hill Formation, with muted Δ33S values (<0.3‰) and predominantly mass-dependent Δ36S/Δ33S systematics, remains in stark contrast to recent reports of pronounced S-MIF within proximal formational equivalents. If reflective of atmospheric processes, these observed kilometer-scale discrepancies disclose heterogenous S-MIF delivery to the Transvaal Basin and/or poorly resolved fleeting returns to S-MIF production. Rigorous bulk and grain-scale analytical campaigns remain paramount to refine our understanding of Earth’s oxygenation and substantiate claims of post-2.3 Ga oscillations in atmospheric oxygen.
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Berg JS, Ahmerkamp S, Pjevac P, Hausmann B, Milucka J, Kuypers MMM. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6517451. [PMID: 35094062 PMCID: PMC9075580 DOI: 10.1093/femsre/fuac006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 12/01/2022] Open
Abstract
Oxygen (O2) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O2 down to nanomolar concentrations. The respiration of O2 at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O2 sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O2 at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here, we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.
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Affiliation(s)
- Jasmine S Berg
- Corrresponding author: Géopolis, Quartier Unil-Mouline, Université de Lausanne, 1015 Lausanne, Switzerland. E-mail:
| | - Soeren Ahmerkamp
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna 1090, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1090, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna 1090, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria
| | - Jana Milucka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
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Cooke GJ, Marsh DR, Walsh C, Black B, Lamarque JF. A revised lower estimate of ozone columns during Earth's oxygenated history. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211165. [PMID: 35070343 PMCID: PMC8728182 DOI: 10.1098/rsos.211165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/25/2021] [Indexed: 05/17/2023]
Abstract
The history of molecular oxygen (O2) in Earth's atmosphere is still debated; however, geological evidence supports at least two major episodes where O2 increased by an order of magnitude or more: the Great Oxidation Event (GOE) and the Neoproterozoic Oxidation Event. O2 concentrations have likely fluctuated (between 10-3 and 1.5 times the present atmospheric level) since the GOE ∼2.4 Gyr ago, resulting in a time-varying ozone (O3) layer. Using a three-dimensional chemistry-climate model, we simulate changes in O3 in Earth's atmosphere since the GOE and consider the implications for surface habitability, and glaciation during the Mesoproterozoic. We find lower O3 columns (reduced by up to 4.68 times for a given O2 level) compared to previous work; hence, higher fluxes of biologically harmful UV radiation would have reached the surface. Reduced O3 leads to enhanced tropospheric production of the hydroxyl radical (OH) which then substantially reduces the lifetime of methane (CH4). We show that a CH4 supported greenhouse effect during the Mesoproterozoic is highly unlikely. The reduced O3 columns we simulate have important implications for astrobiological and terrestrial habitability, demonstrating the relevance of three-dimensional chemistry-climate simulations when assessing paleoclimates and the habitability of faraway worlds.
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Affiliation(s)
- G. J. Cooke
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - D. R. Marsh
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
- National Center for Atmospheric Research, Boulder, CO 80301, USA
| | - C. Walsh
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - B. Black
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ, USA
- Department of Earth and Atmospheric Sciences, CUNY City College, New York, NY, USA
| | - J.-F. Lamarque
- National Center for Atmospheric Research, Boulder, CO 80301, USA
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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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50
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Decreasing extents of Archean serpentinization contributed to the rise of an oxidized atmosphere. Nat Commun 2021; 12:7341. [PMID: 34930924 PMCID: PMC8688491 DOI: 10.1038/s41467-021-27589-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/03/2021] [Indexed: 11/09/2022] Open
Abstract
At present, molecular hydrogen (H2) produced through Fe(II) oxidation during serpentinization of ultramafic rocks represents a small fraction of the global sink for O2 due to limited exposures of ultramafic rocks. In contrast, ultramafic rocks such as komatiites were much more common in the Early Earth and H2 production via serpentinization was a likely factor in maintaining an O2-free atmosphere throughout most of the Archean. Using thermodynamic simulations, this work quantifies the global O2 consumption attributed to serpentinization during the past 3.5 billion years. Results show that H2 generation is strongly dependent on rock compositions where serpentinization of more magnesian lithologies generated substantially higher amounts of H2. Consumption of >2 Tmole O2 yr-1 via low-temperature serpentinization of Archean continents and seafloor is possible. This O2 sink diminished greatly towards the end of the Archean as ultramafic rocks became less common and helped set the stage for the Great Oxidation Event.
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