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Khan IU, Saqib M, Amin A, Manzoor S, Ahmed I, Liu RR, Jiao JY, Zhi XY, Li WJ. Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet Hot Springs, China. Antonie Van Leeuwenhoek 2024; 117:103. [PMID: 39042225 DOI: 10.1007/s10482-024-02001-8] [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: 05/14/2024] [Accepted: 07/09/2024] [Indexed: 07/24/2024]
Abstract
Genus Thermus is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus Thermus in geographically different thermal springs. Sixteen Thermus strains were isolated and sequenced from hot springs, Qucai hot springs in Tibet and Tengchong hot springs in Yunnan, China. 16S rRNA gene based phylogeny and phylogenomic analyses based on concatenated set of 971 Orthologous Protein Families (supermatrix and gene content methods) revealed a mixed distribution of the Thermus strains. Whole genome based phylogenetic analysis showed, all 16 Thermus strains belong to five species; Thermus oshimai (YIM QC-2-109, YIM 1640, YIM 1627, 77359, 77923, 77838), Thermus antranikianii (YIM 73052, 77412, 77311, 71206), Thermus brokianus (YIM 73518, 71318, 72351), Thermus hydrothermalis (YIM 730264 and 77927) and one potential novel species 77420 forming clade with Thermus thalpophilus SYSU G00506T. Although the genomes of different strains of Thermus of same species were highly similar in their metabolic pathways, but subtle differences were found. CRISPR loci were detected through genome-wide screening, which showed that Thermus isolates from two different thermal locations had well developed defense system against viruses and adopt similar strategy for survival. Additionally, comparative genome analysis screened competence loci across all the Thermus genomes which could be helpful to acquire DNA from environment. In the present study it was found that Thermus isolates use two mechanism of incomplete denitrification pathway, some Thermus strains produces nitric oxide while others nitrious oxide (dinitrogen oxide), which show the heterotrophic lifestyle of Thermus genus. All isolated organisms encoded complete pathways for glycolysis, tricarboxylic acid and pentose phosphate. Calvin Benson Bassham cycle genes were identified in genomes of T. oshimai and T. antranikianii strains, while genomes of all T. brokianus strains and organism 77420 were lacking. Arsenic, cadmium and cobalt-zinc-cadmium resistant genes were detected in genomes of all sequenced Thermus strains. Strains 77,420, 77,311, 73,518, 77,412 and 72,351 genomes were found harboring genes for siderophores production. Sox gene clusters were identified in all sequenced genomes, except strain YIM 730264, suggesting a mode of chemolithotrophy. Through the comparative genomic analysis, we also identified 77420 as the genome type species and its validity as novel organism was confirmed by whole genome sequences comparison. Although isolate 77420 had 99.0% 16S rRNA gene sequence similarity with T. thalpophilus SYSU G00506T but based on ANI 95.86% (Jspecies) and digital DDH 68.80% (GGDC) values differentiate it as a potential novel species. Similarly, in the phylogenomic tree, the novel isolate 77,420 forming a separate branch with their closest reference type strain T. thalpophilus SYSU G00506T.
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Affiliation(s)
- Inam Ullah Khan
- Faculty of Veterinary and Animal Sciences, Institute of Microbiology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, 29050, Pakistan
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Muhammad Saqib
- Department of Zoology, Gomal University, Tank Campus, 29050, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Arshia Amin
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, 45500, Pakistan
| | - Sadia Manzoor
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Iftikhar Ahmed
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Rui-Rui Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Yang Zhi
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China.
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Cohen AB, Christensen LN, Weber F, Yagudaeva M, Lo E, Henkes GA, McCormick ML, Taylor GT. Preserved particulate organic carbon is likely derived from the subsurface sulfidic photic zone of the Proterozoic Ocean: evidence from a modern, oxygen-deficient lake. GEOBIOLOGY 2024; 22:e12593. [PMID: 38476006 DOI: 10.1111/gbi.12593] [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: 08/14/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024]
Abstract
Biological processes in the Proterozoic Ocean are often inferred from modern oxygen-deficient environments (MODEs) or from stable isotopes in preserved sediment. To date, few MODE studies have simultaneously quantified carbon fixation genes and attendant stable isotopic signatures. Consequently, how carbon isotope patterns reflect these pathways has not been thoroughly vetted. Addressing this, we profiled planktonic productivity and quantified carbon fixation pathway genes and associated organic carbon isotope values (δ13 CPOC ) of size-fractionated (0.2-2.7 and >2.7 μm) particulate matter from meromictic Fayetteville Green Lake, NY, USA. The high-O2 Calvin-Benson-Bassham (CBB) gene (cbbL) was most abundant in the <2.7 μm size fraction in shallow oxic and deep hypoxic waters, corresponding with cyanobacterial and eukaryote algal populations. The low-O2 CBB gene (cbbM) was most abundant near the lower oxycline boundary in the larger size fraction, coincident with purple sulfur bacteria populations. The reverse citric acid cycle gene (aclB) was equally abundant in both size fractions in the deepest photic zone, coinciding with green sulfur bacteria populations. Methane coenzyme reductase A (mcrA), of anaerobic methane cyclers, was most abundant at the lower oxycline boundary in both size fractions, coinciding with Methanoregula populations. δ13 CPOC values overlapped with the high-O2 CBB fixation range except for two negative excursions near the lower oxycline boundary, likely reflecting assimilation of isotopically-depleted groundwater-derived carbon by autotrophs and sulfate-reducers. Throughout aphotic waters, δ13 CPOC values of the large size fraction became 13 C-enriched, likely reflecting abundant purple sulfur bacterial aggregates. Eukaryote algae- or cyanobacteria-like isotopic signatures corresponded with increases in cbbL, cbbM, and aclB, and enrichment of exopolymer-rich prokaryotic photoautotrophs aggregates. Results suggest that δ13 CPOC values of preserved sediments from areas of the Proterozoic Ocean with sulfidic photic zones may reflect a mixture of alternate carbon-fixing populations exported from the deep photic zone, challenging the paradigm that sedimentary stable carbon isotope values predominantly reflect oxygenic photosynthesis from surface waters.
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Affiliation(s)
- Ashley B Cohen
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | | | - Felix Weber
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Milana Yagudaeva
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Evan Lo
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Gregory A Henkes
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
- Department of Geosciences, Stony Brook University, Stony Brook, New York, USA
| | | | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
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Ubierna N, Holloway-Phillips MM, Wingate L, Ogée J, Busch FA, Farquhar GD. Using Carbon Stable Isotopes to Study C 3 and C 4 Photosynthesis: Models and Calculations. Methods Mol Biol 2024; 2790:163-211. [PMID: 38649572 DOI: 10.1007/978-1-0716-3790-6_10] [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: 04/25/2024]
Abstract
Stable carbon isotopes are a powerful tool to study photosynthesis. Initial applications consisted of determining isotope ratios of plant biomass using mass spectrometry. Subsequently, theoretical models relating C isotope values to gas exchange characteristics were introduced and tested against instantaneous online measurements of 13C photosynthetic discrimination. Beginning in the twenty-first century, laser absorption spectroscopes with sufficient precision for determining isotope mixing ratios became commercially available. This has allowed collection of large data sets at lower cost and with unprecedented temporal resolution. More data and accompanying knowledge have permitted refinement of 13C discrimination model equations, but often at the expense of increased model complexity and difficult parametrization. This chapter describes instantaneous online measurements of 13C photosynthetic discrimination, provides recommendations for experimental setup, and presents a thorough compilation of equations available to researchers. We update our previous 2018 version of this chapter by including recently improved descriptions of (photo)respiratory processes and associated fractionations. We discuss the capabilities and limitations of the diverse 13C discrimination model equations and provide guidance for selecting the model complexity needed for different applications.
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Affiliation(s)
- Nerea Ubierna
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Unité Mixte de Recherche (UMR)1391 ISPA, Villenave D'Ornon, France
| | - Meisha-Marika Holloway-Phillips
- Research Unit of Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmendsorf, Switzerland
| | - Lisa Wingate
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Unité Mixte de Recherche (UMR)1391 ISPA, Villenave D'Ornon, France
| | - Jérôme Ogée
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Unité Mixte de Recherche (UMR)1391 ISPA, Villenave D'Ornon, France
| | - Florian A Busch
- School of Biosciences and The Birmingham Institute of Forest Research, University of Birmingham, Birmingham, UK
| | - Graham D Farquhar
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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Glidden A, Seager S, Petkowski JJ, Ono S. Can Isotopologues Be Used as Biosignature Gases in Exoplanet Atmospheres? Life (Basel) 2023; 13:2325. [PMID: 38137926 PMCID: PMC10744769 DOI: 10.3390/life13122325] [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: 06/15/2023] [Revised: 10/25/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023] Open
Abstract
Isotopologue ratios are anticipated to be one of the most promising signs of life that can be observed remotely. On Earth, carbon isotopes have been used for decades as evidence of modern and early metabolic processes. In fact, carbon isotopes may be the oldest evidence for life on Earth, though there are alternative geological processes that can lead to the same magnitude of fractionation. However, using isotopologues as biosignature gases in exoplanet atmospheres presents several challenges. Most significantly, we will only have limited knowledge of the underlying abiotic carbon reservoir of an exoplanet. Atmospheric carbon isotope ratios will thus have to be compared against the local interstellar medium or, better yet, their host star. A further substantial complication is the limited precision of remote atmospheric measurements using spectroscopy. The various metabolic processes that cause isotope fractionation cause less fractionation than anticipated measurement precision (biological fractionation is typically 2 to 7%). While this level of precision is easily reachable in the laboratory or with special in situ instruments, it is out of reach of current telescope technology to measure isotope ratios for terrestrial exoplanet atmospheres. Thus, gas isotopologues are poor biosignatures for exoplanets given our current and foreseeable technological limitations.
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Affiliation(s)
- Ana Glidden
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Kavli Institute for Astrophysics and Space Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sara Seager
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Kavli Institute for Astrophysics and Space Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Janusz J. Petkowski
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- JJ Scientific, Mazowieckie, 02-792 Warsaw, Poland
- Faculty of Environmental Engineering, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Shuhei Ono
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Wang RZ, Liu AK, Banda DM, Fischer WW, Shih PM. A Bacterial Form I' Rubisco Has a Smaller Carbon Isotope Fractionation than Its Form I Counterpart. Biomolecules 2023; 13:596. [PMID: 37189344 PMCID: PMC10135865 DOI: 10.3390/biom13040596] [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: 02/15/2023] [Revised: 03/14/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Form I rubiscos evolved in Cyanobacteria ≥ 2.5 billion years ago and are enzymatically unique due to the presence of small subunits (RbcS) capping both ends of an octameric large subunit (RbcL) rubisco assembly to form a hexadecameric (L8S8) holoenzyme. Although RbcS was previously thought to be integral to Form I rubisco stability, the recent discovery of a closely related sister clade of octameric rubiscos (Form I'; L8) demonstrates that the L8 complex can assemble without small subunits (Banda et al. 2020). Rubisco also displays a kinetic isotope effect (KIE) where the 3PG product is depleted in 13C relative to 12C. In Cyanobacteria, only two Form I KIE measurements exist, making interpretation of bacterial carbon isotope data difficult. To aid comparison, we measured in vitro the KIEs of Form I' (Candidatus Promineofilum breve) and Form I (Synechococcus elongatus PCC 6301) rubiscos and found the KIE to be smaller in the L8 rubisco (16.25 ± 1.36‱ vs. 22.42 ± 2.37‱, respectively). Therefore, while small subunits may not be necessary for protein stability, they may affect the KIE. Our findings may provide insight into the function of RbcS and allow more refined interpretation of environmental carbon isotope data.
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Affiliation(s)
- Renée Z. Wang
- Division of Geological and Planetary Sciences, Caltech, Pasadena, CA 91125, USA
| | - Albert K. Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Douglas M. Banda
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Woodward W. Fischer
- Division of Geological and Planetary Sciences, Caltech, Pasadena, CA 91125, USA
| | - Patrick M. Shih
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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Chimeric inheritance and crown-group acquisitions of carbon fixation genes within Chlorobiales: Origins of autotrophy in Chlorobiales and implication for geological biomarkers. PLoS One 2022; 17:e0275539. [PMID: 36227849 PMCID: PMC9560492 DOI: 10.1371/journal.pone.0275539] [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: 03/21/2022] [Accepted: 09/16/2022] [Indexed: 11/21/2022] Open
Abstract
The geological record of microbial metabolisms and ecologies primarily consists of stable isotope fractionations and the diagenetic products of biogenic lipids. Carotenoid lipid biomarkers are particularly useful proxies for reconstructing this record, providing information on microbial phototroph primary productivity, redox couples, and oxygenation. The biomarkers okenane, chlorobactane, and isorenieratene are generally considered to be evidence of anoxygenic phototrophs, and provide a record that extends to 1.64 Ga. The utility of the carotenoid biomarker record may be enhanced by examining the carbon isotopic ratios in these products, which are diagnostic for specific pathways of biological carbon fixation found today within different microbial groups. However, this joint inference assumes that microbes have conserved these pathways across the duration of the preserved biomarker record. Testing this hypothesis, we performed phylogenetic analyses of the enzymes constituting the reductive tricarboxylic acid (rTCA) cycle in Chlorobiales, the group of anoxygenic phototrophic bacteria usually implicated in the deposition of chlorobactane and isorenieretane. We find phylogenetically incongruent patterns of inheritance across all enzymes, indicative of horizontal gene transfers to both stem and crown Chlorobiales from multiple potential donor lineages. This indicates that a complete rTCA cycle was independently acquired at least twice within Chlorobiales and was not present in the last common ancestor. When combined with recent molecular clock analyses, these results predict that the Mesoproterzoic lipid biomarker record diagnostic for Chlorobiales should not preserve isotopic fractionations indicative of a full rTCA cycle. Furthermore, we conclude that coupling isotopic and biomarker records is insufficient for reliably reconstructing microbial paleoecologies in the absence of a complementary and consistent phylogenomic narrative.
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Rangan P, Wankhede DP, Subramani R, Chinnusamy V, Malik SK, Baig MJ, Singh K, Henry R. Evolution of an intermediate C 4 photosynthesis in the non-foliar tissues of the Poaceae. PHOTOSYNTHESIS RESEARCH 2022; 153:125-134. [PMID: 35648247 DOI: 10.1007/s11120-022-00926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Carbon concentrating mechanisms (CCMs) in plants are abaptive features that have evolved to sustain plant growth in unfavorable environments, especially at low atmospheric carbon levels and high temperatures. Uptake of CO2 and its storage in the aerenchyma tissues of Lycopsids and diurnal acidity fluctuation in aquatic plants during the Palaeozoic era (ca. 300 Ma.) would represent the earliest evolution of a CCM. The CCM parts of the dark reactions of photosynthesis have evolved many times, while the light reactions are conserved across plant lineages. A C4 type CCM, leaf C4 photosynthesis is evolved in the PACMAD clade of the Poaceae family. The evolution of C4 photosynthesis from C3 photosynthesis was an abaptation. Photosynthesis in reproductive tissues of sorghum and maize (PACMAD clade) has been shown to be of a weaker C4 type (high CO2 compensation point, low carbon isotope discrimination, and lack of Rubisco compartmentalization, when compared to the normal C4 types) than that in the leaves (normal C4 type). However, this does not fit well with the character polarity concept from an evolutionary perspective. In a recent model proposed for CCM evolution, the development of a rudimentary CCM prior to the evolution of a more efficient CCM (features contrasting to a weaker C4 type, leading to greater biomass production rate) has been suggested. An intermediate crassulacean acid metabolism (CAM) type of CCM (rudimentary) was reported in the genera, Brassia, Coryanthes, Eriopsis, Peristeria, of the orchids (well-known group of plants that display the CAM pathway). Similarly, we propose here the evolution of a rudimentary CCM (C4-like type pathway) in the non-foliar tissues of the Poaceae, prior to the evolution of the C4 pathway as identified in the leaves of the C4 species of the PACMAD clade.
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Affiliation(s)
- Parimalan Rangan
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.
| | | | - Rajkumar Subramani
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | | | - Surendra K Malik
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | | | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
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Elling FJ, Evans TW, Nathan V, Hemingway JD, Kharbush JJ, Bayer B, Spieck E, Husain F, Summons RE, Pearson A. Marine and terrestrial nitrifying bacteria are sources of diverse bacteriohopanepolyols. GEOBIOLOGY 2022; 20:399-420. [PMID: 35060273 DOI: 10.1111/gbi.12484] [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: 03/14/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Hopanoid lipids, bacteriohopanols and bacteriohopanepolyols, are membrane components exclusive to bacteria. Together with their diagenetic derivatives, they are commonly used as biomarkers for specific bacterial groups or biogeochemical processes in the geologic record. However, the sources of hopanoids to marine and freshwater environments remain inadequately constrained. Recent marker gene studies suggest a widespread potential for hopanoid biosynthesis in marine bacterioplankton, including nitrifying (i.e., ammonia- and nitrite-oxidizing) bacteria. To explore their hopanoid biosynthetic capacities, we studied the distribution of hopanoid biosynthetic genes in the genomes of cultivated and uncultivated ammonia-oxidizing (AOB), nitrite-oxidizing (NOB), and complete ammonia-oxidizing (comammox) bacteria, finding that biosynthesis of diverse hopanoids is common among seven of the nine presently cultivated clades of nitrifying bacteria. Hopanoid biosynthesis genes are also conserved among the diverse lineages of bacterial nitrifiers detected in environmental metagenomes. We selected seven representative NOB isolated from marine, freshwater, and engineered environments for phenotypic characterization. All tested NOB produced diverse types of hopanoids, with some NOB producing primarily diploptene and others producing primarily bacteriohopanepolyols. Relative and absolute abundances of hopanoids were distinct among the cultures and dependent on growth conditions, such as oxygen and nitrite limitation. Several novel nitrogen-containing bacteriohopanepolyols were tentatively identified, of which the so called BHP-743.6 was present in all NOB. Distinct carbon isotopic signatures of biomass, hopanoids, and fatty acids in four tested NOB suggest operation of the reverse tricarboxylic acid cycle in Nitrospira spp. and Nitrospina gracilis and of the Calvin-Benson-Bassham cycle for carbon fixation in Nitrobacter vulgaris and Nitrococcus mobilis. We suggest that the contribution of hopanoids by NOB to environmental samples could be estimated by their carbon isotopic compositions. The ubiquity of nitrifying bacteria in the ocean today and the antiquity of this metabolic process suggest the potential for significant contributions to the geologic record of hopanoids.
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Affiliation(s)
- Felix J Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas W Evans
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Vinitra Nathan
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Jordon D Hemingway
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Jenan J Kharbush
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, Michigan, USA
| | - Barbara Bayer
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - Eva Spieck
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Fatima Husain
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Roger E Summons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
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9
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Kędzior M, Garcia AK, Li M, Taton A, Adam ZR, Young JN, Kaçar B. Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time. Cell Rep 2022; 39:110726. [PMID: 35476992 DOI: 10.1016/j.celrep.2022.110726] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/26/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022] Open
Abstract
The earliest geochemical indicators of microbes-and the enzymes that powered them-extend back ∼3.8 Ga on Earth. Paleobiologists often attempt to understand these indicators by assuming that the behaviors of extant microbes and enzymes are uniform with those of their predecessors. This consistency in behavior seems at odds with our understanding of the inherent variability of living systems. Here, we examine whether a uniformitarian assumption for an enzyme thought to generate carbon isotope indicators of biological activity, RuBisCO, can be corroborated by independently studying the history of changes recorded within RuBisCO's genetic sequences. We resurrected a Precambrian-age RuBisCO by engineering its ancient DNA inside a cyanobacterium genome and measured the engineered organism's fitness and carbon-isotope-discrimination profile. Results indicate that Precambrian uniformitarian assumptions may be warranted but with important caveats. Experimental studies illuminating early innovations are crucial to explore the molecular foundations of life's earliest traces.
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Affiliation(s)
- Mateusz Kędzior
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amanda K Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Meng Li
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Arnaud Taton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zachary R Adam
- NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Geosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jodi N Young
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Jahan E, Thomson PC, Tissue DT. Mesophyll conductance in two cultivars of wheat grown in glacial to super-elevated CO2 concentrations. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7191-7202. [PMID: 34232298 DOI: 10.1093/jxb/erab320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/04/2021] [Indexed: 05/26/2023]
Abstract
Mesophyll conductance (gm) is an important factor limiting photosynthesis. However, gm response to long-term growth in variable [CO2] is not well understood, particularly in crop plants. Here, we grew two cultivars of wheat (Halberd and Cranbrook), known to differ in gm under current environmental conditions, in four [CO2] treatments: glacial (206 μmol mol-1), pre-industrial (344 μmol mol-1), current ambient (489 μmol mol-1), and super-elevated (1085 μmol mol-1), and two water treatments (well-watered and moderate water limitation), to develop an evolutionary and future climate perspective on gm control of photosynthesis and water-use efficiency (WUE). In the two wheat genotypes, gm increased with rising [CO2] from glacial to ambient [CO2], but declined at super-elevated [CO2]. The responses of gm to different growth [CO2] also depend on water stress; however, the specific mechanism of gm response to [CO2] remains unclear. Although gm and gm/gsc (mesophyll conductance/stomatal conductance) were strongly associated with the variability of photosynthetic rates (A) and WUE, we found that plants with higher gm may increase A without increasing gsc, which increased WUE. These results may be useful to inform plant breeding programmes and cultivar selection for Australian wheat under future environmental conditions.
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Affiliation(s)
- Eisrat Jahan
- The University of Sydney, School of Life and Environmental Sciences, Camden NSW, Australia
| | - Peter C Thomson
- The University of Sydney, School of Life and Environmental Sciences, Camden NSW, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW, Australia
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11
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Garcia AK, Cavanaugh CM, Kacar B. The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution. THE ISME JOURNAL 2021; 15:2183-2194. [PMID: 33846565 PMCID: PMC8319343 DOI: 10.1038/s41396-021-00971-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 11/09/2022]
Abstract
The oldest and most wide-ranging signal of biological activity (biosignature) on our planet is the carbon isotope composition of organic materials preserved in rocks. These biosignatures preserve the long-term evolution of the microorganism-hosted metabolic machinery responsible for producing deviations in the isotopic compositions of inorganic and organic carbon. Despite billions of years of ecosystem turnover, evolutionary innovation, organismic complexification, and geological events, the organic carbon that is a residuum of the global marine biosphere in the rock record tells an essentially static story. The ~25‰ mean deviation between inorganic and organic 13C/12C values has remained remarkably unchanged over >3.5 billion years. The bulk of this record is conventionally attributed to early-evolved, RuBisCO-mediated CO2 fixation that, in extant oxygenic phototrophs, produces comparable isotopic effects and dominates modern primary production. However, billions of years of environmental transition, for example, in the progressive oxygenation of the Earth's atmosphere, would be expected to have accompanied shifts in the predominant RuBisCO forms as well as enzyme-level adaptive responses in RuBisCO CO2-specificity. These factors would also be expected to result in preserved isotopic signatures deviating from those produced by extant RuBisCO in oxygenic phototrophs. Why does the bulk carbon isotope record not reflect these expected environmental transitions and evolutionary innovations? Here, we discuss this apparent discrepancy and highlight the need for greater quantitative understanding of carbon isotope fractionation behavior in extant metabolic pathways. We propose novel, laboratory-based approaches to reconstructing ancestral states of carbon metabolisms and associated enzymes that can constrain isotopic biosignature production in ancient biological systems. Together, these strategies are crucial for integrating the complementary toolsets of biological and geological sciences and for interpretation of the oldest record of life on Earth.
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Affiliation(s)
- Amanda K Garcia
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Colleen M Cavanaugh
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Betul Kacar
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.
- Lunar and Planetary Laboratory and Steward Observatory, University of Arizona, Tucson, AZ, USA.
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12
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Hurley SJ, Wing BA, Jasper CE, Hill NC, Cameron JC. Carbon isotope evidence for the global physiology of Proterozoic cyanobacteria. SCIENCE ADVANCES 2021; 7:7/2/eabc8998. [PMID: 33893090 PMCID: PMC7787495 DOI: 10.1126/sciadv.abc8998] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/11/2020] [Indexed: 05/03/2023]
Abstract
Ancestral cyanobacteria are assumed to be prominent primary producers after the Great Oxidation Event [≈2.4 to 2.0 billion years (Ga) ago], but carbon isotope fractionation by extant marine cyanobacteria (α-cyanobacteria) is inconsistent with isotopic records of carbon fixation by primary producers in the mid-Proterozoic eon (1.8 to 1.0 Ga ago). To resolve this disagreement, we quantified carbon isotope fractionation by a wild-type planktic β-cyanobacterium (Synechococcus sp. PCC 7002), an engineered Proterozoic analog lacking a CO2-concentrating mechanism, and cyanobacterial mats. At mid-Proterozoic pH and pCO2 values, carbon isotope fractionation by the wild-type β-cyanobacterium is fully consistent with the Proterozoic carbon isotope record, suggesting that cyanobacteria with CO2-concentrating mechanisms were apparently the major primary producers in the pelagic Proterozoic ocean, despite atmospheric CO2 levels up to 100 times modern. The selectively permeable microcompartments central to cyanobacterial CO2-concentrating mechanisms ("carboxysomes") likely emerged to shield rubisco from O2 during the Great Oxidation Event.
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Affiliation(s)
- Sarah J Hurley
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO 80302, USA.
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO 80309, USA
| | - Boswell A Wing
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO 80302, USA
| | - Claire E Jasper
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO 80302, USA
| | - Nicholas C Hill
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO 80309, USA
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Jeffrey C Cameron
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO 80309, USA.
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA
- National Renewable Energy Laboratory, Golden, CO 80401, USA
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13
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Raven JA, Suggett DJ, Giordano M. Inorganic carbon concentrating mechanisms in free-living and symbiotic dinoflagellates and chromerids. JOURNAL OF PHYCOLOGY 2020; 56:1377-1397. [PMID: 32654150 DOI: 10.1111/jpy.13050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
Photosynthetic dinoflagellates are ecologically and biogeochemically important in marine and freshwater environments. However, surprisingly little is known of how this group acquires inorganic carbon or how these diverse processes evolved. Consequently, how CO2 availability ultimately influences the success of dinoflagellates over space and time remains poorly resolved compared to other microalgal groups. Here we review the evidence. Photosynthetic core dinoflagellates have a Form II RuBisCO (replaced by Form IB or Form ID in derived dinoflagellates). The in vitro kinetics of the Form II RuBisCO from dinoflagellates are largely unknown, but dinoflagellates with Form II (and other) RuBisCOs have inorganic carbon concentrating mechanisms (CCMs), as indicated by in vivo internal inorganic C accumulation and affinity for external inorganic C. However, the location of the membrane(s) at which the essential active transport component(s) of the CCM occur(s) is (are) unresolved; isolation and characterization of functionally competent chloroplasts would help in this respect. Endosymbiotic Symbiodiniaceae (in Foraminifera, Acantharia, Radiolaria, Ciliata, Porifera, Acoela, Cnidaria, and Mollusca) obtain inorganic C by transport from seawater through host tissue. In corals this transport apparently provides an inorganic C concentration around the photobiont that obviates the need for photobiont CCM. This is not the case for tridacnid bivalves, medusae, or, possibly, Foraminifera. Overcoming these long-standing knowledge gaps relies on technical advances (e.g., the in vitro kinetics of Form II RuBisCO) that can functionally track the fate of inorganic C forms.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Faculty of Science, University of Technology, Sydney, Climate Change Cluster, Ultimo, Sydney, New South Wales, 2007, Australia
- School of Biological Science, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - David J Suggett
- Faculty of Science, University of Technology, Sydney, Climate Change Cluster, Ultimo, Sydney, New South Wales, 2007, Australia
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Algatech, Trebon, Czech Republic
- National Research Council, Institute of Marine Science ISMAR, Venezia, Italy
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14
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Vogado NO, Winter K, Ubierna N, Farquhar GD, Cernusak LA. Directional change in leaf dry matter δ 13C during leaf development is widespread in C3 plants. ANNALS OF BOTANY 2020; 126:981-990. [PMID: 32577724 PMCID: PMC7596372 DOI: 10.1093/aob/mcaa114] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/17/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS The stable carbon isotope ratio of leaf dry matter (δ 13Cp) is generally a reliable recorder of intrinsic water-use efficiency in C3 plants. Here, we investigated a previously reported pattern of developmental change in leaf δ 13Cp during leaf expansion, whereby emerging leaves are initially 13C-enriched compared to mature leaves on the same plant, with their δ 13Cp decreasing during leaf expansion until they eventually take on the δ 13Cp of other mature leaves. METHODS We compiled data to test whether the difference between mature and young leaf δ 13Cp differs between temperate and tropical species, or between deciduous and evergreen species. We also tested whether the developmental change in δ 13Cp is indicative of a concomitant change in intrinsic water-use efficiency. To gain further insight, we made online measurements of 13C discrimination (∆ 13C) in young and mature leaves. KEY RESULTS We found that the δ 13Cp difference between mature and young leaves was significantly larger for deciduous than for evergreen species (-2.1 ‰ vs. -1.4 ‰, respectively). Counter to expectation based on the change in δ 13Cp, intrinsic water-use efficiency did not decrease between young and mature leaves; rather, it did the opposite. The ratio of intercellular to ambient CO2 concentrations (ci/ca) was significantly higher in young than in mature leaves (0.86 vs. 0.72, respectively), corresponding to lower intrinsic water-use efficiency. Accordingly, instantaneous ∆ 13C was also higher in young than in mature leaves. Elevated ci/ca and ∆ 13C in young leaves resulted from a combination of low photosynthetic capacity and high day respiration rates. CONCLUSION The decline in leaf δ 13Cp during leaf expansion appears to reflect the addition of the expanding leaf's own 13C-depleted photosynthetic carbon to that imported from outside the leaf as the leaf develops. This mixing of carbon sources results in an unusual case of isotopic deception: less negative δ 13Cp in young leaves belies their low intrinsic water-use efficiency.
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Affiliation(s)
- Nara O Vogado
- Centre for Tropical Environmental and Sustainability Science, College of Science and Engineering, James Cook University, Cairns, Australia
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Nerea Ubierna
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Graham D Farquhar
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Lucas A Cernusak
- Centre for Tropical Environmental and Sustainability Science, College of Science and Engineering, James Cook University, Cairns, Australia
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15
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Díaz-Álvarez EA, de la Barrera E. Isotopic biomonitoring of anthropic carbon emissions in a megalopolis. PeerJ 2020; 8:e9283. [PMID: 32523817 PMCID: PMC7263291 DOI: 10.7717/peerj.9283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/12/2020] [Indexed: 11/21/2022] Open
Abstract
Atmospheric pollution has become a serious threat for human health and the environment. However, the deployment, operation and maintenance of monitoring networks can represent a high cost for local governments. In certain locations, the use of naturally occurring plants for monitoring pollution can be a useful supplement of existing monitoring networks, and even provide information when other types of monitoring are lacking. In this work, we (i) determined the tissue carbon content and the δ13C values for the epiphytic CAM bromeliad Tillandsia recurvata and the relationship of both parameters with the existing CO concentrations in the Valley of Mexico basin and (ii) mapped the spatial distribution of such elemental and isotopic composition for this plant within the basin, in order to assess its potential as an atmospheric biomonitor of carbon monoxide, a pollutant with important repercussions on public health. The CO concentrations in the basin ranged from 0.41 ppm at rural locations to 0.81 ppm at urban sites. The carbon content of T. recurvata, which averaged 42.9 ± 0.34% (dry weight), was not influenced by the surrounding CO concentration. In contrast, the δ13C depended on the sites where the plants were collected. For example, the values were -13.2‰ in rural areas and as low as -17.5‰ in an urban site. Indeed, the isotopic values had a positive linear relationship with the atmospheric CO concentrations. Given the close relationship observed between the isotopic composition of T. recurvata with the CO concentrations in the Valley of Mexico, the δ13C values can be useful for the detection of atmospheric carbonaceous emissions.
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Affiliation(s)
- Edison A. Díaz-Álvarez
- Instituto de Investigaciones Forestales, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Erick de la Barrera
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
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16
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Probst AJ, Elling FJ, Castelle CJ, Zhu Q, Elvert M, Birarda G, Holman HYN, Lane KR, Ladd B, Ryan MC, Woyke T, Hinrichs KU, Banfield JF. Lipid analysis of CO 2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. ISME JOURNAL 2020; 14:1547-1560. [PMID: 32203118 PMCID: PMC7242380 DOI: 10.1038/s41396-020-0624-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 11/09/2022]
Abstract
Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community.
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Affiliation(s)
- Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA. .,Institute for Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Felix J Elling
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany. .,Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA.
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Qingzeng Zhu
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Giovanni Birarda
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163,5 Basovizza, 34149, Trieste, Italy.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hoi-Ying N Holman
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine R Lane
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Bethany Ladd
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada.,Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - M Cathryn Ryan
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, MA, USA
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA.
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17
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Busch FA, Holloway-Phillips M, Stuart-Williams H, Farquhar GD. Revisiting carbon isotope discrimination in C 3 plants shows respiration rules when photosynthesis is low. NATURE PLANTS 2020; 6:245-258. [PMID: 32170287 DOI: 10.1038/s41477-020-0606-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/23/2020] [Indexed: 05/12/2023]
Abstract
Stable isotopes are commonly used to study the diffusion of CO2 within photosynthetic plant tissues. The standard method used to interpret the observed preference for the lighter carbon isotope in C3 photosynthesis involves the model of Farquhar et al., which relates carbon isotope discrimination to physical and biochemical processes within the leaf. However, under many conditions the model returns unreasonable results for mesophyll conductance to CO2 diffusion (gm), especially when rates of photosynthesis are low. Here, we re-derive the carbon isotope discrimination model using modified assumptions related to the isotope effect of mitochondrial respiration. In particular, we treat the carbon pool associated with respiration as separate from the pool of primary assimilates. We experimentally test the model by comparing gm values measured with different CO2 source gases varying in their isotopic composition, and show that our new model returns matching gm values that are much more reasonable than those obtained with the previous model. We use our results to discuss CO2 diffusion properties within the mesophyll.
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Affiliation(s)
- Florian A Busch
- Research School of Biology and ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Acton, Australian Capital Territory, Australia.
| | - Meisha Holloway-Phillips
- Research School of Biology and ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Acton, Australian Capital Territory, Australia
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Hilary Stuart-Williams
- Research School of Biology and ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Acton, Australian Capital Territory, Australia
| | - Graham D Farquhar
- Research School of Biology and ARC Centre of Excellence for Translational Photosynthesis, Australian National University, Acton, Australian Capital Territory, Australia
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18
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Iñiguez C, Capó-Bauçà S, Niinemets Ü, Stoll H, Aguiló-Nicolau P, Galmés J. Evolutionary trends in RuBisCO kinetics and their co-evolution with CO 2 concentrating mechanisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:897-918. [PMID: 31820505 DOI: 10.1111/tpj.14643] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/15/2019] [Accepted: 11/27/2019] [Indexed: 05/19/2023]
Abstract
RuBisCO-catalyzed CO2 fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5-bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen-rich atmosphere promoted the appearance of CO2 concentrating mechanisms (CCMs) and/or the evolution of a more CO2 -specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO2 /O2 concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co-evolution of RuBisCO and CCMs. Trade-offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO2 specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.
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Affiliation(s)
- Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
- Estonian Academy of Sciences, Kohtu 6, 10130, Tallinn, Estonia
| | - Heather Stoll
- Department of Earth Sciences, ETH Zürich, Sonnegstrasse 5, 8092, Zürich, Switzerland
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain
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19
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Demars BOL, Friberg N, Thornton B. Pulse of dissolved organic matter alters reciprocal carbon subsidies between autotrophs and bacteria in stream food webs. ECOL MONOGR 2020. [DOI: 10.1002/ecm.1399] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Benoît O. L. Demars
- Norwegian Institute for Water Research (NIVA) Gaustaallen 21 Oslo 0349 Norway
- The James Hutton Institute Craigiebuckler Aberdeen AB15 8QH United Kingdom
| | - Nikolai Friberg
- Norwegian Institute for Water Research (NIVA) Gaustaallen 21 Oslo 0349 Norway
- Freshwater Biological Section University of Copenhagen Universitetsparken 4, Third floor Copenhagen 2100 Denmark
- School of Geography University of Leeds Leeds LS2 9JT United Kingdom
| | - Barry Thornton
- The James Hutton Institute Craigiebuckler Aberdeen AB15 8QH United Kingdom
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20
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Cummins PL, Kannappan B, Gready JE. Response: Commentary: Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All. FRONTIERS IN PLANT SCIENCE 2019; 10:1426. [PMID: 31824523 PMCID: PMC6884029 DOI: 10.3389/fpls.2019.01426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 10/15/2019] [Indexed: 05/29/2023]
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21
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Garcia AK, Kaçar B. How to resurrect ancestral proteins as proxies for ancient biogeochemistry. Free Radic Biol Med 2019; 140:260-269. [PMID: 30951835 DOI: 10.1016/j.freeradbiomed.2019.03.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/11/2019] [Accepted: 03/26/2019] [Indexed: 10/27/2022]
Abstract
Throughout the history of life, enzymes have served as the primary molecular mediators of biogeochemical cycles by catalyzing the metabolic pathways that interact with geochemical substrates. The byproducts of enzymatic activities have been preserved as chemical and isotopic signatures in the geologic record. However, interpretations of these signatures are limited by the assumption that such enzymes have remained functionally conserved over billions of years of molecular evolution. By reconstructing ancient genetic sequences in conjunction with laboratory enzyme resurrection, preserved biogeochemical signatures can instead be related to experimentally constrained, ancestral enzymatic properties. We may thereby investigate instances within molecular evolutionary trajectories potentially tied to significant biogeochemical transitions evidenced in the geologic record. Here, we survey recent enzyme resurrection studies to provide a reasoned assessment of areas of success and common pitfalls relevant to ancient biogeochemical applications. We conclude by considering the Great Oxidation Event, which provides a constructive example of a significant biogeochemical transition that warrants investigation with ancestral enzyme resurrection. This event also serves to highlight the pitfalls of facile interpretation of paleophenotype models and data, as applied to two examples of enzymes that likely both influenced and were influenced by the rise of atmospheric oxygen - RuBisCO and nitrogenase.
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Affiliation(s)
- Amanda K Garcia
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Astronomy and Steward Observatory, University of Arizona, Tucson, AZ, 85721, USA.
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22
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Flamholz AI, Prywes N, Moran U, Davidi D, Bar-On YM, Oltrogge LM, Alves R, Savage D, Milo R. Revisiting Trade-offs between Rubisco Kinetic Parameters. Biochemistry 2019; 58:3365-3376. [PMID: 31259528 PMCID: PMC6686151 DOI: 10.1021/acs.biochem.9b00237] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Rubisco
is the primary carboxylase of the Calvin cycle, the most
abundant enzyme in the biosphere, and one of the best-characterized
enzymes. On the basis of correlations between Rubisco kinetic parameters,
it is widely posited that constraints embedded in the catalytic mechanism
enforce trade-offs between CO2 specificity, SC/O, and maximum carboxylation rate, kcat,C. However, the reasoning that established this view
was based on data from ≈20 organisms. Here, we re-examine models
of trade-offs in Rubisco catalysis using a data set from ≈300
organisms. Correlations between kinetic parameters are substantially
attenuated in this larger data set, with the inverse relationship
between kcat,C and SC/O being a key example. Nonetheless, measured kinetic parameters
display extremely limited variation, consistent with a view of Rubisco
as a highly constrained enzyme. More than 95% of kcat,C values are between 1 and 10 s–1, and no measured kcat,C exceeds 15 s–1. Similarly, SC/O varies
by only 30% among Form I Rubiscos and <10% among C3 plant
enzymes. Limited variation in SC/O forces
a strong positive correlation between the catalytic efficiencies (kcat/KM) for carboxylation
and oxygenation, consistent with a model of Rubisco catalysis in which
increasing the rate of addition of CO2 to the enzyme–substrate
complex requires an equal increase in the O2 addition rate.
Altogether, these data suggest that Rubisco evolution is tightly constrained
by the physicochemical limits of CO2/O2 discrimination.
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Affiliation(s)
- Avi I Flamholz
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
| | - Noam Prywes
- Innovative Genomics Institute , University of California , Berkeley , California 94704 , United States
| | - Uri Moran
- Department of Plant and Environmental Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
| | - Rui Alves
- Institute of Biomedical Research of Lleida , IRBLleida , 25198 Lleida , Catalunya , Spain.,Departament de Ciències Mèdiques Bàsiques , University of Lleida , 25198 Lleida , Catalunya , Spain
| | - David Savage
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
| | - Ron Milo
- Department of Plant and Environmental Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
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23
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Boyd RA, Cavanagh AP, Kubien DS, Cousins AB. Temperature response of Rubisco kinetics in Arabidopsis thaliana: thermal breakpoints and implications for reaction mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:231-242. [PMID: 30403800 PMCID: PMC6305185 DOI: 10.1093/jxb/ery355] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/09/2018] [Indexed: 05/04/2023]
Abstract
Enhancement of Rubisco kinetics could improve photosynthetic efficiency, ultimately resulting in increased crop yield. However, imprecise knowledge of the reaction mechanism and the individual rate constants limits our ability to optimize the enzyme. Membrane inlet mass spectrometry (MIMS) may offer benefits over traditional methods for determining individual rate constants of the Rubisco reaction mechanism, as it can directly monitor concentration changes in CO2, O2, and their isotopologs during assays. However, a direct comparison of MIMS with the traditional radiolabel method of determining Rubisco kinetic parameters has not been made. Here, the temperature responses of Rubisco kinetic parameters from Arabidopsis thaliana were measured using radiolabel and MIMS methods. The two methods provided comparable parameters above 25 °C, but temperature responses deviated at low temperature as MIMS-derived catalytic rates of carboxylation, oxygenation, and CO2/O2 specificity showed thermal breakpoints. Here, we discuss the variability and uncertainty surrounding breakpoints in the Rubisco temperature response and the relevance of individual rate constants of the reaction mechanisms to potential breakpoints.
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Affiliation(s)
- Ryan A Boyd
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Amanda P Cavanagh
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - David S Kubien
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Asaph B Cousins
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA
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24
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Thomas PJ, Boller AJ, Satagopan S, Tabita FR, Cavanaugh CM, Scott KM. Isotope discrimination by form IC RubisCO from
Ralstonia eutropha
and
Rhodobacter sphaeroides
, metabolically versatile members of ‘
Proteobacteria
’ from aquatic and soil habitats. Environ Microbiol 2018; 21:72-80. [DOI: 10.1111/1462-2920.14423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/18/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Phaedra J. Thomas
- Department of Integrative Biology University of South Florida Tampa FL USA
| | - Amanda J. Boller
- Department of Integrative Biology University of South Florida Tampa FL USA
| | - Sriram Satagopan
- Department of Microbiology The Ohio State University Columbus OH USA
| | - F. Robert Tabita
- Department of Microbiology The Ohio State University Columbus OH USA
| | - Colleen M. Cavanaugh
- Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Kathleen M. Scott
- Department of Integrative Biology University of South Florida Tampa FL USA
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25
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Aubineau J, El Albani A, Chi Fru E, Gingras M, Batonneau Y, Buatois LA, Geffroy C, Labanowski J, Laforest C, Lemée L, Mángano MG, Meunier A, Pierson-Wickmann AC, Recourt P, Riboulleau A, Trentesaux A, Konhauser KO. Unusual microbial mat-related structural diversity 2.1 billion years ago and implications for the Francevillian biota. GEOBIOLOGY 2018; 16:476-497. [PMID: 29923673 DOI: 10.1111/gbi.12296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/10/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
The 2.1-billion-year-old (Ga) Francevillian series in Gabon hosts some of the oldest reported macroscopic fossils of various sizes and shapes, stimulating new debates on the origin, evolution and organization of early complex life. Here, we document ten representative types of exceptionally well-preserved mat-related structures, comprising "elephant-skin" textures, putative macro-tufted microbial mats, domal buildups, flat pyritized structures, discoidal microbial colonies, horizontal mat growth patterns, wrinkle structures, "kinneyia" structures, linear patterns and nodule-like structures. A combination of petrographic analyses, scanning electron microscopy, Raman spectroscopy and organic elemental analyses of carbon-rich laminae and microtexture, indicate a biological origin for these structures. The observed microtextures encompass oriented grains, floating silt-sized quartz grains, concentrated heavy minerals, randomly oriented clays, wavy-crinkly laminae and pyritized structures. Based on comparisons with modern analogues, as well as an average δ13 C organic matter (Corg ) composition of -32.94 ± 1.17‰ (1 standard deviation, SD) with an outlier of -41.26‰, we argue that the mat-related structures contain relicts of multiple carbon pathways including heterotrophic recycling of photosynthetically derived Corg . Moreover, the relatively close association of the macroscopic fossil assemblages to the microbial mats may imply that microbial communities acted as potential benthic O2 oases linked to oxyphototrophic cyanobacterial mats and grazing grounds. In addition, the mat's presence likely improved the preservation of the oldest large colonial organisms, as they are known to strongly biostabilize sediments. Our findings highlight the oldest community assemblage of microscopic and macroscopic biota in the aftermath of the "Great Oxidation Event," widening our understanding of biological organization during Earth's middle age.
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Affiliation(s)
| | | | - Ernest Chi Fru
- School of Earth and Ocean Sciences, Cardiff University, Cardiff, UK
| | - Murray Gingras
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Yann Batonneau
- UMR CNRS IC2MP 7285, University of Poitiers, Poitiers, France
| | - Luis A Buatois
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Claude Geffroy
- UMR CNRS IC2MP 7285, University of Poitiers, Poitiers, France
| | | | - Claude Laforest
- UMR CNRS IC2MP 7285, University of Poitiers, Poitiers, France
| | - Laurent Lemée
- UMR CNRS IC2MP 7285, University of Poitiers, Poitiers, France
| | - Maria G Mángano
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alain Meunier
- UMR CNRS IC2MP 7285, University of Poitiers, Poitiers, France
| | | | - Philippe Recourt
- UMR 8187 LOG CNRS, University of Lille, ULCO, Villeneuve d'Ascq, France
| | | | - Alain Trentesaux
- UMR 8187 LOG CNRS, University of Lille, ULCO, Villeneuve d'Ascq, France
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
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26
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Tcherkez GG, Bathellier C, Farquhar GD, Lorimer GH. Commentary: Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All. FRONTIERS IN PLANT SCIENCE 2018; 9:929. [PMID: 29997647 PMCID: PMC6030380 DOI: 10.3389/fpls.2018.00929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/11/2018] [Indexed: 05/07/2023]
Affiliation(s)
- Guillaume G. Tcherkez
- Research School of Biology, Australian National University, ANU College of Science, Canberra, ACT, Australia
- *Correspondence: Guillaume G. Tcherkez
| | - Camille Bathellier
- Research School of Biology, Australian National University, ANU College of Science, Canberra, ACT, Australia
| | - Graham D. Farquhar
- Research School of Biology, Australian National University, ANU College of Science, Canberra, ACT, Australia
| | - George H. Lorimer
- Department of Chemistry and Biochemistry, College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park, MD, United States
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27
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Tan W, Bartram S, Boland W. Mechanistic studies of sesquiterpene cyclases based on their carbon isotope ratios at natural abundance. PLANT, CELL & ENVIRONMENT 2018; 41:39-49. [PMID: 28045196 DOI: 10.1111/pce.12901] [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: 09/08/2016] [Revised: 11/27/2016] [Accepted: 11/29/2016] [Indexed: 06/06/2023]
Abstract
During the process of terpene biosynthesis, C-C bond breaking and forming steps are subjected to kinetic carbon isotope effects, leading to distinct carbon isotopic signatures of the products. Accordingly, carbon isotopic signatures could be used to reveal the 'biosynthetic history' of the produced terpenoids. Five known sesquiterpene cyclases, regulating three different pathways, representing simple to complex biosynthetic sequences, were heterologously expressed and used for in vitro assays with farnesyl diphosphate as substrate. Compound specific isotope ratio mass spectrometry measurements of the enzyme substrate farnesyl diphosphate (FDP) and the products of all the five cyclases were performed. The calculated δ13 C value for FDP, based on δ13 C values and relative amounts of the products, was identical with its measured δ13 C value, confirming the reliability of the approach and the precision of measurements. The different carbon isotope ratios of the products reflect the complexity of their structure and are correlated with the frequency of carbon-carbon bond forming and breaking steps on their individual biosynthetic pathways. Thus, the analysis of carbon isotopic signatures of terpenes at natural abundance can be used as a powerful tool in elucidation of associated biosynthetic mechanisms of terpene synthases and in future in vivo studies even without 'touching' the plant.
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Affiliation(s)
- Wenhua Tan
- Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Stefan Bartram
- Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Wilhelm Boland
- Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745, Jena, Germany
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28
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Ubierna N, Holloway-Phillips MM, Farquhar GD. Using Stable Carbon Isotopes to Study C 3 and C 4 Photosynthesis: Models and Calculations. Methods Mol Biol 2018; 1770:155-196. [PMID: 29978402 DOI: 10.1007/978-1-4939-7786-4_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Stable carbon isotopes are a powerful tool to study photosynthesis. Initial applications consisted of determining isotope ratios of plant biomass using mass spectrometry. Subsequently, theoretical models relating C-isotope values to gas exchange characteristics were introduced and tested against instantaneous online measurements of 13C photosynthetic discrimination. Beginning in the twenty-first century, tunable diode laser spectroscopes with sufficient precision for determining isotope mixing ratios became commercially available. This has allowed collection of large data sets, at low cost and with unprecedented temporal resolution. With more data and accompanying knowledge, it has become apparent that there is a need for increased complexity in models and calculations. This chapter describes instantaneous online measurements of 13C photosynthetic discrimination, provides recommendations for experimental setup, and presents a thorough compilation of equations needed for different applications.
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Affiliation(s)
- Nerea Ubierna
- School of Biological Sciences, Molecular Plant Sciences, Washington State University, Pullman, WA, USA.
| | | | - Graham D Farquhar
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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29
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Cummins PL, Kannappan B, Gready JE. Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All. FRONTIERS IN PLANT SCIENCE 2018; 9:183. [PMID: 29545812 PMCID: PMC5838012 DOI: 10.3389/fpls.2018.00183] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/31/2018] [Indexed: 05/19/2023]
Abstract
The ubiquitous enzyme Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) fixes atmospheric carbon dioxide within the Calvin-Benson cycle that is utilized by most photosynthetic organisms. Despite this central role, RuBisCO's efficiency surprisingly struggles, with both a very slow turnover rate to products and also impaired substrate specificity, features that have long been an enigma as it would be assumed that its efficiency was under strong evolutionary pressure. RuBisCO's substrate specificity is compromised as it catalyzes a side-fixation reaction with atmospheric oxygen; empirical kinetic results show a trend to tradeoff between relative specificity and low catalytic turnover rate. Although the dominant hypothesis has been that the active-site chemistry constrains the enzyme's evolution, a more recent study on RuBisCO stability and adaptability has implicated competing selection pressures. Elucidating these constraints is crucial for directing future research on improving photosynthesis, as the current literature casts doubt on the potential effectiveness of site-directed mutagenesis to improve RuBisCO's efficiency. Here we use regression analysis to quantify the relationships between kinetic parameters obtained from empirical data sets spanning a wide evolutionary range of RuBisCOs. Most significantly we found that the rate constant for dissociation of CO2 from the enzyme complex was much higher than previous estimates and comparable with the corresponding catalytic rate constant. Observed trends between relative specificity and turnover rate can be expressed as the product of negative and positive correlation factors. This provides an explanation in simple kinetic terms of both the natural variation of relative specificity as well as that obtained by reported site-directed mutagenesis results. We demonstrate that the kinetic behaviour shows a lesser rather than more constrained RuBisCO, consistent with growing empirical evidence of higher variability in relative specificity. In summary our analysis supports an explanation for the origin of the tradeoff between specificity and turnover as due to competition between protein stability and activity, rather than constraints between rate constants imposed by the underlying chemistry. Our analysis suggests that simultaneous improvement in both specificity and turnover rate of RuBisCO is possible.
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30
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Kacar B, Guy L, Smith E, Baross J. Resurrecting ancestral genes in bacteria to interpret ancient biosignatures. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:20160352. [PMID: 29133450 PMCID: PMC5686408 DOI: 10.1098/rsta.2016.0352] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/17/2017] [Indexed: 05/04/2023]
Abstract
Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the laboratory, which we term palaeophenotype reconstruction.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
- Betul Kacar
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden
| | - Eric Smith
- Earth-Science Life Institute, Meguro-ku, Tokyo 152-8550, Japan
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - John Baross
- The School of Oceanography, University of Washington, Seattle, WA 98105, USA
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31
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Kacar B, Hanson‐Smith V, Adam ZR, Boekelheide N. Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree. GEOBIOLOGY 2017; 15:628-640. [PMID: 28670785 PMCID: PMC5575542 DOI: 10.1111/gbi.12243] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 05/09/2017] [Indexed: 05/04/2023]
Abstract
Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen-sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem-bearing, oxygen-evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen-sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.
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Affiliation(s)
- B. Kacar
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - V. Hanson‐Smith
- Department of Microbiology and ImmunologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Z. R. Adam
- Department of Earth and Planetary SciencesHarvard UniversityCambridgeMAUSA
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32
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Sugar Metabolism in Hummingbirds and Nectar Bats. Nutrients 2017; 9:nu9070743. [PMID: 28704953 PMCID: PMC5537857 DOI: 10.3390/nu9070743] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 12/15/2022] Open
Abstract
Hummingbirds and nectar bats coevolved with the plants they visit to feed on floral nectars rich in sugars. The extremely high metabolic costs imposed by small size and hovering flight in combination with reliance upon sugars as their main source of dietary calories resulted in convergent evolution of a suite of structural and functional traits. These allow high rates of aerobic energy metabolism in the flight muscles, fueled almost entirely by the oxidation of dietary sugars, during flight. High intestinal sucrase activities enable high rates of sucrose hydrolysis. Intestinal absorption of glucose and fructose occurs mainly through a paracellular pathway. In the fasted state, energy metabolism during flight relies on the oxidation of fat synthesized from previously-ingested sugar. During repeated bouts of hover-feeding, the enhanced digestive capacities, in combination with high capacities for sugar transport and oxidation in the flight muscles, allow the operation of the “sugar oxidation cascade”, the pathway by which dietary sugars are directly oxidized by flight muscles during exercise. It is suggested that the potentially harmful effects of nectar diets are prevented by locomotory exercise, just as in human hunter-gatherers who consume large quantities of honey.
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33
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Stable carbon isotope signals in particulate organic and inorganic carbon of coccolithophores – A numerical model study for Emiliania huxleyi. J Theor Biol 2017; 420:117-127. [DOI: 10.1016/j.jtbi.2017.01.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 01/15/2017] [Accepted: 01/19/2017] [Indexed: 11/18/2022]
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34
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Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principle Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01. G3-GENES GENOMES GENETICS 2016; 6:2791-7. [PMID: 27412985 PMCID: PMC5015936 DOI: 10.1534/g3.116.032953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain’s genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin–Benson–Bassham (CBB) cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3- rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01.
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35
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Hanson DT, Stutz SS, Boyer JS. Why small fluxes matter: the case and approaches for improving measurements of photosynthesis and (photo)respiration. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3027-39. [PMID: 27099373 PMCID: PMC4867897 DOI: 10.1093/jxb/erw139] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Since its inception, the Farquhar et al. (1980) model of photosynthesis has been a mainstay for relating biochemistry to environmental conditions from chloroplast to global levels in terrestrial plants. Many variables could be assigned from basic enzyme kinetics, but the model also required measurements of maximum rates of photosynthetic electron transport (J max ), carbon assimilation (Vcmax ), conductance of CO2 into (g s ) and through (g m ) the leaf, and the rate of respiration during the day (R d ). This review focuses on improving the accuracy of these measurements, especially fluxes from photorespiratory CO2, CO2 in the transpiration stream, and through the leaf epidermis and cuticle. These fluxes, though small, affect the accuracy of all methods of estimating mesophyll conductance and several other photosynthetic parameters because they all require knowledge of CO2 concentrations in the intercellular spaces. This review highlights modified methods that may help to reduce some of the uncertainties. The approaches are increasingly important when leaves are stressed or when fluxes are inferred at scales larger than the leaf.
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Affiliation(s)
- David T Hanson
- Department of Biology, MSC03-2020, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Samantha S Stutz
- Department of Biology, MSC03-2020, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - John S Boyer
- Interdisciplinary Plant Group, 1-31 Agriculture Building, University of Missouri, Columbia, MO 65211, USA
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36
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Allen DK, Bates PD, Tjellström H. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future. Prog Lipid Res 2015; 58:97-120. [PMID: 25773881 DOI: 10.1016/j.plipres.2015.02.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/30/2015] [Accepted: 02/11/2015] [Indexed: 11/25/2022]
Abstract
Metabolism is comprised of networks of chemical transformations, organized into integrated biochemical pathways that are the basis of cellular operation, and function to sustain life. Metabolism, and thus life, is not static. The rate of metabolites transitioning through biochemical pathways (i.e., flux) determines cellular phenotypes, and is constantly changing in response to genetic or environmental perturbations. Each change evokes a response in metabolic pathway flow, and the quantification of fluxes under varied conditions helps to elucidate major and minor routes, and regulatory aspects of metabolism. To measure fluxes requires experimental methods that assess the movements and transformations of metabolites without creating artifacts. Isotopic labeling fills this role and is a long-standing experimental approach to identify pathways and quantify their metabolic relevance in different tissues or under different conditions. The application of labeling techniques to plant science is however far from reaching it potential. In light of advances in genetics and molecular biology that provide a means to alter metabolism, and given recent improvements in instrumentation, computational tools and available isotopes, the use of isotopic labeling to probe metabolism is becoming more and more powerful. We review the principal analytical methods for isotopic labeling with a focus on seminal studies of pathways and fluxes in lipid metabolism and carbon partitioning through central metabolism. Central carbon metabolic steps are directly linked to lipid production by serving to generate the precursors for fatty acid biosynthesis and lipid assembly. Additionally some of the ideas for labeling techniques that may be most applicable for lipid metabolism in the future were originally developed to investigate other aspects of central metabolism. We conclude by describing recent advances that will play an important future role in quantifying flux and metabolic operation in plant tissues.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture, Agricultural Research Service, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Philip D Bates
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, United States
| | - Henrik Tjellström
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, United States; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, United States
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Schmidt HL, Robins RJ, Werner RA. Multi-factorial in vivo stable isotope fractionation: causes, correlations, consequences and applications. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2015; 51:155-199. [PMID: 25894429 DOI: 10.1080/10256016.2015.1014355] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Many physical and chemical processes in living systems are accompanied by isotope fractionation on H, C, N, O and S. Although kinetic or thermodynamic isotope effects are always the basis, their in vivo manifestation is often modulated by secondary influences. These include metabolic branching events or metabolite channeling, metabolite pool sizes, reaction mechanisms, anatomical properties and compartmentation of plants and animals, and climatological or environmental conditions. In the present contribution, the fundamentals of isotope effects and their manifestation under in vivo conditions are outlined. The knowledge about and the understanding of these interferences provide a potent tool for the reconstruction of physiological events in plants and animals, their geographical origin, the history of bulk biomass and the biosynthesis of defined representatives. It allows the use of isotope characteristics of biomass for the elucidation of biochemical pathways and reaction mechanisms and for the reconstruction of climatic, physiological, ecological and environmental conditions during biosynthesis. Thus, it can be used for the origin and authenticity control of food, the study of ecosystems and animal physiology, the reconstruction of present and prehistoric nutrition chains and paleaoclimatological conditions. This is demonstrated by the outline of fundamental and application-orientated examples for all bio-elements. The aim of the review is to inform (advanced) students from various disciplines about the whole potential and the scope of stable isotope characteristics and fractionations and to provide them with a comprehensive introduction to the literature on fundamental aspects and applications.
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Affiliation(s)
- Hanns-Ludwig Schmidt
- a Lehrstuhl für Biologische Chemie , Technische Universität München , Freising-Weihenstephan, Germany
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38
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Schneider TW, Angeles-Boza AM. Competitive 13C and 18O kinetic isotope effects on CO2 reduction catalyzed by Re(bpy)(CO)3Cl. Dalton Trans 2015; 44:8784-7. [DOI: 10.1039/c4dt03977g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Competitive 13C and 18O kinetic isotope effects (KIEs) on CO2 reduction reactions catalyzed by Re(bpy)(CO)3Cl are reported.
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Hanson DT, Collins AM, Jones HDT, Roesgen J, Lopez-Nieves S, Timlin JA. On-line stable isotope gas exchange reveals an inducible but leaky carbon concentrating mechanism in Nannochloropsis salina. PHOTOSYNTHESIS RESEARCH 2014; 121:311-22. [PMID: 24844569 PMCID: PMC8078823 DOI: 10.1007/s11120-014-0001-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 03/24/2014] [Indexed: 05/28/2023]
Abstract
Carbon concentrating mechanisms (CCMs) are common among microalgae, but their regulation and even existence in some of the most promising biofuel production strains is poorly understood. This is partly because screening for new strains does not commonly include assessment of CCM function or regulation despite its fundamental role in primary carbon metabolism. In addition, the inducible nature of many microalgal CCMs means that environmental conditions should be considered when assessing CCM function and its potential impact on biofuels. In this study, we address the effect of environmental conditions by combining novel, high frequency, on-line (13)CO2 gas exchange screen with microscope-based lipid characterization to assess CCM function in Nannochloropsis salina and its interaction with lipid production. Regulation of CCM function was explored by changing the concentration of CO2 provided to continuous cultures in airlift bioreactors where cell density was kept constant across conditions by controlling the rate of media supply. Our isotopic gas exchange results were consistent with N. salina having an inducible "pump-leak" style CCM similar to that of Nannochloropsis gaditana. Though cells grew faster at high CO2 and had higher rates of net CO2 uptake, we did not observe significant differences in lipid content between conditions. Since the rate of CO2 supply was much higher for the high CO2 conditions, we calculated that growing cells bubbled with low CO2 is about 40 % more efficient for carbon capture than bubbling with high CO2. We attribute this higher efficiency to the activity of a CCM under low CO2 conditions.
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Affiliation(s)
- David T Hanson
- Department of Biology, University of New Mexico, Albuquerque, NM, USA,
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40
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von Caemmerer S, Ghannoum O, Pengelly JJL, Cousins AB. Carbon isotope discrimination as a tool to explore C4 photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3459-70. [PMID: 24711615 DOI: 10.1093/jxb/eru127] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Photosynthetic carbon isotope discrimination is a non-destructive tool for investigating C4 metabolism. Tuneable diode laser absorption spectroscopy provides new opportunities for making rapid, concurrent measurements of carbon isotope discrimination and CO2 assimilation over a range of environmental conditions, and this has facilitated the use of carbon isotope discrimination as a probe of C4 metabolism. In spite of the significant progress made in recent years, understanding how photosynthetic carbon isotope discrimination measured concurrently with gas exchange relates to carbon isotope composition of leaf and plant dry matter remains a challenge that requires resolution if this technique is to be successfully applied as a screening tool in crop breeding and phylogenetic research. In this review, we update our understanding of the factors and assumptions that underlie variations in photosynthetic carbon isotope discrimination in C4 leaves. Closing the main gaps in our understanding of carbon isotope discrimination during C4 photosynthesis may help advance research aimed at developing higher productivity and efficiency in key C4 food, feed, and biofuel crops.
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Affiliation(s)
- Susanne von Caemmerer
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - Oula Ghannoum
- Hawkesbury Institute for the Environment, University of Western Sydney, Hawkesbury campus, Locked Bag 1797, Penrith 2751, NSW, Australia
| | - Jasper J L Pengelly
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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41
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Gentsch L, Hammerle A, Sturm P, Ogée J, Wingate L, Siegwolf R, Plüss P, Baur T, Buchmann N, Knohl A. Carbon isotope discrimination during branch photosynthesis of Fagus sylvatica: a Bayesian modelling approach. PLANT, CELL & ENVIRONMENT 2014; 37:1516-1535. [PMID: 24372560 DOI: 10.1111/pce.12262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 11/05/2013] [Accepted: 12/04/2013] [Indexed: 06/03/2023]
Abstract
Field measurements of photosynthetic carbon isotope discrimination ((13)Δ) of Fagus sylvatica, conducted with branch bags and laser spectrometry, revealed a high variability of (13)Δ, both on diurnal and day-to-day timescales. We tested the prediction capability of three versions of a commonly used model for (13)Δ [called here comprehensive ((13)(Δcomp)), simplified ((13) Δsimple) and revised ((13)(Δrevised)) versions]. A Bayesian approach was used to calibrate major model parameters. Constrained estimates were found for the fractionation during CO(2) fixation in (13)(Δcomp), but not in (13)(Δsimple), and partially for the mesophyll conductance for CO(2)(gi). No constrained estimates were found for fractionations during mitochondrial and photorespiration, and for a diurnally variable apparent fractionation between current assimilates and mitochondrial respiration, specific to (13)(Δrevised). A quantification of parameter estimation uncertainties and interdependencies further helped explore model structure and behaviour. We found that (13)(Δcomp) usually outperformed (13)(Δsimple) because of the explicit consideration of gi and the photorespiratory fractionation in (13)(Δcomp) that enabled a better description of the large observed diurnal variation (≈9‰) of (13)Δ. Flux-weighted daily means of (13)Δ were also better predicted with (13)(Δcomp) than with (13)(Δsimple).
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Affiliation(s)
- Lydia Gentsch
- Institute of Agricultural Sciences, ETH Zurich, Universitätsstrasse 2, Zurich, 8092, Switzerland; UR1263 Ephyse, INRA, Villenave d'Ornon, 33140, France
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42
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von Caemmerer S, Tazoe Y, Evans JR, Whitney SM. Exploiting transplastomically modified Rubisco to rapidly measure natural diversity in its carbon isotope discrimination using tuneable diode laser spectroscopy. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3759-67. [PMID: 24687980 PMCID: PMC4085952 DOI: 10.1093/jxb/eru036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Carbon isotope discrimination (Δ) during C3 photosynthesis is dominated by the fractionation occurring during CO2-fixation by the enzyme Rubisco. While knowing the fractionation by enzymes is pivotal to fully understanding plant carbon metabolism, little is known about variation in the discrimination factor of Rubisco (b) as it is difficult to measure using existing in vitro methodologies. Tuneable diode laser absorption spectroscopy has improved the ability to make rapid measurements of Δ concurrently with photosynthetic gas exchange. This study used this technique to estimate b in vivo in five tobacco (Nicotiana tabacum L. cv Petit Havana [N,N]) genotypes expressing alternative Rubisco isoforms. For transplastomic tobacco producing Rhodospirillum rubrum Rubisco b was 23.8±0.7‰, while Rubisco containing the large subunit Leu-335-Val mutation had a b-value of 13.9±0.7‰. These values were significantly less than that for Rubisco from wild-type tobacco (b=29‰), a C3 species. Transplastomic tobacco producing chimeric Rubisco comprising tobacco Rubisco small subunits and the catalytic large subunits from either the C4 species Flaveria bidentis or the C3-C4 species Flaveria floridana had b-values of 27.8±0.8 and 28.6±0.6‰, respectively. These values were not significantly different from tobacco Rubisco.
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Affiliation(s)
- Susanne von Caemmerer
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - Youshi Tazoe
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - John R Evans
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - Spencer M Whitney
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
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43
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Jahan E, Amthor JS, Farquhar GD, Trethowan R, Barbour MM. Variation in mesophyll conductance among Australian wheat genotypes. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:568-580. [PMID: 32481014 DOI: 10.1071/fp13254] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/14/2014] [Indexed: 06/11/2023]
Abstract
CO2 diffusion from substomatal intercellular cavities to sites of carboxylation in chloroplasts (mesophyll conductance; gm) limits photosynthetic rate and influences leaf intrinsic water-use efficiency (A/gsw). We investigated genotypic variability of gm and effects of gm on A/gsw among eleven wheat (Triticum aestivum L.) genotypes under light-saturated conditions and at either 2 or 21% O2. Significant variation in gm and A/gsw was found between genotypes at both O2 concentrations, but there was no significant effect of O2 concentration on gm. Further, gm was correlated with photosynthetic rate among the 11 genotypes, but was unrelated to stomatal conductance. The effect of leaf age differed between genotypes, with gm being lower in older leaves for one genotype but not another. This study demonstrates a high level of variation in gm between wheat genotypes; 0.5 to 1.0μmolm-2s-1 bar-1. Further, leaf age effects indicate that great care must be taken to choose suitable leaves in studies of genotypic variation in gm and water-use efficiency.
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Affiliation(s)
- Eisrat Jahan
- Faculty of Agriculture and Environment, The University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
| | - Jeffrey S Amthor
- Faculty of Agriculture and Environment, The University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
| | - Graham D Farquhar
- Research School of Biology, The Australian National University, Biology Place, Canberra, ACT 0200, Australia
| | - Richard Trethowan
- Faculty of Agriculture and Environment, The University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
| | - Margaret M Barbour
- Faculty of Agriculture and Environment, The University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
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44
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Gentsch L, Sturm P, Hammerle A, Siegwolf R, Wingate L, Ogée J, Baur T, Plüss P, Barthel M, Buchmann N, Knohl A. Carbon isotope discrimination during branch photosynthesis of Fagus sylvatica: field measurements using laser spectrometry. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1481-96. [PMID: 24676031 DOI: 10.1093/jxb/eru024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
On-line measurements of photosynthetic carbon isotope discrimination ((13)Δ) under field conditions are sparse. Hence, experimental verification of the natural variability of instantaneous (13)Δ is scarce, although (13)Δ is, explicitly and implicitly, used from leaf to global scales for inferring photosynthetic characteristics. This work presents the first on-line field measurements of (13)Δ of Fagus sylvatica branches, at hourly resolution, using three open branch bags and a laser spectrometer for CO₂ isotopologue measurements (QCLAS-ISO). Data from two August/September field campaigns, in 2009 and 2010, in a temperate forest in Switzerland are shown. Diurnal variability of (13)Δ was substantial, with mean diurnal amplitudes of ~9‰ and maximum diurnal amplitudes of ~20‰. The highest (13)Δ were generally observed during early morning and late afternoon, and the lowest (13)Δ during midday. An assessment of propagated standard deviations of (13)Δ demonstrated that the observed diurnal variation of (13)Δ was not a measurement artefact. Day-to-day variations of (13)Δ were summarized with flux-weighted daily means of (13)Δ, which ranged from 15‰ to 23‰ in 2009 and from 18‰ to 29‰ in 2010, thus displaying a considerable range of 8-11‰. Generally, (13)Δ showed the expected negative relationship with intrinsic water use efficiency. Diurnal and day-to-day variability of (13)Δ was, however, always better predicted by that of net CO₂ assimilation, especially in 2010 when soil moisture was high and vapour pressure deficit was low. Stomatal control of leaf gas exchange, and consequently (13)Δ, could only be identified under drier conditions in 2009.
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Affiliation(s)
- Lydia Gentsch
- Institute of Agricultural Sciences, ETH Zurich, Universitätsstrasse 2, 8092 Zurich, Switzerland
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45
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Tcherkez G. Modelling the reaction mechanism of ribulose-1,5-bisphosphate carboxylase/oxygenase and consequences for kinetic parameters. PLANT, CELL & ENVIRONMENT 2013; 36:1586-96. [PMID: 23305122 DOI: 10.1111/pce.12066] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/12/2012] [Accepted: 12/26/2012] [Indexed: 05/20/2023]
Abstract
Although ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was discovered nearly 60 years ago, the associated chemical mechanism of the reaction is still incompletely understood. The catalytic cycle consists of four major steps: ribulose-1,5-bisphosphate binding, enolization, CO₂ or O₂ addition and hydration, and cleavage of the intermediate. The use of individual rate constants for these elemental steps yields mathematical expressions for usual kinetic constants (k(cat), K(m)), CO₂ versus O₂ specificity (S(c/o)) as well as other chemical parameters such as the ¹²C/¹³C isotope effect. That said, most of them are not simple and thus the interpretation of experimental and observed values of kcat , Km and Sc/o may be more complicated than expected. That is, Rubisco effective catalysis depends on several kinetic parameters that are influenced by both the biological origin and the cellular medium (which, in turn, can vary with environmental conditions). In this brief review, we present the basic model of Rubisco kinetics and describe how subtle biochemical changes (which may have occurred along Evolution) can easily modify Rubisco catalysis.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR 8618, Université Paris-Sud, 91405 Orsay Cedex, France.
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46
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Tcherkez GGB, Bathellier C, Stuart-Williams H, Whitney S, Gout E, Bligny R, Badger M, Farquhar GD. D2O Solvent Isotope Effects Suggest Uniform Energy Barriers in Ribulose-1,5-bisphosphate Carboxylase/Oxygenase Catalysis. Biochemistry 2013; 52:869-77. [DOI: 10.1021/bi300933u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guillaume G. B. Tcherkez
- Institut de Biologie des Plantes,
CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay cedex, France
- Institut Universitaire de France, 103 boulevard Saint-Michel, 75005 Paris,
France
| | - Camille Bathellier
- Institut de Biologie des Plantes,
CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay cedex, France
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Hilary Stuart-Williams
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Spencer Whitney
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Elisabeth Gout
- Laboratoire de
Physiologie Cellulaire
Végétale, CEA-Grenoble, 17
rue des Martyrs, 38009 Grenoble cedex, France
| | - Richard Bligny
- Laboratoire de
Physiologie Cellulaire
Végétale, CEA-Grenoble, 17
rue des Martyrs, 38009 Grenoble cedex, France
| | - Murray Badger
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
| | - Graham D. Farquhar
- Research School of
Biology, Australian National University, Canberra ACT 0200,
Australia
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47
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Tiago I, Veríssimo A. Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization. Environ Microbiol 2012; 15:1687-706. [PMID: 23731249 DOI: 10.1111/1462-2920.12034] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 10/25/2012] [Indexed: 11/27/2022]
Abstract
Microbial and functional diversity were assessed, from a serpentinization-driven subterrestrial alkaline aquifer - Cabeço de Vide Aquifer (CVA) in Portugal. DGGE analyses revealed the presence of a stable microbial community. By 16S rRNA gene libraries and pyrosequencing analyses, a diverse bacterial composition was determined, contrasting with low archaeal diversity. Within Bacteria the majority of the populations were related to organisms or sequences affiliated to class Clostridia, but members of classes Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Deinococci, Gammaproteobacteria and of the phyla Bacteroidetes, Chloroflexi and Nitrospira were also detected. Domain Archaea encompassed mainly sequences affiliated to Euryarchaeota. Only form I RuBisCO - cbbL was detected. Autotrophic carbon fixation via the rTCA, 3-HP and 3-HP/4H-B cycles could not be confirmed. The detected APS reductase alpha subunit - aprA sequences were phylogenetically related to sequences of sulfate-reducing bacteria belonging to Clostridia, and also to sequences of chemolithoautothrophic sulfur-oxidizing bacteria belonging to Betaproteobacteria. Sequences of methyl coenzyme M reductase - mcrA were phylogenetically affiliated to sequences belonging to Anaerobic Methanotroph group 1 (ANME-1). The populations found and the functional key markers detected in CVA suggest that metabolisms related to H2 , methane and/or sulfur may be the major driving forces in this environment.
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Affiliation(s)
- Igor Tiago
- Department of Life Sciences, University of Coimbra, Apartado 3046, 3001-401 Coimbra, Portugal
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48
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Douthe C, Dreyer E, Brendel O, Warren CR. Is mesophyll conductance to CO 2 in leaves of three Eucalyptus species sensitive to short-term changes of irradiance under ambient as well as low O 2? FUNCTIONAL PLANT BIOLOGY : FPB 2012; 39:435-448. [PMID: 32480795 DOI: 10.1071/fp11190] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 03/26/2012] [Indexed: 06/11/2023]
Abstract
Mesophyll conductance to CO2 (g m) limits the diffusion of CO2 to the sites of carboxylation, and may respond rapidly (within minutes) to abiotic factors. Using three Eucalyptus species, we tested the rapid response of g m to irradiance under 21% and 1% O2. We used simultaneous measurements of leaf gas exchange and discrimination against 13CO2 with a tuneable diode laser absorption spectrometer. Measurements under 1% O2 were used to limit uncertainties due to 13C-12C fractionation occurring during photorespiration. Switching irradiance from 600 to 200µmolm-2s-1 led to a ≈60% decrease of g m within minutes in all species under both 21% O2 and 1% O2. The g m response to irradiance is unlikely to be a computation artefact since using different values for the parameters of the discrimination model changed the absolute values of g m but did not affect the relative response to irradiance. Simulations showed that possible rapid changes of any parameter were unable to explain the observed variations of g m with irradiance, except for13C-12C fractionation during carboxylation (b), which, in turn, is dependent on the fraction of leaf C assimilated by phospho-enol pyruvate carboxylase (PEPc) (β). g m apparently increased by ≈30% when O2 was switched from 21% to 1% O2. Again, possible changes of β with O2 could explain this apparent g m response to O2. Nevertheless, large irradiance or O2-induced changes in β would be required to fully explain the observed changes in g m, reinforcing the hypothesis that g m is responsive to irradiance and possibly also to O2.
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Affiliation(s)
- Cyril Douthe
- INRA, Unité Mixte de Recherches 1147 'Ecologie et Ecophysiologie Forestières', F 54280 Champenoux, France
| | - Erwin Dreyer
- INRA, Unité Mixte de Recherches 1147 'Ecologie et Ecophysiologie Forestières', F 54280 Champenoux, France
| | - Oliver Brendel
- INRA, Unité Mixte de Recherches 1147 'Ecologie et Ecophysiologie Forestières', F 54280 Champenoux, France
| | - Charles R Warren
- University of Sydney, School of Biological Sciences, Heydon-Laurence Building, A08, The University of Sydney, NSW 2006, Australia
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49
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Moolna A, Rickaby REM. Interaction of the coccolithophore Gephyrocapsa oceanica with its carbon environment: response to a recreated high-CO2 geological past. GEOBIOLOGY 2012; 10:72-81. [PMID: 22118223 DOI: 10.1111/j.1472-4669.2011.00308.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Coccolithophores have played a key role in the carbon cycle since becoming dominant in the Cretaceous ocean, and their influence depends fundamentally on how they interact with their external carbon environment. Because the photosynthetic carbon-fixing enzyme Rubisco requires high levels of CO(2) for effective catalysis, coccolithophores are known to induce carbon concentrating mechanisms (CCMs) to raise the level of dissolved inorganic carbon (DIC) in an 'internal pool'. The ocean carbon system has varied greatly over the geological past, suggesting that coccolithophore interactions with that external carbon environment will have changed in parallel. The widespread present-day coccolithophore Gephyrocapsa oceanica was acclimated here to a geological scale change in the seawater carbon system (five times higher DIC and alkalinity). Significant acclimation in response to the external carbon environment was demonstrated by a fourfold increase in the K(m) substrate concentration requirement for half-maximum photosynthetic carbon fixation rates (suggesting that CCMs were down-regulated when ambient carbon was more available). There was, however, no difference in growth rate, morphology or calcification, suggesting that calcification is not coupled to photosynthesis as one of the CCMs induced here and that productivity (growth rate and calcification) is not carbon-limited under representative present-day conditions. Beyond the kinetic parameters of photosynthesis, the only other indication of changed cell physiology seen was the increased fractionation of carbon isotopes into organic matter. These findings demonstrate that G. oceanica changes its carbon-use physiology to maintain consistent photosynthetic carbon fixation in concert with different levels of ambient DIC without changing its morphology or calcification.
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Affiliation(s)
- A Moolna
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, UK
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50
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Kodama N, Cousins A, Tu KP, Barbour MM. Spatial variation in photosynthetic CO(2) carbon and oxygen isotope discrimination along leaves of the monocot triticale (Triticum × Secale) relates to mesophyll conductance and the Péclet effect. PLANT, CELL & ENVIRONMENT 2011; 34:1548-62. [PMID: 21707646 DOI: 10.1111/j.1365-3040.2011.02352.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Carbon and oxygen isotope discrimination of CO(2) during photosynthesis (Δ(13)C(obs) and Δ(18)O(obs)) were measured along a monocot leaf, triticale (Triticum × Secale). Both Δ(13)C(obs) and Δ(18)O(obs) increased towards the leaf tip. While this was expected for Δ(18)O(obs) , because of progressive enrichment of leaf water associated with the Péclet effect, the result was surprising for Δ(13) C(obs). To explore parameters determining this pattern, we measured activities of key photosynthetic enzymes [ribulose bis-phosphate carboxylase-oxygenase (Rubisco), phosphoenolpyruvate carboxylase (PEPC) and carbonic anhydrase) as well as maximum carboxylation and electron transport rates (V(cmax) and J(max)) along the leaf. Patterns in leaf internal anatomy along the leaf were also quantified. Mesophyll conductance (g(m)) is known to have a strong influence on Δ(13)C(obs) , so we used three commonly used estimation methods to quantify variation in g(m) along the leaf. Variation in Δ(13)C(obs) was correlated with g(m) and chloroplast surface area facing the intercellular air space, but unrelated to photosynthetic enzyme activity. The observed variation could cause errors at higher scales if the appropriate portion of a leaf is not chosen for leaf-level measurements and model parameterization. Our study shows that one-third of the way from the base of the leaf represents the most appropriate portion to enclose in the leaf chamber.
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Affiliation(s)
- Naomi Kodama
- Agro-meteorology Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan.
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