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Chen P, Ye T, Li C, Praveen P, Hu Z, Li W, Shang C. Embracing the era of antimicrobial peptides with marine organisms. Nat Prod Rep 2024; 41:331-346. [PMID: 37743806 DOI: 10.1039/d3np00031a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Covering: 2018 to Jun of 2023The efficiency of traditional antibiotics has been undermined by the proliferation of antibiotic-resistant pathogenic microorganisms, necessitating the pursuit of innovative therapeutic agents. Antimicrobial peptides (AMPs), which are part of host defence peptides found ubiquitously in nature, exhibiting a wide range of activity towards bacteria, fungi, and viruses, offer a highly promising candidate solution. The efficacy of AMPs can frequently be augmented via alterations to their amino acid sequences or structural adjustments. Given the vast reservoir of marine life forms and their distinctive ecosystems, marine AMPs stand as a burgeoning focal point in the quest for alternative peptide templates extracted from natural sources. Advances in identification and characterization techniques have accelerated the discoveries of marine AMPs, thereby stimulating AMP customization, optimization, and synthesis research endeavours. This review presents an overview of recent discoveries related to the intriguing qualities of marine AMPs. Emphasis will be placed upon post-translational modifications (PTMs) of marine AMPs and how they may impact functionality and potency. Additionally, this review considers ways in which marine PTM might support larger-scale, heterologous AMP manufacturing initiatives, providing insights into translational applications of these important biomolecules.
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Affiliation(s)
- Pengyu Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ting Ye
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Chunyuan Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Praveen Praveen
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science La Trobe University, Victoria, 3086, Australia.
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Wenyi Li
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science La Trobe University, Victoria, 3086, Australia.
| | - Chenjing Shang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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Eilertsen HC, Strømholt J, Bergum JS, Eriksen GK, Ingebrigtsen R. Mass Cultivation of Microalgae: II. A Large Species Pulsing Blue Light Concept. BIOTECH 2023; 12:biotech12020040. [PMID: 37218757 DOI: 10.3390/biotech12020040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023] Open
Abstract
If mass cultivation of photoautotrophic microalgae is to gain momentum and find its place in the new "green future", exceptional optimizations to reduce production costs must be implemented. Issues related to illumination should therefore constitute the main focus, since it is the availability of photons in time and space that drives synthesis of biomass. Further, artificial illumination (e.g., LEDs) is needed to transport enough photons into dense algae cultures contained in large photobioreactors. In the present research project, we employed short-term O2 production and 7-day batch cultivation experiments to evaluate the potential to reduce illumination light energy by applying blue flashing light to cultures of large and small diatoms. Our results show that large diatom cells allow more light penetration for growth compared to smaller cells. PAR (400-700 nm) scans yielded twice as much biovolume-specific absorbance for small biovolume (avg. 7070 μm3) than for large biovolume (avg. 18,703 μm3) cells. The dry weight (DW) to biovolume ratio was 17% lower for large than small cells, resulting in a DW specific absorbance that was 1.75 times higher for small cells compared to large cells. Blue 100 Hz square flashing light yielded the same biovolume production as blue linear light in both the O2 production and batch experiments at the same maximum light intensities. We therefore suggest that, in the future, more focus should be placed on researching optical issues in photobioreactors, and that cell size and flashing blue light should be central in this.
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Affiliation(s)
- Hans Chr Eilertsen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
- Finnfjord AS, N-9305 Finnsnes, Norway
| | | | | | - Gunilla Kristina Eriksen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Richard Ingebrigtsen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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Oh ZG, Askey B, Gunn LH. Red Rubiscos and opportunities for engineering green plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:520-542. [PMID: 36055563 PMCID: PMC9833100 DOI: 10.1093/jxb/erac349] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Nature's vital, but notoriously inefficient, CO2-fixing enzyme Rubisco often limits the growth of photosynthetic organisms including crop species. Form I Rubiscos comprise eight catalytic large subunits and eight auxiliary small subunits and can be classified into two distinct lineages-'red' and 'green'. While red-type Rubiscos (Form IC and ID) are found in rhodophytes, their secondary symbionts, and certain proteobacteria, green-type Rubiscos (Form IA and IB) exist in terrestrial plants, chlorophytes, cyanobacteria, and other proteobacteria. Eukaryotic red-type Rubiscos exhibit desirable kinetic properties, namely high specificity and high catalytic efficiency, with certain isoforms outperforming green-type Rubiscos. However, it is not yet possible to functionally express a high-performing red-type Rubisco in chloroplasts to boost photosynthetic carbon assimilation in green plants. Understanding the molecular and evolutionary basis for divergence between red- and green-type Rubiscos could help us to harness the superior CO2-fixing power of red-type Rubiscos. Here we review our current understanding about red-type Rubisco distribution, biogenesis, and sequence-structure, and present opportunities and challenges for utilizing red-type Rubisco kinetics towards crop improvements.
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Affiliation(s)
- Zhen Guo Oh
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Bryce Askey
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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Biswas H. A story of resilience: Arctic diatom Chaetoceros gelidus exhibited high physiological plasticity to changing CO 2 and light levels. FRONTIERS IN PLANT SCIENCE 2022; 13:1028544. [PMID: 36438134 PMCID: PMC9692007 DOI: 10.3389/fpls.2022.1028544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Arctic phytoplankton are experiencing multifaceted stresses due to climate warming, ocean acidification, retreating sea ice, and associated changes in light availability, and that may have large ecological consequences. Multiple stressor studies on Arctic phytoplankton, particularly on the bloom-forming species, may help understand their fitness in response to future climate change, however, such studies are scarce. In the present study, a laboratory experiment was conducted on the bloom-forming Arctic diatom Chaetoceros gelidus (earlier C. socialis) under variable CO2 (240 and 900 µatm) and light (50 and 100 µmol photons m-2 s-1) levels. The growth response was documented using the pre-acclimatized culture at 2°C in a closed batch system over 12 days until the dissolved inorganic nitrogen was depleted. Particulate organic carbon and nitrogen (POC and PON), pigments, cell density, and the maximum quantum yield of photosystem II (Fv/Fm) were measured on day 4 (D4), 6 (D6), 10 (D10), and 12 (D12). The overall growth response suggested that C. gelidus maintained a steady-state carboxylation rate with subsequent conversion to macromolecules as reflected in the per-cell POC contents under variable CO2 and light levels. A substantial amount of POC buildup at the low CO2 level (comparable to the high CO2 treatment) indicated the possibility of existing carbon dioxide concentration mechanisms (CCMs) that needs further investigation. Pigment signatures revealed a high level of adaptability to variable irradiance in this species without any major CO2 effect. PON contents per cell increased initially but decreased irrespective of CO2 levels when nitrogen was limited (D6 onward) possibly to recycle intracellular nitrogen resources resulting in enhanced C: N ratios. On D12 the decreased dissolved organic nitrogen levels could be attributed to consumption under nitrogen starvation. Such physiological plasticity could make C. gelidus "ecologically resilient" in the future Arctic.
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Affiliation(s)
- Haimanti Biswas
- National Institute of Oceanography - CSIR (Council of Scientific and Industrial Research), Biological Oceanography Division, Goa, India
- Polar Biological Oceanography, Alfred Wegener Institute of Polar and Marine Research, Bremerhaven, Germany
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Zhang B, Shi J, Zhao Y, Wang H, Chu Z, Chen Y, Wu Z, Jiang Z. Pickering interfacial biocatalysis with enhanced diffusion processes for CO2 mineralization. CHINESE JOURNAL OF CATALYSIS 2022. [DOI: 10.1016/s1872-2067(21)63998-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mass Cultivation of Microalgae: I. Experiences with Vertical Column Airlift Photobioreactors, Diatoms and CO2 Sequestration. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12063082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
From 2015 to 2021, we optimized mass cultivation of diatoms in our own developed vertical column airlift photobioreactors using natural and artificial light (LEDs). The project took place at the ferrosilicon producer Finnfjord AS in North Norway as a joint venture with UiT—The Arctic University of Norway. Small (0.1–6–14 m3) reactors were used for initial experiments and to produce inoculum cultures while upscaling experiments took place in a 300 m3 reactor. We here argue that species cultivated in reactors should be large since biovolume specific self-shadowing of light can be lower for large vs. small cells. The highest production, 1.28 cm3 L−1 biovolume (0.09–0.31 g DW day−1), was obtained with continuous culture at ca. 19% light utilization efficiency and 34% CO2 uptake. We cultivated 4–6 months without microbial contamination or biofouling, and this we argue was due to a natural antifouling (anti-biofilm) agent in the algae. In terms of protein quality all essential amino acids were present, and the composition and digestibility of the fatty acids were as required for feed ingredients. Lipid content was ca. 20% of ash-free DW with high EPA levels, and omega-3 and amino acid content increased when factory fume was added. The content of heavy metals in algae cultivated with fume was well within the accepted safety limits. Organic pollutants (e.g., dioxins and PCBs) were below the limits required by the European Union food safety regulations, and bioprospecting revealed several promising findings.
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Blake LI, Cann MJ. Carbon Dioxide and the Carbamate Post-Translational Modification. Front Mol Biosci 2022; 9:825706. [PMID: 35300111 PMCID: PMC8920986 DOI: 10.3389/fmolb.2022.825706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/03/2022] [Indexed: 01/10/2023] Open
Abstract
Carbon dioxide is essential for life. It is at the beginning of every life process as a substrate of photosynthesis. It is at the end of every life process as the product of post-mortem decay. Therefore, it is not surprising that this gas regulates such diverse processes as cellular chemical reactions, transport, maintenance of the cellular environment, and behaviour. Carbon dioxide is a strategically important research target relevant to crop responses to environmental change, insect vector-borne disease and public health. However, we know little of carbon dioxide’s direct interactions with the cell. The carbamate post-translational modification, mediated by the nucleophilic attack by carbon dioxide on N-terminal α-amino groups or the lysine ɛ-amino groups, is one mechanism by which carbon dioxide might alter protein function to form part of a sensing and signalling mechanism. We detail known protein carbamates, including the history of their discovery. Further, we describe recent studies on new techniques to isolate this problematic post-translational modification.
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Iqbal WA, Miller IG, Moore RL, Hope IJ, Cowan-Turner D, Kapralov MV. Rubisco substitutions predicted to enhance crop performance through carbon uptake modelling. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6066-6075. [PMID: 34115846 PMCID: PMC8411856 DOI: 10.1093/jxb/erab278] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/09/2021] [Indexed: 05/03/2023]
Abstract
Improving the performance of the CO2-fixing enzyme Rubisco is among the targets for increasing crop yields. Here, Earth system model (ESM) representations of canopy C3 and C4 photosynthesis were combined with species-specific Rubisco parameters to quantify the consequences of bioengineering foreign Rubiscos into C3 and C4 crops under field conditions. The 'two big leaf' (sunlit/shaded) model for canopy photosynthesis was used together with species-specific Rubisco kinetic parameters including maximum rate (Kcat), Michaelis-Menten constant for CO2 at ambient atmospheric O2 (Kc21%O2), specificity for CO2 to O2 (Sc/o), and associated heat activation (Ha) values. Canopy-scale consequences of replacing native Rubiscos in wheat, maize, and sugar beet with foreign enzymes from 27 species were modelled using data from Ameriflux and Fluxnet databases. Variation among the included Rubisco kinetics differentially affected modelled carbon uptake rates, and Rubiscos from several species of C4 grasses showed the greatest potential of >50% carbon uptake improvement in wheat, and >25% improvement in sugar beet and maize. This study also reaffirms the need for data on fully characterized Rubiscos from more species, and for better parameterization of 'Vcmax' and temperature response of 'Jmax' in ESMs.
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Affiliation(s)
- Wasim A Iqbal
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
- Correspondence:
| | - Isabel G Miller
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Rebecca L Moore
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Iain J Hope
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Daniel Cowan-Turner
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Maxim V Kapralov
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
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Gunn LH, Martin Avila E, Birch R, Whitney SM. The dependency of red Rubisco on its cognate activase for enhancing plant photosynthesis and growth. Proc Natl Acad Sci U S A 2020; 117:25890-25896. [PMID: 32989135 PMCID: PMC7568259 DOI: 10.1073/pnas.2011641117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Plant photosynthesis and growth are often limited by the activity of the CO2-fixing enzyme Rubisco. The broad kinetic diversity of Rubisco in nature is accompanied by differences in the composition and compatibility of the ancillary proteins needed for its folding, assembly, and metabolic regulation. Variations in the protein folding needs of catalytically efficient red algae Rubisco prevent their production in plants. Here, we show this impediment does not extend to Rubisco from Rhodobacter sphaeroides (RsRubisco)-a red-type Rubisco able to assemble in plant chloroplasts. In transplastomic tobRsLS lines expressing a codon optimized Rs-rbcLS operon, the messenger RNA (mRNA) abundance was ∼25% of rbcL transcript and RsRubisco ∼40% the Rubisco content in WT tobacco. To mitigate the low activation status of RsRubisco in tobRsLS (∼23% sites active under ambient CO2), the metabolic repair protein RsRca (Rs-activase) was introduced via nuclear transformation. RsRca production in the tobRsLS::X progeny matched endogenous tobacco Rca levels (∼1 µmol protomer·m2) and enhanced RsRubisco activation to 75% under elevated CO2 (1%, vol/vol) growth. Accordingly, the rate of photosynthesis and growth in the tobRsLS::X lines were improved >twofold relative to tobRsLS. Other tobacco lines producing RsRubisco containing alternate diatom and red algae S-subunits were nonviable as CO2-fixation rates (kcatc) were reduced >95% and CO2/O2 specificity impaired 30-50%. We show differences in hybrid and WT RsRubisco biogenesis in tobacco correlated with assembly in Escherichia coli advocating use of this bacterium to preevaluate the kinetic and chloroplast compatibility of engineered RsRubisco, an isoform amenable to directed evolution.
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Affiliation(s)
- Laura H Gunn
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Elena Martin Avila
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Rosemary Birch
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Spencer M Whitney
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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Young JN, Schmidt K. It's what's inside that matters: physiological adaptations of high-latitude marine microalgae to environmental change. THE NEW PHYTOLOGIST 2020; 227:1307-1318. [PMID: 32391569 DOI: 10.1111/nph.16648] [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: 08/23/2019] [Accepted: 03/23/2020] [Indexed: 05/13/2023]
Abstract
Marine microalgae within seawater and sea ice fuel high-latitude ecosystems and drive biogeochemical cycles through the fixation and export of carbon, uptake of nutrients, and production and release of oxygen and organic compounds. High-latitude marine environments are characterized by cold temperatures, dark winters and a strong seasonal cycle. Within this environment a number of diverse and dynamic habitats exist, particularly in association with the formation and melt of sea ice, with distinct microalgal communities that transition with the season. Algal physiology is a crucial component, both responding to the dynamic environment and in turn influencing its immediate physicochemical environment. As high-latitude oceans shift into new climate regimes the analysis of seasonal responses may provide insights into how microalgae will respond to long-term environmental change. This review discusses recent developments in our understanding of how the physiology of high-latitude marine microalgae is regulated over a polar seasonal cycle, with a focus on ice-associated (sympagic) algae. In particular, physiologies that impact larger scale processes will be explored, with an aim to improve our understanding of current and future ecosystems and biogeochemical cycles.
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Affiliation(s)
- Jodi N Young
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Katrin Schmidt
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
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Goudet MMM, Orr DJ, Melkonian M, Müller KH, Meyer MT, Carmo-Silva E, Griffiths H. Rubisco and carbon-concentrating mechanism co-evolution across chlorophyte and streptophyte green algae. THE NEW PHYTOLOGIST 2020; 227:810-823. [PMID: 32249430 DOI: 10.1111/nph.16577] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/23/2020] [Indexed: 05/19/2023]
Abstract
Green algae expressing a carbon-concentrating mechanism (CCM) are usually associated with a Rubisco-containing micro-compartment, the pyrenoid. A link between the small subunit (SSU) of Rubisco and pyrenoid formation in Chlamydomonas reinhardtii has previously suggested that specific RbcS residues could explain pyrenoid occurrence in green algae. A phylogeny of RbcS was used to compare the protein sequence and CCM distribution across the green algae and positive selection in RbcS was estimated. For six streptophyte algae, Rubisco catalytic properties, affinity for CO2 uptake (K0.5 ), carbon isotope discrimination (δ13 C) and pyrenoid morphology were compared. The length of the βA-βB loop in RbcS provided a phylogenetic marker discriminating chlorophyte from streptophyte green algae. Rubisco kinetic properties in streptophyte algae have responded to the extent of inducible CCM activity, as indicated by changes in inorganic carbon uptake affinity, δ13 C and pyrenoid ultrastructure between high and low CO2 conditions for growth. We conclude that the Rubisco catalytic properties found in streptophyte algae have coevolved and reflect the strength of any CCM or degree of pyrenoid leakiness, and limitations to inorganic carbon in the aquatic habitat, whereas Rubisco in extant land plants reflects more recent selective pressures associated with improved diffusive supply of the terrestrial environment.
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Affiliation(s)
- Myriam M M Goudet
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Michael Melkonian
- Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, 50674, Cologne, Germany
- Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, 45141, Essen, Germany
| | - Karin H Müller
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Moritz T Meyer
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | | | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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Launay H, Huang W, Maberly SC, Gontero B. Regulation of Carbon Metabolism by Environmental Conditions: A Perspective From Diatoms and Other Chromalveolates. FRONTIERS IN PLANT SCIENCE 2020; 11:1033. [PMID: 32765548 PMCID: PMC7378808 DOI: 10.3389/fpls.2020.01033] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/23/2020] [Indexed: 05/08/2023]
Abstract
Diatoms belong to a major, diverse and species-rich eukaryotic clade, the Heterokonta, within the polyphyletic chromalveolates. They evolved as a result of secondary endosymbiosis with one or more Plantae ancestors, but their precise evolutionary history is enigmatic. Nevertheless, this has conferred them with unique structural and biochemical properties that have allowed them to flourish in a wide range of different environments and cope with highly variable conditions. We review the effect of pH, light and dark, and CO2 concentration on the regulation of carbon uptake and assimilation. We discuss the regulation of the Calvin-Benson-Bassham cycle, glycolysis, lipid synthesis, and carbohydrate synthesis at the level of gene transcripts (transcriptomics), proteins (proteomics) and enzyme activity. In contrast to Viridiplantae where redox regulation of metabolic enzymes is important, it appears to be less common in diatoms, based on the current evidence, but regulation at the transcriptional level seems to be widespread. The role of post-translational modifications such as phosphorylation, glutathionylation, etc., and of protein-protein interactions, has been overlooked and should be investigated further. Diatoms and other chromalveolates are understudied compared to the Viridiplantae, especially given their ecological importance, but we believe that the ever-growing number of sequenced genomes combined with proteomics, metabolomics, enzyme measurements, and the application of novel techniques will provide a better understanding of how this important group of algae maintain their productivity under changing conditions.
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Affiliation(s)
- Hélène Launay
- BIP, Aix Marseille Univ CNRS, BIP UMR 7281, Marseille, France
| | - Wenmin Huang
- BIP, Aix Marseille Univ CNRS, BIP UMR 7281, Marseille, France
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Stephen C. Maberly
- UK Centre for Ecology & Hydrology, Lake Ecosystems Group, Lancaster Environment Centre, Lancaster, United Kingdom
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Choi H, Hardy AP, Leissing TM, Chowdhury R, Nakashima Y, Ge W, Markoulides M, Scotti JS, Gerken PA, Thorbjornsrud H, Kang D, Hong S, Lee J, McDonough MA, Park H, Schofield CJ. A human protein hydroxylase that accepts D-residues. Commun Chem 2020; 3:52. [PMID: 36703414 PMCID: PMC9814778 DOI: 10.1038/s42004-020-0290-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/12/2020] [Indexed: 01/29/2023] Open
Abstract
Factor inhibiting hypoxia-inducible factor (FIH) is a 2-oxoglutarate-dependent protein hydroxylase that catalyses C3 hydroxylations of protein residues. We report FIH can accept (D)- and (L)-residues for hydroxylation. The substrate selectivity of FIH differs for (D) and (L) epimers, e.g., (D)- but not (L)-allylglycine, and conversely (L)- but not (D)-aspartate, undergo monohydroxylation, in the tested sequence context. The (L)-Leu-containing substrate undergoes FIH-catalysed monohydroxylation, whereas (D)-Leu unexpectedly undergoes dihydroxylation. Crystallographic, mass spectrometric, and DFT studies provide insights into the selectivity of FIH towards (L)- and (D)-residues. The results of this work expand the potential range of known substrates hydroxylated by isolated FIH and imply that it will be possible to generate FIH variants with altered selectivities.
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Affiliation(s)
- Hwanho Choi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK.,Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 05006, Korea
| | - Adam P Hardy
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Thomas M Leissing
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Yu Nakashima
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Marios Markoulides
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - John S Scotti
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Philip A Gerken
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Helen Thorbjornsrud
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Dahye Kang
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Joongoo Lee
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 05006, Korea.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK.
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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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South PF, Cavanagh AP, Lopez-Calcagno PE, Raines CA, Ort DR. Optimizing photorespiration for improved crop productivity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1217-1230. [PMID: 30126060 DOI: 10.1111/jipb.12709] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/14/2018] [Indexed: 05/24/2023]
Abstract
In C3 plants, photorespiration is an energy-expensive process, including the oxygenation of ribulose-1,5-bisphosphate (RuBP) by ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and the ensuing multi-organellar photorespiratory pathway required to recycle the toxic byproducts and recapture a portion of the fixed carbon. Photorespiration significantly impacts crop productivity through reducing yields in C3 crops by as much as 50% under severe conditions. Thus, reducing the flux through, or improving the efficiency of photorespiration has the potential of large improvements in C3 crop productivity. Here, we review an array of approaches intended to engineer photorespiration in a range of plant systems with the goal of increasing crop productivity. Approaches include optimizing flux through the native photorespiratory pathway, installing non-native alternative photorespiratory pathways, and lowering or even eliminating Rubisco-catalyzed oxygenation of RuBP to reduce substrate entrance into the photorespiratory cycle. Some proposed designs have been successful at the proof of concept level. A plant systems-engineering approach, based on new opportunities available from synthetic biology to implement in silico designs, holds promise for further progress toward delivering more productive crops to farmer's fields.
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Affiliation(s)
- Paul F South
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture/Agricultural Research Service, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Amanda P Cavanagh
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | | | - Christine A Raines
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
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