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Wang C, Lu C, Wang J, Liu X, Wei Z, Qin Y, Zhang H, Wang X, Wei B, Lv W, Mu G. Molecular mechanisms regulating glucose metabolism in quinoa (Chenopodium quinoa Willd.) seeds under drought stress. BMC PLANT BIOLOGY 2024; 24:796. [PMID: 39174961 PMCID: PMC11342610 DOI: 10.1186/s12870-024-05510-w] [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: 01/13/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND Abiotic stress seriously affects the growth and yield of crops. It is necessary to search and utilize novel abiotic stress resistant genes for 2.0 breeding programme in quinoa. In this study, the impact of drought stress on glucose metabolism were investigated through transcriptomic and metabolomic analyses in quinoa seeds. Candidate drought tolerance genes on glucose metabolism pathway were verified by qRT-PCR combined with yeast expression system. RESULTS From 70 quinoa germplasms, drought tolerant material M059 and drought sensitive material M024 were selected by comprehensive evaluation of drought resistance. 7042 differentially expressed genes (DEGs) were indentified through transcriptomic analyses. Gene Ontology (GO) analysis revealed that these DEGs were closely related to carbohydrate metabolic process, phosphorus-containing groups, and intracellular membrane-bounded organelles. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis detected that DEGs were related to pathways involving carbohydrate metabolisms, glycolysis and gluconeogenesis. Twelve key differentially accumulated metabolites (DAMs), (D-galactose, UDP-glucose, succinate, inositol, D-galactose, D-fructose-6-phosphate, D-glucose-6-phosphate, D-glucose-1-phosphate, dihydroxyacetone phosphate, ribulose-5-phosphate, citric acid and L-malate), and ten key candidate DEGs (CqAGAL2, CqINV, CqFrK7, CqCELB, Cqbg1x, CqFBP, CqALDO, CqPGM, CqIDH3, and CqSDH) involved in drought response were identified. CqSDH, CqAGAL2, and Cqβ-GAL13 were candidate genes that have been validated in both transcriptomics and yeast expression screen system. CONCLUSION These findings provide a foundation for elucidating the molecular regulatory mechanisms governing glucose metabolism in quinoa seeds under drought stress, providing insights for future research exploring responses to drought stress in quinoa.
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Affiliation(s)
- Chunmei Wang
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Chuan Lu
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Junling Wang
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Xiaoqing Liu
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Zhimin Wei
- Institute of Millet Crops, Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals(Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, The Key Research Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Yan Qin
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Huilong Zhang
- Shijiazhuang Fubao Ecological Technology Co., LTD, Shijiazhuang, 050000, Hebei Province, P. R. China
| | - Xiaoxia Wang
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Boxiang Wei
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China
| | - Wei Lv
- The S&T Innovation Service Center of Hebei Province, Shijiazhuang, 050000, Hebei Province, P. R. China.
| | - Guojun Mu
- North China State Key Laboratory of Crop Improvement and Regulation, Hebei Provincial Laboratory of Crop Germplasm Resources/College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei Province, P. R. China.
- The Quinoa Industrial Technology Research Institute of Hebei Province, Zhang Jiakou, 075000, Hebei Province, P. R. China.
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Dong X, Rawiwan P, Middleditch M, Guo G, Woo MW, Quek SY. Effects of protein variations by different extraction and dehydration approaches on hempseed protein isolate: Protein pattern, amino acid profiling and label-free proteomics. Food Chem 2024; 460:140426. [PMID: 39047496 DOI: 10.1016/j.foodchem.2024.140426] [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: 03/25/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024]
Abstract
This study evaluates the effects of alkaline and micellisation extraction methods, alongside freeze-drying and spray-drying, on the protein subunits, amino acid profiles, and proteome data of hempseed protein isolate (HPI). Findings revealed that the extraction methods affect protein profiles more than the drying methods. Micellisation-extracted HPI showed higher albumin, oleosin, and sulphur-containing protein levels than alkaline-extracted HPI. The alkali-extracted undried sample (AU) gave more potentially allergenic proteins, including Hsp70 and triosephosphate isomerase, than its micellization-extracted counterpart (MU). Unique potential allergens were identified, including malate dehydrogenase and enolase in AU, and RuBisCo in MU samples. Both drying processes impacted the HPI proteome and reduced RuBisCo in the micellisation-extracted HPI. These insights highlight the crucial role of method selection in HPI processing for optimising production in the food industry.
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Affiliation(s)
- Xuan Dong
- Food Science, School of Chemical Sciences, The University of Auckland, Auckland, 1010, New Zealand.
| | - Pattarasuda Rawiwan
- Food Science, School of Chemical Sciences, The University of Auckland, Auckland, 1010, New Zealand.
| | - Martin Middleditch
- Technical Services, Faculty of Science, The University of Auckland, Auckland, 1010, New Zealand.
| | - George Guo
- Department of Physiology, School of Medical Sciences, University of Auckland, Auckland, New Zealand.
| | - Meng Wai Woo
- Department of Chemical and Materials Engineering, Faculty of Engineering, The University of Auckland, Auckland, 1142, New Zealand.
| | - Siew Young Quek
- Food Science, School of Chemical Sciences, The University of Auckland, Auckland, 1010, New Zealand; Riddet Institute, Centre of Research Excellence for Food Research, Palmerston North 4474, New Zealand.
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Chen S, Qiu G. Physiological and multi-omics analysis reveals the influence of copper on Halophila beccarii Asch. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108785. [PMID: 38824692 DOI: 10.1016/j.plaphy.2024.108785] [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: 02/17/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
High concentrations of copper can pollute coastal waters, primarily from agricultural runoff and mining activities, which can harm marine organisms, including seagrasses. The molecular mechanism of copper toxicity to seagrass currently remains unclear. To determine the response to copper, physiological and multi-omic analyses were conducted to explore the molecular mechanism by which copper affects the global threatened seagrass Halophila beccarii Asch. Excessive copper stress causes oxidative damage and stimulates the activity of the antioxidant enzyme system to remove excess reactive oxygen species (ROS), thereby reducing the damage caused by copper stress. Cu increases the activities of superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), peroxidase (EC 1.11.1.7), ascorbate peroxidase (EC 1.11.1.11), glutathione peroxidase (EC 1.11.1.9), ascorbate oxidase (EC 1.10.3.3), glutathione reductase (EC 1.6.4.2), and dehydroascorbate reductase (EC 1.8.5.1) and the content of malondialdehyde and reduces the activity of monodehydroascorbate reductase (EC 1.6.5.4). Under copper stress, H. beccarii upregulates the metabolic pathways of steroid biosynthesis and cutin, suberin, and wax biosynthesis, downregulates the metabolic pathways of arginine and proline metabolism and fructose and mannose metabolism; the levels of expression of the ribosome-related genes; upregulates the levels of expression of circadian rhythm-related proteins and downregulates the levels of glutathione metabolism and the proteins related to carbon fixation. This study provides new insights into the response of seagrass to copper stress and reports potential candidate metabolites, genes, and proteins that can be considered as biomarkers to improve the protection and management of seagrass meadows.
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Affiliation(s)
- Siting Chen
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Academy of Marine Sciences (Guangxi Mangrove Research Center), Guangxi Academy of Sciences, Beihai, Guangxi, 536007, China.
| | - Guanglong Qiu
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Academy of Marine Sciences (Guangxi Mangrove Research Center), Guangxi Academy of Sciences, Beihai, Guangxi, 536007, China.
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Fang J, Zheng L, Liu G, Zhu H. Comparative Analysis of Chloroplast Genomes in Cephaleuros and Its Related Genus ( Trentepohlia): Insights into Adaptive Evolution. Genes (Basel) 2024; 15:839. [PMID: 39062618 PMCID: PMC11275322 DOI: 10.3390/genes15070839] [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: 06/03/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Cephaleuros species are well-known as plant pathogens that cause red rust or algae spot diseases in many economically cultivated plants that grow in shady and humid environments. Despite their prevalence, the adaptive evolution of these pathogens remains poorly understood. We sequenced and characterized three Cephaleuros (Cephaleuros lagerheimii, Cephaleuros diffusus, and Cephaleuros virescens) chloroplast genomes, and compared them with seven previously reported chloroplast genomes. The chloroplast sequences of C. lagerheimii, C. diffusus, and C. virescens were 480,613 bp, 383,846 bp, and 472,444 bp in length, respectively. These chloroplast genomes encoded 94 genes, including 27 tRNA genes, 3 rRNA genes, and 64 protein-coding genes. Comparative analysis uncovered that the variation in genome size was principally due to the length of intergenic spacer sequences, followed by introns. Furthermore, several highly variable regions (trnY-GTA, trnL-TAG, petA, psbT, trnD-GTC, trnL-TAA, ccsA, petG, psaA, psaB, rps11, rps2, and rps14) were identified. Codon bias analysis revealed that the codon usage pattern of Cephaleuros is predominantly shaped by natural selection. Additionally, six chloroplast protein-coding genes (atpF, chlN, psaA, psaB, psbA, and rbcL) were determined to be under positive selection, suggesting they may play a vital roles in the adaptation of Cephaleuros to low-light intensity habitats.
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Affiliation(s)
- Jiao Fang
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan 430056, China;
| | - Lingling Zheng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (L.Z.); (G.L.)
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (L.Z.); (G.L.)
| | - Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (L.Z.); (G.L.)
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Dong X, Han B, Chen J, Luo D, Zhou Q, Liu Z. Multiomics Analyses Reveal MsC3H29 Positively Regulates Flavonoid Biosynthesis to Improve Drought Resistance of Autotetraploid Cultivated Alfalfa ( Medicago sativa L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14448-14465. [PMID: 38864675 DOI: 10.1021/acs.jafc.4c02472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Alfalfa (Medicago sativa subsp. sativa), the "queen of forage," is the most important perennial legume, with high productivity and an excellent nutritional profile. Medicago sativa subsp. falcata is a subspecies of the alfalfa complex and exhibits better drought tolerance. However, drought stress significantly hampers their development and yield. The molecular mechanisms underlying the aboveground and underground tissues of sativa and falcata responding to drought stress remain obscure. Here, we performed a comprehensive comparative analysis of the physiological and transcriptomic responses of sativa and falcata under drought stress. The results showed that photosynthesis was inhibited, and antioxidant enzymes were activated under drought stress. MsC3H29, a CCCH-type zinc finger protein, was identified as a hub gene through weighted gene coexpression network analysis (WGCNA) and was significantly induced by drought in underground tissue. The MsC3H29 protein was localized in the nucleus. Overexpression (OE) of MsC3H29 can increase the primary root length and fresh weight of transgenic alfalfa hairy roots, while RNA interference (RNAi) decreases them under drought stress. The 2',7'-dichlorodihydrofluorescein diacetate (H2DCFDA) staining revealed that MsC3H29 promoted drought tolerance of alfalfa hairy roots through decreasing ROS accumulation. The targeted metabolome analysis showed that the overexpression of MsC3H29 resulted in higher levels of accumulation for flavonoid monomers, including vicenin, daidzein, apigenin, isorhamnetin, quercetin, and tricin, in transgenic alfalfa hairy roots before and after drought stress, while RNAi led to a reduction. Our study provided a key candidate gene for molecular breeding to improve drought resistance in alfalfa.
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Affiliation(s)
- Xueming Dong
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Bingcheng Han
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Jiwei Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Dong Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Qiang Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
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Yang X, Huang Y, Xia P. The property and function of proteins undergoing liquid-liquid phase separation in plants. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38808958 DOI: 10.1111/pce.14988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 05/30/2024]
Abstract
A wide variety of membrane-less organelles in cells play an essential role in regulating gene expression, RNA processing, plant growth and development, and helping organisms cope with changing external environments. In biology, liquid-liquid phase separation (LLPS) usually refers to a reversible process in which one or more specific molecular components are spontaneously separated from the bulk environment, producing two distinct liquid phases: concentrated and dilute. LLPS may be a powerful cellular compartmentalisation mechanism whereby biocondensates formed via LLPS when biomolecules exceed critical or saturating concentrations in the environment where they are found will be generated. It has been widely used to explain the formation of membrane-less organelles in organisms. LLPS studies in the context of plant physiology are now widespread, but most of the research is still focused on non-plant systems; the study of phase separation in plants needs to be more thorough. Proteins and nucleic acids are the main components involved in LLPS. This review summarises the specific features and properties of biomolecules undergoing LLPS in plants. We describe in detail these biomolecules' structural characteristics, the mechanism of formation of condensates, and the functions of these condensates. Finally, We summarised the phase separation mechanisms in plant growth, development, and stress adaptation.
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Affiliation(s)
- Xuejiao Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yang Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Pengguo Xia
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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Udaypal, Goswami RK, Mehariya S, Verma P. Advances in microalgae-based carbon sequestration: Current status and future perspectives. ENVIRONMENTAL RESEARCH 2024; 249:118397. [PMID: 38309563 DOI: 10.1016/j.envres.2024.118397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/02/2024] [Accepted: 01/30/2024] [Indexed: 02/05/2024]
Abstract
The advancement in carbon dioxide (CO2) sequestration technology has received significant attention due to the adverse effects of CO2 on climate. The mitigation of the adverse effects of CO2 can be accomplished through its conversion into useful products or renewable fuels. In this regard, microalgae is a promising candidate due to its high photosynthesis efficiency, sustainability, and eco-friendly nature. Microalgae utilizes CO2 in the process of photosynthesis and generates biomass that can be utilized to produce various valuable products such as supplements, chemicals, cosmetics, biofuels, and other value-added products. However, at present microalgae cultivation is still restricted to producing value-added products due to high cultivation costs and lower CO2 sequestration efficiency of algal strains. Therefore, it is very crucial to develop novel techniques that can be cost-effective and enhance microalgal carbon sequestration efficiency. The main aim of the present manuscript is to explain how to optimize microalgal CO2 sequestration, integrate valuable product generation, and explore novel techniques like genetic manipulations, phytohormones, quantum dots, and AI tools to enhance the efficiency of CO2 sequestration. Additionally, this review provides an overview of the mass flow of different microalgae and their biorefinery, life cycle assessment (LCA) for achieving net-zero CO2 emissions, and the advantages, challenges, and future perspectives of current technologies. All of the reviewed approaches efficiently enhance microalgal CO2 sequestration and integrate value-added compound production, creating a green and economically profitable process.
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Affiliation(s)
- Udaypal
- Bioprocess and Bioenergy Laboratory (BPBEL), Department of Microbiology, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Rahul Kumar Goswami
- Bioprocess and Bioenergy Laboratory (BPBEL), Department of Microbiology, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Sanjeet Mehariya
- Algal Technology Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, 2713, Qatar
| | - Pradeep Verma
- Bioprocess and Bioenergy Laboratory (BPBEL), Department of Microbiology, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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Song L, Yang T, Wang X, Ye W, Lu G. Magnaporthe oryzae Effector AvrPik-D Targets Rice Rubisco Small Subunit OsRBCS4 to Suppress Immunity. PLANTS (BASEL, SWITZERLAND) 2024; 13:1214. [PMID: 38732428 PMCID: PMC11085154 DOI: 10.3390/plants13091214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Rice blast, caused by the fungal pathogen Magnaporthe oryzae (M. oryzae), is a highly destructive disease that significantly impacts rice yield and quality. During the infection, M. oryzae secretes effector proteins to subvert the host immune response. However, the interaction between the effector protein AvrPik-D and its target proteins in rice, and the mechanism by which AvrPik-D exacerbates disease severity to facilitate infection, remains poorly understood. In this study, we found that the M. oryzae effector AvrPik-D interacts with the Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) small subunit OsRBCS4. The overexpression of the OsRBCS4 gene in transgenic rice not only enhances resistance to M. oryzae but also induces more reactive oxygen species following chitin treatment. OsRBCS4 localizes to chloroplasts and co-localizes with AvrPik-D within these organelles. AvrPik-D suppresses the transcriptional expression of OsRBCS4 and inhibits Rubisco activity in rice. In conclusion, our results demonstrate that the M. oryzae effector AvrPik-D targets the Rubisco small subunit OsRBCS4 and inhibits its carboxylase and oxygenase activity, thereby suppressing rice innate immunity to facilitate infection. This provides a novel mechanism for the M. oryzae effector to subvert the host immunity to promote infection.
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Affiliation(s)
- Linlin Song
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.S.); (T.Y.); (X.W.)
| | - Tao Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.S.); (T.Y.); (X.W.)
| | - Xinxiao Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.S.); (T.Y.); (X.W.)
| | - Wenyu Ye
- China National Engineering Research Center of JUNCAO Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.S.); (T.Y.); (X.W.)
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Zhang H, Lan Y, Jiang C, Cui Y, He Y, Deng J, Lin M, Ye S. Leaf Traits Explain the Growth Variation and Nitrogen Response of Eucalyptus urophylla × Eucalyptus grandis and Dalbergia odorifera in Mixed Culture. PLANTS (BASEL, SWITZERLAND) 2024; 13:988. [PMID: 38611517 PMCID: PMC11013580 DOI: 10.3390/plants13070988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
Mixed cultivation with legumes may alleviate the nitrogen (N) limitation of monoculture Eucalyptus. However, how leaf functional traits respond to N in mixed cultivation with legumes and how they affect tree growth are unclear. Thus, this study investigated the response of leaf functional traits of Eucalyptus urophylla × Eucalyptus grandis (E. urophylla × E. grandis) and Dalbergia odorifera (D. odorifera) to mixed culture and N application, as well as the regulatory pathways of key traits on seedling growth. In this study, a pot-controlled experiment was set up, and seedling growth indicators, leaf physiology, morphological parameters, and N content were collected and analyzed after 180 days of N application treatment. The results indicated that mixed culture improved the N absorption and photosynthetic rate of E. urophylla × E. grandis, further promoting seedling growth but inhibiting the photosynthetic process of D. odorifera, reducing its growth and biomass. Redundancy analysis and path analysis revealed that leaf nitrogen content, pigment content, and photosynthesis-related physiological indicators were the traits most directly related to seedling growth and biomass accumulation, with the net photosynthetic rate explaining 50.9% and 55.8% of the variation in growth indicators for E. urophylla × E. grandis and D. odorifera, respectively. Additionally, leaf morphological traits are related to the trade-off strategy exhibited by E. urophylla × E. grandis and D. odorifera based on N competition. This study demonstrated that physiological traits related to photosynthesis are reliable predictors of N nutrition and tree growth in mixed stands, while leaf morphological traits reflect the resource trade-off strategies of different tree species.
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Affiliation(s)
- Han Zhang
- College of Forestry, Guangxi University, Nanning 530004, China; (H.Z.); (Y.L.); (C.J.); (Y.C.); (Y.H.); (J.D.); (M.L.)
| | - Yahui Lan
- College of Forestry, Guangxi University, Nanning 530004, China; (H.Z.); (Y.L.); (C.J.); (Y.C.); (Y.H.); (J.D.); (M.L.)
| | - Chenyang Jiang
- College of Forestry, Guangxi University, Nanning 530004, China; (H.Z.); (Y.L.); (C.J.); (Y.C.); (Y.H.); (J.D.); (M.L.)
| | - Yuhong Cui
- College of Forestry, Guangxi University, Nanning 530004, China; (H.Z.); (Y.L.); (C.J.); (Y.C.); (Y.H.); (J.D.); (M.L.)
| | - Yaqin He
- College of Forestry, Guangxi University, Nanning 530004, China; (H.Z.); (Y.L.); (C.J.); (Y.C.); (Y.H.); (J.D.); (M.L.)
| | - Jiazhen Deng
- College of Forestry, Guangxi University, Nanning 530004, China; (H.Z.); (Y.L.); (C.J.); (Y.C.); (Y.H.); (J.D.); (M.L.)
| | - Mingye Lin
- College of Forestry, Guangxi University, Nanning 530004, China; (H.Z.); (Y.L.); (C.J.); (Y.C.); (Y.H.); (J.D.); (M.L.)
| | - Shaoming Ye
- College of Forestry, Guangxi University, Nanning 530004, China; (H.Z.); (Y.L.); (C.J.); (Y.C.); (Y.H.); (J.D.); (M.L.)
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi University, Nanning 530004, China
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Sloan DB, Conover JL, Grover CE, Wendel JF, Sharbrough J. Polyploid plants take cytonuclear perturbations in stride. THE PLANT CELL 2024; 36:829-839. [PMID: 38267606 PMCID: PMC10980399 DOI: 10.1093/plcell/koae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/26/2024]
Abstract
Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between nuclear and organellar (mitochondrial and plastid) genomes by creating imbalances in the relative copy number of these genomes and producing genetic incompatibilities between maternally derived organellar genomes and the half of the allopolyploid nuclear genome from the paternal progenitor. Several evolutionary responses have been predicted to ameliorate these effects, including selection for changes in protein sequences that restore cytonuclear interactions; biased gene retention/expression/conversion favoring maternal nuclear gene copies; and fine-tuning of relative cytonuclear genome copy numbers and expression levels. Numerous recent studies, however, have found that evolutionary responses are inconsistent and rarely scale to genome-wide generalities. The apparent robustness of plant cytonuclear interactions to allopolyploidy may reflect features that are general to allopolyploids such as the lack of F2 hybrid breakdown under disomic inheritance, and others that are more plant-specific, including slow sequence divergence in organellar genomes and preexisting regulatory responses to changes in cell size and endopolyploidy during development. Thus, cytonuclear interactions may only rarely act as the main barrier to establishment of allopolyploid lineages, perhaps helping to explain why allopolyploidy is so pervasive in plant evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University,
Fort Collins, CO, USA
| | - Justin L Conover
- Department of Ecology and Evolutionary Biology, University of
Arizona, Tucson, AZ, USA
- Department of Molecular and Cellular Biology, University of
Arizona, Tucson, AZ, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA, USA
| | - Joel Sharbrough
- Department of Biology, New Mexico Institute of Mining and
Technology, Socorro, NM, USA
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11
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Cheng Y, Yang B, Jia T, Hu X. Rubisco Accumulation Factor1-like (RAFL) interacts with RAF1 to mediate Rubisco assembly in Arabidopsis. Biochem Biophys Res Commun 2024; 701:149609. [PMID: 38316092 DOI: 10.1016/j.bbrc.2024.149609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
Rubisco catalysis a rate-limiting step in photosynthesis. It is a complex of eight large (RbcL) and eight small (RbcS) subunits. The biogenesis of Rubisco requires assembly chaperones. One of the key Rubisco assembly chaperones, Rubisco accumulation factor1 (RAF1), assembled as a dimer, acts downstream of chaperonin-assisted RbcL folding by stabilizing RbcL antiparallel dimers for assembly into RbcL8 complexes. In maize, lacking RAF1 causes Rubisco deficient and seedling lethal. A RAF1 homologue, RAF1-like (RAFL), has been detected in Arabidopsis. We found RAFL shares 61.98 % sequence similarity with RAF1. They have similar conserved domains, predicted 3D structures and gene expression pattern. Phylogenetic tree analysis showed that RAFL and RAF1 only present in analyzed dicots, while only one copy of RAF presented in monocots, mosses and green algae. Combined analysis by three different protein-protein interaction methods showed that RAFL interacts with RAF1 both in vivo and in vitro. Taken together, we conclude that RAFL and RAF1 are close paralogous genes, and they can form heterodimer and/or homodimers to mediate Rubisco assembly in Arabidopsis.
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Affiliation(s)
- Yuting Cheng
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Bing Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Ting Jia
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China.
| | - Xueyun Hu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China.
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12
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Bouvier JW, Emms DM, Kelly S. Rubisco is evolving for improved catalytic efficiency and CO 2 assimilation in plants. Proc Natl Acad Sci U S A 2024; 121:e2321050121. [PMID: 38442173 PMCID: PMC10945770 DOI: 10.1073/pnas.2321050121] [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: 11/30/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024] Open
Abstract
Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of the molecular and kinetic evolution of Form I rubisco we uncover the evolutionary trajectory of rubisco kinetic evolution in angiosperms. We show that rbcL is among the 1% of slowest-evolving genes and enzymes on Earth, accumulating one nucleotide substitution every 0.9 My and one amino acid mutation every 7.2 My. Despite this, rubisco catalysis has been continually evolving toward improved CO2/O2 specificity, carboxylase turnover, and carboxylation efficiency. Consistent with this kinetic adaptation, increased rubisco evolution has led to a concomitant improvement in leaf-level CO2 assimilation. Thus, rubisco has been slowly but continually evolving toward improved catalytic efficiency and CO2 assimilation in plants.
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Affiliation(s)
- Jacques W Bouvier
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - David M Emms
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Steven Kelly
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
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13
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Li D, Chen X, Wang Y, Huang W, Wang Y, Zhao X, Song X, Cao X. Panoptic elucidation of algicidal mechanism of Raoultella sp. S1 against the Microcystis aeruginosa by TMT quantitative proteomics. CHEMOSPHERE 2024; 352:141287. [PMID: 38272139 DOI: 10.1016/j.chemosphere.2024.141287] [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: 05/05/2023] [Revised: 11/24/2023] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
Harmful algal blooms (HABs) due to eutrophication are becoming a serious ecological disaster worldwide, threatening human health and the optimal balance of aquatic ecosystems. The traditional approaches to eradicate HABs yield several drawbacks in practical application, while microbial algicidal technology is garnering mounting recognition due to its high efficiency, eco-friendliness, and low cost. In our previous study, we isolated a bacterium strain Raoultella sp. S1 from eutrophic water with high efficiency of algicidal properties. This study further investigated the flocculation and inactivation efficiency of S1 on Microcystis aeruginosa at different eutrophic stages by customizing the algal cell densities. The supernatant extract of S1 strain exhibited remarkable flocculation and inactivation effects against low (1 × 106 cell/mL)and medium (2.7 × 106 cell/mL)concentrations of algal cells, but unexceptional for higher densities. The results further revealed that algal cells at low and medium counts manifested a more apparent antioxidant defense response, while the photosynthetic efficiency and relative electron transport rate were considerably reduced within 24 h. TEM observations confirmed the disruption of thylakoid membranes and cell structure of algal cells by algicidal substances. Moreover, TMT proteomics revealed alterations in protein metabolic pathways of algal cells during the flocculation and lysis stages at the molecular biological level. This signified that the disruption of the photosynthetic system is the core algicidal mechanism of S1 supernatant. In contrast, the photosynthetic metabolic pathways in the HABs were significantly upregulated, increasing the energy supply for the NADPH dehydrogenation process and the upregulation of ATPases in oxidative phosphorylation. Insufficient energy provided by NADPH resulted in a dwindled electron transport rate, stagnation of carbon fixation in dark reactions, and blockage of light energy conversion into chemical energy. Nonetheless, carbohydrate metabolism (gluconeogenesis and glycolysis) proteins were down-regulated and hampered DNA replication and repair. This study aided in unveiling the bacterial management of eutrophication by Raoultella sp. S1 and further arrayed the proteomic mechanism of algal apoptosis.
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Affiliation(s)
- Dongpeng Li
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Xi Chen
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yifei Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Wei Huang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yuhui Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Xiaoxiang Zhao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Xinshan Song
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Xin Cao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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14
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Li Z, Qi L, Cui R, Zhang N, Song C, Li X, Lu X, Fan Y. De novo transcriptome assembly and molecular response mechanism analysis of a diatom Cyclotella meneghiniana Kützing exposed to cadmium. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 272:116020. [PMID: 38306816 DOI: 10.1016/j.ecoenv.2024.116020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 02/04/2024]
Abstract
Cadmium is a persistent heavy metal commonly found in aquatic ecosystems and has a strong toxic effect on organisms. The sensitivity of phytoplankton to environmental changes and its role as an indicator of aquatic ecosystem health have been well-established. However, the mechanisms by which phytoplankton respond to cadmium remain incompletely understood. In this study, we chose the typical planktonic diatom Cyclotella meneghiniana Kützing, by integrating physiological-biochemical data and transcriptome analysis, to reveal the molecular mechanisms of C. meneghiniana responing to cadmium. Under cadmium stress, the cell density and chlorophyll-a content of C. meneghiniana significantly decreased, while MDA content and SOD activity gradually increased. At 72 h of cadmium stress, we found that at this time point, cell abundance and physiological variation were very significant, therefore we selected 72 h for subsequent analysis. To better understand the cadmium stress response mechanisms of C. meneghiniana, a de novo transcriptome method was used to analyse C. meneghiniana under cadmium stress for 72 h, and 1704 (M vs. CK) and 4788 (H vs. CK) differentially expressed genes were found. Our results showed that the changes in gene expression were closely correlated to the physiological-biochemical changes. Although cadmium stress could promote the nitrogen metabolism pathway, ROS scavenging system, and photosynthesis. While, C. meneghiniana under medium and high concentrations of cadmium can also limit various intracellular metabolic pathways, such as the MAPK pathway and phosphatidylinositol metabolic pathway, and the degree of inhibition increases with the increase of stress concentration. In present study, the complete molecular mechanism of the planktonic diatom response to cadmium has been established, which provided important information for further studies on heavy metal pollutants and the multiple functional genes responsible for cadmium sensitivity and tolerance in planktonic diatoms.
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Affiliation(s)
- Zhenxiang Li
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Lin Qi
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Runbo Cui
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Nannan Zhang
- Modern Educational Technology and Experiment Center, Harbin Normal University, Harbin 150025, China
| | - Chunhua Song
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China
| | - Xue Li
- Moutai Institute, Zunyi 564507, China
| | - Xinxin Lu
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China.
| | - Yawen Fan
- College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin 150025, China.
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15
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Trettel DS, Pacheco SL, Laskie AK, Gonzalez-Esquer CR. Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation. FRONTIERS IN PLANT SCIENCE 2024; 15:1346759. [PMID: 38425792 PMCID: PMC10902431 DOI: 10.3389/fpls.2024.1346759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO2-concentrating mechanism. These proteinaceous structures consist of an outer protein shell that partitions Rubisco and carbonic anhydrase from the rest of the cytosol, thereby providing a favorable microenvironment that enhances carbon fixation. The modular nature of carboxysomal architectures makes them attractive for a variety of biotechnological applications such as carbon capture and utilization. In silico approaches, such as molecular dynamics (MD) simulations, can support future carboxysome redesign efforts by providing new spatio-temporal insights on their structure and function beyond in vivo experimental limitations. However, specific computational studies on carboxysomes are limited. Fortunately, all BMC (including the carboxysome) are highly structurally conserved which allows for practical inferences to be made between classes. Here, we review simulations on BMC architectures which shed light on (1) permeation events through the shell and (2) assembly pathways. These models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion. Meanwhile, simulations on BMC assembly demonstrate that assembly pathway is largely dictated kinetically by cargo interactions while final morphology is dependent on shell factors. Overall, these findings are contextualized within the wider experimental BMC literature and framed within the opportunities for carboxysome redesign for biomanufacturing and enhanced carbon fixation.
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Affiliation(s)
- Daniel S. Trettel
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences Group, Los Alamos, NM, United States
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16
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de Souza Celente G, de Cassia de Souza Schneider R, Medianeira Rizzetti T, Lobo EA, Sui Y. Using wastewater as a cultivation alternative for microalga Dunaliella salina: Potentials and challenges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168812. [PMID: 38000734 DOI: 10.1016/j.scitotenv.2023.168812] [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: 08/18/2023] [Revised: 11/03/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
Untreated or poorly treated wastewater still represents environmental issues world-widely. Wastewater, especially saline wastewater treatment, is still primarily associated with high costs from physical and chemical processes, as high salinity hinders biological treatment. One favourable way is to find the suitable biological pathways and organisms to improve the biological treatment efficiency. In this context, halophilic microorganisms could be strong candidates to address the economics and effectiveness of the saline wastewater treatment process. Dunaliella salina is a photoautotrophic microalga that grows in saline environments. It is known for producing marketable bio-compounds such as carotenoids, lipids, and proteins. A biological treatment based on D. salina cultivation offers the opportunity to treat saline wastewater, reducing the threat of possible eutrophication from inappropriate discharge. At the same time, D. salina cultivation could yield compounds of industrial relevance to turn saline wastewater treatment into a profitable and sustainable process. Most research on D. salina has primarily focused on bioproduct generation, leaving thorough reviews of its application in wastewater treatment inadequate. This paper discusses the future challenges and opportunities of using D. salina to treat wastewater from different sources. The main conclusions are (1) D. salina effectively recovers some heavy metals (driven by metal binding capacity and exposure time) and nutrients (driven by pH, their bioavailability, and functional groups in the cell); (2) salinity plays a significant role in bioproducts generation, and (3) wastewater can be combined with the generation of bioproducts.
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Affiliation(s)
- Gleison de Souza Celente
- Environmental Technology Post-graduation Program, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Centre of Excellence in Oleochemical and Biotechnological Products and Processes, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; School of Science, Faculty of Engineering and Science, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | - Rosana de Cassia de Souza Schneider
- Environmental Technology Post-graduation Program, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Centre of Excellence in Oleochemical and Biotechnological Products and Processes, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Tiele Medianeira Rizzetti
- Environmental Technology Post-graduation Program, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Centre of Excellence in Oleochemical and Biotechnological Products and Processes, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Eduardo Alcayaga Lobo
- Environmental Technology Post-graduation Program, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Yixing Sui
- School of Science, Faculty of Engineering and Science, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK.
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17
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Matsushima A, Matsuo K. Removal of plant endogenous proteins from tobacco leaf extract by freeze-thaw treatment for purification of recombinant proteins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111953. [PMID: 38072330 DOI: 10.1016/j.plantsci.2023.111953] [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: 08/15/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/13/2024]
Abstract
Plants are useful as a low-cost source for producing biopharmaceutical proteins. A significant hurdle in the production of recombinant proteins in plants, however, is the complicated process of removing plant-derived components. Removing endogenous plant proteins, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), a major photosynthetic plant enzyme that catalyzes photosynthesis through carboxylation and oxygenation, is important for the purification of recombinant plant proteins. In particular, RuBisCO accounts for 50% of the soluble leaf protein; thus, the removal of RuBisCO is critical for the purification of recombinant proteins from plant materials. An effective conventional method, known as freeze-thaw treatment, was developed for the removal of RuBisCO from Nicotiana benthamiana, which expresses recombinant green fluorescent protein (GFP). Crude extracts or supernatants were frozen at - 30 °C. Upon thawing, most of the RuBisCO was precipitated by centrifugation without significant inactivation and/or yield reduction of GFP. Based on the proteomics analysis, using this method, RuBisCO large and small subunits were reduced to approximately 10% and 20% of those of the unfrozen supernatant solutions, respectively, without the need for specific reagents or equipment. The proteomic analysis also revealed that many ribosomal proteins were removed from the extracts. This method improves the purification process of recombinant proteins from plant materials. Prolonged freezing damaged recombinant β-glucuronidase (GUS), suggesting that the applicability of this treatment should be carefully considered for each recombinant protein.
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Affiliation(s)
- Akito Matsushima
- Frontier Business Division, Chiyoda Corporation, 4-6-2 Minatomirai, Nishi-ku, Yokohama 220-8765, Japan
| | - Kouki Matsuo
- National Institute of Advanced Industrial Science and Technology (AIST), Bioproduction Research Institute, 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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18
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Carpentier P, van der Linden P, Mueller-Dieckmann C. The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF. Acta Crystallogr D Struct Biol 2024; 80:80-92. [PMID: 38265873 PMCID: PMC10836400 DOI: 10.1107/s2059798323010707] [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: 07/25/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024] Open
Abstract
This article describes the High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX) at the ESRF, and highlights new and complementary research opportunities that can be explored using this facility. The laboratory is dedicated to investigating interactions between macromolecules and gases in crystallo, and finds applications in many fields of research, including fundamental biology, biochemistry, and environmental and medical science. At present, the HPMX laboratory offers the use of different high-pressure cells adapted for helium, argon, krypton, xenon, nitrogen, oxygen, carbon dioxide and methane. Important scientific applications of high pressure to macromolecules at the HPMX include noble-gas derivatization of crystals to detect and map the internal architecture of proteins (pockets, tunnels and channels) that allows the storage and diffusion of ligands or substrates/products, the investigation of the catalytic mechanisms of gas-employing enzymes (using oxygen, carbon dioxide or methane as substrates) to possibly decipher intermediates, and studies of the conformational fluctuations or structure modifications that are necessary for proteins to function. Additionally, cryo-cooling protein crystals under high pressure (helium or argon at 2000 bar) enables the addition of cryo-protectant to be avoided and noble gases can be employed to produce derivatives for structure resolution. The high-pressure systems are designed to process crystals along a well defined pathway in the phase diagram (pressure-temperature) of the gas to cryo-cool the samples according to the three-step `soak-and-freeze method'. Firstly, crystals are soaked in a pressurized pure gas atmosphere (at 294 K) to introduce the gas and facilitate its interactions within the macromolecules. Samples are then flash-cooled (at 100 K) while still under pressure to cryo-trap macromolecule-gas complexation states or pressure-induced protein modifications. Finally, the samples are recovered after depressurization at cryo-temperatures. The final section of this publication presents a selection of different typical high-pressure experiments carried out at the HPMX, showing that this technique has already answered a wide range of scientific questions. It is shown that the use of different gases and pressure conditions can be used to probe various effects, such as mapping the functional internal architectures of enzymes (tunnels in the haloalkane dehalogenase DhaA) and allosteric sites on membrane-protein surfaces, the interaction of non-inert gases with proteins (oxygen in the hydrogenase ReMBH) and pressure-induced structural changes of proteins (tetramer dissociation in urate oxidase). The technique is versatile and the provision of pressure cells and their application at the HPMX is gradually being extended to address new scientific questions.
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Affiliation(s)
- Philippe Carpentier
- Université Grenoble Alpes CEA CNRS, IRIG–LCBM UMR 5249, 17 Avenue des Martyrs, 38000 Grenoble, France
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Peter van der Linden
- ESRF, PSCM (Partnership for Soft Condensed Matter), 71 Avenue des Martyrs, 38000 Grenoble, France
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Zhang Z, Zhao J, Li J, Yao J, Wang B, Ma Y, Li N, Wang H, Wang T, Liu B, Gong L. Evolutionary trajectory of organelle-derived nuclear DNAs in the Triticum/Aegilops complex species. PLANT PHYSIOLOGY 2024; 194:918-935. [PMID: 37847157 PMCID: PMC10828211 DOI: 10.1093/plphys/kiad552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/18/2023] [Accepted: 09/23/2023] [Indexed: 10/18/2023]
Abstract
Organelle-derived nuclear DNAs, nuclear plastid DNAs (NUPTs), and nuclear mitochondrial DNAs (NUMTs) have been identified in plants. Most, if not all, genes residing in NUPTs/NUMTs (NUPGs/NUMGs) are known to be inactivated and pseudogenized. However, the role of epigenetic control in silencing NUPGs/NUMGs and the dynamic evolution of NUPTs/NUMTs with respect to organismal phylogeny remain barely explored. Based on the available nuclear and organellar genomic resources of wheat (genus Triticum) and goat grass (genus Aegilops) within Triticum/Aegilops complex species, we investigated the evolutionary fates of NUPTs/NUMTs in terms of their epigenetic silencing and their dynamic occurrence rates in the nuclear diploid genomes and allopolyploid subgenomes. NUPTs and NUMTs possessed similar genomic atlas, including (i) predominantly located in intergenic regions and preferential integration to gene regulation regions and (ii) generating sequence variations in the nuclear genome. Unlike nuclear indigenous genes, the alien NUPGs/NUMGs were associated with repressive epigenetic signals, namely high levels of DNA methylation and low levels of active histone modifications. Phylogenomic analyses suggested that the species-specific and gradual accumulation of NUPTs/NUMTs accompanied the speciation processes. Moreover, based on further pan-genomic analyses, we found significant subgenomic asymmetry in the NUPT/NUMT occurrence, which accumulated during allopolyploid wheat evolution. Our findings provide insight into the dynamic evolutionary fates of organelle-derived nuclear DNA in plants.
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Affiliation(s)
- Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jinyang Yao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yiqiao Ma
- Jilin Academy of Vegetable and Flower Science, Changchun 130033, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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20
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Lee H, Depuydt S, Shin K, De Saeger J, Han T, Park J. Interactive Effects of Blue Light and Water Turbulence on the Growth of the Green Macroalga Ulva australis (Chlorophyta). PLANTS (BASEL, SWITZERLAND) 2024; 13:266. [PMID: 38256819 PMCID: PMC10820934 DOI: 10.3390/plants13020266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/06/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Macroalgal growth and yield are key to sustainable aquaculture. Although light and water turbulence are two important factors that affect algal productivity, research on their interaction is limited. Therefore, in this study, we investigated the effects of different wavelengths of light and the presence or absence of water turbulence on the growth of the green macroalga Ulva australis. Water turbulence was found to enhance the growth of U. australis irrespective of photosynthetic performance, but only in blue light cultures. The quantum dose of blue light required to induce 50% growth promotion was 1.02 mol m-2, which is comparable to the reported values for cryptochrome-mediated effects in other macroalgae. The combined effect of blue light and water turbulence led to the accumulation of photosynthesis-related proteins that support plastid differentiation and facilitate efficient photosynthesis and growth. Our findings thus highlight the potential of harnessing blue light and water turbulence to maximise macroalgal cultivation for sustainable and profitable algal aquaculture.
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Affiliation(s)
- Hojun Lee
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Republic of Korea
| | - Stephen Depuydt
- Erasmus Brussels University of Applied Sciences and Arts, Nijverheidskaai 170, 1070 Brussels, Belgium
| | - Kisik Shin
- Water Environmental Engineering Research Division, National Institute of Environmental Research (NIER), 42, Hwangyeong-ro, Incheon 22689, Republic of Korea
| | - Jonas De Saeger
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Republic of Korea
| | - Taejun Han
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Republic of Korea
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653-Block F, B-9000 Gent, Belgium
| | - Jihae Park
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Republic of Korea
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653-Block F, B-9000 Gent, Belgium
- Center for Environmental and Energy Research, Ghent University Global Campus, 119-5, Songdomunhwa-ro, Incheon 21985, Republic of Korea
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21
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Li D, Wang Y, Qi X, Huang W, Wang Y, Zhao X, Liu Y, Song X, Cao X. A photocatalytic-microbial coupling system for simultaneous removal of harmful algae and enhanced denitrification: Construction, performance and mechanism of action. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132233. [PMID: 37567143 DOI: 10.1016/j.jhazmat.2023.132233] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/10/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
Recently, harmful algal blooms (HABs) have become occurred with increasingly frequency worldwide. High nitrate content is one of the primary causes of eutrophication. Research has shown that photocatalytic materials enhance the effectiveness of microbial denitrification while removing other contaminants, despite some shortcomings. Based on this, we loaded TiO2/C3N4 heterojunctions onto weaveable, flexible carbon fibers and established a novel photocatalytically enhanced microbial denitrification system for the simultaneous removal of harmful algae and Microcystin-LR. We found that 99.35% of Microcystis aeruginosa and 95.34% of MC-LR were simultaneously and effectively removed. Compared to existing denitrification systems, the nitrate removal capacity improved by 72.33%. The denitrifying enzyme activity and electron transport system activity of microorganisms were enhanced by 3.54-3.86 times. Furthermore, the microbial community structure was optimized by the regulation of photogenerated electrons, and the relative abundance of main denitrifying bacteria increased from 50.72% to 66.45%, including Proteobacteria and Bacteroidetes. More importantly, we found that the increased secretion of extracellular polymeric substances by microorganisms may be responsible for the persistence of the reinforcing effect caused by photogenerated electrons in darkness. The higher removal of Microcystis aeruginosa and Microcystin-LR (MC-LR) achieved by the proposed system would reduce the frequency of HAB outbreaks and prevent the associated secondary pollution.
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Affiliation(s)
- Dongpeng Li
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yifei Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiang Qi
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Wei Huang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yuhui Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaoxiang Zhao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yanbiao Liu
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xinshan Song
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xin Cao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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22
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Gao Y, Zhang Y, Ji X, Wang J, Suo N, Liu J, Huo X. Identification of Dioscorea opposite Thunb. CDPK gene family reveals that DoCDPK20 is related to heat resistance. PeerJ 2023; 11:e16110. [PMID: 37744230 PMCID: PMC10517659 DOI: 10.7717/peerj.16110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Temperature affects the growth and yield of yam (Dioscorea opposite Thunb.), and calcium-dependent protein kinases (CDPKs) play an important role in the plant stress response. However, there has been a lack of system analyses of yam's CDPK gene family. In this study, 29 CDPK transcriptome sequences with complete open reading frames (ORFs) were identified from yam RNA sequencing data. The sequences were classified into four groups (I-VI) using phylogenetic analysis. Two DoCDPK genes were randomly selected from each group and the gene patterns of yam leaves were determined using quantitative real-time PCR (qRT-PCR) under high and low temperature stress in order to show their unique functions in mediating specific responses. Among them, DoCDPK20 was significantly induced in high temperatures. The pPZP221-DoCDPK20 was transformed into tobacco leaves using an agrobacterium-mediated method. Under high temperature stress, DoCDPK20 overexpression reduced photosynthesis and improved heat tolerance in transgenic tobacco. Our research offers meaningful perspectives into CDPK genes and new avenues for the genetic engineering and molecular breeding of yam.
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Affiliation(s)
- Yuanli Gao
- Inner Mongolia Agricultural University, Hohhot, China
| | - Yanfang Zhang
- Inner Mongolia Agricultural University, Hohhot, China
| | - Xiang Ji
- Inner Mongolia Agricultural University, Hohhot, China
| | - Jinxin Wang
- Inner Mongolia Agricultural University, Hohhot, China
| | - Ningning Suo
- Inner Mongolia Agricultural University, Hohhot, China
| | - Jiecai Liu
- Inner Mongolia Agricultural University, Hohhot, China
| | - Xiuwen Huo
- Inner Mongolia Agricultural University, Hohhot, China
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23
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Zhou Y, Gunn LH, Birch R, Andersson I, Whitney SM. Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth. NATURE PLANTS 2023; 9:978-986. [PMID: 37291398 DOI: 10.1038/s41477-023-01436-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Improving the carboxylation properties of Rubisco has primarily arisen from unforeseen amino acid substitutions remote from the catalytic site. The unpredictability has frustrated rational design efforts to enhance plant Rubisco towards the prized growth-enhancing carboxylation properties of red algae Griffithsia monilis GmRubisco. To address this, we determined the crystal structure of GmRubisco to 1.7 Å. Three structurally divergent domains were identified relative to the red-type bacterial Rhodobacter sphaeroides RsRubisco that, unlike GmRubisco, are expressed in Escherichia coli and plants. Kinetic comparison of 11 RsRubisco chimaeras revealed that incorporating C329A and A332V substitutions from GmRubisco Loop 6 (corresponding to plant residues 328 and 331) into RsRubisco increased the carboxylation rate (kcatc) by 60%, the carboxylation efficiency in air by 22% and the CO2/O2 specificity (Sc/o) by 7%. Plastome transformation of this RsRubisco Loop 6 mutant into tobacco enhanced photosynthesis and growth up to twofold over tobacco producing wild-type RsRubisco. Our findings demonstrate the utility of RsRubisco for the identification and in planta testing of amino acid grafts from algal Rubisco that can enhance the enzyme's carboxylase potential.
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Affiliation(s)
- Yu Zhou
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Laura H Gunn
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Rosemary Birch
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Norwegian College of Fisheries Sciences, UiT Arctic University of Norway, Tromsø, Norway
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Biocev, Vestec, Czech Republic
| | - Spencer M Whitney
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.
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24
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Shevela D, Kern JF, Govindjee G, Messinger J. Solar energy conversion by photosystem II: principles and structures. PHOTOSYNTHESIS RESEARCH 2023; 156:279-307. [PMID: 36826741 PMCID: PMC10203033 DOI: 10.1007/s11120-022-00991-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/01/2022] [Indexed: 05/23/2023]
Abstract
Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.
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Affiliation(s)
- Dmitry Shevela
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187, Umeå, Sweden.
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Govindjee Govindjee
- Department of Plant Biology, Department of Biochemistry and Center of Biophysics & Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Johannes Messinger
- Department of Chemistry, Chemical Biological Centre, Umeå University, 90187, Umeå, Sweden.
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, 75120, Uppsala, Sweden.
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25
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Cox AJF, Hartley IP, Meir P, Sitch S, Dusenge ME, Restrepo Z, González-Caro S, Villegas JC, Uddling J, Mercado LM. Acclimation of photosynthetic capacity and foliar respiration in Andean tree species to temperature change. THE NEW PHYTOLOGIST 2023; 238:2329-2344. [PMID: 36987979 DOI: 10.1111/nph.18900] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/13/2023] [Indexed: 05/19/2023]
Abstract
Climate warming is causing compositional changes in Andean tropical montane forests (TMFs). These shifts are hypothesised to result from differential responses to warming of cold- and warm-affiliated species, with the former experiencing mortality and the latter migrating upslope. The thermal acclimation potential of Andean TMFs remains unknown. Along a 2000 m Andean altitudinal gradient, we planted individuals of cold- and warm-affiliated species (under common soil and irrigation), exposing them to the hot and cold extremes of their thermal niches, respectively. We measured the response of net photosynthesis (Anet ), photosynthetic capacity and leaf dark respiration (Rdark ) to warming/cooling, 5 months after planting. In all species, Anet and photosynthetic capacity at 25°C were highest when growing at growth temperatures (Tg ) closest to their thermal means, declining with warming and cooling in cold-affiliated and warm-affiliated species, respectively. When expressed at Tg , photosynthetic capacity and Rdark remained unchanged in cold-affiliated species, but the latter decreased in warm-affiliated counterparts. Rdark at 25°C increased with temperature in all species, but remained unchanged when expressed at Tg . Both species groups acclimated to temperature, but only warm-affiliated species decreased Rdark to photosynthetic capacity ratio at Tg as temperature increased. This could confer them a competitive advantage under future warming.
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Affiliation(s)
- Andrew J F Cox
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4RKJ, UK
| | - Iain P Hartley
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4RKJ, UK
| | - Patrick Meir
- School of Geosciences, University of Edinburgh, Edinburgh, EH9 3JN, UK
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Stephen Sitch
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4RKJ, UK
| | - Mirindi Eric Dusenge
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4RKJ, UK
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, Gothenburg, SE-405 30, Sweden
- Department of Biology, The University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Zorayda Restrepo
- Grupo de Investigación en Ecología Aplicada, Universidad de Antioquia, Medellín, Colombia
- UK Centre for Ecology and Hydrology, Crowmarsh-Gifford, Wallingford, OX10 8BB, UK
| | - Sebastian González-Caro
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4RKJ, UK
- UK Centre for Ecology and Hydrology, Crowmarsh-Gifford, Wallingford, OX10 8BB, UK
| | - Juan Camilo Villegas
- Grupo de Investigación en Ecología Aplicada, Universidad de Antioquia, Medellín, Colombia
| | - Johan Uddling
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, Gothenburg, SE-405 30, Sweden
| | - Lina M Mercado
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4RKJ, UK
- UK Centre for Ecology and Hydrology, Crowmarsh-Gifford, Wallingford, OX10 8BB, UK
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26
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Chen Q, Chen L, Teixeira da Silva JA, Yu X. The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia. BMC PLANT BIOLOGY 2023; 23:243. [PMID: 37150831 PMCID: PMC10165817 DOI: 10.1186/s12870-023-04246-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
BACKGROUD Paeonia holds considerable value in medicinal, ornamental horticultural, and edible oil industries, but the incomplete state of phylogenetic research in this genus poses a challenge to the effective conservation and development of wild germplasm, and also impedes the practical utilization of existing cultivars. Due to its uniparental inheritance and lack of recombination, the plastome (i.e., plastid genome), which is a valuable molecular marker for phylogenetic analyses, is characterized by an appropriate rate of nucleotide evolution. METHODS In this study, 10 newly assembled data and available reported data were combined to perform a comparative genomics and phylogenetics analysis of 63 plastomes of 16 Paeonia species, primarily from East Asia, which is the origin and diversity center of Paeonia. RESULTS Ranging between 152,153 and 154,405 bp, most plastomes displayed a conserved structure and relatively low nucleotide diversity, except for six plastomes, which showed obvious IR construction or expansion. A total of 111 genes were annotated in the Paeonia plastomes. Four genes (rpl22, rps3, rps19 and ycf1) showed different copy numbers among accessions while five genes (rpl36, petN, psbI, rpl33 and psbJ) showed strong codon usage biases (ENC < 35). Additional selection analysis revealed that no genes were under positive selection during the domestication of tree peony cultivars whereas four core photosynthesis-related genes (petA, psaA, psaB and rbcL) were under positive selection in herbaceous peony cultivars. This discovery might contribute to the wide adaption of these cultivars. Two types of molecular markers (SSR and SNP) were generated from the 63 plastomes. Even though SSR was more diverse than SNP, it had a weaker ability to delimit Paeonia species than SNP. The reconstruction of a phylogenetic backbone of Paeonia in East Asia revealed significant genetic divergence within the P. ostii groups. Evidence also indicated that the majority of P. suffruticosa cultivars had a maternal origin, from P. ostii. The results of this research also suggest that P. delavayi var. lutea, which likely resulted from hybridization with P. ludlowii, should be classified as a lineage within the broader P. delavayi group. CONCLUSIONS Overall, this study's research findings suggest that the Paeonia plastome is highly informative for phylogenetic and comparative genomic analyses, and could be useful in future research related to taxonomy, evolution, and domestication.
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Affiliation(s)
- Qihang Chen
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, 100083, China
- National Engineering Research Center for Floriculture, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, China
| | - Le Chen
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, 100083, China
- National Engineering Research Center for Floriculture, Beijing, 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, China
| | | | - Xiaonan Yu
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Beijing, 100083, China.
- National Engineering Research Center for Floriculture, Beijing, 100083, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, China.
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27
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Aguiló-Nicolau P, Galmés J, Fais G, Capó-Bauçà S, Cao G, Iñiguez C. Singular adaptations in the carbon assimilation mechanism of the polyextremophile cyanobacterium Chroococcidiopsis thermalis. PHOTOSYNTHESIS RESEARCH 2023; 156:231-245. [PMID: 36941458 PMCID: PMC10154277 DOI: 10.1007/s11120-023-01008-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/16/2023] [Indexed: 05/03/2023]
Abstract
Cyanobacteria largely contribute to the biogeochemical carbon cycle fixing ~ 25% of the inorganic carbon on Earth. However, the carbon acquisition and assimilation mechanisms in Cyanobacteria are still underexplored regardless of being of great importance for shedding light on the origins of autotropism on Earth and providing new bioengineering tools for crop yield improvement. Here, we fully characterized these mechanisms from the polyextremophile cyanobacterium Chroococcidiopsis thermalis KOMAREK 1964/111 in comparison with the model cyanobacterial strain, Synechococcus sp. PCC6301. In particular, we analyzed the Rubisco kinetics along with the in vivo photosynthetic CO2 assimilation in response to external dissolved inorganic carbon, the effect of CO2 concentrating mechanism (CCM) inhibitors on net photosynthesis and the anatomical particularities of their carboxysomes when grown under either ambient air (0.04% CO2) or 2.5% CO2-enriched air. Our results show that Rubisco from C. thermalis possess the highest specificity factor and carboxylation efficiency ever reported for Cyanobacteria, which were accompanied by a highly effective CCM, concentrating CO2 around Rubisco more than 140-times the external CO2 levels, when grown under ambient CO2 conditions. Our findings provide new insights into the Rubisco kinetics of Cyanobacteria, suggesting that improved Sc/o values can still be compatible with a fast-catalyzing enzyme. The combination of Rubisco kinetics and CCM effectiveness in C. thermalis relative to other cyanobacterial species might indicate that the co-evolution between Rubisco and CCMs in Cyanobacteria is not as constrained as in other phylogenetic groups.
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Affiliation(s)
- Pere Aguiló-Nicolau
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain.
| | - Giacomo Fais
- Interdepartmental Centre of Environmental Science and Engineering, University of Cagliari, Via San Giorgio 12, 09124, Cagliari, Italy
| | - Sebastià Capó-Bauçà
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain
| | - Giacomo Cao
- Interdepartmental Centre of Environmental Science and Engineering, University of Cagliari, Via San Giorgio 12, 09124, Cagliari, Italy
- Department of Mechanical, Chemical and Materials Engineering, University of Cagliari, Via Marengo 2, 09123, Cagliari, Italy
| | - Concepción Iñiguez
- Research Group on Plant Biology Under Mediterranean Conditions, Universitat de les Illes Balears, INAGEA, Ctra. Valldemossa km. 7.5, 07122, Palma, Balearic Islands, Spain
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Kupriyanova EV, Pronina NA, Los DA. Adapting from Low to High: An Update to CO 2-Concentrating Mechanisms of Cyanobacteria and Microalgae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1569. [PMID: 37050194 PMCID: PMC10096703 DOI: 10.3390/plants12071569] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
The intracellular accumulation of inorganic carbon (Ci) by microalgae and cyanobacteria under ambient atmospheric CO2 levels was first documented in the 80s of the 20th Century. Hence, a third variety of the CO2-concentrating mechanism (CCM), acting in aquatic photoautotrophs with the C3 photosynthetic pathway, was revealed in addition to the then-known schemes of CCM, functioning in CAM and C4 higher plants. Despite the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of microalgae and cyanobacteria for the CO2 substrate and low CO2/O2 specificity, CCM allows them to perform efficient CO2 fixation in the reductive pentose phosphate (RPP) cycle. CCM is based on the coordinated operation of strategically located carbonic anhydrases and CO2/HCO3- uptake systems. This cooperation enables the intracellular accumulation of HCO3-, which is then employed to generate a high concentration of CO2 molecules in the vicinity of Rubisco's active centers compensating up for the shortcomings of enzyme features. CCM functions as an add-on to the RPP cycle while also acting as an important regulatory link in the interaction of dark and light reactions of photosynthesis. This review summarizes recent advances in the study of CCM molecular and cellular organization in microalgae and cyanobacteria, as well as the fundamental principles of its functioning and regulation.
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29
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Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
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Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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30
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Huang Q, Szebenyi DME. Crystal structure of a type III Rubisco in complex with its product 3-phosphoglycerate. Proteins 2023; 91:330-337. [PMID: 36151846 DOI: 10.1002/prot.26431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 02/04/2023]
Abstract
The crystal structure of the complex of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39) from Archaeoglobus fulgidus (afRubisco) with its products 3PGAs has been determined to a resolution of 1.7 Å and is of the closed form. Type III Rubiscos such as afRubisco have 18 out of the 19 essential amino acid residues of canonical Rubisco; the 19th is Tyr rather than Phe. Superposition with the structure of a complex of the similar tkRubisco with the six-carbon intermediate analog 2CABP shows the same conformation of the 19 residues except for Glu46 and Thr51. Glu46 adopts a unique conformation different from that in other Rubiscos and makes two H-bonds with the ligand 3PGA. Similar to other closed state Rubiscos, the backbone of Thr51 is rotated and the side chain makes an H-bond with the ligand 3PGA. Two product 3PGA molecules are bound at the active site, overlapping well with the 2CABP of tkRubisco/2CABP. The positions of the P1 and P2 phosphate groups differ by 0.4 and 0.53 Å, respectively, between 2CABP and the two 3PGAs. This afRubisco/3PGA complex mimics an intermediate stage of the carboxylation reaction which occurs after the production of the two 3PGA products but before the reopening of the active site. The stability of this complex suggests that the Rubisco active site will not reopen before both 3PGA products are formed.
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Affiliation(s)
- Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York, USA
| | - Doletha M E Szebenyi
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York, USA
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Deslandes-Hérold G, Zanella M, Solhaug E, Fischer-Stettler M, Sharma M, Buergy L, Herrfurth C, Colinas M, Feussner I, Abt MR, Zeeman SC. The PRK/Rubisco shunt strongly influences Arabidopsis seed metabolism and oil accumulation, affecting more than carbon recycling. THE PLANT CELL 2023; 35:808-826. [PMID: 36454674 PMCID: PMC9940875 DOI: 10.1093/plcell/koac338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The carbon efficiency of storage lipid biosynthesis from imported sucrose in green Brassicaceae seeds is proposed to be enhanced by the PRK/Rubisco shunt, in which ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts outside the context of the Calvin-Benson-Bassham cycle to recycle CO2 molecules released during fatty acid synthesis. This pathway utilizes metabolites generated by the nonoxidative steps of the pentose phosphate pathway. Photosynthesis provides energy for reactions such as the phosphorylation of ribulose 5-phosphate by phosphoribulokinase (PRK). Here, we show that loss of PRK in Arabidopsis thaliana (Arabidopsis) blocks photoautotrophic growth and is seedling-lethal. However, seeds containing prk embryos develop normally, allowing us to use genetics to assess the importance of the PRK/Rubisco shunt. Compared with nonmutant siblings, prk embryos produce one-third less lipids-a greater reduction than expected from simply blocking the proposed PRK/Rubisco shunt. However, developing prk seeds are also chlorotic and have elevated starch contents compared with their siblings, indicative of secondary effects. Overexpressing PRK did not increase embryo lipid content, but metabolite profiling suggested that Rubisco activity becomes limiting. Overall, our findings show that the PRK/Rubisco shunt is tightly integrated into the carbon metabolism of green Arabidopsis seeds, and that its manipulation affects seed glycolysis, starch metabolism, and photosynthesis.
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Affiliation(s)
- Gabriel Deslandes-Hérold
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Martina Zanella
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Erik Solhaug
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Michaela Fischer-Stettler
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Mayank Sharma
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Léo Buergy
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Cornelia Herrfurth
- Department for Plant Biochemistry, Albrecht von Haller Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, D-37077 Göttingen, Germany
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, D-37077 Göttingen, Germany
| | - Maite Colinas
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Ivo Feussner
- Department for Plant Biochemistry, Albrecht von Haller Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, D-37077 Göttingen, Germany
- Service Unit for Metabolomics and Lipidomics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, D-37077 Göttingen, Germany
| | - Melanie R Abt
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Samuel C Zeeman
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, CH-8092 Zurich, Switzerland
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Waheeda K, Kitchel H, Wang Q, Chiu PL. Molecular mechanism of Rubisco activase: Dynamic assembly and Rubisco remodeling. Front Mol Biosci 2023; 10:1125922. [PMID: 36845545 PMCID: PMC9951593 DOI: 10.3389/fmolb.2023.1125922] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/31/2023] [Indexed: 02/12/2023] Open
Abstract
Ribulose-1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) enzyme is the limiting step of photosynthetic carbon fixation, and its activation is regulated by its co-evolved chaperone, Rubisco activase (Rca). Rca removes the intrinsic sugar phosphate inhibitors occupying the Rubisco active site, allowing RuBP to split into two 3-phosphoglycerate (3PGA) molecules. This review summarizes the evolution, structure, and function of Rca and describes the recent findings regarding the mechanistic model of Rubisco activation by Rca. New knowledge in these areas can significantly enhance crop engineering techniques used to improve crop productivity.
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Affiliation(s)
- Kazi Waheeda
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States
| | - Heidi Kitchel
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States
| | - Quan Wang
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Po-Lin Chiu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States,*Correspondence: Po-Lin Chiu,
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Lima VS, de Oliveira DRB, da Silva CAS, Santana RDC, Soares NDFF, de Oliveira EB, Martins MA, Coimbra JSDR. Stabilization of oil-water emulsions with protein concentrates from the microalga Tetradesmus obliquus. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:797-808. [PMID: 36712212 PMCID: PMC9873893 DOI: 10.1007/s13197-023-05666-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 11/07/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023]
Abstract
The present work used water-soluble protein concentrates from the microalga Tetradesmus obliquus to stabilize sunflower oil emulsions. Microalgal cells were disrupted by sonication, and proteins were separated from the biomass using two methods, isoelectric and solvent precipitations. The protein extracts were concentrated by lyophilization, and the concentrates were used to produce emulsions with three amounts of Tetradesmus obliquus protein concentrate (TobPC) (0.1, 0.5, and 1.0% w/v). Emulsions were homogenized through sonication and characterized for creaming index, optical microscopy, size distribution, ζ-potential, and rheology. Isoelectric precipitation resulted in TobPC with a high protein content (51.46 ± 2.37%) and a better dispersibility profile. Emulsion stability was higher for both the isoelectric TobPC and control systems than for the TobPC solvent. Solvent TobPC does not efficiently stabilize emulsions at low protein concentrations that showed microscopically larger oil droplets and flocculation spots. A high phase separation velocity was observed for solvent TobPC, probably due to the higher hydrodynamic droplet diameters. The increase in TobPC content in the emulsions resulted in more stable emulsions for all samples. Therefore, Tetradesmus obliquus protein concentrates are a potential emulsifying agent.
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Affiliation(s)
- Viviane Sobreira Lima
- Departamento de Tecnologia de Alimentos (DTA), Universidade Federal de Viçosa (UFV), Campus Universitário S/N, Viçosa, MG CEP 36570-900 Brazil
| | - Davi Rocha Bernardes de Oliveira
- Departamento de Tecnologia de Alimentos (DTA), Universidade Federal de Viçosa (UFV), Campus Universitário S/N, Viçosa, MG CEP 36570-900 Brazil
| | - César Augusto Sodré da Silva
- Departamento de Tecnologia de Alimentos (DTA), Universidade Federal de Viçosa (UFV), Campus Universitário S/N, Viçosa, MG CEP 36570-900 Brazil
| | - Rejane de Castro Santana
- Departamento de Química (DEQ), Universidade Federal de Viçosa (UFV), Campus Universitário S/N, Viçosa, MG CEP 36570-900 Brazil
| | - Nilda de Fátima Ferreira Soares
- Departamento de Tecnologia de Alimentos (DTA), Universidade Federal de Viçosa (UFV), Campus Universitário S/N, Viçosa, MG CEP 36570-900 Brazil
| | - Eduardo Basílio de Oliveira
- Departamento de Tecnologia de Alimentos (DTA), Universidade Federal de Viçosa (UFV), Campus Universitário S/N, Viçosa, MG CEP 36570-900 Brazil
| | - Marcio Aredes Martins
- Departamento de Engenharia Agrícola (DEA), Universidade Federal de Viçosa (UFV), Campus Universitário S/N, Viçosa, MG CEP 36570-900 Brazil
| | - Jane Sélia dos Reis Coimbra
- Departamento de Tecnologia de Alimentos (DTA), Universidade Federal de Viçosa (UFV), Campus Universitário S/N, Viçosa, MG CEP 36570-900 Brazil
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Sytiuk A, Hamard S, Céréghino R, Dorrepaal E, Geissel H, Küttim M, Lamentowicz M, Tuittila ES, Jassey VEJ. Linkages between Sphagnum metabolites and peatland CO 2 uptake are sensitive to seasonality in warming trends. THE NEW PHYTOLOGIST 2023; 237:1164-1178. [PMID: 36336780 PMCID: PMC10108112 DOI: 10.1111/nph.18601] [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: 07/21/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Plants produce a wide diversity of metabolites. Yet, our understanding of how shifts in plant metabolites as a response to climate change feedback on ecosystem processes remains scarce. Here, we test to what extent climate warming shifts the seasonality of metabolites produced by Sphagnum mosses, and what are the consequences of these shifts for peatland C uptake. We used a reciprocal transplant experiment along a climate gradient in Europe to simulate climate change. We evaluated the responses of primary and secondary metabolites in five Sphagnum species and related their responses to gross ecosystem productivity (GEP). When transplanted to a warmer climate, Sphagnum species showed consistent responses to warming, with an upregulation of either their primary or secondary metabolite according to seasons. Moreover, these shifts were correlated to changes in GEP, especially in spring and autumn. Our results indicate that the Sphagnum metabolome is very plastic and sensitive to warming. We also show that warming-induced changes in the seasonality of Sphagnum metabolites have consequences on peatland GEP. Our findings demonstrate the capacity for plant metabolic plasticity to impact ecosystem C processes and reveal a further mechanism through which Sphagnum could shape peatland responses to climate change.
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Affiliation(s)
- Anna Sytiuk
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE)Université Paul Sabatier, CNRSF‐31000ToulouseFrance
| | - Samuel Hamard
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE)Université Paul Sabatier, CNRSF‐31000ToulouseFrance
| | - Régis Céréghino
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE)Université Paul Sabatier, CNRSF‐31000ToulouseFrance
| | - Ellen Dorrepaal
- Department of Ecology and Environmental Science, Climate Impacts Research CentreUmeå UniversitySE‐981 07AbiskoSweden
| | - Honorine Geissel
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE)Université Paul Sabatier, CNRSF‐31000ToulouseFrance
| | - Martin Küttim
- Institute of Ecology, School of Natural Sciences and HealthTallinn UniversityUus‐Sadama 510120TallinnEstonia
| | - Mariusz Lamentowicz
- Climate Change Ecology Research Unit, Faculty of Geographical and Geological SciencesAdam Mickiewicz University in PoznańBogumiła Krygowskiego 1061‐680PoznańPoland
| | - Eeva Stiina Tuittila
- School of Forest SciencesUniversity of Eastern FinlandJoensuu CampusFI‐80100JoensuuFinland
| | - Vincent E. J. Jassey
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE)Université Paul Sabatier, CNRSF‐31000ToulouseFrance
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35
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Su J, Gassmann W. Cytoplasmic regulation of chloroplast ROS accumulation during effector-triggered immunity. FRONTIERS IN PLANT SCIENCE 2023; 14:1127833. [PMID: 36794218 PMCID: PMC9922995 DOI: 10.3389/fpls.2023.1127833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Accumulating evidence suggests that chloroplasts are an important battleground during various microbe-host interactions. Plants have evolved layered strategies to reprogram chloroplasts to promote de novo biosynthesis of defense-related phytohormones and the accumulation of reactive oxygen species (ROS). In this minireview, we will discuss how the host controls chloroplast ROS accumulation during effector-triggered immunity (ETI) at the level of selective mRNA decay, translational regulation, and autophagy-dependent formation of Rubisco-containing bodies (RCBs). We hypothesize that regulation at the level of cytoplasmic mRNA decay impairs the repair cycle of photosystem II (PSII) and thus facilitates ROS generation at PSII. Meanwhile, removing Rubisco from chloroplasts potentially reduces both O2 and NADPH consumption. As a consequence, an over-reduced stroma would further exacerbate PSII excitation pressure and enhance ROS production at photosystem I.
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36
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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Green Biomass-Based Protein for Sustainable Feed and Food Supply: An Overview of Current and Future Prospective. Life (Basel) 2023; 13:life13020307. [PMID: 36836666 PMCID: PMC9966994 DOI: 10.3390/life13020307] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
It is necessary to develop and deploy novel protein production to allow the establishment of a sustainable supply for both humans and animals, given the ongoing expansion of protein demand to meet the future needs of the increased world population and high living standards. In addition to plant seeds, green biomass from dedicated crops or green agricultural waste is also available as an alternative source to fulfill the protein and nutrient needs of humans and animals. The development of extraction and precipitation methods (such as microwave coagulation) for chloroplast and cytoplasmic proteins, which constitute the bulk of leaf protein, will allow the production of leaf protein concentrates (LPC) and protein isolates (LPI). Obtained LPC serves as a sustainable alternative source of animal-based protein besides being an important source of many vital phytochemicals, including vitamins and substances with nutritional and pharmacological effects. Along with it, the production of LPC, directly or indirectly, supports sustainability and circular economy concepts. However, the quantity and quality of LPC largely depend on several factors, including plant species, extraction and precipitation techniques, harvest time, and growing season. This paper provides an overview of the history of green biomass-derived protein from the early green fodder mill concept by Károly Ereky to the state-of-art of green-based protein utilization. It highlights potential approaches for enhancing LPC production, including dedicated plant species, associated extraction methods, selection of optimal technologies, and best combination approaches for improving leaf protein isolation.
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38
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Kulkarni A, Vidal-Henriquez E, Zwicker D. Effective simulations of interacting active droplets. Sci Rep 2023; 13:733. [PMID: 36639416 PMCID: PMC9839783 DOI: 10.1038/s41598-023-27630-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional approaches, like solving the Cahn-Hilliard equation. To overcome this challenge, we here present an alternative, efficient method. The main idea is to focus on the relevant degrees of freedom, like droplet positions and sizes. We derive dynamical equations for these quantities using approximate analytical solutions obtained from a sharp interface limit and linearized equations in the bulk phases. We verify our method against fully-resolved simulations and show that it can describe interacting droplets under the influence of chemical reactions and external gradients using only a fraction of the computational costs of traditional methods. Our method can be extended to include other processes in the future and will thus serve as a relevant platform for understanding the dynamics of droplets in cells.
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Affiliation(s)
- Ajinkya Kulkarni
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany
| | | | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany.
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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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40
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Ang WSL, How JA, How JB, Mueller-Cajar O. The stickers and spacers of Rubiscondensation: assembling the centrepiece of biophysical CO2-concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:612-626. [PMID: 35903998 DOI: 10.1093/jxb/erac321] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Aquatic autotrophs that fix carbon using ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) frequently expend metabolic energy to pump inorganic carbon towards the enzyme's active site. A central requirement of this strategy is the formation of highly concentrated Rubisco condensates (or Rubiscondensates) known as carboxysomes and pyrenoids, which have convergently evolved multiple times in prokaryotes and eukaryotes, respectively. Recent data indicate that these condensates form by the mechanism of liquid-liquid phase separation. This mechanism requires networks of weak multivalent interactions typically mediated by intrinsically disordered scaffold proteins. Here we comparatively review recent rapid developments that detail the determinants and precise interactions that underlie diverse Rubisco condensates. The burgeoning field of biomolecular condensates has few examples where liquid-liquid phase separation can be linked to clear phenotypic outcomes. When present, Rubisco condensates are essential for photosynthesis and growth, and they are thus emerging as powerful and tractable models to investigate the structure-function relationship of phase separation in biology.
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Affiliation(s)
- Warren Shou Leong Ang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Ann How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Boon How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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41
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Cheng X, Li X, Liao B, Xu J, Hu L. Improved performance of proteomic characterization for Panax ginseng by strong cation exchange extraction and liquid chromatography-mass spectrometry analysis. J Chromatogr A 2023; 1688:463692. [PMID: 36549145 DOI: 10.1016/j.chroma.2022.463692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/20/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Panax ginseng is a precious and ancient medicinal plant. The completion of its genome sequencing has laid the foundation for the study of proteome and peptidome. However, the high abundance of secondary metabolites in ginseng reduces the identification efficiency of proteins and peptides in mass spectrometry. In this report, strong cation exchange pretreatment was carried out to eliminate the interference of impurities. Based on the charge separation of proteolytic peptides and metabolites, the sensitivity of mass spectrometry detection was greatly improved. After pretreatment, 2322 and 2685 proteins were identified from the root and stem leaf extract. Further, the ginseng peptidome was analyzed based on this optimized strategy, where 970 and 653 endogenous peptides were identified from root and stem leaf extract, respectively. Functional analysis of proteins and endogenous peptides provided valuable information on the biological activities, metabolic processes, and ginsenoside biosynthesis pathways of ginseng.
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Affiliation(s)
- Xianhui Cheng
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Xiaoying Li
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China.
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42
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Mao Y, Catherall E, Díaz-Ramos A, Greiff GRL, Azinas S, Gunn L, McCormick AJ. The small subunit of Rubisco and its potential as an engineering target. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:543-561. [PMID: 35849331 PMCID: PMC9833052 DOI: 10.1093/jxb/erac309] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/07/2022] [Indexed: 05/06/2023]
Abstract
Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.
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Affiliation(s)
| | | | - Aranzazú Díaz-Ramos
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
| | - George R L Greiff
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stavros Azinas
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Laura Gunn
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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43
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Badger MR, Sharwood RE. Rubisco, the imperfect winner: it's all about the base. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:562-580. [PMID: 36412307 DOI: 10.1093/jxb/erac458] [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: 06/28/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Rubisco catalysis is complex and includes an activation step through the formation of a carbamate at the conserved active site lysine residue and the formation of a highly reactive enediol that is the key to its catalytic reaction. The formation of this enediol is both the basis of its success and its Achilles' heel, creating imperfections to its catalytic efficiency. While Rubisco originally evolved in an atmosphere of high CO2, the earth's multiple oxidation events provided challenges to Rubisco through the fixation of O2 that competes with CO2 at the active site. Numerous catalytic screens across the Rubisco superfamily have identified significant variation in catalytic properties that have been linked to large and small subunit sequences. Despite this, we still have a rudimentary understanding of Rubisco's catalytic mechanism and how the evolution of kinetic properties has occurred. This review identifies the lysine base that functions both as an activator and a proton abstractor to create the enediol as a key to understanding how Rubisco may optimize its kinetic properties. The ways in which Rubisco and its partners have overcome catalytic and activation imperfections and thrived in a world of high O2, low CO2, and variable climatic regimes is remarkable.
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Affiliation(s)
- Murray R Badger
- Research School of Biology, Building 134 Linnaeus Way, Canberra ACT, 2601, Australia
| | - Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Bourke St, Richmond, NSW, 2753, Australia
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Lobus NV, Kulikovskiy MS. The Co-Evolution Aspects of the Biogeochemical Role of Phytoplankton in Aquatic Ecosystems: A Review. BIOLOGY 2023; 12:biology12010092. [PMID: 36671784 PMCID: PMC9855382 DOI: 10.3390/biology12010092] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/12/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023]
Abstract
In freshwater and marine ecosystems, the phytoplankton community is based on microalgae and cyanobacteria, which include phylogenetically very diverse groups of oxygenic photoautotrophs. In the process of evolution, they developed a wide range of bio(geo)chemical adaptations that allow them to effectively use solar radiation, CO2, and nutrients, as well as major and trace elements, to form O2 and organic compounds with a high chemical bond energy. The inclusion of chemical elements in the key processes of energy and plastic metabolism in the cell is determined by redox conditions and the abundance and metabolic availability of elements in the paleoenvironment. Geochemical evolution, which proceeded simultaneously with the evolution of biosystems, contributed to an increase in the number of metals and trace elements acting as cofactors of enzymes involved in metabolism and maintaining homeostasis in the first photoautotrophs. The diversity of metal-containing enzymes and the adaptive ability to replace one element with another without losing the functional properties of enzymes ensured the high ecological plasticity of species and allowed microalgae and cyanobacteria to successfully colonize a wide variety of habitats. In this review, we consider the main aspects of the modern concepts of the biogeochemical evolution of aquatic ecosystems and the role of some metals in the main bioenergetic processes in photosynthetic prokaryotes and eukaryotes. We present generalized data on the efficiency of the assimilation of key nutrients by phytoplankton and their importance in the cycle of carbon, silicon, nitrogen, phosphorus, sulfur, and iron. This article presents modern views on the evolutionary prerequisites for the formation of elemental signatures in different systematic groups of microalgae, as well as the possibility of using the stoichiometric ratio in the study of biological and geochemical processes in aquatic ecosystems.
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Ye C, He Z, Peng J, Wang R, Wang X, Fu M, Zhang Y, Wang A, Liu Z, Jia G, Chen Y, Tian B. Genomic and genetic advances of oiltea-camellia ( Camellia oleifera). FRONTIERS IN PLANT SCIENCE 2023; 14:1101766. [PMID: 37077639 PMCID: PMC10106683 DOI: 10.3389/fpls.2023.1101766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Oiltea-camellia (C. oleifera) is a widely cultivated woody oil crop in Southern China and Southeast Asia. The genome of oiltea-camellia was very complex and not well explored. Recently, genomes of three oiltea-camellia species were sequenced and assembled, multi-omic studies of oiltea-camellia were carried out and provided a better understanding of this important woody oil crop. In this review, we summarized the recent assembly of the reference genomes of oiltea-camellia, genes related to economic traits (flowering, photosynthesis, yield and oil component), disease resistance (anthracnose) and environmental stress tolerances (drought, cold, heat and nutrient deficiency). We also discussed future directions of integrating multiple omics for evaluating genetic resources and mining key genes of important traits, and the application of new molecular breeding and gene editing technologies to accelerate the breeding process of oiltea-camellia.
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Affiliation(s)
- Changrong Ye
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
| | - Zhilong He
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Jiayu Peng
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
| | - Rui Wang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Xiangnan Wang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Mengjiao Fu
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Ying Zhang
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
| | - Ai Wang
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Zhixian Liu
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
| | - Gaofeng Jia
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
| | - Yongzhong Chen
- Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
| | - Bingchuan Tian
- Academy of Innovation and Research, Huazhi Biotechnology Co. Ltd., Changsha, China
- Department of Research and Development, Mountain Yuelu Breeding Innovation Center, Changsha, China
- *Correspondence: Gaofeng Jia, ; Yongzhong Chen, ; Bingchuan Tian,
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Wang H, Hayer-Hartl M. Phase Separation of Rubisco by the Folded SSUL Domains of CcmM in Beta-Carboxysome Biogenesis. Methods Mol Biol 2023; 2563:269-296. [PMID: 36227479 DOI: 10.1007/978-1-0716-2663-4_14] [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: 06/16/2023]
Abstract
Carboxysomes are large, cytosolic bodies present in all cyanobacteria and many proteobacteria that function as the sites of photosynthetic CO2 fixation by the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The carboxysome lumen is enriched with Rubisco and carbonic anhydrase (CA). The polyhedral proteinaceous shell allows the passage of HCO3- ions into the carboxysome, where they are converted to CO2 by CA. Thus, the carboxysome functions as a CO2-concentrating mechanism (CCM), enhancing the efficiency of Rubisco in CO2 fixation. In β-cyanobacteria, carboxysome biogenesis first involves the aggregation of Rubisco by CcmM, a scaffolding protein that exists in two isoforms. Both isoforms contain a minimum of three Rubisco small subunit-like (SSUL) domains, connected by flexible linkers. Multivalent interaction between these linked SSUL domains with Rubisco results in phase separation and condensate formation. Here, we use Rubisco and the short isoform of CcmM (M35) of the β-cyanobacterium Synechococcus elongatus PCC7942 to describe the methods used for in vitro analysis of the mechanism of condensate formation driven by the SSUL domains. The methods include turbidity assays, bright-field and fluorescence microscopy, as well as transmission electron microscopy (TEM) in both negative staining and cryo-conditions.
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Affiliation(s)
- Huping Wang
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
- Membrane Protein Biosynthesis and Quality Control, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
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Pinheiro EDS, Preato AM, Petrucci TVB, dos Santos LS, Glezer I. Phase-separation: a possible new layer for transcriptional regulation by glucocorticoid receptor. Front Endocrinol (Lausanne) 2023; 14:1160238. [PMID: 37124728 PMCID: PMC10145926 DOI: 10.3389/fendo.2023.1160238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
Glucocorticoids (GCs) are hormones involved in circadian adaptation and stress response, and it is also noteworthy that these steroidal molecules present potent anti-inflammatory action through GC receptors (GR). Upon ligand-mediated activation, GR translocates to the nucleus, and regulates gene expression related to metabolism, acute-phase response and innate immune response. GR field of research has evolved considerably in the last decades, providing varied mechanisms that contributed to the understanding of transcriptional regulation and also impacted drug design for treating inflammatory diseases. Liquid-liquid phase separation (LLPS) in cellular processes represents a recent topic in biology that conceptualizes membraneless organelles and microenvironments that promote, or inhibit, chemical reactions and interactions of protein or nucleic acids. The formation of these molecular condensates has been implicated in gene expression control, and recent evidence shows that GR and other steroid receptors can nucleate phase separation (PS). Here we briefly review the varied mechanisms of transcriptional control by GR, which are largely studied in the context of inflammation, and further present how PS can be involved in the control of gene expression. Lastly, we consider how the reported advances on LLPS during transcription control, specially for steroid hormone receptors, could impact the different modalities of GR action on gene expression, adding a new plausible molecular event in glucocorticoid signal transduction.
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de Souza Araújo DM, de Almeida AAF, Pirovani CP, Mora-Ocampo IY, Lima Silva JP, Valle Meléndez RR. Molecular, biochemical and micromorphological responses of cacao seedlings of the Parinari series, carrying the lethal gene Luteus-Pa, in the presence and absence of cotyledons. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:550-569. [PMID: 36525937 DOI: 10.1016/j.plaphy.2022.11.009] [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: 05/29/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Investigations of the compatibility between cacao genotypes of the population of the Parinari series (Pa), resulting from the reciprocal crossing of Pa 30 × Pa 169 and Pa 121 × Pa 169, allowed the verification of the occurrence of the recessive lethal single character called Luteus-Pa. These genotypes have this gene in heterozygosity, which when intercross or self-fertilize, segregate in a 3:1 ratio. Normal (NS) and mutant (MS) seedlings grow normally and, after a period of approximately 30 days of age, MS leaves begin to show a metallic yellow color, followed by necrotic spots, and death of the entire seedling, approximately 40 days after the emergency. The work evaluate the molecular, biochemical and micromorphological responses in NS and MS, with and without cotyledons, resulting from the crossing of the Pa 30 × Pa 169 cacao genotypes, aiming to elucidate the possible lethal mechanisms of the homozygous recessive Luteus-Pa. The presence of the lethal gene Luteus-Pa in the seedlings of the cacao genotypes of the population of the Parinari (Pa), with and without cotyledons, resulting from the crossing of Pa 30 × Pa 169, in addition to regulating the synthesis of proteins related to the photosynthetic and stress defense processes, promoted an increase in the synthesis of proteins involved in the glycolic pathway, induced oxidative stress, altered the mobilization of cotyledonary reserves, the integrity of cell membranes, leaf micromorphology and induced the death of seedlings, soon after depletion of protein and carbohydrate reserves, especially in the absence of cotyledons.
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Affiliation(s)
- D'avila Maria de Souza Araújo
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Alex-Alan Furtado de Almeida
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil.
| | - Carlos Priminho Pirovani
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Irma Yuliana Mora-Ocampo
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - João Paulo Lima Silva
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Raúl René Valle Meléndez
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil; Executive Commission for the Cacao farming Plan, km 22 Jorge Amado Highway, 45650-780, Ilhéus, BA, Brazil
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Extraction of plant protein from green leaves: Biomass composition and processing considerations. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Li D, Wang Y, Song X, Jiang M, Zhao X, Cao X. The inhibitory effects of simulated light sources on the activity of algae cannot be ignored in photocatalytic inhibition. CHEMOSPHERE 2022; 309:136611. [PMID: 36179922 DOI: 10.1016/j.chemosphere.2022.136611] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/06/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Harmful algal blooms (HABs) destroy the balance of the aquatic ecosystem, causing huge economic losses and even further endangers human health. In addition to traditional methods of algae removal, photocatalytic inhibition of algae is drawing more and more interests with rich application scenarios and considerable potential. Simulated visible light sources are used to excite photocatalytic materials and optimize their performance. However, most of the light irradiation intensities used in the study exceeded 50 mW/cm2. And the effects of intense light irradiation conditions on algal growth have rarely been addressed in previous studies. So we focused on the effect of different intensity of light irradiation on the growth of algae. We explored the relationship between light irradiation intensity and algal inactivation rate, and investigated the changes in ROS levels in algal cells under different light irradiation and the resulting response of the antioxidant system. We have found that several major antioxidant enzyme activities, such as SOD and CAT, were significantly higher and lipid peroxidation products (MDA) were accumulating. Intense light irradiation had the most direct effect on the photosynthetic system of algal cells, with the photosynthetic rate and relative electron transfer rate decaying to almost 0 within 30 min, indicating that algal photosynthesis was inhibited in a fairly short period of time. We further observed the physiological and morphological changes of algal cells during this process using TEM and found that the progressive dissolution of the cell membrane system and the damage of organelles associated with photosynthesis play a major role in promoting cell death. We thus conclude that light irradiation has a significant effect on the physiological activity of algal cells and is a non-negligible factor in the study of photocatalytic removal of harmful algae. It will provide theoretical guidance for the future study of photocatalysis on algae inhibition.
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Affiliation(s)
- Dongpeng Li
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yifei Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Xinshan Song
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Mengqi Jiang
- Center for Ecological Research, Kyoto University, Shiga, 520-2113, Japan
| | - Xiaoxiang Zhao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Xin Cao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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