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Rangan P, Furtado A, Chinnusamy V, Henry R. A multi-cell model for the C 4 photosynthetic pathway in developing wheat grains based upon tissue-specific transcriptome data. Biosystems 2024; 238:105195. [PMID: 38555052 DOI: 10.1016/j.biosystems.2024.105195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/20/2024] [Indexed: 04/02/2024]
Abstract
A non-Kranz C4 photosynthesis of the NAD-ME subtype, specifically in developing wheat grains (14 dpa, days post-anthesis) was originally demonstrated using transcriptome-based RNA-seq. Here we present a re-examination of evidence for C4 photosynthesis in the developing grains of wheat and, more broadly, the Pooideae and an investigation of the evolutionary processes and implications. The expression profiles for the genes associated with C4 photosynthesis (C4- and C3-specific) were evaluated using published transcriptome data for the outer pericarp, inner pericarp, and endosperm tissues of the developing wheat grains. The expression of the C4-specific genes across these three tissues revealed the involvement of all three tissues in an orderly fashion to accomplish the non-Kranz NAD-ME-dependent C4 photosynthesis. Based on their expression levels in RPKM (reads per kilobase per million mapped reads) values, a model involving multiple cell- and tissue-types is proposed for C4 photosynthesis involved in the refixation of the respired CO2 from the endosperm tissues in the developing wheat grains. This multi-cell C4 model, proposed to involve more than two cell types, requires further biochemical validation.
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Affiliation(s)
- Parimalan Rangan
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India; Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD4072, Australia.
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD4072, Australia
| | | | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD4072, Australia
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2
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [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: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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3
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Chai K, Chen S, Wang P, Kong W, Ma X, Zhang X. Multiomics Analysis Reveals the Genetic Basis of Volatile Terpenoid Formation in Oolong Tea. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19888-19899. [PMID: 38048088 DOI: 10.1021/acs.jafc.3c06762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Oolong tea has gained great popularity in China due to its pleasant floral and fruity aromas. Although numerous studies have investigated the aroma differences across various tea cultivars, the genetic mechanism is unclear. This study performed multiomics analysis of three varieties suitable for oolong tea and three others with different processing suitability. Our analysis revealed that oolong tea varieties contained higher levels of cadinane sesquiterpenoids. PanTFBS was developed to identify variants of transcription factor binding sites (TFBSs). We found that the CsDCS gene had two TFBS variants in the promoter sequence and a single nucleotide polymorphism (SNP) in the coding sequence. Integrating data on genetic variations, gene expression, and protein-binding sites indicated that CsDCS might be a pivotal gene involved in the biosynthesis of cadinane sesquiterpenoids. These findings advance our understanding of the genetic factors involved in the aroma formation of oolong tea and offer insights into the enhancement of tea aroma.
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Affiliation(s)
- Kun Chai
- College of Life Science, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuai Chen
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Pengjie Wang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Weilong Kong
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xiaokai Ma
- College of Life Science, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xingtan Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
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DiMario RJ, Kophs AN, Apalla AJA, Schnable JN, Cousins AB. Multiple highly expressed phosphoenolpyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses. ANNALS OF BOTANY 2023; 132:413-428. [PMID: 37675505 PMCID: PMC10667006 DOI: 10.1093/aob/mcad116] [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: 04/12/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND AND AIMS Phosphoenolpyruvate (PEP) carboxylase (PEPC) catalyses the irreversible carboxylation of PEP with bicarbonate to produce oxaloacetate. This reaction powers the carbon-concentrating mechanism (CCM) in plants that perform C4 photosynthesis. This CCM is generally driven by a single PEPC gene product that is highly expressed in the cytosol of mesophyll cells. We found two C4 grasses, Panicum miliaceum and Echinochloa colona, that each have two highly expressed PEPC genes. We characterized the kinetic properties of the two most abundant PEPCs in E. colona and P. miliaceum to better understand how the enzyme's amino acid structure influences its function. METHODS Coding sequences of the two most abundant PEPC proteins in E. colona and P. miliaceum were synthesized by GenScript and were inserted into bacteria expression plasmids. Point mutations resulting in substitutions at conserved amino acid residues (e.g. N-terminal serine and residue 890) were created via site-directed PCR mutagenesis. The kinetic properties of semi-purified plant PEPCs from Escherichia coli were analysed using membrane-inlet mass spectrometry and a spectrophotometric enzyme-coupled reaction. KEY RESULTS The two most abundant P. miliaceum PEPCs (PmPPC1 and PmPPC2) have similar sequence identities (>95 %), and as a result had similar kinetic properties. The two most abundant E. colona PEPCs (EcPPC1 and EcPPC2) had identities of ~78 % and had significantly different kinetic properties. The PmPPCs and EcPPCs had different responses to allosteric inhibitors and activators, and substitutions at the conserved N-terminal serine and residue 890 resulted in significantly altered responses to allosteric regulators. CONCLUSIONS The two, significantly expressed C4Ppc genes in P. miliaceum were probably the result of genomes combining from two closely related C4Panicum species. We found natural variation in PEPC's sensitivity to allosteric inhibition that seems to bypass the conserved 890 residue, suggesting alternative evolutionary pathways for increased malate tolerance and other kinetic properties.
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Affiliation(s)
- Robert J DiMario
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Ashley N Kophs
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Anthony J A Apalla
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - James N Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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5
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Wang X, Ma X, Yan G, Hua L, Liu H, Huang W, Liang Z, Chao Q, Hibberd JM, Jiao Y, Zhang M. Gene duplications facilitate C4-CAM compatibility in common purslane. PLANT PHYSIOLOGY 2023; 193:2622-2639. [PMID: 37587696 PMCID: PMC10663116 DOI: 10.1093/plphys/kiad451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 08/18/2023]
Abstract
Common purslane (Portulaca oleracea) integrates both C4 and crassulacean acid metabolism (CAM) photosynthesis pathways and is a promising model plant to explore C4-CAM plasticity. Here, we report a high-quality chromosome-level genome of nicotinamide adenine dinucleotide (NAD)-malic enzyme (ME) subtype common purslane that provides evidence for 2 rounds of whole-genome duplication (WGD) with an ancient WGD (P-β) in the common ancestor to Portulacaceae and Cactaceae around 66.30 million years ago (Mya) and another (Po-α) specific to common purslane lineage around 7.74 Mya. A larger number of gene copies encoding key enzymes/transporters involved in C4 and CAM pathways were detected in common purslane than in related species. Phylogeny, conserved functional site, and collinearity analyses revealed that the Po-α WGD produced the phosphoenolpyruvate carboxylase-encoded gene copies used for photosynthesis in common purslane, while the P-β WGD event produced 2 ancestral genes of functionally differentiated (C4- and CAM-specific) beta carbonic anhydrases involved in the C4 + CAM pathways. Additionally, cis-element enrichment analysis in the promoters showed that CAM-specific genes have recruited both evening and midnight circadian elements as well as the Abscisic acid (ABA)-independent regulatory module mediated by ethylene-response factor cis-elements. Overall, this study provides insights into the origin and evolutionary process of C4 and CAM pathways in common purslane, as well as potential targets for engineering crops by integrating C4 or CAM metabolism.
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Affiliation(s)
- Xiaoliang Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Xuxu Ma
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ge Yan
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lei Hua
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Han Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wei Huang
- National Maize Improvement Center, China Agricultural University, Beijing 100193, China
| | - Zhikai Liang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Qing Chao
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Yuannian Jiao
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Mei Zhang
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Yogadasan N, Doxey AC, Chuong SDX. A Machine Learning Framework Identifies Plastid-Encoded Proteins Harboring C3 and C4 Distinguishing Sequence Information. Genome Biol Evol 2023; 15:evad129. [PMID: 37462292 PMCID: PMC10368328 DOI: 10.1093/gbe/evad129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
C4 photosynthesis is known to have at least 61 independent origins across plant lineages making it one of the most notable examples of convergent evolution. Of the >60 independent origins, a predicted 22-24 origins, encompassing greater than 50% of all known C4 species, exist within the Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) clade of the Poaceae family. This clade is therefore primed with species ideal for the study of genomic changes associated with the acquisition of the C4 photosynthetic trait. In this study, we take advantage of the growing availability of sequenced plastid genomes and employ a machine learning (ML) approach to screen for plastid genes harboring C3 and C4 distinguishing information in PACMAD species. We demonstrate that certain plastid-encoded protein sequences possess distinguishing and informative sequence information that allows them to train accurate ML C3/C4 classification models. Our RbcL-trained model, for example, informs a C3/C4 classifier with greater than 99% accuracy. Accurate prediction of photosynthetic type from individual sequences suggests biologically relevant, and potentially differing roles of these sequence products in C3 versus C4 metabolism. With this ML framework, we have identified several key sequences and sites that are most predictive of C3/C4 status, including RbcL, subunits of the NAD(P)H dehydrogenase complex, and specific residues within, further highlighting their potential significance in the evolution and/or maintenance of C4 photosynthetic machinery. This general approach can be applied to uncover intricate associations between other similar genotype-phenotype relationships.
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Affiliation(s)
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Simon D X Chuong
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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7
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Chen L, Yang Y, Zhao Z, Lu S, Lu Q, Cui C, Parry MAJ, Hu YG. Genome-wide identification and comparative analyses of key genes involved in C 4 photosynthesis in five main gramineous crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1134170. [PMID: 36993845 PMCID: PMC10040670 DOI: 10.3389/fpls.2023.1134170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Compared to C3 species, C4 plants showed higher photosynthetic capacity as well as water and nitrogen use efficiency due to the presence of the C4 photosynthetic pathway. Previous studies have shown that all genes required for the C4 photosynthetic pathway exist in the genomes of C3 species and are expressed. In this study, the genes encoding six key C4 photosynthetic pathway enzymes (β-CA, PEPC, ME, MDH, RbcS, and PPDK) in the genomes of five important gramineous crops (C4: maize, foxtail millet, and sorghum; C3: rice and wheat) were systematically identified and compared. Based on sequence characteristics and evolutionary relationships, their C4 functional gene copies were distinguished from non-photosynthetic functional gene copies. Furthermore, multiple sequence alignment revealed important sites affecting the activities of PEPC and RbcS between the C3 and C4 species. Comparisons of expression characteristics confirmed that the expression patterns of non-photosynthetic gene copies were relatively conserved among species, while C4 gene copies in C4 species acquired new tissue expression patterns during evolution. Additionally, multiple sequence features that may affect C4 gene expression and subcellular localization were found in the coding and promoter regions. Our work emphasized the diversity of the evolution of different genes in the C4 photosynthetic pathway and confirmed that the specific high expression in the leaf and appropriate intracellular distribution were the keys to the evolution of C4 photosynthesis. The results of this study will help determine the evolutionary mechanism of the C4 photosynthetic pathway in Gramineae and provide references for the transformation of C4 photosynthetic pathways in wheat, rice, and other major C3 cereal crops.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yang Yang
- College of Agriculture, Shannxi Agricultural University (Institute of Crop Sciences), Taiyuan, Shanxi, China
| | - Zhangchen Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Shan Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiumei Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunge Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Martin A. J. Parry
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- Institute of Water Saving Agriculture in Arid Regions of China, Northwest A&F University, Yangling, Shaanxi, China
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Behera D, Swain A, Karmakar S, Dash M, Swain P, Baig MJ, Molla KA. Overexpression of Setaria italica phosphoenolpyruvate carboxylase gene in rice positively impacts photosynthesis and agronomic traits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:169-181. [PMID: 36417836 DOI: 10.1016/j.plaphy.2022.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
C4 plants have the inherent capacity to concentrate atmospheric CO2 in the vicinity of RuBisCo, thereby increasing carboxylation, and inhibiting photorespiration. Carbonic anhydrase (CA), the first enzyme of C4 photosynthesis, converts atmospheric CO2 to HCO3-, which is utilized by PEPC to produce C4 acids. Bioengineering of C4 traits into C3 crops is an attractive strategy to increase photosynthesis and water use efficiency. In the present study, we isolated the PEPC gene from the C4 plant Setaria italica and transferred it to C3 rice. Overexpression of SiPEPC resulted in a 2-6-fold increment in PEPC enzyme activity in transgenic lines with respect to non-transformed control. Photosynthetic efficiency was enhanced in transformed plants, which was associated with increased ФPSII, ETR, lower NPQ, and higher chlorophyll accumulation. Water use efficiency was increased by 16-22% in PEPC transgenic rice lines. Increased PEPC activity enhanced quantum yield and carboxylation efficiency of PEPC transgenic lines. Transgenic plants exhibited higher light saturation photosynthesis rate and lower CO2 compensation point, as compared to non-transformed control. An increase in net photosynthesis increased the yield by (23-28.9%) and biomass by (24.1-29%) in transgenic PEPC lines. Altogether, our findings indicate that overexpression of C4-specific SiPEPC enzyme is able to enhance photosynthesis and related parameters in transgenic rice.
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Affiliation(s)
| | - Alaka Swain
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Subhasis Karmakar
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Manaswini Dash
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Padmini Swain
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Mirza J Baig
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India.
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9
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Singh J, Garai S, Das S, Thakur JK, Tripathy BC. Role of C4 photosynthetic enzyme isoforms in C3 plants and their potential applications in improving agronomic traits in crops. PHOTOSYNTHESIS RESEARCH 2022; 154:233-258. [PMID: 36309625 DOI: 10.1007/s11120-022-00978-9] [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: 06/02/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
As compared to C3, C4 plants have higher photosynthetic rates and better tolerance to high temperature and drought. These traits are highly beneficial in the current scenario of global warming. Interestingly, all the genes of the C4 photosynthetic pathway are present in C3 plants, although they are involved in diverse non-photosynthetic functions. Non-photosynthetic isoforms of carbonic anhydrase (CA), phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), the decarboxylating enzymes NAD/NADP-malic enzyme (NAD/NADP-ME), and phosphoenolpyruvate carboxykinase (PEPCK), and finally pyruvate orthophosphate dikinase (PPDK) catalyze reactions that are essential for major plant metabolism pathways, such as the tricarboxylic acid (TCA) cycle, maintenance of cellular pH, uptake of nutrients and their assimilation. Consistent with this view differential expression pattern of these non-photosynthetic C3 isoforms has been observed in different tissues across the plant developmental stages, such as germination, grain filling, and leaf senescence. Also abundance of these C3 isoforms is increased considerably in response to environmental fluctuations particularly during abiotic stress. Here we review the vital roles played by C3 isoforms of C4 enzymes and the probable mechanisms by which they help plants in acclimation to adverse growth conditions. Further, their potential applications to increase the agronomic trait value of C3 crops is discussed.
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Affiliation(s)
- Jitender Singh
- National Institute of Plant Genome Research, New Delhi, 110067, India.
| | - Sampurna Garai
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Shubhashis Das
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Jitendra Kumar Thakur
- National Institute of Plant Genome Research, New Delhi, 110067, India.
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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10
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Chen G, Ren Y, Mohi Ud Din A, Gul H, Chen H, Liang B, Pu T, Sun X, Yong T, Liu W, Liu J, Du J, Yang F, Wu Y, Wang X, Yang W. Comparative analysis of farmer practices and high yield experiments: Farmers could get more maize yield from maize-soybean relay intercropping through high density cultivation of maize. FRONTIERS IN PLANT SCIENCE 2022; 13:1031024. [PMID: 36457530 PMCID: PMC9706207 DOI: 10.3389/fpls.2022.1031024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
Intercropping is a high-yield, resource-efficient planting method. There is a large gap between actual yield and potential yield at farmer's field. Their actual yield of intercropped maize remains unclear under low solar radiation-area, whether this yield can be improved, and if so, what are the underlying mechanism for increasing yield? In the present study, we collected the field management and yield data of intercropping maize by conducting a survey comprising 300 farmer households in 2016-2017. Subsequently, based on surveyed data, we designed an experiment including a high density planting (Dense cultivation and high N fertilization with plough tillage; DC) and normal farmer practice (Common cultivation; CC) to analyze the yield, canopy structure, light interception, photosynthetic parameters, and photosynthetic productivity. Most farmers preferred rotary tillage with a low planting density and N fertilization. Survey data showed that farmer yield ranged between 4-6 Mg ha-1, with highest yield recorded at 10-12 Mg ha-1, suggesting a possibility for yield improvement by improved cropping practices. Results from high density experiment showed that the two-years average yield for DC was 28.8% higher than the CC. Compared to CC, the lower angle between stem and leaf (LA) and higher leaf area index (LAI) in DC resulted in higher light interception in middle canopy and increased the photosynthetic productivity under DC. Moreover, in upper and lower canopies, the average activity of phosphoenolpyruvate (PEP) carboxylase was 70% higher in DC than CC. Briefly, increase in LAI and high Pn improved both light interception and photosynthetic productivity, thereby mediating an increase in the maize yield. Overall, these results indicated that farmer's yields on average can be increased by 2.1 Mg ha-1 by increasing planting density and N fertilization, under plough tillage.
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Affiliation(s)
- Guopeng Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Yongfu Ren
- Agriculture Technology Extension Station, Liangzhou County Bureau of Agriculture and Rural Affairs, Wuwei, China
| | - Atta Mohi Ud Din
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
- National Research Center of Intercropping, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hina Gul
- National Center of Industrial Biotechnology, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Shamsabad, Pakistan
| | - Hanlin Chen
- Agriculture Technology Extension Station, Pingchang County Bureau of Agriculture and Rural Affairs, Bazhong, China
| | - Bing Liang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Tian Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Xin Sun
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Taiwen Yong
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Weiguo Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Jiang Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Junbo Du
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Feng Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Yushan Wu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Xiaochun Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
| | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), Chengdu, China
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11
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Wu C, Guo D. Computational Docking Reveals Co-Evolution of C4 Carbon Delivery Enzymes in Diverse Plants. Int J Mol Sci 2022; 23:ijms232012688. [PMID: 36293547 PMCID: PMC9604239 DOI: 10.3390/ijms232012688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins are modular functionalities regulating multiple cellular activities in prokaryotes and eukaryotes. As a consequence of higher plants adapting to arid and thermal conditions, C4 photosynthesis is the carbon fixation process involving multi-enzymes working in a coordinated fashion. However, how these enzymes interact with each other and whether they co-evolve in parallel to maintain interactions in different plants remain elusive to date. Here, we report our findings on the global protein co-evolution relationship and local dynamics of co-varying site shifts in key C4 photosynthetic enzymes. We found that in most of the selected key C4 photosynthetic enzymes, global pairwise co-evolution events exist to form functional couplings. Besides, protein-protein interactions between these enzymes may suggest their unknown functionalities in the carbon delivery process. For PEPC and PPCK regulation pairs, pocket formation at the interactive interface are not necessary for their function. This feature is distinct from another well-known regulation pair in C4 photosynthesis, namely, PPDK and PPDK-RP, where the pockets are necessary. Our findings facilitate the discovery of novel protein regulation types and contribute to expanding our knowledge about C4 photosynthesis.
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12
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Tian H, Zhou Q, Liu W, Zhang J, Chen Y, Jia Z, Shao Y, Wang H. Responses of photosynthetic characteristics of oat flag leaf and spike to drought stress. FRONTIERS IN PLANT SCIENCE 2022; 13:917528. [PMID: 35968085 PMCID: PMC9365945 DOI: 10.3389/fpls.2022.917528] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/12/2022] [Indexed: 05/27/2023]
Abstract
Raising crops production via improving photosynthesis has always been focused. Recently excavating and increasing the photosynthetic capacity of non-leaf organs becomes an important approach to crops yield increase. Here we studied the photosynthetic characteristics of the flag leaf and the non-leaf organs including the sheath, the glume and the lemma under greenhouse. The relative water content (RWC), the stomatal characteristics, the photosynthetic pigment contents, the enzyme activities in C3 and C4 pathway and the malate content of the flag leaf and the non-leaf organs on 7, 14, 21, and 28 days after anthesis (denoted by 7DAA, 14DAA, 21DAA, and 28DAA) were determined under well-watered (CK) and water-stressed (D) treatments. Drought stress significantly reduced the RWC of the flag leaf and the non-leaf organs, while the variation of RWC in the glume and the lemma was lower than in the flag leaf. The chlorophyll a content, the chlorophyll b content, the total chlorophyll content and the xanthophyll content in the flag leaf were significantly decreased under D. However, drought stress significantly increased the photosynthetic pigment contents in the glume at the late stage (21DAA and 28DAA). In addition, the induced activities of PEPC, NADP-MDH, NADP-ME, NAD-ME, and PPDK in non-leaf organs under drought stress suggested that the C4 photosynthetic pathway in non-leaf organs compensated the limited C3 photosynthesis in the flag leaf. Non-leaf organs, in particular the glume, showed the crucial function in maintaining the stable photosynthetic performance of oat.
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Affiliation(s)
- Haoqi Tian
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
| | - Qingping Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
| | - Wenhui Liu
- Academy of Animal Science and Veterinary Medicine of Qinghai Province, Xining, China
| | - Jing Zhang
- Sichuan Animal Science Academy, Chengdu, China
| | - Youjun Chen
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
| | - Zhifeng Jia
- Academy of Animal Science and Veterinary Medicine of Qinghai Province, Xining, China
| | - Yuqiao Shao
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
| | - Hui Wang
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Southwest Minzu University, Chengdu, China
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13
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Zhang C, Ottenheim C, Weingarten M, Ji L. Microbial Utilization of Next-Generation Feedstocks for the Biomanufacturing of Value-Added Chemicals and Food Ingredients. Front Bioeng Biotechnol 2022; 10:874612. [PMID: 35480982 PMCID: PMC9035589 DOI: 10.3389/fbioe.2022.874612] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Global shift to sustainability has driven the exploration of alternative feedstocks beyond sugars for biomanufacturing. Recently, C1 (CO2, CO, methane, formate and methanol) and C2 (acetate and ethanol) substrates are drawing great attention due to their natural abundance and low production cost. The advances in metabolic engineering, synthetic biology and industrial process design have greatly enhanced the efficiency that microbes use these next-generation feedstocks. The metabolic pathways to use C1 and C2 feedstocks have been introduced or enhanced into industrial workhorses, such as Escherichia coli and yeasts, by genetic rewiring and laboratory evolution strategies. Furthermore, microbes are engineered to convert these low-cost feedstocks to various high-value products, ranging from food ingredients to chemicals. This review highlights the recent development in metabolic engineering, the challenges in strain engineering and bioprocess design, and the perspectives of microbial utilization of C1 and C2 feedstocks for the biomanufacturing of value-added products.
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Affiliation(s)
- Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Congqiang Zhang, ,
| | - Christoph Ottenheim
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Melanie Weingarten
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - LiangHui Ji
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
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14
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Huang W, Zhang L, Columbus JT, Hu Y, Zhao Y, Tang L, Guo Z, Chen W, McKain M, Bartlett M, Huang CH, Li DZ, Ge S, Ma H. A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C 4 photosynthesis. MOLECULAR PLANT 2022; 15:755-777. [PMID: 35093593 DOI: 10.1016/j.molp.2022.01.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/09/2021] [Accepted: 01/24/2022] [Indexed: 05/11/2023]
Abstract
Poaceae (the grasses) includes rice, maize, wheat, and other crops, and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11 000 species with a global distribution that contributes to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong phylogenetic support for their monophyly. However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain. To better resolve the Poaceae phylogeny, we generated 342 transcriptomic and seven genomic datasets; these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1200 low-copy nuclear genes were retrieved from these datasets, with several subsets obtained using additional criteria, and used for coalescent analyses to reconstruct a Poaceae phylogeny. Our results strongly support the monophyly of 11 subfamilies; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. Molecular clock analyses estimated the crown age of Poaceae to be ∼101 million years old. Ancestral character reconstruction of C3/C4 photosynthesis supports the hypothesis of multiple independent origins of C4 photosynthesis. These origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which suggests that members of three paralogous subclades (ppc-aL1a, ppc-aL1b, and ppc-B2) were recruited as functional C4ppc genes. This study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.
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Affiliation(s)
- Weichen Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - J Travis Columbus
- Rancho Santa Ana Botanic Garden and Claremont Graduate University, 1500 North College Avenue, Claremont, CA 91711, USA
| | - Yi Hu
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Yiyong Zhao
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Lin Tang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhenhua Guo
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Wenli Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Michael McKain
- Department of Biological Sciences, University of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL 35487, USA
| | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, 611 North Pleasant Street, 221 Morrill 3, Amherst, MA 01003 USA
| | - Chien-Hsun Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA.
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15
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Shu JP, Yan YH, Wang RJ. Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C 4 and crassulacean acid metabolism plants. PeerJ 2022; 10:e12828. [PMID: 35116203 PMCID: PMC8784020 DOI: 10.7717/peerj.12828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/03/2022] [Indexed: 01/10/2023] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.
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Affiliation(s)
- Jiang-Ping Shu
- Key laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yue-Hong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Jiang Wang
- Key laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China,University of Chinese Academy of Sciences, Beijing, China
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16
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Moody NR, Phansopal C, Reid JD. An in vitro Coupled Assay for PEPC with Control of Bicarbonate Concentration. Bio Protoc 2021; 11:e4264. [PMID: 35087923 DOI: 10.21769/bioprotoc.4264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 11/02/2022] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) catalyzes a critical step in carbon metabolism in plants and bacteria, the irreversible reaction between bicarbonate and phosphoenolpyruvate to produce the C4 compound oxaloacetate. This enzyme is particularly important in the context of C4 photosynthesis, where it is the initial carbon-fixing enzyme. Many studies have used kinetic approaches to characterize the properties of PEPCs from different species, different post-translational states, and after mutagenesis. Most of these studies have worked at a fixed saturating concentration of bicarbonate. Controlling the concentration of bicarbonate is difficult at low concentrations because of equilibration with atmospheric CO2. We describe here a simple, repeatable, and gas-tight assay system for PEPC that allows bicarbonate concentrations to be controlled above ca. 50 µM.
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Affiliation(s)
- Nicholas R Moody
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield, S3 7HF, United Kingdom
| | - Chatawal Phansopal
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield, S3 7HF, United Kingdom
| | - James D Reid
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield, S3 7HF, United Kingdom
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17
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Sales CRG, Wang Y, Evers JB, Kromdijk J. Improving C4 photosynthesis to increase productivity under optimal and suboptimal conditions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5942-5960. [PMID: 34268575 PMCID: PMC8411859 DOI: 10.1093/jxb/erab327] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/09/2021] [Indexed: 05/05/2023]
Abstract
Although improving photosynthetic efficiency is widely recognized as an underutilized strategy to increase crop yields, research in this area is strongly biased towards species with C3 photosynthesis relative to C4 species. Here, we outline potential strategies for improving C4 photosynthesis to increase yields in crops by reviewing the major bottlenecks limiting the C4 NADP-malic enzyme pathway under optimal and suboptimal conditions. Recent experimental results demonstrate that steady-state C4 photosynthesis under non-stressed conditions can be enhanced by increasing Rubisco content or electron transport capacity, both of which may also stimulate CO2 assimilation at supraoptimal temperatures. Several additional putative bottlenecks for photosynthetic performance under drought, heat, or chilling stress or during photosynthetic induction await further experimental verification. Based on source-sink interactions in maize, sugarcane, and sorghum, alleviating these photosynthetic bottlenecks during establishment and growth of the harvestable parts are likely to improve yield. The expected benefits are also shown to be augmented by the increasing trend in planting density, which increases the impact of photosynthetic source limitation on crop yields.
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Affiliation(s)
- Cristina R G Sales
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Yu Wang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jochem B Evers
- Centre for Crops Systems Analysis (WUR), Wageningen University, Wageningen, The Netherlands
| | - Johannes Kromdijk
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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18
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Cao J, Cheng G, Wang L, Maimaitijiang T, Lan H. Genome-Wide Identification and Analysis of the Phosphoenolpyruvate Carboxylase Gene Family in Suaeda aralocaspica, an Annual Halophyte With Single-Cellular C 4 Anatomy. FRONTIERS IN PLANT SCIENCE 2021; 12:665279. [PMID: 34527003 PMCID: PMC8435749 DOI: 10.3389/fpls.2021.665279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) plays pivotal roles in the carbon fixation of photosynthesis and a variety of metabolic and stress pathways. Suaeda aralocaspica belongs to a single-cellular C4 species and carries out a photosynthetic pathway in an unusually elongated chlorenchyma cell, which is expected to have PEPCs with different characteristics. To identify the different isoforms of PEPC genes in S. aralocaspica and comparatively analyze their expression and regulation patterns as well as the biochemical and enzymatic properties in this study, we characterized a bacterial-type PEPC (BTPC; SaPEPC-4) in addition to the two plant-type PEPCs (PTPCs; SaPEPC-1 and SaPEPC-2) using a genome-wide identification. SaPEPC-4 presented a lower expression level in all test combinations with an unknown function; two SaPTPCs showed distinct subcellular localizations and different spatiotemporal expression patterns but positively responded to abiotic stresses. Compared to SaPEPC-2, the expression of SaPEPC-1 specifically in chlorenchyma cell tissues was much more active with the progression of development and under various stresses, particularly sensitive to light, implying the involvement of SaPEPC-1 in a C4 photosynthetic pathway. In contrast, SaPEPC-2 was more like a non-photosynthetic PEPC. The expression trends of two SaPTPCs in response to light, development, and abiotic stresses were also matched with the changes in PEPC activity in vivo (native) or in vitro (recombinant), and the biochemical properties of the two recombinant SaPTPCs were similar in response to various effectors while the catalytic efficiency, substrate affinity, and enzyme activity of SaPEPC-2 were higher than that of SaPEPC-1 in vitro. All the different properties between these two SaPTPCs might be involved in transcriptional (e.g., specific cis-elements), posttranscriptional [e.g., 5'-untranslated region (5'-UTR) secondary structure], or translational (e.g., PEPC phosphorylation/dephosphorylation) regulatory events. The comparative studies on the different isoforms of the PEPC gene family in S. aralocaspica may help to decipher their exact role in C4 photosynthesis, plant growth/development, and stress resistance.
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19
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Lyu MJA, Gowik U, Kelly S, Covshoff S, Hibberd JM, Sage RF, Ludwig M, Wong GKS, Westhoff P, Zhu XG. The coordination of major events in C 4 photosynthesis evolution in the genus Flaveria. Sci Rep 2021; 11:15618. [PMID: 34341365 PMCID: PMC8329263 DOI: 10.1038/s41598-021-93381-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/31/2021] [Indexed: 12/13/2022] Open
Abstract
C4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C4 photosynthesis from its ancestral C3 pathway can help us better understand the generic principles of the evolution of complex traits and guide the engineering of C3 crops for higher yields. Here, we used the genus Flaveria that contains C3, C3-C4, C4-like and C4 species as a system to study the evolution of C4 photosynthesis. We first mapped transcript abundance, protein sequence and morphological features onto the phylogenetic tree of the genus Flaveria, and calculated the evolutionary correlation of different features; we then predicted the relative changes of ancestral nodes of those features to illustrate the major events during the evolution of C4 photosynthesis. We found that gene expression and protein sequence showed consistent modification patterns in the phylogenetic tree. High correlation coefficients ranging from 0.46 to 0.9 among gene expression, protein sequence and morphology were observed. The greatest modification of those different features consistently occurred at the transition between C3-C4 species and C4-like species. Our results show highly coordinated changes in gene expression, protein sequence and morphological features, which support evolutionary major events during the evolution of C4 metabolism.
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Affiliation(s)
- Ming-Ju Amy Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Udo Gowik
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany
| | - Steve Kelly
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Martha Ludwig
- School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Department of Medicine and Department of Biological Sciences, The University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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20
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Meng X, Xu J, Zhang M, Du R, Zhao W, Zeng Q, Tu Z, Chen J, Chen B. Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings. BMC Genomics 2021; 22:543. [PMID: 34271866 PMCID: PMC8283932 DOI: 10.1186/s12864-021-07873-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 07/05/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Most plants rely on photosynthesis; therefore, albinism in plants with leaves that are white instead of green causes slow growth, dwarfing, and even death. Although albinism has been characterized in annual model plants, little is known about albino trees. Jackfruit (Artocarpus heterophyllus) is an important tropical fruit tree species. To gain insight into the mechanisms underlying the differential growth and development between albino jackfruit mutants and green seedlings, we analyzed root, stem, and leaf tissues by combining PacBio single-molecule real-time (SMRT) sequencing, high-throughput RNA-sequencing (RNA-seq), and metabolomic analysis. RESULTS We identified 8,202 differentially expressed genes (DEGs), including 225 genes encoding transcription factors (TFs), from 82,572 full-length transcripts. We also identified 298 significantly changed metabolites (SCMs) in albino A. heterophyllus seedlings from a set of 692 metabolites in A. heterophyllus seedlings. Pathway analysis revealed that these DEGs were highly enriched in metabolic pathways such as 'photosynthesis', 'carbon fixation in photosynthetic organisms', 'glycolysis/gluconeogenesis', and 'TCA cycle'. Analysis of the metabolites revealed 76 SCMs associated with metabolic pathways in the albino mutants, including L-aspartic acid, citric acid, succinic acid, and fumaric acid. We selected 225 differentially expressed TF genes, 333 differentially expressed metabolic pathway genes, and 76 SCMs to construct two correlation networks. Analysis of the TF-DEG network suggested that basic helix-loop-helix (bHLH) and MYB-related TFs regulate the expression of genes involved in carbon fixation and energy metabolism to affect light responses or photomorphogenesis and normal growth. Further analysis of the DEG-SCM correlation network and the photosynthetic carbon fixation pathway suggested that NAD-ME2 (encoding a malic enzyme) and L-aspartic acid jointly inhibit carbon fixation in the albino mutants, resulting in reduced photosynthetic efficiency and inhibited plant growth. CONCLUSIONS Our preliminarily screening identified candidate genes and metabolites specifically affected in albino A. heterophyllus seedlings, laying the foundation for further study of the regulatory mechanism of carbon fixation during photosynthesis and energy metabolism. In addition, our findings elucidate the way genes and metabolites respond in albino trees.
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Affiliation(s)
- Xiangxu Meng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Jiahong Xu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Maoning Zhang
- School of Agricultural Sciences, Zhengzhou University, 450001, Zhengzhou, People's Republic of China
| | - Ruyue Du
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Wenxiu Zhao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Qing Zeng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Zhihua Tu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China
| | - Jinhui Chen
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China.
- Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, 570228, Haikou, People's Republic of China.
| | - Beibei Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, 524088, Zhanjiang, People's Republic of China.
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21
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Nomura K, Sakurai Y, Dozono M. Molecular Cloning of Novel-Type Phospho enolpyruvate Carboxylase Isoforms in Pitaya ( Hylocereus undatus). PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091241. [PMID: 32967083 PMCID: PMC7569800 DOI: 10.3390/plants9091241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is an important enzyme involved in the initial CO2 fixation of crassulacean acid metabolism (CAM) photosynthesis. To understand the cultivation characteristics of a CAM plant pitaya, it is necessary to clarify the characteristics of PEPC in this species. Here, we cloned three PEPC cDNAs in pitaya, HuPPC1, HuPPC2, and HuPPC3, which encode 942, 934, and 966 amino acid residues, respectively. Phylogenetic analysis indicated that these PEPC belonged to plant-type PEPC (PTPC), although HuPPC1 and HuPPC2 have no Ser-phosphorylation motif in N-terminal region, which is a crucial regulation site in PTPC and contributes to CAM periodicity. HuPPC1 and HuPPC2 phylogenetically unique to the Cactaceae family, whereas HuPPC3 was included in a CAM clade. Two isoforms were partially purified at the protein level and were assigned as HuPPC2 and HuPPC3 using MASCOT analysis. The most distinct difference in enzymatic properties between the two was sensitivity to malate and aspartate, both of which are allosteric inhibitors of PEPC. With 2 mM malate, HuPPC3 was inhibited to 10% of the initial activity, whereas HuPPC2 activity was maintained at 70%. Aspartate inhibited HuPPC3 activity by approximately 50% at 5 mM; however, such inhibition was not observed for HuPPC2 at 10 mM. These results suggest that HuPPC3 corresponds to a general CAM-related PEPC, whereas HuPPC1 and HuPPC2 are related to carbon and/or nitrogen metabolism, with a characteristic regulation mechanism similar to those of Cactaceae plants.
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Affiliation(s)
- Keiichi Nomura
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
| | - Yuho Sakurai
- Faculty of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
| | - Mayu Dozono
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan;
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22
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Recurrent sequence evolution after independent gene duplication. BMC Evol Biol 2020; 20:98. [PMID: 32770961 PMCID: PMC7414715 DOI: 10.1186/s12862-020-01660-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/17/2020] [Indexed: 11/10/2022] Open
Abstract
Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.
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23
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Moody NR, Christin PA, Reid JD. Kinetic Modifications of C 4 PEPC Are Qualitatively Convergent, but Larger in Panicum Than in Flaveria. FRONTIERS IN PLANT SCIENCE 2020; 11:1014. [PMID: 32719709 PMCID: PMC7350407 DOI: 10.3389/fpls.2020.01014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
C4 photosynthesis results from a set of anatomical features and biochemical components that act together to concentrate CO2 within the leaf and boost productivity. This complex trait evolved independently many times, resulting in various realizations of the phenotype, but in all C4 plants the primary fixation of atmospheric carbon is catalyzed by phosphoenolpyruvate carboxylase. Comparisons of C4 and non-C4 PEPC from a few closely related species suggested that the enzyme was modified to meet the demands of the C4 cycle. However, very few C4 groups have been investigated, hampering general conclusions. To test the hypothesis that distant C4 lineages underwent convergent biochemical changes, we compare the kinetic variation between C4 and non-C4 PEPC from a previously assessed young lineage (Flaveria, Asteraceae) with those from an older lineage found within the distantly related grass family (Panicum). Despite the evolutionary distance, the kinetic changes between the non-C4 and C4 PEPC are qualitatively similar, with a decrease in sensitivity for inhibitors, an increased specificity (k cat/K m) for bicarbonate, and a decreased specificity (k cat/K m) for PEP. The differences are more pronounced in the older lineage Panicum, which might indicate that optimization of PEPC for the C4 context increases with evolutionary time.
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Affiliation(s)
- Nicholas R. Moody
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
| | | | - James D. Reid
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
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24
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Lyu MJA, Wang Y, Jiang J, Liu X, Chen G, Zhu XG. What Matters for C 4 Transporters: Evolutionary Changes of Phospho enolpyruvate Transporter for C 4 Photosynthesis. FRONTIERS IN PLANT SCIENCE 2020; 11:935. [PMID: 32695130 PMCID: PMC7338763 DOI: 10.3389/fpls.2020.00935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
C4 photosynthesis is a complex trait that evolved from its ancestral C3 photosynthesis by recruiting pre-existing genes. These co-opted genes were changed in many aspects compared to their counterparts in C3 species. Most of the evolutionary changes of the C4 shuttle enzymes are well characterized, however, evolutionary changes for the recruited metabolite transporters are less studied. Here we analyzed the evolutionary changes of the shuttle enzyme phosphoenolpyruvate (PEP) transporter (PPT) during its recruitment from C3 to C4 photosynthesis. Our analysis showed that among the two PPT paralogs PPT1 and PPT2, PPT1 was the copy recruited for C4 photosynthesis in multiple C4 lineages. During C4 evolution, PPT1 gained increased transcript abundance, shifted its expression from predominantly in root to in leaf and from bundle sheath cell to mesophyll cell, and gained more rapid and long-lasting responsiveness to light. Modifications occurred in both regulatory and coding regions in C4 PPT1 as compared to C3 PPT1, however, the PEP transporting function of PPT1 remained. We found that PPT1 of a Flaveria C4 species recruited a MEM1 B submodule in the promoter region, which might be related to the increased transcript abundance of PPT1 in C4 mesophyll cells. The case study of PPT further suggested that high transcript abundance in a proper location is of high priority for PPT to support C4 function.
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Affiliation(s)
- Ming-Ju Amy Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence In Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yaling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence In Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jianjun Jiang
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin, Madison, WI, United States
| | - Xinyu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence In Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Genyun Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence In Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence In Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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25
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Structural and biochemical evidence of the glucose 6-phosphate-allosteric site of maize C4-phosphoenolpyruvate carboxylase: its importance in the overall enzyme kinetics. Biochem J 2020; 477:2095-2114. [PMID: 32459324 DOI: 10.1042/bcj20200304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
Activation of phosphoenolpyruvate carboxylase (PEPC) enzymes by glucose 6-phosphate (G6P) and other phospho-sugars is of major physiological relevance. Previous kinetic, site-directed mutagenesis and crystallographic results are consistent with allosteric activation, but the existence of a G6P-allosteric site was questioned and competitive activation-in which G6P would bind to the active site eliciting the same positive homotropic effect as the substrate phosphoenolpyruvate (PEP)-was proposed. Here, we report the crystal structure of the PEPC-C4 isozyme from Zea mays with G6P well bound into the previously proposed allosteric site, unambiguously confirming its existence. To test its functionality, Asp239-which participates in a web of interactions of the protein with G6P-was changed to alanine. The D239A variant was not activated by G6P but, on the contrary, inhibited. Inhibition was also observed in the wild-type enzyme at concentrations of G6P higher than those producing activation, and probably arises from G6P binding to the active site in competition with PEP. The lower activity and cooperativity for the substrate PEP, lower activation by glycine and diminished response to malate of the D239A variant suggest that the heterotropic allosteric activation effects of free-PEP are also abolished in this variant. Together, our findings are consistent with both the existence of the G6P-allosteric site and its essentiality for the activation of PEPC enzymes by phosphorylated compounds. Furthermore, our findings suggest a central role of the G6P-allosteric site in the overall kinetics of these enzymes even in the absence of G6P or other phospho-sugars, because of its involvement in activation by free-PEP.
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26
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Abstract
C4 photosynthesis evolved multiple times independently from ancestral C3 photosynthesis in a broad range of flowering land plant families and in both monocots and dicots. The evolution of C4 photosynthesis entails the recruitment of enzyme activities that are not involved in photosynthetic carbon fixation in C3 plants to photosynthesis. This requires a different regulation of gene expression as well as a different regulation of enzyme activities in comparison to the C3 context. Further, C4 photosynthesis relies on a distinct leaf anatomy that differs from that of C3, requiring a differential regulation of leaf development in C4. We summarize recent progress in the understanding of C4-specific features in evolution and metabolic regulation in the context of C4 photosynthesis.
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Affiliation(s)
- Urte Schlüter
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany; ,
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany; ,
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27
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Alvarez CE, Bovdilova A, Höppner A, Wolff CC, Saigo M, Trajtenberg F, Zhang T, Buschiazzo A, Nagel-Steger L, Drincovich MF, Lercher MJ, Maurino VG. Molecular adaptations of NADP-malic enzyme for its function in C 4 photosynthesis in grasses. NATURE PLANTS 2019; 5:755-765. [PMID: 31235877 DOI: 10.1038/s41477-019-0451-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
In C4 grasses of agronomical interest, malate shuttled into the bundle sheath cells is decarboxylated mainly by nicotinamide adenine dinucleotide phosphate (NADP)-malic enzyme (C4-NADP-ME). The activity of C4-NADP-ME was optimized by natural selection to efficiently deliver CO2 to Rubisco. During its evolution from a plastidic non-photosynthetic NADP-ME, C4-NADP-ME acquired increased catalytic efficiency, tetrameric structure and pH-dependent inhibition by its substrate malate. Here, we identified specific amino acids important for these C4 adaptions based on strict differential conservation of amino acids, combined with solving the crystal structures of maize and sorghum C4-NADP-ME. Site-directed mutagenesis and structural analyses show that Q503, L544 and E339 are involved in catalytic efficiency; E339 confers pH-dependent regulation by malate, F140 is critical for the stabilization of the oligomeric structure and the N-terminal region is involved in tetramerization. Together, the identified molecular adaptations form the basis for the efficient catalysis and regulation of one of the central biochemical steps in C4 metabolism.
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Affiliation(s)
- Clarisa E Alvarez
- Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina
| | - Anastasiia Bovdilova
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Astrid Höppner
- Center for Structural Studies, Hreinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christian-Claus Wolff
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Mariana Saigo
- Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich Heine University, Düsseldorf, Germany
- Institut of Complex Systems, Structural Biochemistry (ICS-6), Jülich, Germany
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Integrative Microbiology of Zoonotic Agents, Department of Microbiology, Institut Pasteur, Paris, France
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich Heine University, Düsseldorf, Germany
- Institut of Complex Systems, Structural Biochemistry (ICS-6), Jülich, Germany
| | - Maria F Drincovich
- Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina
| | - Martin J Lercher
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
- Institute for Computer Science and Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Veronica G Maurino
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany.
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28
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Gandullo J, Monreal JA, Álvarez R, Díaz I, García-Mauriño S, Echevarría C. Anionic Phospholipids Induce Conformational Changes in Phosphoenolpyruvate Carboxylase to Increase Sensitivity to Cathepsin Proteases. FRONTIERS IN PLANT SCIENCE 2019; 10:582. [PMID: 31143196 PMCID: PMC6521631 DOI: 10.3389/fpls.2019.00582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a cytosolic, homotetrameric enzyme that serves a variety of functions in plants, acting as the primary form of CO2 fixation in the C4 photosynthesis pathway (C4-PEPC). In a previous work we have shown that C4-PEPC bind anionic phospholipids, resulting in PEPC inactivation. Also, we showed that PEPC can associate with membranes and to be partially proteolyzed. However, the mechanism controlling this remains unknown. Using semi purified-PEPC from sorghum leaf and a panel of PEPC-specific antibodies, we analyzed the conformational changes in PEPC induced by anionic phospholipids to cause the inactivation of the enzyme. Conformational changes observed involved the exposure of the C-terminus of PEPC from the native, active enzyme conformation. Investigation of the protease activity associated with PEPC demonstrated that cysteine proteases co-purify with the enzyme, with protease-specific substrates revealing cathepsin B and L as the major protease species present. The anionic phospholipid-induced C-terminal exposed conformation of PEPC appeared highly sensitive to the identified cathepsin protease activity and showed initial proteolysis of the enzyme beginning at the N-terminus. Taken together, these data provide the first evidence that anionic phospholipids promote not only the inactivation of the PEPC enzyme, but also its proteolysis.
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Affiliation(s)
- Jacinto Gandullo
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - José-Antonio Monreal
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Rosario Álvarez
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Isabel Díaz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
| | - Sofía García-Mauriño
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Cristina Echevarría
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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29
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Ünlü ES, Ünüvar ÖC, Aydın M. Identification of alternative oxidase encoding genes in Caulerpa cylindracea by de novo RNA-Seq assembly analysis. Mar Genomics 2019; 46:41-48. [PMID: 30922784 DOI: 10.1016/j.margen.2019.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/06/2019] [Accepted: 03/06/2019] [Indexed: 11/29/2022]
Abstract
Alternative oxidases (AOX) are defined in plants, fungi and algae. The main function of AOX proteins has been described for electron flow through electron transport chain and regulation of mitochondrial retrograde signaling pathway. The roles of AOX proteins have been characterized in reproduction and resistance against oxidative stress, cold stress, starvation, and biotic attacks. Caulerpa cylindracea is an invasive marine green alga. Although the natural habitats of the species are Australia coasts, the impact of the invasion has been monitored through the Mediterranean Sea and the Aegean Sea. C. cylindracea species have advantages against others by showing higher resistance to stress conditions such as cold, starvation, pathogen attacks and by their capability of sexual and vegetative reproduction. Comparing the advantages of C. cylindracea over the niche and defined functional roles of mitochondrial AOX proteins, it is evident that AOX proteins are likely involved in developing those advantageous skills in C. cylindracea. However, there is limited data about biochemical and molecular mechanisms that take part in stress resistance and invasion characteristics. We aimed to identify mitochondrial alternative oxidase encoding genes in C. cylindracea while annotating whole transcriptome data for the species. Samples were collected from Seferihisar/İzmir. Transcriptome analysis from pooled RNA samples revealed 47,400 assembled contigs represented by 33,340 unigenes. Using standalone Blast analysis, we were able to identify two alternative oxidase encoding genes.
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Affiliation(s)
- Ercan Selçuk Ünlü
- Bolu Abant İzzet Baysal University, Faculty of Arts and Science, Department of Chemistry, Bolu 14280, Turkey.
| | - Ömer Can Ünüvar
- Bolu Abant İzzet Baysal University, Faculty of Arts and Science, Department of Chemistry, Bolu 14280, Turkey
| | - Meryem Aydın
- Bolu Abant İzzet Baysal University, Faculty of Arts and Science, Department of Chemistry, Bolu 14280, Turkey
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30
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DiMario RJ, Cousins AB. A single serine to alanine substitution decreases bicarbonate affinity of phosphoenolpyruvate carboxylase in C4Flaveria trinervia. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:995-1004. [PMID: 30517744 PMCID: PMC6363079 DOI: 10.1093/jxb/ery403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/20/2018] [Indexed: 05/12/2023]
Abstract
Phosphoenolpyruvate (PEP) carboxylase (PEPc) catalyzes the first committed step of C4 photosynthesis generating oxaloacetate from bicarbonate (HCO3-) and PEP. It is hypothesized that PEPc affinity for HCO3- has undergone selective pressure for a lower KHCO3 (Km for HCO3-) to increase the carbon flux entering the C4 cycle, particularly during conditions that limit CO2 availability. However, the decrease in KHCO3 has been hypothesized to cause an unavoidable increase in KPEP (Km for PEP). Therefore, the amino acid residue S774 in the C4 enzyme, which has been shown to increase KPEP, should lead to a decrease in KHCO3. Several studies reported the effect S774 has on KPEP; however, the influence of this amino acid substitution on KHCO3 has not been tested. To test these hypotheses, membrane-inlet mass spectrometry (MIMS) was used to measure the KHCO3 of the photosynthetic PEPc from the C4Flaveria trinervia and the non-photosynthetic PEPc from the C3F. pringlei. The cDNAs for these enzymes were overexpressed and purified from the PEPc-less PCR1 Escherichia coli strain. Our work in comparison with previous reports suggests that KHCO3 and KPEP are linked by specific amino acids, such as S774; however, these kinetic parameters respond differently to the tested allosteric regulators, malate and glucose-6-phosphate.
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Affiliation(s)
- Robert J DiMario
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA, USA
- Correspondence:
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31
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Minges A, Janßen D, Offermann S, Groth G. Efficient In Vivo Screening Method for the Identification of C 4 Photosynthesis Inhibitors Based on Cell Suspensions of the Single-Cell C 4 Plant Bienertia sinuspersici. FRONTIERS IN PLANT SCIENCE 2019; 10:1350. [PMID: 31736996 PMCID: PMC6831552 DOI: 10.3389/fpls.2019.01350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/01/2019] [Indexed: 05/17/2023]
Abstract
The identification of novel herbicides is of crucial importance to modern agriculture. We developed an efficient in vivo assay based on oxygen evolution measurements using suspensions of chlorenchyma cells isolated from the single-cell C4 plant Bienertia sinuspersici to identify and characterize inhibitors of C4 photosynthesis. This novel approach fills the gap between conventional in vitro assays for inhibitors targeting C4 key enzymes and in vivo experiments on whole plants. The assay addresses inhibition of the target enzymes in a plant context thereby taking care of any reduced target inhibition due to metabolization or inadequate uptake of small molecule inhibitors across plant cell walls and membranes. Known small molecule inhibitors targeting C4 photosynthesis were used to validate the approach. To this end, we tested pyruvate phosphate dikinase inhibitor bisindolylmaleimide IV and phosphoenolpyruvate carboxylase inhibitor okanin. Both inhibitors show inhibition of plant photosynthesis at half-maximal inhibitory concentrations in the sub-mM range and confirm their potential to act as a new class of C4 selective inhibitors.
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Affiliation(s)
- Alexander Minges
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Biochemical Plant Physiology, Heinrich Heine University, Düsseldorf, Germany
| | - Dominik Janßen
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Biochemical Plant Physiology, Heinrich Heine University, Düsseldorf, Germany
| | | | - Georg Groth
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Biochemical Plant Physiology, Heinrich Heine University, Düsseldorf, Germany
- *Correspondence: Georg Groth,
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32
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Connell MB, Lee MJY, Li J, Plaxton WC, Jia Z. Structural and biochemical characterization of citrate binding to AtPPC3, a plant-type phosphoenolpyruvate carboxylase from Arabidopsis thaliana. J Struct Biol 2018; 204:507-512. [PMID: 30419358 DOI: 10.1016/j.jsb.2018.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/02/2018] [Accepted: 11/09/2018] [Indexed: 11/30/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a tightly regulated cytosolic enzyme situated at a crucial branch point of central plant metabolism. The structure of AtPPC3, a C3 PEPC isozyme of the model plant Arabidopsis thaliana, in complex with the inhibitors aspartate and citrate was solved at 2.2-Å resolution. This represents the first PEPC structure with citrate bound. Aspartate and citrate binding sites are in close proximity (5.1-5.3 Å) and interactions between citrate and specific residues were identified. Citrate functions as a mixed (allosteric) inhibitor as it reduced AtPPC3's Vmax while increasing Km(PEP) values. The PEP saturation data gave an excellent fit to the mixed inhibition model, yielding Ki and Ki' (citrate) values of 9.3 and 42.5 mM, respectively. Citrate and aspartate inhibition of AtPPC3 was non-additive, likely due to their closely positioned binding sites, their similar negative charge, and type of binding residues. Fewer interactions and lower affinity for citrate support its observed weaker inhibition of AtPPC3 relative to aspartate. Citrate does not appear to induce further conformational change beyond aspartate owing to the similar structural mechanism of inhibition. AtPPC3 largely exhibits root-specific expression in Arabidopsis, where it is markedly upregulated during stresses such as excessive salinity or nutritional Pi deprivation that necessitate large increases in anaplerotic PEP carboxylation. The cytosolic citrate concentration of potato tubers suggests that AtPPC3's inhibition by citrate may be physiologically relevant. Our results provide novel insights into the structural basis of allosteric PEPC control and the kinetic effects brought about upon inhibitor binding.
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Affiliation(s)
- Matthew B Connell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Michael J Y Lee
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Jerry Li
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - William C Plaxton
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada; Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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Dwivedi SL, Siddique KHM, Farooq M, Thornton PK, Ortiz R. Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments. FRONTIERS IN PLANT SCIENCE 2018; 9:1249. [PMID: 30210519 PMCID: PMC6120061 DOI: 10.3389/fpls.2018.01249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/06/2018] [Indexed: 05/29/2023]
Abstract
Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO2), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C3 crops by harnessing novel variations (genes and network) in crops' (C3, C4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.
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Affiliation(s)
| | | | - Muhammad Farooq
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud, Oman
- University of Agriculture, Faisalabad, Pakistan
| | - Philip K. Thornton
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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González-Segura L, Mújica-Jiménez C, Juárez-Díaz JA, Güémez-Toro R, Martinez-Castilla LP, Muñoz-Clares RA. Identification of the allosteric site for neutral amino acids in the maize C 4 isozyme of phosphoenolpyruvate carboxylase: The critical role of Ser-100. J Biol Chem 2018; 293:9945-9957. [PMID: 29743237 PMCID: PMC6028945 DOI: 10.1074/jbc.ra118.002884] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/01/2018] [Indexed: 11/06/2022] Open
Abstract
The isozymes of photosynthetic phosphoenolpyruvate carboxylase from C4 plants (PEPC-C4) play a critical role in their atmospheric CO2 assimilation and productivity. They are allosterically activated by phosphorylated trioses or hexoses, such as d-glucose 6-phosphate, and inhibited by l-malate or l-aspartate. Additionally, PEPC-C4 isozymes from grasses are activated by glycine, serine, or alanine, but the allosteric site for these compounds remains unknown. Here, we report a new crystal structure of the isozyme from Zea mays (ZmPEPC-C4) with glycine bound at the monomer-monomer interfaces of the two dimers of the tetramer, making interactions with residues of both monomers. This binding site is close to, but different from, the one proposed to bind glucose 6-phosphate. Docking experiments indicated that d/l-serine or d/l-alanine could also bind to this site, which does not exist in the PEPC-C4 isozyme from the eudicot plant Flaveria, mainly because of a lysyl residue at the equivalent position of Ser-100 in ZmPEPC-C4 Accordingly, the ZmPEPC-C4 S100K mutant is not activated by glycine, serine, or alanine. Amino acid sequence alignments showed that PEPC-C4 isozymes from the monocot family Poaceae have either serine or glycine at this position, whereas those from Cyperaceae and eudicot families have lysine. The size and charge of the residue equivalent to Ser-100 are not only crucial for the activation of PEPC-C4 isozymes by neutral amino acids but also affect their affinity for the substrate phosphoenolpyruvate and their allosteric regulation by glucose 6-phosphate and malate, accounting for the reported kinetic differences between PEPC-C4 isozymes from monocot and eudicot plants.
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Affiliation(s)
| | | | - Javier Andrés Juárez-Díaz
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, México
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Nuccio ML, Potter L, Stiegelmeyer SM, Curley J, Cohn J, Wittich PE, Tan X, Davis J, Ni J, Trullinger J, Hall R, Bate NJ. Strategies and tools to improve crop productivity by targeting photosynthesis. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0377. [PMID: 28808096 DOI: 10.1098/rstb.2016.0377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2017] [Indexed: 12/15/2022] Open
Abstract
Crop productivity needs to substantially increase to meet global food and feed demand for a rapidly growing world population. Agricultural technology developers are pursuing a variety of approaches based on both traditional technologies such as genetic improvement, pest control and mechanization as well as new technologies such as genomics, gene manipulation and environmental modelling to develop crops that are capable of meeting growing demand. Photosynthesis is a key biochemical process that, many suggest, is not yet optimized for industrial agriculture or the modern global environment. We are interested in identifying control points in maize photoassimilation that are amenable to gene manipulation to improve overall productivity. Our approach encompasses: developing and using novel gene discovery techniques, translating our discoveries into traits and evaluating each trait in a stepwise manner that reflects a modern production environment. Our aim is to provide step change advancement in overall crop productivity and deliver this new technology into the hands of growers.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.
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Affiliation(s)
- Michael L Nuccio
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Laura Potter
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Suzy M Stiegelmeyer
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Joseph Curley
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Jonathan Cohn
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Peter E Wittich
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Xiaoping Tan
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Jimena Davis
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Junjian Ni
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Jon Trullinger
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Rick Hall
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
| | - Nicholas J Bate
- Syngenta Crop Protection, LLC., 9 Davis Drive, Research Triangle Park, NC 541-8500, USA
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36
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Ecoevolutionary Dynamics of Carbon Cycling in the Anthropocene. Trends Ecol Evol 2018; 33:213-225. [DOI: 10.1016/j.tree.2017.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 12/06/2017] [Accepted: 12/13/2017] [Indexed: 11/17/2022]
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Lauterbach M, Schmidt H, Billakurthi K, Hankeln T, Westhoff P, Gowik U, Kadereit G. De novo Transcriptome Assembly and Comparison of C 3, C 3-C 4, and C 4 Species of Tribe Salsoleae (Chenopodiaceae). FRONTIERS IN PLANT SCIENCE 2017; 8:1939. [PMID: 29184562 PMCID: PMC5694442 DOI: 10.3389/fpls.2017.01939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/27/2017] [Indexed: 05/29/2023]
Abstract
C4 photosynthesis is a carbon-concentrating mechanism that evolved independently more than 60 times in a wide range of angiosperm lineages. Among other alterations, the evolution of C4 from ancestral C3 photosynthesis requires changes in the expression of a vast number of genes. Differential gene expression analyses between closely related C3 and C4 species have significantly increased our understanding of C4 functioning and evolution. In Chenopodiaceae, a family that is rich in C4 origins and photosynthetic types, the anatomy, physiology and phylogeny of C4, C2, and C3 species of Salsoleae has been studied in great detail, which facilitated the choice of six samples of five representative species with different photosynthetic types for transcriptome comparisons. mRNA from assimilating organs of each species was sequenced in triplicates, and sequence reads were de novo assembled. These novel genetic resources were then analyzed to provide a better understanding of differential gene expression between C3, C2 and C4 species. All three analyzed C4 species belong to the NADP-ME type as most genes encoding core enzymes of this C4 cycle are highly expressed. The abundance of photorespiratory transcripts is decreased compared to the C3 and C2 species. Like in other C4 lineages of Caryophyllales, our results suggest that PEPC1 is the C4-specific isoform in Salsoleae. Two recently identified transporters from the PHT4 protein family may not only be related to the C4 syndrome, but also active in C2 photosynthesis in Salsoleae. In the two populations of the C2 species S. divaricata transcript abundance of several C4 genes are slightly increased, however, a C4 cycle is not detectable in the carbon isotope values. Most of the core enzymes of photorespiration are highly increased in the C2 species compared to both C3 and C4 species, confirming a successful establishment of the C2 photosynthetic pathway. Furthermore, a function of PEP-CK in C2 photosynthesis appears likely, since PEP-CK gene expression is not only increased in S. divaricata but also in C2 species of other groups.
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Affiliation(s)
- Maximilian Lauterbach
- Institute for Molecular Physiology, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute for Organismic and Molecular Evolutionary Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Hanno Schmidt
- Institute for Organismic and Molecular Evolutionary Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Kumari Billakurthi
- Institute for Developmental and Molecular Biology of Plants, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Thomas Hankeln
- Institute for Organismic and Molecular Evolutionary Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Peter Westhoff
- Institute for Developmental and Molecular Biology of Plants, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Udo Gowik
- Institute for Developmental and Molecular Biology of Plants, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Institute for Biology and Environmental Science (IBU), Plant Evolutionary Genetics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Gudrun Kadereit
- Institute for Molecular Physiology, Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute for Organismic and Molecular Evolutionary Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
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Moore AJ, Vos JMD, Hancock LP, Goolsby E, Edwards EJ. Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales). Syst Biol 2017; 67:367-383. [DOI: 10.1093/sysbio/syx078] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/18/2017] [Indexed: 01/01/2023] Open
Affiliation(s)
- Abigail J Moore
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, Providence, RI 02912, USA
- Department of Microbiology and Plant Biology and Oklahoma Biological Survey, University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019, USA
| | - Jurriaan M De Vos
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, Providence, RI 02912, USA
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Department of Environmental Sciences—Botany, University of Basel, Totengässlein 3, 4051 Basel, Switzerland
| | - Lillian P Hancock
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, Providence, RI 02912, USA
| | - Eric Goolsby
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, Providence, RI 02912, USA
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520, USA
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, Providence, RI 02912, USA
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT 06520, USA
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Dick M, Erlenkamp G, Nguyen GTT, Förster K, Groth G, Gohlke H. Pyrazolidine-3,5-dione-based inhibitors of phosphoenolpyruvate carboxylase as a new class of potential C 4 plant herbicides. FEBS Lett 2017; 591:3369-3377. [PMID: 28889573 DOI: 10.1002/1873-3468.12842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 11/10/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme in the C4 photosynthetic pathway of many of the world's worst weeds and a valuable target to develop C4 plant-selective herbicides. By virtual screening, analog synthesis, and in vitro validation, we identified pyrazolidine-3,5-diones as a new class of small molecules with inhibitory potential down to the submicromolar range against C4 PEPC and a selectivity factor of up to 16 over C3 PEPC. No other biological activity has yet been reported for the best compound, (3-bromophenyl)-4-(3-hydroxybenzylidene)-pyrazolidine-3,5-dione. A systematic variation in the substituents allowed the derivation of a qualitative structure-activity relationship. These findings make this compound class highly interesting for further investigations toward generating potent, C4 plant-selective herbicides with a low potential for unwanted effects.
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Affiliation(s)
- Markus Dick
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich-Heine-Universität Düsseldorf, Germany
| | - German Erlenkamp
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich-Heine-Universität Düsseldorf, Germany
| | - Giang T T Nguyen
- Institute of Biochemical Plant Physiology and Bioeconomy Science Center (BioSC), Heinrich-Heine-Universität Düsseldorf, Germany
| | - Kerstin Förster
- Institute of Biochemical Plant Physiology and Bioeconomy Science Center (BioSC), Heinrich-Heine-Universität Düsseldorf, Germany
| | - Georg Groth
- Institute of Biochemical Plant Physiology and Bioeconomy Science Center (BioSC), Heinrich-Heine-Universität Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich-Heine-Universität Düsseldorf, Germany
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40
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Cañas RA, Yesbergenova-Cuny Z, Simons M, Chardon F, Armengaud P, Quilleré I, Cukier C, Gibon Y, Limami AM, Nicolas S, Brulé L, Lea PJ, Maranas CD, Hirel B. Exploiting the Genetic Diversity of Maize Using a Combined Metabolomic, Enzyme Activity Profiling, and Metabolic Modeling Approach to Link Leaf Physiology to Kernel Yield. THE PLANT CELL 2017; 29:919-943. [PMID: 28396554 PMCID: PMC5466022 DOI: 10.1105/tpc.16.00613] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 03/07/2017] [Accepted: 04/06/2017] [Indexed: 05/18/2023]
Abstract
A combined metabolomic, biochemical, fluxomic, and metabolic modeling approach was developed using 19 genetically distant maize (Zea mays) lines from Europe and America. Considerable differences were detected between the lines when leaf metabolic profiles and activities of the main enzymes involved in primary metabolism were compared. During grain filling, the leaf metabolic composition appeared to be a reliable marker, allowing a classification matching the genetic diversity of the lines. During the same period, there was a significant correlation between the genetic distance of the lines and the activities of enzymes involved in carbon metabolism, notably glycolysis. Although large differences were observed in terms of leaf metabolic fluxes, these variations were not tightly linked to the genome structure of the lines. Both correlation studies and metabolic network analyses allowed the description of a maize ideotype with a high grain yield potential. Such an ideotype is characterized by low accumulation of soluble amino acids and carbohydrates in the leaves and high activity of enzymes involved in the C4 photosynthetic pathway and in the biosynthesis of amino acids derived from glutamate. Chlorogenates appear to be important markers that can be used to select for maize lines that produce larger kernels.
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Affiliation(s)
- Rafael A Cañas
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique (CNRS) 3559, F-78026 Versailles cedex, France
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Zhazira Yesbergenova-Cuny
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique (CNRS) 3559, F-78026 Versailles cedex, France
| | - Margaret Simons
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Fabien Chardon
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique (CNRS) 3559, F-78026 Versailles cedex, France
| | - Patrick Armengaud
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique (CNRS) 3559, F-78026 Versailles cedex, France
| | - Isabelle Quilleré
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique (CNRS) 3559, F-78026 Versailles cedex, France
| | - Caroline Cukier
- University of Angers, Institut de Recherche en Horticulture et Semences, INRA, Structure Fédérative de Recherche 4207, Qualité et Santé du Végétal, F-49045 Angers, France
| | - Yves Gibon
- Unité Mixte Recherche 1332, Biologie du Fruit et Pathologie, Bordeaux Métabolome Platform, INRA de Bordeaux-Aquitaine, F-33883 Villenave d'Ornon cedex, France
| | - Anis M Limami
- University of Angers, Institut de Recherche en Horticulture et Semences, INRA, Structure Fédérative de Recherche 4207, Qualité et Santé du Végétal, F-49045 Angers, France
| | - Stéphane Nicolas
- Station de Génétique Végétale, INRA-UPS-INAPG-CNRS, Ferme du Moulon, F-91190 Gif/Yvette, France
| | - Lenaïg Brulé
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique (CNRS) 3559, F-78026 Versailles cedex, France
| | - Peter J Lea
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Bertrand Hirel
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318, INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique (CNRS) 3559, F-78026 Versailles cedex, France
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Allosteric Inhibition of Phosphoenolpyruvate Carboxylases is Determined by a Single Amino Acid Residue in Cyanobacteria. Sci Rep 2017; 7:41080. [PMID: 28117365 PMCID: PMC5259782 DOI: 10.1038/srep41080] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/14/2016] [Indexed: 01/04/2023] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is an important enzyme for CO2 fixation and primary metabolism in photosynthetic organisms including cyanobacteria. The kinetics and allosteric regulation of PEPCs have been studied in many organisms, but the biochemical properties of PEPC in the unicellular, non-nitrogen-fixing cyanobacterium Synechocystis sp. PCC 6803 have not been clarified. In this study, biochemical analysis revealed that the optimum pH and temperature of Synechocystis 6803 PEPC proteins were 7.3 and 30 °C, respectively. Synechocystis 6803 PEPC was found to be tolerant to allosteric inhibition by several metabolic effectors such as malate, aspartate, and fumarate compared with other cyanobacterial PEPCs. Comparative sequence and biochemical analysis showed that substitution of the glutamate residue at position 954 with lysine altered the enzyme so that it was inhibited by malate, aspartate, and fumarate. PEPC of the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120 was purified, and its activity was inhibited in the presence of malate. Substitution of the lysine at position 946 (equivalent to position 954 in Synechocystis 6803) with glutamate made Anabaena 7120 PEPC tolerant to malate. These results demonstrate that the allosteric regulation of PEPC in cyanobacteria is determined by a single amino acid residue, a characteristic that is conserved in different orders.
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42
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Schlüter U, Bräutigam A, Gowik U, Melzer M, Christin PA, Kurz S, Mettler-Altmann T, Weber AP. Photosynthesis in C3-C4 intermediate Moricandia species. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:191-206. [PMID: 28110276 PMCID: PMC5853546 DOI: 10.1093/jxb/erw391] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 09/29/2016] [Indexed: 05/09/2023]
Abstract
Evolution of C4 photosynthesis is not distributed evenly in the plant kingdom. Particularly interesting is the situation in the Brassicaceae, because the family contains no C4 species, but several C3-C4 intermediates, mainly in the genus Moricandia Investigation of leaf anatomy, gas exchange parameters, the metabolome, and the transcriptome of two C3-C4 intermediate Moricandia species, M. arvensis and M. suffruticosa, and their close C3 relative M. moricandioides enabled us to unravel the specific C3-C4 characteristics in these Moricandia lines. Reduced CO2 compensation points in these lines were accompanied by anatomical adjustments, such as centripetal concentration of organelles in the bundle sheath, and metabolic adjustments, such as the balancing of C and N metabolism between mesophyll and bundle sheath cells by multiple pathways. Evolution from C3 to C3-C4 intermediacy was probably facilitated first by loss of one copy of the glycine decarboxylase P-protein, followed by dominant activity of a bundle sheath-specific element in its promoter. In contrast to recent models, installation of the C3-C4 pathway was not accompanied by enhanced activity of the C4 cycle. Our results indicate that metabolic limitations connected to N metabolism or anatomical limitations connected to vein density could have constrained evolution of C4 in Moricandia.
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Affiliation(s)
- Urte Schlüter
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
- Network Analysis and Modelling, Leibniz Institute of Plant Genetics and Crop Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | - Udo Gowik
- Institute of Plant Molecular and Developmental Biology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Michael Melzer
- Structural Cell Biology, Leibniz Institute of Plant Genetics and Crop Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Samantha Kurz
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Tabea Mettler-Altmann
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Andreas Pm Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
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43
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Sayed MA, Umekawa Y, Ito K. Metabolic interplay between cytosolic phosphoenolpyruvate carboxylase and mitochondrial alternative oxidase in thermogenic skunk cabbage, Symplocarpus renifolius. PLANT SIGNALING & BEHAVIOR 2016; 11:e1247138. [PMID: 27739913 PMCID: PMC5157899 DOI: 10.1080/15592324.2016.1247138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/05/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
Skunk cabbage (Symplocarpus renifolius) blooms in early spring and its inflorescence, referred to as the spadix, can produce enough heat to melt snow. Here, we investigated glycolytic carbon flow at the PEP branch-point in thermogenic spadices. Our analyses revealed that petals and pistils in thermogenic florets exhibited higher expression of SrPEPC and SrAOX transcripts than those of SrPK, SrPEPCK, and SrPEPtase. Moreover, enzymatic analyses showed high activities of PEPC in the extracts from thermogenic florets. Finally, mitochondria from thermogenic florets showed low respiratory activities when pyruvate was used as a substrate, although a significant malate-mediated cyanide-insensitive respiration was observed. Collectively, these results suggest that PEP metabolism, primarily catabolized by PEPC, plays a critical role in thermogenesis in S. renifolius.
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Affiliation(s)
- Md. Abu Sayed
- United Graduate School of Agricultural Science, Iwate University, Ueda, Morioka, Iwate, Japan
| | - Yui Umekawa
- United Graduate School of Agricultural Science, Iwate University, Ueda, Morioka, Iwate, Japan
| | - Kikukatsu Ito
- United Graduate School of Agricultural Science, Iwate University, Ueda, Morioka, Iwate, Japan
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Ueda, Morioka, Iwate, Japan
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Rangan P, Furtado A, Henry RJ. New evidence for grain specific C4 photosynthesis in wheat. Sci Rep 2016; 6:31721. [PMID: 27530078 PMCID: PMC4987656 DOI: 10.1038/srep31721] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/22/2016] [Indexed: 11/30/2022] Open
Abstract
The C4 photosynthetic pathway evolved to allow efficient CO2 capture by plants where effective carbon supply may be limiting as in hot or dry environments, explaining the high growth rates of C4 plants such as maize. Important crops such as wheat and rice are C3 plants resulting in efforts to engineer them to use the C4 pathway. Here we show the presence of a C4 photosynthetic pathway in the developing wheat grain that is absent in the leaves. Genes specific for C4 photosynthesis were identified in the wheat genome and found to be preferentially expressed in the photosynthetic pericarp tissue (cross- and tube-cell layers) of the wheat caryopsis. The chloroplasts exhibit dimorphism that corresponds to chloroplasts of mesophyll- and bundle sheath-cells in leaves of classical C4 plants. Breeding to optimize the relative contributions of C3 and C4 photosynthesis may adapt wheat to climate change, contributing to wheat food security.
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Affiliation(s)
- Parimalan Rangan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia.,Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi-110012, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia
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45
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Bisson MMA, Kessenbrock M, Müller L, Hofmann A, Schmitz F, Cristescu SM, Groth G. Peptides interfering with protein-protein interactions in the ethylene signaling pathway delay tomato fruit ripening. Sci Rep 2016; 6:30634. [PMID: 27477591 PMCID: PMC4967898 DOI: 10.1038/srep30634] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 07/07/2016] [Indexed: 01/18/2023] Open
Abstract
The plant hormone ethylene is involved in the regulation of several processes with high importance for agricultural applications, e.g. ripening, aging and senescence. Previous work in our group has identified a small peptide (NOP-1) derived from the nuclear localization signal of the Arabidopsis ethylene regulator ETHYLENE INSENSITIVE-2 (EIN2) C-terminal part as efficient inhibitor of ethylene responses. Here, we show that NOP-1 is also able to efficiently disrupt EIN2-ETR1 complex formation in tomato, indicating that the NOP-1 inhibition mode is conserved across plant species. Surface application of NOP-1 on green tomato fruits delays ripening similar to known inhibitors of ethylene perception (MCP) and ethylene biosynthesis (AVG). Fruits treated with NOP-1 showed similar ethylene production as untreated controls underlining that NOP-1 blocks ethylene signaling by targeting an essential interaction in this pathway, while having no effect on ethylene biosynthesis.
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Affiliation(s)
- Melanie M. A. Bisson
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Mareike Kessenbrock
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Lena Müller
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Alexander Hofmann
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Florian Schmitz
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Simona M. Cristescu
- Department of Molecular and Laser Physics, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Georg Groth
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
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46
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Nguyen GTT, Erlenkamp G, Jäck O, Küberl A, Bott M, Fiorani F, Gohlke H, Groth G. Chalcone-based Selective Inhibitors of a C4 Plant Key Enzyme as Novel Potential Herbicides. Sci Rep 2016; 6:27333. [PMID: 27263468 PMCID: PMC4893628 DOI: 10.1038/srep27333] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/18/2016] [Indexed: 11/08/2022] Open
Abstract
Weeds are a challenge for global food production due to their rapidly evolving resistance against herbicides. We have identified chalcones as selective inhibitors of phosphoenolpyruvate carboxylase (PEPC), a key enzyme for carbon fixation and biomass increase in the C4 photosynthetic pathway of many of the world's most damaging weeds. In contrast, many of the most important crop plants use C3 photosynthesis. Here, we show that 2',3',4',3,4-Pentahydroxychalcone (IC50 = 600 nM) and 2',3',4'-Trihydroxychalcone (IC50 = 4.2 μM) are potent inhibitors of C4 PEPC but do not affect C3 PEPC at a same concentration range (selectivity factor: 15-45). Binding and modeling studies indicate that the active compounds bind at the same site as malate/aspartate, the natural feedback inhibitors of the C4 pathway. At the whole plant level, both substances showed pronounced growth-inhibitory effects on the C4 weed Amaranthus retroflexus, while there were no measurable effects on oilseed rape, a C3 plant. Growth of selected soil bacteria was not affected by these substances. Our chalcone compounds are the most potent and selective C4 PEPC inhibitors known to date. They offer a novel approach to combat C4 weeds based on a hitherto unexplored mode of allosteric inhibition of a C4 plant key enzyme.
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Affiliation(s)
- G. T. T. Nguyen
- Biochemical Plant Physiology, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
| | - G. Erlenkamp
- Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
| | - O. Jäck
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - A. Küberl
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - M. Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - F. Fiorani
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - H. Gohlke
- Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
| | - G. Groth
- Biochemical Plant Physiology, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
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47
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Zhang L, Chen F, Zhang GQ, Zhang YQ, Niu S, Xiong JS, Lin Z, Cheng ZMM, Liu ZJ. Origin and mechanism of crassulacean acid metabolism in orchids as implied by comparative transcriptomics and genomics of the carbon fixation pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:175-85. [PMID: 26959080 DOI: 10.1111/tpj.13159] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 05/20/2023]
Abstract
Crassulacean acid metabolism (CAM) is a CO2 fixation pathway that maximizes water-use efficiency (WUE), compared with the C3/C4 CO2 pathway, which permits CAM plants to adapt to arid environments. The CAM pathway provides excellent opportunities to genetically design plants, especially bioenergy crops, with a high WUE and better photosynthetic performance than C3/C4 in arid environments. The information available on the origin and evolution of CAM is scant, however. Here, we analyzed transcriptomes from 13 orchid species and two existing orchid genomes, covering CAM and C3 plants, with an emphasis on comparing 13 gene families involved in the complete carbon fixation pathway. The dosage of the core photosynthesis-related genes plays no substantial role in the evolution of CAM in orchids; however, CAM may have evolved primarily by changes at the transcription level of key carbon fixation pathway genes. We proposed that in both dark and light, CO2 is primarily fixed and then released through two metabolic pathways via known genes, such as PPC1, PPDK and PPCK. This study reports a comprehensive comparison of carbon fixation pathway genes across different photosynthetic plants, and reveals the importance of the level of expression of key genes in the origin and evolution of CAM.
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Affiliation(s)
- Liangsheng Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Shance Niu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Jin-Song Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St Louis, MO, 63103, USA
| | - Zong-Ming Max Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
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48
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Brilhaus D, Bräutigam A, Mettler-Altmann T, Winter K, Weber APM. Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare. PLANT PHYSIOLOGY 2016; 170:102-22. [PMID: 26530316 PMCID: PMC4704576 DOI: 10.1104/pp.15.01076] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/03/2015] [Indexed: 05/14/2023]
Abstract
Drought tolerance is a key factor for agriculture in the 21st century as it is a major determinant of plant survival in natural ecosystems as well as crop productivity. Plants have evolved a range of mechanisms to cope with drought, including a specialized type of photosynthesis termed Crassulacean acid metabolism (CAM). CAM is associated with stomatal closure during the day as atmospheric CO2 is assimilated primarily during the night, thus reducing transpirational water loss. The tropical herbaceous perennial species Talinum triangulare is capable of transitioning, in a facultative, reversible manner, from C3 photosynthesis to weakly expressed CAM in response to drought stress. The transcriptional regulation of this transition has been studied. Combining mRNA-Seq with targeted metabolite measurements, we found highly elevated levels of CAM-cycle enzyme transcripts and their metabolic products in T. triangulare leaves upon water deprivation. The carbohydrate metabolism is rewired to reduce the use of reserves for growth to support the CAM-cycle and the synthesis of compatible solutes. This large-scale expression dataset of drought-induced CAM demonstrates transcriptional regulation of the C3-CAM transition. We identified candidate transcription factors to mediate this photosynthetic plasticity, which may contribute in the future to the design of more drought-tolerant crops via engineered CAM.
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Affiliation(s)
- Dominik Brilhaus
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany (D.B., A.B., T.M.-A., A.P.M.W.); and Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama (K.W.)
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany (D.B., A.B., T.M.-A., A.P.M.W.); and Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama (K.W.)
| | - Tabea Mettler-Altmann
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany (D.B., A.B., T.M.-A., A.P.M.W.); and Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama (K.W.)
| | - Klaus Winter
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany (D.B., A.B., T.M.-A., A.P.M.W.); and Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama (K.W.)
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany (D.B., A.B., T.M.-A., A.P.M.W.); and Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama (K.W.)
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49
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Rosnow JJ, Evans MA, Kapralov MV, Cousins AB, Edwards GE, Roalson EH. Kranz and single-cell forms of C4 plants in the subfamily Suaedoideae show kinetic C4 convergence for PEPC and Rubisco with divergent amino acid substitutions. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:7347-58. [PMID: 26417023 PMCID: PMC4765798 DOI: 10.1093/jxb/erv431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The two carboxylation reactions performed by phosphoenolpyruvate carboxylase (PEPC) and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) are vital in the fixation of inorganic carbon for C4 plants. The abundance of PEPC is substantially elevated in C4 leaves, while the location of Rubisco is restricted to one of two chloroplast types. These differences compared with C3 leaves have been shown to result in convergent enzyme optimization in some C4 species. Investigation into the kinetic properties of PEPC and Rubisco from Kranz C4, single cell C4, and C3 species in Chenopodiaceae s. s. subfamily Suaedoideae showed that these major carboxylases in C4 Suaedoideae species lack the same mutations found in other C4 systems which have been examined; but still have similar convergent kinetic properties. Positive selection analysis on the N-terminus of PEPC identified residues 364 and 368 to be under positive selection with a posterior probability >0.99 using Bayes empirical Bayes. Compared with previous analyses on other C4 species, PEPC from C4 Suaedoideae species have different convergent amino acids that result in a higher K m for PEP and malate tolerance compared with C3 species. Kinetic analysis of Rubisco showed that C4 species have a higher catalytic efficiency of Rubisco (k catc in mol CO2 mol(-1) Rubisco active sites s(-1)), despite lacking convergent substitutions in the rbcL gene. The importance of kinetic changes to the two-carboxylation reactions in C4 leaves related to amino acid selection is discussed.
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Affiliation(s)
- Josh J Rosnow
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Marc A Evans
- Department of Mathematics, Washington State University, Pullman, WA 99164-3113, USA
| | - Maxim V Kapralov
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Gerald E Edwards
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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50
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Wen W, Li K, Alseekh S, Omranian N, Zhao L, Zhou Y, Xiao Y, Jin M, Yang N, Liu H, Florian A, Li W, Pan Q, Nikoloski Z, Yan J, Fernie AR. Genetic Determinants of the Network of Primary Metabolism and Their Relationships to Plant Performance in a Maize Recombinant Inbred Line Population. THE PLANT CELL 2015; 27:1839-56. [PMID: 26187921 PMCID: PMC4531352 DOI: 10.1105/tpc.15.00208] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/30/2015] [Indexed: 05/16/2023]
Abstract
Deciphering the influence of genetics on primary metabolism in plants will provide insights useful for genetic improvement and enhance our fundamental understanding of plant growth and development. Although maize (Zea mays) is a major crop for food and feed worldwide, the genetic architecture of its primary metabolism is largely unknown. Here, we use high-density linkage mapping to dissect large-scale metabolic traits measured in three different tissues (leaf at seedling stage, leaf at reproductive stage, and kernel at 15 d after pollination [DAP]) of a maize recombinant inbred line population. We identify 297 quantitative trait loci (QTLs) with moderate (86.2% of the mapped QTL, R(2) = 2.4 to 15%) to major effects (13.8% of the mapped QTL, R(2) >15%) for 79 primary metabolites across three tissues. Pairwise epistatic interactions between these identified loci are detected for more than 25.9% metabolites explaining 6.6% of the phenotypic variance on average (ranging between 1.7 and 16.6%), which implies that epistasis may play an important role for some metabolites. Key candidate genes are highlighted and mapped to carbohydrate metabolism, the tricarboxylic acid cycle, and several important amino acid biosynthetic and catabolic pathways, with two of them being further validated using candidate gene association and expression profiling analysis. Our results reveal a metabolite-metabolite-agronomic trait network that, together with the genetic determinants of maize primary metabolism identified herein, promotes efficient utilization of metabolites in maize improvement.
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Affiliation(s)
- Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Nooshin Omranian
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Lijun Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Alexandra Florian
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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