Structural, functional, and phylogenetic characterization of phosphoenolpyruvate carboxylase (PEPC) in C<sub>4</sub>and CAM plants

Darabi, Maryam; Seddigh, Samin

doi:10.1080/00087114.2018.1465762

Cited by 4 publications

(6 citation statements)

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“…1). These results clearly indicated that PEPC genes family was extremely conserved throughout its evolutionary history of more than 500 Mya since origin from algae [14,20,28]. However, so conserved gene family performed hyper-diverse housekeeping functions including photosynthesis and nonphotosynthesis for survival in the terrestrial environments [19].…”

Section: Resultsmentioning

confidence: 80%

“…In plants, phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) is a key enzyme that catalyzes the primary xation reaction of photosynthesis CO 2 assimilation in C4 and CAM photosynthesis [12][13][14]. Additionally, PEPC genes also play crucial roles in a variety of non-photosynthesis functions, such as carbon and nitrogen metabolism [15], seed development and germination [16], abiotic stresses [17,18] and so on [12,19,20]. As the so-called housekeeping functions, PEPC genes are highly conserved, which makes it valuable molecular markers for phylogenetic reconstruction of plants [21].…”

Section: Introductionmentioning

confidence: 99%

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Convergent Molecular Evolution of PEPC Gene Family in C4 and CAM Plants

Shu¹,

Yan²,

Wang³

2020

Preprint

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Background: Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4 and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulted in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remained lack of understanding. Results: In present study, we identified the members of PEPC gene family across green plants with genomic data, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructed PEPC gene family tree and reconciled with species tree, we found PEPC genes occurred 71 gene duplications and 16 gene losses, which might result from whole-genome duplication events in plants. Based on the integral phylogenetic tree of PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but no one in CAM species. Conclusions: PEPC gene family was ubiquitous and highly conservative in green plants. After originated from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that facilitated the convergent evolution of C4 photosynthesis in Angiosperms, but PEPC gene did not exist molecular convergence corresponded to the multiple independent evolution of CAM photosynthesis. Our findings help to understand the origin and evolution of C4 and CAM pathways and shed new light on the adaptation of plants in drought and high-temperature habitats.

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Section: Resultsmentioning

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Convergent Molecular Evolution of PEPC Gene Family in C4 and CAM Plants

Shu¹,

Yan²,

Wang³

2020

Preprint

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“…The overall model quality Z-Score from ProSA-web is shown in Fig. 5.The positive Z-score shows that the structure is not stabilized while zero and negative score is an indication of one of the best ideal structures [27,28]. The Z-score of the template sequence (6VSB) was -6.57 as shown in Fig.…”

Section: (Ii) Z-scorementioning

confidence: 99%

“…While the graph in Fig. 6, below for the target is mostly below from the zero on x-axis, based on this graph, the modeled 3D structure for the target can be constructed [27].…”

Section: (Ii) Z-scorementioning

confidence: 99%

In silico study to predict and characterize of SARS CoV 2 Surface glycoprotein

Kumar

Sharma

2020

vacres

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Introduction: Coronavirus family member SARS-CoV-2 is a current worldwide threat. It enters into the epithelium membrane of respiratory tract with the help of its antigenic spike proteins and cause Coronavirus disease 2019 (COVID-19). Methods: Considering SARS-CoV-2 a potent vaccine or diagnostic candidate, a bioinformatical study was done to determine its structure homology modeling, physiological properties and structure validation with presence of antigenic sites. Results: The surface glycoprotein of SARS-CoV-2 was found to be a stable protein with stereochemically good structure. It also contains 65 antigenic sites. Conclusion: The present study suggests further wet-lab research to develop a vaccine or diagnostic kit using this promising surface glycoprotein.

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“…PEPC is a highly regulated enzyme that catalyzes the irreversible β -carboxylation of phosphoenolpyruvate in the presence of bicarbonate and magnesium to yield oxaloacetate and inorganic phosphate, a reaction that serves a variety of physiological functions in plants ( Jiao & Chollet, 1991 ; Lepiniec et al, 1994 ; Chollet, Vidal & O’Leary, 1996 ). Additionally, PEPC genes play crucial roles in a variety of non-photosynthetic functions, including carbon and nitrogen metabolism, seed development and germination and response to abiotic stresses ( Lepiniec et al, 1994 ; O’Leary, Park & Plaxton William, 2011 ; Shi et al, 2015 ; Ruiz-Ballesta et al, 2016 ; Wang et al, 2016 ; Darabi & Seddigh, 2018 ; Zhao et al, 2019 ). As housekeeping genes, PEPC genes are highly conserved, which makes them valuable molecular markers for phylogenetic reconstruction of plants ( Gehrig, Heute & Kluge, 2001 ).…”

Section: Introductionmentioning

confidence: 99%

Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C₄ and crassulacean acid metabolism plants

Shu

Yan

Wang

2022

PeerJ

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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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Structural, functional, and phylogenetic characterization of phosphoenolpyruvate carboxylase (PEPC) in C₄and CAM plants

Cited by 4 publications

References 78 publications

Convergent Molecular Evolution of PEPC Gene Family in C4 and CAM Plants

Convergent Molecular Evolution of PEPC Gene Family in C4 and CAM Plants

In silico study to predict and characterize of SARS CoV 2 Surface glycoprotein

Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C₄ and crassulacean acid metabolism plants

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Structural, functional, and phylogenetic characterization of phosphoenolpyruvate carboxylase (PEPC) in C4and CAM plants

Cited by 4 publications

References 78 publications

Convergent Molecular Evolution of PEPC Gene Family in C4 and CAM Plants

Convergent Molecular Evolution of PEPC Gene Family in C4 and CAM Plants

In silico study to predict and characterize of SARS CoV 2 Surface glycoprotein

Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants

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Product

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Structural, functional, and phylogenetic characterization of phosphoenolpyruvate carboxylase (PEPC) in C₄and CAM plants

Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C₄ and crassulacean acid metabolism plants