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Jia X, Luo S, Ye X, Liu L, Wen W. Evolution of the biochemistry underpinning purine alkaloid metabolism in plants. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230366. [PMID: 39343019 PMCID: PMC11449220 DOI: 10.1098/rstb.2023.0366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 10/01/2024] Open
Abstract
Purine alkaloids are naturally occurring nitrogenous methylated derivatives of purine nucleotide degradation products, having essential roles in medicine, food and various other aspects of our daily lives. They are generated through convergent evolution in different plant species. The pivotal reaction steps within the purine alkaloid metabolic pathways have been largely elucidated, and the convergent evolution of purine alkaloids has been substantiated through bioinformatic, biochemical and other research perspectives within S-adenosyl-ʟ-methionine-dependent N-methyltransferases. Currently, the biological and ecological roles of purine alkaloids, further refinement of the purine alkaloid metabolic pathways and the investigation of purine alkaloid adaptive evolutionary mechanisms continue to attract widespread research interest. The exploration of the purine alkaloid metabolic pathways also enhances our comprehension of the biochemical mechanism, providing insights into inter-species interactions and adaptive evolution and offering potential value in drug development and agricultural applications. Here, we review the progress of research in the distribution, metabolic pathway elucidation and regulation, evolutionary mechanism and ecological roles of purine alkaloids in plants. The opportunities and challenges involved in elucidating the biochemical basis and evolutionary mechanisms of the purine alkaloid metabolic pathways, as well as other research aspects, are also discussed. This article is part of the theme issue 'The evolution of plant meta-bolism'.
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Affiliation(s)
- Xinxin Jia
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Shijie Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Xiali Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Lin Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
| | - Weiwei Wen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University , Wuhan 430070, People's Republic of China
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Ruffinatti FA, Scarpellino G, Chinigò G, Visentin L, Munaron L. The Emerging Concept of Transportome: State of the Art. Physiology (Bethesda) 2023; 38:0. [PMID: 37668550 DOI: 10.1152/physiol.00010.2023] [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: 04/12/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
The array of ion channels and transporters expressed in cell membranes, collectively referred to as the transportome, is a complex and multifunctional molecular machinery; in particular, at the plasma membrane level it finely tunes the exchange of biomolecules and ions, acting as a functionally adaptive interface that accounts for dynamic plasticity in the response to environmental fluctuations and stressors. The transportome is responsible for the definition of membrane potential and its variations, participates in the transduction of extracellular signals, and acts as a filter for most of the substances entering and leaving the cell, thus enabling the homeostasis of many cellular parameters. For all these reasons, physiologists have long been interested in the expression and functionality of ion channels and transporters, in both physiological and pathological settings and across the different domains of life. Today, thanks to the high-throughput technologies of the postgenomic era, the omics approach to the study of the transportome is becoming increasingly popular in different areas of biomedical research, allowing for a more comprehensive, integrated, and functional perspective of this complex cellular apparatus. This article represents a first effort for a systematic review of the scientific literature on this topic. Here we provide a brief overview of all those studies, both primary and meta-analyses, that looked at the transportome as a whole, regardless of the biological problem or the models they used. A subsequent section is devoted to the methodological aspect by reviewing the most important public databases annotating ion channels and transporters, along with the tools they provide to retrieve such information. Before conclusions, limitations and future perspectives are also discussed.
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Affiliation(s)
- Federico Alessandro Ruffinatti
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Scarpellino
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Chinigò
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Luca Visentin
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Luca Munaron
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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Fu X, Li G, Hu F, Huang J, Lou Y, Li Y, Li Y, He H, Lv Y, Cheng J. Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes. BMC Genom Data 2023; 24:12. [PMID: 36849914 PMCID: PMC9969625 DOI: 10.1186/s12863-022-01098-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/15/2022] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND The peaberry bean in Arabica coffee has exceptional quality compared to the regular coffee bean. Understanding the molecular mechanism of bean quality is imperative to introduce superior coffee quality traits. Despite high economic importance, the regulatory aspects of bean quality are yet largely unknown in peaberry. A transcriptome analysis was performed by using peaberry and regular coffee beans in this study. RESULTS The result of phenotypic analysis stated a difference in the physical attributes of both coffee beans. In addition, transcriptome analysis revealed low genetic differences. Only 139 differentially expressed genes were detected in which 54 genes exhibited up-regulation and 85 showed down-regulations in peaberry beans compared to regular beans. The majority of differentially expressed genes had functional annotation with cell wall modification, lipid binding, protein binding, oxidoreductase activity, and transmembrane transportation. Many fold lower expression of Ca25840-PMEs1, Ca30827-PMEs2, Ca30828-PMEs3, Ca25839-PMEs4, Ca36469-PGs. and Ca03656-Csl genes annotated with cell wall modification might play a critical role to develop different bean shape patterns in Arabica. The ERECTA family genes Ca15802-ERL1, Ca99619-ERL2, Ca07439-ERL3, Ca97226-ERL4, Ca89747-ERL5, Ca07056-ERL6, Ca01141-ERL7, and Ca32419-ERL8 along lipid metabolic pathway genes Ca06708-ACOX1, Ca29177-ACOX2, Ca01563-ACOX3, Ca34321-CPFA1, and Ca36201-CPFA2 are predicted to regulate different shaped bean development. In addition, flavonoid biosynthesis correlated genes Ca03809-F3H, Ca95013-CYP75A1, and Ca42029-CYP75A2 probably help to generate rarely formed peaberry beans. CONCLUSION Our results provide molecular insights into the formation of peaberry. The data resources will be important to identify candidate genes correlated with the different bean shape patterns in Arabica.
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Affiliation(s)
- Xingfei Fu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Guiping Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Faguang Hu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Jiaxiong Huang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Yuqiang Lou
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Yaqi Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Hongyan He
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - YuLan Lv
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Jinhuan Cheng
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China.
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