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Wong A, Chi W, Yu J, Bi C, Tian X, Yang Y, Gehring C. Plant adenylate cyclases have come full circle. Nat Plants 2023; 9:1389-1397. [PMID: 37709954 DOI: 10.1038/s41477-023-01486-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/07/2023] [Indexed: 09/16/2023]
Abstract
In bacteria, fungi and animals, 3'-5'-cyclic adenosine monophosphate (cAMP) and adenylate cyclases (ACs), enzymes that catalyse the formation of 3',5'-cAMP from ATP, are recognized as key signalling components. In contrast, the presence of cAMP and its biological roles in higher plants have long been a matter of controversy due to the generally lower amounts in plant tissues compared with that in animal and bacterial cells, and a lack of clarity on the molecular nature of the generating and degrading enzymes, as well as downstream effectors. While treatment with 3',5'-cAMP elicited many plant responses, ACs were, however, somewhat elusive. This changed when systematic searches with amino acid motifs deduced from the conserved catalytic centres of annotated ACs from animals and bacteria identified candidate proteins in higher plants that were subsequently shown to have AC activities in vitro and in vivo. The identification of active ACs moonlighting within complex multifunctional proteins is consistent with their roles as molecular tuners and regulators of cellular and physiological functions. Furthermore, the increasing number of ACs identified as part of proteins with different domain architectures suggests that there are many more hidden ACs in plant proteomes and they may affect a multitude of mechanisms and processes at the molecular and systems levels.
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Affiliation(s)
- Aloysius Wong
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China.
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China.
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China.
| | - Wei Chi
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Jia Yu
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Chuyun Bi
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Xuechen Tian
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Yixin Yang
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
- Zhejiang Bioinformatics Internatiosnal Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy.
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Liu Z, Yuan Y, Wang L, Cao H, Wang C, Zhao X, Wang L, Liu M. Establishment and characterization of a new class of adenylate cyclases (class VII ACs) in plants. Heliyon 2023; 9:e18612. [PMID: 37593644 PMCID: PMC10427991 DOI: 10.1016/j.heliyon.2023.e18612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
Adenylate cyclase is the key enzyme in the synthesis of cAMP. Now, more and more plant genes which possessing AC function are being identified, but the classification of plant ACs has not yet been systematically studied and the relationship of plant ACs with other existing six classes ACs in animals and microorganisms is still unclear. In this study, we found that 7 of the 15 reported plant ACs with conserved CYTH-like_AC_Ⅳ-like domain were clustered into a group with high confidence (Group Ⅳ), while the other plant ACs were clustered into other three groups with no common domain. In addition, we also found that the Group Ⅳ plant ACs were grouped into an independent and specific class (Class VII), separated from the existing six classes of ACs. The Group Ⅳ plant ACs, compared to the existing six classes of ACs, own unique CYTH-like_AC_Ⅳ-like conserved domain and EXEXK signature motif, characteristic protein tertiary structures, specific subcellular localization and catalytic conditions. In view of the above, we regarded the Group Ⅳ plant ACs as the seventh class of AC (VII AC). This study does the systematic classification of plant ACs which could lay a foundation for further identification and study of the biological functions of the plant-specific VII ACs.
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Affiliation(s)
- Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, 071001, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
- Jujube Industry Technology Research Institute of Hebei, Baoding, Hebei, 071001, China
| | - Ye Yuan
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Haonan Cao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Chenyu Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Xuan Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei, 071001, China
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071001, China
- Jujube Industry Technology Research Institute of Hebei, Baoding, Hebei, 071001, China
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Yuan Y, Liu Y, Chen S, Wang L, Wang L, Niu Y, Zhao X, Zhao Z, Liu Z, Liu M. A triphosphate tunnel metalloenzyme from pear (PbrTTM1) moonlights as an adenylate cyclase. Front Plant Sci 2023; 14:1183931. [PMID: 37426988 PMCID: PMC10324617 DOI: 10.3389/fpls.2023.1183931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023]
Abstract
Adenylyl cyclase (AC) is the vital enzyme for generating 3',5'-cyclic adenosine monophosphate, an important signaling molecule with profound nutritional and medicinal values. However, merely, a dozen of AC proteins have been reported in plants so far. Here, a protein annotated as triphosphate tunnel metalloenzyme (PbrTTM1) in pear, the important worldwide fruit plant, was firstly identified to possess AC activity with both in vivo and in vitro methods. It exhibited a relatively low AC activity but was capable of complementing AC functional deficiencies in the E. coli SP850 strain. Its protein conformation and potential catalytic mechanism were analyzed by means of biocomputing. The active site of PbrTTM1 is a closed tunnel constructed by nine antiparallel β-folds surrounded with seven helices. Inside the tunnel, the charged residues were possibly involved in the catalytic process by coordinating with divalent cation and ligand. The hydrolysis activity of PbrTTM1 was tested as well. Compared to the much higher capacity of hydrolyzing, the AC activity of PbrTTM1 tends to be a moonlight function. Through a comparison of protein structures in various plant TTMs, it is reasonable to speculate that many plant TTMs might possess AC activity as a form of moonlighting enzyme function.
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Affiliation(s)
- Ye Yuan
- College of Horticulture, Hebei Agricultural University, Hebei, China
| | - Yuye Liu
- College of Horticulture, Hebei Agricultural University, Hebei, China
| | - Shuangjiang Chen
- College of Horticulture, Hebei Agricultural University, Hebei, China
| | - Lili Wang
- College of Horticulture, Hebei Agricultural University, Hebei, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Hebei, China
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Hebei, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Hebei, China
| | - Yahong Niu
- College of Horticulture, Hebei Agricultural University, Hebei, China
| | - Xin Zhao
- College of Horticulture, Hebei Agricultural University, Hebei, China
| | - Zhihui Zhao
- College of Horticulture, Hebei Agricultural University, Hebei, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Hebei, China
| | - Zhiguo Liu
- College of Horticulture, Hebei Agricultural University, Hebei, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Hebei, China
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Hebei, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Hebei, China
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Świeżawska-Boniecka B, Szmidt-Jaworska A. Phytohormones and cyclic nucleotides - Long-awaited couples? J Plant Physiol 2023; 286:154005. [PMID: 37186984 DOI: 10.1016/j.jplph.2023.154005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Affiliation(s)
- Brygida Świeżawska-Boniecka
- Nicolaus Copernicus University, Faculty of Biological and Veterinary Sciences, Department of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
| | - Adriana Szmidt-Jaworska
- Nicolaus Copernicus University, Faculty of Biological and Veterinary Sciences, Department of Plant Physiology and Biotechnology, Lwowska St. 1, PL 87-100, Torun, Poland.
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