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Zhang H, He Q, Xing L, Wang R, Wang Y, Liu Y, Zhou Q, Li X, Jia Z, Liu Z, Miao Y, Lin T, Li W, Du H. The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones. PLANT COMMUNICATIONS 2024; 5:100677. [PMID: 37634079 PMCID: PMC10811376 DOI: 10.1016/j.xplc.2023.100677] [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: 04/23/2023] [Revised: 06/05/2023] [Accepted: 08/24/2023] [Indexed: 08/28/2023]
Abstract
Rheum officinale, a member of the Polygonaceae family, is an important medicinal plant that is widely used in traditional Chinese medicine. Here, we report a 7.68-Gb chromosome-scale assembly of R. officinale with a contig N50 of 3.47 Mb, which was clustered into 44 chromosomes across four homologous groups. Comparative genomics analysis revealed that transposable elements have made a significant contribution to its genome evolution, gene copy number variation, and gene regulation and expression, particularly of genes involved in metabolite biosynthesis, stress resistance, and root development. We placed the recent autotetraploidization of R. officinale at ∼0.58 mya and analyzed the genomic features of its homologous chromosomes. Although no dominant monoploid genomes were observed at the overall expression level, numerous allele-differentially-expressed genes were identified, mainly with different transposable element insertions in their regulatory regions, suggesting that they functionally diverged after polyploidization. Combining genomics, transcriptomics, and metabolomics, we explored the contributions of gene family amplification and tetraploidization to the abundant anthraquinone production of R. officinale, as well as gene expression patterns and differences in anthraquinone content among tissues. Our report offers unprecedented genomic resources for fundamental research on the autopolyploid herb R. officinale and guidance for polyploid breeding of herbs.
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Affiliation(s)
- Hongyu Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Qiang He
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Longsheng Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Ruyu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yu Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yu Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Qinghong Zhou
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Xuanzhao Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Zheng Jia
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Ze Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Yuqing Miao
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Tao Lin
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Wei Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Basic Science Center for Biotic Interaction in Hebei, Hebei University, Baoding 071000, China.
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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. NATURE 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] [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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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. FRONTIERS IN PLANT SCIENCE 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] [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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Feng YR, Li TT, Wang SJ, Lu YT, Yuan TT. Triphosphate Tunnel Metalloenzyme 2 Acts as a Downstream Factor of ABI4 in ABA-Mediated Seed Germination. Int J Mol Sci 2023; 24:ijms24108994. [PMID: 37240339 DOI: 10.3390/ijms24108994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Seed germination is a complex process that is regulated by various exogenous and endogenous factors, in which abscisic acid (ABA) plays a crucial role. The triphosphate tunnel metalloenzyme (TTM) superfamily exists in all living organisms, but research on its biological role is limited. Here, we reveal that TTM2 functions in ABA-mediated seed germination. Our study indicates that TTM2 expression is enhanced but repressed by ABA during seed germination. Promoted TTM2 expression in 35S::TTM2-FLAG rescues ABA-mediated inhibition of seed germination and early seedling development and ttm2 mutants exhibit lower seed germination rate and reduced cotyledon greening compared with the wild type, revealing that the repression of TTM2 expression is required for ABA-mediated inhibition of seed germination and early seedling development. Further, ABA inhibits TTM2 expression by ABA insensitive 4 (ABI4) binding of TTM2 promoter and the ABA-insensitive phenotype of abi4-1 with higher TTM2 expression can be rescued by mutation of TTM2 in abi4-1 ttm2-1 mutant, indicating that TTM2 acts downstream of ABI4. In addition, TTM1, a homolog of TTM2, is not involved in ABA-mediated regulation of seed germination. In summary, our findings reveal that TTM2 acts as a downstream factor of ABI4 in ABA-mediated seed germination and early seedling growth.
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Affiliation(s)
- Yu-Rui Feng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ting-Ting Li
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang 222005, China
| | - Shi-Jia Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ting-Ting Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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5
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Liu Z, Yuan Y, Wang L, Zhao X, Wang L, Wang L, Zhao Z, Zhao X, Chu Y, Gao Y, Yang F, Wang Y, Zhang Q, Zhao J, Liu M. Three Novel Adenylate Cyclase Genes Show Significant Biological Functions in Plant. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1149-1161. [PMID: 36601683 DOI: 10.1021/acs.jafc.2c07683] [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: 06/17/2023]
Abstract
Adenylate cyclase is the key enzyme solely synthesizing cAMP which participates in cell metabolism regulations and functions as an intracellular second messenger. However, the biological functions of plant ACs have not been elucidated clearly for their poor conservative sequences and low detectable cAMP. We performed a systematic study of plant ACs by using Chinese jujube, whose fruit exhibits the highest cAMP content among plants. Three novel ACs were identified from Chinese jujube, and two types of methods including in vitro and in vivo were used to certificate ZjAC1-3 which can catalyze the conversion of ATP into cAMP. The biological functions of significant accelerations of seed germination, root growth, and flowering were found via overexpression of these AC genes in Arabidopsis, and these functions of ACs were further demonstrated by treating the AC-overexpressing transgenic lines and wild type Arabidopsis with bithionol and dibutyryl-cAMP. At last, transcriptome data revealed that the underlying mechanism of the biological functions of ACs might be regulation of the key genes involved in the circadian rhythm pathway and the hormone signal transduction pathway. This research established a foundation for further investigating plant AC genes and provided strong evidence for cAMP serving as a signaling molecule in plants.
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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
| | - Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xuan Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
- "Dongzao" Research Institute of Zhanhua District, Binzhou, Shandong 256800, China
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, China
| | - Zhihui Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xin Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Yuetong Chu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Yaning Gao
- Beijing Pharma and Biotech Center, Beijing 100176, China
| | - Fangyuan Yang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Yulu Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Qiong Zhang
- Shandong Institute of Pomology, Tai'an, Shandong 271000, China
| | - Jin Zhao
- College of Life Science, 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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6
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Yuan Y, Liu Z, Wang L, Wang L, Chen S, Niu Y, Zhao X, Liu P, Liu M. Two triphosphate tunnel metalloenzymes from apple exhibit adenylyl cyclase activity. FRONTIERS IN PLANT SCIENCE 2022; 13:992488. [PMID: 36275530 PMCID: PMC9582125 DOI: 10.3389/fpls.2022.992488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Adenylyl cyclase (AC) is the key catalytic enzyme for the synthesis of 3',5'-cyclic adenosine monophosphate. Various ACs have been identified in microorganisms and mammals, but studies on plant ACs are still limited. No AC in woody plants has been reported until now. Based on the information on HpAC1, three enzymes were screened out from the woody fruit tree apple, and two of them (MdTTM1 and MdTTM2) were verified and confirmed to display AC activity. Interestingly, in the apple genome, these two genes were annotated as triphosphate tunnel metalloenzymes (TTMs) which were widely found in three superkingdoms of life with multiple substrate specificities and enzymatic activities, especially triphosphate hydrolase. In addition, the predicted structures of these two proteins were parallel, especially of the catalytic tunnel, including conserved domains, motifs, and folded structures. Their tertiary structures exhibited classic TTM properties, like the characteristic EXEXK motif and β-stranded anti-parallel tunnel capable of coordinating divalent cations. Moreover, MdTTM2 and HpAC1 displayed powerful hydrolase activity to triphosphate and restricted AC activity. All of these findings showed that MdTTMs had hydrolysis and AC activity, which could provide new solid evidence for AC distribution in woody plants as well as insights into the relationship between ACs and TTMs.
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Affiliation(s)
- Ye Yuan
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Zhiguo Liu
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Lili Wang
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Shuangjiang Chen
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yahong Niu
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xin Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Ping Liu
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
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7
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Pesquera M, Martinez J, Maillot B, Wang K, Hofmann M, Raia P, Loubéry S, Steensma P, Hothorn M, Fitzpatrick TB. Structural and functional studies of Arabidopsis thaliana triphosphate tunnel metalloenzymes reveal roles for additional domains. J Biol Chem 2022; 298:102438. [PMID: 36049521 PMCID: PMC9582702 DOI: 10.1016/j.jbc.2022.102438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/04/2022] Open
Abstract
Triphosphate tunnel metalloenzymes (TTMs) are found in all biological kingdoms and have been characterized in microorganisms and animals. Members of the TTM family have divergent biological functions and act on a range of triphosphorylated substrates (RNA, thiamine triphosphate, and inorganic polyphosphate). TTMs in plants have received considerably less attention and are unique in that some homologs harbor additional domains including a P-loop kinase and transmembrane domain. Here, we report on structural and functional aspects of the multimodular TTM1 and TTM2 of Arabidopsis thaliana. Our tissue and cellular microscopy studies show that both AtTTM1 and AtTTM2 are expressed in actively dividing (meristem) tissue and are tail-anchored proteins at the outer mitochondrial membrane, mediated by the single C-terminal transmembrane domain, supporting earlier studies. In addition, we reveal from crystal structures of AtTTM1 in the presence and absence of a nonhydrolyzable ATP analog a catalytically incompetent TTM tunnel domain tightly interacting with the P-loop kinase domain that is locked in an inactive conformation. Our structural comparison indicates that a helical hairpin may facilitate movement of the TTM domain, thereby activating the kinase. Furthermore, we conducted genetic studies to show that AtTTM2 is important for the developmental transition from the vegetative to the reproductive phase in Arabidopsis, whereas its closest paralog AtTTM1 is not. We demonstrate through rational design of mutations based on the 3D structure that both the P-loop kinase and TTM tunnel modules of AtTTM2 are required for the developmental switch. Together, our results provide insight into the structure and function of plant TTM domains.
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Affiliation(s)
- Marta Pesquera
- Vitamins & Environmental Stress Responses in Plants, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Jacobo Martinez
- Structural Plant Biology, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Benoît Maillot
- Vitamins & Environmental Stress Responses in Plants, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Kai Wang
- Vitamins & Environmental Stress Responses in Plants, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Manuel Hofmann
- Vitamins & Environmental Stress Responses in Plants, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Pierre Raia
- Structural Plant Biology, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Sylvain Loubéry
- Plant Imaging Unit, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Priscille Steensma
- Vitamins & Environmental Stress Responses in Plants, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Michael Hothorn
- Structural Plant Biology, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland.
| | - Teresa B Fitzpatrick
- Vitamins & Environmental Stress Responses in Plants, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland.
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8
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Bettendorff L. Update on Thiamine Triphosphorylated Derivatives and Metabolizing Enzymatic Complexes. Biomolecules 2021; 11:biom11111645. [PMID: 34827643 PMCID: PMC8615392 DOI: 10.3390/biom11111645] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 12/12/2022] Open
Abstract
While the cellular functions of the coenzyme thiamine (vitamin B1) diphosphate (ThDP) are well characterized, the triphosphorylated thiamine derivatives, thiamine triphosphate (ThTP) and adenosine thiamine triphosphate (AThTP), still represent an intriguing mystery. They are present, generally in small amounts, in nearly all organisms, bacteria, fungi, plants, and animals. The synthesis of ThTP seems to require ATP synthase by a mechanism similar to ATP synthesis. In E. coli, ThTP is synthesized during amino acid starvation, while in plants, its synthesis is dependent on photosynthetic processes. In E. coli, ThTP synthesis probably requires oxidation of pyruvate and may play a role at the interface between energy and amino acid metabolism. In animal cells, no mechanism of regulation is known. Cytosolic ThTP levels are controlled by a highly specific cytosolic thiamine triphosphatase (ThTPase), coded by thtpa, and belonging to the ubiquitous family of the triphosphate tunnel metalloenzymes (TTMs). While members of this protein family are found in nearly all living organisms, where they bind organic and inorganic triphosphates, ThTPase activity seems to be restricted to animals. In mammals, THTPA is ubiquitously expressed with probable post-transcriptional regulation. Much less is known about the recently discovered AThTP. In E. coli, AThTP is synthesized by a high molecular weight protein complex from ThDP and ATP or ADP in response to energy stress. A better understanding of these two thiamine derivatives will require the use of transgenic models.
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Affiliation(s)
- Lucien Bettendorff
- Laboratory of Neurophysiology, GIGA Neurosciences, University of Liège, 4000 Liège, Belgium
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9
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Karia P, Yoshioka K, Moeder W. Multiple phosphorylation events of the mitochondrial membrane protein TTM1 regulate cell death during senescence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:766-780. [PMID: 34409658 DOI: 10.1111/tpj.15470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
The role of mitochondria in programmed cell death (PCD) during animal growth and development is well documented, but much less is known for plants. We previously showed that the Arabidopsis thaliana triphosphate tunnel metalloenzyme (TTM) proteins TTM1 and TTM2 are tail-anchored proteins that localize in the mitochondrial outer membrane and participate in PCD during senescence and immunity, respectively. Here, we show that TTM1 is specifically involved in senescence induced by abscisic acid (ABA). Moreover, phosphorylation of TTM1 by multiple mitogen-activated protein (MAP) kinases regulates its function and turnover. A combination of proteomics and in vitro kinase assays revealed three major phosphorylation sites of TTM1 (Ser10, Ser437, and Ser490). Ser437, which is phosphorylated upon perception of senescence cues such as ABA and prolonged darkness, is phosphorylated by the MAP kinases MPK3 and MPK4, and Ser437 phosphorylation is essential for TTM1 function in senescence. These MPKs, together with three additional MAP kinases (MPK1, MPK7, and MPK6), also phosphorylate Ser10 and Ser490, marking TTM1 for protein turnover, which likely prevents uncontrolled cell death. Taken together, our results show that multiple MPKs regulate the function and turnover of the mitochondrial protein TTM1 during senescence-associated cell death, revealing a novel link between mitochondria and PCD.
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Affiliation(s)
- Purva Karia
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Keiko Yoshioka
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Center for the Analysis of Genome Evolution and Function (CAGEF), University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Wolfgang Moeder
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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10
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Vogt MS, Ngouoko Nguepbeu RR, Mohr MKF, Albers SV, Essen LO, Banerjee A. The archaeal triphosphate tunnel metalloenzyme SaTTM defines structural determinants for the diverse activities in the CYTH protein family. J Biol Chem 2021; 297:100820. [PMID: 34029589 PMCID: PMC8233210 DOI: 10.1016/j.jbc.2021.100820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022] Open
Abstract
CYTH proteins make up a large superfamily that is conserved in all three domains of life. These enzymes have a triphosphate tunnel metalloenzyme (TTM) fold, which typically results in phosphatase functions, e.g., RNA triphosphatase, inorganic polyphosphatase, or thiamine triphosphatase. Some CYTH orthologs cyclize nucleotide triphosphates to 3′,5′-cyclic nucleotides. So far, archaeal CYTH proteins have been annotated as adenylyl cyclases, although experimental evidence to support these annotations is lacking. To address this gap, we characterized a CYTH ortholog, SaTTM, from the crenarchaeote Sulfolobus acidocaldarius. Our in silico studies derived ten major subclasses within the CYTH family implying a close relationship between these archaeal CYTH enzymes and class IV adenylyl cyclases. However, initial biochemical characterization reveals inability of SaTTM to produce any cyclic nucleotides. Instead, our structural and functional analyses show a classical TTM behavior, i.e., triphosphatase activity, where pyrophosphate causes product inhibition. The Ca2+-inhibited Michaelis complex indicates a two-metal-ion reaction mechanism analogous to other TTMs. Cocrystal structures of SaTTM further reveal conformational dynamics in SaTTM that suggest feedback inhibition in TTMs due to tunnel closure in the product state. These structural insights combined with further sequence similarity network–based in silico analyses provide a firm molecular basis for distinguishing CYTH orthologs with phosphatase activities from class IV adenylyl cyclases.
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Affiliation(s)
- Marian S Vogt
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | | | - Michael K F Mohr
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany; Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany.
| | - Ankan Banerjee
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany; Department of Genetics, Philipps-Universität Marburg, Marburg, Germany.
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11
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Xu R, Guo Y, Peng S, Liu J, Li P, Jia W, Zhao J. Molecular Targets and Biological Functions of cAMP Signaling in Arabidopsis. Biomolecules 2021; 11:biom11050688. [PMID: 34063698 PMCID: PMC8147800 DOI: 10.3390/biom11050688] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
Cyclic AMP (cAMP) is a pivotal signaling molecule existing in almost all living organisms. However, the mechanism of cAMP signaling in plants remains very poorly understood. Here, we employ the engineered activity of soluble adenylate cyclase to induce cellular cAMP elevation in Arabidopsis thaliana plants and identify 427 cAMP-responsive genes (CRGs) through RNA-seq analysis. Induction of cellular cAMP elevation inhibits seed germination, disturbs phytohormone contents, promotes leaf senescence, impairs ethylene response, and compromises salt stress tolerance and pathogen resistance. A set of 62 transcription factors are among the CRGs, supporting a prominent role of cAMP in transcriptional regulation. The CRGs are significantly overrepresented in the pathways of plant hormone signal transduction, MAPK signaling, and diterpenoid biosynthesis, but they are also implicated in lipid, sugar, K+, nitrate signaling, and beyond. Our results provide a basic framework of cAMP signaling for the community to explore. The regulatory roles of cAMP signaling in plant plasticity are discussed.
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Affiliation(s)
- Ruqiang Xu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: ; Tel.: +86-0371-6778-5095
| | - Yanhui Guo
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Song Peng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Jinrui Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Panyu Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Wenjing Jia
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
| | - Junheng Zhao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.G.); (S.P.); (J.L.); (P.L.); (W.J.); (J.Z.)
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12
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Crystal structure and enzymatic characterization of the putative adenylyl cyclase HpAC1 from Hippeastrum reveal dominant triphosphatase activity. J Struct Biol 2020; 212:107649. [PMID: 33075486 DOI: 10.1016/j.jsb.2020.107649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/05/2020] [Accepted: 10/11/2020] [Indexed: 11/24/2022]
Abstract
HpAC1, a protein from Hippeastrum hybrid cultivars, was previously suggested to be a plant adenylyl cyclase. We describe a structural and enzymatic characterization of HpAC1. A crystal structure of HpAC1 in complex with a non-hydrolyzable GTP analog confirms a generic CYTH architecture, comprising a β-barrel with an internal substrate site. The structure reveals significant active site differences to AC proteins with CYTH fold, however, and we find that HpAC1 lacks measurable AC activity. Instead, HpAC1 has substantial triphosphatase activity, indicating this protective activity or a related activity as the protein's physiological function.
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13
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Takagi Y, Kuwabara N, Dang TT, Furukawa K, Ho CK. Crystal structures of the RNA triphosphatase from Trypanosoma cruzi provide insights into how it recognizes the 5'-end of the RNA substrate. J Biol Chem 2020; 295:9076-9086. [PMID: 32381506 PMCID: PMC7335777 DOI: 10.1074/jbc.ra119.011811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/06/2020] [Indexed: 11/06/2022] Open
Abstract
RNA triphosphatase catalyzes the first step in mRNA cap formation, hydrolysis of the terminal phosphate from the nascent mRNA transcript. The RNA triphosphatase from the protozoan parasite Trypanosoma cruzi, TcCet1, belongs to the family of triphosphate tunnel metalloenzymes (TTMs). TcCet1 is a promising antiprotozoal drug target because the mechanism and structure of the protozoan RNA triphosphatases are completely different from those of the RNA triphosphatases found in mammalian and arthropod hosts. Here, we report several crystal structures of the catalytically active form of TcCet1 complexed with a divalent cation and an inorganic tripolyphosphate in the active-site tunnel at 2.20-2.51 Å resolutions. The structures revealed that the overall structure, the architecture of the tunnel, and the arrangement of the metal-binding site in TcCet1 are similar to those in other TTM proteins. On the basis of the position of three sulfate ions that cocrystallized on the positively charged surface of the protein and results obtained from mutational analysis, we identified an RNA-binding site in TcCet1. We conclude that the 5'-end of the triphosphate RNA substrate enters the active-site tunnel directionally. The structural information reported here provides valuable insight into designing inhibitors that could specifically block the entry of the triphosphate RNA substrate into the TTM-type RNA triphosphatases of T. cruzi and related pathogens.
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Affiliation(s)
- Yuko Takagi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Naoyuki Kuwabara
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, Japan
| | - Truong Tat Dang
- Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Koji Furukawa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - C Kiong Ho
- Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki Japan.
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14
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Zhu J, Loubéry S, Broger L, Zhang Y, Lorenzo-Orts L, Utz-Pugin A, Fernie AR, Young-Tae C, Hothorn M. A genetically validated approach for detecting inorganic polyphosphates in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:507-516. [PMID: 31816134 DOI: 10.1111/tpj.14642] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/08/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Inorganic polyphosphates (polyPs) are linear polymers of orthophosphate units linked by phosphoanhydride bonds. Polyphosphates represent important stores of phosphate and energy, and are abundant in many pro- and eukaryotic organisms. In plants, the existence of polyPs has been established using microscopy and biochemical extraction methods that are now known to produce artifacts. Here we use a polyP-specific dye and a polyP-binding domain to detect polyPs in plant and algal cells. To develop the staining protocol, we induced polyP granules in Nicotiana benthamiana and Arabidopsis cells by heterologous expression of Escherichia coli polyphosphate kinase 1 (PPK1). Over-expression of PPK1 but not of a catalytically impaired version of the enzyme leads to severe growth phenotypes, suggesting that ATP-dependent synthesis and accumulation of polyPs in the plant cytosol is toxic. We next crossed stable PPK1-expressing Arabidopsis lines with plants expressing the polyP-binding domain of E. coli exopolyphosphatase (PPX1c), which co-localized with PPK1-generated polyP granules. These granules were stained by the polyP-specific dye JC-D7 and appeared as electron-dense structures in transmission electron microscopy sections. Using the polyP staining protocol derived from these experiments, we screened for polyP stores in different organs and tissues of both mono- and dicotyledonous plants. While we could not detect polyP granules in higher plants, we could visualize the polyP-rich acidocalcisomes in the green alga Chlamydomonas reinhardtii.
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Affiliation(s)
- Jinsheng Zhu
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Sylvain Loubéry
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Larissa Broger
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Youjun Zhang
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Center of Plant System Biology and Biotechnology, Ruski Blvd. 139, Plovdiv, 4000, Bulgaria
| | - Laura Lorenzo-Orts
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Anne Utz-Pugin
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Alisdair R Fernie
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Chang Young-Tae
- Center for Self-assembly and Complexity, IBS and Department of Chemistry, POSTECH, 50, Jigok-ro 127beon-gil, Nam-gu, Pohang-si, Gyeongsangbuk-do, Pohang, 37673, Republic of Korea
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
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15
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Zhu J, Loubéry S, Broger L, Zhang Y, Lorenzo-Orts L, Utz-Pugin A, Fernie AR, Young-Tae C, Hothorn M. A genetically validated approach for detecting inorganic polyphosphates in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:507-516. [PMID: 31816134 DOI: 10.1101/630129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/08/2019] [Accepted: 12/03/2019] [Indexed: 05/22/2023]
Abstract
Inorganic polyphosphates (polyPs) are linear polymers of orthophosphate units linked by phosphoanhydride bonds. Polyphosphates represent important stores of phosphate and energy, and are abundant in many pro- and eukaryotic organisms. In plants, the existence of polyPs has been established using microscopy and biochemical extraction methods that are now known to produce artifacts. Here we use a polyP-specific dye and a polyP-binding domain to detect polyPs in plant and algal cells. To develop the staining protocol, we induced polyP granules in Nicotiana benthamiana and Arabidopsis cells by heterologous expression of Escherichia coli polyphosphate kinase 1 (PPK1). Over-expression of PPK1 but not of a catalytically impaired version of the enzyme leads to severe growth phenotypes, suggesting that ATP-dependent synthesis and accumulation of polyPs in the plant cytosol is toxic. We next crossed stable PPK1-expressing Arabidopsis lines with plants expressing the polyP-binding domain of E. coli exopolyphosphatase (PPX1c), which co-localized with PPK1-generated polyP granules. These granules were stained by the polyP-specific dye JC-D7 and appeared as electron-dense structures in transmission electron microscopy sections. Using the polyP staining protocol derived from these experiments, we screened for polyP stores in different organs and tissues of both mono- and dicotyledonous plants. While we could not detect polyP granules in higher plants, we could visualize the polyP-rich acidocalcisomes in the green alga Chlamydomonas reinhardtii.
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Affiliation(s)
- Jinsheng Zhu
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Sylvain Loubéry
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Larissa Broger
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Youjun Zhang
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
- Center of Plant System Biology and Biotechnology, Ruski Blvd. 139, Plovdiv, 4000, Bulgaria
| | - Laura Lorenzo-Orts
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Anne Utz-Pugin
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
| | - Alisdair R Fernie
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Chang Young-Tae
- Center for Self-assembly and Complexity, IBS and Department of Chemistry, POSTECH, 50, Jigok-ro 127beon-gil, Nam-gu, Pohang-si, Gyeongsangbuk-do, Pohang, 37673, Republic of Korea
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, Geneva, 1211, Switzerland
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16
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Świeżawska B, Duszyn M, Kwiatkowski M, Jaworski K, Pawełek A, Szmidt‐Jaworska A. Brachypodium distachyon
triphosphate tunnel metalloenzyme 3 is both a triphosphatase and an adenylyl cyclase upregulated by mechanical wounding. FEBS Lett 2020; 594:1101-1111. [DOI: 10.1002/1873-3468.13701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Brygida Świeżawska
- Chair of Plant Physiology and Biotechnology Nicolaus Copernicus University Torun Poland
| | - Maria Duszyn
- Chair of Plant Physiology and Biotechnology Nicolaus Copernicus University Torun Poland
| | - Mateusz Kwiatkowski
- Chair of Plant Physiology and Biotechnology Nicolaus Copernicus University Torun Poland
| | - Krzysztof Jaworski
- Chair of Plant Physiology and Biotechnology Nicolaus Copernicus University Torun Poland
| | - Agnieszka Pawełek
- Chair of Plant Physiology and Biotechnology Nicolaus Copernicus University Torun Poland
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17
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Lorenzo‐Orts L, Couto D, Hothorn M. Identity and functions of inorganic and inositol polyphosphates in plants. THE NEW PHYTOLOGIST 2020; 225:637-652. [PMID: 31423587 PMCID: PMC6973038 DOI: 10.1111/nph.16129] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/22/2019] [Indexed: 05/08/2023]
Abstract
Inorganic polyphosphates (polyPs) and inositol pyrophosphates (PP-InsPs) form important stores of inorganic phosphate and can act as energy metabolites and signaling molecules. Here we review our current understanding of polyP and inositol phosphate (InsP) metabolism and physiology in plants. We outline methods for polyP and InsP detection, discuss the known plant enzymes involved in their synthesis and breakdown, and summarize the potential physiological and signaling functions for these enigmatic molecules in plants.
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Affiliation(s)
- Laura Lorenzo‐Orts
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
| | - Daniel Couto
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
| | - Michael Hothorn
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
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18
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Dossa K, Li D, Zhou R, Yu J, Wang L, Zhang Y, You J, Liu A, Mmadi MA, Fonceka D, Diouf D, Cissé N, Wei X, Zhang X. The genetic basis of drought tolerance in the high oil crop Sesamum indicum. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1788-1803. [PMID: 30801874 PMCID: PMC6686131 DOI: 10.1111/pbi.13100] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 05/18/2023]
Abstract
Unlike most of the important food crops, sesame can survive drought but severe and repeated drought episodes, especially occurring during the reproductive stage, significantly curtail the productivity of this high oil crop. Genome-wide association study was conducted for traits related to drought tolerance using 400 diverse sesame accessions, including landraces and modern cultivars. Ten stable QTLs explaining more than 40% of the phenotypic variation and located on four linkage groups were significantly associated with drought tolerance related traits. Accessions from the tropical area harboured higher numbers of drought tolerance alleles at the peak loci and were found to be more tolerant than those from the northern area, indicating a long-term genetic adaptation to drought-prone environments. We found that sesame has already fixed important alleles conferring survival to drought which may explain its relative high drought tolerance. However, most of the alleles crucial for productivity and yield maintenance under drought conditions are far from been fixed. This study also revealed that pyramiding the favourable alleles observed at the peak loci is of high potential for enhancing drought tolerance in sesame. In addition, our results highlighted two important pleiotropic QTLs harbouring known and unreported drought tolerance genes such as SiABI4, SiTTM3, SiGOLS1, SiNIMIN1 and SiSAM. By integrating candidate gene association study, gene expression and transgenic experiments, we demonstrated that SiSAM confers drought tolerance by modulating polyamine levels and ROS homeostasis, and a missense mutation in the coding region partly contributes to the natural variation of drought tolerance in sesame.
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Affiliation(s)
- Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS)ThièsSénégal
- Laboratoire Campus de Biotechnologies VégétalesDépartement de Biologie VégétaleFaculté des Sciences et TechniquesUniversité Cheikh Anta DiopDakarSénégal
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
| | - Jingyin Yu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
| | - Yanxin Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
| | - Aili Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
| | - Marie A. Mmadi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS)ThièsSénégal
- Laboratoire Campus de Biotechnologies VégétalesDépartement de Biologie VégétaleFaculté des Sciences et TechniquesUniversité Cheikh Anta DiopDakarSénégal
| | - Daniel Fonceka
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS)ThièsSénégal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies VégétalesDépartement de Biologie VégétaleFaculté des Sciences et TechniquesUniversité Cheikh Anta DiopDakarSénégal
| | - Ndiaga Cissé
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS)ThièsSénégal
| | - Xin Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
- College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubeiChina
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19
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Lorenzo-Orts L, Hohmann U, Zhu J, Hothorn M. Molecular characterization of CHAD domains as inorganic polyphosphate-binding modules. Life Sci Alliance 2019; 2:2/3/e201900385. [PMID: 31133615 PMCID: PMC6537752 DOI: 10.26508/lsa.201900385] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 12/23/2022] Open
Abstract
A domain of unknown function termed CHAD, present in all kingdoms of life, is characterized as a specific inorganic polyphosphate-binding domain. Inorganic polyphosphates (polyPs) are linear polymers of orthophosphate units linked by phosphoanhydride bonds. Here, we report that bacterial, archaeal, and eukaryotic conserved histidine α-helical (CHAD) domains are specific polyP-binding modules. Crystal structures reveal that CHAD domains are formed by two four-helix bundles, giving rise to a central pore surrounded by conserved basic surface patches. Different CHAD domains bind polyPs with dissociation constants ranging from the nano- to mid-micromolar range, but not nucleic acids. A CHAD—polyP complex structure reveals the phosphate polymer binding across the central pore and along the two basic patches. Mutational analysis of CHAD—polyP interface residues validates the complex structure. The presence of a CHAD domain in the polyPase ygiF enhances its enzymatic activity. The only known CHAD protein from the plant Ricinus communis localizes to the nucleus/nucleolus when expressed in Arabidopsis and tobacco, suggesting that plants may harbor polyPs in these compartments. We propose that CHAD domains may be used to engineer the properties of polyP-metabolizing enzymes and to specifically localize polyP stores in eukaryotic cells and tissues.
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Affiliation(s)
- Laura Lorenzo-Orts
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Ulrich Hohmann
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Jinsheng Zhu
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
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20
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Lorenzo-Orts L, Witthoeft J, Deforges J, Martinez J, Loubéry S, Placzek A, Poirier Y, Hothorn LA, Jaillais Y, Hothorn M. Concerted expression of a cell cycle regulator and a metabolic enzyme from a bicistronic transcript in plants. NATURE PLANTS 2019; 5:184-193. [PMID: 30737513 DOI: 10.1038/s41477-019-0358-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/04/2019] [Indexed: 05/15/2023]
Abstract
Eukaryotic mRNAs frequently contain upstream open reading frames (uORFs), encoding small peptides that may control translation of the main ORF (mORF). Here, we report the characterization of a distinct bicistronic transcript in Arabidopsis. We analysed loss-of-function phenotypes of the inorganic polyphosphatase TRIPHOSPHATE TUNNEL METALLOENZYME 3 (AtTTM3), and found that catalytically inactive versions of the enzyme could fully complement embryo and growth-related phenotypes. We could rationalize these puzzling findings by characterizing a uORF in the AtTTM3 locus encoding CELL DIVISION CYCLE PROTEIN 26 (CDC26), an orthologue of the cell cycle regulator. We demonstrate that AtCDC26 is part of the plant anaphase promoting complex/cyclosome (APC/C), regulates accumulation of APC/C target proteins and controls cell division, growth and embryo development. AtCDC26 and AtTTM3 are translated from a single transcript conserved across the plant lineage. While there is no apparent biochemical connection between the two gene products, AtTTM3 coordinates AtCDC26 translation by recruiting the transcript into polysomes. Our work highlights that uORFs may encode functional proteins in plant genomes.
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Affiliation(s)
- Laura Lorenzo-Orts
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
| | - Janika Witthoeft
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Jules Deforges
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Jacobo Martinez
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Sylvain Loubéry
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Aleksandra Placzek
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Ludwig A Hothorn
- Institute of Biostatistics, Leibniz University, Hannover, Germany
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
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21
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Kasahara M, Suetsugu N, Urano Y, Yamamoto C, Ohmori M, Takada Y, Okuda S, Nishiyama T, Sakayama H, Kohchi T, Takahashi F. An adenylyl cyclase with a phosphodiesterase domain in basal plants with a motile sperm system. Sci Rep 2016; 6:39232. [PMID: 27982074 PMCID: PMC5159850 DOI: 10.1038/srep39232] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/18/2016] [Indexed: 01/03/2023] Open
Abstract
Adenylyl cyclase (AC), which produces the signalling molecule cAMP, has numerous important cellular functions in diverse organisms from prokaryotes to eukaryotes. Here we report the identification and characterization of an AC gene from the liverwort Marchantia polymorpha. The encoded protein has both a C-terminal AC catalytic domain similar to those of class III ACs and an N-terminal cyclic nucleotide phosphodiesterase (PDE) domain that degrades cyclic nucleotides, thus we designated the gene MpCAPE (COMBINED AC with PDE). Biochemical analyses of recombinant proteins showed that MpCAPE has both AC and PDE activities. In MpCAPE-promoter-GUS lines, GUS activity was specifically detected in the male sexual organ, the antheridium, suggesting MpCAPE and thus cAMP signalling may be involved in the male reproductive process. CAPE orthologues are distributed only in basal land plants and charophytes that use motile sperm as the male gamete. CAPE is a subclass of class III AC and may be important in male organ and cell development in basal plants.
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Affiliation(s)
- Masahiro Kasahara
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yuki Urano
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Chiaki Yamamoto
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Mikiya Ohmori
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Yuki Takada
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Shujiro Okuda
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Ishikawa 920-0934, Japan
| | - Hidetoshi Sakayama
- Department of Biology, Graduate School of Science, Kobe University, Hyogo 657-8501, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Fumio Takahashi
- Graduate School of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
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22
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Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res 2016; 44:7511-26. [PMID: 27317694 PMCID: PMC5027499 DOI: 10.1093/nar/gkw551] [Citation(s) in RCA: 448] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 12/19/2022] Open
Abstract
The 5′ m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2′O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose.
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Affiliation(s)
- Anand Ramanathan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - G Brett Robb
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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23
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Martinez J, Truffault V, Hothorn M. Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes. J Biol Chem 2015. [PMID: 26221030 PMCID: PMC4641920 DOI: 10.1074/jbc.m115.674473] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Triphosphate tunnel metalloenzymes (TTMs) are present in all kingdoms of life and catalyze diverse enzymatic reactions such as mRNA capping, the cyclization of adenosine triphosphate, the hydrolysis of thiamine triphosphate, and the synthesis and breakdown of inorganic polyphosphates. TTMs have an unusual tunnel domain fold that harbors substrate- and metal co-factor binding sites. It is presently poorly understood how TTMs specifically sense different triphosphate-containing substrates and how catalysis occurs in the tunnel center. Here we describe substrate-bound structures of inorganic polyphosphatases from Arabidopsis and Escherichia coli, which reveal an unorthodox yet conserved mode of triphosphate and metal co-factor binding. We identify two metal binding sites in these enzymes, with one co-factor involved in substrate coordination and the other in catalysis. Structural comparisons with a substrate- and product-bound mammalian thiamine triphosphatase and with previously reported structures of mRNA capping enzymes, adenylate cyclases, and polyphosphate polymerases suggest that directionality of substrate binding defines TTM catalytic activity. Our work provides insight into the evolution and functional diversification of an ancient enzyme family.
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Affiliation(s)
- Jacobo Martinez
- From the Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland and
| | - Vincent Truffault
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Michael Hothorn
- From the Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland and
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24
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Ung H, Moeder W, Yoshioka K. Arabidopsis triphosphate tunnel metalloenzyme2 is a negative regulator of the salicylic acid-mediated feedback amplification loop for defense responses. PLANT PHYSIOLOGY 2014; 166:1009-21. [PMID: 25185123 PMCID: PMC4213072 DOI: 10.1104/pp.114.248757] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The triphosphate tunnel metalloenzyme (TTM) superfamily represents a group of enzymes that is characterized by their ability to hydrolyze a range of tripolyphosphate substrates. Arabidopsis (Arabidopsis thaliana) encodes three TTM genes, AtTTM1, AtTTM2, and AtTTM3. Although AtTTM3 has previously been reported to have tripolyphosphatase activity, recombinantly expressed AtTTM2 unexpectedly exhibited pyrophosphatase activity. AtTTM2 knockout mutant plants exhibit an enhanced hypersensitive response, elevated pathogen resistance against both virulent and avirulent pathogens, and elevated accumulation of salicylic acid (SA) upon infection. In addition, stronger systemic acquired resistance compared with wild-type plants was observed. These enhanced defense responses are dependent on SA, PHYTOALEXIN-DEFICIENT4, and NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1. Despite their enhanced pathogen resistance, ttm2 plants did not display constitutively active defense responses, suggesting that AtTTM2 is not a conventional negative regulator but a negative regulator of the amplification of defense responses. The transcriptional suppression of AtTTM2 by pathogen infection or treatment with SA or the systemic acquired resistance activator benzothiadiazole further supports this notion. Such transcriptional regulation is conserved among TTM2 orthologs in the crop plants soybean (Glycine max) and canola (Brassica napus), suggesting that TTM2 is involved in immunity in a wide variety of plant species. This indicates the possible usage of TTM2 knockout mutants for agricultural applications to generate pathogen-resistant crop plants.
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Affiliation(s)
- Huoi Ung
- Department of Cell and Systems Biology (H.U., W.M., K.Y.) andCenter for the Analysis of Genome Evolution and Function (K.Y.), University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Wolfgang Moeder
- Department of Cell and Systems Biology (H.U., W.M., K.Y.) andCenter for the Analysis of Genome Evolution and Function (K.Y.), University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Keiko Yoshioka
- Department of Cell and Systems Biology (H.U., W.M., K.Y.) andCenter for the Analysis of Genome Evolution and Function (K.Y.), University of Toronto, Toronto, Ontario, Canada M5S 3B2
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25
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Albi T, Serrano A. Two exopolyphosphatases with distinct molecular architectures and substrate specificities from the thermophilic green-sulfur bacterium Chlorobium tepidum TLS. Microbiology (Reading) 2014; 160:2067-2078. [DOI: 10.1099/mic.0.080952-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The genome of the thermophilic green-sulfur bacterium Chlorobium tepidum TLS possesses two genes encoding putative exopolyphosphatases (PPX; EC 3.6.1.11), namely CT0099 (ppx1, 993 bp) and CT1713 (ppx2, 1557 bp). The predicted polypeptides of 330 and 518 aa residues are Ppx-GppA phosphatases of different domain architectures – the largest one has an extra C-terminal HD domain – which may represent ancient paralogues. Both ppx genes were cloned and overexpressed in Escherichia coli BL21(DE3). While CtPPX1 was validated as a monomeric enzyme, CtPPX2 was found to be a homodimer. Both PPX homologues were functional, K+-stimulated phosphohydrolases, with an absolute requirement for divalent metal cations and a marked preference for Mg2+. Nevertheless, they exhibited remarkably different catalytic specificities with regard to substrate classes and chain lengths. Even though both enzymes were able to hydrolyse the medium-size polyphosphate (polyP) P13–18 (polyP mix with mean chain length of 13–18 phosphate residues), CtPPX1 clearly reached its highest catalytic efficiency with tripolyphosphate and showed substantial nucleoside triphosphatase (NTPase) activity, while CtPPX2 preferred long-chain polyPs (>300 Pi residues) and did not show any detectable NTPase activity. These catalytic features, taken together with the distinct domain architectures and molecular phylogenies, indicate that the two PPX homologues of Chl. tepidum belong to different Ppx-GppA phosphatase subfamilies that should play specific biochemical roles in nucleotide and polyP metabolisms. In addition, these results provide an example of the remarkable functional plasticity of the Ppx-GppA phosphatases, a family of proteins with relatively simple structures that are widely distributed in the microbial world.
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Affiliation(s)
- Tomás Albi
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, CSIC-Universidad de Sevilla, Spain
| | - Aurelio Serrano
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, CSIC-Universidad de Sevilla, Spain
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26
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Bettendorff L, Wins P. Thiamine triphosphatase and the CYTH superfamily of proteins. FEBS J 2013; 280:6443-55. [DOI: 10.1111/febs.12498] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/01/2013] [Indexed: 11/28/2022]
Affiliation(s)
| | - Pierre Wins
- GIGA-Neuroscience; University of Liège; Belgium
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