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Kurogi K, Suiko M, Sakakibara Y. Evolution and multiple functions of sulfonation and cytosolic sulfotransferases across species. Biosci Biotechnol Biochem 2024; 88:368-380. [PMID: 38271594 DOI: 10.1093/bbb/zbae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
Organisms have conversion systems for sulfate ion to take advantage of the chemical features. The use of biologically converted sulfonucleotides varies in an evolutionary manner, with the universal use being that of sulfonate donors. Sulfotransferases have the ability to transfer the sulfonate group of 3'-phosphoadenosine 5'-phosphosulfate to a variety of molecules. Cytosolic sulfotransferases (SULTs) play a role in the metabolism of low-molecular-weight compounds in response to the host organism's living environment. This review will address the diverse functions of the SULT in evolution, including recent findings. In addition to the diversity of vertebrate sulfotransferases, the molecular aspects and recent studies on bacterial and plant sulfotransferases are also addressed.
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Affiliation(s)
- Katsuhisa Kurogi
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Miyazaki, Japan
| | - Masahito Suiko
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Miyazaki, Japan
| | - Yoichi Sakakibara
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Miyazaki, Japan
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2
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Alves RM, de Abreu VAC, Oliveira RP, Almeida JVDA, de Oliveira MDM, Silva SR, Paschoal AR, de Almeida SS, de Souza PAF, Ferro JA, Miranda VFO, Figueira A, Domingues DS, Varani AM. Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation. Gigascience 2024; 13:giae027. [PMID: 38837946 PMCID: PMC11152179 DOI: 10.1093/gigascience/giae027] [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: 12/23/2023] [Revised: 03/21/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family. FINDINGS The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species. CONCLUSIONS The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.
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Affiliation(s)
| | - Vinicius A C de Abreu
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Rafaely Pantoja Oliveira
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - João Victor dos Anjos Almeida
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Mauro de Medeiros de Oliveira
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Saura R Silva
- Departamento de Biologia, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Alexandre R Paschoal
- Departamento de Ciência da Computação (DACOM), Grupo de e Bioinformática e Reconhecimento de Padrões (bioinfo-cp), Universidade Tecnológica Federal do Paraná (UTFPR), 80230-901 Cornélio Procópio, PR, Brazil
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, OX110QX Didcot, UK
| | - Sintia S de Almeida
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Pedro A F de Souza
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil
| | - Jesus A Ferro
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Vitor F O Miranda
- Departamento de Biologia, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, 13416-000 Piracicaba, SP, Brazil
| | - Douglas S Domingues
- Departamento de Genética, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), 13418-900 Piracicaba, SP, Brazil
| | - Alessandro M Varani
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil
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Brouckaert M, Peng M, Höfer R, El Houari I, Darrah C, Storme V, Saeys Y, Vanholme R, Goeminne G, Timokhin VI, Ralph J, Morreel K, Boerjan W. QT-GWAS: A novel method for unveiling biosynthetic loci affecting qualitative metabolic traits. MOLECULAR PLANT 2023; 16:1212-1227. [PMID: 37349988 PMCID: PMC7614782 DOI: 10.1016/j.molp.2023.06.004] [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: 11/10/2022] [Revised: 04/06/2023] [Accepted: 06/16/2023] [Indexed: 06/24/2023]
Abstract
Although the plant kingdom provides an enormous diversity of metabolites with potentially beneficial applications for humankind, a large fraction of these metabolites and their biosynthetic pathways remain unknown. Resolving metabolite structures and their biosynthetic pathways is key to gaining biological understanding and to allow metabolic engineering. In order to retrieve novel biosynthetic genes involved in specialized metabolism, we developed a novel untargeted method designated as qualitative trait GWAS (QT-GWAS) that subjects qualitative metabolic traits to a genome-wide association study, while the conventional metabolite GWAS (mGWAS) mainly considers the quantitative variation of metabolites. As a proof of the validity of QT-GWAS, 23 and 15 of the retrieved associations identified in Arabidopsis thaliana by QT-GWAS and mGWAS, respectively, were supported by previous research. Furthermore, seven gene-metabolite associations retrieved by QT-GWAS were confirmed in this study through reverse genetics combined with metabolomics and/or in vitro enzyme assays. As such, we established that CYTOCHROME P450 706A5 (CYP706A5) is involved in the biosynthesis of chroman derivatives, UDP-GLYCOSYLTRANSFERASE 76C3 (UGT76C3) is able to hexosylate guanine in vitro and in planta, and SULFOTRANSFERASE 202B1 (SULT202B1) catalyzes the sulfation of neolignans in vitro. Collectively, our study demonstrates that the untargeted QT-GWAS method can retrieve valid gene-metabolite associations at the level of enzyme-encoding genes, even new associations that cannot be found by the conventional mGWAS, providing a new approach for dissecting qualitative metabolic traits.
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Affiliation(s)
- Marlies Brouckaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Meng Peng
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - René Höfer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ilias El Houari
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Chiarina Darrah
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Véronique Storme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Yvan Saeys
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, 9000 Ghent, Belgium; VIB Center for Inflammation Research, 9052 Ghent, Belgium
| | - Ruben Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert Goeminne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium; VIB Metabolomics Core, 9052 Ghent, Belgium
| | - Vitaliy I Timokhin
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John Ralph
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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He Z, Liu H, Gui S, Liu H, Yang J, Guo Q, Ye X, Zhang B. Procoagulant substances and mechanisms of hemostatic herb Eclipta alba. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5
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Bhinder G, Sharma S, Kaur H, Akhatar J, Mittal M, Sandhu S. Genomic Regions Associated With Seed Meal Quality Traits in Brassica napus Germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:882766. [PMID: 35909769 PMCID: PMC9333065 DOI: 10.3389/fpls.2022.882766] [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: 02/24/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
The defatted Brassica napus (rapeseed) meal can be high-protein feed for livestock as the protein value of rapeseed meal is higher than that of the majority of other vegetable proteins. Extensive work has already been carried out on developing canola rapeseed where the focus was on reducing erucic acid and glucosinolate content, with less consideration to other antinutritional factors such as tannin, phytate, sinapine, crude fiber, etc. The presence of these antinutrients limits the use and marketing of rapeseed meals and a significant amount of it goes unused and ends up as waste. We investigated the genetic architecture of crude protein, methionine, tryptophan, total phenols, β-carotene, glucosinolates (GLSs), phytate, tannins, sinapine, and crude fiber content of defatted seed meal samples by conducting a genome-wide association study (GWAS), using a diversity panel comprising 96 B. napus genotypes. Genotyping by sequencing was used to identify 77,889 SNPs, spread over 19 chromosomes. Genetic diversity and phenotypic variations were generally high for the studied traits. A total of eleven genotypes were identified which showed high-quality protein, high antioxidants, and lower amount of antinutrients. A significant negative correlation between protein and limiting amino acids and a significant positive correlation between GLS and phytic acid were observed. General and mixed linear models were used to estimate the association between the SNP markers and the seed quality traits and quantile-quantile (QQ) plots were generated to allow the best-fit algorithm. Annotation of genomic regions around associated SNPs helped to predict various trait-related candidates such as ASP2 and EMB1027 (amino acid biosynthesis); HEMA2, GLU1, and PGM (tryptophan biosynthesis); MS3, CYSD1, and MTO1 (methionine biosynthesis); LYC (β-carotene biosynthesis); HDR and ISPF (MEP pathway); COS1 (riboflavin synthesis); UGT (phenolics biosynthesis); NAC073 (cellulose and hemicellulose biosynthesis); CYT1 (cellulose biosynthesis); BGLU45 and BGLU46 (lignin biosynthesis); SOT12 and UGT88A1 (flavonoid pathway); and CYP79A2, DIN2, and GSTT2 (GLS metabolism), etc. The functional validation of these candidate genes could confirm key seed meal quality genes for germplasm enhancement programs directed at improving protein quality and reducing the antinutritional components in B. napus.
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Affiliation(s)
| | - Sanjula Sharma
- Oilseeds Section, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | | | - Javed Akhatar
- Oilseeds Section, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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Ortigosa F, Lobato-Fernández C, Shikano H, Ávila C, Taira S, Cánovas FM, Cañas RA. Ammonium regulates the development of pine roots through hormonal crosstalk and differential expression of transcription factors in the apex. PLANT, CELL & ENVIRONMENT 2022; 45:915-935. [PMID: 34724238 DOI: 10.1111/pce.14214] [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: 07/21/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Ammonium is a prominent source of inorganic nitrogen for plant nutrition, but excessive amounts can be toxic for many species. However, most conifers are tolerant to ammonium, a relevant physiological feature of this ancient evolutionary lineage. For a better understanding of the molecular basis of this trait, ammonium-induced changes in the transcriptome of maritime pine (Pinus pinaster Ait.) root apex have been determined by laser capture microdissection and RNA sequencing. Ammonium promoted changes in the transcriptional profiles of multiple transcription factors, such as SHORT-ROOT, and phytohormone-related transcripts, such as ACO, involved in the development of the root meristem. Nano-PALDI-MSI and transcriptomic analyses showed that the distributions of IAA and CKs were altered in the root apex in response to ammonium nutrition. Taken together, the data suggest that this early response is involved in the increased lateral root branching and principal root growth, which characterize the long-term response to ammonium supply in pine. All these results suggest that ammonium induces changes in the root system architecture through the IAA-CK-ET phytohormone crosstalk and transcriptional regulation.
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Affiliation(s)
- Francisco Ortigosa
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - César Lobato-Fernández
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Hitomi Shikano
- Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Concepción Ávila
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Shu Taira
- Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Francisco M Cánovas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Rafael A Cañas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
- Integrative Molecular Biology Lab, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
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7
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Chan KX, Phua SY, Van Breusegem F. Secondary sulfur metabolism in cellular signalling and oxidative stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4237-4250. [PMID: 30868163 DOI: 10.1093/jxb/erz119] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/08/2019] [Indexed: 05/27/2023]
Abstract
The sulfur metabolism pathway in plants produces a variety of compounds that are central to the acclimation response to oxidative stresses such as drought and high light. Primary sulfur assimilation provides the amino acid cysteine, which is utilized in protein synthesis and as a precursor for the cellular redox buffer glutathione. In contrast, the secondary sulfur metabolism pathway produces sulfated compounds such as glucosinolates and sulfated peptides, as well as a corresponding by-product 3'-phosphoadenosine 5'-phosphate (PAP). Emerging evidence over the past decade has shown that secondary sulfur metabolism also has a crucial engagement during oxidative stress. This occurs across various cellular, tissue, and organismal levels including chloroplast-to-nucleus retrograde signalling events mediated by PAP, modulation of hormonal signalling by sulfated compounds and PAP, control of physiological responses such as stomatal closure, and potential regulation of plant growth. In this review, we examine the contribution of the different components of plant secondary metabolism to oxidative stress homeostasis, and how this pathway is metabolically regulated. We further outline the key outstanding questions in the field that are necessary to understand how and why this 'specialized' metabolic pathway plays significant roles in plant oxidative stress tolerance.
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Affiliation(s)
- Kai Xun Chan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
| | - Su Yin Phua
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
| | - Frank Van Breusegem
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark, Ghent, Belgium
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8
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Jin L, Ouyang N, Huang Y, Liu C, Ruan Y. Genome-wide analysis of sulfotransferase genes and their responses to abiotic stresses in Chinese cabbage (Brassica rapa L.). PLoS One 2019; 14:e0221422. [PMID: 31425555 PMCID: PMC6699706 DOI: 10.1371/journal.pone.0221422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/06/2019] [Indexed: 01/08/2023] Open
Abstract
Sulfotransferases (SOTs; EC 2.8.2.-), which are widespread from prokaryotes to eukaryotes, constitute a multi-protein family that plays crucial roles in plant growth, development and stress adaptation. However, this family has not been systemically investigated in Brassica rapa. Here, a genome-wide systemic analysis of SOT genes in B. rapa subsp. pekinensis, a globally cultivated vegetable, were conducted. We identified 56 SOT genes from the whole B. rapa genome using Arabidopsis SOT sequences as queries and classified them into nine groups, rather than the eight groups of previous research. 56 B. rapa SOT genes (BraSOTs) were distributed on all 10 chromosomes except for chromosome 5. Of these, 27 BraSOTs were distributed in seven clusters on five chromosomes (ChrA01, ChrA02, Chr03, ChrA07, and Chr09). Among the BraSOT proteins, 48 had only one SOT_1 domain and 6 had two, while 2 had one SOT_3 domain. Additionally, 47 BraSOT proteins contained only known SOT domains. The remaining nine proteins, five in group-VIII and two in group-IX, contained additional transmembrane domains. Specific motif regions I and IV for 3′-phosphoadenosine 5′-phosphosulfate binding were found in 41 BraSOT proteins. Introns were present in only 18 BraSOT genes, and all seven BraSOT genes in groups VIII and IX had more than three introns. To identify crucial SOTs mediating the response to abiotic stress in B. rapa, expression changes in 56 BraSOT genes were determined by quantitative RT-PCR after drought, salinity, and ABA treatments, and some BraSOT genes were associated with NaCl, drought and ABA stress, e.g. Bra017370, Bra009300, Bra027880.
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Affiliation(s)
- Lu Jin
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, China
| | - Ning Ouyang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, China
| | - Yong Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, China
| | - Chunlin Liu
- Agricultural College of Hunan Agricultural University, Changsha, China
| | - Ying Ruan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Key Laboratory of Crop Epigenetic Regulation and Development in Hunan Province, Changsha, China
- Key Laboratory of Plant Genetics and Molecular Biology of Education Department in Hunan Province, Changsha, China
- * E-mail:
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Abstract
Sulfur is present in the amino acids cysteine and methionine and in a large range of essential coenzymes and cofactors and is therefore essential for all organisms. It is also a constituent of sulfate esters in proteins, carbohydrates, and numerous cellular metabolites. The sulfation and desulfation reactions modifying a variety of different substrates are commonly known as sulfation pathways. Although relatively little is known about the function of most sulfated metabolites, the synthesis of activated sulfate used in sulfation pathways is essential in both animal and plant kingdoms. In humans, mutations in the genes encoding the sulfation pathway enzymes underlie a number of developmental aberrations, and in flies and worms, their loss-of-function is fatal. In plants, a lower capacity for synthesizing activated sulfate for sulfation reactions results in dwarfism, and a complete loss of activated sulfate synthesis is also lethal. Here, we review the similarities and differences in sulfation pathways and associated processes in animals and plants, and we point out how they diverge from bacteria and yeast. We highlight the open questions concerning localization, regulation, and importance of sulfation pathways in both kingdoms and the ways in which findings from these "red" and "green" experimental systems may help reciprocally address questions specific to each of the systems.
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Affiliation(s)
- Süleyman Günal
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne 50674, Germany
| | - Rebecca Hardman
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne 50674, Germany.
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham B15 2TH, United Kingdom.
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Sugimoto MA, Vago JP, Perretti M, Teixeira MM. Mediators of the Resolution of the Inflammatory Response. Trends Immunol 2019; 40:212-227. [DOI: 10.1016/j.it.2019.01.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/13/2019] [Accepted: 01/14/2019] [Indexed: 02/06/2023]
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11
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Chu LL, Dhakal D, Shin HJ, Jung HJ, Yamaguchi T, Sohng JK. Metabolic Engineering of Escherichia coli for Enhanced Production of Naringenin 7-Sulfate and Its Biological Activities. Front Microbiol 2018; 9:1671. [PMID: 30100899 PMCID: PMC6072979 DOI: 10.3389/fmicb.2018.01671] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/04/2018] [Indexed: 01/09/2023] Open
Abstract
Flavonoids are one of the predominant groups of plant polyphenols, and these compounds have significant effects on human health and nutrition. Sulfated flavonoids have more favorable attributes compared to their parent compounds such as increased solubility, stability, and bioavailability. In this research, we developed a microbial system to produce sulfated naringenin using Escherichia coli expressing a sulfotransferase (ST) from Arabidopsis thaliana (At2g03770). This wild-type strain was used as a model system for testing clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) metabolic engineering strategies. Using synthetic sgRNA to mediate transcriptional repression of cysH, a gene encoding 3'-phosphoadenosine-5'-phosphosulfate (PAPS) ST, which is involved in sulfur metabolism, resulted in an increase in intracellular PAPS accumulation by over 3.28-fold without impairing cell growth. Moreover, naringenin 7-sulfate production by engineering E. coli with its cysH gene repressed in the open reading frame through CRISPRi was enhanced by 2.83-fold in compared with the wild-type control. To improve the efficiency of biotransformation, the concentration of SO42- , glucose, and substrate were optimized. The bioproductivity of naringenin 7-sulfate was 135.49 μM [∼143.1 mg (47.7 mg L-1)] in a 3-L fermenter at 36 h. These results demonstrated that the CRISPRi system was successfully applied for the first time in E. coli to develop an efficient microbial strain for production of a sulfated flavonoid. In addition, antibacterial and anticancer activities of naringenin 7-sulfate were investigated and found to be higher than the parent compound.
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Affiliation(s)
- Luan L Chu
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, South Korea
| | - Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, South Korea
| | - Hee J Shin
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, South Korea
| | - Hye J Jung
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, South Korea.,Department of BT Convergence Pharmaceutical Engineering, Sun Moon University, Asan, South Korea
| | - Tokutaro Yamaguchi
- Department of BT Convergence Pharmaceutical Engineering, Sun Moon University, Asan, South Korea
| | - Jae K Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, South Korea.,Department of BT Convergence Pharmaceutical Engineering, Sun Moon University, Asan, South Korea
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Gallo C, Nuzzo G, d'Ippolito G, Manzo E, Sardo A, Fontana A. Sterol Sulfates and Sulfotransferases in Marine Diatoms. Methods Enzymol 2018; 605:101-138. [PMID: 29909823 DOI: 10.1016/bs.mie.2018.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sterol sulfates are widely occurring molecules in marine organisms. Their importance has been so far underestimated although many of these compounds are crucial mediators of physiological and ecological functions in other organisms. Biosynthesis of sterol sulfates is controlled by cytosolic sulfotransferases (SULTs), a varied family of enzymes that catalyze the transfer of a sulfo residue (-SO3H) from the universal donor 3'-phosphoadenosine-5'-phosphosulfate to the hydroxyl function at C-3 of the steroid skeleton. The absence of molecular tools has been the main impediment to the development of a biosynthetic study of this class of compounds in marine organisms. In fact, there is very limited information about these enzymes in marine environments. SULT activity has, however, been reported in several marine species, and, recently, the production of sterol sulfates has been linked to the control of growth in marine diatoms. In this chapter, we describe methods for the study of sterol sulfates in this lineage of marine microalgae. The main aim is to provide the tools useful to deal with the biosynthesis and regulation of these compounds and to circumvent the bottleneck of the lack of molecular information. The protocols have been designed for marine diatoms, but most of the procedures can be used for other marine organisms.
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Affiliation(s)
- Carmela Gallo
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy
| | - Genoveffa Nuzzo
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy
| | - Giuliana d'Ippolito
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy.
| | - Emiliano Manzo
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy
| | - Angela Sardo
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy
| | - Angelo Fontana
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy.
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Cao X, Liao Y, Rong S, Hu C, Zhang X, Chen R, Xu Z, Gao X, Li L, Zhu J. Identification and characterization of a novel abiotic stress responsive sulphotransferase gene (OsSOT9) from rice. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2015.1136237] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Chen J, Gao L, Baek D, Liu C, Ruan Y, Shi H. Detoxification function of the Arabidopsis sulphotransferase AtSOT12 by sulphonation of xenobiotics. PLANT, CELL & ENVIRONMENT 2015; 38:1673-1682. [PMID: 25736839 DOI: 10.1111/pce.12525] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
Cytosolic sulphotransferases have been implicated in inactivation of endogenous steroid hormones and detoxification of xenobiotics in human and animals. Yet, the function of plant sulphotransferases in xenobiotic sulphonation and detoxification has not been reported. In this study, we show that the Arabidopsis sulphotransferase AtSOT12 could sulphonate the bacterial-produced toxin cycloheximide. Loss-of-function mutant sot12 exhibited hypersensitive phenotype to cycloheximide, and expression of AtSOT12 protein in yeast cells conferred resistance to this toxic compound. AtSOT12 exhibited broad specificity and could sulphonate a variety of xenobiotics including phenolic and polycyclic compounds. Enzyme kinetics analysis indicated that AtSOT12 has different selectivity for simple phenolics with different side chains, and the position of the side chain in the simple phenolic compounds affects substrate binding affinity and catalytic efficiency. We proposed that the broad specificity and induced production of AtSOT12 may have rendered this enzyme to not only modify endogenous molecules such as salicylic acid as we previously reported, but also sulphonate pathogen-produced toxic small molecules to protect them from infection. Sulphonation of small molecules in plants may constitute a rapid way to inactivate or change the physiochemical properties of biologically active molecules that could have profound effects on plant growth, development and defence.
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Affiliation(s)
- Jinhua Chen
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Liqiong Gao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Dongwon Baek
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Chunlin Liu
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Ying Ruan
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
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Hirschmann F, Papenbrock J. The fusion of genomes leads to more options: A comparative investigation on the desulfo-glucosinolate sulfotransferases of Brassica napus and homologous proteins of Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 91:10-9. [PMID: 25827495 DOI: 10.1016/j.plaphy.2015.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 03/25/2015] [Indexed: 05/11/2023]
Abstract
Sulfotransferases (SOTs) (EC 2.8.2.-) play a crucial role in the glucosinolate (Gl) biosynthesis, by catalyzing the final step of the core glucosinolate formation. In Arabidopsis thaliana the three desulfo (ds)-Gl SOTs AtSOT16, AtSOT17 and AtSOT18 were previously characterized, showing different affinities to ds-Gls. But can the knowledge about these SOTs be generally transferred to other Gl-synthesizing plants? It was investigated how many SOTs are present in the economically relevant crop plant Brassica napus L., and if it is possible to predict their characteristics by sequence analysis. The recently sequenced B. napus is a hybrid of Brassica rapa and Brassica oleracea. By database research, 71 putative functional BnSOT family members were identified and at least eleven of those are putative ds-Gl SOTs. Besides the homologs of AtSOT16 - 18, phylogenetic analyses revealed new subfamilies of ds-Gl SOTs, which are not present in A. thaliana. Three of the B. napus ds-Gl SOT proteins were expressed and purified, and characterized by determining the substrate affinities to different ds-Gls. Two of them, BnSOT16-a and BnSOT16-b, showed a significantly higher affinity to an indolic ds-Gl, similarly to AtSOT16. Additionally, BnSOT17-a was characterized and showed a higher affinity to long chained aliphatic Gls, similarly to AtSOT17. Identification of homologs to AtSOT18 was less reliable, because putative SOT18 sequences are more heterogeneous and confirmation of similar characteristics was not possible.
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Affiliation(s)
- Felix Hirschmann
- Institute of Botany, Leibniz University Hannover, Herrenhäuserstr. 2, D-30419 Hannover, Germany
| | - Jutta Papenbrock
- Institute of Botany, Leibniz University Hannover, Herrenhäuserstr. 2, D-30419 Hannover, Germany.
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Gilroy D, De Maeyer R. New insights into the resolution of inflammation. Semin Immunol 2015; 27:161-8. [PMID: 26037968 DOI: 10.1016/j.smim.2015.05.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/06/2015] [Accepted: 05/13/2015] [Indexed: 12/31/2022]
Abstract
The goal of treating chronic inflammatory diseases must be to inhibit persistent inflammation and restore tissue function. To achieve this we need to improve our understanding of the pathways that drive inflammation as well as those that bring about its resolution. In particular, resolution of inflammation is driven by a complex set of mediators that regulate cellular events required to clear inflammatory cells from sites of injury or infection and restore homeostasis. Indeed, it may be argued that dysfunctional resolution may underpin the aetiology of some chronic inflammatory disease and that a novel goal in treating such diseases is to develop drugs based on the mode of endogenous pro-resolution factors in order to drive on-going inflammation down a pro-resolution pathway. And while we are improving our understanding of the resolution of acute and chronic inflammation, much remains to be discovered. Here we will discuss the key endogenous checkpoints necessary for mounting an effective yet limited inflammatory response and the crucial biochemical pathways necessary to prevent its persistence and trigger its resolution. In doing so, we will provide an update on what is known about resolution of acute inflammation, in particular its link with adaptive immunity.
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Affiliation(s)
- Derek Gilroy
- Centre for Clinical Pharmacology and Therapeutics, Division of Medicine, 5 University Street, University College London, London WC1E 6JJ, United Kingdom.
| | - Roel De Maeyer
- Centre for Clinical Pharmacology and Therapeutics, Division of Medicine, 5 University Street, University College London, London WC1E 6JJ, United Kingdom
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Brenner WG, Schmülling T. Summarizing and exploring data of a decade of cytokinin-related transcriptomics. FRONTIERS IN PLANT SCIENCE 2015; 6:29. [PMID: 25741346 PMCID: PMC4330702 DOI: 10.3389/fpls.2015.00029] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/13/2015] [Indexed: 05/17/2023]
Abstract
The genome-wide transcriptional response of the model organism Arabidopsis thaliana to cytokinin has been investigated by different research groups as soon as large-scale transcriptomic techniques became affordable. Over the last 10 years many transcriptomic datasets related to cytokinin have been generated using different technological platforms, some of which are published only in databases, culminating in an RNA sequencing experiment. Two approaches have been made to establish a core set of cytokinin-regulated transcripts by meta-analysis of these datasets using different preferences regarding their selection. Here we add another meta-analysis derived from an independent microarray platform (CATMA), combine all the meta-analyses available with RNAseq data in order to establish an advanced core set of cytokinin-regulated transcripts, and compare the results with the regulation of orthologous rice genes by cytokinin. We discuss the functions of some of the less known cytokinin-regulated genes indicating areas deserving further research to explore cytokinin function. Finally, we investigate the promoters of the core set of cytokinin-induced genes for the abundance and distribution of known cytokinin-responsive cis elements and identify a set of novel candidate motifs.
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Affiliation(s)
- Wolfram G. Brenner
- *Correspondence: Wolfram G. Brenner and Thomas Schmülling, Dahlem Centre of Plant Sciences, Institute of Biology/Applied Genetics, Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195 Berlin, Germany e-mail: ;
| | - Thomas Schmülling
- *Correspondence: Wolfram G. Brenner and Thomas Schmülling, Dahlem Centre of Plant Sciences, Institute of Biology/Applied Genetics, Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195 Berlin, Germany e-mail: ;
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Hirschmann F, Krause F, Papenbrock J. The multi-protein family of sulfotransferases in plants: composition, occurrence, substrate specificity, and functions. FRONTIERS IN PLANT SCIENCE 2014; 5:556. [PMID: 25360143 PMCID: PMC4199319 DOI: 10.3389/fpls.2014.00556] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 09/28/2014] [Indexed: 05/20/2023]
Abstract
All members of the sulfotransferase (SOT, EC 2.8.2.-) protein family transfer a sulfuryl group from the donor 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to an appropriate hydroxyl group of several classes of substrates. The primary structure of these enzymes is characterized by a histidine residue in the active site, defined PAPS binding sites and a longer SOT domain. Proteins with this SOT domain occur in all organisms from all three domains, usually as a multi-protein family. Arabidopsis thaliana SOTs, the best characterized SOT multi-protein family, contains 21 members. The substrates for several plant enzymes have already been identified, such as glucosinolates, brassinosteroids, jasmonates, flavonoids, and salicylic acid. Much information has been gathered on desulfo-glucosinolate (dsGl) SOTs in A. thaliana. The three cytosolic dsGl SOTs show slightly different expression patterns. The recombinant proteins reveal differences in their affinity to indolic and aliphatic dsGls. Also the respective recombinant dsGl SOTs from different A. thaliana ecotypes differ in their kinetic properties. However, determinants of substrate specificity and the exact reaction mechanism still need to be clarified. Probably, the three-dimensional structures of more plant proteins need to be solved to analyze the mode of action and the responsible amino acids for substrate binding. In addition to A. thaliana, more plant species from several families need to be investigated to fully elucidate the diversity of sulfated molecules and the way of biosynthesis catalyzed by SOT enzymes.
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Affiliation(s)
| | | | - Jutta Papenbrock
- Institute of Botany, Leibniz University HannoverHannover, Germany
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Incorporation of post-translational modified amino acids as an approach to increase both chemical and biological diversity of conotoxins and conopeptides. Amino Acids 2013; 46:125-51. [DOI: 10.1007/s00726-013-1606-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 10/17/2013] [Indexed: 02/06/2023]
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Hashiguchi T, Sakakibara Y, Shimohira T, Kurogi K, Yamasaki M, Nishiyama K, Akashi R, Liu MC, Suiko M. Identification of a novel flavonoid glycoside sulfotransferase in Arabidopsis thaliana. J Biochem 2013; 155:91-7. [PMID: 24202284 DOI: 10.1093/jb/mvt102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The discovery of sulfated flavonoids in plants suggests that sulfation may play a regulatory role in the physiological functions of flavonoids. Sulfation of flavonoids is mediated by cytosolic sulfotransferases (SULTs), which utilize 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as the sulfate donor. A novel SULT from Arabidopsis thaliana, designated AtSULT202B7 (AGI code: At1g13420), was cloned and expressed in Escherichia coli. Using various compounds as potential substrates, we demonstrated, for the first time, that AtSULT202B7 displayed sulfating activity specific for flavonoids. Intriguingly, the recombinant enzyme preferred flavonoid glycosides (e.g. kaempferol-3-glucoside and quercetin-3-glucoside) rather than their aglycone counterparts. Among a series of hydroxyflavones tested, AtSULT202B7 showed the enzymatic activity only for 7-hydroxyflavone. pH-dependency study showed that the optimum pH was relatively low (pH 5.5) compared with those (pH 6.0-8.5) previously reported for other isoforms. Based on the comparison of high performance (pressure) liquid chromatography (HPLC) retention times between sulfated kaempferol and the deglycosylated product of sulfated kaempferol-3-glucoside, the sulfation site in sulfated kaempferol-3-glucoside appeared to be the hydroxyl group of the flavonoid skeleton. In addition, by using direct infusion mass spectrometry, it was found that the sulfated product had one sulfonate group within the molecule. These results indicated that AtSULT202B7 functions as a flavonoid glycoside 7-sulfotransferase.
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Affiliation(s)
- Takuyu Hashiguchi
- Department of Biochemistry and Applied Biosciences; Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki 889-2192, Japan; and Department of Pharmacology, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo, OH 43614, USA
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