The arabidopsis bookPub Date : 2011-01-01Epub Date: 2011-11-02DOI: 10.1199/tab.0151
Steven D Clouse
{"title":"Brassinosteroids.","authors":"Steven D Clouse","doi":"10.1199/tab.0151","DOIUrl":"10.1199/tab.0151","url":null,"abstract":"<p><p>Brassinosteroids (BRs) are endogenous plant hormones essential for the proper regulation of multiple physiological processes required for normal plant growth and development. Since their discovery more than 30 years ago, extensive research on the mechanisms of BR action using biochemistry, mutant studies, proteomics and genome-wide transcriptome analyses, has helped refine the BR biosynthetic pathway, identify the basic molecular components required to relay the BR signal from perception to gene regulation, and expand the known physiological responses influenced by BRs. These mechanistic advances have helped answer the intriguing question of how BRs can have such dramatic pleiotropic effects on a broad range of diverse developmental pathways and have further pointed to BR interactions with other plant hormones and environmental cues. This chapter briefly reviews historical aspects of BR research and then summarizes the current state of knowledge on BR biosynthesis, metabolism and signal transduction. Recent studies uncovering novel phosphorelays and gene regulatory networks through which BR influences both vegetative and reproductive development are examined and placed in the context of known BR physiological responses including cell elongation and division, vascular differentiation, flowering, pollen development and photomorphogenesis.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0151"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268510/pdf/tab.0151.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The arabidopsis bookPub Date : 2011-01-01Epub Date: 2011-02-02DOI: 10.1199/tab.0141
Robert A Ingle
{"title":"Histidine biosynthesis.","authors":"Robert A Ingle","doi":"10.1199/tab.0141","DOIUrl":"https://doi.org/10.1199/tab.0141","url":null,"abstract":"<p><p>Histidine (His) is one of the standard amino acids in proteins, and plays a critical role in plant growth and development. The chemical properties of the imidazole side group allow His to participate in acid-base catalysis, and in the co-ordination of metal ions. Despite the biological importance of this molecule, His biosynthesis has been somewhat neglected in plants, in stark contrast to micro-organisms where the study of this pathway was fundamental in the discovery of operon structure and regulation by attenuation. With the recent isolation of histidinol-phosphate phosphatase, all the enzymes of His biosynthesis have now been identified in Arabidopsis, and several lines of evidence have implicated ATP-phosphoribosyl transferase (which catalyses the first committed step of the pathway) as playing an important role in the regulation of this pathway. However, little is known about the transcriptional regulation of the His biosynthetic genes, nor how demand for this amino acid is balanced with other metabolic requirements in plants. Similarly, the pathway of His catabolism has yet to be determined.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0141"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1199/tab.0141","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The arabidopsis bookPub Date : 2011-01-01Epub Date: 2011-12-06DOI: 10.1199/tab.0152
Christopher M Fraser, Clint Chapple
{"title":"The phenylpropanoid pathway in Arabidopsis.","authors":"Christopher M Fraser, Clint Chapple","doi":"10.1199/tab.0152","DOIUrl":"https://doi.org/10.1199/tab.0152","url":null,"abstract":"<p><p>The phenylpropanoid pathway serves as a rich source of metabolites in plants, being required for the biosynthesis of lignin, and serving as a starting point for the production of many other important compounds, such as the flavonoids, coumarins, and lignans. In spite of the fact that the phenylpropanoids and their derivatives are sometimes classified as secondary metabolites, their relevance to plant survival has been made clear via the study of Arabidopsis and other plant species. As a model system, Arabidopsis has helped to elucidate many details of the phenylpropanoid pathway, its enzymes and intermediates, and the interconnectedness of the pathway with plant metabolism as a whole. These advances in our understanding have been made possible in large part by the relative ease with which mutations can be generated, identified, and studied in Arabidopsis. Herein, we provide an overview of the research progress that has been made in recent years, emphasizing both the genes (and gene families) associated with the phenylpropanoid pathway in Arabidopsis, and the end products that have contributed to the identification of many mutants deficient in the phenylpropanoid metabolism: the sinapate esters.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0152"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1199/tab.0152","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The arabidopsis bookPub Date : 2011-01-01Epub Date: 2011-04-06DOI: 10.1199/tab.0143
Dorothea Tholl, Sungbeom Lee
{"title":"Terpene Specialized Metabolism in Arabidopsis thaliana.","authors":"Dorothea Tholl, Sungbeom Lee","doi":"10.1199/tab.0143","DOIUrl":"10.1199/tab.0143","url":null,"abstract":"<p><p>Terpenes constitute the largest class of plant secondary (or specialized) metabolites, which are compounds of ecological function in plant defense or the attraction of beneficial organisms. Using biochemical and genetic approaches, nearly all Arabidopsis thaliana (Arabidopsis) enzymes of the core biosynthetic pathways producing the 5-carbon building blocks of terpenes have been characterized and closer insight has been gained into the transcriptional and posttranscriptional/translational mechanisms regulating these pathways. The biochemical function of most prenyltransferases, the downstream enzymes that condense the C(5)-precursors into central 10-, 15-, and 20-carbon prenyldiphosphate intermediates, has been described, although the function of several isoforms of C(20)-prenyltranferases is not well understood. Prenyl diphosphates are converted to a variety of C(10)-, C(15)-, and C(20)-terpene products by enzymes of the terpene synthase (TPS) family. Genomic organization of the 32 Arabidopsis TPS genes indicates a species-specific divergence of terpene synthases with tissue- and cell-type specific expression profiles that may have emerged under selection pressures by different organisms. Pseudogenization, differential expression, and subcellular segregation of TPS genes and enzymes contribute to the natural variation of terpene biosynthesis among Arabidopsis accessions (ecotypes) and species. Arabidopsis will remain an important model to investigate the metabolic organization and molecular regulatory networks of terpene specialized metabolism in relation to the biological activities of terpenes.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0143"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268506/pdf/tab.0143.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The arabidopsis bookPub Date : 2011-01-01Epub Date: 2011-10-06DOI: 10.1199/tab.0144
Søren Bak, Fred Beisson, Gerard Bishop, Björn Hamberger, René Höfer, Suzanne Paquette, Danièle Werck-Reichhart
{"title":"Cytochromes p450.","authors":"Søren Bak, Fred Beisson, Gerard Bishop, Björn Hamberger, René Höfer, Suzanne Paquette, Danièle Werck-Reichhart","doi":"10.1199/tab.0144","DOIUrl":"10.1199/tab.0144","url":null,"abstract":"<p><p>There are 244 cytochrome P450 genes (and 28 pseudogenes) in the Arabidopsis genome. P450s thus form one of the largest gene families in plants. Contrary to what was initially thought, this family diversification results in very limited functional redundancy and seems to mirror the complexity of plant metabolism. P450s sometimes share less than 20% identity and catalyze extremely diverse reactions leading to the precursors of structural macromolecules such as lignin, cutin, suberin and sporopollenin, or are involved in biosynthesis or catabolism of all hormone and signaling molecules, of pigments, odorants, flavors, antioxidants, allelochemicals and defense compounds, and in the metabolism of xenobiotics. The mechanisms of gene duplication and diversification are getting better understood and together with co-expression data provide leads to functional characterization.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0144"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268508/pdf/tab.0144.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The arabidopsis bookPub Date : 2011-01-01Epub Date: 2011-12-06DOI: 10.1199/tab.0153
Joohyun Kang, Jiyoung Park, Hyunju Choi, Bo Burla, Tobias Kretzschmar, Youngsook Lee, Enrico Martinoia
{"title":"Plant ABC Transporters.","authors":"Joohyun Kang, Jiyoung Park, Hyunju Choi, Bo Burla, Tobias Kretzschmar, Youngsook Lee, Enrico Martinoia","doi":"10.1199/tab.0153","DOIUrl":"10.1199/tab.0153","url":null,"abstract":"<p><p>ABC transporters constitute one of the largest protein families found in all living organisms. ABC transporters are driven by ATP hydrolysis and can act as exporters as well as importers. The plant genome encodes for more than 100 ABC transporters, largely exceeding that of other organisms. In Arabidopsis, only 22 out of 130 have been functionally analyzed. They are localized in most membranes of a plant cell such as the plasma membrane, the tonoplast, chloroplasts, mitochondria and peroxisomes and fulfill a multitude of functions. Originally identified as transporters involved in detoxification processes, they have later been shown to be required for organ growth, plant nutrition, plant development, response to abiotic stresses, pathogen resistance and the interaction of the plant with its environment. To fulfill these roles they exhibit different substrate specifies by e.g. depositing surface lipids, accumulating phytate in seeds, and transporting the phytohormones auxin and abscisic acid. The aim of this review is to give an insight into the functions of plant ABC transporters and to show their importance for plant development and survival.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0153"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268509/pdf/tab.0153.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The arabidopsis bookPub Date : 2011-01-01Epub Date: 2011-09-26DOI: 10.1199/tab.0150
Yoshikatsu Matsubayashi
{"title":"Small post-translationally modified Peptide signals in Arabidopsis.","authors":"Yoshikatsu Matsubayashi","doi":"10.1199/tab.0150","DOIUrl":"https://doi.org/10.1199/tab.0150","url":null,"abstract":"<p><p>Recent biochemical, genetic and bioinformatic studies have demonstrated that peptide signaling plays a greater than anticipated role in various aspects of plant growth and development. More than a dozen secreted peptides are now recognized as important signals that mediate cell-to-cell communication. Secreted peptide signals often undergo post-translational modification and proteolytic processing, which are important for their function. Such \"small post-translationally modified peptide signals\" constitute one of the largest groups of peptide signals in plants. In parallel with the discovery of peptide signals, specific receptors for such peptides were identified as being membrane-localized receptor kinases, the largest family of receptor-like molecules in plants. These findings illustrate the critical roles of small peptide ligand-receptor pairs in plant growth and development. This review outlines recent research into secreted peptide signals in plants by focusing on small post-translationally modified peptides.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0150"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1199/tab.0150","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Cryptochrome Blue Light Receptors.","authors":"Xuhong Yu, Hongtao Liu, John Klejnot, Chentao Lin","doi":"10.1199/tab.0135","DOIUrl":"10.1199/tab.0135","url":null,"abstract":"<p><p>Cryptochromes are photolyase-like blue light receptors originally discovered in Arabidopsis but later found in other plants, microbes, and animals. Arabidopsis has two cryptochromes, CRY1 and CRY2, which mediate primarily blue light inhibition of hypocotyl elongation and photoperiodic control of floral initiation, respectively. In addition, cryptochromes also regulate over a dozen other light responses, including circadian rhythms, tropic growth, stomata opening, guard cell development, root development, bacterial and viral pathogen responses, abiotic stress responses, cell cycles, programmed cell death, apical dominance, fruit and ovule development, seed dormancy, and magnetoreception. Cryptochromes have two domains, the N-terminal PHR (Photolyase-Homologous Region) domain that bind the chromophore FAD (flavin adenine dinucleotide), and the CCE (CRY C-terminal Extension) domain that appears intrinsically unstructured but critical to the function and regulation of cryptochromes. Most cryptochromes accumulate in the nucleus, and they undergo blue light-dependent phosphorylation or ubiquitination. It is hypothesized that photons excite electrons of the flavin molecule, resulting in redox reaction or circular electron shuttle and conformational changes of the photoreceptors. The photoexcited cryptochrome are phosphorylated to adopt an open conformation, which interacts with signaling partner proteins to alter gene expression at both transcriptional and posttranslational levels and consequently the metabolic and developmental programs of plants.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"8 ","pages":"e0135"},"PeriodicalIF":0.0,"publicationDate":"2010-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155252/pdf/tab.0135.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30077242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The arabidopsis bookPub Date : 2010-01-01Epub Date: 2010-08-23DOI: 10.1199/tab.0137
Stefan Binder
{"title":"Branched-Chain Amino Acid Metabolism in Arabidopsis thaliana.","authors":"Stefan Binder","doi":"10.1199/tab.0137","DOIUrl":"https://doi.org/10.1199/tab.0137","url":null,"abstract":"<p><p>Valine, leucine and isoleucine form the small group of branched-chain amino acids (BCAAs) classified by their small branched hydrocarbon residues. Unlike animals, plants are able to de novo synthesize these amino acids from pyruvate, 2-oxobutanoate and acetyl-CoA. In plants, biosynthesis follows the typical reaction pathways established for the formation of these amino acids in microorganisms. Val and Ile are synthesized in two parallel pathways using a single set of enzymes. The pathway to Leu branches of from the final intermediate of Val biosynthesis. The formation of this amino acid requires a three-step pathway generating a 2-oxoacid elongated by a methylene group. In Arabidopsis thaliana and other Brassicaceae, a homologous three-step pathway is also involved in Met chain elongation required for the biosynthesis of aliphatic glucosinolates, an important class of specialized metabolites in Brassicaceae. This is a prime example for the evolutionary relationship of pathways from primary and specialized metabolism. Similar to animals, plants also have the ability to degrade BCAAs. The importance of BCAA turnover has long been unclear, but now it seems apparent that the breakdown process might by relevant under certain environmental conditions. In this review, I summarize the current knowledge about BCAA metabolism, its regulation and its particular features in Arabidopsis thaliana.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"8 ","pages":"e0137"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1199/tab.0137","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The arabidopsis bookPub Date : 2010-01-01Epub Date: 2010-01-22DOI: 10.1199/tab.0129
Iván F Acosta, Edward E Farmer
{"title":"Jasmonates.","authors":"Iván F Acosta, Edward E Farmer","doi":"10.1199/tab.0129","DOIUrl":"https://doi.org/10.1199/tab.0129","url":null,"abstract":"<p><p>ARABIDOPSIS IS A SUPERB MODEL FOR THE STUDY OF AN IMPORTANT SUBGROUP OF OXYLIPINS: the jasmonates. Jasmonates control many responses to cell damage and invasion and are essential for reproduction. Jasmonic acid (JA) is a prohormone and is conjugated to hydrophobic amino acids to produce regulatory ligands. The major receptor for active jasmonate ligands is closely related to auxin receptors and, as in auxin signaling, jasmonate signaling requires the destruction of repressor proteins. This chapter uses a frequently asked question (FAQ) approach and concludes with a practical section.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"8 ","pages":"e0129"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1199/tab.0129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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