The arabidopsis bookPub Date : 2012-01-01Epub Date: 2012-01-19DOI: 10.1199/tab.0157
Jorge J Casal
{"title":"Shade avoidance.","authors":"Jorge J Casal","doi":"10.1199/tab.0157","DOIUrl":"https://doi.org/10.1199/tab.0157","url":null,"abstract":"<p><p>The presence of neighboring vegetation modifies the light environment experienced by plants, generating signals that are perceived by phytochromes and cryptochromes. These signals cause large changes in plant body form and function, including enhanced growth of the hypocotyl and petioles, a more erect position of the leaves and early flowering in Arabidopsis thaliana. Collectively, these so-called shade-avoidance responses tend to reduce the degree of current or future shade by neighbors. Shade light signals increase the abundance of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5 proteins, promote the synthesis and redirection of auxin, favor the degradation of DELLA proteins and increase the expression of auxin, gibberellins and brassinosteroid-promoted genes, among other events downstream the photoreceptors. Selectively disrupting these events by genetic or pharmacological approaches affects shade-avoidance responses with an intensity that depends on the developmental context and the environment. Shade-avoidance responses provide a model to investigate the signaling networks used by plants to take advantage of the cues provided by the environment to adjust to the challenges imposed by the environment itself.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"10 ","pages":"e0157"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1199/tab.0157","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30614657","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 : 2012-01-01Epub Date: 2012-01-19DOI: 10.1199/tab.0158
M Águila Ruiz-Sola, Manuel Rodríguez-Concepción
{"title":"Carotenoid biosynthesis in Arabidopsis: a colorful pathway.","authors":"M Águila Ruiz-Sola, Manuel Rodríguez-Concepción","doi":"10.1199/tab.0158","DOIUrl":"10.1199/tab.0158","url":null,"abstract":"<p><p>Plant carotenoids are a family of pigments that participate in light harvesting and are essential for photoprotection against excess light. Furthermore, they act as precursors for the production of apocarotenoid hormones such as abscisic acid and strigolactones. In this review, we summarize the current knowledge on the genes and enzymes of the carotenoid biosynthetic pathway (which is now almost completely elucidated) and on the regulation of carotenoid biosynthesis at both transcriptional and post-transcriptional levels. We also discuss the relevance of Arabidopsis as a model system for the study of carotenogenesis and how metabolic engineering approaches in this plant have taught important lessons for carotenoid biotechnology.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"10 ","pages":"e0158"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350171/pdf/tab.0158.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30614658","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: 2011-12-20DOI: 10.1199/tab.0156
D'Maris Amick Dempsey, A Corina Vlot, Mary C Wildermuth, Daniel F Klessig
{"title":"Salicylic Acid biosynthesis and metabolism.","authors":"D'Maris Amick Dempsey, A Corina Vlot, Mary C Wildermuth, Daniel F Klessig","doi":"10.1199/tab.0156","DOIUrl":"https://doi.org/10.1199/tab.0156","url":null,"abstract":"<p><p>Salicylic acid (SA) has been shown to regulate various aspects of growth and development; it also serves as a critical signal for activating disease resistance in Arabidopsis thaliana and other plant species. This review surveys the mechanisms involved in the biosynthesis and metabolism of this critical plant hormone. While a complete biosynthetic route has yet to be established, stressed Arabidopsis appear to synthesize SA primarily via an isochorismate-utilizing pathway in the chloroplast. A distinct pathway utilizing phenylalanine as the substrate also may contribute to SA accumulation, although to a much lesser extent. Once synthesized, free SA levels can be regulated by a variety of chemical modifications. Many of these modifications inactivate SA; however, some confer novel properties that may aid in long distance SA transport or the activation of stress responses complementary to those induced by free SA. In addition, a number of factors that directly or indirectly regulate the expression of SA biosynthetic genes or that influence the rate of SA catabolism have been identified. An integrated model, encompassing current knowledge of SA metabolism in Arabidopsis, as well as the influence other plant hormones exert on SA metabolism, is presented.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0156"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1199/tab.0156","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434260","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: 2011-12-16DOI: 10.1199/tab.0154
Rüdiger Hell, Markus Wirtz
{"title":"Molecular Biology, Biochemistry and Cellular Physiology of Cysteine Metabolism in Arabidopsis thaliana.","authors":"Rüdiger Hell, Markus Wirtz","doi":"10.1199/tab.0154","DOIUrl":"10.1199/tab.0154","url":null,"abstract":"<p><p>Cysteine is one of the most versatile molecules in biology, taking over such different functions as catalysis, structure, regulation and electron transport during evolution. Research on Arabidopsis has contributed decisively to the understanding of cysteine synthesis and its role in the assimilatory pathways of S, N and C in plants. The multimeric cysteine synthase complex is present in the cytosol, plastids and mitochondria and forms the centre of a unique metabolic sensing and signaling system. Its association is reversible, rendering the first enzyme of cysteine synthesis active and the second one inactive, and vice-versa. Complex formation is triggered by the reaction intermediates of cysteine synthesis in response to supply and demand and gives rise to regulation of genes of sulfur metabolism to adjust cellular sulfur homeostasis. Combinations of biochemistry, forward and reverse genetics, structural- and cell-biology approaches using Arabidopsis have revealed new enzyme functions and the unique pattern of spatial distribution of cysteine metabolism in plant cells. These findings place the synthesis of cysteine in the centre of the network of primary metabolism.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0154"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268551/pdf/tab.0154.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434258","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 Function of the CLE Peptides in Plant Development and Plant-Microbe Interactions.","authors":"Shigeyuki Betsuyaku, Shinichiro Sawa, Masashi Yamada","doi":"10.1199/tab.0149","DOIUrl":"10.1199/tab.0149","url":null,"abstract":"<p><p>The CLAVATA3 (CLV3)/ENDOSPERM SURROUNDING REGION (ESR) (CLE) peptides consist of 12 or 13 amino acids, including hydroxylated proline residues that may or may not contain sugar modifications, and function in a non-cell-autonomous fashion. The CLE gene was first reported in Zea mays (maize) as an endosperm-specific gene, ESR, in 1997 (Opsahl-Ferstad et al., 1997). CLE genes encode secreted peptides that function in the extracellular space as intercellular signaling molecules and bind to cellular surface receptor-like proteins to transmit a signal. CLE peptides regulate various physiological and developmental processes and its signaling pathway are conserved in diverse land plants. Recent CLE functional studies have pointed to their significance in regulating meristematic activity in plant meristems, through the CLE-receptor kinase-WOX signaling node. CLV3 and CLE40 are responsible for maintenance of shoot apical meristem (SAM) and root apical meristem (RAM) function, regulating homeodomain transcription factors, WUSCHEL (WUS) and WUSCHEL-related homeobox 5 (WOX5), respectively. CLE and WOX form an interconnected and self-correcting feedback loop to provide robustness to stem cell homeostasis. CLE peptides are required for certain plant-microbe interactions, such as those that occur during legume symbiosis and phytopathogenic nematode infection. Understanding the molecular properties of CLE peptides may provide insight into plant cell-cell communication, and therefore also into plant-microbe interactions.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0149"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268505/pdf/tab.0149.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434389","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: 2011-02-18DOI: 10.1199/tab.0142
Graham Noctor, Guillaume Queval, Amna Mhamdi, Sejir Chaouch, Christine H Foyer
{"title":"Glutathione.","authors":"Graham Noctor, Guillaume Queval, Amna Mhamdi, Sejir Chaouch, Christine H Foyer","doi":"10.1199/tab.0142","DOIUrl":"10.1199/tab.0142","url":null,"abstract":"<p><p>Glutathione is a simple sulfur compound composed of three amino acids and the major non-protein thiol in many organisms, including plants. The functions of glutathione are manifold but notably include redox-homeostatic buffering. Glutathione status is modulated by oxidants as well as by nutritional and other factors, and can influence protein structure and activity through changes in thiol-disulfide balance. For these reasons, glutathione is a transducer that integrates environmental information into the cellular network. While the mechanistic details of this function remain to be fully elucidated, accumulating evidence points to important roles for glutathione and glutathione-dependent proteins in phytohormone signaling and in defense against biotic stress. Work in Arabidopsis is beginning to identify the processes that govern glutathione status and that link it to signaling pathways. As well as providing an overview of the components that regulate glutathione homeostasis (synthesis, degradation, transport, and redox turnover), the present discussion considers the roles of this metabolite in physiological processes such as light signaling, cell death, and defense against microbial pathogen and herbivores.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0142"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267239/pdf/tab.0142.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434464","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: 2011-08-29DOI: 10.1199/tab.0148
Jigang Li, Gang Li, Haiyang Wang, Xing Wang Deng
{"title":"Phytochrome signaling mechanisms.","authors":"Jigang Li, Gang Li, Haiyang Wang, Xing Wang Deng","doi":"10.1199/tab.0148","DOIUrl":"10.1199/tab.0148","url":null,"abstract":"<p><p>Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0148"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268501/pdf/tab.0148.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434390","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: 2011-12-26DOI: 10.1199/tab.0155
Gary N Drews, Anna M G Koltunow
{"title":"The female gametophyte.","authors":"Gary N Drews, Anna M G Koltunow","doi":"10.1199/tab.0155","DOIUrl":"https://doi.org/10.1199/tab.0155","url":null,"abstract":"<p><p>The angiosperm female gametophyte is critical for plant reproduction. It contains the egg cell and central cell that become fertilized and give rise to the embryo and endosperm of the seed, respectively. Female gametophyte development begins early in ovule development with the formation of a diploid megaspore mother cell that undergoes meiosis. One resulting haploid megaspore then develops into the female gametophyte. Genetic and epigenetic processes mediate specification of megaspore mother cell identity and limit megaspore mother cell formation to a single cell per ovule. Auxin gradients influence female gametophyte polarity and a battery of transcription factors mediate female gametophyte cell specification and differentiation. The mature female gametophyte secretes peptides that guide the pollen tube to the embryo sac and contains protein complexes that prevent seed development before fertilization. Post-fertilization, the female gametophyte influences seed development through maternal-effect genes and by regulating parental contributions. Female gametophytes can form by an asexual process called gametophytic apomixis, which involves formation of a diploid female gametophyte and fertilization-independent development of the egg into the embryo. These functions collectively underscore the important role of the female gametophyte in seed and food production.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0155"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1199/tab.0155","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434259","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: 2011-07-31DOI: 10.1199/tab.0146
Matthew R Willmann, Matthew W Endres, Rebecca T Cook, Brian D Gregory
{"title":"The Functions of RNA-Dependent RNA Polymerases in Arabidopsis.","authors":"Matthew R Willmann, Matthew W Endres, Rebecca T Cook, Brian D Gregory","doi":"10.1199/tab.0146","DOIUrl":"https://doi.org/10.1199/tab.0146","url":null,"abstract":"<p><p>One recently identified mechanism that regulates mRNA abundance is RNA silencing, and pioneering work in Arabidopsis thaliana and other genetic model organisms helped define this process. RNA silencing pathways are triggered by either self-complementary fold-back structures or the production of double-stranded RNA (dsRNA) that gives rise to small RNAs (smRNAs) known as microRNAs (miRNAs) or small-interfering RNAs (siRNAs). These smRNAs direct sequence-specific regulation of various gene transcripts, repetitive sequences, viruses, and mobile elements via RNA cleavage, translational inhibition, or transcriptional silencing through DNA methylation and heterochromatin formation. Early genetic screens in Arabidopsis were instrumental in uncovering numerous proteins required for these important regulatory pathways. Among the factors identified by these studies were RNA-dependent RNA polymerases (RDRs), which are proteins that synthesize siRNA-producing dsRNA molecules using a single-stranded RNA (ssRNA) molecule as a template. Recently, a growing body of evidence has implicated RDR-dependent RNA silencing in many different aspects of plant biology ranging from reproductive development to pathogen resistance. Here, we focus on the specific functions of the six Arabidopsis RDRs in RNA silencing, their ssRNA substrates and resulting RDR-dependent smRNAs, and the numerous biological functions of these proteins in plant development and stress responses.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0146"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1199/tab.0146","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434387","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: 2011-07-31DOI: 10.1199/tab.0145
Ryouichi Tanaka, Koichi Kobayashi, Tatsuru Masuda
{"title":"Tetrapyrrole Metabolism in Arabidopsis thaliana.","authors":"Ryouichi Tanaka, Koichi Kobayashi, Tatsuru Masuda","doi":"10.1199/tab.0145","DOIUrl":"10.1199/tab.0145","url":null,"abstract":"<p><p>Higher plants produce four classes of tetrapyrroles, namely, chlorophyll (Chl), heme, siroheme, and phytochromobilin. In plants, tetrapyrroles play essential roles in a wide range of biological activities including photosynthesis, respiration and the assimilation of nitrogen/sulfur. All four classes of tetrapyrroles are derived from a common biosynthetic pathway that resides in the plastid. In this article, we present an overview of tetrapyrrole metabolism in Arabidopsis and other higher plants, and we describe all identified enzymatic steps involved in this metabolism. We also summarize recent findings on Chl biosynthesis and Chl breakdown. Recent advances in this field, in particular those on the genetic and biochemical analyses of novel enzymes, prompted us to redraw the tetrapyrrole metabolic pathways. In addition, we also summarize our current understanding on the regulatory mechanisms governing tetrapyrrole metabolism. The interactions of tetrapyrrole biosynthesis and other cellular processes including the plastid-to-nucleus signal transduction are discussed.</p>","PeriodicalId":74946,"journal":{"name":"The arabidopsis book","volume":"9 ","pages":"e0145"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268503/pdf/tab.0145.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30434388","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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