Showing papers in "Annual Review of Plant Biology in 2004"

REACTIVE OXYGEN SPECIES: Metabolism, Oxidative Stress, and Signal Transduction

Abstract: Several reactive oxygen species (ROS) are continuously produced in plants as byproducts of aerobic metabolism. Depending on the nature of the ROS species, some are highly toxic and rapidly detoxified by various cellular enzymatic and nonenzymatic mechanisms. Whereas plants are surfeited with mechanisms to combat increased ROS levels during abiotic stress conditions, in other circumstances plants appear to purposefully generate ROS as signaling molecules to control various processes including pathogen defense, programmed cell death, and stomatal behavior. This review describes the mechanisms of ROS generation and removal in plants during development and under biotic and abiotic stress conditions. New insights into the complexity and roles that ROS play in plants have come from genetic analyses of ROS detoxifying and signaling mutants. Considering recent ROS-induced genome-wide expression analyses, the possible functions and mechanisms for ROS sensing and signaling in plants are compared with those in animals and yeast.

Rising atmospheric carbon dioxide: plants FACE the future

Abstract: Atmospheric CO(2) concentration ([CO(2)]) is now higher than it was at any time in the past 26 million years and is expected to nearly double during this century. Terrestrial plants with the C(3) photosynthetic pathway respond in the short term to increased [CO(2)] via increased net photosynthesis and decreased transpiration. In the longer term this increase is often offset by downregulation of photosynthetic capacity. But much of what is currently known about plant responses to elevated [CO(2)] comes from enclosure studies, where the responses of plants may be modified by size constraints and the limited life-cycle stages that are examined. Free-Air CO(2) Enrichment (FACE) was developed as a means to grow plants in the field at controlled elevation of CO(2) under fully open-air field conditions. The findings of FACE experiments are quantitatively summarized via meta-analytic statistics and compared to findings from chamber studies. Although trends agree with parallel summaries of enclosure studies, important quantitative differences emerge that have important implications both for predicting the future terrestrial biosphere and understanding how crops may need to be adapted to the changed and changing atmosphere.

How do crop plants tolerate acid soils? Mechanisms of aluminum tolerance and phosphorous efficiency.

Abstract: Acid soils significantly limit crop production worldwide because approximately 50% of the world's potentially arable soils are acidic. Because acid soils are such an important constraint to agriculture, understanding the mechanisms and genes conferring tolerance to acid soil stress has been a focus of intense research interest over the past decade. The primary limitations on acid soils are toxic levels of aluminum (Al) and manganese (Mn), as well as suboptimal levels of phosphorous (P). This review examines our current understanding of the physiological, genetic, and molecular basis for crop Al tolerance, as well as reviews the emerging area of P efficiency, which involves the genetically based ability of some crop genotypes to tolerate P deficiency stress on acid soils. These are interesting times for this field because researchers are on the verge of identifying some of the genes that confer Al tolerance in crop plants; these discoveries will open up new avenues of molecular/physiological inquiry that should greatly advance our understanding of these tolerance mechanisms. Additionally, these breakthroughs will provide new molecular resources for improving crop Al tolerance via both molecular-assisted breeding and biotechnology.

The ubiquitin 26S proteasome proteolytic pathway

Abstract: Much of plant physiology, growth, and development is controlled by the selective removal of short-lived regulatory proteins. One important proteolytic pathway involves the small protein ubiquitin (Ub) and the 26S proteasome, a 2-MDa protease complex. In this pathway, Ub is attached to proteins destined for degradation; the resulting Ub-protein conjugates are then recognized and catabolized by the 26S proteasome. This review describes our current understanding of the pathway in plants at the biochemical, genomic, and genetic levels, using Arabidopsis thaliana as the model. Collectively, these analyses show that the Ub/26S proteasome pathway is one of the most elaborate regulatory mechanisms in plants. The genome of Arabidopsis encodes more than 1400 (or >5% of the proteome) pathway components that can be connected to almost all aspects of its biology. Most pathway components participate in the Ub-ligation reactions that choose with exquisite specificity which proteins should be ubiquitinated. What remains to be determined is the identity of the targets, which may number in the thousands in plants.

RHAMNOGALACTURONAN II: Structure and Function of a Borate Cross-Linked Cell Wall Pectic Polysaccharide

Abstract: ▪ Abstract Rhamnogalacturonan II (RG-II) is a structurally complex pectic polysaccharide that was first identified in 1978 as a quantitatively minor component of suspension-cultured sycamore cell walls. Subsequent studies have shown that RG-II is present in the primary walls of angiosperms, gymnosperms, lycophytes, and pteridophytes and that its glycosyl sequence is conserved in all vascular plants examined to date. This is remarkable because RG-II is composed of at least 12 different glycosyl residues linked together by more than 20 different glycosidic linkages. However, only a few of the genes and proteins required for RG-II biosynthesis have been identified. The demonstration that RG-II exists in primary walls as a dimer that is covalently cross-linked by a borate diester was a major advance in our understanding of the structure and function of this pectic polysaccharide. Dimer formation results in the cross-linking of the two homogalacturonan chains upon which the RG-II molecules are constructed and ...

Symbioses of grasses with seedborne fungal endophytes

Abstract: Grasses (family Poaceae) and fungi of the family Clavicipitaceae have a long history of symbiosis ranging in a continuum from mutualisms to antagonisms. This continuum is particularly evident among symbioses involving the fungal genus Epichloe (asexual forms = Neotyphodium spp.). In the more mutualistic symbiota, the epichloe endophytes are vertically transmitted via host seeds, and in the more antagonistic symbiota they spread contagiously and suppress host seed set. The endophytes gain shelter, nutrition, and dissemination via host propagules, and can contribute an array of host fitness enhancements including protection against insect and vertebrate herbivores and root nematodes, enhancements of drought tolerance and nutrient status, and improved growth particularly of the root. In some systems, such as the tall fescue N. coenophialum symbioses, the plant may depend on the endophyte under many natural conditions. Recent advances in endophyte molecular biology promise to shed light on the mechanisms of the symbioses and host benefits.

Naturally occurring genetic variation in Arabidopsis thaliana.

Abstract: Currently, genetic variation is probably the most important basic resource for plant biology. In addition to the variation artificially generated by mutants in model plants, naturally occurring genetic variation is extensively found for most species, including Arabidopsis. In many cases, natural variation present among accessions is multigenic, which has historically hampered its analysis. However, the exploitation of this resource down to the molecular level has now become feasible, especially in model species like Arabidopsis, where several genes accounting for natural variation have already been identified. Dissecting this variation requires first a quantitative trait locus (QTL) analysis, which in Arabidopsis has proven very effective by using recombinant inbred lines (RILs). Second, identifying the particular gene and the nucleotide polymorphism underlying QTL is the major challenge, and is now feasible by combining high-throughput genetics and functional genomic strategies. The analysis of Arabidopsis natural genetic variation is providing unique knowledge from functional, ecological, and evolutionary perspectives. This is illustrated by reviewing current research in two different biological fields: flowering time and plant growth. The analysis of Arabidopsis natural variation for flowering time revealed the identity of several genes, some of which correspond to genes with previously unknown function. In addition, for many other traits such as those related to primary metabolism and plant growth, Arabidopsis QTL analyses are detecting loci with small effects that are not easily amenable by mutant approaches, and which might provide new insights into the networks of gene regulation.

Molecular mechanism of gibberellin signaling in plants

Abstract: The hormone gibberellin (GA) plays an important role in modulating diverse processes throughout plant development. In recent years, significant progress has been made in the identification of upstream GA signaling components and trans- and cis-acting factors that regulate downstream GA-responsive genes in higher plants. GA appears to derepress its signaling pathway by inducing proteolysis of GA signaling repressors (the DELLA proteins). Recent evidence indicates that the DELLA proteins are targeted for degradation by an E3 ubiquitin ligase SCF complex through the ubiquitin-26S proteasome pathway.

Metabolic channeling in plants.

Abstract: The organization of cooperating enzymes into macromolecular complexes is a central feature of cellular metabolism. A major advantage of such spatial organization is the transfer of biosynthetic intermediates between catalytic sites without diffusion into the bulk phase of the cell. This so-called "metabolic channeling" offers unique opportunities for enhancing and regulating cellular biochemistry. Studies in a number of plant primary and secondary metabolic systems continue to contribute to our understanding of the nature and importance of this phenomenon. This article reviews advances in four systems: the cysteine synthase complex, the Calvin cycle, cyanogenic glucoside biosynthesis, and the phenylpropanoid pathway. Each of these systems is providing new evidence for the importance of enzyme organization in cellular biochemistry as well as exclusive insights into the molecular basis of enzyme complex assembly. This review also explores current prospects for understanding metabolon structure, assembly, and biological function.

Plastid transformation in higher plants.

Abstract: ▪ Abstract Plastids of higher plants are semi-autonomous organelles with a small, highly polyploid genome and their own transcription-translation machinery. This review provides an overview of the technology for the genetic modification of the plastid genome including: vectors, marker genes and gene design, the use of gene knockouts and over-expression to probe plastid function and the application of site-specific recombinases for excision of target DNA. Examples for applications in basic science include the study of plastid gene transcription, mRNA editing, photosynthesis and evolution. Examples for biotechnological applications are incorporation of transgenes in the plastid genome for containment and high-level expression of recombinant proteins for pharmaceutical and industrial applications. Plastid transformation is routine only in tobacco. Progress in implementing the technology in other crops is discussed.

The generation of Ca(2+) signals in plants.

Abstract: The calcium ion is firmly established as a ubiquitous intracellular second messenger in plants. At their simplest, Ca(2+)-based signaling systems are composed of a receptor, a system for generating the increase in [Ca(2+)]cyt, downstream components that are capable of reacting to the increase in [Ca(2+)]cyt, and other cellular systems responsible for returning [Ca(2+)]cyt to its prestimulus level. Here we review the various mechanisms responsible for generating the stimulus-induced increases in [Ca(2+)]cyt known as Ca(2+) signals. We focus particularly on the mechanisms responsible for generating [Ca(2+)]cyt oscillations and transients and use Nod Factor signaling in legume root hairs and stimulus-response coupling in guard cells to assess the physiological significance of these classes of Ca(2+) signals.

Decoding Ca(2+) signals through plant protein kinases.

Abstract: ▪ Abstract Plants harbor four families of kinases that have been implicated in Ca2+ signaling (CDPKs, CRKs, CCaMKs, and SnRK3s) Although each family appears to respond to Ca2+ via different mechanisms, they all utilize Ca2+ sensors that bind Ca2+ through multiple EF-hands The CDPK (Ca2+-dependent protein kinase) family is represented by the most genes, with 12 subfamilies comprised of 34 isoforms in Arabidopsis and 27 in rice Some of the calcium-regulated kinases also show potential for regulation by lipid signals and kinase cascades Thus, Ca2+-regulated kinases provide potential nodes of cross-talk for multiple signaling pathways that integrate Ca2+ signals into all aspects of plant growth and development

Transport mechanisms for organic forms of carbon and nitrogen between source and sink

Abstract: Sugars and amino acids are generated in plants by assimilation from inorganic forms. Assimilated forms cross multiple membranes on their way from production sites to storage or use locations. Specific transport systems are responsible for vacuolar uptake and release, for efflux from the cells, and for uptake into the vasculature. Detailed phylogenetic analyses suggest that only proton-coupled cotransporters involved in phloem loading have been identified to date, whereas systems for vacuolar transport and efflux still await identification. Novel imaging approaches may provide the means to characterize the cellular events and elucidate whole plant control of assimilate partitioning and allocation.

Biosynthesis and accumulation of sterols

Abstract: In recent years, the impressive development of molecular genetics tools, the sequencing of the Arabidopsis thaliana genome, the availability of DNA or transposon tagged mutants, and the multiple possibilities offered by stable transformation with DNA in sense and antisense orientation have enabled the application of a strategy of gain or loss of function to study the sterol biosynthesis pathway. Here we describe the results obtained with these techniques. The results essentially confirm data obtained previously with sterol biosynthesis inhibitors (SBIs) and enable the precise dissection of biosynthetic pathways. We discuss the advantages and disadvantages of molecular genetics techniques as applied to sterol metabolism. The greater selectivity of these techniques constitutes an invaluable advantage and has led to the discovery of a role for sterols in plant development.

Dna methylation and epigenetics

Abstract: ▪ Abstract In many eukaryotes, including plants, DNA methylation provides a heritable mark that guides formation of transcriptionally silent heterochromatin. In plants, aberrant RNA signals direct DNA methylation to target sequences, sometimes appropriately and sometimes inappropriately. This chapter discusses the generation of RNA signals for epigenetic changes, the factors that mediate those changes, and some of the consequences of those changes for plant gene expression and genome integrity.

VIGS vectors for gene silencing: many targets, many tools.

Abstract: The discovery that plants recognize and degrade invading viral RNA caused a paradigm shift in our understanding of viral/host interactions. Combined with the discovery that plants cosuppress their own genes if they are transformed with homologous transgenes, new models for both plant intercellular communication and viral defense have emerged. Plant biologists adapted homology-based defense mechanisms triggered by incoming viruses to target individual genes for silencing in a process called virus-induced gene silencing (VIGS). Both VIGS- and dsRNA-containing transformation cassettes are increasingly being used for reverse genetics as part of an integrated approach to determining gene function. Virus-derived vectors silence gene expression without transformation and selection. However, because viruses also alter gene expression in their host, the process of VIGS must be understood. This review examines how DNA and RNA viruses have been modified to silence plant gene expression. I discuss advantages and disadvantages of VIGS in determining gene function and guidelines for the safe use of viral vectors.

Alternative nad(p)h dehydrogenases of plant mitochondria

Abstract: Plant mitochondria have a highly branched electron transport chain that provides great flexibility for oxidation of cytosolic and matrix NAD(P)H. In addition to the universal electron transport chain found in many organisms, plants have alternative NAD(P)H dehydrogenases in the first part of the chain and a second oxidase, the alternative oxidase, in the latter part. The alternative activities are nonproton pumping and allow for NAD(P)H oxidation with varying levels of energy conservation. This provides a mechanism for plants to, for example, remove excess reducing power and balance the redox poise of the cell. This review presents our current understanding of the alternative NAD(P)H dehydrogenases present in plant mitochondria.

Genetic regulation of time to flower in arabidopsis thaliana

Abstract: In Arabidopsis thaliana, the initiation of flowering is carried out by four genetic pathways: gibberellin, autonomous, vernalization, and light-dependent pathways. These processes are integrated by the function of the genes FD, FE, FWA, PDF2, SOC1, and FT at the integration pathway. The integrated signal of the floral induction is transmitted to the floral meristem identity genes LFY and AP1, and floral morphogenesis is performed.

Single-cell c4 photosynthesis versus the dual-cell (kranz) paradigm

Abstract: ▪ Abstract The efficiency of photosynthetic carbon assimilation in higher plants faces significant limitations due to the oxygenase activity of the enzyme Rubisco, particularly under warmer temperatures or water stress. A drop in atmospheric CO2 and rise in O2 as early as 300 mya provided selective pressure for the evolution of mechanisms to concentrate CO2 around Rubisco in order to minimize oxygenase activity and the resultant loss of carbon through photorespiration. It is well established that a carbon-concentrating mechanism occurs in some terrestrial plants through the process of C4 photosynthesis. These plants are characterized as having Kranz-type leaf anatomy, with two structurally and biochemically specialized photosynthetic cell types, mesophyll and bundle sheath, that function coordinately in carbon assimilation. C4 photosynthesis has evolved independently many times with great diversity in forms of Kranz anatomy, structure of dimorphic chloroplasts, and biochemistry of the C4 cycle. The most d...

Phosphoenolpyruvate carboxylase: a new era of structural biology.

Abstract: There have been remarkable advances in our knowledge of this important enzyme in the last decade. This review focuses on three recent topics: the three-dimensional structure of the protein, molecular mechanisms of catalytic and regulatory functions, and the molecular cloning and characterization of PEPC kinases, which are Ser/Thr kinases involved specifically in regulatory phosphorylation of vascular plant PEPC. Analysis by X-ray crystallography and site-directed mutagenesis for E. coli and maize PEPC identified the catalytic site and allosteric effector binding sites, and revealed the functional importance of mobile loops. We present the reaction mechanism of PEPC in which we assign the roles of individual amino acid residues. We discuss the unique molecular property of PEPC kinase and its possible regulation at the post-translational level.

Visualizing chromosome structure/organization

Abstract: With the rapid development of sequencing technologies in the past decade, many eukaryotic genomes have been resolved at the primary sequence level. However, organization of the genome within nuclei and the principles that govern such properties remain largely unclear. Optimization of fluorescence probe-based hybridization technologies combined with new advances in the instrumentation for microscopy has steadily yielded more structural information on chromosome organization in eukaryote model systems. These studies provide static snapshots of the detailed organization of chromatin. More recently, the successful application of a chromatin tagging strategy utilizing auto fluorescent fusion proteins opened a new era of chromatin studies in which the dynamic organization of the genome can be tracked in near real time. This review focuses on these new approaches to studying chromatin organization and dynamics in plants, and on future prospects in unraveling the basic principle of chromosome organization.