Trends in Plant Science

Published by Elsevier
Print ISSN: 1360-1385
Guidelines for submitting commentsPolicy: Comments that contribute to the discussion of the article will be posted within approximately three business days. We do not accept anonymous comments. Please include your email address; the address will not be displayed in the posted comment. Cell Press Editors will screen the comments to ensure that they are relevant and appropriate but comments will not be edited. The ultimate decision on publication of an online comment is at the Editors' discretion. Formatting: Please include a title for the comment and your affiliation. Note that symbols (e.g. Greek letters) may not transmit properly in this form due to potential software compatibility issues. Please spell out the words in place of the symbols (e.g. replace “α” with “alpha”). Comments should be no more than 8,000 characters (including spaces ) in length. References may be included when necessary but should be kept to a minimum. Be careful if copying and pasting from a Word document. Smart quotes can cause problems in the form. If you experience difficulties, please convert to a plain text file and then copy and paste into the form.
Nonhost disease resistance is the most common form of disease resistance exhibited by plants against the majority of potentially pathogenic microorganisms. Recently, several components of nonhost disease resistance have been identified. Nonhost resistance exhibited against bacteria, fungi and oomycetes can be of two types. Type I nonhost resistance does not produce any visible symptoms whereas type II nonhost resistance results in a rapid hypersensitive response with cell death. Strong similarities exist between nonhost and gene-for-gene resistance responses but it is still not clear if the same mechanism is involved in producing these resistance responses.
For many years it has been known that plants perform rapid long-distance signalling using classical action potentials that have impacts on diverse processes in plants. Plants also synthesize numerous neuronal molecules and fulfill some criteria for intelligent behaviour. Analysis of recent breakthrough data from ecophysiology studies has revealed that plant roots can discriminate between 'self' and 'non-self'; in animals, this ability to discriminate is dependent on the activities of neuronal synapses. Here, we propose that plant cells establish modes of information exchange between each other that have properties in common with neuronal synapses. Moreover, plants also assemble adhesive contacts that orchestrate cell-to-cell communication between the host cells when challenged with pathogens, parasites and potential symbionts. We propose that these adhesive contacts resemble the immunological synapses found in animals.
Conservation and variability of histone methylation marks in Arabidopsis thaliana, Hordeum vulgare and Vicia faba. (a) Heterochromatin in Arabidopsis is organized as condensed chromocentres. Left: intensely DAPI stained chromocentres (scale barZ5 mm). Middle: immunostaining with antibodies against euchromatin-specific methylation marks shows intense labelling of the euchromatin, whereas the nucleolus and the chromocentres remain unlabelled. Right: by contrast, antibodies against heterochromatin-specific methylation marks yield signals preferentially at the chromocentres. (b) Chromatin organization in H. vulgare resembles the so-called Rablorientation, with the gene-rich chromosome termini clustered in one hemisphere of the nucleus, and pericentromeric heterochromatin, including the centromeres, in the opposite hemisphere. Left: FISH with probes to highlight the centromeres (BAC7-cyan) and the telomeres (HvT01-green) (modified from [91]) (scale barZ5 mm). Middle:
Heterochromatin-specificity of chromatin modifications in different organisms
Cell-cycle-regulated histone H3 phosphorylation in plants. (a-e) Mitosis. (a) H3T11ph correlates with condensation of plant metaphase chromosomes (scale barZ 10 mm). (b) On monocentric chromosomes, the pericentromeric regions show H3S10ph (scale barZ10 mm), whereas H3S28ph is confined to the central part of the pericentromeric region (inset). DAPI-stained interphase nuclei (blue) display no detectable H3 phosphorylation. (c) The polycentric chromosomes of Luzula luzuloides are entirely labelled with H3 phosphorylated at both serine positions (scale barZ5 mm). (d) Anti-AtAurora antibodies label the pericentromeric regions where sister chromatids cohere and where H3 is phosphorylated at S10 and S28 (scale barZ5 mm). (e) Model: in plants, the cell-cycle-dependent phosphorylation at H3T11 can serve as a signal for other proteins involved in chromosome condensation, whereas H3S10ph and H3S28ph is apparently needed for sister chromatid cohesion at pericentromeres of metaphase chromosomes during mitosis and meiosis II. (f-h) Meiosis. (f) H3S28ph and H3T11ph during metaphase I (entire chromosomes labelled) (scale barZ10 mm) and (g) during metaphase II (the pericentromeric regions show H3S28ph, whereas H3T11ph decorates the entire chromosome) (scale barZ10 mm). (h) Single chromatids (arrow), resulting from equational division of univalents at anaphase I, show no pericentromeric H3S10ph during the second meiotic division (scale barZ10 mm).
Cell-cycle dependence and subnuclear distribution patterns of histone acetylation in plants. (a) Cell-cycle dynamics and intensity of acetylation at various H3 and H4 lysine residues within distinct chromatin domains of Vicia faba, Hordeum vulgare and Arabidopsis thaliana. (The acetylation intensity patterns show no clear cell-cycle dependency for H3K9 and/or K18, H3K14, H3K23 and H4K8 of V. faba, for H3K9 and/or K18, H3K14 and H4K16 of H. vulgare and for H3K9, H3K14, H4K5, H4K8 and H4K12 of Arabidopsis, not shown.) (b) Distribution of H4K5ac along V. faba metaphase chromosomes; scheme of karyotype ACB with heterochromatin marked is shown above (scale barZ10 mm). (c) Distribution of H4K5ac along V. faba metaphase chromosomes after treatment of root tips with the HDAC inhibitor trichostatin A for 2 h before fixation (scale barZ10 mm). Note the reverse signal pattern at heterochromatin compared with that shown in (b). (b,c) modified from [87]. (d) Distribution of H3K14ac along V. faba chromosomes reveals clustering at the NOR and some heterochromatic regions, whereas other heterochromatin positions are less labelled than the euchromatin positions (scale barZ10 mm) (modified from [86]). (e) V. faba G1-nucleus showing enrichment of H4K5ac (green) within the nucleolus, whereas euchromatin shows moderate signals and heterochromatin (represented by tandem-repetitive FokI-elements, red) no signals (scale barZ10 mm). (f) V. faba nucleus in late S to early G2 showing clustering of H4K5ac (green) at late replicating heterochromatin (represented by tandem-repetitive FokI-elements, red) (scale barZ10 mm). (g) V. faba nucleus in early S phase after 'run on transcription' showing BrUTP signals (red) mainly within the nucleolus and less dense signals across the euchromatin; the nucleolus and heterochromatin domains are free of H4K5ac (green) (scale barZ10 mm). (h) V. faba nucleus in early G2 phase with BrUTP signals (red) over the nucleolus and the euchromatin, whereas H4K5ac is clustered at heterochromatic domains that do not coincide with BrUTP signals (scale barZ10 mm). Note the rare overlap of red and green signals within the euchromatin in (g) and (h). (a and e-h) reproduced from [90]. (i) A barley translocation chromosome with both NORs on one chromosome; both are enriched with H4K5ac (right), but only NOR6 forms a nucleolus (modified from [91]) (scale barZ5 mm).
The organization of DNA into chromatin regulates expression and maintenance (replication, repair, recombination, segregation) of genetic information in a dynamic manner. The N-terminal tails of the nucleosomal core histones are subjected to post-translational modifications such as acetylation, methylation, phosphorylation, ubiquitination, glycosylation, ADP-ribosylation, carbonylation and sumoylation. These modifications, together with DNA methylation, control the folding of the nucleosomal array into higher order structures and mediate signalling for cellular processes. Although histones and their modifications are highly conserved, recent data show that chromosomal distribution of individual modifications (acetylation, methylation, phosphorylation) can differ along the cell cycle as well as among and between groups of eukaryotes. This implies the possibility of evolutionary divergence in reading the "histone code".
Many agronomically important traits are governed by several genes known as quantitative trait loci (QTLs). The identification of important, QTL-controlled agricultural traits has been difficult because of their complex inheritance; however, completion of the rice genomic sequence has facilitated the cloning of QTLs and their pyramiding for breeding. Because QTLs are derived from natural variation, the use of a wider range of variations such as that found in wild species is important. In addition, Introgression Lines (ILs) developed from wild species in combination with Marker Assisted Selection should facilitate efficient gene identification. This review describes recent developments in rice QTL analysis including mapping, cloning and pyramiding QTLs.
There is little relationship between eukaryotic RNA-directed RNA polymerases (RDRs), viral RNA-dependent RNA polymerases (RdRps) and DNA-dependent RNA polymerases, indicating that RDRs evolved as an independent class of enzymes early in evolution. In fungi, plants and several animal systems, RDRs play a key role in RNA-mediated gene silencing [post-transcriptional gene silencing (PTGS) in plants and RNA interference (RNAi) in non-plants] and are indispensable for heterochromatin formation, at least, in Schizosaccharomyces pombe and plants. Recent findings indicate that PTGS, RNAi and heterochromatin formation not only function as host defence mechanisms against invading nucleic acids but are also involved in natural gene regulation. RDRs are required for these processes, initiating a broad interest in this enzyme class.
Non-model Arabidopsis species have been widely used as outgroup taxa in studies of molecular evolution. In Arabidopsis lyrata, Arabidopsis halleri and Arabidopsis arenosa, traits pertaining to self-incompatibility, heavy metal tolerance and inter-specific hybridization have been subjected to detailed genetic analysis. However, the full potential for exploring the causes and consequences of natural variation in complex traits within the genus Arabidopsis has not been widely appreciated or realized. Here, we draw on broadly dispersed information to characterize the basic biology, ecology, population genetics and molecular evolution for these three non-model Arabidopsis species. We illustrate how the wealth of functional and genomic tools pioneered in A. thaliana can be applied to gain insights into adaptive evolution of ecologically important traits and genome-wide processes, such as polyploidy, speciation and reticulate evolution, within and among Arabidopsis species.
The chemical defence of pine against herbivorous insects has been intensively studied with respect to its effects on the performance and behaviour of the herbivores as well as on the natural enemies of pine herbivores. The huge variety of terpenoid pine components play a major role in mediating numerous specific food web interactions. The constitutive terpenoid pattern can be adjusted to herbivore attack by changes induced by insect feeding or oviposition activity. Recent studies on folivorous pine sawflies have highlighted the role of induced pine responses in herbivore attack and have demonstrated the importance of analysing the variability of pine defence and its finely tuned specificity with respect to the herbivore attacker in a multitrophic context.
Recessive resistance genes against plant viruses have been recognized for a long time but their molecular nature has only recently been linked to components of the eukaryotic translation initiation complex. Translation initiation factors, and particularly the eIF4E and eIF4G protein families, were found to be essential determinants in the outcome of RNA virus infections. Viruses affected by these genes belong mainly to potyviruses; natural viral resistance mechanisms as well as mutagenesis analysis in Arabidopsis all converged to identify the same set of translation initiation factors. Their role in plant resistance against RNA viruses remains to be elucidated. Although the interaction with the protein synthesis machinery is probably a key element for successful RNA virus infection, other possible mechanisms will also be discussed.
Despite significant progress in understanding protein trafficking and compartmentation in plants, the identification and protein compartmentalization for organelles that belong to both the secretory and endocytic pathways have been difficult because protein trafficking has generally been studied separately in these two pathways. However, recent data indicate that the trans-Golgi network serves as an early endosome merging the secretory and endocytic pathways in plant cells. Here, we discuss the proteins identified as markers for post-Golgi compartments in these two pathways and propose that the trans-Golgi network is a pivotal organelle with multiple sorting domains for post-Golgi protein trafficking in plant cells.
Several classes of endogenous small RNAs of 20-26 nucleotides, such as microRNAs and small interfering (si)RNAs, have been described in plants and animals. Arabidopsis currently seems to be an exception because a novel genetically distinguishable small RNA class, termed natural-antisense transcript derived siRNAs, was recently identified. Pathways for the biogenesis and function of each class are already well characterized, enabling their classification on the basis of both size and proteins required for their function. However, each pathway requires proteins belonging to conserved protein families, and recent genetic studies confirmed an expected partial redundancy between members of the Dicer-like (DCL) family. Moreover, several experimental results indicate redundancies among double-strand RNA binding proteins and ARGONAUTE proteins, which probably create a complex network of small RNA pathways.
Metabolite profiling is a fast growing technology and is useful for phenotyping and diagnostic analyses of plants. It is also rapidly becoming a key tool in functional annotation of genes and in the comprehensive understanding of the cellular response to biological conditions. Metabolomics approaches have recently been used to assess the natural variance in metabolite content between individual plants, an approach with great potential for the improvement of the compositional quality of crops. Here, we assess the contribution of metabolite profiling to these areas.
Glucosinolates and their associated degradation products have long been recognized for their distinctive benefits to human nutrition and plant defense. Because most of the structural genes of glucosinolate metabolism have been identified and functionally characterized in Arabidopsis thaliana, current research increasingly focuses on questions related to the regulation of glucosinolate synthesis, distribution and degradation as well as to the feasibility of engineering customized glucosinolate profiles. Here, we highlight recent progress in glucosinolate research, with particular emphasis on the biosynthetic pathway and its metabolic relationships to auxin homeostasis. We further discuss emerging insight into the signaling networks and regulatory proteins that control glucosinolate accumulation during plant development and in response to environmental challenge.
Root hairs and pollen tubes show strictly polar cell expansion called tip growth. Recent studies of tip growth in root hairs and pollen tubes have revealed that small GTPases of the Rab, Arf and Rho/Rac families, along with their regulatory proteins, are essential for spatio-temporal regulation of vesicular trafficking, cytoskeleton organization and signalling. ROP/RAC GTPases are involved in a multiplicity of functions including the regulation of cytoskeleton organization, calcium signalling and endocytosis in pollen tubes and root hairs. One of the most exciting recent discoveries is the preferential localization of vesicles of the trans-Golgi network (TGN), defined by specific RAB GTPases, in the apical "clear zone" and the definition of TGN as a bona fide organelle involved in both polarized secretion and endocytosis. The TGN is thought to serve the function of an early endosome in plants because it is involved in early endocytosis and rapid vesicular recycling of the plasma membrane in root epidermal cells.
Self-incompatibility (SI) is a genetic barrier to inbreeding that is broadly distributed in angiosperms. In finite populations of SI plants, the loss of S-allele diversity can limit plant reproduction by reducing the availability of compatible mates. Many studies have shown that small or fragmented plant populations suffer from mate limitation. The advent of molecular typing of S-alleles in many species has paved the way to address quantitatively the importance of mate limitation, and to provide greater insight into why and how SI systems breakdown frequently in nature. In this review, we highlight the ecological factors that contribute to mate limitation in SI taxa, discuss their consequences for the evolution and functioning of SI, and propose new empirical research directions.
Natural (13)C abundance is now an unavoidable tool to study ecosystem and plant carbon economies. A growing number of studies take advantage of isotopic fractionation between carbon pools or (13)C abundance in respiratory CO(2) to examine the carbon source of respiration, plant biomass production or organic matter sequestration in soils. (12)C/(13)C isotope effects associated with plant metabolism are thus essential to understand natural isotopic signals. However, isotope effects of enzymes do not influence metabolites separately, but combine to yield a (12)C/(13)C isotopologue redistribution orchestrated by metabolic flux patterns. In this review, we summarise key metabolic isotope effects and integrate them into the corpus of plant primary carbon metabolism.
Example of cis and trans eQTLs. In this example, transcription factor A (TF A) has gene B as regulatory target. The Y axis represents the LOD score, which is the logarithm of odds. The horizontal dashed lines indicate the significance threshold for the LOD score for TF A and gene B. Roman numerals represent the chromosome number (Chr.I–V). (a) Expression of TF A and gene B in parent accessions z and q for the RIL population used for the analyses in (b) and (c) . The protein level or functionality of TF A is indicated by the number of blue ovals. The expression levels of all genes are measured for all RILs in the population using microarray, and the expression level of the gene of interest is now the trait that is analyzed. (b) eQTL for TF A. An expression polymorphism is observed for TF A. The genomic location of the polymorphic locus is identical to the genomic position of TF A. Therefore, this is a cis eQTL. Explanation: the polymorphism is located within the promoter of TF A [marked in green in (a) ] causing a difference between the parent lines z and q. This expression polymorphism results in an eQTL for TF A at the same position as the genomic position of TF A. (c) eQTL for gene B. An expression polymorphism is observed for gene B. However, the genomic location of the responsible locus is different to the genomic position of gene B. Therefore, this is a trans eQTL for gene B. The location of the eQTL for gene B coincides with the location of the cis eQTL for TFA. Explanation: The polymorphism in the promoter of TF A [marked in green in (a) ] results in an expression polymorphism of TF A. This results in expression polymorphism of gene B, which generates an eQTL for gene B at the genomic position of TF A on Chr.V and not at the genomic position of gene B on Chr.I. 
Natural genetic variation within plant species is at the core of plant science ranging from agriculture to evolution. Whereas much progress has been made in mapping quantitative trait loci (QTLs) controlling this natural variation, the elucidation of the underlying molecular mechanisms has remained a bottleneck. Recent systems biology tools have significantly shortened the time required to proceed from a mapped locus to testing of candidate genes. These tools enable research on natural variation to move from simple reductionistic studies focused on individual genes to integrative studies connecting molecular variation at multiple loci with physiological consequences. This review focuses on recent examples that demonstrate how expression QTL data can be used for gene discovery and exploited to untangle complex regulatory networks.
We are currently in an interesting phase of plant biotechnology releases, both for the scientists responsible for these innovations who are beginning to see their ideas realized, and for the biotechnology companies that are starting to see a return on their investment. One of the most notable examples, is the introduction of transgenic crops that are engineered to express a Bacillus thuringiensis toxin that confers resistance to insect predation. However, the picture is not altogether positive - there is concern that the introduction of this technology was premature or should not have happened at all, and that the valuable insecticidal properties of Bacillus thuringiensis will be lost.
Although the plant growth hormone auxin has long been recognized as a regulator of plant defense, the molecular mechanisms involved are still largely unknown. Recent studies reviewed here reveal new insights into the role of auxin in plant defense. Similar to the signaling pathways of the defense-associated plant hormones salicylic acid (SA) and jasmonic acid (JA), auxin signaling differentially affects resistance to separate pathogen groups. Recent evidence suggests that the auxin and SA pathways act in a mutually antagonistic manner during plant defense, whereas auxin and JA signaling share many commonalities. Auxin also affects disease outcomes indirectly through effects on development. Here, we discuss the multiple ways in which auxin regulation of plant growth and development might be intimately linked to plant defense.
14-3-3 proteins are phosphoserine-binding proteins that regulate the activities of a wide array of targets via direct protein-protein interactions. In animal cells, the majority of their known targets are involved in signal transduction and transcription. In plants, we know about them primarily through their regulation of the plasma membrane H(+)-ATPase and enzymes of carbon and nitrogen metabolism. Nevertheless, an increasing number of plant signalling proteins are now being recognized as 14-3-3-interacting proteins. Plant 14-3-3 proteins bind a range of transcription factors and other signalling proteins, and have roles regulating plant development and stress responses. Important mechanisms of regulation by 14-3-3 include shuttling proteins between different cellular locations and acting as scaffolds for the assembly of larger signalling complexes.
Signal transduction and enzyme regulation are known to occur via phosphorylation, but it is becoming increasingly apparent that phosphorylation might be only a necessary preamble to regulation. In many cases, the phosphorylated target protein must associate with a specialized adapter protein, known as 14-3-3, to complete the regulatory action. There are several prominent examples of 14-3-3 participation in plant regulatory events, including the regulation of plasma membrane H+-ATPase, nitrate reductase and sucrose phosphate synthase. However, emerging data on 14-3-3s in the nucleus might extend the roles for 14-3-3s well beyond the regulation of cytoplasmic enzymes.
Singlet oxygen ((1)O(2)) is a singular reactive oxygen species (ROS) that is produced constitutively in plant leaves in light via chlorophylls that act as photosensitizers. This (1)O(2) production is spatially resolved within thylakoid membranes and is enhanced under light stress conditions. (1)O(2) can also be produced by phytotoxins during plant-pathogen interactions. (1)O(2) is highly reactive, can be toxic to cells and can be involved in the signaling of programmed cell death or acclimation processes. Here, we summarize current knowledge on (1)O(2) management in plants and on the biological effects of this peculiar ROS. Compared with other ROS, (1)O(2) has received relatively little attention, but recent developments indicate that it has a crucial role in the responses of plants to light.
Mendel's paper 'Versuche über Pflanzen-Hybriden' is the best known in a series of studies published in the late 18th and 19th centuries that built our understanding of the mechanism of inheritance. Mendel investigated the segregation of seven gene characters of pea (Pisum sativum), of which four have been identified. Here, we review what is known about the molecular nature of these genes, which encode enzymes (R and Le), a biochemical regulator (I) and a transcription factor (A). The mutations are: a transposon insertion (r), an amino acid insertion (i), a splice variant (a) and a missense mutation (le-1). The nature of the three remaining uncharacterized characters (green versus yellow pods, inflated versus constricted pods, and axial versus terminal flowers) is discussed.
The creation of transgenic plants has brought significant advances to light in plant biotechnology. However, in spite of the fact that transgenic plants are beginning to be grown widely, controlled transgene integration into a pre-determined site remains to be achieved. Here we suggest two alternative approaches for gene targeting in plants: manipulating the host and donor sequence, and targeting during active homologous recombination stages.
New sequencing technologies are dramatically accelerating progress in forward genetics, and the use of such methods for the rapid identification of mutant alleles will be soon routine in many laboratories. A straightforward extension will be the cloning of major-effect genetic variants in crop species. In the near future, it can be expected that mapping by sequencing will become a centerpiece in efforts to discover the genes responsible for quantitative trait loci. The largest impact, however, might come from the use of these strategies to extract genes from non-model, non-crop plants that exhibit heritable variation in important traits. Deployment of such genes to improve crops or engineer microbes that produce valuable compounds heralds a potential paradigm shift for plant biology.
The plant hormone auxin is frequently observed to be asymmetrically distributed across adjacent cells during crucial stages of growth and development. These auxin gradients depend on polar transport and regulate a wide variety of processes, including embryogenesis, organogenesis, vascular tissue differentiation, root meristem maintenance and tropic growth. Auxin can mediate such a perplexing array of developmental processes by acting as a general trigger for the change in developmental program in cells where it accumulates and by providing vectorial information to the tissues by its polar intercellular flow. In recent years, a wealth of molecular data on the mechanism of auxin transport and its regulation has been generated, providing significant insights into the action of this versatile coordinative signal.
Most plant mRNAs are synthesized as precursors containing one or more intervening sequences (introns) that are removed during the process of splicing. The basic mechanism of spliceosome assembly and intron excision is similar in all eukaryotes. However, the recognition of introns in plants has some unique features, which distinguishes it from the reactions in vertebrates and yeast. Recent progress has occurred in characterizing the splicing signals in plant pre-mRNAs, in identifying the mutants affected in splicing and in discovering new examples of alternatively spliced mRNAs. In combination with information provided by the Arabidopsis genome-sequencing project, these studies are contributing to a better understanding of the splicing process and its role in the regulation of gene expression in plants.
Reactive oxygen species (ROS) are highly reactive molecules able to damage cellular components but they also act as cell signalling elements. ROS are produced by many different enzymatic systems. Plant NADPH oxidases, also known as respiratory burst oxidase homologues (RBOHs), are the most thoroughly studied enzymatic ROS-generating systems and our understanding of their involvement in various plant processes has increased considerably in recent years. In this review we discuss their roles as ROS producers during cell growth, plant development and plant response to abiotic environmental constraints and biotic interactions, both pathogenic and symbiotic. This broad range of functions suggests that RBOHs may serve as important molecular 'hubs' during ROS-mediated signalling in plants.
Membrane heredity was central to the unique symbiogenetic origin from cyanobacteria of chloroplasts in the ancestor of Plantae (green plants, red algae, glaucophytes) and to subsequent lateral transfers of plastids to form even more complex photosynthetic chimeras. Each symbiogenesis integrated disparate genomes and several radically different genetic membranes into a more complex cell. The common ancestor of Plantae evolved transit machinery for plastid protein import. In later secondary symbiogeneses, signal sequences were added to target proteins across host perialgal membranes: independently into green algal plastids (euglenoids, chlorarachneans) and red algal plastids (alveolates, chromists). Conservatism and innovation during early plastid diversification are discussed.
The WRKY proteins are a superfamily of transcription factors with up to 100 representatives in Arabidopsis. Family members appear to be involved in the regulation of various physio-logical programs that are unique to plants, including pathogen defense, senescence and trichome development. In spite of the strong conservation of their DNA-binding domain, the overall structures of WRKY proteins are highly divergent and can be categorized into distinct groups, which might reflect their different functions.
In 1999, the amount of land planted with genetically modified (GM) crops around the world is expected to have increased by >40%. Significant increases were in China, Argentina, Canada and South Africa. Three countries, Portugal, Romania and Ukraine, had commercial plantings for the first time in 1999.
Searching for cytosolic phosphofructokinase (PFK) in the Arabidopsis genome. The tree shows the phylogeny of open reading frames (ORFs) of genes predicted to encode pyrophosphate-dependent phosphofructokinase (PFP) subunits and subunits of PFK and putative PFKs. The Arabidopsis genome was searched for genes with homology to bacterial and mammalian PFKs, the potato PFP-a-subunit or the PFP-b-subunit. The Arabidopsis genes are indicated by their gene numbers. For the remaining genes, GenBank Accession numbers are indicated. Two Arabidopsis genes group with the potato PFP a-subunits (yellow area), and two genes group with the potato PFP b-subunit (blue area). Seven Arabidopsis genes group together (green area) and have some homology to PFK and PFP. These genes are most similar to bacterial PFK-I. Two of these putative Arabidopsis PFKs (highlighted in dark green) are predicted to be chloroplast located by the ChloroP 1.1 server ( [75]. Arabidopsis cytosolic PFK isoforms are likely to be found among the five remaining putative PFKs. The neighbor-joining phylogenetic tree created using the Clustal X, was bootstrapped (1000 times) and graphically presented using Treeview. The scale indicates the average substitutions per site. All the Arabidopsis genes shown appear to be expressed proteins because cDNA clones can be found in the databases.
Fructose-2,6-bisphosphate (Fru-2,6-P(2)) regulates key reactions of the primary carbohydrate metabolism in all eukaryotes. In plants, Fru-2,6-P(2) coordinates the photosynthetic carbon flux into sucrose and starch biosynthesis. The use of transgenic plants has allowed the regulatory models to be tested by modifying the Fru-2,6-P(2) levels and the enzymes regulated by Fru-2,6-P(2). Genes for the bifunctional plant enzyme that synthesizes and degrades Fru-2,6-P(2) have been isolated and molecular characterization has provided new insight into structure and molecular regulation of the enzyme. Advances in Fru-2,6-P(2) physiology and molecular biology are discussed. These advances have not only enlightened in vivo operation of Fru-2,6-P(2) but also revealed that the Fru-2,6-P(2) regulatory system is highly complex and interacts with other regulatory mechanisms.
The Fourth International Fructan Symposium, Arolla, Switzerland, 16–20 August 2000.
Guidelines for submitting commentsPolicy: Comments that contribute to the discussion of the article will be posted within approximately three business days. We do not accept anonymous comments. Please include your email address; the address will not be displayed in the posted comment. Cell Press Editors will screen the comments to ensure that they are relevant and appropriate but comments will not be edited. The ultimate decision on publication of an online comment is at the Editors' discretion. Formatting: Please include a title for the comment and your affiliation. Note that symbols (e.g. Greek letters) may not transmit properly in this form due to potential software compatibility issues. Please spell out the words in place of the symbols (e.g. replace “α” with “alpha”). Comments should be no more than 8,000 characters (including spaces ) in length. References may be included when necessary but should be kept to a minimum. Be careful if copying and pasting from a Word document. Smart quotes can cause problems in the form. If you experience difficulties, please convert to a plain text file and then copy and paste into the form.
Diagram of signals and typical seasons corresponding to the different types of dormancy. Dormancy is generally defined as the temporary suspension of visible growth of any plant structure (e.g. buds containing meristems). Lang et al. [1] further categorized dormancy into paradormancy, endodormancy and ecodormancy. This figure illustrates the cycle of three types of dormancy and the general signals and seasons that are associated with dormancy of perennial weeds, woody plants (shrubs and trees) and shoot buds of tubers (potato and yam). 
Pathways regulating dormancy in plants. Growth inhibition in paradormancy is primarily controlled by auxin and sugar, via abscisic acid (ABA) inhibition and gibberellic acid (GA) and cytokinin signaling. ABA is the primary signal regulating ecodormancy. Endodormancy is primarily regulated by phytochrome and/or ethylene, and might act via a chromatin remodeling epigenetic-like mechanism and/or ABA-mediated growth arrest. Cross talk of signal transduction pathways between ethylene/ phytochrome and ABA plays a role in dormancy. Question marks represent likely pathways that have not yet been shown to exist. TRENDS in Plant Science 
Dormancy regulation in vegetative buds is a complex process necessary for plant survival, development and architecture. Our understanding of and ability to manipulate these processes are crucial for increasing the yield and availability of much of the world's food. In many cases, release of dormancy results in increased cell division and changes in developmental programs. Much can be learned about dormancy regulation by identifying interactions of signals in these crucial processes. Internal signals such as hormones and sugar, and external signals such as light act through specific, overlapping signal transduction pathways to regulate endo-, eco- and paradormancy. Epigenetic-like regulation of endodormancy suggests a possible role for chromatin remodeling similar to that known for the vernalization responses during flowering.
Photochemistry observed for the phototropin light, oxygen or voltage (LOV) domains (modified from Ref. [44]). A sample of purified Arabidopsis phot1 LOV2 is shown in the upper right. Purified LOV domains bind the chromophore FMN (flavin mononucleotide) and exhibit green fluorescence when viewed under ultraviolet light. The graph illustrates the light-induced absorbance changes observed for purified phot1 LOV2 over several seconds. The absorption spectrum that is uppermost at 450 nm represents the protein sample in the dark state. The sample is then irradiated with blue light and spectra recorded at 1-s intervals. The following light-induced absorbance changes result in the formation of three isosbestic points, indicated by the red arrows, which are characteristic of the formation of a flavin–cysteinyl adduct. Proposed light-induced formation of the covalent adduct between the FMN chromophore and a conserved cysteine residue within the LOV domain is shown in the lower right. Recent studies [50] indicate that this reaction involves an, as yet unidentified, proton donor–acceptor (designated X).  
Blue-light-induced phototropic responses, chloroplast migration and stomatal opening observed for wild-type (WT) Arabidopsis plants and single and double phototropin-deficient mutants (phot1, phot2 and phot1 phot2). (a) The phototropic response to low-and high-intensity unilateral blue light. (b) A side view of the chloroplast migration responses in leaf mesophyll cells. (c) The opening response of stomatal guard cells. The size of the black arrows shown for all three responses corresponds to the relative intensity of the blue-light treatment.  
Blue and ultraviolet-A light regulate a wide range of responses in plants, including phototropism, chloroplast migration and stomatal opening. However, the photoreceptors for these light responses have been identified only recently. The phototropins (phot1 and phot2) represent a new class of receptor kinases that appear to be exclusive to plants. Recent genetic analysis has shown that phot1 and phot2 exhibit partially overlapping functions in mediating phototropism, chloroplast migration, and stomatal opening in Arabidopsis. Although significant progress has been made in understanding the early photochemical and biochemical events that follow phototropin excitation, the details of how this excitation activates such different responses remain to be elucidated.
A null allele and point mutation of Fus3 suggest different roles of Kss1p in haploid cells [7.8]. (a) fus3D: Kss1p functionally compensates for Fus3p by interacting with a protein complex that usually recognizes Fus3p. In this genetic background, Kss1p functions in the mating pathway. (b) fus3-M: a mutant form of Fus3 protein interacts with a protein complex and Kss1p is excluded. In this genetic background, strains are sterile. TRENDS in Plant Science 
The abundance of Arabidopsis insert mutants portends the day when null alleles in every gene will be obtained. Once these are created, all plant scientists can become geneticists. However, this brief technical highlight of genetic concepts cautions against ascribing gene function based exclusively on phenotypic analysis of null alleles.
Plants synthesize many fatty acid derivatives, several of which play important regulatory roles. Jasmonates are the best characterized examples. Jasmonate-insensitive mutants and mutants with a constitutive jasmonate response have given us new insights into jasmonate signalling. The jasmonate biosynthesis mutant opr3 allowed the dissection of cyclopentanone and cyclopentenone signalling, thus defining specific roles for these molecules. Jasmonate signalling is a complex network of individual signals and recent findings on specific activities of methyl jasmonate and (Z)-jasmone add to this picture. In addition, there are keto, hydroxy and hydroperoxy fatty acids that might be involved in cell death and the expression of stress-related genes. Finally, there are bruchins and volicitin, signal molecules from insects that are perceived by plants in the picomole to femtomole range. They highlight the importance of fatty acid-derived molecules in interspecies communication and in plant defence.
Selection responses in the Illinois Protein Strains (a) and Illinois Oil Strains (b). Selection has been performed for 103 cycles in each of the Illinois High Protein (IHP), Illinois Low Protein (ILP), Illinois High Oil (IHO) and Illinois Low Oil (ILO) strains. Selection was reversed in each of these four strains beginning at cycle 48 to produce the Reverse High Protein (RHP), Reverse Low Protein (RLP), Reverse High Oil (RHO) and Reverse Low Oil (RLO) strains. The Switchback High Oil (SHO) strain was initiated from RLO at cycle 55 and Reverse Low Protein 2 (RLP2) was initiated from ILP at cycle 90. Each cycle measured grain from 60-120 plants, with seeds from the highest or lowest 20% (depending on the direction of selection) selected to form the next generation. Grain was produced by controlled pollinations among sibling plants to minimize inbreeding. Cross-sections of mature kernels from cycle 100 of nine strains (all except RLP2) show phenotypic differences in protein (largely localized in tan areas at the periphery of kernels), starch (white areas), seed size and scutellum size (yellow tissue at right in each kernel). The selection response graphs are adapted from Ref. [3].
The Illinois Long-Term Selection Experiment for grain protein and oil concentration in maize (Zea mays) is the longest continuous genetics experiment in higher plants. A total of 103 cycles of selection have produced nine related populations that exhibit phenotypic extremes for grain composition and a host of correlated traits. The use of functional genomics tools in this unique genetic resource provides exciting opportunities not only to discover the genes that contribute to phenotypic differences but also to investigate issues such as the response of plant genomes to artificial selection, the genetic architecture of quantitative traits and the source of continued genetic variation within domesticated crop genomes.
Model of phosphatidic acid (PA) signalling in plants. PA is produced by the activation of two different signalling pathways: those of phospholipases C and D (PLC and PLD). PLC hydrolyses PtdIns(4,5)P 2 into Ins(1,4,5)P 3 and diacylglycerol (DAG). Ins(1,4,5)P 3 diffuses into the cytosol, where it releases Ca 2+ from intracellular stores, whereas DAG remains in the membrane, where it is phosphorylated to PA by DAG kinase. PLD generates PA directly by hydrolysing structural lipids such as phosphatidylcholine. Increased PA levels affect several plant processes via various intracellular targets (Table 1). PA signalling is attenuated by phosphorylating it to diacylglycerol pyrophosphate (DGPP) via a PA kinase. Because DGPP is a minor lipid that dramatically increases in concentration when cells are activated, DGPP could itself be a signalling molecule (indicated by '?'). The putative involvement of G-protein-coupled receptors (Rec) is indicated. For further details, see text or Ref. 1. Abbreviations: DGK, DAG kinase; Ins(1,4,5)P 3 , inositol 1,4,5-trisphosphate; PA kin, PA kinase; PtdCho, phosphatidylcholine; PtdIns(4,5)P 2 , phosphatidylinositol 4,5-bisphosphate.
Evidence is accumulating that phosphatidic acid is a second messenger. Its level increases within minutes of a wide variety of stress treatments including ethylene, wounding, pathogen elicitors, osmotic and oxidative stress, and abscisic acid. Enhanced signal levels are rapidly attenuated by phosphorylating phosphatidic acid to diacylglycerol pyrophosphate. Phosphatidic acid is the product of two signalling pathways, those of phospholipases C and D, the former in combination with diacylglycerol kinase. Families of these genes are now being cloned from plants. Several downstream targets of phosphatidic acid have been identified, including protein kinases and ion channels.
PP2C-type protein phosphatases are monomeric enzymes present in both prokaryotes and eukaryotes. Members of this family of phosphoprotein phosphatases are involved in the regulation of several signaling pathways. A database analysis of Arabidopsis reveals PP2Cs to be the largest protein phosphatase family in plants, with 76 members, displaying high complexity, and greatly outnumbering PP2Cs in other eukaryotes. Plant PP2Cs have been found as regulators of signal transduction pathways and also involved in development. PP2C functions emphasize the existence of sophisticated signaling pathways in plants, in which protein dephosphorylation plays a crucial role towards determining specificities.
Grasses are the single most important plant family in agriculture. In the past years, comparative genetic mapping has revealed conserved gene order (colinearity) among many grass species. Recently, the first studies at gene level have demonstrated that microcolinearity of genes is less conserved: small scale rearrangements and deletions complicate the microcolinearity between closely related species, such as sorghum and maize, but also between rice and other crop plants. In spite of these problems, rice remains the model plant for grasses as there is limited useful colinearity between Arabidopsis and grasses. However, studies in rice have to be complemented by more intensive genetic work on grass species with large genomes (maize, Triticeae). Gene-rich chromosomal regions in species with large genomes, such as wheat, have a high gene density and are ideal targets for partial genome sequencing.
There are surprising similarities between how animals and plants perceive pathogens. In animals, innate immunity is based on the recognition of pathogen-associated molecular patterns. This is mediated by the Toll-like receptor (TLR) family, which rapidly induce the innate immunity response, a first line of defence against infectious disease. Plants have highly sensitive perception systems for general elicitors and they respond to these stimuli with a defence response. One of these general elicitors is flagellin, the main component of the bacterial flagellum. Genetic analysis in Arabidopsis has shown that FLS2, which encodes a receptor-like kinase, is essential for flagellin perception. FLS2 shares homology with the TLR family, and TLR5 is responsible for flagellin perception in mammals.
Living organisms have evolved to contain a wide variety of receptors and signaling pathways that are essential for their survival in a changing environment. Of these, the phosphoinositide pathway is one of the best conserved. The ability of the phosphoinositides to permeate both hydrophobic and hydrophilic environments, and their diverse functions within cells have contributed to their persistence in nature. In eukaryotes, phosphoinositides are essential metabolites as well as labile messengers that regulate cellular physiology while traveling within and between cells. The stereospecificity of the six hydroxyls on the inositol ring provides the basis for the functional diversity of the phosphorylated isomers that, in turn, generate a selective means of intracellular and intercellular communication for coordinating cell growth. Although such complexity presents a difficult challenge for bench scientists, it is ideal for the regulation of cellular functions in living organisms.
Until recently, most scientists have tacitly assumed that individual stomata respond independently and similarly to stimuli, showing minor random variation in aperture and behaviour. This implies that stomatal behaviour should not depend on the scale of observation. However, it is now clear that these assumptions are often incorrect. Leaves frequently exhibit dramatic spatial and temporal heterogeneity in stomatal behaviour. This phenomenon, in which small 'patches' of stomata respond differently from those in adjacent regions of the leaf, is called 'patchy stomatal conductance'. It appears to represent a hitherto unknown type of emergent collective behaviour that manifests itself in populations of stomata in intact leaves.
Methionine, lysine and threonine are essential amino acids required in the diets of non-ruminant animals. Major crops, such as corn, soybean and rice, are low in one or more of these amino acids. Currently, these amino acids are supplemented to animal feed to allow optimal growth--a costly process for farmers and consumer, therefore there is a great deal of interest in increasing essential amino acids in crops. The metabolism of methionine in plants is linked to the regulation of the aspartate pathway and is important for plant growth. In recent years, several key steps of this pathway have been identified at the molecular level, enabling us to initiate transgenic approaches to engineer the methionine content of plants.
Top-cited authors
Frank Van Breusegem
  • Ghent University
Martin Gollery
  • University of Nevada, Reno
Jian-Kang Zhu
  • Purdue University
Mansour Karimi
  • Ghent University
Wang-Xia Wang
  • University of Kentucky