The plant kinetochore

Kinetochores are large protein complexes that bind to centromeres. By interacting with microtubules and their associated motor proteins, kinetochores both generate and regulate chromosome movement. Kinetochores also function in the spindle checkpoint; a surveillance mechanism that ensures that metaphase is complete before anaphase begins. Although the ultrastructure of plant kinetochores has been known for many years, only recently have specific kinetochore proteins been identified. The recent data indicate that plant kinetochores contain homologs of many of the proteins implicated in animal and fungal kinetochore function, and that the plant kinetochore is a redundant structure with distinct biochemical subdomains.     

Towards plant pangenomics

As an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species.     

Top 10 plant viruses in molecular plant pathology

Many scientists, if not all, feel that their particular plant virus should appear in any list of the most important plant viruses. However, to our knowledge, no such list exists. The aim of this review was to survey all plant virologists with an association with Molecular Plant Pathology and ask them to nominate which plant viruses they would place in a 'Top 10' based on scientific/economic importance. The survey generated more than 250 votes from the international community, and allowed the generation of a Top 10 plant virus list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Tobacco mosaic virus, (2) Tomato spotted wilt virus, (3) Tomato yellow leaf curl virus, (4) Cucumber mosaic virus, (5) Potato virus Y, (6) Cauliflower mosaic virus, (7) African cassava mosaic virus, (8) Plum pox virus, (9) Brome mosaic virus and (10) Potato virus X, with honourable mentions for viruses just missing out on the Top 10, including Citrus tristeza virus, Barley yellow dwarf virus, Potato leafroll virus and Tomato bushy stunt virus. This review article presents a short review on each virus of the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant virology community, as well as laying down a benchmark, as it will be interesting to see in future years how perceptions change and which viruses enter and leave the Top 10.     

Transposition-based plant transformation

Agrobacterium T-DNAs were used to deliver transposable Dissociation (Ds) elements into the nuclei of potato (Solanum tuberosum) cells. A double-selection system was applied to enrich for plants that only contained a transposed Ds element. This system consisted of a positive selection for the neomycin phosphotransferase (nptII) gene positioned within Ds followed by a negative selection against stable integration of the cytosine deaminase (codA) gene-containing T-DNA. Sixteen of 29 transgenic plants were found to contain a transposed element while lacking any superfluous T-DNA sequences. The occurrence of this genotype indicates that Ds elements can transpose from relatively short extrachromosomal DNA molecules into the plant genome. The frequency of single-copy Ds transformation was determined at 0.3%, which is only about 2.5-fold lower than the potato transformation frequency for backbone-free and single-copy T-DNAs. Because of the generally high expression levels of genes positioned within transposed elements, the new transformation method may find broad applicability to crops that are accessible to Agrobacterium T-DNA transfer.     

Role of plant hormones in plant defence responses

Plant hormones play important roles in regulating developmental processes and signaling networks involved in plant responses to a wide range of biotic and abiotic stresses. Significant progress has been made in identifying the key components and understanding the role of salicylic acid (SA), jasmonates (JA) and ethylene (ET) in plant responses to biotic stresses. Recent studies indicate that other hormones such as abscisic acid (ABA), auxin, gibberellic acid (GA), cytokinin (CK), brassinosteroids (BR) and peptide hormones are also implicated in plant defence signaling pathways but their role in plant defence is less well studied. Here, we review recent advances made in understanding the role of these hormones in modulating plant defence responses against various diseases and pests.     

Illuminating plant development

Throughout 1994 remarkable progress was made with molecular and genetic studies on signal transduction pathways of photomorphogenesis, the lightdependent development of plants. Analysis of Arabidopsis DET and COP genes suggests that they are involved in suppression of photomorphogenic development in the dark and that this is then reversed by light. Studies with COP1 indicate that this is achieved by redistribution of COP1 from the nucleus, in the dark, to the cytosol in the light⁽¹⁾. Overexpression of COP1 in the light, however, was able to partially suppress photomorphogenic development, confirming its role as a light-inactivatable repressor⁽²⁾. Evidence also suggests that some of the COP gene products may interact directly to form a large complex⁽³⁾.     

Quantitative plant proteomics

Quantitation is an inherent requirement in comparative proteomics and there is no exception to this for plant proteomics. Quantitative proteomics has high demands on the experimental workflow, requiring a thorough design and often a complex multi-step structure. It has to include sufficient numbers of biological and technical replicates and methods that are able to facilitate a quantitative signal read-out. Quantitative plant proteomics in particular poses many additional challenges but because of the nature of plants it also offers some potential advantages. In general, analysis of plants has been less prominent in proteomics. Low protein concentration, difficulties in protein extraction, genome multiploidy, high Rubisco abundance in green tissue, and an absence of well-annotated and completed genome sequences are some of the main challenges in plant proteomics. However, the latter is now changing with several genomes emerging for model plants and crops such as potato, tomato, soybean, rice, maize and barley. This review discusses the current status in quantitative plant proteomics (MS-based and non-MS-based) and its challenges and potentials. Both relative and absolute quantitation methods in plant proteomics from DIGE to MS-based analysis after isotope labeling and label-free quantitation are described and illustrated by published studies. In particular, we describe plant-specific quantitative methods such as metabolic labeling methods that can take full advantage of plant metabolism and culture practices, and discuss other potential advantages and challenges that may arise from the unique properties of plants.     

Facilitative plant interactions and climate simultaneously drive alpine plant diversity

Interactions among species determine local‐scale diversity, but local interactions are thought to have minor effects at larger scales. However, quantitative comparisons of the importance of biotic interactions relative to other drivers are rarely made at larger scales. Using a data set spanning 78 sites and five continents, we assessed the relative importance of biotic interactions and climate in determining plant diversity in alpine ecosystems dominated by nurse‐plant cushion species. Climate variables related with water balance showed the highest correlation with richness at the global scale. Strikingly, although the effect of cushion species on diversity was lower than that of climate, its contribution was still substantial. In particular, cushion species enhanced species richness more in systems with inherently impoverished local diversity. Nurse species appear to act as a ‘safety net’ sustaining diversity under harsh conditions, demonstrating that climate and species interactions should be integrated when predicting future biodiversity effects of climate change.     

Top 10 plant pathogenic bacteria in molecular plant pathology

Many plant bacteriologists, if not all, feel that their particular microbe should appear in any list of the most important bacterial plant pathogens. However, to our knowledge, no such list exists. The aim of this review was to survey all bacterial pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate the bacterial pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 458 votes from the international community, and allowed the construction of a Top 10 bacterial plant pathogen list. The list includes, in rank order: (1) Pseudomonas syringae pathovars; (2) Ralstonia solanacearum; (3) Agrobacterium tumefaciens; (4) Xanthomonas oryzae pv. oryzae; (5) Xanthomonas campestris pathovars; (6) Xanthomonas axonopodis pathovars; (7) Erwinia amylovora; (8) Xylella fastidiosa; (9) Dickeya (dadantii and solani); (10) Pectobacterium carotovorum (and Pectobacterium atrosepticum). Bacteria garnering honourable mentions for just missing out on the Top 10 include Clavibacter michiganensis (michiganensis and sepedonicus), Pseudomonas savastanoi and Candidatus Liberibacter asiaticus. This review article presents a short section on each bacterium in the Top 10 list and its importance, with the intention of initiating discussion and debate amongst the plant bacteriology community, as well as laying down a benchmark. It will be interesting to see, in future years, how perceptions change and which bacterial pathogens enter and leave the Top 10.     

Ask the plant: investigating and teaching plant structure

The discipline of comparative plant morphology can play an important role in both teaching and research at a comprehensive university. Natural variation can be used as the basis for studies that begin with the simple premise of 'ask the plant'. Research questions from a variety of disciplines can be examined using the unique methods and perspectives of comparative morphology. In addition to its common application in clarifying developmental relationships and processes, comparative morphology is naturally and has been historically suited to examining the adaptations of plants to their environments. Two examples (one from grasses and another from native Utah shrubs) of studies relating plant form to patterns of growth and competition will be used to illustrate this interface between morphology and ecology. The potential role of comparative morphology in teaching will be described for three different levels in the university curriculum: Biology I (an introductory course for first-year students); Plant Structure (an elective for third- or fourth-year students); and Ecological Plant Morphology and Anatomy (post-baccalaureate or postgraduate level). Describing and explaining plant diversity and variation in the context of common structural adaptations, rather than from a strictly taxonomic perspective, has been an effective 'hook' to interest students in plants in the introductory course. In the more advanced courses it has provided a useful framework for understanding how plant diversity reflects adaptive value as well as common descent and has provided a broader perspective for student research projects in the basic and applied plant sciences.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 73–78.     

Animal and plant space-use drive plant diversity–productivity relationships

Plant community productivity generally increases with biodiversity, but the strength of this relationship exhibits strong empirical variation. In meta-food-web simulations, we addressed if the spatial overlap in plants' resource access and animal space-use can explain such variability. We found that spatial overlap of plant resource access is a prerequisite for positive diversity–productivity relationships, but causes exploitative competition that can lead to competitive exclusion. Space-use of herbivores causes apparent competition among plants, resulting in negative relationships. However, space-use of larger top predators integrates sub-food webs composed of smaller species, offsetting the negative effects of exploitative and apparent competition and leading to strongly positive diversity–productivity relationships. Overall, our results show that spatial overlap of plants' resource access and animal space-use can greatly alter the strength and sign of such relationships. In particular, the scaling of animal space-use effects opens new perspectives for linking landscape processes without effects on biodiversity to productivity patterns.     

Plant hormones and plant growth regulators in plant tissue culture

Summary This is a short review of the classical and new, natural and synthetic plant hormones and growth regulators (phytohormones) and highlights some of their uses in plant tissue culture. Plant hormones rarely act alone, and for most processes— at least those that are observed at the organ level—many of these regulators have interacted in order to produce the final effect. The following substances are discussed: (a) Classical plant hormones (auxins, cytokinins, gibberellins, abscisic acid, ethylene and growth regulatory substances with similar biological effects. New, naturally occurring substances in these categories are still being discovered. At the same time, novel structurally related compounds are constantly being synthesized. There are also many new but chemically unrelated compounds with similar hormone-like activity being produced. A better knowledge of the uptake, transport, metabolism, and mode of action of phytohormones and the appearance of chemicals that inhibit synthesis, transport, and action of the native plant hormones has increased our knowledge of the role of these hormones in growth and development. (b) More recently discovered natural growth substances that have phytohormonal-like regulatory roles (polyamines, oligosaccharins, salicylates, jasmonates, sterols, brassinosteroids, dehydrodiconiferyl alcohol glucosides, turgorins, systemin, unrelated natural stimulators and inhibitors), as well as myoinositol. Many of these growth active substances have not yet been examined in relation to growth and organized developmentin vitro.     

The plant cytoskeleton-cell-wall continuum

Two of the most challenging mysteries of morphogenesis are how cells receive positional information from neighbouring cells and how receipt of this information triggers events that initiate cell differentiation. The concept that the cytoskeleton and éxocellular matrix' (ECM) form an interactive scaffold for perception and transduction of positional information is relatively new. Research is beginning to indicate that a continuous cytoskeleton-ECM scaffold may be a feature of all eukaryotic cells and that many of the molecules participating in this structure may be shared by plants, fungi and animals.     

Shaping in plant cells

Plant cells adopt a diversity of different shapes that are adapted to their specific functions. Central to the development of specialised form is the modification of cell-wall composition and organisation. A number of recent papers emphasise the importance of the cell wall to cell shaping, in the definition of both localised regions that are expandable and regions that are more resistant to mechanical forces. The organisation and activity of the cytoskeleton, and the activity of signalling pathways, are also essential in defining regions of the cell wall that will grow and those that will not. Although turgor has long been assumed to be a rather passive contributor to cell shaping, recent reports show that, in some cells, differential changes in turgor may have a role in establishing specialised cell form.     

Concepts in plant stress physiology. Application to plant tissue cultures

Because the term stress is used, most often subjectively, with variousmeanings, this paper first attempts to clarify the physiological definition,andthe appropriate terms as responses in different situations. The flexibility ofnormal metabolism allows the development of responses to environmental changeswhich fluctuate regularly and predictably over daily and seasonal cycles. Thusevery deviation of a factor from its optimum does not necessarily result instress. Stress begins with a constraint or with highly unpredictablefluctuations imposed on regular metabolic patterns that cause bodily injury,disease, or aberrant physiology. Stress is the altered physiological conditioncaused by factors that tend to alter an equilibrium. Strain is any physicaland/or chemical change produced by a stress, i.e. every established condition,which forces a system away from its thermodynamic optimal state. The papersecondly summarises the Strasser's state-change concept which is preciselythat suboptimality is the driving force for acclimation (genotype level) oradaptation (population level) to stress. The paper continues with the actualknowledge on the mechanisms of stress recognition and cell signalling. Briefly:plasma membranes are the sensors of environmental changes; phytohormones andsecond messengers are the transducers of information from membranes tometabolism; carbon balance is the master integrator of plant response; betwixtand between, some genes are expressed more strongly, whereas others arerepressed. Reactive oxygen species play key roles in up- and down-regulation ofmetabolism and structure. The paper shows finally that the above concepts canbeapplied to plant tissue cultures where the accumulating physiological andgenetical deviations (from a normal plant behaviour) are related to thestressing conditions of the in vitro culture media and ofthe confined environment. The hyperhydrated state of shoots and the cancerousstate of cells, both induced under conditions of stress in invitro cultures, are identified and detailed, because they perfectlyillustrate the stress-induced state-change concept. It is concluded that stressresponses include either pathologies or adaptive advantages. Stress may thuscontain both destructive and constructive elements : it is a selection factoraswell as a driving force for improved resistance and adaptive evolution.     

Nucleopolyhedrovirus infection enhances plant defences by increasing plant volatile diversity

Plant–herbivore–entomopathogen tri-trophic interactions and biodiversity are relatively understudied topics in ecology. Particularly, the effects of entomopathogens on herbivore-induced plant volatiles and plant volatile diversity on the defensive function of plants have not been studied in detail. We used soybean (Glycine max), beet armyworm larvae (Spodoptera exigua), and nucleopolyhedrovirus (NPV) as a tri-trophic system to determine whether NPV infection can promote the emission and diversity of volatiles from plants. We also investigated whether NPV infection affects the attraction of Microplitis pallidipes, an important endoparasitoid of larval S. exigua. Uninfested soybean plants released 7 detectable volatile compounds while plants fed upon by healthy and NPV-infected S. exigua larvae released 12 and 15 volatiles, respectively. Female parasitoids were more attracted to the volatiles from plants that were fed upon by NPV-infected larvae than healthy larvae, and more attracted to the volatiles from plants that were fed upon by healthy larvae than no larvae. The selective responses of parasitoids to plant odours increased as plant volatile diversity increased. Our study suggests that the NPV infection facilitates the release of plant volatiles and enhances the defensive function of plants by increasing plant volatile diversity which in turn attracts more parasitoids. Also, this work reveals that plants might accrue two indirect benefits from NPV infection, cessation of herbivore feeding and more parasitisation.     

Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks

MicroRNAs (miRNAs) are key regulators of gene expression in development and stress responses in most eukaryotes. We globally profiled plant miRNAs in response to infection of bacterial pathogen Pseudomonas syringae pv. tomato (Pst). We sequenced 13 small-RNA libraries constructed from Arabidopsis at 6 and 14 h post infection of non-pathogenic, virulent and avirulent strains of Pst. We identified 15, 27 and 20 miRNA families being differentially expressed upon Pst DC3000 hrcC, Pst DC3000 EV and Pst DC3000 avrRpt2 infections, respectively. In particular, a group of bacteria-regulated miRNAs targets protein-coding genes that are involved in plant hormone biosynthesis and signaling pathways, including those in auxin, abscisic acid, and jasmonic acid pathways. Our results suggest important roles of miRNAs in plant defense signaling by regulating and fine-tuning multiple plant hormone pathways. In addition, we compared the results from sequencing-based profiling of a small set of miRNAs with the results from small RNA Northern blot and that from miRNA quantitative RT-PCR. Our results showed that although the deep-sequencing profiling results are highly reproducible across technical and biological replicates, the results from deep sequencing may not always be consistent with the results from Northern blot or miRNA quantitative RT-PCR. We discussed the procedural differences between these techniques that may cause the inconsistency.     

Neotropical plant morphology

An analysis on plant morphology and the sources that are important to the morphologic interpretations is done. An additional analysis is presented on all published papers in this subject by the Revista de Biología Tropical since its foundation, as well as its contribution to the plant morphology development in the neotropics.