Programmed cell death in the plant immune system

Cell death has a central role in innate immune responses in both plants and animals. Besides sharing striking convergences and similarities in the overall evolutionary organization of their innate immune systems, both plants and animals can respond to infection and pathogen recognition with programmed cell death. The fact that plant and animal pathogens have evolved strategies to subvert specific cell death modalities emphasizes the essential role of cell death during immune responses. The hypersensitive response (HR) cell death in plants displays morphological features, molecular architectures and mechanisms reminiscent of different inflammatory cell death types in animals (pyroptosis and necroptosis). In this review, we describe the molecular pathways leading to cell death during innate immune responses. Additionally, we present recently discovered caspase and caspase-like networks regulating cell death that have revealed fascinating analogies between cell death control across both kingdoms.     

Plasticity comparisons between plants and animals: Concepts and mechanisms

This review attempts to present an integrated update of the issue of comparisons of phenotypic plasticity between plants and animals by presenting the problem and its integrated solutions via a whole-organism perspective within an evolutionary framework. Plants and animals differ in two important aspects: mobility and longevity. These features can have important implications for plasticity, and plasticity may even have facilitated greater longevity in plants. Furthermore, somatic genetic mosaicism, intra-organismal selection, and genomic instability contribute to the maintenance of an adaptive phenotype that is especially relevant to long-lived plants. It is contended that a cross-kingdom phylogenetic examination of sensors, messengers and responses that constitute the plasticity repertoire would be more useful than dichotomizing the plant and animal kingdoms. Furthermore, physicochemical factors must be viewed cohesively in the signal reception and transduction pathways leading to plastic responses. Comparison of unitary versus modular organisms could also provide useful insights into the range of expected plastic responses. An integrated approach that combines evolutionary theory and evolutionary history with signal-response mechanisms will yield the most insights into phenotypic plasticity in all its forms.Key words: electrical signaling, genomic instability, mechanotransduction, phenotypic plasticity, plant volatiles, reactive oxygen species, ROS signaling     

ABA in bryophytes: how a universal growth regulator in life became a plant hormone?

Abscisic acid (ABA) is not a plant-specific compound but one found in organisms across kingdoms from bacteria to animals, suggesting that it is a ubiquitous and versatile substance that can modulate physiological functions of various organisms. Recent studies have shown that plants developed an elegant system for ABA sensing and early signal transduction mechanisms to modulate responses to environmental stresses for survival in terrestrial conditions. ABA-induced increase in stress tolerance has been reported not only in vascular plants but also in non-vascular bryophytes. Since bryophytes are the key group of organisms in the context of plant evolution, clarification of their ABA-dependent processes is important for understanding evolutionary adaptation of land plants. Molecular approaches using Physcomitrella patens have revealed that ABA plays a role in dehydration stress tolerance in mosses, which comprise a major group of bryophytes. Furthermore, we recently reported that signaling machinery for ABA responses is also conserved in liverworts, representing the most basal members of extant land plant lineage. Conservation of the mechanism for ABA sensing and responses in angiosperms and basal land plants suggests that acquisition of this mechanism for stress tolerance in vegetative tissues was one of the critical evolutionary events for adaptation to the land. This review describes the role of ABA in basal land plants as well as non-land plant organisms and further elaborates on recent progress in molecular studies of model bryophytes by comparative and functional genomic approaches.     

Generalized fire response strategies in plants and animals

Despite the existing large body of research on plant–animal interactions, plant research and animal research are still relatively independent and asymmetrical in relation to disturbance. Animals and plants are likely to have different fire responses, yet biodiversity studies in relation to disturbance may benefit from a more integrated functional approach across kingdoms. This would also force us to go deeper into the biological mechanisms and scales for persistence than a taxonomic‐based classification. An integrated view of plant and animal responses would enable us to learn from a great variety of life forms and benefit from expertise in complementary disciplines. To achieve this integrated view, I propose a functional classification for both plants and animals in relation to their fire response strategy. This classification includes the following strategies: resistance, refugia, avoidance, dormancy, recolonization, crypsis and intolerance. Given the limited knowledge of fire responses for many organisms, and especially for many animals, this classification may require further development. However, it provides a framework that facilitates finding knowledge gaps and directing future research for gaining a better understanding of the role of fire on biodiversity.     

Not plants or animals: a brief history of the origin of Kingdoms Protozoa, Protista and Protoctista.

In the wake of Darwin's evolutionary ideas, mid-nineteenth century naturalists realized the shortcomings of the long established two-kingdom system of organismal classification. Placement in a natural scheme of Protozoa, Protophyta, Phytozoa and Bacteria, microorganisms that exhibited plant-like and animal-like characteristics but obviously differed in organization from larger plants and animals, challenged traditional classification. The attempts of naturalists to classify these organisms outside the constraints of the plant and animal kingdoms led to concepts of additional kingdoms (Protozoa, Protista, Protoctista, etc.) to accommodate the nature of these organisms as not true plants or animals.     

Pollen and sperm heteromorphism: convergence across kingdoms?

Sperm competition theory predicts that males should produce many, similar sperm. However, in some species of animals and plants, males exhibit a heteromorphism that results in the production of at least two different types of sperm or pollen grains. In animals, sperm heteromorphism typically corresponds to the production of one fertile morph and one (or more) sterile morph(s), whereas in plants two or more pollen morphs (one of which can be either sterile or fertile) are produced in all flowers but sometimes in different anthers. Heteromorphism has arisen independently several times across phyla and at different phylogenetic levels. Here, we compare and contrast sperm and pollen heteromorphism and discuss the evolutionary hypotheses suggested to explain heteromorphism in these taxa. These hypotheses include facilitation, nutritive contribution, blocking, cheap filler, sperm flushing or killing for animals; outcrossing and precise cross-pollen transfer or bet-hedging strategy for plants; cryptic female choice for both. We conclude that heteromorphism in the two phyla is most likely linked to a general evolutionary response to sexual selection, either to increase one male's sperm or pollen success in competition with other males, or mediate male/female interactions. Therefore, although sperm and pollen are not homologous, we suggest that heteromorphism represents an example of convergence across kingdoms.     

Stem-cell niches: nursery rhymes across kingdoms

Despite the large evolutionary distance between the plant and animal kingdoms, stem cells in both reside in specialized cellular contexts called stem-cell niches. Although stem-cell-specification factors have been recruited from plant-specific gene families, maintenance factors that repress stem-cell differentiation are conserved between plants and animals. Recent evidence indicates that stem cells in multicellular organisms can be specified by kingdom-specific patterning mechanisms that connect to a related core of epigenetic stem-cell factors.     

Colonization outwith the colon: plants as an alternative environmental reservoir for human pathogenic enterobacteria

Members of the Enterobacteriaceae have the capacity to adapt to a wide variety of environments and can be isolated from a range of host species across biological kingdoms. Bacteria that are pathogenic to animals, in particular humans, are increasingly found to be transmitted through the food chain by fruits and vegetables. Rather than simply contaminating plant surfaces, there is a growing body of evidence to show that these bacteria actively interact with plants and can colonize them as alternative hosts. This review draws together evidence from studies that investigate proven and potential mechanisms involved in colonization of plants by human pathogenic enterobacteria.     

植物与草食动物之间的协同适应及进化

通常协同进化是指一个物种 (或种群 )的遗传结构由于回应于另一个物种 (或种群 )遗传结构的变化而发生的相应改变。广义的理解 ,协同进化是相互作用的物种之间的互惠进化。生物之间、特别是植物与草食动物之间的协同适应与进化 ,已经成为生物进化、生态、遗传等学科十分关注的问题 ,可能成为生物学中各学科研究的交汇点或结点。作者具体阐述了 :(1)生物之间协同进化的研究意义 ,包括对生物学与生态学的价值 ;(2 )生物之间协同进化研究的限制或困难 ,诸如时间、研究对象、进化等级尺度和研究方法的限制 ;(3)植物与草食动物之间协同进化的主要研究对象 (系统 ) ,即昆虫传粉系统、昆虫诱导植物反应系统、种子散布系统、以及大型草食动物采食与植物反应系统 ;(4 )植物与草食动物之间协同进化的主要研究内容 ,包括适应特征 (性状 )——物种的可塑性 ,以及适应机制——物种适应过程与策略两个方面 ;(5 )植物与草食动物之间协同进化研究的存在问题及研究方向     

Time zones: a comparative genetics of circadian clocks

The circadian clock is a widespread cellular mechanism that underlies diverse rhythmic functions in organisms from bacteria and fungi, to plants and animals. Intense genetic analysis during recent years has uncovered many of the components and molecular mechanisms comprising these clocks. Although autoregulatory genetic networks are a consistent feature in the design of all clocks, the weight of evidence favours their independent evolutionary origins in different kingdoms.     

Slicing across kingdoms: regeneration in plants and animals

Multicellular organisms possessing relatively long life spans are subjected to diverse, constant, and often intense intrinsic and extrinsic challenges to their survival. Animal and plant tissues wear out as part of normal physiological functions and can be lost to predators, disease, and injury. Both kingdoms survive this wide variety of insults by strategies that include the maintenance of adult stem cells or the induction of stem cell potential in differentiated cells. Repatterning mechanisms often deploy embryonic genes, but the question remains in both plants and animals whether regeneration invokes embryogenesis, generic patterning mechanisms, or unique circuitry comprised of well-established patterning genes.     

Ferritin gene organization: Differences between plants and animals suggest possible kingdom-specific selective constraints

Ferritin, a protein widespread in nature, concentrates iron ∼10¹¹–10¹²-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor (based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization in plants and animals, made possible by the cloning of a dicot (soybean) ferritin gene presented here and the recent cloning of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In plant ferritin genes, the number of introns (n= 7) is higher than in animals (n= 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding sequences and the high conservation of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid, the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling. Received: 25 July 1995 / Accepted: 3 October 1995     

Induction of plant responses to oviposition and feeding by herbivorous arthropods: a comparison

Plants may respond both to feeding and oviposition by herbivorous insects. While responses of plants to feeding damage by herbivores have been studied intensively during the past decades, only a few, but growing number of studies consider the reactions of plants towards egg deposition by herbivorous insects. Plants showing defensive response to oviposition by herbivores do not `wait' until being damaged by feeding, but may instead react towards one of the initial steps of herbivore attack, the egg deposition. Direct plant defensive responses to feeding act directly against the feeding stages of the herbivores. However, a plant may also show direct defensive responses to egg deposition by (a) formation of neoplasms, (b) formation of necrotic tissue (= hypersensitive response), and (c) production of oviposition deterrents. All these plant reactions have directly negative effects on the eggs, hatching larvae, or on the ovipositing females. Indirect plant defensive responses to feeding result in the emission of volatiles (= synomones) that attract predators or parasitoids of the feeding stages. A few recent studies have shown that plants are able to emit volatiles also in response to egg deposition and that these volatiles attract egg parasitoids. Studies on the mechanisms of induction of synomones by egg deposition show several parallels to the mechanisms of induction of plant responses by feeding damage. When considering induced plant defence against herbivores from an evolutionary point of view, the question arises whether herbivores evolved the ability to circumvent or even to exploit the plant's defensive responses. The reactions of herbivores to oviposition induced plant responses are compared with their reactions to feeding induced plant responses.     

Polar delivery in plants; commonalities and differences to animal epithelial cells

Although plant and animal cells use a similar core mechanism to deliver proteins to the plasma membrane, their different lifestyle, body organization and specific cell structures resulted in the acquisition of regulatory mechanisms that vary in the two kingdoms. In particular, cell polarity regulators do not seem to be conserved, because genes encoding key components are absent in plant genomes. In plants, the broad knowledge on polarity derives from the study of auxin transporters, the PIN-FORMED proteins, in the model plant Arabidopsis thaliana. In animals, much information is provided from the study of polarity in epithelial cells that exhibit basolateral and luminal apical polarities, separated by tight junctions. In this review, we summarize the similarities and differences of the polarization mechanisms between plants and animals and survey the main genetic approaches that have been used to characterize new genes involved in polarity establishment in plants, including the frequently used forward and reverse genetics screens as well as a novel chemical genetics approach that is expected to overcome the limitation of classical genetics methods.     

Phylogenetic analysis of the UDP-glycosyltransferase multigene family of Arabidopsis thaliana

A class of UDP-glycosyltransferases (UGTs) defined by the presence of a C-terminal consensus sequence is found throughout the plant and animal kingdoms. Whereas mammalian enzymes use UDP-glucuronic acid, the plant enzymes typically use UDP-glucose in the transfer reactions. A diverse array of aglycones can be glucosylated by these UGTs. In plants, the aglycones include plant hormones, secondary metabolites involved in stress and defense responses, and xenobiotics such as herbicides. Glycosylation is known to regulate many properties of the aglycones such as their bioactivity, their solubility, and their transport properties within the cell and throughout the plant. As a means of providing a framework to start to understand the substrate specificities and structure-function relationships of plant UGTs, we have now applied a molecular phylogenetic analysis to the multigene family of 99 UGT sequences in Arabidopsis. We have determined the overall organization and evolutionary relationships among individual members with a surprisingly high degree of confidence. Through constructing a composite phylogenetic tree that also includes all of the additional plant UGTs with known catalytic activities, we can start to predict both the evolutionary history and substrate specificities of new sequences as they are identified. The tree already suggests that while the activities of some subgroups of the UGT family are highly conserved among different plant species, others subgroups shift substrate specificity with relative ease.     

A meta‐analysis of the strength and nature of cytoplasmic genetic effects

Genetic variation in cytoplasmic genomes (i.e. the mitochondrial genome in animals, and the combined mitochondrial and chloroplast genomes in plants) was traditionally assumed to accumulate under a neutral equilibrium model. This view has, however, come under increasing challenge from studies that have experimentally linked cytoplasmic genetic effects to the expression of life history phenotypes. Such results suggest that genetic variance located within the cytoplasm might be of evolutionary importance and potentially involved in shaping population evolutionary trajectories. As a step towards assessing this assertion, here we conduct a formal meta‐analytic review to quantitatively assess the extent to which cytoplasmic genetic effects contribute to phenotypic expression across animal and plant kingdoms. We report that cytoplasmic effect sizes are generally moderate in size and associated with variation across a range of factors. Specifically, cytoplasmic effects on morphological traits are generally larger than those on life history or metabolic traits. Cytoplasmic effect sizes estimated at the between‐species scale (via interspecies mix‐and‐matching of cytoplasmic and nuclear genomes) are larger than those at the within‐species scale. Furthermore, cytoplasmic effects tied to epistatic interactions with the nuclear genome tend to be stronger than additive cytoplasmic effects, at least when restricting the data set to gonochorous animal species. Our results thus confirm that cytoplasmic genetic variation is commonly tied to phenotypic expression across plants and animals, implicate the cytoplasmic–nuclear interaction as a key unit on which natural selection acts and generally suggest that the genetic variation that lies within the cytoplasm is likely to be entwined in adaptive evolutionary processes.     

No escape: The influence of substrate sodium on plant growth and tissue sodium responses

1. As an essential micronutrient for many organisms, sodium plays an important role in ecological and evolutionary dynamics. Although plants mediate trophic fluxes of sodium, from substrates to higher trophic levels, relatively little comparative research has been published about plant growth and sodium accumulation in response to variation in substrate sodium. Accordingly, we carried out a systematic review of plants'' responses to variation in substrate sodium concentrations.
2. We compared biomass and tissue‐sodium accumulation among 107 cultivars or populations (67 species in 20 plant families), broadly expanding beyond the agricultural and model taxa for which several generalizations previously had been made. We hypothesized a priori response models for each population''s growth and sodium accumulation as a function of increasing substrate NaCl and used Bayesian Information Criterion to choose the best model. Additionally, using a phylogenetic signal analysis, we tested for phylogenetic patterning of responses across taxa.
3. The influence of substrate sodium on growth differed across taxa, with most populations experiencing detrimental effects at high concentrations. Irrespective of growth responses, tissue sodium concentrations for most taxa increased as sodium concentration in the substrate increased. We found no strong associations between the type of growth response and the type of sodium accumulation response across taxa. Although experiments often fail to test plants across a sufficiently broad range of substrate salinities, non‐crop species tended toward higher sodium tolerance than domesticated species. Moreover, some phylogenetic conservatism was apparent, in that evolutionary history helped predict the distribution of total‐plant growth responses across the phylogeny, but not sodium accumulation responses.
4. Our study reveals that saltier plants in saltier soils proves to be a broadly general pattern for sodium across plant taxa. Regardless of growth responses, sodium accumulation mostly followed an increasing trend as substrate sodium levels increased.

     

Recent advances in plant immunity: recognition, signaling, response, and evolution

Innate immune system is employed by plants to defend against phytopathogenic microbes through specific perception of non-self molecules and subsequent initiation of resistance responses. Current researches elucidate that plants mostly rely on cell surface-located pattern recognition receptors (PRRs) and intracellular nucleotide-binding leucine-rich repeat proteins (NB-LRRs) to recognize pathogen-associated molecular patterns (PAMPs) and effector proteins from microbial pathogens, initiating PAMP- and effector-triggered immunity (PTI and ETI), respectively. Some pathogenic bacterial effector proteins are usually secreted into plant cells and play a virulence function by suppressing plant PTI, implying an evolutionary process of plant immunity from PTI to ETI. In the past several years, a great progress has been achieved to reveal fascinating molecular mechanisms underlying the pathogenic recognition, resistance signaling transduction, and plant immunity evolution. Here, we summarized the latest breakthroughs about these topics, and offered an integral understanding of plant molecular immunity.