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Annual Review of Cell and Developmental... 2015Plant-pathogen interactions can result in dramatic visual changes in the host, such as galls, phyllody, pseudoflowers, and altered root-system architecture, indicating... (Review)
Review
Plant-pathogen interactions can result in dramatic visual changes in the host, such as galls, phyllody, pseudoflowers, and altered root-system architecture, indicating that the invading microbe has perturbed normal plant growth and development. These effects occur on a cellular level but range up to the organ scale, and they commonly involve attenuation of hormone homeostasis and deployment of effector proteins with varying activities to modify host cell processes. This review focuses on the cellular-reprogramming mechanisms of filamentous and bacterial plant pathogens that exhibit a biotrophic lifestyle for part, if not all, of their lifecycle in association with the host. We also highlight strategies for exploiting our growing knowledge of microbial host reprogramming to study plant processes other than immunity and to explore alternative strategies for durable plant resistance.
Topics: Bacteria; Fungi; Host-Pathogen Interactions; Plant Diseases; Plant Roots; Plants
PubMed: 26436707
DOI: 10.1146/annurev-cellbio-102314-112502 -
Biochimica Et Biophysica Acta. Gene... Jan 2017Regulation of gene expression depends on specific cis-regulatory sequences located in the gene promoter regions. These DNA sequences are recognized by transcription... (Review)
Review
Regulation of gene expression depends on specific cis-regulatory sequences located in the gene promoter regions. These DNA sequences are recognized by transcription factors (TFs) in a sequence-specific manner, and their identification could help to elucidate the regulatory networks that underlie plant physiological responses to developmental programs or to environmental adaptation. Here we review recent advances in high throughput methodologies for the identification of plant TF binding sites. Several approaches offer a map of the TF binding locations in vivo and of the dynamics of the gene regulatory networks. As an alternative, high throughput in vitro methods provide comprehensive determination of the DNA sequences recognized by TFs. These advances are helping to decipher the regulatory lexicon and to elucidate transcriptional network hierarchies in plants in response to internal or external cues. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
Topics: Binding Sites; Gene Expression Regulation, Plant; Gene Regulatory Networks; Plants; Promoter Regions, Genetic; Protein Binding; Transcription Factors
PubMed: 27155066
DOI: 10.1016/j.bbagrm.2016.05.001 -
Biochimica Et Biophysica Acta. Gene... Jan 2017Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental... (Review)
Review
Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
Topics: DNA, Plant; DNA-Binding Proteins; Evolution, Molecular; Gene Expression Regulation, Plant; Plant Proteins; Plants; Transcription Factors; Transcription, Genetic
PubMed: 27522016
DOI: 10.1016/j.bbagrm.2016.08.005 -
Plant Science : An International... Mar 2015The genomic makeup and phenotypes of plants are diversifying, in part due to artificial or natural selection in agricultural and natural environments. Utilization of... (Review)
Review
The genomic makeup and phenotypes of plants are diversifying, in part due to artificial or natural selection in agricultural and natural environments. Utilization of these variations to enhance crop productivity requires an understanding of the relationships between genotype and phenotype in inbreds and hybrids derived from crosses between these populations. This review highlights recent studies on hybrid vigor (heterosis) and the related phenomenon of hybrid weakness - two types of non-additive inheritance. Heterosis is a phenomenon whereby the phenotype of first-generation hybrids is superior to that of their parents. Intralocus interactions between alleles, complementation of dominant alleles, or inter-loci epistatic interactions are genetic mechanisms that may cause non-additive phenotypic inheritance in hybrids. However, there are different views on what portion of the heterotic variation is modulated by each of these mechanisms. Another aspect of plant vigor is phenotypic stability or robustness in different environments and how this is influenced by gene heterozygosity. Hybrids are not necessarily more phenotypically stable than inbreds since local heterozygosity might be associated with negative effects on biochemical activities. This review integrates genetic and biochemical considerations to illustrate how these relationships may be tightly linked with breeding system and sequence divergence.
Topics: Genotype; Heterozygote; Hybrid Vigor; Hybridization, Genetic; Phenotype; Plants
PubMed: 25617321
DOI: 10.1016/j.plantsci.2014.11.014 -
Biological Reviews of the Cambridge... Jun 2019The biota of New Caledonia is one of the most unusual in the world. It displays high diversity and endemism, many peculiar absences, and far-flung biogeographic... (Review)
Review
The biota of New Caledonia is one of the most unusual in the world. It displays high diversity and endemism, many peculiar absences, and far-flung biogeographic affinities. For example, New Caledonia is the only place on Earth with both main clades of flowering plants - the endemic Amborella and 'all the rest', and it also has the highest concentration of diversity in conifers. The discovery of Amborella's phylogenetic position led to a surge of interest in New Caledonian biogeography, and new studies are appearing at a rapid rate. This paper reviews work on the topic (mainly molecular studies) published since 2013. One current debate is focused on whether any biota survived the marine transgressions of the Paleocene and Eocene. Total submersion would imply that the entire fauna was derived by long-distance dispersal from continental areas since the Eocene, but only if no other islands (now submerged) were emergent. A review of the literature suggests there is little actual evidence in geology for complete submersion. An alternative explanation for New Caledonia's diversity is that the archipelago acted as a refugium, and that the biota avoided the extinctions that occurred in Australia. However, this is contradicted by the many groups that are anomalously absent or depauperate in New Caledonia, although represented there by a sister group. The anomalous absences, together with the unusual levels of endemism, can both be explained by vicariance at breaks in and around New Caledonia. New Caledonia has always been situated at or near a plate boundary, and its complex geological history includes the addition of new terranes (by accretion), orogeny, and rifting. New Caledonia comprises 'basement' terranes that were part of Gondwana, as well as island arc and forearc terranes that accreted to the basement after it separated from Gondwana. The regional tectonic history helps explain the regional biogeography, as well as distribution patterns within New Caledonia. These include endemics on the basement terranes (for example, the basal angiosperm, Amborella), disjunctions at the West Caledonian fault zone, and great biotic differences between Grande Terre and the Loyalty Islands.
Topics: Biodiversity; Biological Evolution; Demography; New Caledonia; Phylogeny; Plants
PubMed: 30523662
DOI: 10.1111/brv.12485 -
Protoplasma Jan 2022Plants are characterized by a post-embryonic mode of organ development, which results in a need for these photoautotrophic organisms to regenerate lost parts in the... (Review)
Review
Plants are characterized by a post-embryonic mode of organ development, which results in a need for these photoautotrophic organisms to regenerate lost parts in the course of their life cycle. This capacity depends on the presence of "pluripotent stem cells," which are part of the meristems within the plant body. One hundred years ago, the botanist Gottlieb Haberlandt (1854-1945) published experiments showing wounding-induced callus formation, which led ultimately to plant regeneration in tissue culture and thence to the techniques of "plant biotechnology," with practical applications for mankind. Here, we recount Haberlandt's discovery within the context of his long research life and his most influential book Physiologische Pflanzenanatomie. In the second part, we describe and analyze a plant tissue-culture regeneration system using sterile, dark-grown sunflower (Helianthus annuus) seedlings as experimental material. We document that excised hook segments, which contain a "stem cell niche," can regenerate entire miniature H. annuus-plantlets that, raised in a light/dark regime, develop flowers. Finally, we discuss molecular data relevant to plant regeneration with reference to phytohormones and conclude that, one century after Haberlandt, 1921, the exact biochemical/genetic mechanisms responsible for the capability of stem cells to remain "forever young" are, although already complex, really just beginning to become known.
Topics: Helianthus; Plant Growth Regulators; Plants; Seedlings; Stem Cells
PubMed: 34292403
DOI: 10.1007/s00709-021-01683-5 -
International Journal of Molecular... Mar 2021Adaptation and response to environmental changes require dynamic and fast information distribution within the plant body. If one part of a plant is exposed to stress,... (Review)
Review
Adaptation and response to environmental changes require dynamic and fast information distribution within the plant body. If one part of a plant is exposed to stress, attacked by other organisms or exposed to any other kind of threat, the information travels to neighboring organs and even neighboring plants and activates appropriate responses. The information flow is mediated by fast-traveling small metabolites, hormones, proteins/peptides, RNAs or volatiles. Electric and hydraulic waves also participate in signal propagation. The signaling molecules move from one cell to the neighboring cell, via the plasmodesmata, through the apoplast, within the vascular tissue or-as volatiles-through the air. A threat-specific response in a systemic tissue probably requires a combination of different traveling compounds. The propagating signals must travel over long distances and multiple barriers, and the signal intensity declines with increasing distance. This requires permanent amplification processes, feedback loops and cross-talks among the different traveling molecules and probably a short-term memory, to refresh the propagation process. Recent studies show that volatiles activate defense responses in systemic tissues but also play important roles in the maintenance of the propagation of traveling signals within the plant. The distal organs can respond immediately to the systemic signals or memorize the threat information and respond faster and stronger when they are exposed again to the same or even another threat. Transmission and storage of information is accompanied by loss of specificity about the threat that activated the process. I summarize our knowledge about the proposed long-distance traveling compounds and discuss their possible connections.
Topics: Biological Transport; Biomarkers; Calcium; Disease Resistance; Electrophysiological Phenomena; Environment; Host-Pathogen Interactions; Light; Organ Specificity; Photosynthesis; Phytochrome; Plant Diseases; Plant Physiological Phenomena; Plants; RNA, Plant; Reactive Oxygen Species; Signal Transduction; Volatile Organic Compounds
PubMed: 33808792
DOI: 10.3390/ijms22063152 -
Current Pharmaceutical Biotechnology 2015Protein-based biopharmaceuticals are often produced in mammalian cell cultures, which are more expensive than microbial systems but capable of authentic... (Review)
Review
Protein-based biopharmaceuticals are often produced in mammalian cell cultures, which are more expensive than microbial systems but capable of authentic post-translational modifications. The costs are lower if plants are used as an alternative platform to produce complex proteins such as monoclonal antibodies, vaccines and enzymes. This review highlights recent advances that have been achieved in plant-based biopharmaceutical production platforms in terms of expression strategies, product yields and process development. The first generation of plant-derived pharmaceuticals now entering the market is also discussed. Finally, the review considers the downstream processing of plant-derived pharmaceuticals which can account for up to 80% of the production costs. In this context, recent improvements in clarification and integrated process methods will have a strong impact on the economic feasibility of production, especially if supported by and combined with process analytical technology as part of the quality-by-design initiative.
Topics: Animals; Biomass; Gene Expression Regulation, Plant; Humans; Molecular Farming; Plant Proteins; Plants, Genetically Modified; Technology, Pharmaceutical
PubMed: 26343135
DOI: 10.2174/138920101611150902115413 -
Plant Science : An International... Jan 2023The plant science community has identified various regulatory components involved in gene expression. With the advancement of approaches and technologies, new layers of... (Review)
Review
The plant science community has identified various regulatory components involved in gene expression. With the advancement of approaches and technologies, new layers of gene regulation have been identified, which play essential roles in fine-tuning biological processes. In this area, recently, small peptides emerged as key regulators in gene regulation to control developmental and physiological processes in plants. Various small peptides have also been identified and characterized to elucidate their roles. A class of small peptides, microProteins (miPs), have been shown to contain at least a protein-protein interaction domain with the potential to regulate multi-domain proteins by becoming a part of protein complexes. Recent studies suggest that some pri-miRNAs encode peptides (miPEPs), which are essential components in plant growth and development. This review provides updates about these small peptides, in general, summarizing their potential role in gene regulation and possible mechanism(s) in plants. We also propose that in-depth research on newly identified plant peptides in crops help to provide solutions enabling sustainable agriculture and food production.
Topics: Gene Expression Regulation, Plant; MicroRNAs; Plants; Peptides; Micropeptides
PubMed: 36330966
DOI: 10.1016/j.plantsci.2022.111519 -
International Journal of Molecular... Apr 2019Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental... (Review)
Review
Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as 'omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined.
Topics: Bacteria; Cell Wall; Endophytes; Plant Development; Plants; Signal Transduction
PubMed: 31010043
DOI: 10.3390/ijms20081947