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Plant, Cell & Environment Feb 2019Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide... (Review)
Review
Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.
Topics: Plant Physiological Phenomena; Plant Proteins; Plants; Protein Interaction Mapping
PubMed: 30156707
DOI: 10.1111/pce.13433 -
International Journal of Molecular... Jan 2022Cold stress limits plant geographical distribution and influences plant growth, development, and yields. Plants as sessile organisms have evolved complex biochemical and... (Review)
Review
Cold stress limits plant geographical distribution and influences plant growth, development, and yields. Plants as sessile organisms have evolved complex biochemical and physiological mechanisms to adapt to cold stress. These mechanisms are regulated by a series of transcription factors and proteins for efficient cold stress acclimation. It has been established that the signaling pathway in plants regulates how plants acclimatize to cold stress. Cold stress is perceived by receptor proteins, triggering signal transduction, and () genes are activated and regulated, consequently upregulating the transcription and expression of the () genes. The protein binds to the (), a homeopathic element of the genes ( gene) promoter, activating their transcription. Transcriptional regulations and post-translational modifications regulate and modify these entities at different response levels by altering their expression or activities in the signaling cascade. These activities then lead to efficient cold stress tolerance. This paper contains a concise summary of the pathway elucidating on the cross interconnections with other repressors, inhibitors, and activators to induce cold stress acclimation in plants.
Topics: Cold-Shock Response; Gene Expression Regulation, Plant; Plant Physiological Phenomena; Plant Proteins; Protein Processing, Post-Translational; Signal Transduction; Trans-Activators; Transcriptional Activation
PubMed: 35163471
DOI: 10.3390/ijms23031549 -
Molecules (Basel, Switzerland) Nov 2016This review provides a historical overview of the research on plant ribosome-inactivating proteins (RIPs), starting from the first studies at the end of eighteenth... (Review)
Review
This review provides a historical overview of the research on plant ribosome-inactivating proteins (RIPs), starting from the first studies at the end of eighteenth century involving the purification of abrin and ricin, as well as the immunological experiments of Paul Erlich. Interest in these plant toxins was revived in 1970 by the observation of their anticancer activity, which has given rise to a large amount of research contributing to the development of various scientific fields. Biochemistry analyses succeeded in identifying the enzymatic activity of RIPs and allowed for a better understanding of the ribosomal machinery. Studies on RIP/cell interactions were able to detail the endocytosis and intracellular routing of ricin, thus increasing our knowledge of how cells handle exogenous proteins. The identification of new RIPs and the finding that most RIPs are single-chain polypeptides, together with their genetic sequencing, has aided in the development of new phylogenetic theories. Overall, the biological properties of these proteins, including their abortifacient, anticancer, antiviral and neurotoxic activities, suggest that RIPs could be utilized in agriculture and in many biomedical fields, including clinical drug development.
Topics: Animals; Endocytosis; Humans; Immunotoxins; Phylogeny; Plant Proteins; Protein Conformation; Ribosome Inactivating Proteins
PubMed: 27898041
DOI: 10.3390/molecules21121627 -
International Journal of Molecular... Mar 2020Lateral organ boundaries (LOB) domain () genes, a gene family encoding plant-specific transcription factors, play important roles in plant growth and development. At... (Review)
Review
Lateral organ boundaries (LOB) domain () genes, a gene family encoding plant-specific transcription factors, play important roles in plant growth and development. At present, though there have been a number of genome-wide analyses on gene families and functional studies on individual LBD proteins, the diverse functions of LBD family members still confuse researchers and an effective strategy is required to summarize their functional diversity. To further integrate and improve our understanding of the phylogenetic classification, functional characteristics and regulatory mechanisms of LBD proteins, we review and discuss the functional characteristics of LBD proteins according to their classifications under a phylogenetic framework. It is proved that this strategy is effective in the anatomy of diverse functions of LBD family members. Additionally, by phylogenetic analysis, one monocot-specific and one eudicot-specific subclade of LBD proteins were found and their biological significance in monocot and eudicot development were also discussed separately. The review will help us better understand the functional diversity of LBD proteins and facilitate further studies on this plant-specific transcription factor family.
Topics: Conserved Sequence; Phylogeny; Plant Proteins; Protein Domains; Transcription Factors
PubMed: 32224847
DOI: 10.3390/ijms21072278 -
Peptides Oct 2021Plants have evolved diverse peptide hormones and cognate receptors to orchestrate plant growth and development. Secreted peptide ligands are mainly sensed by membrane... (Review)
Review
Plants have evolved diverse peptide hormones and cognate receptors to orchestrate plant growth and development. Secreted peptide ligands are mainly sensed by membrane receptor kinases that mediate cell-cell communication. The secreted peptides are categorized into two groups: small linear post-translationally modified peptides and cysteine-rich peptides. The small linear peptides are recognized by the corresponding receptors and co-receptors in a conserved manner. By contrast, the cysteine-rich peptides are perceived by various types of receptor proteins using diverse binding modes. Recent studies have revealed the molecular and mechanistic origins of peptide recognition and receptor activation. This review summarizes plant-peptide binding modes and receptor-activation mechanisms that have been structurally characterized in recent studies.
Topics: Peptides; Plant Proteins; Protein Kinases; Receptors, Cell Surface
PubMed: 34332962
DOI: 10.1016/j.peptides.2021.170614 -
Current Opinion in Plant Biology Apr 2016Fifteen years into sequencing entire plant genomes, more than 30 paleopolyploidy events could be mapped on the tree of flowering plants (and many more when also... (Review)
Review
Fifteen years into sequencing entire plant genomes, more than 30 paleopolyploidy events could be mapped on the tree of flowering plants (and many more when also transcriptome data sets are considered). While some genome duplications are very old and have occurred early in the evolution of dicots and monocots, or even before, others are more recent and seem to have occurred independently in many different plant lineages. Strikingly, a majority of these duplications date somewhere between 55 and 75 million years ago (mya), and thus likely correlate with the K/Pg boundary. If true, this would suggest that plants that had their genome duplicated at that time, had an increased chance to survive the most recent mass extinction event, at 66mya, which wiped out a majority of plant and animal life, including all non-avian dinosaurs. Here, we review several processes, both neutral and adaptive, that might explain the establishment of polyploid plants, following the K/Pg mass extinction.
Topics: Biological Evolution; Evolution, Molecular; Genome, Plant; Phylogeny; Plant Proteins; Polyploidy
PubMed: 26894611
DOI: 10.1016/j.pbi.2016.01.006 -
International Journal of Molecular... Feb 2021Plants are constantly exposed to a wide range of potential pathogens and to protect themselves, have developed a variety of chemical and physical defense mechanisms.... (Review)
Review
Plants are constantly exposed to a wide range of potential pathogens and to protect themselves, have developed a variety of chemical and physical defense mechanisms. Callose is a β-(1,3)-D-glucan that is widely distributed in higher plants. In addition to its role in normal growth and development, callose plays an important role in plant defense. Callose is deposited between the plasma membrane and the cell wall at the site of pathogen attack, at the plasmodesmata, and on other plant tissues to slow pathogen invasion and spread. Since it was first reported more than a century ago, defense-related callose deposition has been extensively studied in a wide-spectrum of plant-pathogen systems. Over the past 20 years or so, a large number of studies have been published that address the dynamic nature of pathogen-induced callose deposition, the complex regulation of synthesis and transport of defense-related callose and associated callose synthases, and its important roles in plant defense responses. In this review, we summarize our current understanding of the regulation and function of defense-related callose deposition in plants and discuss both the progresses and future challenges in addressing this complex defense mechanism as a critical component of a plant immune system.
Topics: Gene Expression Regulation, Plant; Glucans; Glucosyltransferases; Host-Pathogen Interactions; Plant Physiological Phenomena; Plant Proteins
PubMed: 33673633
DOI: 10.3390/ijms22052393 -
Molecular Plant Jan 2021The endoplasmic reticulum, chloroplasts, and mitochondria are major plant organelles for protein synthesis, photosynthesis, metabolism, and energy production. Protein... (Review)
Review
The endoplasmic reticulum, chloroplasts, and mitochondria are major plant organelles for protein synthesis, photosynthesis, metabolism, and energy production. Protein homeostasis in these organelles, maintained by a balance between protein synthesis and degradation, is essential for cell functions during plant growth, development, and stress resistance. Nucleus-encoded chloroplast- and mitochondrion-targeted proteins and ER-resident proteins are imported from the cytosol and undergo modification and maturation within their respective organelles. Protein folding is an error-prone process that is influenced by both developmental signals and environmental cues; a number of mechanisms have evolved to ensure efficient import and proper folding and maturation of proteins in plant organelles. Misfolded or damaged proteins with nonnative conformations are subject to degradation via complementary or competing pathways: intraorganelle proteases, the organelle-associated ubiquitin-proteasome system, and the selective autophagy of partial or entire organelles. When proteins in nonnative conformations accumulate, the organelle-specific unfolded protein response operates to restore protein homeostasis by reducing protein folding demand, increasing protein folding capacity, and enhancing components involved in proteasome-associated protein degradation and autophagy. This review summarizes recent progress on the understanding of protein quality control in the ER, chloroplasts, and mitochondria in plants, with a focus on common mechanisms shared by these organelles during protein homeostasis.
Topics: Homeostasis; Organelles; Plant Proteins; Protein Folding; Proteolysis; Unfolded Protein Response
PubMed: 33137518
DOI: 10.1016/j.molp.2020.10.011 -
Molecular Plant Aug 2015The plant hormone auxin regulates numerous aspects of plant growth and development. Early auxin response genes mediate its genomic effects on plant growth and... (Review)
Review
The plant hormone auxin regulates numerous aspects of plant growth and development. Early auxin response genes mediate its genomic effects on plant growth and development. Discovered in 1987, small auxin up RNAs (SAURs) are the largest family of early auxin response genes. SAUR functions have remained elusive, however, presumably due to extensive genetic redundancy. However, recent molecular, genetic, biochemical, and genomic studies have implicated SAURs in the regulation of a wide range of cellular, physiological, and developmental processes. Recently, crucial mechanistic insight into SAUR function was provided by the demonstration that SAURs inhibit PP2C.D phosphatases to activate plasma membrane (PM) H(+)-ATPases and promote cell expansion. In addition to auxin, several other hormones and environmental factors also regulate SAUR gene expression. We propose that SAURs are key effector outputs of hormonal and environmental signals that regulate plant growth and development.
Topics: Biological Transport; Environment; Plant Development; Plant Growth Regulators; Plant Proteins; Signal Transduction
PubMed: 25983207
DOI: 10.1016/j.molp.2015.05.003 -
Current Opinion in Plant Biology Aug 2017Plant pathogens are a serious threat to agriculture and to global food security, causing diverse crop diseases which lead to extensive annual yield losses. Production of... (Review)
Review
Plant pathogens are a serious threat to agriculture and to global food security, causing diverse crop diseases which lead to extensive annual yield losses. Production of effector proteins by pathogens, to manipulate host cellular processes, is central to their success. An understanding of fundamental effector biology is key to addressing the threat posed by these pathogens. Recent advances in 'omics' technologies have facilitated high-throughput identification of putative effector proteins, while evolving cellular, structural and biochemical approaches have assisted in characterising their function. Furthermore, structures of effectors in complex with host factors now provide opportunities for applying our knowledge of effector biology to influence disease outcomes. In this review, we highlight recent advances in the field and suggest avenues for future research.
Topics: Agriculture; Host-Pathogen Interactions; Plant Diseases; Plant Proteins
PubMed: 28460241
DOI: 10.1016/j.pbi.2017.04.013