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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... 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 -
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 -
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 -
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 -
Biochemical Society Transactions Apr 2021Asparaginyl endopeptidases (AEPs) are versatile enzymes that in biological systems are involved in producing three different catalytic outcomes for proteins, namely (i)... (Review)
Review
Asparaginyl endopeptidases (AEPs) are versatile enzymes that in biological systems are involved in producing three different catalytic outcomes for proteins, namely (i) routine cleavage by bond hydrolysis, (ii) peptide maturation, including macrocyclisation by a cleavage-coupled intramolecular transpeptidation and (iii) circular permutation involving separate cleavage and transpeptidation reactions resulting in a major reshuffling of protein sequence. AEPs differ in their preference for cleavage or transpeptidation reactions, catalytic efficiency, and preference for asparagine or aspartate target residues. We look at structural analyses of various AEPs that have laid the groundwork for identifying important determinants of AEP function in recent years, with much of the research impetus arising from the potential biotechnological and pharmaceutical applications.
Topics: Catalytic Domain; Cysteine Endopeptidases; Hydrolysis; Molecular Dynamics Simulation; Peptides; Plant Proteins; Protein Binding; Protein Conformation; Seed Storage Proteins; Substrate Specificity
PubMed: 33666219
DOI: 10.1042/BST20200908 -
Protein Science : a Publication of the... Feb 2008Plant lipid-transfer proteins (LTPs) are abundant, small, lipid binding proteins that are capable of exchanging lipids between membranes in vitro. Despite their name, a... (Review)
Review
Plant lipid-transfer proteins (LTPs) are abundant, small, lipid binding proteins that are capable of exchanging lipids between membranes in vitro. Despite their name, a role in intracellular lipid transport is considered unlikely, based on their extracellular localization. A number of other biological roles, including antimicrobial defense, signaling, and cell wall loosening, have been proposed, but conclusive evidence is generally lacking, and these functions are not well correlated with in vitro activity or structure. A survey of sequenced plant genomes suggests that the two biochemically characterized families of LTPs are phylogenetically restricted to seed plants and are present as substantial gene families. This review aims to summarize the current understanding of LTP biochemistry, as well as the evidence supporting the proposed in vivo roles of these proteins within the emerging post-genomic framework.
Topics: Antigens, Plant; Carrier Proteins; Evolution, Molecular; Genes, Plant; Models, Molecular; Plant Proteins; Plants; Protein Conformation; Seeds
PubMed: 18096636
DOI: 10.1110/ps.073300108 -
Cellular and Molecular Life Sciences :... Apr 2008The zinc finger domain enables different proteins to interact with or bind DNA, RNA, or other proteins, and is present in the proteomes of many different organisms.... (Review)
Review
The zinc finger domain enables different proteins to interact with or bind DNA, RNA, or other proteins, and is present in the proteomes of many different organisms. Proteins containing zinc finger domain(s) were found to play important roles in eukaryotic cells regulating different signal transduction pathways and controlling processes, such as development and programmed cell death. There are many types of zinc finger proteins, classified according to the number and order of the Cys and His residues that bind the Zinc ion. Among these, the C2H2-type zinc finger proteins, with 176 members in Arabidopsis thaliana, constitute one of the largest families of transcriptional regulators in plants. They are mostly plant-specific and contain a conserved QALGGH sequence within their zinc finger domain. Recent studies revealed that C2H2 zinc finger proteins could function as key transcriptional repressors involved in the defense and acclimation response of plants to different environmental stress conditions. Here we highlight recent functional characterization studies of different C2H2 proteins in Arabidopsis, and suggest that many of these proteins function as part of a large regulatory network that senses and responds to different environmental stimuli.
Topics: Amino Acid Sequence; Molecular Sequence Data; Plant Proteins; Plants; Zinc Fingers
PubMed: 18193167
DOI: 10.1007/s00018-007-7473-4 -
Molecular Plant Pathology Jun 2023The pathogenesis-related (PR) proteins of plants have originally been identified as proteins that are strongly induced upon biotic and abiotic stress. These proteins... (Review)
Review
The pathogenesis-related (PR) proteins of plants have originally been identified as proteins that are strongly induced upon biotic and abiotic stress. These proteins fall into 17 distinct classes (PR1-PR17). The mode of action of most of these PR proteins has been well characterized, except for PR1, which belongs to a widespread superfamily of proteins that share a common CAP domain. Proteins of this family are not only expressed in plants but also in humans and in many different pathogens, including phytopathogenic nematodes and fungi. These proteins are associated with a diverse range of physiological functions. However, their precise mode of action has remained elusive. The importance of these proteins in immune defence is illustrated by the fact that PR1 overexpression in plants results in increased resistance against pathogens. However, PR1-like CAP proteins are also produced by pathogens and deletion of these genes results in reduced virulence, suggesting that CAP proteins can exert both defensive and offensive functions. Recent progress has revealed that plant PR1 is proteolytically cleaved to release a C-terminal CAPE1 peptide, which is sufficient to activate an immune response. The release of this signalling peptide is blocked by pathogenic effectors to evade immune defence. Moreover, plant PR1 forms complexes with other PR family members, including PR5, also known as thaumatin, and PR14, a lipid transfer protein, to enhance the host's immune response. Here, we discuss possible functions of PR1 proteins and their interactors, particularly in light of the fact that these proteins can bind lipids, which have important immune signalling functions.
Topics: Humans; Proteins; Plants; Plant Diseases; Plant Proteins
PubMed: 36932700
DOI: 10.1111/mpp.13320 -
Molecular Plant-microbe Interactions :... May 2008Plants are hosts to a wide array of pathogens from all kingdoms of life. In the absence of an active immune system or combinatorial diversifications that lead to... (Review)
Review
Plants are hosts to a wide array of pathogens from all kingdoms of life. In the absence of an active immune system or combinatorial diversifications that lead to recombination-driven somatic gene flexibility, plants have evolved different strategies to combat both individual pathogen strains and changing pathogen populations. The receptor-like kinase (RLK) gene-family expansion in plants was hypothesized to have allowed accelerated evolution among domains implicated in signal reception, typically a leucine-rich repeat (LRR). Under that model, the gene-family expansion represents a plant-specific adaptation that leads to the production of numerous and variable cell surface and cytoplasmic receptors. More recently, it has emerged that the LRR domains of RLK interact with a diverse group of proteins leading to combinatorial variations in signal response specificity. Therefore, the RLK appear to play a central role in signaling during pathogen recognition, the subsequent activation of plant defense mechanisms, and developmental control. The future challenges will include determinations of RLK modes of action, the basis of recognition and specificity, which cellular responses each receptor mediates, and how both receptor and kinase domain interactions fit into the defense signaling cascades. These challenges will be complicated by the limited information that may be derived from the primary sequence of the LRR domain. The review focuses upon implications derived from recent studies of the secondary and tertiary structures of several plant RLK that change understanding of plant receptor function and signaling. In addition, the biological functions of plant and animal RLK-containing receptors were reviewed and commonalities among their signaling mechanisms identified. Further elucidated were the genomic and structural organizations of RLK gene families, with special emphasis on RLK implicated in resistance to disease and development.
Topics: Models, Biological; Plant Cells; Plant Diseases; Plant Proteins; Plants; Protein Serine-Threonine Kinases; Signal Transduction
PubMed: 18393610
DOI: 10.1094/MPMI-21-5-0507