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International Journal of Molecular... Apr 2013The endoplasmic reticulum (ER) stress response is a highly conserved mechanism that results from the accumulation of unfolded or misfolded proteins in the ER. The... (Review)
Review
The endoplasmic reticulum (ER) stress response is a highly conserved mechanism that results from the accumulation of unfolded or misfolded proteins in the ER. The response plays an important role in allowing plants to sense and respond to adverse environmental conditions, such as heat stress, salt stress and pathogen infection. Since the ER is a well-controlled microenvironment for proper protein synthesis and folding, it is highly susceptible to stress conditions. Accumulation of unfolded or misfolded proteins activates a signaling pathway, called the unfolded protein response (UPR), which acts to relieve ER stress and, if unsuccessful, leads to cell death. Plants have two arms of the UPR signaling pathway, an arm involving the proteolytic processing of membrane-associated basic leucine zipper domain (bZIP) transcription factors and an arm involving RNA splicing factor, IRE1, and its mRNA target. These signaling pathways play an important role in determining the cell's fate in response to stress conditions.
Topics: Animals; Autophagy; Endoplasmic Reticulum Stress; Endoplasmic Reticulum-Associated Degradation; Evolution, Molecular; Mammals; Models, Biological; Plant Cells; Plant Development; Plant Physiological Phenomena; Plant Proteins; Protein Folding; Signal Transduction; Unfolded Protein Response
PubMed: 23591838
DOI: 10.3390/ijms14048188 -
Plant Signaling & Behavior 2019INDETERMINATE-DOMAIN proteins (IDDs) belong to a diverse plant-specific family of transcriptional regulators that coordinate distinct functions during plant growth and... (Review)
Review
INDETERMINATE-DOMAIN proteins (IDDs) belong to a diverse plant-specific family of transcriptional regulators that coordinate distinct functions during plant growth and development. The functions of several of these IDD members are transcriptionally regulated, but so far nothing is known about the regulation at the post-translational level in spite of the fact that post-translational modifications of these proteins have been reported in several large-scale proteomics studies. Recently, we showed that IDD4 is a repressor of basal immunity and its characteristic traits are predominantly determined by the phosphorylation at two distinct phosphorylation sites. This finding prompted us to comprehensively review phosphorylation of the various IDD members from the plethora of phosphoproteomics studies demonstrating the post-translational modification of IDDs at highly conserved sites under various experimental conditions. We reckon that the phosphorylation of IDDs is an underrated mechanistic aspect in their regulation and we postulate their importance in IDD/BIRD functioning.
Topics: Amino Acid Sequence; Environment; Phosphorylation; Phylogeny; Plant Development; Plant Proteins; Protein Domains
PubMed: 31314681
DOI: 10.1080/15592324.2019.1642037 -
Molecules (Basel, Switzerland) Sep 2021Chitin-binding hevein-like peptides (CB-HLPs) belong to a family of cysteine-rich peptides that play important roles in plant stress and defense mechanisms. CB-HLPs are...
Chitin-binding hevein-like peptides (CB-HLPs) belong to a family of cysteine-rich peptides that play important roles in plant stress and defense mechanisms. CB-HLPs are ribosomally synthesized peptides that are known to be bioprocessed from the following two types of three-domain CB-HLP precursor architectures: cargo-carrying and non-cargo-carrying. Here, we report the identification and characterization of chenotides biosynthesized from the third type of precursors, which are cleavable hololectins of the quinoa () family. Chenotides are 6-Cys-CB-HLPs of 29-31 amino acids, which have a third type of precursor architecture that encompasses a canonical chitin-binding domain that is involved in chitin binding and anti-fungal activities. Microbroth dilution assays and microscopic analyses showed that chenotides are effective against phyto-pathogenic fungi in the micromolar range. Structure determination revealed that chenotides are cystine knotted and highly compact, which could confer resistance against heat and proteolytic degradation. Importantly, chenotides are connected by a novel 18-residue Gly/Ala-rich linker that is a target for bioprocessing by cathepsin-like endopeptidases. Taken together, our findings reveal that chenotides are a new family of CB-HLPs from quinoa that are synthesized as a single multi-modular unit and bioprocessed to yield individual mature CB-HLPs. Importantly, such precursors constitute a new family of cleavable hololectins. This unusual feature could increase the biosynthetic efficiency of anti-fungal CB-HLPs, to provide an evolutionary advantage for plant survival and reproduction.
Topics: Amino Acid Sequence; Antimicrobial Cationic Peptides; Chenopodium quinoa; Peptide Fragments; Plant Lectins; Plant Proteins; Protein Conformation; Sequence Homology
PubMed: 34641455
DOI: 10.3390/molecules26195909 -
Cellular and Molecular Life Sciences :... Jul 2007The PIN-FORMED (PIN) protein family is a group of plant transmembrane proteins with a predicted function as secondary transporters. PINs have been shown to play a... (Review)
Review
The PIN-FORMED (PIN) protein family is a group of plant transmembrane proteins with a predicted function as secondary transporters. PINs have been shown to play a rate-limiting role in the catalysis of efflux of the plant growth regulator auxin from cells, and their asymmetrical cellular localization determines the direction of cell-to-cell auxin flow. There is a functional redundancy of PINs and their biochemical activity is regulated at many levels. PINs constitute a flexible network underlying the directional auxin flux (polar auxin transport) which provides cells in any part of the plant body with particular positional and temporal information. Thus, the PIN network, together with downstream auxin signalling system(s), coordinates plant development. This review summarizes recent progress in the elucidation of the role of PIN proteins in polar auxin transport at the cellular level, with emphasis on their structure and evolution and regulation of their function.
Topics: Biological Transport; Evolution, Molecular; Indoleacetic Acids; Models, Biological; Plant Proteins; Sequence Analysis, Protein
PubMed: 17458499
DOI: 10.1007/s00018-007-6566-4 -
Open Biology Jan 2018Molecular and genomic studies have shown the presence of a large number of gene family members in plants, some of which have been proved to act in P signalling and... (Review)
Review
Molecular and genomic studies have shown the presence of a large number of gene family members in plants, some of which have been proved to act in P signalling and homeostasis. In this study, the molecular and evolutionary characteristics of the gene family in plants were comprehensively analysed, and the mechanisms underlying the function of genes in P signalling and homeostasis in the model plant species () and rice (), and in important crops, including wheat (), soya beans () and rapeseed (), were described. Emerging findings on the involvement of genes in other important processes (i.e. disease resistance, iron deficiency response, low oxygen response and phytochrome-mediated light signalling) were also highlighted. The available data suggest that genes are important regulators in the P signalling network, and may be valuable targets for enhancing crop tolerance to low P stress. Further studies on SPX proteins should include more diverse members, which may reveal SPX proteins as important regulatory hubs for multiple processes including P signalling and homeostasis in plants.
Topics: Crops, Agricultural; Evolution, Molecular; Phosphorus; Plant Proteins; Stress, Physiological
PubMed: 29298909
DOI: 10.1098/rsob.170231 -
Biochemistry. Biokhimiia Dec 2014The respiratory chain in the majority of organisms with aerobic type metabolism features the concomitant existence of the phosphorylating cytochrome pathway and the... (Review)
Review
The respiratory chain in the majority of organisms with aerobic type metabolism features the concomitant existence of the phosphorylating cytochrome pathway and the cyanide- and antimycin A-insensitive oxidative route comprising a so-called alternative oxidase (AOX) as a terminal oxidase. In this review, the history of AOX discovery is described. Considerable evidence is presented that AOX occurs widely in organisms at various levels of organization and is not confined to the plant kingdom. This enzyme has not been found only in Archaea, mammals, some yeasts and protists. Bioinformatics research revealed the sequences characteristic of AOX in representatives of various taxonomic groups. Based on multiple alignments of these sequences, a phylogenetic tree was constructed to infer their possible evolution. The ways of AOX activation, as well as regulatory interactions between AOX and the main respiratory chain are described. Data are summarized concerning the properties of AOX and the AOX-encoding genes whose expression is either constitutive or induced by various factors. Information is presented on the structure of AOX, its active center, and the ubiquinone-binding site. The principal functions of AOX are analyzed, including the cases of cell survival, optimization of respiratory metabolism, protection against excess of reactive oxygen species, and adaptation to variable nutrition sources and to biotic and abiotic stress factors. It is emphasized that different AOX functions complement each other in many instances and are not mutually exclusive. Examples are given to demonstrate that AOX is an important tool to overcome the adverse aftereffects of restricted activity of the main respiratory chain in cells and whole animals. This is the first comprehensive review on alternative oxidases of various organisms ranging from yeasts and protists to vascular plants.
Topics: Bacteria; Electron Transport; Mitochondrial Proteins; Nutritional Physiological Phenomena; Oxidoreductases; Phylogeny; Plant Proteins; Protein Conformation
PubMed: 25749168
DOI: 10.1134/S0006297914130112 -
Plant Physiology Mar 2019Prospects are reviewed for the use of synthetic enzyme complexes as a metabolic engineering tool. (Review)
Review
Prospects are reviewed for the use of synthetic enzyme complexes as a metabolic engineering tool.
Topics: Metabolic Engineering; Metabolic Networks and Pathways; Plant Proteins; Plants; Synthetic Biology
PubMed: 30455287
DOI: 10.1104/pp.18.01280 -
Genome Biology 2008Proteins of the phytochrome superfamily of red/far-red light receptors have a variety of biological roles in plants, algae, bacteria and fungi and demonstrate a... (Review)
Review
Proteins of the phytochrome superfamily of red/far-red light receptors have a variety of biological roles in plants, algae, bacteria and fungi and demonstrate a diversity of spectral sensitivities and output signaling mechanisms. Over the past few years the first three-dimensional structures of phytochrome light-sensing domains from bacteria have been determined.
Topics: Algal Proteins; Bacterial Proteins; Evolution, Molecular; Fungal Proteins; Light Signal Transduction; Multigene Family; Photoreceptors, Plant; Phylogeny; Phytochrome; Plant Proteins; Protein Structure, Tertiary
PubMed: 18771590
DOI: 10.1186/gb-2008-9-8-230 -
The New Phytologist Jul 2011The pentatricopeptide repeat (PPR) is a degenerate 35-amino-acid structural motif identified from analysis of the sequenced genome of the model plant Arabidopsis... (Review)
Review
The pentatricopeptide repeat (PPR) is a degenerate 35-amino-acid structural motif identified from analysis of the sequenced genome of the model plant Arabidopsis thaliana. From the wealth of sequence information now available from plant genomes, the PPR protein family is now known to be one of the largest families in angiosperm species, as most genomes encode 400-600 members. As the number of PPR genes is generally only c. 10-20 in other eukaryotic organisms, including green algae, the family has obviously greatly expanded during land plant evolution. This provides a rare opportunity to study selection pressures driving a 50-fold expansion of a single gene family. PPR proteins are sequence-specific RNA-binding proteins involved in many aspects of RNA processing in organelles. In this review, we will summarize our current knowledge about the evolution of PPR genes, and will discuss the relevance of the dramatic expansion in the family to the functional diversification of plant organelles, focusing primarily on RNA editing.
Topics: Amino Acid Motifs; Evolution, Molecular; Genetic Drift; Genome, Plant; Multigene Family; Phylogeny; Plant Proteins; RNA Editing; RNA, Plant
PubMed: 21557747
DOI: 10.1111/j.1469-8137.2011.03746.x -
Scientific Reports Feb 2020Plants produce an array of peptides as part of their innate defense mechanism against pathogens. The potential use of these peptides for various therapeutic purposes is...
Plants produce an array of peptides as part of their innate defense mechanism against pathogens. The potential use of these peptides for various therapeutic purposes is increasing per diem. In order to excel in this research, the community requires web repositories that provide reliable and accurate information about these phyto-peptides. This work is an attempt to bridge the gaps in plant-based peptide research. PlantPepDB is a manually curated database that consists of 3848 plant-derived peptides among which 2821 are experimentally validated at the protein level, 458 have experimental evidence at the transcript level, 530 are predicted and only 39 peptides are inferred from homology. Incorporation of physicochemical properties and tertiary structure into PlantPepDB will help the users to study the therapeutic potential of a peptide, thus, debuts as a powerful resource for therapeutic research. Different options like Simple, Advanced, PhysicoChem and AA composition search along with browsing utilities are provided in the database for the users to execute dynamic search and retrieve the desired data. Interestingly, many peptides that were considered to possess only a single property were found to exhibit multiple properties after careful curation and merging the duplicate data that was collected from published literature and already available databases. Overall, PlantPepDB is the first database comprising detailed analysis and comprehensive information of phyto-peptides from a broad functional range which will be useful for peptide-based applied research. PlantPepDB is freely available at http://www.nipgr.ac.in/PlantPepDB/.
Topics: Data Management; Databases, Protein; Peptides; Plant Proteins; Plants; Software
PubMed: 32042035
DOI: 10.1038/s41598-020-59165-2