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Cellular and Molecular Life Sciences :... Oct 2019Nitrogen (N) is one of the most important essential macro-elements for plant growth and development, and nitrate represents the most abundant inorganic form of N in... (Review)
Review
Nitrogen (N) is one of the most important essential macro-elements for plant growth and development, and nitrate represents the most abundant inorganic form of N in soils. The nitrate uptake and assimilation processes are finely tuned according to the available nitrate in the surroundings as well as by the internal finely coordinated signaling pathways. The NIN-like proteins (NLPs) harbor both RWP-RK, and Phox and Bem1 (PB1) domains, and they belong to the well-characterized plant-specific RWP-RK transcription factor gene family. NLPs are known to be involved in the nitrate signaling pathway by activating downstream target genes, and thus they are implicated in the primary nitrate response in the nucleus via their RWP-RK domains. The PB1 domain is a ubiquitous protein-protein interaction domain and it comprises another regulatory layer for NLPs via the protein interactions within NLPs or with other essential components. Recently, Ca-Ca sensor protein kinase-NLP signaling cascades have been identified and they allow NLPs to have central roles in mediating the nitrate signaling pathway. NLPs play essential roles in many aspects of plant growth and development via the finely tuned nitrate signaling pathway. Furthermore, recent studies have highlighted the emerging roles played by NLPs in the N starvation response, nodule formation in legumes, N and P interactions, and root cap release in higher plants. In this review, we consider recent advances in the identification, evolution, molecular characteristics, and functions of the NLP gene family in plant growth and development.
Topics: Biological Evolution; Nitrates; Nitrogen; Phosphates; Plant Development; Plant Proteins; Plant Root Nodulation; Plants; Signal Transduction; Transcription Factors
PubMed: 31161283
DOI: 10.1007/s00018-019-03164-8 -
FEBS Letters Feb 2018The plant-specific GAI-RGA-and-SCR (GRAS) family of proteins function as transcriptional regulators and play critical roles in development and signalling. Recent... (Review)
Review
The plant-specific GAI-RGA-and-SCR (GRAS) family of proteins function as transcriptional regulators and play critical roles in development and signalling. Recent structural studies have shed light on the molecular functions at the structural level. The conserved GRAS domain comprises an α-helical cap and α/β core subdomains. The α-helical cap mediates head-to-head heterodimerization between SHR and SCR GRAS domains. This type of dimerization is predicted for the NSP1-NSP2 heterodimer and DELLA proteins such as RGA and SLR1 homodimers. The α/β core subdomain possesses a hydrophobic groove formed by surface α3- and α7-helices and mediates protein-protein interactions. The groove of the SHR GRAS domain accommodates the zinc fingers of JKD, a BIRD/IDD family transcription factor, while the groove of the SCL7 GRAS domain mediates the SCL7 homodimerization.
Topics: Plant Proteins; Protein Binding; Protein Domains; Protein Multimerization; Protein Structure, Quaternary; Substrate Specificity
PubMed: 29364510
DOI: 10.1002/1873-3468.12987 -
International Journal of Molecular... Mar 2020Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence-structure-function... (Review)
Review
Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence-structure-function relationship. Hence, classic sequence- or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism.
Topics: Animals; Evolution, Molecular; Gene Expression Regulation; Humans; Intrinsically Disordered Proteins; Plant Proteins; Plants; Protein Conformation; Protein Folding
PubMed: 32204351
DOI: 10.3390/ijms21062105 -
Journal of Experimental Botany Mar 2020The Multiprotein Bridging Factor 1 (MBF1) proteins are transcription co-factors whose molecular function is to form a bridge between transcription factors and the basal... (Review)
Review
The Multiprotein Bridging Factor 1 (MBF1) proteins are transcription co-factors whose molecular function is to form a bridge between transcription factors and the basal machinery of transcription. MBF1s are present in most archaea and all eukaryotes, and numerous reports show that they are involved in developmental processes and in stress responses. In this review we summarize almost three decades of research on the plant MBF1 family, which has mainly focused on their role in abiotic stress responses, in particular the heat stress response. However, despite the amount of information available, there are still many questions that remain about how plant MBF1 genes, transcripts, and proteins respond to stress, and how they in turn modulate stress response transcriptional pathways.
Topics: Gene Expression Regulation, Plant; Genes, Plant; Plant Proteins; Plants; Stress, Physiological; Transcription Factors
PubMed: 32037452
DOI: 10.1093/jxb/erz525 -
International Journal of Molecular... Oct 2019In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial... (Review)
Review
In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial roles. Among them, atlas analysis of plants under different abiotic stresses, including salinity, drought, and toxic conditions, has become more important for uncovering the potential key genes and proteins in different plant tissues. High-quality genomic data and integrated analyses of transcriptomic, proteomic, metabolomics, and phenomic patterns provide a deeper understanding of how plants grow and survive under environmental stresses. This editorial mini-review aims to synthesize the 27 papers including two timely reviews that have contributed to this Special Issue, which focuses on concluding the recent progress in the Protein and Proteome Atlas in plants under different stresses. It covers various aspects of plant proteins ranging from agricultural proteomics, structure and function of proteins, novel techniques and approaches for gene and protein identification, protein quantification, proteomics for post-translational modifications (PTMs), and new insights into proteomics. The proteomics-based results in this issue will help the readers to gain novel insights for the understanding of complicated physiological processes in crops and other important plants in response to stressed conditions. Furthermore, these target genes and proteins that are important candidates for further functional validation in economic plants and crops can be studied.
Topics: Atlases as Topic; Gene Expression Regulation, Plant; Plant Physiological Phenomena; Plant Proteins; Protein Conformation; Proteomics; Stress, Physiological
PubMed: 31640274
DOI: 10.3390/ijms20205222 -
Bioengineered Apr 2022Owing to various undesirable health effects of sugar overconsumption, joint efforts are being made by industrial sectors and regulatory authorities to reduce sugar... (Review)
Review
Owing to various undesirable health effects of sugar overconsumption, joint efforts are being made by industrial sectors and regulatory authorities to reduce sugar consumption practices, worldwide. Artificial sweeteners are considered potential substitutes in several products, e.g., sugar alcohols (polyols), high-fructose corn syrup, powdered drink mixes, and other beverages. Nevertheless, their long-standing health effects continue to be debatable. Consequently, growing interest has been shifted in producing non-caloric sweetenersfrom renewable resources to meet consumers' dietary requirements. Except for the lysozyme protein, various sweet proteins including thaumatin, mabinlin, brazzein, monellin, miraculin, pentadin, and curculin have been identified in tropical plants. Given the high cost and challenging extortion of natural resources, producing these sweet proteins using engineered microbial hosts, such as and represents an appealing choice. Engineering techniques can be applied for large-scale biosynthesis of proteins, which can be used in biopharmaceutical, food, diagnostic, and medicine industries. Nevertheless, extensive work needs to be undertaken to address technical challenges in microbial production of sweet-tasting proteins in bulk. This review spotlights historical aspects, physicochemical properties (taste, safety, stability, solubility, and cost), and recombinant biosynthesis of sweet proteins. Moreover, future opportunities for process improvement based on metabolic engineering strategies are also discussed.
Topics: Bioprospecting; Biotechnology; Plant Proteins; Recombinant Proteins; Sweetening Agents; Taste
PubMed: 35435127
DOI: 10.1080/21655979.2022.2061147 -
International Review of Cell and... 2016Biosynthesis of the photosynthetic apparatus is a complex operation, which includes the concerted synthesis and assembly of lipids, pigments and metal cofactors, and... (Review)
Review
Biosynthesis of the photosynthetic apparatus is a complex operation, which includes the concerted synthesis and assembly of lipids, pigments and metal cofactors, and dozens of proteins. Research conducted in recent years has shown that these processes, as well as the stabilization and repair of this molecular machinery, are facilitated by transiently acting regulatory proteins, many of which belong to the superfamily of helical repeat proteins. Here, we focus on one of its families in photoautotrophic model organisms, the tetratricopeptide repeat (TPR) proteins, which participate in almost all of these steps and are crucial for biogenesis of the thylakoid membrane.
Topics: Amino Acid Sequence; Models, Biological; Photosynthesis; Plant Proteins; Protein Domains; Repetitive Sequences, Amino Acid; Thylakoids
PubMed: 27017009
DOI: 10.1016/bs.ircmb.2016.01.005 -
Journal of Experimental Botany Aug 2016Cell-to-cell communication is crucial for the coherent functioning of multicellular organisms, and they have evolved intricate molecular mechanisms to achieve such... (Review)
Review
Cell-to-cell communication is crucial for the coherent functioning of multicellular organisms, and they have evolved intricate molecular mechanisms to achieve such communication. Small, secreted peptide hormones participate in cell-to-cell communication to regulate various physiological processes. One such family of plant peptide hormones is the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-related (CLE) family, whose members play crucial roles in the differentiation of shoot and root meristems. Recent biochemical and genetic studies have characterized various CLE signaling modules, which include CLE peptides, transmembrane receptors, and downstream intracellular signaling components. CLE signaling systems are conserved across the plant kingdom but have divergent modes of action in various developmental processes in different species. Moreover, several CLE peptides play roles in symbiosis, parasitism, and responses to abiotic cues. Here we review recent studies that have provided new insights into the mechanisms of CLE signaling.
Topics: Plant Development; Plant Growth Regulators; Plant Proteins; Signal Transduction
PubMed: 27229733
DOI: 10.1093/jxb/erw208 -
International Journal of Molecular... Mar 2021Studies implicating an important role for apyrase (NTPDase) enzymes in plant growth and development began appearing in the literature more than three decades ago. After... (Review)
Review
Studies implicating an important role for apyrase (NTPDase) enzymes in plant growth and development began appearing in the literature more than three decades ago. After early studies primarily in potato, and legumes, especially important discoveries that advanced an understanding of the biochemistry, structure and function of these enzymes have been published in the last half-dozen years, revealing that they carry out key functions in diverse other plants. These recent discoveries about plant apyrases include, among others, novel findings on its crystal structures, its biochemistry, its roles in plant stress responses and its induction of major changes in gene expression when its expression is suppressed or enhanced. This review will describe and discuss these recent advances and the major questions about plant apyrases that remain unanswered.
Topics: Apyrase; Catalytic Domain; Chemical Phenomena; Drug Discovery; Enzyme Inhibitors; Gene Expression Regulation, Plant; Models, Molecular; Plant Proteins; Protein Conformation; Structure-Activity Relationship
PubMed: 33807069
DOI: 10.3390/ijms22063283 -
Molecular Biology Reports Jul 2022CIPK protein family is a key protein family in Ca mediated plant signaling pathway, which plays an indispensable role in plant response to stress and development. Every... (Review)
Review
CIPK protein family is a key protein family in Ca mediated plant signaling pathway, which plays an indispensable role in plant response to stress and development. Every gene in this family encodes specific proteins. They interact with calcium ion signals, make plants to deal with various stress or stimuli. This article mainly reviews the mechanism, positioning and physiological functions of the CIPK family in different species in recent years. According to our team's research, CIPK8 interacts with CBL5 to improve salt tolerance, and CIPK23 interacts with TGA1 to regulate nitrate uptake negatively in chrysanthemum. In addition, we discussed current limitations and future research directions. The article will enhance the understanding of the functional characteristics of the CIPK gene family under different stresses, provide insights for future breeding and the development of new crop varieties with enhanced stress tolerance.
Topics: Gene Expression Regulation, Plant; Plant Breeding; Plant Proteins; Signal Transduction; Stress, Physiological
PubMed: 35229240
DOI: 10.1007/s11033-022-07255-x