The Experts below are selected from a list of 228 Experts worldwide ranked by ideXlab platform
Hunseung Kang - One of the best experts on this subject based on the ideXlab platform.
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chloroplast or mitochondria targeted dead box RNA helicases play essential roles in organellar RNA Metabolism and abiotic stress responses
Frontiers in Plant Science, 2017Co-Authors: Ghazala Nawaz, Hunseung KangAbstract:The yields and productivity of crops are greatly diminished by various abiotic stresses, including drought, cold, heat, and high salinity. Chloroplasts and mitochondria are cellular organelles that can sense diverse environmental stimuli and alter gene expression to cope with adverse environmental stresses. Organellar gene expression is mainly regulated at posttranscriptional levels, including RNA processing, intron splicing, RNA editing, RNA turnover, and translational control, during which a variety of nucleus-encoded RNA-binding proteins (RBPs) are targeted to chloroplasts or mitochondria where they play essential roles in organellar RNA Metabolism. DEAD-box RNA helicases (RHs) are enzymes that can alter RNA structures and affect RNA Metabolism in all living organisms. Although a number of DEAD-box RHs have been found to play important roles in RNA Metabolism in the nucleus and cytoplasm, our understanding on the roles of DEAD-box RHs in the regulation of RNA Metabolism in chloroplasts and mitochondria is only at the beginning. Considering that organellar RNA Metabolism and gene expression are tightly regulated by anterograde signaling from the nucleus, it is imperative to determine the functions of nucleus-encoded organellar RBPs. In this review, we summarize the emerging roles of nucleus-encoded chloroplast- or mitochondria- targeted DEAD-box RHs in organellar RNA Metabolism and plant response to diverse abiotic stresses.
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Regulation of RNA Metabolism in Plant Adaptation to Cold
Plant and Microbe Adaptations to Cold in a Changing World, 2013Co-Authors: Hunseung Kang, Su Jung ParkAbstract:Posttranscriptional regulation of RNA Metabolism, including RNA processing, splicing, transport, turnover, and translational control, is recognized as a key regulatory process in plant response to diverse environmental stresses, during which a variety of RNA-binding proteins (RBPs) perform as central regulators in cells. Over the past decades, several classes of RBPs have been identified from diverse plant species and their roles in stress response determined. In particular, the stress-responsive expression and functional roles of glycine-rich RNA-binding proteins (GRPs), cold shock domain proteins (CSPs), and DEAD-box RNA helicases (RHs) have been extensively investigated in Arabidopsis thaliana, rice (Oryza sativa), and wheat (Triticum aestivum). In this chapter, we will review the recent progress of our understanding of the roles of these RBPs during the cold adaptation process in monocotyledonous plants as well as in dicotyledonous plants, which shed new light on the importance of the regulation of mRNA Metabolism and the role of RBPs as a central regulator in plant adaptation to cold.
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Regulation of RNA Metabolism in plant development and stress responses
Journal of Plant Biology, 2013Co-Authors: Hyun Ju Jung, Su Jung Park, Hunseung KangAbstract:Posttranscriptional regulation of RNA Metabolism, including RNA processing, splicing, editing, transport, translational control and turnover, is a key regulatory process in plant growth, development, and stress responses. A variety of RNA-binding proteins (RBPs) plays central roles during these cellular processes. Over the last decades, a considerable progress has been made in the identification and functional analysis of RBPs involved in growth, development, and stress response of plants. Identification of different family members of RBPs and determination of their functional roles in RNA Metabolism shed light on the importance of the regulation of RNA Metabolism and the role of RBPs as a central regulator in diverse cellular processes. In particular, recent reports demonstrate the emerging idea that certain RBPs perform a function as RNA chaperones during growth, development, and stress response of plants.
Patrick Linder - One of the best experts on this subject based on the ideXlab platform.
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Dead-box proteins: The driving forces behind RNA Metabolism
Nature Reviews Molecular Cell Biology, 2004Co-Authors: Sanda Rocak, Patrick LinderAbstract:RNA helicases from the DEAD-box family are found in almost all organisms and have important roles in RNA Metabolism. They are associated with many processes ranging from RNA synthesis to RNA degradation. DEAD-box proteins use the energy from ATP hydrolysis to rearrange inter- or intra-molecular RNA structures or dissociate RNA–protein complexes. Such dynamic rearrangements are fundamental for many, if not all, steps in the life of an RNA molecule. Recent biochemical, genetic and structural data shed light on how these proteins power the Metabolism of RNA within a cell.
L Aravind - One of the best experts on this subject based on the ideXlab platform.
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The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA Metabolism
Genome Biology, 2003Co-Authors: L Aravind, Lakshminarayan M Iyer, Vivek AnantharamanAbstract:Background There is considerable heterogeneity in the phyletic patterns of major chromosomal DNA-binding proteins in archaea. Alba is a well-characterized chromosomal protein from the crenarchaeal genus Sulfolobus . While Alba has been detected in most archaea and some eukaryotic taxa, its exact functions in these taxa are not clear. Here we use comparative genomics and sequence profile analysis to predict potential alteRNAtive functions of the Alba proteins. Results Using sequence-profile searches, we were able to unify the Alba proteins with RNAse P/MRP subunit Rpp20/Pop7, human RNAse P subunit Rpp25, and the ciliate Mdp2 protein, which is implicated in macronuclear development. The Alba superfamily contains two eukaryote-specific families and one archaeal family. We present different lines of evidence to show that both eukaryotic families perform functions related to RNA Metabolism. Several members of one of the eukaryotic families, typified by Mdp2, are combined in the same polypeptide with RNA-binding RGG repeats. We also investigated the relationships of the unified Alba superfamily within the ancient RNA-binding IF3-C fold, and show that it is most closely related to other RNA-binding members of this fold, such as the YhbY and IF3-C superfamilies. Based on phyletic patterns and the principle of phylogenetic bracketing, we predict that at least some of the archaeal members may also possess a role in RNA Metabolism. Conclusions The Alba superfamily proteins appear to have originated as RNA-binding proteins which formed various ribonucleoprotein complexes, probably including RNAse P. It was recruited as a chromosomal protein possibly only within the crenarchaeal lineage. The evolutionary connections reported here suggest how a diversity of functions based on a common biochemical basis emerged in proteins of the Alba superfamily.
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comparative genomics and evolution of proteins involved in RNA Metabolism
Nucleic Acids Research, 2002Co-Authors: Vivek Anantharaman, Eugene V Koonin, L AravindAbstract:RNA Metabolism, broadly defined as the compendium of all processes that involve RNA, including transcription, processing and modification of transcripts, translation, RNA degradation and its regulation, is the central and most evolutionarily conserved part of cell physiology. A comprehensive, genome-wide census of all enzymatic and non-enzymatic protein domains involved in RNA Metabolism was conducted by using sequence profile analysis and structural comparisons. Proteins related to RNA Metabolism comprise from 3 to 11% of the complete protein repertoire in bacteria, archaea and eukaryotes, with the greatest fraction seen in parasitic bacteria with small genomes. Approximately one-half of protein domains involved in RNA Metabolism are present in most, if not all, species from all three primary kingdoms and are traceable to the last universal common ancestor (LUCA). The principal features of LUCA’s RNA Metabolism system were reconstructed by parsimony-based evolutionary analysis of all relevant groups of orthologous proteins. This reconstruction shows that LUCA possessed not only the basal translation system, but also the principal forms of RNA modification, such as methylation, pseudouridylation and thiouridylation, as well as simple mechanisms for polyadenylation and RNA degradation. Some of these ancient domains form paralogous groups whose evolution can be traced back in time beyond LUCA, towards low-specificity proteins, which probably functioned as cofactors for ribozymes within the RNA world framework. The main lineage-specific innovations of RNA Metabolism systems were identified. The most notable phase of innovation in RNA Metabolism coincides with the advent of eukaryotes and was brought about by the merge of the archaeal and bacterial systems via mitochondrial endosymbiosis, but also involved emergence of several new, eukaryote-specific RNA-binding domains. Subsequent, vast expansions of these domains mark the origin of alteRNAtive splicing in animals and probably in plants. In addition to the reconstruction of the evolutionary history of RNA Metabolism, this analysis produced numerous functional predictions, e.g. of previously undetected enzymes of RNA modification.
Michael J. Strong - One of the best experts on this subject based on the ideXlab platform.
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RNA Metabolism in ALS: when normal processes become pathological.
Amyotrophic Lateral Sclerosis, 2014Co-Authors: Cristian A. Droppelmann, Danae Campos-melo, Muhammad Ishtiaq, Kathryn Volkening, Michael J. StrongAbstract:AbstractAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease caused by the death of motor neurons. While the exact molecular and cellular basis for motor neuron death is not yet fully understood, the current conceptualization is that multiple aberrant biological processes contribute. Among these, one of the most compelling is based on alterations of RNA Metabolism. In this review, we examine how the normal process of cellular response to stress leading to RNA stress granule formation might become pathological, resulting in the formation of stable protein aggregates. We discuss the emerging roles of post-translational modifications of RNA binding proteins in the genesis of these aggregates. We also review the contemporary literature regarding the potential role for more widespread alterations in RNA Metabolism in ALS, including alterations in miRNA biogenesis, spliceosome integrity and RNA editing. A hypothesis is presented in which aberrant RNA processing, modulated through pathologica...
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the evidence for altered RNA Metabolism in amyotrophic lateral sclerosis als
Journal of the Neurological Sciences, 2010Co-Authors: Michael J. StrongAbstract:In this review, the role of aberrant RNA Metabolism in ALS is examined, including the evidence that a majority of the genetic mutations observed in familial ALS (including mutations in TDP-43, FUS/TLS, SOD1, angiogenin (ANG) and senataxin (SETX)) can impact directly on either gene transcription, pre-mRNA splicing, ribonucleoprotein complex formation, transport, RNA translation or degradation. The evidence that perturbed expression or function of RNA binding proteins is causally related to the selective suppression of the low molecular weight subunit protein (NFL) steady state mRNA levels in degenerating motor neurons in ALS is examined. The discovery that mtSOD1, TDP-43 and 14-3-3 proteins, all of which form cytosolic aggregates in ALS, can each modulate the stability of NFL mRNA, suggests that a fundamental alteration in the interaction of mRNA species with key trans-acting binding factors has occurred in ALS. These observations lead directly to the hypothesis that ALS can be viewed as a disorder of RNA Metabolism, thus providing a novel pathway for the development of molecular pharmacotherapies.
Vivek Anantharaman - One of the best experts on this subject based on the ideXlab platform.
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The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA Metabolism
Genome Biology, 2003Co-Authors: L Aravind, Lakshminarayan M Iyer, Vivek AnantharamanAbstract:Background There is considerable heterogeneity in the phyletic patterns of major chromosomal DNA-binding proteins in archaea. Alba is a well-characterized chromosomal protein from the crenarchaeal genus Sulfolobus . While Alba has been detected in most archaea and some eukaryotic taxa, its exact functions in these taxa are not clear. Here we use comparative genomics and sequence profile analysis to predict potential alteRNAtive functions of the Alba proteins. Results Using sequence-profile searches, we were able to unify the Alba proteins with RNAse P/MRP subunit Rpp20/Pop7, human RNAse P subunit Rpp25, and the ciliate Mdp2 protein, which is implicated in macronuclear development. The Alba superfamily contains two eukaryote-specific families and one archaeal family. We present different lines of evidence to show that both eukaryotic families perform functions related to RNA Metabolism. Several members of one of the eukaryotic families, typified by Mdp2, are combined in the same polypeptide with RNA-binding RGG repeats. We also investigated the relationships of the unified Alba superfamily within the ancient RNA-binding IF3-C fold, and show that it is most closely related to other RNA-binding members of this fold, such as the YhbY and IF3-C superfamilies. Based on phyletic patterns and the principle of phylogenetic bracketing, we predict that at least some of the archaeal members may also possess a role in RNA Metabolism. Conclusions The Alba superfamily proteins appear to have originated as RNA-binding proteins which formed various ribonucleoprotein complexes, probably including RNAse P. It was recruited as a chromosomal protein possibly only within the crenarchaeal lineage. The evolutionary connections reported here suggest how a diversity of functions based on a common biochemical basis emerged in proteins of the Alba superfamily.
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comparative genomics and evolution of proteins involved in RNA Metabolism
Nucleic Acids Research, 2002Co-Authors: Vivek Anantharaman, Eugene V Koonin, L AravindAbstract:RNA Metabolism, broadly defined as the compendium of all processes that involve RNA, including transcription, processing and modification of transcripts, translation, RNA degradation and its regulation, is the central and most evolutionarily conserved part of cell physiology. A comprehensive, genome-wide census of all enzymatic and non-enzymatic protein domains involved in RNA Metabolism was conducted by using sequence profile analysis and structural comparisons. Proteins related to RNA Metabolism comprise from 3 to 11% of the complete protein repertoire in bacteria, archaea and eukaryotes, with the greatest fraction seen in parasitic bacteria with small genomes. Approximately one-half of protein domains involved in RNA Metabolism are present in most, if not all, species from all three primary kingdoms and are traceable to the last universal common ancestor (LUCA). The principal features of LUCA’s RNA Metabolism system were reconstructed by parsimony-based evolutionary analysis of all relevant groups of orthologous proteins. This reconstruction shows that LUCA possessed not only the basal translation system, but also the principal forms of RNA modification, such as methylation, pseudouridylation and thiouridylation, as well as simple mechanisms for polyadenylation and RNA degradation. Some of these ancient domains form paralogous groups whose evolution can be traced back in time beyond LUCA, towards low-specificity proteins, which probably functioned as cofactors for ribozymes within the RNA world framework. The main lineage-specific innovations of RNA Metabolism systems were identified. The most notable phase of innovation in RNA Metabolism coincides with the advent of eukaryotes and was brought about by the merge of the archaeal and bacterial systems via mitochondrial endosymbiosis, but also involved emergence of several new, eukaryote-specific RNA-binding domains. Subsequent, vast expansions of these domains mark the origin of alteRNAtive splicing in animals and probably in plants. In addition to the reconstruction of the evolutionary history of RNA Metabolism, this analysis produced numerous functional predictions, e.g. of previously undetected enzymes of RNA modification.
