The Experts below are selected from a list of 210 Experts worldwide ranked by ideXlab platform
Hunseung Kang - One of the best experts on this subject based on the ideXlab platform.
-
Rice DEAD-box RNA helicase OsRH53 has negative impact on Arabidopsis response to abiotic stresses
Plant Growth Regulation, 2018Co-Authors: Ghazala Nawaz, Hunseung KangAbstract:DEAD-box RNA Helicases (RHs) play key roles in the regulation of RNA metabolism at the posttranscriptional level. In this study, the expression patterns under abiotic stresses and the functions of a rice (Oryza sativa) RH, OsRH53, in stress response were determined using transgenic Arabidopsis plants. The level of OsRH53 decreased upon abiotic stress treatment, including, drought, salt, cold, and UV stress, and by abscisic acid (ABA). Although OsRH53 contains a putative chloroplast transit peptide at the N-terminal end, confocal analysis of OsRH53–GFP fusion proteins transiently expressed in tobacco leaves revealed that OsRH53 is localized to the nucleus. OsRH53-expressing transgenic Arabidopsis displayed retarded germination and reduced growth under high salinity or dehydration stress but not under cold stress. OsRH53 negatively affected the growth and cotyledon greening of seedlings upon ABA application by activating the genes related to ABA signaling such as ABI3 and ABI4. The ability of OsRH53 to recover growth-defect phenotype of Escherichia coli mutant, and both in vitro and in vivo base pair-breaking ability confirmed that OsRH53 harbors RNA chaperone activity. Collectively, these results suggest that OsRH53 negatively affects plant abiotic stress responses via modulating RNA metabolism through its RNA chaperone activity.
-
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.
-
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.
-
Functional characterization of DEAD-box RNA Helicases in Arabidopsis thaliana under abiotic stress conditions.
Plant and Cell Physiology, 2008Co-Authors: Tae Rin Oh, Chul Min Park, Hunseung KangAbstract:DEAD-box RNA Helicases have been implicated to have a function during stress adaptation processes, but their functional roles in plant stress responses remain to be clearly elucidated. Here, we assessed the expression patterns and functional roles of two RNA Helicases, AtRH9 and AtRH25, in Arabidopsis thaliana under abiotic stress conditions. The transcript levels of AtRH9 and AtRH25 were up-regulated markedly in response to cold stress, whereas their transcript levels were down-regulated by salt or drought stress. Phenotypic analysis of the transgenic plants and T-DNA-tagged mutants showed that the constitutive overexpression of AtRH9 or AtRH25 resulted in the retarded seed germination of Arabidopsis plants under salt stress conditions. AtRH25, but not AtRH9, enhanced freezing tolerance in Arabidopsis plants. Both AtRH9 and AtRH25 complemented the cold-sensitive phenotype of BX04 Escherichia coli mutant cells, but AtRH25 had much more prominent complementation ability than AtRH9. An in vitro nucleic acid binding assay showed that AtRH9 binds equally to all homoribopolymers, whereas AtRH25 binds preferentially to poly(G). Taken together, these results demonstrate that AtRH9 and AtRH25 impact on the seed germination of Arabidopsis plants under salt stress conditions, and suggest that the difference in cold tolerance capability between AtRH9 and AtRH25 arises from their different nucleic acid-binding properties.
Jie Xu - One of the best experts on this subject based on the ideXlab platform.
-
a rice dead box RNA helicase protein osrh17 suppresses 16s ribosomal RNA maturation in escherichia coli
Gene, 2015Co-Authors: Jie Xu, Meiru Li, Jiang Hu, Dali Zeng, Yaolong Yang, Youlin Peng, Banpu Ruan, Hongqing LiAbstract:Abstract DEAD-box proteins comprise a large protein family. These proteins function in all types of processes in RNA metabolism and are highly conserved among eukaryotes. However, the precise functions of DEAD-box proteins in rice physiology and development remain unclear. In this study, we identified a rice DEAD-box protein, OsRH17, that contains a DEAD domain and all of the common conserved motifs of DEAD-box RNA Helicases. OsRH17 was specifically expressed in pollen and differentiated callus and upregulated by application of the plant hormones naphthyl acetic acid (NAA) and abscisic acid (ABA). The OsRH17:GFP fusion protein was localized to the nucleus. Tiny amounts of OsRH17 and partial fragments (N-427 and C-167) were detected when they were expressed in Escherichia coli, a prokaryote. Growth of the host cells was suppressed in E. coli by OsRH17, N-427 or C-167, and this suppression was independent of the concentration of the NaCl in the medium. Expression analysis of rRNAs in E. coli revealed that the 16S rRNA precursor accumulated in transgenic E. coli cells, and the relative growth rate was inversely proportional to the levels of pre-16S rRNA accumulation. Results suggested that OsRH17 may play a role in ribosomal biogenesis and suppress 16S rRNA maturation in E. coli. No visible phenotype was observed in transgenic yeast and rice (overexpressing OsRH17, N-427, and C-167, as well as OsRH17 knockdown), and even in some abiotic and biotic stresses, which could be due to the redundancy in rice under normal conditions.
David B. Mckay - One of the best experts on this subject based on the ideXlab platform.
-
Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif
Journal of Molecular Biology, 2010Co-Authors: John W. Hardin, Yao Xiong Hu, David B. MckayAbstract:DEAD-box RNA Helicases of the bacterial DbpA subfamily are localized to their biological substrate when a carboxy-terminal RNA recognition motif domain binds tightly and specifically to a segment of 23S ribosomal RNA (rRNA) that includes hairpin 92 of the peptidyl transferase center. A complex between a fragment of 23S rRNA and the RNA binding domain (RBD) of the Bacillus subtilis DbpA protein YxiN was crystallized and its structure was determined to 2.9 Å resolution, revealing an RNA recognition mode that differs from those observed with other RNA recognition motifs. The RBD is bound between two RNA strands at a three-way junction. Multiple phosphates of the RNA backbone interact with an electropositive band generated by lysines of the RBD. Nucleotides of the single-stranded loop of hairpin 92 interact with the RBD, including the guanosine base of G2553, which forms three hydrogen bonds with the peptide backbone. A G2553U mutation reduces the RNA binding affinity by 2 orders of magnitude, confirming that G2553 is a sequence specificity determinant in RNA binding. Binding of the RBD to 23S rRNA in the late stages of ribosome subunit maturation would position the ATP-binding duplex destabilization fragment of the protein for interaction with rRNA in the peptidyl transferase cleft of the subunit, allowing it to "melt out" unstable secondary structures and allow proper folding. © 2010 Elsevier Ltd.
Eckhard Jankowsky - One of the best experts on this subject based on the ideXlab platform.
-
Coupling between the DEAD-box RNA Helicases Ded1p and eIF4A
eLife, 2016Co-Authors: Andrea A. Putnam, Heath A. Bowers, Ulf Peter Guenther, Xuan Ye, Audrey Kindsfather, Angela K. Hilliker, Eckhard JankowskyAbstract:Eukaryotic translation initiation involves two conserved DEAD-box RNA Helicases, eIF4A and Ded1p. Here we show that S. cerevisiae eIF4A and Ded1p directly interact with each other and simultaneously with the scaffolding protein eIF4G. We delineate a comprehensive thermodynamic framework for the interactions between Ded1p, eIF4A, eIF4G, RNA and ATP, which indicates that eIF4A, with and without eIF4G, acts as a modulator for activity and substrate preferences of Ded1p, which is the RNA remodeling unit in all complexes. Our results reveal and characterize an unexpected interdependence between the two RNA Helicases and eIF4G, and suggest that Ded1p is an integral part of eIF4F, the complex comprising eIF4G, eIF4A, and eIF4E.
-
Division of Labor in an Oligomer of the DEAD-box RNA Helicase Ded1p
Molecular Cell, 2015Co-Authors: Andrea A. Putnam, Quansheng Yang, Eckhard JankowskyAbstract:Summary Most aspects of RNA metabolism involve DEAD-box RNA Helicases, enzymes that bind and remodel RNA and RNA-protein complexes in an ATP-dependent manner. Here we show that the DEAD-box helicase Ded1p oligomerizes in the cell and in vitro, and unwinds RNA as a trimer. Two protomers bind the single-stranded region of RNA substrates and load a third protomer to the duplex, which then separates the strands. ATP utilization differs between the strand-separating protomer and those bound to the single-stranded region. Binding of the eukaryotic initiation factor 4G to Ded1p interferes with oligomerization and thereby modulates unwinding activity and RNA affinity of the helicase. Our data reveal a strict division of labor between the Ded1p protomers in the oligomer. This mode of oligomerization fundamentally differs from other Helicases. Oligomerization represents a previously unappreciated level of regulation for DEAD-box helicase activities.
-
The Ded1/DDX3 subfamily of DEAD-box RNA Helicases
Critical Reviews in Biochemistry and Molecular Biology, 2014Co-Authors: Deepak Sharma, Eckhard JankowskyAbstract:AbstractIn eukaryotic organisms, the orthologs of the DEAD-box RNA helicase Ded1p from yeast and DDX3 from human form a well-defined subfamily that is characterized by high sequence conservation in their helicase core and their N- and C- termini. Individual members of this Ded1/DDX3 subfamily perform multiple functions in RNA metabolism in both nucleus and cytoplasm. Ded1/DDX3 subfamily members have also been implicated in cellular signaling pathways and are targeted by diverse viruses. In this review, we discuss the considerable body of work on the biochemistry and biology of these proteins, including the recently discovered link of human DDX3 to tumorigenesis.
-
AMP sensing by DEAD-box RNA Helicases
Journal of Molecular Biology, 2013Co-Authors: Andrea A. Putnam, Eckhard JankowskyAbstract:Abstract In eukaryotes, cellular levels of adenosine monophosphate (AMP) signal the metabolic state of the cell. AMP concentrations increase significantly upon metabolic stress, such as glucose deprivation in yeast. Here, we show that several DEAD-box RNA Helicases are sensitive to AMP, which is not produced during ATP hydrolysis by these enzymes. We find that AMP potently inhibits RNA binding and unwinding by the yeast DEAD-box Helicases Ded1p, Mss116p, and eIF4A. However, the yeast DEAD-box Helicases Sub2p and Dbp5p are not inhibited by AMP. Our observations identify a subset of DEAD-box Helicases as enzymes with the capacity to directly link changes in AMP concentrations to RNA metabolism.
Hongqing Li - One of the best experts on this subject based on the ideXlab platform.
-
a rice dead box RNA helicase protein osrh17 suppresses 16s ribosomal RNA maturation in escherichia coli
Gene, 2015Co-Authors: Jie Xu, Meiru Li, Jiang Hu, Dali Zeng, Yaolong Yang, Youlin Peng, Banpu Ruan, Hongqing LiAbstract:Abstract DEAD-box proteins comprise a large protein family. These proteins function in all types of processes in RNA metabolism and are highly conserved among eukaryotes. However, the precise functions of DEAD-box proteins in rice physiology and development remain unclear. In this study, we identified a rice DEAD-box protein, OsRH17, that contains a DEAD domain and all of the common conserved motifs of DEAD-box RNA Helicases. OsRH17 was specifically expressed in pollen and differentiated callus and upregulated by application of the plant hormones naphthyl acetic acid (NAA) and abscisic acid (ABA). The OsRH17:GFP fusion protein was localized to the nucleus. Tiny amounts of OsRH17 and partial fragments (N-427 and C-167) were detected when they were expressed in Escherichia coli, a prokaryote. Growth of the host cells was suppressed in E. coli by OsRH17, N-427 or C-167, and this suppression was independent of the concentration of the NaCl in the medium. Expression analysis of rRNAs in E. coli revealed that the 16S rRNA precursor accumulated in transgenic E. coli cells, and the relative growth rate was inversely proportional to the levels of pre-16S rRNA accumulation. Results suggested that OsRH17 may play a role in ribosomal biogenesis and suppress 16S rRNA maturation in E. coli. No visible phenotype was observed in transgenic yeast and rice (overexpressing OsRH17, N-427, and C-167, as well as OsRH17 knockdown), and even in some abiotic and biotic stresses, which could be due to the redundancy in rice under normal conditions.