Structure-function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2
Abstract not provided
Chen, Shoudeng↗
SEARCH · Engineering Papers
Results for “RNA”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides
Selenium-derivatized oligonucleotides may facilitate phase determination and high-resolution structure determination for protein–nucleic acid crystallography. The Se atom-specific mutagenesis (SAM) strategy may also enhance the study of nuclease catalysis. The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Crystal structures of the methyltransferase and helicase from the ZIKA 1947 MR766 Uganda strain
Two nonstructural proteins encoded by Zika virus strain MR766 RNA, a methyltransferase and a helicase, were crystallized and their structures were solved and refined at 2.10 and 2.01 Å resolution, respectively. The NS5 methyltransferase contains a bound S -adenosyl-L-methionine (SAM) co-substrate. The NS3 helicase is in the apo form. Comparison with published crystal structures of the helicase in the apo, nucleotide-bound and single-stranded RNA (ssRNA)-bound states suggests that binding of ssRNA to the helicase may occur through conformational selection rather than induced fit.
59 BASIC BIOLOGICAL SCIENCES↗
Identification and analysis of stem‐specific promoters from sugarcane and energy cane for oil accumulation in their stems
Abstract Considerable recent progress has been achieved in bioengineering oil accumulation in the vegetative tissues of plants, opening an opportunity for large scale production of biodiesel, jet fuel, lubricants, and high‐value lipid bioproducts. For the highly productive C4 crops, such as sugarcane, energy cane, Miscanthus, and fiber sorghums, the bulk of the biomass is the stem. However, little success has been made in accumulating oil in the stem. Since engineering a trait with a constitutive promoter often results in pleiotropic effects that counter trait improvement, identification of stem parenchyma‐specific promoters is a prerequisite for efficient use of the ample photoassimilates stored in mature stem parenchyma cells. In this study, we first identified two TST genes encoding homologues of tonoplast sugar transporters that were strongly and almost exclusively expressed in the stems of canes via a combination of RNA‐seq atlas analysis, in silico analysis of a sugarcane genome, phylogenetic analysis, and quantitative PCR analysis. They were further confirmed in the pith parenchyma cells of the mature stem by RNA in situ hybridization. When fused with the β‐Glucuronidase (GUS) reporter gene, the promoters of two alleles, TST2b‐1A and TST2b‐1C , from one TST gene demonstrated that they could drive the GUS expression exclusively in the stem in Arabidopsis.
09 BIOMASS FUELS↗
Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in A laska
Abstract Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S r RNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S r RNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical–chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha‐ and Gamma‐Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta‐Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near‐surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga , etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw.
Deng, Jie↗
Spray‐induced gene silencing to identify powdery mildew gene targets and processes for powdery mildew control
Abstract Spray‐induced gene silencing (SIGS) is an emerging tool for crop pest protection. It utilizes exogenously applied double‐stranded RNA to specifically reduce pest target gene expression using endogenous RNA interference machinery. In this study, SIGS methods were developed and optimized for powdery mildew fungi, which are widespread obligate biotrophic fungi that infect agricultural crops, using the known azole‐fungicide target cytochrome P450 51 (CYP51) in the Golovinomyces orontii–Arabidopsis thaliana pathosystem. Additional screening resulted in the identification of conserved gene targets and processes important to powdery mildew proliferation: apoptosis‐antagonizing transcription factor in essential cellular metabolism and stress response; lipid catabolism genes lipase a , lipase 1 , and acetyl‐CoA oxidase in energy production ; and genes involved in manipulation of the plant host via abscisic acid metabolism ( 9‐cis‐epoxycarotenoid dioxygenase , xanthoxin dehydrogenase , and a putative abscisic acid G‐protein coupled receptor ) and secretion of the effector protein, effector candidate 2 . Powdery mildew is the dominant disease impacting grapes and extensive powdery mildew resistance to applied fungicides has been reported. We therefore developed SIGS for the Erysiphe necator–Vitis vinifera system and tested six successful targets identified using the G. orontii–A. thaliana system. For all targets tested, a similar reduction in powdery mildew disease was observed between systems. This indicates screening of broadly conserved targets in the G. orontii–A. thaliana pathosystem identifies targets and processes for the successful control of other powdery mildew fungi. The efficacy of SIGS on powdery mildew fungi makes SIGS an exciting prospect for commercial powdery mildew control.
59 BASIC BIOLOGICAL SCIENCES↗
Suppression of a single BAHD gene in Setaria viridis causes large, stable decreases in cell wall feruloylation and increases biomass digestibility
Summary Feruloylation of arabinoxylan ( AX ) in grass cell walls is a key determinant of recalcitrance to enzyme attack, making it a target for improvement of grass crops, and of interest in grass evolution. Definitive evidence on the genes responsible is lacking so we studied a candidate gene that we identified within the BAHD acyl‐CoA transferase family. We used RNA interference (RNAi) silencing of orthologs in the model grasses Setaria viridis ( Sv BAHD 01 ) and Brachypodium distachyon ( Bd BAHD 01 ) and determined effects on AX feruloylation. Silencing of Sv BAHD 01 in Setaria resulted in a c . 60% decrease in AX feruloylation in stems consistently across four generations. Silencing of Bd BAHD 01 in Brachypodium stems decreased feruloylation much less, possibly due to higher expression of functionally redundant genes. Setaria Sv BAHD 01 RNA i plants showed: no decrease in total lignin, approximately doubled arabinose acylated by p ‐coumarate, changes in two‐dimensional NMR spectra of unfractionated cell walls consistent with biochemical estimates, no effect on total biomass production and an increase in biomass saccharification efficiency of 40–60%. We provide the first strong evidence for a key role of the BAHD 01 gene in AX feruloylation and demonstrate that it is a promising target for improvement of grass crops for biofuel, biorefining and animal nutrition applications.
59 BASIC BIOLOGICAL SCIENCES↗
Amplification and adaptation of centromeric repeats in polyploid switchgrass species
Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats from a single satellite repeat family. Why centromeres are dominated by a single satellite repeat and how the satellite repeats originate and evolve are among the most intriguing and long-standing questions in centromere biology. We identified eight satellite repeats in the centromeres of tetraploid switchgrass (Panicum virgatum). Seven repeats showed characteristics associated with classical centromeric repeats with monomeric lengths ranging from 166 to 187 bp. Interestingly, these repeats share an 80-bp DNA motif. We demonstrate that this 80-bp motif may dictate translational and rotational phasing of the centromeric repeats with the cenH3 nucleosomes. The sequence of the last centromeric repeat, Pv156, is identical to the 5S ribosomal RNA genes. We demonstrate that a 5S ribosomal RNA gene array was recruited to be the functional centromere for one of the switchgrass chromosomes. Our findings reveal that certain types of satellite repeats, which are associated with unique sequence features and are composed of monomers in mono-nucleosomal length, are favorable for centromeres. Centromeric repeats may undergo dynamic amplification and adaptation before the centromeres in the same species become dominated by the best adapted satellite repeat.
59 BASIC BIOLOGICAL SCIENCES↗
BUZZ : an essential gene for postinitiation root hair growth and a mediator of root architecture in Brachypodium distachyon
Here, we discover a player in root development. Recovered from a forward-genetic screen in Brachypodium distachyon, the buzz mutant initiates root hairs but they fail to elongate. In addition, buzz roots grow twice as fast as wild-type roots. Also, lateral roots show increased sensitivity to nitrate, whereas primary roots are less sensitive to nitrate. Using whole-genome resequencing, we identified the causal single nucleotide polymorphism as occurring in a conserved but previously uncharacterized cyclin-dependent kinase (CDK)-like gene. The buzz mutant phenotypes are rescued by the wild-type B. distachyon BUZZ coding sequence and by an apparent homolog in Arabidopsis thaliana. Moreover, T-DNA mutants in A. thaliana BUZZ have shorter root hairs. BUZZ mRNA localizes to epidermal cells and develops root hairs and, in the latter, partially colocalizes with the NRT1.1A nitrate transporter. Based on qPCR and RNA-Seq, buzz overexpresses ROOT HAIRLESS LIKE SIX-1 and -2 and misregulates genes related to hormone signaling, RNA processing, cytoskeletal, and cell wall organization, and to the assimilation of nitrate. Overall, these data demonstrate that BUZZ is required for tip growth after root hair initiation and root architectural responses to nitrate.
59 BASIC BIOLOGICAL SCIENCES↗
Osmotic stress-responsive promoter upstream transcripts (PROMPTs) act as carriers of MYB transcription factors to induce the expression of target genes in Populus simonii
Complex RNA transcription and processing produces a diverse range catalog of long noncoding RNAs (lncRNAs), important biological regulators that have been implicated in osmotic stress responses in plants. Promoter upstream transcript (PROMPT) lncRNAs share some regulatory elements with the promoters of their neighbouring protein-coding genes. However, their function remains unknown. Here, using strand-specific RNA sequencing, we identified 209 differentially regulated osmotic-responsive PROMPTs in poplar (Populus simonii). PROMPTs are transcribed bidirectionally and are more stable than other lncRNAs. Co-expression analysis of PROMPTs and protein-coding genes divided the regulatory network into five independent subnetworks including 27 network modules. Significantly enriched PROMPTs in the network were selected to validate their regulatory roles. We used delaminated layered double hydroxide lactate nanosheets (LDH-lactate-NS) to transport synthetic nucleic acids into live tissues to mimic overexpression and interference of a specific PROMPT. The altered expression of PROMPT_1281 induced the expression of its cis and trans targets, and this interaction was governed by its secondary structure rather than just its primary sequence. Based on this example, we proposed a model that a concentration gradient of PROMPT_1281 is established, which increases the probability of its interaction with targets near its transcription site that shares common motifs. Our results firstly demonstrated that PROMPT_1281 act as carriers of MYB transcription factors to induce the expression of target genes under osmotic stress. In sum, our study identified and validated a set of poplar PROMPTs that likely have regulatory functions in osmotic responses.
59 BASIC BIOLOGICAL SCIENCES↗
De novo transcriptome sequencing of Capsicum frutescens . L and comprehensive analysis of salt stress alleviating mechanism by Bacillus atrophaeus WU ‐9
Abstract Salt stress, as one of the most severe environmental stresses, can cause a series of changes in plants. However, the explanation of plant salt stress alleviating mechanism of plant growth–promoting rhizobacteria (PGPR) was hindered by the limited availability of transcriptomic information for salt stress‐treated plants grown in a microorganism‐controlled environment. Our previous reports have selected Bacillus atrophaeus WU‐9 as PGPR significantly alleviating pepper ( Capsicum frutescens . L) salt stress. In this work, the RNA‐seq analysis of salt stress‐treated and untreated plants, grown with and without WU‐9 in a microorganism‐controlled environment, was used to reveal the plant salt stress alleviating mechanisms of WU‐9. Twelve sequencing libraries, prepared by treating with WU‐9 and salt (150 mM NaCl for 36 h), were constructed by RNA‐Seq technique. Non‐inoculated seedlings mainly respond to salt stress through regulation of signal transduction, such as ethylene‐activated signaling pathway, signaling and cell communication, etc. And ethylene signal participated in salt stress response in pepper through regulating defense responses, fruit ripening and senescence. WU‐9 inoculation under salt stress mainly improves salt tolerance and plant growth by regulating salt stress‐responding ethylene and auxin signal transduction, utilization of proline, photosynthesis, antioxidant enzyme activities and cell enlargement. Furthermore, 86 differentially expressed genes and 20 transcription factors were identified as associated with salt stress response and tolerance. Thus, this innovative transcriptomic study identified the salt stress response and alleviation in C. frutescens . L with PGPR inoculation. This result provided novel insights into the salinity alleviation in pepper regulated by PGPR.
Wang, Wenfei↗
A systems biology approach identifies new regulators of poplar root development under low nitrogen
Summary In Populus , low nitrogen ( LN ) elicits rapid and vigorous lateral root ( LR ) proliferation, which is closely mirrored by corresponding transcriptomic changes. Using transcriptomic data, we built a genetic network encompassing a large proportion of the differentially regulated transcriptome. The network is organized in a hierarchical fashion, centered on 11 genes. Transgenic manipulations of only three of the 11 genes had a strong impact on root development under LN . These three genes encoded an F‐box protein similar to Hawaiian Skirt ( Pta HWS ) and two transcription factors ( Pta RAP 2.11 and Pta NAC 1 ). Up‐ and downregulation of the three genes caused increased and decreased root proliferation under LN conditions, respectively. The transgenic manipulations had a strong positive effect on growth under greenhouse conditions including increased shoot and root biomass. The three genes appeared to encompass a putative yet‐unknown mechanism that underlies root development under LN . Specifically, the genes are predominantly expressed in roots and have a similar temporal response to LN . More importantly, transgenic manipulation for each of the three genes had a highly significant impact on the expression of the other two. The transgenic manipulations appear to also affect the expression of the regulatory mi RNA ( Ptami RNA 164e ) of one of the transcription factors ( Pta NAC 1 ), albeit in an opposite fashion. Consistent with a putative function of Pta HWS in proteasome degradation, treatment with proteasome inhibitor reversed the expression changes in the transgenic plants. The insights from this study will allow genetic modifications of root architecture for more efficient and dynamic nitrogen foraging in biofuel crops like poplar.
Dash, Madhumita↗
Know your enemy, embrace your friend: using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms
Summary Microorganisms, or ‘microbes’, have formed intimate associations with plants throughout the length of their evolutionary history. In extant plant systems microbes still remain an integral part of the ecological landscape, impacting plant health, productivity and long‐term fitness. Therefore, to properly understand the genetic wiring of plants, we must first determine what perception systems plants have evolved to parse beneficial from commensal from pathogenic microbes. In this review, we consider some of the most recent advances in how plants respond at the molecular level to different microbial lifestyles. Further, we cover some of the means by which microbes are able to manipulate plant signaling pathways through altered destructiveness and nutrient sinks, as well as the use of effector proteins and micro‐ RNA s (mi RNA s). We conclude by highlighting some of the major questions still to be answered in the field of plant‐microbe research, and suggest some of the key areas that are in greatest need of further research investment. The results of these proposed studies will have impacts in a wide range of plant research disciplines and will, ultimately, translate into stronger agronomic crops and forestry stock, with immune perception and response systems bred to foster beneficial microbial symbioses while repudiating pathogenic symbioses.
Plett, Jonathan M.↗
Virus-induced gene editing of stomatal regulators in Nicotiana benthamiana enables rapid functional genomics
Virus-induced gene editing (VIGE) holds promise as a rapid and scalable approach for functional genomics in plants. Here, we apply a tobacco rattle virus (TRV)-based single-guide RNA (sgRNA) delivery system to target key regulators of stomatal development in Nicotiana benthamiana using transgenic Cas9-expressing lines. sgRNAs fused to a mobile RNA element and co-delivered with TRV enabled both somatic and heritable genome editing across orthologs of STOMAGEN, EPF2, YODA, and SPEECHLESS. Somatic editing frequencies reached up to 95%, and heritable tetra-allelic mutations were recovered in multiple target genes. Mutants exhibited significant, gene-specific changes in stomatal density, with corresponding effects on leaf temperature indicative of altered evaporative cooling. Additionally, sgRNAs fused to an AmCyan reporter enabled visualization of virus-infected tissues, allowing stomatal phenotyping in edited M0 sectors. This TRV-based platform facilitates functional assessment of genes influencing stomatal patterning and offers a powerful tool for dissecting gene function in a developmentally and physiologically relevant context.
60 APPLIED LIFE SCIENCES↗
Development and evaluation of a Novel RT‐PCR system for reliable and rapid SARS‐CoV ‐2 screening of blood donations
Abstract Background The ongoing outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has caused great global concerns. In contrast to SARS, some SARS‐CoV‐2–infected people can be asymptomatic or have only mild nonspecific symptoms. Furthermore, there is evidence that SARS‐CoV‐2 may be infectious during an asymptomatic incubation period. With the discovery that SARS‐CoV‐2 can be detected in plasma or serum, blood safety is worthy of consideration. Study Design and Methods We developed a nucleic acid test (NAT) screening system for SARS‐CoV‐2 targeting nucleocapsid protein (N) and open reading frame 1ab (ORF 1ab) gene that could screen 5076 samples every 24 hours. The 2019 novel coronavirus RNA standard was used to evaluate linearity of standard curves. Diagnostic sensitivity and reproducibility were evaluated using artificial SARS‐CoV‐2. Specificity was evaluated with 61 other respiratory pathogens. Diagnostic performance was evaluated by testing two sputum and nine oropharyngeal swab specimens. The reverse transcription polymerase chain reaction (RT‐PCR) assay was used to screen SARS‐CoV‐2 RNA in blood donor specimens collected during the outbreak of SARS‐CoV‐2 in Chengdu. Results Limits of detection of the SARS‐CoV‐2 RT‐PCR assay for N and ORF 1ab gene were 12.5 and 27.58 copies/mL, respectively. Intra‐assay and interassay for the SARS‐CoV‐2 RT‐PCR assay based on cycle threshold were acceptably low. No cross‐reactivity was observed with other respiratory virus and bacterial isolates. The overall agreement value between the SARS‐CoV‐2 RT‐PCR assay and clinical diagnostic results was 100%. A total of 16 287 blood specimens collected from blood donors during SARS‐CoV‐2 surveillance were tested negative. Conclusions A high‐throughput NAT screening system was developed for SARS‐CoV‐2 screening of blood donations during the outbreak of SARS‐CoV‐2.
Li, Meng↗
Validation of Numerical Models of the Offshore Wind Turbine From the Alpha Ventus Wind Farm Against Full-Scale Measurements Within OC5 Phase III
The main objective of the Offshore Code Comparison Collaboration Continuation, with Correlation (OC5) project is validation of aero-hydro-servo-elastic simulation tools for offshore wind turbines (OWTs) through comparison of simulated results to the response data of physical systems. Phase III of the OC5 project validates OWT models against the measurements recorded on a Senvion 5M wind turbine supported by the OWEC Quattropod from the alpha ventus offshore wind farm. The following operating conditions of the wind turbine were chosen for the validation: (1) idling below the cut-in wind speed, (2) rotor-nacelle assembly (RNA) rotation maneuver below the cut-in wind speed, (3) power production below and above the rated wind speed, and (4) shutdown. A number of validation load cases were defined based on these operating conditions. The following measurements were used for validation: (1) strains and accelerations recorded on the support structure and (2) pitch, yaw, and azimuth angles, generator speed, and electrical power recorded from the RNA. Strains were not directly available from the majority of the OWT simulation tools; therefore, strains were calculated based on out-of-plane bending moments, axial forces, and cross-sectional properties of the structural members. The simulation results and measurements were compared in terms of time series, discrete Fourier transforms, power spectral densities, and probability density functions of strains and accelerometers. A good match was achieved between the measurements and models setup by OC5 Phase III participants.
17 WIND ENERGY↗
Validation of Numerical Models of the Offshore Wind Turbine From the Alpha Ventus Wind Farm Against Full-Scale Measurements Within OC5 Phase III
The main objective of the Offshore Code Comparison Collaboration Continuation, with Correlation (OC5) project is validation of aero-hydro-servo-elastic simulation tools for offshore wind turbines (OWTs) through comparison of simulated results to the response data of physical systems. Phase III of the OC5 project validates OWT models against the measurements recorded on a Senvion 5M wind turbine supported by the OWEC Quattropod from the alpha ventus offshore wind farm. The following operating conditions of the wind turbine were chosen for the validation: (1) Idling below the cut-in wind speed; (2) Rotor-nacelle assembly (RNA) rotation maneuver below the cut-in wind speed; (3) Power production below and above the rated wind speed; and (4) Shutdown. A number of validation load cases were defined based on these operating conditions. The following measurements were used for validation: (1) Strains and accelerations recorded on the support structure; (2) Pitch, yaw, and azimuth angles, generator speed, and electrical power recorded from the RNA. Strains were not directly available from the majority of the OWT simulation tools. Therefore, strains were calculated based on out-of-plane bending moments, axial forces, and cross-sectional properties of the structural members. Also, a number of issues arose during the validation: (1) The need for a thorough quality check of sensor measurements; (2) The sensitivity of the turbine loads to the controller and airfoil properties, which were only approximated in the modeling approach; (3) The importance of estimating and applying an appropriate damping value for the structure; and (4) The importance of wind characteristics beyond turbulence on the loads. The simulation results and measurements were compared in terms of time series, discrete Fourier transforms, power spectral densities, probability density functions of strains and accelerometers. A good match was achieved between the measurements and models set up by OC5 Phase III participants.
17 WIND ENERGY↗
A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9
The Cas9 endonuclease is widely used for genome engineering applications by programming its single-guide RNA, and ongoing work is aimed at improving the accuracy and efficiency of DNA targeting. DNA cleavage of Cas9 is controlled by the conformational state of the HNH nuclease domain, but the mechanism that governs HNH activation at on-target DNA while reducing cleavage activity at off-target sites remains poorly understood. Using single-molecule Förster resonance energy transfer, we identified an intermediate state of Streptococcus pyogenes Cas9, representing a conformational checkpoint between DNA binding and cleavage. Upon DNA binding, the HNH domain transitions between multiple conformations before docking into its active state. HNH docking requires divalent cations, but not strand scission, and this docked conformation persists following DNA cleavage. Sequence mismatches between the DNA target and guide RNA prevent transitions from the checkpoint intermediate to the active conformation, providing selective avoidance of DNA cleavage at stably bound off-target sites.
59 BASIC BIOLOGICAL SCIENCES↗
Refine your search to explore more results.