PRMD: an integrated database for plant RNA modifications.

The scope and function of RNA modifications in model plant systems have been extensively studied, resulting in the identification of an increasing number of novel RNA modifications in recent years. Researchers have gradually revealed that RNA modifications, especially N6-methyladenosine (m6A), which is one of the most abundant and commonly studied RNA modifications in plants, have important roles in physiological and pathological processes. These modifications alter the structure of RNA, which affects its molecular complementarity and binding to specific proteins, thereby resulting in various of physiological effects. The increasing interest in plant RNA modifications has necessitated research into RNA modifications and associated datasets. However, there is a lack of a convenient and integrated database with comprehensive annotations and intuitive visualization of plant RNA modifications. Here, we developed the Plant RNA Modification Database (PRMD; http://bioinformatics.sc.cn/PRMD and http://rnainformatics.org.cn/PRMD) to facilitate RNA modification research. This database contains information regarding 20 plant species and provides an intuitive interface for displaying information. Moreover, PRMD offers multiple tools, including RMlevelDiff, RMplantVar, RNAmodNet and Blast (for functional analyses), and mRNAbrowse, RNAlollipop, JBrowse and Integrative Genomics Viewer (for displaying data). Furthermore, PRMD is freely available, making it useful for the rapid development and promotion of research on plant RNA modifications.

The genetic basis of grain protein content in rice by genome-wide association analysis.

The grain protein content (GPC) of rice is an important factor that determines its nutritional, cooking, and eating qualities. To date, although a number of genes affecting GPC have been identified in rice, most of them have been cloned using mutants, and only a few genes have been cloned in the natural population. In this study, 135 significant loci were detected in a genome-wide association study (GWAS), many of which could be repeatedly detected across different years and populations. Four minor quantitative trait loci affecting rice GPC at four significant association loci, qPC2.1, qPC7.1, qPC7.2, and qPC1.1, were further identified and validated in near-isogenic line F2 populations (NIL-F2), explaining 9.82, 43.4, 29.2, and 13.6% of the phenotypic variation, respectively. The role of the associated flo5 was evaluated with knockdown mutants, which exhibited both increased grain chalkiness rate and GPC. Three candidate genes in a significant association locus region were analyzed using haplotype and expression profiles. The findings of this study will help elucidate the genetic regulatory network of protein synthesis and accumulation in rice through cloning of GPC genes and provide new insights on dominant alleles for marker-assisted selection in the genetic improvement of rice grain quality. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01347-z.

Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling.

Upstream open reading frames (uORFs) are typically defined as translation sites located within the 5' untranslated region upstream of the main protein coding sequence (CDS) of messenger RNAs (mRNAs). Although uORFs are prevalent in eukaryotic mRNAs and modulate the translation of downstream CDSs, a comprehensive resource for uORFs is currently lacking. We developed Ribo-uORF (http://rnainformatics.org.cn/RiboUORF) to serve as a comprehensive functional resource for uORF analysis based on ribosome profiling (Ribo-seq) data. Ribo-uORF currently supports six species: human, mouse, rat, zebrafish, fruit fly, and worm. Ribo-uORF includes 501 554 actively translated uORFs and 107 914 upstream translation initiation sites (uTIS), which were identified from 1495 Ribo-seq and 77 quantitative translation initiation sequencing (QTI-seq) datasets, respectively. We also developed mRNAbrowse to visualize items such as uORFs, cis-regulatory elements, genetic variations, eQTLs, GWAS-based associations, RNA modifications, and RNA editing. Ribo-uORF provides a very intuitive web interface for conveniently browsing, searching, and visualizing uORF data. Finally, uORFscan and UTR5var were developed in Ribo-uORF to precisely identify uORFs and analyze the influence of genetic mutations on uORFs using user-uploaded datasets. Ribo-uORF should greatly facilitate studies of uORFs and their roles in mRNA translation and posttranscriptional control of gene expression.

OsPP65 Negatively Regulates Osmotic and Salt Stress Responses Through Regulating Phytohormone and Raffinose Family Oligosaccharide Metabolic Pathways in Rice.

Although type 2C protein phosphatases (PP2Cs) have been demonstrated to play important roles in regulating plant development and various stress responses, their specific roles in rice abiotic stress tolerance are still largely unknown. In this study, the functions of OsPP65 in rice osmotic and salt stress tolerance were investigated. Here, we report that OsPP65 is responsive to multiple stresses and is remarkably induced by osmotic and salt stress treatments. OsPP65 was highly expressed in rice seedlings and leaves and localized in the nucleus and cytoplasm. OsPP65 knockout rice plants showed enhanced tolerance to osmotic and salt stresses. Significantly higher induction of genes involved in jasmonic acid (JA) and abscisic acid (ABA) biosynthesis or signaling, as well as higher contents of endogenous JA and ABA, were observed in the OsPP65 knockout plants compared with the wild-type plants after osmotic stress treatment. Further analysis indicated that JA and ABA function independently in osmotic stress tolerance conferred by loss of OsPP65. Moreover, metabolomics analysis revealed higher endogenous levels of galactose and galactinol but a lower content of raffinose in the OsPP65 knockout plants than in the wild-type plants after osmotic stress treatment. These results together suggest that OsPP65 negatively regulates osmotic and salt stress tolerance through regulation of the JA and ABA signaling pathways and modulation of the raffinose family oligosaccharide metabolism pathway in rice. OsPP65 is a promising target for improvement of rice stress tolerance using gene editing.

The Inhibitory Effects of Ketamine on Human Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels and Action Potential in Rabbit Sinoatrial Node.

AIMS: To investigate the effects of ketamine on human hyperpolarization-activated cyclic nucleotide-gated (hHCN) 1, 2, 4 channel currents expressed in Xenopus oocytes and spontaneous action potentials (APs) of rabbit sinoatrial node (SAN). METHODS: The 2-electrode voltage clamp and standard microelectrode techniques were respectively applied to record hHCN channels currents expressed in Xenopus oocytes and APs of SAN separated from rabbit heart. RESULTS: Ketamine (1-625 µmol/L) blocked hHCN1, 2, and 4 currents with IC50 of 67.0, 89.1, and 84.0 µmol/L, respectively, in a concentration-dependent manner. The currents were rapidly blocked by ketamine and partially recovered after washout. The steady-state activation curves of hHCN1, 2, and 4 currents demonstrated a concentration-dependent shift to the left and the rates of activation were significantly decelerated. But ketamine blocked hHCN channels in a voltage-independence and non-use-dependent manner, and did not modify the voltage dependence of activation and reversal potentials. Furthermore, ketamine suppressed phase-4 spontaneous depolarization rate in isolated rabbit SAN and decreased the beat rates in a concentration-dependent manner. CONCLUSION: Ketamine could inhibit hHCN channels expressed in Xenopus oocytes in a concentration-dependent manner as a close-state blocker and decrease beat rates of isolated rabbit SAN. This study may provide novel insights into other unexplained actions of ketamine.

Blockade of the human ether-a-go-go-related gene potassium channel by ketamine.

OBJECTIVES: The inhibition of the cardiac rapid delayed rectifier potassium current (IKr ) and its cloned equivalent human ether-a-go-go-related gene (hERG) channel illustrate QT interval prolonging effects of a wide range of clinically used drugs. In this study, the direct interaction of the intravenous anaesthetic ketamine with wild-type (WT) and mutation hERG currents (IhERG ) was investigated. METHODS: The hERG channel (WT, Y652A and F656A) was expressed in Xenopus oocytes and studied using standard two-microelectrode voltage-clamp techniques. KEY FINDINGS: WT hERG is blocked in a concentration-dependent manner with IC50 = 12.05 ± 1.38 µm by ketamine, and the steady-state inactivation curves are shifted to more negative potentials (about -27 mV). The mutation to Ala of Y652 and F656 located on the S6 domain attenuate IhERG blockade by ketamine, and produced approximately 9-fold and 2.5-fold increases in IC50 compared with that of WT hERG channel, respectively. CONCLUSIONS: Ketamine blocks WT IhERG expressed in Xenopus oocytes in a concentration-dependent manner and predominantly interacts with the open hERG channels. The interaction of ketamine with hERG channel may involve the aromatic residues Tyr652 and Phe656.

Blocking effects of acehytisine on pacemaker currents (I(f)) in sinoatrial node cells and human HCN4 channels expressed in Xenopus laevis oocytes.

ETHNOPHARMACOLOGICAL RELEVANCE: The root of Aconitum coreanum (Levl.) Raipaics has been extensively used to treat various kinds of disorders including cardiovascular disease in China for a long time. According to recent studies, its antiarrhythmic actions are attributable to the active component, acehytisine. However, the underlying mechanism remains poorly understood. AIM OF THE STUDY: The effects of acehytisine on the spontaneous activity in sinoatrial nodes and the electropharmacological action of this drug on I(f) in pacemaker cells and hHCN4 channels in oocytes were to be investigated. MATERIALS AND METHODS: Sinoatrial nodes were cut from rabbit heart, and transmembrane potentials were recorded by standard microelectrode technique. A whole-cell patch clamp technique was employed to record I(f) isolated enzymatically from rabbit sinoatrial node pacemaker cells. Human HCN4 channels were heterologously expressed in Xenopus oocytes and studied using the two-electrode voltage clamp technique. RESULTS: Acehytisine decreased the pacemaker rate of firing and slope of diastolic depolarization, modified the action potential configurations and blocked I(f) in rabbit sinoatrial node cells and hHCN4 channels expressed in Xenopus oocytes in a concentration-dependent, voltage-independent and non-use-dependent manner. Its electropharmacological properties were consistent with those of a close-state blocker. CONCLUSION: Our findings are likely to shed light on the clinical application of acehytisine in the treatment of cardiovascular disorders.

Novel electropharmacological activity of amiodarone on human HCN channels heterologously expressed in the Xenopus oocytes.

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels underlie the pacemaker currents (I(f)) in cardiac cells. The objectives of this study were to investigate the electropharmacological activity of amiodarone on human HCN channels heterologously expressed in Xenopus laevis oocytes. hHCN channels were expressed in oocytes and studied using the standard two-electrode voltage-clamp techniques. The results show that amiodarone blocks hHCN channels heterologously expressed in the Xenopus oocytes in a concentration- and use-dependent manner, but doesn't modify the voltage dependence of activation and reversal potentials. And the removal of blockage of HCN channels by amiodarone was favored by inward current flow, not by hyperpolarizing potential. Characteristics of blockage on hHCN channels were consistent with those of amiodarone as "trapped" drugs on human ether-a-go-go-related gene (HERG) channels. These results will be useful for elucidating the potentially antiarrhythmic mechanism of amiodarone.

Blocking effect of methylflavonolamine on human Na(V)1.5 channels expressed in Xenopus laevis oocytes and on sodium currents in rabbit ventricular myocytes.

AIM: To investigate the blocking effects of methylflavonolamine (MFA) on human Na(V)1.5 channels expressed in Xenopus laevis oocytes and on sodium currents (I(Na)) in rabbit ventricular myocytes. METHODS: Human Na(V)1.5 channels were expressed in Xenopus oocytes and studied using the two-electrode voltage-clamp technique. I(Na) and action potentials in rabbit ventricular myocytes were studied using the whole-cell recording. RESULTS: MFA and lidocaine inhibited human Na(V)1.5 channels expressed in Xenopus oocytes in a positive rate-dependent and concentration-dependent manner, with IC(50) values of 72.61 micromol/L and 145.62 micromol/L, respectively. Both of them markedly shifted the steady-state activation curve of I(Na) toward more positive potentials, shifted the steady-state inactivation curve of I(Na) toward more negative potentials and postponed the recovery of the I(Na) inactivation state. In rabbit ventricular myocytes, MFA inhibited I(Na) with a shift in the steady-state inactivation curve toward more negative potentials, thereby postponing the recovery of the I(Na) inactivation state. This shift was in a positive rate-dependent manner. Under current-clamp mode, MAF significantly decreased action potential amplitude (APA) and maximal depolarization velocity (V(max)) and shortened action potential duration (APD), but did not alter the resting membrane potential (RMP). The demonstrated that the kinetics of sodium channel blockage by MFA resemble those of class I antiarrhythmic agents such as lidocaine. CONCLUSION: MFA protects the heart against arrhythmias by its blocking effect on sodium channels.

Block effect of capsaicin on hERG potassium currents is enhanced by S6 mutation at Y652.

The objectives of this study were to investigate the inhibitory action of capsaicin on wild-type (WT) and mutation human ether-a-go-go-related gene (hERG) potassium channel currents (I(hERG)), and to determine whether mutations in the S6 region are significant for the inhibition of I(hERG) by capsaicin. The hERG channel (WT, Y652A and F656A) was expressed in Xenopus oocytes and studied using standard two-microelectrode voltage-clamp techniques. The results show that capsaicin blocks WT hERG in a concentration-dependent manner, with an IC(50) of 17.45microM and a negative shift in the steady-state inactivation curve. Characteristics of blockade were consistent with capsaicin causing components of block in both the closed and open channel states. However, mutating the Y652 residue to Ala enhances the blockade effect of capsaicin with an IC(50) of 4.11microM, whereas mutation of F656A does not significantly alter drug potency. Simultaneously, for Y652A, the steady-state activation parameter is shifted to a more positive value by 5mV and the inactivation parameter is shifted to a more negative value by -29mV in the presence of 25microM capsaicin. In conclusion, capsaicin blocks hERG channels by binding to both the closed and open channel states.Y652 was important as a molecular determinant of blockade. Mutation Y652A enhances the drug block, which may cause some patients to be particularly sensitive to capsaicin clinically.