A Novel Target of IscS in Escherichia coli: Participating in DNA Phosphorothioation

Many bacterial species modify their DNA with the addition of sulfur to phosphate groups, a modification known as DNA phosphorothioation. DndA is known to act as a cysteine desulfurase, catalyzing a key biochemical step in phosphorothioation. However, bioinformatic analysis revealed that 19 out of the 31 known dnd gene clusters, contain only four genes (dndB-E), lacking a key cysteine desulfurase corresponding gene. There are multiple cysteine desulfurase genes in Escherichia coli, but which one of them participates into DNA phosphorothioation is unknown. Here, by employing heterologous expression of the Salmonella enterica dnd gene cluster named dptBCDE in three E. coli mutants, each of which lacked a different cysteine desulfurase gene, we show that IscS is the only cysteine desulfurase that collaborates with dptB-E, resulting in DNA phosphorothioation. Using a bacterial two-hybrid system, protein interactions between IscS and DptC, and IscS and DptE were identified. Our findings revealed IscS as a key participant in DNA phosphorothioation and lay the basis for in-depth analysis of the DNA phosphorothioation biochemical pathway.     

Phenylalanine 90 and 93 are localized within the phenol binding site of human UDP-glucuronosyltransferase 1A10 as determined by photoaffinity labeling, mass spectrometry, and site-directed mutagenesis

4-Azido-2-hydroxybenzoic acid (4-AzHBA), a novel photoactive benzoic acid derivative, has been synthesized and used as a photoprobe to identify the phenol binding site of UDP-glucuronosyltransferases (UGTs). Analysis of recombinant His-tag UGTs from the 1A family for their ability to glucuronidate p-nitrophenol (pNP) and 4-methylumbelliferone (4-MU) revealed that UGT1A10 shows high activity toward phenols and phenol derivatives. Purified UGT1A10 was photolabeled with 4-AzHBA, digested with trypsin, and analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-mass spectrometry. A single modified peak corresponding to amino acid residues 89-98 (EFMVFHAQWK) of UGT1A10 was identified. The attachment site of the 4-AzHBA probe was localized to the quadruplet Phe(90)-Met(91)-Val(92)-Phe(93) using ESI LC-MS/MS. Sequence alignment revealed that the Phe(90) and Phe(93) are conserved in UGT1A7-10. Site-directed mutagenesis of these two amino acids was then followed by kinetic analysis of the mutants with two phenolic substrates, pNP and 4-MU, containing one and two planar rings, respectively. Using the combination of photoaffinity labeling, enzymatic digestion, MALDI-TOF and LC-MS mass spectrometry, and site-directed mutagenesis, we have determined for the first time that Phe(90) and Phe(93) are directly involved in the catalytic activity of UGT1A10 toward 4-MU and pNP.     

Polymorphism of rs3737597 in DISC1 Gene on Chromosome 1q42.2 in sALS Patients: a Chinese Han Population Case-Control Study

Although lots of genes have been revealed to relate to sporadic amyotrophic lateral sclerosis (sALS), its genetic mechanisms still need to be further explored. We aimed to search the novel genetic factors of sALS and assess their contribution. We constructed an integrative dataset based on the 3227 subsignificant genes (P value?<?0.01) from two sALS-related genome-wide association studies (GWAS) (the US and Irish studies). A significant replication between both studies was confirmed by the gene set enrichment analysis in the integral level (P value?<?10^?4). Using the pathway overrepresentation analysis, we revealed the 34 shared Gene Ontology (GO) biological processes from the two independent studies (P value?<?0.01). Among these pathways, the nervous system developmental pathway (NSD function, GO:0007399) was further supported by the previously reported genes related to sALS (P value?=?3.28e?12). Importantly, four of 17 NSD-function-related target genes (disrupted-in-schizophrenia-1 (DISC1), CNTN4, NRXN3, and ERBB4) presented a considerable association with sALS in both studies. To further verify the association between the NSD function target genes and sALS, we preformed a two-stage case–control study based on 500 sALS patients and 500 controls of Chinese Han populations from mainland. A polymorphism of rs3737597 in DISC1 gene involved in the nervous system developmental pathway was closely associated with sALS. The nervous system developmental pathway is a potential pathogenesis of sALS, among them, the polymorphism of rs3737597 in DISC1 might play some roles.     

Distribution of shrublands in relation to soil and climate in mid-subtropical China

Aims Understanding relationships between vegetation and environments is of importance for ecosystem restoration and management. However, information on how environments influence the floristic patterns of shrublands is lack, especially in the subtropical China. In this study, we explored how environments regulate species composition of shrublands at landscape scale in mid-subtropical China.Methods We investigated species composition and measured the climate and soil environments for 207 shrubland plots in mid-subtropical China (24°39′–30°08′N, 108°47′–114°15′E). We applied a hierarchical cluster analysis and indicator species analysis based on the Bray–Curtis similarity index to identify the main shrubland types and employed principal coordinate analysis (PCoA) to explore the relationship between floristic composition and environment.Important findings We identified four shrubland types occurring in different environmental conditions. Montane shrubland, dominated by species suitable for cool climates (e.g. Rhododendron simsii), were distributed in steep areas at comparatively high altitudes; foothill shrubland, dominated by mesophilous species (e.g. Loropetalum chinense), were distributed in low mountains and hills; pioneer shrubland, dominated by fast grow and short-life cycles species (e.g. Rhus chinensis), were distributed at low altitudes with dense population; and finally, limestone shrubland, dominated by calcicole plants (e.g. Coriaria nepalensis), were distributed in the extensive karst areas. Communities occurring in high pH soils were completely separated from those in low pH soils according to the hierarchical cluster analysis. PCoA ordination associated the four types with distinct edaphic and climatic gradients. Soil pH explained 63.3% of variation in PCoA, followed by soil depth and soil bulk density.     

GID1 modulates stomatal response and submergence tolerance involving abscisic acid and gibberellic acid signaling in rice

Plant responses to abiotic stresses are coordinated by arrays of growth and developmental programs.Gibberellic acid(CA) and abscisic acid(ABA) play critical roles in the developmental programs and environmental responses,respectively,through complex signaling and metabolism networks.However,crosstalk between the two phytohormones in stress responses remains largely unknown.In this study,we report that CIBBERELLIN-INSENSITIVE DWARF 1(GID1),a soluble receptor for GA,regulates stomatal development and patterning in rice(Oryza sativa L.).The gid1 mutant showed impaired biosynthesis of endogenous ABA under drought stress conditions,but it exhibited enhanced sensitivity to exogenous ABA.Scanning electron microscope and infrared thermal image analysis indicated an increase in the stomatal conductance in the gid1 mutant under drought conditions.Interestingly,the gid1 mutant had increased levels of chlorophyll and carbohydrates under submergence conditions,and showed enhanced reactive oxygen species(ROS)-scavenging ability and submergence tolerance compared with the wild-type.Further analyses suggested that the function of GID1 in submergence responses is partially dependent on ABA,and GA signaling by GID1 is involved in submergence tolerance by modulating carbohydrate consumption.Taken together,these findings suggest GID1 plays distinct roles in stomatal response and submergence tolerance through both the ABA and GA signaling pathways in rice.