Streptomyces herbicida sp. nov., a novel actinomycete with antibacterial and herbicidal activity isolated from soil.

A novel actinobacterial strain (NEAU-HV9T) showing antibacterial activity against Ralstonia solanacearum and herbicidal activity against Amaranthus retroflexus L. was isolated from soil sampled in Bama yao Autonomous County, Hechi City, Guangxi Zhuang Autonomous Region. The strain is aerobic and Gram-positive. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-HV9T belonged to the genus Streptomyces and showed high 16S rRNA sequence similarity to Streptomyces panaciradicis 1MR-8T (98.90 %), Streptomyces sasae JR-39T (98.89 %) and Streptomyces barringtoniae JA03T (98.69 %) and less than 98.5 % similarity to other members of the genus Streptomyces. The cell wall of strain NEAU-HV9T contained ll-diaminopimelic acid and the whole-cell hydrolysates were galactose, mannose and ribose. The predominant menaquinones were composed of MK-9(H2) and MK-9(H8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The major fatty acids were C16 : 0, iso-C16 : 0 and C17 : 1 ω8c. The genomic DNA G+C content of strain NEAU-HV9T was 70.6 mol%. Furthermore, the strain could be clearly distinguished from its closely related type strains by the combination of DNA-DNA hybridization results and some phenotypic characteristics. Meanwhile, strain NEAU-HV9T displayed herbicidal activity. Therefore, strain NEAU-HV9T represents a novel species within the genus Streptomyces, for which the name Streptomyces herbicida sp. nov. is proposed, with strain NEAU-HV9T (=CCTCC AA 2019088T=DSM 113364T) as the type strain.

Structure-based prediction of protein-protein interaction network in rice.

Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.

RNA-seq analysis reveals an immunomodulatory peptide from highland barley activating RAW264.7 macrophages via TNF/NF-κB signaling pathway.

Highland barley (HB) is an important cereal crop distributed in the plateau region. Bioactive peptides (BAPs) derived from cereal proteins have shown biological functions. However, the knowledge of highland barley peptide (HBP) is limited. This study aims to explore the immunomodulatory activity of HBP and the relationship between immunomodulatory activity and related gene expression through RNA-seq. Firstly, HBP is isolated from protease hydrolysates of HB protein, yielding 12.04% of crude HB protein. The molecular weight of HBP is about 1702 Da analyzed by gel filtration chromatography, and HBP has a specific amino acid sequence as Gln-Pro-Gln-Gln-Pro-Phe-Pro-Gln (QPQPFPQ) analyzed by LC-MS. Besides, HBP contains 42.20% hydrophobic amino acids and 10.86% basic amino acids. Next, the immunomodulatory activity of HBP in vitro shows that HBP enhances the phagocytosis of RAW264.7 macrophages, promotes nitric oxide (NO) production and the mRNA expression of pro-inflammatory genes including tumor necrosis factor α (TNF-α), interleukin 1ß (IL-1ß), and inducible nitric oxide synthase (iNOS), and decreases the mRNA expression of anti-inflammatory gene, transforming growth factor ß1 (TGF-ß1). RNA-seq analysis reveals TNF and nuclear factor kappa B (NF-κB) pathways are upregulated, and RT-qPCR is performed to verify RNA-seq analysis. In conclusion, HBP activates RAW264.7 macrophages via TNF/NF-κB signaling pathway. HBP, as a significant immunomodulatory peptide, might be a promising resource for future functional foods.

The transcription factor EMB1444-like affects tomato fruit ripening by regulating YELLOW-FRUITED TOMATO 1, a core component of ethylene signaling transduction.

The fleshy fruit of tomato (Solanum lycopersicum) are climacteric and, as such, ethylene plays a pivotal role in their ripening and quality traits. In this study, a basic helix-loop-helix transcription factor, EMB1444-like, was found to induce the expression of YELLOW-FRUITED TOMATO 1 (YFT1), which encodes the SlEIN2 protein, a key element in the ethylene signaling pathway. Yeast one-hybrid and EMSA analyses revealed that EMB1444-like binds to the E-box motif (CACTTG, -1295 bp to -1290 bp upstream of the ATG start codon) of the YFT1 promoter (pYFT1). Suppression of EMB1444-like expression in tomato lines (sledl) using RNAi reduced ethylene production by lowering the expression of 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2/4 (ACS2/4) and ACC OXIDASE1 (ACO1) in a positive feedback loop. sledl tomato also showed differences in numerous quality traits related to fruit ripening, compared with the wild type, such as delayed chromoplast differentiation, a decrease in carotenoid accumulation, and delayed fruit ripening in an ethylene-independent manner, or at least upstream of ripening mediated by YFT1/SlEIN2. This study elucidates the regulatory framework of fruit ripening in tomato, providing information that may be used to breed tomato hybrid cultivars with an optimal balance of shelf-life, durability, and high quality.

Analysis of EEG features and study of automatic classification in first-episode and drug-naïve patients with major depressive disorder.

BACKGROUND: Major depressive disorder (MDD) has a high incidence and an unknown mechanism. There are no objective and sensitive indicators for clinical diagnosis. OBJECTIVE: This study explored specific electrophysiological indicators and their role in the clinical diagnosis of MDD using machine learning. METHODS: Forty first-episode and drug-naïve patients with MDD and forty healthy controls (HCs) were recruited. EEG data were collected from all subjects in the resting state with eyes closed for 10 min. The severity of MDD was assessed by the Hamilton Depression Rating Scale (HAMD-17). Machine learning analysis was used to identify the patients with MDD. RESULTS: Compared to the HC group, the relative power of the low delta and theta bands was significantly higher in the right occipital region, and the relative power of the alpha band in the entire posterior occipital region was significantly lower in the MDD group. In the MDD group, the alpha band scalp functional connectivity was overall lower, while the scalp functional connectivity in the gamma band was significantly higher than that in the HC group. In the feature set of the relative power of the ROI in each band, the highest accuracy of 88.2% was achieved using the KNN classifier while using PCA feature selection. In the explanatory model using SHAP values, the top-ranking influence feature is the relative power of the alpha band in the left parietal region. CONCLUSIONS: Our findings reveal that the abnormal EEG neural oscillations may reflect an imbalance of excitation, inhibition and hyperactivity in the cerebral cortex in first-episode and drug-naïve patients with MDD. The relative power of the alpha band in the left parietal region is expected to be an objective electrophysiological indicator of MDD.

Two homologous Salmonella serogroup C1-specific genes are required for flagellar motility and cell invasion.

BACKGROUND: Salmonella is a major bacterial pathogen associated with a large number of outbreaks of foodborne diseases. Many highly virulent serovars that cause human illness belong to Salmonella serogroup C1, and Salmonella ser. Choleraesuis is a prominent cause of invasive infections in Asia. Comparative genomic analysis in our previous study showed that two homologous genes, SC0368 and SC0595 in Salmonella ser. Choleraesuis were unique to serogroup C1. In this study, two single-deletion mutants (Δ0368 and Δ0595) and one double-deletion mutant (Δ0368Δ0595) were constructed based on the genome. All these mutants and the wild-type strain were subjected to RNA-Seq analysis to reveal functional relationships of the two serogroup C1-specific genes. RESULTS: Data from RNA-Seq indicated that deletion of SC0368 resulted in defects in motility through repression of σ28 in flagellar regulation Class 3. Consistent with RNA-Seq data, results from transmission electron microcopy (TEM) showed that flagella were not present in △0368 and △0368△0595 mutants resulting in both swimming and swarming defects. Interestingly, the growth rates of two non-motile mutants △0368 and △0368△0595 were significantly greater than the wild-type, which may be associated with up-regulation of genes encoding cytochromes, enhancing bacterial proliferation. Moreover, the △0595 mutant was significantly more invasive in Caco-2 cells as shown by bacterial enumeration assays, and the expression of lipopolysaccharide (LPS) core synthesis-related genes (rfaB, rfaI, rfaQ, rfaY, rfaK, rfaZ) was down-regulated only in the △0368△0595 mutant. In addition, this study also speculated that these two genes might be contributing to serotype conversion for Salmonella C1 serogroup based on their apparent roles in biosynthesis of LPS and the flagella. CONCLUSION: A combination of biological and transcriptomic (RNA-Seq) analyses has shown that the SC0368 and SC0595 genes are involved in biosynthesis of flagella and complete LPS, as well as in bacterial growth and virulence. Such information will aid to revealing the role of these specific genes in bacterial physiology and evolution within the serogroup C1.

The transcription factor WRKY32 affects tomato fruit colour by regulating YELLOW FRUITED-TOMATO 1, a core component of ethylene signal transduction.

Fruit quality in most fleshy fruit crops is fundamentally linked to ripening-associated traits, including changes in colour. In many climacteric fruits, including tomato (Solanum lycopersicum), the phytohormone ethylene plays a key role in regulating ripening. Previous map-based cloning of YELLOW FRUITED-TOMATO 1 (YFT1) revealed that it encodes the EIN2 protein, a core component in ethylene signal transduction. A YFT1 allele with a genetic lesion was found to be down-regulated in the yft1 tomato mutant that has a yellow fruit phenotype and perturbed ethylene signalling. Based on bioinformatic analysis, yeast one hybrid assays and electrophoretic mobility shift assays, we report that transcription factor WRKY32 regulates tomato fruit colour formation. WRKY32 binds to W-box and W-box-like motifs in the regulatory region of the YFT1 promoter and induces its expression. In tomato fruits of WRKY32-RNAi generated lines, ethylene signalling was reduced, leading to a suppression in ethylene emission, a delay in chromoplast development, decreased carotenoid accumulation, and a yellow fruit phenotype. These results provide new insights into the regulatory networks that govern tomato fruit colour formation via ethylene signal transduction.

Microbacterium helvum sp. nov., a novel actinobacterium isolated from cow dung.

A Gram-positive, aerobic, non-motile, non-spore-forming, short rod-shaped strain, NEAU-LLCT, was isolated from cow dung in Shangzhi City, Heilongjiang Province, Northeast China and identified by a polyphasic taxonomic study. Colonies was light yellow, round, with entire margin. Strain NEAU-LLCT was grown at 15-45 â„ƒ and pH 6.0-10.0. NaCl concentration ranged from 0 to 5% (W/V). The 16S rRNA gene sequence of NEAU-LLCT showed the high similarities with Microbacterium kyungheense JCM 18735T (98.5%), Microbacterium trichothecenolyticum JCM 1358T (98.3%) and Microbacterium jejuense JCM 18734T (98.2%). The whole-cell sugars were glucose, rhamnose and ribose. The menaquinones contained MK-12 and MK-13. Ornithine, glutamic acid, lysine and a small amount of alanine and glycine were the amino acids in the hydrolyzed products of the cell wall. The major fatty acids were iso-C16:0, iso-C18:0, anteiso-C15:0 and anteiso-C17:0. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The genome of NEAU-LLCT was 4,369,375 bp and G + C content is 70.28 mol%. A combination of DNA-DNA hybridization result and some phenotypic characteristics demonstrated that strain NEAU-LLCT could be distinguished from its closely related strains. Therefore, the strain NEAU-LLCT was considered to represent a novel species, which was named Microbacterium helvum sp. (Type strain NEAU-LLCT = CCTCC AA 2018026T = JCM 32661T).

Microbacterium stercoris sp. nov., an indole acetic acid-producing actinobacterium isolated from cow dung.

A novel growth-promoting and indole acetic acid-producing strain, designated NEAU-LLBT, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, PR China. Cells of strain NEAU-LLBT were Gram-stain-positive, non-motile, aerobic and non-spore-forming. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-LLBT belonged to the genus Microbacterium. Strain NEAU-LLBT had high 16S rRNA sequence similarities of 98.81 and 98.41 % to Microbacterium paludicola DSM 16915T and Microbacterium marinilacus DSM 18904T, and less than 98 % to other members of the genus Microbacterium. Chemotaxonomic characteristics showed that MK-11 and MK-12 were detected as the predominant menaquinones. The peptidoglycan contained glutamic acid, aspartic acid, glycine, ornithine and a small amount of alanine, with ornithine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The major fatty acids were identified as anteiso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. The genomic DNA G+C content of strain NEAU-LLBT was 70.2 mol%. In addition, the average nucleotide identity values between strain NEAU-LLBT and its reference strains, M. paludicola DSM 16915T, M. marinilacus DSM 18904T and M. album SYSU D8007T, were found to be 81.1, 79.4 and 78.7 %, respectively, and the level of digital DNA-DNA hybridization between them were 23.8, 22.6 and 21.8 %, respectively. Based on the phenotypic, phylogenetic and genotypic data, strain NEAU-LLBT is considered to represent a novel species of the genus Microbacterium, for which the name Microbacterium stercoris sp. nov is proposed, with NEAU-LLBT (=CCTCC AA 2018028T=JCM 32660T) as the type strain.

PRAP: Pan Resistome analysis pipeline.

BACKGROUND: Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species. Therefore, a pan-genome approach to analyzing resistomes is necessary for thoroughly characterizing patterns of ARGs distribution within particular pathogen populations. Software tools are readily available for either ARGs identification or pan-genome analysis, but few exist to combine the two functions. RESULTS: We developed Pan Resistome Analysis Pipeline (PRAP) for the rapid identification of antibiotic resistance genes from various formats of whole genome sequences based on the CARD or ResFinder databases. Detailed annotations were used to analyze pan-resistome features and characterize distributions of ARGs. The contribution of different alleles to antibiotic resistance was predicted by a random forest classifier. Results of analysis were presented in browsable files along with a variety of visualization options. We demonstrated the performance of PRAP by analyzing the genomes of 26 Salmonella enterica isolates from Shanghai, China. CONCLUSIONS: PRAP was effective for identifying ARGs and visualizing pan-resistome features, therefore facilitating pan-genomic investigation of ARGs. This tool has the ability to further excavate potential relationships between antibiotic resistance genes and their phenotypic traits.

Interaction of bZIP transcription factor TGA6 with salicylic acid signaling modulates artemisinin biosynthesis in Artemisia annua.

Artemisinin is a sesquiterpene lactone produced by the Chinese traditional herb Artemisia annua and is used for the treatment of malaria. It is known that salicylic acid (SA) can enhance artemisinin content but the mechanism by which it does so is not known. In this study, we systematically investigated a basic leucine zipper family transcription factor, AaTGA6, involved in SA signaling to regulate artemisinin biosynthesis. We found specific in vivo and in vitro binding of the AaTGA6 protein to a 'TGACG' element in the AaERF1 promoter. Moreover, we demonstrated that AaNPR1 can interact with AaTGA6 and enhance its DNA-binding activity to its cognate promoter element 'TGACG' in the promoter of AaERF1, thus enhancing artemisinin biosynthesis. The artemisinin contents in AaTGA6-overexpressing and RNAi transgenic plants were increased by 90-120% and decreased by 20-60%, respectively, indicating that AaTGA6 plays a positive role in artemisinin biosynthesis. Importantly, heterodimerization with AaTGA3 significantly inhibits the DNA-binding activity of AaTGA6 and plays a negative role in target gene activation. In conclusion, we demonstrate that binding of AaTGA6 to the promoter of the artemisinin-regulatory gene AaERF1 is enhanced by AaNPR1 and inhibited by AaTGA3. Based on these findings, AaTGA6 has potential value in the genetic engineering of artemisinin production.

Beam Focusing and Reduction of Quantum Uncertainty in Width at the Few-Photon Level via Multi-Spatial-Mode Squeezing.

We show for the first time that it is possible to realize laser beam focusing at the few-photon level in the four-wave-mixing process, and at the same time reduce the quantum uncertainty in width. The reduction in quantum uncertainty results directly from the strong suppression of local intensity fluctuations. This surprising effect of simultaneous focusing and reduction of width uncertainty is enabled by multi-spatial-mode (MSM) squeezing, and is not possible via any classical optical approach or single-spatial-mode squeezing. Our results open promising possibilities for quantum-enhanced imaging and metrology; as an example, the limit on the measurement of very small beam displacement can be enhanced within feasible experimental parameters because of beam focusing and the noiseless amplification in the MSM squeezing process.

Nocardia bovistercoris sp. nov., an actinobacterium isolated from cow dung.

A novel actinobacterium, designated strain NEAU-351T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, northeast PR China and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-351T belonged to the genus Nocardia, with the highest similarity (98.96 %) to Nocardia takedensis DSM 44801T and less than 98.0 % identity with other type strains of the genus Nocardia. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major menaquinone was observed to contain MK-8(H4, ω-cycl) (78.2 %). The fatty acid profile mainly consisted of C16 : 0, C18 : 1 ω9c and 10-methyl C18 : 0. Mycolic acids were present. The genomic DNA G+C content of strain NEAU-351T was 68.1 mol%. In addition, the average nucleotide identity values between strain NEAU-351T and its reference strains, Nocardia takedensis DSM 44801T and Nocardia arizonensis NBRC 108935T, were found to be 81.4 and 82.9 %, respectively, and the level of digital DNA-DNA hybridization between them were 24.8 % (22.5-27.3 %) and 26.3 % (24-28.8 %), respectively. Here we report on the taxonomic characterization and classification of the isolate and propose that strain NEAU-351T represents a new species of the genus Nocardia, for which the name Nocardia bovistercoris is proposed. The type strain is NEAU-351T (=CCTCC AA 2019090T=DSM 110681T).

A computational interactome for prioritizing genes associated with complex agronomic traits in rice (Oryza sativa).

Rice (Oryza sativa) is one of the most important staple foods for more than half of the global population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet) using machine learning with structural relationship and functional information. RicePPINet contained 708 819 predicted interactions for 16 895 non-transposable element related proteins. The power of the network for discovering novel protein interactions was demonstrated through comparison with other publicly available protein-protein interaction (PPI) prediction methods, and by experimentally determined PPI data sets. Furthermore, global analysis of domain-mediated interactions revealed RicePPINet accurately reflects PPIs at the domain level. Our studies showed the efficiency of the RicePPINet-based method in prioritizing candidate genes involved in complex agronomic traits, such as disease resistance and drought tolerance, was approximately 2-11 times better than random prediction. RicePPINet provides an expanded landscape of computational interactome for the genetic dissection of agronomically important traits in rice.

Chiral Spin Density Wave and d+id Superconductivity in the Magic-Angle-Twisted Bilayer Graphene.

We model the newly synthesized magic-angle-twisted bilayer graphene superconductor with two p_{x,y}-like Wannier orbitals on the superstructure honeycomb lattice, where the hopping integrals are constructed via the Slater-Koster formulism by symmetry analysis. The characteristics exhibited in this simple model are well consistent with both the rigorous calculations and experiment observations. A van Hove singularity and Fermi-surface (FS) nesting are found in the doping levels relevant to the correlated insulator and unconventional superconductivity revealed experimentally, based on which we identify the two phases as weak-coupling FS instabilities. Then, with repulsive Hubbard interactions turned on, we performed random-phase-approximation based calculations to identify the electron instabilities. As a result, we find chiral d+id topological superconductivity bordering the correlated insulating state near half-filling, identified as noncoplanar chiral spin-density wave ordered state, featuring the quantum anomalous Hall effect. The phase diagram obtained in our approach is qualitatively consistent with experiments.

Helicobacter pylori infection-induced H3Ser10 phosphorylation in stepwise gastric carcinogenesis and its clinical implications.

BACKGROUND: Our previous works have demonstrated that Helicobacter pylori (Hp) infection can alter histone H3 serine 10 phosphorylation status in gastric epithelial cells. However, whether Helicobacter pylori-induced histone H3 serine 10 phosphorylation participates in gastric carcinogenesis is unknown. We investigate the expression of histone H3 serine 10 phosphorylation in various stages of gastric disease and explore its clinical implication. MATERIALS AND METHODS: Stomach biopsy samples from 129 patients were collected and stained with histone H3 serine 10 phosphorylation, Ki67, and Helicobacter pylori by immunohistochemistry staining, expressed as labeling index. They were categorized into nonatrophic gastritis, chronic atrophic gastritis, intestinal metaplasia, low-grade intraepithelial neoplasia, high-grade intraepithelial neoplasia, and intestinal-type gastric cancer groups. Helicobacter pylori infection was determined by either 13 C-urea breath test or immunohistochemistry staining. RESULTS: In Helicobacter pylori-negative patients, labeling index of histone H3 serine 10 phosphorylation was gradually increased in nonatrophic gastritis, chronic atrophic gastritis, intestinal metaplasia groups, peaked at low-grade intraepithelial neoplasia, and declined in high-grade intraepithelial neoplasia and gastric cancer groups. In Helicobacter pylori-infected patients, labeling index of histone H3 serine 10 phosphorylation followed the similar pattern as above, with increased expression over the corresponding Helicobacter pylori-negative controls except in nonatrophic gastritis patient whose labeling index was decreased when compared with Helicobacter pylori-negative control. Labeling index of Ki67 in Helicobacter pylori-negative groups was higher in gastric cancer than chronic atrophic gastritis and low-grade intraepithelial neoplasia groups, and higher in intestinal metaplasia group compared with chronic atrophic gastritis group. In Helicobacter pylori-positive groups, Ki67 labeling index was increased stepwise from nonatrophic gastritis to gastric cancer except slightly decrease in chronic atrophic gastritis group. In addition, we noted that histone H3 serine 10 phosphorylation staining is accompanied with its location changes from gastric gland bottom expanded to whole gland as disease stage progress. CONCLUSIONS: These results indicate that stepwise gastric carcinogenesis is associated with altered histone H3 serine 10 phosphorylation, Helicobacter pylori infection enhances histone H3 serine 10 phosphorylation expression in these processes; it is also accompanied with histone H3 serine 10 phosphorylation location change from gland bottom staining expand to whole gland expression. The results suggest that epigenetic dysregulation may play important roles in Helicobacter pylori-induced gastric cancer.

Network analysis of ABA-dependent and ABA-independent drought responsive genes in Arabidopsis thaliana.

Drought is one of the most severe abiotic factors restricting plant growth and yield. Numerous genes functioning in drought response are regulated by abscisic acid (ABA) dependent and independent pathways, but knowledge of interplay between the two pathways is still limited. Here, we integrated transcriptome sequencing and network analyses to explore interplays between ABA-dependent and ABA-independent pathways responding to drought stress in Arabidopsis thaliana. We identified 211 ABA-dependent differentially expressed genes (DEGs) and 1,118 ABA-independent DEGs under drought stress. Functional analysis showed that ABA-dependent DEGs were significantly enriched in expected biological processes in response to water deprivation and ABA stimulus, while ABA-independent DEGs were preferentially enriched in response to jasmonic acid (JA), salicylic acid (SA) and gibberellin (GA) stimuli. We found significantly enriched interactions between ABA-dependent and ABA-independent pathways with 94 genes acting as core interacting components by combining network analyses. A link between ABA and JA signaling mediated through a direct interaction of the ABA responsive elements-binding factor ABF3 with the basic helix-loop-helix transcription factor MYC2 was validated by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Our study provides a systematic view of the interplay between ABA-dependent and ABA-independent pathways in response to drought stress.

Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes.

BACKGROUND: Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD1), G. barbadense (AD2), G. raimondii (D5) and G. arboreum (A2), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium. RESULTS: Six Gossypium mitochondrial genomes, including three diploid species from D and three allotetraploid species from AD genome groups (G. thurberi D1, G. davidsonii D3-d and G. trilobum D8; G. tomentosum AD3, G. mustelinum AD4 and G. darwinii AD5), were assembled as the single circular molecules of lengths about 644 kb in diploid species and 677 kb in allotetraploid species, respectively. The genomic structures of mitochondrial in D group species were identical but differed from the mitogenome of G. arboreum (A2), as well as from the mitogenomes of five species of the AD group. There mainly existed four or six large repeats in the mitogenomes of the A + AD or D group species, respectively. These variations in repeat sequences caused the major inversions and translocations within the mitochondrial genome. The mitochondrial genome complexity in Gossypium presented eight unique segments in D group species, three specific fragments in A + AD group species and a large segment (more than 11 kb) in diploid species. These insertions or deletions were most probably generated from crossovers between repetitive or homologous regions. Unlike the highly variable genome structure, evolutionary distance of mitochondrial genes was 1/6th the frequency of that in chloroplast genes of Gossypium. RNA editing events were conserved in cotton mitochondrial genes. We confirmed two near full length of the integration of the mitochondrial genome into chromosome 1 of G. raimondii and chromosome A03 of G. hirsutum, respectively, with insertion time less than 1.03 MYA. CONCLUSION: Ten Gossypium mitochondrial sequences highlight the insights to the evolution of cotton mitogenomes.

GLANDULAR TRICHOME-SPECIFIC WRKY 1 promotes artemisinin biosynthesis in Artemisia annua.

Artemisinin is a type of sesquiterpene lactone well known as an antimalarial drug, and is specifically produced in glandular trichomes of Artemisia annua. However, the regulatory network for the artemisinin biosynthetic pathway remains poorly understood. Exploration of trichome-specific transcription factors would facilitate the elucidation of regulatory mechanism of artemisinin biosynthesis. The WRKY transcription factor GLANDULAR TRICHOME-SPECIFIC WRKY 1 (AaGSW1) was cloned and analysed in A. annua. AaGSW1 exhibited similar expression patterns to the trichome-specific genes of the artemisinin biosynthetic pathway and AP2/ERF transcription factor AaORA. A ß-glucuronidase (GUS) staining assay further demonstrated that AaGSW1 is a glandular trichome-specific transcription factor. AaGSW1 positively regulates CYP71AV1 and AaORA expression by directly binding to the W-box motifs in their promoters. Overexpression of AaGSW1 in A. annua significantly improves artemisinin and dihydroartemisinic acid contents; moreover, AaGSW1 can be directly regulated by AaMYC2 and AabZIP1, which are positive regulators of jasmonate (JA)- and abscisic acid (ABA)-mediated artemisinin biosynthetic pathways, respectively. These results demonstrate that AaGSW1 is a glandular trichome-specific WRKY transcription factor and a positive regulator in the artemisinin biosynthetic pathway. Moreover, we propose that two trifurcate feed-forward pathways involving AaGSW1, CYP71AV1 and AaMYC2/AabZIP1 function in the JA/ABA response in A. annua.

Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling.

Protein-protein interactions (PPIs) are essential to almost all cellular processes. To better understand the relationships of proteins in Arabidopsis (Arabidopsis thaliana), we have developed a genome-wide protein interaction network (AraPPINet) that is inferred from both three-dimensional structures and functional evidence and that encompasses 316,747 high-confidence interactions among 12,574 proteins. AraPPINet exhibited high predictive power for discovering protein interactions at a 50% true positive rate and for discriminating positive interactions from similar protein pairs at a 70% true positive rate. Experimental evaluation of a set of predicted PPIs demonstrated the ability of AraPPINet to identify novel protein interactions involved in a specific process at an approximately 100-fold greater accuracy than random protein-protein pairs in a test case of abscisic acid (ABA) signaling. Genetic analysis of an experimentally validated, predicted interaction between ARR1 and PYL1 uncovered cross talk between ABA and cytokinin signaling in the control of root growth. Therefore, we demonstrate the power of AraPPINet (http://netbio.sjtu.edu.cn/arappinet/) as a resource for discovering gene function in converging signaling pathways and complex traits in plants.