RGA1 Negatively Regulates Thermo-tolerance by Affecting Carbohydrate Metabolism and the Energy Supply in Rice.

BACKGROUND: Signal transduction mediated by heterotrimeric G proteins, which comprise the α, ß, and γ subunits, is one of the most important signaling pathways in rice plants. RGA1, which encodes the Gα subunit of the G protein, plays an important role in the response to various types of abiotic stress, including salt, drought, and cold stress. However, the role of RGA1 in the response to heat stress remains unclear. RESULTS: The heat-resistant mutant ett1 (enhanced thermo-tolerance 1) with a new allele of the RGA1 gene was derived from an ethane methyl sulfonate-induced Zhonghua11 mutant. After 45 °C heat stress treatment for 36 h and recovery for 7 d, the survival rate of the ett1 mutants was significantly higher than that of wild-type (WT) plants. The malondialdehyde content was lower, and the maximum fluorescence quantum yield of photosystem II, peroxidase activity, and hsp expression were higher in ett1 mutants than in WT plants after 12 h of exposure to 45 °C. The RNA-sequencing results revealed that the expression of genes involved in the metabolism of carbohydrate, nicotinamide adenine dinucleotide, and energy was up-regulated in ett1 under heat stress. The carbohydrate content and the relative expression of genes involved in sucrose metabolism indicated that carbohydrate metabolism was accelerated in ett1 under heat stress. Energy parameters, including the adenosine triphosphate (ATP) content and the energy charge, were significantly higher in the ett1 mutants than in WT plants under heat stress. Importantly, exogenous glucose can alleviate the damages on rice seedling plants caused by heat stress. CONCLUSION: RGA1 negatively regulates the thermo-tolerance in rice seedling plants through affecting carbohydrate and energy metabolism.

Sterile line Dexiang074A enhances drought tolerance in hybrid rice.

Heterosis has been widely used in rice breeding, especially in improving rice yield. But it has rarely been studied in rice abiotic stress, including the drought tolerance, which is becoming one of the most important threaten in decreasing rice yield. Therefore, it is essential to studying the mechanism underlying heterosis in improving drought tolerance of rice breeding. In this study, Dexiang074B (074B) and Dexiang074A (074A) served as maintainer lines and sterile lines. Mianhui146 (R146), Chenghui727 (R727), LuhuiH103 (RH103), Dehui8258 (R8258), Huazhen (HZ), Dehui938 (R938), Dehui4923 (R4923), and R1391 served as restorer lines. The progeny were Dexiangyou (D146), Deyou4727 (D4727), Dexiang 4103 (D4103), Deyou8258 (D8258), Deyou Huazhen (DH), Deyou 4938 (D4938), Deyou 4923 (D4923), and Deyou 1391 (D1391). The restorer line and hybrid offspring were subjected to drought stress at the flowering stage. The results showed that Fv/Fm values were abnormal and oxidoreductase activity and MDA content were increased. However, the performance of hybrid progeny was significantly better than their respective restorer lines. Although the yield of hybrid progeny and restorer lines decreased simultaneously, the yield in hybrid offspring is significantly lower than the respective restorer line. Total soluble sugar content was consistent with the yield result, so we found that 074A can enhance drought tolerance in hybrid rice.

Genome Resource of Sphingomonas carotinifaciens L9-754T, an Endophyte Isolated From Leaf Tissues of Jatropha curcas.

Sphingomonas carotinifaciens strain L9-754T (DSM 27347) is a gram-negative, chemoheterotrophic, and rod-shaped endophyte isolated from the stem tissues of Jatropha curcas L. This strain has putative in vitro antagonistic ability against the plant pathogenic fungus Magnaporthe grisea. A draft genome of L9-754T was obtained using the PacBio SMRT cell platform. By analyzing the genome of strain L9-754T, a gene cluster (GQR91_18700 - GQR91_18715) related to an antioxidant enzyme was identified in the obtained draft genome. The information obtained from the draft genome is expected to reveal the putative properties helpful in biocontrol applications.

Analysis of Gene Expression in Bladder Cancer: Possible Involvement of Mitosis and Complement and Coagulation Cascades Signaling Pathway.

This study focused on identifying bladder cancer (BC)-associated genes, transcription factors (TFs), and microRNAs (miRNAs). Two microarray data sets GSE37815 and GSE40355 were utilized to screen common differentially expressed genes (DEGs) associated with BC. Then, functional enrichment analysis was performed for elucidating the involved functions of DEGs. Subsequently, the protein-protein interaction (PPI) network and submodule of PPI network were analyzed. Finally, the regulation relationships of TF-DEGs and miRNA-DEGs were obtained to construct miRNA-target-TF regulatory network. DEGs were identified across BC and normal bladder tissues samples. Functional enrichment analysis results showed that most upregulated DEGs were closely associated with the Gene Ontology function of "mitotic spindle assembly checkpoint" and pathway of "Cell cycle," whereas most downregulated DEGs were significantly associated with "Complement and coagulation cascades" pathway (e.g., A2M and F13A1) and "Ras signaling pathway" (e.g., GNG11). DEGs such as F13A1 and A2M were highlighted in the PPI network and Submodule 1. In addition, three centromere-associated CENPK, CENPF, and CENPO were enriched in Submodule 2. Moreover, miR-519d had high degree in the regulatory network and CENPO was predicted to be one target of miR-519d. The upregulated CENPK, CENPF, and CENPO, and downregulated A2M, F13A1, and GNG11 might contribute to the progression of BC. In addition, the downregulated miR-519d might lead to the development of BC by upregulating the expression of CENPO. However, future investigation of those findings should be needed.

Complete genome sequence of Achromobacter spanius type strain DSM 23806T, a pathogen isolated from human blood.

OBJECTIVES: Achromobacter spanius is a newly described, non-fermenting, Gram-negative, coccoid pathogen isolated from human blood. Whole-genome sequencing of the A. spanius type strain was performed to investigate the mechanism of pathogenesis of this strain at a genomic level. METHODS: The complete genome of A. spanius type strain DSM 23806T was sequenced using single-molecule real-time (SMRT) DNA sequencing. RESULTS: The complete genome of DSM 23806T consists of one circular DNA chromosome of 6425783bp with a G+C content of 64.26%. The entire genome contains 5804 predicted coding sequences (CDS) and 55 tRNAs. Genomic island (GI) analysis showed that this strain encodes several important pathogenesis- and resistance-related genes. CONCLUSIONS: These results strongly suggest that GIs provide some fitness advantages in A. spanius type strain DSM 23806T. This report provides an extensive understanding of A. spanius at a genomic level as well as an understanding of the evolution of A. spanius.

Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed.

Barnyardgrass (Echinochloa crus-galli) is a pernicious weed in agricultural fields worldwide. The molecular mechanisms underlying its success in the absence of human intervention are presently unknown. Here we report a draft genome sequence of the hexaploid species E. crus-galli, i.e., a 1.27 Gb assembly representing 90.7% of the predicted genome size. An extremely large repertoire of genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with detoxification are found. Two gene clusters involved in the biosynthesis of an allelochemical 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and a phytoalexin momilactone A are found in the E. crus-galli genome, respectively. The allelochemical DIMBOA gene cluster is activated in response to co-cultivation with rice, while the phytoalexin momilactone A gene cluster specifically to infection by pathogenic Pyricularia oryzae. Our results provide a new understanding of the molecular mechanisms underlying the extreme adaptation of the weed.

Complete genome sequence of Achromobacter insolitus type strain LMG 6003T, a pathogen isolated from leg wound.

Achromobacter insolitus is a newly described, Gram-negative, small (1-2 mm long) and coccoid pathogen that has been isolated from leg wound. Due to its potential threat to human beings, the type strain of this species LMG 6003T was completely sequenced in this study. The genomic analysis revealed that the genome of LMG 6003T consists of one circular DNA chromosome of 6 492 697 bp with a GC content of 65.10%. The entire genome contains 6208 predicted coding genes, 61 tRNAs and 13 rRNA genes. Comparative genome analysis between LMG 6003T and another selected 10 sequenced Achromobacter revealed that 725 genes only exist in LMG 6003T. In particular, these genes include several important pathogenic-related genes such as Type IV prepilin peptidase (TadV/CpaA), Type VI secretion lipoprotein (VasD) and type 1 fimbriae major subunit (FimA). Genomic island (GI) analysis also suggests the existence of GIs in LMG 6003T. All these results strongly suggest the unique genomic features in LMG 6003T against other Achromobacter species. This report will provide us with an extended understanding of A. insolitus at the genomic level and would be helpful for understanding the evolution of the Achromobacter genus.

Down-Regulation of a Nicotinate Phosphoribosyltransferase Gene, OsNaPRT1, Leads to Withered Leaf Tips.

Premature leaf senescence affects plant growth and yield in rice. NAD plays critical roles in cellular redox reactions and remains at a sufficient level in the cell to prevent cell death. Although numerous factors affecting leaf senescence have been identified, few involving NAD biosynthetic pathways have been described for plants. Here, we report the cloning and characterization of Leaf Tip Senescence 1 (LTS1) in rice (Oryza sativa), a recessive mutation in the gene encoding O. sativa nicotinate phosphoribosyltransferase (OsNaPRT1) in the NAD salvage pathway. A point mutation in OsNaPRT1 leads to dwarfism and the withered leaf tip phenotype, and the lts1 mutant displays early leaf senescence compared to the wild type. Leaf nicotinate and nicotinamide contents are elevated in lts1, while NAD levels are reduced. Leaf tissue of lts1 exhibited significant DNA fragmentation and H2O2 accumulation, along with up-regulation of genes associated with senescence. The lts1 mutant also showed reduced expression of SIR2-like genes (OsSRT1 and OsSRT2) and increased acetylation of histone H3K9. Down-regulation of OsSRTs induced histone H3K9 acetylation of senescence-related genes. These results suggest that deficiency in the NAD salvage pathway can trigger premature leaf senescence due to transcriptional activation of senescence-related genes.

Full genome sequence of Brevibacillus laterosporus strain B9, a biological control strain isolated from Zhejiang, China.

Brevibacillus laterosporus was newly classified from Bacillus laterosporus, which has ability to be used as a biological control agent in crop field. B. laterosporus strain B9 is an aerobic, motile, Gram-positive, spore-forming rod that was isolated from a field of Oryza sativa in Zhejiang, China in 2011. This bacterium has been confirmed to be a strong antagonist against bacterial brown strip of rice caused by Acidovorex avenae subsp. avenae. Here we describe the features of B. laterosporus strain B9, together with the complete genome sequence and its annotation. The 5,272,435bp genome contains 4804 protein-coding genes and 227 RNA-only encoding genes with 2 plasmids.

Whole genome sequence of Enterobacter ludwigii type strain EN-119T, isolated from clinical specimens.

Enterobacter ludwigii strain EN-119(T) is the type strain of E. ludwigii, which belongs to the E. cloacae complex (Ecc). This strain was first reported and nominated in 2005 and later been found in many hospitals. In this paper, the whole genome sequencing of this strain was carried out. The total genome size of EN-119(T) is 4952,770 bp with 4578 coding sequences, 88 tRNAs and 10 rRNAs. The genome sequence of EN-119(T) is the first whole genome sequence of E. ludwigii, which will further our understanding of Ecc.

Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species.

The genus Echinochloa (Poaceae) includes numerous problematic weeds that cause the reduction of crop yield worldwide. To date, DNA sequence information is still limited in the genus Echinochloa. In this study, we completed the entire chloroplast genomes of two Echinochloa species (Echinochloa oryzicola and Echinochloa crus-galli) based on high-throughput sequencing data from their fresh green leaves. The two Echinochloa chloroplast genomes are 139,891 and 139,800 base pairs in length, respectively, and contain 131 protein-coding genes, 79 indels and 466 substitutions helpful for discrimination of the two species. The divergence between the genus Echinochloa and Panicum occurred about 21.6 million years ago, whereas the divergence between E. oryzicola and E. crus-galli chloroplast genes occurred about 3.3 million years ago. The two reported Echinochloa chloroplast genome sequences contribute to better understanding of the diversification of this genus.

A point mutation in the zinc finger motif of RID1/EHD2/OsID1 protein leads to outstanding yield-related traits in japonica rice variety Wuyunjing 7.

BACKGROUND: Flowering time, which is often associated with the length of the growth period in rice, determines the adaptability of a plant to various environments. However, little is known about how flowering-time genes affect panicle development and yield formation potential in rice after inducing the transition from vegetative growth to reproductive growth. RESULTS: To explore the relationship between floral induction and yield formation and the molecular mechanism of panicle development in rice, a novel mutant, ghd10, was identified from japonica variety Wuyunjing 7 plants subjected to ethyl methane sulfonate (EMS) treatment. The ghd10 mutant exhibited delayed flowering time, tall stalks and increased panicle length and primary branch number. Map-based cloning revealed that Ghd10 encodes a transcription factor with Cys-2/His-2-type zinc finger motifs. Ghd10 is orthologous to INDETERMINATE1 (ID1), which promotes flowering in maize (Zea mays) and is identical to the previously cloned genes Rice Indeterminate1 (RID1), Early heading date2 (Ehd2) and OsId1. Transient expression analysis of the Ghd10-GFP fusion protein in tobacco mesophyll cells showed that this protein is expressed in the nucleus. Ghd10 mRNA accumulated most abundantly in developing leaves and panicle structures, but rarely in roots. Expression analysis revealed that the expression levels of Ehd1, Hd1, RFT1, Hd3a and OsMADS15 decreased dramatically under both short-day and long-day conditions in ghd10. CONCLUSION: These results indicate that Ghd10, which encodes a promoter of flowering, influences plant height and panicle development by regulating the expression levels of some flowering-related genes, such as Ehd1, Hd1, OsMADS15 and others. The ghd10 allele is a useful resource for improvement of panicle traits in rice grown in tropical and low-latitude areas.