Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and other important regulatory elements (CpG islands and tandem repeats) in a promoter or a set of plant promoters. Additionally, TFBSs, CpG islands, and tandem repeats in the conserve regions between similar gene promoters are also identified. The current PlantPAN release (version 2.0) contains 16 960 TFs and 1143 TF binding site matrices among 76 plant species. In addition to updating of the annotation information, adding experimentally verified TF matrices, and making improvements in the visualization of transcriptional regulatory networks, several new features and functions are incorporated. These features include: (i) comprehensive curation of TF information (response conditions, target genes, and sequence logos of binding motifs, etc.), (ii) co-expression profiles of TFs and their target genes under various conditions, (iii) protein-protein interactions among TFs and their co-factors, (iv) TF-target networks, and (v) downstream promoter elements. Furthermore, a dynamic transcriptional regulatory network under various conditions is provided in PlantPAN 2.0. The PlantPAN 2.0 is a systematic platform for plant promoter analysis and reconstructing transcriptional regulatory networks.

Plant responses to abiotic stresses are coordinated by arrays of growth and developmental processes. Indole-3-acetic acid (IAA) and abscisic acid (ABA) play critical roles in developmental programmes and environmental responses, respectively, through complex signalling and metabolism networks. However, crosstalk between the two phytohormones in the stress responses remains largely unknown. Here, it is reported that a GH3 family gene, OsGH3-2, encoding an enzyme catalysing IAA conjugation to amino acids, is involved in the modulation of ABA level and stress tolerance. Expression of OsGH3-2 was induced by drought but was suppressed by cold. Overexpression of OsGH3-2 in rice caused significant morphological aberrations related to IAA deficiency, such as dwarfism, smaller leaves, and fewer crown roots and root hairs. The overexpressing line showed significantly reduced carotene, ABA, and free IAA levels, greater stomata aperture, and faster water loss, and was hypersensitive to drought stress. However, the overexpressing line showed increased cold tolerance, which was due to the combined effects of reduced free IAA content, alleviated oxidative damage, and decreased membrane penetrability. Furthermore, expression levels of some ABA synthesis- and stress-related genes were significantly changed in the overexpression line. It was conclude that OsGH3-2 modulates both endogenous free IAA and ABA homeostasis and differentially affects drought and cold tolerance in rice.

Many plants have evolved a drought escape (DE) mechanism to shorten their life cycle when facing water-deficit conditions. While drought tolerance has been intensively investigated, the genetic and molecular mechanisms of DE remain elusive. In this study, we found that low water-deficit treatment (LWT) at the early stage of rice development can trigger early flowering and reduced tiller numbers. LWT induced the accumulation of abscisic acid (ABA), which in turn has feed-back effects on light perception and circadian clock by synchronously regulating many flowering-related genes to promote early flowering. Moreover, some of light receptors, circadian components, and flowering-related genes including OsTOC1, Ghd7, and PhyB were found to be involved in LWT in an ABA-dependent manner, whereas some of the other flowering-related genes including OsGI, OsELF3, OsPRR37, and OsMADS50 were involved in the regulation of DE independent of ABA. In addition, we found that strigolactones and OsTB1 are involved in the tillering inhibition under LWT, which is independent of the flowering pathway in rice. Taken together, our findings provide compelling evidence that DE in rice is coordinately regulated by multiple pathways during the reproduction (flowering) switch.

Plant responses to abiotic stresses are coordinated by arrays of growth and developmental programs. Phytohormones such as abscisic acid (ABA) and indole-3-acetic acid (IAA) play critical roles in developmental progresses and environmental responses through complex signalling networks. However, crosstalk between the two hormones at the biosynthesis level remains largely unknown. Here, we report that carotenoid-deficient mutants (phs1, phs2, phs3-1, phs4, and PDS-RNAi transgenic rice) were impaired in the biosynthesis of ABA and IAA. Under drought conditions, phs3-1 and PDS-RNAi transgenic rice showed larger stomata aperture and earlier wilting compared to the wild type at both seedling and panicle developmental stage. Interestingly, these carotenoid-deficient lines showed increased cold resistance, which was likely due to the combined effects of reduced IAA content, alleviated oxidative damage and decreased membrane penetrability. Furthermore, we found that IAA content was significantly declined in rice treated with fluridone (a carotenoid and ABA biosynthesis inhibitor), and expression of auxin synthesis and metabolism-related genes were altered in the fluridone-treated rice similar to that in the carotenoid-deficient mutants. In addition, exogenous IAA, but not ABA, could restore the dwarf phenotype of phs3-1 and PDS-RNAi transgenic rice. These results support a crosstalk between ABA and IAA at the biosynthesis level, and this crosstalk is involved in development and differentially affects drought and cold tolerance in rice.

SUMMARYSubmergence and drought are major limiting factors for crop production. However, very limited studies have been reported on the distinct or overlapping mechanisms of plants in response to the two water extremes. Here we report an ETHYLENE OVERPRODUCER 1-like gene (OsETOL1) that modulates differentially drought and submergence tolerance in rice (Oryza sativa L.). Two allelic mutants of OsETOL1 showed increased resistance to drought stress at the panicle development stage. Interestingly, the mutants exhibited a significantly slower growth rate under submergence stress at both the seedling and panicle development stages. Over-expression (OE) of OsETOL1 in rice resulted in reverse phenotypes when compared with the mutants. The OsETOL1 transcript was differentially responsive to abiotic stresses. OsETOL1 was found to interact with OsACS2, a homolog of 1-amino-cyclopropane-1-carboxylate (ACC) synthase (ACS), which acts as a rate-limiting enzyme for ethylene biosynthesis. In the osacs2 mutant and OsETOL1-OE plants, ACC and ethylene content were decreased significantly, and exogenous ACC restored the phenotype of osetol1 and OsETOL1-OE to wild-type under submergence stress, implying a negative role for OsETOL1 in ethylene biosynthesis. The expression of several genes related to carbohydrate catabolism and fermentation showed significant changes in the osetol1 and OsETOL1-OE plants, implying that OsETOL1 may affect energy metabolism. These results together suggest that OsETOL1 plays distinct roles in drought and submergence tolerance by modulating ethylene production and energy metabolism. Findings from the expression and functional comparison of three ethylene overproducer (ETOL) family members in rice further supported the specific role of OsETOL1 in the responses to the two water stresses.