SUMMARYFew regulators of phenylpropanoids have been identified in monocots having potential as biofuel crops. Here we demonstrate the role of the maize (Zea mays) R2R3-MYB factor ZmMYB31 in the control of the phenylpropanoid pathway. We determined its in vitro consensus DNA-binding sequence as ACC T / A ACC, and chromatin immunoprecipitation (ChIP) established that it interacts with two lignin gene promoters in vivo. To explore the potential of ZmMYB31 as a regulator of phenylpropanoids in other plants, its role in the regulation of the phenylpropanoid pathway was further investigated in Arabidopsis thaliana. ZmMYB31 downregulates several genes involved in the synthesis of monolignols and transgenic plants are dwarf and show a significantly reduced lignin content with unaltered polymer composition. We demonstrate that these changes increase cell wall degradability of the transgenic plants. In addition, ZmMYB31 represses the synthesis of sinapoylmalate, resulting in plants that are more sensitive to UV irradiation, and induces several stress-related proteins. Our results suggest that, as an indirect effect of repression of lignin biosynthesis, transgenic plants redirect carbon flux towards the biosynthesis of anthocyanins. Thus, ZmMYB31 can be considered a good candidate for the manipulation of lignin biosynthesis in biotechnological applications.

SummaryPre-harvest sprouting (PHS) or vivipary in cereals is an important agronomic trait that results in significant economic loss. A considerable number of mutations that cause PHS have been identified in several species. However, relatively few viviparous mutants in rice (Oryza sativa L.) have been reported. To explore the mechanism of PHS in rice, we carried out an extensive genetic screening and identified 12 PHS mutants (phs). Based on their phenotypes, these phs mutants were classified into three groups. Here we characterize in detail one of these groups, which contains mutations in genes encoding major enzymes of the carotenoid biosynthesis pathway, including phytoene desaturase (OsPDS), f-carotene desaturase (OsZDS), carotenoid isomerase (OsCRTISO) and lycopene b-cyclase (b-OsLCY), which are essential for the biosynthesis of carotenoid precursors of ABA. As expected, the amount of ABA was reduced in all four phs mutants compared with that in the wild type. Chlorophyll fluorescence analysis revealed the occurrence of photoinhibition in the photosystem and decreased capacity for eliminating excess energy by thermal dissipation. The greatly increased activities of reactive oxygen species (ROS) scavenging enzymes, and reduced photosystem (PS) II core proteins CP43, CP47 and D1 in leaves of the Oscrtiso/phs3-1mutant and OsLCY RNAi transgenic rice indicated that photo-oxidative damage occurred in PS II, consistent with the accumulation of ROS in these plants. These results suggest that the impairment of carotenoid biosynthesis causes photo-oxidation and ABA-deficiency phenotypes, of which the latter is a major factor controlling the PHS trait in rice.

Cold stress resulting from chilling and freezing temperatures substantially reduces crop production worldwide. To identify genes critical for cold tolerance in plants, we screened Arabidopsis thaliana mutants for deregulated expression of a firefly luciferase reporter gene under the control of the C-REPEAT BINDING FACTOR2 (CBF2) promoter (CBF2:LUC). A regulator of CBF gene expression1 (rcf1-1) mutant that is hypersensitive to cold stress was chosen for in-depth characterization. RCF1 encodes a cold-inducible DEAD (Asp-Glu-Ala-Asp) box RNA helicase. Unlike a previously reported DEAD box RNA helicase (LOW EXPRESSION OF OSMOTICALLY RESPONSIVE GENES4 [LOS4]) that regulates mRNA export, RCF1 does not play a role in mRNA export. Instead, RCF1 functions to maintain proper splicing of pre-mRNAs; many cold-responsive genes are misspliced in rcf1-1 mutant plants under cold stress. Functional characterization of four genes (PSEUDO-RESPONSE, and SPFH/PHB DOMAIN-CONTAINING MEMBRANE-ASSOCIATED PROTEIN [SPFH]) that are misspliced in rcf1-1 revealed that these genes are cold-inducible positive (CIR1 and SPFH) and negative (PRR5 and SK12) regulators of cold-responsive genes and cold tolerance. Together, our results suggest that the cold-inducible RNA helicase RCF1 is essential for pre-mRNA splicing and is important for cold-responsive gene regulation and cold tolerance in plants.

Eutrophication has become increasingly serious and noxious algal blooms have been of more frequent occurrence in the Yangtze River Estuary and in the adjacent East China Sea. In 2003 and 2004, four cruises were undertaken in three zones in the estuary and in the adjacent sea to investigate nitrate (NO 3 -N), ammonium (NH 4 -N), nitrite (NO 2 -N), soluble reactive phosphorus (SRP), dissolved reactive silica (DRSi), dissolved oxygen (DO), phytoplankton chlorophyll a (Chl a) and suspended particulate matter (SPM). The highest concentrations of DIN (NO 3 -N+NH 4 -N+NO 2 -N), SRP and DRSi were 131.6, 1.2 and 155.6 lM, respectively. The maximum Chl a concentration was 19.5 mg m )3 in spring. An analysis of historical and recent data revealed that in the last 40 years, nitrate and SRP concentrations increased from 11 to 97 lM and from 0.4 to 0.95 lM, respectively. From 1963 to 2004, N:P ratios also increased from 30-40 up to 150. In parallel with the N and P enrichment, a significant increase of Chl a was detected, Chl a maximum being 20 mg m )3 , nearly four times higher than in the 1980s. In 2004, the mean DO concentration in bottom waters was 4.35 mg l )1 , much lower than in the 1980s. In comparison with other estuaries, the Yangtze River Estuary was characterized by high DIN and DRSi concentrations, with low SRP concentrations. Despite the higher nutrient concentrations, Chl a concentrations were lower in the inner estuary (Zones 1 and 2) than in the adjacent sea (Zone 3). Based on nutrient availability, SPM and hydrodynamics, we assumed that in Zones 1 and 2 phytoplankton growth was suppressed by high turbidity, large tidal amplitude and short residence time. Furthermore, in Zone 3 water stratification was also an important factor that resulted in a greater phytoplankton biomass and lower DO concentrations. Due to hydrodynamics and turbidity, the open sea was unexpectedly more sensitive to nutrient enrichment and related eutrophication processes.

The maize R2R3-MYB regulator C1 cooperates with the basic helixloop-helix (bHLH) factor R to activate the expression of anthocyanin biosynthetic genes coordinately. As is the case for other bHLH factors, R harbors several protein-protein interaction domains. Here we show that not the classical but rather a briefly extended R bHLH region forms homodimers that bind canonical G-box DNA motifs. This bHLH DNA-binding activity is abolished if the C-terminal ACT (aspartokinase, chorismate, and TyrA) domain is licensed to homodimerize. Then the bHLH remains in the monomeric form, allowing it to interact with R-interacting factor 1 (RIF1). In this configuration, the R-RIF1 complex is recruited to the promoters of a subset of anthocyanin biosynthetic genes, such as A1, through the interaction with its MYB partner C1. If, however, the ACT domain remains monomeric, the bHLH region dimerizes and binds to G-boxes present in several anthocyanin genes, such as Bz1. Our results provide a mechanism by which a dimerization domain in a bHLH factor behaves as a switch that permits distinct configurations of a regulatory complex to be tethered to different promoters. Such a combinatorial gene regulatory framework provides one mechanism by which genes lacking obviously conserved cis-regulatory elements are regulated coordinately.gene regulation | promoter switch T he evolution of multicellular organisms was accompanied by an increase in the complexity of gene-regulatory mechanisms, reflected in the expansion of transcription factor families and in the intricacy of the interactions between regulatory proteins and cis-regulatory elements in what is known today as "combinatorial transcriptional control." A premise of combinatorial control is that different arrangements of a discrete number of regulatory proteins can be used to regulate a much larger number of genes. Therefore, understanding how interactions between different regulatory proteins impact their ability to deploy the expression of specific gene sets is of fundamental biological importance.The basic helix-loop-helix (bHLH) family of transcription factors is among the largest in multicellular organisms (1). The hallmark of the family is a bHLH domain, which consists of two functionally distinct regions. Generally, the basic region of the bHLH domain directly contacts DNA harboring an E-box sequence (CANNTG), and the HLH region provides the potential for homo-and heterodimerization. In addition to the HLH motif, bHLH factors often contain additional protein-protein interaction domains. For example, members of the MYC family of mammalian cell proliferation regulators, such as MAD or MNT, contain a leucine-zipper (LZ) region that contributes to the selective interaction with MAX, another bHLH-LZ protein (2). MAX can form homo-or heterodimers with several related proteins, including MAD (3) and MNT (4). Providing a textbook example of combinatorial transcriptional control, MYC-MAX and MAX-MAX complexes bind E-boxes, but only the MYC-MAX heterodimer activates cell-proliferation gene...

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BackgroundThe plant phytohormone auxin controls many aspects of plant growth and development, which largely depends on its uneven distribution in plant tissues. Transmembrane proteins of the PIN family are auxin efflux facilitators. They play a key role in polar auxin transport and are associated with auxin asymmetrical distribution in plants. PIN genes have been characterized in several plant species, while comprehensive analysis of this gene family in soybean has not been reported yet.ResultsIn this study, twenty-three members of the PIN gene family were identified in the soybean genome through homology searches. Analysis of chromosome distribution and phylogenetic relationships of the soybean PIN genes indicated nine pairs of duplicated genes and a legume specific subfamily. Organ/tissue expression patterns and promoter activity assays of the soybean PINs suggested redundant functions for most duplicated genes and complementary and tissue-specific functions during development for non-duplicated genes. The soybean PIN genes were differentially regulated by various abiotic stresses and phytohormone stimuli, implying crosstalk between auxin and abiotic stress signaling pathways. This was further supported by the altered auxin distribution under these conditions as revealed by DR5::GUS transgenic soybean hairy root. Our data indicates that GmPIN9, a legume-specific PIN gene, which was responsive to several abiotic stresses, might play a role in auxin re-distribution in soybean root under abiotic stress conditions.ConclusionsThis study provided the first comprehensive analysis of the soybean PIN gene family. Information on phylogenetic relationships, gene structure, protein profiles and expression profiles of the soybean PIN genes in different tissues and under various abiotic stress treatments helps to identity candidates with potential roles in specific developmental processes and/or environmental stress conditions. Our study advances our understanding of plant responses to abiotic stresses and serves as a basis for uncovering the biological role of PIN genes in soybean development and adaption to adverse environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2149-1) contains supplementary material, which is available to authorized users.

Background: Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja.