RESUMEN

IRE1, BI-1, and bZIP60 monitor compatible plant-potexvirus interactions though recognition of the viral TGB3 protein. This study was undertaken to elucidate the roles of three IRE1 isoforms, the bZIP60U and bZIP60S, and BI-1 roles in genetic reprogramming of cells during potexvirus infection. Experiments were performed using Arabidopsis thaliana knockout lines and Plantago asiatica mosaic virus infectious clone tagged with the green fluorescent protein gene (PlAMV-GFP). There were more PlAMV-GFP infection foci in ire1a/b, ire1c, bzip60, and bi-1 knockout than wild-type (WT) plants. Cell-to-cell movement and systemic RNA levels were greater bzip60 and bi-1 than in WT plants. Overall, these data indicate an increased susceptibility to virus infection. Transgenic overexpression of AtIRE1b or StbZIP60 in ire1a/b or bzip60 mutant background reduced virus infection foci, while StbZIP60 expression influences virus movement. Transgenic overexpression of StbZIP60 also confers endoplasmic reticulum (ER) stress resistance following tunicamycin treatment. We also show bZIP60U and TGB3 interact at the ER. This is the first demonstration of a potato bZIP transcription factor complementing genetic defects in Arabidopsis. Evidence indicates that the three IRE1 isoforms regulate the initial stages of virus replication and gene expression, while bZIP60 and BI-1 contribute separately to virus cell-to-cell and systemic movement.

Asunto(s)

Proteínas de Arabidopsis , Arabidopsis , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico , Enfermedades de las Plantas , Plantas Modificadas Genéticamente , Potexvirus , Arabidopsis/virología , Arabidopsis/genética , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Enfermedades de las Plantas/virología , Enfermedades de las Plantas/genética , Proteínas de Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Potexvirus/fisiología , Regulación de la Expresión Génica de las Plantas , Retículo Endoplásmico/metabolismo , Estrés del Retículo Endoplásmico , Mutación/genética , Tunicamicina/farmacología , Proteínas de la Membrana , Proteínas Quinasas

RESUMEN

The phylogenetic relationships of ninety-five rose rosette virus (RRV) isolates with full-length genomic sequences were analyzed. These isolates were recovered mostly from commercial roses that are vegetatively propagated rather than grown from seed. First, the genome segments were concatenated, and the maximum likelihood (ML) tree shows that the branches arrange independent of their geographic origination. There were six major groups of isolates, with 54 isolates in group 6 and distributed in two subgroups. An analysis of nucleotide diversity across the concatenated isolates showed lower genetic differences among RNAs encoding the core proteins required for encapsidation than the latter genome segments. Recombination breakpoints were identified near the junctions of several genome segments, suggesting that the genetic exchange of segments contributes to differences among isolates. The ML analysis of individual RNA segments revealed different relationship patterns among isolates, which supports the notion of genome reassortment. We tracked the branch positions of two newly sequenced isolates to highlight how genome segments relate to segments of other isolates. RNA6 has an interesting pattern of single-nucleotide mutations that appear to influence amino acid changes in the protein products derived from ORF6a and ORF6b. The P6a proteins were typically 61 residues, although three isolates encoded P6a proteins truncated to 29 residues, and four proteins extended 76-94 residues. Homologous P5 and P7 proteins appear to be evolving independently. These results suggest greater diversity among RRV isolates than previously recognized.

RESUMEN

We treated potato (Solanum tuberosum L.) plantlets with TM and performed gene expression studies to identify genome-wide changes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). An extensive network of responses was identified, including chromatin remodeling, transcriptional reprogramming, as well as changes in the structural components of the endomembrane network system. Limited genome-wide changes in alternative RNA splicing patterns of protein-coding transcripts were also discovered. Significant changes in RNA metabolism, components of the translation machinery, as well as factors involved in protein folding and maturation occurred, which included a broader set of genes than expected based on Arabidopsis research. Antioxidant defenses and oxygen metabolic enzymes are differentially regulated, which is expected of cells that may be experiencing oxidative stress or adapting to protect proteins from oxidation. Surges in protein kinase expression indicated early signal transduction events. This study shows early genomic responses including an array of differentially expressed genes that have not been reported in Arabidopsis. These data describe novel ER stress responses in a solanaceous host.

Asunto(s)

Arabidopsis , Solanum tuberosum , Solanum tuberosum/genética , Arabidopsis/genética , Arabidopsis/metabolismo , Estrés del Retículo Endoplásmico/genética , Retículo Endoplásmico/metabolismo , Perfilación de la Expresión Génica

RESUMEN

Sugarcane mosaic virus (SCMV) is a widely distributed potyvirus that causes mosaic disease in sugarcane, maize, sorghum, canna, and other monocot species worldwide. This study used 139 SCMV full-length genome sequences to analyze the phylogenetic relatedness of geographically distinct isolates. The phylogenetic analysis revealed four major groups of SCMV isolates that relate to their primary host. The geographic locations for some isolates appear to be mismatched within the tree, suggesting either that convergent molecular evolution has occurred or that the tree reconstruction produces statistically significant incongruences that create uncertainty in the true evolutionary relationships of these virus isolates. Recombination analysis showed hot spots across most of the genome except in the coat protein (CP) coding region. We examined 161 SCMV CP sequences from the GenBank database, including sequences from samples collected in Pakistan, a region that has not been included in prior phylogenetic studies. These data suggest that the SCMV isolates from sugarcane (Saccharum officinarum) predate isolates from all other hosts, regardless of their geographic origins.

Asunto(s)

Potyvirus , Saccharum , Evolución Molecular , Variación Genética , Filogenia , Enfermedades de las Plantas , Potyvirus/genética , Zea mays

RESUMEN

The endoplasmic reticulum (ER) houses sensors that respond to environmental stress and underly plants' adaptative responses. These sensors transduce signals that lead to changes in nuclear gene expression. The ER to nuclear signaling pathways are primarily attributed to the unfolded protein response (UPR) and are also integrated with a wide range of development, hormone, immune, and stress signaling pathways. Understanding the role of the UPR in signaling network mechanisms that associate with particular phenotypes is crucially important. While UPR-associated genes are the subject of ongoing investigations in a few model plant systems, most remain poorly annotated, hindering the identification of candidates across plant species. This open-source curated database provides a centralized resource of peer reviewed knowledge of ER to nuclear signaling pathways for the plant community. We provide a UPRome interactive viewer for users to navigate through the pathways and to access annotated information. The plant ER UPRome website is located at http://uprome.tamu.edu. We welcome contributions from the researchers studying the ER UPR to incorporate additional genes into the database through the "contact us" page.

RESUMEN

Potato virus X (PVX) belongs to genus Potexvirus. This study characterizes the cellular transcriptome responses to PVX infection in Russet potato at 2 and 3 days post infection (dpi). Among the 1242 differentially expressed genes (DEGs), 268 genes were upregulated, and 37 genes were downregulated at 2 dpi while 677 genes were upregulated, and 265 genes were downregulated at 3 dpi. DEGs related to signal transduction, stress response, and redox processes. Key stress related transcription factors were identified. Twenty-five pathogen resistance gene analogs linked to effector triggered immunity or pathogen-associated molecular pattern (PAMP)-triggered immunity were identified. Comparative analysis with Arabidopsis unfolded protein response (UPR) induced DEGs revealed genes associated with UPR and plasmodesmata transport that are likely needed to establish infection. In conclusion, this study provides an insight on major transcriptional regulatory networked involved in early response to PVX infection and establishment.

Asunto(s)

Regulación de la Expresión Génica de las Plantas , Enfermedades de las Plantas/genética , Inmunidad de la Planta/genética , Potexvirus/genética , Solanum tuberosum/genética , Factores de Transcripción/genética , Transcriptoma , Arabidopsis/genética , Arabidopsis/inmunología , Arabidopsis/virología , Perfilación de la Expresión Génica , Redes Reguladoras de Genes , Interacciones Huésped-Patógeno/genética , Interacciones Huésped-Patógeno/inmunología , Moléculas de Patrón Molecular Asociado a Patógenos/inmunología , Moléculas de Patrón Molecular Asociado a Patógenos/metabolismo , Enfermedades de las Plantas/inmunología , Enfermedades de las Plantas/virología , Proteínas de Plantas/clasificación , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Potexvirus/crecimiento & desarrollo , Potexvirus/patogenicidad , Transducción de Señal , Solanum tuberosum/inmunología , Solanum tuberosum/virología , Factores de Transcripción/clasificación , Factores de Transcripción/metabolismo , Transcripción Genética , Respuesta de Proteína Desplegada

RESUMEN

Bunyavirales are negative-sense segmented RNA viruses infecting arthropods, protozoans, plants, and animals. This study examines the phylogenetic relationships of plant viruses within this order, many of which are recently classified species. Comprehensive phylogenetic analyses of the viral RNA dependent RNA polymerase (RdRp), precursor glycoprotein (preGP), the nucleocapsid (N) proteins point toward common progenitor viruses. The RdRp of Fimoviridae and Tospoviridae show a close evolutional relationship while the preGP of Fimoviridae and Phenuiviridae show a closed relationship. The N proteins of Fimoviridae were closer to the Phasmaviridae, the Tospoviridae were close to some Phenuiviridae members and the Peribunyaviridae. The plant viral movement proteins of species within the Tospoviridae and Phenuiviridae were more closely related to each other than to members of the Fimoviridae. Interestingly, distal ends of 3' and 5' untranslated regions of species within the Fimoviridae shared similarity to arthropod and vertebrate infecting members of the Cruliviridae and Peribunyaviridae compared to other plant virus families. Co-phylogeny analysis of the plant infecting viruses indicates that duplication and host switching were more common than co-divergence with a host species.

Asunto(s)

Filogenia , Enfermedades de las Plantas/virología , Virus de Plantas/genética , Virus ARN/genética , Animales , Artrópodos/virología , Evolución Molecular , Genoma Viral , Virus de Plantas/clasificación , Virus de Plantas/aislamiento & purificación , Virus de Plantas/fisiología , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , Virus ARN/fisiología

RESUMEN

Plant potexvirus and potyvirus infection can trigger endoplasmic reticulum (ER) stress. ER stress signaling increases the expression of cytoprotective ER-chaperones, especially the BiP chaperones which contribute to pro-survival functions when plants are subjected to infection. The inositol requiring enzyme (IRE1) is one ER stress sensor that is activated to splice the bZIP60 mRNA which produces a truncated transcription factor that activates gene expression in the nucleus. The IRE1/bZIP60 pathway is associated with restricting potyvirus and potexvirus infection. Recent data also identified the IRE1-independent UPR pathways led by bZIP28 and bZIP17 contribute to potexvirus and potyvirus infection. These three bZIP pathways recognize cis-regulatory elements in the BiP promoters to enhance gene expression. BiP is part of a negative feedback loop that regulates the activities of the ER stress transducers IRE1, bZIP28, and bZIP17 to block their activation. We discuss a model in which bZIP60 and bZIP17 synergistically induce BiP and other genes restricting Plantago asiatica mosaic virus (PlAMV; a potexvirus) infection while bZIP60 and bZIP28 independently induce genes supporting PlAMV infection. Regarding Turnip mosiac virus (TuMV, a potyvirus) infection, bZIP60 and bZIP28 serve to repress local and systemic infection. Finally, tauroursodeoxycholic acid treatments were used to demonstrate that the protein folding capacity significantly influences PlAMV accumulation.

Asunto(s)

Potexvirus/patogenicidad , Potyvirus/patogenicidad , Respuesta de Proteína Desplegada/fisiología , Arabidopsis/metabolismo , Arabidopsis/virología , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Chaperón BiP del Retículo Endoplásmico , Estrés del Retículo Endoplásmico/genética , Estrés del Retículo Endoplásmico/fisiología , Endorribonucleasas/genética , Endorribonucleasas/metabolismo , Proteínas de Choque Térmico/genética , Proteínas de Choque Térmico/metabolismo , Respuesta de Proteína Desplegada/genética

RESUMEN

Rose rosette virus (RRV) is a negative-sense RNA virus with a seven-segmented genome that is enclosed by a double membrane. We constructed an unconventional minireplicon system encoding the antigenomic (ag)RNA1 (encoding the viral RNA-dependent RNA polymerase [RdRp]), agRNA3 (encoding the nucleocapsid protein [N]), and a modified agRNA5 containing the coding sequence for the iLOV protein in place of the P5 open reading frame (R5-iLOV). iLOV expression from the R5-iLOV template was amplified by activities of the RdRp and N proteins in Nicotiana benthamiana leaves. A mutation was introduced into the RdRp catalytic domain and iLOV expression was eliminated, indicating RNA1-encoded polymerase activity drives iLOV expression from the R5-iLOV template. Fluorescence from the replicon was highest at 3 days postinoculation (dpi) and declined at 7 and 13 dpi. Addition of the tomato bushy stunt virus (TBSV) P19 silencing-suppressor protein prolonged expression until 7 dpi. A full-length infectious clone system was constructed of seven binary plasmids encoding each of the seven genome segments. Agro-delivery of constructs encoding RRV RNAs 1 through 4 or RNAs 1 through 7 to N. benthamiana plants produced systemic infection. Finally, agro-delivery of the full-length RRV infectious clone including all segments produced systemic infection within 60 dpi. This advance opens new opportunities for studying RRV infection biology.

Asunto(s)

Nicotiana/virología , ARN Viral/genética , ARN Polimerasa Dependiente del ARN/genética , Genética Inversa , Tombusvirus/genética , Enfermedades de las Plantas/virología , Tombusvirus/patogenicidad

RESUMEN

The endoplasmic reticulum (ER) immunoglobulin binding proteins (BiPs) are molecular chaperones involved in normal protein maturation and refolding malformed proteins through the unfolded protein response (UPR). Plant BiPs belong to a multi-gene family contributing to development, immunity, and responses to environmental stresses. This study identified three BiP homologs in the Solanum tuberosum (potato) genome using phylogenetic, amino acid sequence, 3-D protein modeling, and gene structure analysis. These analyses revealed that StBiP1 and StBiP2 grouped with AtBiP2, whereas StBiP3 grouped with AtBiP3. While the protein sequences and folding structures are highly similar, these StBiPs are distinguishable by their expression patterns in different tissues and in response to environmental stressors such as treatment with heat, chemicals, or virus elicitors of UPR. Ab initio promoter analysis revealed that potato and Arabidopsis BiP1 and BiP2 promoters were highly enriched with cis-regulatory elements (CREs) linked to developmental processes, whereas BiP3 promoters were enriched with stress related CREs. The frequency and linear distribution of these CREs produced two phylogenetic branches that further resolve the groups identified through gene phylogeny and exon/intron phase analysis. These data reveal that the CRE architecture of BiP promoters potentially define their spatio-temporal expression patterns under developmental and stress related cues.

Asunto(s)

Proteínas Portadoras/genética , Chaperonas Moleculares/genética , Proteínas de Plantas/genética , Regiones Promotoras Genéticas , Solanum tuberosum/genética , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Retículo Endoplásmico/metabolismo , Regulación de la Expresión Génica de las Plantas , Conformación Proteica , Estrés Fisiológico

RESUMEN

Pathogens and other adverse environmental conditions can trigger endoplasmic reticulum (ER) stress. ER stress signaling increases the expression of cytoprotective ER-chaperones. The inositol-requiring enzyme (IRE1) is one ER stress sensor that is activated to splice the bZIP60 mRNA that produces a truncated transcription factor that activates gene expression in the nucleus. The IRE1/bZIP60 pathway is associated with restricting potyvirus and potexvirus infection. This study shows that the Plantago asiatica mosaic virus (PlAMV) triple gene block 3 (TGB3) and the Turnip mosaic virus (TuMV) 6K2 proteins activate alternative transcription pathways involving the bZIP17, bZIP28, BAG7, NAC089 and NAC103 factors in Arabidopsis thaliana. Using the corresponding knockout mutant lines, we show that bZIP17, bZIP60, BAG7 and NAC089 are factors in reducing PlAMV infection, whereas bZIP28 and bZIP60 are factors in reducing TuMV infection. We propose a model in which bZIP60 and bZIP17 synergistically induce genes restricting PlAMV infection, while bZIP60 and bZIP28 independently induce genes supporting PlAMV infection. Regarding TuMV-green fluorescent protein (GFP) infection, bZIP60 and bZIP28 serve to repress local and systemic infection. Finally, tauroursodeoxycholic acid treatments were used to demonstrate that the protein folding capacity significantly influences PlAMV accumulation.

Asunto(s)

Arabidopsis/virología , Núcleo Celular/metabolismo , Retículo Endoplásmico/metabolismo , Enfermedades de las Plantas/virología , Potexvirus/metabolismo , Potyvirus/metabolismo , Transducción de Señal , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Regulación de la Expresión Génica de las Plantas , Regulación Viral de la Expresión Génica , Respuesta de Proteína Desplegada

RESUMEN

Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies.

RESUMEN

The basic region-leucine zipper (bZIP) transcription factors (TFs) form homodimers and heterodimers via the coil-coil region. The bZIP dimerization network influences gene expression across plant development and in response to a range of environmental stresses. The recent release of the most comprehensive potato reference genome was used to identify 80 StbZIP genes and to characterize their gene structure, phylogenetic relationships, and gene expression profiles. The StbZIP genes have undergone 22 segmental and one tandem duplication events. Ka/Ks analysis suggested that most duplications experienced purifying selection. Amino acid sequence alignments and phylogenetic comparisons made with the Arabidopsis bZIP family were used to assign the StbZIP genes to functional groups based on the Arabidopsis orthologs. The patterns of introns and exons were conserved within the assigned functional groups which are supportive of the phylogeny and evidence of a common progenitor. Inspection of the leucine repeat heptads within the bZIP domains identified a pattern of attractive pairs favoring homodimerization, and repulsive pairs favoring heterodimerization. These patterns of attractive and repulsive heptads were similar within each functional group for Arabidopsis and S. tuberosum orthologs. High-throughput RNA-seq data indicated the most highly expressed and repressed genes that might play significant roles in tissue growth and development, abiotic stress response, and response to pathogens including Potato virus X. These data provide useful information for further functional analysis of the StbZIP gene family and their potential applications in crop improvement.

Asunto(s)

Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Familia de Multigenes , Solanum tuberosum/genética , Secuencias de Aminoácidos , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Sitios de Unión , Mapeo Cromosómico , Secuencia Conservada , Exones , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Orden Génico , Genoma de Planta , Intrones , Especificidad de Órganos , Filogenia , Regiones Promotoras Genéticas , Solanum tuberosum/clasificación , Solanum tuberosum/metabolismo , Estrés Fisiológico , Transcriptoma

RESUMEN

Grain number, plant height and heading date 7 (GhD7) is considered to be one of the key yield-related genes in the production of high-yielding and climate-ready super rice varieties. GhD7 delays the plant's flowering under long-day conditions, which ultimately results in increased yield. Recent findings indicate that GhD7 also plays a major role in the abiotic stress response; however, the fine regulatory mechanisms controlling Ghd7 expression have yet to be uncovered. This study was carried out to explore the transcription factor binding site (TFBS) architecture of the GhD7 promoter to identify the regulatory dynamics of GhD7 transcription. The promoter sequence (-2000 to +200 base pairs from the transcription start site) was retrieved from the PlantPAN 2.0 database. Ab initio promoter analysis, DNase I hypersensitive site (DHS) analysis, and methylation analysis were carried out to identify TFBSs. The TFBS diversity among rice varieties was also assessed. In addition to the previously identified 8 cis-elements, 448 novel cis-elements were identified in the GhD7 promoter that provide binding sites for 25 transcription factor families. Furthermore, a DNase I hypersensitive site and a CpG island were also identified. The identified transcription factor families include key transcription factors involved in both development and abiotic stress responses, revealing the regulatory dynamics of GhD7. Comparative analysis of multiple GhD7 promoters identified 31 single-nucleotide polymorphisms that result in TFBS variations among rice accessions. These variations are mostly found in relation to flowering and abiotic stress responsive TFBSs on the promoter. This study supports the model that GhD7 acts as a central regulator of rice growth, development, and the abiotic stress response.

Asunto(s)

ADN de Plantas/genética , Oryza/genética , Regiones Promotoras Genéticas , Sitios de Carácter Cuantitativo , Estrés Fisiológico/genética , Análisis por Conglomerados , Bases de Datos de Proteínas/estadística & datos numéricos , Regulación de la Expresión Génica de las Plantas , Oryza/crecimiento & desarrollo , Factores de Transcripción/genética

RESUMEN

Dehydration-responsive element- (DREB) proteins are considered as the master regulators of plant abiotic stress responses including drought, salinity and cold. They are also involved in other developmental processes such as embryo and endosperm development. DREB family of transcription factors consist of two sub families namely CBF1/DREB1 and DREB2. In this study, a genome-wide in silico analysis was carried out to dissect the structure and function of DREB2 family transcription factors in the rice genome. Using Arabidopsis DREB2 sequences a total of five rice DREB2 homologs were identified and they were distributed among four chromosomes. All OsDREBs contained the AP2 domain and unique [K/R]GKKGPxN motif characteristic to DREB2 family. During rice growth and development, three OsDREB2s namely OsDREB2A, OsDREB2B and OsABI4 were expressed and their expression was confined to embryo and endosperm tissues. OsDREB2A, OsDREB2B and OsDREB2C were expressed under abiotic stress conditions. OsDREB2B was expressed under drought, salinity and cold stress conditions while OsDREB2A and OsDREB2C were expressed only under drought and salinity conditions. The putative promoter regions of OsDREB2s were enriched with elements related to cellular development, hormonal regulation and stress response validating the observed expression dynamics. Co-expression analysis revealed that embryo development and stress related genes were expressed together with OsDREB2s. Predicted post-translational modifications indicated the fine regulation of OsDREB2s. These findings may shed light in uncovering the complex abiotic stress signaling networks and future genomics studies targeting the development of climate ready crops.

Asunto(s)

Oryza/metabolismo , Proteínas de Plantas/metabolismo , Factores de Transcripción/metabolismo , Simulación por Computador , Genes de Plantas , Oryza/genética , Proteínas de Plantas/genética , Factores de Transcripción/genética

RESUMEN

Rice is a chilling-sensitive plant that is particularly prone to injury during the early stages of seedling development and during flowering. Significant variation exists between subspecies with japonica cultivars generally being less sensitive than most indica cultivars. In most temperate and subtropical countries where rice is grown, crop damage often occurs during the early stages of seedling development due to occasional cold snaps coinciding with the first few weeks after direct seeding in late spring to early summer. Irreversible injuries often result in seedling mortality or if the crop survives a stress episode, plant vigor and resistance to pests and diseases are severely compromised. Recent physiological and molecular studies have shown that oxidative stress is the primary cause of early chilling injuries in rice and the differential responses of indica and japonica cultivars are defined to a large extent by gene expression related to oxidative signaling and defenses. In this chapter, we summarize basic phenotypic, physiological, and molecular procedures that can be adopted for routine evaluation of differential responses between cultivars as well as for functional genomics studies.

Asunto(s)

Frío , Oryza/genética , Fenotipo , Plantones/genética , Estrés Fisiológico , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Oryza/crecimiento & desarrollo , Oryza/metabolismo , Hojas de la Planta , Plantones/crecimiento & desarrollo , Plantones/metabolismo , Estrés Fisiológico/genética

RESUMEN

BACKGROUND: The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa) formed ten clusters of orthologous groups (COG) with genes from the monocot sorghum (Sorghum bicolor) and dicot Arabidopsis (Arabidopsis thaliana). The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns. RESULTS: The most apparent pattern observed was the occurrence of spatially conserved 'core modules' among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS) classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic) or organ-associated signals, which may be functioning as 'regulatory fine-tuners' and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis. CONCLUSIONS: Patterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in conjunction with lineage-specific or species-specific regulatory fine-tuners. This synergy may be critical for finer-scale spatio-temporal regulation, hence unique expression profiles of homologous transcription factors from different species with distinct zones of ecological adaptation such as rice, sorghum and Arabidopsis. The patterns revealed from these comparisons set the stage for further empirical validation by functional genomics.

Asunto(s)

Arabidopsis/genética , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Regulación de la Expresión Génica de las Plantas , Oryza/genética , Proteínas de Plantas/genética , Sorghum/genética , Adaptación Fisiológica/genética , Secuencia de Bases , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/clasificación , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Sitios de Unión , Secuencia Conservada , Datos de Secuencia Molecular , Familia de Multigenes , Filogenia , Proteínas de Plantas/clasificación , Proteínas de Plantas/metabolismo , Regiones Promotoras Genéticas , Homología de Secuencia de Ácido Nucleico , Especificidad de la Especie , Estrés Fisiológico/genética

RESUMEN

Unlike other cereal species, rice is able to germinate and elongate under anoxia. The regulatory mechanism that configures the transcriptome of rice during anaerobic germination is yet to be established. In this study, the major regulatory modules among anoxia-responsive genes in rice identified from published microarray data were predicted by ab initio analysis of cis-regulatory information content. Statistically overrepresented sequence motifs were detected from bona fide promoter sequences [-1000 to +200], revealing various patterns of cis-element enrichment that are highly correlated with bZIP, ERF and MYB types of transcription factors. As implied by the cis-element enrichment patterns, combinatorial mechanisms configure the overall changes in gene expression during anoxic germination and coleoptile elongation. High enrichment of cis-elements associated with ARF, bZIP, ERF, MYB and WRKY (SUSIBA2) transcription factors was also detected among the glycolytic and fermentative associated genes that were upregulated during anoxia. The patterns established from the global analysis of cis-element distribution for upregulated and downregulated genes and their associations with potential cognate regulatory transcription factors indicate the significant roles of ethylene and abscisic acid mediated signaling during coleoptile elongation under anoxia. In addition, the regulation of genes encoding enzymes in the glycolytic and fermentative metabolism could be associated with abscisic acid and auxin in rice coleoptiles to maintain sugar and ATP levels for longer survival.

Asunto(s)

Regulación de la Expresión Génica de las Plantas , Oryza/fisiología , Oxígeno/metabolismo , Secuencias Reguladoras de Ácidos Nucleicos , Transcripción Genética , Genes de Plantas , Familia de Multigenes , Oryza/genética , Oryza/metabolismo , Regiones Promotoras Genéticas

RESUMEN

The R2R3-type OsMyb4 transcription factor of rice has been shown to play a role in the regulation of osmotic adjustment in heterologous overexpression studies. However, the exact composition and organization of its underlying transcriptional network has not been established to be a robust tool for stress tolerance enhancement by regulon engineering. OsMyb4 network was dissected based on commonalities between the global chilling stress transcriptome and the transcriptome configured by OsMyb4 overexpression. OsMyb4 controls a hierarchical network comprised of several regulatory sub-clusters associated with cellular defense and rescue, metabolism and development. It regulates target genes either directly or indirectly through intermediary MYB, ERF, bZIP, NAC, ARF and CCAAT-HAP transcription factors. Regulatory sub-clusters have different combinations of MYB-like, GCC-box-like, ERD1-box-like, ABRE-like, G-box-like, as1/ocs/TGA-like, AuxRE-like, gibberellic acid response element (GARE)-like and JAre-like cis-elements. Cold-dependent network activity enhanced cellular antioxidant capacity through radical scavenging mechanisms and increased activities of phenylpropanoid and isoprenoid metabolic processes involving various abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), ethylene and reactive oxygen species (ROS) responsive genes. OsMyb4 network is independent of drought response element binding protein/C-repeat binding factor (DREB/CBF) and its sub-regulons operate with possible co-regulators including nuclear factor-Y. Because of its upstream position in the network hierarchy, OsMyb4 functions quantitatively and pleiotrophically. Supra-optimal expression causes misexpression of alternative targets with costly trade-offs to panicle development.

Asunto(s)

Regulación de la Expresión Génica de las Plantas , Redes Reguladoras de Genes , Oryza/metabolismo , Estrés Fisiológico , Factores de Transcripción/metabolismo , Frío , Copas de Floración/crecimiento & desarrollo , Oryza/genética , Oryza/crecimiento & desarrollo , Fenotipo , Plantas Modificadas Genéticamente/crecimiento & desarrollo , Plantas Modificadas Genéticamente/metabolismo