Repression of the defense gene PR-10a by the single-stranded DNA binding protein SEBF

Stress responsive OsHyPRP16 promoter driven early expression of resistance gene Pi54 potentiate the resistance against Magnaporthe oryzae in transgenic rice

The rice Hybrid Proline Rich Protein (HyPRP) encoding gene, OsHyPRP16 expression exhibit early upregulation in response to Magnaporthe oryzae inoculation. Here, we functionally characterized the OsHyPRP16 promoter through deletion analysis in transgenic Arabidopsis using GUS (β-glucuronidase) reporter assay. The promoter fragments, sequentially deleted from the 5' end could induce differential GUS activity in response to stresses induced by different hormones and abiotic stress conditions. In addition, a strong GUS induction was observed in M. oryzae inoculated transgenic Arabidopsis. Based on the insilico and stress-inducibility of D1 promoter fragment against various phytohormones and rice blast fungus, and with no basal activity under control conditions, we rationally selected D1 promoter fragment to drive the expression of a major rice blast resistance gene; Pi54 in the genetic background of blast susceptible TP309 rice line. The D1 promoter fragment was able to induce the expression of Pi54 at immediate-early stages of M. oryzae infection in transgenic rice. The transgenic plants with Pi54 under the control of D1 promoter fragment displayed complete resistance against M. oryzae infection as compared to control plants. The present study suggests that the D1 fragment of OsHyPRP16 promoter is a valuable tool for breeding and development of rice lines with early-inducible and pathogen-responsive enhanced disease resistance.

Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches

Single-stranded DNA (ssDNA) binding proteins (SSBs) are critical in maintaining genome stability by protecting the transient existence of ssDNA from damage during essential biological processes, such as DNA replication and gene transcription. The single-stranded region of telomeres also requires protection by ssDNA binding proteins from being attacked in case it is wrongly recognized as an anomaly. In addition to their critical roles in genome stability and integrity, it has been demonstrated that ssDNA and SSB-ssDNA interactions play critical roles in transcriptional regulation in all three domains of life and viruses. In this review, we present our current knowledge of the structure and function of SSBs and the structural features for SSB binding specificity. We then discuss the machine learning-based approaches that have been developed for the prediction of SSBs from double-stranded DNA (dsDNA) binding proteins (DSBs).

Genome-Wide Analysis of LysM-Containing Gene Family in Wheat: Structural and Phylogenetic Analysis during Development and Defense

The lysin motif (LysM) family comprise a number of defense proteins that play important roles in plant immunity. The LysM family includes LysM-containing receptor-like proteins (LYP) and LysM-containing receptor-like kinase (LYK). LysM generally recognizes the chitin and peptidoglycan derived from bacteria and fungi. Approximately 4000 proteins with the lysin motif (Pfam PF01476) are found in prokaryotes and eukaryotes. Our study identified 57 LysM genes and 60 LysM proteins in wheat and renamed these genes and proteins based on chromosome distribution. According to the phylogenetic and gene structure of intron-exon distribution analysis, the 60 LysM proteins were classified into seven groups. Gene duplication events had occurred among the LysM family members during the evolution process, resulting in an increase in the LysM gene family. Synteny analysis suggested the characteristics of evolution of the LysM family in wheat and other species. Systematic analysis of these species provided a foundation of LysM genes in crop defense. A comprehensive analysis of the expression and cis-elements of LysM gene family members suggested that they play an essential role in defending against plant pathogens. The present study provides an overview of the LysM family in the wheat genome as well as information on systematic, phylogenetic, gene duplication, and intron-exon distribution analyses that will be helpful for future functional analysis of this important protein family, especially in Gramineae species.

GhABP19, a Novel Germin-Like Protein From Gossypium hirsutum, Plays an Important Role in the Regulation of Resistance to Verticillium and Fusarium Wilt Pathogens

Germin-like proteins (GLPs) are water-soluble plant glycoproteins belonging to the cupin superfamily. The important role of GLPs in plant responses against various abiotic and biotic stresses, especially pathogens, is well validated. However, little is known about cotton GLPs in relation to fungal pathogens. Here, a novel GLP gene was isolated from Gossypium hirsutum and designated as GhABP19. The expression of GhABP19 was upregulated in cotton plants inoculated with Verticillium dahliae and Fusarium oxysporum and in response to treatment with jasmonic acid (JA) but was suppressed in response to salicylic acid treatment. A relatively small transient increase in GhABP19 was seen in H2O2 treated samples. The three-dimensional structure prediction of the GhABP19 protein indicated that the protein has three histidine and one glutamate residues responsible for metal ion binding and superoxide dismutase (SOD) activity. Purified recombinant GhABP19 exhibits SOD activity and could inhibit growth of V. dahliae, F. oxysporum, Rhizoctonia solani, Botrytis cinerea, and Valsa mali in vitro. To further verify the role of GhABP19 in fungal resistance, GhABP19-overexpressing Arabidopsis plants and GhABP19-silenced cotton plants were developed. GhABP19-transgenic Arabidopsis lines showed much stronger resistance to V. dahliae and F. oxysporum infection than control (empty vector) plants did. On the contrary, silencing of GhABP19 in cotton conferred enhanced susceptibility to fungal pathogens, which resulted in necrosis and wilt on leaves and vascular discoloration in GhABP19-silenced cotton plants. The H2O2 content and endogenous SOD activity were affected by GhABP19 expression levels in Arabidopsis and cotton plants after inoculation with V. dahliae and F. oxysporum, respectively. Furthermore, GhABP19 overexpression or silencing resulted in activation or suppression of JA-mediated signaling, respectively. Thus, GhABP19 plays important roles in the regulation of resistance to verticillium and fusarium wilt in plants. These modulatory roles were exerted by its SOD activity and ability to activate the JA pathway. All results suggest that GhABP19 was involved in plant disease resistance.

Computational analysis of atpB gene promoter from different Pakistani apple varieties

Apple is the fourth most important fruit crop grown in temperate areas of the world belongs to the family Rosaceae. In the present study, the promoter (∼1000bp) region of atpB gene was used to evaluate the genetic diversity and phylogeny of six local apple varieties. atpB gene is one of the large chloroplastic region which encodes β-subunit of ATP synthase and previously it had been used largely in phylogenetic studies. During the present study, atpB promoter was amplified, sequenced and analyzed using various bioinformatics tools including Place Signal Scan, MEGA6 and BLASTn. During the phylogenetic analysis, obtained phylogram divided the studied varieties into two clusters revealing the monophyletic origin of studied apple varieties. Pairwise distance revealed moderate genetic diversity that ranges from 0.047-0.170 with an average of 0.101. While identifying different cis-acting elements present in the atpB promoter region, results exhibited the occurrence of 56 common and 20 unique cis-regulatory elements among studied varieties. The identified cis-acting regulatory elements were mapped as well. It was observed that Kala Kulu has the highest unique features with reference to the availability of cis-acting elements. Moreover, the possible functions of all regulatory elements present on the promoter sequence of atpB gene were predicted based on already reported information regarding their in vivo role.

Multifunctionality of plastid nucleoids as revealed by proteome analyses

Protocols aimed at the isolation of nucleoids and transcriptionally active chromosomes (TACs) from plastids of higher plants have been established already decades ago, but only recent improvements in the mass spectrometry methods enabled detailed proteomic characterization of their components. Here we present a comprehensive analysis of the protein compositions obtained from two proteomic studies of TAC fractions isolated from Arabidopsis/mustard and spinach chloroplasts, respectively, as well as nucleoid fractions from Arabidopsis, maize and pea. Interestingly, different approaches as well as the use of diverse starting materials resulted in the detection of varying protein catalogues with a number of shared proteins. Possible reasons for the discrepancies between the protein repertoires and for missing out some of the nucleoid proteins that have been identified previously by other means than mass spectrometry as well as the repeated identification of "unexpected" proteins indicating potential links between DNA/RNA-associated nucleoid core functions and energy metabolism as well as biosynthetic activities of plastids will be discussed. In accordance with the nucleoid association of proteins involved in key functions of plastids including photosynthesis, the phenotypes of mutants lacking one or the other plastid nucleoid-associated protein (ptNAP) show the importance of nucleoid proteins for overall plant development and growth. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Pathogenesis related-10 proteins are small, structurally similar but with diverse role in stress signaling

Pathogenesis related-10 proteins are small proteins with cytosolic localization, conserved three dimensional structures and single intron at 185 bp position. These proteins have a broad spectrum of roles significantly in biotic and abiotic stresses. The RNase activity, ligand binding activity, posttranslational modification (phosphorylation) and phytohormone signaling provide some information into the mechanism of the regulation of PR-10 proteins, however the presence of isoforms makes it difficult to decipher its exact mode of function. The involvement of phosphorylation/dephosphorylation events in its activation is interesting and provides unique and unbiased insights into the complexity of its regulation. Studies on upstream region of different PR-10 genes indicate the presence of cis-acting elements for WRKY, RAVI, bZ1P, ERF, SEBF and Pti4 transcription factors indicating their role in regulating PR-10 promoter. In this review, we discuss in detail the structure and mechanism of regulation of PR-10 proteins.

The NPR1 ortholog PhaNPR1 is required for the induction of PhaPR1 in Phalaenopsis aphrodite

BACKGROUND

Systematic acquired resistance (SAR) is an effective broad-spectrum defense mechanism that confers long-lasting protection against biotrophic pathogens trough defense related salicylic acid (SA) signaling. Gene(s) involved in SAR have been extensively studied in dicot plants; however, remains largely unresolved in monocot plants. NPR1, an evolutionary conserved gene, plays a central role in SAR, and PR-1 is widely used as a marker for effective SA signaling.

RESULTS

We identified NPR1 and PR-1 homologous genes, PhaNPR1 and PhaPR1, from an economically important orchid, Phalaenopsis aphrodite, and characterized their roles in SA signaling and Cymbidium mosaic virus (CymMV) resistance. A phylogenetic analysis of NPR1 homologs showed that these genes appear to have evolved before angiospermy. Similar to Arabidopsis NPR1, PhaNPR1 was only moderately induced upon SA treatment and CymMV infection. Although PhaPR1 shows only 36% identity with AtPR1, its promoter shared conserved elements with those of other PR-1 genes, and it was induced upon SA treatment and CymMV infection. After CymMV infection, silencing on PhaNPR1 also reduced PhaPR1 expression; however, CymMV accumulation was not affected.

CONCLUSIONS

In conclusion, after virus infection, PhaNPR1 is required for PhaPR1 induction, but plays little role in defense against CymMV.

Impacts of pr-10a overexpression at the molecular and the phenotypic level

Biotechnological approaches using genetic modifications such as homologous gene overexpression can be used to decode gene functions under well-defined circumstances. However, only the recording of the resulting phenotypes allows inferences about the impact of the modification on the organisms’ evolutionary, ecological or economic performance. We here compare a potato wild-type cell line with two genetically engineered cell cultures homologously overexpressing Pathogenesis Related Protein 10a (pr-10a). A detailed analysis of the relative gene-expression patterns of pr-10a and its regulators sebf and pti4 over time provides insights into the molecular response of heterotrophic cells to distinct osmotic and salt-stress conditions. Furthermore, this system serves as an exemplar for the tracing of respiration kinetics as a faster and more sensitive alternative to the laborious and time-consuming recording of growth curves. The utility and characteristics of the resulting data type and the requirements for its appropriate analysis are figured out. It is demonstrated how this novel type of phenotypic information together with the gene-expression-data provides valuable insights into the effect of genetic modifications on the behaviour of cells on both the molecular and the macroscopic level.

Dual targeting and retrograde translocation: regulators of plant nuclear gene expression can be sequestered by plastids

Changes in the developmental or metabolic state of plastids can trigger profound changes in the transcript profiles of nuclear genes. Many nuclear transcription factors were shown to be controlled by signals generated in the organelles. In addition to the many different compounds for which an involvement in retrograde signaling is discussed, accumulating evidence suggests a role for proteins in plastid-to-nucleus communication. These proteins might be sequestered in the plastids before they act as transcriptional regulators in the nucleus. Indeed, several proteins exhibiting a dual localization in the plastids and the nucleus are promising candidates for such a direct signal transduction involving regulatory protein storage in the plastids. Among such proteins, the nuclear transcription factor WHIRLY1 stands out as being the only protein for which an export from plastids and translocation to the nucleus has been experimentally demonstrated. Other proteins, however, strongly support the notion that this pathway might be more common than currently believed.

Cloning and characterization of PR5 gene from Curcuma amada and Zingiber officinale in response to Ralstonia solanacearum infection

Ginger (Zingiber officinale Roscoe), is an important spice crop that is badly affected by Ralstonia solanacearum wilt. Ginger does not set seed and sexual recombination has never been reported. In spite of extensive search in its habitats, no resistance source to Ralstonia induced bacterial wilt, could be located in ginger. Curcuma amada Roxb. is a potential donor for bacterial wilt resistance to Z. officinale, if the exact mechanism of resistance is understood. Pathogenesis-related (PR)-5 proteins are a family of proteins that are induced by different phytopathogens in many plants and share significant sequence similarity with thaumatin. Two putative PR5 genes, CaPR5 and ZoPR5, were amplified from C. amada and ginger, which encode precursor proteins of 227 and 224 amino acid residues, respectively, and share high homology with a number of other PR5 genes. The secondary and three-dimensional structure comparison did not reveal any striking differences between these two proteins. The expression of Ca and ZoPR5s under R. solanacearum inoculation was analyzed at different time points using quantitative real-time PCR (qRT-PCR). Our results reveal that CaPR5 is readily induced by the bacterium in C. amada, while ZoPR5 induction was very weak and slow in ginger. These results suggest that the CaPR5 could play a role in the molecular defense response of C. amada to pathogen attack. This is the first report of the isolation of PR5 gene from the C. amada and Z. officinale. Promoter analysis indicates the presence of a silencing element binding factor in ZoPR5-promoter, but not in CaPR5. Prospective promoter elements, such as GT-1 box and TGTCA, implicated as being positive regulatory elements for expression of PR proteins, occur in the 5'-flanking sequences of the CaPR5. Transient GUS expression study confirms its action with a weaker GUS expression in ginger, indicating that the PR5 expression may be controlled in the promoter.

Cold-inducible expression of AZI1 and its function in improvement of freezing tolerance of Arabidopsis thaliana and Saccharomyces cerevisiae

AZI1 (AZELAIC ACID INDUCED 1) of Arabidopsis thaliana could be induced by azelaic acid and was involved in priming of systemic plant immunity. In the present work, expression of AZI1 in response to low temperature was investigated via RNA gel blot analysis. AZI1 could be induced slowly by cold stress and more than 6h treatment at 4°C was required to detect an increase in mRNA abundance. However, the high expression state could not be maintained stably and would decline to basal level when the plants were transferred to room temperature. In order to clarify the function of AZI1 in resistance to abiotic stresses, overexpressing, RNA interference and T-DNA knockout lines of this gene were used in electrolyte leakage assays. Overexpression of AZI1 resulted in reduced electrolyte leakage during freezing damage. In contrast, AZI1 knockdown and knockout lines showed increased tendencies in cellular damage after freezing treatment. To further validate the potential resistance of AZI1 to low-temperature stress, Saccharomyces cerevisiae cells were transformed with pESC-AZI1 in which AZI1 was under the control of GAL1 promoter. Compared to yeast cells containing empty pESC-URA, the survival rate of yeast cells harboring AZI1 increased obviously after freezing treatment. All these results suggested that AZI1 might be multifunctional and associated with cold tolerance of Arabidopsis.

The RNA-recognition motif in chloroplasts

Chloroplast RNA metabolism is characterized by multiple RNA processing steps that require hundreds of RNA binding proteins. A growing number of RNA binding proteins have been shown to mediate specific RNA processing steps in the chloroplast, but little do we know about their regulatory importance or mode of molecular action. This review summarizes knowledge on chloroplast proteins that contain an RNA recognition motif, a classical RNA binding domain widespread in pro- and eukaryotes. Several members of this family respond to external and internal stimuli by changes in their expression levels and protein modification state. They therefore appear as ideal candidates for regulating chloroplast RNA processing under shifting environmental conditions.

Molecular cloning and function assay of a chalcone isomerase gene (GbCHI) from Ginkgo biloba

Chalcone isomerase (CHI, EC 5.5.1.6) is one of the key enzymes in the flavonoid biosynthesis pathway catalyzing the stereospecific isomerization of chalcones into their corresponding (2S)-flavanones. In this investigation, both the cDNA sequence and the genomic sequence encoding the chalcone isomerase from Ginkgo biloba L. (designated as GbCHI) were isolated from the leaves. The GbCHI gene contained two introns and three extrons and encoded a peptide of 244 amino acids with a predicted molecular mass of 26.29 kDa and a pI of 7.76. RQPCR showed that GbCHI was expressed in a tissue-specific manner in G. biloba. Expression of GbCHI was also up-regulated by UV-B irradiation or treatment with 5-aminolevulinic acid or three plant growth regulator-ethylene, abscisic acid, and chlormequat-and these effects were consistent with analysis of the GbCHI promoter region. The recombinant protein was successfully expressed in an E.coli strain with the pET-28a vector. In vitro enzyme activity, assayed by HPLC, indicated that recombinant GbCHI protein could catalyze the formation of naringenin from 6'-hydroxychalcone. RQPCR analysis showed that CHI activity correlated with changes in transcription level of the CHI gene, GbCHI activity was also positively correlated with total flavonoid levels in ginkgo leaves, suggesting CHI as a key gene regulating flavonoid accumulation in ginkgo leaves.

FaRE1: a transcriptionally active Ty1-copia retrotransposon in strawberry

Retrotransposons are ubiquitous in the plant kingdom and constitute a large fraction of many plant genomes. Although most retrotransposons from plants were thought to be transcriptionally silent in somatic tissues, evidence of activity under certain conditions is available in some cases. In this study, a complete LTR retrotransposon was isolated from the cultivated strawberry (Fragaria x ananassa) genome using genome walking. The element, named FaRE1, has all the features of a typical Ty1-copia retrotransposon. Its total length was 5,104 bp, comprising a single 3,891 bp open reading frame. It is represented by approximately 96 copies per genome, equivalent to approximately 0.33% of the genome. Transcription of FaRE1 was detected in leaf tissue treated with various phytohormones, such as naphthalene acetic acid, 2,4-dichlorophenoxyacetic acid or abscisic acid . To our knowledge, this is the first report of the isolation of a complete LTR retrotransposon with transcriptional activity in strawberry.

Dual-function transcription factors and their entourage: unique and unifying themes governing two pathogenesis-related genes

Much of what we, as plant molecular biologists studying gene regulation, know comes from paradigms characterized or developed in mammalian systems. Although plants, animals, and fungi have been diverging for a very long time, a great deal of the machineries and components discovered in yeast and mammals seem to have been maintained in plants. Nevertheless, despite this apparent conservation, evolutionary pressures on the mechanisms of gene regulation are likely to be different between these kingdoms, given their different environmental constraints. As such, it is imperative for plant molecular biologists to develop their own paradigms, even on seemingly conserved systems. It is with this intent that we compare and contrast the regulation of two pathogenesis-related genes, the arabidopsis PR-1 and potato PR-10a genes. The transcription factors regulating these genes present prime paradigms for the study of plant signal- and context-dependent dual-function transcription factors.

Molecular cloning and characterization of five annexin genes from Indian mustard (Brassica juncea L. Czern and Coss)

Plant annexins constitute a multigene family having suggested roles in a variety of cellular processes including stress responses. We have isolated and characterized five different cDNAs of mustard, Brassica juncea (AnnBj1, AnnBj2, AnnBj3, AnnBj6 and AnnBj7) encoding annexin proteins using a RT-PCR/RACE-PCR based strategy. The predicted molecular masses of these annexins are approximately 36.0 kDa with acidic pIs. At the amino acid level, they share high sequence similarity with each other and with annexins from higher plants. Phylogenetic analysis revealed their evolutionary relationship with corresponding orthologous sequences in Arabidopsis and deduced proteins in various plant species. Expression analysis by semi-quantitative RT-PCR revealed that these genes are differentially expressed in various tissues. The expression patterns of these genes also showed regulation by various stress conditions such as exposure to signaling molecules, salinity and oxidative stress and wounding. Additionally, the in silico promoter analysis (of AnnBj1, AnnBj2 and AnnBj3) showed the presence of different cis-responsive elements that could respond to various stress conditions. These results indicate that AnnBj genes may play important roles in adaptation of plants to various environmental stresses.

Involvement of HbPIP2;1 and HbTIP1;1 aquaporins in ethylene stimulation of latex yield through regulation of water exchanges between inner liber and latex cells in Hevea brasiliensis

Natural rubber is synthesized in specialized articulated cells (laticifers) located in the inner liber of Hevea brasiliensis. Upon bark tapping, the laticifer cytoplasm (latex) is expelled due to liber tissue turgor pressure. In mature virgin (untapped) trees, short-term kinetic studies confirmed that ethylene, the rubber yield stimulant used worldwide, increased latex yield, with a concomitant decrease in latex total solid content, probably through water influx in the laticifers. As the mature laticifers are devoid of plasmodesmata, the rapid water exchanges with surrounding liber cells probably occur via the aquaporin pathway. Two full-length aquaporin cDNAs (HbPIP2;1 and HbTIP1;1, for plasma membrane intrinsic protein and tonoplast intrinsic protein, respectively) were cloned and characterized. The higher efficiency of HbPIP2;1 than HbTIP1;1 in increasing plasmalemma water conductance was verified in Xenopus laevis oocytes. HbPIP2;1 was insensitive to HgCl(2). In situ hybridization demonstrated that HbPIP2;1 was expressed in all liber tissues in the young stem, including the laticifers. HbPIP2;1 was up-regulated in both liber tissues and laticifers, whereas HbTIP1;1 was down-regulated in liber tissues but up-regulated in laticifers in response to bark Ethrel treatment. Ethylene-induced HbPIP2;1 up-regulation was confirmed by western-blot analysis. The promoter sequences of both genes were cloned and found to harbor, among many others, ethylene-responsive and other chemical-responsive (auxin, copper, and sulfur) elements known to increase latex yield. Increase in latex yield in response to ethylene was emphasized to be linked with water circulation between the laticifers and their surrounding tissues as well as with the probable maintenance of liber tissue turgor, which together favor prolongation of latex flow.

Nuclear regulators with a second home in organelles

In plants, increasing evidence points towards the existence of nuclear proteins that are also targeted to either mitochondria - a well-known phenomenon from yeast and mammalians - or to plastids. One such protein is Whirly1, which was the first protein to be identified in the nucleus and plastids of the same plant cell. Like Whirly1, most of the dual targeted (nucleus and organelle) proteins have functions in the maintenance of DNA, telomere structuring or gene expression. In some instances, proteins were even shown to be relocated from one compartment to another upon environmental or developmental clues. We hypothesize that one rationale of dual targeting is storage or sequestration of these proteins inside the organelles until specific conditions require their activity in the nucleus.

Arabidopsis cold shock domain proteins: relationships to floral and silique development

Cold shock domain proteins (CSPs) are highly conserved from bacteria to higher plants and animals. Bacterial cold shock proteins function as RNA chaperones by destabilizing RNA secondary structures and promoting translation as an adaptative mechanism to low temperature stress. In animals, cold shock domain proteins exhibit broad functions related to growth and development. In order to understand better the function of CSPs in planta, detailed analyses were performed for Arabidopsis thaliana CSPs (AtCSPs) on the transcript and protein levels using an extensive series of tissue harvested throughout developmental stages within the entire life cycle of Arabidopsis. On both the transcript and protein levels, AtCSPs were enriched in shoot apical meristems and siliques. Although all AtCSPs exhibited similar expression patterns, AtCSP2 was the most abundantly expressed gene. In situ hybridization analyses were also used to confirm that AtCSP2 and AtCSP4 transcripts accumulate in developing embryos and shoot apices. AtCSPs transcripts were also induced during a controlled floral induction study. In vivo ChIP analysis confirmed that an embryo expressed MADS box transcription factor, AGL15, interacts within two AtCSP promoter regions and alters the respective patterns of AtCSP transcription. Comparative analysis of AtCSP gene expression between Landsberg and Columbia ecotypes confirmed a 1000-fold reduction of AtCSP4 gene expression in the Landsberg background. Analysis of the AtCSP4 genomic locus identified multiple polymorphisms in putative regulatory cis-elements between the two ecotypes. Collectively, these data support the hypothesis that AtCSPs are involved in the transition to flowering and silique development in Arabidopsis.

The transcriptional activator Pti4 is required for the recruitment of a repressosome nucleated by repressor SEBF at the potato PR-10a gene

Transcriptional reprogramming is critical for plant disease resistance responses. In potato (Solanum tuberosum), the marker gene PATHOGENESIS-RELATED-10a (PR-10a) is transcriptionally activated by pathogens, wounding, or elicitor treatment. Activation of PR-10a requires the recruitment of the activator Why1 to its promoter. In addition, PR-10a is negatively regulated by the repressor SEBF (for Silencer Element Binding Factor). Here, we show through a yeast two-hybrid screen that SEBF interacts with Pti4, which has been shown to be a transcriptional activator. SEBF recruits Pti4 via its consensus sequence-type RNA binding domain, while Pti4 is recruited to SEBF by means of its ethylene-response factor domain. In vivo plant transcription assays confirmed that SEBF interacts with Pti4 to form a repressosome, showing that Pti4 can also play a role in transcriptional repression. Chromatin immunoprecipitation revealed that both SEBF and Pti4 are recruited to the PR-10a promoter in uninduced conditions only and that the recruitment of Pti4 is dependent on the presence of SEBF, consistent with the fact that there is no Pti4 consensus binding site in PR-10a. Unexpectedly, we also demonstrated that recruitment of SEBF was dependent on the presence of Pti4, thereby explaining why SEBF, itself a repressor, requires Pti4 for its repressing function.

Regulation of a virus-induced lethal disease in tomato revealed by LongSAGE analysis

Infection of Cucumber mosaic virus (CMV) and D satellite RNA (satRNA) in tomato plants induces rapid plant death, which has caused catastrophic crop losses. We conducted long serial analysis of gene expression (LongSAGE) in control and virus-infected plants to identify the genes that may be involved in the development of this lethal tomato disease. The transcriptomes were compared between mock-inoculated plants and plants infected with CMV, CMV/D satRNA, or CMV/Dm satRNA (a nonnecrogenic mutant of D satRNA with three mutated nucleotides). The analysis revealed both general and specific changes in the tomato transcriptome after infection with these viruses. A massive transcriptional difference of approximately 400 genes was found between the transcriptomes of CMV/D and CMV/Dm satRNA-infected plants. Particularly, the Long-SAGE data indicated the activation of ethylene synthesis and signaling by CMV/D satRNA infection. Results from inoculation tests with an ethylene-insensitive mutant and treatments with an ethylene action inhibitor further confirmed the role of ethylene in mediating the epinastic leaf symptoms and the secondary cell death in the stem. Results from Northern blot analysis demonstrated the partial contribution of ethylene in the induced defense responses in CMV/D satRNA-infected plants.

Survey of differentially expressed proteins and genes in jasmonic acid treated rice seedling shoot and root at the proteomics and transcriptomics levels

Two global approaches were applied to develop an inventory of differentially expressed proteins and genes in rice (cv. Nipponbare) seedling grown on Murashige and Skoog medium with and without jasmonic acid (JA). JA significantly reduced the growth of shoot, root, leaf, and leaf sheath depending on JA concentration (1, 2, 5, 10, 25, and 50 microM) as compared with control. Almost 50% growth inhibition of seedling was observed with 5 microM JA. Shoots and roots of seedlings grown on 5 microM JA for 7 days were then used for proteomics and transcriptomics analyses. Two-dimensional gel electrophoresis revealed 66 and 68 differentially expressed protein spots in shoot and root, respectively, compared to their respective controls. Tandem mass spectrometry analysis of these proteins identified 52 (shoot) and 56 (root) nonredundant proteins, belonging to 10 functional categories. Proteins involved in photosynthesis (44%), cellular respiratory (11%), and protein modification and chaperone (11%) were highly represented in shoot, whereas antioxidant system (18%), cellular respiratory (17%), and defense-related proteins (15%) were highly represented in root. Transcriptomics analysis of shoot and root identified 107 and 325 induced genes and 34 and 213 suppressed genes in shoot and root, respectively. Except of unknown genes with over 57% of the total, most genes encode for proteins involved in secondary metabolism, energy production, protein modification and chaperone, transporters, and cytochrome P450. These identified proteins and genes have been discussed with respect to the JA-induced phenotype providing a new insight into the role of JA in rice seedling growth and development.

KEYWORDS

phytohormone * inhibitory concentration * growth * gel-based approach * mass spectrometry * DNA microarray.

Transcriptional activation and localization of expression of Brassica juncea putative metal transport protein BjMTP1

BACKGROUND

Metal hyperaccumulators, including various Thlaspi species, constitutively express the putative metal transporter MTP1 to high levels in shoots. Here we present data on the transcriptional regulation and localization of expression of the homologous gene BjMTP1 in Brassica juncea. Though B. juncea lacks the ability to hyperaccumulate metals, its relatively high biomass, rapid growth and relatedness to true metal hyperaccumulating plants makes it a promising starting point for the development of plants for phytoremediation. Our goal in this study is to determine the transcriptional regulation of MTP1 in order to start to better understanding the physiological role of MTP1 in B. juncea.

RESULTS

Steady-state mRNA levels of BjMTP1 were found to be enhanced 8.8, 5.9, and 1.6-fold in five-day-old B. juncea seedlings after exposure to Ni2+, Cd2+ or Zn2+, respectively. This was also reflected in enhanced GUS activity in B. juncea seedlings transformed with BjMTP1 promoter::GUSPlus after exposure to these metals over a similar range of toxicities from mild to severe. However, no increase in GUS activity was observed after exposure of seedlings to cold or heat stress, NaCl or hydrogen peroxide. GUS expression in Ni2+ treated seedlings was localized in roots, particularly in the root-shoot transition zone. In four- week- old transgenic plants BjMTP1 promoter activity also primarily increased in roots in response to Ni2+ or Cd2+ in plants transformed with either GUS or mRFP1 as reporter genes, and expression was localized to the secondary xylem parenchyma. In leaves, BjMTP1 promoter activity in response to Ni2+ or Cd2+ spiked after 24 h then decreased. In shoots GUS expression was prominently present in the vasculature of leaves, and floral parts.

CONCLUSION

Our studies establish that a 983 bp DNA fragment upstream of the BjMTP1 translational start site is sufficient for the specific activation by Ni2+ and Cd2+ of BjMTP1 expression primarily in roots. Activation of expression by both metals in roots is primarily localized to the xylem parenchyma cells. This study is the first to identify specific Ni2+ and Cd2+ transcriptional regulation and tissue localization of BjMTP1.

Comparative survey of plastid and mitochondrial targeting properties of transcription factors in Arabidopsis and rice

A group of nuclear transcription factors, the Whirly proteins, were recently shown to be targeted also to chloroplasts and mitochondria. In order to find out whether other proteins might share this feature, an in silico-based screening of transcription factors from Arabidopsis and rice was carried out with the aim of identifying putative N-terminal chloroplast and mitochondrial targeting sequences. For this, the individual predictions of several independent programs were combined to a consensus prediction using a naïve Bayes method. This consensus prediction shows a higher specificity at a given sensitivity value than each of the single programs. In both species, transcription factors from a variety of protein families that possess putative N-terminal plastid or mitochondrial target peptides as well as nuclear localization sequences, were found. A search for homologues within members of the AP2/EREBP protein family revealed that target peptide-containing proteins are conserved among monocotyledonous and dicotyledonous species. Fusion of one of these proteins to GFP revealed, indeed, a dual targeting activity of this protein. We propose that dually targeted transcription factors might be involved in the communication between the nucleus and the organelles in plant cells. We further discuss how recent results on the physical interaction between the organelles and the nucleus could have significance for the regulation of the localization of these proteins.

A comparative proteome and phosphoproteome analysis of differentially regulated proteins during fertilization in the self-incompatible speciesSolanum chacoense Bitt

We have used 2-DE for a time-course study of the changes in protein and phosphoprotein expression that occur immediately after fertilization in Solanum chacoense. The phosphorylation status of the detected proteins was determined with three methods: in vivo labeling, immunodetection, and phosphoprotein-specific staining. Using a pI range of 4-7, 262 phosphorylated proteins could be mapped to the 619 proteins detected by Sypro Ruby staining, representing 42% of the total proteins. Among these phosphoproteins, antibodies detected 184 proteins from which 78 were also detected with either of the other two methods (42%). Pro-Q Diamond phosphoprotein stain detected 111 proteins, of which 76 were also detected with either of the other two methods (68%). The 32P in vivo labeling method detected 90 spots from which 78 were also detected with either of other two methods (87%). On comparing before and after fertilization profiles, 38 proteins and phosphoproteins presented a reproducible change in their accumulation profiles. Among these, 24 spots were selected and analyzed by LC-MS/MS using a hybrid quadrupole-TOF (Q-TOF) instrument. Peptide data were searched against publicly available protein and EST databases, and the putative roles of the identified proteins in early fertilization events are discussed.

Transcriptional Repression Distinguishes Somatic from Germ Cell Lineages in a Plant

In flowering plants, the male germline begins with an asymmetric division, after which one of the resulting cells, the generative cell, divides symmetrically to produce two sperm cells. We show here that the male germline is initiated by transcriptional control. We identify GRSF, germline-restrictive silencing factor, from the lily. GRSF is ubiquitous in nongerm cells and is absent from male germ cells. GRSF recognizes silencer sequences in promoters of genes specific to the germline, stably repressing these genes in cells that are not destined to become germ cells.

Rice GTPase OsRacB: potential accessory factor in plant salt-stress signaling

As the sole ubiquitous signal small guanosine triphosphate-binding protein in plants, Rop gene plays an important role in plant growth and development. In this study, we focus on the relationship between the novel rice Rop gene OsRacB and plant salt tolerance. Results show that OsRacB transcription is highly accumulated in roots after treatment with salinity, but only slightly accumulated in stems and leaves under the same treatment. Promoter analysis showed that OsRacB promoter is induced by salinity and exogenous salicylic acid, not abscisic acid. To elucidate its physiological function, we generated OsRacB sense and antisense transgenic tobacco and rice. Under proper salinity treatment, sense transgenic plants grew much better than the control. This suggests that overexpression of OsRacB in tobacco and rice can improve plant salt tolerance. But under the same treatment, no difference could be observed between OsRacB antisense plants and the control. The results indicated that OsRacB is only an accessory factor in plant salt tolerance.

Promoter activation of pepper class II basic chitinase gene, CAChi2, and enhanced bacterial disease resistance and osmotic stress tolerance in the CAChi2-overexpressing Arabidopsis

The activation of the CAChi2 promoter as the result of bacterial infection and osmotic stresses was examined using the Agrobacterium-mediated transient expression assay. Several stress-related cis-acting elements were revealed within the upstream genomic sequence of the CAChi2 gene. In tobacco leaf tissues transiently transformed with the CAChi2 promoter-beta-glucuronidase (GUS) gene, the CAChi2 promoter was up-regulated by Pseudomonas syringae pv. tabaci infection. The CAChi2-GUS activation was closely related to osmotic stresses, including treatment with mannitol and NaCl. The -378 CAChi2 promoter was sufficient for the CAChi2 gene induction by salicylic acid treatment. CAChi2 overexpression in the transgenic Arabidopsis plants enhanced bacterial disease resistance against Pseudomonas syringae pv. tomato infection. CAChi2-overexpressing Arabidopsis plants also exhibited increased tolerance to NaCl-induced osmotic stresses during seed germination and seedling growth. CAChi2 overexpression induced the expression of the NaCl stress-responsive gene RD29A in the absence of NaCl stress. The CAChi2-overexpressing transgenic plants exhibited increased sensitivity to abscisic acid during seed germination.

Molecular cloning of a pathogen/wound-inducible PR10 promoter from Pinus monticola and characterization in transgenic Arabidopsis plants

In Pinus monticola (Dougl. ex D. Don), the class ten pathogenesis-related (PR10) proteins comprise a family of multiple members differentially expressed upon pathogen infection and other environmental stresses. One of them, PmPR10-1.13, is studied here by investigating its transcriptional regulation in transgenic Arabidopsis plants. For functional analyses of the PmPR10-1.13 promoter, a 1,316-bp promoter fragment and three 5' deletions were translationally fused to the ss-glucuronidase (GUS) reporter gene. The 1,316-bp promoter-driven GUS activity first appeared in hypocotyls and cotyledons in 2- to 3-day-old seedlings. As transgenic plants grew, GUS activity was detected strongly in apical meristems, next in stems and leaves. No GUS activity was detected in roots and in reproductive tissues of flower organs. In adult plants, the PmPR10-1.13 promoter-directed GUS expression was upregulated following pathogen infection and by wounding treatment, which generally mimic the endogenous expression pattern in western white pine. Promoter analysis of 5' deletions demonstrated that two regions between -1,316 and -930, and between -309 and -100 were responsible for the wound responsiveness. By structural and functional comparisons with PmPR10-1.14 promoter, putative wound-responsive elements were potentially identified in the PmPR10-1.13 promoter. In conclusion, PmPR10-1.13 showed properties of a defence-responsive gene, being transcriptionally upregulated upon biotic and abiotic stresses.

Whirly transcription factors: defense gene regulation and beyond

Members of the Whirly family of proteins are found throughout the plant kingdom and are predicted to share the ability to bind to single-stranded DNA. Arabidopsis and potato Whirly orthologs act as transcription factors that regulate defense gene expression; the Arabidopsis Whirly protein AtWhy1 contributes to both basal and specific defense responses. Analysis of the crystal structure of potato StWhy1 has provided insight into the DNA-binding mechanism of this family of proteins, their mode of action and possible autoregulation. There is evidence to suggest that Whirly proteins might play roles in processes other than defense responses and could function in the chloroplast as well as in the nucleus.

Identification of novel cis-acting elements, IDE1 and IDE2, of the barley IDS2 gene promoter conferring iron-deficiency-inducible, root-specific expression in heterogeneous tobacco plants

The molecular mechanisms of plant responses to iron (Fe) deficiency remain largely unknown. To identify the cis-acting elements responsible for Fe-deficiency-inducible expression in higher plants, the barley IDS2 (iron deficiency specific clone no. 2) gene promoter was analyzed using a transgenic tobacco system. Deletion analysis revealed that the sequence between -272 and -91 from the translational start site (-272/-91) was both sufficient and necessary for specific expression in tobacco roots. Further deletion and linker-scanning analysis of this region clearly identified two cis-acting elements: iron-deficiency-responsive element 1 (IDE1) at -153/-136 (ATCAAGCATGCTTCTTGC) and IDE2 at -262/-236 (TTGAACGGCAAGTTTCACGCTGTCACT). The co-existence of IDE1 and IDE2 was essential for specific expression when the -46/+8 region (relative to the transcriptional start site) of the CaMV 35S promoter was used as a minimal promoter. Expression occurred mainly in the root pericycle, endodermis, and cortex. When the -90/+8 region of the CaMV 35S promoter was fused, the -272/-227 region, which consists of IDE2 and an additional 19 bp, could drive Fe-deficiency-inducible expression without IDE1 throughout almost the entire root. The principal modules of IDE1 and IDE2 were homologous. Sequences homologous to IDE1 were also found in many other Fe-deficiency-inducible promoters, including: nicotianamine aminotransferase (HvNAAT)-A, HvNAAT-B, nicotianamine synthase (HvNAS1), HvIDS3, OsNAS1, OsNAS2, OsIRT1, AtIRT1, and AtFRO2, suggesting the conservation of cis-acting elements in various genes and species. The identification of novel cis-acting elements, IDE1 and IDE2, will provide powerful tools to clarify the molecular mechanisms regulating Fe homeostasis in higher plants.

A novel protein from Brassica napus has a putative KID domain and responds to low temperature

To identify factors that interact with histone deacetylase (HDAC) in Brassica napus, a yeast two-hybrid library was screened using the Arabidopsis HDA19 as bait. A novel protein, bnKCP1, containing a putative kinase-inducible domain (KID) was found to interact with HDA19. Southern blot analysis indicated that the bnKCP1 gene belongs to a small gene family of at least three members. Northern blot analysis showed bnKCP1 to be strongly expressed in stems, flowers, roots, and immature siliques, but not in leaf blades of seedlings. The accumulation of bnKCP1 transcript in the leaf blades was induced significantly within 4 h of exposure of B. napus seedlings to cold stress, whereas treatment of leaf blades with inomycin, an ionophore of Ca2+, caused a rapid (30 min) but transient induction of bnKCP1 expression. In contrast to that observed in leaf blades, expression of bnKCP1 in the stems was repressed upon cold treatment. In vitro and in vivo protein-binding assays showed that bnKCP1 interacts with HDA19 via the KID domain, and that S188 is critical for bnKCP1-HDA19 interaction. BnKCP1 also exerted modest transactivation of the lacZ reporter gene in yeast through its N-terminal region. These assays suggest that bnKCP1 may function as a transcription factor, which regulates gene expression through interaction with HDA19.