Sequence-specific interaction between S1F, a spinach nuclear factor, and a negative cis-element conserved in plastid-related genes

Functional analysis of root-preferential oil palm metallothionein promoter in tobacco

Root-specific or preferential promoters are essential to genetically modify plants with beneficial root traits. We have characterised the promoter from an oil palm metallothionein gene (EgMT) and performed a serial 5' deletion analysis to identify the region(s) essential for transgenes expression in roots. Stable functional characterisation of tobacco transgenic lines using the T1 generation showed that a deletion construct, designated as RSP-2D (1107 bp), directed strong GUS expression at all stages of root development, particularly in mature roots. Other constructs, RSP-2A (2481 bp) and RSP-2C (1639 bp), drove GUS expression in roots with an intensity lower than RSP-2D. The promoter activity was also detectable in seed pods and immature seeds, albeit at lower levels than CaMV35S. The promoter activity may also be induced by wounding as intact GUS staining was observed at the flower- and leaf-cutting sites of T1 samples carrying either RSP-2C or RSP-2D constructs. The promoter sequence contains cis-acting elements that may act as negative regulators and be responsible for root specificity. The results further indicated that the 5' UTR and ATATT sequences are essential for strong promoter activity. This study highlights the potential of RSP-2D promoter as a tool for modifying root traits through genetic engineering.

Genome-Wide Identification and Characterization of Chinese Cabbage S1fa Transcription Factors and Their Roles in Response to Salt Stress

The S1fa transcription factor is part of a small family involved in plant growth and development and abiotic stress tolerance. However, the roles of the S1fa genes in abiotic stress tolerance in Chinese cabbage are still unclear. In this study, four S1fa genes in the Chinese cabbage genome were identified and characterized for abiotic stress tolerance. Tissue-specific expression analysis suggested that three of these four S1fa genes were expressed in all tissues of Chinese cabbage, while Bra006994 was only expressed in the silique. Under Hg and Cd stresses, the S1fa genes were significantly expressed but were downregulated under NaCl stresses. The Bra034084 and Bra029784 overexpressing yeast cells exhibited high sensitivity to NaCl stresses, which led to slower growth compared with the wild type yeast cells (EV) under 1 M NaCl stress. In addition, the growth curve of the Bra034084 and Bra029784 overexpressing cells shows that the optical density was reduced significantly under salt stresses. The activities of the antioxidant enzymes, SOD, POD and CAT, were decreased, and the MDA, H₂O₂ and O₂⁻ contents were increased under salt stresses. The expression levels of cell wall biosynthesis genes Ccw14p, Cha1p, Cwp2p, Sed1p, Rlm1p, Rom2p, Mkk1p, Hsp12p, Mkk2p, Sdp1p and YLR194c were significantly enhanced, while Bck1p, and Ptc1p were downregulated under salt stresses. These results suggest that the Bra034084 and Bra029784 genes regulate cell wall biosynthesis and the defense regulatory system under salt stresses. These findings provide a fundamental basis for the further investigation of crop genetic modification to improve crop production and abiotic stress tolerance in Chinese cabbage.

Overexpression of Rice OsS1Fa1 Gene Confers Drought Tolerance in Arabidopsis

Small peptides and proteins play critical regulatory roles in plant development and environmental stress responses; however, only a few of these molecules have been identified and characterized to date because of their poor annotation and other experimental challenges. Here, we present that rice (Oryza sativa L.) OsS1Fa1, a small 76-amino acid protein, confers drought stress tolerance in Arabidopsis thaliana. OsS1Fa1 was highly expressed in leaf, culm, and root tissues of rice seedlings during vegetative growth and was significantly induced under drought stress. OsS1Fa1 overexpression in Arabidopsis induced the expression of selected drought-responsive genes and enhanced the survival rate of transgenic lines under drought. The proteasome inhibitor MG132 protected the OsS1Fa1 protein from degradation. Together, our data indicate that the small protein OsS1Fa1 is induced by drought and is post-translationally regulated, and the ectopic expression of OsS1Fa1 protects plants from drought stress.

The pathogen-inducible promoter of defense-related LsGRP1 gene from Lilium functioning in phylogenetically distinct species of plants

A suitable promoter greatly enhances the efficiency of target gene expression of plant molecular breeding and farming; however, only very few promoters are available for economically important non-graminaceous ornamental monocots. In this study, an 868-bp upstream region of defense-related LsGRP1 of Lilium, named PLsGRP1, was cloned by genome walking and proven to exhibit promoter activity in Nicotiana benthamiana and Lilium 'Stargazer' as assayed by agroinfiltration-based β-glucuronidase (GUS) expression system. Many putative biotic stress-, abiotic stress- and physiological regulation-related cis-acting elements were found in PLsGRP1. Serial deletion analysis of PLsGRP1 performed in Nicotiana tabacum var. Wisconsin 38 accompanied with types of treatments indicated that 868-bp PLsGRP1 was highly induced upon pathogen challenges and cold stress while the 131-bp 3'-end region of PLsGRP1 could be dramatically induced by many kinds of abiotic stresses, biotic stresses and phytohormone treatments. Besides, transient GUS expression in a fern, gymnosperms, monocots and dicots revealed good promotor activity of PLsGRP1 in many phylogenetically distinct plant species. Thus, pathogen-inducible PLsGRP1 and its 131-bp 3'-end region are presumed potential as tools for plant molecular breeding and farming.

Trihelix transcription factor GT-4 mediates salt tolerance via interaction with TEM2 in Arabidopsis

BACKGROUND

Trihelix transcription factor family is plant-specific and plays important roles in developmental processes. However, their function in abiotic stress response is largely unclear.

RESULTS

We studied one member GT-4 from Arabidopsis in relation to salt stress response. GT-4 expression is induced by salt stress and GT-4 protein is localized in nucleus and cytoplasm. GT-4 acts as a transcriptional activator and its C-terminal end is the activation domain. The protein can bind to the cis-elements GT-3 box, GT-3b box and MRE4. GT-4 confers enhanced salt tolerance in Arabidopsis likely through direct binding to the promoter and activation of Cor15A, in addition to possible regulation of other relevant genes. The gt-4 mutant shows salt sensitivity. TEM2, a member of AP2/ERF family was identified to interact with GT-4 in yeast two-hybrid, BiFC and Co-IP assays. Loss-of-function of TEM2 exerts no significant difference on salt tolerance or Cor15A expression in Arabidopsis. However, double mutant gt-4/tem2 shows greater sensitivity to salt stress and lower transcript level of Cor15A than gt-4 single mutant. GT-4 plus TEM2 can synergistically increase the promoter activity of Cor15A.

CONCLUSIONS

GT-4 interacts with TEM2 and then co-regulates the salt responsive gene Cor15A to improve salt stress tolerance.

Soybean Trihelix transcription factors GmGT-2A and GmGT-2B improve plant tolerance to abiotic stresses in transgenic Arabidopsis

BACKGROUND

Trihelix transcription factors play important roles in light-regulated responses and other developmental processes. However, their functions in abiotic stress response are largely unclear. In this study, we identified two trihelix transcription factor genes GmGT-2A and GmGT-2B from soybean and further characterized their roles in abiotic stress tolerance.

FINDINGS

Both genes can be induced by various abiotic stresses, and the encoded proteins were localized in nuclear region. In yeast assay, GmGT-2B but not GmGT-2A exhibits ability of transcriptional activation and dimerization. The N-terminal peptide of 153 residues in GmGT-2B was the minimal activation domain and the middle region between the two trihelices mediated the dimerization of the GmGT-2B. Transactivation activity of the GmGT-2B was also confirmed in plant cells. DNA binding analysis using yeast one-hybrid assay revealed that GmGT-2A could bind to GT-1bx, GT-2bx, mGT-2bx-2 and D1 whereas GmGT-2B could bind to the latter three elements. Overexpression of the GmGT-2A and GmGT-2B improved plant tolerance to salt, freezing and drought stress in transgenic Arabidopsis plants. Moreover, GmGT-2B-transgenic plants had more green seedlings compared to Col-0 under ABA treatment. Many stress-responsive genes were altered in GmGT-2A- and GmGT-2B-transgenic plants.

CONCLUSION

These results indicate that GmGT-2A and GmGT-2B confer stress tolerance through regulation of a common set of genes and specific sets of genes. GmGT-2B also affects ABA sensitivity.

Co-regulation of nuclear genes encoding plastid ribosomal proteins by light and plastid signals during seedling development in tobacco and Arabidopsis

Genes encoding plastid ribosomal proteins are distributed between the nuclear and plastid genomes in higher plants, and coordination of their expression is likely to be required for functional plastid protein synthesis. A custom microarray has been used to examine the patterns of accumulation of transcripts from plastid and nuclear genes encoding plastid ribosomal proteins during seedling development in tobacco and Arabidopsis. The transcripts accumulate coordinately during early seedling development and show similar responses to light and to inhibitors, such as norflurazon and lincomycin, affecting plastid signaling. Computational analysis of the promoters of these genes revealed a shared initiator motif and common cis-elements characteristic of photosynthesis genes, specifically the GT-1 element, and the I-box. Analysis of the RPL27 gene of Arabidopsis thaliana indicated that transcription initiates from an initiator-like region. Deletion analysis of the RPL27 promoter in transgenic plants revealed that the identified shared cis-elements were not all required for wild-type expression patterns, and full developmental, light- and plastid-regulation can be conveyed by a region of the promoter from -235 to +1 relative to the transcription start site.

Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis

The ZFHD recognition sequence (ZFHDRS) and NAC recognition sequence (NACRS) play an important role in the dehydration-inducible expression of the Arabidopsisthaliana EARLY RESPONSIVETO DEHYDRATION STRESS 1 (ERD1) gene. Using the yeast one-hybrid system, we isolated a cDNA encoding the ZFHD1 transcriptional activator that specifically binds to the 62 bp promoter region of ERD1, which contains the ZFHDRS. Both in vitro and in vivo analyses confirmed specific binding of the ZFHD1 to ZFHDRS, and the expression of ZFHD1 was induced by drought, high salinity and abscisic acid. The DNA-binding and activation domains of ZFHD1 were localized on the C-terminal homeodomain and N-terminal zinc finger domain, respectively. Microarray analysis of transgenic plants over-expressing ZFHD1 revealed that several stress-inducible genes were upregulated in the transgenic plants. Transgenic plants exhibited a smaller morphological phenotype and had a significant improvement of drought stress tolerance. Using the yeast two-hybrid system, we detected an interaction between ZFHD1 and NACRS-binding NAC proteins. Moreover, co-over-expression of the ZFHD1 and NAC genes restored the morphological phenotype of the transgenic plants to a near wild-type state and enhanced expression of ERD1 in both Arabidopsis T87 protoplasts and transgenic Arabidopsis plants.

Identification of functional apple scab resistance gene promoters

Apple scab (Venturia inaequalis) is one of the most damaging diseases affecting commercial apple production. Some wild Malus species possess resistance against apple scab. One gene, HcrVf2, from a cluster of three genes derived from the wild apple Malus floribunda clone 821, has recently been shown to confer resistance to apple scab when transferred into a scab-susceptible apple variety. For this proof-of-function experiment, the use of the 35S promoter from Cauliflower mosaic virus was reliable and appropriate. However, in order to reduce the amount of non-plant DNA in genetically modified apple to a minimum, with the aim of increasing genetically modified organism acceptability, these genes would ideally be regulated by their own promoters. In this study, sequences from the promoter region of the three members of the HcrVf gene family were compared. Promoter constructs containing progressive 5' deletions were prepared and used for functional analyses. Qualitative assessment confirmed promoter activity in apple. Quantitative promoter comparison was carried out in tobacco (Nicotiana glutinosa) and led to the identification of several promoter regions with different strengths from a basal level to half the strength of the 35S promoter from Cauliflower mosaic virus.

Expression analysis of a chicory fructan 1-exohydrolase gene reveals complex regulation by cold

The gene for a recently identified cDNA, 1-FEH IIa, encoding a fructan 1-exohydrolase was isolated and cloned from Cichorium intybus and a 1149 bp promoter fragment was characterized. An analysis of the genomic 1-FEH IIa sequence indicated that the gene (FEHIIa) consists of six introns and seven exons, which is similar to plant invertase genes. Like invertase genes, FEHIIa also contains the 9 nt mini-exon encoding the tripeptide DPN. A database search for cis-acting response elements within its promoter identified multiple elements that appear to have relevance to cold-induced expression of the gene in field-grown roots. Promoter analysis by transient expression assay demonstrated that the FEHIIa gene promoter is highly expressed in etiolated Cichorium leaves and cold-stored roots, which correlated well with the high level expression detected by RNA blot analysis. Cold also enhanced FEHIIa reporter gene expression in green leaves, however, the reporter gene activity was much lower compared with similar induction experiments in etiolated leaves. Promoter deletion analysis demonstrated the presence of potential cold-responsive ABRE and/or CRT/DRE elements in the -22 to -172 region, while regions -933 to -717 and -493 to -278 contain elements that can down-regulate expression at the conditions used. Characterization of the FEHIIa promoter may provide tools to study cold-induced expression and to increase freezing tolerance in agricultural crops.

Analysis of GT-3a identifies a distinct subgroup of trihelix DNA-binding transcription factors inArabidopsis

Trihelix DNA-binding factors (or GT factors) bind to GT elements found in the promoters of many plant genes. Although the binding specificity and the transcriptional activity of some members (e.g. GT-1 and GT-2) have been studied, the regulatory function of this family of transcription factors remains largely unknown. In this work, we have characterised a new GT factor, namely GT-3a, and a closely related member, GT-3b. We show that (1) they can form either homo- or heterodimers but do not interact with GT-1; (2) they are predominantly expressed in floral buds and roots; (3) GT-3a cannot bind to the binding sites of GT-1 or GT-2, but binds to the cab2 and rbcS-1A gene promoters via the 5'-GTTAC sequence, which has been previously shown to be the core of the Site 1 type of GT elements. These results suggest that GT-3a and GT-3b belong to a distinct subgroup of GT factors and that each subgroup of GT factors binds to a functionally distinct type of cis-acting GT elements.

Analysis of the alternative oxidase promoters from soybean

Alternative oxidase (Aox) is a nuclear-encoded mitochondrial protein. In soybean (Glycine max), the three members of the gene family have been shown to be differentially expressed during normal plant development and in response to stresses. To examine the function of the Aox promoters, genomic fragments were obtained for all three soybean genes: Aox1, Aox2a, and Aox2b. The regions of these fragments immediately upstream of the coding regions were used to drive beta-glucuronidase (GUS) expression during transient transformation of soybean suspension culture cells and stable transformation of Arabidopsis. The expression patterns of the GUS reporter genes in soybean cells were in agreement with the presence or absence of the various endogenous Aox proteins, determined by immunoblotting. Deletion of different portions of the upstream regions identified sequences responsible for both positive and negative regulation of Aox gene expression in soybean cells. Reporter gene analysis in Arabidopsis plants showed differential tissue expression patterns driven by the three upstream regions, similar to those reported for the endogenous proteins in soybean. The expression profiles of all five members of the Arabidopsis Aox gene family were examined also, to compare with GUS expression driven by the soybean upstream fragments. Even though the promoter activity of the upstream fragments from soybean Aox2a and Aox2b displayed the same tissue specificity in Arabidopsis as they do in soybean, the most prominently expressed endogenous genes in all tissues of Arabidopsis were of the Aox1 type. Thus although regulation of Aox expression generally appears to involve the same signals in different species, different orthologs of Aox may respond variously to these signals. A comparison of upstream sequences between soybean Aox genes and similarly expressed Arabidopsis Aox genes identified common motifs.

Two different novel cis-acting elements of erd1, a clpA homologous Arabidopsis gene function in induction by dehydration stress and dark-induced senescence

Many plant genes have been shown to be induced by water stress and function in stress tolerance. The erd1 gene has been shown to be upregulated in response to both water stress and etiolation. Promoter studies using the erd1 promoter region fused to the luciferase (LUC) reporter gene in Arabidopsis thaliana were performed to identify the putative cis elements involved. Results indicated that the cis elements, responsible for gene expression during dehydration and etiolation, are separately located in two discrete portions of the erd1 promoter. Base substitution analysis showed that a 14-bp region from -599 to -586, and a myc recognition motif from -466 to -461 are necessary for the induction of LUC activity in dehydrated plants. On the other hand, base substitution analysis revealed that both an abscisic acid responsive element (ABRE)-like sequence (from -199 to -195) and an ACGT sequence (from -155 to -152) are required for an etiolation-induced increase in LUC activity. LUC activity measurements from etiolated transgenic plants incubated in either water, N6-benzyleadenine (BA), or a 1% sucrose solution found that while BA was able to delay the increase in LUC activity seen in water-treated plants, no increase in LUC activity was seen in plants incubated in sucrose. These results indicate that the erd1 promoter contains two different regulatory systems that are involved in upregulation by dehydration stress and dark-induced senescence.

Characterization of an iron-dependent regulatory sequence involved in the transcriptional control of AtFer1 and ZmFer1 plant ferritin genes by iron

In eukaryotic cells, ferritin synthesis is controlled by the intracellular iron status. In mammalian cells, iron derepresses ferritin mRNA translation, whereas it induces ferritin gene transcription in plants. Promoter deletion and site-directed mutagenesis analysis, combined with gel shift assays, has allowed identification of a new cis-regulatory element in the promoter region of the ZmFer1 maize ferritin gene. This Iron-Dependent Regulatory Sequence (IDRS) is responsible for transcriptional repression of ZmFer1 under low iron supply conditions. The IDRS is specific to the ZmFer1 iron-dependent regulation and does not mediate the antioxidant response that we have previously reported (Savino et al. (1997) J. Biol. Chem. 272, 33319-33326). In addition, we have cloned AtFer1, the Arabidopsis thaliana ZmFer1 orthologue. The IDRS element is conserved in the AtFer1 promoter region and is functional as shown by transient assay in A. thaliana cells and stable transformation in A. thaliana transgenic plants, demonstrating its ubiquity in the plant kingdom.

Transcriptional activation by Arabidopsis GT-1 may be through interaction with TFIIA-TBP-TATA complex

GT-1 belongs to the class of trihelix DNA-binding proteins and binds to a promoter sequence found in many different genes. Data presented in this report show that GT-1 contains a trans-activation function in yeast and in plant cells. However, in tobacco BY-2 protoplasts, this activity functions only when an internal region containing the DNA-binding domain is deleted. Gel-shift and co-immunoprecipitation assays have revealed that GT-1 can interact with and stabilize the TFIIA-TBP-TATA complex. These results suggest that GT-1 may activate transcription through direct inter- action with the transcriptional pre-initiation complex.

Differential expression of Xenopus ribosomal protein gene XlrpS1c

Components of the translational machinery of the cell, including ribosomal proteins, are generally considered to be clear examples of housekeeping genes with a spatially ubiquitous distribution of messenger RNA during embryonic development. Here we present data based upon in situ hybridization experiments as well as RNase protection assays, demonstrating that Xenopus ribosomal protein gene S1 is differentially expressed in a complex and spatially distinct pattern during embryogenesis. We observed dramatically high levels of expression in some tissues, such as the branchial arches, otic vesicles, optic vesicles and somites and virtually no expression in other tissues, such as the cement gland, epidermis and notochord. Moreover, ribosomal protein genes S22, L1, and L5 display expression patterns nearly identical to S1. Our data is consistent with a model of ribosomal gene expression according to which ribosomal protein genes (or perhaps a subset of ribosomal protein genes) may be expressed at low levels in all tissues, but are abundantly expressed in other cell types reflecting a dynamic and complex pattern of transcriptional control throughout embryonic development.

The mechanism of GT element-mediated cell type-specific transcriptional control

Promoter studies have revealed that sequences related to the GT-1 binding site, known as GT elements, are conserved in plant nuclear genes of diverse functions. In this work, we addressed the issue of whether GT elements are involved in cell type-specific transcriptional regulation. We found that the inactivation of GT-1 site-mediated transcription in roots is correlated with the absence of the GT-1 binding activity in root extracts. In addition, the mutation of the related GT-1 (from the pea rbcs-3A) and the S1F (from the spinach rps1) sites resulted in an increase of their transcriptional activity in roots that contain a distinct GT element-binding factor, referred to as RGTF. Although specific to GT elements, RGTF has a different sequence requirement and a lower sequence specificity than GT-1. Interestingly, RGTF has a higher binding affinity to the mutant GT-1 and S1F sites than to the wild-type sequences. This correlation suggests that RGTF may have some role in transcriptional regulation in roots. Furthermore, root cellular protein extracts contain an inhibitory activity that prevents GT-1 from binding to DNA. This helps to explain the absence of the GT-1 binding activity in roots in which the gene of GT-1 is expressed. Together, these data suggest that the cell type-specific transcription modulation by GT elements is achieved by using two different strategies.

A ribosomal protein gene (rpl32) from tobacco chloroplast DNA is transcribed from alternative promoters: similarities in promoter region organization in plastid housekeeping genes

Multiple transcriptional start sites have been identified in the tobacco plastid ribosomal protein gene rpl32 by RNA mapping and in vitro capping techniques. A promotor with a canonical -10 Pribnow Box (P1) produces a major transcript in leaf chloroplasts. Transcription is also driven from additional promoters in non-photosynthetic plastids from heterotrophically cultured cells (BY2 line). Among them, a second promoter located downstream (P2) generates the most prominent transcript in this type of cell. The absence of typical plastid promoter motifs upstream of this site and the higher steady-state level of the P2-derived transcript in BY2 cells suggest a distinct modulation of transcription. Mobility shift experiments also seem to indicate the existence of differences in protein-DNA binding between both kinds of plastids with respect to a DNA fragment including the sequence upstream from the P2 starting site. The structure of the rpl32 promoter region is discussed in relation to that of other plastid housekeeping genes encoding elements of the genetic machinery.

Cis-acting elements and expression pattern of the spinach rps22 gene coding for a plastid-specific ribosomal protein

In order to study the regulation of nuclear genes coding for plastid ribosomal proteins, we have analysed the promoter region of spinach rps22 using both in vitro and in vivo approaches. By footprinting analyses, we have identified eight DNA elements interacting with spinach leaf nuclear factors in the 300 bp promoter region upstream of the transcription start site. Among these elements, four are short AT-rich sequences and one is identical to the Hex motif characterized initially in wheat histone genes. In transgenic tobacco plants, the reporter gene coding for the beta-glucuronidase (GUS) directed by a 1.2 kb upstream region of rps22 was expressed in several plant organs, with high levels in leaf mesophyll, embryo cotyledons and root meristematic cells and very low levels in other cell types. Interestingly, when deleted to -295, the promoter, which contained all the foot-printed elements, was still able to confer the same expression pattern, although the activity was relatively lower than with the 1.2 kb promoter. When deleted further to -154, the promoter, from which the AT-rich elements were eliminated, loses its activity almost completely, suggesting that these AT-rich elements are important for the rps22 promoter activity. Altogether, our results show that rps22 gene expression is controlled by specific cis elements not present in other nuclear-encoded plastid ribosomal protein genes studied so far.

Structure and differential expression of two distinct genes encoding the chloroplast elongation factor Tu in tobacco

We have isolated two nuclear genes, tufA and tufB, encoding chloroplast EF-Tu from a tobacco (Nicotiana sylvestris) genomic library. The tufA gene encodes a polypeptide of 478 amino-acid residues, consisting of a putative transit peptide of 70 residues and a mature EF-TuA of 408 residues. The tufB gene codes for a precursor proteins of 485 residues, containing a transit peptide of 77 residues and a mature EF-TuB of 408 residues. No introns were found in either gene. The sequence similarity within the coding regions of the two genes is 84.3% for nucleotides and 89.7% for amino acids. Multiple 5' ends of transcripts were observed for both tuf genes. Northern analysis revealed that the EF-Tu mRNA accumulated at least 30-fold more in leaf than in root tissue. Ribonuclease protection assays using gene-specific probes showed that the level of tufB mRNA is three-fold higher than that of tufA mRNA in leaves but in roots the tufB mRNA levels is less than half that of tufA mRNA. The relative amount of tufB mRNA is 30-fold higher in leaves than in roots whereas tufA messages are only five-fold higher in leaves. These data suggest that expression of both tuf genes is differentially regulated according to tissue and plastid type.

Molecular genetics of chloroplast ribosomal proteins

Chloroplasts contain a complete translational apparatus which, in land plants, synthesizes the 80 or so polypeptides encoded by the organelle's own small genome. Recent molecular genetic studies have revealed much about the chloroplast ribosomal proteins (RPs). Some of these proteins are encoded by the chloroplast genome and others by the nuclear genome. Many of these genes have now been cloned and characterized, including some that have no prokaryotic homologues.