Isolation and characterization of three families of auxin down-regulated cDNA clones

Genome-wide identification and expression analysis of the BURP domain-containing genes in Gossypium hirsutum

Background

Many BURP domain-containing proteins, which are unique to plants, have been identified. They performed diverse functions in plant development and the stress response. To date, only a few BURP domain-containing genes have been studied, and no comprehensive analysis of the gene family in cotton has been reported.

Results

In this study, 18, 17 and 30 putative BURP genes were identified in G. raimondii (D₅), G. arboreum (A₂) and G. hirsutum (AD₁), respectively. These BURP genes were phylogenetically classified into eight subfamilies, which were confirmed by analyses of gene structures, motifs and protein domains. The uneven distribution of BURPs in chromosomes and gene duplication analysis indicated that segmental duplication might be the main driving force of the GhBURP family expansion. Promoter regions of all GhBURPs contained at least one putative stress-related cis-elements. Analysis of transcriptomic data and qRT-PCR showed that GhBURPs showed different expression patterns in different organs, and all of them, especially the members of the RD22-like subfamily, could be induced by different stresses, such as abscisic acid (ABA) and salicylic acid (SA), which indicated that the GhBURPs may performed important functions in cotton’s responses to various abiotic stresses.

Conclusions

Our study comprehensively analyzed BURP genes in G. hirsutum, providing insight into the functions of GhBURPs in cotton development and adaptation to stresses.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5948-y) contains supplementary material, which is available to authorized users.

The divergence and positive selection of the plant-specific BURP-containing protein family

BURP domain-containing proteins belong to a plant-specific protein family and have diverse roles in plant development and stress responses. However, our understanding about the genetic divergence patterns and evolutionary rates of these proteins remain inadequate. In this study, 15 plant genomes were explored to elucidate the genetic origins, divergence, and functions of these proteins. One hundred and twenty-five BURP protein-encoding genes were identified from four main plant lineages, including 13 higher plant species. The absence of BURP family genes in unicellular and multicellular algae suggests that this family (1) appeared when plants shifted from relatively stable aquatic environments to land, where conditions are more variable and stressful, and (2) is critical in the adaptation of plants to adverse environments. Promoter analysis revealed that several responsive elements to plant hormones and external environment stresses are concentrated in the promoter region of BURP protein-encoding genes. This finding confirms that these genes influence plant stress responses. Several segmentally and tandem-duplicated gene pairs were identified from eight plant species. Thus, in general, BURP domain-containing genes have been subject to strong positive selection, even though these genes have conformed to different expansion models in different species. Our study also detected certain critical amino acid sites that may have contributed to functional divergence among groups or subgroups. Unexpectedly, all of the critical amino acid residues of functional divergence and positive selection were exclusively located in the C-terminal region of the BURP domain. In conclusion, our results contribute novel insights into the genetic divergence patterns and evolutionary rates of BURP proteins.

AtRD22 and AtUSPL1, members of the plant-specific BURP domain family involved in Arabidopsis thaliana drought tolerance

Crop plants are regularly challenged by a range of environmental stresses which typically retard their growth and ultimately compromise economic yield. The stress response involves the reprogramming of approximately 4% of the transcriptome. Here, the behavior of AtRD22 and AtUSPL1, both members of the Arabidopsis thaliana BURP (BNM2, USP, RD22 and polygalacturonase isozyme) domain-containing gene family, has been characterized. Both genes are up-regulated as part of the abscisic acid (ABA) mediated moisture stress response. While AtRD22 transcript was largely restricted to the leaf, that of AtUSPL1 was more prevalent in the root. As the loss of function of either gene increased the plant's moisture stress tolerance, the implication was that their products act to suppress the drought stress response. In addition to the known involvement of AtUSPL1 in seed development, a further role in stress tolerance was demonstrated. Based on transcriptomic data and phenotype we concluded that the enhanced moisture stress tolerance of the two loss-of-function mutants is a consequence of an enhanced basal defense response.

A crosstalk of auxin and GA during tuber development

Several hormones have been studied for their effect on tuber initiation and development. Until recently, the hormone with the most prominent role in tuber initiation was attributed to GA. Genes involved in GA degradation do exhibit an upregulated profile during early stages of tuber development, leading to a rapid decrease of active GA content, thereby facilitating stolon-tip swelling. While GA is known to be involved in shoot and stolon elongation, the development of the new tuberorgan requires changes in meristem identity and the reorientation ofthe plane of cell division. In other developmental processes, such as embryo patterning, flower development and lateral root initiation auxin plays a key role. Recent evidence on the involvement of auxin in tuber formation was providedby the measurement of auxin content in swelling stolons. Auxin content in the stolon tips increased several fold prior to tuber swelling. In vitro tuberisation experiments with auxin applications support the role of auxin during tuber initiation. Taken together, it is becoming clear that the initiation and induction of tubers in potato is a developmental process that appears to be regulated by a crosstalk between GA and auxin.

Genome-scale identification of soybean BURP domain-containing genes and their expression under stress treatments

BACKGROUND

Multiple proteins containing BURP domain have been identified in many different plant species, but not in any other organisms. To date, the molecular function of the BURP domain is still unknown, and no systematic analysis and expression profiling of the gene family in soybean (Glycine max) has been reported.

RESULTS

In this study, multiple bioinformatics approaches were employed to identify all the members of BURP family genes in soybean. A total of 23 BURP gene types were identified. These genes had diverse structures and were distributed on chromosome 1, 2, 4, 6, 7, 8, 11, 12, 13, 14, and 18. Phylogenetic analysis suggested that these BURP family genes could be classified into 5 subfamilies, and one of which defines a new subfamily, BURPV. Quantitative real-time PCR (qRT-PCR) analysis of transcript levels showed that 15 of the 23 genes had no expression specificity; 7 of them were specifically expressed in some of the tissues; and one of them was not expressed in any of the tissues or organs studied. The results of stress treatments showed that 17 of the 23 identified BURP family genes responded to at least one of the three stress treatments; 6 of them were not influenced by stress treatments even though a stress related cis-element was identified in the promoter region. No stress related cis-elements were found in promoter region of any BURPV member. However, qRT-PCR results indicated that all members from BURPV responded to at least one of the three stress treatments. More significantly, the members from the RD22-like subfamily showed no tissue-specific expression and they all responded to each of the three stress treatments.

CONCLUSIONS

We have identified and classified all the BURP domain-containing genes in soybean. Their expression patterns in different tissues and under different stress treatments were detected using qRT-PCR. 15 out of 23 BURP genes in soybean had no tissue-specific expression, while 17 out of them were stress-responsive. The data provided an insight into the evolution of the gene family and suggested that many BURP family genes may be important for plants responding to stress conditions.

Flux of transcript patterns during soybean seed development

BACKGROUND

To understand gene expression networks leading to functional properties of the soybean seed, we have undertaken a detailed examination of soybean seed development during the stages of major accumulation of oils, proteins, and starches, as well as the desiccating and mature stages, using microarrays consisting of up to 27,000 soybean cDNAs. A subset of these genes on a highly-repetitive 70-mer oligonucleotide microarray was also used to support the results.

RESULTS

It was discovered that genes related to cell growth and maintenance processes, as well as energy processes like photosynthesis, decreased in expression levels as the cotyledons approached the mature, dry stage. Genes involved with some storage proteins had their highest expression levels at the stage of highest fresh weight. However, genes encoding many transcription factors and DNA binding proteins showed higher expression levels in the desiccating and dry seeds than in most of the green stages.

CONCLUSIONS

Data on 27,000 cDNAs have been obtained over five stages of soybean development, including the stages of major accumulation of agronomically-important products, using two different types of microarrays. Of particular interest are the genes found to peak in expression at the desiccating and dry seed stages, such as those annotated as transcription factors, which may indicate the preparation of pathways that will be needed later in the early stages of imbibition and germination.

Protein storage vacuoles of Brassica napus zygotic embryos accumulate a BURP domain protein and perturbation of its production distorts the PSV

BNM2is a prototypical member of the enigmatic BURP domain protein family whose members contain the signature FX6-7GX10-28PX25-31CX11-12X2SX45-56CHX10 CHX25-29CHX2TX15-16PX5CH in the C-terminus. This protein family occurs only in plants, and the cognate genes vary very widely in their expression contexts in vegetative and reproductive tissues. None of theBURP family members has been assigned any biochemical function. BNM2 was originally discovered as a gene expressed in microspore derived embryos (MDE) of Brassica napus but we found that MDE do not contain the corresponding protein. We show that BNM2 protein production is confined to the seeds and localized to the protein storage vacuoles (PSV) even though the transcript is found in vegetative parts and floral buds as well. In developing seeds, transcript accumulation precedes protein appearance by more than 18 days. RNA accumulation peaks at approximately 20 days post anthesis (DPA) whereas protein accumulation reaches its maximum at approximately 40 DPA. Transgenic expression of BNM2 does not abrogate this regulation to yield ectopic protein production or to alter the temporal aspect ofBNM2 accumulation. Overexpression ofBNM2 led to spatial distortion of storage protein accumulation within PSV and to some morphological alterations of PSVs. However, the overall storage protein content was not altered.

The BURP domain protein AtUSPL1 of Arabidopsis thaliana is destined to the protein storage vacuoles and overexpression of the cognate gene distorts seed development

BURP domain proteins comprise a broadly distributed, plant-specific family of functionally poorly understood proteins. VfUSP (Vicia faba Unknown Seed Protein) is the founding member of this family. The BURP proteins are characterized by a highly conserved C-terminal protein domain with a characteristic cysteine-histidine pattern. The Arabidopsis genome contains five BURP-domain encoding genes. Three of them are similar to the non-catalytic beta-subunit of the polygalacturonase of tomato and form a distinct subgroup. The remaining two genes are AtRD22 and AtUSPL1. The deduced product of AtUSPL1 is similar in size and sequence to VfUSP and that of the Brassica napus BNM2 gene which is expressed during microspore-derived embryogenesis. The protein products of BURP genes have not been found, especially that of VfUSP despite a great deal of interest arising from copious transcription of the gene in seeds. Here, we demonstrate that VfUSP and AtUSPL1 occur in cellular compartments essential for seed protein synthesis and storage, like the Golgi cisternae, dense vesicles, prevaculoar vesicles and the protein storage vacuoles in the parenchyma cells of cotyledons. Ectopic expression of AtUSPL1 leads to a shrunken seed phenotype; these seeds show structural alterations in their protein storage vacuoles and lipid vesicles. Furthermore, there is a reduction in the storage protein content and a perturbation in the seed fatty acid composition. However, loss of AtUSP1 gene function due to T-DNA insertions does not lead to a phenotypic change under laboratory conditions even though the seeds have less storage proteins. Thus, USP is pertinent to seed development but its role is likely shared by other proteins that function well enough under the laboratory growth conditions.

Genome-wide identification of BURP domain-containing genes in rice reveals a gene family with diverse structures and responses to abiotic stresses

Increasing evidence suggests that a gene family encoding proteins containing BURP domains have diverse functions in plants, but systematic characterization of this gene family have not been reported. In this study, 17 BURP family genes (OsBURP01-17) were identified and analyzed in rice (Oryza sativa L.). These genes have diverse exon-intron structures and distinct organization of putative motifs. Based on the phylogenetic analysis of BURP protein sequences from rice and other plant species, the BURP family was classified into seven subfamilies, including two subfamilies (BURP V and BURP VI) with members from rice only and one subfamily (BURP VII) with members from monocotyledons only. Two BURP gene clusters, belonging to BURP V and BURP VI, were located in the duplicated region on chromosome 5 and 6 of rice, respectively. Transcript level analysis of BURP genes of rice in various tissues and organs revealed different tempo-spatial expression patterns, suggesting that these genes may function at different stages of plant growth and development. Interestingly, all the genes of the BURP VII subfamily were predominantly expressed in flower organs. We also investigated the expression patterns of BURP genes of rice under different stress conditions. The results suggested that, except for two genes (OsBURP01 and OsBURP13), all other members were induced by at least one of the stresses including drought, salt, cold, and abscisic acid treatment. Two genes (OsBURP05 and OsBURP16) were responsive to all the stress treatments and most of the OsBURP genes were responsive to salt stress. Promoter sequence analysis revealed an over-abundance of stress-related cis-elements in the stress-responsive genes. The data presented here provide important clues for elucidating the functions of genes of this family.

Transcriptome response to glyphosate in sensitive and resistant soybean

The majority of soybeans planted in the United States are resistant to glyphosate due to introduction of a gene encoding for a glyphosate-insensitive 5-enolypyruvylshikimate-3-phosphate synthase. Gene expression profiling was conducted using cDNA microarrays to address questions related to potential secondary effects of glyphosate. When glyphosate-sensitive plants were treated with glyphosate, 3, 170, and 311 genes were identified as having different transcript levels at 1, 4, and 24 h post-treatment (hpt), respectively. Differentially expressed genes were classified into functional categories, and their possible roles in response to glyphosate are briefly discussed. Gene expression profiling of glyphosate-resistant plants treated with glyphosate indicated that the plants were marginally affected at 1 hpt and then quickly adjusted to glyphosate treatment. Ten, four, and four genes were identified as differentially expressed at 1, 4, and 24 hpt. When gene expression profiles of cotyledons from developing seed were compared between the near-isogenic resistant and sensitive lines, two genes were identified as significantly differentially expressed out of 27000, which was less than the empirical false-discovery rate determined from a control experiment. Quantitative real-time reverse-transcribed Polymerase Chain Reaction was conducted on selected genes and yielded results consistent with those from the microarrays. Collectively, these data indicate that there are no major transcriptomic changes associated with currently used glyphosate-resistant soybean.

Specific elements of the glyoxylate pathway play a significant role in the functional transition of the soybean cotyledon during seedling development

BACKGROUND

The soybean (Glycine max) cotyledon is a specialized tissue whose main function is to serve as a nutrient reserve that supplies the needs of the young plant throughout seedling development. During this process the cotyledons experience a functional transition to a mainly photosynthetic tissue. To identify at the genetic level the specific active elements that participate in the natural transition of the cotyledon from storage to photosynthetic activity, we studied the transcript abundance profile at different time points using a new soybean oligonucleotide chip containing 19,200 probes (70-mer long).

RESULTS

After normalization and statistical analysis we determined that 3,594 genes presented a statistically significant altered expression in relation to the imbibed seed in at least one of the time points defined for the study. Detailed analysis of this data identified individual, specific elements of the glyoxylate pathway that play a fundamental role during the functional transition of the cotyledon from nutrient storage to photosynthesis. The dynamics between glyoxysomes and peroxisomes is evident during these series of events. We also identified several other genes whose products could participate co-ordinately throughout the functional transition and the associated mechanisms of control and regulation and we described multiple unknown genetic elements that by association have the potential to make a major contribution to this biological process.

CONCLUSION

We demonstrate that the global transcript profile of the soybean cotyledon during seedling development is extremely active, highly regulated and dynamic. We defined the expression profiles of individual gene family members, enzymatic isoforms and protein subunits and classified them accordingly to their involvement in different functional activities relevant to seedling development and the cotyledonary functional transition in soybean, especially the ones associated with the glyoxylate cycle. Our data suggests that in the soybean cotyledon a very complex and synchronized system of control and regulation of several metabolic pathways is essential to carry out the necessary functions during this developmental process.

Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub)

BACKGROUND

Guar, Cyamopsis tetragonoloba (L.) Taub, is a member of the Leguminosae (Fabaceae) family and is economically the most important of the four species in the genus. The endosperm of guar seed is a rich source of mucilage or gum, which forms a viscous gel in cold water, and is used as an emulsifier, thickener and stabilizer in a wide range of foods and industrial applications. Guar gum is a galactomannan, consisting of a linear (1-->4)-beta-linked D-mannan backbone with single-unit, (1-->6)-linked, alpha-D-galactopyranosyl side chains. To better understand regulation of guar seed development and galactomannan metabolism we created cDNA libraries and a resulting EST dataset from different developmental stages of guar seeds.

RESULTS

A database of 16,476 guar seed ESTs was constructed, with 8,163 and 8,313 ESTs derived from cDNA libraries I and II, respectively. Library I was constructed from seeds at an early developmental stage (15-25 days after flowering, DAF), and library II from seeds at 30-40 DAF. Quite different sets of genes were represented in these two libraries. Approximately 27% of the clones were not similar to known sequences, suggesting that these ESTs represent novel genes or may represent non-coding RNA. The high flux of energy into carbohydrate and storage protein synthesis in guar seeds was reflected by a high representation of genes annotated as involved in signal transduction, carbohydrate metabolism, chaperone and proteolytic processes, and translation and ribosome structure. Guar unigenes involved in galactomannan metabolism were identified. Among the seed storage proteins, the most abundant contig represented a conglutin accounting for 3.7% of the total ESTs from both libraries.

CONCLUSION

The present EST collection and its annotation provide a resource for understanding guar seed biology and galactomannan metabolism.

Developmental expression of ASG- 1 during gametogenesis in apomictic guinea grass (Panicum maximum)

We have used Western blue-visualized in situ-hybridization (ISH) to monitor the expression of apomixis-specific gene-1 (ASG-1, GenBank accession number AB000809) during gametogenesis in obligate-sexual and facultative-apomictic (aposporic) genotypes of guinea grass (Panicum maximum). The in situ-analysis revealed that ASG-1 is not expressed in the ovule during early floral development in both, the facultative apomicts (A1 stage) and the obligate sexuals (S1 stage). With the appearance of the aposporous initial cell(s) in the ovule of the apomictic type (A2-1 stage), ASG-1 expression is strong and specific to this apomixis-specific cell. ASG-1 expression continued through different stages of aposporous embryo sac development (A2-2 stage), indicating that the gene may play a role in this developmental process. Regular embryo sacs in sexual types did not show hybridization signals (S2 stage). However, strong ASG-1 expression was detected in immature pollen grains and young embryos in both reproductive types, suggesting that ASG-1 may be an allele derived from the obligate-sexual wild type. Expression in pollen grains faded with maturation. In a heterologous system, using Paspalum notatum, a facultative-aposporic tropical grass (bahia grass), identical results were obtained. The results are discussed in view of the fact, that ASG-1 shows some homology to genes known to be seed- or embryo-specific or involved in processes related to cell growth.

Tuber on a chip: differential gene expression during potato tuber development

Potato tuber development has proven to be a valuable model system for studying underground sink organ formation. Research on this topic has led to the identification of many genes involved in this complex process and has aided in the unravelling of the mechanisms underlying starch synthesis. However, less attention has been paid to the biochemical pathways of other important metabolites or to the changing metabolic fluxes occurring during potato tuber development. In this paper, we describe the construction of a potato complementary DNA (cDNA) microarray specifically designed for genes involved in processes related to tuber development and tuber quality traits. We present expression profiles of 1315 cDNAs during tuber development where the predominant profiles were strong up- and down-regulation. Gene expression profiles showing transient increases or decreases were less abundantly represented and followed more moderate changes, mainly during tuber initiation. In addition to the confirmation of gene expression patterns during tuber development, many novel differentially expressed genes were identified and are considered as candidate genes for direct involvement in potato tuber development. A detailed analysis of starch metabolism genes provided a unique overview of expression changes during tuber development. Characteristic expression profiles were often clearly different between gene family members. A link between differential gene expression during tuber development and potato tissue specificity is described. This dataset provides a firm basis for the identification of key regulatory genes in a number of metabolic pathways that may provide researchers with new tools to achieve breeding goals for use in industrial applications.

The classical Ubisch bodies carry a sporophytically produced structural protein (RAFTIN) that is essential for pollen development

Pollen fecundity is crucial to crop productivity and also to biodiversity in general. Pollen development is supported by the tapetum, a metabolically active sporophytic nurse layer that devotes itself to this process. The tapetum in cereals and a vast majority of other plants is of the nonamoeboid type. Unable to reach out to microspores, it secretes nutrients into the anther locule where the microspores reside and develop. Orbicules (Ubisch bodies), studied in various plants since their discovery approximately 140 years ago, are a hallmark of the secretory tapetum. Their significance to tapetal or pollen development has not been established. We have identified in wheat and rice an anther-specific single-copy gene (per haploid genome equivalent) whose suppression in rice by RNA interference nearly eliminated the seed set. The flowers in the transgenics were normal for female functions, but the pollen collapsed and became less viable. Further characterization of the gene product, named RAFTIN, in wheat has shown that it is present in pro-orbicule bodies and it is accumulated in Ubisch bodies. Furthermore, it is targeted to microspore exine. Although the carboxyl portion of RAFTINs shares short, dispersed amino acid sequences (BURP domain) in common with a variety of proteins of disparate biological contexts, the occurrence RAFTIN per se is limited to cereals; neither the Arabidopsis genome nor the vast collection of ESTs suggests any obvious dicot homologs. Furthermore, our results show that RAFTIN is essential for the late phase of pollen development in cereals.

beta-alanine N-methyltransferase of Limonium latifolium. cDNA cloning and functional expression of a novel N-methyltransferase implicated in the synthesis of the osmoprotectant beta-alanine betaine

Beta-alanine (Ala) betaine, an osmoprotectant suitable under saline and hypoxic environments, is found in most members of the halophytic plant family Plumbaginaceae. In Limonium latifolium (Plumbaginaceae), it is synthesized via methylation of beta-Ala by the action of a trifunctional S-adenosyl L-methionine (Ado-Met): beta-Ala N-methyltransferase (NMTase). Peptide sequences from purified beta-Ala NMTase were used to design primers for reverse transcriptase-PCR, and several cDNA clones were isolated. The 5' end of the cDNA was cloned using a 5'-rapid amplification of cDNA ends protocol. A 500-bp cDNA was used as a probe to screen a lambda-gt10 L. latifolium leaf cDNA library. Partial cDNA clones represented two groups, NMTase A and NMTase B, differing only in their 3'-untranslated regions. The full-length NMTase A cDNA was 1,414 bp and included a 1128-bp open reading frame and a 119-bp 5'-untranslated region. The deduced amino acid sequence of 375 residues had motifs known to be involved in the binding of Ado-Met. The NMTase mRNA was expressed in L. latifolium leaves but was absent in Limonium sinuatum, a member of the genus that lacks the synthetic pathway for beta-Ala betaine. NMTase mRNA expression was high in young and mature leaves and was enhanced by light. NMTase cDNA was expressed in yeast (Saccharomyces cerevisiae) under the control of a galactose-inducible promoter. Protein extracts of galactose-induced recombinant yeast had Ado-Met-specific NMTase activities that were highly specific to beta-Ala, N-methyl beta-Ala, and N,N-dimethyl beta-Ala as methyl acceptors. NMTase activities were not detectable in comparable protein extracts of yeast, transformed with vector control. The NMTase protein sequence shared homology with plant caffeic acid O-methyltransferases and related enzymes. Phylogenetic analyses suggested that beta-Ala NMTase represents a novel family of N-methyltransferases that are evolutionarily related to O-methyltransferases.

Clustering of microarray data reveals transcript patterns associated with somatic embryogenesis in soybean

Globular somatic embryos can be induced from immature cotyledons of soybean (Glycine max L. Merr. cv Jack) placed on high levels of the auxin 2,4-dichlorophenoxyacetic acid (2,4-D). Somatic embryos develop from the adaxial side of the cotyledon, whereas the abaxial side evolves into a callus. Using a 9,280-cDNA clone array, we have compared steady-state RNA from the adaxial side from which embryos develop and from the abaxial callus at five time points over the course of the 4 weeks necessary for the development of globular embryos. In a second set of experiments, we have profiled the expression of each clone in the adaxial side during the same period. A total of 495 genes differentially expressed in at least one of these experiments were grouped according to the similarity of their expression profiles using a nonhierarchical clustering algorithm. Our results indicate that the appearance of somatic embryos is preceded by dedifferentiation of the cotyledon during the first 2 weeks on auxin. Changes in mRNA abundance of genes characteristic of oxidative stress and genes indicative of cell division in the adaxial side of the cotyledons suggest that the arrangement of the new cells into organized structures might depend on a genetically controlled balance between cell proliferation and cell death. Our data also suggest that the formation of somatic globular embryos is accompanied by the transcription of storage proteins and the synthesis of gibberellic acid.

Differential gene expression in proteoid root clusters of white lupin (Lupinus albus)

Proteoid root clusters are induced by P deficiency in white lupin. In their mature stage, these roots excrete organic acids (mainly citrate), thus allowing this species to acquire P from sparingly soluble sources. To screen for P-regulated genes expressed during the period of citrate efflux, an experimental model based on proteoid root clusters contrasting in citrate efflux was developed. The feasibility of this model in identifying differential gene expression was assessed over a population of mRNAs from P-starved and P-starved rescued proteoid root clusters, sampled 24 and 72 h after P addition to 24 days P-starved white lupin. Approximately 1500 bands of cDNA were displayed by differential display of 21-primer pair's combination; 52 differentially expressed bands, either up- or down-regulated after P addition, were observed. Sequence analysis of 17 of them revealed that they represent distinct cDNAs. A subsample of seven cDNAs was analysed by northern-blot, showing that six were truly differential products. Transcripts coding for enzymes involved in carbon flux (glyceraldehyde 3-phosphate dehydrogenase), glycolytic bypass (phosphoenolpyruvate carboxylase), Pi recycling (sulpholipid synthase), and two unknown cDNAs were shown to be down-regulated by P supply. Besides, an up-regulated transcript coding for a putative auxin-induced protein was identified, whereas P addition did not significantly affect expression of a transcript for cyclophilins. These results show the feasibility of using P-starved and P-starved rescued proteoid root clusters as an experimental model to detect and examine the molecular changes occurring in root clusters during the period of citrate efflux in white lupin.

Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. I. Large-scale changes in the accumulation of growth- and defense-related plant mRNAs

Plants respond to herbivore attack with a dramatic functional reorganization that involves the activation of direct and indirect defenses and tolerance, which in turn make large demands on primary metabolism. Here we provide the first characterization of the transcriptional reorganization that occurs after insect attack in a model plant-herbivore system: Nicotiana attenuata Torr. ex Wats.-Manduca sexta. We used mRNA differential display to characterize one-twentieth of the insect-responsive transcriptome of N. attenuata and verified differential expression for 27 cDNAs. Northern analyses were used to study the effects of folivory and exposure to airborne methyl jasmonate and for kinetic analyses throughout a 16-h- light/8-h-dark cycle. Sequence similarity searches allowed putative functions to be assigned to 15 transcripts. Genes were related to photosynthesis, electron transport, cytoskeleton, carbon and nitrogen metabolism, signaling, and a group responding to stress, wounding, or invasion of pathogens. Overall, transcripts involved in photosynthesis were strongly down-regulated, whereas those responding to stress, wounding, and pathogens and involved in shifting carbon and nitrogen to defense were strongly up-regulated. The majority of transcripts responded similarly to airborne methyl jasmonate and folivory, and had tissue- and diurnal-specific patterns of expression. Transcripts encoding Thr deaminase (TD) and a putative retrotransposon were absent in control plants, but were strongly induced after herbivory. Full-length sequences were obtained for TD and the pathogen-inducible alpha-dioxygenase, PIOX. Effects of abiotic and biotic stimuli were investigated for transcripts encoding TD, importin alpha, PIOX, and a GAL83-like kinase cofactor.

The plant translational apparatus

Protein synthesis in both eukaryotic and prokaryotic cells is a complex process requiring a large number of macromolecules: initiation factors, elongation factors, termination factors, ribosomes, mRNA, amino-acylsynthetases and tRNAs. This review focuses on our current knowledge of protein synthesis in higher plants.

Regulation of an embryogenic carrot gene (DC 2.15) and identification of its active promoter sites

According to previous studies the expression of the gene DC 2.15 is induced in cultured carrot cells after a transfer to an auxin-free medium, where somatic embryo development occurs. This embryogenic gene encodes a prolinerich protein, which resembles proteins involved in auxin-controlled developmental processes. To understand the mechanism underlying the regulation of DC 2.15, an experimental approach has been employed which allows the direct identification of the DC 2.15 promoter structure by applying PCR techniques. We demonstrate the presence of five distinct promoter sequences highly similar in structure, but slightly different in a common region of about 15 nucleotides, which contain the binding site for the GATA factor originally found in the human HOX gene. Activity of each promoter structure was assessed in developing somatic embryos containing the specific sequence fused to the beta-glucuronidase (GUS) reporter gene. For two of the five promoter structures a drastic increase in activity was registered during the torpedo stage while the remaining three were inactive throughout the stages of somatic embryogenesis.

Transcripts of a gene encoding a putative cell wall-plasma membrane linker protein are specifically cold-induced in Brassica napus

We have isolated a gene and cDNA from Brassica napus encoding a hybrid-proline-rich protein. The putative protein is modular in structure. The N-terminal domain has properties of a signal peptide which would direct the protein into the ER. Amino acids 27 to 287 comprise three domains which contain high levels of proline and several other amino acids common in proline-rich cell wall proteins. These domains are characterised by repeating amino acid motifs. The C-terminal domain (amino acids 288 to 376) contains three putative membrane-spanning regions and shows a high degree of amino acid similarity to known hybrid-proline-rich proteins from several species. It is likely that the protein is secreted from the cell, located in the cell wall and anchored in the plasma membrane via the C-terminal domain. Transcripts encoding this protein are induced in leaf tissue within 8 h of cold treatment and decrease rapidly when plants are returned to normal temperatures. The transcripts are not induced by heat shock, dehydration, exogenous ABA or wounding, whereas transcripts of a control B. napus gene are induced by dehydration and ABA. The possible function of this protein in cold tolerance is discussed.

Characterization of a cDNA encoding a proline-rich 14 kDa protein in developing cortical cells of the roots of bean (Phaseolus vulgaris) seedlings

A cDNA clone, corresponding to mRNAs preferentially expressed in the roots of bean (Phaseolus vulgaris L.) seedlings, was isolated. This clone contains a 381 bp open reading frame encoding a polypeptide of 13.5 kDa, designated PVR5 (Phaseolus vulgaris root 5). The amino acid sequence of this clone is rich in proline (13.5%) and leucine (12.7%) and shares significant amino acid sequence homology with root-specific and proline-rich proteins from monocots (maize and rice), and proline-rich proteins from dicots (carrot, oilseed rape, and Madagascar periwinkle). The precise biological roles of these polypeptides are unknown. PVR5 mRNA accumulation is developmentally regulated within the root, with high levels at the root apex and declining levels at distances further from the root tip. In situ hybridization shows that PVR5 mRNA specifically accumulates in the cortical ground meristem in which maximal cell division occurs. Southern blot analysis suggests that genomic DNA corresponding to PVR5 cDNA is encoded by a single gene or a small gene family.

The auxin signal

Recent work on the auxin signal has yielded clear answers to some questions and produced puzzling new data to explain. It is now established that the auxin-binding protein functions extracellularly, but it is unclear how it reaches that location. Important clues on the mechanism(s) by which auxin achieves its genetic and cell biological effects are emerging.

Auxin action and auxin-binding proteins

The plant growth regulator auxin mediates an enormous range of developmental and growth responses, some of which are manifest rapidly and others manifest only after considerable lag periods. The protein that perceives auxin, the auxin receptor, has been sought by many laboratories and the search has identified a good number of candidates. However, a receptor must not only bind auxin, but also transduce the auxin stimulus into the responses we recognize. Finding evidence for this second condition has always proved very demanding. A key requisite is a convenient assay for auxin activity and preferably one involving a rapid response because this is likely to be linked directly to the perception event. For one auxin-binding protein (ABP1) there is growing evidence that it is a functional auxin receptor. The assays used in this work have been rapid auxin-induced changes in protoplast electrophysiology. There are many other responses induced rapidly by auxin for which a link to ABP1 has yet to be established. We have reviewed the whole range of rapid auxin-mediated responses and by doing so we hope to have provided a comprehensive picture of the many events to which a receptor (or receptors) must connect. Against this framework we match the known properties of all putative receptors, including ABP1. Not only have we tried to identify auxin-binding proteins unlikely to be receptors, but we also highlight the remaining gaps in our understanding of the more likely receptor candidates. Contents Summary 167 I. Introduction 168 II. Gene activation 168 III. Mutants 179 IV. Auxin-induced elongation growth 179 V. Other auxin-binding proteins 191 VI. Auxins and signal transduction 192 VII. Overview 194 Acknowledgements 195 References 195.

Post-transcriptional regulation of a salt-inducible alfalfa gene encoding a putative chimeric proline-rich cell wall protein

A cDNA previously shown to identify a salt-inducible root-specific transcript in Medicago sativa was used to screen an alfalfa library for the corresponding genomic sequence. One positive clone was recovered. The nucleotide sequence of a subclone contained a 329 bp 5' region upstream of the first ATG codon, a 1143 bp coding segment, and a 447 bp 3'-untranslated region interrupted by a single 475 bp intron. Translation of the coding segment, which was designated MsPRP2, suggested it encodes a chimeric 40,569 Da cell wall protein with an amino-terminal signal sequence, a repetitive proline-rich sequence, and a cysteine-rich carboxyl-terminal sequence homologous to nonspecific lipid transfer proteins. The 3'-untranslated region of MsPRP2 contained a sequence similar to one found to destabilize mRNAs transcribed from the elicitor-regulated proline-rich protein gene PvPRP1. Transcription run-on experiments using nuclei from salt-sensitive and salt-tolerant alfalfa callus suggested that the accumulation of MsPRP2 transcripts in salt-tolerant alfalfa cells grown in the presence of salt is due primarily to increased mRNA stability. The MsPRP2 gene thus may be a useful model for studying post-transcriptional salt-regulated expression of cell wall proteins.