An Arabidopsis gene regulatory network for secondary cell wall synthesis.

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein-DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

The calmodulin-binding transcription factor SIGNAL RESPONSIVE1 is a novel regulator of glucosinolate metabolism and herbivory tolerance in Arabidopsis.

The Arabidopsis Ca(2+)/calmodulin (CaM)-binding transcription factor SIGNAL RESPONSIVE1 (AtSR1/CAMTA3) was previously identified as a key negative regulator of plant immune responses. Here, we report a new role for AtSR1 as a critical component of plant defense against insect herbivory. Loss of AtSR1 function impairs tolerance to feeding by the generalist herbivore Trichoplusia ni as well as wound-induced jasmonate accumulation. The susceptibility of the atsr1 mutant is associated with decreased total glucosinolate (GS) levels. The two key herbivory deterrents, indol-3-ylmethyl (I3M) and 4-methylsulfinylbutyl (4MSOB), showed the most significant reductions in atsr1 plants. Further, changes in AtSR1 transcript levels led to altered expression of several genes involved in GS metabolism including IQD1, MYB51 and AtST5a. Overall, our results establish AtSR1 as an important component of plant resistance to insect herbivory as well as one of only three described proteins involved in Ca(2+)/CaM-dependent signaling to function in the regulation of GS metabolism, providing a novel avenue for future investigations of plant-insect interactions.

A trans-acting factor that binds to a GT-motif in a phytochrome gene promoter.

The regulatory photoreceptor, phytochrome, controls the expression of numerous genes, including its own phyA genes, which are transcriptionally repressed in response to light. Functional analysis of a rice phyA gene promoter, by means of microprojectile-mediated gene transfer, indicates that a GT motif, GCGGTAATT, closely related to elements in the promoters of a number of other light-regulated genes, is critical for expression. Partial complementary DNA clones have been obtained for a rice nuclear protein, designated GT-2, that binds in a highly sequence-specific fashion to this motif. Mutational analysis shows that the paired G's are most crucial to binding. GT-2 has domains related to certain other transcription factors. Northern blot analysis shows that GT-2 messenger RNA levels decline in white light although red and far red light pulses are ineffective.

The crystal structure of beta-ketoacyl-acyl carrier protein synthase II from Synechocystis sp. at 1.54 A resolution and its relationship to other condensing enzymes.

Condensing enzymes, catalyzing the formation of carbon-carbon bonds in several biosynthetic pathways, have lately been recognized as potential drug targets against cancer and tuberculosis, as crucial for combinatorial biosynthesis of antibiotics and related compounds, and as determinants of plant oil composition. beta-Ketoacyl-ACP synthases (KAS) are the condensing enzymes present in the fatty acid biosynthesis pathway and are able to elongate an acyl chain bound to either co-enzyme A (CoA) or acyl carrier protein (ACP) with a two-carbon unit derived from malonyl-ACP. Several isoforms of KAS with different substrate specificity are present in most species. We have determined the crystal structure of KAS II from Synechocystis sp. PCC 6803 to 1.54 A resolution giving a detailed description of the active site geometry. In order to analyze the structure-function relationships in this class of enzymes in more detail, we have compared all presently known three-dimensional structures of condensing enzymes from different pathways. The comparison reveals that these enzymes can be divided into three structural and functional classes. This classification can be related to variations in the catalytic mechanism and the set of residues in the catalytic site, e.g. due to differences in the nature of the second substrate providing the two-carbon elongation unit. The variation in the acyl-carrier (ACP or CoA) specificity might also be connected to this classification and residues involved in ACP binding in structure class 2 can be suggested based on the comparison. Finally, the two subunits in the dimer contribute differently to formation of the substrate binding-pocket in the three structural classes.

Cloning of the fabF gene in an expression vector and in vitro characterization of recombinant fabF and fabB encoded enzymes from Escherichia coli.

Analysis of the beta-ketoacyl-ACP synthase (KAS) encoded by the fabF gene of Escherichia coli has been hampered by a reported instability of the cloned gene. Here we describe biochemical characterization of purified, active protein from the recombinant fabF gene. This enzyme has the properties ascribed to KAS II and not those of a putative KAS IV reported to be encoded by fabJ, a genomic clone with DNA sequence identical to that of fabF. We also characterize active protein from a recombinant fabB gene and suggest that this method may have a general utility for analysis of KAS enzymes.

The Arabidopsis phytochrome A gene has multiple transcription start sites and a promoter sequence motif homologous to the repressor element of monocot phytochrome A genes.

We have determined the sequence of the phytochrome A gene (PHYA) and its flanking DNA from Arabidopsis thaliana and have identified transcription start sites for three nested transcripts of increasing length. The overall structure of the gene is similar as regards exon/intron organization to other angiosperm PHY genes characterized. The triple transcription start site arrangement is similar to that of pea PHYA but different from the single start site of oat, rice and maize PHYA genes, indicating a possible monocot-dicot difference. Comparison of the Arabidopsis PHYA promoter sequence with others available indicates that both pea and Arabidopsis promoters contain a DNA element with a core sequence motif identical to one conserved in all existing monocot PHYA sequences and defined by functional assay in the oat PHYA gene as repressor element, RE1, responsible for negative light regulation.

Rice HYDROPEROXIDE LYASES with unique expression patterns generate distinct aldehyde signatures in Arabidopsis.

HYDROPEROXIDE LYASE (HPL) genes encode enzymes that catalyze the cleavage of fatty acid hydroperoxides into aldehydes and oxoacids. There are three HPLs in rice (Oryza sativa), designated OsHPL1 through OsHPL3. To explore the possibility of differential functional activities among these genes, we have examined their expression patterns and biochemical properties of their encoded products. Transcript analysis indicates that these genes have distinct patterns and levels of expression. OsHPL1 is ubiquitously expressed, OsHPL2 is expressed in the leaves and leaf sheaths, whereas OsHPL3 is wound inducible and expressed exclusively in leaves. OsHPLs also differ in their substrate preference as determined by in vitro enzyme assays using 9-/13-hydroperoxy linolenic and 9-/13-hydroperoxy linoleic acids as substrates. OsHPL1 and OsHPL2 metabolize 9-/13-hydroperoxides, whereas OsHPL3 metabolizes 13-hydroperoxy linolenic acid exclusively. Sequence alignments of the HPL enzymes have identified signature residues potentially responsible for the substrate specificity/preference of these enzymes. All three OsHPLs are chloroplast localized as determined by chloroplast import assays and green fluorescent protein (GFP) fusion studies. Aldehyde measurements in transgenic Arabidopsis (Arabidopsis thaliana) plants overexpressing individual OsHPL-GFP fusions indicate that all rice HPLs are functional in a heterologous system, and each of them generates a distinct signature of the metabolites. Interestingly, these aldehydes were only detectable in leaves, but not in roots, despite similar levels of OsHPL-GFP proteins in both tissues. Similarly, there were undetectable levels of aldehydes in rice roots, in spite of the presence of OsHPL1 transcripts. Together, these data suggest that additional tissue-specific mechanism(s) beyond transcript and HPL enzyme abundance, regulate the levels of HPL-derived metabolites.

The function of proteases during the light-dependent transformation of etioplasts to chloroplasts in barley (Hordeum vulgare L.).

The role of proteolysis during the light-induced rapid decrease of the NADPH: protochlorophyllide oxidoreductase in barley was studied. A proteolytic activity with a pH optimum of 4.5 was present in a plastid preparation of etiolated barley seedlings. No other proteolytic activity could be detected. The temperature optimum for the proteolysis was 50°C, and the highest specific activity was measured with hemoglobin as the substrate. In contrast to previous proposals, no evidence for the specific involvement of this protease was found during the light-induced transformation of etioplasts to chloroplasts.

The NADPH-protochlorophyllide oxidoreductase is the major protein constituent of prolamellar bodies in wheat (Triticum aestivum L.).

A fraction of highly purified prolamellar bodies was isolated from etioplasts of wheat (Triticum aestivum L. cv. Starke II, Weibull), as previously described by Ryberg and Sundqvist (1982, Physiol. Plant., 56, 125-132). Studies on the protein composition revealed that only one major polypeptide of an apparent molecular weight of 36000 is present in the fraction of prolamellar bodies. This polypeptide was identified as the NADPH-protochlorophyllide oxidoreductase. The highest specific activity of the enzyme in etiolated leaf tissue was confirmed to be in the fraction of prolamellar bodies.

Light-induced changes in the amounts of the 36000-Mr polypeptide of NADPH-protochlorophyllide oxidoreductase and its mRNA in barley plants grown under a diurnal light/dark cycle.

Seedlings of barley were grown either in continuous darkness or under a diurnal 12 h light/12 h dark cycle and the effects on NADPH-protochlorophyllide oxidoreductase were followed at two different levels. Firstly, the relative content of the mRNA encoding the NADPH-protochlorophyllide oxidoreductase was measured by dot-blot hybridization. Secondly, changes in the enzyme polypeptide were monitored either by the method of immunoblotting or by immunogold labelling of ultrathin sections of Lowicryl-embedded leaf tissue. Our results demonstrate that drastic diurnal changes in the level of mRNA sequences and the enzyme protein are unlikely to occur in plants which have been grown under natural light/dark conditions. In the dark, protein and mRNA accumulation occurs at an early developmental stage. These results are difficult to reconcile with the suggestion that the massive accumulation of mRNA and enzyme protein in dark-grown seedlings is primarily the consequence of an artificially extended darkperiod. In addition to the plastid-specific NADPH-protochlorophyllide oxidoreductase a closely related polypeptide has been detected outside the plastid in the surrounding cytoplasm (Dehseh et al. 1986b, Planta 169, 172-183). During the diurnal light/dark treatment of seedlings the concentrations of the two protein populations did not show any variation indicative of an exchange between the two protein populations across the plastid envelope.

The proteolytic degradation in vitro of the NADPH-protochlorophyllide oxidoreductase of barley (Hordeum vulgare L.).

A cell-free membrane system has been developed from isolated barley etioplasts which displays a highly selective decrease of the NADPH-protochlorophyllide oxidoreductase in vitro which is indistinguishable from that observed previously in the intact plant. The rapid breakdown of the enzyme protein in vitro is caused by a membrane-bound proteolytic activity. The protease is essentially independent of pH in the physiological pH range of 6 to 8.5. The optimum temperature for the reaction is approximately 40 degrees C. In the presence of excessive protochlorophyllide the enzyme is no longer degraded or inactivated during illumination of dark-grown plants. In the isolated membrane fraction protochlorophyllide also enhances the stability of the enzyme, a similar effect is exerted by NADPH but not by NADH. The results suggest that the inactivation of the NADPH-protochlorophyllide oxidoreductase is influenced by the interaction of the enzyme with protochlorophyllide and NADPH. In the absence of these two components the enzyme becomes susceptible to proteolytic degradation.

The biosynthesis of chlorophyll in greening barley (Hordeum vulgare). Is there a light-independent protochlorophyllide reductase?

Recently, some evidence for the occurence of a light-independent protochlorophyllide-reducing enzyme in greening barley plants has been presented. In the present work this problem was reinvestigated. δ-[(14)C] Aminolevulinic acid was fed to isolated barley shoots from plants which had been preilluminated for various lengths of time. Porphyrins which had been synthesized during the dark incubation were analyzed by high-performance liquid chromatography. There was no evidence for a light-independent synthesis of chlorophyll(ide). The (14)C-labelled precursor was incorporated almost exclusively into protochlorophyllide. The reduction of labelled protochlorophyllide to chlorophyllide was strictly light-dependent. These results are not consistent with the existence of a light-independent protochlorophyllide-reductase in barley as proposed previously.

The light-dependent accumulation of the P700 chlorophyll a protein of the photosystem I reaction center in barley. Evidence for translational control.

The light-dependent accumulation of the P700 chlorophyll a protein of the photosystem I reaction center has been studied in greening barley (Hordeum vulgare L.) seedlings. Immunoblot analysis of total cellular protein fractions and immunogold labelling of the P700 chlorophyll a protein in ultrathin sections of Lowicryl-embedded leaf tissue revealed that the concentration of this chlorophyll-binding protein in plastids of dark-grown barley seedlings is below the limit of detection. Upon illumination with white light, a rapid accumulation of this protein is induced. This light effect seems not to be regulated at the level of transcription. The gene for the P700 chlorophyll a protein has been mapped within the large single-copy region of the plastid DNA of barley. High levels of transcripts of this gene are present already in dark-grown seedlings and remain fairly constant throughout an extended illumination period. Polysomes were isolated from etioplasts and chloroplasts. The same high relative concentration of mRNA encoding the P700 chlorophyll a protein was present in both polysome fractions. This result suggests that the light-dependent accumulation of the P700 chlorophyll a protein during chloroplast formation in barley seedlings is regulated at the translational, or posttranslational, level.

The distribution of NADPH-protochlorophyllide oxidoreductase in relation to chlorophyll accumulation along the barley leaf gradient.

The possible regulatory role of NADPH-protochlorophyllide oxidoreductase for chlorophyll accumulation has been investigated in barley plants. Within the primary leaf of etiolated plants the different maturation stages of etioplasts are found in a linear series with the youngest in cells near the base and the oldest in cells near the tip. This distribution of different plastid forms is paralleled by drastic differences in the NADPH-protochlorophyllide-oxidoreductase content of the plastids and their capacity to accumulate chlorophyll during illumination. The amount of enzyme and the rate of chlorophyll accumulation are highest in the mature etioplast in the tip of the leaf and both decline rapidly with decreasing age of the leaf tissue, being almost undetectable in the leaf base. The translatable mRNA coding for the enzyme shows a different distribution pattern within the leaf. The highest concentration is found in the middle part of the leaf while in the top part only traces of this mRNA are detectable. It is concluded that during leaf development the enzyme is synthesized rapidly only during a limited time period and that it is stored subsequently in the mature etioplast as a stable protein. The close correlation between the distribution of the enzyme within the barley leaf and that of the potential to accumulate chlorophyll during illumination would favour a control of chlorophyll accumulation by the amount of NADPH-protochlorophyllide oxidoreductase. Dark-grown plants which were exposed to far-red light were used to test this possibility. The far-red-absorbing form of phytochrome (Pfr) has an inverse effect on the kinetics of chlorophyll accumulation and the enzyme concentration. Our results indicate that the rate of chlorophyll accumulation in barley is not determined by the level of NADPH-protochlorophyllide oxidoreductase present in the leaves.

Light-induced changes in the distribution of the 36000-Mr polypeptide of NADPH-protochlorophyllide oxidoreductase within different cellular compartments of barley (Hordeum vulgare L.) : I. Localization by immunoblotting in isolated plastids and total leaf extracts.

Changes in the relative content of NADPH-protochlorophyllide oxidoreductase during the light-induced greening of barley plants were measured both in the total leaf extract as well as in intact and broken plastids. The enzyme protein was identified by its apparent molecular weight and its immunological crossreactivity with an antiserum directed against the NADPH-protochlorophyllide oxidoreductase. The monospecificity of the antiserum was tested by two different criteria: i. The antiserum was purified by affinity chromatography. ii. It was demonstrated that the antiserum crossreacts with only those polypeptides which appear to be enzymatically active. In the fraction of broken plastids isolated from leaves of briefly illuminated barley plants the concentration of the enzyme protein was reduced drastically. Our results indicate that this decrease in enzyme protein content is the consequence of an artificial proteolytic breakdown of the membrane-bound enzyme protein. In intact plastids and in the total leaf extract the concentration of the enzyme protein did not change dramatically during the first 4 to 6 h of illumination. However, when the exposure to continuous white light was extended further the concentration of the enzyme protein in intact plastids began to decline rapidly while in total leaf extracts the concentration remained almost constant for the next 10 h of light. These results indicate that part of the enzyme protein may be localized outside of the plastid compartment.

Light-induced changes in the distribution of the 36000-Mr polypeptide of NADPH-protochlorophyllide oxidoreductase within different cellular compartments of barley (Hordeum vulgare L.) : II. Localization by immunogold labelling in ultrathin sections.

The cellular distribution of the 36000-Mr polypeptide of NADPH-protochlorophyllide oxidoreductase has been determined in ultrathin sections of barley leaves by the method of immunogold labelling. In leaves of etiolated seedlings a large portion of the immunoreactive protein was localized within the prolamellar body. However, approximately one third of the total immunoreactive protein was present outside the plastid in the area of the plasmalemma. During illumination of etiolated seedlings the two polypeptide populations were differentially affected by light. While the concentration of the plastid-localized immunoreactive protein rapidly decreased and was hardly detectable after 16 h of continuous white-light treatment, the concentration of the extraplastidic polypeptide did not decline significantly during this illumination period. A similar distribution pattern of the immunoreactive polypeptide was also found in maize and rye. The chlorophyll-deficient barley mutant xantha-l(81) contained the immunoreactive 36000-Mr polypeptide, even though the prolamellar body was not detectable in etioplasts of this mutant. All of the immunoreactive polypeptide was localized outside the plastid in the area of the plasmalemma. Despite the apparent absence of the enzyme protein from the plastid, dark-grown mutant plants contained the same relative concentration of mRNA activity for the NADPH-protochlorophyllide oxidoreductase, which declined rapidly during illumination, as in wild-type plants. The antigenic properties and the apparent molecular weight of the plastid-localized NADPH-protochlorophyllide oxidoreductase and the 36000-Mr immunoreactive polypeptide outside the plastid were so similar as to indicate that the two proteins may be of common origin.

DNA binding factor GT-2 from Arabidopsis.

Complementary DNA clones encoding a DNA-binding factor have been obtained from Arabidopsis by DNA hybridization with a GT-2 factor cDNA clone from rice. The GT-2 gene appears to be present as a single copy in the Arabidopsis genome and is transcribed as a 2.1 kb mRNA which is not light-regulated. The longest open reading frame in the sequenced clones predicts a protein of 65 kDa, beginning with the first in-frame methionine. The protein contains basic, acidic, and proline/glutamine-rich motifs and has significant amino acid sequence homology to the rice GT-2 factor, including three regions of 50-75 amino acids each of greater than 60% identity. Two of these regions are predicted to form similar trihelix structures postulated to be involved in selective binding to specific variations of a GT-box motif DNA sequence found in the promoter regions of several plant genes. Except for weak similarity to a tobacco GT-box binding factor, GT-1a/B2F, Arabidopsis GT-2 has no similarity to other sequences in the databases. DNA-binding studies show that Arabidopsis GT-2 has binding characteristics similar to those of the rice GT-2 factor, but dissimilar to those of the tobacco GT-1a/B2F factor. The data indicate that a DNA-binding factor containing domains of similar structure and target-sequence specificity has been conserved between monocots and dicots.

The distribution of caprylate, caprate and laurate in lipids from developing and mature seeds of transgenic Brassica napus L.

The composition and positional distribution of lipids in developing and mature transgenic Brassica napus seeds accumulating up to 7 mol% of caprylate (8:0), 29 mol% caprate (10:0) or 63 mol% of laurate (12:0) were examined. The accumulation of 8:0 and 10:0 resulted from over-expression of the medium-chain-specific thioesterase (Ch FatB2) alone or together with the respective chain-length-specific condensing enzyme (Ch KASIV). Seeds containing high levels of 12:0 were obtained from plants expressing bay thioesterase (BTE) alone or crossed with a line over-expressing the coconut lysophosphatidic acid acyltransferase (LPAAT), an enzyme responsible for the increase in acylation of 12:0 at the sn-2 position. In all instances, 10:0 and 12:0 fatty acids were present in substantial amounts in phosphatidylcholine during seed development with a drastic decrease of 80-90% in mature seeds. At all stages of seed development however, 8:0 was barely detectable in this membrane lipid. Altogether, these results indicate that these transgenic seeds exclude and/or remove the medium-chain fatty acids from their membrane and that this mechanism(s) is more effective with the shorter-chain fatty acids. Furthermore, seeds of 8:0- and 10:0-producing lines had only negligible levels of these fatty acids present in the sn-2 position of the triacylglycerols. In contrast, all 12:0-producing seeds had a substantial amount of this fatty acid in the sn-2 position of the triacylglycerols, suggesting that the endogenous LPAAT is able to acylate 12:0 if no other acyl-CoA species are available.

ACX3, a novel medium-chain acyl-coenzyme A oxidase from Arabidopsis.

In a database search for homologs of acyl-coenzyme A oxidases (ACX) in Arabidopsis, we identified a partial genomic sequence encoding an apparently novel member of this gene family. Using this sequence information we then isolated the corresponding full-length cDNA from etiolated Arabidopsis cotyledons and have characterized the encoded recombinant protein. The polypeptide contains 675 amino acids. The 34 residues at the amino terminus have sequence similarity to the peroxisomal targeting signal 2 of glyoxysomal proteins, including the R-[I/Q/L]-X5-HL-XL-X15-22-C consensus sequence, suggesting a possible microsomal localization. Affinity purification of the encoded recombinant protein expressed in Escherichia coli followed by enzymatic assay, showed that this enzyme is active on C8:0- to C14:0-coenzyme A with maximal activity on C12:0-coenzyme A, indicating that it has medium-chain-specific activity. These data indicate that the protein reported here is different from previously characterized classes of ACX1, ACX2, and short-chain ACX (SACX), both in sequence and substrate chain-length specificity profile. We therefore, designate this new gene AtACX3. The temporal and spatial expression patterns of AtACX3 during development and in various tissues were similar to those of the AtSACX and other genes expressed in glyoxysomes. Currently available database information indicates that AtACX3 is present as a single copy gene.