Structure, organization and putative function of the genes identified within a 23.9-kb fragment from Arabidopsis thaliana chromosome IV

Microarray expression profiling and functional characterization of AtTPS genes: duplicated Arabidopsis thaliana sesquiterpene synthase genes At4g13280 and At4g13300 encode root-specific and wound-inducible (Z)-gamma-bisabolene synthases

The Arabidopsis thaliana genome contains at least 32 terpenoid synthase (AtTPS) genes [Aubourg et al., Mol. Genet. Genom. 267 (2002) 730] a few of which have recently been characterized. Based on hierarchical cluster analysis of AtTPS gene expression, measured by microarray profiling and validated with published expression data, we identified two groups of predominantly root expressed AtTPS genes containing five members with previously unknown biochemical functions (At4g13280, At4g13300, At5g48110, At1g33750, and At3g29410). Among the root expressed AtTPS genes, a pair of tandem-organized genes, At4g13280 (AtTPS12) and At4g13300 (AtTPS13), shares 91% predicted amino acid identity indicating recent gene duplication. Bacterial expression of cDNAs and enzyme assays showed that both At4g13280 and At4g13300 encode sesquiterpene synthases catalyzing the conversion of farnesyl diphosphate to (Z)-gamma-bisabolene and the additional minor products E-nerolidol and alpha-bisabolol. Expression of beta-glucuronidase (GUS) reporter gene fused to upstream genomic regions of At4g13280 or At4g13300 showed constitutive promoter activities in the cortex and sub-epidermal layers of Arabidopsis roots. In addition, highly localized promoter activities were found in leaf hydathodes and flower stigmata. Mechanical wounding of Arabidopsis leaves induced local expression of At4g13280 and At4g13300. The functional characterization of At4g13280 gene product AtTPS12 and At4g13230 gene product AtTPS13 as (Z)-gamma-bisabolene synthases, together with the recent characterization of two flower-specific AtTPS [At5g23960 and At5g44630; Tholl et al., Plant J. 42 (2005) 757], concludes the biochemical functional annotation of all four predicted Arabidopsis sesquiterpene synthase genes. Our data suggest biological functions for At4g13280 and At4g13300 in the rhizosphere with additional roles in aerial plant tissues.

DEFENSIVE RESIN BIOSYNTHESIS IN CONIFERS

Tree killing bark beetles and their vectored fungal pathogens are the most destructive agents of conifer forests worldwide. Conifers defend against attack by the constitutive and inducible production of oleoresin, a complex mixture of mono-, sesqui-, and diterpenoids that accumulates at the wound site to kill invaders and both flush and seal the injury. Although toxic to the bark beetle and fungal pathogen, oleoresin also plays a central role in the chemical ecology of these boring insects, from host selection to pheromone signaling and tritrophic level interactions. The biochemistry of oleoresin terpenoids is reviewed, and the regulation of production of this unusual plant secretion is described in the context of bark beetle infestation dynamics with respect to the function of the turpentine and rosin components. Recent advances in the molecular genetics of terpenoid biosynthesis provide evidence for the evolutionary origins of oleoresin and permit consideration of genetic engineering strategies to improve conifer defenses as a component of modern forest biotechnology.

Terpenoid secondary metabolism in Arabidopsis thaliana: cDNA cloning, characterization, and functional expression of a myrcene/(E)-beta-ocimene synthase

The Arabidopsis genome project has recently reported sequences with similarity to members of the terpene synthase (TPS) gene family of higher plants. Surprisingly, several Arabidopsis terpene synthase-like sequences (AtTPS) share the most identity with TPS genes that participate in secondary metabolism in terpenoid-accumulating plant species. Expression of a putative Arabidopsis terpene synthase gene, designated AtTPS03, was demonstrated by amplification of a 392-bp cDNA fragment using primers designed to conserved regions of plant terpene synthases. Using the AtTPS03 fragment as a hybridization probe, a second AtTPS cDNA, designated AtTPS10, was isolated from a jasmonate-induced cDNA library. The partial AtTPS10 cDNA clone contained an open reading frame of 1665 bp encoding a protein of 555 amino acids. Functional expression of AtTPS10 in Escherichia coli yielded an active monoterpene synthase enzyme, which converted geranyl diphosphate (C(10)) into the acyclic monoterpenes beta-myrcene and (E)-beta-ocimene and small amounts of cyclic monoterpenes. Based on sequence relatedness, AtTPS10 was classified as a member of the TPSb subfamily of angiosperm monoterpene synthases. Sequence comparison of AtTPS10 with previously cloned monoterpene synthases suggests independent events of functional specialization of terpene synthases during the evolution of terpenoid secondary metabolism in gymnosperms and angiosperms. Functional characterization of the AtTPS10 gene was prompted by the availability of Arabidopsis genome sequences. Although Arabidoposis has not been reported to form terpenoid secondary metabolites, the unexpected expression of TPS genes belonging to the TPSb subfamily in this species strongly suggests that terpenoid secondary metabolism is active in the model system Arabidopsis.

Diversity and variability of terpenoid defences in conifers: molecular genetics, biochemistry and evolution of the terpene synthase gene family in grand fir (Abies grandis)

This review focuses on the molecular genetics, biochemistry and evolution of terpenoid synthases relevant to terpenoid defences in conifers. In grand fir (Abies grandis) biosynthesis of terpenoids of the three classes of monoterpenes, sesquiterpenes and diterpenes is inducible by stem wounding at the level of gene activation and increase of enzyme activity of the respective terpene synthases. The monoterpene, sesquiterpene and diterpene synthases utilize prenyl diphosphates of appropriate size as substrates to generate the large diversity of carbon skeletons characteristic of the terpenoid resin of conifers. A large and diverse gene family of grand fir terpene synthases has been cloned and cDNAs are actively expressed in Escherichia coli for enzyme characterization. The monophyletic group of grand fir monoterpene, sesquiterpene and diterpene synthases represents both constitutively expressed and inducible genes encoding single product and multiple product enzymes. Several events of gene duplication and functional specialization of new synthases occurred during the evolution of terpenoid biosynthesis in grand fir, and gave rise to the enormous diversity and variability of this ancient and successful plant defence against herbivores and pathogens. The review concludes with a perspective of the biotechnological applications of terpenoid synthases for the genetic engineering of agricultural crops and forest trees.

Isolation and analysis of cDNA within a 300 kb Arabidopsis thaliana genomic region located around the 100 map unit of chromosome 1

In order to analyze the organization of genes located at the 100 map unit of chromosome 1, we screened cDNAs hybridized with approximately 300kb contiguous DNA using four P1 clones and one YAC clone. A total of 40 kinds of cDNA were isolated, and their entire sequences were determined. A comparison with the GenBank/EMBL database indicated that three of the cDNAs have been found in Arabidopsis, and that similar sequences to 18 of the cDNAs had been detected in Arabidopsis or other organisms. cDNAs were aligned on a physical map of the contiguous DNA, and the transcriptional direction of each cDNA was determined. This contiguous DNA contains a large direct repeat, which contains five genes. In addition, identical or very similar sequences to two cDNAs are located in a narrow region. Thus, a total of 50 genes were identified, and the gene density was revealed to be approximately one gene every 6kb. In addition, cDNA sequencing revealed the existence of unusual transcripts. A sequence of seven cDNAs seemed to have no significant open reading frames. Furthermore, the existence of antisense RNA and the possibility of alternative splicing were also revealed.

Plant MAP kinase kinase kinases structure, classification and evolution

The increasing number of reports describing plant MAP kinase signalling components reflects the cardinal role that MAP kinase pathways are likely to play during plant growth and development. Relationship and structural analyses of plant MAP kinase kinase kinase related cDNAs and genes established, on one hand, the PMEKKs, which may be distinguished into the alpha, beta, gamma, and zeta groups, and, on the other hand, the PRAFs that consist of the delta, eta and theta groups. Plant MAP3Ks are characterized by different primary structures, but conserved within a single group. A relationship analysis, which included animal, fungal and plant MAP3Ks, revealed a high degree of diversity among this biochemically established set of proteins, thus suggesting a range of biological functions. Four major families emerged, namely the MEKK/STE11, including the PMEKKs, the RAF, including the PRAFs, as well as the MLK and CDC7 families. These four families showed phylum-dependent distributions. Signature sequences characterizing the RAF family and the RAF subfamilies have been evidenced. However, no equivalent sequence motifs were identified for the MEKK/STE11 family, which is highly heterogeneous.

Structure and expression of three src2 homologues and a novel subfamily of flavoprotein monooxygenase genes revealed by the analysis of a 25kb fragment from Arabidopsis thaliana chromosome IV

Biological and computer-assisted analyses of a 25kb fragment from Arabidopsis thaliana chromosome IV led to the characterization of two multigene families and three novel orphan genes, not previously described. The first gene family named AtMO1-4 encodes monooxygenases, related to the prokaryotic salicylate hydroxylases. The second gene family contains three members, two on the analysed 25kb fragment and one on chromosome I. The latter three genes lack introns and are homologous to the previously studied Glycine max src2 gene which is overexpressed at low temperature. Gene expression and primary structure of the deduced proteins are described and compared. Three genes of unknown function, showing tissue specific expressions, are characterized on the 25kb fragment. Full length or partial cognate cDNAs have been sequenced for all the genes studied.

Characterisation of novel plant genes encoding MEKK/STE11 and RAF-related protein kinases

Various elements of the MAP kinase module have been isolated in plants. We describe here the characterisation of 14 new plant cDNAs and genes encoding putative MAP kinase kinase kinases (MAP3Ks) related to the MEKK/STE11 and RAF protein kinases. Plant MAP3Ks are characterised by a variety of primary structures conserved within closely related proteins. Southern blot analysis suggests that plant MAP3Ks are heterogenous in their genomic structure, existing either as single copy genes or as small gene families. An RT-PCR analysis showed that in Arabidopsis thaliana, all organs studied contain detectable levels of transcripts of each of the MAP3K genes identified; however, signals obtained with mature pollen were weak or non-existent except for AtMAP3Kgamma. None of the reported genes share a cell-cycle or a cold stress regulated expression.

Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction

While genomic sequences are accumulating, finding the location of the genes remains a major issue that can be solved only for about a half of them by homology searches. Prediction methods are thus required, but unfortunately are not fully satisfying. Most prediction methods implicitly assume a unique model for genes. This is an oversimplification as demonstrated by the possibility to group coding sequences into several classes in Escherichia coli and other genomes. As no classification existed for Arabidopsis thaliana, we classified genes according to the statistical features of their coding sequences. A clustering algorithm using a codon usage model was developed and applied to coding sequences from A. thaliana, E. coli, and a mixture of both. By using it, Arabidopsis sequences were clustered into two classes. The CU1 and CU2 classes differed essentially by the choice of pyrimidine bases at the codon silent sites: CU2 genes often use C whereas CU1 genes prefer T. This classification discriminated the Arabidopsis genes according to their expressiveness, highly expressed genes being clustered in CU2 and genes expected to have a lower expression, such as the regulatory genes, in CU1. The algorithm separated the sequences of the Escherichia-Arabidopsis mixed data set into five classes according to the species, except for one class. This mixed class contained 89 % Arabidopsis genes from CU1 and 11 % E. coli genes, mostly horizontally transferred. Interestingly, most genes encoding organelle-targeted proteins, except the photosynthetic and photoassimilatory ones, were clustered in CU1. By tailoring the GeneMark CDS prediction algorithm to the observed coding sequence classes, its quality of prediction was greatly improved. Similar improvement can be expected with other prediction systems.

Distribution of genes in the genome of Arabidopsis thaliana and its implications for the genome organization of plants

Previous work has shown that, in the large genomes of three Gramineae [rice, maize, and barley: 415, 2,500, and 5,300 megabases (Mb), respectively] most genes are clustered in long DNA segments (collectively called the "gene space") that represent a small fraction (12-24%) of nuclear DNA, cover a very narrow (0.8-1.6%) GC range, and are separated by vast expanses of gene-empty sequences. In the present work, we have analyzed the small (ca. 120 Mb) nuclear genome of Arabidopsis thaliana and shown that its organization is drastically different from that of the genomes of Gramineae. Indeed, (i) genes are distributed over about 85% of the main band of DNA in CsCl and cover an 8% GC range; (ii) ORFs are fairly evenly distributed in long (>50 kb) sequences from GenBank that amount to about 10 Mb; and (iii) the GC levels of protein-coding sequences (and of their third codon positions) are correlated with the GC levels of their flanking sequences. The different pattern of gene distribution of Arabidopsis compared with Gramineae appears to be because the genomes of the latter comprise (i) many large gene-empty regions separating gene clusters and (ii) abundant transposons in the intergenic sequences of gene clusters. Both sequences are absent or very scarce in the Arabidopsis genome. These observations provide a comparative view of angiosperm genome organization.

Structure and expression of an asparaginyl-tRNA synthetase gene located on chromosome IV of Arabidopsis thaliana and adjacent to a novel gene of 15 exons

The gene AtNS1 coding for an asparaginyl-tRNA synthetase and located on chromosome IV of Arabidopsis thaliana has been characterized. AtNS1 is the first asparaginyl-tRNA synthetase gene described in higher plants. The genomic environment of AtNS1 has been studied, as well as a partial cDNA of a second homologous asparaginyl-tRNA synthetase gene, AtNS2. Both AtNS1 and AtNS2 exhibit the highest similarity with prokaryotic homologues. A large novel gene of 15 exons, named AtG2484-1, is located adjacent to AtNS1. AtG2484-1 shows features rarely described in plants including large exons and one 3' non-coding exon. PCR and Northern analyses were carried out to obtain information about the expression of these genes in various A. thaliana tissues.

Plant terpenoid synthases: molecular biology and phylogenetic analysis

This review focuses on the monoterpene, sesquiterpene, and diterpene synthases of plant origin that use the corresponding C10, C15, and C20 prenyl diphosphates as substrates to generate the enormous diversity of carbon skeletons characteristic of the terpenoid family of natural products. A description of the enzymology and mechanism of terpenoid cyclization is followed by a discussion of molecular cloning and heterologous expression of terpenoid synthases. Sequence relatedness and phylogenetic reconstruction, based on 33 members of the Tps gene family, are delineated, and comparison of important structural features of these enzymes is provided. The review concludes with an overview of the organization and regulation of terpenoid metabolism, and of the biotechnological applications of terpenoid synthase genes.

Analysis of a 14-kb fragment containing a putative cell wall gene and a candidate for the ARA1, arabinose kinase, gene from chromosome IV of Arabidopsis thaliana

An Arabidopsis thaliana genomic DNA fragment of 14kb has been characterized in the framework of the E.S.S.A. programme. Computational and molecular approaches identified three novel gene sequences coding, respectively, for a protein of unknown function, a putative membrane-anchored cell wall protein and an arabinose kinase gene corresponding to the locus ARA1. The latter two genes named AtSEB1 and AtISA1 have been characterized in detail. They are very different in their organization, codon usage and level of expression. Homologues of AtSEB1 and AtISA1 have been identified. Sequence comparisons showed that the former genes contained a long 5' extension coding for an N-terminal domain probably specifying subcellular localization. Cloning and sequencing of the cognate cDNA for the AtISA1 homologue in A. thaliana, named GAL1, indicate that it encodes for a galactokinase-like protein. Our results highlight the integrative outcome of a systematic sequencing project in which links between biochemically and genetically characterized mutants, ESTs and genomic sequence data are generated.