The chalcone synthase multigene family of Petunia hybrida (V30): sequence homology, chromosomal localization and evolutionary aspects

Type III polyketide synthase repertoire in Zingiberaceae: computational insights into the sequence, structure and evolution

Zingiberaceae or 'ginger family' is the largest family in the order 'Zingiberales' with more than 1300 species in 52 genera, which are mostly distributed throughout Asia, tropical Africa and the native regions of America with their maximum diversity in Southeast Asia. Many of the members are important spice, medicinal or ornamental plants including ginger, turmeric, cardamom and kaempferia. These plants are distinguished for the highly valuable metabolic products, which are synthesised through phenylpropanoid pathway, where type III polyketide synthase is the key enzyme. In our present study, we used sequence, structural and evolutionary approaches to scrutinise the type III polyketide synthase (PKS) repertoire encoded in the Zingiberaceae family. Highly conserved amino acid residues in the sequence alignment and phylogram suggested strong relationships between the type III PKS members of Zingiberaceae. Sequence and structural level investigation of type III PKSs showed a small number of variations in the substrate binding pocket, leading to functional divergence among these PKS members. Molecular evolutionary studies indicate that type III PKSs within Zingiberaceae evolved under strong purifying selection pressure, and positive selections were rarely detected in the family. Structural modelling and protein-small molecule interaction studies on Zingiber officinale PKS 'a representative from Zingiberaceae' suggested that the protein is comparatively stable without much disorder and exhibited wide substrate acceptance.

Tandemly arranged chalcone synthase A genes contribute to the spatially regulated expression of siRNA and the natural bicolor floral phenotype in Petunia hybrida

The natural bicolor floral traits of the horticultural petunia (Petunia hybrida) cultivars Picotee and Star are caused by the spatial repression of the chalcone synthase A (CHS-A) gene, which encodes an anthocyanin biosynthetic enzyme. Here we show that Picotee and Star petunias carry the same short interfering RNA (siRNA)-producing locus, consisting of two intact CHS-A copies, PhCHS-A1 and PhCHS-A2, in a tandem head-to-tail orientation. The precursor CHS mRNAs are transcribed from the two CHS-A copies throughout the bicolored petals, but the mature CHS mRNAs are not found in the white tissues. An analysis of small RNAs revealed the accumulation of siRNAs of 21 nucleotides that originated from the exon 2 region of both CHS-A copies. This accumulation is closely correlated with the disappearance of the CHS mRNAs, indicating that the bicolor floral phenotype is caused by the spatially regulated post-transcriptional silencing of both CHS-A genes. Linkage between the tandemly arranged CHS-A allele and the bicolor floral trait indicates that the CHS-A allele is a necessary factor to confer the trait. We suppose that the spatially regulated production of siRNAs in Picotee and Star flowers is triggered by another putative regulatory locus, and that the silencing mechanism in this case may be different from other known mechanisms of post-transcriptional gene silencing in plants. A sequence analysis of wild Petunia species indicated that these tandem CHS-A genes originated from Petunia integrifolia and/or Petunia inflata, the parental species of P. hybrida, as a result of a chromosomal rearrangement rather than a gene duplication event.

Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type III Polyketide Synthase Family

Type III polyketide synthases have a substantial role in the biosynthesis of various polyketides in plants and microorganisms. Comparative proteomic analysis of type III polyketide synthases showed evolutionarily and structurally related positions in a compilation of amino acid sequences from different families. Bacterial and fungal type III polyketide synthase proteins showed <50% similarity but in higher plants, it exhibited >80% among chalcone synthases and >70% in the case of non-chalcone synthases. In a consensus phylogenetic tree based on 1000 replicates; bacterial, fungal and plant proteins were clustered in separate groups. Proteins from bryophytes and pteridophytes grouped immediately near to the fungal cluster, demonstrated how evolutionary lineage has occurred among type III polyketide synthase proteins. Upon physicochemical analysis, it was observed that the proteins localized in the cytoplasm and were hydrophobic in nature. Molecular structural analysis revealed comparatively stable structure comprising of alpha helices and random coils as major structural components. It was found that there was a decline in the structural stability with active site mutation as prophesied by the in silico mutation studies.

Molecular linkage mapping and phylogeny of the chalcone synthase multigene family in soybean

Chalcone synthase (CHS), the key enzyme in the flavonoid biosynthesis pathway, is encoded by a multigene family, CHS1-CHS8 and dCHS1 in soybean. A tandem repeat of CHS1, CHS3 and CHS4, and dCHS1 that is believed to be located in the vicinity comprises the I locus that suppresses coloration of the seed coat. This study was conducted to determine the location of all CHS members by using PCR-based DNA markers. Primers were constructed based on varietal differences in either the nucleotide sequence of the 5'-upstream region or the first intron of two cultivars, Misuzudaizu, with a yellow seed coat (II), and Moshidou Gong 503, with a brown seed coat (ii). One hundred and fifty recombinant inbred lines that originated from a cross between these two cultivars were used for linkage mapping together with 360 markers. Linkage mapping confirmed that CHS1, CHS3, CHS4, dCHS1, and the I locus are located at the same position in molecular linkage group (MLG) A2. CHS5 was mapped at a distance of 0.3 cM from the gene cluster. CHS2 and CHS6 were located in the middle region of MLGs A1 and K, respectively, while CHS7 and CHS8 were found at the distal end of MLGs D1a and B1, respectively. Phylogenetic analysis indicated that CHS1, CHS3, CHS4, and CHS5 are closely related, suggesting that gene duplication may have occurred repeatedly to form the I locus. In addition, CHS7 and CHS8 located at the distal end and CHS2, CHS6, and CHS members around the I locus located around the middle of the MLG are also related. Ancient tetraploidization and repeated duplication may be responsible for the evolution of the complex genetic loci of the CHS multigene family in soybean.

Features of a 103-kb gene-rich region in soybean include an inverted perfect repeat cluster of CHS genes comprising the I locus

The I locus in soybean (Glycine max) corresponds to a region of chalcone synthase (CHS) gene duplications affecting seed pigmentation. We sequenced and annotated BAC clone 104J7, which harbors a dominant i(i) allele from Glycine max 'Williams 82', to gain insight into the genetic structure of this multigenic region in addition to examining its flanking regions. The 103-kb BAC encompasses a gene-rich region with 11 putatively expressed genes. In addition to six copies of CHS, these genes include: a geranylgeranyltransferase type II beta subunit (E.C.2.5.1.60), a beta-galactosidase, a putative spermine and (or) spermidine synthase (E.C.2.5.1.16), and an unknown expressed gene. Strikingly, sequencing data revealed that the 10.91-kb CHS1, CHS3, CHS4 cluster is present as a perfect inverted repeat separated by 5.87 kb. Contiguous arrangement of CHS paralogs could lead to folding into multiple secondary structures, hypothesized to induce deletions that have previously been shown to effect CHS expression. BAC104J7 also contains several gene fragments representing a cation/hydrogen exchanger, a 40S ribosomal protein, a CBL-interacting protein kinase, and the amino terminus of a subtilisin. Chimeric ESTs were identified that may represent read-through transcription from a flanking truncated gene into a CHS cluster, generating aberrant CHS RNA molecules that could play a role in CHS gene silencing.

A family of polyketide synthase genes expressed in ripening Rubus fruits

Quality traits of raspberry fruits such as aroma and color derive in part from the polyketide derivatives, benzalacetone and dihydrochalcone, respectively. The formation of these metabolites during fruit ripening is the result of the activity of polyketide synthases (PKS), benzalcetone synthase and chalcone synthase (CHS), during fruit development. To gain an understanding of the regulation of these multiple PKSs during fruit ripening, we have characterized the repertoire of Rubus PKS genes and studied their expression patterns during fruit ripening. Using a PCR-based homology search, a family of ten PKS genes (Ripks1-10) sharing 82-98% nucleotide sequence identity was identified in the Rubus idaeus genome. Low stringency screening of a ripening fruit-specific cDNA library, identified three groups of PKS cDNAs. Group 1 and 2 cDNAs were also represented in the PCR amplified products, while group 3 represented a new class of Rubus PKS gene. The Rubus PKS gene-family thus consists of at least eleven members. The three cDNAs exhibit distinct tissue-specific and developmentally regulated patterns of expression. RiPKS5 has high constitutive levels of expression in all organs, including developing flowers and fruits, while RiPKS6 and RiPKS11 expression is consistent with developmental and tissue-specific regulation in various organs. The recombinant proteins encoded by the three RiPKS cDNAs showed a typical CHS-type PKS activity. While phylogenetic analysis placed the three Rubus PKSs in one cluster, suggesting a recent duplication event, their distinct expression patterns suggest that their regulation, and thus function(s), has evolved independently of the structural genes themselves.

Organization of soybean chalcone synthase gene clusters and characterization of a new member of the family

Chalcone synthase (CHS; EC 2.3.1.74), the first committed enzyme of the multibranched pathway of flavonoid/isoflavonoid biosynthesis is encoded by a multigene family in soybean, (Glycine max L. Merrill). Our results suggest that this gene family comprises at least seven members, some of which are clustered. We have identified four chs clusters in the allo-tetraploid G. max genome and chs5, a newly characterized member of the chs gene family is present in two of them. We describe the complete nucleotide sequence of chs5, the identification of its immediate neighbors and the organization of the four hitherto identified chs clusters in the Gm genome.

Origin, distribution and mapping of RAPD markers from wildPetunia species inPetunia hybrida Hort lines

We have established the first linkage map forPetunia hybrida based upon both RAPD and phenotypical markers. The progeny studied consisted of 100 BC1 individuals derived from the [(St40xTlvl)xTlvl] back-cross. Each morphological marker has previously been mapped onto one of the seven chromosomes. The map consists of 35 RAPD loci of which 24 were affected onto chromosomes while 10 loci were not affected. The loci covered 262.9 cM with a mean distance of 8.2 cM. They are dispersed over seven linkage groups, of which six are carried on identified chromosomes. The RAPD markers were also applied on a set of tenP. hybrida, lines chosen for their diversity and on a set of seven wild species corresponding to the possible ancestors of theP. hybrida species. The markers were found both in the wild species as well as inP. hybrida lines indicating that they are inherited and are stable enough to establish similarities and to suggest relationships between species. Eight out of the ten lines carry different linkage groups of RAPD markers, which suggest that recombinant events occurred between chromosomes which originated in the wild species.

In Trifolium subterraneum, chalcone synthase is encoded by a multigene family

Chalcone synthase (CHS) catalyzes the first and key regulatory step in flavonoid biosynthesis. We report the existence and characterization of a CHS multigene family present in Trifolium subterraneum L. cultivar Karridale. The CHS family consists of at least four members, which are tightly clustered in a 15-kb region. The complete sequences of two of these genes (CHS1 and CHS2) are presented. The putative promoters of these genes have sequences which are homologous to those known, or implicated, in regulation of the expression of phenylpropanoid-encoding genes.

Stress responses in alfalfa (Medicago sativa L.). 15. Characterization and expression patterns of members of a subset of the chalcone synthase multigene family

We have identified five different full length chalcone synthase (CHS) cDNA clones from a cDNA library produced from transcripts isolated from an elicitor-treated alfalfa cell suspension culture. Nucleotide sequence similarity between the clones varied from 88-93%. Oligonucleotides based on divergent sequences in the 5'-untranslated regions of the clones could distinguish individual genes, or groups of genes, and their corresponding transcripts. Developmentally regulated expression of the CHS transcripts was predominantly in roots and root nodules; other unidentified members of the CHS gene family are expressed in stems, leaves and nodules. One of the CHS transcripts was strongly expressed in floral tissue. All the CHS transcripts studied were induced in elicitor-treated cell suspension cultures. Transcripts were also induced in roots in response to wounding or spraying with various elicitors, and in leaves infected with Phoma medicaginis (but not in wounded leaves). The induction kinetics of CHS2 transcripts were more rapid and/or transient than those of other members of the CHS family in CuCl2-treated roots and Phoma-infected leaves. The results are discussed in terms of the evolution and functions of the CHS gene family in legumes.