Abstract
Sequences from the sugarcane expressed sequence tag (SUCEST) database were analyzed based on their identities to genes encoding chalcone-synthase-like enzymes. The sorghum (Sorghum bicolor) chalcone-synthase (CHS, EC 2.3.1.74) protein sequence (gi|12229613) was used to search the SUCEST database for clusters of sequencing reads that were most similar to chalcone synthase. We found 121 reads with homology to sorghum chalcone synthase, which we were then able to sort into 14 clusters which themselves were divided into two groups (group 1 and group 2) based on the similarity of their deduced amino acid sequences. Clusters in group 1 were more similar to the sorghum enzyme than those in group 2, having the consensus sequence of the active site of chalcone and stilbene synthase. Analysis of gene expression (based on the number of reads from a specific library present in each group) indicated that most of the group 1 reads were from sugarcane flower and root libraries. Group 2 clusters were more similar to the amino acid sequence of an uncharacterized pathogen-induced protein (PI1, gi|9855801) from the S. bicolor expressed sequence tag (EST) database. The group 2 clusters sequences and PI1 proteins are 90% identical, having two amino acid changes at the chalcone and stilbene synthase consensi but conserving the cysteine residue at the active site. The PI1 EST has not been previously associated with chalcone synthase and has a different consensus sequence from the previously described chalcone synthase of sorghum. Most of the group 2 reads were from libraries prepared from sugarcane roots and plants infected with Herbaspirillum rubrisubalbicans and Gluconacetobacter diazotroficans. Our results indicate that we have identified a sugarcane chalcone synthase similar to the pathogen-induced PI1 protein found in the sorghum cDNA libraries, and it appears that both proteins represent new members of the chalcone and stilbene synthase super-family.
Highlights
Chalcone synthase (CHS) operates early in the biosynthetic pathway of flavonoids, secondary metabolites which play important roles in the interactions which occur between plants and their environment
We found that 121 sugarcane expressed sequence tag (EST) showed high levels of sequence similarity to sorghum chalcone synthase
We found that the deduced amino acid sequence of sugarcane chalcone synthase 1 was 402 amino acids long and 97% identical to all seven S. bicolor chalcone synthases described, 95% identical to Zea mays chalcone synthase c2 (Franken et al, 1991) and 93% identical to Oryza sativa chalcone synthase
Summary
Chalcone synthase (CHS) operates early in the biosynthetic pathway of flavonoids, secondary metabolites which play important roles in the interactions which occur between plants and their environment. Phytoalexins (which play a role in plant-microbe interactions) can be derived from the flavonoid pathway and activation of the plant defense-response can often be detected by checking for the accumulation of chalcone synthase mRNA or by measuring the activity of this enzyme after inoculating a plant with microorganisms (Cui et al, 1996). The chalcone synthase genes present a high degree of sequence similarity at the amino acid level and have been the object of numerous studies in dicotyledonous plants, where up to seven copies have been identified in several species (Koes et al, 1987; 1989; Durbin et al, 2000). Most of the genera studied (i.e. Zea, Oryza, Hordeum and Secale) have two copies of the chalcone synthase gene (Wienand et a.l, 1986; Franken et al, 1991; Rhode et al, 1991), seven copies have been identified in Sorghum bicolor by Lo and Nicholson (1999), (gi|5305906|, gi|5305908|, gi|5305910|, gi|5305912|, gi|5305914|, gi|5305916|, gi|5305918|). Durbin et al (2000) have pointed out that chalcone synthase is suitable for studies of gene duplication and investigations on the origin of gene families
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