Analysis of Heat Shock Proteins Based on Amino Acids for the Tomato Genome

Abstract

This research aimed to investigate heat shock proteins in the tomato genome through the analysis of amino acids. The highest length among sequences was found in seq19 with 3534 base pairs. This seq19 was reported and contained a family of proteins known as HsfA that have a domain of transcriptional activation for tolerance to heat and other abiotic stresses. The values of the codon adaptation index (CAI) ranged from 0.80 in Seq19 to 0.65 in Seq10, based on the mRNA of heat shock proteins for tomatoes. Asparagine (AAT, AAC), aspartic acid (GAT, GAC), phenylalanine (TTT, TTC), and tyrosine (TAT, TAC) have relative synonymous codon usage (RSCU) values bigger than 0.5. In modified relative codon bias (MRCBS), the high gene expressions of the amino acids under heat stress were histidine, tryptophan, asparagine, aspartic acid, lysine, phenylalanine, isoleucine, cysteine, and threonine. RSCU values that were less than 0.5 were considered rare codons that affected the rate of translation, and thus selection could be effective by reducing the frequency of expressed genes under heat stress. The normal distribution of RSCU shows about 68% of the values drawn from the standard normal distribution were within 0.22 and -0.22 standard deviations that tend to cluster around the mean. The most critical component based on principal component analysis (PCA) was the RSCU. These findings would help plant breeders in the development of growth habits for tomatoes during breeding programs.

Keywords: amino acids; codon adaptation index; modified relative codon bias; principal component analysis; relative synonymous codon usage.

Figure 1

The RSCU mean in heat shock protein sequences based on mRNA for the Solanum lycopersicum cultivar Heinz 1706, excluding Methionine and Tryptophan, with standard error shown by the red line and label with standard deviation (±).

Figure 2

The normal distribution of the RSCU values in heat shock protein sequences based on mRNA for the Solanum lycopersicum cultivar Heinz 1706.

Figure 3

The MRCBS mean in heat shock protein sequences for the Solanum lycopersicum cultivar Heinz 1706, excluding Methionine and Tryptophan, with standard error shown by the red line and label with standard deviation (±).

Figure 4

The percentage of two dominations explains variability through principal components for 19 mRNA sequences related to heat shock proteins for the Solanum lycopersicum cultivar Heinz 1706, the right legend shows the contributions of variables to PCs. Dim1 expresses dimension 1 while Dim2 expresses dimension 2.