Trimer Distribution Patterns in the Protein Sense and Antisense Sequences on the two Replichores of the Burkholderia Lata Chromosomes

Abstract

Burkholderia lata is a bacterium whose cell has three circular chromosomes, which are different in both size and nucleotide sequence. Each chromosome has a replication origin and a replication terminus, which divide the chromosome into two halves, forming the two replichores during the process of DNA replication. The complete bacterial chromosomal sequence is made of protein sense and antisense sequences, intergenic sequences, and sequences that encode for ribosomal RNAs and transfer RNAs. The natural nucleotide distribution in the bacterial chromosome has not much been known, while it is vital to the DNA replication rate, the cell division process and the chromosomal stability, which can in turn exert effects on the success of the genetic experiments manipulating the bacterial chromosomes. We used computer, and randomly chose a pair of trimer/trimer's reverse complement, GCG/CGC, among 32 possible trimer/trimer's reverse complement pairs, to perform our investigation on their distribution in the protein sense and antisense sequences of each of the B. lata chromosomes. We found that, although the chromosomes were different in size and nucleotide sequence, the distribution patterns of the GCG and CGC were the same in all these chromosomes, in that the frequencies of certain distances (frequencies of D) between the adjacent GCGs in the sense sequences (S) on one replichore (R1) of a chromosome were almost similar to those between the adjacent CGCs in the antisense sequences (AS) on the other replichore (R2) of that chromosome; also, the frequencies of D between the adjacent GCGs in the AS on R1 were almost similar to those between the adjacent CGCs in the S on R2, and vice versa. This finding provides key information of the natural nucleotide distribution in the bacterial chromosomes, which can help in experimental design for success in manipulation of the bacterial chromosomal sequences or in evolutionary analysis of protein sequences.