Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method

Feng-Biao Guo,Xiu-Juan Yu

doi:10.1186/1471-2164-8-366

Abstract

BackgroundThe nucleotide compositional asymmetry between the leading and lagging strands in bacterial genomes has been the subject of intensive study in the past few years. It is interesting to mention that almost all bacterial genomes exhibit the same kind of base asymmetry. This work aims to investigate the strand biases in Chlamydia muridarum genome and show the potential of the Z curve method for quantitatively differentiating genes on the leading and lagging strands.ResultsThe occurrence frequencies of bases of protein-coding genes in C. muridarum genome were analyzed by the Z curve method. It was found that genes located on the two strands of replication have distinct base usages in C. muridarum genome. According to their positions in the 9-D space spanned by the variables u1 – u9 of the Z curve method, K-means clustering algorithm can assign about 94% of genes to the correct strands, which is a few percent higher than those correctly classified by K-means based on the RSCU. The base usage and codon usage analyses show that genes on the leading strand have more G than C and more T than A, particularly at the third codon position. For genes on the lagging strand the biases is reverse. The y component of the Z curves for the complete chromosome sequences show that the excess of G over C and T over A are more remarkable in C. muridarum genome than in other bacterial genomes without separating base and/or codon usages. Furthermore, for the genomes of Borrelia burgdorferi, Treponema pallidum, Chlamydia muridarum and Chlamydia trachomatis, in which distinct base and/or codon usages have been observed, closer phylogenetic distance is found compared with other bacterial genomes.ConclusionThe nature of the strand biases of base composition in C. muridarum is similar to that in most other bacterial genomes. However, the base composition asymmetry between the leading and lagging strands in C. muridarum is more significant than that in other bacteria. It's supposed that the remarkable strand biases of G/C and T/A are responsible for the appearance of separate base or codon usages in C. muridarum. On the other hand, the closer phylogenetic distance among the four bacterial genomes with separate base and/or codon usages is necessary rather than occasional. It's also shown that the Z curve method may be more sensitive than RSCU when being used to quantitatively analyze DNA sequences.

Highlights

The nucleotide compositional asymmetry between the leading and lagging strands in bacterial genomes has been the subject of intensive study in the past few years
It is interesting that almost all bacterial genomes exhibit the same kind of asymmetry [3,5,8,9] i.e., there is an excess of nucleotides G relative to C in the leading strand and of C to G in the lagging strand, which is frequently accompanied by an abundance of T over A in the leading strand [3,8,9,10,11]
We show that C. muridarum genes have two separate base usages depending on whether the gene is transcribed on the leading or lagging strand, using the Z curve and Correspondence analysis (CA) methods (Different from [19,20,21], where CA of RSCU was carried out)

Summary

Introduction

The nucleotide compositional asymmetry between the leading and lagging strands in bacterial genomes has been the subject of intensive study in the past few years. The compositional asymmetry between the leading and lagging strands in bacterial genomes has been the subject of intensive study in the past few years [1,2,3,4,5,6,7,8,9,10,11]. Several plausible explanations have been proposed that account for the biases in base composition, which have been partly summarized in four recent papers [5,7,8,9] It seems that the cytosine deamination theory enjoys the most attention among the theories aimed at explaining strand biases [6,9]. The C to T mutation occurs more frequently in the leading stand than in the lagging strand and the excesses of G(C) relative to C(G) and T(A) relative to A(T) are formed in the leading(lagging) strand

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