Putative essential and core-essential genes in Mycoplasma genomes

Abstract

Mycoplasma, which was used to create the first "synthetic life", has been an important species in the emerging field, synthetic biology. However, essential genes, an important concept of synthetic biology, for both M. mycoides and M. capricolum, as well as 14 other Mycoplasma with available genomes, are still unknown. We have developed a gene essentiality prediction algorithm that incorporates information of biased gene strand distribution, homologous search and codon adaptation index. The algorithm, which achieved an accuracy of 80.8% and 78.9% in self-consistence and cross-validation tests, respectively, predicted 5880 essential genes in the 16 Mycoplasma genomes. The intersection set of essential genes in available Mycoplasma genomes consists of 153 core essential genes. The predicted essential genes (available from pDEG, tubic.tju.edu.cn/pdeg) and the proposed algorithm can be helpful for studying minimal Mycoplasma genomes as well as essential genes in other genomes.

Figure 1. The flow chart of the proposed algorithm in training and prediction phases.

Figure 2. Accuracy indices and the ROC curve for the current algorithm.

(A) Sensitivity, specificity and positive prediction rate in relation to the parameter s defined in eq. (8). The value of s (s ≥ s₀) was chosen such that the sensitivity S_n is roughly equal to the specificity S_p. (B) The ROC curve (blue) and AUC (Area Under Curve). The red line denotes an extrapolation of the ROC curve to the point where 1 − S_p = 1. The AUC value is found to be 0.812.

Figure 3. The phylogenetic tree of the 18 Mycoplasma genomes based on the 16S rRNA.

The intersection set of (A) genes and (B) essential genes in the 18 Mycoplasma genomes. The numbers on the left indicate gene numbers in intersection sets between genomes, whereas those on the right denote total gene number in a genome. The intersection set of the 5880 predicted essential genes and those experimentally identified in M. genitalium and M. pulmonis genomes consists of 153 core essential genes for the Mycoplasma family.

Figure 4. Functional classification of genes in the M. genitalium genome based on COG.

(A) COG classification of core-essential, non-core-essential and non-essential genes in M. genitalium. (B) Distribution of COG classification of the 153 core-essential genes.