On the biased nucleotide composition of the human coronavirus RNA genome

Abstract

We investigated the nucleotide composition of the RNA genome of the six human coronaviruses. Some general coronavirus characteristics were apparent (e.g. high U, low C count), but we also detected species-specific signatures. Most strikingly, the high U and low C proportions are quite variable and act like communicating vessels, C goes down when U goes up and vice versa. U ranges among virus isolates from 30.7% to 40.3%, and C makes the opposite movement from 20.0% to 12.9%, respectively. The nucleotide biases are more pronounced in the unpaired regions of the structured RNA genome, which may suggest a certain biological function for these distinctive sequence signatures. Coronaviruses have an atypical codon usage that has been linked to mutational events operating on the viral RNA genome on an evolutionary time scale. We suggest that the atypical nucleotide bias may serve a distinct biological function and that it is the direct cause of the characteristic codon usage in these viruses. The relevance for evolution of the novel human pathogens MERS and SARS is discussed.

Keywords: Coronavirus; MERS; Nucleotide signature; RNA genome; SARS.

Fig. 1

Summary of the nucleotide composition of coronavirus RNA genomes. A and G proportions are relatively invariant among coronaviruses, while in contrast U and C are highly variable and represent communicating vessels.

Fig. 2

Basepair composition in RNA structure model of MERS, HKU and HIV-1. Only the top MFold predictions were analyzed. Coronavirus RNA genomes (30,000 nts) were split in four fragments (3 × 8500 + rest) with 500-nts overlaps.

Fig. 3

Skew analysis of RNA genomes of MERS and HKU. Skew values (N1 − N2)/(N1 + N2) have been calculated in overlapping windows along the sequence (“all nts”, “ds nts” and “ss nts”). Window size was set at 1% of the length of the sequence with a step size of 20% of the window size resulting in approximately 500 datapoints comprising the X-axis. We used the same Y-axis for the cumulative skew values to allow a direct comparison of the compositional signatures of different coronavirus RNA genomes. It should be noted that the labels next to each line do not indicate a basepair, but refer to the two nucleotides for which the skew values were calculated.

Fig. 4

Codon ENC analysis of MERS and HKU. The effective number of codons (ENC-values, Y-axis) of coronavirus genes was plotted against the GC-content at the 3rd synonymous codon positions (GC3-values, X-axis). The continuous line indicates theoretical ENC values with random codon usage as a function of GC3. Deviation from this line in the direction of lower ENC-values points to translational selection acting in favor of a preferred set of codons. Codon usage data for the nuclear genes of the host species were obtained from the following numbers of codons (number of genes in parentheses): human: 40,662,582 (93,487), dromedary: 6414 (21) and bats (3 species): 3522 (10).