GC-Skew and OriC in E. Coli

5 Jul 2017

GC-skew describes the equifrequency, or lack thereof, of G and C bases in a nucleotide sequence, defined by the following simple formula:

 

 G - C 

 G + C 

 

In [1], it is shown that there is a stark change in the GC-skew at the origin of replication (OriC) in the genomes of E.coli and other bacteria. This notion was later confirmed and extended in [2], where this same change was observed at the terminus of replication in E. coli.

 

The below image, taken from [2], shows the structure of the E. coli genome, and the loci of its origin and terminus of replication.

 

 

The are a number of bioinformatic tools that compute and plot skew data for any pair of bases:

The author of [1] went on to develop a tool with the precise aim of finding the locus of OriC in bacterial genomes, named Oriloc [3].

 

The only other similar tool I have come across is OriFinder [4]. Note that the same team have developed OriFinder 2 [5] as an equivalent for archaeal genomes.

 

[185]

 

References:

1. Lobry, J.R., 1996. Asymmetric substitution patterns in the two DNA strands of bacteria. Molecular biology and evolution, 13(5), pp.660-665.

2. Blattner, F.R., Plunkett, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F. and Gregor, J., 1997. The complete genome sequence of Escherichia coli K-12. science, 277(5331), pp.1453-1462.

3. Frank, A.C. and Lobry, J.R., 2000. Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics, 16(6), pp.560-561.

4. Gao, F. and Zhang, C.T., 2008. Ori-Finder: a web-based system for finding oriC s in unannotated bacterial genomes. BMC bioinformatics, 9(1), p.79.

5. Luo, H., Zhang, C.T. and Gao, F., 2014. Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes. Frontiers in microbiology, 5.

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PhDomics by Fatima