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Life 2015, 5(1), 921-948; doi:10.3390/life5010921

Highly Iterated Palindromic Sequences (HIPs) and Their Relationship to DNA Methyltransferases

Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA
Academic Editors: John C. Meeks and Robert Haselkorn
Received: 1 January 2015 / Revised: 24 February 2015 / Accepted: 9 March 2015 / Published: 17 March 2015
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Abstract

The sequence GCGATCGC (Highly Iterated Palindrome, HIP1) is commonly found in high frequency in cyanobacterial genomes. An important clue to its function may be the presence of two orphan DNA methyltransferases that recognize internal sequences GATC and CGATCG. An examination of genomes from 97 cyanobacteria, both free-living and obligate symbionts, showed that there are exceptional cases in which HIP1 is at a low frequency or nearly absent. In some of these cases, it appears to have been replaced by a different GC-rich palindromic sequence, alternate HIPs. When HIP1 is at a high frequency, GATC- and CGATCG-specific methyltransferases are generally present in the genome. When an alternate HIP is at high frequency, a methyltransferase specific for that sequence is present. The pattern of 1-nt deviations from HIP1 sequences is biased towards the first and last nucleotides, i.e., those distinguish CGATCG from HIP1. Taken together, the results point to a role of DNA methylation in the creation or functioning of HIP sites. A model is presented that postulates the existence of a GmeC-dependent mismatch repair system whose activity creates and maintains HIP sequences. View Full-Text
Keywords: repeated sequence; methyltransferase; HIP1; cyanobacteria; restriction/modification repeated sequence; methyltransferase; HIP1; cyanobacteria; restriction/modification
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Elhai, J. Highly Iterated Palindromic Sequences (HIPs) and Their Relationship to DNA Methyltransferases. Life 2015, 5, 921-948.

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