Document Type
Article
Original Publication Date
2015
Journal/Book/Conference Title
Life
Volume
5
DOI of Original Publication
10.3390/life5010921
Date of Submission
December 2015
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 In some of these cases, it appears to have been replaced by a different GC-rich palindromic sequence, alternate HIPs.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.
Rights
© 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).
Is Part Of
VCU Study of Biological Complexity Publications
Table S4
HIP-Suppl-Figures.pdf (1629 kB)
HIP Figures
Suppl-Table-S1-cb-data-150130.xlsx (28 kB)
Table S1
Suppl-Table-S2-Data-for-Fig2-and-FigS1-150212.xlsx (145 kB)
Table S2
Suppl-Table-S3-most-frequent-oligomers.xlsx (168 kB)
Comments
Originally published at http://dx.doi.org/10.3390/life5010921