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

Life
Jeff Elhai

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 In some of these cases, it appears to have been replaced by a different GC-rich palindromic sequence, alternate HIPs.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.

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Citations

Aug 15, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Otilia Cheregi, Christiane Funk
Jul 3, 2019·BMC Microbiology·Ingeborg ScholzWolfgang R Hess
May 11, 2018·Applied Microbiology and Biotechnology·Annesha SenguptaPramod P Wangikar
Nov 25, 2016·Frontiers in Microbiology·Corinne Cassier-ChauvatFranck Chauvat
Jun 20, 2020·ACS Synthetic Biology·Annesha SenguptaPramod P Wangikar

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Datasets Mentioned

BETA
UTEX
2349

Software Mentioned

CyanoBIKE
BioBIKE
REBASE
SEQWARE
Gblocks
BLAST
PHYLIP
PhyML
Clustal W

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