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

Elhai J - Life (Basel) (2015)

Bottom Line: The sequence GCGATCGC (Highly Iterated Palindrome, HIP1) is commonly found in high frequency in cyanobacterial genomes.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 Article: PubMed Central - PubMed

Affiliation: Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA. ElhaiJ@vcu.edu.

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 In some of these cases, it appears to have been replaced by a different GC-rich palindromic sequence, alternate HIPs.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

No MeSH data available.


Occurrences of highly iterated palindromes and the enzymes that may recognize them.
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life-05-00921-f005: Occurrences of highly iterated palindromes and the enzymes that may recognize them.

Mentions: As previously noted [4], dmtA, a gene capable of encoding a type II alpha m6A MTase that recognizes GATC within HIP1 sites, is found in almost all cyanobacteria outside of Group C1 (Figure 5, column 3). The sole exceptions are Mastigocladopsis repens PCC 10914, whose incomplete genome sequence shows no sign of any recognizable GATC-specific MTase, Trichodesmium erythreum IMS101, whose gene is interrupted at the 17th codon by an apparent retroelement (thereby deleting the conserved Motif X), and UCYN-A, whose gene suffers from a frame shift that leads to the loss of the final 51 amino acids. Even the two Gloeobacter strains possess DmtA orthologs. The phylogeny of the DmtA proteins overall does not match the phylogeny of the strains (Supplemental Figure S2A), indicating multiple instances of horizontal gene transfer. Some genomes have two versions of GATC-methylating proteins (Figure 5, columns 3 and 4), in some cases similar to the highly unusual enzyme DmtE [7].


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

Elhai J - Life (Basel) (2015)

Occurrences of highly iterated palindromes and the enzymes that may recognize them.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390886&req=5

life-05-00921-f005: Occurrences of highly iterated palindromes and the enzymes that may recognize them.
Mentions: As previously noted [4], dmtA, a gene capable of encoding a type II alpha m6A MTase that recognizes GATC within HIP1 sites, is found in almost all cyanobacteria outside of Group C1 (Figure 5, column 3). The sole exceptions are Mastigocladopsis repens PCC 10914, whose incomplete genome sequence shows no sign of any recognizable GATC-specific MTase, Trichodesmium erythreum IMS101, whose gene is interrupted at the 17th codon by an apparent retroelement (thereby deleting the conserved Motif X), and UCYN-A, whose gene suffers from a frame shift that leads to the loss of the final 51 amino acids. Even the two Gloeobacter strains possess DmtA orthologs. The phylogeny of the DmtA proteins overall does not match the phylogeny of the strains (Supplemental Figure S2A), indicating multiple instances of horizontal gene transfer. Some genomes have two versions of GATC-methylating proteins (Figure 5, columns 3 and 4), in some cases similar to the highly unusual enzyme DmtE [7].

Bottom Line: The sequence GCGATCGC (Highly Iterated Palindrome, HIP1) is commonly found in high frequency in cyanobacterial genomes.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 Article: PubMed Central - PubMed

Affiliation: Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA. ElhaiJ@vcu.edu.

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.

No MeSH data available.