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 In some of these cases, it appears to have been replaced by a different GC-rich palindromic sequence, alternate HIPs.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


Distributions of most overrepresented oligomers in cyanobacterial genomes. The most overrepresented of a specific class of oligomer was determined for each of 97 genomes. Filled boxes: number of most overrepresented oligomers not contained within HIP1. Unfilled boxes: number of most overrepresented oligomers contained within HIP1 (visible only when the number is higher than filled boxes). (A) Nondegenerate palindromic 6-mers, with a bin size of 1; (B) Palindromic 5-mers (the central nucleotide is either [AT] or [CG]), with a bin size of 0.1; (C) Degenerate palindromic 6-mers, with a bin size of 0.2. Oligomers not contained with HIP1 have been split between those in Group C1 and Gloeobacter (red) and those in other groups (blue).
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life-05-00921-f004: Distributions of most overrepresented oligomers in cyanobacterial genomes. The most overrepresented of a specific class of oligomer was determined for each of 97 genomes. Filled boxes: number of most overrepresented oligomers not contained within HIP1. Unfilled boxes: number of most overrepresented oligomers contained within HIP1 (visible only when the number is higher than filled boxes). (A) Nondegenerate palindromic 6-mers, with a bin size of 1; (B) Palindromic 5-mers (the central nucleotide is either [AT] or [CG]), with a bin size of 0.1; (C) Degenerate palindromic 6-mers, with a bin size of 0.2. Oligomers not contained with HIP1 have been split between those in Group C1 and Gloeobacter (red) and those in other groups (blue).

Mentions: There is nothing unusual about finding an overrepresented oligomer in a genome, but these three stand out as remarkable outliers. GGCGCC in Calothrix PCC 7103 is by far the most overrepresented 6-mer in all 97 genomes, 4-times as overrepresented as the next palindromic hexamer apart from the central 6-mer of HIP1 (Figure 4A). The O/E ratio of GGCGCC in the 19,301 nt available for Calothrix D253 is slightly lower — 15.5 — but it is still a decided outlier. Similarly, GCsGC of Cyanothece PCC 7822 is the most overrepresented palindromic 5-mer found in any of the cyanobacterial genomes (Figure 4B). Finally, rCCGGy of Oscillatoria PCC 10802 is the most overrepresented degenerate 6‑mer palindrome amongst all cyanobacteria outside of the picocyanobacteria, if one excludes those 6‑mers contained within HIP1 (Figure 4C).


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

Elhai J - Life (Basel) (2015)

Distributions of most overrepresented oligomers in cyanobacterial genomes. The most overrepresented of a specific class of oligomer was determined for each of 97 genomes. Filled boxes: number of most overrepresented oligomers not contained within HIP1. Unfilled boxes: number of most overrepresented oligomers contained within HIP1 (visible only when the number is higher than filled boxes). (A) Nondegenerate palindromic 6-mers, with a bin size of 1; (B) Palindromic 5-mers (the central nucleotide is either [AT] or [CG]), with a bin size of 0.1; (C) Degenerate palindromic 6-mers, with a bin size of 0.2. Oligomers not contained with HIP1 have been split between those in Group C1 and Gloeobacter (red) and those in other groups (blue).
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00921-f004: Distributions of most overrepresented oligomers in cyanobacterial genomes. The most overrepresented of a specific class of oligomer was determined for each of 97 genomes. Filled boxes: number of most overrepresented oligomers not contained within HIP1. Unfilled boxes: number of most overrepresented oligomers contained within HIP1 (visible only when the number is higher than filled boxes). (A) Nondegenerate palindromic 6-mers, with a bin size of 1; (B) Palindromic 5-mers (the central nucleotide is either [AT] or [CG]), with a bin size of 0.1; (C) Degenerate palindromic 6-mers, with a bin size of 0.2. Oligomers not contained with HIP1 have been split between those in Group C1 and Gloeobacter (red) and those in other groups (blue).
Mentions: There is nothing unusual about finding an overrepresented oligomer in a genome, but these three stand out as remarkable outliers. GGCGCC in Calothrix PCC 7103 is by far the most overrepresented 6-mer in all 97 genomes, 4-times as overrepresented as the next palindromic hexamer apart from the central 6-mer of HIP1 (Figure 4A). The O/E ratio of GGCGCC in the 19,301 nt available for Calothrix D253 is slightly lower — 15.5 — but it is still a decided outlier. Similarly, GCsGC of Cyanothece PCC 7822 is the most overrepresented palindromic 5-mer found in any of the cyanobacterial genomes (Figure 4B). Finally, rCCGGy of Oscillatoria PCC 10802 is the most overrepresented degenerate 6‑mer palindrome amongst all cyanobacteria outside of the picocyanobacteria, if one excludes those 6‑mers contained within HIP1 (Figure 4C).

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.