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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 In some of these cases, it appears to have been replaced by a different GC-rich palindromic sequence, alternate HIPs.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 HIP1 and other oligomers in cyanobacterial genomes. The O/E ratio (observed/expected counts) (A) and filtered normalized counts (B) of specific sequences are shown for 97 genomes, presented on the x-axis in phylogenetic order according to the tree given in Figure 1. The calculations are described in the Methods section, and the underlying numbers are given in Supplemental Table S2. Calculating expectations from first-order or second-order Markov analyses (thereby taking into account dinucleotide- and trinucleotide-frequencies) produces qualitatively similar graphs (see Supplemental Figure S1 and Supplemental Table S2). Certain genomes of interest are marked with letters a through w, and their identities are given in Table 2.
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life-05-00921-f002: Occurrences of HIP1 and other oligomers in cyanobacterial genomes. The O/E ratio (observed/expected counts) (A) and filtered normalized counts (B) of specific sequences are shown for 97 genomes, presented on the x-axis in phylogenetic order according to the tree given in Figure 1. The calculations are described in the Methods section, and the underlying numbers are given in Supplemental Table S2. Calculating expectations from first-order or second-order Markov analyses (thereby taking into account dinucleotide- and trinucleotide-frequencies) produces qualitatively similar graphs (see Supplemental Figure S1 and Supplemental Table S2). Certain genomes of interest are marked with letters a through w, and their identities are given in Table 2.

Mentions: To lay the foundation for a detailed assessment of exceptions to the general rule of highly overrepresented HIP1 sequences in cyanobacteria, I examined the oligonucleotide content of 97 genomes. The abundance of oligonucleotide sequences may be expressed as the count of the sequence (normalized to some standard length) or the observed number of instances in a genome divided by the number expected based on genomic characteristics (the O/E ratio). The former quantity may conceivably be closer to what is physiologically important, and the latter quantity distinguishes meaningful occurrences from those that might arise by chance and therefore indicates either selection or heightened production. The expected number of occurrences was calculated on the basis of nucleotide frequency. The O/E ratio is shown for HIP1 sequences in cyanobacteria in Figure 2A and the count of HIP1 sequences normalized to genome length shown in Figure 2B (red lines in both cases).


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

Elhai J - Life (Basel) (2015)

Occurrences of HIP1 and other oligomers in cyanobacterial genomes. The O/E ratio (observed/expected counts) (A) and filtered normalized counts (B) of specific sequences are shown for 97 genomes, presented on the x-axis in phylogenetic order according to the tree given in Figure 1. The calculations are described in the Methods section, and the underlying numbers are given in Supplemental Table S2. Calculating expectations from first-order or second-order Markov analyses (thereby taking into account dinucleotide- and trinucleotide-frequencies) produces qualitatively similar graphs (see Supplemental Figure S1 and Supplemental Table S2). Certain genomes of interest are marked with letters a through w, and their identities are given in Table 2.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00921-f002: Occurrences of HIP1 and other oligomers in cyanobacterial genomes. The O/E ratio (observed/expected counts) (A) and filtered normalized counts (B) of specific sequences are shown for 97 genomes, presented on the x-axis in phylogenetic order according to the tree given in Figure 1. The calculations are described in the Methods section, and the underlying numbers are given in Supplemental Table S2. Calculating expectations from first-order or second-order Markov analyses (thereby taking into account dinucleotide- and trinucleotide-frequencies) produces qualitatively similar graphs (see Supplemental Figure S1 and Supplemental Table S2). Certain genomes of interest are marked with letters a through w, and their identities are given in Table 2.
Mentions: To lay the foundation for a detailed assessment of exceptions to the general rule of highly overrepresented HIP1 sequences in cyanobacteria, I examined the oligonucleotide content of 97 genomes. The abundance of oligonucleotide sequences may be expressed as the count of the sequence (normalized to some standard length) or the observed number of instances in a genome divided by the number expected based on genomic characteristics (the O/E ratio). The former quantity may conceivably be closer to what is physiologically important, and the latter quantity distinguishes meaningful occurrences from those that might arise by chance and therefore indicates either selection or heightened production. The expected number of occurrences was calculated on the basis of nucleotide frequency. The O/E ratio is shown for HIP1 sequences in cyanobacteria in Figure 2A and the count of HIP1 sequences normalized to genome length shown in Figure 2B (red lines in both cases).

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.