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 In some of these cases, it appears to have been replaced by a different GC-rich palindromic sequence, alternate HIPs.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


Phylogenetic tree of 16S rDNA from organisms used in this study. The maximum likelihood tree was based on complete 16S rDNA sequences and rooted by Gloeobacter, in accordance with previous trees that used various eubacterial sequences as outgroups [11,12]. Organism abbreviations are explained in Supplemental Table S1. The categories of organisms, Groups A through C are taken from Shih et al. (2013) [11], Figure 1A. Branches are color-coded to facilitate identification with the categories shown to the right of the tree. Gray branches lead to organisms not in the set used by Shih et al. (2013). Circles at nodes indicate those that are supported by at least 70 of 100 bootstrap trials. Leptolyngbya Heron Island J was omitted from the construction of the tree because only 71% of its 16S rRNA sequence is known. However, by inspection of the aligned sequences, it is very close to Leptolyngbya PCC 6406. The bar represents the horizontal distance corresponding to 0.05 mutations per aligned nucleotide.
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life-05-00921-f001: Phylogenetic tree of 16S rDNA from organisms used in this study. The maximum likelihood tree was based on complete 16S rDNA sequences and rooted by Gloeobacter, in accordance with previous trees that used various eubacterial sequences as outgroups [11,12]. Organism abbreviations are explained in Supplemental Table S1. The categories of organisms, Groups A through C are taken from Shih et al. (2013) [11], Figure 1A. Branches are color-coded to facilitate identification with the categories shown to the right of the tree. Gray branches lead to organisms not in the set used by Shih et al. (2013). Circles at nodes indicate those that are supported by at least 70 of 100 bootstrap trials. Leptolyngbya Heron Island J was omitted from the construction of the tree because only 71% of its 16S rRNA sequence is known. However, by inspection of the aligned sequences, it is very close to Leptolyngbya PCC 6406. The bar represents the horizontal distance corresponding to 0.05 mutations per aligned nucleotide.

Mentions: The genomes considered in this study, taken from those currently in the CyanoBIKE database [10], are shown in a phylogenetic tree based on 16S rRNA sequences (Figure 1), with additional information provided in Supplemental Table S1. The tree adds 14 genomes to those in the 16S tree of Shih et al. (2013, their Figure S2) [11]. The two trees are completely concordant, except for a discrepancy in the placement of Prochlorococcus marinus CCMP 1375 (ss120), and both suffer from low bootstrap support, as compared to the tree constructed by Shih et al. [11] by the alignment of conserved protein. The differences between the 16S and protein trees (seen in Figure 1 as branches with anomalous colors) are minor and unimportant for this study).


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

Elhai J - Life (Basel) (2015)

Phylogenetic tree of 16S rDNA from organisms used in this study. The maximum likelihood tree was based on complete 16S rDNA sequences and rooted by Gloeobacter, in accordance with previous trees that used various eubacterial sequences as outgroups [11,12]. Organism abbreviations are explained in Supplemental Table S1. The categories of organisms, Groups A through C are taken from Shih et al. (2013) [11], Figure 1A. Branches are color-coded to facilitate identification with the categories shown to the right of the tree. Gray branches lead to organisms not in the set used by Shih et al. (2013). Circles at nodes indicate those that are supported by at least 70 of 100 bootstrap trials. Leptolyngbya Heron Island J was omitted from the construction of the tree because only 71% of its 16S rRNA sequence is known. However, by inspection of the aligned sequences, it is very close to Leptolyngbya PCC 6406. The bar represents the horizontal distance corresponding to 0.05 mutations per aligned nucleotide.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00921-f001: Phylogenetic tree of 16S rDNA from organisms used in this study. The maximum likelihood tree was based on complete 16S rDNA sequences and rooted by Gloeobacter, in accordance with previous trees that used various eubacterial sequences as outgroups [11,12]. Organism abbreviations are explained in Supplemental Table S1. The categories of organisms, Groups A through C are taken from Shih et al. (2013) [11], Figure 1A. Branches are color-coded to facilitate identification with the categories shown to the right of the tree. Gray branches lead to organisms not in the set used by Shih et al. (2013). Circles at nodes indicate those that are supported by at least 70 of 100 bootstrap trials. Leptolyngbya Heron Island J was omitted from the construction of the tree because only 71% of its 16S rRNA sequence is known. However, by inspection of the aligned sequences, it is very close to Leptolyngbya PCC 6406. The bar represents the horizontal distance corresponding to 0.05 mutations per aligned nucleotide.
Mentions: The genomes considered in this study, taken from those currently in the CyanoBIKE database [10], are shown in a phylogenetic tree based on 16S rRNA sequences (Figure 1), with additional information provided in Supplemental Table S1. The tree adds 14 genomes to those in the 16S tree of Shih et al. (2013, their Figure S2) [11]. The two trees are completely concordant, except for a discrepancy in the placement of Prochlorococcus marinus CCMP 1375 (ss120), and both suffer from low bootstrap support, as compared to the tree constructed by Shih et al. [11] by the alignment of conserved protein. The differences between the 16S and protein trees (seen in Figure 1 as branches with anomalous colors) are minor and unimportant for this study).

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.