Abundance and distribution of the highly iterated palindrome 1 (HIP1) among prokaryotes

Abstract

Abbreviations: HIP1, highly iterated palindrome 1; HGT, horizontal gene transfer; SDR, small dispersed repeat;OpcA, glucose 6-phosphate dehydrogenase assembly proteinWe have studied the abundance and phylogenetic distribution of the Highly Iterated Palindrome 1 (HIP1) among sequenced prokaryotic genomes. We show that an overrepresentation of HIP1 is exclusive of some lineages of cyanobacteria, and that this abundance was gained only once during evolution and was subsequently lost in the lineage leading to marine pico-cyanobacteria. We show that among cyanobacterial protein sequences with annotated Pfam domains, only OpcA (glucose 6-phosphate dehydrogenase assembly protein) has a phylogenetic distribution fully matching HIP1 abundance, suggesting a functional relationship; we also show that DAM methylase (an enzyme that has the four central nucleotides of HIP1 as is site of action) is present in all cyanobacterial genomes (independently of their HIP1 content) with the exception of marine pico-cyanobacteria whom might have lost this enzyme during the process of genome reduction. Our analyses also show that in some prokaryotic lineages (particularly in those species with large genomes), HIP1 is unevenly distributed between coding and non-coding DNA (being more common in coding regions; with the exception of Cyanobacteria Yellowstone B' and Synechococcus elongates where the reverse pattern is true). Finally, we explore the hypothesis that the HIP1 can be used as a molecular "water-mark" to identify horizontally transferred genes from cyanobacteria to other species.

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

“…A third class was described by Robinson et al (1995) [ 3 ], HIP1 (Highly Iterated Palindrome) sites found overrepresented in many cyanobacteria [ 3 , 4 ]. The sequence, GCGATCGC, is the same in all described instances [ 4 ], although a larger sequence, GGCGATCGCC, has been recognized in two cyanobacteria [ 2 , 5 ].…”

“…A third class was described by Robinson et al (1995) [ 3 ], HIP1 (Highly Iterated Palindrome) sites found overrepresented in many cyanobacteria [ 3 , 4 ]. The sequence, GCGATCGC, is the same in all described instances [ 4 ], although a larger sequence, GGCGATCGCC, has been recognized in two cyanobacteria [ 2 , 5 ]. Little is known about the biological significance of the sequence, but there is some indication that it may function in site-specific recombination in Synechococcus PCC 7002 [ 5 ] and (at a much lower efficiency) illegitimate recombination between cloned sequences in Synechococcus PCC 7942 and Escherichia coli [ 6 ].…”

“…A possible connection between HIP1 sequences and two DNA methyltransferases (MTases) has been previously noted [ 4 , 7 , 8 ]. The internal four nucleotides, GATC, is methylated by the MTase DmtA, found in Anabaena PCC 7120, an essential protein under standard laboratory conditions [ 7 ].…”

Genomic Fingerprinting Using Highly Repetitive Sequences to Differentiate Close Cyanobacterial Strains

“…The HIP primers used in this investigation were constructed on the basis of this frequently occurring octa palindromic sequence, which permits DNA amplification between adjacent repeated HIP sequences. The utility of HIP sequences in differentiating members of Anabaena has been reported earlier (Delaye and Moya, 2011). In a further modification of this technique, Shalini et al (2007) utilized a blend of HIP and random primer sets to create fingerprint patterns for Calothrix.…”

“…While there are no similar sequences to HIP1 in different organisms, the explanations behind this overrepresentation are obscure, although it is guessed that it might be a recombination hotspot. The HIP1 sequence can also be used to fingerprint organisms (Delaye and Moya, 2011). The HIP primers used in this investigation were constructed on the basis of this frequently occurring octa palindromic sequence, which permits DNA amplification between adjacent repeated HIP sequences.…”