HIP1 propagates in cyanobacterial DNA via nucleotide substitutions but promotes excision at similar frequencies in Escherichia coli and Synechococcus PCC 7942

Abstract

SummaryThe sequence 5Ј-GCGATCGC-3Ј, designated HIP1, for highly iterated palindrome, was first identified at the borders of a gene-deletion event and subsequently shown to constitute up to 2.5% of the DNA in some cyanobacteria. It is now reported that HIP1 is polyphyletic, occurring in several distinct cyanobacterial lineages and not defining a clade. HIP1 does not introduce gaps into sequence alignments. It aligns with partial HIP1 sites in related sequences showing that it propagates by nucleotide substitutions rather than insertion. Constructs have been created to determine the frequencies at which deletion events occur between palindromes located within the selectable marker neo. Deletion between HIP1 sites was more frequent in Synechococcus PCC 7942 than deletion between control palindromes, 5Ј-CCGATCGG-3Ј, designated PAL0. However, this is not due to a recombinase that recognises HIP1 and is peculiar to cyanobacteria because similar deletion frequencies were detected in Escherichia coli. Furthermore, the frequency of deletion of DNA flanked asymmetrically by one HIP1 site and one PAL0 site was less than the frequency of deletion of DNA flanked symmetrically by identical copies of either palindrome. This is consistent with deletion by copy-choice.

Genetic diversity of inorganic carbon uptake systems causes variation in CO2 response of the cyanobacterium Microcystis

“…Other evidence for a common bicA history is that the detected small bicA fragments were very similar in these Eurasian strains, the African strain PCC 9443 and the Australian strain PCC 9808. The bicA fragments consisted of two short sequences at the 5 0 -end part of bicA (inset in Figure 1), whereas the area missing in between has the HIP1 sequences (5 0 -CGATCG-3 0 ) at the outer ends, which have been associated with early gene deletion events (Robinson et al, 1995(Robinson et al, , 1997. One exception was HUB 5-2-4, which contained the same bicA fragment but clustered together in the sbtAB tree with strains that had complete bicA.…”

Tansley Review No. 116

“…Other genomic rearrangements might also occur to bring about adaptation to changes in environmental conditions (Robinson et al, 1997). Furthermore, genetic differences might occur between cyanobacterial isolates in culture and those in symbiotic tissues of Azolla (Nierzwicki-Bauer & Bushnell, 1998) and the lichen Nephroma .…”

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

“…Regarding the origin and mobility of this sequence, it was suggested (based on the lack of gaps surrounding HIP1 motifs into aligned homologous sequences), that HIP1 propagates in cyanobacteria via nucleotide substitutions. 3 The rationale behind previous conclusion was as follow, if HIP1 would propagate through insertion events in coding sequences, downstream-frameshifts generated by this octanucleotide would have to be accommodate via additional insertion or deletions events. The analysis of 68 genes from Synechococcus PCC 7942 aligned to their corresponding homologs from Escherichia coli showed a lack of such additional deletion or insertions, therefore supporting the hypothesis of propagation via nucleotide substitutions.…”

“…The analysis of 68 genes from Synechococcus PCC 7942 aligned to their corresponding homologs from Escherichia coli showed a lack of such additional deletion or insertions, therefore supporting the hypothesis of propagation via nucleotide substitutions. 3 It is not known whether HIP1 confers some kind of advantage to its host, or if it is a molecular parasite (or the footprint left by a selfish genetic element). If HIP1 propagates through nucleotide substitutions (i.e., point mutations originating an HIP1 sequence are selected for), then a legitimate question is, what is the function encoded by this sequence?…”