PMC:3514855 / 25083-29392 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3514855","sourcedb":"PMC","sourceid":"3514855","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3514855","text":"4.1. Strain history\n‘PCC-M’ shows sequence differences in several genes compared with the reference sequence of ‘GT-Kazusa’ and also to the recently sequenced ‘GT-S’ strain. Kanesaki et al.9 concluded that 15 differences between the resequenced strains and the published GT-Kazusa sequence were annotation errors in the latter due to sequencing artefacts, a list to which we add two more putative errors in the database, differences #4 and #42 in Table 1. According to the proposed strain history in Ikeuchi and Tabata,8 the early division of Synechocystis sp. PCC 6803 into two branches occurred due to an insertion in spkA. Thus, our data suggest that the motile ‘PCC-M’ strain belongs to the motile PCC 6803 branch, whereas the non-motile ‘GT-Kazusa’, ‘GT-S’ and ‘GT-V’ strains are more closely related to each other and belong to the ATCC 27 184 branch. However, the 1-bp insertion in the pilC leading to ‘GT-Kazusa’ as described in the proposed strain history8 is not present in either ‘GT-S’ or ‘GT-V’, characterizing ‘GT-Kazusa’ as a more derived substrain.\nThat ‘PCC-M’ belongs to the motile PCC 6803 branch is further reinforced by our finding of six SNPs specifically shared between the ‘PCC-M’ and the ‘PCC-N and PCC-P’ substrains (Tables 1 and 2).9 These six SNPs are in slr1865, in sll1951, encoding a haemolysin-like protein, in ssr1176, encoding a transposase and, interestingly, in genes encoding sensor and/or regulatory proteins (slr1983, slr0222 and slr0302) (Tables 1 and 2) and must already have been present in the progenitor strain to ‘PCC-M’, ‘PCC-N’ and ‘PCC-P’. Additional support comes from the analysis of two larger indels (#2 and #6 in Table 1). The preceding paper, Kanesaki et al.,9 described difficulties in finding indels between direct repeat sequences such as slr1084 and slr2031 by short read type re-sequencing data. Therefore, these two regions were analysed by PCR and Sanger sequencing in addition to the re-sequencing analysis. Indeed, the finding of indels between direct repeat sequences in genes slr1084 and slr2031 turned out as not been straightforward in our analysis as well. Compared with the reference, we found in both cases the additional sequences of 102 and 154 bp to be present in ‘PCC-M’. This result is relevant for lineage relationships among substrains. The additional 102 bp in gene slr1084 are shared between ‘PCC-M’ and the other substrains ‘PCC-P’, ‘PCC-N’ and ‘GT-I’. Therefore, this must be a deletion in the lineage leading to GT-Kazusa and GT-S. In contrast, the additional 154 bp within and upstream of gene slr2031 are shared between ‘PCC-M’, ‘PCC-P’ and ‘PCC-N’ and are absent from all studied GT substrains. These 154 bp comprise the conserved start codon of slr2031 and extend the gene by 29 codons compared with ‘GT-Kazusa’. Hence, the lack of these 154 bp in GT strains indicate a functionally adverse deletion there. In fact, the 154-bp deletion in GT substrains was noticed before,46 as well as the activity of slr2031 in the original Synechocystis sp. PCC 6803 substrains.47 From these considerations, the tree shown in Fig. 3 can be derived. In this tree, ‘GT-Kazusa’ is displayed as the strain with the longest evolutionary distance from the original isolate, whereas the ‘PCC-M’ substrain belongs to the ‘PCC’ group of substrains and is probably close to the original characteristics. All strains belonging to the ‘PCC’ group of substrains exhibit twitching motility as was shown also for the original PCC strain deposited in the Pasteur Culture Collection6 with variations in the motility behaviour.48,49 Since ‘PCC-M’ shows motility and is tolerant to glucose, it appears physiologically as a sort of intermediate between the two major branches: the motile and GT branches, consistent with its characterization as being close to the original characteristics.\nFigure 3. Visualization of phylogenetic relationships between various strains of Synechocystis sp. PCC 6803. The occurrence of the identified SNPs and other known events are indicated along the branches. The eight events separating the ‘GT’ and ‘PCC’ strains from each other are given at the branch point where these two lineages split or on the respective branches where they occurred. Putative insertions and deletions are labelled ‘Ins’. and ‘Del’., respectively.","divisions":[{"label":"title","span":{"begin":6,"end":20}},{"label":"p","span":{"begin":21,"end":1065}}],"tracks":[{"project":"2_test","denotations":[{"id":"23069868-22193367-25970128","span":{"begin":190,"end":191},"obj":"22193367"},{"id":"23069868-16228363-25970129","span":{"begin":520,"end":521},"obj":"16228363"},{"id":"23069868-16228363-25970130","span":{"begin":965,"end":966},"obj":"16228363"},{"id":"23069868-22193367-25970131","span":{"begin":1260,"end":1261},"obj":"22193367"},{"id":"23069868-22193367-25970132","span":{"begin":1714,"end":1715},"obj":"22193367"},{"id":"23069868-16354116-25970133","span":{"begin":3582,"end":3584},"obj":"16354116"},{"id":"23069868-22065076-25970134","span":{"begin":3585,"end":3587},"obj":"22065076"}],"attributes":[{"subj":"23069868-22193367-25970128","pred":"source","obj":"2_test"},{"subj":"23069868-16228363-25970129","pred":"source","obj":"2_test"},{"subj":"23069868-16228363-25970130","pred":"source","obj":"2_test"},{"subj":"23069868-22193367-25970131","pred":"source","obj":"2_test"},{"subj":"23069868-22193367-25970132","pred":"source","obj":"2_test"},{"subj":"23069868-16354116-25970133","pred":"source","obj":"2_test"},{"subj":"23069868-22065076-25970134","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ccec93","default":true}]}]}}