PMC:3514855 / 17277-19677 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":"3.3. Point mutations in IGRs\nCompared with the reference, eight SNPs are located in IGRs, three of these (#7, 24 and 36) are ‘PCC-M’ specific. One of these (#36 in Table 1) SNPs is predicted to affect one of the recently reported cis-antisense RNAs.33 The additional A between positions 3194022 and 3194023 is located in the IGR between genes slr0533 and slr0534, encoding histidine kinase 10 (Hik10) and the soluble lytic transglycosylase Slt. On the reverse strand, the additional T falls within the predicted −10 element of the slr0534_as3 promoter. Instead of the high-scoring CATAAT,33 the motif is changed to ATTAAT. Hence, a modulation of slr0534_as3 expression compared with the reference is possible. In contrast to its designation, this cis-antisense RNA overlaps the 3′ end of genes slr0533 and hik10 (due to an error in the annotation used as the reference). In microarray analyses, slr0534_as3 of strain ‘PCC-M’ was found to be moderately to highly expressed under four tested conditions. Compared with the accumulation of the hik10 mRNA, it appeared even stronger.33 A function for Hik10 has been found in the perception of salt stress or transduction of the signal.35 The slr0534_as3 transcript may play a silencing role with regard to hik10 under non-inducing conditions. Mutation of its promoter element may hence cause a physiological effect in the salt stress response.\nTwo other SNPs (at positions 831 647 and 2 400 722; #7 and #24 in Table 1) could have an impact on the promoter strength or the regulation of the genes infA and glcP. For glcP, the initiation site of transcription was mapped to position 2 400 66633 and for infA to position 831 635 (unpublished). Thus, these two SNPs are located 12 and 56 nt upstream of the respective initiation site of transcription. In the case of the infA promoter, the transition replaces a nucleotide within the putative −10 element, changing it from TGTGAT to TATGAT, a much more typical motif for a −10 element in Synechocystis.33 The mutation 56 nt upstream of the initiation site of transcription of glcP might be functionally relevant as well. The gene product, a glucose transporter, is directly relevant for the physiological ability to use glucose; its gene expression is affected by mutation of the gene for the AbrB-type transcription factor Sll0822.36 The region at position −56 might well be part of the recognized sequence.","divisions":[{"label":"title","span":{"begin":6,"end":29}},{"label":"p","span":{"begin":30,"end":1389}}],"tracks":[{"project":"2_test","denotations":[{"id":"23069868-21245330-25970113","span":{"begin":250,"end":252},"obj":"21245330"},{"id":"23069868-21245330-25970114","span":{"begin":589,"end":591},"obj":"21245330"},{"id":"23069868-21245330-25970115","span":{"begin":1079,"end":1081},"obj":"21245330"},{"id":"23069868-15805106-25970116","span":{"begin":1181,"end":1183},"obj":"15805106"},{"id":"23069868-21245330-25970117","span":{"begin":1633,"end":1638},"obj":"21245330"},{"id":"23069868-21245330-25970118","span":{"begin":1994,"end":1996},"obj":"21245330"},{"id":"23069868-18667724-25970119","span":{"begin":2324,"end":2326},"obj":"18667724"}],"attributes":[{"subj":"23069868-21245330-25970113","pred":"source","obj":"2_test"},{"subj":"23069868-21245330-25970114","pred":"source","obj":"2_test"},{"subj":"23069868-21245330-25970115","pred":"source","obj":"2_test"},{"subj":"23069868-15805106-25970116","pred":"source","obj":"2_test"},{"subj":"23069868-21245330-25970117","pred":"source","obj":"2_test"},{"subj":"23069868-21245330-25970118","pred":"source","obj":"2_test"},{"subj":"23069868-18667724-25970119","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#939bec","default":true}]}]}}