Analysis of loci encoding proteins of the CP43/IsiA/Pcb family.

A. Organization of the chromosomal region harboring the isiA and psbC-like genes (psbC-lk1-3) of N. spumigena and the separate psbDC operon. The PsaL–coding domain in psbC-lk2 (nsp37500) is highlighted in orange. B. Phylogenetic analysis of CP43, IsiA and related chlorophyll-binding proteins from N. spumigena and of selected other cyanobacteria was inferred using the Minimum Evolution method. The optimal tree with the sum of branch length = 3,97009738 is shown. The percentage of replicate trees in which the associated taxa clustered in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated from the dataset (complete deletion option). There were a total of 279 positions in the final dataset. C. Transcriptional organization around the isiA, isiB and psbC-like gene cluster. There are three mapped TSS in the region displayed in Fig. 3A, all associated with or close to the 5′ end of nsp37510. TSS are indicated by blue arrows and the number of cDNA reads associated with them are given as approximation for their activity. One gTSS gives rise to the 83 nt long 5′ UTR upstream of nsp37510 (blue) and the gene or operon mRNA. An antisense RNA originates from a single aTSS in the opposite direction (purple). The third TSS is a putative nTSS driving the transcription of an ncRNA in the nsp37510- nsp37520 intergenic spacer. Except for the nsp37510 5′ UTR, all TSS displayed are drawn with a 100 nt-long box that corresponded to the maximum read length in the dRNAseq approach.