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

<p><b>A.</b> Organization of the chromosomal region harboring the <i>isiA</i> and <i>psbC</i>-like genes (<i>psbC-lk1-3</i>) of <i>N. spumigena</i> and the separate <i>psbDC</i> operon. The PsaL–coding domain in <i>psbC-lk2</i> (<i>nsp37500</i>) is highlighted in orange. <b>B.</b> Phylogenetic analysis of CP43, IsiA and related chlorophyll-binding proteins from <i>N. spumigena</i> 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. <b>C.</b> Transcriptional organization around the <i>isiA, isiB</i> and <i>psbC</i>-like gene cluster. There are three mapped TSS in the region displayed in <b>Fig. 3A</b>, all associated with or close to the 5′ end of <i>nsp37510.</i> 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 <i>nsp37510</i> (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 <i>nsp37510</i>- <i>nsp37520</i> intergenic spacer. Except for the <i>nsp37510</i> 5′ UTR, all TSS displayed are drawn with a 100 nt-long box that corresponded to the maximum read length in the dRNAseq approach.</p

The 50 gTSS of protein-coding genes associated with the highest number of reads.

<p>For each gTSS, the position with respect to the forward strand, the orientation (S), the number of reads, the gene ID, gene name (if known) and gene annotation is given. The gTSS are ordered according to the number of reads.</p

General features of <i>N. spumigena</i> CCY9414.

<p><b>A</b>. Photomicrograph of <i>N. spumigena</i> CCY9414 trichomes. The arrows point to heterocysts. The vertical bar corresponds to 40 µm. <b>B</b>. Phylogenetic position of <i>N. spumigena</i> CCY9414 (boxed) within the cyanobacterial phyum, based on its two 16S rRNA sequences (labeled a and b). The two sub-clades within the Nostocales, clade I and clade II, are indicated. Species for which a total genome sequence is publicly available, are in blue. The sequence of <i>Chlorobium tepidum</i> TLS served as outgroup. The numbers at nodes refer to bootstrap support values (1000 repetitions) if >60%. The phylogenetic tree was generated using the Minimum Evolution method within MEGA5 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060224#pone.0060224-Tamura1" target="_blank">[158]</a>. The optimal tree with the sum of branch length  =  0.85445647 is shown. 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 and are given in the number of base substitutions per site. The multiple sequence alignment was shortened to a total of 1407 positions in the final dataset to include also 16S rRNA sequences from species without a genome sequence.</p

Classification of the predicted <i>N. spumigena</i> CCY9414 proteome.

<p><b>A.</b> Comparison of all predicted proteins of <i>N. spumigena</i> (N_spumi) against the proteomes of other well-studied Nostocales, <i>Nostoc punctiforme</i> sp. PCC 73102 (N_punct), <i>Anabaena variabilis</i> sp. ATCC 29413 (A_var) and <i>Anabaena</i> PCC 7120 (N_7120) based on MCL clustering of BLASTp results (minimum e-value: 10^-8). The numbers refer to the number of protein clusters in each category, the numbers in brackets to the total number of individual proteins. <b>B.</b> Taxonomic top hits for the 1,098 <i>N. spumigena</i> CCY9414 singletons from part A (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060224#pone.0060224.s005" target="_blank">Table S3</a>) visualized by MEGAN.</p

Proteins related to the uptake of iron in <i>N. spumigena</i> CCY9414 identified on the basis of gene clusters present in the genome of <i>Anabaena</i> PCC 7120.

<p>The first row contains the ORF ID, annotation and gene name (if available) of the respective <i>Anabaena</i> protein (according to the published sequence <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060224#pone.0060224-Kaneko1" target="_blank">[163]</a> in Genbank file NC_003272.1), followed by the ORF ID in <i>N. spumigena</i> CCY9414 (NsORF), the detailed annotation, the% ID in a pairwise alignment and the reference, if available.</p