Figure 2 Organization and co-transcription of four cbb gene

clusters in A. ferrooxidans ATCC 23270. (A) cbb1 (B) cbb2 (C) cbb3 and (D) cbb4. The following are represented in each of the panels A-E: (a) nucleotide sequences of the predicted σ70-like promoter region (-10 and -35 sites in italics) and potential CbbR-binding sites in grey boxes with the LysR-type TNA-N7-TNA and T-N11-A consensus binding HDAC assay sites in bold letters, (b) gene organization of the respective operons with predicted rho-independent transcriptional stop sites indicated as stem-loop symbols, (c) locations of PCR primers used for RT-PCR experiments (indicated by numbers) or EMSA assays (indicated by letters) and (d) gel electrophoresis of fragments amplified by RT-PCR using purified cellular RNA as template. A 1-kb scale bar is shown. One of the T-N11-A consensus binding sites HSP990 cost in the cbb4 operon is part of a larger pseudo-palindrome indicated by inverted arrows. Predicted gene functions are provided in Table 3. Table 3 Predicted genes of cbb operons *Accession aGene name bPredicted function cBest BlastP hit d% Similarity eScore fE-value gDomains and motifs Operon cbb1               ACK78724.1 cbbR LysR family transcriptional regulatory protein CbbR Nitrococcus mobilis 76 363 7e-99 PD462572, PD756396, Pfam03466, Pfam00126, COG0583 ACK79627.1 cbbL1 Ribulose bisphosphate carboxylase large subunit 1 [4.1.1.39]

Halothiobacillus neapolitanus 94 882 0 PD417314, PD000044, Pfam00016, Pfam02788, COG1850 ACK77836.1 cbbS1 Ribulose bisphosphate carboxylase small subunit 1 [4.1.1.39] Methylococcus capsulatus 80

161 8e-39 PD000290, Pfam00101, COG4451 ACK78689.1 csoS2 Carboxysome structural peptide Thiobacillus denitrificans Galeterone 59 325 9e-87 PD579361, tat signal peptide ACK80925.1 csoS3 Carboxysome structural peptide Thiobacillus denitrificans 65 537 5e-151 PD191834, Pfam08936 ACK80352.1 csoS4A Carboxysome peptide A Thiobacillus denitrificans 93 139 6e-32 PD012510, Pfam03319, COG4576, tat signal peptide ACK79436.1 csoS4B Carboxysome peptide B Thiobacillus denitrificans 82 119 7e-26 PD012510, Pfam03319, COG4576 ACK78722.1 csoS1C Microcompartments protein Nitrosomonas eutropha 97 142 6e-33 PD003442, Pfam00936, COG4577 ACK79154.1 csoS1A Microcompartments protein Nitrosomonas eutropha 97 144 1e-33 PD003442, Pfam00936, COG4577 ACK79584.1 csoS1B Microcompartments protein Nitrosomonas eutropha 95 146 3e-34 PD003442, Pfam00936, COG4577 ACK79096.1 bfrA Bacterioferritin Thiobacillus denitrificans 70 135 6e-31 PDA00179, Pfam00210, COG1633 ACK77923.1 hyp1 Hypothetical protein Thiobacillus denitrificans 81 68 2e-10 PDA1E0I5 ACK80576.1 parA Partition protein A Thiobacillus denitrificans 72 196 6e-49 PD194671, Pfam01656, COG1192 ACK78664.1 hyp2 Hypothetical protein Acidithiobacillus ferrooxidans 100 156 1e-09   ACK80060.1 cbbQ1 Rubisco activation protein Nitrosomonas europaea 92 489 5e-137 PD490543, Pfam08406, Pfam07728, COG0714, COG5271 ACK80817.