Introduction Streptomyces Streptomyces Streptomyces coelicolor Streptomyces avermitilis 2002 2003 Streptomyces Streptomyces S. coelicolor S. avermitilis Borrelia burgdorferi Agrobacterium tumefaciens Streptomyces 1993 2002 1999 2004 Streptomyces Streptomyces Streptomyces S. avermitilis S. coelicolor Streptomyces. S. avermitilis Streptomyces maritimus Streptomyces. Streptomyces cattleya S. coelicolor Streptomyces Streptomyces cattleya Kitasatospora aureofaciens Streptomyces S. coelicolor 2004 2001 2005 Streptomyces S. coelicolor E. coli S. coelicolor Streptomyces S. coelicolor Streptomyces 2001 2001 1999 2003 2001 2001 2002 2001 2002 2003 2001 2002 2000 2001 2004 Campylobacter jejuni Vibrio cholerae Staphylococcus aureus 2001 2002 2001 Sodalis glossinidius Escherichia coli Salmonella bongori Salmonella enterica Shewanella Shewanella oneidensis E. coli Brucella Brucella melitensis 2001 2003 2001 2004 S. coelicolor Streptomyces Kitasatospora Streptomyces Streptomyces Streptomyces Materials and methods 16S phylogeny 1997 S. maritimus Arrays Streptomyces coelicolor 2004 Strains and growth conditions S. coelicolor + S. avermitilis S. cattleya S. maritimus K. aureofaciens Preparation of labeled DNA 1995 2 Microarray hybridization and data analysis 1998 2003 2 2002 S. coelicolor 1998 S. avermitilis S. avermitilis 2003 S. coelicolor S. avermitilis Analysis of gene presence across the chromosome A graphical display was created by counting the number of gene detected as present from the signal based on the 2SD cutoff from each normalized microarray dataset using a moving window of 10 genes in steps of one. Results and discussion S. avermitilis S. cattleya S. maritimus K. aureofaciens S. coelicolor In total, after spot and data validation, a total of 7,083 open reading frames were included in this analysis as presence on both types of array and giving analyzable signal on all three arrays. Validity in this study was initially obtained by using microarrays from two sources that presumably use different PCR products to create the arrays. In addition, the University of Surrey array was hybridized and analyzed in duplicate. In terms of gene absence based on two standard deviations as described in the “Materials and methods" section, the agreement between the Stanford array and the duplicated University of Surrey array was about 95%, while the agreement between the two University of Surrey arrays was about 98%. In order to minimize the effect of divergent individual array spots, the signal mean for each gene from the three arrays was used throughout this study. Streptomyces Kitasatospora S. coelicolor S. coelicolor S. avermitilis Streptomyces Mycobacterium tuberculosis Corynebacteriun glutamicum 2002 Streptomyces S. coelicolor S. coelicolor S. cattleya K. aureofaciens S. maritimus S.avermitilis 1 S. cattleya K. aureofaciens S. avermitilis S. maritimus S. cattleya K aureofaciens Kitasatospora K. aureofaciens Streptomyces Kitasatospora Streptomyces Fig. 1 Streptomyces  2 S. coelicolor S. avermitilis S. avermitilis Fig. 2 Streptomyces coelicolor Streptomyces avermitilis S. avermitilis S. avermitilis  S. coelicolor Streptomyces Streptomyces 3 S. coelicolor 2002 Streptomyces S. coelicolor S. avermitilis 3 S. ambofaciens 2006a b Fig. 3 Y  2005 S. coelicolor Mycobacterium Corynebacterium S. coelicolor S. coelicolor S. cattleya S. maritimus K. aurefaciens S. avermitilis 2003 1 S. coelicolor Streptomyces S. coelicolor 2002 2002 Table 1 Streptomyces coelicolor Region Area of chromosome a a Significant features Region A SCO0996–SCO1010 17/29 59 Integrase, insertion sequence Region B SCO2860–SCO2879 53/76 69 Rifampin ribosyl transferase Region C SCO3249–SCO3288 94/156 60 Integrase, excisionase Region D SCO3471–SCO3538 198/268 73 Agarase Region E SCO3584–SCO3599 30/60 50  Region F SCO3929–SCO3937 22/32 68 fstK Region G SCO3980–SCO4001 56/64 88 Hypothetical proteins Region H SCO4052–SCO4066 132/144 92 dnaZ Region I SCO4210–SCO4223 37/54 69  Region J SCO4247–SCO4257 21/36 58 Hypothetical proteins Region K SCO4340–SCO4354 34/40 85 Integrase, DNA invertase Region L SCO4509–SCO4547 106/144 74 Hypothetical proteins Region M SCO4613–SCO4631 40/68 59 Integrase, excisionase Region N SCO4686–SCO4700 24/44 55 Boundary ribosomal proteins operon Region O SCO5323–SCO5351 57/80 71 Integrase, excisionase Region P SCO5605–SCO5620 46/64 72 whiG Region Q SCO5632–SCO5644 40/44 91 korSA Region R SCO5715–SCO5735 57/72 79 bldB Region S SCO5906–SCO5924 28/56 50 Hypothetical proteins, xylanase Region T SCO6372–SCO6406 82/100 82 Recombinase Region V SCO6607–SCO6648 62/120 52 Helicase Region W SCO6806–SCO6953 73/133 55 Hypothetical proteins a Streptomyces 3 Streptomyces tpgA tapA 2002 2001 tpgA Streptomyces S. avermitilis tpgA S. coelicolor S. avermitilis tapA S. maritimus 2000 1999 1998 1997 ttrA S. coelicolor S. avermitilis Streptomyces Streptomyces 2a 2b TpgA TapA Streptomyces 2a 2b Table 2 Streptomyces coelicolor (a) ttrA SCO0800 putative TetR-family transcriptional regulatory protein SCO0142 hypothetical protein SCO0802 hypothetical protein SCO0150 hypothetical protein SCO0810 putative ABC transporter permease SCO0201 putative integral membrane protein SCO0830 putative penicillin-binding protein SCO0232 hypothetical protein SCO0839 putative transmembrane transport protein SCO0415 hypothetical protein SCO0840 putative marR-family transcriptional regulator SCO0443 hypothetical protein SCO0854 hypothetical protein SCO0452 putative SIR2-like regulatory protein SCO0883 polypeptide deformylase SCO0466 araC family transcriptional regulator SCO0887 putative TetR-family transcriptional regulator SCO0471 putative araC family transcriptional regulator SCO0894 putative membrane protein SCO0496 putative iron-siderophore permease transmembrane protein SCO0895 RNA polymerase principal sigma factor HrdC SCO0536 hypothetical protein SCO0900 putative transmembrane efflux protein SCO0538 probable sugar transporter sugar binding lipoprotein SCO0905 putative membrane protein SCO0544 hypothetical secreted protein SCO0907 putative dehydrogenase SCO0546 pyruvate carboxylase SCO0925 putative lysR-family transcriptional regulator SCO0551 putative histidine kinase protein SCO0926 hypothetical protein SCO0552 putative response regulator SCO0931 putative secreted proline-rich protein SCO0565 putative polyprenyl synthetase SCO0942 putative RNA polymerase sigma factor SCO0584 putative cytochrome SCO0943 hypothetical protein SCO0591 putative lysozyme precursor SCO0947 putative integral membrane protein SCO0592 hypothetical protein SCO0949 hypothetical protein SCO0614 hypothetical protein SCO1011 conserved hypothetical protein SCO0619 putative membrane protein SCO1015 hypothetical protein SCO0637 hypothetical protein SCO1018 putative isomerase SCO0690 possible oxidoreductase SCO1021 hypothetical protein SCO0695 hypothetical protein SCO1022 hypothetical protein SCO0701 hypothetical protein SCO1024 hypothetical protein SCO0707 putative branched-chain amino acid ABC transport permease SCO1034 putative tetR-family regulatory protein SCO0708 putative branched-chain amino acid ABC transport protein SCO1036 putative phosphotriesterase-family protein SCO0709 putative branched-chain amino acid transport ATP-binding protein SCO1040 putative DNA repair protein SCO0710 putative branched-chain amino acid transport ATP-binding protein SCO1041 hypothetical protein SCO0765 secreted endoglucanase SCO1043 putative transcriptional regulatory protein SCO0779 conserved hypothetical protein SCO1044 putative secreted protein SCO0788 hypothetical protein SCO1046 putative metal transporter ATPase SCO0790 putative hydrolase  (b) SCO7649 putative two-component system sensor kinase SCO7677 putative secreted solute-binding protein SCO7678 putative metal transport integral membrane protein SCO7679 putative transport system integral membrane protein SCO7680 putative ABC transporter ATP-binding protein SCO7681 putative AMP-binding ligase SCO7682 putative non-ribosomal peptide synthase SCO7684 conserved hypothetical protein SCO7685 conserved hypothetical protein SCO7687 putative thioesterase SCO7688 hypothetical protein SCO7689 putative ABC transporter ATP-binding protein SCO7718 hypothetical protein SCO7720 hypothetical protein SCO7724 hypothetical protein SCO7734 Tpg protein Bold indicates groups of consecutive genes that may form a single transcriptional unit Streptomyces Streptomyces ftsK S. coelicolor E. coli S. coelicolor 3 S. avermitilis K. aureofaciens S. coelicolor Streptomyces Table 3 Microarray data for ribosomal proteins from the four species   S. avermitilis S. cattleya S. maritimus K. aureofaciens SCO0436 probable 50S ribosomal protein 0.35 −0.13 0.44 −0.29 SCO0569 putative 50S ribsomomal protein fragment 0.75 0.63 −0.42 0.27 SCO1150 50S ribosomal protein L31 0.56 −0.47 −0.24 0.14 SCO1505 30S ribosomal protein S4 0.36 −0.35 0.76 −0.31 SCO1598 50S ribosomal protein L20 1.50 0.63 0.89 0.34 SCO1599 50S ribosomal protein L35 0.23 0.41 0.49 −0.51 SCO1998 30S ribosomal protein S1 1.39 0.77 0.99 0.91 SCO2563 30s ribosomal protein S20 0.34 −0.34 0.77 0.33 SCO2596 50S ribosomal protein L27 1.01 0.59 0.08 0.82 SCO2597 ribosomal protein L21 0.27 0.08 0.64 −0.18 SCO3124 ribosomal L25p family protein 0.39 0.31 −0.23 −0.89 SCO3427 putative 50S ribosomal protein L31 0.24 0.37 0.22 0.60 SCO3428 putative 50S ribosomal protein L33 0.15 0.28 0.54 0.09 SCO3429 putative 50S ribosomal protein L28 0.68 0.16 0.55 0.45 SCO3430 putative 30S ribosomal protein S14 0.80 0.10 −0.17 −0.19 SCO3880 putative 50S ribosomal protein L34 1.02 0.13 0.24 0.71 SCO3906 putative 30S ribosomal protein S6 0.70 0.94 1.11 −0.18 SCO3909 putative 50S ribosomal protein L9 1.30 0.01 0.87 1.27 SCO4648 50S ribosomal protein L11 1.67 0.43 0.90 0.47 SCO4649 50S ribosomal protein L1 0.62 0.53 −0.25 0.92 SCO4652 50S ribosomal protein L10 0.42 −0.43 0.64 −0.35 SCO4653 50S ribosomal protein L7/L12 1.22 1.03 0.79 0.45 SCO4659 30S ribosomal protein S12 0.74 0.65 0.70 −0.53 SCO4660 30S ribosomal protein S7 0.57 −0.23 0.68 0.12 SCO4701 30S ribosomal protein S10 1.19 1.17 1.16 −0.21 SCO4702 50S ribosomal protein L3 0.92 0.02 0.84 0.49 SCO4703 50S ribosomal protein L4 1.16 0.91 0.59 0.23 SCO4704 50S ribosomal protein L23 0.85 1.44 1.24 0.36 SCO4705 50S ribosomal protein L2 0.85 −0.12 0.84 0.22 SCO4706 30S ribosomal protein S19 0.06 0.24 0.32 −0.26 SCO4707 50S ribosomal protein L22 0.96 0.69 0.64 0.15 SCO4708 30S ribosomal protein S3 1.15 0.38 0.78 1.07 SCO4709 50S ribosomal protein L16 0.52 0.67 1.09 1.26 SCO4710 50S ribosomal protein L29 0.33 −0.06 −0.19 0.41 SCO4711 30S ribosomal protein S17 0.59 0.92 0.51 −0.13 SCO4712 50S ribosomal protein L14 1.05 0.35 0.48 0.82 SCO4713 50S ribosomal protein L24 1.09 0.88 0.63 0.64 SCO4714 50S ribosomal protein L5 1.24 0.78 0.77 1.03 SCO4715 30S ribosomal protein S14 0.39 0.03 0.19 0.12 SCO4716 30S ribosomal protein S8 1.18 −0.11 0.64 0.76 SCO4717 50S ribosomal protein L6 0.96 0.82 0.79 −0.02 SCO4718 50S ribosomal protein L18 0.09 0.30 0.57 0.74 SCO4719 30S ribosomal protein S5 1.56 0.66 1.02 −0.09 SCO4720 50S ribosomal protein L30 0.13 0.39 0.64 0.26 SCO4721 50S ribosomal protein L15 1.79 0.42 0.80 0.84 SCO4726 50S ribosomal protein L36 0.46 −0.13 0.35 −0.10 SCO4727 30S ribosomal protein S13 0.63 −0.23 0.62 −0.17 SCO4728 30S ribosomal protein S11 1.12 0.55 0.87 0.27 SCO4730 50S ribosomal protein L17 0.69 0.27 0.86 0.51 SCO4734 50S ribosomal protein L13 −0.27 0.45 0.50 0.40 SCO4735 30S ribosomal protein S9 0.36 −0.02 0.00 −0.01 SCO5359 50S ribosomal protein L31 0.86 0.22 1.40 0.46 SCO5564 putative 50S ribosomal protein L28 0.60 0.28 0.21 0.51 SCO5591 30S ribosomal protein S16 0.44 0.03 0.57 0.60 SCO5595 50S ribosomal protein L19 0.77 0.78 1.54 −0.03 SCO5624 30S ribosomal protein S2 1.16 0.48 1.52 0.30 SCO5736 30S ribosomal protein S15 0.70 0.41 0.79 −0.46 Mean hybridization score for ribosomal protein genes 0.67 0.35 0.61 0.18 Bold values indicate that the signal for that gene is more than 2SD below the mean core signal for that species and such a value is suggestive of either gene absence or very low similarity 4 S. coelicolor S. coelicolor Streptomyces Table 4 Streptomyces coelicolor   S.avermitilis S.cattleya S. maritimus K. aureofaciens   SCO0037 putative sigma factor 1.04 0.90 0.88 1.49  SCO0159 putative ECF sigma factor 1.26 0.65 2.05 0.60  SCO0194 putative sigma factor 0.87 0.35 0.61 0.52  SCO0255 putative transcriptional regulator 0.64 0.37 0.99 0.46  SCO0414 putative RNA polymerase sigma factor −0.05 −0.28 −0.15 −0.22 Conserved SCO0598 putative anti anti sigma factor 0.11 0.50 −0.08 0.57 Conserved SCO0599 putative regulator of sig8 1.41 1.07 0.84 1.08  SCO0632 putative RNA polymerase sigma factor −0.14 0.19 0.82 0.11  SCO0672 putative anti-sigma factor antagonist −0.10 0.40 −0.19 0.12  SCO0781 putative anti sigma factor antagonist 0.79 0.86 1.06 0.83  SCO0803 putative RNA polymerase sigma factor −0.25 −0.09 0.51 −0.01  SCO0864 probable ECF-family sigma factor 0.74 0.86 1.04 0.50  SCO0866 probable ECF-family sigma factor −0.13 0.19 −0.28 0.23 Conserved SCO0869 putative anti-sigma factor antagonist 0.59 0.90 1.23 0.90  SCO0895 RNA polymerase principal sigma factor HrdC 0.52 0.43 1.12 0.34 Conserved SCO0942 putative RNA polymerase sigma factor 0.34 0.81 0.61 0.45 Conserved SCO1263 putative ECF-sigma factor −0.17 −0.26 0.08 0.35 Conserved SCO1276 RNA polymerase ECF sigma factor 1.22 0.55 0.60 0.88  SCO1564 putative RNA polymerase sigma factor 1.04 −0.33 1.34 0.47  SCO1723 putative RNA polymerase sigma factor 0.19 −0.39 −0.15 0.52 Conserved SCO1876 putative RNA polymerase sigma factor 1.01 0.93 0.77 0.50  SCO2465 RNA polymerase principal sigma factor 0.76 0.74 0.97 0.64 Conserved SCO2639 putative RNA polymerase sigma factor 0.74 0.22 0.01 0.27 Conserved SCO2954 putative RNA polymerase sigma factor 1.12 0.51 0.94 0.46  SCO3066 putative regulator of Sig15 0.53 0.29 0.88 0.31 Conserved SCO3067 putative anti anti sigma factor 0.74 1.25 0.89 0.42  SCO3068 putative RNA polymerase sigma factor 0.33 −0.06 1.07 0.41 Conserved SCO3202 RNA polymerase principal sigma factor 0.98 0.29 1.40 0.19 Conserved SCO3323 putative RNA polymerase sigma factor 0.76 0.49 1.08 0.27 Conserved SCO3356 ECF sigma factor 37 −0.05 0.11 0.73 0.46 Conserved SCO3450 putative RNA polymerase sigma factor (ECF subfamily) 0.16 −0.09 0.79 −0.23  SCO3548 putative anti-sigma factor 0.57 0.50 0.49 −0.06  SCO3549 bldG putative anti-sigma factor antagonist −0.03 −0.16 0.21 −0.20 Conserved SCO3613 putative RNA polymerase sigma factor 0.57 0.15 0.08 0.46 Conserved SCO3692 putative anti-sigma factor antagonist 0.14 0.64 −0.27 0.13 Conserved SCO3709 putative ECF sigma factor 0.02 0.06 −0.21 0.61 Conserved SCO3715 putative ECF sigma factor 0.45 0.92 −0.28 −0.27 Conserved SCO3736 putative RNA polymerase ECF sigma factor −0.06 −0.29 0.28 −0.09 Conserved SCO3892 putative RNA polymerase sigma factor 0.68 0.21 0.80 −0.27 Conserved SCO4027 putative anti sigma factor antagonist −0.04 1.11 0.59 0.58  SCO4034 putative RNA polymerase sigma factor 0.98 1.27 1.26 0.22 Conserved SCO4035 RNA polymerase sigma factor (fragment) 1.04 1.27 0.88 0.45 Conserved SCO4146 putative ECF subfamily sigma factor −0.23 0.53 0.58 0.16 Conserved SCO4409 putative RNA polymerase sigma factor −0.10 0.12 0.10 0.64 Conserved SCO4410 putative anti anti sigma factor 0.89 0.07 0.16 0.81  SCO4452 putative sigma factor −0.17 −0.21 −0.08 0.27 Conserved SCO4769 ECF sigma factor 0.09 0.38 0.68 0.61  SCO4864 putative ECF sigma factor 0.02 −0.34 −0.12 0.73  SCO4866 putative ECF sigma factor 0.12 0.19 0.09 0.38 Conserved SCO4895 putative ECF sigma factor 0.32 1.15 −0.11 0.56  SCO4938 putative ECF-sigma factor 0.17 0.43 0.24 0.64 Conserved SCO4960 possible sigma factor −0.04 0.05 0.66 0.60  SCO4996 putative RNA polymerase ECF sigma factor 0.54 −0.04 0.58 0.48  SCO5147 putative ECF-subfamily sigma factor 0.39 0.35 0.79 0.59  SCO5217 anti-sigma factor 0.47 −0.05 0.28 0.80  SCO5244 anti-sigma factor 0.32 0.54 −0.37 −0.29  SCO5386 putative anti-sigma factor antagonist 0.15 0.37 0.00 -0.07 Conserved SCO5621 RNA polymerase sigma factor WhiG 0.79 0.92 0.64 −0.27 Conserved SCO5820 hrdB, major vegetative sigma factor 1.36 1.06 1.53 1.09 Conserved SCO5934 putative sigma factor 0.07 0.25 -0.58 0.17  SCO6239 putative sigma factor 0.92 1.27 1.84 0.74  SCO6996 putative RNA polymerase s
gma factor -0.34 0.29 0.00 −0.04 Conserved SCO7099 putative RNA polymerase sigma factor −0.20 0.38 0.38 0.29  SCO7104 putative RNA polymerase sigma factor 0.70 −0.02 0.79 0.56  SCO7112 putative ECF-family RNA polymerase sigma factor 0.35 −0.25 1.65 −0.38  SCO7144 putative ECF sigma factor 0.62 0.13 0.91 0.34  SCO7314 probable RNA polymerase sigma factor −0.25 −0.11 0.23 0.46 Conserved SCO7323 anti-sigma factor antagonist 0.30 −0.01 0.23 0.31 Conserved SCO7325 anti-sigma factor antagonist -0.37 -0.68 −0.23 1.15  SCO7341 putative RNA polymerase secondary sigma factor −0.09 0.54 0.29 0.44 Conserved SCO7573 putative anti-sigma factor antagonist −0.18 0.03 1.69 0.21  SCO7619 putative anti sigma factor antagonist −0.28 0.37 0.97 0.64  SCO7754 putative anti-sigma factor antagonist 1.20 0.51 1.89 0.02  Mean hybridization score for ribosomal protein genes 0.01 0.06 0.10 0.05 NA Bold values indicate that the signal for that gene is more than 2SD below the mean core signal for that species and such a value is suggestive of either gene absence or very low similarity. A conserved gene is one that seems to be present in all four species. NA, Not applicable 5 K. aureofaciens Streptomyces sapA Streptomyces Streptomyces ftsK bldB bldB S. coelicolor S. avermitilis Table 5 Streptomyces coelicolor   S. avermitilis S. cattleya S. maritimus  K. aureofaciens SCO0409 sapA spore-associated protein precursor 1.99 1.39 0.59 0.67 SCO1454 putative amino oxidase 1.00 0.45 1.18 −0.17 SCO1489 bldD putative DNA binding protein 0.99 0.76 1.02 0.58 SCO1772 putative partitioning or sporulation protein 0.69 0.35 0.39 0.54 SCO2082 ftsZ cell division protein 1.44 0.89 0.97 0.95 SCO2083 ftsQ sporulation protein 0.32 0.74 0.06 0.26 SCO2084 murG 0.86 −0.01 0.49 0.32 SCO2085 fts W putative cell division protein 0.82 0.81 0.59 0.50 SCO2086 murD 0.58 0.23 0.35 0.45 SCO2087 murX 0.41 0.05 0.51 −0.30 SCO2088 murF 1.18 0.73 0.67 0.01 SCO2089 murE 0.73 0.47 0.36 0.31 SCO2090 ftsl cell division protein 0.80 0.01 0.45 −0.50 SCO2607 Sfr protein 0.73 0.73 0.91 −0.01 SCO2608 penicillin binding protein −0.04 −0.25 0.45 −0.92 SCO2609 mreD rod shape-determining protein 0.09 0.07 0.66 0.43 SCO2610 mreC rod shape-determining protein 0.42 −0.16 0.17 0.52 SCO2611 mreB rod shape-determining protein 0.98 0.80 0.68 0.19 SCO2620 putative cell division trigger factor 0.81 −0.12 0.50 0.25 SCO2968 putative cell division protein 0.35 −0.17 0.34 −0.39 SCO2969 ftsE cell division ATP-binding protein 0.37 0.43 0.00 0.51 SCO3034 whiB sporulation regulatory protein 0.23 0.50 0.81 0.26 SCO3323 bldB putative RNA polymerase sigma factor 0.76 0.49 1.08 0.27 SCO3404 ftsH2 cell division protein ftsH homolog 1.11 0.51 1.07 0.15 SCO3549 bldG putative anti-sigma factor antagonist −0.03 −0.16 0.21 −0.20 SCO3557 putative septum site determining protein 0.31 0.45 −0.19 0.92 SCO3558 putative morphological differentiation-associated protein 0.69 −0.26 1.62 −0.20 SCO3846 putative FtsW/RodA/SpoVE family cell cycle protein 1.11 0.31 1.07 0.61 SCO3886 putative partitioning or sporulation protein 0.00 0.83 0.43 0.98 SCO3887 putative partitioning or sporulation protein −0.19 −0.19 0.24 1.04 SCO3934 ftsK/spoIIIE family protein 0.56 0.39 1.18 0.53 SCO4014 sporulation associated protein 0.87 0.93 0.81 1.17 SCO4184 mfC aerial mycelium formation 0.12 0.17 0.01 −0.05 SCO4508 putative cell division-related protein 0.62 −0.27 0.07 0.59 SCO4531 putative septum determining protein 0.56 0.88 0.12 −0.09 SCO4620 traB1 putative sporulation-related protein 0.49 0.68 0.19 −0.34 SCO4621 traA1 putative sporulation-related protein −0.03 0.51 1.33 −0.38 SCO4767 putative regulatory protein 0.14 0.00 1.67 −0.01 SCO4768 bldM putative two-component regulator 1.06 1.00 0.92 0.61 SCO5006 minD1 putative septum site-determining protein −0.31 −0.04 0.58 −0.28 SCO5008 minD3 putative septum site-determining protein 0.04 −0.21 −0.11 −0.07 SCO5112 BldKA 0.42 0.92 0.75 0.51 SCO5114 BldKC 0.39 −0.08 1.23 −0.23 SCO5115 BldKD 0.01 −0.18 0.89 −0.15 SCO5116 bldKE putative peptide transport system ATP-binding protein −0.04 −0.22 0.70 −0.03 SCO5314 whiE protein VII 1.24 −0.23 0.03 0.67 SCO5315 polyketide cyclase −0.39 0.82 −0.31 −0.25 SCO5316 acyl carrier protein 0.42 −0.29 0.75 0.03 SCO5318 polyketide beta-ketoacyl synthase alpha −0.03 −0.13 0.86 0.43 SCO5321 polyketide hydroxylase 0.12 −0.09 1.50 0.27 SCO5587 ftsH cell division protein FtsH homolog −0.05 0.31 0.23 0.21 SCO5621 whiG RNA polymerase sigma factor WhiG 0.79 0.92 0.64 −0.27 SCO5723 bldB putative regulator, BldB 1.47 0.76 1.27 1.05 SCO5750 ftsK homolog 0.67 0.16 0.65 2.52 SCO5819 whiH, sporulation transcription factor 0.68 0.12 0.16 0.13 SCO6029 whiI two-component regulator 0.14 −0.26 0.77 0.92 Mean hybridization score for ribosomal protein genes 0.05 −0.05 0.27 −0.02 Bold values indicate that the signal for that gene is more than 2SD below the mean core signal for that species and such a value is suggestive of either gene absence or very low similarity 6 Streptomyces S. lividans S. maritimus S. avermitilis S. cattleya Streptomyces 1989 mutT 2004 recA recF recR recX S. cattleya S. maritimus Streptomyces S. avermitilis gyrA gyrB gyrB2 ruvB ruvC ruvA Streptomyces ruvA Streptomyces Table 6 Streptomyces coelicolor   S. avermitilis S. cattleya S. maritimus K. aureofaciens SCO0183 putative deoxyribodipyrimidine photolyase 1.38331 0.76404 1.15786 0.78973 SCO0760 putative methyltransferase −0.23598 −0.17603 0.079613 −0.16712 SCO0842 putative deoxyribodipyrimidine photolyase 0.002475 0.167429 −0.05198 0.35453 SCO0918 putative excinuclease ABC subunit A −0.28707 −0.34813 0.010852 −0.46861 SCO0945 putative formamidopyrimidine-DNA glycosylase 0.34857 0.60698 0.4371 −0.38083 SCO1040 putative DNA repair protein 0.047315 0.568723 0.456168 0.367071 SCO1050 putative DNA protection protein −0.47479 0.093299 0.451487 0.92697 SCO1114 uracil DNA glycosylase 0.34573 0.357182 0.433902 0.950894 SCO1167 putative helicase (fragment) 0.604813 0.072648 −0.40455 −0.25074 SCO1180 putative DNA polymerase III beta chain 0.347 −0.21511 0.42838 −0.20922 SCO1202 putative DNA ligase 0.308497 0.202188 −0.15524 0.096586 SCO1203 putative MutT-like protein −0.17791 −0.3705 0.324233 −0.28871 SCO1255 G/U mismatch-specific DNA glycosylase 0.521679 0.41904 0.321208 0.429148 SCO1343 uracil-DNA glycosylase 0.61294 0.00339 0.311478 0.036821 SCO1380 putative DNA damage inducible protein 0.763064 0.313948 0.214931 0.677262 SCO1395 mutT-like protein 0.068215 0.572527 0.17071 0.414092 SCO1475 putative primosomal protein 0.048892 0.689232 0.53545 0.457655 SCO1518 ruvB holliday junction DNA helicase 1.136489 0.638803 0.930067 1.045593 SCO1519 ruvA holliday junction DNA helicase 0.57721 −0.23275 −0.15374 0.008274 SCO1520 ruvC crossover junction endodeoxyribonuclease 1.079786 0.708131 0.886363 0.979821 SCO1534 putative DNA polymerase III 0.3296 0.371242 −0.10025 0.090739 SCO1739 putative DNA polymerase III 1.128049 0.423158 1.111964 0.326701 SCO1780 putative DNA repair protein −0.14578 −0.09175 0.258713 −0.32746 SCO1792 putative 3-methyladenine DNA glycosylase −0.20485 −0.07755 0.083499 −0.2824 SCO1827 putative DNA polymerase III 0.559715 0.711265 0.512873 0.343849 SCO1966 ABC excision nuclease subunit B 0.047382 0.06896 1.085903 −0.05934 SCO1969 putative DNA-methyltransferase −0.19025 −0.12184 0.143367 0.56545 SCO2003 DNA polymerase I 1.172176 0.188493 0.498126 0.201411 SCO2468 DNA primase 0.82715 0.520552 1.25613 0.69797 SCO2626 putative DNA repair hydrolase (fragment) 0.289916 0.337365 0.567783 0.326821 SCO2863 putative helicase 0.47935 0.68124 1.92881 0.81052 SCO2952 putative helicase protein 0.513952 0.38864 0.750517 0.379556 SCO3109 putative transcriptional-repair coupling factor 0.87255 −0.29611 0.759684 −0.33637 SCO3351 putative DNA repair protein −0.95043 0.68521 0.24637 0.48466 SCO3352 putative DNA-binding protein 0.090569 −0.09602 0.536392 −0.2275 SCO3434 putative DNA polymerase I 0.8554 1.651768 0.874246 1.328528 SCO3510 putative DNA methylase 0.402433 1.11393 2.15274 2.07607 SCO3541 putative DNA polymerase 0.003597 0.40289 0.297076 0.75003 SCO3543 probable DNA topoisomerase I 0.798705 1.33477 0.87884 1.226661 SCO3550 putative helicase 0.263644 0.13935 0.559872 0.216127 SCO3618 putative recomination protein 0.533404 0.052623 0.511469 −0.36893 SCO3873 DNA gyrase subunit A 1.293458 −0.20851 0.985546 1.2494 SCO3874 DNA gyrase subunit B 0.99333 0.958247 1.250669 0.37466 SCO3878 DNA polymerase III 0.05375 0.026053 0.328502 0.62343 SCO3879 chromosomal replication initiator protein (fragment) 1.25983 1.572531 0.731065 −0.12482 SCO4092 ATP-dependent helicase −0.00752 0.055194 0.978098 −0.21188 SCO4143 putative mutT-like protein 0.021035 0.435471 0.479161 −0.28423 SCO4272 putative mutT-like protein −0.1352 0.016206 −0.32968 0.527274 SCO4351 putative DNA invertase 1.26688 0.78144 1.29284 0.68489 SCO4495 putative DNA polymerase related protein −0.09624 0.75937 0.582419 0.316259 SCO4577 putative helicase 0.726962 0.053196 1.044155 −0.09189 SCO4797 putative ATP-dependent DNA helicase II 0.323366 0.286421 0.749868 0.026912 SCO5064 putative bifunctional protein −0.20262 0.49259 1.90763 −0.29433 SCO5143 DNA-3-methyladenine glycosylase I −0.86594 0.342489 0.276611 0.981316 SCO5183 putative ATP-dependent DNA helicase 0.235633 0.120765 0.767504 0.591935 SCO5184 putative ATP-dependent DNA helicase 0.180638 −0.17587 0.208839 0.666073 SCO5188 putative ATP-dependent DNA helicase 0.204048 0.36005 0.808168 −0.04087 SCO5331 putative DNA methylase 1.52864 2.37483 3.76436 2.18209 SCO5494 putative DNA ligase 0.124781 0.288429 0.215946 −0.0149 SCO5566 putative ATP-dependent DNA helicase 0.408995 1.186714 0.428183 0.825946 SCO5567 putative methylase 0.338198 0.82207 0.596196 0.83241 SCO5573 formamidopyrimidine-DNA glycosylase 0.387552 −0.08353 0.601585 0.435209 SCO5760 DNA glycosylase 0.846985 0.02235 0.675876 0.46121 SCO5770 RecX protein −0.1193 0.72104 0.58075 0.079675 SCO5802 putative ATP-dependent helicase 0.823429 −0.10433 0.511595 0.058287 SCO5803 SOS regulatory protein LexA 0.143322 0.78751 −0.0905 −0.16946 SCO5805 ribonucleotide reductase 0.235182 0.271514 0.98906 −0.06823 SCO5815 probable ATP-dependent DNA helicase 0.52023 −0.31138 0.75254 0.71096 SCO5822 gyrB2, probable DNA gyrase 0.167275 0.223473 0.426849 0.393883 SCO5836 DNA gyrase-like protein 0.725708 0.507498 0.937531 0.073608 SCO6084 putative DNA polymerase −0.05381 0.165634 0.084564 −0.16407 SCO6151 putative methylated-DNA-protein-cysteine methyltransferase 0.88705 −0.08112 0.375214 0.207725 SCO6262 putative helicase 6884138:6887071 forward MW:103912 0.260624 −0.28836 0.753508 −0.08897 SCO6405 putative DNA recombinase −0.16958 0.65562 1.15936 −0.30768 SCO6462 putative methylated-DNA-protein-cysteine methyltransferase −0.09961 −0.00285 0.231836 0.026866 SCO6640 putative ATP-dependent helicase 0.56659 0.52367 1.18266 −0.38994 SCO6707 putative DNA ligase −0.25409 0.618121 −0.0252 −0.3333 SCO6844 putative DNA methylase. 0.487806 0.475711 0.59387 0.230037 SCO6907 putative DNA ligase. 0.71491 0.181384 0.67564 0.69734 SCO7345 probable ATP-dependent DNA ligase 0.176692 0.207606 0.340255 0.085159 SCO7522 putative DNA ligase −0.31874 −0.0533 0.63701 0.470458 Mean hybridization score 0.113633 0.007441 0.153752 −0.04491 Bold values indicate that the signal for that gene is more than 2SD below the mean core signal for that species and such a value is suggestive of either gene absence or very low similarity 7 murA, murA2, murB, murD, murE, murF,murG murX Streptomyces D D Table 7 Streptomyces coelicolor   S. avermitilis S.cattleya S. maritimus K. aureofaciens SCO0237 putative oxidoreductase −0.07526 1.14854 −0.09821 0.57347 SCO0286 putative peptidoglycan binding protein 0.9459 0.93949 1.83967 1.02755 SCO0830 putative penicillin-binding protein 0.243458 0.081341 0.556096 0.08585 SCO0936 putative oligosaccharide deacetylase 0.78759 1.38608 0.58892 1.00821 SCO1018 putative isomerase 0.390534 0.519204 0.392605 0.600019 SCO1875 putative secreted penicillin binding protein 0.44831 0.039598 0.320356 0.256976 SCO2084 murG 0.85602 −0.00677 0.485989 0.319639 SCO2085 putative cell division protein 0.816624 0.80742 0.592214 0.502565 SCO2086 murD 0.580506 0.225348 0.347674 0.449973 SCO2087 murX 0.405731 0.049645 0.509959 −0.3047 SCO2088 murF 1.175078 0.730925 0.667383 0.006107 SCO2089 murE 0.734068 0.470869 0.363458 0.308295 SCO2345 putative peptidodoglycan-binding membrane protein −0.0329 0.016338 0.133355 0.069404 SCO2451 putative rod shape-determining protein 0.604327 0.180028 0.612243 0.205981 SCO2589 putative glycosyl transferase 0.093285 0.41217 0.478809 −0.09528 SCO2590 putative glycosyltransferase 0.069933 0.52938 1.18523 0.89326 SCO2608 penicillin binding protein −0.0413 −0.24681 0.445143 0.92429 SCO2609 rod shape-determining protein 0.085879 0.06721 0.663609 0.427758 SCO2610 rod shape-determining protein 0.41695 −0.15798 0.168038 0.52083 SCO2611 rod shape-determining protein 0.979884 0.796403 0.675204 0.186331 SCO2706 putative transferase 0.233423 0.505652 0.55544 0.407847 SCO2707 putative transferase 0.014126 0.37225 0.088105 −0.12772 SCO2897 probable penicillin-binding protein 0.576646 0.409388 0.693237 0.120551 SCO2949 murA 0.418363 0.209024 0.335159 0.062475 SCO3580 putative transpeptidase −0.09884 0.76666 1.13347 0.212152 D D 0.77707 1.21402 1.61266 1.31715 D D 1.47294 0.65926 1.4814 0.85496 D D 0.50714 0.58617 0.155077 0.78413 SCO3847 putative penicillin-binding protein 0.128622 0.43643 0.640849 −0.18456 SCO3901 putative penicillin-binding protein 0.59684 0.78306 −0.26692 −0.39905 SCO4013 putative penicillin binding protein −0.09095 −0.01844 −0.04797 0.164779 SCO4132 putative secreted transglycosylase 0.237226 −0.17562 −0.03522 −0.2261 D 0.74865 0.93049 0.177585 1.21329 SCO4643 murB −0.01505 −0.20659 0.197283 −0.35551 SCO5039 putative penicillin-binding protein 0.590106 −0.70926 0.891819 0.313533 SCO5301 putative penicillin-binding protein −0.19347 −0.13131 0.547233 −0.22028 SCO5365 putative transferase 1.11236 −0.27334 0.569152 1.16844 SCO5467 muramoyl-pentapeptide carboxypeptidase −0.15448 0.387477 −0.49044 −0.02243 D D 0.728112 0.209602 0.167769 0.330255 SCO5998 murA2 0.800726 0.792975 1.291368 0.051102 N L 0.19941 0.377004 0.817329 0.527531 D D 0.605949 0.70203 0.343827 0.524521 Mean hybridization score 0.125637 −0.10744 0.118866 −0.14494 Bold values indicate that the signal for that gene is more than 2SD below the mean core signal for that species and such a value is suggestive of either gene absence or very low similarity Conserved genes with no known function S. avermitilis Streptomyces Streptomyces Streptomyces Streptomyces Streptomyces Streptomyces Streptomyces 8 Streptomyces Streptomyces 2005 Table 8 S. coelicolor Genes (SCO) a b 0614, 0616, 0617, 0618 None – 1317, 1318, 1319, 1320 None – 1521, 1522, 1523, 1524 Possible operon Recombination 1634, 1635, 1636 Possible operon – 1650, 1651, 1652, 1653 Possible operon Proteosome 1788, 1789, 1790, 1791, 1794, 1795, 1796 Possible operon Both flanks of rRNA gene homologues 2030, 2031, 2032 Possible operon – 2124, 2125, 2127, 2129, 2130 Possible operon Glucose kinase 2268, 2269, 2270 Possible operon Close to heme oxygenase 2913, 2915, 2916, 2917 None – 3115, 3117, 3118, 3119 None – 3150, 3151, 3152, 3153 None – 3406, 3407, 3408 Possible operon Penicillin binding protein 3950, 3951, 3952 Possible operon Oxidoreductase 4028, 4029, 4030 None – 4801, 4803, 4804, 4805 None – 5307, 5308, 5309, 5310, 5312 None – 5600, 5601, 5602, 5603, 5604 Possible operon Mycobacterium tuberculosis 5762, 5763, 5764, 5765 Possible operon DNA helicase 6413, 6415, 6416, 6417, 6419, 6420, 6421, 6422 None – 6574, 6575, 6576, 6577, 6578, 6579, 6580 Possible operon Possible DNA binding protein 6671, 6672, 6674, 6675, 6676 Possible operon – 7070, 7071, 7072 None – a b Conservation of genes involved in secondary metabolism and similar functions Streptomyces S. coelicolor S. maritimus S. coelicolor S. cattleya K. aureofaciens S. coelicolor S. maritimus S. avermitilis S. cattleya S. maritimus K. aureofaciens S. cattleya S. maritimus K. aureofaciens Streptomyces Streptomyces melC1 melC2 1992 Streptomyces Kitasatospora S. coelicolor Streptomyces S. coelicolor 9 Streptomyces Table 9 Streptomyces SCO0333 Dioxygenase SCO0560 Catalase/Peroxidase SCO0765 Endoglucanase SCO1187 Cellulase SCO1188 Cellulose binding protein SCO1338 M
nooxygenase SCO1451 Endoglucanase SCO1923 Dioxygenase SCO2016 Monooxygenase SCO2267 Heme oxygenase SCO2700 Tyrosinase (monophenol monooxygenase) SCO2701 Tyrosinase cofactor SCO2783 Monooxygenase SCO2798 Cellobiose hydrolase SCO2838 Endoglucanase SCO3172 Monooxygenase SCO3236 Oxygenase SCO4416 Monooxygenase SCO4870 Monooxygenase SCO5033 Hydrogen peroxide sensing regulator SCO5293 Oxygenase SCO5390 Alkanal monoxygenase SCO5773 Monooxygenase SCO6545 Cellulase SCO7223 Monooxygenase SCO7637 Endoglucanase Note that the oxygeneases included as possible enzymes that make be able to attack lignin are all unclassified yet as to their real function. The core region is in bold Conclusions Streptomyces S. coelicolor/S. avermitilis Streptomyces S. coelicolor, Streptomyces S. coelicolor Streptomyces Kitasatospora Saccharomonospora viridis Streptosporangium roseum Streptomyces rimosus Streptomyces Electronic supplementary material Below is the link to the electronic supplementary material
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