Table 1.
Conserved actinobacterial signature proteins/genes identified by Gao et al. (2006) and Gao & Gupta (2012)†. (A) The 26 most frequent actinobacterial signature proteins include at least six with likely developmental roles (asterisks). (B) Seven actinomycete signature proteins referred to in the text‡
| SCO number | ML number | Comments such as gene or protein name, function, conserved linkage, references, etc. |
|---|---|---|
| (A) | ||
| 5199 | 0642 | Often next to conserved gene for ‘epimerase/dehydratase’. Similar to SCO3407 (25% identity over 336 aa overlap), which is also very widespread and actinospecific, but is not listed in Gao et al. (2006). SCO3407 is neighboured by SCO3408 (= ML00211, actinospecific, widely conserved, predicted D-ala, D-ala carboxypeptidase, PBP4 class, similar to dacB of E. coli) and by a cluster conserved even in B. subtilis (SCO3406, possible MesJ-like cell division-associated ATPase; SCO3405, probable hypoxanthine phosphoribosyl transferase; SCO3405, FtsH2, ATP-dependent protease) |
| 1997* | 1009 | Closely similar to ParJ. Function unknown, but structure established (Gao et al., 2009). May perhaps interact with ParA or the ubiquitous ParA2 (= SCO1772). Absent from nonactinomycete actinobacteria and from two actinomycetes, Trophyrema whipplei and Saccharopolyspora erythraea. |
| 5869 | 1029 | DUF3710 domain; probably cotranscribed with SCO5868 (3nt in between; dut, probable deoxyuridine 5′-triphosphate nucleotidohydrolase) and SCO5867 (phenylacetic acid thioesterase, Paa1). Linkage with dut conserved throughout actinomycetes |
| 1662* | 1306 | parJ. ParJ interacts with ParA (Ditkowski et al., 2010) |
| 3034* | 0760 | whiB, developmental regulatory gene (Fowler-Goldsworthy et al., 2011) |
| 5240* | 0804 | wblE, encodes WhiB-like protein of uncertain role, possibly essential in streptomycetes but not in C. glutamicum (Kim et al., 2005; Fowler-Goldsworthy et al., 2011) |
| 2196 | 0857 | 234 aa, probable integral membrane protein |
| 2169 | 0869 | 251 aa, DUF3034, probable integral membrane protein |
| 2947 | 1016 | 97 aa, DUF3039 |
| 5864 | 1026 | 98 aa; note conserved linkage of SCO5864 and 5869, and ML1026 and 1029 |
| 1381 | 2073 | 228 aa; present in all actinobacteria except Acidimicrobium ferrooxidans and Coriobacteriales. Removed by Gao & Gupta (2012) |
| 5855 | 2137 | 252 aa, DUF3071 |
| 4088 | 2204 | 84 aa, DUF3073 |
| 3854* | 0013 | crgA (whiP in S. avermitilis), 84-aa membrane protein, septation inhibitor, absent from nonactinomycete actinobacteria (Del Sol et al., 2003, 2006; Plocinski et al., 2011, 2012) |
| 3872 | 0007 | 185 aa, DUF3566, invariably very close to oriC |
| 1938 | 0580 | opcA; assembly of glucose-6-phosphate dehydrogenase (also in cyanobacteria: Hagen & Meeks, 2001; and next to the zwf2 gene); a less widely occurring paralogue, SCO6660, is downstream of zwf1 in S. coelicolor |
| 2078 | 0921 | 94 aa, possible transmembrane protein, invariably next to divIVA |
| 1421 | 1439 | rpbA, RNA polymerase-binding protein (Tabib-Salazar et al., 2013; Bortoluzzi et al., 2013; note that ML1439 was listed twice by Gao et al. (2006)) |
| 5601 | 1610 | 102aa, DUF2469, conserved linkage with SCO5602 |
| 4084 | 2207 | 437 aa. Note conserved linkage of SCO4084 and 4088, and ML2207 and 2204 |
| 3095* | 0256 | divIC; part of cell division apparatus, interacts with FtsL (Bennett et al., 2007; sequence divergence of DivIC orthologues in other bacteria took them beyond the threshold adopted by Gao et al., 2006; but they were removed by Gao & Gupta, 2012) |
| 3011 | 0775 | lpqB/Putative lipoprotein |
| 3031 | 0761 | 117 aa, DUF1025. Note conserved linkage of SCO3031 and another signature gene, SCO3034 (whiB) |
| 5169 | 0814 | 94 aa, DUF3107, possible ATP-binding protein |
| 2370 | 1649 | 159 aa, DUF3052, invariably next to gene for possible thiol-specific antioxidant protein |
| 4330 | 2142 | 308 aa, DUF3027 |
| (B) | ||
| 3375 | 0234 | lsr2/HNS-like DNA-bridging protein, iron-regulated in M. tuberculosis (Gordon et al., 2010) |
| 2097 | 0904 | 135 aa, DUF3040, part of spore wall-synthesising complex (Kleinschnitz et al., 2011) |
| 4179 | 2200 | 191 aa, cd07821, likely nitrobindin. NO or fatty acid-binding protein domain, structure known for M. tuberculosis (Shepard et al., 2007), conserved synteny with adjacent fur homologue |
| 1480 | 0540 | 107 aa, nucleoid-binding protein sIHF (Yang et al., 2012; Swiercz et al., 2013) |
| 1664 | 1300 | 265 aa, generally very close to mshC gene for mycothiol biosynthesis |
| 3097 | 2030 | rpfC/RPF, secreted protein, peptidoglycan binding, several paralogues |
| 4205 | 2442 | 168 aa, DUF2596, downstream of and overlapping mshA |
The gene identifiers listed by Gao et al. (2006) were for the Mycobacterium leprae genome. Here, we have listed S. coelicolor orthologues as defined by reciprocal best-hit BLASTP analysis. The function descriptions are based on the cited papers where given, but where no reference is given, the commentary is derived from synteny and conserved domain analysis carried out for this review, using StrepDB (http://strepdb.streptomyces.org.uk).
The remaining 39 actinomycete signature genes identified by Gao et al. (2006) were as follows (M. leprae, L. xyli or T. fusca designations given in brackets after SCO equivalent): SCO numbers: 0908 (Tfu_0365), 1372 (Lxx16410), 1383 (ML2075), 1437 (ML0561), 1653 (ML1312), 1665 (ML1299), 1929 (ML0589), 2105 (ML0898), 2153 (ML2446), 2154 (ML0876), 2197 (Lxx10090), 2391 (ML1781), 2460 (Tfu_1340), 2557 (Lxx08190), 2643 (ML1485), 2893 (ML0169), 2915 (ML1166), 2916 (ML1165), 3016 (Tfu_2498), 3030 (ML0762), 3576 (Lxx03620), 3647 (ML0284), 3822 (ML0115), 3902 (ML2687), 4043 (Tfu_0030), 4287 (ML1927), 4579 (ML2064), 4590 (Tfu_1240), 5145 (ML1067), 5167 (Tfu_0515), 5173 (ML0816), 5414 (ML1176), 5493 (ML1706), 5697 (Tfu_0751), 5766 (ML0986), 5866 (ML1027), 6030 (ML1041). One (ML2428A) was similar to SCO3327, but did not give a reciprocal blastp best hit, and another (ML0899) was absent from S. coelicolor, but present in S. avermitilis (SAV1313) and many other streptomycetes.