Table 1.
SARPs encoded in antibiotic biosynthetic gene clusters from diverse streptomycetesa
| Pathway type | Antibiotic | Organism | SARP length |
No. of TTA codons | Gene name | |
|---|---|---|---|---|---|---|
| <400 aa | >400 aa | |||||
| Type II polyketides | Aranciamycin | S. echinatus | 270 | 70 | orf15 | |
| 943 | orf4 | |||||
| Lactonamycin | S. rishiriensis | 626 | lct23 | |||
| 277 | lct15 | |||||
| 221 | lct21 | |||||
| 510 | lct22 | |||||
| FD-594 | Streptomycessp. strain TA-0256 | 636 | 620 | pxnR2 | ||
| Griseorhodin | Streptomyces sp. strain JP95 | 274 | grhR2 | |||
| 274 | grhR1 | |||||
| A-74528 | Streptomyces sp. strain SANK 61196 | 611 | sanR1 | |||
| Aclacinomycin | S. galilaeus | 281 | acl1 | |||
| 273 | aknO | |||||
| Medermycin | Streptomyces sp. strain AM-7161 | 259 | med-ORFII | |||
| Auricin | S. aureofaciens | 274 | sa35 | |||
| 269 | sa23 | |||||
| 293 | sa37 | |||||
| 273 | sa24 | |||||
| Polyketomycin | S. diastatochromogenes | 271 | 8 | pokR2 | ||
| 1,066 | pokR1 | |||||
| Chartreusin | S. chartreusis | 217 | chaR1 | |||
| Lysolipin | S. tendae | 614 | 30 | llpR4 | ||
| Gilvocarcin | S. griseoflavus | 1,090 | gilS | |||
| Hedamycin | S. griseoruber | 273 | orf16 | |||
| Granaticin | S. violaceoruber | 284 | gra-ORF9 | |||
| Polyketide 5 | S. avermitilis | 271 | 129 | ? | ||
| Frenolicin | S. roseofulvus | 283 | frnG | |||
| Fredericamycin | S. griseus | 612 | 191 | fdmR1 | ||
| Alnumycin | Streptomyces sp. strain CM020 | 272 | 5 | alnR3 | ||
| Enterocin | S. maritimus | 284 | encF | |||
| Chromomycin | S. griseus | 301 | 13 | cmmR | ||
| Steffimycin | S. steffisburgensis | 291 | 241 | stfR1 | ||
| Mithramycin | S. argillaceus | 277 | 6, 226 | mtmR | ||
| SF2575 | Streptomyces sp. strain 2575 | 271 | 8 | ssfT1 | ||
| Totals | 22 pathways | 22 organisms | 24 small SARPs | 9 medium or large SARPs | 11 genes with TTA codons | |
| Type I polyketides | Reveromycin | Streptomyces sp. strain SN-593 | 278 | 27, 30 | revQ | |
| AHBA | Kitasatospora putterlickiae | 769 | orf18 | |||
| Tetronasin | S. longisporus | 257 | tsn17 | |||
| Pactamycin | S. pactum | 399 | orf27 | |||
| Furaquinocin A | Streptomyces sp. strain KO-3988 | 344 | 56, 75, 78 | ? | ||
| Oxazolomycin | S. albus | 930 | ozmU | |||
| Chlorothricin | S. antibioticus | 262 | chlF2 | |||
| Natamycin | S. chattanoogensis | 1,177 | 37, 351 | scnR1 | ||
| Piericidin | S. piemogenus | 200 | pieR | |||
| Salinomycin | S. albus | 856 | orf15 | |||
| Bafilomycin | S. lohii | 610 | 172 | bafG | ||
| Nangchangmycin | S. nangchangensis | 254 | 31 | nanR2 | ||
| 242 | nanR1 | |||||
| Polyketide 5 | S. avermitilis | 271 | 129 | ? | ||
| Virginiamycin | S. virginiae | 330 | vrmS | |||
| Rubradirin | S. achromogenes subsp. rubradiris | 291 | rubRg3 | |||
| 267 | rubRg1 | |||||
| Tetronomycin | Streptomyces sp. strain NRRL 11266 | 257 | 31 | trrn18 | ||
| Aureothin | S. thioluteus | 272 | 11 | aurD | ||
| Dorrigocin/migrastatin | S. platensissubsp. rosaceus | 1,218 | 447, 1059 | |||
| Asukamycin | S. nodosussubsp. asukaensis | 255 | asuR5 | |||
| Concanamycin A | S. neyagawaensis | 702 | 5 | orf17 | ||
| Tylosin | S. fradiae | 278 | 68 | tylS | ||
| Totals | 21 pathways | 21 organisms | 16 small SARPs | 8 medium or large SARPs | 12 genes with TTA codons | tylT |
| Nonpolyketides | Nosiheptide (thiopeptide) | S. actuosus | 324 | nosP | ||
| Skyllamycin (nonribosomal peptide) | Streptomyces sp. strain Acta 2897 | 647 | sky44 | |||
| Polyoxin (nucleoside) | S. cacaoisubsp. asoensis | 1,112 | 63 | polR | ||
| 963 | 152, 360 | ? | ||||
| Peptide-2 (nonribosomal peptide) | S. avermitilis | 616 | ? | |||
| Thienamycin (atypical beta-lactam) | S. cattleya | 267 | thnU | |||
| 4-Hydroxy-3-nitrosobenzamide | S. murayamaensis | 323 | 41 | nspR | ||
| Nikkomycin | S. tendae | 1,063 | orfR | |||
| Himastatin | S. himastatinicus | 1,049 | ? | |||
| Virginiamycin (two polyketide/peptide components) | S. virginiae | 330 | vmsS | |||
| Phenalinolactone (terpene) | Streptomyces sp. strain Tu6071 | 266 | plaR1 | |||
| Heboxidiene (?) | S. chromofuscus | 262 | 200 | ? | ||
| Prodigiosin (pyrrole) | S. griseoviridis | 254 | rphD | |||
| Rubrinomycin (?) | S. collinus | 662 | rubS | |||
| Cinnamycin (lantibiotic) | S. cinnamoneus | 262 | 72 | cinR1 | ||
| Totals | 14 pathways | 14 organisms | 8 small SARPs | 7 medium or large SARPs | 5 genes with TTA codons | |
Gene clusters were initially identified by searching the NCBI database for “Streptomyces” under the field “organism” and for “cluster” under the field “title.” Limits of 5,000 to 500,000 nucleotides were set. The exact query submitted to the database was, “Streptomyces [organism] AND cluster [title] AND 5000:5000000 [sequence length].” From 365 clusters initially listed, manual editing was used to eliminate clusters that were not for antibiotic biosynthesis. Further manual editing eliminated clusters that were SARP free but incomplete. From a final total of 236 clusters, 24% (57 clusters) encoded at least one SARP (homologues of ActII-ORF4 using BLASTP analysis). These are listed here in relation to the general type of biosynthetic pathway. “Small” SARPs are up to 400 aa long, “medium” are 401 to 799 bp, and “large” 800 bp or more. AHBA, 3-amino-5-hydroxybenzoic acid.