Table 1

SARPs encoded in antibiotic biosynthetic gene clusters from diverse streptomycetesa

Pathway typeAntibioticOrganismSARP lengthNo. of TTA codonsGene name
<400 aa>400 aa
Type II polyketidesAranciamycinS. echinatus27070orf15
943orf4
LactonamycinS. rishiriensis626lct23
277lct15
221lct21
510lct22
FD-594Streptomycessp. strain TA-0256636620pxnR2
GriseorhodinStreptomyces sp. strain JP95274grhR2
274grhR1
A-74528Streptomyces sp. strain SANK 61196611sanR1
AclacinomycinS. galilaeus281acl1
273aknO
MedermycinStreptomyces sp. strain AM-7161259med-ORFII
AuricinS. aureofaciens274sa35
269sa23
293sa37
273sa24
PolyketomycinS. diastatochromogenes2718pokR2
1,066pokR1
ChartreusinS. chartreusis217chaR1
LysolipinS. tendae61430llpR4
GilvocarcinS. griseoflavus1,090gilS
HedamycinS. griseoruber273orf16
GranaticinS. violaceoruber284gra-ORF9
Polyketide 5S. avermitilis271129?
FrenolicinS. roseofulvus283frnG
FredericamycinS. griseus612191fdmR1
AlnumycinStreptomyces sp. strain CM0202725alnR3
EnterocinS. maritimus284encF
ChromomycinS. griseus30113cmmR
SteffimycinS. steffisburgensis291241stfR1
MithramycinS. argillaceus2776, 226mtmR
SF2575Streptomyces sp. strain 25752718ssfT1
    Totals22 pathways22 organisms24 small SARPs9 medium or large SARPs11 genes with TTA codons
Type I polyketidesReveromycinStreptomyces sp. strain SN-59327827, 30revQ
AHBAKitasatospora putterlickiae769orf18
TetronasinS. longisporus257tsn17
PactamycinS. pactum399orf27
Furaquinocin AStreptomyces sp. strain KO-398834456, 75, 78?
OxazolomycinS. albus930ozmU
ChlorothricinS. antibioticus262chlF2
NatamycinS. chattanoogensis1,17737, 351scnR1
PiericidinS. piemogenus200pieR
SalinomycinS. albus856orf15
BafilomycinS. lohii610172bafG
NangchangmycinS. nangchangensis25431nanR2
242nanR1
Polyketide 5S. avermitilis271129?
VirginiamycinS. virginiae330vrmS
RubradirinS. achromogenes subsp. rubradiris291rubRg3
267rubRg1
TetronomycinStreptomyces sp. strain NRRL 1126625731trrn18
AureothinS. thioluteus27211aurD
Dorrigocin/migrastatinS. platensissubsp. rosaceus1,218447, 1059
AsukamycinS. nodosussubsp. asukaensis255asuR5
Concanamycin AS. neyagawaensis7025orf17
TylosinS. fradiae27868tylS
    Totals21 pathways21 organisms16 small SARPs8 medium or large SARPs12 genes with TTA codonstylT
NonpolyketidesNosiheptide (thiopeptide)S. actuosus324nosP
Skyllamycin (nonribosomal peptide)Streptomyces sp. strain Acta 2897647sky44
Polyoxin (nucleoside)S. cacaoisubsp. asoensis1,11263polR
963152, 360?
Peptide-2 (nonribosomal peptide)S. avermitilis616?
Thienamycin (atypical beta-lactam)S. cattleya267thnU
4-Hydroxy-3-nitrosobenzamideS. murayamaensis32341nspR
NikkomycinS. tendae1,063orfR
HimastatinS. himastatinicus1,049?
Virginiamycin (two polyketide/peptide components)S. virginiae330vmsS
Phenalinolactone (terpene)Streptomyces sp. strain Tu6071266plaR1
Heboxidiene (?)S. chromofuscus262200?
Prodigiosin (pyrrole)S. griseoviridis254rphD
Rubrinomycin (?)S. collinus662rubS
Cinnamycin (lantibiotic)S. cinnamoneus26272cinR1
    Totals14 pathways14 organisms8 small SARPs7 medium or large SARPs5 genes with TTA codons
  • a 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.