In Silico Analysis of PKS and NRPS Gene Clusters in Arisostatin- and Kosinostatin-Producers and Description of Micromonospora okii sp. nov.
Abstract
:1. Introduction
2. Results
2.1. Classification of Micromonospora sp. TP-A0316 and Micromonospora sp. TP-A0468
2.2. PKS and NRPS Gene Clusters in Micromonospora sp. TP-A0316 and M. okii TP-A0468T
2.3. Distribution of Quinmuinolidomicin-BGC Orthologs in the Genus Micromonospora
3. Discussion
4. Description of Micromonospora okii sp. nov.
5. Materials and Methods
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Character | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
Melanine formation | + | nd | nd | nd | − |
Soluble pigment | − | nd | + | nd | − |
Whole cell sugar | Gal, Xyl, Ara, Glu | Ara, Xyl, Glu | Ara, Glu, Rib, Xyl | Ara, Glu, Xyl | Glu, Xyl, Man |
Phospholipid | PE, PI | PE, DPG, PIM | DPG, PE, PG, PI, PIMs | DPG, PE, PIM | DPG, PE, PIM |
Starch hydrolysis | + | + | + | v | + |
Milk peptonization | + | nd | + | nd | − |
Cellulose decomposition | − | + | nd | + | − |
Gelatin liquefaction | + | + | − | nd | − |
Utilization of carbon source | |||||
l-Arabinose | + | − | + | − | − |
d-Fructose | + | v | + | v | − |
d-Galactose | + | v | + | − | + |
Inositol | − | nd | − | nd | + |
Maltose | + | − | nd | + | + |
d-Mannitol | − | v | − | v | + |
d-Mannose | + | − | + | + | + |
d-Raffinose | − | + | w | + | + |
d-Xylose | − | v | + | v | − |
Growth temperature (optimum, °C) | 13–41 (25–39) | nd | 20–45 (30) | nd | 15–40 (28) |
pH for growth (optimum) | 6–10 (7–8) | 5–8.5 | 5–10 (7) | nd | 6–10 (7) |
NaCl tolerance (%) | <4 | 3 | 4 | 3 | 3.5 |
Cluster | ORF | Domain Organization | Predicted Product |
---|---|---|---|
t1pks-1 | 11-150 (tcaA1) | KS/AT/ACP-KS/AT/DH/KR/ACP-KS/AT/DH/KR/ACP-KS | arisostatins A & B, tetrocarcin A |
11-151 (tcaA1) | ATmm/DH/KR/ACP | ||
11-152 (tcaA2) | KS/ATm/DH/KR/ACP-KS/AT/DH/KR/ACP-KS/ATm/DH/KR/ACP- | ||
KS/ATm/DH/KR/ACP | |||
11-153 (tcaA4) | KS/ATmm/DH/KR/ACP | ||
11-154 (tcaA5) | KS/ATm/KR/ACP | ||
11-166 (tcaA3) | KS/AT/DH/ER/KR/ACP- KS/ATmm/DH/KR/ACP | ||
t1pks-2 * | 1-1073 | CoL/KR/ACP-KS/ATm/DH/KR/ACP-KS/ATmm/DH/ER/KR/ACP | quinolidomicin congener |
1-1077 | KS/ATm/DH/KR/ACP | ||
1-1078 | KS/ATm/KR/ACP-KS/ATm/KR/ACP-KS/ATm/KR/ACP | ||
1-1080 | KS/ATm/DH/ER/KR/ACP-KS/ATmm/DH/ER/KR/ACP-KS/ATm/DH/ER/KR/ACP- | ||
KS/ATm/KR/ACP | |||
1-1081 | KS/ATmm/KR/ACP-KS/ATm/DH/KR/ACP-KS/ATm/DH/KR/ACP- | ||
KS/ATm/DH/KR/ACP-KS/ATm/KR/ACP-KS/ATm/KR/ACP | |||
1-1091 | KS/ATm/KR/ACP-KS/ATmm/DH/KR/ACP | ||
1-1092 | KS/ATm/DH/KR/ACP-KS/ATmm/KR/ACP-KS/ATm/KR/ACP | ||
1-1093 | KS/ATm/KR/ACP-KS/ATmm/DH/ER/KR/ACP | ||
1-1094 | KS/ATm/KR/ACP- KS/ATmm/KR/ACP- KS/ATmm/KR/ACP | ||
1-1095 | KS/ATm/DH/KR/ACP-KS/ATmm/DH/KR/ACP | ||
1-1096 | KS/ATmm/KR/ACP | ||
1-1097 | KS/ATmm/KR/ACP-KS/ATm/KR/ACP | ||
1-1098 | KS/ATm/ACP-Te | ||
t1pks-3 | 4-330 | KS/AT/KR/DH | sporolide |
t1pks-4P | 14-64 P | KS/AT… | unpredictable |
16-1 P | …KR | ||
16-2 | KS/AT | ||
16-3 | ACP | ||
t2pks-1 | 4-99 | KSα | aromatic polyketide |
4-100 | KSβ (CLF) | ||
4-101 | ACP | ||
t3pks-1 * | 2-674 | KS | alkyl-O-dihydrogeranyl-methoxyhydroquinone |
nrps-1 | 1-336 | C/A/T-C/Athr/T/E | pentapeptide (x-thr-phe-ser-ile) |
1-337 | C/Aphe/T/E-C/Aser/T | ||
1-339 | C/Aile/T | ||
nrps-2 | 4-510 | C-C | tripeptide (x-gly-x) |
4-511 | C/A/T-Te | ||
4-512 | A | ||
4-513 | C/Agly/T | ||
4-514 | T | ||
nrps-3 | 6-252 | C/Acys/T-Te | tetrapeptide (x-x-cys-cys) |
6-258 | A-C/Acys/T | ||
6-265 | C | ||
6-266 | A | ||
6-270 | A/T | ||
nrps-4P | 8-247 | A/T-C | unpredictable |
8-248 | A/T | ||
nrps-5 | 12-31 | C/Aser/T-C/Apro/T-Te | ser-pro |
pks/nrps-1 | 4-217 4-220 4-223 4-227 4-228 4-229 4-247 | CoL/ACP-KS/ATm/ACP-C/A/T-C Aala/T-C Aglu/T-C/T Athr/T T-C Aser/T-C/T-Te A/T | heptapeptide with polyketide moieties (st-pk-x-ala-glu-y-thr-ser-y) |
pks/nrps-2 * | 6-50 6-51 6-52 6-53 6-54 6-55 | C/A/T KS ACP C/Aval/T KS/ATm/ACP Aser | tripeptide with polyketide moiety (ser-x-val-pk) |
pks/nrps-3 * | 6-307 6-310 6-311 6-313 6-314 | A/T-KS/DH A/T-C/T KS/ATm/KR/DH/ACP C/Aasn/T C/Aser/T-Te | pentapeptide with polyketide moiety (x-pk-x-y-pk-asn-ser) |
pks/nrps-4 | 8-41 8-40 8-39 8-37 | Agly/T-KS/ACP-KS/ATm DH/KR/ACP-KS/ACP-KS/KR/ACP KS/DH/ACP-KS/ATm DH/KR/ACP-AmT | hexaketide with gly |
M * | Quinolidomicin (qnm) | t1pks-2 | |
---|---|---|---|
in M. chalcea AK-AN57 | in Micromonospora sp. TP-A0316 | in M. okii TP-A0468T | |
(qnmA1) | (1-1073) | (8-118) | |
L | CoL/ACP | CoL/KR/ACP | CoL/ACP |
1 | KS/ATm/DH/KR/ACP | KS/ATm/DH/KR/ACP | KS/ATm/DH/KR/ACP |
2 | KS/ATmm/DH/ER/KR/ACP | KS/ATmm/DH/ER/KR/ACP | KS/ATmm/DH/ER/KR/ACP |
(qnmA2) | (1-1077) | (8-122) | |
3 | KS/ATm/DH/KR/ACP | KS/ATm/DH/KR/ACP | KS/ATm/DH/KR/ACP |
(qnmA3) | (1-1078) | (8-123) | |
4 5 6 7 | KS/ATm/DH/KR/ACP KS/ATm/KR/ACP KS/ATm/KR/ACP KS/ATm/KR/ACP | - KS/ATm/KR/ACP KS/ATm/KR/ACP KS/ATm/KR/ACP | - KS/ATm/KR/ACP KS/ATm/KR/ACP KS/ATm/KR/ACP |
(qnmA4) | (1-1080) | (8-135) | |
8 9 10 11 | KS/ATm/DH/ER/KR/ACP KS/AT/DH/ER/KR/ACP KS/ATm/DH/KR/ACP KS/ATm/KR/ACP | KS/ATm/DH/ER/KR/ACP KS/ATmm/DH/ER/KR/ACP KS/ATm/DH/ER/KR/ACP KS/ATm/KR/ACP | KS/ATm/DH/ER/KR/ACP KS/AT/DH/ER/KR/ACP KS/ATm/DH/ER/KR/ACP KS/ATm/KR/ACP |
(qnmA5) | (1-1081) | (8-136) | |
12 | KS/ATm/KR/ACP | KS/ATmm/KR/ACP | KS/ATmm/KR/ACP |
(8-137) | |||
13 | KS/ATm/DH/KR/ACP | KS/ATm/DH/KR/ACP | KS/ATm/DH/KR/ACP |
14 | KS/ATm/DH/KR/ACP | KS/ATm/DH/KR/ACP | KS/ATm/DH/KR/ACP |
15 | KS/ATm/DH/KR/ACP | KS/ATm/DH/KR/ACP | KS/ATm/DH/KR/ACP |
16 | KS/ATm/KR/ACP | KS/ATm/KR/ACP | KS/ATm/KR/ACP |
17 | KS/ATm/KR/ACP | KS/ATm/KR/ACP | KS/ATm/KR/ACP |
(qnmA6) | (1-1091) | (8-146) | |
18 19 | KS/ATm/KR/ACP KS/DH/KR/ACP | KS/ATm/KR/ACP KS/ATmm/DH/KR/ACP | KS/ATm/KR/ACP KS/ATmm/DH/KR/ACP |
(qnmA7) | (1-1092) | (8-147) | |
20 21 22 | KS/ATm/DH/KR/ACP KS/ATmm/KR/ACP KS/ATm/KR/ACP | KS/ATm/DH/KR/ACP KS/ATmm/KR/ACP KS/ATm/KR/ACP | KS/ATm/DH/KR/ACP KS/KR/ACP KS/ATm/KR/ACP |
(qnmA8) | (1-1093) | (8-148) | |
23 24 | KS/ATm/KR/ACP KS/ATmm/DH/ER/KR/ACP | KS/ATm/KR/ACP KS/ATmm/DH/ER/KR/ACP | KS/AT/KR/ACP KS/ATmm/DH/ER/KR/ACP |
(qnmA9) | (1-1094) | (8-149) | |
25 | KS/ATm/KR/ACP | KS/ATm/KR/ACP | KS/ATm |
(8-150) | |||
26 27 | KS/ATmm/KR/ACP KS/ATmm/KR/ACP | KS/ATmm/KR/ACP KS/ATmm/KR/ACP | KS/ATmm/KR/ACP KS/ATmm/KR/ACP |
(qnmA10) | (1-1095) | (8-151) | |
28 29 | KS/ATm/DH/KR/ACP KS/ATmm/DH/KR/ACP | KS/ATm/DH/KR/ACP KS/ATmm/DH/KR/ACP | KS/ATm/DH/KR/ACP KS/ATmm/DH/KR/ACP |
(qnmA11) | (1-1096) | (8-152) | |
30 | KS/ATmm/KR/ACP | KS/ATmm/KR/ACP | KS/ATmm/KR/ACP |
(qnmA12) | (1-1097) | (8-153) | |
31 32 | KS/ATmm/KR/ACP KS/ATm/KR/ACP | KS/ATmm/KR/ACP KS/ATm/KR/ACP | KS/ATmm/KR/ACP KS/ATm/KR/ACP |
(qnmA13) | (1-1098) | (8-154) | |
33 | KS/ATm/KR/ACP/Te | KS/ATm/ACP/Te | KS/ATm/ACP/Te |
Gene Cluster | ORF | Domain Organization | Predicted Product |
---|---|---|---|
t1pks-2 * | 8-118 | CoL/ACP-KS/ATm/DH/KR/ACP-KS/ATmm/DH/ER/KR/ACP | quinolidomicin congener |
8-122 | KS/ATm/DH/KR/ACP | ||
8-123 | KS/ATm/KR/ACP-KS/ATm/KR/ACP-KS/ATm/KR/ACP | ||
8-135 | KS/ATm/DH/ER/KR/ACP-KS/AT/DH/ER/KR/ACP- | ||
KS/ATm/DH/ER/KR/ACP-KS/ATm/KR/ACP | |||
8-136 | KS/ATmm/KR/ACP | ||
8-137 | KS/ATm/DH/KR/ACP-KS/ATm/DH/KR/ACP-KS/ATm/DH/KR/ACP- | ||
KS/ATm/KR/ACP-KS/ATm/KR/ACP | |||
8-146 8-147 8-148 8-149 8-150 8-151 8-152 8-153 8-154 | KS/ATm/KR/ACP-KS/ATmm/DH/KR/ACP KS/ATm/DH/KR/ACP-KS/KR/ACP-KS/ATm/KR/ACP KS/AT/KR/ACP-KS/ATmm/DH/ER/KR/ACP KS/ATm KS/ATmm/KR/ACP-KS/ATmm/KR/ACP KS/ATm/DH/KR/ACP-KS/ATmm/DH/KR/ACP KS/ATmm/KR/ACP KS/ATmm/KR/ACP-KS/ATm/KR/ACP KS/ATm/ACP-Te | ||
t1pks-5 | 17-167 | CoL/ACP-KS/ATmm/DH/KR/ACP-KS/ATmm/ACP-KS/ATmm/KR/ACP | 16-demethylrifamycins |
KS/ATmm/DH/KR/ACP-KS/ATmm/DH/KR/ACP-KS/ATmm/DH/KR/ACP | |||
17-166 | KS/ATmm/DH/KR/ACP | ||
KS/ATmm/DH/KR/ACP | |||
17-165 | KS/ATm/DH/KR/ACP-KS/ATm/DH/KR/ACP | ||
17-164 | |||
17-163 | |||
t2pks-2 | 8-66 8-67 8-68 | KSα KSβ (CLF) ACP | kosinostatin |
t2pks-3 | 15-39 15-40 15-41 | KSα KSβ (CLF) ACP | aromatic polyketide |
t3pks-1 * | 13-182 | KS | alkyl-O-dihydrogeranyl-methoxyhydroquinone |
t3pks-2 | 9-577 | KS | polyketide with guanidinotide moiety |
nrps-6P | 8-1 P 8-2 8-14 | …T C/Acys/MT/T Adhb | pyochelin |
nrps-7 | 9-387 | Aglu/T-TD | glu with β-lactone |
nrps-8 | 16-60 16-59 16-58 | T Aval C/Apro/T-TD | dipeptide (val-pro) |
nrps-9 | 19-118 19-110 | A/T C/A/T | dipeptide (x-x) |
nrps-10 | 20-72 20-83 | A A/T/E | dipeptide (x-x) |
pks/nrps-2 * | 24-73 24-74 24-75 24-76 24-77 24-78 | C/A/T KS ACP C/Aval/T KS/ATm/ACP Aser | tripeptide with polyketide moiety (ser-x-val-pk) |
pks/nrps-3 * | 17-59 17-56 17-55 17-52 17-51 | A/T-KS/DH A/T-C/T KS/ATm/KR/DH/ACP C/Aasn/T C/Aser/T-Te | pentapeptide with polyketide moiety (x-pk-x-y-pk-asn-ser) |
pks/nrps-5 | 21-43 21-44 21-45 21-46 21-47 21-48 21-50 21-51 21-53 21-62 | C/Aasn/T-C/A/T C/Aser/T KS/ATm/MT/KR/ACP C/A/T CoL/T-C/Aser/T-C T-C C/Ab-ala/T-C/Acys/T-C A/T C A/T | methyltallysomycin |
pks/nrps-6 | 26-56 | A/T-KS/ATm/ACP-C/A/T-C | dipeptide with polyketide moiety (x-pk-x) |
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Komaki, H.; Ichikawa, N.; Hosoyama, A.; Hamada, M.; Igarashi, Y. In Silico Analysis of PKS and NRPS Gene Clusters in Arisostatin- and Kosinostatin-Producers and Description of Micromonospora okii sp. nov. Antibiotics 2021, 10, 1447. https://doi.org/10.3390/antibiotics10121447
Komaki H, Ichikawa N, Hosoyama A, Hamada M, Igarashi Y. In Silico Analysis of PKS and NRPS Gene Clusters in Arisostatin- and Kosinostatin-Producers and Description of Micromonospora okii sp. nov. Antibiotics. 2021; 10(12):1447. https://doi.org/10.3390/antibiotics10121447
Chicago/Turabian StyleKomaki, Hisayuki, Natsuko Ichikawa, Akira Hosoyama, Moriyuki Hamada, and Yasuhiro Igarashi. 2021. "In Silico Analysis of PKS and NRPS Gene Clusters in Arisostatin- and Kosinostatin-Producers and Description of Micromonospora okii sp. nov." Antibiotics 10, no. 12: 1447. https://doi.org/10.3390/antibiotics10121447