Synthetic Biology Journal ›› 2022, Vol. 3 ›› Issue (6): 1277-1291.DOI: 10.12211/2096-8280.2022-004
• Invited Review • Previous Articles
Liangliang WU1, Yingying CHANG1, Zixin DENG1,2, Tiangang LIU1,2
Received:
2022-01-05
Revised:
2022-02-23
Online:
2023-01-17
Published:
2022-12-31
Contact:
Tiangang LIU
吴亮亮1, 常莹莹1, 邓子新1,2, 刘天罡1,2
通讯作者:
刘天罡
作者简介:
基金资助:
Liangliang WU, Yingying CHANG, Zixin DENG, Tiangang LIU. Efficient synthesis of gentamicin and its related products in industrial chassis cells[J]. Synthetic Biology Journal, 2022, 3(6): 1277-1291.
吴亮亮, 常莹莹, 邓子新, 刘天罡. 庆大霉素及其相关产物在工业底盘细胞中的高效合成[J]. 合成生物学, 2022, 3(6): 1277-1291.
Add to citation manager EndNote|Ris|BibTeX
URL: https://synbioj.cip.com.cn/EN/10.12211/2096-8280.2022-004
Strain | Description | Reference |
---|---|---|
M. echinospora J1-020 | Wild-type | This study |
DH10B | F–mcrA ∆(mrr-hsdRMS-mcrBC) | Gibco-BRL |
ET12567(pUZ8002) | damdcmhsdS/pUZ8002, for intergeneric conjugation | [ |
ET12567(pUB307) | dam dcm hsdS/pUB307, for intergeneric conjugation | [ |
YC001 | genP gene overexpression strain | This study |
YC002 | genP gene overexpression strain | This study |
YC003 | genP gene overexpression strain | This study |
YC004 | genP gene overexpression strain | This study |
YC005 | genQ gene knockout strain | This study |
YC006 | genB4 gene knockout strain | This study |
YC007 | genB4 and genK gene knockout strain | This study |
Plasmid | ||
pWHU77 | int, att, tsr, ermE* | [ |
pYH7 | sti-, rep*, orf85-, R1-, tsr, aac(3)IV | [ |
pXS001 | E.coli-actinomycete integrated shuttle plasmid, pWHU77 carries genP under the control of the ermE* promoter | This study |
pXS002 | E.coli-actinomycete integrated shuttle plasmid, pWHU77 carries genP under the control of the kasOp* promoter | This study |
pXS003 | E.coli-actinomycete integrated shuttle plasmid, pWHU77 carries genP under the control of the rpsLp-cf promoter | This study |
pXS004 | E.coli-actinomycete replicating shuttle plasmid, pYH7 carries genP under the control of the rpsLp-cf promoter | This study |
pXS005 | E.coli-actinomycete replicating shuttle plasmid, genQ gene knockout plasmid | This study |
pXS006 | E.coli-actinomycete replicating shuttle plasmid, genB4 gene knockout plasmid | This study |
pXS007 | E.coli-actinomycete replicating shuttle plasmid, genK gene knockout plasmid | This study |
Tab. 1 Strains and plasmids used in this study
Strain | Description | Reference |
---|---|---|
M. echinospora J1-020 | Wild-type | This study |
DH10B | F–mcrA ∆(mrr-hsdRMS-mcrBC) | Gibco-BRL |
ET12567(pUZ8002) | damdcmhsdS/pUZ8002, for intergeneric conjugation | [ |
ET12567(pUB307) | dam dcm hsdS/pUB307, for intergeneric conjugation | [ |
YC001 | genP gene overexpression strain | This study |
YC002 | genP gene overexpression strain | This study |
YC003 | genP gene overexpression strain | This study |
YC004 | genP gene overexpression strain | This study |
YC005 | genQ gene knockout strain | This study |
YC006 | genB4 gene knockout strain | This study |
YC007 | genB4 and genK gene knockout strain | This study |
Plasmid | ||
pWHU77 | int, att, tsr, ermE* | [ |
pYH7 | sti-, rep*, orf85-, R1-, tsr, aac(3)IV | [ |
pXS001 | E.coli-actinomycete integrated shuttle plasmid, pWHU77 carries genP under the control of the ermE* promoter | This study |
pXS002 | E.coli-actinomycete integrated shuttle plasmid, pWHU77 carries genP under the control of the kasOp* promoter | This study |
pXS003 | E.coli-actinomycete integrated shuttle plasmid, pWHU77 carries genP under the control of the rpsLp-cf promoter | This study |
pXS004 | E.coli-actinomycete replicating shuttle plasmid, pYH7 carries genP under the control of the rpsLp-cf promoter | This study |
pXS005 | E.coli-actinomycete replicating shuttle plasmid, genQ gene knockout plasmid | This study |
pXS006 | E.coli-actinomycete replicating shuttle plasmid, genB4 gene knockout plasmid | This study |
pXS007 | E.coli-actinomycete replicating shuttle plasmid, genK gene knockout plasmid | This study |
Primers | Sequence(5′ to 3′) | Restriction site |
---|---|---|
XS001-genP-F | CCA | NdeⅠ |
XS001-genP-R | TAC | EcoRⅠ |
XS001-YZ-F | GCGAGTGTCCGTTCGAGTGG | |
XS001-YZ-R | TCAGAGAAATTCGTCCAGCAG | |
XS002-kasOp*-F | GCAGGTCGACTCTAGTATGCAT | XbaⅠ |
XS002- kasOp*-R | GTGCTGCAACCATCTTCATATGGCGTATCCCCTTTCAGATACC | |
XS002-genP-F | TCTGAAAGGGGATACGCCATATGAAGATGGTTGCAGCACC | |
XS002-genP-R | GGAAACAGCTATGACATGATTAC | EcoRⅠ |
XS002-YZ-F | GGAACGATCGTTGGCTGTGTTC | |
XS003-rpsLp-cf-F | AGGTCGACTCTAGTATGCAT | XbaⅠ |
XS003-rpsLp-cf-R | GGTGCTGCAACCATCTTCATATGGCGTATCCCCTTTCAGATAC | |
XS003-genP-F | TCTGAAAGGGGATACGCCATATGAAGATGGTTGCAGCACC | |
XS003-genP-R | TTTCACACAGGAAACAGCTATGACATGATTAC | EcoRⅠ |
XS003-YZ-F | GGAACGATCGTTGGCTGCCCGCCGCGGGCGCTG | |
XS004-leftarm-F | ACCTGCAGGTCGACTCTAGACACGTCTGAA | NheⅠ |
XS004-leftarm-R | CCTCCAGCGCCCGCGGCGGGCAGCCAACGATCGTTCCTCACGCCTTGTGGATCGCCACC | |
XS004-rpsLp-cf-F | CCTGGTGGCGATCCACAAGGCGTGAGGAACGATCGTTGGCTGCCCGCCGCGGGCGCTGG | |
XS004-genP-R | AGACCACCGCGATCGTCGAGCGCCTCTGGGAGGACTGATCAGAGAAATTCGTCCAGCAG | |
XS004-rightarm-F | GCTGACCTACATCCAACTGCTGGACGAATTTCTCTGATCAGTCCTCCCAGAGGCGCTCG | |
XS004-rightarm-R | TAGGCGTATCACGAGGCCCTTTCGTCTTCAA | EcoRⅠ |
XS004-YZ-F | CCGTTCACCGTGCCCTGGCTGCGCGAGGTG | |
XS004-YZ-R | CTCGACCCGGCCGTCTGGATCGTGGCGAAG | |
XS005-leftarm-F | CGGCCATCGTGCCTCCCCACTCCTGC | HindⅢ |
XS005-leftarm-R | GTGCGGCCTTCCGCGAATTCCGGGACCGGGCCCGACTGGAG | |
XS005-rightarm-F | CGGGCCCGGTCCCGGAATTCGCGGAAGGCCGCACCGCCGAAG | |
XS005-rightarm-R | AGCGGAAAAGATCCGTCGACCTGCAGGCATGC | BglⅡ |
XS005-YZ-F | TCCGCTCGATTCGTTCCGTTCCGAC | |
XS005-YZ-R | GCACGGGACCACCGGGCAGGTGCTC | |
XS006-leftarm-F | CTGCAGGTCGACTCTAGACACGTCTGAA | NheⅠ |
XS006-leftarm-R | AAGCTGACCTACATCCAACTGCTGGACGAATTTCTCTGATCAGCGCTGGTAGGTGCTCG | |
XS006-rightarm-F | AGCGCTGGCGGCTGCGCGCACCTACCAGCGCTGCTAAGAGAAATTCGTCCAGCAGTTGG | |
XS006-rightarm-R | GGCGTATCACGAGGCCCTTTCGTCTTCAA | EcoRⅠ |
XS006-YZ-F | GGCAGCCGGACTGGGCGACCATCCGGATCG | |
XS006-YZ-R | CCGAGGACGATCTCGTCGTCTGCCACGGTG | |
XS007-leftarm-F | CTGCAGGTCGACTCTAGACACGTCTGAA | NheⅠ |
XS007-leftarm-R | CCCCCTACTACGAGAGCGCCTACGAGCTGGCCCGGATGATGGCGCAGCTCGACCCGGAG | |
XS007-rightarm-F | GTTCCTCCGGGCTCTCCGGGTCGAGCtGCGCCATCATCCGGGCCAGCTCGAGGCGCTC | |
XS007-rightarm-R | ATAGGCGTATCACGAGGCCCTTTCGTCTTCAA | EcoRⅠ |
XS007-YZ-F | CGTCACGCGATGGGAGCAGGGCGGAGTATC | |
XS007-YZ-R | CCGAGCATCACGCTGCCGAAGGAGTTGGAG |
Tab. 2 Oligonucleotide primers used in this study
Primers | Sequence(5′ to 3′) | Restriction site |
---|---|---|
XS001-genP-F | CCA | NdeⅠ |
XS001-genP-R | TAC | EcoRⅠ |
XS001-YZ-F | GCGAGTGTCCGTTCGAGTGG | |
XS001-YZ-R | TCAGAGAAATTCGTCCAGCAG | |
XS002-kasOp*-F | GCAGGTCGACTCTAGTATGCAT | XbaⅠ |
XS002- kasOp*-R | GTGCTGCAACCATCTTCATATGGCGTATCCCCTTTCAGATACC | |
XS002-genP-F | TCTGAAAGGGGATACGCCATATGAAGATGGTTGCAGCACC | |
XS002-genP-R | GGAAACAGCTATGACATGATTAC | EcoRⅠ |
XS002-YZ-F | GGAACGATCGTTGGCTGTGTTC | |
XS003-rpsLp-cf-F | AGGTCGACTCTAGTATGCAT | XbaⅠ |
XS003-rpsLp-cf-R | GGTGCTGCAACCATCTTCATATGGCGTATCCCCTTTCAGATAC | |
XS003-genP-F | TCTGAAAGGGGATACGCCATATGAAGATGGTTGCAGCACC | |
XS003-genP-R | TTTCACACAGGAAACAGCTATGACATGATTAC | EcoRⅠ |
XS003-YZ-F | GGAACGATCGTTGGCTGCCCGCCGCGGGCGCTG | |
XS004-leftarm-F | ACCTGCAGGTCGACTCTAGACACGTCTGAA | NheⅠ |
XS004-leftarm-R | CCTCCAGCGCCCGCGGCGGGCAGCCAACGATCGTTCCTCACGCCTTGTGGATCGCCACC | |
XS004-rpsLp-cf-F | CCTGGTGGCGATCCACAAGGCGTGAGGAACGATCGTTGGCTGCCCGCCGCGGGCGCTGG | |
XS004-genP-R | AGACCACCGCGATCGTCGAGCGCCTCTGGGAGGACTGATCAGAGAAATTCGTCCAGCAG | |
XS004-rightarm-F | GCTGACCTACATCCAACTGCTGGACGAATTTCTCTGATCAGTCCTCCCAGAGGCGCTCG | |
XS004-rightarm-R | TAGGCGTATCACGAGGCCCTTTCGTCTTCAA | EcoRⅠ |
XS004-YZ-F | CCGTTCACCGTGCCCTGGCTGCGCGAGGTG | |
XS004-YZ-R | CTCGACCCGGCCGTCTGGATCGTGGCGAAG | |
XS005-leftarm-F | CGGCCATCGTGCCTCCCCACTCCTGC | HindⅢ |
XS005-leftarm-R | GTGCGGCCTTCCGCGAATTCCGGGACCGGGCCCGACTGGAG | |
XS005-rightarm-F | CGGGCCCGGTCCCGGAATTCGCGGAAGGCCGCACCGCCGAAG | |
XS005-rightarm-R | AGCGGAAAAGATCCGTCGACCTGCAGGCATGC | BglⅡ |
XS005-YZ-F | TCCGCTCGATTCGTTCCGTTCCGAC | |
XS005-YZ-R | GCACGGGACCACCGGGCAGGTGCTC | |
XS006-leftarm-F | CTGCAGGTCGACTCTAGACACGTCTGAA | NheⅠ |
XS006-leftarm-R | AAGCTGACCTACATCCAACTGCTGGACGAATTTCTCTGATCAGCGCTGGTAGGTGCTCG | |
XS006-rightarm-F | AGCGCTGGCGGCTGCGCGCACCTACCAGCGCTGCTAAGAGAAATTCGTCCAGCAGTTGG | |
XS006-rightarm-R | GGCGTATCACGAGGCCCTTTCGTCTTCAA | EcoRⅠ |
XS006-YZ-F | GGCAGCCGGACTGGGCGACCATCCGGATCG | |
XS006-YZ-R | CCGAGGACGATCTCGTCGTCTGCCACGGTG | |
XS007-leftarm-F | CTGCAGGTCGACTCTAGACACGTCTGAA | NheⅠ |
XS007-leftarm-R | CCCCCTACTACGAGAGCGCCTACGAGCTGGCCCGGATGATGGCGCAGCTCGACCCGGAG | |
XS007-rightarm-F | GTTCCTCCGGGCTCTCCGGGTCGAGCtGCGCCATCATCCGGGCCAGCTCGAGGCGCTC | |
XS007-rightarm-R | ATAGGCGTATCACGAGGCCCTTTCGTCTTCAA | EcoRⅠ |
XS007-YZ-F | CGTCACGCGATGGGAGCAGGGCGGAGTATC | |
XS007-YZ-R | CCGAGCATCACGCTGCCGAAGGAGTTGGAG |
Type | Morphology of actinomycetes | Plasmid | The mixing ratio (Donor: Receptor) | Incubation time/h | Number of conjugants (Cultivate to 9d) |
---|---|---|---|---|---|
Diparental conjugation | mycelia | pWHU77 | 10∶1、4∶1、1∶1 | 14、16 | 100~200 |
mycelia | pYH7 | 20∶1、10∶1 | 1 | ||
Triparental conjugation | mycelia | pWHU77 | 4∶4∶1、1∶1∶1 | 100~200 | |
mycelia | pYH7 | 4∶4∶1、1∶1∶1 | 50~100 | ||
spore | pYH7 | 10∶10∶1、1∶1∶1 | 13 | >200 |
Tab. 3 Exploration of the conjugation conditions of M. echinospora J1-020
Type | Morphology of actinomycetes | Plasmid | The mixing ratio (Donor: Receptor) | Incubation time/h | Number of conjugants (Cultivate to 9d) |
---|---|---|---|---|---|
Diparental conjugation | mycelia | pWHU77 | 10∶1、4∶1、1∶1 | 14、16 | 100~200 |
mycelia | pYH7 | 20∶1、10∶1 | 1 | ||
Triparental conjugation | mycelia | pWHU77 | 4∶4∶1、1∶1∶1 | 100~200 | |
mycelia | pYH7 | 4∶4∶1、1∶1∶1 | 50~100 | ||
spore | pYH7 | 10∶10∶1、1∶1∶1 | 13 | >200 |
1 | LLEWELLYN N M, SPENCER J B. Biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics[J]. Natural Product Reports, 2006, 23(6): 864-874. |
2 | Waksman SA. Antibiotics and chemotherapy[J]. California medicine, 1953,78(5):417-423. |
3 | SWART E A, HUTCHISON D, WAKSMAN S A. Neomycin, recovery and purification[J]. Archives of Biochemistry, 1949, 24(1): 92-103. |
4 | UMEZAWA H, UEDA M, MAEDA K, et al. Production and isolation of a new antibiotic: kanamycin[J]. The Journal of Antibiotics, 1957, 10(5): 181-188. |
5 | WEINSTEIN M J, LUEDEMANN G M, ODEN E M, et al. Gentamicin, a new antibiotic complex from micromonospora[J]. Journal of Medicinal Chemistry, 1963, 6: 463-464. |
6 | FOURMY D, RECHT M I, BLANCHARD S C, et al. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic[J]. Science, 1996, 274(5291): 1367-1371. |
7 | TESTA R T, TILLEY B C. Biotransformation, a new approach to aminoglycoside biosynthesis: II. Gentamicin[J]. The Journal of Antibiotics, 1976, 29(2): 140-146. |
8 | KHAREL M K, BASNET D B, LEE H C, et al. Molecular cloning and characterization of a 2-deoxystreptamine biosynthetic gene cluster in gentamicin-producing Micromonospora echinospora ATCC 15835[J]. Molecules and Cells, 2004, 18(1): 71-78. |
9 | PARK J W, HONG J S J, PARAJULI N, et al. Genetic dissection of the biosynthetic route to gentamicin A2 by heterologous expression of its minimal gene set[J]. Proceedings of the National Academy of Sciences of the United States of America, 2008, 105(24): 8399-8404. |
10 | KIM J Y, SUH J W, KANG S H, et al. Gene inactivation study of gntE reveals its role in the first step of pseudotrisaccharide modifications in gentamicin biosynthesis[J]. Biochemical and Biophysical Research Communications, 2008, 372(4): 730-734. |
11 | HONG W R, YAN L B. Identification of gntK, a gene required for the methylation of purpurosamine C-6' in gentamicin biosynthesis[J]. The Journal of General and Applied Microbiology, 2012, 58(5): 349-356. |
12 | KIM H J, MCCARTY R M, OGASAWARA Y, et al. GenK-catalyzed C-6′ methylation in the biosynthesis of gentamicin: isolation and characterization of a cobalamin-dependent radical SAM enzyme[J]. Journal of the American Chemical Society, 2013, 135(22): 8093-8096. |
13 | HUANG C, HUANG F L, MOISON E, et al. Delineating the biosynthesis of gentamicin X2, the common precursor of the gentamicin C antibiotic complex[J]. Chemistry & Biology, 2015, 22(2): 251-261. |
14 | GUO J H, HUANG F L, HUANG C, et al. Specificity and promiscuity at the branch point in gentamicin biosynthesis[J]. Chemistry & Biology, 2014, 21(5): 608-618. |
15 | SHAO L, CHEN J S, WANG C X, et al. Characterization of a key aminoglycoside phosphotransferase in gentamicin biosynthesis[J]. Bioorganic & Medicinal Chemistry Letters, 2013, 23(5): 1438-1441. |
16 | ZHOU S T, CHEN X T, NI X P, et al. Pyridoxal-5′-phosphate-dependent enzyme GenB3 catalyzes C-3′, 4′-dideoxygenation in gentamicin biosynthesis[J]. Microbial Cell Factories, 2021, 20(1): 65. |
17 | CHEN X T, ZHANG H, ZHOU S T, et al. The bifunctional enzyme, GenB4, catalyzes the last step of gentamicin 3′, 4′-di-deoxygenation via reduction and transamination activities[J]. Microbial Cell Factories, 2020, 19(1): 62. |
18 | LI S, GUO J, REVA A, et al. Methyltransferases of gentamicin biosynthesis[J]. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(6): 1340-1345. |
19 | BAN Y H, SONG M C, HWANG J Y, et al. Complete reconstitution of the diverse pathways of gentamicin B biosynthesis[J]. Nature Chemical Biology, 2019, 15(3): 295-303. |
20 | CHANG Y Y, CHAI B Z, DING Y K, et al. Overproduction of gentamicin B in industrial strain Micromonospora echinospora CCTCC M 2018898 by cloning of the missing genes genR and genS [J]. Metabolic Engineering Communications, 2019, 9: e00096. |
21 | MACNEIL D J, OCCI J L, GEWAIN K M, et al. Complex organization of the Streptomyces avermitilis genes encoding the avermectin polyketide synthase[J]. Gene, 1992, 115(1/2): 119-125. |
22 | FLETT F, MERSINIAS V, SMITH C P. High efficiency intergeneric conjugal transfer of plasmid DNA from Escherichia coli to methyl DNA-restricting streptomycetes[J]. FEMS Microbiology Letters, 1997, 155(2): 223-229. |
23 | SUN Y H, HONG H, SAMBORSKYY M, et al. Organization of the biosynthetic gene cluster in Streptomyces sp. DSM 4137 for the novel neuroprotectant polyketide meridamycin[J]. Microbiology, 2006, 152(Pt 12): 3507-3515. |
24 | WEBER T, BLIN K, DUDDELA S, et al. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters[J]. Nucleic Acids Research, 2015, 43(W1): W237-W243. |
25 | BILYK O, LUZHETSKYY A. Metabolic engineering of natural product biosynthesis in actinobacteria[J]. Current Opinion in Biotechnology, 2016, 42: 98-107. |
26 | SASAKI K, MIZUSAWA H, ISHIDATE M, et al. Regulation of G418 selection efficiency by cell-cell interaction in transfection[J]. Somatic Cell and Molecular Genetics, 1992, 18(6): 517-527. |
27 | BAIAZITOV R Y, FRIESEN W, JOHNSON B, et al. Chemical modifications of G418 (geneticin): synthesis of novel readthrough aminoglycosides results in an improved in vitro safety window but no improvements in vivo [J]. Carbohydrate Research, 2020, 495: 108058. |
28 | NI X P, SUN Z P, ZHANG H Y, et al. Genetic engineering combined with random mutagenesis to enhance G418 production in Micromonospora echinospora [J]. Journal of Industrial Microbiology & Biotechnology, 2014, 41(9): 1383-1390. |
29 | SHAEER K M, ZMARLICKA M T, CHAHINE E B, et al. Plazomicin: a next-generation aminoglycoside[J]. Pharmacotherapy, 2019, 39(1): 77-93. |
30 | NI X P, SUN Z P, GU Y W, et al. Assembly of a novel biosynthetic pathway for gentamicin B production in Micromonospora echinospora [J]. Microbial Cell Factories, 2016, 15: 1. |
31 | WU Z, GAO W L, ZHOU S T, et al. Improving gentamicin B and gentamicin C1a production by engineering the glycosyltransferases that transfer primary metabolites into secondary metabolites biosynthesis[J]. Microbiological Research, 2017, 203: 40-46. |
32 | LI D, LI H, NI X P, et al. Construction of a gentamicin C1a-overproducing strain of Micromonospora purpurea by inactivation of the gacD gene[J]. Microbiological research, 2013, 168(5): 263-267. |
No related articles found! |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||