Reference
Andreani, J., Le Bideau, M., Duflot,
I., Jardot, P., Rolland, C., Boxberger, M., . . . Raoult, D. (2020). In
vitro testing of combined hydroxychloroquine and azithromycin on
SARS-CoV-2 shows synergistic effect. Microbial Pathogenesis, 145 .
doi: 10.1016/j.micpath.2020.104228
Butler, M. J., Bruheim, P., Jovetic,
S., Marinelli, F., Postma, P. W., & Bibb, M. J. (2002). Engineering of
primary carbon metabolism for improved antibiotic production in
Streptomyces lividans. Appl Environ Microbiol, 68 (10), 4731-4739.
doi: 10.1128/aem.68.10.4731-4739.2002
Carata, E., Peano, C., Tredici, S. M.,
Ferrari, F., Tala, A., Corti, G., . . . Alifano, P. (2009). Phenotypes
and gene expression profiles of Saccharopolyspora erythraea
rifampicin-resistant (rif) mutants affected in erythromycin production.Microb Cell Fact, 8 , 18. doi: 10.1186/1475-2859-8-18
Chen, C., Hong, M., Chu, J., Huang,
M., Ouyang, L., Tian, X., & Zhuang, Y. (2017). Blocking the flow of
propionate into TCA cycle through a mutB knockout leads to a significant
increase of erythromycin production by an industrial strain of
Saccharopolyspora erythraea. Bioprocess Biosyst Eng, 40 (2),
201-209. doi: 10.1007/s00449-016-1687-5
Chen, Y., Huang, M., Wang, Z., Chu,
J., Zhuang, Y., & Zhang, S. (2013). Controlling the feed rate of
glucose and propanol for the enhancement of erythromycin production and
exploration of propanol metabolism fate by quantitative metabolic flux
analysis. Bioprocess Biosyst Eng, 36 (10), 1445-1453. doi:
10.1007/s00449-013-0883-9
Chng, C., Lum, A. M., Vroom, J. A., &
Kao, C. M. (2008). A key developmental regulator controls the synthesis
of the antibiotic erythromycin in Saccharopolyspora erythraea.Proc Natl Acad Sci U S A, 105 (32), 11346-11351. doi:
10.1073/pnas.0803622105
Cortés, J., Velasco, J., Foster, G.,
Blackaby, A. P., Rudd, B. A., & Wilkinson, B. (2002). Identification
and cloning of a type III polyketide synthase required for diffusible
pigment biosynthesis in Saccharopolyspora erythraea. Mol
Microbiol, 44 (5), 1213-1224. doi:
doi.org/10.1046/j.1365-2958.2002.02975.x
Darzi, Y., Letunic, I., Bork, P., &
Yamada, T. (2018). iPath3.0: interactive pathways explorer v3.Nucleic Acids Res, 46 (W1), W510-W513. doi: 10.1093/nar/gky299
Dhakal, D., Sohng, J. K., & Pandey,
R. P. (2019). Engineering actinomycetes for biosynthesis of macrolactone
polyketides. Microb Cell Fact, 18 (1), 137. doi:
10.1186/s12934-019-1184-z
El-Enshasy, H. A., Mohamed, N. A.,
Farid, M. A., & El-Diwany, A. I. (2008). Improvement of erythromycin
production by Saccharopolyspora erythraea in molasses based medium
through cultivation medium optimization. Bioresour Technol,
99 (10), 4263-4268. doi: 10.1016/j.biortech.2007.08.050
Ferro, A. M., Ramos, P., Guerreiro,
O., Jeronimo, E., Pires, I., Capel, C., . . . Goncalves, S. (2017).
Impact of novel SNPs identified in Cynara cardunculus genes on
functionality of proteins regulating phenylpropanoid pathway and their
association with biological activities. BMC Genomics, 18 (1), 183.
doi: 10.1186/s12864-017-3534-8
Fischer, M., Falke, D., Naujoks, C.,
& Sawers, R. G. (2018). Cytochrome bd oxidase has an important role in
sustaining growth and development of Streptomyces coelicolor A3 (2)
under oxygen-limiting conditions. J Bacteriol, 200 (16),
e00239-00218.
Fujimoto, M., Chijiwa, M., Nishiyama,
T., Takano, H., & Ueda, K. (2016). Developmental defect of cytochrome
oxidase mutants of Streptomyces coelicolor A3(2). Microbiology,
162 (8), 1446-1455. doi: 10.1099/mic.0.000332
Hong, M., Huang, M., Chu, J., Zhuang,
Y., & Zhang, S. (2016). Impacts of proline on the central metabolism of
an industrial erythromycin-producing strain Saccharopolyspora erythraea
via (13)C labeling experiments. J Biotechnol, 231 , 1-8. doi:
10.1016/j.jbiotec.2016.05.026
Hopwood, D. A. (1985). Genetic
manipulation of Streptomyces: a laboratory manual.
Huerta-Cepas, J., Szklarczyk, D.,
Forslund, K., Cook, H., Heller, D., Walter, M. C., . . . Kuhn, M.
(2016). eggNOG 4.5: a hierarchical orthology framework with improved
functional annotations for eukaryotic, prokaryotic and viral sequences.Nucleic Acids Res, 44 (D1), D286-D293. doi:
doi.org/10.1093/nar/gkv1248
Karnicar, K., Drobnak, I., Petek, M.,
Magdevska, V., Horvat, J., Vidmar, R., . . . Petkovic, H. (2016).
Integrated omics approaches provide strategies for rapid erythromycin
yield increase in Saccharopolyspora erythraea. Microb Cell Fact,
15 , 93. doi: 10.1186/s12934-016-0496-5
Kiss, J., Szabo, M., & Olasz, F.
(2003). Site-specific recombination by the DDE family member mobile
element IS30 transposase. Proc Natl Acad Sci U S A, 100 (25),
15000-15005. doi: 10.1073/pnas.2436518100
Li, X., Chen, J., Andersen, J. M.,
Chu, J., & Jensen, P. R. (2020). Cofactor engineering redirects
secondary metabolism and enhances erythromycin production in
Saccharopolyspora erythraea. ACS Synth Biol, 9 (3), 655-670. doi:
10.1021/acssynbio.9b00528
Li, X., Chu, J., & Jensen, P. R.
(2020). The expression of NOX from synthetic promoters reveals an
important role of the redox status in regulating secondary metabolism of
Saccharopolyspora erythraea. Front Bioeng Biotechnol, 8 , 818.
doi: 10.3389/fbioe.2020.00818
Li, Y., Chang, X., Yu, W., Li, H.,
Ye, Z., Yu, H., . . . Ye, B. (2013). Systems perspectives on
erythromycin biosynthesis by comparative genomic and transcriptomic
analyses of S. erythraea E3 and NRRL23338 strains. BMC Genomics,
14 (1), 523. doi: doi.org/10.1186/1471-2164-14-523
Liao, C., Yao, L., Xu, Y., Liu, W.,
Zhou, Y., & Ye, B. (2015). Nitrogen regulator GlnR controls uptake and
utilization of non-phosphotransferase-system carbon sources in
actinomycetes. Proc. Natl. Acad. Sci. U. S. A., 112 (51),
15630-15635. doi: doi:10.1073/pnas.1508465112
Licona-Cassani, C., Marcellin, E.,
Quek, L. E., Jacob, S., & Nielsen, L. K. (2012). Reconstruction of the
Saccharopolyspora erythraea genome-scale model and its use for enhancing
erythromycin production. Antonie van Leeuwenhoek, 102 (3),
493-502. doi: 10.1007/s10482-012-9783-2
Liu, J., Chen, Y., Wang, W., Ren, M.,
Wu, P., Wang, Y., . . . Zhang, B. (2017). Engineering of an Lrp family
regulator SACE_Lrp improves erythromycin production in
Saccharopolyspora erythraea. Metab Eng, 39 , 29-37. doi:
10.1016/j.ymben.2016.10.012
Liu, Y., Ren, C. Y., Wei, W. P., You,
D., Yin, B. C., & Ye, B. C. (2019). A CRISPR-Cas9 Strategy for
Activating the Saccharopolyspora erythraea Erythromycin Biosynthetic
Gene Cluster with Knock-in Bidirectional Promoters. ACS Synth
Biol, 8 (5), 1134-1143. doi: 10.1021/acssynbio.9b00024
Lum, A. M., Huang, J., Hutchinson, C.
R., & Kao, C. M. (2004). Reverse engineering of industrial
pharmaceutical-producing actinomycete strains using DNA microarrays.Metab Eng, 6 (3), 186-196. doi: 10.1016/j.ymben.2003.12.001
Manteca, A., & Yague, P. (2018).
Streptomyces Differentiation in Liquid Cultures as a Trigger of
Secondary Metabolism. Antibiotics (Basel), 7 (2). doi:
10.3390/antibiotics7020041
Marcellin, E., Mercer, T. R.,
Licona-Cassani, C., Palfreyman, R. W., Dinger, M. E., Steen, J. A., . .
. Nielsen, L. K. (2013). Saccharopolyspora erythraea’s genome is
organised in high-order transcriptional regions mediated by targeted
degradation at the metabolic switch. BMC Genomics, 14 (1), 15.
doi: doi.org/10.1186/1471-2164-14-15
Mironov, V., Sergienko, O.,
Nastasyak, I., & Danilenko, V. (2004). Biogenesis and regulation of
biosynthesis of erythromycins in Saccharopolyspora erythraea.Appl. Biochem. Microbiol., 40 (6), 531-541. doi:
doi.org/10.1023/B:ABIM.0000046985.66328.7a
Molle, V., Palframan, W. J., Findlay,
K. C., & Buttner, M. J. (2000). WhiD and WhiB, homologous proteins
required for different stages of sporulation in Streptomyces coelicolor
A3 (2). J Bacteriol, 182 (5), 1286-1295. doi: Biogenesis and
regulation of biosynthesis of erythromycins in Saccharopolyspora
erythraeadoi: 10.1128/JB.182.5.1286-1295.2000
Nagy, Z., & Chandler, M. (2004).
Regulation of transposition in bacteria. Res Microbiol, 155 (5),
387-398. doi: 10.1016/j.resmic.2004.01.008
Nakken, S., Alseth, I., & Rognes, T.
(2007). Computational prediction of the effects of non-synonymous single
nucleotide polymorphisms in human DNA repair genes. Neuroscience,
145 (4), 1273-1279. doi: 10.1016/j.neuroscience.2006.09.004
Newman, D. J., & Cragg, G. M.
(2016). Natural Products as Sources of New Drugs from 1981 to 2014.J Nat Prod, 79 (3), 629-661. doi: 10.1021/acs.jnatprod.5b01055
Oliynyk, M., Samborskyy, M., Lester,
J. B., Mironenko, T., Scott, N., Dickens, S., . . . Leadlay, P. F.
(2007). Complete genome sequence of the erythromycin-producing bacterium
Saccharopolyspora erythraea NRRL23338. Nat Biotechnol, 25 (4),
447-453. doi: 10.1038/nbt1297
Peano, C., Bicciato, S., Corti, G.,
Ferrari, F., Rizzi, E., Bonnal, R. J., . . . De Bellis, G. (2007).
Complete gene expression profiling of Saccharopolyspora erythraea using
GeneChip DNA microarrays. Microb Cell Fact, 6 , 37. doi:
10.1186/1475-2859-6-37
Peano, C., Damiano, F., Forcato, M.,
Pietrelli, A., Palumbo, C., Corti, G., . . . Alifano, P. (2014).
Comparative genomics revealed key molecular targets to rapidly convert a
reference rifamycin-producing bacterial strain into an overproducer by
genetic engineering. Metab Eng, 26 , 1-16. doi:
10.1016/j.ymben.2014.08.001
Peano, C., Tala, A., Corti, G.,
Pasanisi, D., Durante, M., Mita, G., . . . Alifano, P. (2012).
Comparative genomics and transcriptional profiles of Saccharopolyspora
erythraea NRRL 2338 and a classically improved erythromycin
over-producing strain. Microb Cell Fact, 11 , 32. doi:
10.1186/1475-2859-11-32
Qiao, L., Li, X., Ke, X., & Chu, J.
(2020). A two-component system gene SACE_0101 regulates copper
homeostasis in Saccharopolyspora erythraea. Bioresources and
Bioprocessing, 7 (1), 12. doi: 10.1186/s40643-020-0299-8
Radchenko, M. V., Thornton, J., &
Merrick, M. (2013). P(II) signal transduction proteins are ATPases whose
activity is regulated by 2-oxoglutarate. Proc Natl Acad Sci U S A,
110 (32), 12948-12953. doi: 10.1073/pnas.1304386110
Redenbach, M., Scheel, J., &
Schmidt, U. (2000). Chromosome topology and genome size of selected
actinomycetes species. Antonie van Leeuwenhoek, 78 (3-4), 227-235.
doi: doi.org/10.1023/A:1010289326752
Reeves, A. R., Brikun, I. A.,
Cernota, W. H., Leach, B. I., Gonzalez, M. C., & Weber, J. M. (2006).
Effects of methylmalonyl-CoA mutase gene knockouts on erythromycin
production in carbohydrate-based and oil-based fermentations of
Saccharopolyspora erythraea. J Ind Microbiol Biotechnol, 33 (7),
600-609. doi: 10.1007/s10295-006-0094-3
Reeves, A. R., Brikun, I. A.,
Cernota, W. H., Leach, B. I., Gonzalez, M. C., & Weber, J. M. (2007).
Engineering of the methylmalonyl-CoA metabolite node of
Saccharopolyspora erythraea for increased erythromycin production.Metab Eng, 9 (3), 293-303. doi: 10.1016/j.ymben.2007.02.001
Sayed, A. M., Abdel-Wahab, N. M.,
Hassan, H. M., & Abdelmohsen, U. R. (2019). Saccharopolyspora: an
underexplored source for bioactive natural products. J Appl
Microbiol . doi: 10.1111/jam.14360
Scott, R. I., Salmon, I., & Poole,
R. K. (1992). The cytochromes of the filamentous bacteria Streptomyces
clavuligerus and Saccharopolyspora erythraea (FormerlyStreptomyces
erythraeus). Curr Microbiol, 24 (2), 105-109. doi:
doi.org/10.1007/BF01570906
Sivapragasam, S., & Grove, A.
(2019). The Link between Purine Metabolism and Production of Antibiotics
in Streptomyces. Antibiotics (Basel), 8 (2). doi:
10.3390/antibiotics8020076
Smolke, C. D., & Keasling, J. D.
(2002). Effect of gene location, mRNA secondary structures, and RNase
sites on expression of two genes in an engineered operon.Biotechnol Bioeng, 80 (7), 762-776. doi: 10.1002/bit.10434
Summers, R. G., Donadio, S., Staver,
M. J., Wendt-Pienkowski, E., Hutchinson, C. R., & Katz, L. (1997).
Sequencing and mutagenesis of genes from the erythromycin biosynthetic
gene cluster of Saccharopolyspora erythraea that are involved in
L-mycarose and D-desosamine production. Microbiology, 143 (10),
3251-3262.
Tong, Y., Charusanti, P., Zhang, L.,
Weber, T., & Lee, S. Y. (2015). CRISPR-Cas9 Based Engineering of
Actinomycetal Genomes. ACS Synth Biol, 4 (9), 1020-1029. doi:
10.1021/acssynbio.5b00038
Varemo, L., Nielsen, J., & Nookaew,
I. (2013). Enriching the gene set analysis of genome-wide data by
incorporating directionality of gene expression and combining
statistical hypotheses and methods. Nucleic Acids Res, 41 (8),
4378-4391. doi: 10.1093/nar/gkt111
Wang, W., Li, S., Li, Z., Zhang, J.,
Fan, K., Tan, G., . . . Zhang, L. (2020). Harnessing the intracellular
triacylglycerols for titer improvement of polyketides in Streptomyces.Nat. Biotechnol., 38 (1), 76-83. doi:
doi.org/10.1038/s41587-019-0335-4
Wang, Y., Wang, Y., Chu, J., Zhuang,
Y., Zhang, L., & Zhang, S. (2007). Improved production of erythromycin
A by expression of a heterologous gene encoding S-adenosylmethionine
synthetase. Appl Microbiol Biotechnol, 75 (4), 837-842. doi:
10.1007/s00253-007-0894-z
Weber, T., Blin, K., Duddela, S.,
Krug, D., Kim, H. U., Bruccoleri, R., . . . Medema, M. H. (2015).
antiSMASH 3.0-a comprehensive resource for the genome mining of
biosynthetic gene clusters. Nucleic Acids Res, 43 (W1), W237-243.
doi: 10.1093/nar/gkv437
Weber, T., Charusanti, P.,
Musiol-Kroll, E. M., Jiang, X., Tong, Y., Kim, H. U., & Lee, S. Y.
(2015). Metabolic engineering of antibiotic factories: new tools for
antibiotic production in actinomycetes. Trends Biotechnol, 33 (1),
15-26. doi: 10.1016/j.tibtech.2014.10.009
Xu, Y., You, D., Yao, L. L., Chu, X.,
& Ye, B. C. (2019). Phosphate regulator PhoP directly and indirectly
controls transcription of the erythromycin biosynthesis genes in
Saccharopolyspora erythraea. Microb Cell Fact, 18 (1), 206. doi:
10.1186/s12934-019-1258-y
Xu, Z., Liu, Y., & Ye, B. C. (2018).
PccD Regulates Branched-Chain Amino Acid Degradation and Exerts a
Negative Effect on Erythromycin Production in Saccharopolyspora
erythraea. Appl Environ Microbiol, 84 (8). doi:
10.1128/AEM.00049-18
Xu, Z., You, D., Tang, L. Y., Zhou,
Y., & Ye, B. C. (2019). Metabolic engineering strategies based on
secondary messengers (p)ppGpp and C-di-GMP to increase erythromycin
yield in Saccharopolyspora erythraea. ACS Synth Biol, 8 (2),
332-345. doi: 10.1021/acssynbio.8b00372
Yuzawa, S., Keasling, J. D., & Katz,
L. (2017). Bio-based production of fuels and industrial chemicals by
repurposing antibiotic-producing type I modular polyketide synthases:
opportunities and challenges. J Antibiot (Tokyo), 70 (4), 378-385.
doi: 10.1038/ja.2016.136
Zeng, W., Guo, L., Xu, S., Chen, J.,
& Zhou, J. (2020). High-Throughput Screening Technology in Industrial
Biotechnology. Trends Biotechnol . doi:
10.1016/j.tibtech.2020.01.001
Zhang, Q., Chen, Y., Hong, M., Gao,
Y., Chu, J., Zhuang, Y.-p., & Zhang, S.-l. (2014). The dynamic
regulation of nitrogen and phosphorus in the early phase of fermentation
improves the erythromycin production by recombinant Saccharopolyspora
erythraea strain. Bioresources and Bioprocessing, 1 (1), 15. doi:
doi.org/10.1186/s40643-014-0015-7
Zheng, F., Long, Q., & Xie, J.
(2012). The function and regulatory network of WhiB and WhiB-like
protein from comparative genomics and systems biology perspectives.Cell Biochem Biophys, 63 (2), 103-108. doi:
10.1007/s12013-012-9348-z
Zhuang, Z., Huang, M., & Chu, J.
(2018). In silico reconstruction and experimental validation of
Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that
accounts for 1685 ORFs. Bioresour Bioprocess, 5 (1), 26. doi:
doi.org/10.1186/s40643-018-0212-x
Zhuo, Y., Zhang, W., Chen, D., Gao,
H., Tao, J., Liu, M., . . . Zhang, Q. (2010). Reverse biological
engineering of hrdB to enhance the production of avermectins in an
industrial strain of Streptomyces avermitilis. Proceedings of the
National Academy of Sciences, 107 (25), 11250-11254. doi:
doi:10.1073/pnas.1006085107
Zou, X., Hang, H.-f., Chu, J.,
Zhuang, Y.-p., & Zhang, S.-l. (2009a). Enhancement of erythromycin A
production with feeding available nitrogen sources in erythromycin
biosynthesis phase. Bioresour Technol, 100 (13), 3358-3365. doi:
doi.org/10.1016/j.biortech.2009.01.064
Zou, X., Hang, H.-f., Chu, J.,
Zhuang, Y.-p., & Zhang, S.-l. (2009b). Oxygen uptake rate optimization
with nitrogen regulation for erythromycin production and scale-up from
50 L to 372 m3 scale. Bioresour Technol, 100 (3), 1406-1412. doi:
doi.org/10.1016/j.biortech.2008.09.017