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Valverde JR, Gullón S, Mellado RP. Modelling the metabolism of protein secretion through the Tat route in Streptomyces lividans. BMC Microbiol 2018; 18:59. [PMID: 29898665 PMCID: PMC6000921 DOI: 10.1186/s12866-018-1199-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/30/2018] [Indexed: 01/03/2023] Open
Abstract
Background Streptomyces lividans has demonstrated its value as an efficient host for protein production due to its ability to secrete functional proteins directly to the media. Secretory proteins that use the major Sec route need to be properly folded outside the cell, whereas secretory proteins using the Tat route appear outside the cell correctly folded. This feature makes the Tat system very attractive for the production of natural or engineered Tat secretory proteins. S. lividans cells are known to respond differently to overproduction and secretion of Tat versus Sec proteins. Increased understanding of the impact of protein secretion through the Tat route can be obtained by a deeper analysis of the metabolic impact associated with protein production, and its dependence on protein origin, composition, secretion mechanisms, growth phases and nutrients. Flux Balance Analysis of Genome-Scale Metabolic Network models provides a theoretical framework to investigate cell metabolism under different constraints. Results We have built new models for various S. lividans strains to better understand the mechanisms associated with overproduction of proteins secreted through the Tat route. We compare models of an S. lividans Tat-dependent agarase overproducing strain with those of the S. lividans wild-type, an S. lividans strain carrying the multi-copy plasmid vector and an α-amylase Sec-dependent overproducing strain. Using updated genomic, transcriptomic and experimental data we could extend existing S. lividans models and produce a new model which produces improved results largely extending the coverage of S. lividans strains, the number of genes and reactions being considered, the predictive behaviour and the dependence on specification of exchange constraints. Comparison of the optimized solutions obtained highlights numerous changes between Tat- and Sec-dependent protein secreting strains affecting the metabolism of carbon, amino acids, nucleotides, lipids and cofactors, and variability analysis predicts a large potential for protein overproduction. Conclusions This work provides a detailed look to metabolic changes associated to Tat-dependent protein secretion reproducing experimental observations and identifying changes that are specific to each secretory route, presenting a novel, improved, more accurate and strain-independent model of S. lividans, thus opening the way for enhanced metabolic engineering of protein overproduction in S. lividans. Electronic supplementary material The online version of this article (10.1186/s12866-018-1199-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José R Valverde
- Scientific Computing Service. Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
| | - Sonia Gullón
- Departamento de Biotecnología Microbiana. Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Rafael P Mellado
- Departamento de Biotecnología Microbiana. Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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Exploring the Feasibility of the Sec Route to Secrete Proteins Using the Tat Route in Streptomyces lividans. Mol Biotechnol 2016. [PMID: 26202494 DOI: 10.1007/s12033-015-9883-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Streptomyces lividans uses mainly two pathways to target secretory proteins to the cytoplasmic membrane. The major pathway (Sec pathway) transports pre-proteins using the signal recognition particle, and the minor Tat pathway is responsible for the secretion using a folded conformation of a relatively low number of proteins. The signal peptides of the Sec-dependent alpha-amylase and the Tat-dependent agarase were interchanged and fused in-frame to the corresponding mature part of the other enzyme. Alpha-amylase was unable to use the Tat route when fused to the agarase signal peptide, while agarase used the Sec route when it was targeted by the alpha-amylase signal peptide. In addition to the signal peptide some yet unidentified parts of the secreted proteins may play a role in selecting the secretory route. Structure predictions for the Tat- and Sec-dependent proteins suggest that less structured proteins are more likely to be candidates for the Tat route.
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Gullón S, Marín S, Mellado RP. Overproduction of a Model Sec- and Tat-Dependent Secretory Protein Elicits Different Cellular Responses in Streptomyces lividans. PLoS One 2015. [PMID: 26200356 PMCID: PMC4511581 DOI: 10.1371/journal.pone.0133645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Streptomyces lividans is considered an efficient host for the secretory production of homologous and heterologous proteins. To identify possible bottlenecks in the protein production process, a comparative transcriptomic approach was adopted to study cellular responses during the overproduction of a Sec-dependent model protein (alpha-amylase) and a Tat-dependent model protein (agarase) in Streptomyces lividans. The overproduction of the model secretory proteins via the Sec or the Tat route in S. lividans does elicit a different major cell response in the bacterium. The stringent response is a bacterial response to nutrients’ depletion, which naturally occurs at late times of the bacterial cell growth. While the induction of the stringent response at the exponential phase of growth may limit overall productivity in the case of the Tat route, the induction of that response does not take place in the case of the Sec route, which comparatively is an advantage in secretory protein production processes. Hence, this study identifies a potential major drawback in the secretory protein production process depending on the secretory route, and provides clues to improving S. lividans as a protein production host.
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Affiliation(s)
- Sonia Gullón
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049, Madrid, Spain
| | - Silvia Marín
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049, Madrid, Spain
| | - Rafael P. Mellado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049, Madrid, Spain
- * E-mail:
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Vockenhuber MP, Suess B. Streptomyces coelicolor sRNA scr5239 inhibits agarase expression by direct base pairing to the dagA coding region. MICROBIOLOGY-SGM 2011; 158:424-435. [PMID: 22075028 DOI: 10.1099/mic.0.054205-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transcriptional regulation of primary and secondary metabolism is well-studied in Streptomyces coelicolor, a model organism for antibiotic production and cell differentiation. In contrast, little is known about post-transcriptional regulation and the potential functions of small non-coding RNAs (sRNAs) in this Gram-positive, GC-rich soil bacterium. Here, we report the identification and characterization of scr5239, an sRNA highly conserved in the genus Streptomyces. The sRNA is 159 nt long, composed of five stem-loops, and encoded in the intergenic region between SCO5238 and SCO5239. scr5239 expression is constitutive under several stress and growth conditions but dependent on the nitrogen supply. scr5239 decreases the production of the antibiotic actinorhodin, and represses expression of the extracellular agarase dagA at the post-transcriptional level by direct base pairing to the coding region 33 nt downstream of the ribosome-binding site.
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Affiliation(s)
- Michael-Paul Vockenhuber
- Institut für Molekulare Biowissenschaften, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Beatrix Suess
- Institut für Molekulare Biowissenschaften, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
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Temuujin U, Chi WJ, Lee SY, Chang YK, Hong SK. Overexpression and biochemical characterization of DagA from Streptomyces coelicolor A3(2): an endo-type β-agarase producing neoagarotetraose and neoagarohexaose. Appl Microbiol Biotechnol 2011; 92:749-59. [DOI: 10.1007/s00253-011-3347-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/20/2011] [Accepted: 04/20/2011] [Indexed: 12/01/2022]
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Vallin C, Ramos A, Pimienta E, Rodríguez C, Hernández T, Hernández I, Del Sol R, Rosabal G, Van Mellaert L, Anné J. Streptomyces as host for recombinant production of Mycobacterium tuberculosis proteins. Tuberculosis (Edinb) 2006; 86:198-202. [PMID: 16644285 DOI: 10.1016/j.tube.2006.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 02/27/2006] [Indexed: 11/30/2022]
Abstract
The 45/47 kDa APA protein (Rv1860) of Mycobacterium tuberculosis was produced by Streptomyces lividans. The recombinant protein could be recovered from the culture medium of an S. lividans clone containing the apa gene under control of the promoter and signal sequence of the Streptomyces coelicolor agarase gene. The recombinant protein production was further scaled-up using fermentation conditions. The APA protein was subsequently purified from the culture supernatant by means of immunochromatography. About 80 mg of recombinant protein were obtained per liter of culture media. In vivo tests with the APA protein purified from S. lividans TK24/pRGAPA1 revealed that the recombinant protein was antigenic and could induce high titers of specific antibodies in the mouse biological model. Results obtained concerning heterologous production of APA, its immunogenic and antigenic capacity, demonstrated the potential of S. lividans as a valuable host for the production of recombinant proteins from M. tuberculosis.
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Affiliation(s)
- Carlos Vallin
- Department of Biomedical Research, Center of Pharmaceutical Chemistry, Atabey, Playa, Havana, Cuba.
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Rivas LA, Parro VC, Moreno-Paz M, Mellado RP. The Bacillus subtilis 168 csn gene encodes a chitosanase with similar properties to a streptomyces enzyme. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 11):2929-2936. [PMID: 11065371 DOI: 10.1099/00221287-146-11-2929] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Bacillus subtilis 168 csn gene encodes a chitosanase. It was found that transcription of the csn gene was temporally regulated and was not subject to metabolic repression. Chitosanase synthesis was abolished in a csn mutant strain. Csn was overproduced in B. subtilis, partially purified and characterized. The deduced amino acid sequence, K(m), and optimal pH and temperature of the B. subtilis enzyme were closer to those of a chitosanase from Streptomyces sp. N174 than to those of chitosanases from other Bacillus strains.
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Affiliation(s)
- Luis A Rivas
- Centro Nacional de Biotecnologı́a (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain1
| | - Vı Ctor Parro
- Centro Nacional de Biotecnologı́a (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain1
| | - Mercedes Moreno-Paz
- Centro Nacional de Biotecnologı́a (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain1
| | - Rafael P Mellado
- Centro Nacional de Biotecnologı́a (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain1
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Parro V, Mellado RP. A new signal peptidase gene from Streptomyces lividans TK21. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1999; 9:71-7. [PMID: 10520735 DOI: 10.3109/10425179809086431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Using synthetic oligonucleotides derived from known signal peptidase genes and a multicopy plasmid as a vector, a signal peptidase gene (sipZ) from Streptomyces lividansTK21 has been cloned. The primary structure of the gene has been determined and the amino acid composition of the SipZ protein inferred. SipZ is 258 aa long and showed homology to other type I signal peptidases, containing like them an N-terminal transmembrane anchor. Alignment of SipZ with other known SPases allowed the identification of a conserved sequence of amino acids specific for Gram-positive bacteria.
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Affiliation(s)
- V Parro
- Centro Nacional de Biotecnología (CSIC), Madrid, Spain
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Parro VC, Schacht S, Anné J, Mellado RP. Four genes encoding different type I signal peptidases are organized in a cluster in Streptomyces lividans TK21. MICROBIOLOGY (READING, ENGLAND) 1999; 145 ( Pt 9):2255-2263. [PMID: 10517578 DOI: 10.1099/00221287-145-9-2255] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Four adjacent genes (sipW, sipX, sipY and sipZ) encoding different type I signal peptidases, were isolated on a 7860 bp DNA fragment from Streptomyces lividans TK21. Three of the sip genes constitute an operon and the fourth is the first gene of another operon encompassing three additional, unrelated genes. A DNA fragment containing the four sip genes complemented an Escherichia coli type I signal peptidase mutant when cloned in a multicopy plasmid. Clustering of four different type I signal peptidase genes seems, so far, to be a unique feature of Streptomyces.
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Affiliation(s)
- Vı Ctor Parro
- Centro Nacional de Biotecnologı́a (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain1
| | - Sabine Schacht
- Laboratory of Bacteriology, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium2
| | - Jozef Anné
- Laboratory of Bacteriology, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium2
| | - Rafael P Mellado
- Centro Nacional de Biotecnologı́a (CSIC), Campus de la Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain1
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Fernández-Moreno MA, Carbó L, Cuesta T, Vallín C, Malpartida F. A silent ABC transporter isolated from Streptomyces rochei F20 induces multidrug resistance. J Bacteriol 1998; 180:4017-23. [PMID: 9696745 PMCID: PMC107393 DOI: 10.1128/jb.180.16.4017-4023.1998] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the search for heterologous activators for actinorhodin production in Streptomyces lividans, 3.4 kb of DNA from Streptomyces rochei F20 (a streptothricin producer) were characterized. Subcloning experiments showed that the minimal DNA fragment required for activation was 0.4 kb in size. The activation is mediated by increasing the levels of transcription of the actII-ORF4 gene. Sequencing of the minimal activating fragment did not reveal any clues about its mechanism; nevertheless, it was shown to overlap the 3' end of two convergent genes, one of whose translated products (ORF2) strongly resembles that of other genes belonging to the ABC transporter superfamily. Computer-assisted analysis of the 3.4-kb DNA sequence showed the 3' terminus of an open reading frame (ORF), i.e., ORFA, and three complete ORFs (ORF1, ORF2, and ORFB). Searches in the databases with their respective gene products revealed similarities for ORF1 and ORF2 with ATP-binding proteins and transmembrane proteins, respectively, which are found in members of the ABC transporter superfamily. No similarities for ORFA and ORFB were found in the databases. Insertional inactivation of ORF1 and ORF2, their transcription analysis, and their cloning in heterologous hosts suggested that these genes were not expressed under our experimental conditions; however, cloning of ORF1 and ORF2 together (but not separately) under the control of an expressing promoter induced resistance to several chemically different drugs: oleandomycin, erythromycin, spiramycin, doxorubicin, and tetracycline. Thus, this genetic system, named msr, is a new bacterial multidrug ABC transporter.
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Affiliation(s)
- M A Fernández-Moreno
- Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma de Madrid, Cantoblanco 28049, Madrid, Spain
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Parro V, Mellado RP, Harwood CR. Effects of phosphate limitation on agarase production by Streptomyces lividansTK21. FEMS Microbiol Lett 1998. [DOI: 10.1111/j.1574-6968.1998.tb12808.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Parro V, Vives C, Godia F, Mellado RP. Overproduction and purification of an agarase of bacterial origin. J Biotechnol 1997; 58:59-66. [PMID: 9335178 DOI: 10.1016/s0168-1656(97)00128-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The agarase gene from Streptomyces coelicolor has been cloned in the non-producer bacterium Streptomyces lividans under the control of its own set of promoters and under the control of a heterologous promoter that is functional only during exponential growth. The best level of overproduction was obtained when the strain containing the natural gene was cultivated in fed batch with mannitol as carbon source. The protein, with a relative molecular mass of 32 kDa, has been purified following an affinity purification method. Contaminating activities seem to be absent from the purified enzyme preparation that can be used to purify DNA from agarose gels.
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Affiliation(s)
- V Parro
- Centro Nacional de Biotecnologia (CSIC), Campus de la Universidad Autónoma, Cantoblanco, Madrid, Spain
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Romero NM, Mellado RP. Activation of the actinorhodin biosynthetic pathway in Streptomyces lividans. FEMS Microbiol Lett 1995; 127:79-84. [PMID: 7737486 DOI: 10.1111/j.1574-6968.1995.tb07453.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Production of the antibiotic actinorhodin was activated in Streptomyces lividans under conditions in which it is not normally produced when transformed with an activator gene from S. lividans. The gene encodes a 86-nucleotide transcript, responsible for the actinorhodin production phenotype, which is homologous to the 132 nucleotide transcript from S. fradiae, thought to act as a putative antisense RNA.
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Affiliation(s)
- N M Romero
- Centro Nacional de Biotecnología (CSIC), Campus de la Universidad Autónoma, Madrid, Spain
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Abstract
The Streptomyces coelicolor dagA gene, coding for an extracellular agarase, has been propagated on a multicopy plasmid in S. coelicolor A3(2), the natural agarase producer strain and in S. lividans TK21, a closely related, nonproducer strain. The effect of the carbon source on the production of agarase by both strains, upon cultivation in liquid medium, revealed that the glucose repression affected the synthesis of agarase at the level of secretion, rather than at the level of transcription. In the presence of glucose, the pre-agarase was degraded intracellularly and the overall secretion of proteases decreased considerably in both strains, suggesting a negative regulatory role for glucose in the overall secretion in Streptomyces.
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Affiliation(s)
- V Parro
- Centro Nacional de Biotecnologia (CSIC), Madrid, Spain
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Romero NM, Parro V, Mellado RP. Expression of an heterologous gene activating actinorhodin biosynthesis in Streptomyces lividans and Streptomyces coelicolor. FEMS Microbiol Lett 1994; 116:301-6. [PMID: 7514144 DOI: 10.1111/j.1574-6968.1994.tb06719.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Production of the blue-pigmented antibiotic actinorhodin resulted in activation in the non-producer strain Streptomyces lividans, but not in the natural producer strain Streptomyces coelicolor, when transformed with an heterologous activator gene from Streptomyces fradiae. The gene encodes a 132 nucleotide-long transcript, responsible for the actinorhodin production phenotype, and thought to act as a putative antisense RNA, which has been detected in the transformed S. lividans cultures by reverse transcription followed by cyclic amplification.
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Affiliation(s)
- N M Romero
- Centro Nacional de Biotecnología (CSIC), Madrid, Spain
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