Streptomyces clavuligerus strain selection for clavulanic acid biosynthesis: a study based on culture composition effects and statistical analysis

Pinilla, Laura; Toro, León F.; Rossa, Claudio Avignone; Peñuela, Mariana; Ríos‐Estepa, Rigoberto

doi:10.15446/dyna.v85n205.69560

Cited by 4 publications

(6 citation statements)

References 28 publications

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“…Trends for the production profiles are in agreement with those found in related studies [6,12,20,21]. Likewise, the presence of phosphate, at the end, remained in the margins of restrictive concentration thus favoring antibiotic biosynthesis [21].…”

Section: Discussionsupporting

confidence: 89%

“…CA, as a secondary metabolite, is non-essential for growth; a reduction in the growth rate was observed past 48 h of cultivation (Figure 2), in both the GSPG and SB- media, which coincides with the onset of secondary metabolism [2,13]. Trends for the production profiles are in agreement with those found in related studies [6,12,20,21]. Likewise, the presence of phosphate, at the end, remained in the margins of restrictive concentration thus favoring antibiotic biosynthesis [21].…”

Section: Discussionsupporting

confidence: 86%

“…As observed, the phosphate source was completely depleted at 75 h in GSPG; meanwhile, in SB-M, the phosphate consumption was slower, rendering a residual concentration of 0.82 g/L at 114 h. The main carbon source, glycerol, was completely consumed at 75 h in GSPG, in contrast to SB-M for which the lowest concentration was obtained at 114 h; 0.08 g/L of glycerol remained unused in SB-M due to the presence of alternative carbon sources such as starch, peptides and carbohydrates in isolated soybean protein [20,21]. CA production was considerably higher in SB-M (1015.16 μgCA/mgDNA) at 104 h compared to the maximum CA reached in GSPG (238.37 μgCA/mgDNA) at 72 h.…”

Section: Resultsmentioning

confidence: 99%

“…It is known that there is a possible interference of peptidoglycan synthesis when ß-lactam compounds are produced at high concentrations. However, for the case of the GSPG, CA levels are not that high compared with those observed in SB-M [21]. Regarding regulatory genes, the TetR-family transcriptional regulator, encoded by SCLAV_2302, is a protein involved in the transcriptional control of multidrug efflux pumps, antibiotic biosynthetic pathways, response to osmotic stress and toxic chemicals, catabolic pathway control and differentiation processes [59].…”

Section: Discussionmentioning

confidence: 99%

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Comparative Transcriptome Analysis of Streptomyces Clavuligerus in Response to Favorable and Restrictive Nutritional Conditions

Pinilla

Toro²,

Laing³

et al. 2019

Antibiotics

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Background: Clavulanic acid (CA), a β-lactamase inhibitor, is industrially produced by the fermentation of Streptomyces clavuligerus. The efficiency of CA production is associated with media composition, culture conditions and physiological and genetic strain characteristics. However, the molecular pathways that govern CA regulation in S. clavuligerus remain unknown. Methods and Results: Here we used RNA-seq to perform a comparative transcriptome analysis of S. clavuligerus ATCC 27064 wild-type strain grown in both a favorable soybean-based medium and in limited media conditions to further contribute to the understanding of S. clavuligerus metabolism and its regulation. A total of 350 genes were found to be differentially expressed between conditions; 245 genes were up-regulated in favorable conditions compared to unfavorable. Conclusion: The up-regulated expression of many regulatory and biosynthetic CA genes was positively associated with the favorable complex media condition along with pleiotropic regulators, including proteases and some genes whose biological function have not been previously reported. Knowledge from differences between transcriptomes from complex/defined media represents an advance in the understanding of regulatory paths involved in S. clavuligerus’ metabolic response, enabling the rational design of future experiments.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionsupporting

confidence: 86%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Comparative Transcriptome Analysis of Streptomyces Clavuligerus in Response to Favorable and Restrictive Nutritional Conditions

Pinilla

Toro²,

Laing³

et al. 2019

Antibiotics

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“…Experimental conditions were set up at 28 • C, pH 6.8 and shaking at 220 rpm. For the high CA production condition, an isolated soy-protein based medium was used [32]; for the low production condition, the chemically-defined media GSPG medium was employed [33]. RNA extraction was performed using the TRIzol®RNA Isolation Protocol [34].…”

Section: Rna Extraction Library Preparation and Sequencingmentioning

confidence: 99%

Comparative Analysis of Strategies for De Novo Transcriptome Assembly in Prokaryotes: Streptomyces clavuligerus as a Case Study

et al. 2019

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The performance of software tools for de novo transcriptome assembly greatly depends on the selection of software parameters. Up to now, the development of de novo transcriptome assembly for prokaryotes has not been as remarkable as that for eukaryotes. In this contribution, Rockhopper2 was used to perform a comparative transcriptome analysis of Streptomyces clavuligerus exposed to diverse environmental conditions. The study focused on assessing the incidence of software parameters on software performance for the identification of differentially expressed genes as a final goal. For this, a statistical optimization was performed using the Transrate Assembly Score (TAS). TAS was also used for evaluating the software performance and for comparing it with related tools, e.g., Trinity. Transcriptome redundancy and completeness were also considered for this analysis. Rockhopper2 and Trinity reached a TAS value of 0.55092 and 0.58337, respectively. Trinity assembles transcriptomes with high redundancy, with 55.6% of transcripts having some duplicates. Additionally, we observed that the total number of differentially expressed genes (DEG) and their annotation greatly depends on the method used for removing redundancy and the tools used for transcript quantification. To our knowledge, this is the first work aimed at assessing de novo assembly software for prokaryotic organisms. complete transcription map [1]. De novo transcriptome assembly is necessary for organisms whose genomes have been neither sequenced nor annotated, e.g., for non-model organisms, when analyzing complex microbial communities, in meta-transcriptome studies, or while investigating uncultivable microorganisms [5][6][7]. Many software tools have been developed to assemble transcriptomes using the de novo strategy. The most commonly used are: Trinity [3,8], Oases [6], Bridger [9], SOAPdenovo-Trans [10], IDBA-Trans [11], SSP [12], Shannon [13], BinPacker [14] and Rockhopper2 [5].De novo assembly is very sensitive to software parameters due to the lack of a genome to guide the assembly and the type of algorithms used which are mostly based on the De Bruijn graphs. Thus, they depend on the k-mer length [14] or on the minimum k-mer coverage [3]. Moreover, the consistency and biological relevance of the data, obtained from different sources, make it challenging to select the most accurate assembly [15,16], and the same data can generate substantially different assemblies, both within and between assembly methods, affecting the biological analysis and its conclusions [17]. In this regard, some authors have undertaken the task of evaluating the impact of different methodologies and software configurations on the quality of the assembled transcriptome [18][19][20][21][22].Different software are available for evaluating the quality of a de novo assembly, e.g., SCAN [23], rnaQUAST [24], DETONATE [16], Transrate [17] and recently, a topology-based method called Branching Measure [25]. For the case of Transrate, it renders a Transrate Assembly Score (TAS) that allow...

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Biotechnological and industrial applications of Streptomyces metabolites

Khushboo

Kumar

Dubey

et al. 2021

Biofuels Bioprod Bioref

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Streptomyces sp. produces clinically important bioactive compounds with anticancer, antiviral, and antibacterial properties. These compounds have important roles in various fields like agriculture, and medicine, with bio-economic benefits. Progress in genome mining has resulted in the characterization of various secondary metabolites such as lipstatin, macrolide lactones, clavulanic acid, and cholesterol oxidase. Integration of DNA sequencing with computational tools has provided information regarding the biosynthetic pathways of secondary metabolites. This information is leading to the modulation of associated metabolic pathways to expand the biotechnological and industrial applications of metabolites. The increased utilization of bioactive compounds requires sustainable production to improve the bioeconomy. In this review, the authors discuss the bioactive compounds isolated from Streptomyces and advanced approaches to improve their production.

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Streptomyces clavuligerus strain selection for clavulanic acid biosynthesis: a study based on culture composition effects and statistical analysis

Cited by 4 publications

References 28 publications

Comparative Transcriptome Analysis of Streptomyces Clavuligerus in Response to Favorable and Restrictive Nutritional Conditions

Comparative Transcriptome Analysis of Streptomyces Clavuligerus in Response to Favorable and Restrictive Nutritional Conditions

Comparative Analysis of Strategies for De Novo Transcriptome Assembly in Prokaryotes: Streptomyces clavuligerus as a Case Study

Biotechnological and industrial applications of Streptomyces metabolites

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