Isolation of soluble proteins from an industrial strain Streptomyces avermitilis in complex culture medium for two-dimensional gel electrophoresis

Occurrence of Streptomyces tauricus in mangrove soil of Mangalore region in Dakshina Kannada as a source for antimicrobial peptide

Microbial resistance and deprivation of the effective drugs have become the foremost problem that propels to seek out for advanced approach. This concept initiated a need to search for more effective antimicrobial compounds from reliable sources. The Streptomyces is grouped under phylum Actinobacteria and are considered prolific producers of antibiotics, around 70% of presently available antibiotics are contributed by Streptomyces alone. In this study, Mangroves of the Mangalore Coast offered a unique source for screening Actinomyces group of microorganisms. We investigated on the four soil samples collected from Mangrove swamps of Mangalore, Karnataka, India. Based on their culture traits, the 18 distinct Actinomyces isolates were analyzed through a series of morphological and biochemical tests on starch casein nitrate (SCN) media. Culture biomasses were subjected for intracellular protein extraction through acetone precipitation method; the extracted proteins from each Actinomyces isolate were examined for antimicrobial activity against test organisms. The isolate ANTB-YKMU4 showed potential antimicrobial activity against significant number of test organisms; Bacillus cereus, Proteus vulgaris, Staphylococcus aureus, Salmonella typhimurium, and Pseudomonas aeruginosa. The isolate ANTB-YKMU4 through 16 s rRNA gene sequence analysis was identified as Streptomyces tauricus strain with GenBank accession no. MW785875.1. The S. tauricus further cultivated for efficient biomass growth on SCN media for subsequent protein extraction and purification by a series of Electrophoretic and chromatographic techniques. Thus, by intracellular extractions from S. tauricus resulted in the identification of peptide with a molecular weight of 266 Da that was characterized by LC-MS.

Streptomyces griseus KJ623766: A Natural Producer of Two Anthracycline Cytotoxic Metabolites β- and γ-Rhodomycinone

Background: This study aimed to produce, purify, structurally elucidate, and explore the biological activities of metabolites produced by Streptomyces (S.) griseus isolate KJ623766, a recovered soil bacterium previously screened in our lab that showed promising cytotoxic activities against various cancer cell lines. Methods: Production of cytotoxic metabolites from S. griseus isolate KJ623766 was carried out in a 14L laboratory fermenter under specified optimum conditions. Using a 3-(4,5-dimethylthazol-2-yl)-2,5-diphenyl tetrazolium-bromide assay, the cytotoxic activity of the ethyl acetate extract against Caco2 and Hela cancer cell lines was determined. Bioassay-guided fractionation of the ethyl acetate extract using different chromatographic techniques was used for cytotoxic metabolite purification. Chemical structures of the purified metabolites were identified using mass, 1D, and 2D NMR spectroscopic analysis. Results: Bioassay-guided fractionation of the ethyl acetate extract led to the purification of two cytotoxic metabolites, R1 and R2, of reproducible amounts of 5 and 1.5 mg/L, respectively. The structures of R1 and R2 metabolites were identified as β- and γ-rhodomycinone with CD₅₀ of 6.3, 9.45, 64.8 and 9.11, 9.35, 67.3 µg/mL against Caco2, Hela and Vero cell lines, respectively. Values were comparable to those of the positive control doxorubicin. Conclusions: This is the first report about the production of β- and γ-rhodomycinone, two important scaffolds for synthesis of anticancer drugs, from S. griseus.

Proteomic analysis of a hom-disrupted, cephamycin C overproducing Streptomyces clavuligerus

BACKGROUND

Streptomyces clavuligerus is prolific producer of cephamycin C, a medically important antibiotic. In our former study, cephamycin C titer was 2-fold improved by disrupting homoserine dehydrogenase (hom) gene of aspartate pahway in Streptomyces clavuligerus NRRL 3585.

OBJECTIVE

In this article, we aimed to provide a comprehensive understanding at the proteome level on potential complex metabolic changes as a consequence of hom disruption in Streptomyces clavuligerus AK39.

METHODS

A comparative proteomics study was carried out between the wild type and its hom disrupted AK39 strain by 2 Dimensional Electrophoresis-Matrix Assisted Laser Desorption and Ionization Time-Of-Flight Mass Spectrometry (2DE MALDI-TOF/MS) and Nanoscale Liquid Chromatography- Tandem Mass Spectrometry (nanoLC-MS/MS) analyses. Clusters of Orthologous Groups (COG) database was used to determine the functional categories of the proteins. The theoretical pI and Mw values of the proteins were calculated using Expasy pI/Mw tool.

RESULTS

"Hypothetical/Unknown" and "Secondary Metabolism" were the most prominent categories of the differentially expressed proteins. Upto 8.7-fold increased level of the positive regulator CcaR was a key finding since CcaR was shown to bind to cefF promoter thereby direcly controlling its expression. Consistently, CeaS2, the first enzyme of CA biosynthetic pathway, was 3.3- fold elevated. There were also many underrepresented proteins associated with the biosynthesis of several Non-Ribosomal Peptide Synthases (NRPSs), clavams, hybrid NRPS/Polyketide synthases (PKSs) and tunicamycin. The most conspicuously underrepresented protein of amino acid metabolism was 4-Hydroxyphenylpyruvate dioxygenase (HppD) acting in tyrosine catabolism. The levels of a Two Component System (TCS) response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain as well as DNA-binding protein HU were elevated while a TetR-family transcriptional regulator was underexpressed.

CONCLUSION

The results obtained herein will aid in finding out new targets for further improvement of cephamycin C production in Streptomyces clavuligerus.

Proteome-wide alterations in an industrial clavulanic acid producing strain of Streptomyces clavuligerus

The usefulness of genetic/metabolic engineering for further improvement of industrial strains is subject of discussion because of the general lack of knowledge on genetic alterations introduced by iterative cycles of random mutagenesis in such strains. An industrial clavulanic acid (CA)-overproducer Streptomyces clavuligerus DEPA was assessed to understand proteome-wide changes that have occurred in a local industrial CA overproducer developed through succesive mutagenesis programs. The proteins that could be identified corresponded to 33 distinct ORFs for underrepresented ones and 60 ORFs for overrepresented ones. Three CA biosynthetic enzymes were overrepresented in S. clavuligerus DEPA; carboxyethylarginine synthase (Ceas2), clavaldehyde dehydrogenase (Car) and carboxyethyl-arginine beta-lactam-synthase (Bls2) whereas the enzymes of two other secondary metabolites were underrepresented along with two important global regulators [two-component system (TCS) response regulator (SCLAV_2102) and TetR-family transcriptional regulator (SCLAV_3146)] that might be related with CA production and/or differentiation. γ-butyrolactone biosynthetic protein AvaA2 was 2.6 fold underrepresented in S. clavuligerus DEPA. The levels of two glycolytic enzymes, 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase and phosophoglycerate kinase were found decreased while those of dihydrolipoyl dehydrogenase (E3) and isocitrate dehydrogenase, with two isoforms were found as significantly increased. A decrease of amino acid metabolism, methionine biosynthesis in particular, as well as S-adenosylmethionine synthetase appeared as one of the prominent mechanisms of success of S. clavuligerus DEPA strain as a prolific producer of CA. The levels of two enzymes of shikimate pathway that leads to the production of aromatic amino acids and aromatic secondary metabolites were also underrepresented. Some of the overrepresented stress proteins in S. clavuligerus DEPA included polynucleotide phosphorylase/polyadenylase (PNPase), ATP-dependent DNA helicase, two isoforms of an anti-sigma factor and thioredoxin reductase. Downregulation of important proteins of cell wall synthesis and division was recorded and a protein with β-lactamase domain (SCLAV_p1007) appeared in 12 isoforms, 5 of which were drastically overrepresented in DEPA strain. These results described herein provide useful information for rational engineering to improve CA production in Streptomyces clavuligerus.

The investigation of different pollutants and operation processes on sludge toxicity in sequencing batch bioreactors

The influence of different target pollutants and operation modes in sequencing batch bioreactors (SBRs) on sludge toxicity was compared in this study. Sludge toxicity was characterized by the inhibiting luminosity through using luminescent bacterium Photobacterium phosphoreum (P. phosphoreum) during either gradual acclimation or impaction processes with synthetic wastewater containing high-strength bisphenol A (BPA) or N, N-dimethylformamide (DMF). When the activated sludge was first acclimated with either 120 mg/L DMF or 20 mg/L BPA, and then respectively increased to 200 mg/L DMF and 40 mg/L BPA it was defined as gradual acclimation process, whereas when the activated sludge was, respectively, injected with 200 mg/L DMF and 40 mg/L BPA directly it was defined as impaction process. Results showed that the toxicity of the impacted sludge was greater than that of the gradual acclimated sludge, especially in the initial stage before 10 d. Activated sludge treating BPA synthetic wastewater exhibited higher toxicity due to the more inhibition of BPA to sludge activity compared to that of DMF. The proteomics analysis indicated that the stress responses of activated sludge to DMF and BPA stimulation were both significant. In turn, the secretions from two kinds of sludge under stress conditions contributed to sludge toxicity.

Interrogation of Streptomyces avermitilis for efficient production of avermectins

The 2015 Nobel Prize in Physiology or Medicine has been awarded to avermectins and artemisinin, respectively. Avermectins produced by Streptomyces avermitilis are excellent anthelmintic and potential antibiotic agents. Because wild-type strains only produce low levels of avermectins, much research effort has focused on improvements in avermectin production to meet the ever increasing demand for such compounds. This review describes the strategies that have been widely employed and the future prospects of synthetic biology applications in avermectin yield improvement. With the help of genome sequencing of S. avermitilis and an understanding of the avermectin biosynthetic/regulatory pathways, synthetic and systems biotechnology approaches have been applied for precision engineering. We focus on the design and synthesis of biological chassis, parts, devices, and modules from diverse microbes to reconstruct and optimize their dynamic processes, as well as predict favorable effective overproduction of avermectins by a 4Ms strategy (Mine, Model, Manipulation, and Measurement).

Taxonomy, Physiology, and Natural Products of Actinobacteria

Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.

Isolation, Characterization and Selection of Avermectin-Producing Streptomyces avermitilis Strains From Soil Samples

Background:

Streptomyces avermitilis, belonging to Actinomycetes, is specialized for production of avermectin, used as an anthelmintic and insecticidal agent. It is mostly found in soil and its isolation is very crucial for medically important avermectin production.

Objectives:

In the present study, 10 bacterial isolates lacking antimicrobial activities were isolated from the soil samples collected from different areas of Lahore, Pakistan.

Materials and Methods:

Three distinctive localities of Lahore were opted for soil assortment to isolate S. avermitilis. About 50 isolates of Streptomyces species were attained through selective prescreening procedures. All of these isolates were studied for production of the secondary metabolite, avermectin. Different test like soluble pigment color and melanin formation were used for identification. Biochemical characterizations of those isolates closely resembling the control in morphological characteristics, soluble pigment color and melanin formation tests were performed.

Results:

The 10 selected isolates were identified as the avermectin-producing strain by fermentation and characterized on ISP2 medium for aerial and reverse side mycelia color, soluble pigment color and melanin formation, in comparison with S. avermitilis DSM 41445. The best avermectin-producing isolate S1-C (10.15 mg/L) showed similar result as S. avermitilis DSM 41445, when subjected for culture characteristics analysis in different media along with biochemical characterization.

Conclusions:

From the results, it was concluded that agricultural lands around Pakistan Council of Scientific and Industrial Research (PCSIR) Campus Lahore were rich sources of industrially important Streptomyces, especially S. avermitilis.

Feature-matching pattern-based support vector machines for robust peptide mass fingerprinting

Peptide mass fingerprinting, regardless of becoming complementary to tandem mass spectrometry for protein identification, is still the subject of in-depth study because of its higher sample throughput, higher level of specificity for single peptides and lower level of sensitivity to unexpected post-translational modifications compared with tandem mass spectrometry. In this study, we propose, implement and evaluate a uniform approach using support vector machines to incorporate individual concepts and conclusions for accurate PMF. We focus on the inherent attributes and critical issues of the theoretical spectrum (peptides), the experimental spectrum (peaks) and spectrum (masses) alignment. Eighty-one feature-matching patterns derived from cleavage type, uniqueness and variable masses of theoretical peptides together with the intensity rank of experimental peaks were proposed to characterize the matching profile of the peptide mass fingerprinting procedure. We developed a new strategy including the participation of matched peak intensity redistribution to handle shared peak intensities and 440 parameters were generated to digitalize each feature-matching pattern. A high performance for an evaluation data set of 137 items was finally achieved by the optimal multi-criteria support vector machines approach, with 491 final features out of a feature vector of 35,640 normalized features through cross training and validating a publicly available "gold standard" peptide mass fingerprinting data set of 1733 items. Compared with the Mascot, MS-Fit, ProFound and Aldente algorithms commonly used for MS-based protein identification, the feature-matching patterns algorithm has a greater ability to clearly separate correct identifications and random matches with the highest values for sensitivity (82%), precision (97%) and F1-measure (89%) of protein identification. Several conclusions reached via this research make general contributions to MS-based protein identification. Firstly, inherent attributes showed comparable or even greater robustness than other explicit. As an inherent attribute of an experimental spectrum, peak intensity should receive considerable attention during protein identification. Secondly, alignment between intense experimental peaks and properly digested, unique or non-modified theoretical peptides is very likely to occur in positive peptide mass fingerprinting. Finally, normalization by several types of harmonic factors, including missed cleavages and mass modification, can make important contributions to the performance of the procedure.

Reverse biological engineering of hrdB to enhance the production of avermectins in an industrial strain of Streptomyces avermitilis

Avermectin and its analogues are produced by the actinomycete Streptomyces avermitilis and are widely used in the field of animal health, agriculture, and human health. Here we have adopted a practical approach to successfully improve avermectin production in an industrial overproducer. Transcriptional levels of the wild-type strain and industrial overproducer in production cultures were monitored using microarray analysis. The avermectin biosynthetic genes, especially the pathway-specific regulatory gene, aveR, were up-regulated in the high-producing strain. The upstream promoter region of aveR was predicted and proved to be directly recognized by sigma(hrdB) in vitro. A mutant library of hrdB gene was constructed by error-prone PCR and selected by high-throughput screening. As a result of evolved hrdB expressed in the modified avermectin high-producing strain, 6.38 g/L of avermectin B1a was produced with over 50% yield improvement, in which the transcription level of aveR was significantly increased. The relevant residues were identified to center in the conserved regions. Engineering of the hrdB gene can not only elicit the overexpression of aveR but also allows for simultaneous transcription of many other genes. The results indicate that manipulating the key genes revealed by reverse engineering can effectively improve the yield of the target metabolites, providing a route to optimize production in these complex regulatory systems.