0000000000613616
AUTHOR
Giovanni Renzone
Adaptative biochemical pathways and regulatory networks in Klebsiella oxytoca BAS-10 producing a biotechnologically relevant exopolysaccharide during Fe(III)-citrate fermentation.
Abstract Background A bacterial strain previously isolated from pyrite mine drainage and named BAS-10 was tentatively identified as Klebsiella oxytoca. Unlikely other enterobacteria, BAS-10 is able to grow on Fe(III)-citrate as sole carbon and energy source, yielding acetic acid and CO2 coupled with Fe(III) reduction to Fe(II) and showing unusual physiological characteristics. In fact, under this growth condition, BAS-10 produces an exopolysaccharide (EPS) having a high rhamnose content and metal-binding properties, whose biotechnological applications were proven as very relevant. Results Further phylogenetic analysis, based on 16S rDNA sequence, definitively confirmed that BAS-10 belongs t…
Additional file 4: of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Supplementary Results section. (PDF 123 kb)
The Odorant-Binding Proteins of the Spider Mite Tetranychus urticae
Spider mites are one of the major agricultural pests, feeding on a large variety of plants. As a contribution to understanding chemical communication in these arthropods, we have characterized a recently discovered class of odorant-binding proteins (OBPs) in Tetranychus urticae. As in other species of Chelicerata, the four OBPs of T. urticae contain six conserved cysteines paired in a pattern (C1–C6, C2–C3, C4–C5) differing from that of insect counterparts (C1–C3, C2–C5, C4–C6). Proteomic analysis uncovered a second family of OBPs, including twelve members that are likely to be unique to T. urticae. A three-dimensional model of TurtOBP1, built on the recent X-ray structure of Varroa destruc…
Differential proteomic analysis highlights metabolic strategies associated with balhimycin production in Amycolatopsis balhimycina chemostat cultivations
Abstract Background Proteomics was recently used to reveal enzymes whose expression is associated with the production of the glycopeptide antibiotic balhimycin in Amycolatopsis balhimycina batch cultivations. Combining chemostat fermentation technology, where cells proliferate with constant parameters in a highly reproducible steady-state, and differential proteomics, the relationships between physiological status and metabolic pathways during antibiotic producing and non-producing conditions could be highlighted. Results Two minimal defined media, one with low Pi (0.6 mM; LP) and proficient glucose (12 g/l) concentrations and the other one with high Pi (1.8 mM) and limiting (6 g/l; LG) glu…
Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024.
Background The filamentous actinomycete Microbispora ATCC-PTA-5024 produces the lantibiotic NAI-107, which is an antibiotic peptide effective against multidrug-resistant Gram-positive bacteria. In actinomycetes, antibiotic production is often associated with a physiological differentiation program controlled by a complex regulatory and metabolic network that may be elucidated by the integration of genomic, proteomic and bioinformatic tools. Accordingly, an extensive evaluation of the proteomic changes associated with NAI-107 production was performed on Microbispora ATCC-PTA-5024 by combining two-dimensional difference in gel electrophoresis, mass spectrometry and gene ontology approaches. R…
Expression in Streptomyces lividans of Nonomuraea genes cloned in an artificial chromosome
A bacterial artificial chromosomal library of Nonomuraea sp. ATCC39727 was constructed using Escherichia coli-Streptomyces artificial chromosome (ESAC) and screened for the presence of dbv genes known to be involved in the biosynthesis of the glycopeptide A40926. dbv genes were cloned as two large, partially overlapping, fragments and transferred into the host Streptomyces lividans, thus generating strains S. lividansColon, two colonsNmESAC50 and S. lividansColon, two colonsNmESAC57. The heterologous expression of Nonomuraea genes in S. lividans was successfully demonstrated by using combined RT-PCR and proteomic approaches. MALDI-TOF analysis revealed that a Nonomuraea ABC transporter is e…
NovelAmycolatopsis balhimycinabiochemical abilities unveiled by proteomics
Amycolatopsis balhimycina DSM5908 is an actinomycete producer of balhimycin, an analogue of vancomycin, the antibiotic of ‘last resort’ against multidrug-resistant Gram-positive pathogens. Most knowledge on glycopeptide biosynthetic pathways comes from studies on A. balhimycina as this strain, among glycopeptide producers, is genetically more amenable. The recent availability of its genome sequence allowed to perform differential proteomic analyses elucidating key metabolic pathways leading to antibiotic production in different growth conditions. To implement proteomic data on A. balhimycina derived from 2-DE approaches and to identify novel components, a combined approach based on protein …
Streptomyces coelicolor Vesicles: Many Molecules To Be Delivered
ABSTRACT Streptomyces coelicolor is a model organism for the study of Streptomyces, a genus of Gram-positive bacteria that undergoes a complex life cycle and produces a broad repertoire of bioactive metabolites and extracellular enzymes. This study investigated the production and characterization of membrane vesicles (MVs) in liquid cultures of S. coelicolor M145 from a structural and biochemical point of view; this was achieved by combining microscopic, physical and -omics analyses. Two main populations of MVs, with different sizes and cargos, were isolated and purified. S. coelicolor MV cargo was determined to be complex, containing different kinds of proteins and metabolites. In particul…
Additional file 5: of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Figure S1-S6 with corresponding figure legends. (PDF 511 kb)
Tryptophan promotes morphological and physiological differentiation in Streptomyces coelicolor.
The molecular mechanisms regulating tryptophan biosynthesis in actinomycetes are poorly understood; similarly, the possible roles of tryptophan in the differentiation program of microorganism life-cycle are still underexplored. To unveil the possible regulatory effect of this amino acid on gene expression, an integrated study based on quantitative teverse transcription-PCR (qRT-PCR) and proteomic approaches was performed on the actinomycete model Streptomyces coelicolor. Comparative analyses on the microorganism growth in a minimal medium with or without tryptophan supplementation showed that biosynthetic trp gene expression in S. coelicolor is not subjected to a negative regulation by the …
Additional file 5: of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Figure S1-S6 with corresponding figure legends. (PDF 511 kb)
Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina.
A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially and constitutively expressed protein isoforms, which were associated to 203 ORFs in the A. balhimycina genome. These data, providing insights on the major metabolic pathways/molecular processes operating in this organism, were used to compile 2-DE reference maps covering 3-10, 4-7 and 4.5-5.5 pH gradients available over the World Wide Web as interactive web pages (http://www.unipa.it/ampuglia/Abal-prot…
Differential proteomic analysis of an engineered Streptomyces coelicolor strain reveals metabolic pathways supporting growth on n-hexadecane
The alkB gene, encoding an alkane monooxygenase in the actinomycete Gordonia sp. SoCg, was expressed in the non-alkane-degrading actinomycete Streptomyces coelicolor M145. The resulting engineered strain, M145-AH, can grow on n-hexadecane as sole carbon source. To unravel proteins associated with growth on n-alkanes, proteome of M145-AH after 6, 24, and 48 h of incubation in the Bushnell-Haas (BH) mineral medium containing n-hexadecane as sole carbon source (H condition) and in BH without any carbon source (0 condition) were compared using 2D-differential gel electrophoresis. Proteome analysis revealed significant changes only at 48 h, showing 48 differentially abundant proteins identified …
TrpM, a Small Protein Modulating Tryptophan Biosynthesis and Morpho-Physiological Differentiation in Streptomyces coelicolor A3(2).
In the model actinomycete Streptomyces coelicolor A3(2), small open reading frames encoding proteins with unknown functions were identified in several amino acid biosynthetic gene operons, such as SCO2038 (trpX) in the tryptophan trpCXBA locus. In this study, the role of the corresponding protein in tryptophan biosynthesis was investigated by combining phenotypic and molecular analyses. The 2038KO mutant strain was characterized by delayed growth, smaller aerial hyphae and reduced production of spores and actinorhodin antibiotic, with respect to the WT strain. The capability of this mutant to grow on minimal medium was rescued by tryptophan and tryptophan precursor (serine and/or indole) su…
Additional file 4: of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Supplementary Results section. (PDF 123 kb)
Pirin: A novel redox-sensitive modulator of primary and secondary metabolism in Streptomyces
Pirins are evolutionarily conserved iron-containing proteins that are found in all kingdoms of life, and have been implicated in diverse molecular processes, mostly associated with cellular stress. In the present study, we started from the evidence that the insertional inactivation of pirin-like gene SAM23877_RS18305 (pirA) by Phi C31 Att/Int system-based vectors in spiramycin-producing strain Streptomyces ambofaciens ATCC 23877 resulted in marked effects on central carbon and energy metabolism gene expression, high sensitivity to oxidative injury and repression of polyketide antibiotic production. By using integrated transcriptomic, proteomic and metabolite profiling, together with genetic…
The Streptomyces coelicolor Small ORF trpM Stimulates Growth and Morphological Development and Exerts Opposite Effects on Actinorhodin and Calcium-Dependent Antibiotic Production
In actinomycetes, antibiotic production is often associated with a morpho-physiological differentiation program that is regulated by complex molecular and metabolic networks. Many aspects of these regulatory circuits have been already elucidated and many others still deserve further investigations. In this regard, the possible role of many small open reading frames (smORFs) in actinomycete morpho-physiological differentiation is still elusive. In Streptomyces coelicolor, inactivation of the smORF trpM (SCO2038) – whose product modulates L-tryptophan biosynthesis – impairs production of antibiotics and morphological differentiation. Indeed, it was demonstrated that TrpM is able to interact w…
An integrated proteomic and metabolomic study to evaluate the effect of nucleus-cytoplasm interaction in a diploid citrus cybrid between sweet orange and lemon.
Key message: Our results provide a comprehensive overview how the alloplasmic condition might lead to a significant improvement in citrus plant breeding, developing varieties more adaptable to a wide range of conditions. Abstract: Citrus cybrids resulting from somatic hybridization hold great potential in plant improvement. They represent effective products resulting from the transfer of organelle-encoded traits into cultivated varieties. In these cases, the plant coordinated array of physiological, biochemical, and molecular functions remains the result of integration among different signals, which derive from the compartmentalized genomes of nucleus, plastids and mitochondria. To dissect …
Additional file 2: Table S2. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from global proteome analysis at D substages. (XLS 107 kb)
Additional file 6: Table S5. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Description, abundance profile and mass spectrometry identification parameters of differentially represented spots containing multiple protein components. (XLS 45 kb)
Additional file 3: Table S3. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from membrane proteome analysis at A substages. (XLSX 37 kb)
Additional file 2: Table S2. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from global proteome analysis at D substages. (XLS 107 kb)
Additional file 6: Table S5. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Description, abundance profile and mass spectrometry identification parameters of differentially represented spots containing multiple protein components. (XLS 45 kb)
Additional file 7: Table S4. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented proteins due to NAI-107 exposure in Microbispora ATCC-PTA-5024 RP0 strain. (XLSX 32 kb)
Additional file 1: Table S1. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from global proteome analysis at A substages. (XLSX 48 kb)
Additional file 8: Table S6. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Numbers of KEGG orthology groups participating in molecular and metabolic processes as inferred from genome and proteome analyses, respectively. (XLS 24 kb)
Additional file 3: Table S3. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from membrane proteome analysis at A substages. (XLSX 37 kb)
Additional file 7: Table S4. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented proteins due to NAI-107 exposure in Microbispora ATCC-PTA-5024 RP0 strain. (XLSX 32 kb)
Additional file 8: Table S6. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Numbers of KEGG orthology groups participating in molecular and metabolic processes as inferred from genome and proteome analyses, respectively. (XLS 24 kb)
Additional file 1: Table S1. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024
Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from global proteome analysis at A substages. (XLSX 48 kb)