Genome sequencing and genomic analysis of Amycolatopsis tucumanensis DSM 45259 applicable in gray, red, and nano-biotechnology.

Through the years, the genus Amycolatopsis has demonstrated its biotechnological potential. The need to clean up the environment and produce new antimicrobial molecules led to exploit promising bacterial genera such as Amycolatopsis. In this present work, we analyze the genome of the strain Amycolatopsis tucumanensis AB0 previously isolated from copper-polluted sediments. Phylogenomic and comparative analysis with the closest phylogenetic neighbor was performed. Our analysis showed the genetic potential of the strain to deal with heavy metals such as copper and mitigate oxidative stress. In addition, the ability to produce copper oxide nanoparticles and the presence of genes potentially involved in the synthesis of secondary metabolites suggest that A. tucumanensis may find utility in gray, red, and nano-biotechnology. To our knowledge, this is the first genomic analysis of an Amycolatopsis strain with potential for different biotechnological fields.

Determination of the metabolic pathways for degradation of naphthalene and pyrene in Amycolatopsis sp. Poz14.

Polycyclic aromatic hydrocarbons (PAHs) constitute important soil contaminants derived from petroleum. Poz14 strain can degrade pyrene and naphthalene. Its genome presented 9333 genes, among them those required for PAHs degradation. By phylogenomic analysis, the strain might be assigned to Amycolatopsis nivea. The strain was grown in glucose, pyrene, and naphthalene to compare their proteomes; 180 proteins were detected in total, and 90 of them were exclusives for xenobiotic conditions. Functions enriched with the xenobiotics belonged to transcription, translation, modification of proteins and transport of inorganic ions. Enriched pathways were pentose phosphate, proteasome and RNA degradation; in contrast, in glucose were glycolysis/gluconeogenesis and glyoxylate cycle. Proteins proposed to participate in the upper PAHs degradation were multicomponent oxygenase complexes, Rieske oxygenases, and dioxygenases; in the lower pathways were ortho-cleavage of catechol, phenylacetate, phenylpropionate, benzoate, and anthranilate. The catechol dioxygenase activity was measured and found increased when the strain was grown in naphthalene. Amycolatopsis sp. Poz14 genome and proteome revealed the PAHs degradation pathways and functions helping to contend the effects of such process.

First Confirmed Diagnosis of Nocardioform Placentitis (Amycolatopsis lexingtonensis) in South America.

Nocardioform placentitis is a pathologically unique form of placental disease first diagnosed in central Kentucky in the mid-80s. Since then, the occurrence of nocardioform placentitis in the region has varied over the years, from sporadic cases to outbreaks. The disease has been sporadically detected in other countries and has not been confirmed in South America. A 13-year-old multiparous Mangalarga delivered a healthy filly at 340d gestation. The mare passed the fetal membranes 33 minute after foaling. Gross examination of the fetal membranes identified two focal lesions on the chorionic surface consistent with focal mucoid placentitis. Histopathologic evaluation revealed hyperplasia and degeneration of the allantoic mesoderm, intense mononuclear inflammatory infiltrates with marked lymphocytes and plasma, and occasional macrophages and neutrophils in the microvilli. Necrotic debris and exudate were identified in the chorionic epithelium, with macrophages, plasma cells, and neutrophils confirming the diagnosis of focal mucoid placentitis. The exudate culture revealed white, firm, punctiform colonies of ∼1 mm diameter. Gram staining revealed bacilli with rounded ends and branching aspect typical of actinomycetes. PCR using primers for the 16S rRNA identified the genera of bacteria as Amycolatopsis. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis identified the isolate as Amycolatopsis lexingtonensis. In conclusion, we described the first confirmed case of nocardioform placentitis in South America. The present case was associated with the birth of a full-term healthy live foal; this result is consistent with Amycolatopsis spp and, in this case, was caused by A. lexingtonensis.

Proteomic analysis reveals the metabolic versatility of Amycolatopsis sp. BX17: A strain native from milpa agroecosystem soil.

Amycolatopsis sp. BX17 is an actinobacterium isolated from milpa soils, which antagonizes the phytopathogenic fungus Fusarium graminearum. Metabolites secreted by the actinobacterium cultured in glucose-free medium inhibited 100% of the mycelial growth of F. graminearum RH1, while the inhibition rate was 65% in medium supplemented with 20 g/L glucose. With the aim of studying how the metabolism of strain BX17 is modulated by glucose as the main carbon source, media with 0 and 20 g/L glucose were selected to analyze the intracellular proteins by quantitative label-free proteomic analysis. Data are available via ProteomeXchange with identifier PXD028644. Proteins identified in bacteria cultured in medium without glucose were involved in glutamate metabolism, the Krebs cycle and the shikimate pathway, suggesting that amino acids are metabolized to synthesize antifungal compounds. In glucose-containing medium, carbon flux was directed mainly toward the synthesis of energy and cell growth. This study shows the metabolic versatility of Amycolatopsis BX17, and strengthens its potential use in designing biotechnological strategies for phytopathogen control. SIGNIFICANCE: Amycolatopsis BX17 is a bacterium isolated from milpa agroecosystems that antagonizes the phytopathogenic fungus Fusarium graminearum. Currently, there is scarce information about the metabolism involved in the biosynthesis of antifungal agents by this genus. We used a label-free proteomic approach to identify the differences in metabolic routes for antifungal biosynthesis in Amycolatopsis BX17 grown in media with 0 and 20 g/L glucose. Taken together the results suggest that the BX17 strain could be synthesizing the antifungal metabolite(s) from the Shikimate pathway through the synthesis and degradation of the amino acid tyrosine, which is a known precursor of glycopeptides with antibiotic and antifungal activity. While the lower antifungal activity of the metabolites secreted by Amycolatopsis BX17 when grown in a medium with glucose as the main carbon source, may be correlated with a lower synthesis of antifungal compounds, due to the directing of carbon flux toward metabolic pathways involved with energy synthesis and cell growth. Likewise, it is possible that the bacteria synthesize other compounds with biological activity, such as glycopeptides with antibiotic activity. These findings are relevant because they represent the first stage to understand the metabolic regulation involved in the biosynthesis of antifungal metabolites by the genus Amycolatopsis. Finally, improving our understanding of the metabolic regulation involved in the biosynthesis of antifungal metabolites is essential to design of strategies in agricultural biotechnology for phytopathogen control.

Differential Activation of Ferulic Acid Catabolic Pathways of Amycolatopsis sp. ATCC 39116 in Submerged and Surface Cultures.

Amycolatopsis sp. ATCC 39116 catabolizes ferulic acid by the non-oxidative deacetylation and ß-oxidation pathways to produce vanillin and vanillic acid, respectively. In submerged culture, vanillin productivity decreased more than 8-fold, when ferulic, p-coumaric, and caffeic acids were employed in pre-cultures of the microorganism in order to activate the ferulic acid catabolic pathways, resulting in a carbon redistribution since vanillic acid and guaiacol productivities increased more than 5-fold compared with control. In contrast, in surface culture, the effects of ferulic and sinapic acids in pre-cultures were totally opposite to those of the submerged culture, directing the carbon distribution into vanillin formation. In surface culture, more than 30% of ferulic acid can be used as carbon source for other metabolic processes, such as ATP regeneration. In this way, the intracellular ATP concentration remained constant during the biotransformation process by surface culture (100 µg ATP/mg protein), demonstrating a high energetic state, which can maintain active the non-oxidative deacetylation pathway. In contrast, in submerged culture, it decreased 3.15-fold at the end of the biotransformation compared with the initial content, showing a low energetic state, while the NAD+/NADH ratio (23.15) increased 1.81-fold. It seems that in submerged culture, low energetic and high oxidative states are the physiological conditions that can redirect the ferulic catabolism into ß-oxidative pathway and/or vanillin oxidation to produce vanillic acid.