Natural Products from Nocardia and Their Role in Pathogenicity

Nocardia spp. are filamentous Actinobacteria of the order Corynebacteriales and mostly known for their ability to cause localized and systemic infections in humans. However, the onset and progression of nocardiosis is only poorly understood, in particular the mechanisms of strain-specific presentations. Recent genome sequencing has revealed an extraordinary capacity for the production of specialized small molecules. Such secondary metabolites are often crucial for the producing microbe to survive the challenges of different environmental conditions. An interesting question thus concerns the role of these natural products in Nocardia-associated pathogenicity and immune evasion in a human host. In this review, a summary and discussion of Nocardia metabolites is presented, which may play a part in nocardiosis because of their cytotoxic, immunosuppressive and metal-chelating properties or otherwise vitally important functions. This review also contains so far unpublished data concerning the biosynthesis of these molecules that were obtained by detailed bioinformatic analyses.

Secondary metabolites and biodiversity of actinomycetes

BACKGROUND

The ability to produce microbial bioactive compounds makes actinobacteria one of the most explored microbes among prokaryotes. The secondary metabolites of actinobacteria are known for their role in various physiological, cellular, and biological processes.

MAIN BODY

Actinomycetes are widely distributed in natural ecosystem habitats such as soil, rhizosphere soil, actinmycorrhizal plants, hypersaline soil, limestone, freshwater, marine, sponges, volcanic cave-hot spot, desert, air, insects gut, earthworm castings, goat feces, and endophytic actinomycetes. The most important features of microbial bioactive compounds are that they have specific microbial producers: their diverse bioactivities and their unique chemical structures. Actinomycetes represent a source of biologically active secondary metabolites like antibiotics, biopesticide agents, plant growth hormones, antitumor compounds, antiviral agents, pharmacological compounds, pigments, enzymes, enzyme inhibitors, anti-inflammatory compounds, single-cell protein feed, and biosurfactant.

SHORT CONCLUSIONS

Further highlight that compounds derived from actinobacteria can be applied in a wide range of industrial applications in biomedicines and the ecological habitat is under-explored and yet to be investigated for unknown, rare actinomycetes diversity.

Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters in the genus Acrocarpospora

Acrocarpospora is a rare, recently established actinomycete genus of the family Streptosporangiaceae. In the present study, we sequenced whole genomes of the type strains of Acrocarpospora corrugate, Acrocarpospora macrocephala, and Acrocarpospora pleiomorpha to assess their potency as secondary metabolite producers; we then surveyed their nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters. The genome sizes of A. corrugate NBRC 13972^T, A. macrocephala NBRC 16266^T, and A. pleiomorpha NBRC 16267^T were 9.3 Mb, 12.1 Mb, and 11.8 Mb, respectively. Each genome contained 12-17 modular NRPS and PKS gene clusters. Among the 23 kinds of NRPS and PKS gene clusters identified from the three strains, eight clusters were conserved in all the strains, six were shared between A. macrocephala and A. pleiomorpha, and the remaining nine were strain-specific. We predicted the chemical structures of the products synthesized by these gene clusters based on bioinformatic analyses. Since the chemical structures are diverse, Acrocarpospora strains are considered an attractive source of diverse nonribosomal peptide and polyketide compounds.

Comparative Genomics and Metabolomics in the Genus Nocardia

Using automated genome analysis tools, it is often unclear to what degree genetic variability in homologous biosynthetic pathways relates to structural variation. This hampers strain prioritization and compound identification and can lead to overinterpretation of chemical diversity. Here, we assessed the metabolic potential of Nocardia, an underinvestigated actinobacterial genus that is known to comprise opportunistic human pathogens. Our analysis revealed a plethora of putative biosynthetic gene clusters of various classes, including polyketide, nonribosomal peptide, and terpenoid pathways. Furthermore, we used the highly conserved biosynthetic pathway for nocobactin-like siderophores to investigate how gene cluster differences correlate to structural differences in the produced compounds. Sequence similarity networks generated by BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) showed the presence of several distinct gene cluster families. Metabolic profiling of selected Nocardia strains using liquid chromatography-mass spectrometry (LC-MS) metabolomics data, nuclear magnetic resonance (NMR) spectroscopy, and GNPS (Global Natural Product Social molecular networking) revealed that nocobactin-like biosynthetic gene cluster (BGC) families above a BiG-SCAPE threshold of 70% can be assigned to distinct structural types of nocobactin-like siderophores.IMPORTANCE Our work emphasizes that Nocardia represent a prolific source for natural products rivaling better-characterized genera such as Streptomyces or Amycolatopsis Furthermore, we showed that large-scale analysis of biosynthetic gene clusters using similarity networks with high stringency allows the distinction and prediction of natural product structural variations. This will facilitate future genomics-driven drug discovery campaigns.

Bioactive molecules from Nocardia: diversity, bioactivities and biosynthesis

Nocardia spp. are catalase positive, aerobic, and non-motile Gram-positive filamentous bacteria. Many Nocarida spp. have been reported as unusual causes of diverse clinical diseases in both humans and animals. Therefore, they have been studied for a long time, primarily focusing on strain characterization, taxonomic classification of new isolates, and host pathophysiology. Currently, there are emerging interests in isolating bioactive molecules from diverse actinobacteria including Nocardia spp. and studying their biosynthetic mechanisms. In addition, these species possess significant metabolic capacity, which has been utilized for generating diverse functionalized bioactive molecules by whole cell biotransformation. This review summarizes the structural diversity and biological activities of compounds biosynthesized or biotransformed by Nocardia spp. Furthermore, the recent advances on biosynthetic mechanisms and genetic engineering approaches for enhanced production or structural/functional modification are presented.

Antimicrobial profile of Arthrobacter kerguelensis VL-RK_09 isolated from Mango orchards

An actinobacterial strain VL-RK_09 having potential antimicrobial activities was isolated from a mango orchard in Krishna District, Andhra Pradesh (India) and was identified as Arthrobacter kerguelensis. The strain A. kerguelensis VL-RK_09 exhibited a broad spectrum of in vitro antimicrobial activity against bacteria and fungi. Production of bioactive metabolites by the strain was the highest in modified yeast extract malt extract dextrose broth, as compared to other media tested. Lactose (1%) and peptone (0.5%) were found to be the most suitable carbon and nitrogen sources, respectively, for the optimum production of the bioactive metabolites. The maximum production of the bioactive metabolites was detected in the culture medium with an initial pH of 7, in which the strain was incubated for five days at 30°C under shaking conditions. Screening of secondary metabolites obtained from the culture broth led to the isolation of a compound active against a wide variety of Gram-positive and negative bacteria and fungi. The structure of the first active fraction was elucidated using Fourier transform infrared spectroscopy, electrospray ionization mass spectrometry, 1H and 13C nuclear magnetic resonance spectroscopy. The compound was identified as S,S-dipropyl carbonodithioate. This study is the first report of the occurrence of this compound in the genus Arthrobacter.

Functional diversity of Nocardia in metabolism

Bacteria affiliated in the genus Nocardia are aerobic and Gram-positive actinomycetes that are widely found in aquatic and terrestrial habitats. As occasional pathogens, several of them cause infection diseases called 'nocardiosis' affecting lungs, central nervous system, cutaneous tissues and others. In addition, members of the genus Nocardia exhibit an enormous metabolic versatility. On one side, many secondary metabolites have been isolated from members of this genus that exhibit various biological activities such as antimicrobial, antitumor, antioxidative and immunosuppressive activities. On the other side, many species are capable of degrading or converting aliphatic and aromatic toxic hydrocarbons, natural or synthetic polymers, and other widespread environmental pollutants. Because of these valuable properties and the application potential, Nocardia species have attracted much interest in academia and industry in recent years. A solid basis of genetic tools including a set of shuttle vectors and an efficient electroporation method for further genetic and metabolic engineering studies has been established to conduct efficient research. Associated with the increasing data of nocardial genome sequences, the functional diversity of Nocardia will be much faster and better understood.

Pharmaceutically active secondary metabolites of marine actinobacteria

Marine actinobacteria are one of the most efficient groups of secondary metabolite producers and are very important from an industrial point of view. Many representatives of the order Actinomycetales are prolific producers of thousands of biologically active secondary metabolites. Actinobacteria from terrestrial sources have been studied and screened since the 1950s, for many important antibiotics, anticancer, antitumor and immunosuppressive agents. However, frequent rediscovery of the same compounds from the terrestrial actinobacteria has made them less attractive for screening programs in the recent years. At the same time, actinobacteria isolated from the marine environment have currently received considerable attention due to the structural diversity and unique biological activities of their secondary metabolites. They are efficient producers of new secondary metabolites that show a range of biological activities including antibacterial, antifungal, anticancer, antitumor, cytotoxic, cytostatic, anti-inflammatory, anti-parasitic, anti-malaria, antiviral, antioxidant, anti-angiogenesis, etc. In this review, an evaluation is made on the current status of research on marine actinobacteria yielding pharmaceutically active secondary metabolites. Bioactive compounds from marine actinobacteria possess distinct chemical structures that may form the basis for synthesis of new drugs that could be used to combat resistant pathogens. With the increasing advancement in science and technology, there would be a greater demand for new bioactive compounds synthesized by actinobacteria from various marine sources in future.

A novel anticancer and antifungus phenazine derivative from a marine actinomycete BM-17

A marine actinomycete, designated strain BM-17, was isolated from a sediment sample collected in the Arctic Ocean. The strain was identified as Nocardia dassonvillei based on morphological, cultural, physiological, biochemical characteristics, along with the cell wall analysis and 16S rDNA gene sequence analysis. A new secondary metabolite (1), N-(2-hydroxyphenyl)-2-phenazinamine (NHP), and six known antibiotics (2-7) have been isolated from the saline culture broth of the stain by sequentially purification over macroporous resin D101, silica gel, Sephadex LH-20 column chromatography and preparative HPLC after the stain was incubated in soy bean media at 28°C for 7 days. The chemical structures of the compounds were elucidated on the basis of spectroscopic analysis, including two-dimensional (2D) NMR and HR-ESI-MS data. The new compound showed significant antifungal activity against Candida albicans, with a MIC of 64 μg/ml and high cancer cell cytotoxicity against HepG2, A549, HCT-116 and COC1 cells.

Production of bioactive metabolites by Nocardia levis MK-VL_113

AIMS

To isolate and identify the bioactive compounds produced by Nocardia levis MK-VL_113.

METHODS AND RESULTS

Cultural characteristics of Noc. levis isolated from laterite soils of Guntur region were recorded on International Streptomyces Project media. Morphological studies of the strain through scanning electron microscopy revealed the clear pattern of its hyphal fragmentation into rod-shaped bacilli. Chemical examination of the secondary metabolites of the strain grown on sucrose-tryptone broth led to the isolation of three fractions active against Bacillus cereus. Further analysis of second fraction resulted in the isolation of two active subfractions. Two different phthalate esters, namely, bis-(2-ethylhexyl) phthalate and bis-(5-ethylheptyl) phthalate, were purified from the first active subfraction, and the structural elucidation of these compounds was confirmed on the basis of FT-IR, mass and NMR spectroscopy. The partially purified second subfraction subjected to Gas Chromatography-Mass spectroscopy contained nine components: decanedioic acid; 2,6-piperdione monooxime; 1-eicosanol; beta-1-arabinopyranoside, methyl; cyclopentaneundecanoic acid; hexadecanoic acid; silane, trichloro eicosyl; 1-hexacosanol; and 1,2-dodecanediol. The antimicrobial activity of the bioactive compounds produced by Noc. levis was expressed in terms of minimum inhibitory concentration.

CONCLUSIONS

The present study clearly revealed that the metabolites of Noc. levis act as bioactive compounds against gram-positive and gram-negative bacteria, yeast and filamentous fungi. It also supports the idea that there are a number of rare actinomycetes remained to be explored for new bioactive compounds.

SIGNIFICANCE AND IMPACT OF THE STUDY

Metabolites of Noc. levis exhibited antibacterial and antifungal activities. This is the first report of bis-(5-ethylheptyl) phthalate as well as the nine partially purified compounds from actinomycetes. In addition, this is also the first report of bis-(2-ethylhexyl) phthalate from the genus Nocardia.