Traditional utilization of bamboo in the Central Siwalik region, Nepal.

Bamboo are the fastest growing perennial woody grasses that have versatile applications. Most of the local people inhabiting the riverine area of the Siwalik region of Nepal rely on bamboo products for economic benefits and medicinal uses. Our objective was to identify the diversity of bamboo species, their ethnomedicinal practices, and economic and ecological importance. Data were collected by direct observation, key informant interviews, participatory rural appraisal, inventory technique, focus group discussions, and a household survey using semi-structured and structured questionnaires. We recorded four genera and nine species of bamboo, of which eight species have been used for agriculture, five for medicine, four for construction, food, fodder, artifacts and religious purpose, three for river embankment, and two for ornamental purpose. As the local people in the study area were deprived of medical facilities, using traditional herbal medicine to cure various diseases was a common practice. The inhabitants responded that they use bamboo-based primary ethnomedicinal care even against snake and scorpion bites. Similarly, they use bamboo young culm for reducing body weight and control diabetes. The value of the informant consensus factor was found to be maximum for the bamboo against snake and scorpion bites (1.0) and minimum for weight loss (0.81). This study concludes that the traditional utilization of all kinds of bamboo in the region is vast despite their less diversity. The recorded bamboo species are used not only for food and fodder but also in preparing artifacts, soil nutrients restoration in the fallow land, construction materials for the rural people, river embankments, and religious and spiritual purposes. Therefore, if grown on a large scale, bamboo can provide sustainable benefits for the local users and ecological aspects. Bambusa tulda and Dendrocalamus strictus have a broad spectrum of pharmacological agents. Considering the multifaceted application of bamboo in the Siwalik area, it is worthwhile to encourage the local people to bamboo plantation, which would contribute to supplement their household requirements and be one of the alternative livelihood options.

Draft Genome Analysis of Antimicrobial Streptomyces Isolated from Himalayan Lichen.

There have been several studies regarding lichen-associated bacteria obtained from diverse environments. Our screening process identified 49 bacterial species in two lichens from the Himalayas: 17 species of Actinobacteria, 19 species of Firmicutes, and 13 species of Proteobacteria. We discovered five types of strong antimicrobial agent-producing bacteria. Although some strains exhibited weak antimicrobial activity, NP088, NP131, NP132, NP134, and NP160 exhibited strong antimicrobial activity against all multidrug-resistant strains. Polyketide synthase (PKS) fingerprinting revealed results for 69 of 148 strains; these had similar genes, such as fatty acid-related PKS, adenylation domain genes, PfaA, and PksD. Although the association between antimicrobial activity and the PKS fingerprinting results is poorly resolved, NP160 had six types of PKS fingerprinting genes, as well as strong antimicrobial activity. Therefore, we sequenced the draft genome of strain NP160, and predicted its secondary metabolism using antiSMASH version 4.2. NP160 had 46 clusters and was predicted to produce similar secondary metabolites with similarities of 5-100%. Although NP160 had 100% similarity with the alkylresorcinol biosynthetic gene cluster, our results showed low similarity with existing members of this biosynthetic gene cluster, and most have not yet been revealed. In conclusion, we expect that lichen-associated bacteria from the Himalayas can produce new secondary metabolites, and we found several secondary metabolite-related biosynthetic gene clusters to support this hypothesis.

Heterologous production of spectinomycin in Streptomyces venezuelae by exploiting the dTDP-D-desosamine pathway.

Spectinomycin is an aminoglycoside antibiotic composed of actinamine and actinospectose, which are fused together by a putative glycosyltransferase, SpcG, during spectinomycin biosynthesis. Although previous studies have revealed the involvement of SpcA (myo-inositol monophosphatase), SpcB (dehydrogenase), SpcS2 (aminotransferase), and SpcM (methyltransferase) in the biosynthesis of actinamine, heterologous biosynthesis of spectinomycin via actinospectose has not been clearly elucidated. In this study, Streptomyces venezuelae was utilized as a source of dTDP-actinospectose from the pikromycin biosynthetic desosamine sugar pathway, and a recombinant vector, pSM5, carrying spcA, spcB, spcS2, spcM, and spcG was inserted into S. venezuelae. The formation of dTDP-spectinose was suspected through the use of dehydrogenase in the S. venezuelae chromosome. Herewith, the genetically engineered strain, S. venezuelae SM5, effectively produced up to 89.2mg/L in optimized medium. However, pSM5 in S. venezuelae YJ003, a dTDP-actinospectose-deficient strain, did not produce spectinomycin. This result demonstrates the use of a dTDP-actinospectose precursor produced in the desosamine pathway for heterologous production of spectinomycin in S. venezuelae.

Enhancement of herboxidiene production in Streptomyces chromofuscus ATCC 49982.

Structurally, herboxidiene contains the tetrahydropyran acetic acid moiety and a side chain including a conjugated diene, and has been isolated from Streptomyces chromofuscus ATCC 49982. Its production was significantly elevated nearly 13.5-fold (0.74 g/l) in a medium supplemented with glycerol (medium No. 6A6), and was more efficacious (1.08 g/l; 19.8-fold) in fed-batch fermentation at 36 h in medium No. 6A6, from Streptomyces chromofuscus. For further enhancement, regulatory genes metK1-sp and afsR-sp from Streptomyces peucetius were overexpressed using an expression vector, pIBR25, and similarly ACCase from Streptomyces coelicolor and two genes, metK1-sp and afsR-sp, were also overexpressed using an integration vector, pSET152, under the control of the strong ermE* promoter in Streptomyces chromofuscus. Only the recombinant strains S. chromofuscus SIBR, S. chromofuscus GIBR, and S. chromofuscus AFS produced more herboxidiene than the parental strain in optimized medium No. 6A6 with an increment of 1.32-fold (0.976 g/l), 3.85-fold (2.849 g/l), and 1.7-fold(1.258 g/l) respectively.

Biosynthesis of the nargenicin A1 pyrrole moiety from Nocardia sp. CS682.

A number of structurally diverse natural products harboring pyrrole moieties possess a wide range of biological activities. Studies on biosynthesis of pyrrole ring have shown that pyrrole moieties are derived from L-proline. Nargenicin A(1), a saturated alicyclic polyketide from Nocardia sp. CS682, is a pyrrole-2-carboxylate ester of nodusmicin. We cloned and identified a set of four genes from Nocardia sp. CS682 that show sequence similarity to the respective genes involved in the biosynthesis of the pyrrole moieties of pyoluteorin in Pseudomonas fluorescens, clorobiocin in Streptomyces roseochromogenes subsp. Oscitans, coumermycin A(1) in Streptomyces rishiriensis, one of the pyrrole rings of undecylprodigiosin in Streptomyces coelicolor, and leupyrrins in Sorangium cellulosum. These genes were designated as ngnN4, ngnN5, ngnN3, and ngnN2. In this study, we presented the evidences that the pyrrole moiety of nargenicin A(1) was also derived from L-proline by the coordinated action of three proteins, NgnN4 (proline adenyltransferase), NgnN5 (proline carrier protein), and NgnN3 (flavine-dependent acyl-coenzyme A dehydrogenases). Biosynthesis of pyrrole moiety in nargenicin A(1) is initiated by NgnN4 that catalyzes ATP-dependent activation of L-proline into L-prolyl-AMP, and the latter is transferred to NgnN5 to create prolyl-S-peptidyl carrier protein (PCP). Later, NgnN3 catalyzes the two-step oxidation of prolyl-S-PCP into pyrrole-2-carboxylate. Thus, this study presents another example of a pyrrole moiety biosynthetic pathway that uses a set of three genes to convert L-proline into pyrrole-2-carboxylic acid moiety.

Biosynthesis of rubradirin as an ansamycin antibiotic from Streptomyces achromogenes var. rubradiris NRRL3061.

The four overlapping cosmids from the rubradirin producer, Streptomyces achromogenes var rubradiris NRRL 3061, have 58 ORFs within a 105.6 kb fragment. These ORFs harbored essential genes responsible for the formation and attachment of four distinct moieties, along with the genes associated with regulatory, resistance, and transport functions. The PKS (rubA) and glycosyltransferase (rubG2) genes were disrupted in order to demonstrate a complete elimination of rubradirin production. The rubradirin biosynthetic pathway was proposed based on the putative functions of the gene products, the functional identification of sugar genes, and the mutant strains.

Functional characterization of ketoreductase (rubN6) and aminotransferase (rubN4) genes in the gene cluster of Streptomyces achromogenes var. rubradiris.

ORF's for rubN6 and rubN4 have been annotated as thymidine diphosphate glucose 4-ketoreductase and thymidine diphosphate glucose 3-aminotransferase by sequence analysis of the rubradirin biosynthetic gene cluster cloned from Streptomyces achromogenes var. rubradiris NRRL 3061. Both ORFs were heterologously expressed in Escherichia coli as His-tagged fusion proteins. The functionalities of TDP-glucose 4-ketoreductase and TDP-glucose 3-aminotransferase were verified by in vitro enzyme assay, and a biosynthetic pathway for TDP-D: -rubranitrose is proposed.