Access to and use of marine genetic resources : understanding the legal framework

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Acknowledgements This work was supported by the PharmaSea project funded by the EU Seventh Framework Programme, and reects only the authors' views. Contract number 312184. www.pharma-sea.eu.Peer reviewedPublisher PD

Differential expression of genes involved in iron metabolism in Aspergillus fumigatus

The ability of fungi to survive in many environments is linked to their capacity to acquire essential nutrients. Iron is generally complexed and available in very limited amounts. Like bacteria, fungi have evolved highly specific systems for iron acquisition. Production and uptake of iron-chelating siderophores has been shown to be important for certain human bacterial pathogens, as well as in fungal pathogens such as Cryptococcus neoformans and Fusarium graminearum. This system also enables the opportunistic fungal pathogen Aspergillus fumigatus to infect and subsequently colonize the human lung. In this study, advantage was taken of genome sequence data available for both Aspergillus nidulans and A. fumigatus either to partially clone or to design PCR primers for 10 genes putatively involved in siderophore biosynthesis or uptake in A. fumigatus. The expression of these genes was then monitored by semi-quantitative and quantitative real-time PCR over a range of iron concentrations. As expected, the putative biosynthetic genes sidA, sidC and sidD were all strongly up-regulated under iron starvation conditions, although the variable degree of induction indicates complex regulation by a number of transcriptional factors, including the GATA family protein SreA. In contrast, the gene sidE shows no iron-regulation, suggesting that SidE may not be involved in siderophore biosynthesis. The characterisation of the expression patterns of this subset of genes in the iron regulon facilitates further studies into the importance of iron acquisition for pathogenesis of A. fumigatus. [Int Microbiol 2006; 9(4):281-287

Mycotoxins in spices and herbs - an update

Spices and herbs have been used since ancient times as flavor and aroma enhancers, colorants, preservatives, and traditional medicines. There are more than 30 spices and herbs of global economic and culinary importance. Among the spices, black pepper, capsicums, cumin, cinnamon, nutmeg, ginger, turmeric, saffron, coriander, cloves, dill, mint, thyme, sesame seed, mustard seed, and curry powder are the most popular spices worldwide. In addition to their culinary uses, a number of functional properties of aromatic herbs and spices are also well described in the scientific literature. However, spices and herbs cultivated mainly in tropic and subtropic areas can be exposed to contamination with toxigenic fungi and subsequently mycotoxins. This review provides an overview on the mycotoxin risk in widely consumed spices and aromatic herbs

Draft genome sequence of the antimycin-producing bacterium Streptomyces sp. strain SM8, isolated from the marine sponge Haliclona simulans

Streptomyces sp. strain SM8, isolated from Haliclona simulans, possesses antifungal and antibacterial activities and inhibits the calcineurin pathway in yeast. The draft genome sequence is 7,145,211 bp, containing 5,929 predicted coding sequences. Several secondary metabolite biosynthetic gene clusters are present, encoding known and novel metabolites, including antimycin

Draft genome sequence of Pseudomonas putida CA-3, a bacterium capable of styrene degradation and medium-chain-length polyhydroxyalkanoate synthesis

Pseudomonas putida strain CA-3 is an industrial bioreactor isolate capable of synthesizing biodegradable polyhydroxyalkanoate polymers via the metabolism of styrene and other unrelated carbon sources. The pathways involved are subject to regulation by global cellular processes. The draft genome sequence is 6,177,154 bp long and contains 5,608 predicted coding sequences

Cloning and characterization of novel methylsalicylic acid synthase gene involved in the biosynthesis of isoasperlactone and asperlactone in Aspergillus westerdijkiae

Aspergillus westerdijkiae is the main producer of several biologically active polyketide metabolites including isoasperlactone and asperlactone. A 5298 bp polyketide synthase gene ‘‘aomsas” has been cloned in Aspergillus westerdijkiae by using gene walking approach and RACE-PCR. The predicted amino acid sequence of aomsas shows an identity of 40–56% with different methylsalicylic acid synthase genes found in Byssochlamys nivea, P. patulum, A. terreus and Streptomyces viridochromogenes. Based on the reverse transcription PCR and kinetic secondary metabolites production studies, aomsas expression was found to be associated with the biosynthesis of isoasperlactone and asperlactone. Moreover an aomsas knockout mutant ‘‘aoDmsas” of A. westerdijkiae, not only lost the capacity to produce isoasperlactone and asperlactone,but also 6-methylsalicylic acid. The genetically complemented mutant ao+msas restored the biosynthesis of all the missing metabolites. Chemical complementation through the addition of 6-methylsalicylic acid, aspyrone and diepoxide to growing culture of aoDmsas mutant revealed that these compounds play intermediate roles in the biosynthesis of asperlactone and isoasperlactone

Synthesis of Nm-PHB (nanomelanin-polyhydroxy butyrate) nanocomposite film and its protective effect against biofilm-forming multi drug resistant Staphylococcus aureus

Melanin is a dark brown ubiquitous photosynthetic pigment which have many varied and ever expanding applications in fabrication of radio-protective materials, food packaging, cosmetics and in medicine. In this study, melanin production in a Pseudomonas sp. which was isolated from the marine sponge Tetyrina citirna was optimized employing one-factor at a time experiments and characterized for chemical nature and stability. Following sonication nucleated nanomelanin (Nm) particles were formed and evaluated for antibacterial and antioxidant properties. Nanocomposite film was fabricated using combinations (% w/v) of polyhydroxy butyrate-nanomelanin (PHB: Nm) blended with 1% glycerol. The Nm was found to be spherical in shape with a diameter of 100-140 nm and showed strong antimicrobial activity against both Gram positive and Gram negative bacteria. The Nm-PHB nanocomposite film was homogeneous, smooth, without any cracks, and flexible. XRD and DSC data indicated that the film was crystalline in nature, and was thermostable up to 281.87 degrees C. This study represents the first report on the synthesis of Nm and fabrication of Nm-PHB nanocomposite film which show strong protective effect against multidrug resistant Staphyloccoccus aureus. Thus this Nm-PHB nanocomposite film may find utility as packaging material for food products by protecting the food products from oxidation and bacterial contamination

Methanosarcina play an important role in anaerobic co-digestion of the seaweed Ulva lactuca: metagenomics structure and predicted metabolism of functional microbial communities.

Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1) and strongest (R6) performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA) showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation

Extending the "one strain many compounds" (OSMAC) principle to marine microorganisms

Genomic data often highlights an inconsistency between the number of gene clusters identified using bioinformatic approaches as potentially producing secondary metabolites and the actual number of chemically characterized secondary metabolites produced by any given microorganism. Such gene clusters are generally considered as "silent", meaning that they are not expressed under laboratory conditions. Triggering expression of these "silent" clusters could result in unlocking the chemical diversity they control, allowing the discovery of novel molecules of both medical and biotechnological interest. Therefore, both genetic and cultivation-based techniques have been developed aimed at stimulating expression of these "silent" genes. The principles behind the cultivation based approaches have been conceptualized in the "one strain many compounds" (OSMAC) framework, which underlines how a single strain can produce different molecules when grown under different environmental conditions. Parameters such as, nutrient content, temperature, and rate of aeration can be easily changed, altering the global physiology of a microbial strain and in turn significantly affecting its secondary metabolism. As a direct extension of such approaches, co-cultivation strategies and the addition of chemical elicitors have also been used as cues to activate "silent" clusters. In this review, we aim to provide a focused and comprehensive overview of these strategies as they pertain to marine microbes. Moreover, we underline how changes in some parameters which have provided important results in terrestrial microbes, but which have rarely been considered in marine microorganisms, may represent additional strategies to awaken "silent" gene clusters in marine microbes. Unfortunately, the empirical nature of the OSMAC approach forces scientists to perform extensive laboratory experiments. Nevertheless, we believe that some computation and experimental based techniques which are used in other disciplines, and which we discuss; could be effectively employed to help streamline the OSMAC based approaches. We believe that natural products discovery in marine microorganisms would be greatly aided through the integration of basic microbiological approaches, computational methods, and technological innovations, thereby helping unearth much of the as yet untapped potential of these microorganisms

HPLC-ESI-MS/MS characterisation of metabolites produced by Pseudovibrio sp. W64, a marine sponge-derived bacterium isolated from Irish waters

Rationale: In recent years, metabolites produced by Pseudovibrio species have gained scientific attention due to their potent antimicrobial activity. Recently we also have assessed antibacterial activities of Pseudovibrio sp. W64 isolates against Staphylococcus aureus, where only the dominant tropodithietic acid (TDA) was identified. However characterisation of other metabolites is necessary as these metabolites may also serve as potent antimicrobial agents. Methods: LC-MS/MS, aided by accurate mass measurements, was employed to screen and characterise a range of metabolites produced by Pseudovibrio sp. W64 via assessment of ethyl acetate fractions generated from bacterial cultures. Results: Thirteen metabolites unique to the bacterial culture were detected and their chemical structures were assigned by tandem mass spectrometry and accurate mass measurement. Among the thirteen metabolites, a methyl ester of TDA, a number of cholic acid derivatives, and amino diols and triols were characterised. Conclusions: Pseudovibrio sp. W64 produces methylated TDA in addition to TDA, and metabolises lipids and amino acids in the cell-culture medium. To the best of our knowledge, this is the first report of methylated TDA, cholic acid and its various analogs, and sphinganine being detected in this Pseudovibrio strain. The data generated may help to better understand the biochemical processes and metabolism of bacterial strains towards discovery of antimicrobial agents from marine sources