Steven Anthony Fish

Recovery of 16S ribosomal RNA gene fragments from ancient halite

During the last decade, sensitive techniques for detecting DNA have been successfully applied to archaeological and other samples that were a few hundred to a few thousand years old. Nevertheless, there is still controversy and doubt over claims of exceptionally ancient DNA. Additional accounts stretching back nearly a century suggest that microorganisms may survive over geological time in evaporite deposits. There is, however, often doubt over the age relationship between evaporite formation and the incorporation of microorganisms. Here, we have used petrographic and geochemical techniques (laser ablation microprobe–inductively coupled plasma–mass spectrometry) to verify the estimated geological age of halite (NaCl) evaporite samples. Fragments of 16S ribosomal RNA genes were detected by polymerase chain reaction amplification of DNA extracted from halite samples ranging in age from 11 to 425 Myr (millions of years). Haloarchaeal 16S rDNA amplicons were present in one sample (11–16 Myr), whereas other samples (65–425 Myr) yielded only bacterial 16S rDNA amplicons. Terminal restriction fragment length polymorphism analyses indicate complex and different populations of microorganisms or their free DNA in ancient halites of different ages.

The tylosin-biosynthetic genes of Streptomyces fradiae

The tylosin-biosynthetic (tyl) gene cluster occupies about 1% of the genome of Streptomyces fradiae and includes at least 43 open reading frames. In addition to structural genes required for tylosin production, the tylcluster contains three resistance determinants and several regulatory genes. Tylosin production is evidently controlled by pathway-specific and pleiotropic regulators with the likely involvement of γ-butyrolactone signalling factors. Accumulation of the polyketide aglycone is controlled by glycosylated macrolides and optimal performance of the complex polyketide synthase enzyme requires the activity of an editing thioesterase.

Stimulation of polyketide metabolism in Streptomyces fradiae by tylosin and its glycosylated precursors

Three glycosyltransferases are involved in tylosin biosynthesis in Streptomyces fradiae. The first sugar to be added to the polyketide aglycone (tylactone) is mycaminose and the gene encoding mycaminosyltransferase is orf2* (tylM2). However, targeted disruption of orf2* did not lead to the accumulation of tylactone under conditions that normally favour tylosin production; instead, the synthesis of tylactone was virtually abolished. This may, in part, have resulted from a polar effect on the expression of genes downstream of orf2*, particularly orf4* (ccr) which encodes crotonyl-CoA reductase, an enzyme that supplies 4-carbon extender units for polyketide metabolism. However, that cannot be the entire explanation, since tylosin production was restored at about 10% of the wild-type level when orf2* was re-introduced into the disrupted strain. When glycosylated precursors of tylosin were fed to the disrupted strain, they were converted to tylosin, confirming that two of the three glycosyltransferase activities associated with tylosin biosynthesis were still intact. Interestingly, however, tylactone also accumulated under such conditions and, to a much lesser extent, when tylosin was added to similar fermentations. It is concluded that glycosylated macrolides exert a pronounced positive effect on polyketide metabolism in S. fradiae.

Bioactive compound production by thermophilic and thermotolerant cyanobacteria (blue-green algae)

A thermotolerant species of Phormidium produced extracellular anti-microbial material during batch culture. Although this material was inactive when screened against a number of other cyanobacteria, it inhibited the growth of a wide range of Gram-positive and Gram-negative heterotrophic bacteria, Candida albicans and Cladosporium resinae.

Characterization of a family of ice-active proteins from the Ryegrass, Lolium perenne☆

Five genes coding for ice-active proteins were identified from an expressed sequence tag database of Lolium perenne cDNA libraries. Each of the five genes were characterized by the presence of an N-terminal signal peptide, a region enriched in hydrophilic amino acids and a leucine-rich region in four of the five genes that is homologous with the receptor domain of receptor-like protein kinases of plants. The C-terminal region of all five genes contains sequence homologous with Lolium and Triticum ice-active proteins. Of the four ice-active proteins (IAP1, IAP2, IAP3 and IAP5) cloned, three could be expressed in Escherichia coli and recovered in a functional form in order to study their ice activity. All three ice-active proteins had recrystallization inhibition activity but showed no detectable antifreeze or ice nucleation activity at the concentration tested. IAP2 and IAP5 formed distinct hexagonal-shaped crystals in the nanolitre osmometer as compared to the weakly hexagonal crystals produced by IAP3.

Modelling real-time simultaneous saccharification and fermentation of lignocellulosic biomass and organic acid accumulation using dielectric spectroscopy.

Dielectric spectroscopy (DS) is routinely used in yeast and mammalian fermentations to quantitatively monitor viable biomass through the inherent capacitance of live cells; however, the use of DS to monitor the enzymatic break down of lignocellulosic biomass has not been reported. The aim of the current study was to examine the application of DS in monitoring the enzymatic saccharification of high sugar perennial ryegrass (HS-PRG) fibre and to relate the data to changes in chemical composition. DS was capable of both monitoring the on-line decrease in PRG fibre capacitance (C=580 kHz) during enzymatic hydrolysis, together with the subsequent increase in conductivity (G=580 kHz) resulting from the production of organic acids during microbial growth. Analysis of the fibre fractions revealed >50% of HS-PRG lignocellulose had undergone enzymatic hydrolysis. These data demonstrated the utility of DS biomass probes for on-line monitoring of simultaneous saccharification and fermentation (SSF).

Analysis of culture conditions controlling the yield of bioactive material produced by the thermotolerant cyanobacterium (blue-green alga) Phormidium

Growth conditions were investigated in batch culture of the thermotolerant cyanobacterium Phormidium sp. with the aim of identifying which culture conditions modulated an increase in the yield of bioactive material. This was achieved using a factorial experimental design, followed by a method of steepest ascent. Although temperature, nitrilotriacetic acid, nitrate and ferric iron chloride all influenced regulation of the production of compounds which inhibit the growth of Staphylococcus aureus and Candida albicans, it was found that ferric iron chloride exerted the greatest effect.

corrigendum: Recovery of 16S ribosomal RNA gene fragments from ancient halite

This corrects the article DOI: 417432a

Antimicrobial and cytotoxic activity produced by an isolate of the thermotolerant cyanobacterium (blue-green alga) Phormidium sp.

Extracellular material from a thermotolerant isolate ofPhormidium sp. from the Azores was chromatographed using Amberlite XAD-7 in conjunction with C18 Sep-Paks to reveal antimicrobial activity. Further examination indicated the possibility of anticancer activity, elucidated using a biochemical induction assay and the inhibition of the V79 cell line.