The ability to specifically attach chemical probes to individual proteins represents a powerful approach to the study and manipulation of protein function in living cells. It provides a simple, robust and versatile approach to the imaging of fusion proteins in a wide range of experimental settings. However, a potential drawback of detection using chemical probes is the fluorescence background from unreacted or nonspecifically bound probes. In this report we present the design and application of novel fluorogenic probes for labeling SNAP-tag fusion proteins in living cells. SNAP-tag is an engineered variant of the human repair protein O6-alkylguanine-DNA alkyltransferase (hAGT) that covalently reacts with benzylguanine derivatives. Reporter groups attached to the benzyl moiety become covalently attached to the SNAP tag while the guanine acts as a leaving group. Incorporation of a quencher on the guanine group ensures that the benzylguanine probe becomes highly fluorescent only upon labeling of the SNAP-tag protein. We describe the use of intramolecularly quenched probes for wash-free labeling of cell surface-localized epidermal growth factor receptor (EGFR) fused to SNAP-tag and for direct quantification of SNAP-tagged β-tubulin in cell lysates. In addition, we have characterized a fast-labeling variant of SNAP-tag, termed SNAPf, which displays up to a tenfold increase in its reactivity towards benzylguanine substrates. The presented data demonstrate that the combination of SNAPf and the fluorogenic substrates greatly reduces the background fluorescence for labeling and imaging applications. This approach enables highly sensitive spatiotemporal investigation of protein dynamics in living cells.

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BackgroundThe initiating nucleotide found at the 5’ end of primary transcripts has a distinctive triphosphorylated end that distinguishes these transcripts from all other RNA species. Recognizing this distinction is key to deconvoluting the primary transcriptome from the plethora of processed transcripts that confound analysis of the transcriptome. The currently available methods do not use targeted enrichment for the 5′end of primary transcripts, but rather attempt to deplete non-targeted RNA.ResultsWe developed a method, Cappable-seq, for directly enriching for the 5' end of primary transcripts and enabling determination of transcription start sites at single base resolution. This is achieved by enzymatically modifying the 5′ triphosphorylated end of RNA with a selectable tag. We first applied Cappable-seq to E. coli, achieving up to 50 fold enrichment of primary transcripts and identifying an unprecedented 16539 transcription start sites (TSS) genome-wide at single base resolution. We also applied Cappable-seq to a mouse cecum sample and identified TSS in a microbiome.ConclusionsCappable-seq allows for the first time the capture of the 5′ end of primary transcripts. This enables a unique robust TSS determination in bacteria and microbiomes.  In addition to and beyond TSS determination, Cappable-seq depletes ribosomal RNA and reduces the complexity of the transcriptome to a single quantifiable tag per transcript enabling digital profiling of gene expression in any microbiome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2539-z) contains supplementary material, which is available to authorized users.

There has been a recent upsurge of interest in mushrooms as a source of biological active compounds of medicinal value including anti-cancer, anti-viral, immunopotentiating, hypocholesterolaemic and hepatoprotective agents. This new class of compounds, termed 'mushroom nutriceuticals', are extractable from either the fungal mycelium or fruiting body and represent an important component of the expanding mushroom biotechnology industry.

Lentinula (Lentinus) edodes, strain LS4, produces manganese‐dependent peroxidase (MnP) and laccase, but not lignin peroxidase, when grown on a defined medium with glucose as sole carbon source. MnP production is suppressed by nitrogen whereas highest levels of laccase were observed when the fungus was grown under high nitrogen (26 mM) conditions. Both the titre and time of appearance of MnP were affected by the concentration of Mn in the culture medium with highest enzyme levels recorded in cultures supplemented with 1.1 ppm Mn. Purified MnP from L. edodes LS4 has an apparent Mr of 59000 and a pI of 5.6, and differs in several respects from a MnP isolated from L. edodes grown on a commercial wood substrate.

Background: The initiating nucleotide found at the 5' end of primary transcripts has a distinctive triphosphorylated end that distinguishes these transcripts from all other RNA species. Recognizing this distinction is key to deconvoluting the primary transcriptome from the plethora of processed transcripts that confound analysis of the transcriptome. The currently available methods do not use targeted enrichment for the 5′end of primary transcripts, but rather attempt to deplete non-targeted RNA.

A Flexibacter columnaris-like bacterium (Strain NCMB 2158), isolated from Dover sole suffering from 'black patch necrosis' (BPN) in Scotland, was compared to F. columnaris, F. psychrophilus, F. maritimus, and to all other valid Flexibacter and Cytophaga species Investigation of phenotypic characteristics showed the unidentified isolate to be more closely related to F. nlanhmus to than F. columnaris. DNA was subsequently extracted from each of the studied strains and compared using the DNA/DNA hybridization method. The very high DNA relatedness of Strain NCMB 2158 with 2 F. maritimus reference strains and its insignificant homology with all of the other strains confirmed that the Dover sole isolate belonged to the species F rnaritimus. These results have resolved the bacterial aetiology of BPN and reveal for the first time the existence of F maritimus elsewhere than in Japan.

One of the most economically-viable processes for the bioconversion of many types of lignocellulosic wastes is represented by edible mushroom cultivation. Lentinula edodes, Volvariella volvacea and Pleurotus sajor-caju are three important commercially cultivated mushrooms which exhibit varying abilities to utilise different lignocellulosics as growth substrate. Examination of the lignocellulolytic enzyme profiles of the three species show this diversity to be reflected in qualitative variations in the major enzymic determinants (i.e. cellulases, ligninases) required for substrate bioconversion. For example, L. edodes, which is cultivated on highly lignified substrates such as wood or sawdust, produces two extracellular enzymes which have been associated with lignin depolymerisation in other fungi, (manganese peroxidase and laccase). Conversely, V. volvacea, which prefers high cellulose-, low lignin-containing substrates produces a family of cellulolytic enzymes including at least five endoglucanases, five cellobiohydrolases and two β-glucosidases, but none of the recognised lignin-degrading enzymes.