ALBERT

Description: Background: The ability to adapt to environments with fluctuating nutrient availability is vital for bacterial survival. Although essential for growth, few nitrogen metabolism genes have been identified or fully characterised in mycobacteria and nitrogen stress survival mechanisms are unknown. Results: A global transcriptional analysis of the mycobacterial response to nitrogen stress, showed a significant change in the differential expression of 16% of the Mycobacterium smegmatis genome. Gene expression changes were mapped onto the metabolic network using Active Modules for Bipartite Networks (AMBIENT) to identify metabolic pathways showing coordinated transcriptional responses to the stress. AMBIENT revealed several key features of the metabolic response not identified by KEGG enrichment alone. Down regulated reactions were associated with the general reduction in cellular metabolism as a consequence of reduced growth rate. Up-regulated modules highlighted metabolic changes in nitrogen assimilation and scavenging, as well as reactions involved in hydrogen peroxide metabolism, carbon scavenging and energy generation. Conclusions: Application of an Active Modules algorithm to transcriptomic data identified key metabolic reactions and pathways altered in response to nitrogen stress, which are central to survival under nitrogen limiting environments.

Description: Background: Nitrogen is an essential element for bacterial growth and an important component of biological macromolecules. Consequently, responding to nitrogen limitation is critical for bacterial survival and involves the interplay of signalling pathways and transcriptional regulation of nitrogen assimilation and scavenging genes. In the soil dwelling saprophyte Mycobacterium smegmatis the OmpR-type response regulator GlnR is thought to mediate the transcriptomic response to nitrogen limitation. However, to date only ten genes have been shown to be in the GlnR regulon, a vastly reduced number compared to other organisms. Results: We investigated the role of GlnR in the nitrogen limitation response and determined the entire GlnR regulon, by combining expression profiling of M. smegmatis wild type and glnR deletion mutant, with GlnR-specific chromatin immunoprecipitation and high throughput sequencing. We identify 53 GlnR binding sites during nitrogen limitation that control the expression of over 100 genes, demonstrating that GlnR is the regulator controlling the assimilation and utilisation of nitrogen. We also determine a consensus GlnR binding motif and identify key residues within the motif that are required for specific GlnR binding. Conclusions: We have demonstrated that GlnR is the global nitrogen response regulator in M. smegmatis, directly regulating the expression of more than 100 genes. GlnR controls key nitrogen stress survival processes including primary nitrogen metabolism pathways, the ability to utilise nitrate and urea as alternative nitrogen sources, and the potential to use cellular components to provide a source of ammonium. These studies further our understanding of how mycobacteria survive nutrient limiting conditions.

Description: A new luminescence erosion meter has huge potential for inferring erosion rates on sub-millennial scales for both steady and transient states of erosion, which is not currently possible with any existing techniques capable of measuring erosion. This study applies new rock luminescence techniques to a well-constrained scenario provided by the Beinn Alligin rock avalanche, NW Scotland. Boulders in this deposit are lithologically consistent and have known cosmogenic nuclide ages and independently derived Holocene erosion rates. We find that luminescence-derived exposure ages for the Beinn Alligin rock avalanche were an order of magnitude younger than existing cosmogenic nuclide exposure ages, suggestive of high erosion rates (as supported by field evidence of quartz grain protrusions on the rock surfaces). Erosion rates determined by luminescence were consistent with independently derived rates measured from boulder edge roundness. Inversion modelling indicates a transient state of erosion reflecting the stochastic nature of erosional processes over the last ∼4.5 kyr in the wet, temperate climate of NW Scotland. Erosion was likely modulated by known fluctuations in moisture availability and to a lesser extent temperature, which controlled the extent of chemical weathering of these highly lithified rocks prior to erosion. The use of a multi-elevated temperature, post-infra-red, infra-red stimulated luminescence (MET-pIRIR) protocol (50, 150 and 225 ∘C) was advantageous as it identified samples with complexities that would not have been observed using only the standard infra-red stimulated luminescence (IRSL) signal measured at 50 ∘C, such as that introduced by within-sample variability (e.g. surficial coatings). This study demonstrates that the luminescence erosion meter can infer accurate erosion rates on sub-millennial scales and identify transient states of erosion (i.e. stochastic processes) in agreement with independently derived erosion rates for the same deposit.