Biochemical characterization of Serpula lacrymans iron-reductase enzymes in lignocellulose breakdown
Irnia Nurika, Daniel C Eastwood, Timothy DH Bugg, Guy C Barker
Putative iron-reductase (IR) genes from Serpula lacrymans with similarity to the conserved iron-binding domains of cellobiose dehydrogenase (CDH) enzymes have been identified. These genes were cloned and expressed to functionally characterize their activity and role in the decomposition of lignocellulose. Our results suggest that both IR enzymes mediate a non-enzymatic depolymerisation of lignocellulose and highlight the potential of chelator-mediated Fenton systems in the industrial pre-treatment of biomass.
NeuRiPP: Neural network identification of RiPP precursor peptides
Significant progress has been made in the past few years on the computational identification of biosynthetic gene clusters (BGCs) that encode ribosomally synthesized and post-translationally modified peptides (RiPPs). This is done by identifying both RiPP tailoring enzymes (RTEs) and RiPP precursor peptides (PPs). However, identification of PPs, particularly for novel RiPP classes remains challenging. To address this, machine learning has been used to accurately identify PP sequences. NeuRiPP was able to successfully identify PP sequences from novel RiPP classes that were recently characterized experimentally, highlighting its utility in complementing existing bioinformatics tools.
Electrical polarization enables integrative quality control during bacterial differentiation into spores
Teja Sirec, Jonatan M. Benarroch, Pauline Buffard, Jordi Garcia-Ojalvo, Munehiro Asally
Quality control of offspring is important for the survival of cells. However, the mechanisms by which quality of offspring cells may be checked while running genetic programs of cellular differentiation remain unclear. Here we investigated quality control during sporulating in Bacillus subtilis by combining single-cell time-lapse microscopy, molecular biology and mathematical modelling. Our results revealed that the quality control via premature germination is coupled with the electrical polarization of outer membranes of developing forespores.
Increasing sulphate levels show a differential impact on synthetic communities comprising different methanogens and a sulphate reducer
Jing Chen, Matthew J. Wade, Jan Dolfing, Orkun S. Soyer
Methane-producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulfate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulfate availability are not well understood. Here, we construct model synthetic communities using a sulfate reducer and two types of methanogens representing different methanogenesis routes. Our findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities.
Electrically induced bacterial membrane-potential dynamics correspond to cellular proliferation capacity
James P Stratford, Conor LA Edwards, Manjari J Ghanshyam, Dmitry Malyshev, Marco A Delise, Yoshikatsu Hayashi, and Munehiro Asally
Transmembrane voltage in bacteria plays a central role both in electrical signaling and cell proliferation. However, whether proliferation state influences the response to electrical signals was unknown. Combining fluorescence time-lapse microscopy with a bespoke device and mathematical modelling, we show that proliferative and inhibited cells respond in opposite directions to an identical electrical signal. The response differentiation can be seen within a minute after stimulation. Therefore, our findings offer a novel approach for rapid detection of proliferative bacteria at the single-cell level. PNAS. April 2019