Pattern Engineering of Living Bacterial Colonies Using Meniscus Driven Fluidic Channels
Vasily Kantsler, Elena Ontañón-McDonald, Cansu Kuey, Manjari J. Ghanshyam, Maria Chiara Roffin, and Munehiro Asally
Transcription factors control gene expression in all life. This raises the question of what is the smallest protein that can support such activity. In nature, Cro from bacteriophage l is one of the smallest known repressors (66 amino acids), and activators are typically much larger (e.g., l cI, 237 amino acids). In this study, we show that directed evolution results in a new Cro activator-repressor that functions as efficiently as l cI in vivo. This is the smallest protein activator that enables polymerase recruitment, highlighting the capacity of transcription factors to evolve from very short peptide sequences.
Bioelectrical understanding and engineering of cell biology
The last five decades of molecular and systems biology research have provided unprecedented insights into the molecular and genetic basis of many cellular processes. Despite these insights, however, it is arguable that there is still only limited predictive understanding of cell behaviours. In particular, the basis of heterogeneity in single-cell behaviour and the initiation of many different metabolic, transcriptional or mechanical responses to environmental stimuli remain largely unexplained. To go beyond the status quo, the understanding of cell behaviours emerging from molecular genetics must be complemented with physical and physiological ones, focusing on the intracellular and extracellular conditions within and around cells. Here, we argue that such a combination of genetics, physics and physiology can be grounded on a bioelectrical conceptualization of cells.
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.