Biology subjects

Carlson, A.

Publications and source records attributed to Carlson, A..

3 recordsLinked to original sources

bioRxiv2018

A nanotube-mediated path to protocell formation

Cellular compartments are membrane-enclosed, spatially distinct microenvironments which confine and protect biochemical reactions in the biological cell. On the early Earth, the autonomous formation of compartments is thought to have led to the encapsulation of nucleotides, thereby satisfying a starting condition for the emergence of life. Recently, surfaces have come into focus as potential platforms for the self-assembly of prebiotic compartments, as significantly enhanced vesicle formation was reported in the presence of solid interfaces. The detailed mechanism of such formation at the mesoscale is still under discussion. We report here on the spontaneous transformation of solid surface-adhered lipid deposits to unilamellar membrane compartments through a straightforward sequence of topological changes, proceeding via a network of interconnected lipid nanotubes. We show that this transformation is entirely driven by surface-free energy minimization and does not require hydrolysis of organic molecules, or external stimuli such as electrical currents or mechanical agitation. The vesicular structures take up and encapsulate their external environment during formation, and can subsequently separate and migrate upon exposure to hydrodynamic flow. This may link, for the first time, the self-directed transition from weakly organized bioamphiphile assemblies on solid surfaces to protocells with secluded internal contents.\n\nSignificanceThe nature of the physical and chemical mechanisms behind the formation, growth and division of the earliest protocells is among the key questions concerning the origin of life. Establishing a simple pathway for the assembly of protocell structures from the primordial soup is a particular challenge. Emerging evidence supporting the assumption that solid surfaces have a governing role in protocell formation has recently expanded the scope, and created new inspiration for investigation. By presenting a physical path from self-assembled amphiphile-based membranes on solid surfaces to spherical single-membrane compartments via a consistent sequence of transformations, solely driven by the materials properties of the interfaces, a direct link between the presence of functional biomolecules and the development of protocells can be established.

biophysics↗

bioRxiv2018

Kluyveromyces marxianus as a robust synthetic biology platform host

Throughout history, the yeast Saccharomyces cerevisiae has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However S. cerevisiae has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineer the thermotolerant yeast Kluyveromyces marxianus to create a new synthetic biology platform. Using CRISPR-Cas9 mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits- thermotolerance, lipid production, and facile transformation with exogenous DNA-into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals.

synthetic biology↗

bioRxiv2016

Artificial Microbiome-Selection to Engineer Microbiomes That Confer Salt-Tolerance to Plants

We develop a method to artificially select for rhizosphere microbiomes that confer salt-tolerance to the model grass Brachypodium distachyon. We differentially propagate microbiomes within the background of a non-evolving, highly-inbred plant population, and therefore only microbiomes evolve in our experiment, but not the plants. To optimize methods, we conceptualize artificial microbiome-selection as a special case of indirect selection: We do not measure microbiome properties directly, but we use host performance (e.g., biomass; seed set) as an indicator to infer association with rhizosphere microbiomes that confer salt-tolerance to a plant. We previously called this indirect-selection scheme host-mediated indirect selection on microbiomes (Mueller & Sachs 2015). Our methods aim to maximize evolutionary changes due to differential microbiome-propagation, while minimizing some (but not all) ecological processes affecting microbiome composition. Specifically, our methods aim to maximize microbiome perpetuation between selection-cycles and maximize response to artificial microbiome-selection by (a) controlling microbiome assembly when inoculating seeds at the beginning of each selection cycle; (b) using low-carbon soil to enhance host-control mediated by carbon secretions of plants during initial microbiome assembly and subsequent microbiome persistence; (c) fractionating microbiomes before transfer between plants to perpetuate and select only on bacterial and viral (but not fungal) microbiome components; and (d) ramping of salt-stress between selection-cycles to minimize the chance of over-stressing plants. Our selection protocol generates microbiomes that enhance plant fitness after only 1-3 rounds of artificial selection on rhizosphere microbiomes. Relative to fallow-soil control treatments, artificially-selected microbiomes increase plant fitness by 75% under sodium-sulfate stress, and by 38% under aluminum-sulfate stress. Relative to null control treatments, artificially-selected microbiomes increase plant fitness by 13% under sodium-sulfate stress, and by 12% under aluminum-sulfate stress. When testing microbiomes after nine rounds of differential microbiome propagation, the effect of bacterial microbiomes selected to confer tolerance to sodium-sulfate stress appears specific (these microbiomes do not confer tolerance to aluminum-sulfate stress), but the effect of microbiomes selected to confer tolerance to aluminum-sulfate stress appears non-specific (selected microbiomes ameliorate both sodium- and aluminum-sulfate stresses). Complementary metagenomic analyses of the artificially selected microbiomes will help elucidate metabolic properties of microbiomes that confer specific versus non-specific salt-tolerance to plants.

plant biology↗