Biology subjects

Wood, C. W.

Publications and source records attributed to Wood, C. W..

22 records · Page 2Linked to original sources

bioRxiv2020

De Novo Designed Peptide and Protein Hairpins that Self-assemble into Sheets and Nanoparticles.

The design and assembly of peptide based materials has advanced considerably, leading to a variety of fibrous, sheet and nanoparticle structures. A remaining challenge is to account for and control different possible supramolecular outcomes accessible to the same or similar peptide building blocks. Here we present a de novo peptide system that forms nanoparticles or sheets depending on the strategic placement of a disulfide pin between two elements of secondary structure that drive self-assembly. Specifically, we join homodimerizing and homotrimerizing de novo coiled-coil -helices with a flexible linker to generate a series of linear peptides. The helices are pinned back-to-back, constraining them as hairpins by a disulfide bond placed either proximal or distal to the linker. Computational modeling and advanced microscopy show that the proximally pinned hairpins self-assemble into nanoparticles, whereas the distally pinned constructs form sheets. These peptides can be made synthetically or recombinantly to allow both chemical modifications and the introduction of whole protein cargoes as required.

synthetic biology↗

bioRxiv2019

Common genetic variants shape broad patterns of within-population variation in gene expression.

Understanding the persistence of genetic variation within populations has long been a goal of evolutionary biology. One promising route towards achieving this goal is using population genetic approaches to describe how selection acts on the loci associated with trait variation. Gene expression provides a model trait for addressing the challenge of the maintenance of variation because it can be measured genome-wide without information about how gene expression affects traits. Previous work has shown that loci affecting the expression of nearby genes (local or cis-eQTLs) are under negative selection, but we lack a clear understanding of the selective forces acting on variants that affect the expression of genes in trans. Here, we identify loci that affect gene expression in trans using genomic and transcriptomic data from one population of the obligately outcrossing plant, Capsella grandiflora. The allele frequencies of trans-eQTLs are consistent with stronger negative selection acting on trans-eQTLs than cis-eQTLs, and even more strongly on trans-eQTLs associated with the expression of multiple genes. However, despite this general pattern, we still observe the presence of a trans-eQTL at intermediate frequency that affects the expression of a large number of genes in the same coexpression module. Overall, our work highlights the different selective pressures shaping variation in cis- and trans- gene regulation.

evolutionary biology↗

bioRxiv2018

Navigating the structural landscape of de novo α-helical bundles

The association of amphipathic helices in water leads to -helical-bundle protein structures. However, the driving force for this--the hydrophobic effect--is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle--the -helical coiled coils--relationships have been established that discriminate between all-parallel dimers, trimers and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less-well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high-resolution X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of -helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.

biochemistry↗

bioRxiv2017

Genetic conflict with a parasitic nematode disrupts the legume-rhizobia mutualism

Genetic variation for partner quality in mutualisms is an evolutionary paradox. One possible resolution to this puzzle is that there is a tradeoff between partner quality and other fitness-related traits. Here, we tested whether a susceptibility to parasitism is one such tradeoff in the mutualism between legumes and nitrogen-fixing bacteria (rhizobia). We performed two greenhouse experiments with the legume Medicago truncatula. In the first, we inoculated each plant with the rhizobia Ensifer meliloti and with one of 40 genotypes of the parasitic root-knot nematode Meloidogyne hapla. In the second experiment, we inoculated all plants with rhizobia and half of the plants with a genetically variable population of nematodes. Using the number of nematode galls as a proxy for infection severity, we found that plant genotypes differed in susceptibility to nematode infection, and nematode genotypes differed in infectivity. Second, we showed that there was a genetic correlation between the number of mutualistic structures formed by rhizobia (nodules) and the number of parasitic structures formed by nematodes (galls). Finally, we found that nematodes disrupt the rhizobia mutualism: nematode-infected plants formed fewer nodules and had less nodule biomass than uninfected plants. Our results demonstrate that there is genetic conflict between attracting rhizobia and repelling nematodes in Medicago. If genetic conflict with parasitism is a general feature of mutualism, it could account for the maintenance of genetic variation in partner quality and influence the evolutionary dynamics of positive species interactions.\n\nImpact summaryCooperative species interactions, known as mutualisms, are vital for organisms from plants to humans. For example, beneficial microbes in the human gut are a necessary component of digestive health. However, parasites often infect their hosts via mechanisms that are extraordinarily similar to those used by mutualists, which may create a tradeoff between attracting mutualists and resisting parasites. In this study, we investigated whether this tradeoff exists, and how parasites impact mutualism function in the barrelclover Medicago truncatula, a close relative of alfalfa. Legumes like Medicago depend on nitrogen provided by mutualistic bacteria (rhizobia) to grow, but they are also infected by parasitic worms called nematodes, which steal plant nutrients. Both microorganisms live in unique structures (nodules and galls) on plant roots. We showed that the benefits of mutualism and the costs of parasitism are predicted by the number of mutualistic structures (nodules) and the number of parasitic structures (galls), respectively. Second, we found that there is a genetic tradeoff between attracting mutualists and repelling parasites in Medicago truncatula: plant genotypes that formed more rhizobia nodules also formed more nematode galls. Finally, we found that nematodes disrupt the rhizobia mutualism. Nematode-infected plants formed fewer rhizobia nodules and less total nodule biomass than uninfected plants. Our research addresses an enduring evolutionary puzzle: why is there so much variation in the benefits provided by mutualists when natural selection should weed out low-quality partners? Tradeoffs between benefits provided by mutualists and their susceptibility to parasites could resolve this paradox.

evolutionary biology↗