Biology subjects

Williams, T. A.

Publications and source records attributed to Williams, T. A..

4 recordsLinked to original sources

bioRxiv2018

Extensive transfer of membrane lipid biosynthetic genes between Archaea and Bacteria

One of the key differences between Bacteria and Archaea are their canonical membrane phospholipids, which are synthesized by distinct biosynthetic pathways with non-homologous enzymes. This \"lipid divide\" has important implications for the early evolution of cells and the type of membrane phospholipids present in the last universal common ancestor (LUCA). One of the main challenges in studies of membrane evolution is that the key biosynthetic genes are ancient and their evolutionary histories are poorly resolved. This poses major challenges for traditional rooting methods because the only available outgroups are distantly related. Here, we address this issue by using the best available substitution models for single gene trees, by expanding our analyses to the diversity of uncultivated prokaryotes recently revealed by environmental genomics, and by using two complementary approaches to rooting that do not depend on outgroups. Consistent with some previous analyses, our rooted gene trees support extensive inter-domain horizontal transfer of membrane phospholipid biosynthetic genes, primarily from Archaea to Bacteria. They also suggest that the capacity to make archaeal-type membrane phospholipids was already present in LUCA.

evolutionary biology↗

bioRxiv2018

Elongation during segmentation shows axial variability, low mitotic rates, and synchronized cell cycle domains in the crustacean, Thamnocephalus platyurus

Segmentation in arthropods typically occurs by sequential addition of segments from a posterior growth zone, but cell behaviors producing posterior elongation are not well known. Using precisely staged larvae of the crustacean, Thamnocephalus platyurus, we systematically examined cell division patterns and morphometric changes associated with posterior elongation during segmentation. We show that cell division is required for normal elongation but that cells in the growth zone need only divide ~1.5 times to meet that requirement; correspondingly, direct measures of cell division in the growth zone are low. Morphometric measurements of the growth zone and of newly formed segments suggest tagma-specific features of segment generation. Using methods for detecting two different phases in the cell cycle, we show distinct domains of synchronized cells in the posterior. Borders of cell cycle domains correlate with domains of segmental gene expression, suggesting an intimate link between segment generation and cell cycle regulation.\n\nSummary StatementPosterior growth zone has synchronized cell cycle domains but shows little cell division during segment addition in a crustacean. Dimensions of the shrinking posterior growth zone change at tagma boundaries.

developmental biology↗

bioRxiv2018

Mitochondrial targeting of glycolysis in a major lineage of eukaryotes

Glycolysis is a major cytosolic catabolic pathway that provides ATP for many organisms1. Mitochondria play an even more important role in the provision of additional cellular ATP for eukaryotes2. Here, we show that in many stramenopiles, the C3 part of glycolysis is localised in mitochondria. We discovered genuine mitochondrial targeting signals on the six last enzymes of glycolysis. These targeting signals are recognised and sufficient to import GFP into mitochondria of a heterologous host. Analysis of eukaryotic genomes identified these targeting signals on many glycolytic C3 enzymes in a large group of eukaryotes found in the SAR supergroup3, in particular the stramenopiles. Stramenopiles, or heterokonts, are a large group of ecologically important eukaryotes that includes multi- and unicellular algae such as kelp and diatoms, but also economically important oomycete pathogens such as Phytophthora infestans. Confocal immunomicroscopy confirmed the mitochondrial location of glycolytic enzymes for the human parasite Blastocystis. Enzyme assays on cellular fractions confirmed the presence of the C3 part of glycolysis in Blastocystis mitochondria. These activities are sensitive to treatment with proteases and Triton X-100 but not proteases alone. Our work clearly shows that core cellular metabolism is more plastic than previously imagined and suggests new strategies to combat stramenopile pathogens such as the causative agent of late potato blight, P. infestans.

evolutionary biology↗

bioRxiv2017

Gene transfers, like fossils, can date the Tree of Life

Biodiversity has always been predominantly microbial and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here we show that patterns of lateral gene transfer deduced from the analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use new phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukaryotes. An inspection of discrepancies between transfers and clocks and a comparison with mammal fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.

evolutionary biology↗