Biology subjects

Howland, K.

Publications and source records attributed to Howland, K..

4 recordsLinked to original sources

bioRxiv2022

Autophagy receptor NDP52 alters DNA conformation to modulate RNA Polymerase II transcription

NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear function for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We found that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene-expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover novel nuclear roles for NDP52 in gene expression and DNA structure regulation.

biophysics↗

bioRxiv2019

Trophic variation within a piscivorous lake trout morph from Great Bear Lake, Canada: The initial step toward ecological specialization?

In a polymorphic species, stable differences in resource use are expected among ecotypes, and homogeneity in resource use is predicted within an ecotype. Yet, using a broad resource spectrum has been identified as a strategy for fishes living in unproductive northern environments, where food is patchily distributed and ephemeral. We investigated whether individual specialization of trophic resources occurred within the generalist piscivore ecotype of lake trout from Great Bear Lake, Canada, reflective of a form of diversity. Four distinct dietary patterns of resource use within the lake trout ecotype were detected from fatty acid composition, with some variation linked to spatial patterns within Great Bear Lake. Feeding habits of different groups within the ecotype were not associated with detectable morphological or genetic differentiation, suggesting that behavioral plasticity caused the trophic differences. A low level of genetic differentiation was detected between exceptionally large-sized individuals and other individuals. Investigating a geologically young system that displays high levels of intraspecific diversity and focusing on individual variation in diet suggested that individual trophic specialization can occur within an ecotype. The characterization of niche use among individuals, as done in this study, is necessary to understand the role that individual variation can play at the beginning of differentiation processes.

ecology↗

bioRxiv2019

Dietary vs non-dietary fatty acid profiles of lake trout morphs from Lake Superior and Great Bear Lake: Are fish really what they eat?

Fatty acids are well-established biomarkers used to characterize trophic ecology, food-web linkages, and the ecological niche of many different taxa. Most often, fatty acids that are examined include only those previously identified as "dietary" or "extended dietary" biomarkers. Fatty acids considered as non-dietary biomarkers, however, represent numerous fatty acids that can be extracted. Some studies may include non-dietary fatty acids (i.e., combined with dietary fatty acids), but do not specifically assess them, whereas in other studies, these data are discarded. In this study, we explored whether non-dietary biomarkers fatty acids can provide worthwhile information by assessing their ability to discriminate intraspecific diversity within and between lakes. Non-dietary fatty acids used as biomarkers delineated variation among regions, among locations within a lake, and among ecotypes within a species. Physiological differences that arise from differences in energy processing can be adaptive and linked to habitat use by a species ecotypes, and likely explains why non-dietary fatty acids biomarkers can be a relevant tool to delineate intraspecific diversity. Little is known about the non-dietary-mediated differences in fatty acid composition, but our results showed that non-dietary fatty acids biomarkers can be useful tool in identifying variation.

ecology↗

bioRxiv2017

Codon-Dependent Translational Accuracy Controls Protein Quality in Escherichia coli but not in Saccharomyces cerevisiae

In order to generate a functional proteome, gene expression pathways must assemble proteins accurately according to the rules of the genetic code. General gene expression accuracy is known to be high, but errors nevertheless occur with measurable frequencies. Here we develop a mass-spectrometry (MS) based assay for the detection of a particular type of gene expression error, amino acid misincorporation. This assay allows assessing a much broader range of misincorporation events compared to current, very sensitive but also very specific enzyme reporter assays. Our assay uncovers a remarkably rich pool of error products for a model protein expressed in E. coli, which depend quantitatively on codon usage in the expression construct. This codon usage dependence can be explained in part as a function of the composition of the tRNA pool in this organism. We further show that codon-dependent differences in error levels correlate with measurable changes in specific protein activity. In contrast to E. coli, error levels are lower, and appear not to be codon usage dependent, when the same model protein is expressed in S. cerevisiae.

molecular biology↗