Biology subjects

Trudeau, A.

Publications and source records attributed to Trudeau, A..

4 recordsLinked to original sources

bioRxiv2025

What determines trophic niche breadth? A global analysis of freshwater fishes using isospaces

Trophic niche is one of the most tractable dimensions of a species niche. Several hypotheses have been proposed to explain global variation in species trophic niches, but empirical tests are limited. Stable isotope analysis (SIA) of {delta}{superscript 1}3C (a proxy for basal sources) and {delta}{superscript 1} N (a proxy for vertical trophic position) has increasingly been used to estimate trophic niche variation. We performed SIA on a dataset of over 33,000 stable isotope samples from freshwater fishes across six ecoregions. For 541 populations (358 species), we estimated the size of {delta}{superscript 1}3C x {delta}{superscript 1} N isospace--a bivariate representation of trophic niche breadth. We evaluated isospace variation in relation to environmental factors, species traits, and sampling scale, testing both novel and long-standing hypotheses about the drivers of trophic niche variation. A Boosted Regression Tree Model best predicted isospace, with environmental and trait-based variables among the strongest predictors. Fish isospaces were broader in regions with warmer temperatures, higher humidity, and precipitation variability, suggesting that more productive, diverse, and seasonal ecosystems are associated with broader trophic niches. Conversely, isospace size declined with increasing basin fish richness, which may reflect heightened interspecific competition or historical competitive exclusion. Isospace size was slightly smaller in large lakes compared to rivers, streams, and small lakes. Within-population variation in body size was strongly and positively associated with isospace size, highlighting the role of ontogenetic dietary shifts. Fish with truncate-rounded fins had broader isospaces than those with forked-lunate fins, likely due to the former having more limited movement and greater spatial isolation that resulted in greater between-individual niche variation. Primary consumers had larger isospaces than intermediate and top consumers. Predators showed relationships consistent those observed from analysis encompassing all trophic guilds, but non-predators deviated with regards to four variables--solar radiation, basin richness, average body size, and caudal fin aspect ratio. Isospace size increased with the number of sampled individuals, habitats and years surveyed. Although isospace patterns have well-documented limitations as trophic ecology metrics, our findings nonetheless conform with several longstanding hypotheses for trophic niche variation and stimulate new ideas about environmental and biological drivers of niche breadth.

ecology↗

bioRxiv2022

Reduction of a heme cofactor initiates N-nitroglycine degradation by NnlA

The NnlA enzyme from Variovorax sp. strain JS1663 degrades the linear nitramine N-nitroglycine (NNG)--a natural product produced by some bacteria--to glyoxylate and nitrite (NO2-). Ammonium (NH4+) was predicted as the third product of this reaction. A source of non-heme FeII was shown to be required for initiation of NnlA activity. However, it was unclear if this FeII was being used as a metallocofactor or a reductant. This study reveals that NnlA contains a b-type heme cofactor. Reduction of this heme is required to initiate NnlA activity. Reduction can occur either by addition of a non-heme FeII source or by reduction with dithionite. Therefore, FeII is not an essential substrate for holoenzyme activity. Data are presented showing that reduced NnlA (FeII-NnlA) can catalyze at least 100 turnovers. In addition, this catalysis occurred in the absence of O2. Finally, NH4+ was verified as the third product, accounting for the complete nitrogen mass balance. Size exclusion chromatography showed that NnlA is a dimer in solution. Additionally, FeII-NnlA is oxidized by O2 and NO2- and binds carbon monoxide (CO) and nitric oxide (NO). These are characteristics shared with PAS domains; NnlA was previously shown to exhibit homology with such domains. Providing further evidence, a structural homology model of NnlA was generated based on the structure of the PAS domain from Pseudomonas aeruginosa Aer2. The structural homology model suggested His73 is the axial ligand of the NnlA heme. Site-directed mutagenesis of His73 to alanine decreased the heme occupancy of NnlA and eliminated NNG activity, providing evidence that the homology model is valid. We conclude that NnlA forms a homodimeric heme-binding PAS domain protein that requires reduction for initiation of the activity. ImportanceLinear nitramines are potential carcinogens. These compounds result from environmental degradation of high-energy cyclic nitramines and as by-products of carbon capture technologies. Mechanistic understanding of the biodegradation of linear nitramines is critical to inform approaches for their remediation. The best understood biodegradation of a linear nitramine is NNG degradation by NnlA from Variovorax sp. strain JS 1663; however, it is unclear why non-heme iron was required to initiate enzymatic turnover. This study shows that non-heme iron is unnecessary. Instead, our study reveals that NnlA contains a heme cofactor, the reduction of which is critical for activating NNG degradation activity. These studies constrain the proposals for NnlA reaction mechanisms, thereby informing mechanistic studies of degradation of anthropogenic nitramine contaminants. In addition, these results will future work to design biocatalysts to degrade these nitramine contaminants.

biochemistry↗

bioRxiv2021

Spatial structure affects evolutionary dynamics and drives genomic diversity in experimental populations of Pseudomonas fluorescens

Most populations live in spatially structured environments and that structure has the potential to impact the evolutionary dynamics in a number of important ways. Theoretical models tracking evolution in structured environments using a range of different approaches, suggest that local interactions and spatial heterogeneity can increase the adaptive benefits of motility, impact both the rate and extent of adaptation, and increase the probability of parallel evolution. We test these general predictions in a microbial evolution experiment tracking phenotypic and genomic changes in replicate populations of Pseudomonas fluorescens evolved in both well-mixed and spatially-structured environments, where spatial structure was generated through the addition of semi-solid agar. In contrast to the well-mixed environment, populations evolved in the spatially-structured environment adapted more slowly, retained the ability to disperse more rapidly, and had a greater putatively neutral population genomic diversity. The degree of parallel evolution measured at the gene-level, did not differ across these two types of experimental environments, perhaps because the populations had not evolved for long enough to near their fitness optima. These results confirm important general impacts of spatial structure on evolutionary dynamics at both the phenotypic and genomic level.

evolutionary biology↗

bioRxiv2020

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic

Three-dimensional structures of SARS-CoV-2 and other coronaviral proteins archived in the Protein Data Bank were used to analyze viral proteome evolution during the first six months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48,000 viral proteome sequences showed how each one of the 29 viral study proteins have undergone amino acid changes. Structural models computed for every unique sequence variant revealed that most substitutions map to protein surfaces and boundary layers with a minority affecting hydrophobic cores. Conservative changes were observed more frequently in cores versus boundary layers/surfaces. Active sites and protein-protein interfaces showed modest numbers of substitutions. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for six drug discovery targets and four structural proteins comprising the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and functional interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.

molecular biology↗