Biology subjects

Girguis, P. R.

Publications and source records attributed to Girguis, P. R..

6 recordsLinked to original sources

bioRxiv2026

Ether linkages in phospholipids provide modular control of membrane mechanics

The structures of phospholipid headgroups and chains are well-established determinants of membrane elastic properties, but functions for different chemistries that join these moieties together are poorly understood. While common phospholipids feature ester linkages, alkyl ether- and plasmenyl-linked species emerged in prokaryotes, are highly abundant in metazoans, and have been implicated in neurodegeneration and aging. Multiple pathways for ether lipid synthesis evolved convergently, suggesting conserved functions for ether linkage chemistry in the structure of cell membranes. Here we combine experiments and molecular simulations to show that backbone linkage chemistry provides modular control of membrane mechanics and topology through a set of discrete drivers. Alkyl linkages provide the first of these by additively promoting negative intrinsic curvature, which destabilizes bilayers. Ethers also decouple membrane stiffness from viscosity, softening membranes while maintaining packing in the hydrophobic core. The plasmenyl C=C bond represents a second, distinct driver that stabilizes the inverted hexagonal phase by relieving interstitial packing frustration. These results explain the fusogenicity of ether lipids, show how they regulate membrane topology through multiple physical mechanisms, and provide a rationale for convergent evolution of the complex plasmenyl linkage moiety.

biophysics↗

bioRxiv2025

Homeostatic regulation of intrinsic lipid curvature in eukaryotic cells

Cell membranes are composed of both bilayer-supporting and non-bilayer phospholipids, with the latters negative intrinsic curvature aiding in membrane trafficking and the dynamics of membrane proteins. Phospholipid metabolism has long been recognized to maintain membrane fluidity, but whether it also acts to maintain the function of high-curvature lipids is not resolved. Here, we find that cells grown under hydrostatic pressure - used to artificially reduce lipid curvature - maintain lipidome curvature through metabolic acclimation. We first observed that manipulation of the lipidome curvature via the phosphatidylethanolamine (PE) to phosphatidylcholine (PC) ratio affects high-pressure growth and viability of yeast independently of membrane fluidity. In wild-type cells, X-ray scattering measurements revealed an increased propensity for lipid extracts to form non-lamellar phases after extended pressure incubations. Unexpectedly, this change in phase behavior was not due to increased levels of PE, but of phosphatidylinositol (PI), the only major phospholipid class whose curvature had not been previously characterized. We found that PI is a non-bilayer lipid, with a negative curvature intermediate to that of PE and PC. Accounting for PI, mean lipidome curvature was defended in response to pressure by two distantly related yeasts. Lipidome curvature also responded to pressure in a human cancer cell line through ether phospholipid metabolism and chain remodeling, but not in bacterial cells. These findings indicate that eukaryotic phospholipid metabolism uses diverse mechanisms to maintain curvature frustration in cell membranes.

biophysics↗

bioRxiv2025

Contrasting genomic responses of hydrothermal vent animals and their symbionts to population decline after the Hunga volcanic eruption

Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a populations ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusk-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, symbiont populations exhibited a notable decrease in genomic variation, including loss of certain habitat-specific strains. However, detection of environmental symbiont sequences suggests that lost strain diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and levels of gene flow, although the full extent of population bottlenecks in the host animals might only be recognizable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to potential future anthropogenic impacts.

evolutionary biology↗

bioRxiv2022

Ancient electrogenic survival metabolism of β-proteobacterial ammonia oxidizers for oxygen deficiency

Oxygen availability is critical for microbes as some are obligatorily dependent on oxygen for energy conservation. However, aerobic microbes that live in environments with varying oxygen concentrations experience pressures over evolutionary time, selecting alternative energy metabolisms that relax the dependence on oxygen. One such capacity is extracellular electron transfer (or EET), which is the ability to transfer electrons from central metabolism to extracellular oxidants such as iron and manganese oxides. We posit that the {beta}-proteobacterial ammonia-oxidizing bacteria, highly specialized lineages heretofore recognized as strict aerobes, can be capable of EET as they have been constantly observed in oxygen-limiting and depleted environments. Here, we show that a strictly aerobic ammonia-oxidizer, Nitrosomonas communis, utilized a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multi-heme cytochromes suggested that direct electron transfer is the mechanism underlying EET. Molecular clock models suggest that the ancestors of {beta}-proteobacterial ammonia oxidizers appeared after the oxygenation of Earth when the oxygen levels were >10-4 pO2 (PAL), suggesting their aerobic origins. Phylogenetic reconciliations of gene and species trees show that the multi-heme c-type EET proteins in Nitrosomonas and Nitrosospira were acquired by gene transfer from {beta}-proteobacteria during oxygen scarcity. The preservation of EET metabolism over billions of years under fluctuating oxygen levels and aspects of EET physiology in {beta}-proteobacterial ammonia oxidizers might explain how they have been coped with oxygen stress and survived under oxygen deprivation. SIGNIFICANCEMetabolic versatility can permit typically aerobic microbes to survive in anaerobic conditions when oxygen is deficient as a terminal electron acceptor. This article demonstrates a previously unidentified anaerobic extracellular electron transfer metabolism that operates in aerobic {beta}-proteobacterial ammonia oxidizers and reconstructs the evolutionary history of this metabolism, linking it to the early history of Earths oxygenation. Our approach contributes to the understanding of metabolisms in the N-cycle and their evolution on Earth, as well as how aerobic microbes manage to retain energy generation under oxygen-limiting or depleted conditions. AUTHOR CONTRIBUTIONSAG designed the physiological research with PRG and the phylogenetic research with GF; AG performed the research, AG analyzed the data with PRG and GF. AG wrote the paper, and all authors edited and approved the manuscript.

evolutionary biology↗

bioRxiv2020

Mud, microbes, and macrofauna: seasonal dynamics of the iron biogeochemical cycle in an intertidal mudflat

Microorganisms and burrowing animals exert a pronounced impact on the cycling of redox sensitive metals in coastal sediments. Sedimentary metal cycling is likely controlled by seasonal processes including changes in temperature, animal feeding behavior due to food availability, and availability of organic matter in sediments. We hypothesized that the iron biogeochemical cycle and associated sedimentary microbial community will respond to seasonal changes in a bioturbated intertidal mudflat. In this study, we monitored the spatiotemporal dynamics of porewater and highly reactive solid phase iron with the corresponding prokaryotic and eukaryotic sedimentary microbial communities over one annual cycle from November 2015 to November 2016. Continuous and seasonally variable pools of both porewater Fe(II) and highly reactive iron (FeHR) were observed throughout the season with significant increases of Fe(II) and FeHR in response to increased sediment temperature in summer months. Maximum concentrations of Fe(II) and FeHR were predominantly confined to the upper 5 cm of sediment throughout the season. Iron-oxidizing and -reducing microorganisms were present and stable throughout the season, and exhibited strong depth-dependent stratification likely due to availability of Fe(II) and FeHR pools, respectively. Otherwise, the community was dominated by Deltaproteobacteria, which are involved in sulfur and potentially iron cycling, as well as Gammaproteobacteria and Bacteroidetes. The microbial community was relatively stable throughout the seasonal cycle, but showed strong separation with depth, probably driven by changes in oxygen availability and organic matter. The relative abundance of diatoms revealed a noticeable seasonal signature, which we attribute to spring and fall blooms recorded in the sediments. Macro-, meio, and microfauna were detected throughout the season with some seasonal variations that may influence sedimentary iron transformations by active microbial grazing. The seasonal dynamics of the sedimentary iron cycle are controlled by numerous, interdependent processes, with macrobiota-microbiota relationships and depth stratification comprising primary components. Deciphering these processes in natural ecosystems is essential to understand how they might respond to future environmental perturbations, such as anthropogenic nutrient release to coastal systems.

microbiology↗

bioRxiv2019

Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens

DNA from formalin-preserved tissue could unlock a vast repository of genetic information stored in museums worldwide. However, formaldehyde crosslinks proteins and DNA, and prevents ready amplification and DNA sequencing. Formaldehyde acylation also fragments the DNA. Treatment with proteinase K proteolyzes crosslinked proteins to rescue the DNA, though the process is quite slow. To reduce processing time and improve rescue efficiency, we applied the mechanical energy of a vortex fluidic device (VFD) to drive the catalytic activity of proteinase K and recover DNA from American lobster tissue (Homarus americanus) fixed in 3.7% formalin for >1-year. A scan of VFD rotational speeds identified the optimal rotational speed for recovery of PCR-amplifiable DNA and while 500+ base pairs were sequenced, shorter read lengths were more consistently obtained. This VFD-based method also effectively recovered DNA from formalin-preserved samples. The results provide a roadmap for exploring DNA from millions of historical and even extinct species.

biochemistry↗