Biology subjects

Luque, A.

Publications and source records attributed to Luque, A..

15 recordsLinked to original sources

bioRxiv2026

Computational Rational Design of Larger AAV Icosahedral Capsids

Adeno-associated virus (AAV) is the preferred viral vector platform in gene therapy. Yet its packaging capacity, about 4.7 kb (kilobases), limits its therapeutic potential and represents a major bottleneck in the field. The packaging capacity of AAV is constrained by its small capsid, which forms a 26-nm-diameter shell assembled from 60 capsid proteins in a T=1 icosahedral architecture. Here, we propose increasing the cargo capacity of AAV vectors by engineering the next possible icosahedral architecture, T=3 (180 capsid proteins), which is predicted to provide a fivefold increase in volume capacity. Oligomers of VP3, the main capsid protein of AAV, were folded using AI-based methods. This identified triangular trimers as the optimal multimer compatible with the tiles of icosahedral lattices in the geometrical theory of capsids. The VP3 trimers were assembled into a T=3 architecture and coarse-grained at 5[A] resolution. It was necessary to introduce 15 deletions (VP3{Delta}15) to accommodate the T=3 curvature. Molecular simulations under physiological conditions demonstrated the stability of the 45 nm-diameter T=3 capsid. Structural analysis measured a five- to sixfold increase in internal volume and estimated a potential upper cargo limit of 35 kb. The engineered VP3{Delta}15 could enable delivery of multicistronic constructs, larger regulatory elements, and CRISPR systems beyond the reach of current AAV vectors. Additionally, the introduced generalized protein design framework could be used to engineer capsids with larger T-numbers and to modify the capacity of other icosahedral delivery systems.

biophysics↗

bioRxiv2026

Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes

Meromictic lakes serve as analogs for redox-stratified ancient oceans with well-mixed surface waters and anoxic bottoms. Purple and green sulfur bacteria (PSB, GSB) dominate the anoxic zones where light penetrates, and their biosignatures can be used to guide interpretations of geologic records. However, PSB and GSB biosignatures do not directly reflect the microbial community composition of modern lakes, posing a challenge for their interpretation. Here, we investigate this decoupling by integrating metagenomics, metatranscriptomics, and metaHi-C virus-host linkages with the geochemical profiles of three meromictic lakes. In the phototrophic microbial plates, PSBs transcriptional activity far exceeded their abundance (73% of the total microbial community activity versus 30% of the abundance), while GSBs displayed the opposite pattern. Concurrently, PSBs were exclusively associated with temperate viruses, while GSBs were targeted by lytic infections. Sulfate-reducing bacteria (SRB) and viruses encoding genes for sulfate reduction were most active where sulfide concentration was lowest. These results reveal that viral replication strategies are associated with the decoupling between abundance and activity in anoxygenic phototrophs and sulfate reducers. These relationships could accelerate sulfur regeneration, contribute to sustaining phototrophy, and ultimately reflect in the lakes bulk biosignatures.

microbiology↗

bioRxiv2025

A novel mobile genetic element with virus-like characteristics is widespread in the world's oceans

While the majority of viruses falls within a handful of well-defined realms, many novel viruses and virus-like genetic elements remain to be discovered. Given the abundance and diversity of small, circular DNA genomes in animal gut viromes, we hypothesized that viruses of similar size might have been overlooked in other environments. Re-analyzing existing ocean virome datasets for small viruses, we discover a novel group of circular mobile genetic elements of [~]4.6kb in size, likely with double-stranded DNA, which we term Charybdis elements. Charybdis elements form a singular group based on cohesive gene content, encode around 10 hypothetical genes but apparently contain no virus, transposon or plasmid associated hallmark proteins. They are detected exclusively in marine datasets ranging from surface water to hydrothermal vents and sediments, from the Arctic to the Antarctic. Virome datasets separating virus-like particles by density gradients show that Charybdis elements accumulate in the fraction representing extracellular vesicles and small, tail-less viruses that are often associated with lipid membranes. One specific clade of Charybdis elements is shown to integrate into the genomes of the common marine group II archaeon candidate order Poseidoniales, the putative host of these elements. Analysis of thousands genomes shows a common genome architecture consisting of two modules: An accessory module containing a diverse range methyltransferases and other genes likely involved in host interactions, and a more conserved (putative) structural module. The structural module encodes proteins that are confidently predicted to form striking tri- or pentameric structures. These structures show stark resemblance and in some cases homology to protrusion or tail-elements on the capsids of viruses from the realms Varidnaviria and Duplodnaviria. Given these traits, Charybdis elements likely represent a hitherto undiscovered group of virus or virus-satellites, with at least one protein of a novel double-Greek-key fold serving as a potential capsid element. However, since their hosts remain unculturable, the true nature of these ubiquitous marine elements remains as of yet unresolvable.

genomics↗

bioRxiv2025

Small uncultured viral-like entities redraw the origin of viruses and cellular compartments

The HK97-fold is an ancient, conserved protein structure that forms protein shells. It is the building block of capsids that protect the genome of viruses in the Duplodnaviria realm, infecting organisms across all domains of life. It is also the building block of encapsulins, compartments that confine biochemical reactions in prokaryotes. Recent genomic studies have hypothesized that encapsulins evolved from HK97-fold viruses. However, this evolutionary pathway is challenging to justify biophysically because HK97-fold viruses form larger and more complex protein shells than encapsulins. We addressed this paradox by searching for smaller and simpler HK97-fold viral capsids across ecosystems. The investigation yielded a well-defined group of viral entities, which encode HK97-fold proteins displaying molecular similarities with encapsulins and lacking portal and tail genes. The structural phylogenetic analysis of HK97-fold entities revealed bidirectional evolutionary transitions between encapsulins and HK97-fold viruses. An evolutionary mechanism responsible for such transitions was proposed based on the presence of lysogeny-associated genes in the viral entities and the structural and molecular parallels between encapsulins and procapsids, the immature state of viral capsids before genome packaging. We concluded that procapsids are akin to the common HK97-fold protein shell ancestor and might still facilitate transitions between modern viruses and encapsulins. The potential genomic and biochemical functions of HK97-fold procapsids make them an ideal candidate model for the early evolution of life and might require a revision of the role of viral capsids in the biosphere.

bioinformatics↗

bioRxiv2023

Emerging dynamic regimes and tipping points from finite empirical principles

The dynamics of biogeochemical, ecological, and astronomical systems are transient. Yet, predicting the occurrence of dynamical shifts remains a challenge due to inferential uncertainties from datasets and the limitations of asymptotic-dependent theories. To address this problem, we developed a theoretical framework that builds on the finite nature of observations. This framework assesses the relative importance of processes, defined as the mechanisms that contribute to the rate of change of the systems dynamic variables, and it predicts the critical values that would trigger a shift into a new regime. The number of observable dynamic regimes within the framework increases exponentially with the number of processes. Observers, however, only experience dynamic regimes associated with relevant processes-- those exceeding a tipping point--within their reference framework. A case study of the framework was tested for a classic predator-prey system with four processes parameterized for bacteria (prey) and lytic bacteriophages (predator). The analysis recovered the sixteen dynamic regimes predicted by the framework, including two non-trivial quasi-equilibrium dynamics. An adaptive Boolean model, which used only relevant observable processes, validated the accuracy of the framework, recovering the dynamics of the full model. The observational framework introduced here provides a strategy for identifying the processes and conditions that lead to tipping points, representing a conceptual paradigm shift in transient dynamics, placing the focus on the specific, finite context of the observer, rather than the intrinsic, asymptotic states of the system. SIGNIFICANCESudden shifts in ecological, climate, and biological systems--so-called tipping points or critical transitions--are notoriously difficult to predict. This study introduces a mathematical framework that redefines these transitions as outcomes shaped by the observers empirical limits. By accounting for finite observation time and resolution, the framework uncovers a rich spectrum of dynamic regimes that classical theories overlook. Its conceptual rigor and practical value are demonstrated in a predator-prey system. This new approach reframes how to forecast regime shifts in complex systems and offers a tool with broad relevance, from microbial ecosystems to planetary climate.

ecology↗

bioRxiv2023

A novel stabilization mechanism accommodating genome length variation in evolutionarily related viral capsids

Tailed bacteriophages are one of the most numerous and diverse group of viruses. They store their genome at quasi-crystalline densities in capsids built from multiple copies of proteins adopting the HK97-fold. The high density of the genome exerts an internal pressure, requiring a maturation process that reinforces their capsids. However, it is unclear how capsid stabilization strategies have adapted to accommodate the evolution of larger genomes in this virus group. Here we characterized a novel capsid reinforcement mechanism in two evolutionary-related actinobacteriophages that modifies the length of a stabilization protein to accommodate a larger genome while maintaining the same capsid size. We used cryo-EM to reveal that capsids contained split hexamers of HK97-fold proteins with a stabilization protein in the chasm. The observation of split hexamers in mature capsids was unprecedented, so we rationalized this result mathematically, discovering that icosahedral capsids can be formed by all split or skewed hexamers as long as their T-number is not a multiple of three. Our results suggest that analogous stabilization mechanisms can be present in other icosahedral capsids, and they provide a strategy for engineering capsids accommodating larger DNA cargoes as gene delivery systems. Significance StatementHow capsids are stabilized and change size is an important part of understanding how to design protein containers and understand viral evolution. We describe a novel capsid stability mechanism that allows the capsid to package a larger genome without changing the capsid architecture and have predicted other capsids using this mechanism. Beyond the evolutionary implications, our findings provide a mechanism to increase the amount of DNA packaged in a capsid, offering a solution to engineer gene delivery systems with larger DNA content, a pressing challenge in gene therapy.

molecular biology↗

bioRxiv2023

The Promise and Pitfalls of Prophages

Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion. Many prophages benefit their host, and prophages are responsible for genotypic and phenotypic differences that separate individual microbial strains. However, the microbes also endure a cost to maintain those phages: additional DNA to replicate and proteins to transcribe and translate. We have never quantified those benefits and costs. Here, we analysed over two and a half million prophages from over half a million bacterial genome assemblies. Analysis of the whole dataset and a representative subset of taxonomically diverse bacterial genomes demonstrated that the normalised prophage density was uniform across all bacterial genomes above 2 Mbp. We identified a constant carrying capacity of phage DNA per bacterial DNA. We estimated that each prophage provides cellular services equivalent to approximately 2.4 % of the cells energy or 0.9 ATP per bp per hour. We demonstrate analytical, taxonomic, geographic, and temporal disparities in identifying prophages in bacterial genomes that provide novel targets for identifying new phages. We anticipate that the benefits bacteria accrue from the presence of prophages balance the energetics involved in supporting prophages. Furthermore, our data will provide a new framework for identifying phages in environmental datasets, diverse bacterial phyla, and from different locations.

bioinformatics↗

bioRxiv2023

Novel crAssphage isolates exhibit conserved gene order and purifying selection of the host specificity protein

Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. tikkala strain Bc01, Kolpuevirus sp. frurule strain Bc03, and Rudgehvirus jaberico strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome. Impact statementBacteriophages play a crucial role in shaping microbial communities within the human gut. Among the most dominant bacteriophages in the human gut microbiome are Crassvirales phages, which infect Bacteroides. Despite being widely distributed, only a few Crassvirales genomes have been isolated, leading to a limited understanding of their biology, ecology, and evolution. This study isolated and characterized three novel Crassvirales genomes belonging to two different families, and three genera, but infecting one bacterial host, Bacteroides cellulosilyticus WH2. Notably, the observation confirmed the phages are not co-evolving with their bacterial hosts, rather have a shared ability to exploit similar features in their bacterial host. Additionally, the identification of a critical viral protein undergoing purifying selection and interacting with the bacterial receptors opens doors to targeted therapies against bacterial infections. Given Bacteroides role in polysaccharide degradation in the human gut, our findings advance our understanding of the phage-host interactions and could have important implications for the development of phage-based therapies. These discoveries may hold implications for improving gut health and metabolism to support overall well-being. Data summaryThe genomes used in this research are available on Sequence Read Archive (SRA) within the project, PRJNA737576. Bacteroides cellulosilyticus WH2, Kehishuvirus sp. tikkala strain Bc01, Kolpuevirus sp. frurule strain Bc03, and Rudgehvirus jaberico strain Bc11 are all available on GenBank with accessions NZ_CP072251.1 (B. cellulosilyticus WH2), QQ198717 (Bc01), QQ198718 (Bc03), and QQ198719 (Bc11), and we are working on making the strains available through ATCC. The 3D protein structures for the three Crassvirales genomes are available to download at doi.org/10.25451/flinders.21946034.

bioinformatics↗

bioRxiv2023

pyCapsid: Identifying dominant dynamics and quasi-rigid mechanical units in protein shells

Structured AbstractO_ST_ABSSummaryC_ST_ABSpyCapsid is a Python package developed to facilitate the characterization of the dynamics and mechanical units of protein shells and other protein complexes. The package was developed in response to the rapid increase of high-resolution structures, particularly capsids of viruses, requiring multiscale biophysical analyses. Given a protein shell, pyCapsid generates the collective vibrations of its amino-acid residues, identifies quasi-rigid mechanical regions, and maps the results back to the input proteins for interpretation. pyCapsid summarizes the main results in a report that includes publication-quality figures. Availability and ImplementationpyCapsids source code is available under MIT License on GitHub (https://github.com/luquelab/pycapsid). It is compatible with Python 3.8-3.10 and has been deployed in two leading Python package-management systems, PIP (https://pypi.org/project/pyCapsid/) and Conda (https://anaconda.org/luque_lab/pycapsid). Installation instructions and tutorials are available in the GitHub Page-style online documentation (https://luquelab.github.io/pyCapsid). Additionally, a cloud-based implementation of pyCapsid is available as a Google Colab notebook (https://colab.research.google.com/github/luquelab/pyCapsid/blob/main/notebooks/pyCapsid_colab_notebook.ipynb). pyCapsid Colab does not require installation and generates the same report and outputs as the installable version. Users can post issues regarding pyCapsid in the GitHub repository (https://github.com/luquelab/pyCapsid/issues).

bioinformatics↗

bioRxiv2020

Unifying framework for the diffusion of microscopic particles in mucus

Mucus is a fluid that protects animals against pathogens while promoting interactions with commensal microbes. Changes in the diffusivity of particles in mucus alter viruses infectivity, the efficiency of bacterial pathogens to invade a host, and the effectivity of drug delivery. Multiple physicochemical properties modulate the diffusion of microscopic particles in mucus, but their combined effect is unclear. Here, we analyzed the impact of particle size, charge, chemistry, anomalous diffusion exponent, and mucus composition in the diffusivity of particles from 106 published experiments. We used a time window sampling of one second to define a consistent, effective diffusion across experiments. The effective diffusion spanned seven orders of magnitude from 10-5 to 102 {micro}m2/s. The anomalous exponent was the strongest predictor among all variables tested. It displayed an exponential relationship with the effective diffusion that explained 90% of the empirical data variance. We showed that the relationship and dominance of the anomalous diffusion exponent resulted from a general mathematical relationship obtained from first-principles for any subdiffusion mechanism. Our derivation demonstrated that the generalized diffusion coefficient is not a measurable physical quantity and must be replaced by the length and time scales associated with the underlying mobility mechanisms. This led us to a fundamental reformulation of the classic subdiffusion equation, which calls for a reinterpretation of anomalous diffusion in physical systems. We also discussed how our results impact the characterization of microscopic particle diffusion in mucus and other hydrogels.

biophysics↗

bioRxiv2020

Quantification of lysogeny caused by phage coinfections in microbial communities from biophysical principles

Temperate phages can integrate in their bacterial host genome to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbial-dense environment of the mammalian-gut. This observation contrasts with the long-standing hypothesis of lysogeny being favored in microbial communities with low densities. Here we hypothesized that phage coinfections--the most studied molecular mechanism of lysogeny in lambda phage--increases at high microbial abundances. To test this hypothesis, we developed a biophysical model of coinfection and stochastically sampled ranges of phage and bacterial concentrations, adsorption rates, lysogenic commitment times, and community diversity from marine and gut microbiomes. Based on lambda experiments, a Poisson process assessed the probability of lysogeny via coinfection in these ecosystems. In 90% of the sampled marine ecosystems, lysogeny stayed below 10% of the bacterial community. In contrast, 25% of the sampled gut communities stayed above 25% of lysogeny, representing an estimated nine trillion lysogens formed via phage coinfection in the human gut every day. The prevalence of lysogeny in the gut was a consequence of the higher densities and faster adsorption rates. In marine communities, which were characterized by lower densities and phage adsorption rates, lysogeny via coinfection was still possible for communities with long lysogenic commitments times. Our study suggests that physical mechanisms can favor coinfection and cause lysogeny at poor growth conditions (long commitment times) and in rich environments (high densities and adsorption rates). ImportancePhage integration in bacterial genomes manipulate microbial dynamics from the oceans to the human gut. This phage-bacteria interaction, called lysogeny, is well-studied in laboratory models, but its environmental drivers remain unclear. Here we quantified the frequency of lysogeny via phage coinfection--the most studied mechanism of lysogeny--by developing a biophysical model that incorporated a meta-analysis of the properties of marine and gut microbiomes. Lysogeny was found to be more frequent in high-productive environments like the gut, due to higher phage and bacterial densities and faster phage adsorption rates. At low cell densities, lysogeny via coinfection was possible for hosts with long duplication times. Our research bridges the molecular understanding of lysogeny with the ecology of complex microbial communities.

microbiology↗

bioRxiv2020

Phage and bacteria diversification through a prophage acquisition ratchet

Lysogeny is prevalent in the microbial-dense mammalian gut. This contrasts the classical view of lysogeny as a refuge used by phages under poor host growth conditions. Here we hypothesize that as carrying capacity increases, lysogens escape phage top-down control through superinfection exclusion, overcoming the canonical trade-off between competition and resistance. This hypothesis was tested by developing an ecological model that combined lytic and lysogenic communities and a diversification model that estimated the accumulation of prophages in bacterial genomes. The ecological model sampled phage-bacteria traits stochastically for communities ranging from 1 to 1000 phage-bacteria pairs, and it included a fraction of escaping lysogens proportional to the increase in carrying capacity. The diversification model introduced new prophages at each diversification step and estimated the distribution of prophages per bacteria using combinatorics. The ecological model recovered the range of abundances and sublinear relationship between phage and bacteria observed across eleven ecosystems. The diversification model predicted an increase in the number of prophages per genome as bacterial abundances increased, in agreement with the distribution of prophages on 833 genomes from marine and human-associated bacteria. The study of lysogeny presented here offers a framework to interpret viral and microbial abundances and reconciles the Kill-the-Winner and Piggyback-the-Winner paradigms in viral ecology.

ecology↗

bioRxiv2019

Bean yellow mosaic virus infecting broad bean in the green belt of Cordoba, Argentina

Broad bean (Vicia faba L) is the fourth most important pulse crop in the world. In Argentina, broad bean production was of 1,841 hectares and 16,500 tons during the 2017 growing season. Broad bean is commonly used in rotations; especially by farmers located in \"green belts\" that are peri-urban areas surrounding large cities that include horticultural family farms. Plants showing marked foliar mosaic symptoms, typical of viral infection, were collected during the 2015 growing season in the green belt of Cordoba city, Argentina. Preparations of symptomatic tissues were mechanically inoculated onto healthy broad bean plants in the greenhouse, which developed symptoms similar to those observed in the field. In addition, symptomatic samples were positive when tested by indirect ELISA with the anti-potyvirus group monoclonal antibody. Further, flexuous filamentous particles typical of potyviruses were observed under the electronic microscope on dip preparations. Lastly, total RNA was extracted from a symptomatic leaf and high-throughput sequenced, which allowed the assembly of a single virus sequence corresponding to a new highly divergent strain of Bean yellow mosaic virus (BYMV). Phylogenetic insights clustered this Argentinean broad bean isolate (BYMV-ARGbb) within group IX of BYMV. Given the economical importance of this virus and its associated disease, the results presented here are a pivotal first step oriented to explore the eventual incidence and epidemiological parameters of BYMV in broad bean in Argentina.

microbiology↗

bioRxiv2018

Biophysical and physiological causes of coral reef microbialization

Coral reefs are declining globally as their primary producer communities shift from stony coral to fleshy macroalgae dominance. Previously, we have shown that the rise of fleshy macroalgae produces dissolved organic carbon (DOC) that lead to microbialization and coral death. Here we test the hypothesis that the biophysical cause of bacterial biomass accumulation is a relative decrease in electron acceptors relative to electron donors due to O2 loss from macroalgae. We show that 37 % of photosynthetic O2 produced by reef fleshy macroalgae is lost in the form of gas through ebullition from algae surfaces. O2 loss increases DOC:O2 ratios, decoupling the photosynthetically fixed carbon from oxidative potential for respiration. This biogeochemical environment drives heterotrophic microbes to increase cell-specific DOC consumption and cell sizes, accumulating biomass. In contrast, corals do not lose oxygen and support the growth of smaller and fewer bacteria. In situ biomass and metagenomic analyses of 87 reefs across the Pacific and Caribbean show that on algae-dominated reefs bacteria accumulate organic carbon through a Warburg-like increase in aerobic glycolytic metabolism. Because of its biophysical basis, microbialization is predicted to occur in other marine ecosystems shifting primary producer assemblages, such as planktonic communities in warming and acidifying conditions.

ecology↗

bioRxiv2018

Relevance of coral geometry in the outcomes of the coral-algal benthic war

Corals have built reefs on the benthos for millennia, becoming an essential element in marine ecosystems. Climate change and human impact, however, are favoring the invasion of non-calcifying benthic algae and reducing coral coverage. Corals rely on energy derived from photosynthesis and heterotrophic feeding, which depends on their surface area, to defend their outer perimeter. But the relation between geometric properties of corals and the outcome of competitive coral-algal interactions is not well known. To address this, 50 coral colonies interacting with algae were sampled in the Caribbean island of Curacao. 3D and 2D digital models of corals were reconstructed to measure their surface area, perimeter, and polyp sizes. A box counting algorithm was applied to calculate their fractal dimension. The perimeter and surface dimensions were statistically non-fractal, but differences in the mean surface fractal dimension captured relevant features in the structure of corals. The mean fractal dimension and surface area were negatively correlated with the percentage of losing perimeter and positively correlated with the percentage of winning perimeter. The combination of coral perimeter, mean surface fractal dimension, and coral species explained 19% of the variability of losing regions, while the surface area, perimeter, and perimeter-to-surface area ratio explained 27% of the variability of winning regions. Corals with surface fractal dimensions smaller than two and small perimeters displayed the highest percentage of losing perimeter, while corals with large surface areas and low perimeter-to-surface ratios displayed the largest percentage of winning perimeter. This study confirms the importance of fractal surface dimension, surface area, and perimeter of corals in coral-algal interactions. In combination with non-geometrical measurements such as microbial composition, this approach could facilitate environmental conservation and restoration efforts on coral reefs.

ecology↗