Biology subjects

Iranzo, J.

Publications and source records attributed to Iranzo, J..

16 recordsLinked to original sources

bioRxiv2026

Self-organized division of labor and selection for long-term antiviral defense in CRISPR arrays.

CRISPR-Cas is an adaptive immunity system that protects prokaryotes from viruses and other genetic parasites. CRISPR-Cas immunity is guided by short DNA sequences, called spacers, that are acquired upon encounters with parasites and stored in the CRISPR array. Although the mechanisms driving spacer acquisition are relatively well understood, the timespan of CRISPR immune memory and, consequently, the very nature of CRISPR-Cas as a short-term or long-term defense mechanism remain controversial. Because CRISPR arrays have limited size, CRISPR-Cas systems face a fundamental trade-off between acquiring new spacers against recent infections and retaining old spacers for long-term defense. To investigate how CRISPR-Cas systems resolve this "fast response-versus-memory" trade-off, we developed a stochastic model that captures CRISPR array dynamics under varying abundances of endemic and episodic viruses. Simulations reveal three distinct evolutionary regimes that result in short-term, long-term, and "dual memory" arrays. These regimes are governed by the ratio of two measurable parameters: the length of the CRISPR array and the time required for transient epidemics to decay below basal endemic viral abundance. Spontaneous division of labor emerges in the dual memory regime, with spacers near the leader and distal ends specialized in short-term and long-term memory, respectively. Within-array division of labor results in a U-shaped longitudinal profile for the probability of finding the targets of CRISPR immunity among the local virome. Such profiles, that have been empirically observed in CRISPR arrays from the human gut microbiome, could inform future research on the environmental persistence of poorly characterized viromes.

microbiology↗

bioRxiv2026

Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?

BackgroundMobile genetic elements (MGEs), including viruses, plasmids, and transposons, are major drivers of evolution in bacteria and archaea. Host-parasite conflicts drive the emergence of a broad variety of defense and counter-defense systems. Recent advances in metagenomics and functional annotation have shown that many defense systems are located on MGEs. The fact that MGEs are, essentially, genomic parasites raises an intriguing question: why do these parasites carry defense systems at high prevalence, often even higher than the host chromosome? ResultsWe developed a simple mathematical model to investigate the factors that promote evolution of defense systems in MGEs and the ecological implications of MGE-encoded defense. Our analysis points to the strength of inter-MGE interference as a key determinant of the evolution of defense systems in MGEs. We identify two qualitatively distinct regimes, depending on the basic reproductive number in mixed coinfections. Weakly interfering MGEs tend to carry low-cost defense systems that enhance the survival of their hosts upon exposure to more damaging MGEs. Although these systems can be occasionally transferred to the host, they typically remain in MGEs. In contrast, strongly interfering MGEs, such as plasmids from the same incompatibility group, can carry high-cost defense systems that are detrimental to the host and the population as a whole, but help their carriers spread by actively replacing their competitors. ConclusionsAnalysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as MGE banks, typically carrying low-cost defense systems that can benefit the host by protecting it from more damaging MGEs. In contrast, strongly interfering MGEs would carry costly defense systems that mediate inter-MGE conflicts but are deleterious to the host. These MGEs could serve as proving grounds for emerging defense systems, which might eventually become cost-effective once optimized by selection.

evolutionary biology↗

bioRxiv2026

Glyphosate as a driver of antimicrobial resistance evolution in bacteria

Glyphosate, the worlds most widely used herbicide, targets the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which is conserved across plants and many bacteria. While its environmental effects are increasingly recognized, its role on antimicrobial resistance (AMR) remains incompletely understood. In particular, the link between intrinsic glyphosate sensitivity and AMR gene content or evolutionary dynamics has not been systematically explored. We examined the relationship between bacterial sensitivity to glyphosate, AMR profiles, and the evolution of AMR genes. We analyzed genome datasets from the human gut microbiota and the Alignable Tight Genomic Clusters (ATGC). EPSPS sequences were identified via BLAST and annotations and classified based on the intrinsic sensitivity to glyphosate using the EPSPSClass webserver. AMR genes, including associated drug classes and resistance mechanisms, were annotated using the Comprehensive Antibiotic Resistance Database (CARD). Across datasets, glyphosate-sensitive bacteria carried a greater diversity of AMR genes and mechanisms. In contrast, probabilistic modeling revealed that glyphosate-resistant bacteria accumulate AMR genes at significantly higher rates. Phylogenetic birth-and-death analyses and stochastic mapping further revealed elevated AMR gene gain, loss, expansion, and reduction in resistant strains. These results indicate a decoupling between AMR gene diversity and evolutionary dynamics: sensitive bacteria maintain more resistance genes, whereas resistant bacteria display accelerated AMR gene turnover. This suggests that glyphosate resistance is linked to increased genome dynamics, potentially enhancing bacterias adaptability under combined herbicide and antimicrobial pressures. Given glyphosates extensive agricultural use and potential human exposure, these findings highlight an underappreciated link between herbicide resistance and the evolution of AMR in bacterial populations.

microbiology↗

bioRxiv2025

Stability and diversity of interactions in complex microbiomes

Complex microbial communities abound in nature, yet designing robust and stable microbial consortia for use in biotechnology and One Health applications remains a major challenge. Inspired by a large body of work on community ecology, we used mathematical models to investigate what makes a microbiome stable. Our approach integrates three factors that characterize many free-living and host-associated microbial communities but have seldom been jointly considered: sustained growth, high-order interactions, and a broad diversity of interaction profiles. We derived a simple expression that relates community stability to basic statistical properties of the underlying interaction networks. Analytical and numerical results show that synergistic high-order interactions, such as those derived from complex auxotrophies, play a critical role in stabilizing species-rich microbial communities with highly diverse interaction profiles. In contrast, in the absence of high-order interactions, viability is restricted to communities with very sparse or fully mutualistic interaction networks. Our findings have the potential to inform microorganism-based interventions in areas in which sustained growth and long-term stability are desirable properties. We propose that incorporating high-order mutualism into engineered microbial consortia could improve their robustness by buffering design uncertainty about the underlying interaction networks.

ecology↗

bioRxiv2025

Long-term evolution of prokaryotic genomes in a chemolithotrophic cave over 5.5 million years of isolation

Fluctuating conditions drive adaptive evolution, yet understanding how genomes evolve under stable conditions over extended periods remains a major challenge, since most research on microbial evolution relies on short-term experiments or phylogenetic comparisons. The Movile Cave, isolated from external influences 5.5 million years, offers a unique opportunity to explore microbial evolution under prolonged environmental stability. Here, we analyzed metagenome-assembled genomes from this cave, revealing that prokaryotes exhibit lower gene diversity and higher levels of pseudogenization compared to those from non-isolated environments, mainly affecting housekeeping functions involved in translation. Functional redundancy across genomes remained comparable to related habitats. Our results suggest that pseudogenization may serve as a fine-tuning mechanism to reduce excess redundancy. Although horizontal gene transfer is limited overall, the cave virome seems to contribute to microbial adaptation through the transfer of auxiliary metabolic genes. Movile microorganisms harbor fewer phage-defense systems than counterparts in related environments, suggesting a long-term adaptation to a relatively stable virosphere. Our findings indicate that prolonged isolation under stable selective pressures does not necessarily lead to major genomic divergence, but rather promotes adaptive gene loss. This study provides key insights into how long-term stability shapes microbial genome evolution and ecosystem function.

microbiology↗

bioRxiv2024

Timescales and genetic linkage explain the variable impact of defense systems on horizontal gene transfer

Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGE). However, because MGE are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short and long terms. By combining comparative genomics and phylogeny-aware statistical methods, we quantified the association between the presence of 7 widespread defense systems and the abundance of MGE in the genomes of 196 bacterial and 1 archaeal species. We also calculated the differences in the rates of gene gain and loss between lineages that possess and lack each defense system. Our results show that the impact of defense systems on HGT is highly taxon- and system-dependent. CRISPR-Cas stands out as the defense system that most often associates with a decrease in the number of MGE and reduced gene acquisition. Timescale analysis reveals that defense systems must persist in a lineage for a relatively long time to exert an appreciable negative impact on HGT. In contrast, at short evolutionary times, defense systems, MGE, and gene gain rates tend to be positively correlated. Based on these results and given the high turnover rates experienced by defense systems, we propose that the inhibitory effect of most defense systems on HGT is masked by recent co-transfer events involving MGE.

microbiology↗

bioRxiv2024

Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome

Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals to study how the interplay of genetic parasites and CRISPR-Cas immunity reflects on the dynamics and composition of the human gut microbiome. Based on the coordinated study of 80,000 CRISPR-Cas loci and their targets, we show that CRISPR-Cas immunity effectively modulates bacteriophage abundances in the gut. Acquisition of CRISPR-Cas immunity typically leads to a decrease in the abundance of lytic phages, but does not necessarily cause their complete disappearance. Much smaller effects are observed for lysogenic phages and plasmids. Conversely, phage-CRISPR interactions shape bacterial microdiversity by producing weak selective sweeps that benefit immune host lineages. Interestingly, distal (and chronologically older) regions of CRISPR arrays are enriched in spacers that are potentially functional and target crass-like phages and local prophages. This suggests that exposure to reactivated prophages and other endemic viruses is a major selective pressure in the gut microbiome that drives the maintenance of long-lasting immune memory.

microbiology↗

bioRxiv2022

DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation

Somatic DNA methylation is established early during mammalian development, as embryonic cells transition from naive to primed pluripotency. This precedes the emergence of the three somatic germ layers, but also the segregation of the germline that undergoes genome-wide DNA demethylation after specification. While DNA methylation is essential for embryogenesis, the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Using culture modeling of cellular transitions, we found that DNA methylation-free embryonic stem cells (ESCs) with a triple DNA methyltransferase knockout (TKO) normally progressed through the continuum of pluripotency states, but demonstrated skewed differentiation abilities towards neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells (PGCLCs), even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that the neural and germline lineages are linked by a similar enhancer dynamics during priming, defined by common sets of methyl-sensitive transcription factors that fail to be decommissioned in absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of preferred differentiation route during early development.

developmental biology↗

bioRxiv2022

Operational Gene Clusters and intrinsic uncertainty in pangenome analyses

BackgroundA key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers, that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multi-copy gene families (recognizable by synteny conservation) and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes. ResultsClustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, which allows for robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables. ConclusionsChoosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.

genomics↗

bioRxiv2022

Pervasive conditional selection of driver mutations and modular epistasis networks in cancer

Cancer driver mutations often display mutual exclusion or co-occurrence, underscoring the key role of epistasis in carcinogenesis. However, estimating the magnitude of epistasis and quantifying its effect on tumor evolution remains a challenge. We developed a method to quantify COnditional SELection on the Excess of Nonsynonymous Substitutions (Coselens) in cancer genes. Coselens infers the number of drivers per gene in different partitions of a cancer genomics dataset using covariance-based mutation models and determines whether coding mutations in a gene affect selection for drivers in any other gene. Using Coselens, we identified 296 conditionally selected gene pairs across 16 cancer types in the TCGA dataset. Conditional selection affects 25-50% of driver substitutions in tumors with >2 drivers. Conditionally co-selected genes form modular networks, whose structures challenge the traditional interpretation of within-pathway mutual exclusivity and across-pathway synergy, suggesting a more complex scenario, where gene-specific across-pathway epistasis shapes differentiated cancer subtypes.

cancer biology↗

bioRxiv2021

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions

Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.

evolutionary biology↗

bioRxiv2021

The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates

Genomic imprinting refers to the mono-allelic and parent-specific expression of a subset of genes. While long recognized for their role in embryonic development, imprinted genes have recently emerged as important modulators of postnatal physiology, notably through hypothalamus-driven functions. Here, using mouse models of loss, gain and parental inversion of expression, we report that the paternally expressed Zdbf2 gene controls neonatal growth in mice, in a dose-sensitive but parent-of-origin-independent manner. We further found that Zdbf2-KO neonates failed to fully activate hypothalamic circuits that stimulate appetite, and suffered milk deprivation and diminished circulating Insulin Growth Factor 1 (IGF-1). Consequently, only half of Zdbf2-KO pups survived the first days after birth and those surviving were smaller. This study demonstrates that precise imprinted gene dosage is essential for vital physiological functions at the transition from intra- to extra-uterine life, here the adaptation to oral feeding and optimized body weight gain.

molecular biology↗

bioRxiv2019

Homologous recombination substantially delays sequence but not gene content divergence of prokaryotic populations

Evolution of bacterial and archaeal genomes is a highly dynamic process that involves extensive gain and loss of genes. Therefore, phylogenetic trees of prokaryotes can be constructed both by the traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we found that the terminal branches of gene trees were systematically compressed compared to those of genome trees. Thus, sequence evolution seems to be significantly delayed with respect to genome evolution by gene gain and loss. The extent of this delay widely differs among bacterial and archaeal lineages. We develop and explore mathematical models demonstrating that the delay of sequence divergence can be explained by sequence homogenization that is caused by homologous recombination. Once evolving genomes become isolated by barriers that impede homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation. This model of prokaryotic genome evolution gives a mechanistic explanation of our previous finding that archaeal genomes contain a class of genes that turn over rapidly, before significant sequence divergence occurs, and provides a framework for correcting phylogenetic trees, to make them consistent with the dynamics of gene turnover.

evolutionary biology↗

bioRxiv2018

Origins and Evolution of the Global RNA Virome

Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches, 2 of which include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded (ds) RNA viruses, and 2 consist of dsRNA and negative-sense (-) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas -RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, particularly, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.\n\nIMPORTANCEThe majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than what was attainable previously. This reconstruction reveals the relationships between different Baltimore Classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.

microbiology↗

bioRxiv2017

The cancer-mutation network and the number and specificity of driver mutations

Cancer genomics has produced extensive information on cancer-associated genes but the number and specificity of cancer driver mutations remains a matter of debate. We constructed a bipartite network in which 7665 tumors from 30 cancer types are connected via shared mutations in 198 previously identified cancer-associated genes. We show that 27% of the tumors can be assigned to statistically supported modules, most of which encompass 1-2 cancer types. The rest of the tumors belong to a diffuse network component suggesting lower gene-specificity of driver mutations. Linear regression of the mutational loads in cancer-associated genes was used to estimate the number of drivers required for the onset of different cancers. The mean number of drivers is ~2, with a range of 1 to 5. Cancers that are associated to modules had more drivers than those from the diffuse network component, suggesting that unidentified and/or interchangeable drivers exist in the latter.

cancer biology↗

bioRxiv2017

Disentangling The Effects Of Selection And Loss Bias On Gene Dynamics

We combine mathematical modelling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most non-parasitic genes is low albeit positive, compatible with the observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in anti-parasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction-modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not the duplication to loss ratio, correlates with genome size, potentially explaining the increased abundance of neutral and costly elements in larger genomes.\n\nSIGNIFICANCEEvolution of microbes is dominated by horizontal gene transfer and the incessant host-parasite arms race that promotes the evolution of diverse anti-parasite defense systems. The evolutionary factors governing these processes are complex and difficult to disentangle but the rapidly growing genome databases provide ample material for testing evolutionary models. Rigorous mathematical modeling of evolutionary processes, combined with computer simulation and comparative genomics, allowed us to elucidate the evolutionary regimes of different classes of microbial genes. Only genes involved in key informational and metabolic pathways are subject to strong selection whereas most of the others are effectively neutral or even burdensome. Mobile genetic elements and defense systems are costly, supporting the understanding that their evolution is governed by the same factors.

evolutionary biology↗