Biology subjects

Bravo, I. G.

Publications and source records attributed to Bravo, I. G..

14 recordsLinked to original sources

bioRxiv2026

Sialidase variability in Gardnerella: genetics, taxonomy, function, and clinical presentation

Bacterial vaginosis (BV) is the most common vaginal condition among women of reproductive age. Despite over six decades of research, the pathogenesis and etiology of BV remain largely unknown. Members of the Gardnerella genus are common components of the healthy vaginal microbiota, although their uncontrolled proliferation plays a key role in BV pathogenesis. Recent taxonomic revisions have highlighted extensive genetic and functional diversity among Gardnerella spp., but the relationship between genetics, taxonomy, and virulence remains elusive. Sialidases are key virulence factors in BV, degrading the protective epithelial mucus layer, facilitating colonization and releasing carbon and nitrogen sources. However, robust clinical evidence linking sialidases to increased BV risk remains limited. Here, we analyzed clinical Gardnerella isolates from BV-positive (75%) and BV-negative (25%) samples (n = 66) collected at the University Hospital of Montpellier, France. We inferred phylogenetic relationships, characterised the nanH sialidase gene repertoire, quantified in vitro sialidase activity, and evaluated antibiotic resistance profiles. Most isolates belonged to Gardnerella clades 1, 2, and 4 (63.6%, 19.7%, and 16.7%, respectively). The three nanH genes were unevenly distributed across clades: nanH1 was most common ([~]80%), highly prevalent in clades 1-3; nanH2 was rare (6%); and nanH3 ([~]38%) was predominantly found in clade 2 - typically co-occurring with nanH1. Sialidase activity varied both between and within clades, and was only weakly associated with the nanH gene repertoire. Neither taxonomy nor sialidase-associated traits were reliable predictors of BV status, and we found no clear link between taxonomy and antibiotic resistance. Together, these results reveal substantial discordance in the genotype-phenotype relationship in Gardnerella, suggesting epigenetic, physiological and/or ecological modulation. Our findings highlight the need for a better understanding of bacterial physiology, plasticity, and ecology to explain microbial traits of clinical importance.

microbiology↗

bioRxiv2025

Environmental complexity constrains evolutionary adaptation across taxa

Complex environments combining multiple stressors are the new norm worldwide. Adaptive evolution will be critical to population persistence under these combined challenges, but how environmental complexity affects the pace of evolution remains poorly understood. Using a meta-experimental evolution approach, we exposed 14 species, from bacteria to unicellular eukaryotes and plants, to single stressors and their pairwise combinations for multiple generations, while keeping the overall stress level comparable. Populations evolving under combined stressors tended to have lower fitness increase in the selective environments, higher fitness reductions in the control environment, and shallower relation between initial maladaptation and fitness gain, than under single stressors. However, these responses varied with species and stressor type. Accounting for such constraints on evolutionary dynamics should prove crucial for the management of biodiversity. Significance StatementA pressing challenges for modern science and society in the face of ongoing global change is understanding what limits the capacity of living organisms to adapt to complex environments combining multiple stressors. To answer to this question, we conducted a large-scale meta-experimental evolution design across a diversity of organisms, exposing them for multiple generations to either single or combined-stress treatments. Combined stressors led to less adaptive fitness gain than single stressors, and imposed additional costs through reduced fitness in non-stressful conditions. This unique combination of meta-experimental approach with a careful distinction between environmental complexity and overall stress allowed us to gain robust quantitative evidence on how environmental complexity can impact the pace of evolution.

evolutionary biology↗

bioRxiv2025

The Population Genetics of Biological Noise

Information transmission is intrinsic to life, and noise is intrinsic to information transmission. Biological noise during development is essential for the flexibility and plasticity of individual organisms, but also underlies some diseases. Biological noise during reproduction is the fuel for evolution, including the evolution of therapy resistance in pathogenic microbes and in cancer. Recent technological advances in our ability to characterize many sources of biological noise have demonstrated that its amount is often heritable. Here, we frame the population genetics of loci that influence the amount of any source of biological noise. While analogous theory for heritable changes in mean trait values has been established for nearly a century, to our knowledge this is the first general approach for studying the evolution of heritable changes in their statistical distributions. This represents a critical theoretical contribution to an important and rapidly growing domain of intellectual inquiry. It also sheds light on the hypothesis that natural selection can increase evolvability, and generalizes modifier theory used in the tradition of Feldman and colleagues. Author summaryBiological noise is a fact of life. Genetically identical organisms reared in identical environments invariably exhibit random phenotypic differences. And siblings born of the same parent(s) in the same environment are endowed with inheritances that invariably differ at random. While the specific consequences of biological noise are unpredictable, extraordinary experimental advances now make clear that its amount can be influenced by an organisms genetics. For example, high- and low-noise promoter, and high- and low-noise DNA polymerase alleles are well known. This raises the question of when and how natural selection favors high- or low-noise alleles. While biological noise is on average deleterious, it can also occasionally induce high fitness phenotypes. Here, we solve a simple analytic model for the fitness difference between noise alleles that captures both these features. Our model predicts the existence of an evolutionary equilibrium in the amount of noise, whose location reflects just four features of an organisms biology. In light the clinical importance of biological noise, as well as its central role more broadly in both development and evolution, this work provides an urgently needed evolutionary framework for understanding its long-term determinants.

evolutionary biology↗

bioRxiv2024

Resource landscape shapes the composition and stability of the human vaginal microbiota

The vaginal microbiota is associated with the health of women and newborns alike. Despite its comparatively simple composition relative to other human microbiota systems, the mechanisms underpinning the dynamics and stability of vaginal microbial communities remain elusive. A crucial, yet so far underexplored, aspect of vaginal microbiota ecology is the role played by nutritional resources. Glycogen and its derivatives, produced by vaginal epithelia, are accessible to all bacterial constituents of the microbiota. Concurrently, free sialic acid and fucose offer supplementary nutritional resources to bacterial strains capable of cleaving them from glycans, which are structurally integral to mucus. Notably, bacteria adept at sialic acid exploitation are often correlated with adverse clinical outcomes and are frequently implicated in bacterial vaginosis (BV). In this study, we introduce a novel mathematical model tailored to human vaginal microbiota dynamics to explore the interactions between bacteria and their respective nutritional landscape. Our resource-based model examines the impact of the relative availability of glycogen derivatives (accessible to all bacterial species) and sialic acid (exclusive to some BV-associated bacteria) on the composition of the vaginal microbiota. Our findings elucidate that the success of BV-associated bacteria is intricately linked to their exclusive access to specific nutritional resources. This private access fortifies communities dominated by BV-associated bacteria, rendering them resilient to compositional transitions. We empirically corroborate our model prediction with longitudinal clinical data on microbiota composition and previously unpublished metabolomic profiles obtained from a North American cohort. The insights gleaned from this study shed light on potential pathways for BV prevention and treatment. Significance statementThe vaginal microbiota has a notable impact on womens health at various stages of life, namely puberty, infection protection, sexual health, fertility, pregnancy, and menopausal changes. At present, most non-anti-microbial products developed to mitigate adverse vaginal symptoms emphasise competitive interactions through acids (boric or lactic acid) or probiotics as a means to "rebalance" microbiota communities. Despite recent advances in profiling the composition of vaginal microbiota communities, there remains a major gap in our mechanistic understanding of how to maintain or reinstate a resilient Lactobacillus-dominated microbiota that improves vaginal health and outcomes. This study explores the role of nutritional resources in the vaginal microbiota by introducing a mathematical model that analyses how access to specific nutrients like glycogen derivatives and sialic acid affects the balance of bacterial vaginosis (BV) and non-BV-associated bacteria. Our findings, supported by original cohort-derived microbiological and metabolomics data, demonstrate that exclusive access to these nutrients is linked to the dominance and resilience of BV-associated bacteria, providing new insights for BV prevention and treatment.

microbiology↗

bioRxiv2024

Pervasive translation of the downstream ORF from bicistronic mRNAs by human cells: impact of the upstream ORF codon usage and splicing

In this work, we present a straightforward model to study gene expression regulation from virus-like bicistronic mRNAs in human cells, composed by a short shble upstream ORF and a reporter egfp downstream ORF. We have engineered thirteen synonymous versions of the shble ORF to explore a large parameter space in compositional and folding features, as well as differences in propensity to undergo splicing. Our experimental model focuses on the control and modulation of shble translation elongation and their effects on downstream translation: i) regarding translation initiation, all constructs share identical 5UTR, ribosomal binding site and shble start codon context; and ii) regarding egfp translation, all constructs share identical shble stop codon context, spacer between shble and egfp and the full egfp sequence. Our results show first that the human translation machinery can translate the downstream ORF in bicistronic mRNAs, independently of the characteristics of the upstream ORF. Even if GFP protein levels are hundreds of times lower than SHBLE protein levels, our results challenge the textbook interpretation positing that the eukaryotic translation machinery does not handle the downstream ORF in bicistronic transcripts. Second, we show that synonymous recoding of the upstream ORF determines its own translation efficiency, can uncover cryptic splice signals, and largely conditions the probability of translation from the downstream ORF. Our results are consistent with a leaky scanning mechanism at play for downstream ORF translation from bicistronic mRNAs in human cells.

molecular biology↗

bioRxiv2024

"This training is bound for glory": selection by experimental evolution of a bacteriophage with expanded host-range and increased virulence

Viral host range expansion is predicted to evolve at the cost of reduced mean fitness. We investigated the adaptive walks of a virulent phage (Tequintavirus) in a spatially variable environment composed of four susceptible bacterial isolates and four resistant ones (Salmonella enterica serotype Tennessee, sequence types ST5018 and ST319 respectively). Starting from a single ancestral phage, we evolved multiple independent populations through serial passages on non-coevolving bacteria, following the Appelmans protocol. The phage populations evolved an expanded host range and increased virulence. Whole-genome sequencing revealed recurrent parallel mutations across populations (i.e. convergent evolution), particularly in genes encoding exo- and endo-nucleases, dUTPase, and caudal proteins. Notably, two parallel mutations in the gene coding for the Long Tail Fibre became fixed early in the evolutionary trajectories. Reverse-genetics experiments introducing these mutations into the ancestral genome expanded the host range but yielded only marginal increases in virulence, highlighting the effect of compensatory mutations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/584857v3_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@cec6b5org.highwire.dtl.DTLVardef@1579ba4org.highwire.dtl.DTLVardef@ab5ad5org.highwire.dtl.DTLVardef@1d88160_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights* A phage (Tequintavirus) was evolved on susceptible and resistant Salmonella enterica strains * Experimentally evolved phage populations displayed expanded host range and increased virulence * Convergent evolution revealed adaptive mutations modifying receptor recognition in caudal proteins * Reverse-genetic showed implication of two Long Tail Fibre mutations in host range expansion In BriefGeneralism is traditionally predicted to evolve at the cost of lower mean fitness. Contrary to this textbook view, we demonstrate that generalist phages with expanded host range and increased virulence can readily evolve in vitro and be purposely optimized for phage therapy applications.

evolutionary biology↗

bioRxiv2022

The non-neutral, multi-level, phenotypic impact of synonymous mutations revealed through heterologous gene expression in human cells.

Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels, with an emphasis on translation elongation. Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analysed by means of: quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single-cell level expression; and real-time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness. We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA levels and in protein levels, leading to differences of over fifteen times in translation efficiency; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade-off between the benefit of antibiotic resistance and the burden of heterologous expression. In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes. IMPORTANCESynonymous codons encode for the same amino acid, but they are not neutral regarding gene expression or protein synthesis. Bias between synonymous codons have evolved naturally and are also applied in biotechnology protein production. We have studied the multilevel impact of codon usage on a human cell system. We show that differences in codon usage lead to transcriptomic, proteomic and functional changes, modulating gene expression and cellular phenotype.

systems biology↗

bioRxiv2021

Human cellular homeostasis buffers trans-acting translational effects of heterologous gene expression with very different codon usage bias

The frequency of synonymous codons in protein coding genes is non-random and varies both between species and between genes within species. Whether this codon usage bias (CUBias) reflects underlying neutral mutational processes or is instead shaped by selection remains an open debate, especially regarding the role of selection for enhanced protein production. Variation in CUBias of a gene (be it natural synonymous mutations or biotechnological synonymous recoding) can have an enormous impact on its expression by diverse cis-acting mechanisms. But expression of genes with extreme CUBias can also lead to strong phenotypic effects by altering the overall intracellular translation homeostasis via competition for ribosomal machinery or tRNA depletion. In this study, we expressed at high levels in human cells six different synonymous versions of a gene and used matched transcriptomic and proteomic data to evaluate the impact of CUBias of the heterologous gene on the translation of cellular transcripts. Our experimental design focused specifically on differences during translation elongation. Response to expression of the different synonymous sequences was assessed by various approaches, ranging from analyses performed on a per-gene basis to more integrated approaches of the cell as a whole. We observe that the transcriptome displayed substantial changes as a result of heterologous gene expression by triggering an intense antiviral and inflammatory response, but that changes in the proteomes were very modest. Most importantly we notice that changes in translation efficiency of cellular transcripts were not associated with the direction of the CUBias of the heterologous sequences, thereby providing only limited support for trans-acting effects of synonymous changes. We interpret that, in human cells in culture, changes in CUBias can lead to important cis-acting effects in gene expression, but that cellular homeostasis can buffer the phenotypic impact of overexpression of heterologous genes with extreme CUBias.

cell biology↗

bioRxiv2021

Variability in codon usage in Coronaviruses is mainly driven by mutational bias and selective constraints on CpG dinucleotide

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third virus within the Orthocoronavirinae causing an emergent infectious disease in humans, the ongoing coronavirus disease 2019 pandemic (COVID-19). Due to the high zoonotic potential of these viruses, it is critical to unravel their evolutionary history of host species shift, adaptation and emergence. Only such knowledge can guide virus discovery, surveillance and research efforts to identify viruses posing a pandemic risk in humans. We present a comprehensive analysis of the composition and codon usage bias of the 82 Orthocoronavirinae members, infecting 47 different avian and mammalian hosts. Our results clearly establish that synonymous codon usage varies widely among viruses and is only weakly dependent on the type of host they infect. Instead, we identify mutational bias towards AT-enrichment and selection against CpG dinucleotides as the main factors responsible of the codon usage bias variation. Further insight on the mutational equilibrium within Orthocoronavirinae revealed that most coronavirus genomes are close to their neutral equilibrium, the exception is the three recently-infecting human coronaviruses, which lie further away from the mutational equilibrium than their endemic human coronavirus counterparts. Finally, our results suggest that while replicating in humans SARS-CoV-2 is slowly becoming AT-richer, likely until attaining a new mutational equilibrium.

evolutionary biology↗

bioRxiv2020

Ecological opportunity as a driving force of radiation events and time-dependent evolutionary rates in papillomaviruses

Papillomaviruses (PVs) have a wide host range, infecting mammals, birds, turtles, and snakes. The recent discovery of PVs in different fish species allows for a more complete reconstruction of the evolutionary history of this viral family. In this study we perform phylogenetic dating to analyse evolutionary events that occurred during PV evolution, as well as to estimate speciation and evolutionary rates. We have used four different data sets to explore and correct for potential biases that particular taxa combinations may introduce during molecular time inference. When considering the evolution of substitution rates we observed that short-term rate estimates are much higher than long-term rate estimates, also known as the time-dependent rate phenomenon. When considering the evolution of viral branching events (as a proxy for speciation rates), we show that these have not been constant through time, suggesting the occurrence of distinct evolutionary events such as adaptive radiations and/or changes in the available host niches. In a joint analysis with host speciation rates, we identified at least four different evolutionary periods, suggesting that the evolution of PVs has been multiphasic, and thus refining the previously suggested biphasic evolutionary scenario. Thanks to the discovery of novel PVs in basal hosts and to the implementation of a time-dependent rate model for molecular dating, our results provide new insights into the evolutionary history of PVs. In this updated evolutionary scenario, ecological opportunity appears as one main driving force for the different radiation and key-innovation events we observe.

evolutionary biology↗

bioRxiv2020

Loop 1 of APOBEC3C regulates its antiviral activity against HIV-1

APOBEC3 deaminases (A3s) provide mammals with an anti-retroviral barrier by catalyzing dC-to-dU deamination on viral ssDNA. Within primates, A3s have evolved diversely via gene duplications and fusions. Human APOBEC3C (hA3C) efficiently restricts the replication of viral infectivity factor (vif)-deficient Simian immunodeficiency virus (SIV{Delta}vif), but for unknown reasons, it inhibits HIV-1{Delta}vif weakly. In catarrhines (Old World monkeys and apes), the A3C loop 1 displays the conserved amino acid pair WE, while the corresponding consensus sequence in A3F and A3D is the largely divergent pair RK, which is also the inferred ancestral sequence for the last common ancestor of A3C|D|F in primates. Here, we report that modifying the WE residues in hA3C loop 1 to RK leads to stronger interactions with ssDNA substrate, facilitating catalytic function, which resulted in a drastic increase in both deamination activity and the ability to restrict HIV-1 and LINE-1 replication. Conversely, the modification hA3F_WE resulted only in a marginal decrease in HIV-1{Delta}vif inhibition. The two series of ancestral gene duplications that generated A3C, A3D-CTD and A3F-CTD allowed neo/subfunctionalization: A3F-CTD maintained the ancestral RK residues in loop 1, while strong evolutionary pressure selected for the RK[->]WE modification in catarrhines A3C, possibly allowing for novel substrate specificity and function. AUTHOR SUMMARYThe restriction factors of the APOBEC3 (A3) family of cytidine deaminases inhibit the replication of Vif-deficient retroviruses mainly by mutating their viral genomes. While there are seven A3 proteins (A3A-A3H) found in humans only A3G and A3F potently inhibit HIV-1 replication. A3C in general and its retroviral restriction capacity have not been widely studied probably due to its weak anti-HIV-1 activity, however, it displays a strong antiviral effect against SIV. Understanding the role of A3C is important because it is highly expressed in CD4+ T cells, is upregulated upon HIV-1 infection, and is distributed cell-wide. In this study, we report that replacing two residues in loop 1 of A3C protein with conserved positively-charged amino acids enhance the substrate DNA binding, which markedly facilitates its deamination-dependent antiviral activity against HIV-1 as well as increasing the restriction of LINE-1 retroelements. Furthermore, our evolutionary analysis demonstrates that the pressure that caused the loss of potential loop 1 residues occurred only in A3C but not in primate homologues. Overall, our study highlights the possibility of A3C acting as a super restriction factor, however, this was likely evolutionarily selected against to achieve a balance between anti-viral/anti-LINE-1 activity and genotoxicity.

microbiology↗

bioRxiv2019

COUSIN (COdon Usage Similarity INdex): a normalized index of Codon Usage Preferences.

Codon Usage Preferences (CUPrefs) describe the unequal usage of synonymous codons at the gene, genomic region or genome scale. Numerous indices have been developed to measure the CUPrefs of a sequence. We introduce a normalized index to calculate CUPrefs called COUSIN for COdon Usage Similarity INdex. This index compares the CUPrefs of a query against those of a reference dataset and normalizes the output over a Null Hypothesis of random codon usage. COUSIN results can be easily interpreted, quantitatively and qualitatively. We exemplify the use of COUSIN and highlight its advantages with an analysis on the complete coding sequences of eight divergent genomes, two of them with extreme nucleotide composition. Strikingly, COUSIN captures a hitherto unreported bimodal distribution in CUPrefs in genes in the human and in the chicken genomes. We show that this bimodality can be explained by the global nucleotide composition bias of the chromosome in which the gene resides, and by the precise location within the chromosome. Our results highlight the power of the COUSIN index and uncover unexpected characteristics of the CUPrefs in human and chicken. An eponymous tool written in python3 to calculate COUSIN is available for online or local use.

bioinformatics↗

bioRxiv2017

Macroecology suggests cancer-causing papillomaviruses form non-neutral communities

Chronic infection by oncogenic Human papillomaviruses (HPVs) leads to cancers. Public health interventions, such as cancer screening and mass vaccination, radically change the ecological conditions encountered by circulating viruses. It is currently unclear how HPVs communities may respond to these environmental changes, because little is known about their ecology. Predicting the impact on viral diversity by the introduction of HPV vaccines requires answering the unresolved question of how HPVs interact. Although it is commonly believed that they do not interact (neutral theory), there are suggestions that HPV types may compete for resources or via the immune response (niche-based or non-neutral theory). Here, we applied for the first time established biodiversity measures and methods to epidemiological data in order to assess whether niche-partitioning or neutral processes are shaping HPV diversity patterns at the population level. We find that as infections progress toward cancer, HPVs communities become more uneven and a few HPVs play a stronger dominance role. By fitting species abundance distributions, we found that neutral models were always out-performed by non-neutral distributions, both in asymptomatic infections and in cancers. Our results suggest that temporally moving from a more even to a less even community implies an increase in competition, probably due to environmental changes linked to infection progression. More ecological thinking will be required to understand present-day interactions and to anticipate the future of the long lasting interactions between HPVs and humans.\n\nSIGNIFICANCE STATEMENTHuman papillomaviruses (HPVs) are very diverse. Infections by HPVs are very common and chronic infections may lead to cancers. The more oncogenic HPVs are now targetted by effective vaccines, and this has raised the question of whether there may be a viral replacement if these dominant types were removed. This is a medical version of a classical ecological controversy, namely how much biodiversity distributions and community dynamics are explained by neutral theory plays out across ecosystems. For HPVs, epidemiologic studies before and after the vaccination have led to the widespread belief that these viruses do not interact. Here, we apply different methods developed in macroecology to the best available epidemiologic data to address this issue. Consistently, we find that HPVs form non-neutral communities. Instead, competitive niche-partitioning process and dominance explain best HPVs communities. We also find that the vaccine might not change such competitive niche processes. Beyond clinical implications, this garners support that niche processes often best explain biodiversity patterns, even in human viral communities.

ecology↗

bioRxiv2017

The underestimated importance of acute infections by human papillomaviruses

Most infections by human papillomaviruses (HPVs) are acute, that is non-persistent. Yet, for HPVs, as for many other oncoviruses, there is a striking gap between our detailed understanding of chronic infections and our limited data on the early stages of infection. Here we argue that studying HPV acute infections is necessary and timely. Focusing on early interactions will help explain why certain infections are cleared while others become chronic or latent. From a molecular perspective, descriptions of immune effectors and pro-inflammatory pathways during the initial stages of infections have the potential to lead to novel treatments or to improved handling algorithms. From a dynamical perspective, adopting concepts from spatial ecology, such as meta-populations or meta-communities, can help explain why HPV acute infections sometimes last for years. Furthermore, cervical cancer screening and vaccines impose novel iatrogenic pressures on HPVs, implying that anticipating any viral evolutionary response remain essential. Finally, hints at the associations between HPV acute infections and fertility deserve further investigation given their high worldwide prevalence. Overall, understanding asymptomatic and benign infections may be instrumental in reducing HPV virulence.

epidemiology↗