Biology subjects

Arevalo, P.

Publications and source records attributed to Arevalo, P..

4 recordsLinked to original sources

bioRxiv2026

HepI and OpsX are functionally coupled but evolutionarily asymmetric heptosyltransferase variants: ecological transitions and operon modularization drive divergent constraints and flexibility

Lipopolysaccharide (LPS) inner-core biosynthesis is classically initiated by a heptosyltransferase enzyme most commonly Heptosyltranferase I (HepI), a conserved WaaC-like enzyme. An alternative heptosyltranferase variant, OpsX, occurs alone in a subset of Gram-negative bacteria and co-exist with WaaC-like enzyme within the same genome of other organisms, raising questions about the origin of these two vairants and their functional partitioning. Here, we present a comparative evolutionary analysis of HepI (K02841) and OpsX (K12982) across Gram-negative bacteria to resolve their functional coupling and divergence. Selection analyses reveal a consistent evolutionary asymmetry, with OpsX exhibiting elevated {omega} values relative to HepI across global datasets and within genomes encoding both systems. Residue-level analyses indicate conserved catalytic cores in both enzymes, but a broader distribution of relaxed constraints in OpsX, suggesting differential partitioning of functional pressure. HepI has undergone intensified purifying selection in host-associated lineages, whereas OpsX shows no corresponding shift, indicating distinct responses to ecological context. Gene-species tree reconciliation further reveals contrasting horizontal gene transfer (HGT) architectures: HepI displays an ecologically structured network enriched in pathogen- and opportunist-associated lineages, with recurrent hub-mediated exchanges and deeper lineage-integrated events, whereas OpsX exhibits a diffuse transfer regime dominated by non-pathogenic taxa and primarily recent terminal acquisitions. These differences persist in genomes co-encoding both systems, where HepI transfer signal remains strongly associated with lifestyle, while OpsX is largely uncoupled from ecological structure. Analysis of operon architecture reveals pathway partitioning between the two genes: HepI is embedded in a conserved downstream operon linked to glycosyltransferase-mediated core assembly, whereas OpsX occurs in a more variable context enriched for upstream ADP-heptose precursor biosynthesis genes. In dual-system genomes, HepI is reduced to a minimal downstream module while OpsX retains upstream functions, indicating coordinated operon modularization. Together, HepI and OpsX form a functionally coupled but evolutionarily asymmetric system shaped by ecological transitions and genomic reorganization. HighlightsO_LIHepI and OpsX represent functionally coupled but evolutionarily asymmetric LPS inner-core biosynthesis systems across Gram-negative bacteria. C_LIO_LIOpsX shows relaxed selective constraint and a diffuse horizontal gene transfer pattern, whereas HepI is under stronger purifying selection and ecologically structured transfer. C_LIO_LIOperon organization reveals pathway modularization, with HepI embedded in conserved downstream assembly modules and OpsX retaining upstream precursor-associated flexibility. C_LI

evolutionary biology↗

bioRxiv2024

Structural Adaptations of HepI Enzymes in Proteobacteria: Insights into Evolutionary Resilience and Functional Dynamics

Since lipopolysaccharide molecules are highly variable in their structure while also being essential for bacterial cell survival, we hypothesized that enzymes involved in its biosynthesis may exhibit differences that could be used to predict the likelihood of survival in different ecological niches. We examined the sequence variability of orthologues of Heptosyltransferase I (HepI), which is found in all lipopolysaccharide (LPS) containing Gram-negative bacteria. We identified two different sequence motifs within the N-terminal domain of HepI, which correlated with differences in the Lipid A portion of the LPS. Further, we compared the protein structure of HepI from Escherichia coli with a structural model we generated that incorporated the alternate sequence motif. Molecular dynamics simulations of these two proteins, recapitulated our findings, that proteins with the E. coli-like sequence motif maintained a larger enzyme active site, while the mutated structural model undergoes rearrangements that lead to a smaller N-terminal active site pocket. This work revealed sequence-structure-function relationships that can be used to determine if a species incorporates a Heptose residue onto Lipid A chains containing one or two 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) residues. Since research suggests that the number of Kdo residues in LPS impacts the overall immune response to the LPS endotoxin, this work could aid in our understanding of the pathogenic effects of human-bacterial interactions. Understanding the sequence-structural adaptations of HepI enzymes across proteobacteria sheds light on their evolutionary resilience and functional versatility. HighlightsO_LILipopolysaccharide (LPS) structure varies between organisms C_LIO_LIHeptosytransferase I sequence motifs allow prediction of LPS structural features C_LIO_LIAdaptations of HepI enzymes reveal evolutionary resilience and functional versatility C_LI

evolutionary biology↗

bioRxiv2021

Rapid evolutionary turnover of mobile genetic elements drives microbial resistance to viruses

Although it is generally accepted that viruses (phages) drive bacterial evolution, how these dynamics play out in the wild remains poorly understood. Here we show that the arms race between phages and their hosts is mediated by large and highly diverse mobile genetic elements. These phage-defense elements display exceedingly fast evolutionary turnover, resulting in differential phage susceptibility among clonal bacterial strains while phage receptors remain invariant. Protection afforded by multiple elements is cumulative, and a single bacterial genome can harbor as many as 18 putative phage-defense elements. Overall, elements account for 90% of the flexible genome amongst closely related strains. The rapid turnover of these elements demonstrates that phage resistance is unlinked from other genomic features and that resistance to phage therapy might be as easily acquired as antibiotic resistance.

microbiology↗

bioRxiv2019

Sympatric and allopatric differentiation delineate population structure in a free-living terrestrial bacterium

In free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several barriers to the study of the processes contributing to microbial diversification. As such, microorganisms are often operationally defined using conserved marker genes (i.e., 16S rRNA gene) or whole-genome measurements (i.e., ANI) to interpret intra-specific processes. However, as in eukaryotes, investigations into microbial populations must consider the potential for interacting genotypes among individuals that are subjected to similar environmental selective pressures. Therefore, we isolated 26 strains within a single bacterial ecotype (equivalent to a eukaryotic species definition) from a common habitat (leaf litter) across a regional climate gradient and asked whether the genetic diversity in a free-living soil bacterium (Curtobacterium) was consistent with patterns of allopatric or sympatric differentiation. By examining patterns of gene flow, our results indicate that microbial populations are delineated by gene flow discontinuities and exhibit evidence for population-specific adaptation. We conclude that the genetic structure within this bacterium is due to both adaptation within localized microenvironments (isolation-by-environment) as well as dispersal limitation between geographic locations (isolation-by-distance).

evolutionary biology↗