Research

Molecular barriers to functional integration of horizontally transferred genes

With the ever increasing number of fully sequenced prokaryotic genomes, there is a growing appreciation that adaptive evolution in prokaryotes is largely driven by horizontal gene transfer (HGT). HGT produces extremely dynamic bacterial genomes in which substantial amounts of DNA from distantly related organisms flow into and from the chromosome, thus effectively shaping the ecological and pathogenic character of bacterial species. Whilst the genetic mechanisms responsible for the horizontal acquisition of foreign genes (i.e., transformation of naked DNA, conjugation, and viral transduction) are well characterized, the molecular barriers to the integration of new genes within the cellular environment and networks of the recipient organism remain largely unexplored.

We aim at elucidating the molecular and systems-level mechanisms that control the accommodation of the horizontally transferred proteins, including the interaction with protein homeostasis machinery and the integration within transcriptional, metabolic and protein-protein interaction networks.

We are particularly interested in the horizontal transfer of genes involved in folate transport and metabolism. We generate and study collections of strains carrying the horizontally transferred genes using bioinformatics, microbial genetics, in vitro biophysical and biochemical molecular characterization, systems-level analysis, and high-throughput experimental evolution.

Dynamics and mechanisms of adaptive evolution facilitated by horizontal gene transfer

Microbial communities, such as gut, oral, and soil microbiomes exhibit many types of complex interaction allowing to colonize and rapidly respond to changes in the environment in which they live. One of the central components of these interactions is the transfer and horizontal acquisition of DNA within this environment from co-resident (but phylogenetically distant) bacterial species, or from exogenous sources. Such an adaptive mechanism is markedly different from an adaptive evolution fueled by point mutations. Indeed, unlike random point mutations that diversify the existing genes, horizontally transferred genes are already products of a purifying selection and, as such, they carry sequence and molecular characteristics that reflect the evolutionary history and physical and cellular properties of the original donor organisms. Collectively, these features shape the trajectories of the adaptive evolution that follows HGT.

We aim (i) to establish the link between the molecular traits of the horizontally acquired proteins and fitness landscape of the recipient organisms; (ii) to determine the role of epistasis and pleiotropy in the evolutionary outcomes of HGT; and (iii) to characterize how the strength and timing of the selection pressure govern the rate and dynamics of the evolutionary trajectories that follow HGT events.

Understanding the dynamics and mechanisms of evolution requires establishing the essential link between the fitness of an organism and the underlying biophysical principles, as well as having an access to the intermediate evolutionary forms co-existing at a population level. In practical terms, it means that the data generated by high-throughput experimental evolution techniques are analyzed at molecular-, cellular-, and population-levels, and quantitative description encompassing the different scales is established. We apply this comprehensive strategy to study the adaptive evolution facilitated by horizontal gene transfer in bacteria. Specifically, we mimic horizontal transfer of genes involved in folate transport and metabolism, and subject the resulting strains to selection in the presence of antifolate compounds.

Co-evolution of protein quality control and proteomes and its role in bacterial speciation

The protein quality control (PQC) constitutes a network of molecular chaperones that maintains the integrity of the proteome through assisted folding or degradation of proteins. While the role of molecular chaperones in sustaining protein homeostasis and buffering fitness effects of deleterious mutations is widely accepted, the dynamics of co-evolution of chaperones and their proteomes remains largely unexplored. Understanding this process is especially important in the context of microbial evolution. Indeed, molecular chaperones can play a central role in mediating the physical accommodation of the newly acquired proteins within the hosting proteome and influence the dynamics of the evolutionary processes that follow HGT events. Furthermore, it remains largely unexplored whether the PQC-client specificity could lead to the emergence of cross-species barriers in bacteria.

We aim at characterizing the molecular mechanisms (thermodynamic/kinetic folding characteristics and specific recognition sequences) that govern the evolution of specific interactions between PQC and clients proteins, and how this evolved specificity affects the HGT-associated fitness effects and adaptive evolution.

We are particularly interested in the co-evolution of proteomes and GroEL/ES chaperonins and ATP-dependent Lon protease.

Novel protein-protein interactions as a driving force of phenotypic evolution

Since most globular proteins are only marginally stable, randomly accumulating destabilizing mutations are expected to promote their misfolding and aggregation, and, unless purged from a population, eventually lead to a reduction in organismal fitness. Yet, there is an increasing body of evidence that suggests that proteins that have acquired destabilizing mutations can nonetheless “escape” the misfoling/aggregation fate by forming a higher order soluble and functional oligomers via self-association (homomers) or by interacting with other cellular proteins that share similar structural motifs (heteromers). Oligomerization can provide the needed thermodynamic and/or kinetic stabilization to the affected proteins and open new evolutionary trajectories to neo-functionalization and regulation at a level of a single protein and at a systems-level through rewiring of protein-protein interaction and regulatory networks. Thus, by triggering homo- and hetero-oligomerization, destabilizing mutations can function as evolutionary capacitors.

We aim (i) to determine the extent of the “escape” response of proteins to destabilizing mutations based on homo- and hetero-oligomerization at a global proteome level; (ii) to characterize the biophysical and structural mechanisms of the oligomerization events; and (iii) to determine the evolutionary potential (neo-functionalization, allosteric regulation, network interaction/regulation) of the newly formed oligomers by experimental and directed evolution;