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Biology subjects

Martinson, J. N. V.

Publications and source records attributed to Martinson, J. N. V..

5 recordsLinked to original sources

Adaptive benefits of motility in cross-feeding mutualisms

Cross-feeding mutualisms, in which partner species exchange essential metabolites, are ubiquitous in microbial communities. In spatially structured environments, motility can improve access to partner-produced resources but also impose metabolic costs and displace cells from nutrient-rich regions, so its net benefit depends on the spatial dynamics of the interaction. Here, we combine competition experiments in a cross-feeding mutualism between Escherichia coli and Salmonella enterica with a spatially explicit consumer-resource model to determine what drives selection on motility. Spatial structure imposes asymmetric selection between partners i.e. S. enterica benefits from motility regardless of partner motility, whereas selection on E. coli switches from favourable to unfavourable depending on whether its partner can move. Competition in well-mixed culture suggests that this reversal reflects the loss of a spatial benefit rather than an increased cost. Our model attributes the asymmetry to three interacting factors: the ratio of metabolite production to consumption which sets whether the cross-fed resource is scarce or abundant; the number of growth-limiting resources which determines whether an alternative gradient can rescue the benefit of motility; and partner motility and growth rate, which shape where metabolites are produced. When a metabolite is scarce, motile cells gain by dispersing into regions it has reached but not yet been depleted from. When it accumulates, this gradient is eroded, and the motility costs offset any benefit it provides. Selection on motility therefore depends on the metabolic structure of the interaction and the spatial behaviour of partners.

ecology↗

Plasmids weaponize conjugation to eliminate non-permissive recipients

Horizontal gene transfer via conjugative plasmids is a major driver of bacterial evolution. While antibiotic exposure selects for the resistance genes carried by some plasmids, much uncertainty remains in how plasmids persist and spread in microbial communities in the absence of such external selection. Here we show that conjugative plasmids drive their own spread, in part, by using their transfer machinery to enforce a join-or-die ultimatum that selectively eliminates non-permissive recipients through the process of lethal zygosis - the T4SS-mediated elimination of recipients that fail to establish the plasmid. We found that this contact-dependent killing effectively clears a competitive niche for plasmid donors by turning bacterial immune systems into a fatal liability. Specifically, cells resisting plasmid establishment via CRISPR-Cas or Restriction-Modification systems are selectively killed because they fail to acquire the protective exclusion genes encoded on the plasmid, leading to lethal unregulated transfer. We leveraged this insight to resolve an obstacle in bacterial editing by developing "shielded" transposon vectors that co-deliver exclusion genes, increasing the efficiency of gene editing by orders of magnitude. Our results reveal the role of "coercive assimilation" in horizontal gene transfer, exposing a trade-off where the advantage of bacterial immunity to foreign DNA is counterbalanced by lethal zygosis.

microbiology↗

Generating functional plasmid origins with OriGen

While generative artificial intelligence (AI) has shown promise for biological design, no computational system has yet created and validated sequences capable of autonomous replication. Focusing on plasmids, one of the smallest types of replicating elements, we develop OriGen, a sequence model that generates new plasmid origins of replication while maintaining key elements essential for their replication. We experimentally validate OriGens ability to create functional origins that diverge from existing wild types, demonstrating the models capacity to capture the complex and often cryptic mechanisms of biological replication.

synthetic biology↗

Identification of Proteins Influencing CRISPR-Associated Transposases for Enhanced Genome Editing

CRISPR-Associated Transposases (CASTs) hold tremendous potential for microbial genome editing due to their ability to integrate large DNA cargos in a programmable and site-specific manner. However, the widespread application of CASTs has been hindered by their low efficiency in diverse, non-model bacteria. In an effort to address this shortcoming, we conducted the first genome-wide screen for host factors impacting Vibrio cholerae CAST (VchCAST) activity and used the findings to increase VchCAST editing efficiency. A genome-wide loss-of-function mutant library in E. coli was screened to identify 15 genes that impact type VchCAST transposition. Of these, seven factors were validated to improve VchCAST activity and two were found to be inhibitory. Informed by homologous recombination involved effectors, RecD and RecA, we tested the {lambda}-Red recombineering system in our VchCAST editing vectors, which increased its insertion meditated-editing efficiency by 25.7-fold in E. coli while maintaining high target specificity and similar insertion arrangements. Furthermore, {lambda}-Red-enhanced VchCAST achieved increased editing efficiency in the industrially important bacteria Pseudomonas putida and the emerging pathogen Klebsiella michiganensis. This study improves understanding of factors impacting VchCAST activity and enhances its efficiency as a bacterial genome editor. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/612086v2_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@12609e5org.highwire.dtl.DTLVardef@53a128org.highwire.dtl.DTLVardef@794e63org.highwire.dtl.DTLVardef@9835f_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Mutualism reduces the severity of gene disruptions in predictable ways across microbial communities.

Predicting evolution in microbial communities is critical for problems from human health to global nutrient cycling. Understanding how species interactions impact the distribution of fitness effects for a focal population would enhance our ability to predict evolution. Specifically, it would be useful to know if the type of ecological interaction, such as mutualism or competition, changes the average effect of a mutation (i.e., the mean of the distribution of fitness effects). Furthermore, how often does increasing community complexity alter the impact of species interactions on mutant fitness? To address these questions, we created a transposon mutant library in Salmonella enterica and measured the fitness of loss of function mutations in 3,550 genes when grown alone versus competitive co-culture or mutualistic co-culture with Escherichia coli and Methylorubrum extorquens. We found that mutualism reduces the average impact of mutations, while competition had no effect. Additionally, mutant fitness in the 3-species communities can be predicted by averaging the fitness in each 2-species community. Finally, the fitness effects of several knockouts in the mutualistic communities were surprising. We discovered that S. enterica is obtaining a different source of carbon and more vitamins and amino acids than we had expected. Our results suggest that species interactions can predictably impact fitness effect distributions, in turn suggesting that evolution may ultimately be predictable in multi-species communities.

microbiology↗