Biology subjects

Mehmetoglu Boz, E.

Publications and source records attributed to Mehmetoglu Boz, E..

2 recordsLinked to original sources

bioRxiv2026

Programmed strain tagging and gene disruption throughout a diverse bacterial genus

Transposons are a convenient vehicle for inserting DNA into a bacterial genome, but widely-used transposons such as Tn7, Tn5, and Mariner do not hit custom targets. Recently, CRISPR-associated transposons (CASTs) have been developed as tools to direct the insertion of a transposon to a chosen site with a short guide sequence. We adapted this system for use in the widespread plant-associated genus Sphingomonas, uniquely tagging genetically diverse strains in several different sites, and we demonstrate the utility of the tags for quantitative strain tracking in complex bacterial populations. Although we initially targeted the conserved site into which Tn7 integrates as a benign transposition location, a genomics search revealed insertions at this site would frequently disrupt genes not only in Sphingomonas but also in widely studied Pseudomonas. Therefore we identified improved genus-wide conserved sites between convergently terminating genes as alternatives. We experimentally validated an improved neutral site in Sphingomonas, and then targeted this site in a heterogeneous uncharacterized Sphingomonas population. Using a tagIM seq, a novel rapid transposon mapping method introduced here, we screened resulting transformant colonies for off-target transposon insertions. This enabled prioritization of correctly tagged novel strains, accelerating the creation of fully tagged synthetic communities for the high-throughput study of fine-scale bacterial natural variation.

microbiology↗

bioRxiv2024

Field conditions greatly modify a major growth-defense tradeoff in Arabidopsis thaliana

When plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off in the plant Arabidopsis thaliana is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild plant populations maintain significant functional variation in the ACD6 gene, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet are of smaller stature, their leaves senesce earlier, and they set fewer seeds. We hypothesized that such hyperactive alleles would not only affect the growth of microbial pathogens, but also more generally leaf microbiome assembly in the wild. To test this, we grew plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both in climate-controlled conditions and outdoors. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. To our surprise, we discovered that mature field plants, in stark contrast to greenhouse plants, were unaffected by their ACD6 genotype, suggesting that additional abiotic and/or microbial signals present outdoors - but not in the greenhouse - greatly modulate ACD6 activity.

plant biology↗