Biology subjects

Xu, Y. C.

Publications and source records attributed to Xu, Y. C..

2 recordsLinked to original sources

bioRxiv2026

HMCES DNA-protein cross-links promote template slippage during DNA replication

During replication, nucleolytic processing of apurinic/apyrimidinic (AP) sites in single-stranded (ss)DNA is attenuated by the evolutionarily conserved 5-hydroxymethylcytosine binding, embryonic-specific (HMCES) protein. HMCES forms a covalent thiazolidine linkage with the ring-opened aldehyde form of a ssDNA AP site to stabilize the AP site and suppress the formation of DNA double-strand breaks. The resulting HMCES DNA-protein cross-link (DPC) can then be digested by the SPRTN protease and bypassed through mutagenic translesion synthesis (TLS). Here, we use Xenopus egg extracts and molecular dynamics simulations to investigate how HMCES-DPC formation influences the mutagenicity of AP site bypass. We show that SPRTN processes the HMCES-DPC to a five amino acid peptide adduct prior to TLS. Surprisingly, the mutagenicity of HMCES-DPC bypass is insensitive to the extent of DPC proteolysis and depends only on cross-link formation, which traps the AP site in a more dynamic ring-opened configuration. We further show that the spectrum of mutations produced during bypass of HMCES-adducts strongly depends on the template strand nucleotide immediately 5 of the AP site. Our data support a model in which HMCES-DPC formation increases the conformational flexibility of the DNA template, allowing template slippage and use of the 5 template nucleotide to direct insertion opposite the adducted AP site.

biochemistry↗

bioRxiv2021

Introduction of probiotic bacterial consortia promotes plant growth via impacts on the resident rhizosphere microbiome

Plant growth depends on a range of functions provided by their associated rhizosphere microbiome, including nutrient mineralization, hormone co-regulation and pathogen suppression. Improving the ability of plant associated microbiome to deliver these functions is thus important for developing robust and sustainable crop production. However, it is yet unclear how beneficial effects of probiotic microbial inoculants can be optimised and how they are mediated. Here, we sought to enhance the tomato plant growth by targeted introduction of probiotic bacterial consortia consisting of up to eight plant-associated Pseudomonas strains. We found that the effect of probiotic consortium inoculation was richness-dependent: consortia that contained more Pseudomonas strains, reached higher densities in the tomato rhizosphere and had clearer beneficial effects on multiple plant growth characteristics. Crucially, these effects were best explained by changes in the resident community diversity, composition and increase in the relative abundance of initially rare taxa, instead of introduction of plant-beneficial traits into the existing community along with probiotic consortia. Together, our results suggest that beneficial effects of microbial introductions can be driven indirectly through effects on the diversity and composition of resident plant rhizosphere microbiome.

ecology↗