Biology subjects

Krasileva, K.

Publications and source records attributed to Krasileva, K..

4 recordsLinked to original sources

bioRxiv2022

Pseudomonas isolates from ponds populated with duckweed prevent disease caused by pathogenic Pseudomonas species

Duckweeds are notoriously invasive plants. They are successful in inhabiting diverse environments, despite their lack of conventional immune pathways that are essential for disease resistance in other plant species. It is unclear how duckweeds thrive in the absence of these immune pathways. In this study, we investigated the effect of bacteria from duckweeds natural habitat on disease progression utilizing the duckweed-Pseudomonas pathosystem. Through nanopore sequencing of 16S and ITS rDNA amplicons we identified duckweed-associated bacterial and fungal genera present at three environmental sites. The pond filtrate from one of the three environmental locations primed duckweeds pathogen defenses leading to a reduction in disease symptoms. Furthermore, we were able to identify bacterial isolates from the filtrate that protect duckweed from disease symptoms upon Pseudomonas pathogen inoculation. The isolated protective bacteria belong to the Pseudomonas genus, and we demonstrated antagonistic interactions between the pathogen and beneficial strains in vitro and in vivo. The ability of our environmental isolates to protect against Pseudomonas pathogens appears to be plant/species specific as environmental strains showed no protective effect against Pseudomonas pathogens in Arabidopsis assays. Genome sequencing of the beneficial Pseudomonas strains showed the presence of several genes involved in bacterial competition. We have thus demonstrated that Pseudomonas species from duckweeds natural habitat can successfully antagonize other plant pathogens.

plant biology↗

bioRxiv2022

Comparative computational structural genomics highlights divergent evolution of fungal effectors

Elucidating the evolution of pathogen effector molecules is critical to understand infection mechanisms of fungal phytopathogens and ensure crop security. However, rapid diversification that diminishes sequence similarities between homologous effectors has largely concealed the roots of effector evolution. We predicted the folds of 26,653 secreted proteins from 21 species with AlphaFold and performed structure-guided comparative analyses on two aspects of effector evolution: uniquely expanded effector families and common folds present across the fungal species. Extreme expansion of nearly lineage-specific effector families was found only in several obligate biotrophs, Blumeria graminis and Puccinia graminis. The highly expanded effector families were the source of conserved sequence motifs, such as the Y/F/WxC motif. We identified additional lineage-specific effector families that include known (a)virulence factors, such as AvrSr35, AvrSr50 and Tin2. These families represented new classes of sequence-unrelated structurally similar effectors. Structural comparisons revealed that the expanded structural folds further diversify through domain duplications and fusion with disordered stretches. Sub-and neo-functionalized structurally similar effectors reconverge on regulation, expanding the functional pools of effectors in the pathogen infection cycle. We also found evidence that many effector families could have originated from ancestral folds that have been conserved across fungi. Collectively, our study highlights diverse mechanisms of effector evolution and supports divergent evolution of effectors that leads to emergence of pathogen virulence from ancestral proteins.

microbiology↗

bioRxiv2022

Engineering of Sr33 and Sr50 plant immune receptors to alter recognition specificity and autoactivity

Plants possess cytoplasmic immune receptors called nucleotide-binding leucine-rich repeat receptors (NLRs) that recognize the presence of a pathogen through a range of mechanisms: direct binding of effectors or indirect recognition of effector actions. The direct binding of effectors has been shown to be mediated through the NLRs leucine-rich repeat (LRR) domain. Accurate prediction of amino acids involved in these direct interactions can greatly enhance understanding of effector recognition and inform efforts to engineer new resistance. In this study, we utilized two homologous NLR resistance genes from wheat, Sr33 and Sr50, that recognize distinct effectors by directly binding to them through their LRR domain. While the effector recognized by Sr50 is known and described as AvrSr50, the effector recognized by Sr33 remains unknown. Through a combination of phylogenetics, allele diversity analysis in the LRR and structural modeling, we identified the amino acids in Sr50 likely to physically interact with its effector. Mutation of these sites helped identify 12 amino acids we hypothesized to be sufficient to mediate effector binding in Sr50. Changing these 12 corresponding amino acids in Sr33, we showed AvrSr50-dependent initiation of cell death in wheat protoplasts and Nicotiana benthamiana. Furthermore, we were able to pinpoint and change amino acid residues that govern autoactivity of Sr50 in the wheat protoplast cell death assay. These findings are a major advance towards the successful engineering of new effector recognition specificities in direct binder NLRs.

plant biology↗

bioRxiv2022

A draft genome assembly for the heterozygous wild tomato Solanum habrochaites highlights haplotypic structural variations of intracellular immune receptors

Solanum habrochaites LA1353 is a self-incompatible, highly heterozygous wild tomato that is a useful germplasm resource for the study of metabolism, reproduction and disease resistance. We generated a draft genome assembly with PacBio HiFi reads and genome annotations, which underscored the expansion of gene families associated with metabolite-production, self-incompatibility, DNA regulation and immunity. After manually curating intracellular nucleotide-binding leucine-rich repeat immune receptors (NLRs), we found that S. habrochaites LA1353 has a larger NLR inventory than other wild tomato species. A great number of heterozygous local copy number variations (CNVs) driven by haplotypic structural variations further expands the inventory, both enhancing NLR diversity and providing more opportunities for sequence evolution. The NLRs associated with local CNVs predominantly appear in the helper NLR (NRC)-related phylogenetic clades and are concentrated in a few physical NLR gene clusters. Synteny analysis points out that these genomic regions correspond to the known NLR clusters from which experimentally validated, functional NLRs, such as Hero, Mi-1.2 and Rpi-amr1, have been identified. Producing and incorporating Resistance Gene Enrichment Sequencing (RenSeq) data across wild tomato species, we reveal that the regions with local CNVs might have been shaped nearly equally by recent NLR gains and losses, along with enhanced sequence diversification that diminishes one-to-one orthology between heterozygous alleles. Our analysis suggests that these genomic regions may have accelerated evolutionary dynamics for NLR diversity generation in S. habrochaites LA1353.

plant biology↗