Biology subjects

Kandasamy, V.

Publications and source records attributed to Kandasamy, V..

3 recordsLinked to original sources

bioRxiv2024

A synthetic platform for multiplex screening of cell-cell communication between soil fungi

Fungi are essential members across ecosystems, yet phytopathogenic fungi pose an increasing risk to crop yields. Despite their ecologic importance, cell-cell communication in fungi is underexplored, partly due to the lack of high-throughput techniques. Here we developed a Yeast Mating Platform (YeMaP) to investigate the interaction between fungal G protein-coupled receptors (GPCRs) and pheromone peptides. We used YeMaP for high- throughput screening of 8,000 pheromone sequences and identified new peptides with improved agonism or antagonism action. We found that these peptides can be applied in a native fungal system such as the plant pathogen Fusarium oxysporum, to control hyphal chemotropism and reduce plant root penetration. Additionally, we utilized YeMaP in a one- pot assay to investigate how abiotic factors influence the communication of multiple pheromone-GPCR combinations and found that the cell-cell communication mediated by the GPCR Ste2 from F. oxysporum signalled robustly across different abiotic factors, while other fungal GPCR-pheromone interactions were more sensitive to changes. Taken together, YeMaP accelerates the identification of fungal GPCR-peptide interactions by enabling one- pot assays, and serves as model system for studying fungal cell-cell communication.

synthetic biology↗

bioRxiv2024

Trade-off Between Resistance and Persistence in High Cell Density Escherichia Coli Cultures

Microbes experience high cell density in many environments that come with diverse resource limitations and stresses. However, high density physiology remains poorly understood. We utilized well-controlled culturing systems to grow wild-type and metabolically engineered Escherichia coli strains into high cell densities (50-80 g Cdry cell weight L-1) and determine the associated transcriptional dynamics. Knowledge-enriched machine-learning-based analytics reveal distinct stress-related gene expression patterns that are consistent with a fundamental trade-off between resistance and persistence. We suggest that this trade-off explains observed growth arrests in high-density cultures and that it results from the disruption of cellular homeostasis, due to reallocation of limited cellular resources from resistance functions towards maintenance requirements of engineered production pathways. This study deepens our understanding of high-density physiology and demonstrates its importance to fundamental biomanufacturing challenges.

microbiology↗

bioRxiv2023

Using the E. coli Alleleome in Strain Design

Leveraging observed variants in strain design is a promising technique for creating strains with specific properties. Adaptive laboratory evolution (ALE) experiments generate variants that enhance fitness under specific conditions and can contribute to application-specific strain designs. Further, the wild-type (WT) coding alleleome of an organism, the complete set of its genes WT alleles, can provide an additional amount and diversity of variants not yet accessible from the aggregation of ALE experiment results. This study used both an ALE mutation database (3093 genomes) and a large set of WT genomes (12,661 genomes) to explore the sequence solution space of genes involved in tolerance to 10 conditions of industrial importance. To accomplish this, ALE variants for 22 genes previously identified as potentially important for industrial chemical tolerance were collected and supplemented with all available variants from the WT coding alleleome. A total of 4879 variants were reintroduced and used in 10 selection experiments. Both ALE and WT contributed highly enriched variants, where the enrichment and benefits depended on the conditions, genes, and gene product regions. The results also revealed that variants not originating from the initial experiment could potentially confer substantially greater benefits. Additionally, ALE and WT variants rarely overlapped on AA positions, but their clustering did coincide with where highly enriched variants were ultimately located. For genes primarily hosting potential gain-of-function variations, substitutions predicted to have a conservative impact frequently outperformed more radical substitutions. Case studies demonstrated that maximizing the amount of variants enabled easier identification of variant trends, which in turn can be used to better understand areas and characteristics of genes that can be feasibly varied, representing what could be thought of as a genome design variable. The combination of ALE and WT variants is a promising approach for use in future projects to better constrain and ultimately achieve practical coverage in the exploration of feasible sequence solution space. Visual Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/558058v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1a8e843org.highwire.dtl.DTLVardef@28a134org.highwire.dtl.DTLVardef@16f6849org.highwire.dtl.DTLVardef@127b43c_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗