Biology subjects

Ahn, S.-J.

Publications and source records attributed to Ahn, S.-J..

7 recordsLinked to original sources

bioRxiv2024

A bacterial site 2 protease contributes to RNA phage resistance by targeting phage lysis protein

Lytic phages culminate their lifecycle by causing lysis of the infected host cell. Despite extensive research on the molecular mechanisms of phage lysis, our understanding of anti-phage resistance mechanisms during the lysis stage remains less understood. Here, we demonstrated that MucP, a site 2 protease of Pseudomonas aeruginosa (PA), mitigates the activity of the RNA phage PP7 lysis protein (LP), which contains a transmembrane (TM) helix, suggesting that MucP act as a resistance mechanism against PP7-induced lysis. We identified an LP variant (LP*) having enhanced helical propensity due to P26L and S40L mutations, which was unaffected by MucP and exhibited killing activity against PA strains that are resistant to the wild type LP, with an inverse correlation between MucP activity and LP susceptibility. A PP7 mutant with LP* exhibited MucP-escaper phenotype such as discernable plaque formation on MucP-expressing cells. These results suggest that MucP targets the RNA phage LP at the TM helix in certain strains, providing a resistance function compromising phage lysis by utilizing an existing bacterial enzyme in PA. IMPORTANCEDespite the importance of cell lysis as the last stage of phage lifecycle, the factors influencing coordinated lysis remain elusive in the context of phage-bacteria interactions. Our study identifies MucP, a membrane protease in Pseudomonas aeruginosa (PA), as a resistance factor against the RNA phage PP7 by destabilizing its lysis protein (LP), with lower helical tendency at transmembrane (TM) domain. An LP variant with higher helical tendency exhibits strong killing activity against PA isolates, revealing an inverse correlation between MucP activity and LP susceptibility. Since MucP is a conserved protease in mucoid conversion of PA, we propose that MucP offers an intrinsic or passive defense or resistance mechanism against the RNA phage, whose activities vary among the diverse PA isolates.

microbiology↗

bioRxiv2024

Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion

Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.

evolutionary biology↗

bioRxiv2023

Comparative genomics and the salivary transcriptome of the redbanded stink bug shed light on its high damage potential to soybean

The redbanded stink bug, Piezodorus guildinii (Westwood) (Hemiptera: Pentatomidae), is a significant soybean pest in the Americas, inflicting more physical damage on soybean than other native stink bugs. Studies suggest that its heightened impact is attributed to the aggressive digestive properties of its saliva. Despite its agricultural importance, the factors driving its greater ability to degrade plant tissues have remained unexplored in a genomic evolutionary context. In this study, we hypothesized that lineage-specific gene family expansions have increased the dosage of digestive genes expressed in the salivary glands. To investigate this, we annotated a previously published genome assembly of the redbanded stink bug and performed a comparative genomic analysis on 11 hemipteran species and reconstructed patterns of gene duplication, gain, and loss in the redbanded stink bug. We also performed RNA-seq on the redbanded stink bugs salivary tissues, along with the rest of the body without salivary glands. We identified hundreds of differentially expressed salivary genes, including a subset lost in other stink bug lineages but retained and expressed in the redbanded stink bugs salivary glands. These genes were significantly enriched with protein families involved in proteolysis, potentially explaining the redbanded stink bugs heightened damage to soybeans. Contrary to our hypothesis, we found no support for an increased dosage of digestive genes in the salivary glands of the redbanded stink bug. Nonetheless, these results provide insight into the evolution of this important crop pest, establishing a link between its genomic history and its agriculturally important physiology. SIGNIFICANCE STATEMENTThe redbanded stink bug, an important soybean pest in the Americas, inflicts greater damage to soybean due to higher salivary digestion. We employed comparative genomics and analyses of the salivary transcriptome to explore this and found that the differential retention of ancestral salivary genes may explain this phenomenon better than gene gains or duplications in the redbanded stink bug genome. We identify a distinct set of genes in the salivary gland that were differentially retained and expressed in the redbanded stink bug lineage, demonstrating enrichment in proteolytic function. This discovery offers a potential explanation for the redbanded stink bugs elevated damage to soybean crops.

genomics↗

bioRxiv2023

Overexpression and nonsynonymous mutations of UDP-glycosyltransferases potentially associated with pyrethroid resistance in Anopheles funestus

UDP-glycosyltransferases (UGTs) constitute a superfamily of enzymes that play a vital role in the biotransformation of diverse hydrophobic substrates into more hydrophilic products, thereby facilitating their excretion from the cell through transporters. The significance of UGTs in conferring insecticide resistance has been emphasized in various insect species. In this study, we characterised Anopheles funestus UGT genes genome-wide and explored their evolution and association with pyrethroid resistance. We combined genome-wide association of pooled-template sequencing (GWAS-PoolSeq) with the transcriptomic profile of pyrethroid-resistant An. funestus populations, and deep targeted sequencing of UGTs from 80 individual mosquitoes collected in Malawi, Uganda, Cameroon and the two laboratory colonies (FANG and FUMOZ) to investigate the role of UGTs in pyrethroid resistance. We identified common overexpression of UGT310B2 (AFUN000679) in the resistant laboratory colony (FUMOZ) and resistant field populations from Malawi, Cameroon and Uganda. Significant gene-wise Fst differentiation between the resistant and putatively susceptible populations was observed for UGT301C2 and UGT302A3 in Malawi, as well as UGT306C2 in Uganda. Furthermore, the gene-wise Tajimas D density curves of the sequenced regions provided insights into genome-wide processes elucidating population structures within An. funestus populations from these three countries, supporting previous observations. Additionally, we identified significantly differentiated nonsynonymous mutations within UGT genes, which may potentially contribute to pyrethroid resistance. The identified role of An. funestus UGT genes in pyrethroid resistance has direct implications for current vector control strategies, management approaches, and the prediction of potential cross-resistance to other insecticides that can be directly detoxified by UGTs.

genetics↗

bioRxiv2019

Environmental Triggers of lrgA Expression in Streptococcus mutans

The lrgAB and cidAB operons of Streptococcus mutans encode proteins that are structurally similar to the bacteriophage lambda family of holin-antiholin proteins, which are believed to facilitate cell death in other bacterial species. Although their precise function is not known, cidAB and lrgAB are linked to multiple virulence traits of S. mutans, including oxidative stress tolerance, biofilm formation, and autolysis. The regulation of cidAB and lrgAB is still not understood, as these operons show opposite patterns of expression as well as a complex dependence on growth conditions. We have used a microfluidic approach, together with single-cell imaging of a fluorescent gene reporter, to identify with greater precision the cues that trigger lrgA expression and characterize cell-to-cell heterogeneity in lrgA activity. lrgA activates very abruptly at stationary phase, with a high degree of synchrony across the population. We find this activation is controlled by a small number of inputs that are sensitive to growth phase: Extracellular pyruvate, glucose, and molecular oxygen. Further, activation of lrgA appears to be self-limiting, so that lrgA is strongly expressed only for a very short interval of time. Consequently, lrgA is programmed to switch on briefly at the end of exponential growth, as glucose and molecular oxygen are exhausted and extracellular pyruvate is available. Our findings are consistent with studies showing that homologs of lrgAB are linked, together with lytST, to the reimport of pyruvate for anaerobic fermentative growth.\n\nImportanceThe function and regulation of cidAB and lrgAB in Streptococcus mutans is not understood, although these operons have been clearly linked to stress responses and they show a complex dependence on environmental inputs and growth phase. Identifying specific environmental cues that trigger activation of lrgAB has been difficult owing to the cells own modification of key inputs such as glucose and oxygen: In S. mutans the lrgAB operon is strongly upregulated at the end of exponential phase, where growth conditions in a bulk culture become poorly defined. Here we have used microfluidics to apply precise control of environmental inputs to S. mutans and identify specific chemical cues that activate lrgAB. We find that rigorously anaerobic conditions and the presence of extracellular pyruvate are sufficient to induce lrgAB expression, suggesting that lrgAB is timed to activate just as pyruvate fermentation becomes favorable.

biophysics↗

bioRxiv2018

Threshold regulation and stochasticity from the MecA/ClpCP proteolytic system in Streptococcus mutans competence

Many bacterial species use the MecA/ClpCP proteolytic system to block entry into genetic competence. In Streptococcus mutans, MecA/ClpCP degrades ComX (also called SigX), an alternative sigma factor for the comY operon and other late competence genes. Although the mechanism of MecA/ClpCP has been studied in multiple Streptococcus species, its role within noisy competence pathways is poorly understood. S. mutans competence can be triggered by two different peptides, CSP and XIP, but it is not known whether MecA/ClpCP acts similarly for both stimuli, how it affects competence heterogeneity, and how its regulation is overcome. We have studied the effect of MecA/ClpCP on the activation of comY in individual S. mutans cells. Our data show that MecA/ClpCP is active under both XIP and CSP stimulation, that it provides threshold control of comY, and that it adds noise in comY expression. Our data agree quantitatively with a model in which MecA/ClpCP prevents adventitious entry into competence by sequestering or intercepting low levels of ComX. Competence is permitted when ComX levels exceed a threshold, but cell-to-cell heterogeneity in MecA levels creates variability in that threshold. Therefore MecA/ClpCP provides a stochastic switch, located downstream of the already noisy comX, that enhances phenotypic diversity.

microbiology↗

bioRxiv2018

The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

The semi-aquatic bugs conquered water surfaces worldwide and occupy ponds, streams, lakes, mangroves, and even open oceans. As such, they inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders thorough investigations of the mechanisms underlying the processes of adaptation and diversification in this group. Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome, the first water strider genome to be sequenced so far. G. buenoi genome is about 1 000Mb and the sequencing effort recovered 20 949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to water surface lifestyle. These expansions affect key processes such as growth, vision, desiccation resistance, detoxification, olfaction and epigenetic components. Strikingly, the G. buenoi genome contains three Insulin Receptors, a unique case among metazoans, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes include wavelength sensitivity shifts in opsin proteins likely in association with the requirements of vision in water habitats. Our findings suggest that local gene duplications might have had an important role during the evolution of water striders. These findings along with the G. buenoi genome open exciting research opportunities to understand adaptation and genome evolution of this unique hemimetabolous insect.

genomics↗