Biology subjects

Bennett, G. M.

Publications and source records attributed to Bennett, G. M..

5 recordsLinked to original sources

bioRxiv2026

Intrahost mutational dynamics parallel long-term genome evolution in endosymbionts

Obligate endosymbionts of insects undergo extreme genome evolution, marked by accelerated molecular evolution, severe base-pair compositional bias, and massive gene loss. However, the microevolutionary processes driving these patterns remain poorly understood, as they occur at intrahost population scales that are rarely captured. To address this gap, we measured intrahost genetic diversity of two endosymbionts, Karelsulcia and Nasuia, from the aster leafhopper, Macrosteles quadrilineatus (Hemiptera: Cicadellidae). Contrary to the theoretical expectation of strict clonality, we found that both endosymbionts harbor measurable intrahost genetic variation, with lineage-specific mutational dynamics that parallels long-term evolutionary trends. Karelsulcia showed sparse intrahost variation dominated by repeat-associated indels, while Nasuia exhibited more abundant single-nucleotide mutations that appear to shape genome-wide A+T bias. Mitochondrial heteroplasmy did not covary with endosymbiont nucleotide diversity, indicating that these patterns are not driven by host-level dynamics. Notably, recurrent nonsynonymous variants in Nasuia affect essential genes for amino acid biosynthesis and translation. The intrahost mutational patterns we observed in endosymbionts are consistent with long-term sequence changes between our population founder genome and contemporary endosymbiont populations after [~]11 years of maintenance. Taken together, our results demonstrate how distinct mutational processes operating at the intrahost populations scale drive macroevolutionary patterns in endosymbiont genomes. Moreover, our study establishes that laboratory endosymbiont systems provide a powerful framework for dissecting and understanding these fundamental evolutionary processes.

evolutionary biology↗

bioRxiv2023

Identification of putative druggable pockets in PRL3, a significant oncology target, using in silico analysis

Due to their active roles in regulating phosphorylations, protein tyrosine phosphatases (PTP) have emerged as attractive targets in diseases characterized by aberrant phosphorylations such as cancers. The activity of the phosphatase of regenerating liver 3, PRL3, has been linked to several oncogenic and metastatic pathways, particularly in breast, ovarian, colorectal, and blood cancers. Development of small molecules that directly target PRL3, however, has been challenging. This is partly due to the lack of structural information on how PRL3 interacts with its inhibitors. Here, computational methods are used to bridge this gap by evaluating the druggability of PRL3. In particular, web-based pocket prediction tools, DoGSite3 and FTMap, were used to identify binding pockets using structures of PRL3 currently available in the Protein Data Bank. Druggability assessment by molecular dynamics simulations with probes was also performed to validate these results and to predict the strength of binding in the identified pockets. While several druggable pockets were identified, those in the closed conformation show more promise given their volume and depth. These two pockets flank the active site loops and roughly correspond to pockets predicted by molecular docking in previous papers. Notably, druggability simulations predict the possibility of low nanomolar affinity inhibitors in these sites implying the potential to identify highly potent small molecule inhibitors for PRL3. Putative pockets identified here can be leveraged for high-throughput virtual screening to further accelerate the drug discovery against PRL3 and development of PRL3-directed therapeutics.

biochemistry↗

bioRxiv2022

Genome comparison reveals inversions and alternative evolutionary history of nutritional endosymbionts in planthoppers (Hemiptera: Fulgoromorpha)

The evolutionary success of sap-feeding hemipteran insects in the suborder Auchenorrhyncha was enabled by nutritional contributions from their heritable endosymbiotic bacteria. However, the symbiont diversity, functions, and evolutionary origins in this large insect group have not been broadly characterized using genomic tools. In particular, the origins and relationships among ancient betaproteobacterial symbionts Vidania (in Fulgoromorpha) and Nasuia/Zinderia (in Cicadomorpha) are uncertain. Here, we characterized the genomes of Vidania and Sulcia from three Pyrops planthoppers (family Fulgoridae) to understand their metabolic functions and evolutionary histories. Like in previously characterized planthoppers, these symbionts share nutritional responsibilities, with Vidania providing seven out of ten essential amino acids. Sulcia lineages across the Auchenorrhyncha have a highly conserved genome but with multiple independent rearrangements occurring in an early ancestor of Cicadomorpha or Fulgoromorpha and in a few succeeding lineages. Genomic synteny was also observed within each of the betaproteobacterial symbiont genera Nasuia, Zinderia, and Vidania, but not across them, which challenges the expectation of a shared ancestry for these symbionts. The further comparison of other biological traits strongly suggests an independent origin of Vidania early in the planthopper evolution and possibly of Nasuia and Zinderia in their respective host lineages. Originality-Significance StatementWe sequenced and characterized the genomes of two ancient nutritional symbionts, Sulcia and Vidania, in three species from the genus Pyrops in the species- and symbiont-rich but understudied insect clade, Fulgoromorpha (planthoppers). We describe--for the first time--several independent genome rearrangements in Sulcia, which is often cited as a premier example of extreme genome stability spanning hundreds of millions of years. We also show a global lack of synteny across the genomes of the Auchenorrhynchan betaproteobacterial symbionts (Vidania, Nasuia, and Zinderia). This result is unexpected given previous hypotheses of a common origin for these symbionts >250 million years ago alongside Sulcia. Taken together, we suggest an independent origin of Vidania and possibly of Nasuia and Zinderia symbiont lineages as well. This hypothesis further links the potential acquisition of novel nutritional endosymbiont lineages with the emergence of auchenorrhyncham superfamilies.

genomics↗

bioRxiv2020

Mutational pressure drives differential genome conservation in two bacterial endosymbionts of sap feeding insects

Compared to free-living bacteria, endosymbionts of sap-feeding insects have tiny and rapidly evolving genomes. Increased genetic drift, high mutation rates, and relaxed selection associated with host control of key cellular functions all likely contribute to genome decay. Phylogenetic comparisons have revealed massive variation in endosymbiont evolutionary rate, but such methods make it difficult to partition the effects of mutation vs. selection. For example, the ancestor of auchenorrhynchan insects contained two obligate endosymbionts, Sulcia and a betaproteobacterium (BetaSymb; called Nasuia in leafhoppers) that exhibit divergent rates of sequence evolution and different propensities for loss and replacement in the ensuing [~]300 Ma. Here, we use the auchenorrhynchan leafhopper Macrosteles sp. nr. severini, which retains both of the ancestral endosymbionts, to test the hypothesis that differences in evolutionary rate are driven by differential mutagenesis. We used a high-fidelity technique known as duplex sequencing to measure and compare low-frequency variants in each endosymbiont. Our direct detection of de novo mutations reveals that the rapidly evolving endosymbiont (Nasuia) has a much higher frequency of single-nucleotide variants than the more stable endosymbiont (Sulcia) and a mutation spectrum that is even more AT-biased than implied by the 83.1% AT content of its genome. We show that indels are common in both endosymbionts but differ substantially in length and distribution around repetitive regions. Our results suggest that differences in long-term rates of sequence evolution in Sulcia vs. BetaSymb, and perhaps the contrasting degrees of stability of their relationships with the host, are driven by differences in mutagenesis. SIGNIFICANCE STATEMENTTwo ancient endosymbionts in the same host lineage display stark differences in genome conservation over phylogenetic scales. We show the rapidly evolving endosymbiont has a higher frequency of mutations, as measured with duplex sequencing. Therefore, differential mutagenesis likely drives evolutionary rate variation in these endosymbionts.

genetics↗

bioRxiv2018

Cicada endosymbionts have tRNAs that are correctly processed despite having genomes that do not encode all of the tRNA processing machinery

Gene loss and genome reduction are defining characteristics of nutritional endosymbiotic bacteria. In extreme cases, even essential genes related to core cellular processes such as replication, transcription, and translation are lost from endosymbiont genomes. Computational predictions on the genomes of the two bacterial symbionts of the cicada Diceroprocta semicincta, \"Candidatus Hodgkinia cicadicola\" (Alphaproteobacteria) and \"Ca. Sulcia muelleri\" (Betaproteobacteria), find only 26 and 16 tRNA, and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original \"Ca. Hodgkinia\" genome annotation is missing several essential genes involved in tRNA processing, such as RNase P and CCA tRNA nucleotidyltransferase, as well as several RNA editing enzymes required for tRNA maturation. How \"Ca. Sulcia\" and \"Ca. Hodgkinia\" preform basic translation-related processes without these genes remains unknown. Here, by sequencing eukaryotic mRNA and total small RNA, we show that the limited tRNA set predicted by computational annotation of \"Ca. Sulcia\" and \"Ca. Hodgkinia\" is likely correct. Furthermore, we show that despite the absence of genes encoding tRNA processing activities in the symbiont genomes, symbiont tRNAs have correctly processed 5 and 3 ends, and seem to undergo nucleotide modification. Surprisingly, we find that most \"Ca. Hodgkinia\"and \"Ca. Sulcia\" tRNAs exist as tRNA halves. Finally, and in contrast with other related insects, we show that cicadas have experienced little horizontal gene transfer that might complement the activities missing from the endosymbiont genomes. We conclude that \"Ca. Sulcia\" and \"Ca. Hodgkinia\" tRNAs likely function in bacterial translation, but require host-encoded enzymes to do so.

evolutionary biology↗