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1. Genomic Comparisons Reveal Selection Pressure and Functional Variation Between Nutritional Endosymbionts of Cave-Adapted and Epigean Hawaiian Planthoppers

   https://doi.org/10.1093/gbe/evad031  

   Gossett, Jordan M; Porter, Megan L; Vasquez, Yumary M; Bennett, Gordon M; Chong, Rebecca A (March 2023, Genome Biology and Evolution)

   Angert, Esther (Ed.)

   Abstract Planthoppers in the family Cixiidae (Hemiptera: Auchenorrhyncha: Fulgoromorpha) harbor a diverse set of obligate bacterial endosymbionts that provision essential amino acids and vitamins that are missing from their plant-sap diet. “Candidatus Sulcia muelleri” and “Ca. Vidania fulgoroidea” have been associated with cixiid planthoppers since their origin within the Auchenorrhyncha, whereas “Ca. Purcelliella pentastirinorum” is a more recent endosymbiotic acquisition. Hawaiian cixiid planthoppers occupy diverse habitats including lava tube caves and shrubby surface landscapes, which offer different nutritional resources and environmental constraints. Genomic studies have focused on understanding the nutritional provisioning roles of cixiid endosymbionts more broadly, yet it is still unclear how selection pressures on endosymbiont genes might differ between cixiid host species inhabiting such diverse landscapes, or how variation in selection might impact symbiont evolution. In this study, we sequenced the genomes of Sulcia, Vidania, and Purcelliella isolated from both surface and cave-adapted planthopper hosts from the genus Oliarus. We found that nutritional biosynthesis genes were conserved in Sulcia and Vidania genomes in inter- and intra-host species comparisons. In contrast, Purcelliella genomes retain different essential nutritional biosynthesis genes between surface- and cave-adapted planthopper species. Finally, we see the variation in selection pressures on symbiont genes both within and between host species, suggesting that strong coevolution between host and endosymbiont is associated with different patterns of molecular evolution on a fine scale that may be associated with the host diet. 

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2. Regulation of the Pseudomonas syringae Type III Secretion System by Host Environment Signals

   https://doi.org/10.3390/microorganisms9061227  

   O’Malley, Megan R.; Anderson, Jeffrey C. (June 2021, Microorganisms)

   null (Ed.)

   Pseudomonas syringae are Gram-negative, plant pathogenic bacteria that use a type III secretion system (T3SS) to disarm host immune responses and promote bacterial growth within plant tissues. Despite the critical role for type III secretion in promoting virulence, T3SS-encoding genes are not constitutively expressed by P. syringae and must instead be induced during infection. While it has been known for many years that culturing P. syringae in synthetic minimal media can induce the T3SS, relatively little is known about host signals that regulate the deployment of the T3SS during infection. The recent identification of specific plant-derived amino acids and organic acids that induce T3SS-inducing genes in P. syringae has provided new insights into host sensing mechanisms. This review summarizes current knowledge of the regulatory machinery governing T3SS deployment in P. syringae, including master regulators HrpRS and HrpL encoded within the T3SS pathogenicity island, and the environmental factors that modulate the abundance and/or activity of these key regulators. We highlight putative receptors and regulatory networks involved in linking the perception of host signals to the regulation of the core HrpRS–HrpL pathway. Positive and negative regulation of T3SS deployment is also discussed within the context of P. syringae infection, where contributions from distinct host signals and regulatory networks likely enable the fine-tuning of T3SS deployment within host tissues. Last, we propose future research directions necessary to construct a comprehensive model that (a) links the perception of host metabolite signals to T3SS deployment and (b) places these host–pathogen signaling events in the overall context of P. syringae infection. 

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3. Symbiont Gene Expression Predicts Insect Host's Response to High Temperatures

   https://doi.org/10.1111/mec.70154  

   Stillson, Patrick T; Sim, Sheina B; Corpuz, Renee L; Ravenscraft, Alison (November 2025, Molecular Ecology)

   ABSTRACT Microbial symbionts play crucial roles in host nutrition, defence, and detoxification. However, host‐symbiont interactions are context‐dependent, and environmental stressors can disrupt these benefits. Diverse hosts, including corals, insects and leguminous plants, have been shown to suffer under thermal stress due to the negative impact of high temperatures on their symbionts. This failure is often linked to a symbiont's poor transcriptional regulation of heat shock genes, causing vulnerability at high temperatures. In the bug‐Caballeroniamodel system, insect performance at elevated temperatures varies based on the hosted symbiont species. Here, we explore the underlying mechanisms that drive this variation using comparative metatranscriptomics and two symbionts with contrasting host outcomes at high temperatures. We evaluated both host and symbiont transcriptional responses to elevated temperature, testing the hypothesis that symbionts conferring improved host outcomes at high temperatures will have more upregulated heat shock genes under thermal stress compared to those conferring worse host outcomes. Our findings reveal that host transcription did not change with different symbionts but rather only at different temperatures. Furthermore, symbionts had distinct gene expression profiles across temperatures. At 36°C, the heat‐resistant symbiont not only increased expression of heat shock genes but surprisingly upregulated flagellar genes, which are normally turned off during symbiosis. This suggests that symbiont, not host, transcription underlies host benefits at low versus high temperatures and ultimately furthers our understanding of context dependence in the outcomes of symbiotic associations. 

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4. Rapid de novo evolution of lysis genes in single-stranded RNA phages

   https://doi.org/10.1038/s41467-020-19860-0  

   Chamakura, Karthik R; Tran, Jennifer S; O’Leary, Chandler; Lisciandro, Hannah G; Antillon, Sophia F; Garza, Kameron D; Tran, Elizabeth; Min, Lorna; Young, Ry (December 2020, Nature Communications)

   Abstract Leviviruses are bacteriophages with small single-stranded RNA genomes consisting of 3-4 genes, one of which (sgl) encodes a protein that induces the host to undergo autolysis and liberate progeny virions. Recent meta-transcriptomic studies have uncovered thousands of leviviral genomes, but most of these lack an annotatedsgl, mainly due to the small size, lack of sequence similarity, and embedded nature of these genes. Here, we identifysglgenes in 244 leviviral genomes and functionally characterize them inEscherichia coli. We show that leviviruses readily evolvesglgenes and sometimes have more than one per genome. Moreover, these genes share little to no similarity with each other or to previously knownsglgenes, thus representing a rich source for potential protein antibiotics. 

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5. Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes

   https://doi.org/10.1128/mbio.01823-22  

   Batstone, Rebecca T.; Lindgren, Hanna; Allsup, Cassandra M.; Goralka, Laura A.; Riley, Alex B.; Grillo, Michael A.; Marshall-Colon, Amy; Heath, Katy D. (December 2022, mBio)

   Wilson, Daniel; Parkhill, Julian (Ed.)

   ABSTRACT A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes , being governed by genetic variation encoded not only by the host’s own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype— partner quality , or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis. 

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