Intron-mediated induction of phenotypic heterogeneity

Introns are universally present in the nuclear genomes of eukaryotes. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein (RP) genes differing primarily in their introns. Despite recent findings on the role of RP introns under stress and starvation, understanding the contribution of introns to ribosome regulation remains challenging. Here, combining isogrowth profiling with single-cell protein measurements, we found that introns can mediate inducible phenotypic heterogeneity conferring a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B mediated by 5’UTR-intron retention in its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low Rps22B protein levels resulted in prolonged survival under sustained starvation, while high Rps22B levels enabled cells to resume growth sooner after transient starvation. Further, yeast growing at high sugar concentrations – similar to those in ripe grapes – exhibit bimodal Rps22B expression when approaching stationary phase. Differential intron-mediated regulation of RP genes thus provides a way to diversify the population when starvation looms in natural environments. Our findings reveal intron retention as a new mechanism for inducing phenotypic heterogeneity in changing environments and suggest that duplicated RP genes in yeast serve to resolve the evolutionary conflict between precise expression control and environmental responsiveness.

Intron-mediated induction of phenotypic heterogeneity

Introns are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein (RP) genes differing primarily in their introns2–4. Despite recent findings on the role of RP introns under stress and starvation5–7, understanding the contribution of introns to ribosome regulation remains challenging. Here, combining isogrowth profiling8 with single-cell protein measurements9, we found that introns can mediate inducible phenotypic heterogeneity conferring a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B mediated by 5’UTR-intron retention in its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low Rps22B protein levels resulted in prolonged survival under sustained starvation, while high Rps22B levels enabled cells to resume growth sooner after transient starvation. Further, yeast growing at high sugar concentrations – similar to those in ripe grapes – exhibit bimodal Rps22B expression when approaching stationary phase. Differential intron-mediated regulation of RP genes thus provides a way to diversify the population when starvation looms in natural environments. Our findings reveal intron retention as a new mechanism for inducing phenotypic heterogeneity in changing environments10,11 and suggest that duplicated RP genes in yeast serve to resolve the evolutionary conflict between precise expression control and environmental responsiveness12.

Whose trait is it anyways? Coevolution of joint phenotypes and genetic architecture in mutualisms

Evolutionary biologists typically envision a trait’s genetic basis and fitness effects occurring within a single species. However, traits can be determined by and have fitness consequences for interacting species, thus evolving in multiple genomes. This is especially likely in mutualisms, where species exchange fitness benefits and can associate over long periods of time. Partners may experience evolutionary conflict over the value of a multi-genomic trait, but such conflicts may be ameliorated by mutualism’s positive fitness feedbacks. Here, we develop a simulation model of a host–microbe mutualism to explore the evolution of a multi-genomic trait. Coevolutionary outcomes depend on whether hosts and microbes have similar or different optimal trait values, strengths of selection and fitness feedbacks. We show that genome-wide association studies can map joint traits to loci in multiple genomes and describe how fitness conflict and fitness feedback generate different multi-genomic architectures with distinct signals around segregating loci. Partner fitnesses can be positively correlated even when partners are in conflict over the value of a multi-genomic trait, and conflict can generate strong mutualistic dependency. While fitness alignment facilitates rapid adaptation to a new optimum, conflict maintains genetic variation and evolvability, with implications for applied microbiome science.

Signatures of host–pathogen evolutionary conflict reveal MISTR—A conserved MItochondrial STress Response network

Host–pathogen conflicts leave genetic signatures in genes that are critical for host defense functions. Using these “molecular scars” as a guide to discover gene functions, we discovered a vertebrate-specific MItochondrial STress Response (MISTR) circuit. MISTR proteins are associated with electron transport chain (ETC) factors and activated by stress signals such as interferon gamma (IFNγ) and hypoxia. Upon stress, ultraconserved microRNAs (miRNAs) down-regulate MISTR1(NDUFA4) followed by replacement with paralogs MItochondrial STress Response AntiViral (MISTRAV) and/or MItochondrial STress Response Hypoxia (MISTRH). While cells lacking MISTR1(NDUFA4) are more sensitive to chemical and viral apoptotic triggers, cells lacking MISTRAV or expressing the squirrelpox virus-encoded vMISTRAV exhibit resistance to the same insults. Rapid evolution signatures across primate genomes for MISTR1(NDUFA4) and MISTRAV indicate recent and ongoing conflicts with pathogens. MISTR homologs are also found in plants, yeasts, a fish virus, and an algal virus indicating ancient origins and suggesting diverse means of altering mitochondrial function under stress. The discovery of MISTR circuitry highlights the use of evolution-guided studies to reveal fundamental biological processes.

Retroviral Restriction Factors and Their Viral Targets: Restriction Strategies and Evolutionary Adaptations

The evolutionary conflict between retroviruses and their vertebrate hosts over millions of years has led to the emergence of cellular innate immune proteins termed restriction factors as well as their viral antagonists. Evidence accumulated in the last two decades has substantially increased our understanding of the elaborate mechanisms utilized by these restriction factors to inhibit retroviral replication, mechanisms that either directly block viral proteins or interfere with the cellular pathways hijacked by the viruses. Analyses of these complex interactions describe patterns of accelerated evolution for these restriction factors as well as the acquisition and evolution of their virus-encoded antagonists. Evidence is also mounting that many restriction factors identified for their inhibition of specific retroviruses have broader antiviral activity against additional retroviruses as well as against other viruses, and that exposure to these multiple virus challenges has shaped their adaptive evolution. In this review, we provide an overview of the restriction factors that interfere with different steps of the retroviral life cycle, describing their mechanisms of action, adaptive evolution, viral targets and the viral antagonists that evolved to counter these factors.

Illuminating the complexities of conflict with evolution: validation of the scales of evolutionary conflict measure (SECM)

Background Although personal, familial, and community conflict with evolution have been documented in the literature, these scales require conceptualization as a construct and operationalization as a measure. The Scales of Conflict with Evolution Measure (SECM) instrument was developed in response to these needs. Using a construct validity framework, the content, internal structure, convergent, and substantive validity of the SECM were evaluated using Rasch analysis, Structural Equation Modeling (SEM), and follow up questioning. The conceptual utility of the instrument was explored by examining whether it added explanatory insights into evolution acceptance above and beyond religiosity, evolution knowledge, and background variables. Results A literature review and expert consultation indicated that construct of evolutionary conflict perception should (i) encompass the hierarchical nature of human social structures (personal, family, community) and (ii) probe conflict as it relates to human values, cultures, and beliefs. A three-dimensional construct was operationalized as a nine-item rating scale measure. Using Rasch analyses of SECM responses from a diverse sample of > 1000 students studying evolution, the instrument met criteria of robust measurement, including: fit to model expectations; three-dimensional structure; high reliability; good rating scale function; measurement invariance with time; and convergence with a similar construct. SEM showed that: (i) family and community conflict had unique causal contributions to personal conflict, with family showing a stronger and modest impact, and (ii) personal conflict had a significant and modest causal impact on evolution acceptance above and beyond the contributions of religiosity, evolution knowledge, and background variables. Conclusion The SECM is an easy-to-administer instrument to measure conflict with evolution and is supported by several forms of validity evidence. The SECM has potential for facilitating measurement of evolutionary conflict in educational settings, thereby raising instructor awareness of conflict levels in students, promoting rigorous evaluations of educational interventions designed to reduce conflict, and fostering conceptual advances in the field of evolution education. Future work is needed to gather additional forms of validity evidence and to test current validity claims in additional participant samples. SECM measures should also be incorporated into more complex SEM models that treat evolution knowledge and religiosity as part of the structural paths to evolution acceptance. Such models could provide insights into the most worthwhile targets for the development of educational interventions to mitigate conflict at multiple scales.

Urban resources limit pair coordination over offspring provisioning

The amount of care parents provide to the offspring is complicated by an evolutionary conflict of interest (‘sexual conflict’) between the two parents. Recent theoretical models suggest that pair coordination of the provisioning may reduce this conflict and increase parent and offspring fitness. Despite empirical studies showing that pair coordination is common in avian species, it remains unclear how environmental and ecological conditions might promote or limit the ability of parents to coordinate care. We compared the level of pair coordination, measured as alternation and synchrony of the nest visits, of house wrens Troglodytes aedon pairs breeding in a rural (10 nests) and a suburban (9 nests) site and investigated how differences in parental behaviours were related to habitat composition, prey abundance and how they ultimately related to reproductive success. We found that parents alternated and synchronized their nest visits more in the rural site compared to the suburban one. The suburban site is characterized by a more fragmented habitat with more coniferous trees and less caterpillar availability. Offspring from the rural site were heavier at fledging than at the suburban site. Taken together, these results suggest that environmental conditions play an important role on the emergence of coordinated parental care and that considering environmental variables is pivotal to assess the fitness consequences of parental strategies.

Conflicts between business and government in bike sharing system

Purpose The purpose of this paper is to elaborate on the interactive conflicts between business and governmental authorities in the regulatory process of an emerging business model: sharing economy. Focusing on bike sharing system, the study also investigates the conflict-handling strategy of bike sharing companies and government regulation. Design/methodology/approach An evolutionary game model is introduced to illustrate the interactive conflict between bike sharing companies and government regulation, combined with system dynamics (SD) to simulate the evolutionary conflict-handling strategies between the two players. Findings The dynamic strategies of the two players are observed, and under five conditions the conflict outcomes are evolutionary stable states. Simulations show that each party sacrifices part of its interest and adjust its strategy according to that of the other, indicating the conflict-handling strategy as a compromising mode. Furthermore, the strategies of bike sharing companies are sensitive to additional operation and maintenance costs for producing low-quality bicycles and costs of positive regulation, which provides theoretical guidance for regulatory authorities. Originality/value The station-less bike sharing come up in China recently, and it is an important research field of entrepreneurship. Owing to the uniqueness and novelty of the phenomenon, conflicts and challenges exist during the regulation process. Thus, the study practically contributes to the conflict-handling strategies of businesses and government under the context of sharing economy. Methodologically, as a novel issue with less available data to carry out empirical research, this study combines evolutionary game theory with SD to shed light on the complex interactions between businesses and government. The research method can be applied to other entrepreneurial studies.