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1. Parallel sensory compensation following independent subterranean colonization by groundwater salamanders ( Eurycea )

   https://doi.org/10.1073/pnas.2504850122  

   Tovar, Ruben U; Dobbins, Brittany A; Hartman, Nicholas R; Leelani, Sheena; Devitt, Thomas J; García, Dana M; Gignac, Paul M; Cannatella, David C; Hillis, David M (June 2025, Proceedings of the National Academy of Sciences)

   Lineages that have invaded subterranean environments have repeatedly evolved remarkable adaptations to life in darkness. However, observational and experimental studies in additional natural systems are needed to further our understanding of repeated evolution and convergence. In Texas, a radiation of groundwater salamanders (genusEurycea), with independent invasions of subterranean karstic environments, offers an opportunity to investigate phenotypic convergence, parallel evolution, and the enhancement and regression of sensory systems. Adaptations to a troglobitic life in this clade include morphological, behavioral, and physiological changes within and among species. Intraspecific and interspecific variation in morphology in response to the selective pressures of life underground allows for detailed examination of physical, behavioral, and physiological changes associated with subterranean adaptation within a comparative phylogenetic framework. We find a correlated change between two sensory systems repeated across multiple subterraneanEurycealineages: the degeneration of the eye and the expansion of the mechanosensory lateral line. The increase in anterior neuromast organs in subterranean lineages was positively correlated with the expression ofpax6(Paired-box 6), a conserved transcription factor important for vertebrate neurogenesis. Our results show a decreasing trend of PAX6 labeling in the neuromasts of adult surface salamanders (Eurycea nana) relative to the maintained labeling in subterranean species (Eurycea rathbuni). These lateral line enhancements are correlated with reductions in the development of optic systems in subterranean salamander lineages. Altogether, our findings provide a starting point for future evolutionary developmental investigations examining the genetic underpinnings of adaptive, repeated evolution in a novel system. 

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2. A Novel cis Element Achieves the Same Solution as an Ancestral cis Element During Thiamine Starvation in Candida glabrata

   https://doi.org/10.1534/g3.119.400897  

   Iosue, Christine L.; Gulotta, Anthony P.; Selhorst, Kathleen B.; Mody, Alison C.; Barbour, Kristin M.; Marcotte, Meredith J.; Bui, Lilian N.; Leone, Sarah G.; Lang, Emma C.; Hughes, Genevieve H.; et al (January 2020, G3: Genes|Genomes|Genetics)

   Regulatory networks often converge on very similar cis sequences to drive transcriptional programs due to constraints on what transcription factors are present. To determine the role of constraint loss on cis element evolution, we examined the recent appearance of a thiamine starvation regulated promoter in Candida glabrata . This species lacks the ancestral transcription factor Thi2, but still has the transcription factor Pdc2, which regulates thiamine starvation genes, allowing us to determine the effect of constraint change on a new promoter. We identified two different cis elements in C. glabrata - one present in the evolutionarily recent gene called CgPMU3 , and the other element present in the other thiamine (THI) regulated genes. Reciprocal swaps of the cis elements and incorporation of the S. cerevisiae Thi2 transcription factor-binding site into these promoters demonstrate that the two elements are functionally different from one another. Thus, this loss of an imposed constraint on promoter function has generated a novel cis sequence, suggesting that loss of trans constraints can generate a non-convergent pathway with the same output. 

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3. Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

   https://doi.org/10.1186/s12862-019-1524-y  

   Bogan, Samuel N; Place, Sean P (December 2019, BMC Evolutionary Biology)

   Abstract BackgroundAntarctic fishes of the Notothenioidei suborder constitutively upregulate multiple inducible chaperones, a highly derived adaptation that preserves proteostasis in extreme cold, and represent a system for studying the evolution of gene frontloading. We screened forHsf1-binding sites, asHsf1is a master transcription factor of the heat shock response, and highly-conserved non-coding elements within proximal promoters of chaperone genes across 10 Antarctic notothens, 2 subpolar notothens, and 17 perciform fishes. We employed phylogenetic models of molecular evolution to determine whether (i) changes in motifs associated withHsf1-binding and/or (ii) relaxed purifying selection or exaptation at ancestralcis-regulatory elements coincided with the evolution of chaperone frontloading in Antarctic notothens. ResultsAntarctic notothens exhibited significantly fewerHsf1-binding sites per bp at chaperone promoters than subpolar notothens and Serranoidei, the most closely-related suborder to Notothenioidei included in this study. 90% of chaperone promoters exhibited accelerated substitution rates among Antarctic notothens relative to other perciformes. The proportion of bases undergoing accelerated evolution (i) was significantly greater in Antarctic notothens than in subpolar notothens and Perciformes in 70% of chaperone genes and (ii) increased among bases that were more conserved among perciformes. Lastly, we detected evidence of relaxed purifying selection and exaptation acting on ancestrally conservedcis-regulatory elements in the Antarctic notothen lineage and its major branches. ConclusionA large degree of turnover has occurred in Notothenioidei at chaperone promoter regions that are conserved among perciform fishes following adaptation to the cooling of the Southern Ocean. Additionally, derived reductions inHsf1-binding site frequency suggestcis-regulatory modifications to the classical heat shock response. Of note, turnover events within chaperone promoters were less frequent in the ancestral node of Antarctic notothens relative to younger Antarctic lineages. This suggests thatcis-regulatory divergence at chaperone promoters may be greater between Antarctic notothen lineages than between subpolar and Antarctic clades. These findings demonstrate that strong selective forces have acted uponcis-regulatory elements of chaperone genes among Antarctic notothens. 

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4. Mfd interacts with RNA polymerase to modulate flagellum-dependent motility, chemotaxis, and population heterogeneity in the stationary phase of Bacillus subtilis

   https://doi.org/10.1128/jb.00589-25  

   Grifaldo, Jessica; Leyva-Sanchez, Hilda; Rosales, Khristian; Callaway, Amber; Sotelo, Andres; Martin, Holly Anne; Perez, Ryan King; Chavez_Rios, Jocelyn; Huezo, Elizabeth N; Pedraza-Reyes, Mario; et al (June 2026, Journal of Bacteriology)

   Shank, Elizabeth Anne (Ed.)

   ABSTRACT Bacillus subtilisis a model for cell differentiation, capable of transitioning between distinct states: a sessile, chained state (often associated with biofilm formation), and a motile, planktonic state. This transition is governed by a complex regulatory network that includes alternative sigma factor-D (σ^D), which drives the expression of genes for autolysins, flagellar biosynthesis, and chemotaxis, resulting in separated, flagellated, motile cells. Although the conserved transcription-coupled repair factormutationfrequencydecline (Mfd) is best known for resolving stalled RNA polymerase (RNAP) during DNA repair, its involvement in cell differentiation during the stationary phase remains poorly understood. This research shows that in the absence of Mfd translocation or RNAP recruitment, RNAP completes transcription of motility genes more frequently, despite unchanged σ^Dtranscript levels. Increased transcription of the σ^D-dependent motility regulon led to greater flagellation; however, swimming motility and pH taxis were paradoxically reduced, indicating that Mfd is required to translate flagellar gene expression into functional motility. Notably, Mfd-deficient cells failed to maintain chained subpopulations, indicating an additional role in sustaining population heterogeneity. These findings reveal a previously unrecognized function of Mfd as an RNAP-modulating factor that coordinates motility gene expression, thereby expanding our understanding of how transcription-coupled repair proteins influence bacterial physiology and behavior under non-proliferative conditions.IMPORTANCEThemutationfrequencydecline (Mfd) enzyme mediates transcription-coupled repair in transcribed genes by directly interacting with RNA polymerase (RNAP) during transcription of coding sequences. However, whether the Mfd factor regulates gene expression associated with adaptations unrelated to DNA repair and mutagenesis remains vague. Here, we show that Mfd regulates the completion of full transcripts of genes that confer swimming motility, chemotaxis, and cell heterogeneity inBacillus subtilis. Furthermore, we identified the Mfd’s translocase activity and its interaction with RNAP as key elements of this regulation. Therefore, Mfd’s importance in bacterial physiology and adaptation goes beyond DNA repair. 

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5. Diverse gene regulatory mechanisms alter rattlesnake venom gene expression at fine evolutionary scales

   https://doi.org/10.1093/gbe/evae110  

   Gopalan, Siddharth S; Perry, Blair W; Francioli, Yannick Z; Schield, Drew R; Guss, Hannah D; Bernstein, Justin M; Ballard, Kaas; Smith, Cara F; Saviola, Anthony J; Adams, Richard H; et al (May 2024, Genome Biology and Evolution)

   Gossmann, Toni (Ed.)

   Abstract Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic diversity evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce differences in venom gene expression. Through comparisons within and between species, we find a remarkably high degree of gene expression and regulatory network variation across even a shallow level of evolutionary divergence. We use these data to test hypotheses about the roles of specific trans-factors and cis-regulatory elements, how these roles may vary across venom genes and gene families, and how variation in regulatory systems drive diversity in venom phenotypes. Our results illustrate that differences in chromatin and genotype at regulatory elements play major roles in modulating expression. However, we also find that enhancer deletions, differences in transcription-factor expression, and variation in activity of the insulator protein CTCF also likely impact venom phenotypes. Our findings provide insight into the diversity and gene-specificity of gene regulatory features and highlight the value of comparative studies to link gene regulatory network variation to phenotypic variation. 

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