Expression Differentiation Is Constrained to Low-Expression Proteins over Ecological Timescales

Abstract

Protein expression level is one of the strongest predictors of protein sequence evolutionary rate, with high-expression protein sequences evolving at slower rates than low-expression protein sequences largely because of constraints on protein folding and function. Expression evolutionary rates also have been shown to be negatively correlated with expression level across human and mouse orthologs over relatively long divergence times (i.e., 100 million years). Long-term evolutionary patterns, however, often cannot be extrapolated to microevolutionary processes (and vice versa), and whether this relationship holds for traits evolving under directional selection within a single species over ecological timescales (i.e., ,5000 years) is unknown and not necessarily expected. Expression is a metabolically costly process, and the expression level of a particular protein is predicted to be a tradeoff between the benefit of its function and the costs of its expression. Selection should drive the expression level of all proteins close to values that maximize fitness, particularly for high-expression proteins because of the increased energetic cost of production. Therefore, stabilizing selection may reduce the amount of standing expression variation for high-expression proteins, and in combination with physiological constraints that may place an upper bound on the range of beneficial expression variation, these constraints could severely limit the availability of beneficial expression variants. To determine whether rapid-expression evolution was restricted to low-expression proteins owing to these constraints on highly expressed proteins over ecological timescales, we compared venom protein expression levels across mainland and island populations for three species of pit vipers. We detected significant differentiation in protein expression levels in two of the three species and found that rapid-expression differentiation was restricted to low-expression proteins. Our results suggest that various constraints on high-expression proteins reduce the availability of beneficial expression variants relative to lowexpression proteins, enabling low-expression proteins to evolve and potentially lead to more rapid adaptation.KEYWORDS protein expression; selective constraints; evolutionary rates; adaptation T HE expression level of a protein is one of the strongest predictors of protein sequence evolutionary rate; sequences of highly expressed proteins evolve more slowly than low-expression proteins (Duret and Mouchiroud 1999;Pal et al. 2001;Gout et al. 2010;Yang et al. 2012;Nabholz et al. 2013;Park et al. 2013). This relationship may be a function of specific selective constraints on sequences to avoid protein misfolding (Drummond et al. 2005;Geiler-Samerotte et al. 2011), protein misinteractions (Yang et al. 2012, a decrease in protein function (Cherry 2010;Gout et al. 2010), and/or messenger RNA (mRNA) misfolding (Park et al. 2013). Analyses of microarray data have shown that expression evolutionary rate is also negatively...

Functional characterizations of venom phenotypes in the eastern diamondback rattlesnake (Crotalus adamanteus) and evidence for expression-driven divergence in toxic activities among populations

“…Because of the ontogenetic shift in venom composition (Margres et al, 2015b), specimens ≥102 cm were classified as adults and individuals <102 cm were classified as juveniles (Waldron et al, 2013), consistent with previous analyses (Margres et al, 2015a, b; 2016). All venom samples included in this study had been analyzed previously (i.e., reversed-phase high-performance liquid chromatography (RP-HPLC) and statistical analyses; Margres et al, 2015a, b, 2016). Samples were collected under the following permits: Florida Fish and Wildlife Conservation Commission (FWC) LSSC-13-00004 and LSSC-09-0399, Eglin Air Force Base 96 SFS/SFOIRP, Everglades National Park - EVER-2012-SCI-0053, Florida Department of Environmental Protection - Permit # 04101310, and St. Vincent National Wildlife Refuge - Permit # 41650-2012-08.…”

“…Reversed-phase high-performance liquid chromatography was performed on a Beckman System Gold HPLC (Beckman Coulter, Fullerton, CA) as described previously for each pooled venom as well as a reference venom sample from a single individual (Margres et al, 2015a, 2016, b; Wray et al, 2015). Briefly, 100 μ g of total protein were injected onto a Jupiter C18 column, 250 × 4.6 mm (Phenomenex, Torrence, CA) using the solvent system of A =0.1% trifluoroacetic acid (TFA) in water and B = 0.075% TFA in acetonitrile.…”

“…Snake venoms are modular, polygenic traits that are critical for feeding (Biardi et al, 2000) and defense (Jansa and Voss, 2011), resulting in strong selective pressures on the genes encoding venom components at the sequence (Kordiš and Gubenšek, 2000; Lynch, 2007; Gibbs and Rossiter, 2008; Juárez et al, 2008; Rokyta et al, 2011; Margres et al, 2013; Vonk et al, 2013) and expression levels (Daltry et al, 1996; Barlow et al, 2009; Rokyta et al, 2015; Margres et al, 2016). These strong selective pressures are believed to be responsible for the extensive interspecific (Mackessy, 2008; Sanz et al, 2008; Rokyta et al, 2013; McGivern et al, 2014), intraspecific (Daltry et al, 1996; Creer et al, 2003; Gibbs et al, 2009; Boldrini-França et al, 2010; Margres et al, 2015a, 2016; Rokyta et al, 2015), and ontogenetic venom variation (Mackessy, 1988; Mackessy et al, 2003; Guércio et al, 2006; Madrigal et al, 2012; Zelanis et al, 2012; Durban et al, 2013; Margres et al, 2015b; Wray et al, 2015) because venom variation has been shown to be associated with dietary shifts (Daltry et al, 1996; Barlow et al, 2009).…”

“…These strong selective pressures are believed to be responsible for the extensive interspecific (Mackessy, 2008; Sanz et al, 2008; Rokyta et al, 2013; McGivern et al, 2014), intraspecific (Daltry et al, 1996; Creer et al, 2003; Gibbs et al, 2009; Boldrini-França et al, 2010; Margres et al, 2015a, 2016; Rokyta et al, 2015), and ontogenetic venom variation (Mackessy, 1988; Mackessy et al, 2003; Guércio et al, 2006; Madrigal et al, 2012; Zelanis et al, 2012; Durban et al, 2013; Margres et al, 2015b; Wray et al, 2015) because venom variation has been shown to be associated with dietary shifts (Daltry et al, 1996; Barlow et al, 2009). These spatial and temporal shifts in resource use presumably lead to shifts in phenotypic optima and should be accompanied by functional divergence (Jensen et al, 2012; Margres et al, 2015b).…”

“…Although historically native to seven states in the southeastern United States, this species has been extirpated from Louisiana, is listed as endangered in North Carolina (Palmer and Braswell, 1995), and is currently under consideration for listing as threatened under the Endangered Species Act (United States Fish and Wildlife Service, 2012). Margres et al (2014; 2015a; 2016) used transcriptomics and proteomics to construct a genotype-phenotype map for the venom system of C. adamanteus . This map was used to identify extensive protein expression variation across seven adult populations, identifying five unique phenotypes, as well as the specific loci being differentially expressed across populations (Margres et al, 2015a).…”