Directional divergence of Ep300 duplicates in teleosts and its implications

Abstract

Background EP300 is a conserved protein in vertebrates, which serves as a key mediator of cellular homeostasis. Mutations and dysregulation of EP300 give rise to severe human developmental disorders and malignancy. Danio rerio is a promising model organism to study EP300 related diseases and drugs; however, the effect of EP300 duplicates derived from teleost-specific whole genome duplication should not just be neglected. Results In this study, we obtained EP300 protein sequences of representative teleosts, mammals and sauropsids, with which we inferred a highly supported maximum likelihood tree. We observed that Ep300 duplicates (Ep300a and Ep300b) were widely retained in teleosts and universally expressed in a variety of tissues. Consensus sequences of Ep300a and Ep300b had exactly the same distribution of conserved domains, suggesting that their functions should still be largely overlapped. We analyzed the molecular evolution of Ep300 duplicates in teleosts, using branch-site models, clade models and site models. The results showed that both duplicates were subject to strong positive selection; however, for an extant species, generally at most one copy was under positive selection. At the clade level, there were evident positive correlations between evolutionary rates, the number of positively selected sites and gene expression levels. In Ostariophysi, Ep300a were under stronger positive selection than Ep300b; in Neoteleostei, another species-rich teleost clade, the contrary was the case. We also modeled 3D structures of zf-TAZ domain and its flanking regions of Ep300a and Ep300b of D. rerio and Oryzias latipes and found that in either species the faster evolving copy had more short helixes. Conclusions Collectively, the two copies of Ep300 have undoubtedly experienced directional divergence in main teleost clades. The divergence of EP300 between teleosts and mammals should be greater than the divergence between different teleost clades. Further studies are needed to clarify to what extent the EP300 involved regulatory network has diverged between teleosts and mammals, which would also help explain the huge success of teleosts.

Bertalanffy-Pütter models for avian growth

“…We use life history data from [1][2][3] and environmental data from [4] that were collected between March and June of 2016. [3] investigated the development of nestlings of blue tits and great tits that grew up at various sites in and around Warsaw, Poland.…”

“…[3] investigated the development of nestlings of blue tits and great tits that grew up at various sites in and around Warsaw, Poland. [4] complemented these growth data by reporting environmental data from the nest-box sites. We received from these authors data on 429 nestlings from 56 nest-boxes.…”

“…To study the association between environmental variables and growth we used the following information about the nest-boxes: human activity (explained in [1]), air temperature at the nest-box site (average of the morning temperatures in˚C at the eight visits), light and sound pollution at the nest-box sites (units: lux and decibel), distances to paths and roads (minimal Euclidean distance in m from the nest-box to the center of the next path or road), percentage of impervious surface around the nest (ISA), tree cover in percent around the nest, and NDVI (normalized difference vegetation index). According to [3], the latter indicators were assessed for a circle with radius 100 m around the nest and a pixel-resolution of 20 m. For methodological details we refer to the published sources [1][2][3][4].…”

“…This paper uses nonlinear regression models to study the growth of passerine birds, blue tits (Cyanistes caeruleus) and great tits (Parus major). Our study was based on data from [1][2][3][4] on the development of 81 nestlings of blue tits and great tits, and the environmental characteristics of their nest sites (nest-boxes) in a public park of the Warsaw city center.…”

“…It was used to relate growth to predation [6,7], to environmental variation [8][9][10], to annual adult mortality rates, and to incubation period duration [11]. Literature has considered various environmental factors that may affect growth, such as: tree cover [12], impervious surface [4,13], pollution by light [14,15] and sound [16][17][18], or nest interference by humans and pets [1,2,19]. All these factors are also known to affect the breeding success.…”