Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins

Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function

Background

Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancreas, particularly with respect to their “unusual” energy metabolism (where ketone bodies and amino acids are the main oxidative fuel source) and their paradoxical ability to both maintain stable blood glucose levels and tolerate extensive periods of hypoglycemia. In order to shed light on some of these processes, we carried out the first large-scale comparative transcriptomic survey of multiple cartilaginous fish tissues: the pancreas, brain and liver of the lesser spotted catshark, Scyliorhinus canicula.

Results

We generated a mutli-tissue assembly comprising 86,006 contigs, of which 44,794 were assigned to a particular tissue or combination of tissues based on mapping of sequencing reads. We have characterised transcripts encoding genes involved in insulin regulation, glucose sensing, transcriptional regulation, signaling and digestion, as well as many peptide hormone precursors and their receptors for the first time. Comparisons to mammalian pancreas transcriptomes reveals that mechanisms of glucose sensing and insulin regulation used to establish and maintain a stable internal environment are conserved across jawed vertebrates and likely pre-date the vertebrate radiation. Conservation of pancreatic hormones and genes encoding digestive proteins support the single, early evolution of a distinct pancreatic gland with endocrine and exocrine functions in jawed vertebrates. In addition, we demonstrate that chondrichthyes lack pancreatic polypeptide (PP) and that reports of PP in the literature are likely due cross-reaction with PYY and/or NPY in the pancreas. A three hormone islet organ is therefore the ancestral jawed vertebrate condition, later elaborated upon only in the tetrapod lineage.

Conclusions

The cartilaginous fish are a great untapped resource for the reconstruction of patterns and processes of vertebrate evolution and new approaches such as those described in this paper will greatly facilitate their incorporation into the rank of “model organism”.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1074) contains supplementary material, which is available to authorized users.

Large scale of human duplicate genes divergence

Proteome complexity increases in the evolution mostly by means of gene duplication followed by divergence. In this genome-scale study of human genome I show that density distribution of duplicate gene pairs along the axis of protein divergence between pair members forms two main peaks with a small peak and plateau before the first main peak. This picture indicates the existence of three evolutionary stages of duplicate gene evolution. The analysis of various functional parameters (gene expression level and breadth, transcription factor targets, protein interaction networks) suggests that subfunctionalization (partition of function) is a predominant mode of divergence in the first main peak, whereas neofunctionalization (acquiring of novel functions) prevails in the second main peak. The young duplicate pairs show a much higher expression level compared with singleton genes and more diverged duplicates, which indicates that requirement for high gene dosage is important for retention of duplicates just after the duplication event. Thus, a prevailing route of duplicate evolution seems to be the high gene dosage-subfunctionalization-neofunctionalization. This adaptationist model suggests that an organism is evolving in the direction of its most intensively used functions.