The serine/threonine kinase 33 is present and expressed in palaeognath birds but has become a unitary pseudogene in neognaths about 100 million years ago.

Tobias Lautwein,Steffen Lerch,Erwin R Schmidt,Daniel Schäfer

doi:10.1186/s12864-015-1769-9

Abstract

BackgroundSerine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. It has been shown to phosphorylate vimentin and might play a role in spermatogenesis and organ ontogenesis. In this study we analyzed the genomic locus and expression of stk33 in the class Aves, using a combination of large scale next generation sequencing data analysis and traditional PCR.ResultsWithin the subclass Palaeognathae we analyzed the white-throated tinamou (Tinamus guttatus), the African ostrich (Struthio camelus) and the emu (Dromaius novaehollandiae). For the African ostrich we were able to generate a 62,778 bp long genomic contig and an mRNA sequence that encodes a protein showing highly significant similarity to STK33 proteins from other vertebrates. The emu has been shown to encode and transcribe a functional STK33 as well. For the white-throated tinamou we were able to identify 13 exons by sequence comparison encoding a protein similar to STK33 as well.In contrast, in all 28 neognath birds analyzed, we could not find evidence for the existence of a functional copy of stk33 or its expression. In the genomes of these 28 bird species, we found only remnants of the stk33 locus carrying several large genomic deletions, leading to the loss of multiple exons. The remaining exons have acquired various indels and premature stop codons.ConclusionsWe were able to elucidate and describe the genomic structure and the transcription of a functional stk33 gene within the subclass Palaeognathae, but we could only find degenerate remnants of stk33 in all neognath birds analyzed. This led us to the conclusion that stk33 became a unitary pseudogene in the evolutionary history of the class Aves at the paleognath-neognath branch point during the late cretaceous period about 100 million years ago. We hypothesize that the pseudogenization of stk33 might have become fixed in neognaths due to either genetic redundancy or a non-orthologous gene displacement and present potential candidate genes for such an incident.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1769-9) contains supplementary material, which is available to authorized users.

Highlights

Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates
We screened the whole genome and this region in particular for the presence of stk33. These genomic screens revealed the presence of only eight remnant exons containing both frameshifting indels and multiple stop codons (Fig. 3) in this region and multiple large genomic deletions that have led to the deletion of several exons
Encouraged by our findings that stk33 is expressed in the African ostrich, we investigated if the genomes of other paleognath birds contain a functional stk33 gene

Summary

Introduction

Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. Serine/threonine kinase 33 (stk33) was first discovered in the course of comparative genome analyses of human chromosome 11p15.3 and its orthologous region in the mouse [1,2,3] This region is highly syntenic (see Additional file 1: Figure S1) and known to be associated with several diseases including different types of cancer [4,5,6,7,8]. Stk has attracted attention since it has been identified as an essential component for the survival of KRAS-dependent cancer cells by high-throughput RNA interference (RNAi) screens [12,13,14] It has been associated with pancreatic cancer [15]. Recent studies found an association of stk with colorectal cancer [20], hepatocellular carcinoma [21], hypopharyngeal squamous cell carcinoma [22] and lung cancer [23]

Results

Discussion

Conclusion