Cross-Species Genome-Wide Identification of Evolutionary Conserved MicroProteins

Abstract

MicroProteins are small single-domain proteins that act by engaging their targets into different, sometimes nonproductive protein complexes. In order to identify novel microProteins in any sequenced genome of interest, we have developed miPFinder, a program that identifies and classifies potential microProteins. In the past years, several microProteins have been discovered in plants where they are mainly involved in the regulation of development by fine-tuning transcription factor activities. The miPFinder algorithm identifies all up to date known plant microProteins and extends the microProtein concept beyond transcription factors to other protein families. Here, we reveal potential microProtein candidates in several plant and animal reference genomes. A large number of these microProteins are species-specific while others evolved early and are evolutionary highly conserved. Most known microProtein genes originated from large ancestral genes by gene duplication, mutation and subsequent degradation. Gene ontology analysis shows that putative microProtein ancestors are often located in the nucleus, and involved in DNA binding and formation of protein complexes. Additionally, microProtein candidates act in plant transcriptional regulation, signal transduction and anatomical structure development. MiPFinder is freely available to find microProteins in any genome and will aid in the identification of novel microProteins in plants and animals.

Keywords: metazoa; miPFinder; microProteins; plants; protein–protein interaction.

Fig. 1.—

Flow chart miPFinder. Mandatory steps are with a light gray background. Orange, databases; green, data packages; gray, tools; blue, lists; white, custom functions.

Fig. 2.—

Circos plot of individual microProtein candidates. Links indicate conservation between species based on OrthoFinder. Red, in all 11 species; dark blue, exclusively in all five metazoans; light blue, only in metazoans; dark green, exclusively in all six plants; light green, only in plants.

Fig. 3.—

MicroProtein candidates in transcription factor families in metazoans. The presence of microProtein candidates in human (upper left, red), mouse (upper right, blue), zebrafish (right, yellow), fruit fly (bottom, green) and roundworm (left, gray) in the respective transcription factor family is indicated as bold line.

Fig. 4.—

Gene Ontology and protein class analysis of microProtein-subsets. For all sets, only the most significant ancestor of a microProtein candidate family was analyzed. (A and B) The subsets represent microProtein candidate families with the following conservation in: a: all species; b: all plants; c: all dicots; d: some dicots; e: all monocots; f: some monocots; g: some plants; h: all metazoa; i: all vertebrates; j: some vertebrates; k: nonvertebrates; l: some metazoa. (A) The GO terms are sorted in order of their descending average abundance of all subsets and color coded by their subset specific percent of genes with GO annotation. (B) Selected GO terms extracted from A as indicated by dashed lines. NF, not found. (C) Protein classes that are regulated by Arabidopsis (left) and human (right) high probability microProteins.