Wenkel, Stephan - Small proteins controlling development and adaptation

Research

Portrait photo of Stephan Wenkel We are interested in understanding how plants use small proteins to dynamically adjust growth and development in response to environmental changes.

There is growing evidence that proteomes are more complex than previously anticipated. For instance, until recently, genes coding for proteins with fewer than 100 amino acids were often labeled as artefacts. As a result, many such small open reading frames were excluded in genome annotations. Moreover, in addition to these single, individual, open reading frames, small proteins can also arise through processes such as alternative splicing or alternative use of transcription start sites. Thus, one gene can code for more than one protein. These and other processes result in a much larger number of protein species in a given cell compared to the number of protein-coding genes in the genome.

Figure showing a circle with a blue and green coloured outer circel and lines connecting different parts of the outer circle with each otherFigure 1: 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. Has: Homo sapiens; Mmu: Mus musculus; Dre: Danio rerio; Dme: Drosophila melanogaster; Cel: Caenorhabditis elegans; Ath: Arabidopsis thaliana; Sly: Solanum lycopersicum; Stu: Solanum tuberosum; Sbi: Sorghum bicolor; Osa: Oryza sativa; Zma: Zea mays. From: Straub and Wenkel, Genome Biol. Evol. 9(3):777–789, 2017.

In our research, we use both protein-centric approaches (starting with the identification and characterization of specific small proteins, often microProteins) and process-oriented approaches, where we try to understand how plants dynamically change their developmental decisions in response to environmental changes. To identify small proteins, such as microProteins in any sequenced genome, we developed miPFinder that can classify small proteins as microProteins (Fig. 1, Straub and Wenkel, 2017). Biological processes we study involve the promotion of growth in response to shading or the induction of flowering in response to day length and temperature. One of the things we have been able to show is that small B-box microProteins can strongly influence flowering (Fig.2 and Graeff et al., 2016).

Five Arabidopsis plants in front of a black background, only the first one has inflorescencesFigure 2: Transgenic plants with elevated microProtein levels are late flowering under inductive long day conditions. Image of representative late flowering mutants co and ft and transgenic plants overexpressing two microProteins (35S::miP1a and 35S::miP1b) compared to a Col-0 wild type plant of the same age. From: Graeff et al., PLOS Genetics | DOI:10.1371/journal.pgen.1005959; 2016.

The next steps

Owing to their small size and the predictability of protein interactions, microProteins are suitable for the regulation of biotechnological processes. With the help of new genome engineering tools, we are currently exploring the possibilities of generating microProteins de novo to control developmental pathways at will.