A Comprehensive Analysis of MicroProteins Reveals Their Potentially Widespread Mechanism of Transcriptional Regulation  

Abstract

Truncated transcription factor-like proteins called microProteins (miPs) can modulate transcription factor activities, thereby increasing transcriptional regulatory complexity. To understand their prevalence, evolution, and function, we predicted over 400 genes that encode putative miPs from Arabidopsis (Arabidopsis thaliana) using a bioinformatics pipeline and validated two novel miPs involved in flowering time and response to abiotic and biotic stress. We provide an evolutionary perspective for a class of miPs targeting homeodomain transcription factors in plants and metazoans. We identify domain loss as one mechanism of miP evolution and suggest the possible roles of miPs on the evolution of their target transcription factors. Overall, we reveal a prominent layer of transcriptional regulation by miPs, show pervasiveness of such proteins both within and across genomes, and provide a framework for studying their function and evolution.

Found in translation: functions and evolution of a recently discovered alternative proteome

“…Similar small proteins that contain protein-protein interaction domains and that regulate the assembly of functional protein complexes have been termed microproteins, by analogy with the action of microRNAs on mRNAs [16,17]. Microproteins may be as small as 34 aa long and block the assembly of functional transcription complexes [18]. Future functional studies will determine whether the regulatory role of small proteins in the assembly and function of protein complexes is a common mode of action.…”

TWS1, a Novel Small Protein, Regulates Various Aspects of Seed and Plant Development

“…Large proteins are easily annotated and more often studied, while shorter proteins tend to be ignored because they pose additional experimental challenges compared to larger proteins. However, with the recent availability of a great array of genome and transcriptome data, an increasing number of SPs have been identified and studied, demonstrating that SPs are widespread and have fundamental functions in all domains of life (Su et al, 2013;Magnani et al, 2014). SPs usually contain a single domain, tend to be nonconventional proteins, and seem to possess lineage-specific or tissue-specific functions (Zhao, 2012;Su et al, 2013).…”

MicroProteins: small size – big impact

“…A recent study found a list of potential miPs that show a sequence similarity to TFs but lack a DBD [34]. The authors identified 438 TF-related proteins and referred to these as putative miPs.…”

“…The absence of a domain does not necessarily lead to an inhibitory effect, as evidenced by the two proof-of-concept potential miP candidates that were selected in the above study [34]. The first protein, LITTLE SIPPER (SPPR), is a 52-kDa multidomain protein that regulates HD-Zip IV FLOWERING WAGENINGEN (FWA) [34].…”

“…The first protein, LITTLE SIPPER (SPPR), is a 52-kDa multidomain protein that regulates HD-Zip IV FLOWERING WAGENINGEN (FWA) [34]. Although SPPR contained sequence similarity to FWA and interacted with it, SPPR showed no other characteristics of a miP.…”