RT Journal
A1 Fesenko, Igor
A1 Kirov, Ilya
A1 Kniazev, Andrey
A1 Khazigaleeva, Regina
A1 Lazarev, Vassili
A1 Kharlampieva, Daria
A1 Grafskaia, Ekaterina
A1 Zgoda, Viktor
A1 Butenko, Ivan
A1 Arapidi, Georgy
A1 Mamaeva, Anna
A1 Ivanov, Vadim
A1 Govorun, Vadim
T1 Distinct types of short open reading frames are translated in plant cells
JF Genome Research 
JO Genome Research 
YR 2019 
FD September 01 
VO 29 
IS 9 
SP 1464 
OP 1477 
DO 10.1101/gr.253302.119 
UL http://genome.cshlp.org/content/29/9/1464.abstract 
AB Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Functional analysis of four lncRNA-encoded peptides showed that sORFs-encoded peptides are involved in regulation of growth and differentiation in moss. Knocking out lncRNA-encoded peptides resulted in a decrease of moss growth. In contrast, the overexpression of these peptides resulted in a diverse range of phenotypic effects. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.