Quantitative proteomic dataset of the moss Physcomitrium patens PSEP3 KO and OE mutant lines

Abstract

Small open reading frames (<100 codons) that are located on long noncoding RNAs (lncRNAs) can encode functional microproteins. These microproteins are shown to play important roles in different cellular processes, such as cell proliferation, development and disease response [1] , [2] , [3] , [4] , [5] , [6] . However, there are only a few known lncRNA-encoded functional microproteins in plants. One such microprotein that was named PSEP3, was identified in the moss Physcomitrium patens by mass-spectrometry analysis. 57-aa PSEP3 contains Low Complexity Region (LCR) enriched with proline. We have previously shown that PSEP3 is translated in protonemata and gametophores of P. patens , and its knockout (KO line) or overexpression (OE line) affects protonemata growth [7] . We performed a quantitative proteomic analysis of the mutant lines with PSEP3 knockout and overexpression. 7-days old protonemata of wild type (WT line) and both mutant lines (KO and OE) were collected and used for iTRAQ-based proteomic experiments. LC-MS/MS data were processed using PEAKS Studio v.8 software with protein identification based on a Phytozome protein database. More analysis of PSEP3 effects on plant growth can be obtained in the paper published in Nucleic Acid Research [8] .

Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long “Non-Coding” RNAs

“…Overexpression and knockdown studies of these lncRNA-encoded peptides have revealed morphological variations showing their role in moss growth and development: (i) knocking out a 40-aa peptide encoded by lncRNA Pp3c18_sORF57 showed a slight decrease in moss plant diameter on medium with glucose and without ammonium tartrate. Moreover, no changes have been observed in protonemal architecture and the number of leafy shoots or filament branching in knockouts; (ii) overexpression of a 41-aa peptide encoded by the Pp3c9_sORF1544 results in longer filaments implicated in a rapid radial extension of the protonemal tissues compared to the wild-type lines; (iii) knocking out a 61-aa peptide encoded by conserved Pp3c25_sORF1000 results in a decrease in growth rate and altered protonemal architecture on medium without glucose but supplemented with ammonium tartrate; (iv) the lines with a knockout in a 57-aa peptide encoded by an additional conservative lncRNA Pp3c25_sORF1253 display a decrease in protonemata growth rate and altered filament branching [ 40 , 42 ].…”

“…Particularly, the CRISPR-cas9-mediated gene editing approach can be applied to check the potential activities of peptides. Alternatively, in planta overexpression of small peptides or expression driven by a native promoter, there may also be useful ways to study the lncRNA-encoded peptide functions via genetic approaches [ 17 , 24 , 40 , 41 , 42 ]. On the other hand, the use of artificially produced lncRNA-encoded peptides with a high purity and/or desired labeling provides an effective tool for studying plant small peptide functions.…”

“…In principle, these peptides can be obtained by chemical synthesis. In addition, the in vitro translation and overexpression in microbe cells can be used (for example, see [ 17 , 24 , 42 , 43 ]).…”

Pervasive translation of small open reading frames in plant long non-coding RNAs

“…This shows that a small proportion of the identified lncRNAs are potential pseudogenes. Overexpression and knockout of P.patens lncORFs Pp3c9_sORF1554, Pp3c25_sORF1253, Pp3c25_sORF1000, and Pp3c18_ resulted in morphological changes ( Mamaeva et al., 2022 ).…”

Proteome plasticity during Physcomitrium patens spore germination – from the desiccated phase to heterotrophic growth and reconstitution of photoautotrophy

“…Making use of this genetic resource, several proteomic datasets were acquired in the last two decades giving insights into abiotic stress and desiccation tolerance‐associated proteins in protonema and gametophores (Cho et al., 2006; Cui et al., 2012; Luo et al., 2020; Mamaeva et al., 2022; Sarnighausen et al., 2004; Skripnikov et al., 2009; Toshima et al., 2014; Wang et al., 2010; Wang, Yang, Zhang, et al., 2009; Wang, Yang, Liu, et al., 2009; Wang et al., 2008; Yotsui et al., 2016).…”