YB-3 substitutes YB-1 in global mRNA binding

Abstract

Y-box binding proteins are DNA-and RNA-binding proteins with an evolutionarily ancient and conserved cold shock domain. The Y-box binding protein 1 (YB-1) is the most studied due to its abundance in somatic cells. YB-1 is involved in a variety of cellular processes, including proliferation, differentiation and stress response. Here, using Ribo-Seq and RIP-Seq we confirm that YB-1 binds a wide range of mRNAs and globally acts as a translation inhibitor. Surprisingly, YBX1 knockout results in only minor alterations in the expression of other genes, mostly caused by changes in RNA abundance. But YB-3 mRNA is an exception: it is better translated in the absence of YB-1, thereby producing an increased amount of YB-3 and thus suggesting that its synthesis is under YB-1 negative control. We have shown that the set of mRNAs bound to YB-3 is strikingly similar to that of YB-1, and that the mRNA-binding by YB-3 is enhanced in the absence of YB-1, resulting in a similar global reduction of translation of bound mRNAs in YB-1-null cells. Thus, YB-3 acts as a substitute for YB-1 in mRNA binding and, probably, in global translational control. ARTICLE HISTORY

Y-Box Binding Proteins in mRNP Assembly, Translation, and Stability Control

“…Probably other YB proteins, such as YB-2 and YB-3, or other RBPs functionally compensate for the YB-1 loss. This hypothesis is supported by the observation of even more severe malformations and an earlier death of the YB-1 and MSY4 (mouse YB-3) double knockout embryos [104], as well as by the recent discovery of the functional interchangeability of YB-1 and YB-3 in HEK293T cells [79].…”

“…For YB-3, eCLIP (enhanced CLIP) showed that it binds a broad set of specific RNAs without a discernible binding motif (8727 binding regions within 4018 RNAs) in HeLa cells [78]. In addition, the RIP-Seq (RNA Immunoprecipitation Sequencing) analysis showed that in HEK293T cells, the mRNA sets bound to YB-1 and YB-3 are almost the same, and they amount to about 80% of the transcriptome [79]. Yet, the specificity of these proteins is somewhat different.…”

“…For a long time, doubts were cast upon the role of YB proteins in the global translation inhibition in somatic cells. The recent development of high-throughput techniques allowed demonstrating a decrease in global translation resulting from YB-1 or YB-3 overexpression [79]. Moreover, the magnitude of translation inhibition correlates with the efficiency of YB-1 or YB-3 binding to mRNAs, thus indicating the direct impact of YB proteins [79].…”

“…The recent development of high-throughput techniques allowed demonstrating a decrease in global translation resulting from YB-1 or YB-3 overexpression [79]. Moreover, the magnitude of translation inhibition correlates with the efficiency of YB-1 or YB-3 binding to mRNAs, thus indicating the direct impact of YB proteins [79]. However, the decrease in global translation does not exceed 20%, probably because not all mRNAs are packaged into untranslated mRNPs even with overexpressed YB proteins.…”

“…As was discussed previously, YB-1 acts as the general and specific translation inhibitor for hundreds of mRNAs; hence, an increase in global translation may be expected upon YB-1 knockout. Quite the opposite, YB-1 knockout produces a slight decline in global translation in mouse and human cells [79,103]. This fact can be explained as follows.…”