YB-1, an abundant core mRNA-binding protein, has the capacity to form an RNA nucleoprotein filament: a structural analysis

Abstract

The structural rearrangements accompanying mRNA during translation in mammalian cells remain poorly understood. Here, we discovered that YB-1 (YBX1), a major partner of mRNAs in the cytoplasm, forms a linear nucleoprotein filament with mRNA, when part of the YB-1 unstructured C-terminus has been truncated. YB-1 possesses a cold-shock domain (CSD), a remnant of bacterial cold shock proteins that have the ability to stimulate translation under the low temperatures through an RNA chaperone activity. The structure of the nucleoprotein filament indicates that the CSD of YB-1 preserved its chaperone activity also in eukaryotes and shows that mRNA is channeled between consecutive CSDs. The energy benefit needed for the formation of stable nucleoprotein filament relies on an electrostatic zipper mediated by positively charged amino acid residues in the YB-1 C-terminus. Thus, YB-1 displays a structural plasticity to unfold structured mRNAs into extended linear filaments. We anticipate that our findings will shed the light on the scanning of mRNAs by ribosomes during the initiation and elongation steps of mRNA translation.

Optimization of Golden Gate assembly through application of ligation sequence-dependent fidelity and bias profiling

“…Several other high AT% overhangs, such as AAAA and TTTT, were also seen in reduced numbers as compared to the average overhang. This result mirrored our previous observation in three-base overhangs that TNA overhangs ligate significantly slower than the reciprocal ANT overhangs (21).…”

“…The substrate for the four-base overhang ligation fidelity assay was produced using the protocol previously published for three-base overhangs, with the following modifications (21). Initial PAGEpurified substrate precursor oligonucleotide (IDT) contained a 5′-terminal region, a randomized fourbase region, a BsaI binding site, a constant region, an internal 6-base randomized region as a control for synthesis bias, and a region corresponding to the SMRT-bell sequencing adapter for Pacific Biosciences SMRT sequencing (Supplementary Data, Table S1).…”

“…The oligonucleotide was designed with a short (7-base) complementary region such that they form a primer-template junction hairpin structure ( Figure 1). The precursor oligonucleotide was extended as per the published method (21).…”

“…Here, we report the application of a single-molecule, next-generation sequencing assay to probe the fidelity of DNA ligase end-joining in the context of four-base overhangs (Figure 1). Applying our previously reported sequencing method for profiling ligase end-joining fidelity (21), we have quantified the ligation efficiency of all four-base Watson-Crick pairs and the prevalence of all possible mismatched overhang combinations by T4 DNA ligase at 25 and 37°C with typical buffer conditions lacking molecular crowding agents. We have further applied this data to predict the accuracy of a tenfragment Golden Gate assembly, demonstrating the ability to predict overall assembly fidelity, specific assembly errors, and ligation pairs that exhibit relatively low ligation efficiency despite perfectly complementary overhangs.…”

Class I HDAC inhibitors enhance YB ‐1 acetylation and oxidative stress to block sarcoma metastasis

“…Notably, mutation of YB‐1‐K81 (K81E) has been reported in human tumors (http://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=YBX1), although the functional significance of this finding remains to be established. Of interest, YB‐1 was recently shown to form nucleoprotein filaments with bound mRNAs in the cytoplasm, thus potentially increasing translational efficiency of its target mRNAs by converting them into extended linear forms . It will be of interest to determine how YB‐1 acetylation by MS‐275 affects this function.…”