Cryo-EM structure of the yeast TREX complex and coordination with the SR-like protein Gbp2

Xie, Yihu; Clarke, Bradley P.; Kim, Yong Joon; Ivey, Austin L.; Hill, Pate S.; Shi, Yi; Ren, Yi

doi:10.7554/elife.65699

Cited by 30 publications

(50 citation statements)

References 66 publications

(105 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Nevertheless, Yra1, much like Sub2, is not a component of export-competent mRNP; it dissociates as a consequence of targeted ubiquitination [ 85 , 86 ] ( Figure 3 B). Further mechanistic details of how TREX executes loading of Mex67MTR2 have implicated the SR protein Gbp2 (see “ Section 2.1 ”), which supports Sub2 loading of Mex67/MTR2 on mRNA and has been suggested to work as an alternative adaptor to Yra1 [ 87 ].…”

Section: Mrnp Export Through the Nuclear Pore Complexmentioning

confidence: 99%

“…In addition to the main adaptor Yra1/AlyREF, SR proteins additionally coordinate the loading of Mex67-NXF1, providing a successful splicing checkpoint, both directly and indirectly. In yeast, Gbp2 supports recruitment of Sub2, the adaptor for Yra1, by THO during mRNP biogenesis [ 87 ], but also cooperates with Mex67 loading on mRNA via protein–protein interaction, together with Hrb1 [ 88 ] , in a splicing-dependent fashion. In murine cells, the strongest direct recruitment of NXF1/Mex67 occurs via the SR proteins SRSF3 and SRSF7 [ 35 ] (see “ Section 3.5 ”).…”

Section: Mrnp Export Through the Nuclear Pore Complexmentioning

confidence: 99%

See 1 more Smart Citation

The Great Escape: mRNA Export through the Nuclear Pore Complex

Magistris

2021

IJMS

View full text Add to dashboard Cite

Nuclear export of messenger RNA (mRNA) through the nuclear pore complex (NPC) is an indispensable step to ensure protein translation in the cytoplasm of eukaryotic cells. mRNA is not translocated on its own, but it forms ribonuclear particles (mRNPs) in association with proteins that are crucial for its metabolism, some of which; like Mex67/MTR2-NXF1/NXT1; are key players for its translocation to the cytoplasm. In this review, I will summarize our current body of knowledge on the basic characteristics of mRNA export through the NPC. To be granted passage, the mRNP cargo needs to bind transport receptors, which facilitate the nuclear export. During NPC transport, mRNPs undergo compositional and conformational changes. The interactions between mRNP and the central channel of NPC are described; together with the multiple quality control steps that mRNPs undergo at the different rings of the NPC to ensure only proper export of mature transcripts to the cytoplasm. I conclude by mentioning new opportunities that arise from bottom up approaches for a mechanistic understanding of nuclear export.

show abstract

Section: Mrnp Export Through the Nuclear Pore Complexmentioning

confidence: 99%

Section: Mrnp Export Through the Nuclear Pore Complexmentioning

confidence: 99%

The Great Escape: mRNA Export through the Nuclear Pore Complex

Magistris

2021

IJMS

View full text Add to dashboard Cite

show abstract

“…Our data allow us to map the crosslinking sites on available 3D structures of the THO-Sub2 complex from yeast containing the proteins Tho2, Hpr1, Thp2, Mft1, Tex1 and Sub2, but no RNA (72)(73)(74), and this in turn gives a picture of how RNA interacts with the proteins Tho2, Hpr1, Mft1 and Sub2…”

Section: Discussionmentioning

confidence: 98%

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA

Keil

Wulf²,

Kachariya

et al. 2022

Preprint

View full text Add to dashboard Cite

RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein-RNA and protein-protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate multiple functions at once and likely impact the structural integrity of the large messenger ribonucleoprotein particle (mRNP) assemblies, these proteins often function in. Using UV-induced RNA-protein crosslinking and subsequent mass spectrometric analysis, we first identified more than 100 in vivo RNA crosslinks in 16 nuclear mRNP components in S. cerevisiae. For functional analysis, we chose Npl3, for which we determined crosslinks in its two RNA recognition motifs (RRM) and in the flexible linker region connecting the two. Using NMR and structural analyses, we show that both RRM domains and the linker uniquely contribute to RNA recognition. Interestingly, mutations in these regions cause different phenotypes, indicating distinct functions of the different RNA-binding domains of Npl3. Notably, the npl3-Linker mutation strongly impairs recruitment of several mRNP components to chromatin and incorporation of further mRNP components into nuclear mRNPs, establishing a function of Npl3 in nuclear mRNP assembly. Taken together, we determined the specific function of the RNA-binding activity of the nuclear mRNP component Npl3, an approach that can be applied to many RBPs in any RNA metabolic process.

show abstract

“…Here, we identified for the first time RNA interaction sites on proteins at amino acid resolution after affinity purification of tagged proteins with their crosslinked RNA isolated from UV-crosslinked cells. Alongside providing a valuable source for in vivo mutagenesis studies, which we outline below, our results allow us to map the crosslinking sites on available 3D structures of the THO-Sub2 complex from yeast, which contain the proteins Tho2, Hpr1, Thp2, Mft1, Tex1 and Sub2, but no RNA (73)(74)(75), resulting in a picture of how RNA interacts with the proteins Tho2, Hpr1, Mft1 and Sub2 (Supplementary Figure S11).…”

Section: Discussionmentioning

confidence: 99%

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA

Keil

Wulf²,

Kachariya

et al. 2022

Nucleic Acids Research

View full text Add to dashboard Cite

RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein–RNA and protein–protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate multiple functions at once and likely impact the structural integrity of the large ribonucleoprotein particles (RNPs) these proteins function in. Using UV-induced RNA–protein crosslinking of entire cells, protein complex purification and mass spectrometric analysis, we identified >100 in vivo RNA crosslinks in 16 nuclear mRNP components in Saccharomyces cerevisiae. For functional analysis, we chose Npl3, which displayed crosslinks in its two RNA recognition motifs (RRMs) and in the connecting flexible linker region. Both RRM domains and the linker uniquely contribute to RNA recognition as revealed by NMR and structural analyses. Interestingly, mutations in these regions cause different phenotypes, indicating distinct functions of the different RNA-binding domains. Notably, an npl3-Linker mutation strongly impairs recruitment of several mRNP components to chromatin and incorporation of other mRNP components into nuclear mRNPs, establishing a so far unknown function of Npl3 in nuclear mRNP assembly. Taken together, our integrative analysis uncovers a specific function of the RNA-binding activity of the nuclear mRNP component Npl3. This approach can be readily applied to RBPs in any RNA metabolic process.

show abstract

Cryo-EM structure of the yeast TREX complex and coordination with the SR-like protein Gbp2

Cited by 30 publications

References 66 publications

The Great Escape: mRNA Export through the Nuclear Pore Complex

The Great Escape: mRNA Export through the Nuclear Pore Complex

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA

Contact Info

Product

Resources

About