Pre-ribosomal particles from nucleoli to cytoplasm

References

• Shore D, Albert B. Ribosome biogenesis and the cellular energy economy. Curr Biol. 2022;32(12):R611–12. doi: 10.1016/j.cub.2022.04.083
   PubMed Web of Science ®Google Scholar
• Sloan KE, Gleizes P-E, Bohnsack MT. Nucleocytoplasmic transport of RNAs and RNA-Protein complexes. J Mol Biol. 2015:1–20. Available from 10.1016/j.jmb.2015.09.023
   Web of Science ®Google Scholar
• Baßler J, Hurt E. Eukaryotic Ribosome Assembly. Annu Rev Biochem. 2018;88(1):281–306. doi: 10.1146/annurev-biochem-013118-110817
   PubMedGoogle Scholar
• Dundr M, Hoffmann-Rohrer U, Hu Q, et al. A kinetic framework for a mammalian RNA polymerase in vivo. Science. 2002;298(5598):1623–1626. doi: 10.1126/science.1076164
   PubMed Web of Science ®Google Scholar
• Hori Y, Engel C, Kobayashi T. Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol. 2023;24(6):414–429. doi: 10.1038/s41580-022-00573-9
   PubMed Web of Science ®Google Scholar
• Lam YW, Trinkle-Mulcahy L. New insights into nucleolar structure and function. F1000Prime Rep. 2015;7:48. Available from: http://f1000.com/prime/reports/b/7/48
   PubMedGoogle Scholar
• Yao R-W, Xu G, Wang Y, et al. Nascent pre-rRNA sorting via phase separation drives the assembly of dense fibrillar components in the Human Nucleolus. Mol Cell. 2019;76(5):767–783.e11. doi: 10.1016/j.molcel.2019.08.014
   PubMed Web of Science ®Google Scholar
• Miller OL Jr., Beatty BR. Visualization of Nucleolar Genes. Science. 1969;164:955–957. doi: 10.1126/science.164.3882.955
   PubMed Web of Science ®Google Scholar
• Broeck AV, Klinge S. Principles of human pre-60S biogenesis. Science. 2023;381(6653):eadh3892. doi: 10.1126/science.adh3892
   PubMed Web of Science ®Google Scholar
• Yao R-W, Xu G, Wang Y, et al. Nascent Pre-rRNA sorting via phase separation drives the assembly of dense fibrillar components in the human nucleolus. Mol Cell. 2019;76(5):767–783.e11. doi: 10.1016/j.molcel.2019.08.014
   PubMed Web of Science ®Google Scholar
• Lewis JD, Tollervey D. Like attracts like: getting RNA processing together in the nucleus. Science. 2000;288(5470):1385–1389. doi: 10.1126/science.288.5470.1385
   PubMed Web of Science ®Google Scholar
• Erdmann PS, Hou Z, Klumpe S, et al. In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli. Nat Commun. 2021;12(1):5364. doi: 10.1038/s41467-021-25413-w
   PubMed Web of Science ®Google Scholar
• Kuersten S, Ohno M, Mattaj IW. Nucleocytoplasmic transport: ran, beta and beyond. Trends Cell Biol. 2001;11(12):497–503. doi: 10.1016/S0962-8924(01)02144-4
   PubMed Web of Science ®Google Scholar
• Ameismeier M, Cheng J, Berninghausen O, et al. Visualizing late states of human 40S ribosomal subunit maturation. Nature. 2018;558(7709):249–253. doi: 10.1038/s41586-018-0193-0
   PubMed Web of Science ®Google Scholar
• Liang X, Zuo M-Q, Zhang Y, et al. Structural snapshots of human pre-60S ribosomal particles before and after nuclear export. Nat Commun. 2020;11(1):3542–14. doi: 10.1038/s41467-020-17237-x
   PubMed Web of Science ®Google Scholar
• Cowburn D, Rout M. Improving the hole picture: towards a consensus on the mechanism of nuclear transport. Biochem Soc Trans. 2023;51(2):871–886. doi: 10.1042/BST20220494
   PubMed Web of Science ®Google Scholar
• Ritland Politz JC, Tuft RA, Pederson T. Diffusion-based transport of nascent ribosomes in the nucleus. Mol Biol Cell. 2003;14(12):4805–4812. doi: 10.1091/mbc.e03-06-0395
   PubMed Web of Science ®Google Scholar
• Vargas DY, Raj A, Marras SAE, et al. Mechanism of mRNA transport in the nucleus. Proc Natl Acad Sci. 2005;102(47):17008–17013. doi: 10.1073/pnas.0505580102
   PubMed Web of Science ®Google Scholar
• Veith R, Sorkalla T, Baumgart E, et al. Balbiani Ring mRnps diffuse through and bind to clusters of large intranuclear molecular structures. Biophys J. 2010;99(8):2676–2685. doi: 10.1016/j.bpj.2010.08.004
   PubMed Web of Science ®Google Scholar
• Phair RD, Misteli T. High mobility of proteins in the mammalian cell nucleus. Nature. 2000;404(6778):604–609. doi: 10.1038/35007077
   PubMed Web of Science ®Google Scholar
• Spille J-H, Kaminski TP, Scherer K, et al. Direct observation of mobility state transitions in RNA trajectories by sensitive single molecule feedback tracking. Nucl Acids Res. 2015;43(2):e14. doi: 10.1093/nar/gku1194
   PubMed Web of Science ®Google Scholar
• Landvogt L, Ruland JA, Montellese C, et al. Observing and tracking single small ribosomal subunits in vivo. Methods. 2019;153:63–70. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1046202318300859
   PubMed Web of Science ®Google Scholar
• Ruland JA, Krüger AM, Dörner K, et al. Nuclear export of the pre-60S ribosomal subunit through single nuclear pores observed in real time. Nat Commun. 2021;12(1):6211. doi: 10.1038/s41467-021-26323-7
   PubMed Web of Science ®Google Scholar
• Siebrasse JP, Kaminski T, Kubitscheck U. Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy. Proc Natl Acad Sci. 2012;109(24):9426–9431. doi: 10.1073/pnas.1201781109
   PubMed Web of Science ®Google Scholar
• Woolls HA, Lamanna AC, Karbstein K. Roles of Dim2 in ribosome Assembly*. J Biol Chem. 2011;286(4):2578–2586. doi: 10.1074/jbc.M110.191494
   PubMed Web of Science ®Google Scholar
• Zemp I, Wild T, O’Donohue M-F, et al. Distinct cytoplasmic maturation steps of 40S ribosomal subunit precursors require hRio2. J Cell Biol. 2009;185:1167–1180. doi: 10.1083/jcb.200904048
   PubMed Web of Science ®Google Scholar
• Baum M, Erdel F, Wachsmuth M, et al. Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells. Nat Commun. 2014;5(1):4494. doi: 10.1038/ncomms5494
   PubMedGoogle Scholar
• Hertzog M, Erdel F. The material properties of the cell nucleus: a matter of scale. Cells. 2023;12(15):1958. doi: 10.3390/cells12151958
   PubMed Web of Science ®Google Scholar
• Eliscovich C, Singer RH. RNP transport in cell biology: the long and winding road. Curr Opin Cell Biol. 2017;45:38–46. doi: 10.1016/j.ceb.2017.02.008
   PubMed Web of Science ®Google Scholar
• Basu U, Si K, Warner JR, et al. The Saccharomyces cerevisiae TIF6 gene encoding translation initiation factor 6 is required for 60S ribosomal subunit biogenesis. Mol Cell Biol. 2001;21(5):1453–1462. doi: 10.1128/MCB.21.5.1453-1462.2001
   PubMed Web of Science ®Google Scholar
• Gallo S, Beugnet A, Biffo S. Tagging of functional ribosomes in living cells by HaloTag® technology. Vitro Cell Dev Biol Anim. 2011;47(2):132–138. Available from: http://pubmed.gov/21082278
   PubMed Web of Science ®Google Scholar
• Nehrbass U, Blobel G. Role of the nuclear transport factor p10 in nuclear import. Science. 1996;272(5258):120–122. doi: 10.1126/science.272.5258.120
   PubMed Web of Science ®Google Scholar
• Kubitscheck U, Grünwald D, Hoekstra A, et al. Nuclear transport of single molecules. J Cell Biol. 2005;168(2):233–243. doi: 10.1083/jcb.200411005
   PubMed Web of Science ®Google Scholar
• Presman DM, Ball DA, Paakinaho V, et al. Quantifying transcription factor binding dynamics at the single-molecule level in live cells. Methods. 2017;123:76–88. doi: 10.1016/j.ymeth.2017.03.014
   PubMed Web of Science ®Google Scholar
• Dross N, Spriet C, Zwerger M, et al. Mapping eGFP oligomer mobility in living cell nuclei. PLoS One. 2009;4(4):e5041. doi: 10.1371/journal.pone.0005041
   PubMed Web of Science ®Google Scholar
• Spille J-H, Kubitscheck U. Labelling and imaging of single endogenous messenger RNA particles in vivo. J Cell Sci. 2015;128:3695–3706. doi: 10.1242/jcs.166728
   PubMed Web of Science ®Google Scholar
• Kubitscheck U, Wedekind P, Zeidler O, et al. Single nuclear pores visualized by confocal microscopy and image processing. Biophys J. 1996;70(5):2067–2077. doi: 10.1016/S0006-3495(96)79811-9
   PubMed Web of Science ®Google Scholar
• Ribbeck K, Görlich D. Kinetic analysis of translocation through nuclear pore complexes. Embo J. 2001;20(6):1320–1330. doi: 10.1093/emboj/20.6.1320
   PubMed Web of Science ®Google Scholar
• Lin DH, Hoelz A. The structure of the nuclear pore complex (an update). Ann Rev Biochem. 2019;88(1):725–783. doi: 10.1146/annurev-biochem-062917-011901
   PubMed Web of Science ®Google Scholar
• Frey S, Görlich D. A saturated FG-Repeat Hydrogel can reproduce the permeability properties of nuclear pore complexes. Cell. 2007;130(3):512–523. doi: 10.1016/j.cell.2007.06.024
   PubMed Web of Science ®Google Scholar
• Aramburu IV, Lemke EA. Floppy but not sloppy: Interaction mechanism of FG-nucleoporins and nuclear transport receptors. Semin Cell Dev Biol. 2017;68:34–41. doi: 10.1016/j.semcdb.2017.06.026
   PubMed Web of Science ®Google Scholar
• Schuller AP, Wojtynek M, Mankus D, et al. The cellular environment shapes the nuclear pore complex architecture. Nature. 2021;598(7882):667–671. doi: 10.1038/s41586-021-03985-3
   PubMed Web of Science ®Google Scholar
• Zimmerli CE, Allegretti M, Rantos V, et al. Nuclear pores dilate and constrict in cellulo. Science. 2021;374(6573):eabd9776. doi: 10.1126/science.abd9776
   PubMed Web of Science ®Google Scholar
• Paci G, Zheng T, Caria J, et al. Molecular determinants of large cargo transport into the nucleus. Elife. 2020;9:e55963. doi: 10.7554/eLife.55963
   PubMed Web of Science ®Google Scholar
• Rajan AAN, Montpetit B. Emerging molecular functions and novel roles for the DEAD-box protein Dbp5/DDX19 in gene expression. Cell Mol Life Sci. 2021;78(5):2019–2030. doi: 10.1007/s00018-020-03680-y
   PubMed Web of Science ®Google Scholar
• Tieg B, Krebber H. Dbp5 — from nuclear export to translation. BBA Gene Reg Mech. 2013;1829(8):791–798. doi: 10.1016/j.bbagrm.2012.10.010
   Google Scholar
• Yao W, Roser D, Köhler A, et al. Nuclear export of ribosomal 60S subunits by the general mRNA export receptor Mex67-Mtr2. Mol Cell. 2007;26:51–62. doi: 10.1016/j.molcel.2007.02.018
   PubMed Web of Science ®Google Scholar
• Wild T, Horvath P, Wyler E, et al. A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. PLoS Biol. 2010;8(10):e1000522. doi: 10.1371/journal.pbio.1000522
   PubMed Web of Science ®Google Scholar
• Güttler T, Görlich D. Ran‐dependent nuclear export mediators: a structural perspective. Embo J. 2011;30(17):3457–3474. doi: 10.1038/emboj.2011.287
   PubMed Web of Science ®Google Scholar
• Peña C, Hurt E, Panse VG. Eukaryotic ribosome assembly, transport and quality control. Nat Struct Mol Biol. 2017;24(9):689–699. doi: 10.1038/nsmb.3454
   PubMed Web of Science ®Google Scholar
• Dörner K, Ruggeri C, Zemp I, et al. Ribosome biogenesis factors—from names to functions. Embo J. 2023;42(7):e112699. doi: 10.15252/embj.2022112699
   PubMed Web of Science ®Google Scholar
• Zemp I, Wild T, O’Donohue M-F, et al. Distinct cytoplasmic maturation steps of 40S ribosomal subunit precursors require hRio2. J Cell Bio. 2009;185:1167–1180. doi: 10.1083/jcb.200904048
   PubMed Web of Science ®Google Scholar
• Landry-Voyer A-M, Bilodeau S, Bergeron D, et al. Human PDCD2L is an export substrate of CRM1 that associates with 40S ribosomal subunit precursors. Mol Cell Biol. 2016;36(24):3019–3032. doi: 10.1128/MCB.00303-16
   PubMed Web of Science ®Google Scholar
• Delavoie F, Soldan V, Rinaldi D, et al. The path of pre-ribosomes through the nuclear pore complex revealed by electron tomography. Nat Commun. 2019;10(1):497. doi: 10.1038/s41467-019-08342-7
   PubMedGoogle Scholar
• Winey M, Yarar D, Giddings TH, et al. Nuclear pore complex number and distribution throughout the Saccharomyces cerevisiae cell cycle by three-dimensional reconstruction from electron micrographs of nuclear envelopes. Mol Biol Cell. 1997;8(11):2119–2132. doi: 10.1091/mbc.8.11.2119
   PubMed Web of Science ®Google Scholar
• Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999;24(11):437–440. doi: 10.1016/S0968-0004(99)01460-7
   PubMed Web of Science ®Google Scholar
• Akey CW, Singh D, Ouch C, et al. Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell. 2022;185(2):361–378.e25. doi: 10.1016/j.cell.2021.12.015
   PubMed Web of Science ®Google Scholar
• Li Z, Chen S, Zhao L, et al. Nuclear export of pre-60S particles through the nuclear pore complex. Nature. 2023;618(7964):411–418. doi: 10.1038/s41586-023-06128-y
   PubMed Web of Science ®Google Scholar
• Huff J. The Airyscan detector from ZEISS: confocal imaging with improved signal-to-noise ratio and super-resolution. Nat Methods. 2015;12(12):i–ii. doi: 10.1038/nmeth.f.388
   Web of Science ®Google Scholar
• Junod SL, Tingey M, Kelich JM, et al. Dynamics of nuclear export of pre-ribosomal subunits revealed by high-speed single-molecule microscopy in live cells. iScience. 2023;26(8):107445. doi: 10.1016/j.isci.2023.107445
   PubMed Web of Science ®Google Scholar
• Ribbeck K, Görlich D. The permeability barrier of nuclear pore complexes appears to operate via hydrophobic exclusion. Embo J. 2002;21(11):2664–2671. doi: 10.1093/emboj/21.11.2664
   PubMed Web of Science ®Google Scholar
• Li Y, Aksenova V, Tingey M, et al. Distinct roles of nuclear basket proteins in directing the passage of mRNA through the nuclear pore. Proc Natl Acad Sci. 2021:118. Available from: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=34504007&retmode=ref&cmd=prlinks
   Web of Science ®Google Scholar
• Lowe AR, Siegel JJ, Kalab P, et al. Selectivity mechanism of the nuclear pore complex characterized by single cargo tracking. Nature. 2010. Available from: http://www.nature.com/nature/journal/v467/n7315/abs/nature09285.html
   Web of Science ®Google Scholar
• Tu L-C, Fu G, Zilman A, et al. Large cargo transport by nuclear pores: implications for the spatial organization of FG-nucleoporins. Embo J. 2013;32(24):3220–3230. doi: 10.1038/emboj.2013.239
   PubMed Web of Science ®Google Scholar
• Karbstein K. Quality control mechanisms during ribosome maturation. Trends Cell Biol. 2013;23(5):242–250. doi: 10.1016/j.tcb.2013.01.004
   PubMed Web of Science ®Google Scholar
• Saroufim M-A, Bensidoun P, Raymond P, et al. The nuclear basket mediates perinuclear mRNA scanning in budding yeast. J Cell Bio. 2015;211(6):1131–1140. doi: 10.1083/jcb.201503070
   PubMed Web of Science ®Google Scholar
• Soheilypour M, Mofrad MRK. Quality control of mRNAs at the entry of the nuclear pore: cooperation in a complex molecular system. Nucleus. 2018;9(1):202–211. doi: 10.1080/19491034.2018.1439304
   PubMed Web of Science ®Google Scholar
• Hutten S, Kehlenbach RH. CRM1-mediated nuclear export: to the pore and beyond. Trends Cell Biol. 2007;17(4):193–201. doi: 10.1016/j.tcb.2007.02.003
   PubMed Web of Science ®Google Scholar
• Kehlenbach RH, Dickmanns A, Kehlenbach A, et al. A role for RanBP1 in the release of CRM1 from the nuclear pore complex in a terminal step of nuclear export. J Cell Bio. 1999;145(4):645–657. doi: 10.1083/jcb.145.4.645
   PubMed Web of Science ®Google Scholar
• Hutten S, Kehlenbach RH. Nup214 is required for CRM1-dependent nuclear protein export in vivo. Mol Cell Biol. 2006;26(18):6772–6785. doi: 10.1128/MCB.00342-06
   PubMed Web of Science ®Google Scholar
• Gleizes P-E, Noaillac-Depeyre J, Léger-Silvestre I, et al. Ultrastructural localization of rRNA shows defective nuclear export of preribosomes in mutants of the Nup82p complex. J Cell Bio. 2001;155(6):923–936. doi: 10.1083/jcb.200108142
   PubMed Web of Science ®Google Scholar
• Bernad R, van der VH, Fornerod M, et al. Nup358/RanBP2 attaches to the nuclear pore complex via association with Nup88 and Nup214/CAN and plays a supporting role in CRM1-mediated nuclear protein export. Mol Cell Biol. 2004;24(6):2373–2384. doi: 10.1128/MCB.24.6.2373-2384.2004
   PubMed Web of Science ®Google Scholar
• Lin DH, Correia AR, Cai SW, et al. Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat Commun. 2018;9(1):1–19. doi: 10.1038/s41467-018-04459-3
   PubMedGoogle Scholar
• Li Y, Zhou J, Min S, et al. Distinct RanBP1 nuclear export and cargo dissociation mechanisms between fungi and animals. Elife. 2019;8:e41331. doi: 10.7554/eLife.41331
   PubMed Web of Science ®Google Scholar
• Kubitscheck U, Siebrasse JP. Kinetics of transport through the nuclear pore complex. Semin Cell Dev Biol. 2017;68:18–26. doi: 10.1016/j.semcdb.2017.06.016
   PubMed Web of Science ®Google Scholar
• Ma J, Liu Z, Michelotti N, et al. High-resolution three-dimensional mapping of mRNA export through the nuclear pore. Nat Commun. 2013;4(1):2414–2414. doi: 10.1038/ncomms3414
   PubMedGoogle Scholar
• Chowdhury R, Sau A, Musser SM. Super-resolved 3D tracking of cargo transport through nuclear pore complexes. Nat Cell Biol. 2022;24(1):112–122. doi: 10.1038/s41556-021-00815-6
   PubMed Web of Science ®Google Scholar
• Yu M, Heidari M, Mikhaleva S, et al. Visualizing the disordered nuclear transport machinery in situ. Nature. 2023;617(7959):162–169. doi: 10.1038/s41586-023-05990-0
   PubMed Web of Science ®Google Scholar