Bonmati EM, Fang X, Maple R, Fiedler M, Passmore LA, Dean CA. (2023) The CPSF phosphatase module links transcription termination to chromatin silencing bioRxiv doi.org/10.1101/2023.07.06.547976
Höpfler M, Absmeier E, Peak-Chew SY, Vartholomaiou E, Passmore LA, Gasic I, Hegde RS. (2023) Mechanism of ribosome-associated mRNA degradation during tubulin autoregulation. Mol Cell 83, 2290-2303. doi.org/10.1016/j.molcel.2023.05.020
EMDB: EMD-16155, PDB: 8BPO, EMPIAR-11593
Boreikaite V, Passmore LA*. (2023) 3′-End Processing of Eukaryotic mRNA: Machinery, Regulation, and Impact on Gene Expression. Ann Rev Biochem 92, 199-225. doi.org/10.1146/annurev-biochem-052521-012445
Absmeier E†, Chandrasekaran V†*, O’Reilly FJ, Stowell JAW, Rappsilber J, Passmore LA*. (2023) Specific recognition and ubiquitination of slow-moving ribosomes by human CCR4-NOT. Nat Struct Mol Biol 30, 1314–1322.
bioRxiv doi.org/10.1101/2022.07.24.501325
EMDB: EMD-16052, PDB: 8BHF, EMPIAR-11593
Research Briefing: Mammalian CCR4–NOT binds and ubiquitinates 80S ribosomes to enforce translational stalling (2023) Nat Struct Mol Biol 30, 1254-1255 doi:10.1038/s41594-023-01079-4
Rodríguez-Molina JB, West S*, Passmore LA*. (2023) Knowing when to stop: Transcription termination on protein-coding genes by eukaryotic RNAPII. Mol Cell 83, 404-415. doi: 10.1016/j.molcel.2022.12.021.
Carminati M, Manav MC, Bellini D, Passmore LA*. (2023) A direct interaction between CPF and RNA Pol II RNA 3ʹ-end processing to transcription. Mol Cell 83, 4461-4478.
bioRxiv doi.org/10.1101/2022.07.28.501803
EMDB: EMD-15358, EMD-15359, EMD15360
PDB: 8A8F
Sijacki T, Alcón P, Chen ZA, McLaughlin SH, Shakeel S, Rappsilber J, Passmore LA*. (2022) The DNA-damage kinase ATR activates the FANCD2-FANCI clamp by priming it for ubiquitination. Nat Struct Mol Biol 29, 881–890
News and Views by Cody Rogers & Patrick Sung
EMDB: EMD-15102, EMD-15101, EMD15103
EMPIAR-11748
PDB: 8A2Q
jPOST: JPST001474, PRIDE ID: PXD031632
Boreikaite V, Elliott T, Chin J, Passmore LA*. (2022) RBBP6 activates the pre-mRNA 3’-end processing machinery in humans. Genes Dev 36, 221–224
Outlook by Yoseop Yoon & Yongsheng Shi
bioRxiv 2021.11.02.466915; doi: https://doi.org/10.1101/2021.11.02.466915
Rodríguez-Molina JB, O’Reilly FJ, Sheekey E, Maslen S, Skehel JM, Rappsilber J, Passmore LA*. (2022) Mpe1 senses binding of pre-mRNA and controls 3ʹ-end processing by CPF. Mol Cell 82, 2490-2504
Cover by Shraddha Nayak, MRC LMB
bioRxiv https://doi.org/10.1101/2021.09.02.458805
EMDB: EMD-14710, EMD-14711, EMD-14712
PDB: 7ZGP, 7ZGQ, 7ZGR
ArrayExpress: E-MTAB-10820
ProteomeXchange: PXD027482
Mendeley Data: https://dx.doi.org/10.17632
Passmore LA*, Coller J*. (2022) Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol 23, 93–106. doi: 10.1038/s41580-021-00417-y
Kumar A†, Yu CWH†, Rodríguez-Molina JB, Li XH, Freund SMV*, Passmore LA*. (2021) Dynamics in Fip1 regulate eukaryotic mRNA 3'-end processing. Genes Dev 35, 1510-1526
bioRxiv 2021.07.07.451483; doi: https://doi.org/10.1101/2021.07.07.451483
BMRB 50795, 50796, and 50797
Turtola M, Manav MC, Kumar A, Tudik A, Mroczek S, Krawczyk P, Dziembowski A, Schmid M, Passmore LA, Casañal A*, Heick Jensen T*. (2021) Three-layered control of mRNA poly(A) tail synthesis in Saccharomyces cerevisiae, Genes Dev 35, 1290-1303
Passmore LA, Tang TTL. (2021) The long and the short of it. eLife 10:e70757.
Stowell JAW, Tang TTL, Seidel M, Passmore LA*. (2021) Gel-Based Analysis of Protein–Nucleic Acid Interactions. Methods in Molecular Biology 2263, 321-339
Farrell DP, Anishchenko I, Shakeel S, Lauko A, Passmore LA, Baker D, DiMaio F. “Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM” (2020) IUCrJ 7:881-892
bioRxiv doi: https://doi.org/10.1101/2020.05.01.072751
PDBDEV_00000055
Alcón P*, Shakeel S*, Chen ZA, Rappsilber J, Patel KJ, Passmore LA “FANCD2–FANCI is a clamp stabilized on DNA by monoubiquitination of FANCD2 during DNA repair” (2020) Nature Struct Mol Biol 27:240-248. doi.org/10.1038/s41594-020-0380-1
PDB-6TNF, 6TNG, 6TNI
EMDB-10531, 10532, 10534
EMPIAR-10609, 10610, 10611
F1000 recommendation: https://f1000.com/prime/737383221?bd=1
LMB Insight on Research https://www2.mrc-lmb.cam.ac.uk/how-is-the-fanconi-anaemia-pathway-activated-to-remove-dna-lesions/
Nuevas pistas para reparar el ADN dañado en la anemia de Fanconi
Ross NT*, Lohmann F*, Carbonneau S, Fazal A, Weihofen WA, Gleim S, Salcius M, Sigoillot F, Henault M, Carl SH, Rodríguez-Molina JB, Miller HR, Brittain SM, Murphy J, Zambrowski M, Boynton G, Wang Y, Chen A, Molind GJ, Wilbertz JH, Artus-Revel CG, Jia M, Akinjiyan FA, Turner J, Knehr J, Carbone W, Schuierer S, Reece-Hoyes JS, Xie K, Saran C, Williams ET, Roma G, Spencer M, Jenkins J, George EL, Thomas JR, Michaud G, Schirle M, Tallarico J, Passmore LA, Chao JA, Beckwith REJ “CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing’s sarcoma” (2019) Nat Chem Biol 16:50–59 doi: 10.1038/s41589-019-0424-1
News and views https://t.co/y1kYWHulgs?amp=1
Shakeel S*, Rajendra E*, Alcón P, O’Reilly F, Chorev DS, Maslen S, Degliesposti G, Russo CJ, He S, Hill CH, Skehel JM, Scheres SHW, Patel KJ, Rappsilber J, Robinson CV, Passmore LA “Structure of the Fanconi anemia monoubiquitin ligase complex” (2019) Nature 575:234-237 doi: 10.1038/s41586-019-1703-4
EMDB-10290, EMDB-10291, EMDB-10292, EMDB-10293, EMDB-10294
EMPIAR-10608
PDB 6SRI, 6SRS
PRIDE database PXD014282
Spotlight in Trends in Biochemical Sciences: “FANally…A Structure Emerges of the Fanconi Anemia Core Complex” Aguirre & Thomä.
LMB Insight on Research https://www2.mrc-lmb.cam.ac.uk/decade-long-collaboration-results-in-the-first-structure-of-the-fanconi-anaemia-core-complex/
CRUK highlight https://crukcambridgecentre.org.uk/research/programmes/cellular-and-molecular-biology/publications
Kumar A*, Clerici M*, Muckenfuss LM*, Passmore LA†, Jinek M† “Mechanistic insights into mRNA 3’-end processing” (2019) Curr Opin Struct Biol 59:143-150. doi: 10.1016/j.sbi.2019.08.001
Casañal A†, Shakeel S, Passmore LA† “Interpretation of medium resolution cryoEM maps of multi-protein complexes” (2019) Curr Opin Struct Biol 58:166-174. doi: 10.1016/j.sbi.2019.06.009
Tang TTL, Stowell JAW, Hill CH, Passmore LA “The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases” (2019) Nature Struct Mol Biol 26: 433-442
PDB 6R9I, 6R9J, 6R9M, 6R9O, 6R9P, 6R9Q
Recommended by F1000 https://f1000.com/prime/735791923
Insight on Research https://www2.mrc-lmb.cam.ac.uk/a-novel-mode-of-rna-recognition-based-on-structure-not-sequence/
Lai WS, Stumpo DJ, Wells ML, Gruzdev A, Hicks SN, Nicholson CO, Yang Z, Faccio R, Webster MW, Passmore LA, Blackshear PJ “Importance of the conserved carboxyl-terminal CNOT1 binding domain to tristetraprolin (TTP) activity in vivo” (2019) Mol Cell Biol pii: MCB.00029-19. doi: 10.1128/MCB.00029-19
Hill CH, Boreikaitė V, Kumar A, Casañal A, Kubík P, Degliesposti G, Maslen S, Mariani A, von Loeffelholz O, Girbig M, Skehel M, Passmore LA “Activation of the endonuclease that defines mRNA 3ʹ-ends requires incorporation into an 8-subunit core cleavage and polyadenylation factor complex” (2019) Mol Cell 73, 1217–1231
EMD-0324 and EMD-0325, PDB 6I1D
Recommended by F1000 https://f1000.com/prime/735057887
Featured on CRUK http://goo.gl/Kv4xn7
Featured on Instruct-ERIC, https://instruct-eric.eu/news/how-to-generate-the-end-of-an-mrna
Webster MW, Stowell JAW, Passmore LA “RNA-binding proteins distinguish between similar sequence motifs to promote targeted deadenylation by Ccr4-Not” (2019) eLife 8:e40670 doi: 10.7554/eLife.40670
Lidschreiber M*†, Easter A*, Battaglia S, Rodríguez-Molina J, Casañal A, Carminati M, Baejen C, Grzechnik P, Maier K, Cramer P†, Passmore LA† “The APT complex is involved in non-coding RNA transcription and is distinct from CPF” (2018) Nucleic Acids Research 41: 11528–11538
Webster MW, Chen YH, Stowell JAW, Alhusaini N, Sweet T, Graveley BR, Coller J†, Passmore LA† “mRNA deadenylation is coupled to translation rates by the
differential activities of Ccr4-Not nucleases” (2018) Mol Cell 70:1089-1100.e8.
‘Discovering how translation and mRNA decay are linked’ Insight on Research
Stowell JAW, Wagstaff JL, Hill CH, Yu M, McLaughlin SH, Freund SMV† and Passmore LA† “A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding” (2018) J Mol Biol
Casañal A*, Kumar A*, Hill CH, Easter AD, Emsley P, Degliesposti G, Gordiyenko Y, Santhanam B, Wolf J, Wiederhold K, Dornan GL, Skehel M, Robinson CV and Passmore LA (2017) Architecture of eukaryotic mRNA 3′-end processing machinery Science 348: 1056-1059 *, equal contribution
‘How the poly(A) tail is added to the end of mRNAs’ (MRC LMB Insight on Research)
‘Scientists unveil structure of protein critical for gene expression and targeted by influenza’ (MRC)
‘Tall tails of mRNA’ (Diamond Light Source)
‘Cryo-electron microscopy used to identify CPF protein structure’ (Drug Target Review)
‘A tale of the messenger’s tail’ (Gates Cambridge)
Webster MW, Stowell JA, Tang TTL, Passmore LA (2017) Analysis of mRNA deadenylation by multi-protein complexes Methods 126: 95–104
Stowell JA, Webster MW, Kögel A, Wolf J, Shelley K, Passmore LA (2016) Reconstitution of Targeted Deadenylation by the Ccr4-Not Complex and the YTH Domain Protein Mmi1 Cell Reports 17(8):1978-1989.
Passmore LA, Russo CJ (2016) Specimen Preparation for High-Resolution Cryo-EM Methods in Enzymology 579:51-86.
Passmore LA, Taatjes DJ. (2016) Macromolecular Complexes in Transcription and Co-Transcriptional RNA Processing. Journal of Molecular Biology 428: 2539-2660. (Editorial for special issue)
Russo CJ, Passmore LA. (2016) Progress towards an optimal specimen support for electron cryomicroscopy. Current Opinion in Structural Biology 37:81-9
Russo CJ, Passmore LA. (2016) Ultrastable gold substrates: Properties of a support for high-resolution electron cryomicroscopy of biological specimens. Journal of Structural Biology 193:33-44.
Seweryn S, Van LB, Kjeldgaard M, Russo CJ, Passmore LA, Hove-Jensen B, Jochimsen B, Brodersen DE (2015) Structural insights into the bacterial carbon-phosphorus lyase machinery. Nature 525: 68–72
Bharat TAM, Russo CJ, Löwe J, Passmore LA, Scheres S (2015) Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging Structure 23(9): 1743-1753.
Gibbs-Seymour I, Oka Y, Rajendra E, Weinert BT, Passmore LA, Patel KJ, Olsen JV, Choudhary C, Bekker-Jensen S & Mailand N (2015) Ubiquitin-SUMO circuitry controls activated Fanconi Anemia ID complex dosage in response to DNA damage. Mol Cell 57(1): 150-164
Russo CJ & Passmore LA (2014) Ultrastable gold substrates for electron cryomicroscopy. Science 346(6215):1377-1380
EMDB entry EMD-2788 and PDB entry 4v1w
Rajendra E, Garaycoechea JI, Patel KJ & Passmore LA (2014) Abundance of the Fanconi anaemia core complex is regulated by the RuvBL1 and RuvBL2 AAA+ ATPases. Nucleic Acids Research doi: 10.1093/nar/gku1230
Russo CJ & Passmore LA (2014) Robust evaluation of 3D electron cryomicroscopy data using tilt-pairs. J Struct Biol 187(2):112-8
Link to TiltStats Website where you can download the programs.
Rajendra E, Oestergaard VH, Langevin F, Wang M, Dornan GL, Patel KJ† & Passmore LA† (2014) The genetic and biochemical basis of FANCD2 monoubiquitination. Mol Cell 54(5): 858-869.
Wolf J, Valkov E, Allen MD, Meineke B, Gordiyenko Y, McLaughlin SH, Olsen TM, Robinson CV, Bycroft M, Stewart M & Passmore LA (2014) Structural basis for binding of Pan3 to Pan2 and its function in mRNA recruitment and deadenylation. EMBOJ 33(14):1514-26
Have You Seen? commentary in EMBO J.
News and Views in Nature Structural and Molecular Biology
PDB entries: Pan3 pseudokinase/CTD 4CYI, Pan2 linker–Pan3 pseudokinase/CTD 4CYJ, Pan3 Zn finger 4CYK
Russo C & Passmore LA (2014) Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas Nature Methods 11(6): 649-652.2014
Wolf J & Passmore LA (2014) mRNA deadenylation by Pan2-Pan3 Biochem. Soc. Trans. 42: 184-187
Schreieck A*, Easter AD*, Etzold S, Wiederhold K, Lindschrieber M, Cramer P†, Passmore LA†. (2014) RNA polymerase II termination involves CTD tyrosine dephosphorylation by CPF subunit Glc7 Nat Struct Mol Biol. 21: 175-179
*Equal contribution, †Corresponding authors
Bøggild A, Sofos N, Andersen KR, Feddersen A, Easter AD, Passmore LA, Brodersen DE. (2012) “The Crystal Structure of the Intact E. coli RelBE Toxin-Antitoxin Complex Provides the Structural Basis for Conditional Cooperativity.” Structure 10:1-8.
Henderson R, Chen S, Chen JZ, Grigorieff N, Passmore LA, Ciccarelli L, Rubinstein JL, Crowther RA, Stewart PL, Rosenthal PB. (2011) “Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy.” J Mol Biol. 413(5):1028-46.
Wiederhold K, Passmore LA. (2010) “Cytoplasmic deadenylation: regulation of mRNA fate.” Biochem. Soc. Trans. 38(6):1531-6
Passmore LA, Schmeing TM, Maag D, Applefield DJ, Acker MG, Algire MA, Lorsch JR, Ramakrishnan V. (2007) “The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome”. Mol Cell 26(1): 41-50.
Passmore LA, Booth CR, Vénien-Bryan C, Ludtke SJ, Fioretto C, Johnson LN, Chiu W, Barford D. (2005) “Structural analysis of the anaphase-promoting complex reveals multiple active sites and insights into poly-ubiquitylation”. Mol. Cell 20(6): 855-66.
Passmore LA, Barford D. (2005) “Coactivator functions in a stoichiometric complex with anaphase-promoting complex/cyclosome to mediate substrate recognition. EMBO Rep. 6, 873-878.
Passmore LA, Barford D, Harper JW. (2005) “Purification and Assay of the Budding Yeast Anaphase Promoting Complex.” in Methods in Enzymology Volume 398: Ubiquitin and Protein Degradation. Chapter 17: 195-219.
Passmore LA. (2004) “The Anaphase-Promoting Complex (APC): The sum of its parts?” Biochem. Soc. Trans. 32(5): 724-727.
Passmore LA and Barford D. (2004) “Getting into Position: The catalytic mechanisms of protein ubiquitylation.” Biochem. J. 379(3): 513–525.
Passmore LA, McCormack EA, Au SWN, Paul A, Willison KR, Harper JW, Barford D. (2003) “Doc1 mediates the activity of the anaphase-promoting complex by contributing to substrate recognition.” EMBO J. 22(4): 786-96.
Lim D, Sanschagrin F, Passmore L, De Castro L, Levesque RC, Strynadka NC. (2001) “Insights into the molecular basis for the carbenicillinase activity of PSE-4 beta-lactamase from crystallographic and kinetic studies.” Biochemistry 40(2): 395-402.
Kramer F, White K, Pauleikhoff D, Gehrig A, Passmore L, Rivera A, Rudolph G, Kellner U, Andrassi M, Lorenz B, Rohrschneider K, Blankenagel A, Jurklies B, Schilling H, Schutt F, Holz FG, Weber BH. (2000) “Mutations in the VMD2 gene are associated with juvenile-onset vitelliform macular dystrophy (Best disease) and adult vitelliform macular dystrophy but not age-related macular degeneration.” Eur J Hum Genet 8(4): 286-292.
Passmore LA, Kasmann-Kellner B, Weber BHF. (1999) “Novel and recurrent mutations in the tyrosinase gene and the P gene in the German albino population.” Hum Genet. 105(3): 200-210.
Tognon CE, Kirk HE, Passmore LA, Whitehead IP, Der CJ, Kay RJ. (1998) “Regulation of RasGRP via a phorbol ester-responsive C1 domain.” Mol Cell Biol 18(12): 6995-7008.
Marquardt A, Stoehr H, Passmore LA, Kraemer F, Rivera A, Weber BHF. (1998) “Mutations in a novel gene, VMD2, encoding a protein of unknown properties, cause juvenile-onset vitelliform macular dystrophy (Best's disease).” Hum Mol Genet 7(9): 1517-1525.
Houtzager V, Ouellet M, Falgueyret J-P, Passmore LA, Bayly C, Percival MD. (1996) “Inhibitor induced changes in the intrinsic fluorescence of human cyclooxygenase-2.” Biochemistry 35(33): 10974-10984.
*equal contribution
†co-corresponding authors
Publications
Passmore Lab, MRC Laboratory of Molecular Biology, Cambridge UK