Structure and function of the N-terminal domain of the yeast telomerase reverse transcriptase

Abstract The elongation of single-stranded DNA repeats at the 3′-ends of chromosomes by telomerase is a key process in maintaining genome integrity in eukaryotes. Abnormal activation of telomerase leads to uncontrolled cell division, whereas its down-regulation is attributed to ageing and several pathologies related to early cell death. Telomerase function is based on the dynamic interactions of its catalytic subunit (TERT) with nucleic acids—telomerase RNA, telomeric DNA and the DNA/RNA heteroduplex. Here, we present the crystallographic and NMR structures of the N-terminal (TEN) domain of TERT from the thermotolerant yeast Hansenula polymorpha and demonstrate the structural conservation of the core motif in evolutionarily divergent organisms. We identify the TEN residues that are involved in interactions with the telomerase RNA and in the recognition of the ‘fork’ at the distal end of the DNA product/RNA template heteroduplex. We propose that the TEN domain assists telomerase biological function and is involved in restricting the size of the heteroduplex during telomere repeat synthesis.

[1]  R. A. Wu,et al.  DNA‐binding determinants and cellular thresholds for human telomerase repeat addition processivity , 2017, The EMBO journal.

[2]  C. Armstrong,et al.  Fundamental mechanisms of telomerase action in yeasts and mammals: understanding telomeres and telomerase in cancer cells , 2017, Open Biology.

[3]  E. Skordalakes,et al.  Structural Analysis Reveals the Deleterious Effects of Telomerase Mutations in Bone Marrow Failure Syndromes* , 2017, The Journal of Biological Chemistry.

[4]  Florent Cipriani,et al.  P13, the EMBL macromolecular crystallography beamline at the low-emittance PETRA III ring for high- and low-energy phasing with variable beam focusing , 2017, Journal of synchrotron radiation.

[5]  J. Shay,et al.  Role of Telomeres and Telomerase in Aging and Cancer. , 2016, Cancer discovery.

[6]  O. A. Petrova,et al.  NMR assignments of the N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase , 2016, Biomolecular NMR assignments.

[7]  Duilio Cascio,et al.  Structure of Tetrahymena telomerase reveals previously unknown subunits, functions, and interactions , 2015, Science.

[8]  E. Skordalakes,et al.  Structural Basis of Telomerase Inhibition by the Highly Specific BIBR1532. , 2015, Structure.

[9]  J. Feigon,et al.  Progress in Human and Tetrahymena Telomerase Structure Determination. , 2015, Annual review of biophysics.

[10]  T. Cech,et al.  Human telomerase: biogenesis, trafficking, recruitment, and activation , 2015, Genes & development.

[11]  Michael D. Stone,et al.  The telomerase essential N-terminal domain promotes DNA synthesis by stabilizing short RNA–DNA hybrids , 2015, Nucleic acids research.

[12]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[13]  Woonghee Lee,et al.  NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy , 2014, Bioinform..

[14]  Andrey A Lebedev,et al.  Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the program Zanuda. , 2014, Acta crystallographica. Section D, Biological crystallography.

[15]  O. Dontsova,et al.  Telomere length regulation in budding yeasts , 2014, FEBS letters.

[16]  M. Lei,et al.  Structural basis for protein-RNA recognition in telomerase , 2014, Nature Structural &Molecular Biology.

[17]  Xavier Robert,et al.  Deciphering key features in protein structures with the new ENDscript server , 2014, Nucleic Acids Res..

[18]  R. A. Wu,et al.  Human telomerase specialization for repeat synthesis by unique handling of primer‐template duplex , 2014, The EMBO journal.

[19]  J. Feigon,et al.  Progress in structural studies of telomerase. , 2014, Current opinion in structural biology.

[20]  Pavol Skubák,et al.  Automatic protein structure solution from weak X-ray data , 2013, Nature Communications.

[21]  E. Westhof,et al.  Specific features of telomerase RNA from Hansenula polymorpha , 2013, RNA.

[22]  E. Skordalakes,et al.  A motif in the vertebrate telomerase N-terminal linker of TERT contributes to RNA binding and telomerase activity and processivity. , 2013, Structure.

[23]  Z. Zhou,et al.  Tetrahymena Telomerase Holoenzyme Assembly, Activation, and Inhibition by Domains of the p50 Central Hub , 2013, Molecular and Cellular Biology.

[24]  Philip R. Evans,et al.  How good are my data and what is the resolution? , 2013, Acta crystallographica. Section D, Biological crystallography.

[25]  Z. Zhou,et al.  The architecture of Tetrahymena telomerase holoenzyme , 2013, Nature.

[26]  E. Blackburn,et al.  The telomere syndromes , 2012, Nature Reviews Genetics.

[27]  A. Venteicher,et al.  TPP1 OB-Fold Domain Controls Telomere Maintenance by Recruiting Telomerase to Chromosome Ends , 2012, Cell.

[28]  Evgeny Krissinel,et al.  Enhanced fold recognition using efficient short fragment clustering. , 2012, Journal of molecular biochemistry.

[29]  P. Andrew Karplus,et al.  Linking Crystallographic Model and Data Quality , 2012, Science.

[30]  H. Pickett,et al.  Telomerase Recruitment Requires both TCAB1 and Cajal Bodies Independently , 2012, Molecular and Cellular Biology.

[31]  Jacek Blazewicz,et al.  Automated 3D structure composition for large RNAs , 2012, Nucleic acids research.

[32]  K. Collins,et al.  Roles of Telomerase Reverse Transcriptase N-terminal Domain in Assembly and Activity of Tetrahymena Telomerase Holoenzyme* , 2012, The Journal of Biological Chemistry.

[33]  Joshua D. Podlevsky,et al.  RNA/DNA hybrid binding affinity determines telomerase template‐translocation efficiency , 2012, The EMBO journal.

[34]  G. Guillaume,et al.  A mutation in the catalytic subunit of yeast telomerase alters primer–template alignment while promoting processivity and protein–DNA binding , 2011, Journal of Cell Science.

[35]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[36]  M. Lei,et al.  Telomerase regulatory subunit Est3 in two Candida species physically interacts with the TEN domain of TERT and telomeric DNA , 2011, Proceedings of the National Academy of Sciences.

[37]  Benjamin A. Lewis,et al.  Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step , 2011, Proceedings of the National Academy of Sciences.

[38]  K. Collins,et al.  Human telomerase domain interactions capture DNA for TEN domain-dependent processive elongation. , 2011, Molecular cell.

[39]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[40]  M. Parker,et al.  Direct involvement of the TEN domain at the active site of human telomerase , 2010, Nucleic acids research.

[41]  Dieter Braun,et al.  Protein-binding assays in biological liquids using microscale thermophoresis. , 2010, Nature communications.

[42]  Pavol Skubák,et al.  Multivariate phase combination improves automated crystallographic model building. , 2010, Acta crystallographica. Section D, Biological crystallography.

[43]  Stephen C. West,et al.  InTERTpreting telomerase structure and function , 2010, Nucleic acids research.

[44]  E. Skordalakes,et al.  Structural basis for telomerase catalytic subunit TERT binding to RNA template and telomeric DNA , 2010, Nature Structural &Molecular Biology.

[45]  Kevin Cowtan,et al.  Recent developments in classical density modification , 2010, Acta crystallographica. Section D, Biological crystallography.

[46]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[47]  T. Cech,et al.  Functional interaction between telomere protein TPP1 and telomerase. , 2010, Genes & development.

[48]  T. Cech,et al.  POT1–TPP1 enhances telomerase processivity by slowing primer dissociation and aiding translocation , 2010, The EMBO journal.

[49]  M. Ikura,et al.  The N-terminus of hTERT contains a DNA-binding domain and is required for telomerase activity and cellular immortalization , 2009, Nucleic acids research.

[50]  E. Choi,et al.  A novel kanamycin/G418 resistance marker for direct selection of transformants in Escherichia coli and different yeast species , 2009, Yeast.

[51]  A. Bax,et al.  TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts , 2009, Journal of biomolecular NMR.

[52]  D. Temiakov,et al.  Maintenance of RNA-DNA Hybrid Length in Bacterial RNA Polymerases* , 2009, Journal of Biological Chemistry.

[53]  T. Frenkiel,et al.  Structure and dynamics in solution of the complex of lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate , 2008, Protein science : a publication of the Protein Society.

[54]  E. Skordalakes,et al.  Structure of the Tribolium castaneum telomerase catalytic subunit TERT , 2008, Nature.

[55]  M. Pardue,et al.  Drosophila Telomeres: A Variation on the Telomerase Theme , 2008, Fly.

[56]  E. Skordalakes,et al.  Structure of the RNA-binding domain of telomerase: implications for RNA recognition and binding. , 2007, Structure.

[57]  Tahir H. Tahirov,et al.  Structural basis for transcription elongation by bacterial RNA polymerase , 2007, Nature.

[58]  H. Manor,et al.  High-resolution physical and functional mapping of the template adjacent DNA binding site in catalytically active telomerase , 2007, Proceedings of the National Academy of Sciences.

[59]  Haley D. M. Wyatt,et al.  Characterization of Physical and Functional Anchor Site Interactions in Human Telomerase , 2007, Molecular and Cellular Biology.

[60]  T. Cech,et al.  The POT1–TPP1 telomere complex is a telomerase processivity factor , 2007, Nature.

[61]  Kevin Cowtan,et al.  The Buccaneer software for automated model building. 1. Tracing protein chains. , 2006, Acta crystallographica. Section D, Biological crystallography.

[62]  T. Cech,et al.  Crystal structure of the essential N-terminal domain of telomerase reverse transcriptase , 2006, Nature Structural &Molecular Biology.

[63]  David S Wishart,et al.  A simple method to predict protein flexibility using secondary chemical shifts. , 2005, Journal of the American Chemical Society.

[64]  Deborah S Wuttke,et al.  Soluble domains of telomerase reverse transcriptase identified by high‐throughput screening , 2005, Protein science : a publication of the Protein Society.

[65]  N. Lue A Physical and Functional Constituent of Telomerase Anchor Site*[boxs] , 2005, Journal of Biological Chemistry.

[66]  K. Collins,et al.  Two Purified Domains of Telomerase Reverse Transcriptase Reconstitute Sequence-specific Interactions with RNA* , 2005, Journal of Biological Chemistry.

[67]  J. Lingner,et al.  Telomerase limits the extent of base pairing between template RNA and telomeric DNA , 2005, EMBO reports.

[68]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[69]  D. Bushnell,et al.  Structural Basis of Transcription: Separation of RNA from DNA by RNA Polymerase II , 2004, Science.

[70]  I. Mian,et al.  Conserved N-terminal Motifs of Telomerase Reverse Transcriptase Required for Ribonucleoprotein Assembly in Vivo * , 2003, The Journal of Biological Chemistry.

[71]  K. Pongracz,et al.  Interaction of human telomerase with its primer substrate. , 2003, Biochemistry.

[72]  B. Armbruster,et al.  N-Terminal Domains of the Human Telomerase Catalytic Subunit Required for Enzyme Activity in Vivo , 2001, Molecular and Cellular Biology.

[73]  Claude Lecomte,et al.  Refinement of proteins at subatomic resolution with MOPRO , 2001 .

[74]  James R. Mitchell,et al.  RNA Binding Domain of Telomerase Reverse Transcriptase , 2001, Molecular and Cellular Biology.

[75]  I. Mian,et al.  Identification of Functionally Important Domains in the N-Terminal Region of Telomerase Reverse Transcriptase , 2000, Molecular and Cellular Biology.

[76]  H. Fujiwara,et al.  Detection and distribution patterns of telomerase activity in insects. , 2000, European journal of biochemistry.

[77]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[78]  T. Cech,et al.  Euplotes telomerase: evidence for limited base-pairing during primer elongation and dGTP as an effector of translocation. , 1998, Biochemistry.

[79]  A. Vagin,et al.  MOLREP: an Automated Program for Molecular Replacement , 1997 .

[80]  A M Gronenborn,et al.  Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. , 1997, Journal of magnetic resonance.

[81]  J. Thornton,et al.  AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR , 1996, Journal of biomolecular NMR.

[82]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[83]  A. I. Bogdanova,et al.  Plasmid reorganization during integrative transformation in Hansenula polymorpha , 1995, Yeast.

[84]  C B Harley,et al.  Specific association of human telomerase activity with immortal cells and cancer. , 1994, Science.

[85]  T. Pawson,et al.  Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. , 1994, Biochemistry.

[86]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[87]  A. Gronenborn,et al.  Analysis of the backbone dynamics of interleukin-1.beta. using two-dimensional inverse detected heteronuclear nitrogen-15-proton NMR spectroscopy , 1990 .

[88]  Paul C. Driscoll,et al.  Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins , 1990 .

[89]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[90]  Carol W. Greider,et al.  Identification of a specific telomere terminal transferase activity in tetrahymena extracts , 1985, Cell.

[91]  P. Kitcher Species , 1984, Philosophy of Science.

[92]  A. Szabó,et al.  Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity , 1982 .

[93]  A. Szabó,et al.  Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results , 1982 .

[94]  H. Fujiwara Accumulation of Telomeric-Repeat-Specific Retrotransposons in Subtelomeres of Bombyx mori and Tribolium castaneum , 2014 .

[95]  Nicholas K. Sauter,et al.  The DIALS framework for integration software , 2013 .

[96]  O. A. Petrova,et al.  Hansenula Polymorpha TERT: 
A Telomerase Catalytic Subunit Isolated in Recombinant Form with Limited Reverse Transcriptase Activity , 2012, Acta naturae.

[97]  M. Nilges,et al.  ARIA for solution and solid-state NMR. , 2012, Methods in molecular biology.

[98]  N. Lue A PHYSICAL AND FUNCTIONAL CONSTITUENT OF TELOMERASE ANCHOR SITE , 2008 .

[99]  M. Blackledge,et al.  Overall rotational diffusion and internal mobility in domain II of protein G from Streptococcus determined from 15N relaxation data , 2000, Protein science : a publication of the Protein Society.

[100]  J. Abrahams,et al.  Methods used in the structure determination of bovine mitochondrial F1 ATPase. , 1996, Acta crystallographica. Section D, Biological crystallography.

[101]  A. Gronenborn,et al.  Analysis of the backbone dynamics of interleukin-1 beta using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy. , 1990, Biochemistry.