Imperial College London

ProfessorXiaodongZhang

Faculty of MedicineDepartment of Infectious Disease

Professor of Macromolecular Structure and Function
 
 
 
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Contact

 

+44 (0)20 7594 3151xiaodong.zhang Website

 
 
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Assistant

 

Miss Kelly Butler +44 (0)20 7594 2763

 
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Location

 

104Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

140 results found

Zhang X, Blundell T, Tainer JA, 2021, The renaissance in biophysics and molecular biology enabled by the interface of DNA repair and replication with cancer, PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, Vol: 163, Pages: 1-4, ISSN: 0079-6107

Journal article

Williams RM, Zhang X, 2021, Roles of ATM and ATR in DNA double strand breaks and replication stress, PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, Vol: 163, Pages: 109-119, ISSN: 0079-6107

Journal article

Williams RM, Zhang X, 2021, Roles of ATM and ATR in DNA double strand breaks and replication stress, PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, Vol: 161, Pages: 27-38, ISSN: 0079-6107

Journal article

Zhang X, Carver A, 2021, Rad51 filament dynamics and its antagonistic modulators, Seminars in Cell and Developmental Biology, Vol: 113, Pages: 3-13, ISSN: 1084-9521

Rad51 recombinase is the central player in homologous recombination, the faithful repair pathway for double-strand breaks and key event during meiosis. Rad51 forms nucleoprotein filaments on single-stranded DNA, exposed by a double-strand break. These filaments are responsible for homology search and strand invasion, which lead to homology-directed repair. Due to its central roles in DNA repair and genome stability, Rad51 is modulated by multiple factors and post-translational modifications. In this review, we summarize our current understanding of the dynamics of Rad51 filaments, the roles of other factors and their modes of action in modulating key stages of Rad51 filaments: formation, stability and disassembly.

Journal article

Kaneko Y, Shimoda K, Ayala R, Goto Y, Panico S, Zhang X, Kondo Het al., 2021, p97 and p47 function in membrane tethering in cooperation with FTCD during mitotic Golgi reassembly, EMBO JOURNAL, Vol: 40, ISSN: 0261-4189

Journal article

Tannous EA, Yates LA, Zhang X, Burgers PMet al., 2021, Mechanism of auto-inhibition and activation of Mec1ATR checkpoint kinase, Nature Structural and Molecular Biology, Vol: 28, Pages: 50-61, ISSN: 1545-9985

In response to DNA damage or replication fork stalling, the basal activity of Mec1ATR is stimulated in a cell-cycle-dependent manner, leading to cell-cycle arrest and the promotion of DNA repair. Mec1ATR dysfunction leads to cell death in yeast and causes chromosome instability and embryonic lethality in mammals. Thus, ATR is a major target for cancer therapies in homologous recombination-deficient cancers. Here we identify a single mutation in Mec1, conserved in ATR, that results in constitutive activity. Using cryo-electron microscopy, we determine the structures of this constitutively active form (Mec1(F2244L)-Ddc2) at 2.8 Å and the wild type at 3.8 Å, both in complex with Mg2+-AMP-PNP. These structures yield a near-complete atomic model for Mec1-Ddc2 and uncover the molecular basis for low basal activity and the conformational changes required for activation. Combined with biochemical and genetic data, we discover key regulatory regions and propose a Mec1 activation mechanism.

Journal article

Zhang X, Blundell TL, 2020, Editorial overview: Macromolecular assemblies, CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol: 61, Pages: VI-VIII, ISSN: 0959-440X

Journal article

Williams R, Yates L, Zhang X, 2020, Structures and regulations of ATM and ATR, master kinases in genome integrity, Current Opinion in Structural Biology, Vol: 61, Pages: 98-105, ISSN: 0959-440X

Homologous recombination (HR) is a faithful repair mechanism for double stranded DNA breaks. Two highly homologous master kinases, the tumour suppressors ATM and ATR (Tel1 and Mec1 in yeast), coordinate cell cycle progression with repair during HR. Despite their importance, our molecular understanding of these apical coordinators has been limited, in part due to their large sizes. With the recent development in cryo-electron microscopy, significant advances have been made in structural characterisation of these proteins in the last two years. These structures, combined with new biochemical studies, now provide a more detailed understanding of how a low basal activity is maintained and how activation may occur. In this review, we summarize recent advances in the structural and molecular understanding of these key components in HR, compare the common and distinct features of these kinases and suggest aspects of structural components that are likely to be involved in regulating its activity.

Journal article

Gao F, Danson AE, Ye F, Jovanovic M, Buck M, Zhang Xet al., 2020, Bacterial enhancer binding proteins - AAA+ proteins in transcription activation, Biomolecules, Vol: 10, ISSN: 2218-273X

Bacterial enhancer-binding proteins (bEBPs) are specialised transcriptional activators. bEBPs are hexameric AAA+ ATPases and use ATPase activities to remodel RNA polymerase (RNAP) complexes that contain the major variant sigma factor, σ54 to convert the initial closed complex to the transcription competent open complex. Earlier crystal structures of AAA+ domains alone have led to proposals of how nucleotide-bound states are sensed and propagated to substrate interactions. Recently, the structure of the AAA+ domain of a bEBP bound to RNAP-σ54-promoter DNA was revealed. Together with structures of the closed complex, an intermediate state where DNA is partially loaded into the RNAP cleft and the open promoter complex, a mechanistic understanding of how bEBPs use ATP to activate transcription can now be proposed. This review summarises current structural models and the emerging understanding of how this special class of AAA+ proteins utilises ATPase activities to allow σ54-dependent transcription initiation.

Journal article

Stach L, Morgan RM, Makhlouf L, Douangamath A, von Delft F, Zhang X, Freemont PSet al., 2020, Crystal structure of the catalytic D2 domain of the AAA+ ATPase p97 reveals a putative helical split-washer-type mechanism for substrate unfolding, FEBS Letters, Vol: 594, Pages: 933-943, ISSN: 0014-5793

Several pathologies have been associated with the AAA+ ATPase p97, an enzyme essential to protein homeostasis. Heterozygous polymorphisms in p97 have been shown to cause neurological disease, while elevated proteotoxic stress in tumours has made p97 an attractive cancer chemotherapy target. The cellular processes reliant on p97 are well described. High‐resolution structural models of its catalytic D2 domain, however, have proved elusive, as has the mechanism by which p97 converts the energy from ATP hydrolysis into mechanical force to unfold protein substrates. Here, we describe the high‐resolution structure of the p97 D2 ATPase domain. This crystal system constitutes a valuable tool for p97 inhibitor development and identifies a potentially druggable pocket in the D2 domain. In addition, its P61 symmetry suggests a mechanism for substrate unfolding by p97.

Journal article

Yates L, Williams R, Hailemariam S, Ayala R, Zhang Xet al., 2020, Cryo-EM structure of nucleotide-bound Tel1ATM unravels the molecular basis of inhibition and structural rationale for disease-associated mutations, Structure, Vol: 28, Pages: 96-104.e3, ISSN: 0969-2126

Yeast Tel1 and its highly conserved human orthologue ATM are large protein kinases centralto the maintenance of genome integrity. Mutations in ATM are found in ataxia-telangiectasia(A-T) patients and ATM is one of the most frequently mutated genes in many cancers. Usingcryo electron microscopy, we present the structure of Tel1 in a nucleotide-bound state. Ourstructure reveals molecular details of key residues surrounding the nucleotide binding site andprovides a structural and molecular basis for its intrinsically low basal activity. We show thatthe catalytic residues are in a productive conformation for catalysis, but the PIKK-regulatorydomain-Insert (PRD-I) restricts peptide-substrate access and the N-lobe is in an openconformation, thus explaining the requirement for Tel1 activation. Structural comparisons withother PIKKs suggest a conserved and common allosteric activation mechanism. Our work alsoprovides a structural rationale for many mutations found in A-T and cancer.

Journal article

Sun Y, McCorvie TJ, Yates LA, Zhang Xet al., 2019, Structural basis of homologous recombination, CELLULAR AND MOLECULAR LIFE SCIENCES, Vol: 77, Pages: 3-18, ISSN: 1420-682X

Journal article

Ye F, Kotta-Loizou I, Jovanovic M, Liu X, Dryden D, Buck M, Zhang Xet al., 2019, Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7, eLife, Vol: 9, ISSN: 2050-084X

Abstract Bacteriophage T7 infects Escherichia coli and evades the host defence system. The Ocr protein of T7 was shown to exist as a dimer mimicking DNA and to bind to host restriction enzymes, thus preventing the degradation of the viral genome by the host. Here we report that Ocr can also inhibit host transcription by directly binding to bacterial RNA polymerase (RNAP) and competing with the recruitment of RNAP by sigma factors. Using cryo electron microscopy, we determined the structures of Ocr bound to RNAP. The structures show that an Ocr dimer binds to RNAP in the cleft, where key regions of sigma bind and where DNA resides during transcription synthesis, thus providing a structural basis for the transcription inhibition. Our results reveal the versatility of Ocr in interfering with host systems and suggest possible strategies that could be exploited in adopting DNA mimicry as a basis for forming novel antibiotics. Impact statement DNA mimicry Ocr protein, a well-studied T7 phage protein that inhibits host restriction enzymes, can also inhibit host transcription through competing with sigma factors in binding to RNA polymerase.

Journal article

Ebright RH, Werner F, Zhang X, 2019, RNA Polymerase Reaches 60: Transcription Initiation, Elongation, Termination, and Regulation in Prokaryotes, JOURNAL OF MOLECULAR BIOLOGY, Vol: 431, Pages: 3945-3946, ISSN: 0022-2836

Journal article

Danson AE, Jovanovic M, Buck M, Zhang Xet al., 2019, Mechanisms of sigma(54)-Dependent Transcription Initiation and Regulation, JOURNAL OF MOLECULAR BIOLOGY, Vol: 431, Pages: 3960-3974, ISSN: 0022-2836

Journal article

Daza-Martin M, Starowicz K, Jamshad M, Tye S, Ronson GE, MacKay HL, Chauhan AS, Walker AK, Stone HR, Beesley JFJ, Coles JL, Garvin AJ, Stewart GS, McCorvie TJ, Zhang X, Densham RM, Morris JRet al., 2019, Isomerization of BRCA1-BARD1 promotes replication fork protection, NATURE, Vol: 571, Pages: 521-+, ISSN: 0028-0836

Journal article

Yates LA, Williams RM, Hailemariam S, Ayala R, Burgers P, Zhang Xet al., 2019, Structure of nucleotide-bound Tel1ATM reveals the molecular basis of inhibition and structural rationale for disease mutations

<jats:sec><jats:title>SUMMARY</jats:title><jats:p>Yeast Tel1 and its highly conserved human orthologue ATM are large protein kinases central to the maintenance of genome integrity. Mutations in ATM are found in ataxia-telangiectasia (A-T) patients and ATM is one of the most frequently mutated genes in many cancers. Using cryo electron microscopy, we present the structure of Tel1 in a nucleotide-bound state. Our structure reveals molecular details of key residues surrounding the nucleotide binding site and provides a structural and molecular basis for its intrinsically low basal activity. We show that the catalytic residues are in a productive conformation for catalysis, but the PIKK-regulatory domain-Insert (PRD-I) restricts peptide-substrate access and the N-lobe is in an open conformation, thus explaining the requirement for Tel1 activation. Structural comparisons with other PIKKs suggest a conserved and common allosteric activation mechanism. Our work also provides a structural rationale for many mutations found in A-T and cancer.</jats:p></jats:sec>

Journal article

Danson A, Jovanovic M, Buck M, Zhang Xet al., 2019, Mechanisms of s54-dependent transcription initiation and regulation, Journal of Molecular Biology, ISSN: 0022-2836

Cellular RNA polymerase is a multi-subunit macromolecular assembly responsible for gene transcription, a highly regulated process conserved from bacteria to humans. In bacteria, sigma factors are employed to mediate gene-specific expression in response to a variety of environmental conditions. The major variant σ factor, σ54, has a specific role in stress responses. Unlike σ70-dependent transcription, which often can spontaneously proceed to initiation, σ54-dependent transcription requires an additional ATPase protein for activation. As a result, structures of a number of distinct functional states during the dynamic process of transcription initiation have been captured using the σ54 system with both x-ray crystallography and cryo electron microscopy, furthering our understanding of σ54-dependent transcription initiation and DNA opening. Comparisons with σ70 and eukaryotic polymerases reveal unique and common features during transcription initiation.

Journal article

Yates LA, Aramayo RJ, Pokhrel N, Caldwell CC, Kaplan JA, Perera RL, Spies M, Anthony E, Zhang Xet al., 2018, A structural and dynamic model for the assembly of Replication Protein A on single-stranded DNA, Nature Communications, Vol: 9, ISSN: 2041-1723

Replication Protein A (RPA), the major eukaryotic single stranded DNA-binding protein, binds to exposed ssDNA to protect it from nucleases, participates in a myriad of nucleic acid transactions and coordinates the recruitment of other important players. RPA is a heterotrimer and coats long stretches of single-stranded DNA (ssDNA). The precise molecular architecture of the RPA subunits and its DNA binding domains (DBDs) during assembly is poorly understood. Using cryo electron microscopy we obtained a 3D reconstruction of the RPA trimerisation core bound with ssDNA (∼55 kDa) at ∼4.7 Å resolution and a dimeric RPA assembly on ssDNA. FRET-based solution studies reveal dynamic rearrangements of DBDs during coordinated RPA binding and this activity is regulated by phosphorylation at S178 in RPA70. We present a structural model on how dynamic DBDs promote the cooperative assembly of multiple RPAs on long ssDNA.

Journal article

Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang Xet al., 2018, Structures of bacterial RNA polymerase complexes reveal mechanisms of DNA loading and transcription initiation, Molecular Cell, Vol: 70, Pages: 1111-1120.e3, ISSN: 1097-2765

Gene transcription is carried out by multi-subunit RNA polymerases (RNAP).Transcription initiation is a dynamic multi-step process that involves the opening of the double stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis. Applying cryo electron microscopy to a unique transcription system using 54 (N), the major bacterial variant sigma factor, we capture a new intermediate state at 4.1 Å where promoter DNA is caught at the entrance of the RNAP cleft. Combining with new structures of the open promotercomplex and an initial de novo transcribing complex at 3.4 and 3.7 Å respectively, our studies reveal the dynamics of DNA loading and mechanism of transcription bubble stabilisation that involves coordinated, large scale conformational changes of the universally conserved features within RNAP and DNA. In addition, our studies reveal a novel mechanism of strand separation by 54.

Journal article

Ayala R, Willhoft O, Aramayo R, Wilkinson M, McCormack E, Ocloo L, Wigley D, Zhang Xet al., 2018, Structure and regulation of the human INO80–nucleosome complex, Nature, Vol: 556, Pages: 391-395, ISSN: 0028-0836

Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines1. Biochemical studies2-4 have placed the motor domains of several remodellers on the superhelical location (SHL) 2 region of the nucleosome. Structural studies on Chd1 and Snf2 (RSC) in complex with nucleosomes5-7 have provided insights into the basic mechanism of nucleosome sliding by these complexes. However, how larger, multi-subunit remodelling complexes, such as INO80, interact with nucleosomes or how remodellers carry out functions such as nucleosome sliding8, histone exchange9, and nucleosome spacing10-12 remains poorly understood. Although some remodellers work as monomers13, others work as highly cooperative dimers11,14,15. Here we present the structure of the INO80 chromatin remodeller with a bound nucleosome revealing that INO80 interacts with nucleosomes in a unique manner with the motor domains located at the entry point to the wrap around the histone core rather than at SHL2. The Arp5-Ies6 module of INO80 makes additional contacts on the opposite side of the nucleosome. This unique arrangement allows the H3 tails of the nucleosome to play a role in regulation, differing from other characterised remodellers.

Journal article

Zhang X, Aramayo RJ, Willhoft O, Ayala R, Bythell-Douglas R, Wigley DBet al., 2017, CryoEM structures of the human INO80 chromatin remodelling complex, Nature Structural and Molecular Biology, Vol: 25, Pages: 37-44, ISSN: 1545-9985

Access to chromatin for processes such as DNA repair and transcription requires the sliding of nucleosomes along DNA. The multi-subunit INO80 chromatin remodelling complex has a particular role in DNA repair. Here we present the cryo electron microscopy structures of the active core complex of human INO80 at 9.6 Å with portions at 4.1 Å resolution along with reconstructions of combinations of subunits. Together these structures reveal the architecture of the INO80 complex, including Ino80 and actin-related proteins, which is assembled around a single Tip49a (RUVBL1) and Tip49b (RUVBL2) AAA+ heterohexamer. An unusual spoked-wheel structural domain of the Ino80 subunit is engulfed by this heterohexamer and the intimate association of this Ino80 domain with the heterohexamer is at the core of the complex. We also identify a cleft in RUVBL1 and RUVBL2, which forms a major interaction site for partner proteins and likely communicates partner-interactions with its nucleotide binding sites.

Journal article

Glyde R, Ye F, Darbari V, Zhang N, Buck M, Zhang Xet al., 2017, Structures of RNA polymerase closed and intermediate complexes revealmechanisms of DNA opening and transcription initiation, Molecular Cell, Vol: 67, Pages: 106-116, ISSN: 1097-2765

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo.

Journal article

Wigley DB, Willhoft O, McCormack EA, Aramayo R, Bythell-Douglas R, Ocloo L, Zhang Xet al., 2017, Cross-talk within a functional INO80 complex dimer regulates nucleosome sliding, eLife, Vol: 6, ISSN: 2050-084X

Several chromatin remodellers have the ability to space nucleosomes on DNA. For ISWI remodellers, this involves an interplay between H4 histone tails, the AutoN and NegC motifs of the motor domains that together regulate ATPase activity and sense the length of DNA flanking the nucleosome. By contrast, the INO80 complex also spaces nucleosomes but is not regulated by H4 tails and lacks the AutoN and NegC motifs. Instead nucleosome sliding requires cooperativity between two INO80 complexes that monitor DNA length simultaneously on either side of the nucleosome during sliding. The C-terminal domain of the human Ino80 subunit (Ino80CTD) binds cooperatively to DNA and dimerisation of these domains provides crosstalk between complexes. ATPase activity, rather than being regulated, instead gradually becomes uncoupled as nucleosome sliding reaches an end point and this is controlled by the Ino80CTD. A single active ATPase motor within the dimer is sufficient for sliding.

Journal article

Sawicka M, Aramayo R, Ayala R, Glyde R, Zhang Xet al., 2017, Single-Particle Electron Microscopy Analysis of DNA Repair Complexes, Methods in Enzymology, Vol: 592, Pages: 159-186, ISSN: 0076-6879

DNA repair complexes play crucial roles in maintaining genome integrity, which is essential for the survival of an organism. The understanding of their modes of action is often obscure due to limited structural knowledge. Structural characterizations of these complexes are often challenging due to a poor protein production yield, a conformational flexibility, and a relatively high molecular mass. Single-particle electron microscopy (EM) has been successfully applied to study some of these complexes as it requires low amount of samples, is not limited by the high molecular mass of a protein or a complex, and can separate heterogeneous assemblies. Recently, near-atomic resolution structures have been obtained with EM owing to the advances in technology and image processing algorithms. In this chapter, we review the EM methodology of obtaining three-dimensional reconstructions of macromolecular complexes and provide a workflow that can be applied to DNA repair complex assemblies.

Journal article

Zhang N, Darbari VC, Glyde R, Zhang X, Buck Met al., 2016, The bacterial enhancer-dependent RNA polymerase, Biochemical Journal, Vol: 473, Pages: 3741-3753, ISSN: 1470-8728

Transcription initiation is highly regulated in bacterial cells, allowing adaptive gene regulation in response to environment cues. One class of promoter specificity factor called sigma54 enables such adaptive gene expression through its ability to lock the RNA polymerase down into a state unable to melt out promoter DNA for transcription initiation. Promoter DNA opening then occurs through the action of specialized transcription control proteins called bacterial enhancer-binding proteins (bEBPs) that remodel the sigma54 factor within the closed promoter complexes. The remodelling of sigma54 occurs through an ATP-binding and hydrolysis reaction carried out by the bEBPs. The regulation of bEBP self-assembly into typically homomeric hexamers allows regulated gene expression since the self-assembly is required for bEBP ATPase activity and its direct engagement with the sigma54 factor during the remodelling reaction. Crystallographic studies have now established that in the closed promoter complex, the sigma54 factor occupies the bacterial RNA polymerase in ways that will physically impede promoter DNA opening and the loading of melted out promoter DNA into the DNA-binding clefts of the RNA polymerase. Large-scale structural re-organizations of sigma54 require contact of the bEBP with an amino-terminal glutamine and leucine-rich sequence of sigma54, and lead to domain movements within the core RNA polymerase necessary for making open promoter complexes and synthesizing the nascent RNA transcript.

Journal article

von Nicolai C, Ehlén Å, Martin C, Zhang X, Carreira Aet al., 2016, A second DNA binding site in human BRCA2 promotes homologous recombination., Nature Communications, Vol: 7, Pages: 12813-12813, ISSN: 2041-1723

BRCA2 tumour-suppressor protein is well known for its role in DNA repair by homologous recombination (HR); assisting the loading of RAD51 recombinase at DNA double-strand breaks. This function is executed by the C-terminal DNA binding domain (CTD) which binds single-stranded (ss)DNA, and the BRC repeats, which bind RAD51 and modulate its assembly onto ssDNA. Paradoxically, analysis of cells resistant to DNA damaging agents missing the CTD restore HR proficiency, suggesting another domain may take over its function. Here, we identify a region in the N terminus of BRCA2 that exhibits DNA binding activity (NTD) and provide evidence for NTD promoting RAD51-mediated HR. A missense variant detected in breast cancer patients located in the NTD impairs HR stimulation on dsDNA/ssDNA junction containing substrates. These findings shed light on the function of the N terminus of BRCA2 and have implications for the evaluation of breast cancer variants.

Journal article

Zhang N, Jovanovic G, McDonald C, Ces O, Zhang X, Buck Met al., 2016, Transcription regulation and membrane stress management in enterobacterial pathogens, Advances in Experimental Medicine and Biology, Vol: 915, Pages: 207-230, ISSN: 0065-2598

Transcription regulation in a temporal and conditional manner underpins the lifecycle of enterobacterial pathogens. Upon exposure to a wide array of environmental cues, these pathogens modulate their gene expression via the RNA polymerase and associated sigma factors. Different sigma factors, either involved in general 'house-keeping' or specific responses, guide the RNA polymerase to their cognate promoter DNAs. The major alternative sigma54 factor when activated helps pathogens manage stresses and proliferate in their ecological niches. In this chapter, we review the function and regulation of the sigma54-dependent Phage shock protein (Psp) system-a major stress response when Gram-negative pathogens encounter damages to their inner membranes. We discuss the recent development on mechanisms of gene regulation, signal transduction and stress mitigation in light of different biophysical and biochemical approaches.

Journal article

Sawicka M, Wanrooij PH, Darbari VC, Tannous E, Hailemariam S, Bose D, Makarova AV, Burgers PM, Zhang Xet al., 2016, The dimeric architecture of checkpoint kinases Mec1ATR and Tel1ATM reveal a common structural organisation., Journal of Biological Chemistry, Vol: 291, Pages: 13436-13447, ISSN: 1083-351X

The phosphatidylinositol 3-kinase-related protein kinases (PIKKs) are key regulators controlling a wide range of cellular events. The yeast Tel1 and Mec1-Ddc2 complex (ATM and ATR-ATRIP in humans) play pivotal roles in DNA replication, DNA damage signalling and repair. Here, we present the first structural insight for dimers of Mec1-Ddc2 and Tel1 using single particle electron microscopy. Both kinases reveal a head-to-head dimer with one major dimeric interface through their N-terminal HEAT repeats. Their dimeric interface is significantly distinct from the interface of mTOR Complex 1 dimer, which oligomerises through two spatially separate interfaces. We also observe different structural organisation of kinase domains of Mec1 and Tel1. The kinase domains in the Mec1-Ddc2 dimer are located in close proximity to each other. However, in the Tel1 dimer they are fully separated providing potential access of substrates to this kinase, even in its dimeric form.

Journal article

Zhang N, Schaefer J, Sharma A, Rayner L, Zhang X, Tuma R, Stockley P, Buck Met al., 2015, Mutations in RNA Polymerase Bridge Helix and Switch Regions Affect Active-Site Networks and Transcript-Assisted Hydrolysis, Journal of Molecular Biology, Vol: 427, Pages: 3516-3526, ISSN: 1089-8638

In bacterial RNA polymerase (RNAP), the bridge helix and switch regions form an intricate network with the catalytic active centre and the main channel. These interactions are important for catalysis, hydrolysis and clamp domain movement. By targeting conserved residues in Escherichia coli RNAP, we are able to show that functions of these regions are differentially required during σ70-dependent and the contrasting σ54-dependent transcription activations and thus potentially underlie the key mechanistic differences between the two transcription paradigms. We further demonstrate that the transcription factor DksA directly regulates σ54-dependent activation both positively and negatively. This finding is consistent with the observed impacts of DksA on σ70-dependent promoters. DksA does not seem to significantly affect RNAP binding to a pre-melted promoter DNA but affects extensively activity at the stage of initial RNA synthesis on σ54-regulated promoters. Strikingly, removal of the σ54 Region I is sufficient to invert the action of DksA (from stimulation to inhibition or vice versa) at two test promoters. The RNAP mutants we generated also show a strong propensity to backtrack. These mutants increase the rate of transcript-hydrolysis cleavage to a level comparable to that seen in the Thermus aquaticus RNAP even in the absence of a non-complementary nucleotide. These novel phenotypes imply an important function of the bridge helix and switch regions as an anti-backtracking ratchet and an RNA hydrolysis regulator.

Journal article

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