Lab news

Professor Sanjib Bhakta’s lab featured in The Biologist

Professor Sanjib Bhakta’s lab featured in The Biologist

Professor Sanjib Bhakta (School of Natural Sciences, Faculty of Science, Birkbeck) and his research lab has been featured in the The Royal Society of Biology’s magazine, The Biologist. Full article can be accessed here.

Posted by Cyndy Thooi in Lab news
News about the Mechanisms and Evolution of Transcription!

News about the Mechanisms and Evolution of Transcription!

Transcription is carried out by evolutionary conserved RNA polymerases and subject to regulation by different strategies. The control of individual genes is enabled by a plethora of DNA-binding transcription factors that respond to changes in the environment and enable the up- or downregulation gene expression; the structural basis and mechanisms of genespecific regulation has been characterised in great detail. Much less is known about the global regulation of transcription that is enabled by RNAP-binding factors. Two research articles from the ISMB RNAP laboratory published back-to-back in Nature Communications explore and characterise the global control of the archaeal RNAP in two different scenarios. Firstly, a multidisciplinary study combining functional genomics with in vitro transcription assays hints at a paradigm shift for the regulation of transcription in Archaea (Blombach et al., 2021), and secondly, a cryo-EM analysis elucidates, for the first time, the structural basis of RNAP inhibition by repressors involved in the archaeal virus-host arms race (Pilotto et al., 2021).
Dr Fabian Blombach, the lead author of the first study explains: ‘The current paradigm in the field dictates that transcription regulators positively or negatively interfere with the recruitment of RNA polymerase to the promoter at the stage of initiation. We challenged this hypothesis using a functional genomics approach by mapping the dynamic (re-)distribution of RNAP correlating it with the cellular RNA levels, genome-wide and at single nucleotide resolution. We could show that it is not only simple ‘access’ of RNAP to the promoter that determines the expression level of a gene, but sophisticated mechanisms that occur during early elongation (Fig. 1). The factors Spt4/5 and Elf1 are successively recruited to the transcription elongation complex before the RNA polymerase makes a transition into productive transcription. Quite surprisingly, we also found that RNA polymerases in the early elongation phase recruit a ribonuclease, the transcription termination factor aCPSF1, that negatively regulates transcription likely by RNA cleavage-induced premature termination mechanism, a mode of regulation that is evolutionary conserved in bacteria and eukaryotes.’

Dr Simona Pilotto, the lead author of the second study elaborates on her work: The inhibition of RNAP and the resulting attenuation of the transcriptome plays a crucial role in the interaction between viruses and their hosts during infection. My aim is to understand the structural basis of ‘switching off’ RNAP, as this is highly relevant for the design of novel antibiotics and antiviral drugs. I have solved the cryo-EM structures of the complexes formed between the Sulfolobus acidocaldarius RNAP and two distinct regulators (RIP and TFS4), and my structures provide insights into the detailed mechanisms underlying the very potent inhibition (Fig. 2). RIP is encoded by the Acidianus two-tailed virus (ATV) and sterically interferes with the interaction of template DNA and transcription factors by molecular mimicry of initiation factors. TFS4 is encoded by the Sulfolobus host and is expressed in response to infection with the Sulfolobus Turreted Icosahedral Virus (STIV). TFS4 is related to elongation factors including TFIIS and targets the RNAP NTP entry pore through which it inactivates RNAP in an allosteric fashion by inducing a widening of the DNA-binding channel disrupting the bridge helix and trigger loop active site motifs. The most intriguing conclusion of my work is that the inhibitory strategies and mechanisms reveal the underlying functional conservation
of RNAPs: unrelated inhibitors have evolved to exploit factor- and nucleic acid binding sites, and conformational flexibilities that are intrinsic to all RNAPs to effectively repress its activity.

Blombach, F., Fouqueau, T., Matelska, D., Smollett, K., and Werner, F. (2021). Promoter-proximal elongation regulates transcription in archaea. Nat Commun 12, 5524.
Pilotto, S., Fouqueau, T., Lukoyanova, N., Sheppard, C., Lucas-Staat, S., Diaz-Santin, L.M., Matelska, D., Prangishvili, D., Cheung, A.C.M., and Werner, F. (2021). Structural basis of RNA polymerase inhibition by viral and host factors. Nat Commun 12, 5523.

Posted by ubcg03u in Lab news, News, Publications
Studying protein conformation using a new cyclic ion mobility mass spectrometry (cIMMS) device

Studying protein conformation using a new cyclic ion mobility mass spectrometry (cIMMS) device

Dr Konstantinos Thalassinos

We are the first group to publish a paper on how a new cyclic ion-mobility mass-spectrometry (cIMMS) device, manufactured by Waters, can be used to probe protein structure and dynamics. In particular, the tandem ion mobility capabilities of the instrument allow us to probe in very fine detail protein unfolding pathways and for the first time to do so for co-existing and interconverting conformers. We are now using this technology to study proteins involved in protein misfolding diseases such as human amyloid islet polypeptide.

The paper is:
Eldrid, C.; Ujma, J.; Kalfas, S.; Tomczyk, N.; Giles, K.; Morris, M.; Thalassinos, K. Gas Phase Stability of Protein Ions in a Cyclic Ion Mobility Spectrometry Traveling Wave Device. Anal. Chem. 2019, 91 (12), 7554–7561 https://doi.org/10.1021/acs.analchem.8b05641

A video where I and other people in the field describe the cIMMS technology:
https://vimeo.com/318178536/005117727e

The link to the Waters site:
https://www.waters.com/waters/en_US/SELECT-SERIES-Cyclic-IMS-ion-mobility-mass-spectrometer/nav.htm?cid=135021297&locale=en_PT

 

Posted by ubtowe001 in Lab news, News, Publications, Uncategorised
Arrival of the new Multiwavelength Beckman Optima analytical ultracentrifuge at the UCL Molecular Interactions Facility

Arrival of the new Multiwavelength Beckman Optima analytical ultracentrifuge at the UCL Molecular Interactions Facility

We are very grateful to the UCL Capital Equipment Fund for the purchase of the new Beckman AUC Optima for the UCL Molecular Interactions Facility that arrived on 25th March 2019. This was installed after Easter and is starting to become operational. This is the first machine of its type to be installed permanently at an UK university. The pictures show (1) the arrival of the instrument on wheels, (2) what we found when the boxes were opened, and (3) the big smiles of our user community. The major development with this new AUC machine is the capability to measure macromolecular sedimentation across a full absorbance wavelength range, and not with a single wavelength as with the old Beckman AUC Proteome. Other advantages are the capacity to measure samples that are more dilute than with the old AUC. The instrument is highly complementary in scope to macromolecular data collected by NMR, crystallography, mass spectrometry, calorimetry and X-ray and neutron scattering. This should make a big difference to biophysical studies where measuring monodispersity or dissociation constants Kd values are important. For example, the binding of ligands with different chromophores can be monitored simultaneously but independently of the protein that they bind to. In the study of heterogeneous interactions, protein complexes in which one is labelled and the other is not can be monitored in detail, or likewise proteins with haem groups that absorb strongly in the visible region. We have already completed with Dr Lindsay McDermott (pictured) an interesting first project where different fatty acids with two distinct fluorescently-tagged chromophores bind to a lipid binding protein called zinc alpha2 glycoprotein. An account of how this method can be used to follow DNA or RNA binding to a protein at three wavelengths for DNA/RNA, protein and their complex is reported in a short review by Borries Demeler on the new multiwavelength AUC published in the current issue of the Biochemist, published by our Biochemical Society: http://www.portlandpresspublishing.com/sites/default/files/biochemist/Biochemist%20Biophysics/BioAPR19_All%28Demeler%29.pdf?dm_i=4WUK,532Y,250YBQ,HPBK,1

Do please email Prof Steve Perkins (s.perkins@ucl.ac.uk) or Mr Jayesh Gor (J.gor@ucl.ac.uk) if you are interested in discussing possibilities, or even applying this new instrument for your research.

          

Posted by ubtowe001 in Lab news, News, Uncategorised
Single-Molecule Studies at the ISMB Biophysics Centre

Single-Molecule Studies at the ISMB Biophysics Centre

Single-molecule studies can reveal key molecular behaviours that are difficult or impossible to discern at the ensemble level. At the ISMB Biophysics Centre, we are planning trials of new, user-friendly instruments that enable the measurement of protein localisation, conformation, mass and force at the single-molecule level.

If your research would benefit from any of these technologies, please contact us. As well as yielding preliminary data for your research, your samples could help to win funding to bring these instruments to the Biophysics Centre on a permanent basis.

The three instruments that will be trialled are:

  • A Nanoimager: a user-friendly super-resolution microscope (https://oni.bio/) for cellular imaging, particle tracking (for diffusion or active transport) or single-molecule FRET studies.
  • An interferometric scattering mass spectrometer (iSCAMS) (https://www.aragobio.com/), that uses light scattering to determine the macromolecular weight of single particles. This is a powerful way of determining the oligomeric state or composition of protein complexes for structural biology projects, with very limited sample requirements (only tens of nM and microliters required).
  • A combined optical tweezer and single-molecule imaging setup (https://lumicks.com/) for detailed mechanistic studies of forces and kinetics.

For informal enquires, do not hesitate to contact Tina Daviter (t.daviter@mail.cryst.bbk.ac.uk) or Mark Williams (m.williams@mail.cryst.bbk.ac.uk). Other ISMB members with experience/interest in these areas who are happy to discuss are: Alan Lowe (a.lowe@ucl.ac.uk), Phil Robinson (p.robinson@mail.cryst.bbk.ac.uk) and Anthony Roberts (a.roberts@mail.cryst.bbk.ac.uk 

– Dr Tina Daviter

Posted by ubcg03u in Lab news, News