Postdoctoral position, 24 months with a possibility of extension

The Laboratory for Molecular Infection Medicine Sweden (MIMS) within the Nordic EMBL Partnership for Molecular Medicine, Umeå University, Sweden

Project description:

The focus of the project is biochemical analysis of Bacillus subtilis ribosome-associated stress factors. The project addresses questions generated through bioinformatic analysis of ribosomal factors, and will comprise of a biochemical research programme backed up by a complementary set of microbiological and structural investigations. The position is co-financed by funds from Ragnar Söderberg and Carl Tryggers foundations.

Our laboratory uses a combination of experimental (in vitro biochemistry in a reconstituted translational system, NGS-based techniques for in vivo biochemistry, as well as microbiological approaches) and in silico (molecular evolution) approaches. We are currently supported by the Swedish Research Council, Ragnar Söderberg foundation, Kempe foundation, Carl Tryggers foundation, as well as Umeå University funds.

For further information please contact Dr. Vasili Hauryliuk, vasili.hauryliuk@umu.se or Dr. Gemma C. Atkinson, gemma.atkinson@umu.se. See also our web page.

A successful candidate should meet the following criteria:

Essential:

- Documented proficiency in biochemical assays

- Strong skills in experimental design and interpretation

- A high level of proficiency in written and spoken English, as well as scientific writing

- A strong publication record in international, peer reviewed journals

- An ability to work effectively independently and as a group

- A willingness to learn new techniques

Highly desired:

- Experience in ribosomal biochemistry / RNA biochemistry

- Experience in bacterial genetics, particularly Bacillus subtilis

Applications should be written in English, comprise of a cover letter, CV with a publication list and contact information of at least two referees. Documents should be in MS Word or PDF format and submitted electronically to Dr. Vasili Hauryliuk, vasili.hauryliuk@umu.se, or Dr. Gemma Atkinson, gemma.atkinson@umu.se. The position is available starting spring 2015 (negotiable).

Two PhD and one postdoctoral position at MIMS

Our lab is branching out. This fall we cross the Baltic sea and set up a new lab in Umeå, Sweden - at the Laboratory for Molecular Infection Medicine Sweden, MIMS. Do you like ribosomes? Do you also think that is ppGpp the main G nucleotide in bacteria? Are you stringent enough? Do you know somebody who fits the bill?

If yes, then good news are that we have two PhD and one postdoctoral positions up for grabs. Drop me a line at vasili.hauryliuk@molbiol.umu.se!

Tet(O) cryoEM structure is out!

So it is finally out: the cryoEM structure of Tet(O) on the ribosome we have collaborated on with Joachim Frank's lab is finally published on in Nature Communications. Tet(O) is a bacterial translational GTPase that clears the ribosome from tetracycline antibiotic, and structural data provided in the paper shed light on the mechanism of Tet(O)-mediated resistance. Recently cryoEM of Tet(O)'s close relative, Tet(M) was published by Beckmann and Wilson labs, so now one can compare the two. And yes, they look very similar. No surprise there.

References:

Li et al. Nature Communications (2013) PIMD: 23403578

Dönhöfer at al. PNAS (2012) PIMD:  23027944

ppGpp biosyntehsis pathway summed up nicely

A very nice scheme of the ppGpp biosynthesis pathways can be found on the MetaCyc (1). Seems to be a very useful database in general.

References:

Caspi et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. NAR 2012 Jan;40(Database issue):D742-53 PIMD: 22102576

RiboCOURSE Spring 2013: From Ribosome structure to bacterial physiology

An advanced course on bacterial translation and physiology is to be taught at the RiboCORE, Uppsala University in spring 2013. I will be giving a lecture on the stringent response. You can find the course programme here. Review on the stringent response written by Gem Atkinson and myself is a nice introduction to the subject.

GDP and SRL don't mix

Translational GTPases run the ribosomal cycle, and the ribosome talks back - it recruits the GTPases when it is a certain state, affects trGTPase's affinity to G nucleotides and activates the GTP hydrolysis when needed. Using Isothermal Titration Calorimetry we showed that binding of GDP nucleotide and of SRL rRNA element to translational GTPases IF2 and EF-G are mutually exclusive. This suggests a neat mechanism for the destabilisation of the ribosome-bound GDP form of the GTPase: the moor has done his duty, the moor can go.

Due to the technical limitations, the ITC experiments were performed with a 27-nucleotide long RNA piece mimicking the rRNA element as a model. In order to place our results in the framework of the ribosomal cycle we need experiments with the whole ribosome. 

References:

Mitkevich et al., Scientific Reports 2012 2:843, PIMD: 32150791

First PhD defence in the lab

Our first PhD defence took place on November 2d, 2012. Viktoriya Shyp has defended her work "G nucleotide regulation of translational GTPases and the stringent response factor RelA". Mike Cashel, the discoverer of ppGpp, served as opponent.

Hurray to Vika!