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Manchester Centre for Integrative Systems Biology

Dr. Naglis Malys


Address

Manchester Centre for Integrative Systems Biology

Faculty of Life Sciences

Manchester Interdisciplinary Biocentre

(Room 2.002)

131 Princess Street

Manchester M1 7DN

UK

Phone:+44 (0) 161 30 65197

Email: n.malys@manchester.ac.uk

 

Research interests

Yeast metabolism

We are developing and applying various biochemical, biophysical and modelling techniques for better understanding the metabolism in the cell. As proteins are the chief engines and catalysts of cellular dynamics, in an ongoing project at the Manchester Centre for Integrative Systems Biology we use S. cerevisiae as a protein production factory. Yeast offers many advantages, as its biosynthetic pathways resemble higher eukaryotic cells in many aspects. Moreover, S. cerevisiae has a long and successful track record and is generally regarded as a best studied microorganism. In the systems biology approach we quantitatively measure the enzyme kinetics to establish parameters for modelling of whole metabolic pathways. In addition, we are aiming to develop methods for metabolic engineering and biotechnology.

Protein production

We use S. cerevisiae for protein production. Protein expression is performed using controlled yeast expression system. The affinity tag based protein purification method allows purifying up to 1 mg of protein per 5 g of yeast (wet mass, corresponding to 1 L yeast culture). Available strain collection provides good opportunity to produce almost every yeast protein. Besides, any other eukaryotic gene can be effectively cloned into available expression system and protein of interest produced in yeast.

protein production image

mRNA turnover and scavenger decapping enzymes

Decapping scavenger enzyme Dcs1 catalyses cleavage of 5'end m(7)G-oligoribonucleotide fragments generated by 3'-->5' exonucleolytic mRNA decay, and cleavage of m(7)GDP generated by Dcp1/Dcp2-mediated decapping in the 5'-->3' decay pathway. As a consequence of this scavenger activity, toxic methylated nucleotide derivatives are cleared from the cell. We showed that Dcs1 is active as a homodimer with low Km values for cleavage of m(7)GpppG and m(7)GDP, while the Dcs2 that is closely related to Dcs1 is induced under nutrient stress via the cAMP-PKA signalling pathway. The resulting Dcs2 interferes with Dcs1 function by forming a heterodimer, both modulating Dcs1 substrate specificity and suppressing its k(cat). Fluorescence microscopy studies also reveal that during starvation the GFP labelled Dcs2 protein co-localises with RFP-Lsm1 protein in P-bodies. In addition, we demonstrated that decapping scavenger enzyme plays a complementary role to the translation factor eIF4E in preventing capped 5' fragments of mRNA from interfering with translation initiation.

Postranscriptional control

The formation of translation initiation complex requires a limited number of well-characterized signals, which are clustered within the translation initiation region (TIR) of mRNAs. For the canonical mRNA of prokaryotes, one of the most important signals is the Shine-Dalgarno sequence that base pairs to variable subset of the anti-SD sequence in the 3' end of the 16S rRNA. The SD interaction anchors the TIR of the mRNA to the 30S ribosomal subunit forming the 30S-mRNA complex that allows the kinetic selection of the start codon (AUG, GUG or others) in closer proximity of the ribosomal P site leading to translation initiation. The accessibility of translation initiation signals to ribosome can be controlled by mRNA secondary structure. We investigate special cases when secondary structures enhance translation initiation.

 

Experience

2005 - present
University of Manchester. Experimental officer at the MCISB, University of Manchester, working with Prof Douglas Kell and Prof John McCarthy.

2002 - 2005
UMIST and University of Manchester, Faculty of Life Sciences. Research Associate, working with Prof John McCarthy on decapping scavanger enzymes Dcs1 and Dcs2 in S. cerevisiae and translation initiation factor eIF4E in S. pombe.

2001 - 2002
University of Maryland, Department of Biochemistry and Molecular Biology, Baltimore, MD. Postdoctoral fellow, working with Prof Lindsay Black on development and application of phage display, identifying new role of terminase in transcription regulation through interaction with phage sigma factor gp55.

1998 - 2001
Vilnius University, Faculty of Natural Sciences, Vilnius, Lithuania. Visiting lecturer, Module leader in Genetic Engineering.

1995 - 2000
Vilnius University and Institute of Biochemistry, Vilnius, Lithuania. D.Phil. in Biochemistry, working under the supervision of Dr Rimantas Nivinskas.

 

Publications

Malys, N., and Nivinskas, R. (2009) Non-canonical RNA arrangement in T4-even phages: accomodated ribosome binding site at the gene 26-25 intercistronic junction. Mol. Microbiol., 73, 1115-1127.

Malys, N., and McCarthy, J.E. (2006) Dcs2, a novel stress-induced modulator of m7GpppX pyrophosphatase activity that locates to P bodies. J. Mol. Biol., 363, 370-382.

Malys, N., Carroll, K., Miyan, J., Tollervey, D. and McCarthy, J.E. (2004) The 'scavenger' m7GpppX pyrophosphatase activity of Dcs1 modulates nutrient-induced responses in yeast. Nucleic Acids Res., 32, 3590-3600.

Ptushkina, M., Malys, N. and McCarthy, J.E. (2004) eIF4E isoform 2 in Schizosaccharomyces pombe is a novel stress-response factor. EMBO Rep., 5, 311-316.

Malys, N., Chang, D.Y., Baumann, R.G., Xie, D. and Black, L.W. (2002) A bipartite bacteriophage T4 SOC and HOC randomized peptide display library: detection and analysis of phage T4 terminase (gp17) and late sigma factor (gp55) interaction. J. Mol. Biol., 319, 289-304.

Malys, N., Klausa, V. and Nivinskas, R. (2000) Polarity effect of premature termination of the bacteriophage T4 gene 26 translation on the gene 25 expression in vivo . Biologija Nr. 2 suppl, 82-84.

Klausa, V., Malys, N. and Nivinskas, R. (2000). The product of gene 26 of bacteriophage T4 is virion protein: Direct immunoblot assay evidence. Biologija Nr. 2 suppl, 79-81.

Malys, N. and Nivinskas, R. (2000) Detection of mRNA secondary structure in the translation initiation region of bacteriophage T4 gene 25 by AMV reverse transcriptase. Biologija Nr. 1, 33-36.

Nivinskas, R., Malys, N., Klausa, V., Vaiskunaite, R. and Gineikiene E. (1999) Post-transcriptional control of bacteriophage T4 gene 25 expression: mRNA secondary structure that enhances translational initiation. J. Mol. Biol., 288, 291-304.

Malys, N., Klausa, V., Vaiskunaite, R.and Nivinskas, R. (1998) Construction of bacteriophage T4 mutants carrying mutations in the upstream region of gene 25 . Biologija Nr. 2, 70-73.

Zajanckauskaite, A., Malys, N., Salniene, V. and Nivinskas, R. (1998) Use of gene fusion to confirm the structure and arrangement of overlapping genes 30.3 and 30.3` in bacteriophage T4. Biologija Nr. 2, 86-88.

Malys, N. and Nivinskas, R. (1998) Some features of the expression of bacteriophage T4 gene 26 and 25 . Biologija Nr. 1 suppl, 37-40.

Zajanckauskaite, A., Malys, N. and Nivinskas, R. (1997) A rare type of overlapping genes in bacteriophage T4: gene 30.3' is completely embedded within gene 30.3 by one position downstream. Gene, 194, 157-162.

Malys, N. and Nivinskas, R. (1996). Effect of mRNA secondary structure in the regulation of gene 25 expression of bacteriophage T4. Biologija Nr. 2, 42-44.