Manchester Centre for Integrative Systems Biology
Faculty of Life Sciences
Manchester Interdisciplinary Biocentre
131 Princess Street
Manchester M1 7DN
Phone:+44 (0) 161 30 65197
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
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.
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.
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.
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
1995 - 2000
Vilnius University and Institute of Biochemistry,
Vilnius, Lithuania. D.Phil. in Biochemistry, working under the
supervision of Dr
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.
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.
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.
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.
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,
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.
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.
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.
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.
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.
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.
and Nivinskas, R. (1996). Effect of mRNA secondary structure in the
regulation of gene 25 expression of bacteriophage T4. Biologija Nr.