State-of-the-art and preparatory work

Our team works in collaboration with colleagues from the Justus‐Liebig‐Universität‐Giessen as well as colleagues from the team of Oretskaya and Kubareva, Moscow State University. Our projects concern various aspects of the bioinformatics analysis of enzymes acting on nucleic acids.

First, we are working on predicting mutations on dimerisation interfaces of LAGLIDADG homing endonucleases which will provide information concerning a desired dimerisation interface of LAGLIDADG domains from different proteins. Such kind of approach is promising in terms of constructing chimeric homing endonucleases with changed specificity. Joint results of the work of our group and the Wende group on interfaces of native LAGLIDADG domains are now in press.

Second, we have created new original tools for revealing block structures in multiple alignments of protein sequences and in corresponding 3D structures. Such tools will significantly improve the bioinformatics analysis of protein families of interest. A manuscript describing the first version of the programme was accepted for publication.

Third, we are working on comprehensive bioinformatics analysis of prokaryotic restrictionmodification systems. By now, distribution of restriction sites in available phage genomes has been studied. Sequence based phylogeny of more than 7000 methyltransferases was described. This work, previously discussed with Prof. Pingoud, is currently in progress due to active work of our PhD and undergraduate students.

Fourth, as proposed by Prof. Pingoud, we have started the work on searching for a protein inhibitor for the non‐specific endonuclease EndA of Streptococcus pneumonia and related bacteria. Although it might be that the endonuclease activity of EndA in host cytoplasm is inhibited by different mechanisms, the importance of a possible inhibition of EndA when expressed in E. coli and known examples of protein inhibitors of homologous endonucleases in a number of bacterial taxa encourages this work.

Fifth, we are working in tight collaboration with the team of Oretskaya and Kubareva (Moscow) on several aspects of the interaction of DNA methyltrasferases with their target sites, which are in the sphere of interest of both teams.

References

1 Grishin, A.V., Fonfara, I., Alekseevskii, A.V., Spirin, S.A., Zanegina, O., Karyagina, A., Alexeyevky, D. & Wende, W. (2010) Identification of conserved features of LAGLIDADG homing endonucleases. J Bioinform Comput Biol in press.

2 Burkov, B., Nagaev, B., Spirin, S. & Alexeevski, A. (2010) MALAKITE: An automatic tool for characterization of structure of reliable blocks in multiple alignments of protein sequences. J Bioinform Comput Biol in press.

3 Mitrofanov, S., Panchin, A., Spirin, S., Alexeevski, A., Panchin, Y. (2010) Exclusive sequences of different genomes. J Bioinform Comput Biol in press.

4 Grishin, A.V., Alekseevskii, A.V., Spirin, S.A. & Kariagin, A.S. (2009) Conserved structural features of ETS domain‐‐DNA complexes. Mol Biol (Mosk) 43, 666‐674.

5 Fedotova, E.A., Protsenko, A.S., Zakharova, M.V., Lavrova, N.V., Alekseevsky, A.V., Oretskaya, T.S., Karyagina, A.S., Solonin, A.S. & Kubareva, E.A. (2009) SsoII‐like DNA‐methyltransferase Ecl18kI: interaction between regulatory and methylating functions. Biochemistry (Mosc) 74, 85‐91.

6 Aksianov, E., Zanegina, O., Grishin, A., Spirin, S., Karyagina, A. & Alexeevski, A. (2008) Conserved water molecules in Xray structures highlight the role of water in intramolecular and intermolecular interactions. J Bioinform Comput Biol 6, 775‐788.

7 Spirin, S., Titov, M., Karyagina, A. & Alexeevski, A. (2007) NPIDB: a database of nucleic acids‐protein interactions. Bioinformatics 23, 3247‐3248.

8 Petrova, N.V., Yakutenko, II, Alexeevski, A.V., Verbovoy, V.A., Razin, S.V. & Iarovaia, O.V. (2007) Changes in chromosome positioning may contribute to the development of diseases related to X‐chromosome aneuploidy. J Cell Physiol 213, 278‐283.

Aims

The overall aims of this project are:

I. Bioinformatic analysis of LAGLIDADG homing endonucleases with particular focus on modelling dimerization interfaces for engineering enzymes with new specificities

II. Analysis of the evolution of restriction‐modification systems

III. Development of computer tools for the analysis of sequences and 3D structures of related biomolecules

Work Programme and methods

Predicting interfaces for desirable dimerization of different LAGLIDADG endonucleases’ subunits by virtual screening and sequence analysis approaches.

Developing computer tools for the analysis of multiple protein sequence alignments that have complex block structures. Applying them for the analysis of LAGLIDADG endonucleases and other protein families of interest.

Further developing of NPIDB, a database of 3D structures of complexes of proteins with nucleic acids. Testing comparative genomic approach for searching protein inhibitors of non‐specific bacterial endonucleases EndA.

Reconstructing evolution of type II restriction‐modification systems

Titles for dissertations (prospective)

• LAGLIDADG homing endonucleases: evolution, structure, modelling of dimerization interface

• MALAKITE package for multiple alignment analysis

• Whole genome bioinformatics analysis of prokaryotic restriction‐modification systems

• Comprehensive analysis of 3D structures of Protein‐DNA complexes

Relationships/connections within the research training group

Wende: Modelling of the interface region of the new chimeric homing endonucleases.

Pingoud: End A inhibitor design

Oretskaya, Kubareva: Co‐evolution of phage genomes and bacterial R‐M systems

Benefits of the scientific exchange

The collaboration of teams in the frame of the IRTG project is of great importance for our team, especially for our young scientists. The experience of regular meetings of all teams, successful workshops and visits of our students to Giessen and German students to Moscow made it clear.