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  • Laboratory of Structural Biology: Bochtler Laboratory

Laboratory of Structural Biology: Bochtler Laboratory

Matthias Bochtler, PhD, Professor 

Correspondence address:
Laboratory of Structural Biology
International Institute of Molecular and Cell Biology
4 Ks. Trojdena Street, 02-109 Warsaw, Poland
Email: This email address is being protected from spambots. You need JavaScript enabled to view it. 
tel: +48 (22) 597 0732; fax: +48 (22) 597 0715

2009 Professor of Biological Sciences, nomination by the President of the Republic of Poland
2006 DSc Habil, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
1999 PhD in Biochemistry, Technical University of Munich, Germany
1995 MSc in Experimental Physics, Munich University, Germany

Research Training:
1996-1999 Research Assistant, MPI of Biochemistry, Martinsried, Germany
1995-1996 Internship, Medical Microbiology, University of Regensburg, Germany
1992-1993 Guest Student, Cambridge University, United Kingdom
1990-1992 Studies in physics, Munich University, Germany

Professional Employment:
2010 - Present Head, Structural Biology Laboratory, International Institute of Molecular and Cell Biology, Warsaw, Poland
2007 - 2011 Part-time Director of Structural Biology, Cardiff University, United Kingdom
2001-2010 Head, Joint MPG-PAN Junior Research Group, IIMCB, Warsaw, Poland
2000 Patent training, Weickmann & Weickmann
1999-2000 Postdoctoral Fellow, MPI of Biochemistry, Martinsried, Germany

Honors , Prizes , and Awards:
2005 Pieńkowski Award
2004 EMBO/HHMI Young Investigator Award
2000 Crystal Award, Germany
1998 Crystal Award, Germany
1990-1992 Scholarship from Deutsche Studienstiftung and Bavarian State

   Our group currently works on sequence- and modificationspecific protein-nucleic acid interactions. With an FNP Team grant to support our work, the focus is now almost exclusively on DNA methylation and hydroxymethylation. These modifications are present in prokaryotes and eukaryotes, but they have very different roles in these organisms. Our group seeks to exploit the prokaryotic biology of DNA methylation and hydroxymethylation to develop tools for the study of these modifications in eukaryotes, particularly zebrafish and mice. In 2012, our efforts were concentrated on one story that emphasizes the deep evolutionary roots of DNA methylation.

    DNA cytosine methylation in many eukaryotic species is predominantly found in the context of the CpG dinucleotide. It is thought to be essential in mammals and many other model animals, with the notable exception of the fruit fly Drosophila melanogaster. However, cytosine methylation comes at a price. Genome-wide studies have consistently shown that CpG methylation in eukaryotes is associated with CpG depletion. As a result, the CpG dinucleotide is found several-fold less frequently in nuclear DNA of higher mammals, including humans, than one might expect based on the GC content of the DNA. The reasons for the link between CpG methylation and depletion are both chemical and biological. At the chemical level, cytosine methylation promotes deamination and leads to thymines. More importantly, at the biological level, methylcytosines converted to thymines are difficult to identify as a damage product and difficult to repair to cytosines through DNA repair pathways. Both the chemical and biological arguments for the link between CpG methylation and depletion are fairly fundamental and should apply to all kingdoms of life.

   Hence, one can ask the question, “Is it possible to discover novel prokaryotic CpG methyltransferases (like the previously found CpG specific M.SssI) by searching bacterial genomes for CpG depletion?” We have performed exactly this and scanned all fully sequenced bacterial genomes in the NCBI sequence collection for CpG underrepresentation. We found several drastically (i.e., approximately 10-fold) CpG-depleted bacterial species. Although we found differences in the statistical signatures of CpG depletion when compared with eukaryotes (e.g., in the comparison of coding and on-coding regions), we followed this observation by analyzing bacteria with drastic CpG depletion for CpG methylation. In the case of Mycoplasma penetrans, a genome-wide study of cytosine methylation using bisulfite sequencing identifi ed global CpG methylation and several other universally methylated sequences. To identify the M. penetrans CpG methyltransferase, we picked a candidate protein on the basis of remote amino acid sequence similarity to M.SssI. Using bisulfite sequencing and other CpG methylation assays (i.e., HpaII/MspI digestion), we demonstrated in vitro that our candidate enzyme was indeed a CpG-specific DNA methyltransferase and hence named it M.MpeI in accordance with nomenclature guidelines.

Fig. 1. (A) Initial screen for CpG depletion in bacterial genomes. The GpC/CpG dinucleotide ratio was used as a “proxy” for CpG depletion in order to normalize for the GC content. Every dot in the diagram represents one bacterial genome. (B-D) The same for related dinucleotide ratios as a control.


 How does M.MpeI recognize its CpG target sequence with extraordinary specificity? To answer this question, we crystallized M.MpeI with target DNA and solved the structure. Unsurprisingly, we found typical features of CpG methyltransferase DNA complexes, such as flipping of the substrate cytosine and the proximity of the co-factor to the substrate base for direct transfer of a methyl group. Very interestingly, the DNA structure was perturbed not only in the substrate strand but also in the complementary strand. In this strand, we detected intercalation of a phenylalanine residue between the C and G nucleotides of the CpG site. The 5'-pyrimidine purine-3' steps are thought to be easier to unstack than other dinucleotide steps. Hence, intercalation might contribute to CpG readout. This concept is supported by the recent structure of the eukaryotic DNA maintenance methyltransferase Dnmt1 in complex with target DNA, which also shows unstacking of the CpG step.


Fig. 2. Structures of C5 methyltransferases in productive complexes with target DNA. Only the structure of M.MpeI with DNA is our work, the other two structures were drawn according to coordinates from other laboratories.


    If CpG methylation damages genomes, then what is the benefi t for bacteria to retain a CpG-specific DNA methyltransferase? We are presently unable to answer this question, but several possibilities exist. The methyltransferase might be part of a CpG-specific restriction modification system. Alternatively and somewhat improbably in light of our genome-wide methylation data, it might play a role as an epigenetic regulator. Finally, bacterial CpG methylation might involve host pathogen interactions. Although the claim is still debated, most authors now agree that CpG-unmethylated DNA is far more immunogenic than CpG-methylated DNA.

    Hence, CpG methylation might help bacteria dodge the host immune system. If so, then our findings could also have medical applications because at least some of the CpG-specific DNA methyltransferases are found in human pathogens.

Lab Leader:
Matthias Bochtler, PhD, Professor

Postdoctoral Fellows:
Honorata Czapińska, PhD
Humberto Fernandes, PhD (IBB)
Thomas Fricke, PhD
Joanna Krwawicz, PhD
Małgorzata Perycz, PhD
Anna Piasecka, PhD

Junior Researchers:
Marlena Kisiała, MSc (IBB)
Norbert Osiński, MSc
Michał Pastor, MSc (IBB)
Dominik Rafalski, MSc
Anton Slyvka, MSc
Anna  Stroynowska-Czerwińska, MSc
Katarzyna Szafran, MSc

Lab and Office Manager:
Paulina Okafor, MSc

Agnieszka Olszewska

Past lab members:
Asgar Abbas Kazrani, PhD
Jean-Philippe Borges, PhD
Grzegorz Chojnowski, PhD
Mohamed El-Komy, MSc
Renata Filipek, PhD
Patrycja Haniewicz, PhD
Agnieszka Kolano, PhD
Henryk Korza, PhD
Karolina Mierzejewska, MSc
Katarzyna Misztal, PhD
Izabela Sabała, PhD
Wojciech Siwek, PhD
Monika Sokołowska, PhD
Roman Szczepanowski, PhD
Marta Szychowska, MSc
Marta Wawrzyniak, PhD (shared with Department of Molecular Biology)
Patrycja Wawrzyniecka, MSc (IBB)
Marek Wojciechowski, PhD




Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M.

Activity and structure of EcoKMcrA.

Kisiala M, Copelas A, Czapinska H, Xu S, Bochtler M.

Crystal structure of the modification-dependent SRA-HNH endonuclease TagI

Fernandes H, Czapinska H, Grudziaz K, Bujnicki JM, Nowacka M.

Crystal structure of human Acinus RNA recognition motif domain.

Stroynowska-Czerwinska A, Piasecka A, Bochtler M.

Specificity of MLL1 and TET3 CXXC domains towards naturally occurring cytosine modifications.

Tamulaitiene G, Manakova E, Jovaisaite V, Tamulaitis G, Grazulis S, Bochtler M, Siksnys V.

Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family.

Piasecka A, Czapinska H, Vielberg MT, Szczepanowski RH, Kiefersauer R, Reed S, Groll M, Bochtler M.

The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers.


Perycz M, Krwawicz J, Bochtler M.

A TALE-inspired computational screen for proteins that contain approximate tandem repeats.

Slyvka A, Mierzejewska K, Bochtler M.

Nei-like 1 (NEIL1) excises 5-carboxylcytosine directly and stimulates TDG-mediated 5-formyl and 5-carboxylcytosine excision.


Haniewicz P, Floris D, Farci D, Kirkpatrick J, Loi MC, Büchel C, Bochtler M, Piano D

Isolation of Plant Photosystem II Complexes by Fractional Solubilization

Mierzejewska K, Bochtler M, Czapinska H

On the role of steric clashes in methylation control of restriction endonuclease activity

Bochtler M., Piasecka A

Haloferax volcanii UbaA, catalytic engine for sampylation and sulfur transfer

Szychowska M, Siwek W, Pawolski D, Kazrani AA, Pyrc K, Bochtler M

Type III CRISPR complexes from Thermus thermophilus

Bochtler M, Kolano A, Xu G-L

DNA demethylation pathways: Additional players and regulators


Burmistrz M, Dudek B, Staniec D, Rodriguez Martinez JI, Bochtler M, Potempa J, Pyrc K

Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems

Grabowska M, Jagielska E, Czapinska H, Bochtler M, Sabala I

High resolution structure of an M23 peptidase with a substrate analogue


Gallagher JM, Yamak A, Kirilenko P, Black S, Bochtler M, Lefebvre C, Nemer M, Latinkić BV

Carboxy terminus of GATA4 transcription factor is required for its cardiogenic activity and interaction with CDK4

Jaremko M, Jaremko L, Nowakowski M, Wojciechowski M, Szczepanowski RH, Panecka R, Zhukov I, Bochtler M, Ejchart A

NMR structural studies of the first catalytic half-domain of ubiquitin activating enzyme

Kazrani AA, Kowalska M, Czapinska H, Bochtler M

Crystal structure of the 5hmC specific endonuclease PvuRts1I

Wojciechowski M, Rafalski D, Kucharski R, Misztal K, Maleszka J, Bochtler M, Maleszka R

Insights into DNA hydroxymethylation in the honeybee from in-depth analyses of TET dioxygenase

Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M

Structural basis of the methylation specificity of R.DpnI

Sabala I, Jagielska E, Bardelang PT, Czapinska H, Dahms SO, Sharpe JA, James R, Than ME, Thomas NR, Bochtler M

Crystal structure of the antimicrobial peptidase lysostaphin from Staphylococcus simulans


Wojciechowski M, Czapinska H, Bochtler M

CpG Underrepresentation and the Bacterial CpG Specific DNA Methyltransferase M.MpeI

Haniewicz P, De Sanctis D, Büchel C, Schröder WP, Loi MC, Kieselbach T, Bochtler M, Piano D

Isolation of monomeric photosystem II that retains the subunit PsbS


Chojnowski G, Bujnicki JM, Bochtler M

RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes

Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K

Crystal structure and mechanism of action of the N6-methyladenine dependent type IIM restriction endonuclease

Sabala I, Jonsson IM, Tarkowski A, Bochtler M

Anti-staphylococcal activities of lysostaphin and LytM catalytic domain

Bochtler M

Structural basis of the TAL effector-DNA interaction


Sokolowska M, Czapinska H, Bochtler M

Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis

Braun S, Humphreys C, Fraser E, Brancale A, Bochtler M, Dale TC

Amyloid-associated nucleic acid hybridisation

Antonczak AK, Simova Z, Yonemoto IT, Bochtler M, Piasecka A, Czapinska H, Brancale A, Tippmann EM

Importance of single molecular determinants in the fidelity of expanded genetic codes

Firczuk M, Wojciechowski M, Czapinska H, Bochtler M

DNA intercalation without flipping in the specific ThaI-DNA complex


Piano D, El Alaoui S, Korza HJ, Filipek R, Sabala I, Haniewicz P, Buechel C, De Sanctis D, Bochtler M

Crystallization of the Photosystem II core complex and its chlorophyll binding subunit CP43 from transplastomic plants of Nicotiana tabacum

Chojnowski G, Breer K, Narczyk M, Wielgus-Kutrowska B, Czapinska H, Hashimoto M, Hikishima S, Yokomatsu T, Bochtler M, Girstun A, Staroń K, Bzowska A

1.45 A resolution crystal structure of recombinant PNP in complex with a pM multisubstrate analogue inhibitor bearing one feature of the postulated transition state

Gentsch M, Kaczmarczyk A, van Leeuwen K, de Boer M, Kaus-Drobek M, Dagher MC, Kaiser P, Arkwright PD, Gahr M, Rösen-Wolff A, Bochtler M, Secord E, Britto-Williams P, Saifi GM, Maddalena A, Dbaibo G, Bustamante J, Casanova JL, Roos D, Roesler J

Alu-repeat-induced deletions within the NCF2 gene causing p67-phox-deficient chronic granulomatous disease (CGD)

Chojnowski G, Bochtler M

DIBER: protein, DNA or both?


Sokolowska M, Czapinska H, Bochtler M

Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA


Lipka M, Filipek R, Bochtler M

Crystal structure and mechanism of the Staphylococcus cohnii virginiamycin B lyase (Vgb)

Sukackaite R, Grazulis S, Bochtler M, Siksnys V.

The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution

Breer K, Wielgus-Kutrowska B, Hashimoto M, Hikishima S, Yokomatsu T, Szczepanowski RH, Bochtler M, Girstun A, Starón K, Bzowska A

Thermodynamic studies of interactions of calf spleen PNP with acyclic phosphonate inhibitors

Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V

How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets

Szczepanowski RH, Carpenter MA, Czapinska H, Zaremba M, Tamulaitis G, Siksnys V, Bhagwat AS, Bochtler M

Central base pair flipping and discrimination by PspGI


Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V

Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence

Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M

Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA.

Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Siksnys V, Bochtler M

Restriction endonucleases that resemble a component of the bacterial DNA repair machinery

Kaus-Drobek M, Czapinska H, Sokołowska M, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M

Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically

Firczuk M, Bochtler M

Mutational analysis of peptidoglycan amidase MepA

Firczuk M, Bochtler M

Folds and activities of peptidoglycan amidases

Chojnowski G, Bochtler M

The statistics of the highest E value

Bochtler M, Chojnowski G

The highest reflection intensity in a resolution shell


Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis S, Czapinska H, Manakova E, Siksnys V

Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease


Marcyjaniak M, Odintsov SG, Sabala I, Bochtler M

Peptydoglycan amidase MepA is a LAS metallopeptidase

Potempa J, Golonka E, Filipek R, Shaw LN

Fighting an enemy within: cytoplasmic inhibitors of bacterial cysteine proteases

Szczepanowski RH, Filipek R, Bochtler M

Crystal structure of a fragment of mouse ubiquitin-activating enzyme.

Odintsov SG, Sabała I, Bourenkov G, Rybin V, Bochtler M

Substrate access to the active sites in aminopeptidase T, a representative of a new metallopeptidase clan.

Odintsov SG, Sabała I, Bourenkov G, Rybin V, Bochtler M

Staphylococcus aureus aminopeptidase S is a founding member of a new peptidase clan

Korza HJ, Bochtler M

Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow.

Groll M, Bochtler M, Brandstetter H, Clausen T, Huber R

Molecular machines for protein degradation.

Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V

Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.

Firczuk M, Mucha A, Bochtler M

Crystal structures of active LytM

Filipek R, Potempa J, Bochtler M

A comparison of staphostatin B with standard mechanism serine protease inhibitors

Dandanell G,Szczepanowski RH, Kierdaszuk B, Shugar D, Bochtler M

Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene

Azim MK, Goehring W, Song HK, Ramachandran R, Bochtler M, Goettig P

Characterization of the HslU chaperone affinity for HslV protease


Golonka E, Filipek R, Sabat A, Sinczak A, Potempa J

Genetic characterization of staphopain genes in Staphylococcus aureus

Odintsov SG, Sabala I, Marcyjaniak M, Bochtler M

Latent LytM at 1.3A resolution

Marcyjaniak M, Odintsov SG, Sabala I, Bochtler M

Peptidoglycan amidase MepA is a LAS metallopeptidase

Filipek R, Szczepanowski R, Sabat A, Potempa J, Bochtler M

Prostaphopain B structure: a comparison of proregion-mediated and staphostatin-mediated protease inhibition

Bochtler M, Odintsov SG, Marcyjaniak M, Sabala I

Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases.

Marcyjaniak M, Odintsov SG, Sabala I, Bochtler M

Peptidoglycan amidase MepA is a LAS metallopeptidase.


Rzychon M, Filipek R, Sabat A, Kosowska K, Dubin A, Potempa J, Bochtler M

Staphostatins resemble lipocalins, not cystatins in fold

Filipek R, Rzychon M, Oleksy A, Gruca M, Dubin A, Potempa J, Bochtler M

The Staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease.

Dubin G, Krajewski M, Popowicz G, Stec-Niemczyk J, Bochtler M, Potempa J, Dubin A, Holak TA

A novel class of cysteine protease inhibitors: solution structure of staphostatin A from Staphylococcus aureus.


Ramachandran R, Hartmann C, Song HK, Huber R, Bochtler M

Functional interactions of HslV (ClpQ) with the ATPase HslU (ClpY)


Palczewska M, Groves P, Ambrus A, Kaleta A, Kövér KE, Batta G, Kuźnicki J.

Structural and biochemical characterization of neuronal calretinin domain I-II (residues 1-100). Comparison to homologous calbindin D28k domain I-II (residues 1-93)