Lab Presentation

A unique feature of mitochondria is that they possess their own genome, the mitochondrial DNA (mtDNA), which codes for subunits of the electron transport chain that eventually leads to the synthesis of the ATP molecule. Dysregulation of this genome causes complex diseases and syndromes that are difficult to diagnose and treat. These are mostly classified as rare diseases. In the Structural MitoLab,we are interested in the structural basis underlying mtDNA regulation and packaging. Our research is multidisciplinary and combines macromolecular X-ray crystallography with biochemical and biophysical analyses (chromatography, electrophoresis, SAXS, MALLS, etc.), which can be completed with additional techniques in collaboration with other groups.

Our group is interested in understanding the structural basis of mitochondrial genome regulation. In humans, this genome is a circular DNA molecule of 16.5kbp whose Light and Heavy DNA strands together code for 13 essential subunits (out of approximately 80) of complexes I, III, IV and V of the oxidative phosphorylation pathway (OXPHOS), as well as for two rRNAs and 22tRNAs. The remaining OXPHOS subunits are imported from the cytosol. During mitochondrial fusion and fission, mtDNA is replicated and transmitted to daughter organelles. Therefore, correct transcription, replication and maintenance of the mtDNA are essential for cell viability.

 

tfam twinkle mterf

Gallery of representative projects of the Structural Mitolab.(A) Mitochondrial Transcription Factor A, TFAM. Top panel, the domains of TFAM, HMGbox1 and HMGbox2 are depicted in orange and green respectively; the connecting Linker is in yellow. TFAM’s cognate DNA sequence at LSP is represented in blue. Bottom, representation of the DNA U-turn imposed by TFAM at the transcription initiation site (‘start site’), to which mtRNA polymerase (MTRPOL) and transcription factor B2 (TFB2) bind. The red arrow signals the position of TFAM’s C-terminal tail and its interaction with the transcription machinery. (B) Replicative helicase Twinkle. The top panel shows the different domains of a homology model based on the T7 phage gp4 helicase and E.coli primase fitted into the EM map (1Q57 and 2AU3 PDB codes, respectively). The Zinc-binding domain (ZBD) is shown in blue, the RNA-polymerase domain (RPD) in magenta, and the C-terminal domain in yellow; ZBDs 2 and 3 show different relative positions. Bottom: The EM map is represented in purple and the contacts between subunits are shown. (C) Mitochondrial Termination Factor mTERF. The different TERF motifs I – IX from the termination factor mTERF are represented. Two DNA molecules (one from the asymmetric unit and the second from a symmetry mate) lay along the central axis of the Zurdo left-handed domain.

 

Transcription of the mtDNA strands is initiated at two promoters (light strand promoter, LSP; heavy strand promoter, HSP) that are clustered at the Control Region. The pre-initiation complex is formed by mitochondrial transcription factor A (TFAM, Panel A in the figure), which recruits RNA polymerase (mtRNAP). This is completed by Factor B2, which creates the replication bubble. We have previously solved the structure of TFAM bound to LSP, which corresponds to the first step of the pre-initiation complex formation. This protein encompasses two HMG-box domains, which are typically found in the nucleus. In TFAM, these domains insert residues into the DNA, disrupting the stacking between bases and inducing a strong bend of 180º. In this complex, the protein is intertwined with the DNA, a binding mechanism that is possible by virtue of TFAM’s high flexibility, as shown by SAXS. In addition, the C-terminal tail of TFAM is positioned in an orientation that can recruit mtRNAP to the LSP.

The replicative helicase Twinkle is another protein that has caught our interest. This protein (Panel B in the figure) shows homology to phage helicases, in particular to T7 gp4, since both include a primase and a helicase domain fused in a single molecule. However, Twinkle’s primase domain, although needed for protein function, does not show primase activity. We analyzed the full-length structure by cryo-EM, SAXS and homology modeling. This is the first structure of an SF4 family hexameric helicase that includes all domains. The structural analysis confirmed previous results that showed the formation of flexible hexamers and heptamers. Our results showed that, in the multimeric complex, two-layered N- (NTD) and C-terminal domain (CTD) rings are found. The N-terminal ring is composed of a zinc-binding domain (ZBD) and an RNA-polymerase domain (RPD) and, while all RPDs similarly contact the CTDs, the ZBDs show an asymmetric disorder compatible with asymmetric contacts with the DNA during helicase progression.

A third example of our work is termination factor mTERF (Panel C in the figure), which functions as a roadblock, preventing collision between transcription and replication machineries by binding to specific sites ofmtDNA. We have shown that mTERF displays a novel fold consisting of a left-handed arrangement of α-helices in an elongated structure that harbors the DNA along its longest axis (Fig. 1D). We termed this type of fold ‘Zurdo’ (left-handed in Spanish). Interestingly, in this third case,homologues are only found in mitochondria or plastid organelles.

The structural MitoLab is headed by Dr. Maria Solà. After a tenure-tracked period of four years funded by a Ramón y Cajal contract, Maria Solà was awarded a permanent position as tenured Assistant Professor at the Spanish Research Council (Consejo Superior de Investigaciones Científicas, CSIC) in 2008, joining the Institute of Molecular Biology Barcelona (Institut de Biologia Molecular Barcelona, IBMB), where she established a research laboratory on the structural biology of mitochondrial DNA regulation.

Projects

  • Structural analysis of mitochondrial DNA regulatory proteins. We use biochemical and X-ray crystallography approaches. This is completed by electron microscopy and small-angle X-ray scattering (SAXS) studies through external collaborations.
  • Analysis of mitochondrial DNA structure.
  • Structural studies of bacterial protein/DNA complexes.

Lab People

Maria Solà Vilarrubias

Maria Solà Vilarrubias

Research Scientist CSIC

msvcri@ibmb.csic.es
+34 934 034 950 / +34 934 020 544

Sebastien Lyonnais

Sebastien Lyonnais

Postdoctoral Researcher

slycri@ibmb.csic.es

Reicy Brito De Rosales

Reicy Brito De Rosales

Postdoctoral Researcher

rbrcri@ibmb.csic.es

Arka Chakraborty

Arka Chakraborty

PhD Student

achcri@ibmb.csic.es

Claus Schmitz

Claus Schmitz

PhD Student

cshcri@ibmb.csic.es

Aleix Tarres Sole

Aleix Tarres Sole

PhD Student

atscri@ibmb.csic.es

Javier Bermudez Morales

Javier Bermudez Morales

Research Technician

jbmcri@ibmb.csic.es

Lina Juknaite

Lina Juknaite

Postdoctoral Researcher

ljucri@ibmb.csic.es

Selected Publications

The human mitochondrial transcription factor A is a versatile G-quadruplex binding protein.

Lyonnais, S., Tarrés-Solé, A., Rubio-Cosials, A., Cuppari, A., Brito, R., Jaumot, J., Gargallo, R., Vilaseca, M., Silva, C., Granzhan, A., Teulade-Fichou, M.-P., Eritja, R. & Solà, M*.

Scientific Reports, 2017; 7: 43992.


DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.

Chakraborty, A., Lyonnais, S.; Battistini, F.; Hospital, A.; Medici, G.; Prohens, R.; Orozco, M.; Vilardell, J. & Solà, M*.

Nucleic Acids Research, 2016; 45: 951-967.


Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonasgingivalis peptidyl-argininedeiminase.

Goulas, T., Mizgalska, D., Garcia-Ferrer, I., Kantyka, T., Guevara, T., Szmigielski, B., Sroka, A., Millan, C., Uson, I., Veillard, F., Potempa, B., Mydel, P., Solà, M.*, Potempa, J.*, Gomis-Ruth, F.X.*

Scientific Reports, 2015; 5: 11969


The hexameric structure of the human mitochondrial replicative helicase Twinkle

Fernández-Millán, P., Lázaro, M., Cansız-Arda, S., Gerhold, J. M., Rajala, N., Schmitz, C.A., Silva-Espiña, C., Gil, D., Bernadó, P., Valle, M.*, Spelbrink, J.N.* &Solà, M* (2015).

Nucleic Acids Research, 2015; 43: 4284-4295. DOI:10.1093/nar/gkv189.


A Robust Assay to Measure DNA Topology-Dependent Protein Binding Affinity

Litwin, T., Solà, M., Holt, I. and Neuman, K.*

Nucleic Acids Research, 2014: 43(7): e43.


Solution equilibria of cytosine- and guanine-rich sequences near the promoter region of the n-myc gene that contain stable hairpins within lateral loops

Benabou, S., Ferreira, R., Aviñó, A., González, C., Lyonnais, S., Solà, M., Eritja, R., Jaumot, J., Gargallo, R.

BiochimBiophysActa, 2014 1840: 41-52.


Ultratight crystal packing of a 10 kDa protein

Trillo-Muyo, S., Jasilionis, A.,Domagalski, M.J., Chruszcz, M., Minor, W.,Kuisiene, N., Arolas, J.L., Solà, M., Gomis-Rüth, F.X.

ActaCryst, 2013; D69: 464-470.


U-turn DNA bending by human mitochondrial transcription factor A.

Rubio-Cosials, A. &Solà, M.*

Curr Op StructBiol, 2013; 23: 116-124.


Human mitochondrial transcription factor A induces a U-turn structure in the light strand promoter.

Rubio-Cosials, A., Sydow, J.F., Jiménez-Menéndez, N., Fernández-Millán, P., Montoya, J., Jacobs, H.T., Coll, M., Bernadó, P. & Solà, M.*

Nat StructMolBiol, 2011; 18: 1281-1289.

(Selected as “Article of the Month” in the December 2011 issue of the Spanish Society of Biochemistry and Molecular Biology Journal, Sociedad Española de Bioquímica y Biología Molecular, SEBBM.

First author (from the Structural MitoLab) was awarded the 2nd Prize “Fischer Scientific” to a Young Investigator at the XXXV SEBBM Meeting, held in Seville (Spain) in September 2012.

Article mentioned in News and Views in Nature Structural and Molecular Biology, 2011; 18, 1179–1181).


The structure of a transcription activation sub-complex reveals how σ70 is recruited to PhoB promoters.

Blanco, A.G., Canals, A., Bernués, J., Solà, M. & Coll, M.

EMBO, 2011; J30: 3776 -3785.


Structural basis for antiviral inhibition of the main protease, 3C, from human enterovirus 93

Costenaro, L., Kaczmarska, Z., Arnan, C., Janowski, R., Coutard, B., Solà, M., Gorbalenya, A.E.,Norder, H., Canard, B. & Coll, M.

J Virol, 2011; K 2011; 85: 10764-73.


Picornavirus non-structural proteins as targets for new anti-virals with broad activity

Norder, H., De Palma, A.M., Selisko, B., Costenaro, L., Papageorgiou, N., Arnan, C., Coutard, B., Lantez, V., De Lamballerie, X., Baronti, C., Solà, M., Tan, J., Neyts, J., Canard, B., Coll, M., Gorbalenya, A.E. &Hilgenfeld, R.

Antivir Res; 2011 89: 204-18.


Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain

Nadal, M., Mas, P., Blanco, A.G., Arnan, C., Solà, M., Hart, D. &Coll, M.

ProcNatlAcadSci USA, 2010; 107: 16078-83.


Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat.

Jiménez-Menéndez, N., Fernández-Millán, P., Rubio-Cosials, A., Arnan, C., Montoya, J., Jacobs, H.T., Bernadó, P., Coll, M., Usón, I. & Solà, M.*

Nat StructMolBiol, 2010; 17: 891-3

(Selected as “Article of the Month” in the August 2010 issue of the Spanish Society of Biochemistry and Molecular Biology Journal, SociedadEspañola de Bioquímica y Biología Molecular, SEBBM.

First author (from the Structural MitoLab) was awarded the “José Tormo” Prize to a Young Investigator at the XXXIV SEBBM Meeting, held in Barcelona (Spain) in September 2011).


Structural studies on the full-length LysR-type regulator TsaR from Comamonastestosteroni T-2 reveal a novel open conformation of the tetrameric LTTR fold.

Monferrer, D., Tralau, T., Kertesz, M. A., Dix, I., Solà, M. &Usón, I.

MolMicrobiol, 2010; 75: 1199-1214.


All Publications

The human mitochondrial transcription factor A is a versatile G-quadruplex binding protein.

Lyonnais, S., Tarrés-Solé, A., Rubio-Cosials, A., Cuppari, A., Brito, R., Jaumot, J., Gargallo, R., Vilaseca, M., Silva, C., Granzhan, A., Teulade-Fichou, M.-P., Eritja, R. & Solà, M*.

Scientific Reports, 2017; 7: 43992.


DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.

Chakraborty, A., Lyonnais, S.; Battistini, F.; Hospital, A.; Medici, G.; Prohens, R.; Orozco, M.; Vilardell, J. & Solà, M*.

Nucleic Acids Research, 2016; 45: 951-967.


Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonasgingivalis peptidyl-argininedeiminase.

Goulas, T., Mizgalska, D., Garcia-Ferrer, I., Kantyka, T., Guevara, T., Szmigielski, B., Sroka, A., Millan, C., Uson, I., Veillard, F., Potempa, B., Mydel, P., Solà, M.*, Potempa, J.*, Gomis-Ruth, F.X.*

Scientific Reports, 2015; 5: 11969


The hexameric structure of the human mitochondrial replicative helicase Twinkle

Fernández-Millán, P., Lázaro, M., Cansız-Arda, S., Gerhold, J. M., Rajala, N., Schmitz, C.A., Silva-Espiña, C., Gil, D., Bernadó, P., Valle, M.*, Spelbrink, J.N.* &Solà, M* (2015).

Nucleic Acids Research, 2015; 43: 4284-4295. DOI:10.1093/nar/gkv189.


A Robust Assay to Measure DNA Topology-Dependent Protein Binding Affinity

Litwin, T., Solà, M., Holt, I. and Neuman, K.*

Nucleic Acids Research, 2014: 43(7): e43.


Solution equilibria of cytosine- and guanine-rich sequences near the promoter region of the n-myc gene that contain stable hairpins within lateral loops

Benabou, S., Ferreira, R., Aviñó, A., González, C., Lyonnais, S., Solà, M., Eritja, R., Jaumot, J., Gargallo, R.

BiochimBiophysActa, 2014 1840: 41-52.


Ultratight crystal packing of a 10 kDa protein

Trillo-Muyo, S., Jasilionis, A.,Domagalski, M.J., Chruszcz, M., Minor, W.,Kuisiene, N., Arolas, J.L., Solà, M., Gomis-Rüth, F.X.

ActaCryst, 2013; D69: 464-470.


U-turn DNA bending by human mitochondrial transcription factor A.

Rubio-Cosials, A. &Solà, M.*

Curr Op StructBiol, 2013; 23: 116-124.


Human mitochondrial transcription factor A induces a U-turn structure in the light strand promoter.

Rubio-Cosials, A., Sydow, J.F., Jiménez-Menéndez, N., Fernández-Millán, P., Montoya, J., Jacobs, H.T., Coll, M., Bernadó, P. & Solà, M.*

Nat StructMolBiol, 2011; 18: 1281-1289.

(Selected as “Article of the Month” in the December 2011 issue of the Spanish Society of Biochemistry and Molecular Biology Journal, Sociedad Española de Bioquímica y Biología Molecular, SEBBM.

First author (from the Structural MitoLab) was awarded the 2nd Prize “Fischer Scientific” to a Young Investigator at the XXXV SEBBM Meeting, held in Seville (Spain) in September 2012.

Article mentioned in News and Views in Nature Structural and Molecular Biology, 2011; 18, 1179–1181).


The structure of a transcription activation sub-complex reveals how σ70 is recruited to PhoB promoters.

Blanco, A.G., Canals, A., Bernués, J., Solà, M. & Coll, M.

EMBO, 2011; J30: 3776 -3785.


Structural basis for antiviral inhibition of the main protease, 3C, from human enterovirus 93

Costenaro, L., Kaczmarska, Z., Arnan, C., Janowski, R., Coutard, B., Solà, M., Gorbalenya, A.E.,Norder, H., Canard, B. & Coll, M.

J Virol, 2011; K 2011; 85: 10764-73.


Picornavirus non-structural proteins as targets for new anti-virals with broad activity

Norder, H., De Palma, A.M., Selisko, B., Costenaro, L., Papageorgiou, N., Arnan, C., Coutard, B., Lantez, V., De Lamballerie, X., Baronti, C., Solà, M., Tan, J., Neyts, J., Canard, B., Coll, M., Gorbalenya, A.E. &Hilgenfeld, R.

Antivir Res; 2011 89: 204-18.


Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain

Nadal, M., Mas, P., Blanco, A.G., Arnan, C., Solà, M., Hart, D. &Coll, M.

ProcNatlAcadSci USA, 2010; 107: 16078-83.


Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat.

Jiménez-Menéndez, N., Fernández-Millán, P., Rubio-Cosials, A., Arnan, C., Montoya, J., Jacobs, H.T., Bernadó, P., Coll, M., Usón, I. & Solà, M.*

Nat StructMolBiol, 2010; 17: 891-3

(Selected as “Article of the Month” in the August 2010 issue of the Spanish Society of Biochemistry and Molecular Biology Journal, SociedadEspañola de Bioquímica y Biología Molecular, SEBBM.

First author (from the Structural MitoLab) was awarded the “José Tormo” Prize to a Young Investigator at the XXXIV SEBBM Meeting, held in Barcelona (Spain) in September 2011).


Structural studies on the full-length LysR-type regulator TsaR from Comamonastestosteroni T-2 reveal a novel open conformation of the tetrameric LTTR fold.

Monferrer, D., Tralau, T., Kertesz, M. A., Dix, I., Solà, M. &Usón, I.

MolMicrobiol, 2010; 75: 1199-1214.

Project Funding

Ongoing Projects


Reference: BFU2015-70645-R

Title: Structural analysis of the mitocondrial genome and its regulation

R&Dproject, Fundamental Biology Plan, Molecular and Cellular Biology Subplan, Ministry of Economy and Competitiveness.


Reference: MDM-2014-0435

Title: Appointment of the Department of Structural Biology of IBMB as a “María de Maeztu” Unit of Excellence”

Total awarded: €2,000,000 (1.7.2015 – 30.6.2019)

Spanish Ministry of Economy and Competitivity.


Reference: FP7-HEALTH-2012-306029-2 “TRIGGER”

Title: King of hearts, joints and lungs; periodontal pathogens as etiologic factor in RA, CVD and COPD and their impact on treatment strategies

(1.4.2013 – 31.3.2017)

European Union STREP FP7 Project


Reference: FP7-PEOPLE-2011-290246 “RAPID”

Title: RAPID-Rheumatoid arthritis and periodontal inflammatory disease

Coordinator: Thomas Dietrich (Birmingham, UK). WP nº 3

(1.4.2012 – 31.3.2016)

European Union Marie Curie Initial Training Network (ITN) Project


Project Funding

Concluded Projects


Reference: BFU2012-33516/BMC

Title: Structural Basis of Mitochondrial Genome Regulation

(1.1.2013-31.12.2015)

R&Dproject, Fundamental Biology Plan, Molecular and Cellular Biology Subplan, Ministry of Economy and Competitiveness.


Reference: FP7-HEALTH-2010-261460

Title: Protein citrullination as a link between periodontal diseases and rheumatoid arthritis (RA) and target for development of novel drugs to treat RA

(1.11.2010 – 31.10.2014)

Coordinator: Peter Mydel (Göteborg, Sweden). WP nº 3

European Union STREP FP7 Project


Reference: BFU2009-07134/BMC

Title: Structural Biology of Mitochondrial Genome Regulation

(1.1.2010-31.12.2012)

Coordinator: Peter Mydel (Göteborg, Sweden). WP nº 3

R&Dproject, Fundamental Biology Plan, Molecular, Cellular and Genetics Biology Subplan, Ministry of Science and Innovation.


Reference: BFU2006-09593/BMC

R&D project, Fundamental Biology Plan, Molecular and Cellular Biology Subplan financed by the Ministry of Education and Science.


Reference: PIE 200820I045

C.S.I.C “Intramural” Project.


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