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PD Dr. Basem Soboh

Microbiology, Biochemistry and Genetic Biophysics

My name is Basem Soboh. The major focus of my work is to understand how complex cofactors of gas processing metalloproteins (hydrogenase and nitrogenase) are assembled. I was born in Gaza-Palestine, where I completed my Bachelor degree of Microbiology & Chemistry, then I completed my diploma and doctoral studies at the MPI-Marburg in the group of Rolf Thauer. I studied a wide combination of subjects including Microbiology, Biochemistry, Genetics and Virology. During my post-doc at UC-Berkeley I investigated the in vitro biosynthesis of the FeMo cofactor of Nitrogenase. During my Habilitation at Martin Luther University, an in vitro Synthesis of active [NiFe]-hydrogenase has been developed. Since 2016 I started as a group leader in the laboratories of Heberle for Experimental Biophysics and Schlesinger for Genetic Biophysics. Using a combinations of molecular biology, anaerobic protein biochemistry and biophysical methods, we are currently investigating the biogenesis of [NiFe]-cofactor at the molecular level. Further details can be found in my CV.

basem

Fachbereich Physik

Institut für experimentelle Physik

Experimentelle Molekulare Biophysik

Researcher

Address
Arnimallee 14
Room -1.2.06
14195 Berlin
Fax
(030) 838-453337

PROFESSIONAL POSITIONS

2016–present: Freie Universität Berlin
Group leader at the Department of Physics, Genetic Biophysics
Topic: In vitro biosynthesis of [NiFe]-hydrogenases

2008–2015: Martin Luther University
Group leader at the Department of Biology, Institute of Microbiology
Topic: In vitro biosynthesis of complex Fe-S cofactors

2005–2008: University of California, Berkeley
Postdoctoral Scholar at the Department of Plant and Microbial Biology (with Prof. Paul W. Ludden)
Topic: Biosynthesis of the iron-molybdenum cofactor of nitrogenase

2004–2005: MPI for Terrestrial Microbiology
Postdoctoral Scholar, Department of Biochemistry (with Prof. Rolf Thauer)
Topic: Characterization of energy-conserving [NiFe]-hydrogenases and CO-dehydrogenases

 

EDUCATION

Habilitation in Microbiology 2016, Martin Luther University (Institute of Biology-Microbiology)

Ph.D. (Dr. rer. nat.) 2004, Department of Biochemistry at the MPI Marburg (Thauer Lab)

Diploma in Biology 2001, Philipps-University Marburg (Microbiology, Biochemistry, Genetics & Virology)

Bachelor of Science 1996, Alazhr University-Gaza (Microbiology & Chemistry)

My research focuses on the in vitro biosynthesis of complex Fe-S cofactors. We currently employ hydrogenases that make or oxidize hydrogen gas. [NiFe]-hydrogenase has a complicated catalytic active site that contains nickel and iron bound to the protein in addition to unique non-protein ligands. The biosynthesis of hydrogenases is a multi-step process that requires the coordinated activity of several accessory proteins. My interest lies in determining how this complex cofactor is assembled. Over the last few years, we have developed an in vitro maturation system for the synthesis of active [NiFe]-hydrogenase using only purified components. Our in vitro reconstitution system provides the possibility to study the maturation steps individually and to observe the stepwise synthesis and assembly of the hydrogenase cofactor in real time. The in vitro system will be important for elucidating the biogenesis of [NiFe]-cofactor at the molecular level.

Our biochemical-genetic strategy concept of the in vitro system involves isolation of the maturation proteins, then following the stepwise synthesis and assembly of cofactors using a broad range of methodologies. This includes manipulation of genes, overexpression, anaerobic purification of the maturation protein complexes and intermediates, then in vitro reconstitution of the pathway for cofactor assembly. The analytical methods include anoxic enzyme kinetics, FPLC, metabolite analysis (HPLC, GC), functional protein-protein interaction (thermophoresis), metal detection (ICP-MS), and native gel electrophoresis. Spectroscopic methods include UV/Vis-, electron paramagnetic resonance (EPR)-, Mössbauer-, resonance Raman-, and Fourier-transform infrared (FTIR) spectroscopy and protein film electrochemistry. Furthermore, we apply crystallization and cryo electron microscopy.

Working model for maturation of the large subunit into functional [NiFe]-hydrogenase. A: (i) Incorporation of the Fe(CN)2CO moiety into the hydrogenase large subunit (pro-protein) (ii) Nickel insertion. (iii) Proteolytic cleavage of the C-terminal peptide, (iv) Dimerization of large and small subunit to form functional [NiFe]-hydrogenase. B: Biosynthesis of the Fe(CN)2CO moiety. (1) The HypCD complex is formed upon contact with the [Fe]-CO2 carrying HypC dimer while a HypC monomer is released. (2) The CO2 ligand may undergo an ATP-dependent reduction to CO catalyzed by HypCD complex (3) The CN ligands are generated by the maturation proteins HypE and HypF. (4) Transfer of the CN ligands to the CO-modified iron ion and formation of the [Fe](CN)2CO precursor on the HypCD complex.

1- Stripp S.T., Oltmanns J., Müller C., Ehrenberg D., Schlesinger R., Heberle J., Adrian L., Schünemann V., Pierik A., and Soboh B* (2021) Electron Inventory of the Iron-Sulfur Scaffold Complex HypCD Essential in [NiFe]-Hydrogenase Cofactor Assembly. ChemRxiv https://doi.org/10.26434/chemrxiv.13736632.v1

2- Senger M., Laun K., Soboh B. and Stripp S.T. (2018) Infrared Characterization of the Periplasmatic O2-sensitive [NiFe]-hydrogenase from E. coli. Catalysts, (8), 530

3- Senger M., Stripp S.T. and Soboh B*. (2017) Proteolytic Cleavage Orchestrates Cofactor Insertion and Protein Assembly in [NiFe]-hydrogenase Biosynthesis. J Biol Chem. (28):11670-11681.

4- Stripp ST., Lindenstrauss U., Sawers RG. and Soboh B*. (2015) Identification of an Isothiocyanate on the HypEF Complex Suggests a Route for Efficient Cyanyl-Group Channeling during [NiFe]-Hydrogenase Cofactor Generation. PLoS One e0133118. doi: 10.1371/journal.pone.0133118.

5- Stripp ST., Lindenstrauss U., Granich C., Sawers RG. and Soboh B*. (2014) The influence of oxygen on [NiFe]-hydrogenase cofactor biosynthesis and how ligation of carbon monoxide precedes cyanation. Plos ONE 9 e107488. doi: 10.1371/journal.pone.0107488.

6- Soboh B*., Lindenstrauss U., Granich C., Javaid M., Herzberg M., Claudia T. and Stripp ST. (2014) [NiFe]-hydrogenase maturation in vitro: analysis of the roles of the HybG and HypD accessory proteins. Biochemical journal. 1;464(2):169-77.

7- Soboh B., Stripp ST., Bielak C., Lindenstrauß U., Braussemann M., Javaid M., Hallensleben M., Granich C., Herzberg M., Heberle J. and Sawers RG. (2013) The [NiFe]-hydrogenase accessory chaperones HypC and HybG of Escherichia coli are iron- and carbon dioxide-binding proteins. FEBS Lett. 19;587(16):2512-6.

8- Soboh B. and Sawers RG. (2013) [NiFe]-hydrogenase cofactor assembly. In: Encyclopedia of Inorganic and Bioorganic Chemistry - Metals in Cells, Chapter eibc2154 ISBN: 9781119951438. doi: 10.1002/9781119951438.eibc2154.

9- Stripp ST., Soboh B., Lindenstrauss U., Braussemann M., Herzberg M., Nies DH. , Sawers RG. and Heberle J. (2013) HypD is the Scaffold Protein for Fe-(CN)2CO Cofactor Assembly in [NiFe]-Hydrogenase Maturation. Biochemistry, 52 (19), 3289–32962

10- Trchounian K., Soboh B., Sawers RG. and Trchounian A. (2013) Contribution of hydrogenase 2 to stationary phase H2 production by Escherichia coli during fermentation of glycerol. Cell. Biochem. Biophys. 66-(1)103-108.

11- Soboh B., Stripp ST., Muhr E., Granich C., Braussemann M., Herzberg M., Heberle J. and Sawers RG. (2012) [NiFe]-hydrogenase maturation: isolation of a HypC-HypD complex carrying diatomic CO and CN- ligands.FEBS Lett., 586(21) 3882-3887

12- Soboh B., Kuhns M., Braussemann M., Waclawek M., Muhr E., Pierik AJ. and Sawers RG. (2012) Evidence for an oxygen-sensitive iron-sulfur cluster in an immature large subunit species of Escherichia coli [NiFe]-hydrogenase 2. Biochem Biophys Res Commun. 424(1),158-163

13- Petkun S., Shi R., Li Y., Asinas A., Munger C., Zhang L., Waclawek M., Soboh B., Sawers RG. and Cygler M. (2011) Structure of Hydrogenase Maturation Protein HypF with Reaction Intermediates Shows Two Active Sites. Structure 19 (12), 1773–1783

14- Pinske C., Krüger S., Soboh B., Ihling C., Kuhns M., Braussemann M., Jaroschinsky M., Sauer C., Sargent F., Sinz A. and Sawers RG. (2011) Efficient electron transfer from hydrogen to benzyl viologen by the [NiFe]-hydrogenases of Escherichia coli is dependent on the coexpression of the iron-sulphur cluster-containing small subunit. Arch. Microbiol.193(12),893-903

15- Soboh B., Pinske C., Kuhns M., Waclawek M., Ihling C., Trchounian K., Trchounian A., Sinz. A., and Sawers RG. (2011) The respiratory molybdo-selenoprotein formate dehydrogenases of Escherichia coli have hydrogen: benzyl viologen oxidoreductase activity. BMCMicrobiol.11:173

16- Soboh B., Krüger S., Kuhns M., Pinske C., Lehmann A. and Sawers RG. (2010) Development of a cell-free system reveals an oxygen-labile step in the maturation of [NiFe]-hydrogenase 2 of E. coli.FEBS Lett. 584 (18), 4109-4114

17- Soboh B., Boyd ES., Zhao D, Peters JW. and Rubio LM. ( 2010) Substrate specificity and evolutionary implications of a NifDK enzyme carrying NifB-co at its active site. FEBSLett. 584(8),1487-92

18- Rubio LM., Hernández JA., Soboh B., Zhao D., Igarashi RY. , Curatti L. and Ludden PW. (2008). The Role of Nif Proteins in Nitrogenase Maturation. Plant Science and Biotechnology in Agriculture, Book: Biological Nitrogen Fixation, Volume 42, pp 325-328

19- Curatti L., Hernandez JA., Igarashi RY., Soboh B., Zhao D. and Rubio LM. (2007). In vitro synthesis of the iron-molybdenum cofactor of nitrogenase from iron, sulfur, molybdenum and homocitrate using purified proteins. Proc. Natl. Acad. Sci. 104 (45), 17626-31

20- George SJ., Igarashi RY., Piamonteze C., Soboh B., Cramer SP. and Rubio LM. (2007) Identification of a Mo-Fe-S cluster on NifEN by Mo K-edge EXAFS. J. Am. Chem. Soc.,129(11),3060-3061

21- Hernández JA., Igarashi RY., Soboh B., Curatti L., Dean DR., Ludden PW. and Rubio, LM. (2006) NifX and NifEN exchange biosynthetic precursors of the iron-molybdenum cofactor of nitrogenase. Mol. Microbiol.,63 (1),177-92

22- Soboh B., Igarashi RY., Hernandez JA. and Rubio LM. (2006) Purification of a NifEN protein complex that contains bound Mo and a FeMo-co precursor from an Azotobacter vinelandii ΔnifHDK strain. J. Biol. Chem., 281, 36701-36709cofactor of nitrogenase. Mol. Microbiol.,63 (1),177-92

23- Soboh B., Forzi L., Stojanowic A. and Hedderich R. (2004) Energy-converting [NiFe] hydrogenases from archaea and bacteria: ancestors of complex I. Biochimica et Biophysica Acta (BBA) – Bioenergetics. 1658

24. Soboh B., Linder D. and Hedderich R. (2004) A multisubunit membrane-bound [NiFe] hydrogenase and a NADH-dependent Fe-only hydrogenase in the fermenting bacterium Thermoanaerobacter tengcongensis Microbiology 150, 2451-2463

25. Soboh B., Linder D. and Hedderich R. (2002) Purification and catalytic properties of a CO-oxidizing:H2 evolving enzyme complex from Carboxydothermus hydrogenoformans Eur.J. Biochem. 269, 5712-21.