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Lever M.A.,University of Aarhus | Rogers K.L.,Rensselaer Polytechnic Institute | Lloyd K.G.,University of Tennessee at Knoxville | Overmann J.,Leibniz Institute DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH | And 4 more authors.
FEMS Microbiology Reviews | Year: 2015

The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation. © FEMS 2015. All rights reserved.


Buckel W.,University of Marburg | Buckel W.,Max Planck Institute For Terrestrische Mikrobiologie
Angewandte Chemie - International Edition | Year: 2013

The thiyl radical of cysteine 272 (C272) in the C-P lyase adds to 5-phosphoribose-1-methylphosphonate to give a covalently bound thiophosphonate radical. Reaction with glycine 32 (G32) of the enzyme yields methane, a glycyl radical, and thiophosphate (see scheme). Intramolecular attack of the 2-OH group leads to 5-phosphoribose-1,2-cyclic-phosphate, whereas the glycyl radical oxidizes the liberated SH group back to the thiyl radical. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Netz D.J.A.,University of Marburg | Mascarenhas J.,University of Marburg | Stehling O.,University of Marburg | Pierik A.J.,University of Marburg | And 3 more authors.
Trends in Cell Biology | Year: 2014

Eukaryotic cells contain numerous cytosolic and nuclear iron-sulfur (Fe/S) proteins that perform key functions in metabolic catalysis, iron regulation, protein translation, DNA synthesis, and DNA repair. Synthesis of Fe/S clusters and their insertion into apoproteins are essential for viability and are conserved in eukaryotes. The process is catalyzed in two major steps by the CIA (cytosolic iron-sulfur protein assembly) machinery encompassing nine known proteins. First, a [4Fe-4S] cluster is assembled on a scaffold complex. This step requires a sulfur-containing compound from mitochondria and reducing equivalents from an electron transfer chain. Second, the Fe/S cluster is transferred from the scaffold to specific apoproteins by the CIA targeting complex. This review summarizes our molecular knowledge on CIA protein function during the assembly process. © 2013 Elsevier Ltd.


Srinivasan V.,University of Marburg | Pierik A.J.,University of Marburg | Pierik A.J.,University of Kaiserslautern | Lill R.,University of Marburg | Lill R.,Max Planck Institute For Terrestrische Mikrobiologie
Science | Year: 2014

The yeast mitochondrial ABC transporter Atm1, in concert with glutathione, functions in the export of a substrate required for cytosolic-nuclear iron-sulfur protein biogenesis and cellular iron regulation. Defects in the human ortholog ABCB7 cause the sideroblastic anemia XLSA/A. Here, we report the crystal structures of free and glutathione-bound Atm1 in inward-facing, open conformations at 3.06- and 3.38-angstrom resolution, respectively. The glutathione binding site includes a residue mutated in XLSA/A and is located close to the inner membrane surface in a large cavity. The two nucleotide-free adenosine 5′-triphosphate binding domains do not interact yet are kept in close vicinity through tight interaction of the two C-terminal a-helices of the Atm1 dimer. The resulting protein stabilization may be a common structural feature of all ABC exporters.


Stehling O.,University of Marburg | Lill R.,University of Marburg | Lill R.,Max Planck Institute For Terrestrische Mikrobiologie
Cold Spring Harbor Perspectives in Biology | Year: 2013

Iron-sulfur (Fe/S) clusters belong to the most ancient protein cofactors in life, and fulfill functions in electron transport, enzyme catalysis, homeostatic regulation, and sulfur activation. The synthesis of Fe/S clusters and their insertion into apoproteins requires almost 30 proteins in the mitochondria and cytosol of eukaryotic cells. This review summarizes our current biochemical knowledge of mitochondrial Fe/S protein maturation. Because this pathway is essential for various extra mitochondrial processes, we then explain how mitochondria contribute to the mechanism of cytosolic and nuclear Fe/S protein biogenesis, and to other connected processes including nuclear DNA replication and repair, telomere maintenance, and transcription. We next describe how the efficiency of mitochondria to assemble Fe/S proteins is used to regulate cellular iron homeostasis. Finally, we briefly summarize a number of mitochondrial "Fe/S diseases" in which various biogenesis components are functionally impaired owing to genetic mutations. The thorough understanding of the diverse biochemical disease phenotypes helps with testing the current working model for the molecular mechanism of Fe/S protein biogenesis and its connected processes. © Cold Spring Harbor Laboratory Press; all rights reserved.


Stehling O.,University of Marburg | Wilbrecht C.,University of Marburg | Lill R.,University of Marburg | Lill R.,Max Planck Institute For Terrestrische Mikrobiologie
Biochimie | Year: 2014

Work during the past 14 years has shown that mitochondria are the primary site for the biosynthesis of iron-sulfur (Fe/S) clusters. In fact, it is this process that renders mitochondria essential for viability of virtually all eukaryotes, because they participate in the synthesis of the Fe/S clusters of key nuclear and cytosolic proteins such as DNA polymerases, DNA helicases, and ABCE1 (Rli1), an ATPase involved in protein synthesis. As a consequence, mitochondrial function is crucial for nuclear DNA synthesis and repair, ribosomal protein synthesis, and numerous other extra-mitochondrial pathways including nucleotide metabolism and cellular iron regulation. Within mitochondria, the synthesis of Fe/S clusters and their insertion into apoproteins is assisted by 17 proteins forming the ISC (iron-sulfur cluster) assembly machinery. Biogenesis of mitochondrial Fe/S proteins can be dissected into three main steps: First, a Fe/S cluster is generated de novo on a scaffold protein. Second, the Fe/S cluster is dislocated from the scaffold and transiently bound to transfer proteins. Third, the latter components, together with specific ISC targeting factors insert the Fe/S cluster into client apoproteins. Disturbances of the first two steps impair the maturation of extra-mitochondrial Fe/S proteins and affect cellular and systemic iron homeostasis. In line with the essential function of mitochondria, genetic mutations in a number of ISC genes lead to severe neurological, hematological and metabolic diseases, often with a fatal outcome in early childhood. In this review we briefly summarize our current functional knowledge on the ISC assembly machinery, and we present a comprehensive overview of the various Fe/S protein assembly diseases. © 2014 Elsevier Masson SAS. All rights reserved.


Buckel W.,Max Planck Institute For Terrestrische Mikrobiologie | Buckel W.,University of Marburg | Thauer R.K.,Max Planck Institute For Terrestrische Mikrobiologie | Thauer R.K.,University of Marburg
Biochimica et Biophysica Acta - Bioenergetics | Year: 2013

The review describes four flavin-containing cytoplasmatic multienzyme complexes from anaerobic bacteria and archaea that catalyze the reduction of the low potential ferredoxin by electron donors with higher potentials, such as NAD(P)H or H2 at ≤ 100 kPa. These endergonic reactions are driven by concomitant oxidation of the same donor with higher potential acceptors such as crotonyl-CoA, NAD+ or heterodisulfide (CoM-S-S-CoB). The process called flavin-based electron bifurcation (FBEB) can be regarded as a third mode of energy conservation in addition to substrate level phosphorylation (SLP) and electron transport phosphorylation (ETP). FBEB has been detected in the clostridial butyryl-CoA dehydrogenase/electron transferring flavoprotein complex (BcdA-EtfBC), the multisubunit [FeFe]hydrogenase from Thermotoga maritima (HydABC) and from acetogenic bacteria, the [NiFe]hydrogenase/heterodisulfide reductase (MvhADG-HdrABC) from methanogenic archaea, and the transhydrogenase (NfnAB) from many Gram positive and Gram negative bacteria and from anaerobic archaea. The Bcd/EtfBC complex that catalyzes electron bifurcation from NADH to the low potential ferredoxin and to the high potential crotonyl-CoA has already been studied in some detail. The bifurcating protein most likely is EtfBC, which in each subunit (βγ) contains one FAD. In analogy to the bifurcating complex III of the mitochondrial respiratory chain and with the help of the structure of the human ETF, we propose a conformational change by which γ-FADH- in EtfBC approaches β-FAD to enable the bifurcating one-electron transfer. The ferredoxin reduced in one of the four electron bifurcating reactions can regenerate H2 or NADPH, reduce CO2 in acetogenic bacteria and methanogenic archaea, or is converted to ΔμH+/Na+ by the membrane-associated enzyme complexes Rnf and Ech, whereby NADH and H2 are recycled, respectively. The mainly bacterial Rnf complexes couple ferredoxin oxidation by NAD+ with proton/sodium ion translocation and the more diverse energy converting [NiFe]hydrogenases (Ech) do the same, whereby NAD+ is replaced by H+. Many organisms also use Rnf and Ech in the reverse direction to reduce ferredoxin driven by ΔμH+/Na +. Finally examples are shown, in which the four bifurcating multienzyme complexes alone or together with Rnf and Ech are integrated into energy metabolisms of nine anaerobes. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. © 2012 Elsevier B.V.


Godeke J.,Max Planck Institute For Terrestrische Mikrobiologie | Paul K.,Max Planck Institute For Terrestrische Mikrobiologie | Lassak J.,Max Planck Institute For Terrestrische Mikrobiologie | Thormann K.M.,Max Planck Institute For Terrestrische Mikrobiologie
ISME Journal | Year: 2011

Shewanella oneidensis MR-1 is capable of forming highly structured surface-attached communities. By DNase I treatment, we demonstrated that extracellular DNA (eDNA) serves as a structural component in all stages of biofilm formation under static and hydrodynamic conditions. We determined whether eDNA is released through cell lysis mediated by the three prophages LambdaSo, MuSo1 and MuSo2 that are harbored in the genome of S. oneidensis MR-1. Mutant analyses and infection studies revealed that all three prophages may individually lead to cell lysis. However, only LambdaSo and MuSo2 form infectious phage particles. Phage release and cell lysis already occur during early stages of static incubation. A mutant devoid of the prophages was significantly less prone to lysis in pure culture. In addition, the phage-less mutant was severely impaired in biofilm formation through all stages of development, and three-dimensional growth occurred independently of eDNA as a structural component. Thus, we suggest that in S. oneidensis MR-1 prophage-mediated lysis results in the release of crucial biofilm-promoting factors, in particular eDNA. © 2011 International Society for Microbial Ecology All rights reserved.


Buckel W.,Max Planck Institute For Terrestrische Mikrobiologie | Thauer R.K.,Max Planck Institute For Terrestrische Mikrobiologie
Angewandte Chemie - International Edition | Year: 2011

A surprising mechanism: The enzymatic methylation of adenosine at C-2 consumes two molecules of S-adenosylmethionine (SAM +), one in the S N2 transfer of its methyl group to an active-site cysteine of the methyltransferase, and a second in the formation of a 5′-deoxyadenosine radical (5′-A .) that abstracts a hydrogen atom from the protein-bound methyl group enabling it to attack at C-2 of the adenosine (see scheme). Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Parthasarathy A.,Max Planck Institute For Terrestrische Mikrobiologie
Archives of microbiology | Year: 2013

Evidence is presented for a pathway of phenylalanine catabolism in the hyperthermophilic archaeon Archaeoglobus fulgidus involving the following enzymes-phenylalanine:2-oxoglutarate aminotransferase, phenyllactate dehydrogenase, radical iron-sulphur 3-phenyllactyl-CoA dehydratase, phenylpropionyl-CoA dehydrogenase, aryl pyruvate ferredoxin oxidoreductase, ADP-forming acetyl-CoA synthetase and family III CoA-transferase. Hitherto amino acid degradation pathways involving radical iron-sulphur dehydratases have been characterised only in mesophilic clostridia and related bacteria. The difference here is that the pathway is not fermentative but coupled to sulphate reduction. Initial experiments also show the utilisation of tryptophan as a growth substrate and the decarboxylation of caffeate by cell extracts, suggesting the potential to catabolise different classes of aromatic compounds.

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