Diphenylene iodonium as an inhibitor for the hydrogenase complex of Rhodobacter capsulatus. Evidence for two distinct electron donor sites

Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential

Three-dimensional structures of six closely related hydrogenases from purple bacteria were modeled by combining the template-based and ab initio modeling approach. The results led to the conclusion that there should be a 4Fe3S cluster in the structure of these enzymes. Thus, these hydrogenases could draw interest for exploring their oxygen tolerance and practical applicability in hydrogen fuel cells. Analysis of the 4Fe3S cluster’s microenvironment showed intragroup heterogeneity. A possible function of the C-terminal part of the small subunit in membrane binding is discussed. Comparison of the built models with existing hydrogenases of the same subgroup (membrane-bound oxygen-tolerant hydrogenases) was carried out. Analysis of intramolecular interactions in the large subunits showed statistically reliable differences in the number of hydrophobic interactions and ionic interactions. Molecular tunnels were mapped in the models and compared with structures from the PDB. Protein–protein docking showed that these enzymes could exchange electrons in an oligomeric state, which is important for oxygen-tolerant hydrogenases. Molecular docking with model electrode compounds showed mostly the same results as with hydrogenases from E. coli, H. marinus, R. eutropha, and S. enterica; some interesting results were shown in case of HupSL from Rba. sphaeroides and Rvi. gelatinosus.

Novel properties of photofermentative biohydrogen production by purple bacteria Rhodobacter sphaeroides: effects of protonophores and inhibitors of responsible enzymes

Background

Biohydrogen (H₂) production by purple bacteria during photofermentation is a very promising way among biological H₂ production methods. The effects of protonophores, carbonyl cyanide m-chlorophenylhydrazone (CCCP), 2,4-dinitrophenol (DNP), and inhibitors of enzymes, involved in H₂ metabolism, metronidazole (Met), diphenyleneiodonium (DPI), and dimethylsulphoxide (DMSO) on H₂ production by Rhodobacter sphaeroides MDC6522 isolated from Jermuk mineral springs in Armenia have been investigated in both nitrogen-limited and nitrogen-excess conditions.

Results

With the increase of inhibitors concentrations H₂ yield gradually decreased. The complete inhibition of H₂ production was observed in the presence of DPI and CCCP. DPI’s solvent—DMSO in low concentration did not significantly affect H₂ yield. N,N′-dicyclohexylcarbodiimide (DCCD)-inhibited the F_OF₁-ATPase activity of bacterial membrane vesicles was analyzed in the presence of inhibitors. Low concentrations of DPI and DMSO did not affect ATPase activity, whereas Met and CCCP stimulated enzyme activity. The effect of DNP was similar to CCCP.

Conclusions and significance

The results have shown the low concentration or concentration dependent effects of protonophores and nitrogenase and hydrogenase inhibitors on photofermentative H₂ production by Rh. sphaeroides in nitrogen-limited and nitrogen-excess conditions. They would be significant to understand novel properties in relationship between nitrogenase, hydrogenase and the F_OF₁-ATPase in Rh. sphaeroides, and regulatory pathways of photofermentation. The inhibitors of nitrogenase and hydrogenase can be used in biotechnology for regulation of H₂ production in different technology conditions and development of scale-up applications, for biomass and energy production using purple bacterial cells.

Structural aspects of [NiFe]-hydrogenases

Enzymes that naturally contain an organometallic complex are highly rare. Hydrogenases commonly include iron carbonyl(s) at the active site and play central roles in the hydrogen metabolism of microorganisms. [NiFe]-hydrogenases that harbor an Ni-Fe(CN)2CO complex at the active site most widely exist among organisms, compared with the other two types, [FeFe]- and [Fe]-hydrogenases. Since the first crystal structure report in 1995, structural information of the Ni-Fe cluster with various redox/substrate-bound states has been obtained, although details of the reaction mechanisms are poorly understood. While the subunit composition, physiological function, and spectroscopic/biochemical properties of [NiFe]-hydrogenases are diverse, structural information of only a limited group of the enzymes is available so far. In this paper, structural aspects of [NiFe]-hydrogenases are reviewed and recent progresses in understanding the mechanism of an O2-tolerant property of limited members and active site assembling of [NiFe]-hydrogenases are described.

Relationship of proton motive force and the F(0)F (1)-ATPase with bio-hydrogen production activity of Rhodobacter sphaeroides: effects of diphenylene iodonium, hydrogenase inhibitor, and its solvent dimethylsulphoxide

Rhodobacter sphaeroides MDC 6521 was able to produce bio-hydrogen (H(2)) in anaerobic conditions under illumination. In this study the effects of the hydrogenase inhibitor-diphenylene iodonium (Ph(2)I) and its solvent dimethylsulphoxide (DMSO) on growth characteristics and H(2) production by R. sphaeroides were investigated. The results point out the concentration dependent DMSO effect: in the presence of 10 mM DMSO H(2) yield was ~6 fold lower than that of the control. The bacterium was unable to produce H(2) in the presence of Ph(2)I. In order to examine the mediatory role of proton motive force (∆p) or the F(0)F(1)-ATPase in H(2) production by R. sphaeroides, the effects of Ph(2)I and DMSO on ∆p and its components (membrane potential (∆ψ) and transmembrane pH gradient), and ATPase activity were determined. In these conditions ∆ψ was of -98 mV and the reversed ∆pH was +30 mV, resulting in ∆p of -68 mV. Ph(2)I decreased ∆ψ in concentrations of 20 μM and higher; lower concentrations of Ph(2)I as DMSO had no valuable effect on ∆ψ. The R. sphaeroides membrane vesicles demonstrated significant ATPase activity sensitive to N,N'-dicyclohexylcarbodiimide. The 10-20 μM Ph(2)I did not affect the ATPase activity, whereas 40 μM Ph(2)I caused a marked inhibition (~2 fold) in ATPase activity. The obtained results provide novel evidence on the involvement of hydrogenase and the F(0)F(1)-ATPase in H(2) production by R. sphaeroides. Moreover, these data indicate the role of hydrogenase and the F(0)F(1)-ATPase in ∆p generation. In addition, DMSO might increase an interaction of nitrogenase with CO(2), decreasing nitrogenase activity and affecting H(2) production.

A simplified method for assay of hydrogenase activities of H2 evolution and uptake in Enterobacter aerogenes

Assay of hydrogenase activity pertaining to H2 production needs anaerobic conditions. To establish a simplified method for assay of hydrogenase activities by using intact cells of Enterobater aerogenes, different chemicals capable of enhancing the cell-wall permeability to electron mediators were examined. As a result, Triton X-100 and CTAB were found to be appropriate for H2 uptake and evolution activities of the intact cells, respectively. This method enabled H2 uptake and evolution activities of the intact cells to be easily detected. This is also the first report of the presence of H2 uptake hydrogenase activity in E. aerogenes.

The Tat protein translocation pathway and its role in microbial physiology

The Tat (twin arginine translocation) protein transport system functions to export folded protein substrates across the bacterial cytoplasmic membrane and to insert certain integral membrane proteins into that membrane. It is entirely distinct from the Sec pathway. Here, we describe our current knowledge of the molecular features of the Tat transport system. In addition, we discuss the roles that the Tat pathway plays in the bacterial cell, paying particular attention to the involvement of the Tat pathway in the biogenesis of cofactor-containing proteins, in cell wall biosynthesis and in bacterial pathogenicity.

A subset of bacterial inner membrane proteins integrated by the twin-arginine translocase

A group of bacterial exported proteins are synthesized with N-terminal signal peptides containing a SRRxFLK 'twin-arginine' amino acid motif. Proteins bearing twin-arginine signal peptides are targeted post-translationally to the twin-arginine translocation (Tat) system which transports folded substrates across the inner membrane. In Escherichia coli, most integral inner membrane proteins are assembled by a co-translational process directed by SRP/FtsY, the SecYEG translocase, and YidC. In this work we define a novel class of integral membrane proteins assembled by a Tat-dependent mechanism. We show that at least five E. coli Tat substrate proteins contain hydrophobic C-terminal transmembrane helices (or 'C-tails'). Fusions between the identified transmembrane C-tails and the exclusively Tat-dependent reporter proteins TorA and SufI render the resultant chimeras membrane-bound. Export-linked signal peptide processing and membrane integration of the chimeras is shown to be both Tat-dependent and YidC-independent. It is proposed that the mechanism of membrane integration of proteins by the Tat system is fundamentally distinct from that employed for other bacterial inner membrane proteins.

The response of Leuconostoc mesenteroides to low external oxidoreduction potential generated by hydrogen gas

AIMS

The physiological consequences of low external oxidoreduction potential in Leuconostoc mesenteroides were investigated.

METHODS AND RESULTS

Leuconostoc mesenteroides was grown under two initial oxidoreduction potential conditions (Eh7: +200 mV and -400 mV) using nitrogen and hydrogen as reducing agents. Growth was affected by Eh7; the lag phase increased from 1 h at an initial Eh7 of +200 mV to 6 h at an initial Eh7 of -400 mV; the maximum specific growth rate at -400 mV was 68% of the one observed at +200 mV. The NADH/NAD+ ratio and (NADH + NAD+) pool were independent of the external Eh7.

CONCLUSIONS

This study shows that changing the external oxidoreduction potential from +200 to -400 mV has a strong effect on the Leuc. mesenteroides physiology. The constancy of the maximum carbon and energetic fluxes (qglu, qATP) under the two Eh7 conditions accompanied by the decrease of YX/S and YATP suggested the existence of an uncoupling phenomenon, namely that some catabolized glucose and hence ATP was not associated with biomass production.

SIGNIFICANCE AND IMPACT OF THE STUDY

This paper demonstrates the usefulness of taking into account, the effect of the oxidoreduction potential on the growth of Leuc. mesenteroides in the fermentation process.