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BBA - Bioenergetics (v.1757, #2)

Editorial Board (pp. ii).

Mitochondrial DNA maintenance and bioenergetics by Jeffrey A. Stuart; Melanie F. Brown (pp. 79-89).

Oxidative phosphorylation requires assembly of the protein products of both mitochondrial and of nuclear genomes into functional respiratory complexes. Cellular respiration can be compromised when mitochondrial DNA (mtDNA) sequences are corrupted. Oxidative damage resulting from reactive oxygen species (ROS) produced during respiration is probably a major source of mitochondrial genomic instability leading to respiratory dysfunction. Here, we review mechanisms of mitochondrial ROS production, mtDNA damage and its relationship to mitochondrial dysfunction. We focus particular attention on the roles of mtDNA repair enzymes and processes by which the integrity of the mitochondrial genome is maintained and dysfunction prevented.

Keywords: mtDNA; Mitochondria; Reactive oxygen species; Base excision repair; DNA repair; Oxidative phosphorylation

Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales by Dror Noy; Christopher C. Moser; P. Leslie Dutton (pp. 90-105).

Decades of research on the physical processes and chemical reaction-pathways in photosynthetic enzymes have resulted in an extensive database of kinetic information. Recently, this database has been augmented by a variety of high and medium resolution crystal structures of key photosynthetic enzymes that now include the two photosystems (PSI and PSII) of oxygenic photosynthetic organisms. Here, we examine the currently available structural and functional information from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in de novo designed and custom-built molecular solar energy conversion devices. We find that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Moreover, we find that the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. Thus, for projected de novo designed constructions, the control of spatial organization of cofactor molecules within a dense array is initially given priority. Nevertheless, constructions accommodating dense arrays of different cofactors, some well within 1 nm from each other, still presents a significant challenge for protein design.

Keywords: Chlorophyll; Electron tunneling; F�rster resonance energy transfer; Reaction center; Redox chain

Herbicide binding and thermal stability of photosystem II isolated from Thermosynechococcus elongatus by K. Zimmermann; M. Heck; J. Frank; J. Kern; I. Vass; A. Zouni (pp. 106-114).

Binding of herbicides to photosystem II inhibits the electron transfer from Q_A to Q_B due to competition of herbicides with plastoquinone bound at the Q_B site. We investigated herbicide binding to monomeric and dimeric photosystem II core complexes (PSIIcc) isolated from Thermosynechococcus elongatus by a combination of different methods (isothermal titration and differential scanning calorimetry, CD spectroscopy and measurements of the oxygen evolution) yielding binding constants, enthalpies and stoichiometries for various herbicides as well as information regarding stabilization/destabilization of the complex. Herbicide binding to detergent-solubilized PSIIcc can be described by a model of single independent binding sites present on this important membrane protein. Interestingly, binding stoichiometries herbicide:PSIIcc are lower than 1:1 and vary depending on the herbicide under study. Strong binding herbicides such as terbutryn stabilize PSIIcc in thermal unfolding experiments and endothermically binding herbicides like ioxynil probably cause large structural changes accompanied with the binding process as shown by differential scanning calorimetry experiments of the unfolding reaction of PSIIcc monomer in the presence of ioxynil. In addition we studied the occupancy of the Q_B sites with plastoquinone (PQ9) by measuring flash induced fluorescence relaxation yielding a possible explanation for the deviations of herbicide binding from a 1:1 herbicide/binding site model.

Keywords: Abbreviations; Atrazin; 2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazin; Bromacil; 5-bromo-3-sec-butyl-6-methyluracil; Bromoxynil; 3,5-dibromo-4-hydroxybenzonitrile; Chla; chlorophyll a; 2,6-DBQ; 2,6-dichloro-p-benzoquinone; DCMU; 3-(3,4-dichlorophenyl)-1,1-dimethylurea; DLS; dynamic light scattering; β-DM; n-Dodecyl-β-; d; -maltoside; DSC; differential scanning calorimetry; Ioxynil; 3,5-diiodo-4-hydroxybenzonitrile; ITC; isothermal titration calorimetry; M; molecular mass; MES; 2-(N-morpholino)ethanesulfonic acid; PIPES; piperazine-; N; ,; N; ′-bis(2-ethanesulfonic acid); PQ9; plastoquinone 9; PSIIcc; photosystem II core complex; Terbutryn; 2-t-butylamino-4-ethylamino-6-methylmercapto-s-triazine; Trietazin; 2-chloro-4-diethylamino-6-ethylamino-s-triazin; TRIS; tris-(hydroxymethyl)-aminomethanePhotosystem II; Herbicide; Binding constant; Calorimetry; Flash induced fluorescence

Riboflavin enhances the assembly of mitochondrial cytochrome c oxidase in C. elegans NADH-ubiquinone oxidoreductase mutants by Leslie I. Grad; Bernard D. Lemire (pp. 115-122).

Mitochondrial respiratory chain dysfunction is responsible for a large variety of early and late-onset diseases. NADH-ubiquinone oxidoreductase (complex I) defects constitute the most commonly observed mitochondrial disorders. We have generated Caenorhabditis elegans strains with mutations in the 51 kDa active site subunit of complex I. These strains exhibit decreased NADH-dependent respiration and lactic acidosis, hallmark features of complex I deficiency. Surprisingly, the mutants display a significant decrease in the amount and activity of cytochrome c oxidase (complex IV). The metabolic and reproductive fitness of the mutants is markedly improved by riboflavin. In this study, we have examined how the assembly and activity of complexes I and IV are affected by riboflavin. Our results reveal that the mutations result in variable steady-state levels of different complex I subunits and in a significant reduction in the amount of COXI subunit. Using native gel electrophoresis, we detected assembly intermediates for both complexes I and IV. Riboflavin promotes the assembly of both complexes, resulting in increased catalytic activities. We propose that one primary pathogenic mechanism of some complex I mutations is to destabilize complex IV. Enhancing complex I assembly with riboflavin results in the added benefit of partially reversing the complex IV deficit.

Keywords: Mitochondria; Complex I; Complex IV; C. elegans

Very strong UV-A light temporally separates the photoinhibition of photosystem II into light-induced inactivation and repair by Otto Zsiros; Suleyman I. Allakhverdiev; Shoichi Higashi; Masakatsu Watanabe; Yoshitaka Nishiyama; Norio Murata (pp. 123-129).

When organisms that perform oxygenic photosynthesis are exposed to strong visible or UV light, inactivation of photosystem II (PSII) occurs. However, such organisms are able rapidly to repair the photoinactivated PSII. The phenomenon of photoinactivation and repair is known as photoinhibition. Under normal laboratory conditions, the rate of repair is similar to or faster than the rate of photoinactivation, preventing the detailed analysis of photoinactivation and repair as separate processes. We report here that, using strong UV-A light from a laser, we were able to analyze separately the photoinactivation and repair of photosystem II in the cyanobacterium Synechocystis sp. PCC 6803. Very strong UV-A light at 364 nm and a photon flux density of 2600 μmol photons m⁻² s⁻¹ inactivated the oxygen-evolving machinery and the photochemical reaction center of PSII within 1 or 2 min before the first step in the repair process, namely, the degradation of the D1 protein, occurred. During subsequent incubation of cells in weak visible light, the activity of PSII recovered fully within 30 min and this process depended on protein synthesis. During subsequent incubation of cells in darkness for 60 min, the D1 protein of the photoinactivated PSII was degraded. Further incubation in weak visible light resulted in the rapid restoration of the activity of PSII. These observations suggest that very strong UV-A light is a useful tool for the analysis of the repair of PSII after photoinactivation.

Keywords: Abbreviations; Chl; chlorophyll; DCIP; dichlorophenolindophenol; DPC; diphenylcarbazide; EPR; electron paramagnetic resonance; PSII; photosystem II; Pheo; pheophytinD1 protein; Photoinhibition; Photosystem II; Synechocystis; UV-A light

The phycocyanin-associated rod linker proteins of the phycobilisome of Gloeobacter violaceus PCC 7421 contain unusually located rod-capping domains by Emma Berta Guti�rrez-Cirlos; Bertha P�rez-G�mez; David W. Krogmann; Carlos G�mez-Lojero (pp. 130-134).

Gloeobacter violaceus PCC 7421 is a unique cyanobacterium that has no thylakoids and whose genome has been sequenced [Y. Nakamura, T. Kaneko, S. Sato, M. Mimuro, H. Miyashita, T. Tsuchiya, S. Sasamoto, A. Watanabe, K. Kawashima, Y. Kishida, C. Kiyokawa, M. Kohara, M. Matsumoto, A. Matsuno, N. Nakazaki, S. Shimpo, C. Takeuchi, M. Yamada, S. Tabata, Complete Genome Structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids. DNA Research 10 (2003) 137–145]. Phycobilisomes of G. violaceus were isolated and analyzed by SDS-PAGE followed by N-terminal sequencing. Three rod-linker subunits (CpeC, CpeD and CpeE) were identified as predicted from the genome sequence. The cpcC1 and cpcC2 genes at order locus named (OLN) glr0950 and gll 3219 encoding phycocyanin-associated linker proteins from G. violaceus are 56 and 55 amino acids longer at the N-terminus than the open reading frame proposed in the genome. The two amino acid extensions showed a 66% identity to one another. Also, the N-terminal extensions of these sequences were similar to domains in both the rod-capping-linker protein CpcD2 and to the C-terminus domain of the phycoerythrin-associated linker protein CpeC. These domains are not only unusual in their N-terminal location, but are unusual in that they are more closely related in sequence similarity to the C-terminus domain of the phycoerythrin-associated linker, CpeC of G. violaceus, than to the C-terminus domain of phycocyanin-associated linker CpcC in other cyanobacteria. These linker proteins with unique special domains are indicators of the unusual structure of the phycobilisomes of G. violaceus.

Keywords: Gloeobacter violaceus; Phycobilisome; cpc; C gene; L; _R; ³⁵; protein; CpcD domain

Regulation of plant alternative oxidase activity: A tale of two cysteines by Ann L. Umbach; Vicki S. Ng; James N. Siedow (pp. 135-142).

Two Cys residues, Cys_I and Cys_II, are present in most plant alternative oxidases (AOXs). Cys_I inactivates AOX by forming a disulfide bond with the corresponding Cys_I residue on the adjacent subunit of the AOX homodimer. When reduced, Cys_I associates with α-keto acids, such as pyruvate, to activate AOX, an effect mimicked by charged amino acid substitutions at the Cys_I site. Cys_II may also be a site of AOX activity regulation, through interaction with the small α-keto acid, glyoxylate. Comparison of Arabidopsis AOX1a (AtAOX1a) mutants with single or double substitutions at Cys_I and Cys_II confirmed that glyoxylate interacted with either Cys, while the effect of pyruvate (or succinate for AtAOX1a substituted with Ala at Cys_I) was limited to Cys_I. A variety of Cys_II substitutions constitutively activated AtAOX1a, indicating that neither the catalytic site nor, unlike at Cys_I, charge repulsion is involved. Independent effects at each Cys were suggested by lack of Cys_II substitution interference with pyruvate stimulation at Cys_I, and close to additive activation at the two sites. However, results obtained using diamide treatment to covalently link the AtAOX1a subunits by the disulfide bond indicated that Cys_I must be in the reduced state for activation at Cys_II to occur.

Keywords: Plant alternative oxidase; Plant mitochondria; Disulfide redox regulation; Enzyme activation

Solution structures of tetrahaem ferricytochrome c₃ from Desulfovibrio vulgaris (Hildenborough) and its K45Q mutant: The molecular basis of cooperativity by Ana C. Messias; Ant�nio P. Aguiar; Lorraine Brennan; Carlos A. Salgueiro; L�gia M. Saraiva; Ant�nio V. Xavier; David L. Turner (pp. 143-153).

The NMR structure of the oxidised wild-type cytochrome c₃ from Desulfovibrio vulgaris Hildenborough was determined in solution. Using a newly developed methodology, NMR data from the K45Q mutant was then grafted onto data from the wild-type protein to determine the structure in the region of the mutation. The structural origins of the redox-Bohr effect and haem–haem cooperativities are discussed with respect to the redox-related conformational changes observed in solution.

Keywords: Abbreviations; lovs; lower volume limits; upvs; upper volume limitsCytochrome; c; ₃; Tetrahaem cytochrome; c; ₃; Multihaem cytochromes; Redox proteins; NMR

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BBA - Bioenergetics (v.1757, #2)