BBA - Bioenergetics (v.1858, #3)

Subunit NDUFV3 is present in two distinct isoforms in mammalian complex I by Hannah R. Bridges; Khairunnisa Mohammed; Michael E. Harbour; Judy Hirst (197-207).
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the electron transport chain in mammalian mitochondria. Extensive proteomic and structural analyses of complex I from Bos taurus heart mitochondria have shown it comprises 45 subunits encoded on both the nuclear and mitochondrial genomes; 44 of them are different and one is present in two copies. The bovine heart enzyme has provided a model for studying the composition of complex I in other mammalian species, including humans, but the possibility of additional subunits or isoforms in other species or tissues has not been explored. Here, we describe characterization of the complexes I purified from five rat tissues and from a rat hepatoma cell line. We identify a ~ 50 kDa isoform of subunit NDUFV3, for which the canonical isoform is only ~ 10 kDa in size. We combine LC-MS and MALDI-TOF mass spectrometry data from two different purification methods (chromatography and immuno-purification) with information from blue native PAGE analyses to show the long isoform is present in the mature complex, but at substoichiometric levels. It is also present in complex I in cultured human cells. We describe evidence that the long isoform is more abundant in both the mitochondria and purified complexes from brain (relative to in heart, liver, kidney and skeletal muscle) and more abundant still in complex I in cultured cells. We propose that the long 50 kDa isoform competes with its canonical 10 kDa counterpart for a common binding site on the flavoprotein domain of complex I.
Keywords: Complex I; isoform; mitochondria; NADH:ubiquinone oxidoreductase; NDUFV3; rat;

Identification and evolutionary analysis of tissue-specific isoforms of mitochondrial complex I subunit NDUFV3 by Sergio Guerrero-Castillo; Alfredo Cabrera-Orefice; Martijn A. Huynen; Susanne Arnold (208-217).
Mitochondrial complex I is the largest respiratory chain complex. Despite the enormous progress made studying its structure and function in recent years, potential regulatory roles of its accessory subunits remained largely unresolved. Complex I gene NDUFV3, which occurs in metazoa, contains an extra exon that is only present in vertebrates and thereby evolutionary even younger than the rest of the gene. Alternative splicing of this extra exon gives rise to a short NDUFV3-S and a long NDUFV3-L protein isoform. Complexome profiling revealed that the two NDUFV3 isoforms are constituents of the multi-subunit complex I. Further mass spectrometric analyses of complex I from different murine and bovine tissues showed a tissue-specific expression pattern of NDUFV3-S and NDUFV3-L. Hence, NDUFV3-S was identified as the only isoform in heart and skeletal muscle, whereas in liver, brain, and lung NDUFV3-L was expressed as the dominant isoform, together with NDUFV3-S present in all tissues analyzed. Thus, we identified NDUFV3 as the first out of 30 accessory subunits of complex I present in vertebrate- and tissue-specific isoforms. Interestingly, the tissue-specific expression pattern of NDUFV3-S and NDUFV3-L isoforms was paralleled by changes in kinetic parameters, especially the substrate affinity of complex I. This may indicate a regulatory role of the NDUFV3 isoforms in different vertebrate tissues.
Keywords: Mitochondria; OXPHOS Complex I; Subunit isoforms; Tissue-specificity; NDUFV3;

When grown under intermittent light (IL), the pennate diatom Phaeodactylum tricornutum forms ‘super’ non-photochemical fluorescence quenching (NPQ) in response to excess light. The current model of diatom NPQ mechanism involves two quenching sites, one of which detaches from photosystem II reaction centres (RCIIs) and aggregates into oligomeric complexes. Here we addressed how antenna reorganisation controls NPQ kinetics in P. tricornutum cells grown under continuous light (CL) and IL. Overall, IL acclimation induced: (i) reorganisation of chloroplasts, containing greater pigment pools without a strongly enhanced operation of the xanthophyll cycle, and (ii) ‘super NPQ’ causing a remarkable reduction of the chlorophyll excited state lifetime at Fm′. Regardless of different levels of NPQ formed in both culture conditions, its dark recovery was rapid and similar fractions of their antenna uncoupled (~ 50%). Although antenna detachment relieved excitation pressure, it provided a minor protective contribution equivalent to NPQ ~ 1, while the largest NPQ was 4.4 ± 0.2 (CL) and 13 ± 0.8 (IL). The PSII cross-section decrease took place only at relatively low NPQ values, beyond which the cross-section remained constant whilst NPQ continued to rise. This finding suggests that the energy trapping efficiency of diatom antenna quenchers cannot over-compete that of RCIIs, similarly to what has been observed on higher plants. We conclude that such ‘economic photoprotection’ operates to flexibly adjust the overall efficiency of diatom light harvesting.
Keywords: Non-photochemical quenching; FCP antenna; Photosystem II; Cross-section; Phaeodactylum tricornutum; Antenna reorganisation;

The Cbb3-type cytochrome c oxidases (Cbb3-CcOs), the second most abundant CcOs, catalyze the reduction of molecular oxygen to water, even at micromolar oxygen concentrations. In Pseudomonas stutzeri ZoBell, two tandemly organized cbb 3-operons encode the isoforms Cbb3-1 and Cbb3-2 both possessing subunits CcoN, CcoO and CcoP. However, only the cbb 3-2 operon contains an additional ccoQ gene. CcoQ consists of 62 amino acids and is predicted to possess one transmembrane spanning helix. The physiological role of CcoQ was investigated based on a CcoQ-deletion mutant and wild-type Cbb3-2 crystals not containing subunit CcoQ. Cbb3-2 isolated from the deletion mutant is inactive and appears as a dispersed band on blue native-PAGE gels. Surprisingly, in the absence of ccoQ, Cbb3-1 also shows a strongly reduced activity. Our data suggest that CcoQ primarily functions as an assembly factor for Cbb3-2 but is also required for correct assembly of Cbb3-1. In contrast, once correctly assembled, Cbb3-1 and Cbb3-2 possess a full enzymatic activity even in the absence of CcoQ.
Keywords: Pseudomonas stutzeri; Cytochrome c oxidase; Cbb3; Subunit CcoQ; Knockout mutant; Assembly;

In photosynthesis, electron transport-coupled proton movement initiates the formation of the light-induced electric potential difference, ΔΨ, across the thylakoid membrane (TM). Ions are transported across the TM to counterbalance the charge of protons accumulated in the lumen. The objective of this work is to construct range of mathematical models for simulation of ΔΨ, using the transition state rate theory (TSRT) for description of movement of ions through the channels. The TSRT considers either single-ion (TSRT-SI) or multi-ion occupancy (TSRT-MI) in the channels. Movement of ions through the channel pore is described by means of energy barriers and binding sites; ions move in and out of vacant sites with rate constants that depend on the barrier heights and well depths, as well as on the interionic repulsion in TSRT-MI model. Three energy motifs are used to describe the TSRT-SI model: two-barrier one-site (2B1S), three-barrier two-site (3B2S), and four-barrier three-site (4B3S). The 3B2S energy motif is used for the TSRT-MI model. The accumulation of cations due to the TM surface negative fixed charges is also taken into account. A model employing the electro-diffusion theory instead of the TSRT is constructed for comparison. The dual wavelength transmittance signal (ΔA515-560 nm) measuring the electrochromic shift (ECS) provides a proxy for experimental light-induced ΔΨ. The simulated ΔΨ traces qualitatively agree with the measured ECS traces. The models can simulate different channel conducting regimes and assess their impact on ΔΨ. The ionic flux coupling in the TSRT-MI model suggests that an increase in the internal or external K+ concentration may block the outward or the inward Mg2+ current, respectively.
Keywords: Electric potential difference ΔΨ; Electrochromic shift; Ion channel; Modeling; Transition state rate theory; Thylakoid membrane;

Reevaluating the mechanism of excitation energy regulation in iron-starved cyanobacteria by Hui-Yuan S. Chen; Michelle Liberton; Himadri B. Pakrasi; Dariusz M. Niedzwiedzki (249-258).
This paper presents spectroscopic investigations of IsiA, a chlorophyll a-binding membrane protein produced by cyanobacteria grown in iron-deficient environments. IsiA, if associated with photosystem I, supports photosystem I in light harvesting by efficiently transferring excitation energy. However, if separated from photosystem I, IsiA exhibits considerable excitation quenching observed as a substantial reduction of protein-bound chlorophyll a fluorescence lifetime. Previous spectroscopic studies suggested that carotenoids are involved in excitation energy dissipation and in addition play a second role in this antenna complex by supporting chlorophyll a in light harvesting by absorbing in the spectral range inaccessible for chlorophyll a and transferring excitation to chlorophylls. However, this investigation does not support these proposed roles of carotenoids in this light harvesting protein. This study shows that carotenoids do not transfer excitation energy to chlorophyll a. In addition, our investigations do not support the hypothesis that carotenoids are quenchers of the excited state of chlorophyll a in this protein complex. We propose that quenching of chlorophyll a fluorescence in IsiA is maintained by pigment-protein interaction via electron transfer from an excited chlorophyll a to a cysteine residue, an excitation quenching mechanism that was recently proposed to regulate the light harvesting capabilities of the bacteriochlorophyll a-containing Fenna-Mathews-Olson protein from green sulfur bacteria.
Keywords: IsiA; Carotenoids; Excitation quenching; Cyanobacteria; Transient absorption; Chlorophyll;

Imaging the Photosystem I/Photosystem II chlorophyll ratio inside the leaf by Emilie Wientjes; John Philippi; Jan Willem Borst; Herbert van Amerongen (259-265).
Oxygenic photosynthesis is driven by photosystems I (PSI) and II (PSII). In plants the number of chlorophylls of PSI versus PSII is adjusted to the light irradiance spectrum. On a timescale of days, this is regulated at the level of protein concentration. Instead, on a timescale of minutes, it is regulated by the dynamic association of light-harvesting complex II with either PSI or PSII. Thus far very diverse values have been reported for the PSI/PSII chlorophyll ratio, ranging from 0.54 to 1.4. The methods used require the isolation of chloroplasts and are time consuming. We present a fluorescence lifetime imaging approach that quantifies the PSI/PSII Chl ratio of chloroplasts directly in their natural leaf environment. In wild type Arabidopsis thaliana plants, grown under white light, the PSI/PSII chlorophyll ratio appeared to be 0.99 ± 0.09 at the adaxial side and 0.83 ± 0.05 at the abaxial side of the leaf. When these plants were acclimated to far red light for several days the PSI/PSII chlorophyll ratio decreased by more than a factor of 3 to compensate for the ineffective far red light absorption of PSII. This shows how plants optimize their light-harvesting capacity to the specific light conditions they encounter. Zooming in on single chloroplasts inside the leaf allowed to study the grana/stroma membrane network and their PSI/PSII chlorophyll ratios. The developed method will be useful to study dynamic processes in chloroplasts in intact leaves which involve changes in the grana and the stroma membranes such as state transitions.
Keywords: Microscopy; Fluorescence lifetime imaging; Light-harvesting complex II; LHCII;