Electron transport system supercomplexes affect reactive-oxygen species production and respiration in both a hibernator (Ictidomys tridecemlineatus) and a nonhibernator (Rattus norvegicus).

Across many taxa, the complexes of the electron transport system associate with each other within the inner mitochondrial membrane to form supercomplexes (SCs). These SCs are thought to confer some selective advantage, such as increasing cellular respiratory capacity or decreasing the production of damaging reactive oxygen species (ROS). In this study, we investigate the relationship between supercomplex abundance and performance of liver mitochondria isolated from rats that do not hibernate and hibernating ground squirrels in which metabolism fluctuates substantially. We quantified the abundance of SCs (respirasomes (SCs containing CI, CIII, and CIV) or SCs containing CIII and CIV) and examined the relationship with state 3 (OXPHOS) and state 4 (LEAK) respiration rate, as well as net ROS production. We found that, in rats, state 3 and 4 respiration rate correlated negatively with respirasome abundance, but positively with CIII/CIV SC abundance. Despite the greater range of respiration rates in different hibernation stages, these relationships were similar in ground squirrels. This is, to our knowledge, the first report of differential effects of supercomplex types on mitochondrial respiration and ROS production.

Determination of the DNA/RNA-Associated Subproteome from Chloroplasts and Other Plastid Types.

Plastids of plant and algae cells are of endosymbiotic origin. They possess their own genome and a sophisticated protein machinery to express it. Studies over the recent years uncovered that the regulation of plastid gene expression is highly complex involving a multiplicity of regulatory protein factors that are mostly imported from the cytosol. Proper expression of the chloroplast genome in coordination with nuclear genome was found to be absolutely essential for efficient growth and development of plants especially during early steps of photomorphogenesis, but also at later stages of the plant life cycle. Protein factors being responsible for such essential steps, therefore, are highly interesting for fundamental science as well as for industrial applications targeting crop improvement and yield increase. Nevertheless, many proteins involved in regulation of plastid gene expression are still unidentified and/or uncharacterized. This asks for appropriate methods to analyze this special subproteome. Here, we describe suitable methods that proved to be successful in the analysis of the plastid subproteome of DNA/RNA-binding proteins.

NDUFAF3 variants that disrupt mitochondrial complex I assembly may associate with cavitating leukoencephalopathy.

Genetic abnormalities in mitochondrial complex assembling factors are associated with leukoencephalopathy. We present a 1-year-old girl with consciousness disturbance after a respiratory infection. Brain MRI revealed leukoencephalopathy with bilaterally symmetrical hyperintensity in the substantia nigra, medial thalamic nuclei, and basal nuclei, as well as cavities in the cerebral white matter and corpus callosum. Lactate levels in the spinal fluid were high, while magnetic resonance spectroscopy of the cerebral white matter and basal nuclei showed high peak lactate levels, suggesting mitochondrial dysfunction. The respiratory enzyme activity of complex I was reduced to 17% to 21% in skeletal muscle. Whole exome sequencing identified compound heterozygous variations in NDUFAF3, involved in the assembly of mitochondrial complex I (c.342_343insGTG:p.117Valdup, c.505C > A:p.Pro169Thr). Two-dimensional, blue-native polyacrylamide gel electrophoresis (PAGE) and sodium dodecyl sulfate-PAGE revealed reductions in Q-module (NDUFS2, NDUFS3, and NDUFA9) and P-module (NDUFB10 and NDUFB11) subunits, indicating disruption of mitochondrial complex I assembly. Our report expands the spectrum of clinical phenotypes associated with pathogenic variants of NDUFAF3.

Separation of Thylakoid Protein Complexes with Two-dimensional Native-PAGE.

The hierarchical composition and interactions of the labile thylakoid protein complexes can be assessed by sequential 2D-native gel-electrophoresis system. Mild non-ionic detergent digitonin is used to solubilize labile protein super-and megacomplexes, which are then separated with first-dimension blue native polyacrylamide gel electrophoresis (1D-BN-PAGE). The digitonin derived protein complexes are further solubilized with stronger detergent, ß-DM, and subsequently separated on an orthogonal 2D-BN-PAGE to release smaller protein subcomplexes from the higher-order supercomplexes. Here we describe a detailed method for 2D-BN-PAGE analysis of thylakoid protein complexes from Arabidopsis thaliana.

Blue native-PAGE analysis of membrane protein complexes in Porphyromonas gingivalis.

Membrane complexes of Porphyromonas gingivalis were analyzed using two dimensional-blue native-PAGE. The molecular mass of the gingipain complexes, RgpA and Kgp, ranged from 450 kDa to greater than 1200 kDa, and did not change in single rgpA and kgp mutants indicating that the proteolytically processed polyproteins were independently capable of forming complexes. The outer membrane protein, LptO, which is essential for gingipain secretion, was found in up to seven different complex sizes. PG0026, also important for secretion, was observed to interact with the largest LptO complex [VII] at 480 kDa, supporting a cooperative role in secretion. Two pro-form RgpB intermediates formed a complex before cleavage of their C-terminal secretion signal domains (CTDs) such that complex formation may occur during secretion and processing. This may also be the case for other CTD-proteins as not only modified, mature RgpB, but also CPG70 was found to exist as multi-subunit complexes. RagA and RagB were observed in three different complex sizes. Elimination of the abundant gingipains enabled the identification of many inner and outer membrane protein complexes: TonB:ExbB:ExbD, Omp85, P51:PG2168, PorK:PorN, PG0056, PG0241, PG1430 and five proposed respiratory chain complexes (Mmd, Nqr, Rnf, Frd/Sdh and Atp). BIOLOGICAL SIGNIFICANCE: Porphyromonas gingivalis is a major oral pathogen associated with chronic periodontitis in humans. Secreted gingipains are considered major virulence factors of this pathogen and are secreted by a newly described type IX secretion system. This work has used 2D-BN-PAGE and MS to demonstrate that mature gingipains can independently form complexes and that substrate intermediates and mature secreted proteins of the type IX secretion system form multi-subunit complexes. Based on this work we propose that the substrates of this secretion system are secreted as large multi-subunit protein complexes. Two known important components of the secretion machinery, PG0026 and the integral outer membrane protein, LptO, were found to interact which would anchor PG0026 to the outer membrane and perhaps aid in the function of PG0026 to cleave the CTD from secreted substrates. The work has also identified more than 100 membrane proteins forming multi-subunit complexes.