Order wrapped in chaos: On the roles of intrinsically disordered proteins and RNAs in the arrangement of the mitochondrial enzymatic machines.

The analysis of cryo-electron tomography images of human and rat mitochondria revealed that the mitochondrial matrix is at least as crowded as the cytosol. To mitigate the crowding effects, metabolite transport in the mitochondria primarily occurs through the intermembrane space, which is significantly less crowded. The scientific literature largely ignores how enzyme systems and metabolite transport are organized in the crowded environment of the mitochondrial matrix. Under crowded conditions, multivalent interactions carried out by disordered protein regions (IDRs), may become extremely important. We analyzed the human mitochondrial proteome to determine the presence and physiological significance of IDRs. Despite mitochondrial proteins being generally more ordered than cytosolic or overall proteome proteins, disordered regions plays a significant role in certain mitochondrial compartments and processes. Even in highly ordered enzyme systems, there are proteins with long IDRs. Some IDRs act as binding elements between highly ordered subunits, while the roles of others are not yet established. Mitochondrial systems, like their bacterial ancestors, rely less on IDRs and more on RNA for LLPS compartmentalization. More evolutionarily advanced subsystems that enable mitochondria-cell interactions contain more IDRs. The study highlights the crucial and often overlooked role played by IDRs and non-coding RNAs in mitochondrial organization.

Safari with an Electron Gun: Visualization of Protein and Membrane Interactions in Mitochondria in Natural Environment.

This paper presents new structural data about mitochondria using correlative light and electron microscopy (CLEM) and cryo-electron tomography. These state-of-the-art structural biology methods allow studying biological objects at nanometer scales under natural conditions. Non-invasiveness of these methods makes them comparable to observing animals in their natural environment on a safari. The paper highlights two areas of research that can only be accomplished using these methods. The study visualized location of the Aß42 amyloid aggregates in relation to mitochondria to test a hypothesis of development of mitochondrial dysfunction in Alzheimer's disease. The results showed that the Aß42 aggregates do not interact with mitochondria, although some of them are closely located. Therefore, the study demonstrated that mitochondrial dysfunction is not directly associated with the effects of aggregates on mitochondrial structure. Other processes should be considered as sources of mitochondrial dysfunction. Second unique area presented in this work is high-resolution visualization of the mitochondrial membranes and proteins in them. Analysis of the cryo-ET data reveals toroidal holes in the lamellar structures of cardiac mitochondrial cristae, where ATP synthases are located. The study proposes a new mechanism for sorting and clustering protein complexes in the membrane based on topology. According to this suggestion, position of the OXPHOS system proteins in the membrane is determined by its curvature. High-resolution tomography expands and complements existing ideas about the structural and functional organization of mitochondria. This makes it possible to study the previously inaccessible structural interactions of proteins with each other and with membranes in vivo.

Association of 2-oxoacid dehydrogenase complexes with respirasomes in mitochondria.

In the present study, cryo-electron tomography was used to investigate the localization of 2-oxoacid dehydrogenase complexes (OADCs) in cardiac mitochondria and mitochondrial inner membrane samples. Two classes of ordered OADC inner cores with different symmetries were distinguished and their quaternary structures modeled. One class corresponds to pyruvate dehydrogenase complexes and the other to dehydrogenase complexes of α-ketoglutarate and branched-chain α-ketoacids. OADCs were shown to be localized in close proximity to membrane-embedded respirasomes, as observed both in densely packed lamellar cristae of cardiac mitochondria and in ruptured mitochondrial samples where the dense packing is absent. This suggests the specificity of the OADC-respirasome interaction, which allows localized NADH/NAD+ exchange between OADCs and complex I of the respiratory chain. The importance of this local coupling is based on OADCs being the link between respiration, glycolysis and amino acid metabolism. The coupling of these basic metabolic processes can vary in different tissues and conditions and may be involved in the development of various pathologies. The present study shows that this important and previously missing parameter of mitochondrial complex coupling can be successfully assessed using cryo-electron tomography.

Photosystem II for photoelectrochemical hydrogen production.

Water is a primary source of electrons and protons for photosynthetic organisms. For the production of hydrogen through the process of mimicking natural photosynthesis, photosystem II (PSII)-based hybrid photosynthetic systems have been created, both with and without an external voltage source. In the past 30 years, various PSII immobilization techniques have been proposed, and redox polymers have been created for charge transfer from PSII. This review considers the main components of photosynthetic systems, methods for evaluating efficiency, implemented systems and the ways to improve them. Recently, low-overpotential catalysts have emerged that do not contain precious metals, which could ultimately replace Pt and Ir catalysts and make water electrolysis cheaper. However, PSII competes with semiconductor analogues that are less efficient but more stable. Methods originally created for sensors also allow for the use of PSII as a component of a photoanode. To date, charge transfer from PSII remains a bottleneck for such systems. Novel data about action mechanism of artificial electron acceptors in PSII could develop redox polymers to level out mass transport limitations. Hydrogen-producing systems based on PSII have allowed to work out processes in artificial photosynthesis, investigate its features and limitations. Supplementary Information: The online version contains supplementary material available at 10.1007/s12551-023-01139-5.

Contribution of the Collective Excitations to the Coupled Proton and Energy Transport along Mitochondrial Cristae Membrane in Oxidative Phosphorylation System.

The results of many experimental and theoretical works indicate that after transport of protons across the mitochondrial inner membrane (MIM) in the oxidative phosphorylation (OXPHOS) system, they are retained on the membrane-water interface in nonequilibrium state with free energy excess due to low proton surface-to-bulk release. This well-established phenomenon suggests that proton trapping on the membrane interface ensures vectorial lateral transport of protons from proton pumps to ATP synthases (proton acceptors). Despite the key role of the proton transport in bioenergetics, the molecular mechanism of proton transfer in the OXPHOS system is not yet completely established. Here, we developed a dynamics model of long-range transport of energized protons along the MIM accompanied by collective excitation of localized waves propagating on the membrane surface. Our model is based on the new data on the macromolecular organization of the OXPHOS system showing the well-ordered structure of respirasomes and ATP synthases on the cristae membrane folds. We developed a two-component dynamics model of the proton transport considering two coupled subsystems: the ordered hydrogen bond (HB) chain of water molecules and lipid headgroups of MIM. We analytically obtained a two-component soliton solution in this model, which describes the motion of the proton kink, corresponding to successive proton hops in the HB chain, and coherent motion of a compression soliton in the chain of lipid headgroups. The local deformation in a soliton range facilitates proton jumps due to water molecules approaching each other in the HB chain. We suggested that the proton-conducting structures formed along the cristae membrane surface promote direct lateral proton transfer in the OXPHOS system. Collective excitations at the water-membrane interface in a form of two-component soliton ensure the coupled non-dissipative transport of charge carriers and elastic energy of MIM deformation to ATP synthases that may be utilized in ATP synthesis providing maximal efficiency in mitochondrial bioenergetics.

E/Z isomerization of astaxanthin and its monoesters in vitro under the exposure to light or heat and in overilluminated Haematococcus pluvialis cells.

Thermo- and photoisomerization of astaxanthin was investigated in a model system (solutions in methanol and chloroform), and the dynamics of astaxanthin isomers and esters content was analyzed in Haematococcus pluvialis green algal cells exposed to factors inducing astaxanthin accumulation. In both systems, the astaxanthin isomerization process seems to be defined by a) the action of light (or heat), and b) the dielectric constant of the surrounding medium. Upon heating, the accumulation of Z-isomers occurred in a model system during the entire incubation period. For the first 5 h of illumination, both Z-isomers accumulated in the solutions up to 5%, and then their content decreased. The accumulated amount of the Z-isomers in the cells of H. pluvialis was found to reach 42% of the total content of astaxanthin initially, and then it decreased during the experiment. The results lead to a conclusion that both cultivation of H. pluvialis culture in specific conditions and heat treatment of the resulting extracts from it might be efficient for obtaining large amounts of economically useful astaxanthin Z-isomer.

Draft Genome Sequence of "Halomonas chromatireducens" Strain AGD 8-3, a Haloalkaliphilic Chromate- and Selenite-Reducing Gammaproteobacterium.

Here, we report the complete genome sequence (3.97 Mb) of "Halomonas chromatireducens" AGD 8-3, a denitrifying bacterium capable of chromate and selenite reduction under extreme haloalkaline conditions. This strain was isolated from soda solonchak soils of the Kulunda steppe, Russian Federation.