Biological Energy Transducers

The process of changing one form of energy into another is referred to as transduction. One example of transduction is the chloroplast’s utilisation of light energy to make ATP from ADP. G proteins perform the role of transducers, which are the agents that convey signals from external stimuli to effector enzymes. They slowly catalyse the hydrolysis of bound guanosine 5′-triphosphate (GTP, the guanine analogue of ATP), which results in guanosine 5′-diphosphate. This action is known as GTPase activity.

Biological Energy Transducers

Consistent energy transduction pathways are required for life to exist. The acquired energy, whether from light, inorganic or organic molecules, is transduced into a transmembrane difference of electrochemical potential across the prokaryotic cytoplasmic or mitochondrial membranes in most species, from prokaryotes to eukaryotes. Non-photosynthetic organisms, for example, obtain energy by degrading organic dietary components such proteins, glucides and lipids which provide electrons to the respiratory chain. Here, electron transfer is linked to ion translocation across the membrane, and the energy released by the favourable electron transfer is converted into a transmembrane electrochemical potential difference. This transmembrane potential is required for cell import of solutes and nutrients, ATP production, and motility . In his Chemiosmotic Theory, Peter Mitchell hypothesised the existence of such potential for the first time.

• It is dedicated to three main research lines

1.) 1- Complex I – CpI

Complex I catalyses the oxidation of NADH and the reduction of quinone, both of which are accompanied by charge transfer across the membrane. Deficiencies in this complex have been linked to a variety of diseases, including neurodegenerative diseases including Leber’s hereditary optic neuropathy, Parkinson’s disease, and Dystonia. With a recent accumulation of structural and functional data including its X-ray structure, this enzyme is currently a hot-topic in the field of bioenergetics. 

We’ve been studying complex I using Rhodothermus marinus as a model organism, looking into electron transfer kinetics and quinone reduction, H+ and Na+ translocation, and the electron transfer-ion transport coupling mechanism.E. coli and Paracoccus denitrificans are also used as model organism  for studying complex I

The energy-transducing enzyme Complex I can be found in all three realms of life. The oxidation of NADH and the reduction of quinone are catalysed by this enzyme, which is accompanied by charge transfer across the membrane. It helps to establish the transmembrane difference in electrochemical potential, which is necessary for ATP generation, solute transport and motility. 

The respiratory complex is a membrane enzyme with an L-shaped peripheral and membrane arm . At the catalytic site where NADH is oxidised, the peripheral arm contains a sequence of iron-sulphur centres (binuclear and tetranuclear ones, called N1a, N1b, N2, N3, N4, N5, N6a and N6b) and an FMN. The charge translocating machinery is located in the membrane arm. The bacterial complex I is made up of 14 subunits (called Nqo1-14 or NuoA-N) that can be thought of as modular units and are found in other complexes. The electron input module is made up of Nqo1, 2, and 3, which are similar to the subunits of soluble NAD+ reducing hydrogenases except for the C-terminal region of Nqo3. Nqo3 shares a C-terminal region with molybdopterin enzymes. The subunits Nqo4, 5, 6, 8, and 9 are analogous to membrane-bound NiFe hydrogenases, whereas Nqo11, 12, 13, and 14 are homologous to Mrp-like Na+/H+ antiporters. For the components Nqo7 and Nqo10, no homologues have been found. 

The type of the ion(s) translocated by this enzyme is still a hot topic, with protons and sodium ions being two potential choices. Complex I translocates H+ for a long time, but the H+/electron stoichiometry has only been determined for the mitochondrial system. The concept that all complexes I from all organisms exclusively translocate H+ was challenged a few years ago when it was shown that complex I from Klebsiella pneumoniae can also translocate Na+, which is the system’s coupling ion. 

We recently discovered that some bacterial complexes can transport H+ and Na+ in opposing directions, with H+ serving as the coupling ion. We devised a unique method for monitoring substrate-driven Na+ transport by membrane vesicles using 23Na-NMR spectroscopy, which was the first time this technique had been used. We discovered two H+ translocating sites in Rhodothermus marinus complex I, one of which operates independently of the presence of Na+ and the other of which functions as a Na+/H+ antiporter. We looked at ion translocation by the two best studied bacterial complexes I and II to see if the antiporter site was limited to R. marinus complex I. We discovered that complex I from E. coli has antiporter function, but complex I from Paracoccus denitrificans does not. We anticipated that the type of quinone utilised as substrate and the existence of antiporter activity were linked. Furthermore, we predicted that energy coupling in complex I occurred via an indirect mechanism based on our findings with a common inhibitor of Na+/H+ antiporters. 

2) Alternative Complex III – ACIII

Despite the bacterial electron transfer chains’ great diversity and adaptability, the cytochrome bc1 complex family was assumed to be the only one capable of quinol: electron acceptor oxidoreductase activity. However, for the first time, our research has discovered an alternate complex III, ACIII, that is structurally distinct from the former. 

ACIII is a seven-subunit complex made up of three peripheral proteins, two c-type cytochromes, a multi heme and a monoheme, a large subunit with FeS centres, and four transmembrane proteins from R. marinus . ACIII has been shown to interact with quinol and at least one quinol binding site is found. ACIII can also decrease a high potential iron-sulphur protein (HiPIP), cytochrome c, and form a functional relationship with the caa3 oxygen reductase, according to our findings. 

Most importantly, the presence of ACIII is not limited to R. marinus; genes coding for this complex are found throughout the Bacteria domain, with the majority of genes coding for this complex being found in genomes where the genes coding for the subunits of a typical complex III are missing and the presence of a complex with that activity is predicted. We conducted a comprehensive investigation of the genes and gene clusters that code for ACIII subunits, as well as a thorough examination of the main structures of the various subunits and comparisons with similar proteins. We discovered a link between ACIII and members of the complex iron-sulphur molybdoenzyme family, leading us to believe that ACIII is an unique complex made up of modules previously identified in other respiratory complexes. Despite the existence of the ACIII gene cluster in multiple genomes, only the enzymes from R. marinus and C. aurantiacus have been extracted and described thus far. 

3) 3- Heme-copper oxygen reductases – HCO

Heme-copper The principal enzymes responsible for the reduction of oxygen to water in respiratory chains are oxygen reductases (HCOs). These membrane-bound enzymes catalyse the last reaction of aerobic respiratory chains and are found in Bacteria, Archaea, and Eukarya. HCOs contribute to energy conservation through two mechanisms: I charge separation, in which protons and electrons required for the chemical reaction come from opposite sides of the membrane, and ii) proton translocation, in which a portion of the energy released during the O2 reduction is used to promote thermodynamically unfavourable proton translocation across the membrane. 

Intra-protein proton conducting channels in mitochondrial and mitochondrial-like enzymes were discovered using sequence alignments, site directed mutagenesis, and X-ray crystallographic structural models. These channels were given the letters D and K after certain amino acid residues thought to be involved in proton translocation. 

We found that those specific residues were not conserved across all HCOs and we suggested probable substitutes in various enzymes. We suggested a categorization scheme based on the fingerprint of proton conducting channels, in which HCOs were categorised into three types: A (further divided into A1 and A2), B, and C Type enzymes. A detailed bioinformatics analysis recently confirmed this categorisation. 

The A Type enzymes have the most proteins and are the most thoroughly investigated HCOs. The mitochondrial oxygen reductase belongs to this group, which is distinguished by the presence of two proton conducting channels (the D- and K-channels) and the catalytic tyrosine’s placement in helix VI (Tyr-I). Only one proton conducting channel has been identified in B Type enzymes, the alternative K-channel, and the catalytic tyrosine is also present in helix VI in the majority of those enzymes (Tyr-I). C Type HCOs also have only one channel, an alternate K-channel that is unique to this group and not found in B Type enzymes. Helix VII contains the catalytic tyrosine residue (Tyr-II). 

A programme that can classify any user-supplied sequence was developed in partnership with the Instituto Gulbenkian de Ciência’s Computational Genomics Laboratory. This required the creation of a pipeline in which fresh sequences were categorised based on their best similarity hit against a manually curated dataset. This automated categorization approach is based on the similarity of amino acid sequences generated using local alignments (blast) versus the dataset reported in this paper.

Conclusion 

The chloroplast uses light energy to make ATP from ADP, a process known as transduction. Transduction occurs when one kind of energy is converted into another. Transducers: G proteins convey external stimuli to effector enzymes by acting as transducers. GTPase activity is present in G proteins, which means that they slowly catalyse the hydrolysis of bound guanosine 5′-triphosphate (GTP, the guanine analogue of ATP) to guanosine 5′-diphosphate.