The Leeuwenhoek Lecture, 1981. The biochemical and genetic approach to the study of bioenergetics with the use of Escherichia coli: progress and prospects

How the 'energy currency' of the cell, adenosine triphosphate (ATP), is produced consequent upon the oxidation of foodstuffs (oxidative phosphorylation) is, despite prolonged research, still a matter of debate and the molecular mechanism of the process is unknown. It appears that the problem of oxidative phosphorylation can be approached with the aid of the biochemical genetics of the bacterium Escherichia coli. The ease of manipulation of bacteria and definitive results obtained by this approach have been invaluable in solving other major biochemical problems. Mutants affected in oxidative phosphorylation have been isolated and characterized by genetic and biochemical techniques. These 'unc' mutants are affected in the adenosine triphosphatase (ATPase) multiprotein complex which is part of the cell membrane and responsible for the terminal stages of ATP synthesis. Seven distinct genes concerned with oxidative phosphorylation have been characterized in E. coli and shown to be part of an operon. The relationships between the different classes of unc genes and the various components of the ATPase have been established. Information about the assembly of the ATP synthesizing complex in the cell membrane has also been obtained and the stage set for further studies on the assembly, control and function of the ATP synthesizing system.     

Recognition sites for chemotactic repellents of Bacillus subtilis.

Repellents of Bacillus subtilis include many membrane-active compounds, such as uncouplers of oxidative phosphorylation, local anesthetics, chlorpromazine (a central nervous system depressant), and tetraphenylboron (a lipophilic anion). Normally, bacteria swim smoothly, and occasionally tumble, but addition of repellent causes all bacteria to tumble, then later resume original frequency of swimming and tumbling (adaptation). Bacteria adapted to repellent can then be tested to determine the minimum concentration (threshold) of the same or different repellents that causes tumbling. The results indicate that repellents act at (saturable) recognition sites, which differ for chemically different species. An implication is that uncouplers of oxidative phosphorylation affect cell properties by interaction at specific locations.     

Type 3 peptide deformylases are required for oxidative phosphorylation in Trypanosoma brucei

Peptide deformylase (PDF) catalyses the removal of the formyl group from the first methionine of nascent proteins. Type 1 PDFs are found in bacteria and have orthologues in most eukaryotes. Type 2 PDFs are restricted to bacteria. Type 3 enzymes are found in Archaea and trypanosomatids and have not been studied experimentally yet. Thus, TbPDF1 and TbPDF2, the two PDF orthologues of the parasitic protozoa Trypanosoma brucei, are of type 3. An experimental analysis of these enzymes shows that both are mitochondrially localized, but that only TbPDF1 is essential for normal growth. Recombinant TbPDF1 exhibits PDF activity with a substrate specificity identical to that of bacterial enzymes. Consistent with these results, TbPDF1 is required for oxidative but not for mitochondrial substrate-level phosphorylation. Ablation of TbPDF2, in contrast, does neither affect growth on standard medium nor oxidative phosphorylation. However, a reduced level of TbPDF2 slows down growth in a medium that selects for highly efficient oxidative phosphorylation. Furthermore, combined ablation of TbPDF1 and TbPDF2 results in an earlier growth arrest than is observed by downregulation of TbPDF1 alone. These results suggest that TbPDF2 is functionally linked to TbPDF1, and that it can influence the efficiency of oxidative phosphorylation.     

Purification and some properties of cytochrome P-450 specific for steroid 17 alpha-hydroxylation and C17-C20 bond cleavage from guinea pig adrenal microsomes

The energy requirements for mitochondrial protein synthesis were investigated in isolated rat liver mitochondria. Controlled changes in coupling efficiency were obtained by titration with FCCP in the presence of various substrates. No relationship was observed between the efficiency of oxidative phosphorylation and the inhibition of protein synthesis. With succinate-ADP as the substrate the ADP:O ratio was decreased by 70–80% with no effect on protein synthesis. In contrast, with acetate-ADP as substrate, a 10–20% reduction in the ADP:O ratio gave complete inhibition of protein synthesis. The data suggest that the rate of ATP production is more important for maintenance of protein synthesis than the efficiency of coupling $\text{per se}$. Thus, certain substrates can support maximal rates of protein synthesis even in relatively poorly coupled mitochondria. Analysis of mitochondrial translation products formed in the presence of increasing FCCP concentrations also showed that decreased efficiency of oxidative phosphorylation had no influence on the nature of the products.     

Comparative study of the energy metabolism of anaerobic alkaliphiles from soda lakes

We investigated the influence of inhibitors of energy metabolism and ionophores on the growth and formation of metabolic products in alkaliphilic anaerobes characterized by various catabolism types. It was shown that blockage of oxidative phosphorylation by the addition of N,N'-dicyclohexylcarbodiimide (DCCD), an inhibitor of F1F0 ATP synthase, resulted in a complete arrest of the growth of the acetogenic bacterium Tindallia magadiensis with arginine as electron acceptor. In the presence of pyruvate, substrate-level phosphorylation occurred. The methylotrophic methanogenic archaebacterium Methanosalus zhilinae did not grow with DCCD and vanadate, an inhibitor of E1E2 ATPase, suggesting the presence of two ATPase types in this species. In the saccharolytic alkaliphiles Halonatronum, Amphibacillus tropicus, and Spirochaeta alkalica (which are characterized by different pH optima), the contribution of the H+ gradient to the energy metabolism and, presumably, to the maintenance of the intracellular pH level decreased with an increase in the degree of alkaliphily. Based on the data of an inhibitor assay using protonophores, monensin, and amiloride, we suggest that all of the bacteria tested depend on H+- and Na+-gradients. The Na+/H+ antiport appears to be a universal mechanism of regulating the intracellular pH level and the interaction between the Na+ and the H+ cycles in bacterial cells cultivated under alkaline conditions.     

Down-regulated energy metabolism genes associated with mitochondria oxidative phosphorylation and fatty acid metabolism in viral cardiomyopathy mouse heart

The majority of experimental and clinical studies indicates that the hypertrophied and failing myocardium are characterized by changes in energy and substrate metabolism that attributed to failing heart changes at the genomic level, in fact, heart failure is caused by various diseases, their energy metabolism and substrate are in different genetic variations, then the potential significance of the molecular mechanisms for the aetiology of heart failure is necessary to be evaluated. Persistent viral infection (especially coxsackievirus group B3) of the myocardium in viral myocarditis and viral dilated cardiomyopathy has never been neglected by experts. This study aimed to explore the role and regulatory mechanism of the altered gene expression for energy metabolism involved in mitochondrial oxidative phosphorylation, fatty acid metabolism in viral dilated cardiomyopathy. cDNA Microarray technology was used to evaluate the expression of >35,852 genes in a mice model of viral dilated cardiomyopathy. In total 1385 highly different genes expression, we analyzed 33 altered genes expression for energy metabolism involved in mitochondrial oxidative phosphorylation, fatty acid metabolism and further selected real-time-PCR for quantity one of regulatory mechanisms for energy including fatty acid metabolism—the UCP2 and assayed cytochrome C oxidase activity by Spectrophotometer to explore mitochondrial oxidative phosphorylation function. We found obviously different expression of 33 energy metabolism genes associated with mitochondria oxidative phosphorylation, fatty acid metabolism in cardiomyopathy mouse heart, the regulatory gene for energy metabolism: UCP2 was down-regulated and cytochrome C oxidase activity was decreased. Genes involved in both fatty acid metabolism and mitochondrial oxidative phosphorylation were down-regulated, mitochondrial uncoupling proteins (UCP2) expression did not increase but decrease which might be a kind of adaptive protection response to regulate energy metabolism for ATP produce.     

海藻酸分解菌研究进展

海藻酸分解菌是一类能够自身合成海藻酸裂解酶,能够降解并同化海藻酸的微生物。海藻酸分解菌是海藻酸裂解酶的重要来源,其产生的海藻酸裂解酶具有种类多、反应条件温和、酶活高和易于大规模生产等优点,并且在生物、医疗、化工等领域有重要的应用价值。在过去的几十年里,海藻酸分解菌一直作为海藻酸裂解酶生产者的角色被研究和应用。但随着近年来能源危机的加剧,以海藻酸等海藻生物质为原料转化生物能源成为解决能源危机的潜在途径,因此,海藻酸分解菌又有了崭新的研究领域,即海藻酸分解菌利用海藻酸发酵生产生物能源。本文从海藻酸分解菌及其海藻酸裂解酶的种类和特性、海藻酸分解菌的代谢以及海藻酸分解菌基因工程等方面,介绍海藻酸分解菌的研究现状,并展望未来的发展趋势。     

Phosphorylation in Hydrogen Bacteria

The electron-transport system of cell-free extracts obtained from Hydrogenomonas H-20 has been studied with particular reference to phosphorylation associated with the oxyhydrogen reaction. Cell-free preparations of this organism exhibit oxidative phosphorylation with hydrogen and succinate as electron donors. This activity could be uncoupled with a number of agents. Ratios of phosphorylative activity to oxidative activity observed varied from 0.2 to 0.7. Factors affecting the efficiency of phosphorylation were examined. Inhibitor and spectrophotometric studies indicated that phosphorylation with hydrogen as electron donor occurs exclusively at a site in an abbreviated electron transport chain between H(2) and cytochrome b. The possible occurrence of a cytochrome b oxidase and the requirement for a quinone are discussed, as well as the correlation between the abbreviated pathway and the energy generation by the cell. Evidence is presented which indicates that nicotinamide adenine dinucleotide does not participate in the hydrogen oxidation path which is coupled to adenosine triphosphate formation.     

Metabolic differentiation in the embryonic retina

Unlike healthy adult tissues, cancers produce energy mainly by aerobic glycolysis instead of oxidative phosphorylation. This adaptation, called the Warburg effect, may be a feature of all dividing cells, both normal and cancerous, or it may be specific to cancers. It is not known whether, in a normally growing tissue during development, proliferating and postmitotic cells produce energy in fundamentally different ways. Here we show in the embryonic Xenopus retina in vivo, that dividing progenitor cells depend less on oxidative phosphorylation for ATP production than non-dividing differentiated cells, and instead use glycogen to fuel aerobic glycolysis. The transition from glycolysis to oxidative phosphorylation is connected to the cell differentiation process. Glycolysis is indispensable for progenitor proliferation and biosynthesis, even when it is not used for ATP production. These results suggest that the Warburg effect can be a feature of normal proliferation in vivo, and that the regulation of glycolysis and oxidative phosphorylation is critical for normal development.     

Uncoupling Effect of Fatty Acids in Halo- and Alkalotolerant Bacterium Bacillus pseudofirmus FTU

Natural uncouplers of oxidative phosphorylation, long-chain non-esterified fatty acids, cause uncoupling in the alkalo- and halotolerant bacterium Bacillus pseudofirmus FTU. The uncoupling effect in the bacterial cells was manifested as decrease of membrane potential and increase of respiratory activity. The membrane potential decrease was detected only in bacterial cells exhausted by their endogenous substrates. In proteoliposomes containing reconstituted bacterial cytochrome c oxidase, fatty acids caused a "mild" uncoupling effect by reducing membrane potential only at low rate of membrane potential generation. "Free respiration" induced by the "mild" uncouplers, the fatty acids, can be considered as possible mechanism responsible for adaptation of the bacteria to a constantly changed environment.     

Electron transport phosphorylation coupled to fumarate reduction by H2- and Mg2+-dependent adenosine triphosphatase activity in extracts of the rumen anaerobe Vibrio succinogenes.

Vibrio succinogenes, an anaerobic bacterium, obtains its energy for growth from H2 or formate oxidation coupled to the reduction of fumarate to succinate. Membrane preparations have been obtained from this organism that catalyze the synthesis of ATP during H2 oxidation coupled to fumarate reduction. Esterification of orthophosphate is dependent on electron transfer, as evidenced by the requirement for both H2 and fumarate. Phosphorylation is also dependent on ADP and is destroyed by boiling the membrane preparations. H2 utilized for fumarate reduction and succinate formed are stoichiometric. The phosphorylation is markedly uncoupled by pentachlorophenol and gramicidin, but to a lesser extent by dinitrophenol and methyl viologen. 2-n-Heptyl-4-hydroxyquinoline-N-oxide causes severe inhibition of H2 oxidation as well as phosphorylation, but oligomycin or antimycin A has no demonstrable effect. Among several electron acceptors tested, significant phosphorylation is observed only with fumarate. A Mg2+-dependent adenosine triphosphatase activity is present in both the membrane and soluble protein fractions. Highest activity is obtained with ATP as the substrate, and considerably less activity is obtained with other nucleoside triphosphates. The possibility that phosphorylation during "fumarate respiration" may play an important physiological role in the growth of many anaerobic and facultatively anaerobic bacteria is discussed.     

Energy metabolism in tumor cells

In early studies on energy metabolism of tumor cells, it was proposed that the enhanced glycolysis was induced by a decreased oxidative phosphorylation. Since then it has been indiscriminately applied to all types of tumor cells that the ATP supply is mainly or only provided by glycolysis, without an appropriate experimental evaluation. In this review, the different genetic and biochemical mechanisms by which tumor cells achieve an enhanced glycolytic flux are analyzed. Furthermore, the proposed mechanisms that arguably lead to a decreased oxidative phosphorylation in tumor cells are discussed. As the O(2) concentration in hypoxic regions of tumors seems not to be limiting for the functioning of oxidative phosphorylation, this pathway is re-evaluated regarding oxidizable substrate utilization and its contribution to ATP supply versus glycolysis. In the tumor cell lines where the oxidative metabolism prevails over the glycolytic metabolism for ATP supply, the flux control distribution of both pathways is described. The effect of glycolytic and mitochondrial drugs on tumor energy metabolism and cellular proliferation is described and discussed. Similarly, the energy metabolic changes associated with inherent and acquired resistance to radiotherapy and chemotherapy of tumor cells, and those determined by positron emission tomography, are revised. It is proposed that energy metabolism may be an alternative therapeutic target for both hypoxic (glycolytic) and oxidative tumors.     

THE TOTAL LUMINOUS EFFICIENCY OF LUMINOUS BACTERIA

Methods are described for measuring the light emitted by an emulsion of luminous bacteria of given thickness, and calculating the light emitted by a single bacterium, measuring 1.1 x 2.2 micra, provided there is no absorption of light in the emulsion. At the same time, the oxygen consumed by a single bacterium was measured by recording the time for the bacteria to use up .9 of the oxygen dissolved in sea water from air (20 per cent oxygen). The luminescence intensity does not diminish until the oxygen concentration falls below 2 per cent, when the luminescence diminishes rapidly. Above 2 per cent oxygen (when the oxygen dissolving in sea water from pure oxygen at 760 mm. Hg pressure = 100 per cent) the bacteria use equal amounts of oxygen in equal times, while below 2 per cent oxygen it seems very likely that rate of oxygen absorption is proportional to oxygen concentration. By measuring the time for a tube of luminous bacteria of known concentration saturated with air (20 per cent oxygen) to begin to darken (2 per cent oxygen) we can calculate the oxygen absorbed by one bacterium per second. The bacteria per cc. are counted on a blood counting slide or by a centrifugal method, after measuring the volume of a single bacterium (1.695 x 10^–12 cc.). Both methods gave results in good agreement with each other. The maximum value for the light from a single bacterium was 24 x 10^–14 lumens or 1.9 x 10^–14 candles. The maximum value for lumen-seconds per mg. of oxygen absorbed was 14. The average value for lumen-seconds per mg. O₂ was 9.25. The maximum values were selected in calculating the efficiency of light production, since some of the bacteria counted may not be producing light, although they may still be using oxygen. The "diet" of the bacteria was 60 per cent glycerol and 40 per cent peptone. To oxidize this mixture each mg. of oxygen would yield 3.38 gm. calories or 14.1 watts per second. 1 lumen per watt is therefore produced by a normal bacterium which emits 14 lumen-seconds per mg. O₂ absorbed. Since the maximum lumens per watt are 640, representing 100 per cent efficiency, the total luminous efficiency if .00156. As some of the oxygen is used in respiratory oxidation which may have nothing to do with luminescence, the luminescence efficiency must be higher than 1 lumen per watt. Experiments with KCN show that this substance may reduce the oxygen consumption to 1/20 of its former value while reducing the luminescence intensity only ¼. A partial separation of respiratory from luminescence oxidations is therefore effected by KCN, and our efficiency becomes 5 lumens per watt, or .0078. This is an over-all efficiency, based on the energy value of the "fuel" of the bacteria, regarded as a power plant for producing light. It compares very favorably with the 1.6 lumens per watt of a tungsten vacuum lamp or the 3.9 lumens per watt of a tungsten nitrogen lamp, if we correct the usual values for these illuminants, based on watts at the lamp terminals, for a 20 per cent efficiency of the power plant converting the energy of coal fuel into electric current. The specific luminous emission of the bacteria is 3.14 x 10^–6 lumens per cm². One bacterium absorbs 215,000 molecules of oxygen per second and emits 1,280 quanta of light at λ_max = 510µµ. If we suppose that a molecule of oxygen uniting with luminous material gives rise to the emission of 1 quantum of light energy, only 1/168 of the oxygen absorbed is used in luminescence. On this basis the efficiency becomes 168 lumens per watt or 26.2 per cent.     

Tissue variation of mitochondrial oxidative phosphorylation efficiency in cold-acclimated ducklings

We investigated the oxidative phosphorylation efficiency of liver and gastrocnemius muscle mitochondria in thermoneutral and cold-acclimated ducklings. The yield of oxidative phosphorylation was lower in muscle than in liver mitochondria, a difference that was associated with a higher proton conductance in muscle mitochondria. Cold exposure did not affect oxidative phosphorylation efficiency or basal proton leak in mitochondria. We conclude that the basal proton conductance of mitochondria may regulate mitochondrial oxidative phosphorylation efficiency, but is not an important contributor to thermogenic processes in cold-acclimated ducklings.     

Brown adipose tissue mitochondria: recoupling caused by substrate level phosphorylation and extramitochondrial adenosine phosphates.

1. Uncoupled oxidative phosphorylation in isolated guinea pig brown-adipose-tissue mitochondria is reflected by a low phosphorylation state of adenosine phosphates in the mitochondrial matrix and in the extramitochondrial space during oxidation of succinate or glycerol 1-phosphate in the presence of serum albumin and 100 muM ADP. Recoupling of respiration and phosphorylation in the mitochondria is indicatdd by a dramatic increase in the phosphorylation state of adenine nucleotides in both compartments, when substrates inducing substrate level phosphorylation are respired. In this case ATP/ADP ratios in the extramitochondrial compartment are 10-15 times higher than in the mitochondrial matrix. 2. Recoupling mediated by substrate level phosphorylation depends on the presence of extramitochondrial adenosine phosphate and on intact adenine nucleotide translocation. In the presence of substrate level phosphorylation the amount of extramitochondrial ADP required to restore energy coupling can be extremely low (20 muM ADP or 10 nmol ADP/mg mitochondrial protein respectively). If substrate level phosphorylation is prevented by rotenone or in the presence of atractyloside, 20-50 times higher amounts of extramitochondrial adenine nucleotides are necessary to cause coupled oxidative phosphorylation. The recoupling effect of ATP is significantly stronger than that of ADP. 3. GDP (100 muM) causes a rapid increase of the ATP/ADP ratio in both compartments which is independent of substrate level phosphorylation as well as of the extramitochondrial adenosine phosphate concentration and the adenine nucleotide carrier. 4. The amount of extramitochondrial adenosine phosphate in guinea pig brown-adipose-tissue (18 nmol/mg mitochondrial protein or 2.5 mM respectively) would suffice for recoupling of oxidative phosphorylation mediated by substrate level phosphorylation under conditions in vitro; this suggests that substrate level phosphorylation is of essential importance in brown fat in vivo with respect to energy conditions in the tissue during different states of thermogenesis.     

Influences of light and oxygen conditions on photosynthetic bacteria macromolecule degradation: different metabolic pathways

Direct degradation of macromolecules by photosynthetic bacteria (PSB) is important for the industrial application of PSB wastewater treatment. Light and oxygen are the most important parameters in PSB growth. This paper studied the PSB macromolecule degradation process under three different light and oxygen conditions: light-anaerobic, natural light-microaerobic and dark-aerobic. The results showed that under three different light-oxygen conditions, PSB degradation of macromolecules was higher than 90%; the removal ratios of COD, TN, TP, total sugar and protein were also high; and the biomass yield reached nearly 0.5 mg-biomass/mg-COD-removal. Light and oxygen significantly influenced the efficiency. Macromolecules and pollutants removals were higher under oxygen condition than those under light-anaerobic condition. Theoretical analysis showed that under aerobic condition, PSB carried out oxidative phosphorylation, in which pollutants were sufficiently utilized with high mineralization degree. Under light-anaerobic condition, PSB carried out photophosphorylation and fermentation, which led to low pollutants removal efficiency.     

Proteomics viewed on stress response of thermophilic bacterium Bacillus stearothermophilus TLS33

Thermophilic bacterium Bacillus stearothermophilus TLS33, isolated from a hot spring in Chiang Mai, Thailand, usually produces many enzymes that are very useful for industrial applications. However, the functional properties and mechanisms of this bacterium under stress conditions are rarely reported and still need more understanding on how the bacterium can survive in stress environments. In this study, we examined the oxidative stress induced proteins of this bacterium by proteomic approach combining two-dimensional electrophoresis and mass spectrometry. When the bacterium encountered oxidative stress, peroxiredoxin, as an antioxidant enzyme, is one of the interesting stressed proteins which appeared to be systematically increased with different pI. There are four isoforms of peroxiredoxin, denoted as Prx I, Prx II, Prx III and Prx IV, which are observed at the same molecular weight of 27 kDa but differ in pI values of 5.0, 4.87, 4.81 and 4.79, respectively. The H2O2 concentration directly increased Prx II, Prx III and Prx IV intensities, but decreased Prx I intensity. These shifting of peroxiredoxin isoforms may occur by a post-translational modification. Otherwise, the longer time of oxidative stress had not affected the expression level of peroxiredoxin isoforms. Therefore, this finding of peroxiredoxin intends to know the bacterial adaptation under oxidative stress. Otherwise, this protein plays an important role in many physiological processes and able to use in the industrial applications.     

Chemical modulation of physiological adaptation and cross-protective responses against oxidative stress in soil bacterium and phytopathogen, Xanthomonas

Soil bacteria need to adapt quickly to changes in the environmental conditions. Physiological adaptation plays an important role in microbial survival, especially under stressful conditions. Here the abilities of chemicals and pesticides to modulate physiological adaptive and cross-protective responses, that make the bacteria more resistant to oxidative stress, are examined in the soil bacterium and phytopathogen, Xanthomonas. The genetic basis for the observed stress resistance, as well as the regulatory mechanisms controlling gene expression during the process, has begun to be elucidated.