Bacterial metabolism

See also metabolism

Introduction:

Distinct metabolic strategies allow microbes to extract energy from diverse surroundings and colonize nearly every part of the earth. Microbial energy metabolisms vary greatly but can be generally categorized as possessing fermentative or respiratory properties. Cellular respiration is classically described by a multistep process that initiates with the enzymatic oxidation of organic matter and the accompanying reduction of NAD+ (nicotinamide adenine dinucleotide) to NADH. Respiration of fermentable sugars typically starts with glycolysis, which generates pyruvate and NADH. Pyruvate then enters the tricarboxylic acid (TCA) cycle, where its oxidation to carbon dioxide is coupled to the production of additional NADH. NADH generated by glycolysis and the TCA cycle is then oxidized by NADH dehydrogenase to regenerate NAD+ and the resulting electrons are transferred via an electron transport chain to a terminal electron acceptor. See Light

While mammals strictly use oxygen as a respiratory electron acceptor, microbes reside in diverse oxygen-limited environments and have varying and diverse capabilities to use disparate non-oxygen respiratory electron acceptors. Whatever the electron acceptor, electron transfer in the electron transport chain is often coupled to proton pumping across the bacterial inner membrane. This generates a proton gradient or proton motive force, which powers a variety of processes, including ATP production by ATP synthase.

Respiratory pathways are important for several aspects of bacterial physiology. Respiration’s role in establishing the proton motive force allows bacteria to generate ATP from non-fermentable energy sources (which are not amenable to ATP production by substrate-level phosphorylation) and increases ATP yields from fermentable energy sources. In addition to these roles in ATP production, respiratory electron transport chains are directly involved in many other aspects of bacterial physiology, including the regulation of cytosolic pH, transmembrane solute transport, ferredoxin-dependent metabolisms, protein secretion, protein folding, disulfide formation, and flagellar motility. See Light

The process of bacterial metabolism begins with hydrolysis of large macromolecules in the external cellular environment by specific enzymes. Small molecules produced by this hydrolysis (i.e, fatty acids from lipids, monosaccharides from polysaccharides, short peptides from proteins) are transported into bacteria using a variety of transport mechanisms which all require permeases (binding proteins). These transport mechanisms include (1) facilitated diffusion (passive transport) down a concentration gradient (e.g., glycerol), (2) phosphorylation-linked transport where molecules are chemically altered during uptake (e.g., glucose) by phosphorylation, (3) active transport which requires a proton motive force (e.g, lactose) and (4) siderophores which traps Fe+3 from transferrin and transport it into the cell.

Definitions:

Catabolism: The process of substrate breakdown and conversion into usable energy is known as catabolism. The energy produced may then be used in the synthesis of cellular constituents (cell walls, proteins, nucleic acids, etc.) in a process called anabolism. The specific used by bacteria for catabolism and anabolism are, for the most part, shared by both prokaryotic and eukaryotic cells.

Bacterial respiration, whether done aerobically or anaerobically, utilizes the Krebs cycle and the electron transport system to harvest the energy and products needed to build cell parts. Fermentation does not use the Krebs cycle or the electron transport system.

Glycolysis: The primary pathway used by both bacteria and eukaryotic cells for the conversion of glucose to pyruvate (a universal intermediate) is the glycolytic or Embden-Myerhof-Parnas (EMP) pathway. The reactions which make up this pathway occur under both anaerobic and aerobic conditions. There is a net production of 2 molecules of ATP. Pyruvate is a molecule taht is uniquely suited for chemical reacitons that will produce reducing power which eventually will produce ATP.

Fermentation: In the absence of oxygen, pyruvate undergoes fermentation wherein organic molecules are e acceptors and NAD is regenerated. Synthesis of key intermediates (anabolism) include malate, succinate, oxaloacetate, etc.

Krebs cycle (also known as the tricarboxylic acid (TCA cycle): transfers the eerngy stored in acetyle coA to NAD+ and FAD by reducing them.

Under aerobic conditions, in the TCA cycle, pyruvate is oxidized to water and CO2 along with the generation of GTP and substrates such as alpha ketoglutarate, citrate, etc.. Additional ATP is also generated in the electron transport chain from the oxidation of NADH which is provided by the TCA cycle.

Respiratory chain: electron transport: is the final step in both aerobic and anaerobic respiration. Overall, the electron transport system (ETS) consists of a chain of special redox carriers that receives electrons form reduced carriers (NADH), FADH2) generated by glycolysis and the Krebs cycle and passes them in a sequential and orderly fashion from one redox molecule to the next. The flow of electrons down this chain is full of energy and allows the active transport of hydrogen ions to the outside of the membrane where the respiratory chain is located.

In aerobic respiration, the step that finalizes the transport process is the acceptance of electrons and hydrogen by oxygen, producing water. This process consumes oxygen. The electron transport carriers and enzymes are embedded in the cytoplasmic membrane in bacteria. The equivalent structure for housing them in eukaryotes is the inner mitchondrial membranes.

Aerobic Respiration:

The final step in aerobic respiration, during which oxygen accepts the electrons, is catalzyed by cytochrome aa, also called cytochrome oxidate. This large enzyme complex is adapted to receive electrons from cytochrome c, pick up hydrogens form the solution, and react with oxygen to form a molecule of water.

Most eukaryotic aerobes have a fully functioning cytochrome system, but bacteria exhibit wide ranging variations in this part of the system. Some species lack one or more of the redox steps. Others have several alternative electron transport schemes. Because many bacteria lack cytochrome oxidase, this variation can be used to differentiate among certain genera of bacteria. An oxidase detection test can be used to help identify members of the genera Neiseria and Pseudomonas and some species of Bacillus.

A potential side reaction of the respiratory chain in aerobic organisms is the incomplete reduction of oxygen to superoxide ion (O2-) and hydrogen peroxide (H2O2). These toxic oxygen products can damage the cells. Aerobes have neutralizing enzymes to deal with these products, including superoxide dismutase and catalase. One exception is the genus Streptococcus, which can grow well in oxygen yet lacks both cytochromes and catalase. The tolerance of these organisms to oxygen can be explained by the neutralizing effects of a special peroxidase. The lack of cytochromes, catalase and peroxidases in anaerobes as a rule limits their ability to process free oxygen and contributes to its toxic effects on them.

In the presence of oxygen, aerobic and facultative bacteria utilize molecular oxygen as a terminal electron acceptor. As a consequence of one-electron reduction steps from oxygen to water, the reactive oxygen species superoxide anion (O22) and hydrogen peroxide (H2O2) are formed. on (O22) and hydrogen peroxide (H2O2) are formed (6, 24). Moreover, in the Fenton reaction, free hydrogen peroxide readily reacts with available transition metals such as ferrous iron to form a more powerful and highly reactive oxidant, the hydroxyl radical (OH• ). Superoxide anion and hydrogen peroxide may also be generated by autoxidation of dehydrogenases, catechols, thiols, flavins, and oxidases and by UV radiation. Oxygen radicals are implicated in severe damage to membrane lipids, proteins, and DNA. In order to prevent this damage, microorganisms have developed efficient mechanisms to eliminate harmful oxygen by-products. Superoxide dismutase (SOD) eliminates toxic O22 by dismutation to H2O2 and O2, and the accumulation of toxic H2O2 is prevented by the action of catalases and peroxidases. See Smith

Anaerobic Respiration:

The terminal step in anaerobic respiration utilizes inorganic compounds rather than free oxygen as the final electron acceptor in electron transport. Of these, the nitrate (NO3-) and nitrite (NO2-) reduction systems are best known. The enzyme nitrate reducatase ctalyzes the removal of oxygen from nitrate, leaving nitrite and water as products. A test for this reaction is one of the test used in identifying bacteria.

It has been found that nitrate reducing bacteria in the mouth and gut can contribute to pulmonary and cardiovascular diseases in the host due to the overproduction of nitrate, nitrite, and other forms of nitrogen oxide, which damage blood vessels.

Denitrification: Some species of Pseudomonas adn Bacillus possess enzymes that can further reduce nitrate to nitric oxide (NO), nitrous oxide (N2O) and even nitrogen gase (N2) in a process called denitrification. It is a very important step in recycling nitrogen in the biosphere. (see next section).

In prokaryotes, enhanced respiratory flexibility allows the use of alternative electron acceptors, including nitrogen oxides, sulfate, and oxyanions, and contributes to their ability to colonize microaerobic or anaerobic environments. Denitrification is a respiratory process in which nitrate (NO3) and nitrite (NO2) are reduced into gaseous nitric oxide (NO), nitrous oxide (N2O), and nitrogen (N2) under oxygen-limited conditions. B. suis and B. melitensis possess the four reductases Nar (NO3 reductase), Nir (NO2 reductase), Nor (NO reductase), and Nos (N2O reductase) needed to catalyze the complete denitrification cascade. Denitrification can provide energy for bacterial metabolism in oxygen-poor and/or anaerobic environments, allowing pathogenic bacteria such as Brucella, Neisseria gonorrhoea and Mycobacterium bovis to persist within the host. Denitrification provides these bacteria with an additional defense mechanism against NO, produced by macrophages to kill invading microorganisms. See Kohler

Nitrogen Fixation of Some Bacteria:

Nitrogen fixation or the reduction of oxidized form of nitrogen into usable forms is the most energetically epxensive reaction to occur in any cell, requiring 16 ATP to make two molecules of NH3. This is due to the triple bond in N2.

Plants need ammonia (NH3) or nitrate (NO3-) to build amino acids, but most of the nitrogen in the atomosphere is in the form of gaseous nitrogen (N2). Plants lack the biochemical pathways (including the enzyme nitrogenase) necessary to cnvert N2 to NH3. Some bacteria have this capacity. Some nitrogen fixing bacteria such as Rhizbium fix nitrogen in exchange for carbohydrates from plants. Symboiotic relationships ahve evolved between some plant groups and bacteria that can fix atomospheric nitrogen into usable forms. Legumes for example can form root nodules which host hese bacteria in exchange for carbohydrates. This is important where the soil lacks nitrogen compounds.

Fermentation:

Fermentation is the incomplete oxidation of glucose or other carbohydrates in the absence of oxygen. This process uses organic compounds as the terminal electron acceptors and yields a small amount of ATP. It is used by organism that do not have an electron transport chain and thus cannot respire.

Bacteria that digest cellulose in the rumens of cattle are largely fermentative. After initially hdrolyzing cellulose to glucose, they ferment the glucose to organic acids, which are then absorbed as the bovine’s principal energy source.

Food, beverage -especially wine- and biofuel production industries:

Alcoholic beverages (wine, beer) are the most well known fermentation products. The products of alchoholic fermentation are not only ethanol but also CO2 which accounts for the bubbles in champagne and beer and the rising of bread dough. Other fermentation products are solvents (acetone, butanol), organic acids (lactic, acetic acids), dairy products and many other foods. Derivatives of proteins, nucleic acids and other organic compounds are fermented to produce vitamins, antibiotics and even hormones such as hydrocortisome.

–Saccharomyces cerevisiae: is the best studied eukaryote and a valuable tool for most aspects of basic research on eukaryotic organisms. This is due to its unicellular nature, which often simplifies matters, offering the combination of the facts that nearly all biological functions found in eukaryotes are also present and well conserved in S. cerevisiae. Moreover, unlike other model organisms, S. cerevisiae is concomitantly of great importance for various biotechnological applications, some of which date back to several thousands of years. S. cerevisiae‘s biotechnological usefulness resides in its unique biological characteristics, i.e., its fermentation capacity, accompanied by the production of alcohol and CO2. S. cerevisiae has been an essential component of human civilization because of its extensive use in food and beverage fermentation in which it has a high commercial significance. In regard to beverage industry, S. cerevisiae is involved in the production of many fermented beverages, such as wine, beer and cider; distilled beverages, such as rum, vodka, whisky, brandy, and sake; whereas in other alcoholic beverages worldwide, from fruits, honey, and tea, S. cerevisiae is also involved. The process of producing the fermentation bouquet is complex. It includes a significant number of biosynthetic pathways and genes and is affected by various parameters including the composition of the fermentation medium, the fermentation conditions and the inoculum used. The beans of the tropical plant Theobroma cacao are the basic raw material for the production of chocolate. However, raw cocoa beans are inedible, being bitter and astringent, while their aroma and flavours are not those of chocolate; thus, are subjected to fermentation to reduce the levels of polyphenols and alcaloids, causing the bitterness and astringency, and to develop flavours determining the fine organoleptics of cocoa and chocolate. To this end, after the cocoa rods are opened, cocoa beans covered by the acidic [high concentration of citric acid] and sugar-rich (10–15% sugars) cocoa pulp are exposed to the naturally existing wild microflora and left to undergo a spontaneous fermentation. See Parapouli

Human Muscle Cells:

Even human muscle cells can undergo a form of fermentation that permits short periods of activity after the oxygen supply in the muscle has been exhausted. Muscle cells convert pyruvic acid into lactic acid, which allows anaerobic production of ATP to proceed for a time.But this cannot go on indefinitely, and after a fe minutes, the accumulated lactic acid causes muscle fatigue.

Generally a high serum lactate level indicates poor organ function. Serum lactate levels are frequently requested during infection, especially in cases of suspected sepsis, because they can indicate the severity of the infection and the body’s response to it. Elevated lactate levels suggest that the body is not getting enough oxygen, which can happen due to various factors like tissue hypoperfusion (reduced blood flow to tissues) or cellular dysfunction, both of which are common in severe infections.

Human Gut Microbiota:

The adult human gut microbiota consists of at least as many bacterial cells as our total number of somatic and germ cells3 and their collective genomes (microbiome) contain more than 500-fold more genes than our human genome. Comparative metagenomics has revealed that, compared with the microbiome of patients with type 2 diabetes, a healthy microbiome is frequently associated with an increased microbial diversity and an increased abundance of butyrate-producing bacteria, such as Faecalibacterium prausnitzii.

Human gut microorganisms do not act in isolation but form complex ecological interactions that are important for intestinal homeostasis. One key attribute of the gut microbiota is the fermentation of carbohydrates to short-chain fatty acids (SCFAs), including butyrate, which is associated with several host benefits.

Fermentation is the major energy-generating process utilized by gut microorganisms, and the removal of fermentation electron sink by-products such as lactate and hydrogen is essential to maintain fermentative processes.

Requirement for Iron:

Iron is an essential nutrient for most bacteria and is often growth-limiting during infection, due to the host sequestering free iron as part of the innate immune response. To obtain the iron required for growth, many bacterial pathogens encode transporters capable of extracting the iron-containing cofactor heme directly from host proteins. See Grinter

Transporter Proteins Required:

–ChuA: Pathogenic E. coli and Shigella spp. produce the outer membrane transporter ChuA, which binds host hemoglobin and extracts its heme cofactor, before importing heme into the cell. Heme extraction by ChuA is a dynamic process, with the transporter capable of rapidly extracting heme from hemoglobin in the absence of an external energy source, without forming a stable ChuA-hemoglobin complex. See Grinter

Grinter utilised artificial intelligence-based protein design to create binders capable of inhibiting E. coli growth by blocking hemoglobin binding to ChuA. By screening a limited number of these designs, we identify several binders that inhibit E. coli growth at low nanomolar concentrations, without experimental optimisation. See Grinter