Metabolic pathways in bacteria

The study of sulfide metabolism at hydrothermal vents dictated the development of methods that could process hundreds of samples which contain complex mixtures of sulfur compounds in a variety of blood, seawater and tissues samples. In addition, we needed the capability of using "S-radiolabeled compounds for the tracing of complex sulfur metabolic pathways in bacteria and animal compartments of the different hydrothermal vent symbioses. In some instances, in situ sampling by submersibles at depths of 2500 meters with associated recovery times of two hours necessitated the remote derivatization of samples at depth prior to recovery. None of the above methods completely met our needs. We have adapted the bimane-HPLC method (24.351 for shipboard use and have found it a particularly robust method for studying a number of questions concerning the role of reduced sulfur compounds in the marine environment. 

Stanier, R.Y. 1968. Biochemical and immunological studies on the evolution of a metabolic pathway in bacteria pp. 201-225. In Chemotaxonomy and Serotaxonomy (Ed. J.G. Hawkes). Systematics Association Special Vol. 2. Academic Press, London. 

Biochemical reactions. Biochemical reactions, often referred to as fermentations, can be divided into two broad types. In the first type, the reaction exploits the metabolic pathways in selected microorganisms (especially bacteria,... 

Ormerod, J.G., Gest, H. 1962. IV. Hydrogen photosynthesis and alternative metabolic pathways in photosynthetic bacteria. Bacteriol Rev 26 51-66. 

An attractive hypothesis is the independent evolution in bacteria of their diffusible individualites and the currently recognized secondary metabolic pathways, in parallel with their surface components and their biosynthesis. An indicator for this would be the use of the same gene pool. The theory would include all substances that play a role in the build-up of glycan and other modified surface layers, lipids, murein, (glyco-) proteins (e.g., S-layers), polysaccharides, teichoic... 

Probably the most common and widespread control mechanisms in cells are allosteric inhibition and allosteric activation. These mechanisms are incorporated into metabolic pathways in many ways, the most frequent being feedback inhibition. This occurs when an end product of a metabolic sequence accumulates and turns off one or more enzymes needed for its own formation. It is often the first enzyme unique to the specific biosynthetic pathway for the product that is inhibited. When a cell makes two or more isoenzymes, only one of them may be inhibited by a particular product. For example, in Fig. 11-1 product P inhibits just one of the two isoenzymes that catalyzes conversion of A to B the other is controlled by an enzyme modification reaction. In bacteria such as E. coli, three isoenzymes, which are labeled I, II, and III in Fig. 11-3, convert aspartate to (3-aspartyl phosphate, the precursor to the end products threonine, isoleucine, methionine, and lysine. Each product inhibits only one of the isoenzymes as shown in the figure. 

The thermodynamic yield of the various anaerobic pathways is related to their affinity for substrates. Sulfate-reducing bacteria outcompete methanogens by maintaining H2 concentrations below the threshold for the process to be thermodynamically feasible (Lovley et al., 1982), and Fe(III) reducers do the same to SOU reducers. In fact, the equilibrium concentration of H2 can be used to predict the dominant metabolic pathways in a given environment (Lovley and Goodwin, 1988 Lovley et al., 1994a). 

The acidogenic and solventogenic metabolic pathways in Clostridia have been detailed (41). Clostridial bacteria can also ferment other cheaper alternative biomass such as, lignocellulosic materials due to their saccharolytic ability (42). There, an acidic or enz5miatic hydrolysis of lignocellulosic materials is necessary to convert them into monosaccharides before they can be used as substrates in the... 

The subsequent induction of enzymes which belong to one metabolic pathway by the products of preceding enzymes (sequential gene expression), is a characteristic of catabolic pathways in bacteria. Although sequential formation of secondary products and secondary metabolic enzymes in many plants and microorganisms has been observed the direct influence of secondary products on the expression of enzymes catalyzing their further transformation has been demonstrated in very few organisms. 

The importance of terpenoids to life is highlighted by the fact that two separate pathways have been found to produce the terpenoid precursor C5 units isopentenyl diphosphate (IDP) and dimethylaUyl diphosphate (DMADP). The mevalonic acid (MVA) pathway is functional in archae, animals and fungi, 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway is found in green algae, and terpenoids are produced by both pathways in bacteria and plants [2]. In plants the MVA pathway is active in the cytosol and it provides C5 units for sesquiterpene, triterpene and polyterpene biosynthesis whereas the MEP pathway occurs in plastids and produces C5 units for isoprene, monoterpenes, diterpenes and carotenoids [1]. Recent reports have indicated metabolic crosstalk between biosynthesis pathways and e.g., the homoterpene DMNT may originate from both pathways. 

Lipid A is a category of complex hexa-acylated disaccharide of glucosamine in bacteria. The existence of Lipid A metabolism pathway in plants was demonstrated by LC-MS [28], The structure of the Lipid A-related compounds is confirmed by product-ion analysis utilizing QqTOF-MS [28]. 

Shirai, X, Nakato, A, Izutani, N, Nagahisa, K. et al (2005) Comparative study of flux redistribution of metabolic pathway in glutamate production by two coryneform bacteria. Metah. Eng., 7, 59-69,... 

Over 100 different monomers have been found to be included in bacterial PHAs and the metabolic pathways involved in the synthesis of a variety of these pathways have been elucidated by research scientists. Through bioengineering, it is possible to modify plant cells to incorporate PHA metabolic pathways from bacteria. 

Different pathways are available in nature for metabolism of arabinose and xylose which are converted to xylulose 5-phosphate (intermediate com-poimd) to enter the pentose phosphate pathway as shown in Figure 10.5. In yeasts, xylose is first reduced by xylose reductase to xylitol, which in turn is oxidized to xylulose by xylitol dehydrogenase. In bacteria and some anaerobic fungi, xylose isomerase is responsible for direct conversion of xylose to xylulose. Xylulose is finally phosphorylated to xylulose-5-phos-phate by xylulokinase. In fungi, L-arabinose is reduced to L-arabitol (by arabinose reductase), L-xylulose (by arabitol dehydrogenase), xylitol (by L-xylulose reductase). Xylitol is finally converted to xylulose (by xylitol dehydrogenase), whose activity is also part of xylose utilization pathways. In bacteria, L-arabinose is converted to L-ribulose (by L-arabinose isomerase), L-ribulose-5-P (by L-ribulokinase) and finally D-xylulose-5-P (by L-ribulose-5-P 4-epimerase) (Bettiga et al., 2008). 

Such complexes include fatty acid synthases (FASes), elongases (ELSes) and polyketide synthases (PKSes) which can fimction individually or in concert. FAS synthesizes the 16 and 18 carbon acyl chains of membrane lipids as well as those of the plant cutin and suberin monomers. ELSes use these acyl chains as primers to synthesize longer ones for storage lipids in some seeds and for cuticular and epicuticular waxes. PKSes participate in a wide range of secondary metabolic pathways. In plants chalcone synthase contributes to the carbon skeleton of the flavonoids, in fungi and bacteria, especially... 

Sato T, Atomi H (2011) Novel metabolic pathways in Archaea. Curr Opin Microbiol 14 307-314 Schneider J, Wendisch VF (2011) Biotechnological production of polyamines by bacteria recent achievements and future perspectives. Appl Microbiol Biotechnol 91 17-30 Stetter KO (1996) Hypeithermophilic procaryotes. FEMS Microbiol Rev 18 149-158 Tabor CW, Tabor H (1985) Polyamines in microorganisms. Microbiol Rev 49 81-99 Terui Y, Ohnuma M, Hiraga K, Kawashima E, Oshima T (2005) Stabilization of nucleic acids by unusual polyamines produced by an extreme thermophUe, Thermus thetmophilus. Biochem J 388 427 33... 

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