Catabolism of Organic Compounds

Transcription

1 LECTURE PRESENTATIONS For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark Chapter 14 Lectures by John Zamora Middle Tennessee State University Catabolism of Organic Compounds 2012 Pearson Education, Inc. I. Fermentation 14.1 Energetic and Redox Considerations 14.2 Lactic and Mixed-Acid Fermentations 14.3 Clostridial and Propionic Acid Fermentations 14.4 Fermentations Lacking Substrate-Level Phosphorylation 14.5 Syntrophy 1

2 14.1 Energetic and Redox Considerations Two mechanisms for catabolism of organic compounds: Respiration Exogenous electron acceptors are present to accept electrons generated from the oxidation of electron donors Fermentation Electron donor and acceptor are the same compound Relatively little energy yield 14.1 Energetic and Redox Considerations In the absence of external electron acceptors, organic compounds can be catabolized anaerobically only by fermentation (Figure 14.1) ATP is usually synthesized by substrate-level phosphorylation Energy-rich phosphate bonds from phosphorylated organic intermediates transferred to ADP Redox balance is achieved by production of fermentation products 2

3 Figure 14.1 The essentials of fermentation 14.2 Lactic and Mixed-Acid Fermentations Fermentations are classified by either the substrate fermented or the products formed A wide variety of organic compounds can be fermented Lactic acid bacteria produce lactic acid Lactic acid fermentation can occur by homofermentative and heterofermentative pathways 3

4 14.2 Lactic and Mixed-Acid Fermentations 14.2 Lactic and Mixed-Acid Fermentations Mixed-acid fermentations Generate acids Acetic, lactic, and succinic Sometimes also generate neutral products Example: butanediol Characteristic of enteric bacteria 4

5 14.3 Clostridial and Propionic Acid Fermentations Clostridium species ferment sugars, producing butyric acid Butanol and acetone can also be by-products 14.3 Clostridial and Propionic Acid Fermentations Some Clostridium species ferment amino acids using a complex biochemical pathway known as the Strickland reaction 5

6 14.3 Clostridial 3 Pyruvate and Propionic Acid Fermentations 2 Oxalacetate Acetate CO 2 Secondary fermentation The fermentation of fermentation products 2 Malate CoA transfer Fermentation of ethanol plus acetate by Clostridium kluyveri 2 Propionate 2 Fumarate Propionic acid fermentation Propionibacterium and related 2 prokaryotes Propionyl CoA produce 2 Succinate propionic acid as a major fermentation product 2 Succinyl CoA 2 Methylmalonyl CoA Overall: 3 Lactate 2 propionate acetate CO 2 H 2 O G kj (3 ATP) 14.4 Fermentations Lacking Substrate- Level Phosphorylation Fermentations of certain compounds do not yield sufficient energy to synthesize ATP Catabolism of the compound can then be linked to ion pumps that establish a proton or sodium motive force Propionigenium modestum catabolizes succinate under strictly anoxic conditions Establishes a sodium motive force Sodium motive force forms ATP 6

7 14.4 Fermentations Lacking Substrate-Level Phosphorylation Oxalobacter formigenes catabolizes oxalate and produces formate Formate is excreted from the cell Export of formate from the cell establishes a proton motive force Proton motive force forms ATP 14.5 Syntrophy Syntrophy A process whereby two or more microbes cooperate to degrade a substance neither can degrade alone Most syntrophic reactions are secondary fermentations Most reactions are based on interspecies hydrogen transfer H 2 production by one partner is linked to H 2 consumption by the other Syntrophic reactions are important for the anoxic portion of the carbon cycle 7

8 Figure 14.9 Syntrophy: Interspecies H 2 transfer. Ethanol fermentation: G kj/reaction Methanogenesis: G kj/reaction Coupled reaction: Reactions G kj/reaction Ethanol fermenter Methanogen 2 Ethanol Interspecies hydrogen transfer 2 Acetate Syntrophic transfer of H Syntrophy Syntrophy (cont d) H 2 consumption affects the energetics of the reaction carried out by the H 2 producer, allowing the reaction to be exothermic 8

9 II. Anaerobic Respiration 14.6 Anaerobic Respiration: General Principles 14.7 Nitrate Reduction and Denitrification 14.8 Sulfate and Sulfur Reduction 14.9 Acetogenesis Methanogenesis Proton Reduction Other Electron Acceptors Anoxic Hydrocarbon Oxidation Linked to Anaerobic Respiration 14.6 Anaerobic Respiration: General Principles In anaerobic respiration, electron acceptors other than O 2 are used Anaerobic and aerobic respiratory systems are similar But anaerobic respiration yields less energy than aerobic respiration Energy released from redox reactions can be determined by comparing reduction potentials Animation: Electron Transport: Aerobic & Anaerobic Conditions 2012 Pearson Education, Inc. Marmara University Enve303 Env. Eng. Microbiology Prof. BARIŞ ÇALLI 9

10 14.6 Anaerobic Respiration: General Principles In the assimilative metabolism of an inorganic compound (e.g., NO 3, SO 4 2, CO 2 ) the reduced compounds are used in biosynthesis During anaerobic respiration, the reduction of inorganic compounds is called dissimilative metabolism because the reduced products are excreted 14.7 Nitrate Reduction and Denitrification Inorganic nitrogen compounds are the most common electron acceptors in anaerobic respiration All products of nitrate reduction (denitrification) are gaseous (Figure 14.12) Denitrification is the main biological source of gaseous N 2 10

11 Figure Steps in the dissimilative reduction of nitrate Nitrate Nitrite NO 3 Nitrate reductase NO 2 Nitrate reduction (Escherichia coli) Nitrite reductase Nitric oxide NO Nitric oxide reductase Denitrification (Pseudomonas stutzeri) Gases Nitrous oxide N 2 O Nitrous oxide reductase Dinitrogen N Nitrate Reduction and Denitrification The biochemical pathway for dissimilative nitrate reduction has been well studied Enzymes of the pathway are repressed by oxygen 11

12 14.8 Sulfate and Sulfur Reduction Inorganic sulfur compounds can be used as electron acceptors in anaerobic respiration Reduction of SO 4 2 to H 2 S proceeds through several intermediates and requires activation of sulfate by ATP Sulfate and Sulfur Reduction 12

13 14.8 Sulfate and Sulfur Reduction Many different compounds can serve as electron donors in sulfate reduction Examples: H 2, organic compounds, phosphite 4H 2 + SO H + HS - + 4H 2 O G 0 = -152 kj CH 3 COO - + SO H + CO 2 + H 2 S + 2H 2 O G 0 = kj 4HPO 3 + SO H + 4HPO HS - G 0 = -364 kj 14.9 Acetogenesis Acetogens and methanogens use CO 2 as an electron acceptor in anaerobic respiration H 2 is the major electron donor for both groups of organisms (Figure 14.16) Acetogens carry out the reaction 4H 2 + H + + 2HCO 3 - CH 3 COO - + 4H 2 O G 0 = -105 kj 13

14 Figure The contrasting processes of methanogenesis and acetogenesis Methanogenesis ( G kj) Proton or sodium motive force (plus substrate-level phosphorylation for acetogens) Acetogenesis ( G kj) Methanogenesis Methanogenesis Biological production of methane Carried out by a group of strictly anaerobic Archaea called the methanogens Involves a complex series of biochemical reactions that use novel coenzymes 14

15 14.10 Methanogenesis The autofluorescence of coenzyme F 420 can be used to identify methanogens microscopically (Figure 14.19) Methanosarcina barkeri Methanobacterium formicicum Figure Fluorescence due to the methanogenic coenzyme F 420. The organisms were made visible by excitation with blue light in a fluorescence microscope Methanogenesis H 2 is the major electron donor for methanogenesis (Figure 14.20) Additional electron donors exist Examples: formate, CO, organic compounds 15

16 14.11 Proton Reduction Pyrococcus furiosus Member of the Archaea Grows optimally at 100 C on sugars and small peptides as electron donors May have the simplest anaerobic respiration mechanism (Figure 14.23) Organism uses modified glycolysis and protons in anaerobic respiration linked to ATPase activity Other Electron Acceptors Fe 3+, Mn 4+, ClO 3, and various organic compounds can serve as electron acceptors for bacteria (Figure 14.24) Fe 3+ is abundant in nature and its reduction is a major form of anaerobic respiration 16

17 Figure Some alternative electron acceptors for anaerobic respirations Couple Reaction E 0 Fumarate/ Succinate 0.03 Trimethylamine-N-oxide (TMAO)/ Trimethylamine (TMA) 0.13 Arsenate/ Arsenite 0.14 Dimethyl sulfoxide (DMSO)/ Dimethyl sulfide (DMS) 0.16 Ferric ion/ Ferrous ion 0.20 Selenate/ Selenite 0.48 Manganic ion/ Manganous ion 0.80 Chlorate/ Chloride Other Electron Acceptors The reduction of arsenate has been employed for cleanup of toxic wastes and groundwater (Figure 14.25) Halogenated compounds can also serve as electron acceptors via a process called reductive dechlorination (dehalorespiration) 17

18 Figure Biomineralization during arsenate reduction by the sulfate-reducing bacterium Desulfotomaculum auripigmentum Desulfotomaculum can reduce AsO 4 3- to AsO 3 3-, along with sulfate (SO 4 2- ) to sulfide (HS - ) Appearance of culture bottle after inoculation Synthetic sample of As 2 S 3 Following growth for 2 weeks and biomineralization of arsenic trisulfide, As 2 S Anoxic Hydrocarbon Oxidation Aliphatic and aromatic hydrocarbons and organic compounds containing only carbon and hydrogen can be oxidized anaerobically The first step in degradation is the addition of oxygen to the molecule through the incorporation of fumarate Hydrocarbons are oxidized to intermediates that can be catabolized via the citric acid cycle 18

19 14.13 Anoxic Hydrocarbon Oxidation Aliphatic hydrocarbons are straight-chain saturated or unsaturated compounds Many of them are substrates for denitrifying and sulfate-reducing bacteria Aromatic hydrocarbons are catabolized by ring reduction and cleavage Can be degraded by some denitrifying, ferric iron-reducing, and sulfate-reducing bacteria Anoxic Hydrocarbon Oxidation Methane The simplest hydrocarbon Can be oxidized under anoxic conditions by a consortia containing sulfate-reducing bacteria and methanotrophic archaea CH 4 + SO H + CO 2 + HS - + 2H 2 O G 0 = -18 kj 19

20 Figure Anoxic methane oxidation Methanotrophic Archaea (ANME-types) Sulfate-reducing Bacteria Organic compounds Mechanism for cooperative degradation of CH 4. An organic compound or some other carrier of reducing power transfers electrons from methanotroph to SRB. III. Aerobic Chemoorganotrophic Processes Molecular Oxygen as a Reactant and Aerobic Hydrocarbon Oxidation Methylotrophy and Methanotrophy Sugar and Polysaccharide Metabolism Organic Acid Metabolism Lipid Metabolism 20

21 14.14 Oxygen as a Reactant and Hydrocarbon Oxidation Oxygen used as a direct reactant in certain biochemical reactions Oxygenases Enzymes that catalyze the incorporation of atoms of oxygen from O 2 into organic compounds Two classes: Monooxygenases: incorporate one oxygen atom Dioxygenases: incorporate both oxygen atoms Oxygen as a Reactant and Hydrocarbon Oxidation Many microbes can use aliphatic and aromatic hydrocarbons as electron donors when growing aerobically Oxygenases are central enzymes in these biochemical reactions Aerobic degradation of aromatic compounds involves ring oxidation 21

22 14.15 Methylotrophy and Methanotrophy Methylotrophs use compounds that lack C C bonds as electron donors and carbon sources Methanotrophs are methylotrophs that use CH 4 The initial step in methanotrophy requires methane monooxygenase (MMO) In the MMO reaction, CH 4 is converted to CH 3 OH and H 2 O Other oxidation steps convert CH 3 OH to CO 2 The steps in CH 4 oxidation to CO 2 CH 4 CH 3 OH CH 2 O HCOO - CO Sugar and Polysaccharide Metabolism Sugars and polysaccharides are common substrates for chemoorganotrophs Polysaccharides such as cellulose and starch are common in nature Their breakdown yields hexoses and pentoses Starch is fairly soluble and readily degraded by many fungi and bacteria employing amylases 22

23 14.16 Sugar and Polysaccharide Metabolism Cellulose is fairly insoluble and its degradation typically involves attachment of microbes to cellulose fibrils and production of cellulases (Figure 14.34) Cellulose degradation is restricted to relatively few bacteria groups, including the gliding bacteria Sporocytophaga and Cytophaga (Figure 14.35) Figure Cellulose digestion. Cellulose fiber Bacteria Transmission electron micrograph showing attachment of the cellulosedigesting bacterium Sporocytophaga myxococcoides to cellulose fibers. 23

24 Figure Cytophaga hutchinsonii colonies on a cellulose agar plate Cellulose digestion Areas where cellulose has been hydrolyzed are more translucent Sugar and Polysaccharide Metabolism Pentoses are required for the synthesis of nucleic acids If pentoses are not readily available from the environment, organisms must synthesize them The major pathway for pentose production is the pentose phosphate pathway 24

25 14.17 Organic Acid Metabolism Organic acids can be metabolized as electron donors and carbon sources by many microbes C 4 C 6 citric acid cycle intermediates (e.g., citrate, malate, fumarate, and succinate) are common natural plant and fermentation products and can be readily catabolized through the citric acid cycle alone Catabolism of C 2 and C 3 organic acids typically involves production of oxalacetate through the glyoxylate cycle Lipid Metabolism Lipids are abundant in nature and readily degraded by many microbes Catabolism of fats is initiated by hydrolysis of the ester bond, yielding fatty acids and glycerol, by extracellular lipases (Figure 14.41) Phospholipases are a class of lipases that attack phospholipids Fatty acids are oxidized by beta-oxidation to acetyl-coa, which is then oxidized to CO 2 by citric acid cycle 25

26 Figure Lipases Glycerol Fatty acid Fatty acid Fatty acid Activity of lipases on a fat Lipase Fatty acid Fatty acid Phospholipase B Phospholipase A Phospholipase C Phospholipase activity on phospholipid Phospholipase D 26