Download Catabolism of Organic Compounds Chapter 14

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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
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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
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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
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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
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Figure 14.1 The essentials of fermentation
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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
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14.2 Lactic and Mixed-Acid Fermentations
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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
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14.3 Clostridial and Propionic Acid
Fermentations
• Clostridium species ferment sugars,
producing butyric acid
– Butanol and acetone can also be by-products
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14.3 Clostridial and Propionic Acid
Fermentations
• Some Clostridium species ferment amino acids
using a complex biochemical pathway known as
the Strickland reaction
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3 Lactate
14.3 Clostridial3 Pyruvate
and Propionic Acid
Fermentations Acetate  CO2
2 Oxalacetate
• 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
Propionyl CoA
– Propionibacterium and related 2prokaryotes
2 Succinate
produce
propionic acid as a major
fermentation2 Succinyl
productCoA
2 Methylmalonyl CoA
Overall: 3 Lactate  2 propionate  acetate  CO2  H2O
 G0  171 kJ
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(3 ATP)
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14.4 Fermentations Lacking SubstrateLevel 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
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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
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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
– H2 production by one partner is linked to H2
consumption by the other
• Syntrophic reactions are important for the anoxic
portion of the carbon cycle
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Figure 14.9 Syntrophy: Interspecies H2 transfer.
Ethanol fermentation:
 G0  19.4 kJ/reaction
Methanogenesis:
 G0  130.7 kJ/reaction
Coupled reaction:
 G0  111.3 kJ/reaction
Reactions
Methanogen
Ethanol fermenter
2 Ethanol
Interspecies hydrogen transfer
2 Acetate
Syntrophic transfer of H2
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14.5 Syntrophy
• Syntrophy (cont’d)
– H2 consumption affects the energetics of the
reaction carried out by the H2 producer,
allowing the reaction to be exothermic
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II. Anaerobic Respiration
•
•
•
•
•
•
•
•
14.6 Anaerobic Respiration: General Principles
14.7 Nitrate Reduction and Denitrification
14.8 Sulfate and Sulfur Reduction
14.9 Acetogenesis
14.10 Methanogenesis
14.11 Proton Reduction
14.12 Other Electron Acceptors
14.13 Anoxic Hydrocarbon Oxidation Linked to
Anaerobic Respiration
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14.6 Anaerobic Respiration: General
Principles
• In anaerobic respiration, electron acceptors
other than O2 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
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14.6 Anaerobic Respiration: General
Principles
• In the assimilative metabolism of an inorganic
compound (e.g., NO3, SO42, CO2) 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
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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 N2
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Figure 14.12 Steps in the dissimilative reduction of nitrate
Nitrate
NO3
Nitrate reductase
Nitrite
Nitrate
reduction
(Escherichia
coli)
NO2
Nitrite reductase
Denitrification
Nitric oxide NO
Nitric oxide reductase
Gases
(Pseudomonas
stutzeri)
Nitrous oxide N2O
Nitrous oxide reductase
Dinitrogen N2
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14.7 Nitrate Reduction and Denitrification
• The biochemical pathway for dissimilative
nitrate reduction has been well studied
• Enzymes of the pathway are repressed by
oxygen
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14.8 Sulfate and Sulfur Reduction
• Inorganic sulfur compounds can be used as
electron acceptors in anaerobic respiration
• Reduction of SO42 to H2S proceeds through
several intermediates and requires activation
of sulfate by ATP.
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14.8 Sulfate and Sulfur Reduction
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14.8 Sulfate and Sulfur Reduction
• Many different compounds can serve as electron
donors in sulfate reduction
– Examples: H2, organic compounds, phosphite
4H2 + SO42- + H+HS- + 4H2O
∆G0’ = -152 kJ
CH3COO- + SO42- + 3H+CO2 + H2S + 2H2O
∆G0’ = -57.5 kJ
4HPO3+ SO42- + H+4HPO42- + HS- ∆G0’ = -364 kJ
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14.9 Acetogenesis
• Acetogens and methanogens use CO2 as an
electron acceptor in anaerobic respiration
– H2 is the major electron donor for both groups of
organisms (Figure 14.16)
• Acetogens carry out the reaction
4H2 + H+ + 2HCO3-CH3COO- + 4H2O ∆G0’ = -105 kJ
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Figure 14.16 The contrasting processes of methanogenesis and acetogenesis
Methanogenesis
Proton or sodium
motive force (plus
substrate-level
phosphorylation for
acetogens)
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Acetogenesis
( G0  105 kJ)
( G0  136 kJ)
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14.10 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
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14.10 Methanogenesis
• The autofluorescence of coenzyme F420 can
be used to identify methanogens
microscopically (Figure 14.19)
Methanosarcina barkeri
Methanobacterium formicicum
Figure 14.19 Fluorescence due to the methanogenic coenzyme F420 . The organisms
were made visible by excitation with blue light in a fluorescence microscope
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14.10 Methanogenesis
• H2 is the major electron donor for
methanogenesis (Figure 14.20)
• Additional electron donors exist
– Examples: formate, CO, organic compounds
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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
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14.12 Other Electron Acceptors
• Fe3+, Mn4+, ClO3, and various organic
compounds can serve as electron acceptors for
bacteria (Figure 14.24)
• Fe3+ is abundant in nature and its reduction is a
major form of anaerobic respiration
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Figure 14.24 Some alternative electron acceptors for anaerobic respirations
Couple
Reaction
E0
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
1.00
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14.12 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)
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Figure 14.25 Biomineralization during arsenate reduction by the sulfate-reducing bacterium
Desulfotomaculum auripigmentum
Desulfotomaculum can reduce AsO43- to AsO33-, along with sulfate
(SO42-) to sulfide (HS-)
Appearance of
culture bottle after
inoculation
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Synthetic sample
of As2S3
Following growth for 2 weeks
and biomineralization of
arsenic trisulfide, As2S3
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14.13 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
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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
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14.13 Anoxic Hydrocarbon Oxidation
• Methane
– The simplest hydrocarbon
– Can be oxidized under anoxic conditions by a
consortia containing sulfate-reducing bacteria
and methanotrophic archaea
CH4 + SO42- + H+  CO2 + HS- + 2H2O ∆G0’ = -18 kJ
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Figure 14.28 Anoxic methane oxidation
Methanotrophic Archaea
(ANME-types)
Sulfate-reducing Bacteria
Organic
compounds
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Mechanism for cooperative
degradation of CH4.
An organic compound or
some other carrier of reducing
power transfers electrons
from methanotroph to SRB.
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III. Aerobic Chemoorganotrophic
Processes
• 14.14 Molecular Oxygen as a Reactant and
Aerobic Hydrocarbon Oxidation
• 14.15 Methylotrophy and Methanotrophy
• 14.16 Sugar and Polysaccharide Metabolism
• 14.17 Organic Acid Metabolism
• 14.18 Lipid Metabolism
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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 O2 into organic compounds
– Two classes:
• Monooxygenases: incorporate one oxygen atom
• Dioxygenases: incorporate both oxygen atoms
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14.14 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
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14.15 Methylotrophy and Methanotrophy
• Methylotrophs use compounds that lack C–C
bonds as electron donors and carbon sources
• Methanotrophs are methylotrophs that use CH4
– The initial step in methanotrophy requires
methane monooxygenase (MMO)
– In the MMO reaction, CH4 is converted to CH3OH
and H2O
– Other oxidation steps convert CH3OH to CO2
– The steps in CH4 oxidation to CO2
CH4CH3OH CH2O HCOO-CO2
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14.16 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
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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)
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Figure 14.34 Cellulose digestion.
Cellulose
fiber
Bacteria
Transmission electron micrograph showing attachment of the cellulosedigesting bacterium Sporocytophaga myxococcoides to cellulose fibers.
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Figure 14.35 Cytophaga hutchinsonii colonies on a cellulose–agar plate
Cellulose
digestion
Areas where cellulose has been hydrolyzed are more translucent
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14.17 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
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14.17 Organic Acid Metabolism
• Organic acids can be metabolized as electron
donors and carbon sources by many
microbes
• C4–C6 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 C2 and C3 organic acids
typically involves production of oxalacetate
through the glyoxylate cycle
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14.18 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 CO2 by
citric acid cycle
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Figure 14.41 Lipases
Glycerol
Fatty acid
Fatty acid
Activity of lipases on a fat
Fatty acid
Lipase
Phospholipase B
Fatty acid
Fatty acid
Phospholipase A
Phospholipase C
Phospholipase
activity on
phospholipid
Phospholipase D
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