Chapter 21

Metabolic Diversity: Catabolism of Organic Compounds

I. Fermentations

21.1 Fermentations: Energetic and Redox

Considerations

21.2 Fermentative Diversity: Lactic and Mixed-Acid

Fermentations

21.3 Fermentative Diversity: Clostridial and Propionic

Acid Fermentations

21.4 Fermentations without Substrate-Level

Phosphorylation

21.5 Syntrophy

21.1 Fermentations: 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

- Aerobic and anaerobic respiration

Fermentation

Electron donor and acceptor are the same compound

Relatively little energy yield

In the absence of external electron acceptors, compounds

can be catabolized anaerobically by fermentation

ATP is usually synthesized by substrate-level

phosphorylation

Energy-rich phosphate bonds from phosphorylated organic

intermediates transferred directly to ADP

Redox balance is achieved by production and secretion of

fermentation products

The Essentials of Fermentation

Figure 21.1

A requirement for most fermentations is that organic

intermediates can be generated that contain an

energy-rich phosphate bond or a molecule of

coenzyme-A

Energy-Rich Compounds Involved in SLP

Anaerobic Breakdown of Major Fermentable Substrates

Figure 21.2

In many fermentations, redox balance is maintained by

the production of molecular hydrogen (H2)

H2 production involves

transfer of electrons from

ferredoxin to H+ by

a hydrogenase

Pyruvate-ferredoxin oxidoreductase

21.2 Lactic and Mixed-Acid Fermentations

Fermentations are classified by either the substrate

fermented or the productions formed

A wide variety of organic compounds can be fermented

Common Bacterial Fermentations

Some Unusual Bacterial Fermentations

Lactic Acid Fermentations

Lactic acid fermentation can occur by

homofermentative and heterofermentative pathways

Glucose Fermentation by Homofermentations

Figure 21.4

Glucose Fermentation by Heterofermentations

Figure 21.4

The Entner-Doudoroff Pathway

A variant of the glycolytic pathway (e.g. Pseudomonas)

A widespread pathway for sugar catabolism in bacteria

Entner-Doudoroff Pathway

Mixed-Acid Fermentations

Mixed-Acid Fermentations

Generate acids

Acetic, lactic, and succinic acids

Sometimes also generate neutral products

e.g., butanediol

Characteristic of enteric bacteria

Butanediol Production in Mixed-Acid Fermentations

Figure 21.5

21.3 Clostridial and Propionic Acid Fermentations

Clostridium species ferment sugars, producing

butyric acid

Butanol and acetone can also be byproducts

The Butyric Acid and Butanol/Acetone Fermentation

Figure 21.6

Some Clostridium species ferment amino acids using a

complex biochemical pathway known as the Stickland

reaction

The Stickland Reaction

Figure 21.7

Secondary Fermentations

Secondary Fermentation

The fermentation of fermentation products

C. kluyveri

- Ethanol + Acetate → Caproate + Butyrate

Propionibacterium

- Lactate → Propionate + Acetate

The Propionic Acid Fermentation of Propionibacterium

Figure 21.8

21.4 Non-Substrate-Level Phosphorylation Fermentations

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

Succinate Fermentation by Propionigenium modestum

Figure 21.9a

Oxalate Fermentation by Oxalobacter formigenes

Figure 21.9b

21.5 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

Syntrophy: Interspecies H2 Transfer

Figure 21.10

H2 consumption affects the energetics of the reaction carried out by the H2 producer, allowing the reaction to be exothermic.

Figure 21.10

Energetics of Growth of Syntrophomonas

Figure 21.11a

Energetics of Growth of Syntrophomonas

Figure 21.11b

Disproportionation of crotonate

(anaerobic respiration with crotonate as an electron acceptor)

II. Anaerobic Respiration

21.6 Anaerobic Respiration: General Principles

21.7 Nitrate Reduction and Denitrification

21.8 Sulfate and Sulfur Reduction

21.9 Acetogenesis

21.10 Methanogenesis

21.11 Proton Reduction

21.12 Other Electron Acceptors

21.13 Anoxic Hydrocarbon Oxidation Linked to Anaerobic

Respiration

21.6 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 of each electron

acceptor

Major Forms of Anaerobic Respiration

Figure 21.12

■ Assimilative metabolism of an inorganic compound

(e.g., NO3-, SO4

2-, CO2)

- The reduced compounds are used in biosynthesis

■ Dissimilative metabolism of inorganic compounds

- During anaerobic respiration, the reduced products

are excreted

21.7 Nitrate Reduction and Denitrification

Inorganic nitrogen compounds are the most common

electron acceptors in anaerobic respiration

Most products of nitrate reduction (denitrification)

are gaseous (NO, N2O or N2)

- Some are NO2- and NH4

+

Denitrification is the main biological source of

gaseous N2

Steps in the Dissimilative Reduction of Nitrate

Figure 21.13

The biochemical pathway for dissimilative nitrate

reduction has been well-studied

Enzymes of the pathway are repressed by oxygen

Respiration and Anaerobic Respiration (E. coli)

Figure 21.14a

Respiration and Anaerobic Respiration (P. stutzeri)

Figure 21.14c

Periplasmic proteins

21.8 Sulfate and Sulfur Reduction

Several inorganic sulfur compounds can be used as electron acceptors in anaerobic respiration

The reduction of SO42- to

H2S proceeds through

several intermediates and

requires activation of

sulfate by ATP

Activated sulfates

Schemes of Assimilative and Dissimilative Sulfate Reduction

Figure 21.15b

Many different compounds can serve as electron

donors in sulfate reduction

e.g., H2, organic compounds, phosphite

Electron Transport and Energy Conservation during Sulfate Reduction

Figure 21.16

Membrane-associated propotein complex

Some sulfur-reducing bacteria can gain additional

energy through disproportionation of sulfur

compounds

- S2O32- + H2O → SO4

2- + H2S

21.9 Acetogenesis

Acetogens and methanogens use CO2 as an

electron acceptor in anaerobic respiration

H2 is the major electron donor for both groups of

organisms

The Processes of Methanogenesis and Acetogenesis

Figure 21.17

Acetogens (homo acetogens)

Reduce CO2 to acetate by the acetyl-CoA pathway, a

pathway widely distributed in obligate anaerobes

Reactions of the Acetyl-CoA Pathway

Figure 21.18

Organisms Employing the Acetyl-CoA Pathway

21.10 Methanogenesis

Methanogenesis

Involves a complex series of biochemical reactions that

use novel coenzymes

Coenzymes of Methanogenesis (Methanofuran)

Figure 21.19a

Coenzymes of Methanogenesis (Methanopterin)

Figure 21.19b

Resembles folic acid

Playes a role analogus to THF

Coenzymes of Methanogenesis (Coenzyme M)

Figure 21.19c

Required for the terminal step of methanogenesis

Coenzymes of Methanogenesis (Coenzyme F430)

Figure 21.19d

Contains nickel and required for the terminal step of methanogenesis

Coenzymes of Methanogenesis (Coenzyme F420)

Figure 21.19e

A redox coenzyme structurally resembling FMN

Oxidized form absorbs light at 420 nm and fluoresces blue-green

The autofluorescence of coenzyme F420 can be

used to identify methanogens microscopically

Fluorescence Due to the Methanogenic Coenzyme F420

Figure 21.20

Autofluourescence in Cells of the Methanogen Methanosarcina barkeri

F420 fluorescence in Cells of the Methanogen Methanobacterium formicicum

Coenzymes of Methanogenesis (Coenzyem B)

Figure 21.19f

7-Mercaptoheptanoylthreonine phosphate

Required for the terminal step of methanogenesis catalyzed by the methyl reductase enzyme complex

H2 is the major electron donor for methanogenesis

Methanogenesis from CO2 plus H2

Figure 21.21

Additional electron donors exist

e.g., formate, CO, organic compounds

Methanogenesis from Methanol

Figure 21.22a

Corrin ring Vitamin B12 (cyanocobalamin)

Methanogenesis from Acetate

Figure 21.22b

Autotrophy in methanogenes occurs via the acetyl-

CoA pathway

Energy conservation in methanogenesis is linked to

both proton and sodium motive forces

Energy Conservation in Methanogenesis

Figure 21.23

Methanophenazine

21.11 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 of all anaerobic respiratory mechanisms

This organism ferments glucose by reducing protons in an anerobic respiration linked to ATPase activity

- Electron transport chain is not involved

- But protons are the net electron acceptor

Modified Glycolysis and Proton Reduction in P. furiosus

Fdox/red = ~ -0.42 V

2H+/H2 = ~ -0.42 V

No substrate-level phosphorylation

Figure 21.24

21.12 Other Electron Acceptors

Fe3+, Mn4+, ClO3-, and various organic compounds

can serve as electron acceptors for bacteria

Fe3+ is abundant in nature and its reduction is a

major form of anaerobic respiration

Alternative Electron Acceptors for Anaerobic Respirations

Figure 21.25

toxic

Biomineralization During Arsenate Reduction

Figure 21.26

The reduction of arsenate by sulfate-reducing bacteria has been employed for clean-up of toxic wastes and groundwater

- Spontaneous production of As2S3 during reduction of arsenate to arsenite along with the reduction of sulfate to sulfide

After inoculation Biominerlization after 2 weeks

Synthetic As2S3

Halogenated compounds can also serve as

electron acceptors via a process called reductive

dechlorination (dehalorespiration)

Characteristics of Genera of Reductive Dechlorinators

21.13 Anoxic Hydrocarbon Oxidation

Aliphatic and aromatic hydrocarbons can be oxidized

anaerobically

Hydrocarbons are oxidized to intermediates that can

be catabolized via the citric acid cycle

Anoxic Catabolism of the Aliphatic Hydrocarbon Hexane

Figure 21.27

The first step in degradation is the addition of oxygen to the molecule through the incorporation of fumarate

Anoxic Degradation of Aromatic Hydrocarbon Benzoate

Figure 21.28

Aromatic hydrocarbons are catabolized by ring reduction and cleavage

Anoxic Oxidation of Methane

Methane

The simplest hydrocarbon

Can be oxidized under anoxic conditions by a consortia

containing sulfate-reducing bacteria and

methanotrophic archaea

Figure 21.29a

Methane-oxidizing cell aggregates

Possible mechanism of the cooperative degradation of methane

(or some other carriers of reducing power)

III. Aerobic Chemoorganotrophic Processes

21.14 Molecular Oxygen as a Reactant in Biochemical

Processes

21.15 Aerobic Hydrocarbon Oxidation

21.16 Methylotrophy and Methanotrophy

21.17 Hexose, Pentose, and Polysaccharide Metabolism

21.18 Organic Acid Metabolism

21.19 Lipid Metabolism

21.14 Molecular Oxygen as a Reactant

Oxygen plays an important role as a direct reactant

in certain biochemical reactions

Oxygenases

Enzymes that catalyze the incorporation of atoms of

oxygen from O2 into organic compounds

Two major classes

Monooxygenases: incorporate one oxygen atom

Dioxygenases: incorporate both oxygen atoms

Monooxygenase Activity

Figure 21.30

= Hydroxylase

21.15 Aerobic Hydrocarbon Oxidation

Many bacteria and eukaryotic microbes can use

aliphatic and aromatic hydrocarbons as electron

donors when growing aerobically

Oxygenases are central enzymes in these biochemical

reactions

Aerobic aromatic compound degradation involves ring

oxidation

Hydroxylation of Benzene to Catechol by a Monooxygenase

Figure 21.31a

Cleavage of Catechol by an Intradiol Ring-Cleavage Dioxygenase

Figure 21.31b

Sequential Reaction of Dioxygenases

Figure 21.31c

21.16 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)

- Soluble MMO (sMMO)

- Membrane-bound MMO (particulate MMO, pMMO)

Oxidation of Methane by Methanotrophic Bacteria

Figure 21.32

Methanol dehydrogenase: periplasmic enzyme

Membrane-associated

Methanotrophs are classified into two physiological

groups that differ in the pathways invoked for

assimilation of carbon into cell material

Type I: Ribulose Monophosphate Pathway

- Assimilates formaldehyde

Type II: Serine Pathway

- Assimilates formaldehyde and CO2

Methylosinus sp. (type II)

Methylococcus capsulatus (type I)

Some Characteristics of Methanotrophic Bacteria

The Ribulose Monophosphate Pathway

Figure 21.34

The Serine Pathway

Figure 21.33

21.17 Hexose, Pentose, 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 that are

readily catabolized by microbes

Naturally Occurring Polysaccharides Yielding Sugars

Starch is fairly soluble and readily degraded by

many fungi and bacteria employing amylases

Hydrolysis of Starch by Bacillus subtilis

Figure 21.37

Purple-black color of the starch-iodine complex

Cellulose is fairly insoluble and its degradation typically

involves attachment of microbes to cellulose fibrils and

production of cellulases

Cellulose degradation is restricted to relatively few

bacteria groups, including the gliding bacteria

Sporocytophaga and Cytophaga

Cellulose Digestion

Figure 21.35

(Sporocytophaga myxococcoides)

Cytophaga hutchinsonii Colonies on a Cellulose-Agar Plate

Figure 21.36

Pentoses are required for the synthesis of nucleic acids

If pentoses are not readily available from the environment, organisms must synthesis themselves

The major pathway for pentose production is the pentose phosphate pathway (= hexulose monophosphate pathway)

The Pentose Phosphate Pathway

Figure 21.39

21.18 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-C3 organic acids typically involves

production of oxalacetate through the glyoxylate

cycle

Glyoxylate cycle

- Most TCA cycle reactions + isocitrate lyase &

malate synthase

The Glyoxylate Cycle

Figure 21.40

CHO

COOH

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111

TCA and Glyoxylate cycles

21.19 Lipid Metabolism

Lipids are abundant in nature and readily degraded by

many microbes

Catabolism of fats by microbes is initiated by hydrolysis

of the ester bond, yielding fatty acids and glycerol, by

extracellular lipases

Phospholipases are a class of lipases that attack

phospholipids

Phospholipase Activity

Figure 21.41

Lipases

Figure 21.42

Fatty acids are oxidized by beta-oxidation

A series of reactions in which the compounds are first

activated by coenzyme A

Then two carbons of the fatty acid are successively

removed, generating acetyl-CoA

Acetyl-CoA is then catabolized through the citric

acid cycle

Beta-Oxidation

Figure 21.43

CoA-SH