Catabolic Activities of Aerobic Heterotrophs

Catabolic activities of aerobic
heterotrophs
Ref: Gadd
Organic Acid Utilization
Fatty acid utilization
• Acyl-CoA synthetase forms acyl-CoA from fatty acids
and coenzyme-A before acyl-CoA is converted to
acetyl-CoA through β -oxidation.
• The glyoxylate cycle is employed with the TCA cycle to
convert acetyl-CoA into the carbon skeletons needed
for biosynthesis
β-oxidation
• β-oxidation splits a 2-carbon unit in the form of acetyl-CoA from acyl-CoA and this is
catalyzed by five enzymes including acyl-CoA synthetase.
• Fatty acids with an even number of carbons result solely in acetyl-CoA while
propionyl-CoA remains after β-oxidation of fatty acids with an odd number of
carbons.
• Ex: Palmitate degradation to acetyl-CoA through β-oxidation
Step 2: Oxidation by
FAD
Step 3: Hydration
Step 3: Oxidation by
NAD+
Step 4: Thiolytic
cleavage by CoA
• Propionyl-CoA is a metabolic intermediate of a number of
compounds including the amino acids, L-valine and L-isoleucine.
• The acrylate pathway and the methylmalonyl-CoA pathway were
identified as the oxidative metabolism of propionyl-CoA in earlier work.
• More recent studies have shown that propionyl-CoA is metabolized to
pyruvate through the methylcitrate cycle in many bacteria including
Escherichia coli, Salmonella typhimurium and Ralstonia eutropha, and in
fungi such as Saccharomyces cerevisiae and Aspergillus nidulans.
Propionate can inhibit fungal growth on glucose but can also serve as a
carbon and energy source.
Amino acid Utilization
• Amino acids are used for protein synthesis and are deaminated to the corresponding 2-keto acids.
• The 2-keto acids are oxidized to acyl CoA by 2-keto acid dehydrogenases for use as carbon and
energy sources. They are deaminated through different mechanisms depending on their nature.
Oxidative deamination
Amino acids are deaminated either by amino acid oxidase reducing its prosthetic flavin or by amino
acid dehydrogenase reducing NAD(P)+
Amino acid oxidases have a low specificity for the substrate and a single enzyme can oxidize up to
ten different amino acids. Since bacterial cell walls contain D-amino acids, bacteria have L-amino
acid as well as D-amino acid oxidase.
• Amino acid dehydrogenase oxidizes L-alanine or L-glutamate to pyruvate and 2-ketoglutarate,

respectively. Since transaminases convert pyruvate and 2-ketoglutarate to alanine and glutamate,
all amino acids can be deaminated by the combination of transaminase and amino acid
dehydrogenase.
Transamination
Transamination is an enzymatic reaction that transfers
the -NH2 group from amino acids to 2-keto acids.
alanine and glutamate dehydrogenases deaminate their
substrate.
When coupling transamination and dehydrogenation of
alanine or glutamate, an amino acid is oxidized to the
corresponding 2-keto acid reducing NAD(P)+.
Deamination products of amino acids
• Deamination of amino acids yields various
organic acids
Oxidation of aliphatic hydrocarbons
• Many prokaryotic and eukaryotic microbes can

use aliphatic hydrocarbons, especially those that
are liquid at ambient temperature.
• Hydrocarbons are water insoluble and differ from

water-soluble substrates in terms of transport.
• Since microbes cannot thrive in a pure oil phase, microbes use
hydrocarbons as their carbon and energy source at the water–oil
interface.
• Hydrophobic glycolipids are found on the cell surfaces of bacteria and
fungi that use hydrocarbons. This glycolipid solubilizes the hydrocarbon
before it is transported into the cell. Many bacteria, including
Acinetobacter calcoaceticus, produce a surfactant to improve hydrocarbon
transport as an emulsion.
•
Hydrocarbon monooxygenase oxidizes a hydrocarbon to a primary alcohol
at the cytoplasmic membrane. This enzyme can oxidize two different
substrates using one molecule of oxygen. This kind of enzyme is referred
to as a monooxygenase, mixed function oxidase or hydroxylase.
Oxidation of aromatic compounds
• The complex aromatic polymer lignin comprises about

25% of land based biomass on Earth, and coal and
petroleum contain a variety of aromatic compounds.
• These substances are oxidized mainly under aerobic
conditions due to their high structural stability.
• Aliphatic hydrocarbons are easily oxidized, but the
aromatic portion of petroleum is persistent in natural
ecosystems.
• Aromatic hydrocarbon degradation is best known in
Pseudomonas spp., e.g. Pseudomonas acidovorans and
Pseudomonas putida.
Oxidation of aromatic amino acids
• Phenylalanine monooxygenase oxidizes phenylalanine to

tyrosine that is deaminated to p-hydroxyphenylpyruvate.
• Dioxygenases are involved in the following reactions.
• Enzymes that incorporate both atoms of molecular oxygen

into one substrate are referred to as dioxygenases or
oxidases.
• Homogentisate oxidase opens up the benzene ring, finally

producing fumarate and acetoacetate.
Ortho and meta cleavage, and the gentisate pathway
• The metabolism of aromatic compounds can be divided into two

steps.
• In the first step monooxygenases incorporate hydroxyl groups into the
benzene ring. Through this step, aromatic compounds are converted to
one of three intermediates: protocatechuate, catechol and gentisate.
• Aromatics with a hydroxyl group are mainly converted to protocatechuate
• catechol is derived from aromatic hydrocarbons, aromatic compounds
with amino groups and lignin monomers.
• Some bacteria generate gentisate from naphthalene, 3-hydroxybenzoate,
phenol derivatives, 3,6-dichloro-2-methoxybenzoate, and other
substances. The benzene rings of these intermediates are opened up by
dioxygenases.
• Ring fission is catalyzed by dioxygenases and termed
– ortho cleavage when it occurs between the hydroxyl
groups and
– meta cleavage when it occurs adjacent to one of the hydroxyls.
• Another ring cleavage pathway, the gentisate pathway, is responsible for the
oxidation of aromatic compounds with hydroxyl groups at para positions.
Metabolism of C1 compounds
• C1 compounds that support growth:
1. Carbon dioxide (CO2)
2. Methane (CH4)
3. Methanol (CH3OH)
4. Methylamine (CH3NH2)
Methanotrophy and methylotrophy
• Methanotrophs use C1 compounds but do not use multicarbon
compounds. These are termed obligate methylotrophs.
• Methylotrophs do not use methane. Based on their carbon
assimilation metabolism, methylotrophs are divided
into
– heterotrophic methylotrophs: assimilate formaldehyde through the
ribulose monophosphate pathway or the serine–
isocitrate lyase pathway and
– autotrophic methylotrophs: assimilate carbon dioxide through
the Calvin cycle .
• Methanotrophs are not known in eukaryotes, and methylotrophic

yeasts assimilate formaldehyde through the xylulose
monophosphate pathway.
Methanotrophy
• Methane monooxygenase
oxidizes methane to
methanol using NADH as
the cosubstrate
• Electrons from methanol
oxidation are channelled to
the electron transport
system for ATP synthesis.
Formaldehyde or carbon
dioxide are assimilated for
biosynthesis of cell
materials.
Carbon assimilation by methylotrophs
• Obligate methylotrophs cannot use multicarbon

compounds as
their carbon source.
• Obligate methylotrophs and heterotrophic methylotrophs
employ either the ribulose monophosphate (RMP) pathway
to assimilate formaldehyde or the serine–isocitrate lyase
(SIL) pathway to assimilate formaldehyde and CO2.
• Autotrophic methylotrophs fix CO2 through the Calvin cycle.
• Methylotrophic yeasts growing on methanol employ yet
another novel pathway, the xylulose monophosphate (XMP)
pathway
Ribulose monophosphate (RMP) pathway
Serine–isocitrate lyase (SIL) pathway
Xylulose monophosphate (XMP) pathway
Energy efficiency in C1 metabolism
• Microorganisms assimilate
C1 compounds through the
RMP, SIL and XMP pathways,
and the Calvin cycle.
• However, energy
requirements as ATP and
reduced electron carriers
differ between the pathways.
• Since the starting materials
and the products are
different, calculations can be
made normalizing pyruvate
as the final product

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Catabolic activities of aerobic

• Amino acid dehydrogenase oxidizes L-alanine or L-glutamate to pyruvate and 2-ketoglutarate,

• Many prokaryotic and eukaryotic microbes can

• Hydrocarbons are water insoluble and differ from

• The complex aromatic polymer lignin comprises about

• Phenylalanine monooxygenase oxidizes phenylalanine to

• Dioxygenases are involved in the following reactions.

• Enzymes that incorporate both atoms of molecular oxygen

• Homogentisate oxidase opens up the benzene ring, finally

• The metabolism of aromatic compounds can be divided into two

• Methanotrophs are not known in eukaryotes, and methylotrophic

• Obligate methylotrophs cannot use multicarbon

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