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General Microbiology II

Metabolic Diversity

Catabolism

• Organotrophy - mode of life in which organisms extract chemical bond energy from organic compounds by removal of electrons (oxidation) and use it to generate ATP and NAD(P)H (reducing power), then use these to help form organic compounds from carbon "skeletons" (taken in or generated during catabolism) via biosynthetic reactions
  • fermentation - anaerobic catabolism in which electron donor and electron acceptor are both organic molecules and cytochrome ETS is not used
    • substrate-level phosphorylation-coupled - this type of phosphorylation occurs only when the energy source can be coupled to a high-energy intermediate such as coenzyme A or various phosphates including phosphoenolpyruvate in glycolysis (Embden-Meyerhof glycolytic pathway)
    • energy-linked membrane-bound ion pump (ATPsynthase) coupled phosphorylation generally involves the fermentation of dicarboxylic acids:
      • succinate is oxidized to propionate plus carbon dioxide (coupled to Na ion transport; Na ion gradient used by ATPase as an energy source for phosphorylation of ADP to form ATP)
      • oxalate is oxidized to formate plus carbon dioxide (coupled to proton transport - proton gradient used by ATPase as an energy source for phosphorylation of ADP to form ATP)
  • aerobic respiration - utilizes the TCA cycle, the electron transport system (ETS), proton gradients, ATP synthase, and oxygen as final electron acceptor; covered in previous courses ... overview
    • Embden-Meyerhof glycolytic pathway
    • Entner-Doudoroff Pathway (Pentose Phosphate Pathway)
    • Hexose Monophosphate Shunt
  • anaerobic respiration - dissimilative catabolism that involves cytochrome ETS and which uses a molecule other than oxygen the final electron acceptor
    • general characteristics
      • assimilative vs. dissimilative metabolism
        • assimilative - aerobic or anaerobic metabolism in which small amounts of a molecule (just enough to satisfy growth requirements) are incorporated into the organism
        • dissimilative - anaerobic metabolism (typically associated with anaerobic respiration) in which large amounts of molecules outside the cell are used as electron acceptors
      • ATP generation - ETS generates proton gradient by pumping protons (proton) out while transporting electrons derived by oxidation of substrate to a terminal electron acceptor, then the membrane-bound ATPase (ATP synthase) forms ATP using energy derived as protons flow back in; less energy than when oxygen is used due to the lower reduction potential difference between these terminal electron acceptors and NAD(P)H:
        • carbon dioxide is reduced to acetate
        • sulfate is reduced to sulfur is reduced to sulfide
        • carbon dioxide is reduced to methane
        • nitrate is reduced to nitrite is reduced to nitrous oxide is reduced to nitrogen
        • ferric iron is reduced to ferrous iron
        • fumarate is reduced to succinate
        • glycine is reduced to acetate
        • TMAO (trimethylamine oxide) is reduced to TMA (trimethylamine)
        • DMSO (dimethyl sulfoxide) is reduced to DMS (dimethyl sulfide)
      • facultative vs obligate anaerobes - some anaerobic respirers are facultative aerobes, because they have an electron transport system and use oxygen preferentially as the terminal electron acceptor when it is present; they switch to alternate electron acceptors only when oxygen has been depleted
    • nitrate-reducing bacteria (Pseudomonas denitrificans, Bacillus, Enterics) - denitrification; this is an anaerobic process because the dissimilative nitrate reductase is repressed by oxygen) these bacteria reduce nitrate to nitrite then to nitrous oxide then to nitrogen which is released into the atmosphere
    • sulfate-reducing bacteria (Desulfovibrio) - the electron donor is hydrogen (hydrogenase-mediated); in the presence of ATP and 8 electrons, these bacteria convert sulfate into adenosine phosphosulfate (APS), which is converted into thiosulfate, which is reduced to hydrogen sulfide, which is excreted
    • carbonate-reducing bacteria and archaea reduce carbonate to methane; these
      • carbonate ions are reduced to form methane by methanogens such as Methanococcus, Methanobacterium, etc. (these prokaryotes are actually Archaea, not Bacteria)
      • 2 carbonate ions are reduced to form 1 acetate by homoacetogens such as Clostridium
    • iron and/or manganese-reducing bacteria
      • appears to be carried out by nitrate reductase in many cases, but has its own reductase in others: ferric iron ions are reduced to form ferrous iron ions (Pseudomonas)
      • same enzymes also reduce manganese (+4) to manganous ion (2+) (Shewanella)
    • fumarate reducing bacteria (Wolinella succinogenes, Desulfovibrio gigas, Escherichia coli, Proteus rettgeri) - use reverse TCA cycle to generate succinate from fumarate
    • TMAO-reducing bacteria (several facultative aerobes, purple nonsulfur bacteria) - bacteria which grow on marine fish (which make TMAO as a method of excreting excess nitrogen) produce trimethylamine (TMA)
    • DMSO-reducing bacteria (Campylobacter, Escherichia, many other proteobacteria) reduce DMSO to produce DMS (dimethylsulfide)
• Lithotrophy - mode of life in which organisms utilize chemical bond energy in inorganic compounds to generate ATP and NAD(P)H (reducing power), then use them to reduce carbon dioxide to form organic compounds
• oxidizing bacteria - aerobic facultative lithotrophs
  • general metabolic characteristics
    • ATP generation - ETS generates proton gradient by pumping proton out while transporting electrons derived by enzymatic oxidation of substrate to oxygen, then membrane-bound ATPase (ATP synthase) forms ATP using energy derived as proton flow back in
    • NADH/NADPH generation - electrons generated by reverse electron transport much like anoxygenic phototrophs use reduces NAD+ and NADP+, thus generating reducing power
    • carbon dioxide fixation - occurs via Calvin cycle in oxidizing lithotrophic bacteria
  • hydrogen-oxidizing bacteria (Alkaligenes, Aquaspirillum, Arthrobacter, Pseudomonas)
    • electrons derived from hydrogenase-mediated hydrogen oxidation
    • heterotrophic growth mediated by reverse Calvin cycle
  • sulfur-oxidizing bacteria (Beggiatoa, Thiobacillus)
    • electrons derived by oxidation of hydrogen sulfide, sulfur, thiosulfate
    • those which oxidize sulfur to completion generate sulfate, so they must be acid tolerant
    • when oxidizing hydrogen sulfide, these bacteria frequently accumulate cytoplasmic sulfur granules
    • when oxidizing sulfur, these bacteria must be in close approximation to sulfur granules due to the low solubility of elemental sulfur
  • iron-oxidizing bacteria (Thiobacillus ferrooxidans)
    • acidophilic - ferrous iron ions oxidized by oxygen at neutral pH, but not at low pH
    • oxidation of ferrous iron ions to ferric iron ions does not provide sufficient electrochemical potential to allow ATP generation or NADPH formation by normal mechanisms
    • therefore many iron bacteria also derive electrons from oxidation of hydrogen sulfide, sulfur, thiosulfate
    • Thiobacillus ferrooxidans uses the natural proton gradient in its low pH environment to generate ATP via ATP synthase, then eliminates excess cytoplasmic protons by coupling oxygen reduction to Fe2+ oxidation using rusticyanin, cytochrome c and cytochrome a1 (all in the cytoplasmic membrane): 2 ferrous iron ions plus 1/2 oxygen plus 2 protons leads to oxidation to 2 ferric iron ions plus water
  • nitrifying bacteria - electrons from oxidation of ammonium ions to nitrate, which is accomplished sequentially by two types of bacteria:
    • ammonium-oxidizer (Nitrosomonas) - oxidizes ammonium ions to nitrite (NH₄ NO₂)
    • nitrite-oxidizer (Nitrobacter) - oxidizes nitrite- to nitrate (NO₂ NO₃)
• oxidizing archaea - aerobic facultative lithotrophs
  • general metabolic characteristics
    • ATP generation - ETS generates proton gradient by pumping proton out while transporting electrons derived by enzymatic oxidation of substrate to oxygen, then membrane-bound ATPase (ATP synthase) forms ATP using energy derived as proton flow back in
    • NADH/NADPH generation - electrons generated by reverse electron transport much like anoxygenic phototrophs use reduces NAD+ and NADP+, thus generating reducing power
    • carbon dioxide fixation - occurs via hydroxypropionate pathway in oxidative lithotrophic archaea
  • iron-oxidizing archaea (Sulfolobus)
    • acidophilic - ferrous iron ions oxidized by oxygen at neutral pH, but not at low pH
    • oxidation of ferrous iron ions to ferric iron ions does not provide sufficient electrochemical potential to allow ATP generation or NADPH formation by normal mechanisms
    • therefore iron archaea may also derive electrons from oxidation of hydrogen sulfide, sulfur, thiosulfate
    • carbon dioxide fixation occurs via hydroxypropionate pathway in Sulfolobus
  • sulfur-oxidizing bacteria (Sulfolobus, Thermoproteus, Pyrobaculum)
    • electrons derived by oxidation of hydrogen sulfide, sulfur, thiosulfate
    • those which oxidize sulfur to completion generate sulfate, so they must be acid tolerant
    • when oxidizing hydrogen sulfide, these bacteria frequently accumulate cytoplasmic sulfur granules
    • when oxidizing sulfur, these bacteria must be in close approximation to sulfur granules due to the low solubility of elemental sulfur
    • carbon dioxide fixation
      • hydroxypropionate pathway in Sulfolobus
      • reductive (reverse) TCA pathway in Thermoproteus, Pyrobaculum
• reducing bacteria - many anaerobic, facultative lithotrophs (Desulfovibrio, Desulfomonas, Desulfobacter)
  • anaerobic respiration with sulfate or nitrate as final electron acceptor
  • ATP generation via ETS, proton gradients, ATP synthase
  • NADH/NADPH generation - electrons generated by reverse electron transport, much like anoxygenic phototrophs use; reduces NAD+ and NADP+, thus generating reducing power for biosynthesis
  • carbon dioxide fixation occurs via acetyl-CoA pathway in acetogens and sulfate reducers
• reducing archaea - anaerobic, facultative lithotrophs (methanogens and other anaerobic archaea)
  • anaerobic respiration with sulfate or nitrate as final electron acceptor
  • ATP generation via ETS, proton gradients, ATP synthase
  • NADH/NADPH generation - electrons generated by reverse electron transport, much like anoxygenic phototrophs use; reduces NAD+ and NADP+, thus generating reducing power for biosynthesis
  • carbon dioxide fixation occurs via reductive (reverse) acetyl-CoA pathway in methanogens and other anaerobic archaea
• Phototrophy - mode of life in which organisms utilize photosynthesis to convert light energy into ATP and NAD(P)H (reducing power), then use them to reduce carbon dioxide to form organic compounds
  • light reactions - photosensitive pigments are used to capture and conversion of light (photon) energy into chemical energy by membrane/protein-associated molecules, leading to formation of ATP and NADPH
    • antenna pigments - membrane/protein-associated that collect light energy, then transfer excitons to reaction center pigments by inductive resonance (carotenoids prevent pigment photooxidation)
      • anoxygenic photosynthesis (carried out by purple and green photosynthetic bacteria) - antenna pigments are chlorophylls or bacteriochlorophylls
      • oxygenic photosynthesis (carried out by cyanobacteria) - antenna pigments are phycobiliproteins
    • reaction center pigments - membrane protein-associated molecules that transfer electrons to the electron transport system (ETS), which generates a proton gradient as ETS components are sequentially reduced and oxidized
      • anoxygenic photosynthesis
        • photosystem I (PSI) ... in Chlorobia (Green Bacteria)
          • antenna complex bacteriochlorophyll a transfers light energy to reaction center bacteriochlorophyll P840 in the form of excitons, thus converting P840 from its resting state (Eo' ~ +0.25V) to a strong reductant (Eo' ~ -1.25V)
          • reduced bacteriochlorophyll P840, together with its associated cytochrome c, fosters splitting (photolysis) of H₂S (or an organic electron donor such as succinate) to yield 2H⁺ + 2e^-
          • ATP generation
            • photolysis occurs on the outside of the membrane, so the 2H⁺ liberated set up a proton gradient as H⁺ are used inside the cell during reduction of NAD⁺ (see explanation below)
            • ATP is generated as H⁺ are transported into the cell by ATP synthase
          • reducing power (NADH, NADPH) generation
            • phylloquinone (PQ) transfers the 2e^- liberated via photolysis to ferredoxin (Fd) inside the cell thus reducing it
            • ferrodoxin NADH oxidoreductase (FNR) oxidizes reduced ferredoxin, transferring the 2e^- (together with 2H⁺) to NAD⁺ (or NADP⁺) forming NADH (or NADPH) + H⁺ (reducing power)
        • photosystem II (PSII) ... in Rhodobacteria (Purple alpha-proteobacteria)
          • antenna complex bacteriochlorophyll a transfers light energy to reaction center bacteriochlorophyll P870 in the form of excitons, thus converting P870 from its resting state (Eo' ~ +0.5V) to a weak reductant (Eo' ~ -1.0V)
          • reduced bacteriochlorophyll P870 transfers 2e^- to bacteriophaeophytin a within the reaction center, thus reducing the bacteriophaeophytin a
          • reduced bacteriophaeophytin a transfers the 2e^- to quinols (Q_A to Q_B to Q pool) thus reducing them
          • quinols transfer the 2e^- to cytochrome bc, reducing the cytochrome bc and fostering transport of 2H⁺ outside the cell
          • reduced cytochrome bc transfers the 2e^- to cytochrome c thus reducing it
          • reduced cytochrome c transfers the 2e^- to iron-sulfur proteins thus reducing them
          • reduced iron-sulfur proteins transfer the 2e^- back to bacteriochlorophyll P870, completing this cyclic electron transfer process
          • ATP generation
            • as quinols transfer the 2e^- to cytochrome bc, 2H⁺ are transported outside the cell, setting up a proton gradient
            • ATP is generated as H⁺ are transported into the cell by ATP synthase
          • reducing power (NADH, NADPH) generation
            • PSII does not generate a strong enough reductant to generate NADH or NADPH, so an alternate mechanism is required
            • H₂S (or H₂ or S⁰ or S₂O₂ or Fe⁺⁺) from the environment is oxidized to obtain electrons for generation of reducing power
            • electrons are transported via reverse ETS from the reduced substrate H₂S (etc.) to NAD⁺ (or NADP⁺) forming NADH (or NADPH) + H⁺ (reducing power)
      • oxygenic photosynthesis (aka "Z" photosynthesis)
        • photosystem II (PSII):
          • light energy absorbed by P680 (form of chlorophyll a) is used to cleave H₂O (electron donor)
          • water is broken down to form hydrogen and oxygen ... H₂O O + 2 H⁺ + 2 e^- ... and release a pair of electrons in the process
          • electrons are then transferred to an ETS consisting of I (an unidentified intermediate...phaeophytin a ?), plastoquinones, cytochrome b, cytochrome f and plastocyanin
          • this noncyclic ETS sets up a proton gradient across the membrane and transfers the electrons to the reaction center chlorophyll a of photosystem I (P700)
        • photosystem I: (PSI)
          • when stimulated with light and electrons, P700 transfers electrons to...
          • X (unidentified, may be a chlorophyll a free radical ?), which transfers electrons to one of these...
            • the noncyclic ETS described above, which sets up a proton gradient (can be used for ATP generation) , or
            • ferredoxin (Fd), which reduces NADP+ to form NADPH
    • ATPsynthase - membrane-bound molecule which "uses" the proton gradient to form ATP
      • anoxygenic photosynthesis - cyclic photophosphorylation; reaction center bacteriochlorophyll a is both the electron donor and the final electron acceptor (no net gain or loss of electrons)
      • oxygenic photosynthesis - even though the original source of electrons was O, which is external to the system, PSI can also engage in cyclic photophosphorylation
    • cytochrome oxidase (or ferredoxin reduces NADP+ to NADPH
      • anoxygenic photosynthesis - ATP-requiring reverse electron flow is the driving force; sulfide, sulfur or an organic compound such as succinate is the electron donor (is reduced)
      • oxygenic photosynthesis - ferredoxin reduces NADP+
  • dark reactions - conversion of carbon dioxide into organic compounds at the oxidation level of carbohydrate, utilizing energy stored as ATP and reducing power stored as NADPH (both generated by light reactions)
    • CO₂ fixation allows the cells to convert carbon dioxide into organic compounds at the oxidation level of carbohydrate, using one of these pathways:
  • Calvin cycle (reductive pentose cycle) is used by cyanobacteria and purple bacteria for carbon dioxide fixation:
    • 6 CO₂ + 12 NADPH + 18 ATP glucose + 12 NADP⁺ + 18 ADP + 18 PO₄^-3
    • unique enzymes - ribulose bisphosphate carboxylase (RuBisCo) and phosphoribulokinase
  • reductive (reverse) TCA cycle is used by green sulfur bacteria for carbon dioxide fixation; also use reverse glycolysis for sugar synthesis and storage
    • 3 CO₂ + 12 NADPH + 5 ATP triose phosphate + 12 NADP⁺ + 5 ADP + 5 PO₄^-3
    • unique enzyme is citrate lyase
  • hydroxypropionate pathway is used by green nonsulfur bacteria for carbon dioxide fixation:
    • 2 CO₂ + 4 NADPH + 3 ATP glyoxylate + 8 NADP⁺ + 3 ADP + 3 PO₄^-3
    • acetyl-CoA is carboxylated to form hydroxypropionate, then carboxylated again to form methylmalonyl-CoA, which is oxidized to form malyl-CoA, which is cleaved to (re)form acetyl-CoA plus glyoxylate, which is used to generate glycine or serine which are used as intermediates for generation of cell materials
  • carbohydrates can serve as energy storage molecules - more stable than ATP or NADPH
    • poly-beta-hydroxybutyrate and glycogen - purple and green bacteria
    • starch or sucrose - cyanobacteria and algae

Anabolism

If not available in the environment, organic compounds must be synthesized by the cell

• Carbohydrates (polysaccharides, ribose and deoxyribose in nucleic acids)
  • hexoses are synthesized via gluconeogenesis:
    • after conversion of oxalacetate to form phosphoenolpyruvate hexoses can be synthesized by "reversing" glycolysis
    • after glucose is coupled with uridine diphosphate (UDP), it can be used to synthesize structural or storage polysaccharides
  • pentoses are synthesized via the pentose phosphate shunt
    • hexose is cleaved to form pentose (ribulose-5-phosphate) plus carbon dioxide, which can be used in the Calvin cycle or for ribose synthesis
    • ribulose-5-phosphate is converted to ribose, which can be oxidized to form deoxyribose (both of which are used in synthesis of nucleotides and vitamins such as NAD)
• Amino acids (for proteins ... also used to generate purines for nucleic acids)
  • two major aspects of synthetic reactions:
    • synthesis of the carbon skeleton from metabolic intermediates
    • attachment of an amino group
      • glutamate dehydrogenase adds an amino group to a-ketoglutarate directly, thus generating glutamate
      • other amino acids are generated from different carbon skeletons via transamination using glutamate as the source of the amino group
  • synthesis of amino acids from metabolic intermediates generated by:
    • glycolysis
      • pyruvate transamination generates alanine, a precursor of valine and leucine
      • 3-phosphoglyceraldehyde transamination leads to serine, which is a precursor to serine and glycine
      • phosphoenolpyruvate and erythrose-4-phosphate combine to form chorismate, which is the precursor of the aromatic amino acids tryptophan, phenylalanine and tyrosine
    • TCA cycle
      • alpha-ketoglutarate amination leads to glutamate, which is a precursor to glutamine, proline and arginine
      • oxalacetate transamination leads to aspartate, which is a precursor to asparagine, lysine, methionine, threonine and isoleucine
    • Other sources
      • phosphoribosylpyrophosphate is a precursor to histidine
• Purines and pyrimidines (for RNA, DNA, ATP, NAD)
  • purines (adenine, guanine) are synthesized via complex sequence of reactions in which components are donated by aspartate, glutamate, glycine, carbon dioxide and formate (from folic acid)
  • pyrimidines (cytosine, thymine, uracil) are synthesized from aspartate, carbon dioxide and ammonia (also via several reactions in a sequence)
• Lipids
  • fatty acids are generated by fatty acid synthetase from successive addition of acetate groups donated by acetyl-CoA (derived from pyruvate generated in glycolysis)
  • glycerol is derived from dihydroxyacetone phosphate (in glycolysis) and is subsequently esterified by fatty acids to form mono-, di- or triglycerides (diglycerides may then be modified by addition of phosphate, amino, or other groups to better suit them for their functions in membranes, etc.)