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Lecture 4: Bacterial Fueling and Assimilation

Lecture 4: Bacterial Fueling and Assimilation. Reading assignments in Text: Lengeler et al. 1999 Text: pages 116-122 Assimilation Text: pages 177-182 Assimilation reactions Text: pages 155-157 Storage compounds Lecture 3 Text: pages 114-116, 123-128 Central metabolism

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Lecture 4: Bacterial Fueling and Assimilation

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  1. Lecture 4: Bacterial Fueling and Assimilation Reading assignments in Text: Lengeler et al. 1999 Text: pages 116-122 Assimilation Text: pages 177-182 Assimilation reactions Text: pages 155-157 Storage compounds Lecture 3 Text: pages 114-116, 123-128 Central metabolism Text: pages 52-58 Substrate level phosphorylation Text: pages 62-67 Electrontransport-coupled phosphorylation Text: pages 296-307 Fermentation Text: pages 263-266 Oxygen and metabolism Text: pages 524 Energy generation Lecture 2 Text: pages 343-352 DNA replication Text: pages 362-368, 441 RNA transcription Text: pages 369-376 Translation

  2. Fermentation products Yeast: Bread, beer, wine... Bacteria: Rye breads Butter milk (Lactobacilli) Sourdough bread Yogurt Olives Sausages “Thousand year” eggs Coffee (husk removal) Sauerkraut Vegetables / mushrooms (Lactobacillus plantarum) Vinegar (acetic acid) Organic acids, ketones, alcohols, ... Hydrogen gas

  3. Overview of Metabolism Lecture 1 Lecture 2 Fuelling Pili Flagella DNA, RNA Protein N, S P Fermentation 12 MP’s Met. Precursors ( 2C - 6C units) eTS (electron- Transp. Sys.) Reducing Power NADPH NADH Foods: glucose, ribose, acetate, ... Lectures 3,4 ATP F0F1 ATPase Biosyn. Polymer. Assembly PMF (Proton Motive Force) Strange foods: oils, benzene, pesticides, ... “oxidative phosphorylation” “substrate-level” = Glycolysis (EMP Pw) CM Central Metabolism Pentose phosphate cycle (PPC) PM Peripheral Met. Citric acid [Kreb’s] cycle (TCA) [1-C units]

  4. 1-C unit metabolism, Tetra Hydofolate (THF) and sulfa antibiotics Many Biosyn. Rxns N CH2 COO- Competitive inhibitor O || C--O Sulfanilamide _NH 1st antibiotics people NH2 SO2 NH2 NH bacteria COO- Folic acid (Food, Vitamin) Non-competitive inhibitor Trimethoprin 2nd path way “mobile 1-C carrier” Serine (AA) + THF + THF Glycine (AA) | CH2OH | H || CH2 THF = (1 + 2 +3) +2 p-amino- benzoic acid 1 Pteridine ring +3 Glutamate (AA) Methionine (AA) Purines (A, G) Thiamine (Vit. B1) Thymine (dUMP > dTMP) Coenzyme A, etc... DHF Benefits ? Problems ?

  5. Entner-Doudoroff Pathway and glycolysis 2-Keto, 3-deoxy- 6-P Gluconate -H2O 6-P Gluconate COO- COO- -2 ATP H-C-OH C=O +3 ATP HO-C-H H-C-H NADH 2x +6 ATP +3 ATP H C=O +4 ATP H-C-OH HO-C-H 3-C 3-C 3-C TCA P P P Glycolysis (EMP Pw) Glucose -1 ATP Glucose-6-P (6C) NAD(P)H Fructose-6-P Fructose 1,6-P Triose 3-P (2x 3C) NADH 1, 3-Diphosphoglycerate 3-Phosphoglycerate +2 ATP 2-Phosphoglycerate Phosphoenolpyruvate Net: +8 ATP plus 2x Pyruvate Net: +7 ATP plus 2x Pyruvate Aerobic glucose utilization

  6. Dumping excess electrons (NAD+ from NADH) Bug PH2 ATP NADH CO2 eTS H2 Dissimulatory reduction Assimilatory reduction ? NAD+ Fermentation P S = anaerobic respiration e.g. nitrate > nitrite >> ammonium > nitrogen gas

  7. Sulfur Dominate many subsurface environments Attach to, and reduce insoluble Sulfur, Fe(III) and Mn(IV) oxides Oxidize Organics CO2 Fumarate, Malate, Sulfur, Fe(III), Mn(IV) (terminal electron acceptors, “dissimulatory reduction”) Geobacter sulfurreducens

  8. N Assimilation NH3 NADPH ATP Biosyn. Biosyn. All N-compounds R-NH2 (amino acids) R=N-R’ (purines, etc...) Assimilatory reductases Dissimulatory reductases (anaerobic respiration) Nitrate Nitrite Nitrous oxide NH3 :N N: gas Fixation Lithotrophic oxidation Nitrogen cycle (big pool) GS GDH NH3 a Ketoglutarate (MP) Glutamate (AA) Glutamine (AA) GDH = Glutamate Dehydrogenase GS = Glutamine Synthetase Direct organic sources: ? No preferred N-sources: ~80% atmosphere ~20 Mega-year turnover

  9. Nitrogen fixation, conflict with oxygen poison N2 O2 air NH3 gas soil Clostridium pasteurianum (pages 8, 304) Strict anaerobe Azotobacter vinlandii (pages 8, 44) N2 Obligate aerobe O2 :N N: Air = ~80 nitrogen (food) ~20% oxygen Nitrogenase Proteins (FeS) (Mo) Four fixation strategies: Size, rapid respiration protect Nitrogenase Cyanobacteria sps. PS II makes oxygen Cell differentiation into “Heterocyst” Rhizobia sps. Cell differentiation into “Bacteroid” Symbiosis with plants, form nodule organ

  10. S Assimilation Cysteine (AA) SH2 O-Acetyl serine SH ? Sources: “Assimilatory reduction” Anaerobic respiration NH2 COO- NH2 COO- O-Acetyl CH2 CH2 “Dissimulatory reduction” e.g. Geobacter sp. Geological / volcanic + O2 [S-P-5’Adenosine 3’P] Adenosine phosphosulfate carrier Methionine Lipoic acid Coenzyme A 3 ATP 4 NADPH Thiamine, FeS clusters, etc... SO42-

  11. P Assimilation PO43- R-O-PO32- esters free OM (-) porins PO43- H+ R-OH IM F0F1 ATP + ADP PO43- EMP Rxn, etc... O O O O - P - (O -P- O)n - P - O O O O Alkaline Phosphatase PS 5’ Nucleosidases, etc... Poly-Phosphate Many roles: Storage Inclusion bodies “volutin” n = 1 to 1,000 Pre-biotic Molecular cloning Stress tolerance, virulence, etc... PO43-

  12. Lecture Overview Metabolism (Inside and Out) Growth Survival strategies Cell differentiation Sporulation Symbiosis Diversity and environmental niches Adaptation mechanisms Rapid responses through altered enzyme activities Altering genetic expression

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