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Nitrogen, why is it so important?

Nitrogen, why is it so important?

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Nitrogen, why is it so important?

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  1. Nitrogen, why is it so important? N=N air N=N N=N N=N Source:CRC Handbook of Chemistry and Physicsby David R. Lide, Editor-in-Chief1997 Edition

  2. Excess Nitrogen • Nitrogen Fixation: Atmospheric dinitrogen(N2)  Ammonia(NH3 ) • Nitrogen-fixers – bacteria, free-living and symbiotic http://dragon.seowon.ac.kr/~bioedu/bio/ohp/t-294.jpg

  3. The Big Picture N2 + 8H+ + 8e- + 16 ATP = 2NH3 + H2 + 16ADP + 16 Pi

  4. Nitrogen-Fixing Bacteria

  5. Nitrogen Fixation Mechanism

  6. Nitrogen Dependence : Cryptobiotic Crust http://helios.bto.ed.ac.uk/bto/microbes/nitrogen.htm

  7. How they know how to fix nitrogen:

  8. Nitrogenase

  9. Nitrogenase Enzyme Complex Fe Protein Fe-Mo Protein a b a b http://www.tau.ac.il/~ecology/virtau/2tali/The%20Nitrogenase%20complex.htm

  10. Fe-Mo Protein Regulation Fe Protein b a a b

  11. Activation of NifA Fe-Mo Protein Regulation Fe Protein b a a b NtrC-RNA polymerase

  12. Electron Transport Fe-Mo Protein Regulation Fe Protein b a a b ATP Ferredoxin

  13. Electron Transport Fe-Mo Protein Regulation Reduced Fe Protein b a a b ATP Ferredoxin

  14. Electron Transport Reduction of Fe-Mo Protein Regulation Reduced Fe Protein b a a b ATP Ferredoxin

  15. Electrons Donated to N2 Electron Transport Reduction of Fe-Mo Protein Regulation Reduced Fe Protein b a a b ATP Ferredoxin

  16. Electrons Donated to N2 Formation of NH3 Electron Transport Reduction of Fe-Mo Protein Regulation Reduced Fe Protein b a a b ATP Ferredoxin

  17. Fe-Mo Protein Regulation Fe Protein b a a b

  18. Activation of NifL Fe-Mo Protein Regulation Fe Protein b a a b Oxygen Presence

  19. Activation of NifL Suppression of NifA Fe-Mo Protein Regulation Fe Protein b a a b Oxygen Presence

  20. Electron Transport Fe-Mo Protein Regulation Fe Protein b a a b Ferredoxin

  21. Electron Transport Fe-Mo Protein Regulation Fe Protein b a a b Ferredoxin

  22. Electron Transport Fe-Mo Protein Regulation Fe Protein b a a b Order Importance? Ferredoxin

  23. Is there a correlation among the position of nif genes among nitrogen-fixers?

  24. Methods: • Identify the nif genes involved in nitrogen fixation • Map out the location of specific nif genes in Tery and Cwat • Compare geographic proximity of cyanobacteria to other nitrogen fixers.

  25. Examination of Synteny • Nif genes in Trichodesmium similar to Crocosphaera? • Examine orthologs of specific genes related to NIF

  26. Genes Described By Nif: Trichodesmium/Crocosphaera • (("Tn10-like transposase [Bacteroides uniformis]" "NifU [Trichodesmium sp. IMS101]" "hypothetical protein [Trichodesmium erythraeum IMS101] gi|20138873|sp|O34106|NIFH_TRIS1 Nitro" "hypothetical protein [Trichodesmium erythraeum IMS101] gi|9081910|gb|AAF82641.1| NifX [Tricho" "hypothetical protein [Trichodesmium erythraeum IMS101] gi|20139219|sp|Q9KJL4|NIFW_TRIS1 Nitro" "COG1348: Nitrogenase subunit NifH (ATPase) [Trichodesmium erythraeum IMS101]" "COG1625: Fe-S oxidoreductase, related to NifB/MoaA family [Trichodesmium erythraeum IMS1") ("pyruvate oxidoreductase [Synechocystis sp. PCC 6803] gi|1709285|sp|P52965|NIFJ_SYNY3 Putativ" "Unknown [Vibrio vulnificus CMCP6] gi|27361669|gb|AAO10576.1|AE016804_86 Unknown [Vibrio vulnificus" "NifT protein [Nostoc sp. PCC 7120] gi|25532906|pir||AF1982 NifT protein [imported] - Nostoc sp." "NifP [Cyanothece sp. PCC 8801]" "NifS [Cyanothece sp. PCC 8801]" "Nitrogenase iron protein (Nitrogenase component II) (Nitrogenase Fe protein) (Nitrogenas" "Nitrogenase iron-molybdenum cofactor biosynthesis protein nifE gi|2183304|gb|AAC35194.1| NifE" "Nitrogenase iron-molybdenum cofactor biosynthesis protein nifN gi|2183305|gb|AAC35195.1| NifN" "NifX [Cyanothece sp. PCC 8801]" "Nitrogenase stabilizing/protective protein nifW gi|2183307|gb|AAC35197.1| NifW [Cyanothece sp" "unknown protein [Synechocystis sp. PCC 6803] gi|1652359|dbj|BAA17282.1| ORF_ID:slr2030~unknow" "light-independent protochlorophyllide reductase iron protein subunit; ChlL [Synechocystis sp." "putative NifU-like protein [Synechococcus sp. PCC 7942]")) But what does this mean?

  27. Are the Nif Genes in Different Order? Crocosphaera(CWAT) NifH Trichodesmium (TERY) NifH

  28. Are the Nif Genes in Different Order? Crocosphaera(CWAT) NifH Trichodesmium (TERY) NifH

  29. Genes Downstream… Crocosphaera(CWAT) MOFE NifH Trichodesmium (TERY) NifH MOFE

  30. Genes Upstream… Crocosphaera(CWAT) NifH Trichodesmium (TERY) NifH

  31. Synteny Among Crocosphaera and Trichodesmium Similar Functionally and Geographically Crocosphaera(CWAT) NifH Trichodesmium (TERY) NifH

  32. Synteny Among Crocosphaera and Trichodesmium Crocosphaera(CWAT) MOFE NifH Trichodesmium (TERY) NifH MOFE

  33. Synteny Among Crocosphaera and Trichodesmium Crocosphaera(CWAT) Alpha chain only MOFE NifH Trichodesmium (TERY) NifH MOFE Alpha and beta chain

  34. Synteny Among Crocosphaera and Trichodesmium Makes sense…need e- for transport Crocosphaera(CWAT) Alpha chain only Hypothetical Protein MOFE NifH Trichodesmium (TERY) NifH MOFE Hemolysin activation/secretion protein Alpha and beta chain

  35. Synteny Among Crocosphaera and Trichodesmium Similar Function? Crocosphaera(CWAT) Alpha chain only Hypothetical Protein MOFE NifH Trichodesmium (TERY) NifH MOFE Hemolysin activation/secretion protein Alpha and beta chain

  36. In Reality, Synteny Exists! Crocosphaera(CWAT) Alpha chain only Hypothetical Protein MOFE NifH Trichodesmium (TERY) NifH MOFE Hemolysin activation/secretion protein Alpha and beta chain

  37. Regulators

  38. Gene Conservation Among Other N-Fixers NifA

  39. Gene Conservation NifA Ferrodoxin

  40. Gene Conservation NifA Transcriptional Activator NifA Ferrodoxin

  41. Other Regulators? A L

  42. Electron Transport Fe-Mo Protein Regulation Fe Protein b a a b Ferredoxin

  43. Electron Transport Fe-Mo Protein Regulation Fe Protein b a a b Ferredoxin H D K A L

  44. Mutational Regulation H D K A L

  45. Mutational Regulation H D K A L

  46. Electron Transport Fe-Mo Protein Regulation Fe Protein b a a b Ferredoxin H D K A L

  47. Similarities and Differences of Nif in Nitrogen-fixing bacteria? • Functional conservation between nif-genes of nitrogen fixers