A novel pathway for the biosynthesis of heme in Archaea: Genome-based bioinformatic predictions and experimental evidence

Archaea

Volumn 2010, Issue , 2010, Pages

  Layer, Gunhild ^a   Storbeck, Sonja ^a   Rolfes, Sarah ^a   Raux Deery, Evelyne ^b   Warren, Martin J ^b   Jahn, Dieter ^a  

^a TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^b UNIVERSITY OF KENT   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; METHANOSARCINA BARKERI;

EID: 79251541167     PISSN: 14723646     EISSN: None     Source Type: Journal    
DOI: 10.1155/2010/175050     Document Type: Article

References (57)

1. Layer G., Reichelt J., Jahn D., Heinz D. W., Structure and function of enzymes in heme biosynthesis Protein Science 2010 19 6 1137 1161
2. Battersby A. R., Tetrapyrroles: the pigments of life Natural Product Reports 2000 17 6 507 526
3. Hunter G. A., Ferreira G. C., 5-Aminolevulinate synthase: catalysis of the first step of heme biosynthesis Cellular and Molecular Biology 2009 55 1 102 110
4. Ler C., Schauer S., Mbius K., Schulze J., Schubert W. D., Heinz D. W., Jahn D., Moser J., Complex formation between glutamyl-tRNA reductase and glutamate-1- semialdehyde 2,1-aminomutase in Escherichia coli during the initial reactions of porphyrin biosynthesis Journal of Biological Chemistry 2005 280 19 18568 18572 (Pubitemid 41379554)
5. Jaffe E. K., The porphobilinogen synthase catalyzed reaction mechanism Bioorganic Chemistry 2004 32 5 316 325
6. Shoolingin-Jordan P. M., Porphobilinogen deaminase and uroporphyrinogen III synthase: structure, molecular biology, and mechanism Journal of Bioenergetics and Biomembranes 1995 27 2 181 195
7. Dailey H. A., Terminal steps of haem biosynthesis Biochemical Society Transactions 2002 30 4 590 595
8. Dailey H. A., Dailey T. A., Wu C. K., Medlock A. E., Rose J. P., Wang K. F., Ferrochelatase at the millennium: structures, mechanisms and [2Fe-2S] clusters Cellular and Molecular Life Sciences 2000 57 13-14 1909 1926
9. Frankenberg N., Moser J., Jahn D., Bacterial heme biosynthesis and its biotechnological application Applied Microbiology and Biotechnology 2003 63 2 115 127 (Pubitemid 38130583)
10. Panek H., O'Brian M. R., A whole genome view of prokaryotic haem biosynthesis Microbiology 2002 148 8 2273 2282
11. Cavallaro G., Decaria L., Rosato A., Genome-based analysis of heme biosynthesis and uptake in prokaryotic systems Journal of Proteome Research 2008 7 11 4946 4954
12. Shima S., Sordel-Klippert M., Brioukhanov A., Netrusov A., Linder D., Thauer R. K., Characterization of a heme-dependent catalase from Methanobrevibacter arboriphilus Applied and Environmental Microbiology 2001 67 7 3041 3045 (Pubitemid 33644770)
13. Duwat P., Sourice S., Cesselin B., Lamberet G., Vido K., Gaudu P., Le Loir Y., Violet F., Loubire P., Gruss A., Respiration capacity of the fermenting bacterium Lactococcus lactis and its positive effects on growth and survival Journal of Bacteriology 2001 183 15 4509 4516 (Pubitemid 32646000)
14. Allen J. W. A., Harvat E. M., Stevens J. M., Ferguson S. J., A variant System I for cytochrome c biogenesis in archaea and some bacteria has a novel CcmE and no CcmH FEBS Letters 2006 580 20 4827 4834
15. Bertini I., Cavallaro G., Rosato A., Cytochrome c: occurrence and functions Chemical Reviews 2006 106 1 90 115 (Pubitemid 43159622)
16. Bertini I., Cavallaro G., Rosato A., Evolution of mitochondrial-type cytochrome c domains and of the protein machinery for their assembly Journal of Inorganic Biochemistry 2007 101 11-12 1798 1811 (Pubitemid 47576183)
17. Freitas T. A. K., Hou S., Dioum E. M., Saito J. A., Newhouse J., Gonzalez G., Gilles-Gonzalez M. A., Alam M., Ancestral hemoglobins in Archaea Proceedings of the National Academy of Sciences of the United States of America 2004 101 17 6675 6680 (Pubitemid 38586033)
18. Ho W. W., Li H., Nishida C. R., Ortiz De Montellano P. R., Poulos T. L., Crystal structure and properties of CYP231A2 from the thermoacidophilic archaeon Picrophilus torridus Biochemistry 2008 47 7 2071 2079 (Pubitemid 351287133)
19. Nardini M., Pesce A., Thijs L., Saito J. A., Dewilde S., Alam M., Ascenzi P., Coletta M., Ciaccio C., Moens L., Bolognesi M., Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity EMBO Reports 2008 9 2 157 163 (Pubitemid 351223453)
20. Pereira M. M., Bandeiras T. M., Fernandes A. S., Lemos R. S., Melo A. M. P., Teixeira M., Respiratory chains from aerobic thermophilic prokaryotes Journal of Bioenergetics and Biomembranes 2004 36 1 93 105 (Pubitemid 38500763)
21. Schfer G., Engelhard M., Mller V., Bioenergetics of the Archaea Microbiology and Molecular Biology Reviews 1999 63 3 570 620 (Pubitemid 29422783)
22. Thauer R. K., Kaster A. K., Seedorf H., Buckel W., Hedderich R., Methanogenic archaea: ecologically relevant differences in energy conservation Nature Reviews Microbiology 2008 6 8 579 591
23. Akutsu H., Park J. S., Sano S., L-methionine methyl is specifically incorporated into the C-2 and C-7 positions of the porphyrin of cytochrome c3 in a strictly anaerobic bacterium, Desulfovibrio vulgaris Journal of the American Chemical Society 1993 115 25 12185 12186 (Pubitemid 2004463)
24. Buchenau B., Kahnt J., Heinemann I. U., Jahn D., Thauer R. K., Heme biosynthesis in Methanosarcina barkeri via a pathway involving two methylation reactions Journal of Bacteriology 2006 188 24 8666 8668 (Pubitemid 44894068)
25. Ishida T., Yu L., Akutsu H., Ozawa K., Kawanishi S., Seto A., Inubushi T., Sano S., A primitive pathway of porphyrin biosynthesis and enzymology in Desulfovibrio vulgaris Proceedings of the National Academy of Sciences of the United States of America 1998 95 9 4853 4858 (Pubitemid 28208515)
26. Lobo S. A. L., Brindley A., Warren M. J., Saraiva L. M., Functional characterization of the early steps of tetrapyrrole biosynthesis and modification in Desulfovibrio vulgaris Hildenborough Biochemical Journal 2009 420 2 317 325
27. Storbeck S., Walther J., Mller J., Parmar V., Schiebel H. M., Kemken D., Dlcks T., Warren M. J., Layer G., The Pseudomonas aeruginosa nirE gene encodes the S-adenosyl-L-methionine- dependent uroporphyrinogen III methyltransferase required for heme d biosynthesis FEBS Journal 2009 276 20 5973 5982
28. Uchiyama I., MBGD: microbial genome database for comparative analysis Nucleic Acids Research 2003 31 1 58 62 (Pubitemid 36150333)
29. Uchiyama I., MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups Nucleic Acids Research 2007 35 1 D343 D346 (Pubitemid 46056228)
30. Uchiyama I., Higuchi T., Kawai M., MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity Nucleic Acids Research 2009 38 1 D361 D365
31. Zhang Y., Rodionov D. A., Gelfand M. S., Gladyshev V. N., Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization BMC Genomics 2009 10, article 78
32. Pfaltz A., Kobelt A., Hunster R., Thauer R. K., Biosynthesis of coenzyme F430 in methanogenic bacteria. Identification of 15,17-seco-F430-17-acid as an intermediate European Journal of Biochemistry 1988 170 1-2 459 467 (Pubitemid 18028488)
33. Schubert H. L., Rose R. S., Leech H. K., Brindley A. A., Hill C. P., Rigby S. E. J., Warren M. J., Structure and function of SirC from Bacillus megaterium: a metal-binding precorrin-2 dehydrogenase Biochemical Journal 2008 415 2 257 263
34. Warren M. J., Raux E., Schubert H. L., Escalante-Semerena J. C., The biosynthesis of adenosylcobalamin (vitamin B) Natural Product Reports 2002 19 4 390 412
35. Zajicek R. S., Bali S., Arnold S., Brindley A. A., Warren M. J., Ferguson S. J., D haem biogenesisassessing the roles of three nir gene products FEBS Journal 2009 276 21 6399 6411
36. Zumft W. G., Cell biology and molecular basis of denitrification? Microbiology and Molecular Biology Reviews 1997 61 4 533 616 (Pubitemid 28006959)
37. Brindley A. A., Zajicek R., Warren M. J., Ferguson S. J., Rigby S. E. J., NirJ, a radical SAM family member of the d1 heme biogenesis cluster FEBS Letters 2010 584 11 2461 2466
38. Kawasaki S., Arai H., Kodama T., Igarashi Y., Gene cluster for dissimilatory nitrite reductase (nir) from Pseudomonas aeruginosa: sequencing and identification of a locus for heme d1 biosynthesis Journal of Bacteriology 1997 179 1 235 242 (Pubitemid 26428486)
39. Palmedo G., Seither P., Korner H., Matthews J. C., Burkhalter R. S., Timkovich R., Zumft W. G., Resolution of the nirD locus for heme d1 synthesis of cytochrome cd (respiratory nitrite reductase) from Pseudomonas stutzeri European Journal of Biochemistry 1995 232 3 737 746
40. Suzuki M., Hirai T., Arai H., Ishii M., Igarashi Y., Purification, characterization, and gene cloning of thermophilic cytochrome cd nitrite reductase from Hydrogenobacter thermophilus TK-6 Journal of Bioscience and Bioengineering 2006 101 5 391 397 (Pubitemid 44354419)
41. Booker S. J., Anaerobic functionalization of unactivated C-H bonds Current Opinion in Chemical Biology 2009 13 1 58 73
42. Frey P. A., Hegeman A. D., Ruzicka F. J., The radical SAM superfamily Critical Reviews in Biochemistry and Molecular Biology 2008 43 1 63 88
43. Layer G., Moser J., Heinz D. W., Jahn D., Schubert W. D., Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes EMBO Journal 2003 22 23 6214 6224 (Pubitemid 37522579)
44. Johnson E. F., Mukhopadhyay B., Coenzyme F-dependent sulfite reductase-enabled sulfite detoxification and use of sulfite as a sole sulfur source by Methanococcus maripaludis Applied and Environmental Microbiology 2008 74 11 3591 3595 (Pubitemid 351812814)
45. Schiffer A., Parey K., Warkentin E., Diederichs K., Huber H., Stetter K. O., Kroneck P. M. H., Ermler U., Structure of the Dissimilatory Sulfite Reductase from the Hyperthermophilic Archaeon Archaeoglobus fulgidus Journal of Molecular Biology 2008 379 5 1063 1074
46. Thauer R. K., Bonacker L. G., Biosynthesis of coenzyme F430, a nickel porphinoid involved in methanogenesis Ciba Foundation symposium 1994 180 210 222
47. Fan J., Wang D., Liang Z., Guo M., Teng M., Niu L., Maize uroporphyrinogen III methyltransferase: overexpression of the functional gene fragments in Escherichia coli and one-step purification Protein Expression and Purification 2006 46 1 40 46 (Pubitemid 43246994)
48. Stroupe M. E., Leech H. K., Daniels D. S., Warren M. J., Getzoff E. D., CysG structure reveals tetrapyrrole-binding features and novel regulation of siroheme biosynthesis Nature Structural Biology 2003 10 12 1064 1073
49. Vvodov J., Graham R. M., Raux E., Schubert H. L., Roper D. I., Brindley A. A., Ian Scott A., Roessner C. A., Stamford N. P. J., Elizabeth Stroupe M., Getzoff E. D., Warren M. J., Wilson K. S., Structure/function studies on a S-adenosyl-L-methionine-dependent uroporphyrinogen III C methyltransferase (SUMT), a key regulatory enzyme of tetrapyrrole biosynthesis Journal of Molecular Biology 2004 344 2 419 433 (Pubitemid 39441214)
50. Schubert H. L., Raux E., Brindley A. A., Leech H. K., Wilson K. S., Hill C. P., Warren M. J., The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase EMBO Journal 2002 21 9 2068 2075 (Pubitemid 34516765)
51. Chou Pei-Lin., Ohtsuka M., Minowa T., Yamasato K., Sakano Y., Matsuzawa H., Ohta T., Sakai H., Reddish Escherichia coli cells caused by overproduction of Bacillus stearothermophilus uroporphyrinogen III methylase: cloning, sequencing, and expression of the gene Bioscience, Biotechnology and Biochemistry 1995 59 10 1817 1824 (Pubitemid 3009675)
52. Leustek T., Smith M., Murillo M., Singh D. P., Smith A. G., Woodcock S. C., Awan S. J., Warren M. J., Siroheme biosynthesis in higher plants. Analysis of an S-adenosyl-L- methionine-dependent uroporphyrinogen III methyltransferase from Arabidopsis thaliana Journal of Biological Chemistry 1997 272 5 2744 2752 (Pubitemid 27053318)
53. Sattler I., Roessner C. A., Stolowich N. J., Hardin S. H., Harris-Haller L. W., Yokubaitis N. T., Murooka Y., Hashimoto Y., Scott A. I., Cloning, sequencing, and expression of the uroporphyrinogen III methyltransferase cobA gene of Propionibacterium freudenreichii (shermanii) Journal of Bacteriology 1995 177 6 1564 1569
54. Warren M. J., Stolowich N. J., Santander P. J., Roessner C. A., Sowa B. A., Scott A. I., Enzymatic synthesis of dihydrosirohydrochlorin (precorrin-2) and of a novel pyrrocorphin by uroporphyrinogen III methylase FEBS Letters 1990 261 1 77 80
55. Blanche F., Debussche L., Thibaut D., Crouzet J., Cameron B., Purification and characterization of S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase from Pseudomonas denitrificans Journal of Bacteriology 1989 171 8 4222 4231
56. Blanche F., Robin C., Couder M., Faucher D., Cauchois L., Cameron B., Crouzet J., Purification, characterization, and molecular cloning of S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase from Methanobacterium ivanovii Journal of Bacteriology 1991 173 15 4637 4645
57. Robin C., Blanche F., Cauchois L., Cameron B., Couder M., Crouzet J., Primary structure, expression in Escherichia coli, and properties of S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase from Bacillus megaterium Journal of Bacteriology 1991 173 15 4893 4896