Karboksidotrofik Mikroorganizmaların Karbonmonoksit Dehidrojenazları

Öz

Endüstriyel gazlar içerisinde salınan ve kömür gibi yakıtların yanmasıyla açığa çıkan karbonmonoksitin (CO), ilerleyen sanayi ile birlikte çevre kirleticisi olarak doğada konsantrasyonu artmakta ve insanoğlunun sağlığını tehdit etmektedir. Bununla birlikte, yaşamın doğal dengesi içerisinde karboksidotrofik mikroorganizmalar, sahip oldukları karbonmonoksit dehidrogenaz (CODH) enzimleri ile, CO’i karbon ve enerji kaynağı olarak kullanmaktadırlar. Gerek aerobik gerekse anaerobik koşullarda yaşam formları gösteren bu mikroorganizmalar, çok farklı kofaktörlere sahip çeşitli CODH enzimleri ile yüksek ölçüde toksik CO’inkarbondioksite (CO2)dönüşümünü katalizlerler.Böylece, enerji zengini bileşiklerin oluşturulmasında ve küresel karbon döngüsünde karbonun çevreye katılmasıyla önemli potansiyel etkiye sahiptirler. Enzimkatalizlediği reaksiyon nedeniyle biyoteknoloji için büyük bir potansiyel sunmaktadır. CO dehidrojenazın kullanılacağı tasarımlar ile, biyosensörlerde CO tabanlı problarveya yakıt hücreleri üretilebilir. Bu derlemede endüstriyel olarak oldukça öneme sahip olan CO dehidrojenazlar hakkında bilgi sunulması amaçlanmıştır.

Anahtar Kelimeler

• Karboksidotrofik mikroorganizmalar
• Karbon monoksit dehidrojenaz
• Morella thermoacetica

Carbon Monoxide DehydrogenasesfromCarboxidotrophic Microorganisms

Öz

Carbon monoxide (CO), released in industrial gases and released by the burning of fuels such as coal, increases its concentration in nature as an environmental pollutant with the advancing industry and threatens human health. However, in the natural balance of life, carboxidotrophic microorganisms use CO as a carbon and energy source with their carbon monoxide dehydrogenase (CODH) enzymes. These microorganisms, which show life forms in both aerobic and anaerobic conditions, catalyze the conversion of highlytoxic CO to CO2(carbon dioxide) with various CODH enzymes with very different cofactors. Thus, they have significant potential impact in the creation of energy-rich compounds and the incorporation of carbon into the environment in the global carbon cycle. It offers great potential for biotechnology due to the enzyme catalyzed reaction. With designs using CO dehydrogenase, CO-based probes or fuel cells can be produced in biosensors. In this review, it is aimed to present information about the industrially important CO dehydrogenases.

Anahtar Kelimeler

• Carboxidotrophic microorganims
• Carbon monoxide dehydrogenase
• Morella thermoacetica

Kaynakça

1. Varma,D.R., Mulay, S.,Chemtob,S. (2015).Carbon Monoxide: From Public Health Risk to Painless Killer,In: Handbook of Toxicology of Chemical Warfare Agents (Second Edition), Ed(s): GuptaRC,Academic Press,P:267-286.
2. Anand,A., Satyanarayana,T. (2012). Applicability of carboxydotrophic bacterial carbonmonoxidedehydrogenase(CODH) in carbon sequestration and bioenergy generation. 381-384.
3. Adam,P. S, Borrel, G., Gribaldo,S. (2018).Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. Proceedings of the National Academy of Science. 115(6): E1166–E1173.
4. Ragsdale, S. W. (2004). Life with Carbon Monoxide. Critical Reviews inBiochemistry and Molecular Biology 39:165–195.
5. Cao, Z. ve Mo, Y. (2007). Computational Characterization of the Elusive C-Cluster of Carbon Monoxide Dehydrogenase. Journal of Theoretical and Computational Chemistry, Vol. 7, No. 4, 473–484.
6. Meyer, O., Jacobitz, S., and Kruger,B. (1986). Biochemistry and physiology of aerobic carbon monoxide-utilizing bacteria.FEMS Microbiol Rev 39:161–179.
7. Gnida, M., Ferner, R., Gremer, L., Meyer, O., and Meyer-Klaucke, W. (2003). A novel binuclear [CuSMo] cluster at the active site of carbon monoxide dehydrogenase: characterization by X-ray absorption spectroscopy. Biochemistry 42(1):222–230.
8. Johnson, J.L., Rajagopalan, K.V., and Meyer, O. (1990). Isolation and characterization of a second molybdopterin dinucleotide: molybdopterin cytosine dinucleotide. Arch Biochem Biophys 283:542–545.

9. Bray, R.C., George, G.N., Lange, R., and Meyer, O. (1983). Studies by e.p.r. spectroscopy of carbon monoxide oxidases from Pseudomonas carboxydovorans and Pseudomonas carboxydohydrogena. Biochem J. 211:687–694.
10. Meyer, O., Frunzke, K., and M ̈orsdorf, G. (1993). Biochemistry of the aerobic utilization of carbon monoxide. In Microbial growth on C1 compounds,pp. 433–459. J.C. Murrell, and D.P. Kelly, Eds., Intercept, Ltd., Andover, MA.
11. Inoue,M., Nakamoto,I., Omae,K., Oguro,T., Ogata,H., Yoshida,T.,and Sako,Y.(2019) Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases. Front. Microbiol. 9:3353. doi: 10.3389/fmicb.2018.03353
12. Ensign, S.A., Bonam, D., and Ludden, P.W. (1989). Nickel is required for the transfer of electrons from carbon monoxide to the iron-sulfur center(s) of carbon monoxide dehydrogenase from Rhodospirillum rubrum. Biochem 28(12):4968–4973.
13. Bhatnagar, L., Krzycki, J.A., and Zeikus, J.G. (1987). Analysis of hydrogen metabolism in Methanosarcina barkeri: regulation of hydrogenase and role of CO-dehydrogenase in H2 production. FEMS MicrobiolLett 41:337–343.
14. Menon, S.,and Ragsdale, S.W. (1996). Unleashing hydrogenase activity in pyruvate: ferredoxin oxidoreductase and acetyl-CoA synthase/CO dehydrogenase. Biochemistry 35(49):15814–15821.
15. Santiago, B.,and Meyer, O. (1996). Characterization of hydrogenase activities associated with the molybdenum CO dehydrogenase from Oligotropha carboxidovorans. FEMS Microbiol Lett 136(2):157–162.
16. Darnault, C., Volbeda, A., Kim, E.J., Legrand, P., Vernede, X., Lindahl, P.A., and Fontecilla-Camps, J.C. (2003). Ni-Zn-[Fe(4)-S(4)] and Ni-Ni-[Fe(4)-S(4)] clusters in closed and open alpha subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase. Nat Struct Biol 10(4):271–279.
17. Dobbek, H., Svetlitchnyi, V., Gremer, L., Huber, R., and Meyer, O. (2001). Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster. Science 293(5533):1281–1285.
18. Doukov, T.I., Iverson, T., Seravalli, J., Ragsdale, S.W., and Drennan, C.L. (2002). A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Science 298(5593):567–572. Drennan, C.L., Heo, J., Sintchak, M.D., Schreiter, E., and Ludden, P.W. (2001). Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase. Proc Natl Acad Sci USA 98(21):11973–11978.
19. Kiley, P. J., and Beinert., H.(2003). The role of Fe-S proteins in sensing and regulation in bacteria. Curr. Opin. Microbiol. 6:181–185.
20. Pomposiello, P. J., and Demple., B.(2001). Redox-operated genetic switches: the SoxR and OxyR transcription factors. Trends Biotechnol. 19:109–114.
21. Bernhard, M., Buhrke,T., Bleijlevens,B., De Lacey,A. L., Fernandez,V. M., Albracht,S. P.,and Friedrich., B.(2001). The H2sensor of Ralstonia eutropha. Biochemical characteristics, spectroscopic properties, and its interaction with a histidine protein kinase. J. Biol. Chem. 276:15592–15597.
22. Tosques, I. E., Shi,J.,and Shapleigh, J. P. (1996). Cloning and characterization of nnrR, whose product is required for the expression of proteins involved in nitric oxide metabolism in Rhodobacter sphaeroides2.4.3. J. Bacteriol. 178:4958–4964.
23. Zumft, W. G. (2002). Nitric oxide signaling and NO dependent transcriptional control in bacterial denitrification by members of the FNR-CRP regülatör family. J. Mol. Microbiol. Biotechnol. 4:277–286.
24. Roberts,G. P., Youn H., and Kerby,R. L.(2004). CO-Sensing Mechanisms. Mıcrobiol. Mol. Biol. Rev. 68: 453–473.
25. Tan, X., Loke, H., Fitch, S.,and Lindahl, P. A. (2005). The Tunnel of Acetyl-Coenzyme A Synthase/Carbon Monoxide Dehydrogenase Regulates Delivery of CO to the Active Site. J. Am. Chem. Soc.127, 5833-5839.
26. King,G.M. andWeber C.F.(2007). Distribution, diversity and ecology of aerobic CO oxidising bacteria, Nature Rev, 5: 107-118.
27. King, G.M., (2003).Molecular and Culture-Based Analyses of Aerobic Carbon Monoxide Oxidizer Diversity. Applied and Environmental Microbiology, 69:12, 7257–7265.
28. Meyer, O.,and Rhode, M. (1984). Enzymology and bioenergetics of carbon monoxide-oxidizing bacteria. In Microbial growth on C1compounds, pp. 26–33. R.L. Crawford, and R.S. Hanson, Eds., American Society for Microbiology, Washington, DC.[30] Sokolova,T.G., Henstra,A.M., Sipma,J., Parshina,S.N., Stams,A.J.(2009). Diversity and eco-physiological features of thermophilic carboxydotrophic anaerobes, FEMS MicrobiolEcol, 68: 131-141.
29. Krüger, B., and Meyer, O. (1984).Thermophilic Bacilli growing with carbon monoxide. Arch. Microbiol. 139, 402–408.
30. Bell,J.M., Falconer,C., Colby,J., and Williams,E. (1987). CO metabolism by a thermophilic actinomycetes Streptomyces strain G26, J Gen Microbiol, 133: 3445-3456.
31. Park,S.W., Song,T., Kim,S.Y., Oh,J.I., and Eom,C.Y. (2007). CODH in Mycobacterium possesses a NODH activity, Biochem Biophys Res Commun, 362: 449-453.
32. Lorite,M.J., Tachil,J., Sanjuan,J., Meyer,O., and Bedmar,E.J.(2000). CODH activity in Bradyrhizobium japonicum, Appl Env Microbiol, 66: 1871-1876.
33. Matson,E.G., Gora,K.G., and Leadbetter,J.R.(2011). Anaerobic CODH diversity in the homoacetogenic hindgut microbial communities of lower termites and wood roach, PLOS one, 6: 1-15.
34. Drake, H.L., and Daniel, S.L. (2004). Physiology of the thermophilic acetogen Moorella thermoacetica. Research in Microbiology 155: 869-883.
35. Jiang, B., Henstra, A.M., Paulo, P.L., Balk, M., Van Doesburg, W., and Stams, A.J.M. (2009).Atypical one-carbon metabolism of an acetogenic and hydrogenogenic Moorella thermoacetica strain. Archives of Microbiology 191: 123-131.
36. Pierce,E., Xie,G., Barabote,R. D., Saunders,E., Han,C. S, Detter,J. C., Richardson,P., Brettin,T.S., Das,A., Ljungdahl,L.G.andRagsdale,S.W. (2008).The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol. Oct;10(10):2550-73.
37. Doukov, T. I., Blasiak,L. C., Seravalli,J., Ragsdale,S. W., and Drennan,C. L. (2008). Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase. Biochemistry, 47: 3474–3483.
38. Tomita, T., Gonzalez,G, Chang,A.L., Ikeda-Saito,M., and Gilles-Gonzalez, M.A.(2002). A comparative resonance Raman analysis of heme-binding PAS domains: heme iron coordination structures of the BjFixL, AxPDEA1, EcDos, and MtDos proteins. Biochemistry 41:4819–4826.
39. Uchida, T., Ishikawa,H., Ishimori,K., Morishima,I., Nakajima,H., Aono,S., Mizutani,Y., and Kitagawa, T.(2000). Identification of histidine 77 as the axial heme ligand of carbonmonoxy CooA by picosecond time-resolved resonance Raman spectroscopy. Biochemistry 39:12747–12752.
40. Spiro, T. G., and Jarzecki, A. A.(2001). Heme-based sensors: theoretical modeling of heme-ligand-protein interactions. Curr. Opin. Chem. Biol. 5:715–723.
41. Jeon,W.B., Cheng, J., and Ludden, P.W. (2001). Purification and characterization of membrane-associated CooC protein and its functional role in the insertion of nickel into carbon monoxide dehydrogenase from Rhodospirillum rubrum. J Biol Chem 276(42):38602–38609.
42. Shelver, D., Kerby, R.L., He, Y.P., and Roberts, G.P. (1995). Carbonmonoxide-induced activation of gene expression in Rhodospirillum rubrum requires the product of cooA, a member of the cyclic AMP receptor protein family of transcriptional regulators. J Bacteriol177(8):2157–2163.
43. Watt, R.K. and Ludden, P.W. (1998). The identification, purification, and characterization of CooJ. A nickel-binding protein that is co-regulated with the Ni-containing CO dehydrogenase from Rhodospirillum rubrum. J Biol Chem 273(16):10019–10025.
44. Kerby, R.L., Ludden, P.W., and Roberts, G.P. (1997). In vivo nickel insertion into the carbon monoxide dehydrogenase of Rhodospirillum rubrum: molecular and physiological characterization of cooCTJ. J Bacteriol 179(7):2259–2266.
45. Watt, R.K. and Ludden, P.W. (1999). Nickel-binding proteins. Cell Mol Life Sci 56(7–8):604–625.
46. Dioum, E.M., Rutter, J., Tuckerman, J.R., Gonzalez, G., Gilles-Gonzalez, M.A., and McKnight, S.L. (2002). NPAS2: a gas-responsive transcription factor. Science 298(5602):2385–2387.
47. Aono, S. (2003). Biochemical and biophysical properties of the COsensing transcriptional activator CooA. Acc Chem Res 36:825–831.[50] Lanzilotta, W.N., Schuller, D.J., Thorsteinsson, M.V., Kerby, R.L., Roberts, G.P., and Poulos, T.L. (2000). Structure of the CO sensing transcription activator CooA. Nat Struct Biol 7:876–880.
48. Coyle, C.M., Puranik, M., Youn, H., Nielsen, S.B., Williams, R.D., Kerby, R.L., Roberts, G.P., and Spiro, T.G. (2003). Activation mechanism of the CO sensor CooA. Mutational and resonance Raman spectroscopic studies. J Biol Chem 278(37):35384–35393.
49. Yamamoto, K., Ishikawa, H., Takahashi, S., Ishimori, K., Morishima, I., Nakajima, H., and Aono, S. (2001). Binding of CO at the Pro2 side is crucial for the activation of CO-sensing transcriptional activator CooA. 1H NMR spectroscopic studies. J Biol Chem 276:11473–11476.
50. Leduc, J., Thorsteinsson, M.V., Gaal, T., and Roberts, G.P. (2001). Mapping CooA.RNApolymerase interactions. Identification of activating regions 2 and 3 in CooA, the co-sensing transcriptional activator. J Biol Chem 276(43):39968–39973.
51. Wu,M., Ren,Q., Durkin,A.S., Daugherty,S.C., Brinkac,L.M., Dodson,R.J., Madupu,R., Sullivan,S.A., Kolonay,J.F., Haft,D.H., Nelson,W.C., Tallon,L.J., Jones,K.M., Ulrich,L.E., Gonzalez,J.M., Zhulin,I.B., Robband,F.T., and Eisen,J.A. (2005). Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901, PLoS Genet. 1 0563–0574.
52. Techtmann,S.M., Colman,A.S., Murphy,M.B., Schackwitz,W.S., Goodwin,L.A.,andRobb,F.T. (2011).Regulation of multiple carbon monoxide consumption pathways in anaerobic bacteria, Front. Microbiol. 2 1–12.
53. Lindahl,P.A.,andChang,B. (2001).The evolution of acetyl-CoA synthase, Origins Life Evol. Biosphere 31 403–434.
54. Wang,V.C., Ragsdale,S.W., and Armstrong,F.A. (2013).Investigations of two bidirectional carbon monoxide dehydrogenases from Carboxydothermus hydrogenoformans by protein film electrochemistry. ChemBioChem. 14:1845–1851.
55. Parkin,A., Seravalli,J., Vincent,K.A., Ragsdale,S.W., and Armstrong,F.A. (2007).Rapid and efficient electrocatalytic CO2/CO interconversions by Carboxydothermus hydrogenoformans CO dehydrogenase I on an electrode. J. Am. Chem. Soc.129: 10328–10329.
56. Woolerton,T.W., Sheard,S., Reisner,E., Pierce,E., Ragsdale,S.W., and Armstrong,F.A. (2010).Efficient and clean photoreduction of CO2to CO by enzyme-modified TiO2 nanoparticles using visible light. J. Am. Chem. Soc.132:2132–2133.
57. Can, M., Armstrong, F.A., and Ragsdale, S.W. (2014). Structure, Function, and Mechanism of the Nickel Metalloenzymes,CO Dehydrogenase, and Acetyl-CoA Synthase.
58. Maiga, M., Choi, S.W., Atudorei, V., Sharp, Z.D., Bishai, W.R., and Timmins, G.S. (2014). In Vitro and In Vivo Studies of a Rapid and Selective Breath Test for Tuberculosis Based upon Mycobacterial CO Dehyrogenase.
59. Quiza, L., Lalande, I., Guertin, C., and Constant, P. (2014). Land-use influences the distribution and activity of high affinity CO-oxidizing bacteria associated type I-coxL genotype in soil.