User:Mario Murakami

Mario Murakami is the scientific director of the Brazilian Biorenewables National Laboratory (since 2018) and former coordinator of the macromolecular crystallography village at the Brazilian National Center for Research in Energy and Materials (2010-2017). He obtained Ph.D. degree in molecular biophysics (2006) from the State University of São Paulo with a split Ph.D. at the University of Hamburg and German Electron Synchrotron DESY. He worked with the structural elucidation of macromolecular complexes involved in the inhibition and activation of enzymes during his post-docs at UNESP and Rutgers University. His current research interests encompass the discovery and mechanistic understanding of CAZymes and the genetic engineering of filamentous fungi for enzyme production. He has contributed to structure and function studies of CAZymes from families GH1 [1, 2, 3, 4, 5, 6], GH2 [7], GH5 [8, 9, 10, 11, 12, 13], GH7 [14], GH8 [15], GH10 [16, 17, 18], GH11 [19, 20, 21], GH12 [22, 23, 24], GH16 [25, 26], GH26 [27], GH39 [28, 29], GH42 [30], GH43 [31, 32, 33], GH45 [34], GH51 [35, 36], GH54 [37], GH57 [38], GH128 [39] and AA9 [40]. Recently, his group rationally engineered a publicly available strain (Trichoderma reesei RUT-C30), which can secrete more than 80 g/L of proteins, mostly CAZymes, using a low-cost and byproduct-based bioprocess [41].

Particularly notable works include the systematic biochemical and structural investigation of the GH128 family [39], the development of a cellulase hyper-secreting strain [41], the molecular basis for Man-β-1,4-GlcNAc [13] and xyloglucan [11] specificity in the GH5 family, the discovery of a GH10 reducing end xylose-releasing exo-oligoxylanase [11], the mechanistic understanding and rational design of rumen metagenome GH43 arabinanases [31], the structural determinants for glucose tolerance in the GH1 beta-glucosidases [1].

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Solved structures

PDB ID 3N98 - GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

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References

1. de Giuseppe PO, Souza Tde A, Souza FH, Zanphorlin LM, Machado CB, Ward RJ, Jorge JA, Furriel Rdos P, and Murakami MT. (2014). Structural basis for glucose tolerance in GH1 β-glucosidases. Acta Crystallogr D Biol Crystallogr. 2014;70(Pt 6):1631-9. DOI:10.1107/S1399004714006920 |
2. Crespim E, Zanphorlin LM, de Souza FH, Diogo JA, Gazolla AC, Machado CB, Figueiredo F, Sousa AS, Nóbrega F, Pellizari VH, Murakami MT, and Ruller R. (2016). A novel cold-adapted and glucose-tolerant GH1 β-glucosidase from Exiguobacterium antarcticum B7. Int J Biol Macromol. 2016;82:375-80. DOI:10.1016/j.ijbiomac.2015.09.018 |
3. Santos CA, Zanphorlin LM, Crucello A, Tonoli CCC, Ruller R, Horta MAC, Murakami MT, and de Souza AP. (2016). Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 β-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions. Biotechnol Biofuels. 2016;9:71. DOI:10.1186/s13068-016-0487-0 |
4. Zanphorlin LM, de Giuseppe PO, Honorato RV, Tonoli CC, Fattori J, Crespim E, de Oliveira PS, Ruller R, and Murakami MT. (2016). Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 β-glucosidase from Exiguobacterium antarcticum B7. Sci Rep. 2016;6:23776. DOI:10.1038/srep23776 |
5. Toyama D, de Morais MAB, Ramos FC, Zanphorlin LM, Tonoli CCC, Balula AF, de Miranda FP, Almeida VM, Marana SR, Ruller R, Murakami MT, and Henrique-Silva F. (2018). A novel β-glucosidase isolated from the microbial metagenome of Lake Poraquê (Amazon, Brazil). Biochim Biophys Acta Proteins Proteom. 2018;1866(4):569-579. DOI:10.1016/j.bbapap.2018.02.001 |
6. Santos CA, Morais MAB, Terrett OM, Lyczakowski JJ, Zanphorlin LM, Ferreira-Filho JA, Tonoli CCC, Murakami MT, Dupree P, and Souza AP. (2019). An engineered GH1 β-glucosidase displays enhanced glucose tolerance and increased sugar release from lignocellulosic materials. Sci Rep. 2019;9(1):4903. DOI:10.1038/s41598-019-41300-3 |
7. Domingues MN, Souza FHM, Vieira PS, de Morais MAB, Zanphorlin LM, Dos Santos CR, Pirolla RAS, Honorato RV, de Oliveira PSL, Gozzo FC, and Murakami MT. (2018). Structural basis of exo-β-mannanase activity in the GH2 family. J Biol Chem. 2018;293(35):13636-13649. DOI:10.1074/jbc.RA118.002374 |
8. dos Santos CR, Paiva JH, Meza AN, Cota J, Alvarez TM, Ruller R, Prade RA, Squina FM, and Murakami MT. (2012). Molecular insights into substrate specificity and thermal stability of a bacterial GH5-CBM27 endo-1,4-β-D-mannanase. J Struct Biol. 2012;177(2):469-76. DOI:10.1016/j.jsb.2011.11.021 |
9. Santos CR, Paiva JH, Sforça ML, Neves JL, Navarro RZ, Cota J, Akao PK, Hoffmam ZB, Meza AN, Smetana JH, Nogueira ML, Polikarpov I, Xavier-Neto J, Squina FM, Ward RJ, Ruller R, Zeri AC, and Murakami MT. (2012). Dissecting structure-function-stability relationships of a thermostable GH5-CBM3 cellulase from Bacillus subtilis 168. Biochem J. 2012;441(1):95-104. DOI:10.1042/BJ20110869 |
10. Alvarez TM, Paiva JH, Ruiz DM, Cairo JP, Pereira IO, Paixão DA, de Almeida RF, Tonoli CC, Ruller R, Santos CR, Squina FM, and Murakami MT. (2013). Structure and function of a novel cellulase 5 from sugarcane soil metagenome. PLoS One. 2013;8(12):e83635. DOI:10.1371/journal.pone.0083635 |
11. Dos Santos CR, Cordeiro RL, Wong DW, and Murakami MT. (2015). Structural basis for xyloglucan specificity and α-d-Xylp(1 → 6)-D-Glcp recognition at the -1 subsite within the GH5 family. Biochemistry. 2015;54(10):1930-42. DOI:10.1021/acs.biochem.5b00011 |
12. Ruiz DM, Turowski VR, and Murakami MT. (2016). Effects of the linker region on the structure and function of modular GH5 cellulases. Sci Rep. 2016;6:28504. DOI:10.1038/srep28504 |
13. Cordeiro RL, Pirolla RAS, Persinoti GF, Gozzo FC, de Giuseppe PO, and Murakami MT. (2019). N-glycan Utilization by Bifidobacterium Gut Symbionts Involves a Specialist β-Mannosidase. J Mol Biol. 2019;431(4):732-747. DOI:10.1016/j.jmb.2018.12.017 |
14. Segato F, Damasio AR, Gonçalves TA, Murakami MT, Squina FM, Polizeli M, Mort AJ, and Prade RA. (2012). Two structurally discrete GH7-cellobiohydrolases compete for the same cellulosic substrate fiber. Biotechnol Biofuels. 2012;5:21. DOI:10.1186/1754-6834-5-21 |
15. Scapin SMN, Souza FHM, Zanphorlin LM, de Almeida TS, Sade YB, Cardoso AM, Pinheiro GL, and Murakami MT. (2017). Structure and function of a novel GH8 endoglucanase from the bacterial cellulose synthase complex of Raoultella ornithinolytica. PLoS One. 2017;12(4):e0176550. DOI:10.1371/journal.pone.0176550 |
16. Santos CR, Meza AN, Hoffmam ZB, Silva JC, Alvarez TM, Ruller R, Giesel GM, Verli H, Squina FM, Prade RA, and Murakami MT. (2010). Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1. Biochem Biophys Res Commun. 2010;403(2):214-9. DOI:10.1016/j.bbrc.2010.11.010 |
17. Alvarez TM, Goldbeck R, dos Santos CR, Paixão DA, Gonçalves TA, Franco Cairo JP, Almeida RF, de Oliveira Pereira I, Jackson G, Cota J, Büchli F, Citadini AP, Ruller R, Polo CC, de Oliveira Neto M, Murakami MT, and Squina FM. (2013). Development and biotechnological application of a novel endoxylanase family GH10 identified from sugarcane soil metagenome. PLoS One. 2013;8(7):e70014. DOI:10.1371/journal.pone.0070014 |
18. Santos CR, Hoffmam ZB, de Matos Martins VP, Zanphorlin LM, de Paula Assis LH, Honorato RV, Lopes de Oliveira PS, Ruller R, and Murakami MT. (2014). Molecular mechanisms associated with xylan degradation by Xanthomonas plant pathogens. J Biol Chem. 2014;289(46):32186-32200. DOI:10.1074/jbc.M114.605105 |
19. Murakami MT, Arni RK, Vieira DS, Degrève L, Ruller R, and Ward RJ. (2005). Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1). FEBS Lett. 2005;579(28):6505-10. DOI:10.1016/j.febslet.2005.10.039 |
20. Ribeiro LF, Furtado GP, Lourenzoni MR, Costa-Filho AJ, Santos CR, Nogueira SC, Betini JA, Polizeli Mde L, Murakami MT, and Ward RJ. (2011). Engineering bifunctional laccase-xylanase chimeras for improved catalytic performance. J Biol Chem. 2011;286(50):43026-38. DOI:10.1074/jbc.M111.253419 |
21. Hoffmam ZB, Zanphorlin LM, Cota J, Diogo JA, Almeida GB, Damásio AR, Squina F, Murakami MT, and Ruller R. (2016). Xylan-specific carbohydrate-binding module belonging to family 6 enhances the catalytic performance of a GH11 endo-xylanase. N Biotechnol. 2016;33(4):467-72. DOI:10.1016/j.nbt.2016.02.006 |
22. Damásio AR, Ribeiro LF, Ribeiro LF, Furtado GP, Segato F, Almeida FB, Crivellari AC, Buckeridge MS, Souza TA, Murakami MT, Ward RJ, Prade RA, and Polizeli ML. (2012). Functional characterization and oligomerization of a recombinant xyloglucan-specific endo-β-1,4-glucanase (GH12) from Aspergillus niveus. Biochim Biophys Acta. 2012;1824(3):461-7. DOI:10.1016/j.bbapap.2011.12.005 |
23. Furtado GP, Santos CR, Cordeiro RL, Ribeiro LF, de Moraes LA, Damásio AR, Polizeli Mde L, Lourenzoni MR, Murakami MT, and Ward RJ. (2015). Enhanced xyloglucan-specific endo-β-1,4-glucanase efficiency in an engineered CBM44-XegA chimera. Appl Microbiol Biotechnol. 2015;99(12):5095-107. DOI:10.1007/s00253-014-6324-0 |
24. Segato F, Dias B, Berto GL, de Oliveira DM, De Souza FHM, Citadini AP, Murakami MT, Damásio ARL, Squina FM, and Polikarpov I. (2017). Cloning, heterologous expression and biochemical characterization of a non-specific endoglucanase family 12 from Aspergillus terreus NIH2624. Biochim Biophys Acta Proteins Proteom. 2017;1865(4):395-403. DOI:10.1016/j.bbapap.2017.01.003 |
25. Cota J, Alvarez TM, Citadini AP, Santos CR, de Oliveira Neto M, Oliveira RR, Pastore GM, Ruller R, Prade RA, Murakami MT, and Squina FM. (2011). Mode of operation and low-resolution structure of a multi-domain and hyperthermophilic endo-β-1,3-glucanase from Thermotoga petrophila. Biochem Biophys Res Commun. 2011;406(4):590-4. DOI:10.1016/j.bbrc.2011.02.098 |
26. Cota J, Oliveira LC, Damásio AR, Citadini AP, Hoffmam ZB, Alvarez TM, Codima CA, Leite VB, Pastore G, de Oliveira-Neto M, Murakami MT, Ruller R, and Squina FM. (2013). Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations. Biochim Biophys Acta. 2013;1834(8):1492-500. DOI:10.1016/j.bbapap.2013.02.030 |
27. Mandelli F, de Morais MAB, de Lima EA, Oliveira L, Persinoti GF, and Murakami MT. (2020). Spatially remote motifs cooperatively affect substrate preference of a ruminal GH26-type endo-β-1,4-mannanase. J Biol Chem. 2020;295(15):5012-5021. DOI:10.1074/jbc.RA120.012583 |
28. Santos CR, Polo CC, Corrêa JM, Simão Rde C, Seixas FA, and Murakami MT. (2012). The accessory domain changes the accessibility and molecular topography of the catalytic interface in monomeric GH39 β-xylosidases. Acta Crystallogr D Biol Crystallogr. 2012;68(Pt 10):1339-45. DOI:10.1107/S0907444912028491 |
29. de Morais MAB, Polo CC, Domingues MN, Persinoti GF, Pirolla RAS, de Souza FHM, Correa JBL, Dos Santos CR, and Murakami MT. (2020). Exploring the Molecular Basis for Substrate Affinity and Structural Stability in Bacterial GH39 β-Xylosidases. Front Bioeng Biotechnol. 2020;8:419. DOI:10.3389/fbioe.2020.00419 |
30. Godoy AS, Camilo CM, Kadowaki MA, Muniz HD, Espirito Santo M, Murakami MT, Nascimento AS, and Polikarpov I. (2016). Crystal structure of β1→6-galactosidase from Bifidobacterium bifidum S17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by α-galactose. FEBS J. 2016;283(22):4097-4112. DOI:10.1111/febs.13908 |
31. Santos CR, Polo CC, Costa MC, Nascimento AF, Meza AN, Cota J, Hoffmam ZB, Honorato RV, Oliveira PS, Goldman GH, Gilbert HJ, Prade RA, Ruller R, Squina FM, Wong DW, and Murakami MT. (2014). Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases. J Biol Chem. 2014;289(11):7362-73. DOI:10.1074/jbc.M113.537167 |
32. Diogo JA, Hoffmam ZB, Zanphorlin LM, Cota J, Machado CB, Wolf LD, Squina F, Damásio AR, Murakami MT, and Ruller R. (2015). Development of a chimeric hemicellulase to enhance the xylose production and thermotolerance. Enzyme Microb Technol. 2015;69:31-7. DOI:10.1016/j.enzmictec.2014.11.006 |
33. Zanphorlin LM, de Morais MAB, Diogo JA, Domingues MN, de Souza FHM, Ruller R, and Murakami MT. (2019). Structure-guided design combined with evolutionary diversity led to the discovery of the xylose-releasing exo-xylanase activity in the glycoside hydrolase family 43. Biotechnol Bioeng. 2019;116(4):734-744. DOI:10.1002/bit.26899 |
34. Berto GL, Velasco J, Tasso Cabos Ribeiro C, Zanphorlin LM, Noronha Domingues M, Tyago Murakami M, Polikarpov I, de Oliveira LC, Ferraz A, and Segato F. (2019). Functional characterization and comparative analysis of two heterologous endoglucanases from diverging subfamilies of glycosyl hydrolase family 45. Enzyme Microb Technol. 2019;120:23-35. DOI:10.1016/j.enzmictec.2018.09.005 |
35. Souza TA, Santos CR, Souza AR, Oldiges DP, Ruller R, Prade RA, Squina FM, and Murakami MT. (2011). Structure of a novel thermostable GH51 α-L-arabinofuranosidase from Thermotoga petrophila RKU-1. Protein Sci. 2011;20(9):1632-7. DOI:10.1002/pro.693 |
36. Dos Santos CR, de Giuseppe PO, de Souza FHM, Zanphorlin LM, Domingues MN, Pirolla RAS, Honorato RV, Tonoli CCC, de Morais MAB, de Matos Martins VP, Fonseca LM, Büchli F, de Oliveira PSL, Gozzo FC, and Murakami MT. (2018). The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans. Biotechnol Biofuels. 2018;11:223. DOI:10.1186/s13068-018-1212-y |
37. Gonçalves TA, Damásio AR, Segato F, Alvarez TM, Bragatto J, Brenelli LB, Citadini AP, Murakami MT, Ruller R, Paes Leme AF, Prade RA, and Squina FM. (2012). Functional characterization and synergic action of fungal xylanase and arabinofuranosidase for production of xylooligosaccharides. Bioresour Technol. 2012;119:293-9. DOI:10.1016/j.biortech.2012.05.062 |
38. Santos CR, Tonoli CC, Trindade DM, Betzel C, Takata H, Kuriki T, Kanai T, Imanaka T, Arni RK, and Murakami MT. (2011). Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Proteins. 2011;79(2):547-57. DOI:10.1002/prot.22902 |
39. Santos CR, Costa PACR, Vieira PS, Gonzalez SET, Correa TLR, Lima EA, Mandelli F, Pirolla RAS, Domingues MN, Cabral L, Martins MP, Cordeiro RL, Junior AT, Souza BP, Prates ÉT, Gozzo FC, Persinoti GF, Skaf MS, and Murakami MT. (2020). Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family. Nat Chem Biol. 2020;16(8):920-929. DOI:10.1038/s41589-020-0554-5 |
40. Corrêa TLR, Júnior AT, Wolf LD, Buckeridge MS, Dos Santos LV, and Murakami MT. (2019). An actinobacteria lytic polysaccharide monooxygenase acts on both cellulose and xylan to boost biomass saccharification. Biotechnol Biofuels. 2019;12:117. DOI:10.1186/s13068-019-1449-0 |
41. Fonseca LM, Parreiras LS, and Murakami MT. (2020). Rational engineering of the Trichoderma reesei RUT-C30 strain into an industrially relevant platform for cellulase production. Biotechnol Biofuels. 2020;13:93. DOI:10.1186/s13068-020-01732-w |