Structural and biochemical analysis of Glyceraldehyde-3-Phosphate Dehydrogenase from Clostridium beijerinckii

다국어 초록 (Multilingual Abstract)

Clostridium beijerinckii is a promising industrial microorganism for its ability to produce butanol, acetone, and isopropanol using a wide range of substrates, including pentoses, hexoses, and starch, via fermentation. The ubiquitous and highly abundant glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is essential for most organisms’ energy and carbon metabolism, which plays a critical role in some industrial bacteria. It catalyzes the simultaneous oxidation and phosphorylation of D-glyceraldehyde-3-phosphate into 1,3-bisphosphoglycerate in the presence of inorganic phosphate and nicotinamide adenine dinucleotide (NAD+). We determined the crystal structure of the GAPDH from C. beijerinckii (C. beijerinckii GAPDH). C. beijerinckii GAPDH consists of an α-β-α domain which shares an evolutionarily conserved fold consisting of two juxtaposed domains, an N-terminal NAD+-binding domain (NBD) and a C-terminal catalytic domain (CD). These findings provide insight into the molecular mechanism of action and cofactorbinding of this important industrial bacterial enzyme.

참고문헌 (Reference)

1 Gómez, S., "The antimicrobials anacardic acid and curcumin are not-competitive inhibitors of gram-positive bacterial pathogenic glyceraldehyde-3-phosphate dehydrogenase by a mechanism unrelated to human C5a anaphylatoxin binding" 10 : 326-, 2019

2 Park, S. S., "Streptococcus pneumoniae binds to host GAPDH on dying lung epithelial cells worsening secondary infection following influenza" 35 : 109267-, 2021

3 Madureira, P., "Streptococcus agalactiae GAPDH is a virulenceassociated immunomodulatory protein" 178 : 1379-1387, 2007

4 Butera, G., "Regulation of autophagy by nuclear GAPDH and its aggregates in cancer and neurodegenerative disorders" 20 : 2062-, 2019

5 Xin, F., "Recent advances on conversion and co-production of acetone-butanol-ethanol into high value-added bioproducts" 38 : 529-540, 2018

6 Veza, I., "Recent advances in butanol production by acetone-butanol-ethanol (ABE) fermentation" 144 : 105919-, 2021

7 Tashiro, Y., "Recent advances and future prospects for increased butanol production by acetone-butanol-ethanol fermentation" 13 : 432-445, 2013

8 Otwinowski, Z., "Processing of X-ray diffraction data collected in oscillation mode" 276 : 307-326, 1997

9 Wilkinson, S. R., "Physical map of the Clostridium beijerinckii (formerly Clostridium acetobutylicum) NCIMB 8052 chromosome" 177 : 439-448, 1995

10 Adams, P. D., "PHENIX : building new software for automated crystallographic structure determination" 58 : 1948-1954, 2002

11 Daengbussadee, C., "Novel methods using an Arthrobacter sp. to create anaerobic conditions for biobutanol production from sweet sorghum juice by Clostridium beijerinckii" 9 : 178-, 2021

12 Sirover, M. A., "New insights into an old protein : the functional diversity of mammalian glyceraldehyde-3-phosphate dehydrogenase" 1432 : 159-184, 1999

13 Terao, Y., "Multifunctional glyceraldehyde-3-phosphate dehydrogenase of Streptococcus pyogenes is essential for evasion from neutrophils" 281 : 14215-14223, 2006

14 Centeno-Leija, S., "Metabolic and transcriptional response of Escherichia coli with a NADP(+)-dependent glyceraldehyde 3-phosphate dehydrogenase from Streptococcus mutans" 104 : 913-924, 2013

15 Buehler, E. A., "Kinetic study of acetone-butanolethanol fermentation in continuous culture" 11 : e0158243-, 2016

16 Sirisantimethakom, L., "Improvement of butanol production from sweet sorghum juice by Clostridium beijerinckii using an orthogonal array design" 79 : 287-294, 2016

17 Baker, B. Y., "Highresolution crystal structures of the photoreceptor glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with three and four-bound NAD molecules" 23 : 1629-1639, 2014

18 Oliveira, L., "Group B streptococcus GAPDH is released upon cell lysis, associates with bacterial surface, and induces apoptosis in murine macrophages" 7 : e29963-, 2012

19 Gaspar, P., "From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria" 31 : 764-788, 2013

20 Matsunaga, N., "Expression of glyceraldehyde-3-phosphate dehydrogenase on the surface of Clostridium perfringens cells" 51 : 124-130, 2018

21 Robert, X., "Deciphering key features in protein structures with the new ENDscript server" 42 : W320-W324, 2014

22 Holm, L., "Dali server: conservation mapping in 3D" 38 : W545-W549, 2010

23 Schormann, N., "Crystal structures of group B streptococcus glyceraldehyde-3-phosphate dehydrogenase: apo-form, binary and ternary complexes" 11 : e0165917-, 2016

24 Mukherjee, S., "Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism" 401 : 949-968, 2010

25 Zhang, J. Y., "Critical protein GAPDH and its regulatory mechanisms in cancer cells" 12 : 10-22, 2015

26 Emsley, P., "Coot : model-building tools for molecular graphics" 60 : 2126-2132, 2004

27 Glaser, F., "ConSurf : identification of functional regions in proteins by surface-mapping of phylogenetic information" 19 : 163-164, 2003

28 Ashkenazy, H., "ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules" 44 : W344-W350, 2016

29 Sievers, F., "Clustal Omega for making accurate alignments of many protein sequences" 27 : 135-145, 2018

30 Jie Zhang ; Yuanyuan Chen ; Tingting Bu ; Xue Bai ; Shanru He ; Lulu Wang ; Chunshan Quan ; Yongbin Xu, "Clostridium beijerinckii glyceraldehyde-3-phosphate dehydrogenase GAPDH: purification, crystallization, and X-ray crystallographic analysis" 한국구조생물학회 10 (10): 51-55, 2022

31 Rochón, E., "Bioprocess intensification for isopropanol, butanol and ethanol (IBE) production by fermentation from sugarcane and sweet sorghum juices through a gas strippingpervaporation recovery process" 281 : 118593-, 2020

32 Vélez-Mercado, M. I., "Bioconversion of lignocellulosic biomass into value added products under anaerobic conditions : insight into proteomic studies" 22 : 12249-, 2021

33 Cook, W. J., "An unexpected phosphate binding site in glyceraldehyde 3-phosphate dehydrogenase : crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme" 9 : 9-, 2009