X-ray structure and characterization of a probiotic Lactobacillus rhamnosus Probio-M9 L-rhamnose isomerase.
Lactobacillus rhamnosus Probio-M9
Crystal structure
D-allose
D-allulose
L-rhamnose isomerase
Rare sugar
Journal
Applied microbiology and biotechnology
ISSN: 1432-0614
Titre abrégé: Appl Microbiol Biotechnol
Pays: Germany
ID NLM: 8406612
Informations de publication
Date de publication:
02 Mar 2024
02 Mar 2024
Historique:
received:
31
07
2023
accepted:
16
02
2024
revised:
18
01
2024
medline:
2
3
2024
pubmed:
2
3
2024
entrez:
2
3
2024
Statut:
epublish
Résumé
A recombinant L-rhamnose isomerase (L-RhI) from probiotic Lactobacillus rhamnosus Probio-M9 (L. rhamnosus Probio-M9) was expressed. L. rhamnosus Probio-M9 was isolated from human colostrum and identified as a probiotic lactic acid bacterium, which can grow using L-rhamnose. L-RhI is one of the enzymes involved in L-rhamnose metabolism and catalyzes the reversible isomerization between L-rhamnose and L-rhamnulose. Some L-RhIs were reported to catalyze isomerization not only between L-rhamnose and L-rhamnulose but also between D-allulose and D-allose, which are known as rare sugars. Those L-RhIs are attractive enzymes for rare sugar production and have the potential to be further improved by enzyme engineering; however, the known crystal structures of L-RhIs recognizing rare sugars are limited. In addition, the optimum pH levels of most reported L-RhIs are basic rather than neutral, and such a basic condition causes non-enzymatic aldose-ketose isomerization, resulting in unexpected by-products. Herein, we report the crystal structures of L. rhamnosus Probio-M9 L-RhI (LrL-RhI) in complexes with L-rhamnose, D-allulose, and D-allose, which show enzyme activity toward L-rhamnose, D-allulose, and D-allose in acidic conditions, though the activity toward D-allose was low. In the complex with L-rhamnose, L-rhamnopyranose was found in the catalytic site, showing favorable recognition for catalysis. In the complex with D-allulose, D-allulofuranose and ring-opened D-allulose were observed in the catalytic site. However, bound D-allose in the pyranose form was found in the catalytic site of the complex with D-allose, which was unfavorable for recognition, like an inhibition mode. The structure of the complex may explain the low activity toward D-allose. KEY POINTS: • Crystal structures of LrL-RhI in complexes with substrates were determined. • LrL-RhI exhibits enzyme activity toward L-rhamnose, D-allulose, and D-allose. • The LrL-RhI is active in acidic conditions.
Identifiants
pubmed: 38430263
doi: 10.1007/s00253-024-13075-9
pii: 10.1007/s00253-024-13075-9
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
249Informations de copyright
© 2024. The Author(s).
Références
Bai W, Shen J, Zhu YM, Men Y, Sun YX, Ma YH (2015) Characteristics and kinetic properties of L-rhamnose isomerase from Bacillus subtilis by isothermal titration calorimetry for the production of D-allose. Food Sci Technol Res 21:13–22. https://doi.org/10.3136/fstr.21.13
doi: 10.3136/fstr.21.13
Bhuiyan SH, Itami Y, Izumori K (1997) Isolation of an L-rhamnose isomerase-constitutive mutant of Pseudomonas sp. strain LL172: purification and characterization of the enzyme. J Ferment Bioeng 84:319–323. https://doi.org/10.1016/S0922-338X(97)89251-3
doi: 10.1016/S0922-338X(97)89251-3
Chen Z, Xu W, Zhang W, Zhang T, Jiang B, Mu W (2018a) Characterization of a thermostable recombinant L-rhamnose isomerase from Caldicellulosiruptor obsidiansis OB47 and its application for the production of L-fructose and L-rhamnulose. J Sci Food Agric 98:2184–2193. https://doi.org/10.1002/jsfa.8703
doi: 10.1002/jsfa.8703
pubmed: 28960307
Chen Z, Chen J, Zhang W, Zhang T, Guang C, Mu W (2018b) Improving thermostability and catalytic behavior of L-rhamnose isomerase from Caldicellulosiruptor obsidiansis OB47 toward D-allulose by site-directed mutagenesis. J Agric Food Chem 66:12017–12024. https://doi.org/10.1021/acs.jafc.8b05107
doi: 10.1021/acs.jafc.8b05107
pubmed: 30370768
Dische Z, Borenfreund A (1950) A spectrophotometric method for the microdetermination of hexosamines. J Biol Chem 184:517–522. https://doi.org/10.1016/S0021-9258(19)50982-6
doi: 10.1016/S0021-9258(19)50982-6
pubmed: 15428432
Duan S, Chen Y, Wang G, Li Z, Dong S, Wu Y, Wang Y, Ma C, Wang R (2023) A study of targeted mutation of L-rhamnose isomerase to improve the conversion efficiency of D-allose. Enz Microbial Technol 168:110259. https://doi.org/10.1016/j.enzmictec.2023.110259
doi: 10.1016/j.enzmictec.2023.110259
Domagk GF, Zech R (1963) On the decomposition of desoxy sugars by bacterial enzymes. I. L-rhamnose-isomerase from Lactobacillus plantarum. Biochem Z 339:145–153
pubmed: 14095156
Emsley P, Lohkamp B, Scott W, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501. https://doi.org/10.1107/S0907444910007493
doi: 10.1107/S0907444910007493
pubmed: 20383002
pmcid: 2852313
Hayashi N, Iida T, Yamada T, Okuma K, Takehara I, Yamamoto T, Yamada K, Tokuda M (2010) Study on the postprandial blood glucose suppression effect of D-psicose in borderline diabetes and the safety of long-term ingestion by normal human subjects. Biosci Biotechnol Biochem 74:510–519. https://doi.org/10.1271/bbb.90707
doi: 10.1271/bbb.90707
pubmed: 20208358
Heikkilä MP, Saris PEJ (2003) Inhibition of Staphylococcus aureus by the commensal bacteria of human milk. J Appl Microbiol 95:471–478. https://doi.org/10.1046/j.1365-2672.2003.02002.x
doi: 10.1046/j.1365-2672.2003.02002.x
pubmed: 12911694
Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, Calder PC, Sanders ME (2014) The international scientific association for probiotics and prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 11:506–514. https://doi.org/10.1038/nrgastro.2014.66
doi: 10.1038/nrgastro.2014.66
pubmed: 24912386
Holm L, Laakso LM (2016) Dali server update. Nucleic Acids Res 44:W351–W355. https://doi.org/10.1093/nar/gkw357
doi: 10.1093/nar/gkw357
pubmed: 27131377
pmcid: 4987910
Holm L (2022) Dali server: structural unification of protein families. Nucleic Acids Res 50:W210–W215. https://doi.org/10.1093/nar/gkac387
doi: 10.1093/nar/gkac387
pubmed: 35610055
pmcid: 9252788
Iida T, Yamada T, Hayashi N, Okuma K, Izumori K, Ishii R, Matsuo T (2013) Reduction of abdominal fat accumulation in rats by 8-week ingestion of a newly developed sweetener made from high fructose corn syrup. Food Chem 138:781–785. https://doi.org/10.1016/j.foodchem.2012.11.017
doi: 10.1016/j.foodchem.2012.11.017
pubmed: 23411176
Kabsch W (2010) XDS. Acta Crystallogr D Biol Crystallogr 66:125–132. https://doi.org/10.1107/S0907444909047337
doi: 10.1107/S0907444909047337
pubmed: 20124692
pmcid: 2815665
Kim YS, Shin KC, Lim YR, Oh DK (2013) Characterization of a recombinant L-rhamnose isomerase from Dictyoglomus turgidum and its application for L-rhamnulose production. Biotechnol Lett 35:259–264. https://doi.org/10.1007/s10529-012-1069-2
doi: 10.1007/s10529-012-1069-2
pubmed: 23070627
Korndörfer IP, Fessner WD, Matthews BW (2000) The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution. J Mol Biol 300:917–933. https://doi.org/10.1006/jmbi.2000.3896
doi: 10.1006/jmbi.2000.3896
pubmed: 10891278
Kozak K, Charbonneau D, Sanozky-Dawes R, Klaenhammer T (2015) Characterization of bacterial isolates from the microbiota of mothers’ breast milk and their infants. Gut Microbes 6:341–351. https://doi.org/10.1080/19490976.2015.1103425
doi: 10.1080/19490976.2015.1103425
pubmed: 26727418
Leang K, Takada G, Ishimura A, Okita M, Izumori K (2004a) Cloning, nucleotide sequence, and overexpression of the L-rhamnose isomerase gene from Pseudomonas stutzeri in Escherichia coli. Appl Environ Microbiol 70:3298–3304. https://doi.org/10.1128/AEM.70.6.3298-3304.2004
doi: 10.1128/AEM.70.6.3298-3304.2004
pubmed: 15184124
pmcid: 427750
Leang K, Takada G, Fukai Y, Morimoto K, Granstrom TB, Izumori K (2004b) Novel reactions of L-rhamnose isomerase from Pseudomonas stutzeri and its relation with D-xylose isomerase via substrate specificity. Biochim Biophys Acta 1674:68–77. https://doi.org/10.1016/j.bbagen.2004.06.003
doi: 10.1016/j.bbagen.2004.06.003
pubmed: 15342115
Lin CJ, Tseng WC, Lin TH, Liu SM, Tzou WS, Fang TY (2010) Characterization of a thermophilic L-rhamnose isomerase from Thermoanaerobacterium saccharolyticum NTOU1. J Agric Food Chem 58:10431–10436. https://doi.org/10.1021/jf102063q
doi: 10.1021/jf102063q
pubmed: 20822145
Lin CJ, Tseng WC, Fang TY (2011) Characterization of a thermophilic L-rhamnose isomerase from Caldicellulosiruptor saccharolyticus ATCC 43494. J Agric Food Chem 59:8702–8708. https://doi.org/10.1021/jf201428b
doi: 10.1021/jf201428b
pubmed: 21761877
Liu W, Chen M, Duo L, Wang J, Guo S, Sun H, Menghe B, Zhang H (2020) Characterization of potentially probiotic lactic acid bacteria and bifidobacteria isolated from human colostrum. J Dairy Sci 103:4013–4025. https://doi.org/10.3168/jds.2019-17602
doi: 10.3168/jds.2019-17602
pubmed: 32113772
LoCascio RG, Niñonuevo MR, Kronewitter SR, Freeman SL, German JB, Lebrilla CB, Mills DA (2009) A versatile and scalable strategy for glycoprofiling bifidobacterial consumption of human milk oligosaccharides. Microb Biotechnol 2:333–342. https://doi.org/10.1111/j.1751-7915.2008.00072.x
doi: 10.1111/j.1751-7915.2008.00072.x
pubmed: 21261928
pmcid: 3815754
Marcobal A, Barboza M, Froehlich JW, Block DE, German JB, Lebrilla CB, Mills DA (2010) Consumption of human milk oligosaccharides by gut-related microbes. J Agric Food Chem 58:5334–5340. https://doi.org/10.1021/jf9044205
doi: 10.1021/jf9044205
pubmed: 20394371
pmcid: 2866150
Martín R, Langa S, Reviriego C, Jimínez E, Marín ML, Xaus J, Fernández L, Rodríguez JM (2003) Human milk is a source of lactic acid bacteria for the infant gut. J Pediatr 143:754–758. https://doi.org/10.1016/j.jpeds.2003.09.028
doi: 10.1016/j.jpeds.2003.09.028
pubmed: 14657823
Moralejo P, Egan SM, Hidalgo E, Aguilar J (1993) Sequencing and characterization of a gene cluster encoding the enzymes for l-rhamnose metabolism in Escherichia coli. J Bacteriol 175:5585–5594. https://doi.org/10.1128/jb.175.17.5585-5594.1993
doi: 10.1128/jb.175.17.5585-5594.1993
pubmed: 8396120
pmcid: 206615
Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240–255. https://doi.org/10.1107/S0907444996012255
doi: 10.1107/S0907444996012255
pubmed: 15299926
Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 67:355–367. https://doi.org/10.1107/S0907444911001314
doi: 10.1107/S0907444911001314
pubmed: 21460454
pmcid: 3069751
Noguchi C, Kamitori K, Hossain A, Hoshikawa H, Katagi A, Dong Y, Sui L, Tokuda M, Yamaguchi F (2016) D-Allose inhibits cancer cell growth by reducing GLUT1 expression. Tohoku J Exp Med 238:131–141. https://doi.org/10.1620/tjem.238.131
doi: 10.1620/tjem.238.131
pubmed: 26829886
Park CS, Yeom SJ, Lim YR, Kim YS, Oh DK (2010) Characterization of a recombinant thermostable L-rhamnose isomerase from Thermotoga maritima ATCC 43589 and its application in the production of L-lyxose and L-mannose. Biotechnol Lett 32:1947–1953. https://doi.org/10.1007/s10529-010-0385-7
doi: 10.1007/s10529-010-0385-7
pubmed: 20809285
Park CS (2014) Characterization of a recombinant L-rhamnose isomerase from Bacillus subtilis and its application on production of L-lyxose and L-mannose. Biotechnol Bioproc Eng 19:18–25. https://doi.org/10.1007/s12257-013-0597-5
doi: 10.1007/s12257-013-0597-5
Poonperm W, Takata G, Okada H, Morimoto K, Granström TB, Izumori K (2007) Cloning, sequencing, overexpression and characterization of L-rhamnose isomerase from Bacillus pallidus Y25 for rare sugar production. Appl Microbiol Biotechnol 76:1297–1307. https://doi.org/10.1007/s00253-007-1109-3
doi: 10.1007/s00253-007-1109-3
pubmed: 17653540
Power J (1967) The L-rhamnose genetic system in Escherichia coli K-12. Genetics 55:557–568. https://doi.org/10.1093/genetics/55.3.557
doi: 10.1093/genetics/55.3.557
pubmed: 5341476
pmcid: 1211410
Prabhu P, Doan TT, Jeya M, Kang LW, Lee JK (2011) Cloning and characterization of a rhamnose isomerase from Bacillus halodurans. Appl Microbiol Biotechnol 89:635–644. https://doi.org/10.1007/s00253-010-2844-4
doi: 10.1007/s00253-010-2844-4
pubmed: 20852996
Prabhu P, Doan TN, Tiwari M, Singh R, Kim SC, Hong MK, Kang YC, Kang LW, Lee JK (2014) Structure-based studies on the metal binding of two-metal-dependent sugar isomerases. FEBS J 281:3446–3459. https://doi.org/10.1111/febs.12872
doi: 10.1111/febs.12872
pubmed: 24925069
Ruibo X, Xu L, Weicheng L, Xin S, Heping Z (2023) Reveal the differences in the genome of Lactobacillus rhamnosus Probio-M9 and other Lactobacillus rhamnosus based on comparative genomics. J Chin Inst Food Sci Technol 23:254–264
Ruiz L, García-Carral C, Rodriguez JM (2019) Unfolding the human milk microbiome landscape in the omics era. Front Microbiol 10:1378. https://doi.org/10.3389/fmicb.2019.01378
doi: 10.3389/fmicb.2019.01378
pubmed: 31293535
pmcid: 6604669
Sakwinska O, Moine D, Delley M, Combremont S, Rezzonico E, Descombes P, Vinyes-Pares G, Zhang Y, Wang P, Thakkar SK (2016) Microbiota in breast milk of Chinese lactating mothers. PLoS One 11:e0160856. https://doi.org/10.1371/journal.pone.0160856
doi: 10.1371/journal.pone.0160856
pubmed: 27529821
pmcid: 4987007
Seo MJ, Choi JH, Kang SH, Shin KC, Oh DK (2018) Characterization of L-rhamnose isomerase from Clostridium stercorarium and its application to the production of D-allose from D-allulose (D-psicose). Biotechnol Lett 40:325–334. https://doi.org/10.1007/s10529-017-2468-1
doi: 10.1007/s10529-017-2468-1
pubmed: 29124517
Shintani H, Shintani T, Sato M (2020) D-Allose, a trace component in human serum, and its pharmaceutical applicability. Int J Appl Biol 11:200–213
Sun Y, Hayakawa S, Puangmanee S, Izumori K (2006) Chemical properties and antioxidative activity of glycated α-lactalbumin with a rare sugar, D-allose, by Maillard reaction. Food Chem 95:509–517. https://doi.org/10.1016/j.foodchem.2005.01.033
doi: 10.1016/j.foodchem.2005.01.033
Takagi Y, Sawada H (1964) The metabolism of L-rhamnose in Escherichia coli. Biochim Biophys Acta 92:10–17. https://doi.org/10.1016/0926-6569(64)90264-0
doi: 10.1016/0926-6569(64)90264-0
pubmed: 14243758
Takata G, Uechi K, Taniguchi E, Kanbara Y, Yoshihara A, Morimoto K, Izumori K (2011) Characterization of Mesorhizobium loti L-rhamnose isomerase and its application to L-talose production. Biosci Biotechnol Biochem 75:1006–1009. https://doi.org/10.1271/bbb.110018
doi: 10.1271/bbb.110018
pubmed: 21597169
Tseng WC, Chen YC, Chang HC, Lin CJ, Fang TY (2022) Altering the substrate specificity of recombinant L-rhamnose isomerase from Thermoanaerobacterium saccharolyticum NTOU1 to favour D-allose production. J Biotechnol 358:9–16. https://doi.org/10.1016/j.jbiotec.2022.08.015
doi: 10.1016/j.jbiotec.2022.08.015
pubmed: 36030895
Vagin A, Teplyakov A (1997) MOLREP: An automated program for molecular replacement. J Appl Cryst 30:1022–1025. https://doi.org/10.1107/S0021889897006766
doi: 10.1107/S0021889897006766
Vagin A, Teplyakov A (2010) Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr 66:22–25. https://doi.org/10.1107/S0907444909042589
doi: 10.1107/S0907444909042589
pubmed: 20057045
Wilson DM, Ajl S (1957) Metabolism of l-rhamnose by Escherichia coli. I L-Rhamnose Isomerase J Bacteriol 73:410–414. https://doi.org/10.1128/jb.73.3.410-414.1957
doi: 10.1128/jb.73.3.410-414.1957
pubmed: 13416204
Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AGW, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67:235–242. https://doi.org/10.1107/S0907444910045749
doi: 10.1107/S0907444910045749
pubmed: 21460441
pmcid: 3069738
Yoshida H, Yamada M, Ohyama Y, Takada G, Izumori K, Kamitori S (2007) The structures of l-rhamnose isomerase from Pseudomonas stutzeri in complexes with l-rhamnose and d-allose provide insights into broad substrate specificity. J Mol Biol 365:1505–1516. https://doi.org/10.1016/j.jmb.2006.11.004
doi: 10.1016/j.jmb.2006.11.004
pubmed: 17141803
Yoshida H, Takeda K, Izumori K, Kamitori S (2010a) Elucidation of the role of Ser329 and the C-terminal region in the catalytic activity of Pseudomonas stutzeri L-rhamnose isomerase. Protein Eng Des Sel 23:919–927. https://doi.org/10.1093/protein/gzq077
doi: 10.1093/protein/gzq077
pubmed: 20977999
Yoshida H, Yamaji M, Ishii T, Izumori K, Kamitori S (2010b) Catalytic reaction mechanism of Pseudomonas stutzeri L-rhamnose isomerase deduced from X-ray structures. FEBS J 277:1045–1057. https://doi.org/10.1111/j.1742-4658.2009.07548.x
doi: 10.1111/j.1742-4658.2009.07548.x
pubmed: 20088877
Yoshida H, Yoshihara A, Teraoka M, Yamashita S, Izumori K, Kamitori S (2012) Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site. FEBS Open Bio 3:35–40. https://doi.org/10.1016/j.fob.2012.11.008
doi: 10.1016/j.fob.2012.11.008
pubmed: 23772372
pmcid: 3668531
Yoshida H, Yoshihara A, Kato S, Mochizuki S, Akimitsu K, Izumori K, Kamitori S (2021) Crystal structure of a novel homodimeric l-ribulose 3-epimerase from Methylomonus sp. FEBS Open Bio 11:1621–1637. https://doi.org/10.1002/2211-5463.13159
doi: 10.1002/2211-5463.13159
pubmed: 33838083
pmcid: 8167858