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1.
Nat Commun ; 15(1): 1489, 2024 Feb 27.
Artículo en Inglés | MEDLINE | ID: mdl-38413572

RESUMEN

Blue denim, a billion-dollar industry, is currently dyed with indigo in an unsustainable process requiring harsh reducing and alkaline chemicals. Forming indigo directly in the yarn through indican (indoxyl-ß-glucoside) is a promising alternative route with mild conditions. Indican eliminates the requirement for reducing agent while still ending as indigo, the only known molecule yielding the unique hue of blue denim. However, a bulk source of indican is missing. Here, we employ enzyme and process engineering guided by techno-economic analyses to develop an economically viable drop-in indican synthesis technology. Rational engineering of PtUGT1, a glycosyltransferase from the indigo plant, alleviated the severe substrate inactivation observed with the wildtype enzyme at the titers needed for bulk production. We further describe a mild, light-driven dyeing process. Finally, we conduct techno-economic, social sustainability, and comparative life-cycle assessments. These indicate that the presented technologies have the potential to significantly reduce environmental impacts from blue denim dyeing with only a modest cost increase.


Asunto(s)
Indicán , Carmin de Índigo , Colorantes , Plantas , Ambiente
2.
Biochimie ; 221: 13-19, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38199518

RESUMEN

Sucrose phosphorylases, through transglycosylation reactions, are interesting enzymes that can transfer regioselectively glucose from sucrose, the donor substrate, onto acceptors like flavonoids to form glycoconjugates and hence modulate their solubility and bioactivity. Here, we report for the first time the structure of sucrose phosphorylase from the marine bacteria Alteromonas mediterranea (AmSP) and its enzymatic properties. Kinetics of sucrose hydrolysis and transglucosylation capacities on (+)-catechin were investigated. Wild-type enzyme (AmSP-WT) displayed high hydrolytic activity on sucrose and was devoid of transglucosylation activity on (+)-catechin. Two variants, AmSP-Q353F and AmSP-P140D catalysed the regiospecific transglucosylation of (+)-catechin: 89 % of a novel compound (+)-catechin-4'-O-α-d-glucopyranoside (CAT-4') for AmSP-P140D and 92 % of (+)-catechin-3'-O-α-d-glucopyranoside (CAT-3') for AmSP-Q353F. The compound CAT-4' was fully characterized by NMR and mass spectrometry. An explanation for this difference in regiospecificity was provided at atomic level by molecular docking simulations: AmSP-P140D was found to preferentially bind (+)-catechin in a mode that favours glucosylation on its hydroxyl group in position 4' while the binding mode in AmSP-Q353F favoured glucosylation on its hydroxyl group in position 3'.


Asunto(s)
Catequina , Glucosiltransferasas , Glucosiltransferasas/metabolismo , Glucosiltransferasas/química , Catequina/metabolismo , Catequina/química , Glicosilación , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/genética , Especificidad por Sustrato , Simulación del Acoplamiento Molecular , Cinética , Hidrólisis
3.
Chem Commun (Camb) ; 60(4): 440-443, 2024 Jan 04.
Artículo en Inglés | MEDLINE | ID: mdl-38087900

RESUMEN

TpPL7A and TpPL7B, members of CAZy family PL7, act as ß-glucuronan lyases. TpPL7A diverges by lacking the catalytic histidine, identified as the Brønsted base in PL7 alginate lyases. Our research, including TpPL7A's crystal structure, and mutagenesis studies, reveals a shared syn-ß-elimination mechanism with a single tyrosine serving as both base and acid catalyst. This mechanism may extend to subfamily PL7_4 glucuronan lyases.

4.
Plant J ; 111(6): 1539-1549, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35819080

RESUMEN

Cyanogenic glucosides are important defense molecules in plants with useful biological activities in animals. Their last biosynthetic step consists of a glycosylation reaction that confers stability and increases structural diversity and is catalyzed by the UDP-dependent glycosyltransferases (UGTs) of glycosyltransferase family 1. These versatile enzymes have large and varied substrate scopes, and the structure-function relationships controlling scope and specificity remain poorly understood. Here, we report substrate-bound crystal structures and rational engineering of substrate and stereo-specificities of UGT85B1 from Sorghum bicolor involved in biosynthesis of the cyanogenic glucoside dhurrin. Substrate specificity was shifted from the natural substrate (S)-p-hydroxymandelonitrile to (S)-mandelonitrile by combining a mutation to abolish hydrogen bonding to the p-hydroxyl group with a mutation to provide steric hindrance at the p-hydroxyl group binding site (V132A/Q225W). Further, stereo-specificity was shifted from (S) to (R) by substituting four rationally chosen residues within 6 Å of the nitrile group (M312T/A313T/H408F/G409A). These activities were compared to two other UGTs involved in the biosynthesis of aromatic cyanogenic glucosides in Prunus dulcis (almond) and Eucalyptus cladocalyx. Together, these studies enabled us to pinpoint factors that drive substrate and stereo-specificities in the cyanogenic glucoside biosynthetic UGTs. The structure-guided engineering of the functional properties of UGT85B1 enhances our understanding of the evolution of UGTs involved in the biosynthesis of cyanogenic glucosides and will enable future engineering efforts towards new biotechnological applications.


Asunto(s)
Aminoácidos , Nitrilos , Animales , Glucósidos/metabolismo , Glicósidos , Glicosiltransferasas , Nitrilos/metabolismo , Uridina Difosfato
5.
ACS Sustain Chem Eng ; 10(16): 5078-5083, 2022 Apr 25.
Artículo en Inglés | MEDLINE | ID: mdl-35493695

RESUMEN

Regioselective glycosylation is a chemical challenge, leading to multistep syntheses with protecting group manipulations, ultimately resulting in poor atom economy and compromised sustainability. Enzymes allow eco-friendly and regioselective bond formation with fully deprotected substrates in a single reaction. For the selective glucosylation of silibinin, a pharmaceutical challenged with low solubility, enzyme engineering has previously been employed, but the resulting yields and k cat were limited, prohibiting the application of the engineered catalyst. Here, we identified a naturally regioselective silibinin glucosyltransferase, UGT706F8, a family 1 glycosyltransferase from Zea mays. It selectively and efficiently (k cat = 2.1 ± 0.1 s-1; K M = 36.9 ± 5.2 µM; TTN = 768 ± 22) catalyzes the quantitative synthesis of silibinin 7-O-ß-d-glucoside. We solved the crystal structure of UGT706F8 and investigated the molecular determinants of regioselective silibinin glucosylation. UGT706F8 was the only regioselective enzyme among 18 glycosyltransferases found to be active on silibinin. We found the temperature optimum of UGT706F8 to be 34 °C and the pH optimum to be 7-8. Our results indicate that UGT706F8 is an efficient silibinin glycosyltransferase that enables biocatalytic production of silbinin 7-O-ß-d-glucoside.

6.
Microb Biotechnol ; 15(5): 1622-1632, 2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-35084776

RESUMEN

The fluorinase enzyme represents the only biological mechanism capable of forming stable C-F bonds characterized in nature thus far, offering a biotechnological route to the biosynthesis of value-added organofluorines. The fluorinase is known to operate in a hexameric form, but the consequence(s) of the oligomerization status on the enzyme activity and its catalytic properties remain largely unknown. In this work, this aspect was explored by rationally engineering trimeric fluorinase variants that retained the same catalytic rate as the wild-type enzyme. These results ruled out hexamerization as a requisite for the fluorination activity. The Michaelis constant (KM ) for S-adenosyl-l-methionine, one of the substrates of the fluorinase, increased by two orders of magnitude upon hexamer disruption. Such a shift in S-adenosyl-l-methionine affinity points to a long-range effect of hexamerization on substrate binding - likely decreasing substrate dissociation and release from the active site. A practical application of trimeric fluorinase is illustrated by establishing in vitro fluorometabolite synthesis in a bacterial cell-free system.


Asunto(s)
Streptomyces , Proteínas Bacterianas/metabolismo , Metionina , Oxidorreductasas/metabolismo , S-Adenosilmetionina
7.
Biotechnol Biofuels ; 14(1): 183, 2021 Sep 16.
Artículo en Inglés | MEDLINE | ID: mdl-34530892

RESUMEN

BACKGROUND: Endo-ß-1,4-galactanases are glycoside hydrolases (GH) from the GH53 family belonging to the largest clan of GHs, clan GH-A. GHs are ubiquitous and involved in a myriad of biological functions as well as being widely used industrially. Endo-ß-1,4-galactanases, in particular hydrolyse galactan and arabinogalactan in pectin, a major component of the primary plant cell wall, with important functions in plant defence and application in the food and other industries. Here, we explore the family's biological diversity by characterizing the first archaeal and hyperthermophilic GH53 galactanase, and utilize it as a scaffold for engineering enzymes with different product lengths. RESULTS: A galactanase gene was identified in the genome of the anaerobic hyperthermophilic archaeon Ignisphaera aggregans, and the isolated catalytic domain expressed and characterized (IaGal). IaGal presents the typical (ßα)8 barrel structure of clan GH-A enzymes, with catalytic carboxylates at the end of the 4th and 7th barrel strands. Its activity optimum of at least 95 °C and melting point over 100 °C indicate extreme thermostability, a very advantageous property for industrial applications. If enzyme depletion is reduced, so is the need for re-addition, and thus costs. The main stabilizing features of IaGal compared to other structurally characterized members are π-π and cation-π interactions. The length of the substrate binding site-and thus produced oligosaccharide products-is intermediate compared to previously characterized galactanases. Variants inspired by the structural diversity in the GH53 family were rationally designed to shorten or extend the substrate binding groove, in order to modulate product length. Subsite-deleted variants produced shorter products than IaGal, as do the fungal galactanases inspiring the design. IaGal variants engineered with a longer binding site produced a less expected degradation pattern, though still different from that of wild-type IaGal. All variants remained extremely stable. CONCLUSIONS: We have characterized in detail the most thermophilic endo-ß-1,4-galactanase known to date and successfully engineered it to modify the degradation profile, while maintaining much of its desirable thermostability. This is an important achievement as oligosaccharide products length is an important property for industrial and natural GHs alike.

8.
Nat Commun ; 12(1): 2132, 2021 04 09.
Artículo en Inglés | MEDLINE | ID: mdl-33837197

RESUMEN

Oxidative plant cell-wall processing enzymes are of great importance in biology and biotechnology. Yet, our insight into the functional interplay amongst such oxidative enzymes remains limited. Here, a phylogenetic analysis of the auxiliary activity 7 family (AA7), currently harbouring oligosaccharide flavo-oxidases, reveals a striking abundance of AA7-genes in phytopathogenic fungi and Oomycetes. Expression of five fungal enzymes, including three from unexplored clades, expands the AA7-substrate range and unveils a cellooligosaccharide dehydrogenase activity, previously unknown within AA7. Sequence and structural analyses identify unique signatures distinguishing the strict dehydrogenase clade from canonical AA7 oxidases. The discovered dehydrogenase directly is able to transfer electrons to an AA9 lytic polysaccharide monooxygenase (LPMO) and fuel cellulose degradation by LPMOs without exogenous reductants. The expansion of redox-profiles and substrate range highlights the functional diversity within AA7 and sets the stage for harnessing AA7 dehydrogenases to fine-tune LPMO activity in biotechnological conversion of plant feedstocks.


Asunto(s)
Celulosa/metabolismo , Proteínas Fúngicas/metabolismo , Oomicetos/enzimología , Oxidorreductasas/metabolismo , Pared Celular/química , Pared Celular/metabolismo , Cristalografía por Rayos X , ADN de Hongos/genética , ADN de Hongos/aislamiento & purificación , Flavoproteínas Transportadoras de Electrones/metabolismo , Pruebas de Enzimas , Proteínas Fúngicas/genética , Proteínas Fúngicas/aislamiento & purificación , Proteínas Fúngicas/ultraestructura , Microbiología Industrial/métodos , Espectroscopía de Resonancia Magnética , Oomicetos/genética , Oxidación-Reducción , Oxidorreductasas/genética , Oxidorreductasas/aislamiento & purificación , Oxidorreductasas/ultraestructura , Filogenia , Análisis de Secuencia de ADN , Especificidad por Sustrato
9.
Nat Prod Rep ; 38(3): 432-443, 2021 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-33005913

RESUMEN

Covering: up to 2020C-Glycosyltransferases are enzymes that catalyse the transfer of sugar molecules to carbon atoms in substituted aromatic rings of a variety of natural products. The resulting ß-C-glycosidic bond is more stable in vivo than most O-glycosidic bonds, hence offering an attractive modulation of a variety of compounds with multiple biological activities. While C-glycosylated natural products have been known for centuries, our knowledge of corresponding C-glycosyltransferases is scarce. Here, we discuss commonalities and differences in the known C-glycosyltransferases, review attempts to leverage them as synthetic biocatalysts, and discuss current challenges and limitations in their research and application.


Asunto(s)
Productos Biológicos/química , Biotecnología/métodos , Glicosiltransferasas/química , Glicosiltransferasas/metabolismo , Productos Biológicos/metabolismo , Glicosilación , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Ingeniería de Proteínas
10.
Glycobiology ; 29(12): 839-846, 2019 11 20.
Artículo en Inglés | MEDLINE | ID: mdl-31679023

RESUMEN

l-arabinofuranose is a ubiquitous component of the cell wall and various natural products in plants, where it is synthesized from cytosolic UDP-arabinopyranose (UDP-Arap). The biosynthetic machinery long remained enigmatic in terms of responsible enzymes and subcellular localization. With the discovery of UDP-Arap mutase in plant cytosol, the demonstration of its role in cell-wall arabinose incorporation and the identification of UDP-arabinofuranose transporters in the Golgi membrane, it is clear that the cytosolic UDP-Arap mutases are the key enzymes converting UDP-Arap to UDP-arabinofuranose for cell wall and natural product biosynthesis. This has recently been confirmed by several genotype/phenotype studies. In contrast to the solid evidence pertaining to UDP-Arap mutase function in vivo, the molecular features, including enzymatic mechanism and oligomeric state, remain unknown. However, these enzymes belong to the small family of proteins originally identified as reversibly glycosylated polypeptides (RGPs), which has been studied for >20 years. Here, we review the UDP-Arap mutase and RGP literature together, to summarize and systemize reported molecular characteristics and relations to other proteins.


Asunto(s)
Transferasas Intramoleculares/química , Transferasas Intramoleculares/metabolismo , Oryza/enzimología , Azúcares de Uridina Difosfato/química , Azúcares de Uridina Difosfato/metabolismo , Productos Biológicos/química , Productos Biológicos/metabolismo , Pared Celular/química , Pared Celular/metabolismo , Oryza/citología
11.
J Biol Chem ; 294(47): 17915-17930, 2019 11 22.
Artículo en Inglés | MEDLINE | ID: mdl-31530640

RESUMEN

Alginate is a linear polysaccharide from brown algae consisting of 1,4-linked ß-d-mannuronic acid (M) and α-l-guluronic acid (G) arranged in M, G, and mixed MG blocks. Alginate was assumed to be indigestible in humans, but bacteria isolated from fecal samples can utilize alginate. Moreover, genomes of some human gut microbiome-associated bacteria encode putative alginate-degrading enzymes. Here, we genome-mined a polysaccharide lyase family 6 alginate lyase from the gut bacterium Bacteroides cellulosilyticus (BcelPL6). The structure of recombinant BcelPL6 was solved by X-ray crystallography to 1.3 Å resolution, revealing a single-domain, monomeric parallel ß-helix containing a 10-step asparagine ladder characteristic of alginate-converting parallel ß-helix enzymes. Substitutions of the conserved catalytic site residues Lys-249, Arg-270, and His-271 resulted in activity loss. However, imidazole restored the activity of BcelPL6-H271N to 2.5% that of the native enzyme. Molecular docking oriented tetra-mannuronic acid for syn attack correlated with M specificity. Using biochemical analyses, we found that BcelPL6 initially releases unsaturated oligosaccharides of a degree of polymerization of 2-7 from alginate and polyM, which were further degraded to di- and trisaccharides. Unlike other PL6 members, BcelPL6 had low activity on polyMG and none on polyG. Surprisingly, polyG increased BcelPL6 activity on alginate 7-fold. LC-electrospray ionization-MS quantification of products and lack of activity on NaBH4-reduced octa-mannuronic acid indicated that BcelPL6 is an endolyase that further degrades the oligosaccharide products with an intact reducing end. We anticipate that our results advance predictions of the specificity and mode of action of PL6 enzymes.


Asunto(s)
Bacteroides/enzimología , Microbioma Gastrointestinal , Ácidos Hexurónicos/metabolismo , Polisacárido Liasas/química , Polisacárido Liasas/metabolismo , Alginatos/química , Alginatos/metabolismo , Bacteroides/genética , Genoma Bacteriano , Humanos , Cinética , Simulación del Acoplamiento Molecular , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Mutación/genética , Estructura Secundaria de Proteína , Electricidad Estática , Homología Estructural de Proteína , Relación Estructura-Actividad , Especificidad por Sustrato
12.
J Biol Chem ; 294(46): 17339-17353, 2019 11 15.
Artículo en Inglés | MEDLINE | ID: mdl-31558605

RESUMEN

Feruloyl esterases (EC 3.1.1.73), belonging to carbohydrate esterase family 1 (CE1), hydrolyze ester bonds between ferulic acid (FA) and arabinose moieties in arabinoxylans. Recently, some CE1 enzymes identified in metagenomics studies have been predicted to contain a family 48 carbohydrate-binding module (CBM48), a CBM family associated with starch binding. Two of these CE1s, wastewater treatment sludge (wts) Fae1A and wtsFae1B isolated from wastewater treatment surplus sludge, have a cognate CBM48 domain and are feruloyl esterases, and wtsFae1A binds arabinoxylan. Here, we show that wtsFae1B also binds to arabinoxylan and that neither binds starch. Surface plasmon resonance analysis revealed that wtsFae1B's Kd for xylohexaose is 14.8 µm and that it does not bind to starch mimics, ß-cyclodextrin, or maltohexaose. Interestingly, in the absence of CBM48 domains, the CE1 regions from wtsFae1A and wtsFae1B did not bind arabinoxylan and were also unable to catalyze FA release from arabinoxylan. Pretreatment with a ß-d-1,4-xylanase did enable CE1 domain-mediated FA release from arabinoxylan in the absence of CBM48, indicating that CBM48 is essential for the CE1 activity on the polysaccharide. Crystal structures of wtsFae1A (at 1.63 Å resolution) and wtsFae1B (1.98 Å) revealed that both are folded proteins comprising structurally-conserved hydrogen bonds that lock the CBM48 position relative to that of the CE1 domain. wtsFae1A docking indicated that both enzymes accommodate the arabinoxylan backbone in a cleft at the CE1-CBM48 domain interface. Binding at this cleft appears to enable CE1 activities on polymeric arabinoxylan, illustrating an unexpected and crucial role of CBM48 domains for accommodating arabinoxylan.


Asunto(s)
Carboxilesterasa/química , Hidrolasas de Éster Carboxílico/química , Ácidos Cumáricos/química , Receptores de Superficie Celular/química , Arabinosa/química , Carboxilesterasa/genética , Hidrolasas de Éster Carboxílico/ultraestructura , Cristalografía por Rayos X , Escherichia coli/química , Escherichia coli/enzimología , Hidrólisis , Oligosacáridos/química , Polisacáridos/química , Conformación Proteica , Receptores de Superficie Celular/ultraestructura , Especificidad por Sustrato , Resonancia por Plasmón de Superficie , Aguas Residuales/química , Xilanos/química
13.
J Biol Chem ; 294(31): 11701-11711, 2019 08 02.
Artículo en Inglés | MEDLINE | ID: mdl-31186348

RESUMEN

Bifidobacteria are exposed to substantial amounts of dietary ß-galactosides. Distinctive preferences for growth on different ß-galactosides are observed within Bifidobacterium members, but the basis of these preferences remains unclear. We previously described the first ß-(1,6)/(1,3)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04. This enzyme is relatively promiscuous, exhibiting only 5-fold higher efficiency on the preferred ß-(1,6)-galactobiose than the ß-(1,4) isomer. Here, we characterize the solute-binding protein (Bal6GBP) that governs the specificity of the ABC transporter encoded by the same ß-galactoside utilization locus. We observed that although Bal6GBP recognizes both ß-(1,6)- and ß-(1,4)-galactobiose, Bal6GBP has a 1630-fold higher selectivity for the former, reflected in dramatic differences in growth, with several hours lag on less preferred ß-(1,4)- and ß-(1,3)-galactobiose. Experiments performed in the presence of varying proportions of ß-(1,4)/ß-(1,6)-galactobioses indicated that the preferred substrate was preferentially depleted from the culture supernatant. This established that the poor growth on the nonpreferred ß-(1,4) was due to inefficient uptake. We solved the structure of Bal6GBP in complex with ß-(1,6)-galactobiose at 1.39 Å resolution, revealing the structural basis of this strict selectivity. Moreover, we observed a close evolutionary relationship with the human milk disaccharide lacto-N-biose-binding protein from Bifidobacterium longum, indicating that the recognition of the nonreducing galactosyl is essentially conserved, whereas the adjacent position is diversified to fit different glycosidic linkages and monosaccharide residues. These findings indicate that oligosaccharide uptake has a pivotal role in governing selectivity for distinct growth substrates and have uncovered evolutionary trajectories that shape the diversification of sugar uptake proteins within Bifidobacterium.


Asunto(s)
Transportadoras de Casetes de Unión a ATP/metabolismo , Proteínas Bacterianas/metabolismo , Bifidobacterium animalis/crecimiento & desarrollo , Galactosidasas/metabolismo , Galactósidos/metabolismo , Transportadoras de Casetes de Unión a ATP/química , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Bifidobacterium animalis/enzimología , Bifidobacterium animalis/metabolismo , Sitios de Unión , Dominio Catalítico , Cristalografía por Rayos X , Evolución Molecular , Galactosidasas/química , Galactósidos/química , Cinética , Simulación de Dinámica Molecular , Unión Proteica , Especificidad por Sustrato
14.
Enzyme Microb Technol ; 114: 48-54, 2018 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-29685353

RESUMEN

Carbonic anhydrases (CAs) are extremely fast enzymes, which have attracted much interest in the past due to their medical relevance and their biotechnological potential. An α-type CA gene was isolated from DNA derived from an active hydrothermal vent chimney, in an effort to identify novel CAs with suitable properties for CO2 capture. The gene product was recombinantly produced and characterized, revealing remarkable thermostability, also in the presence of high ionic strength alkaline conditions, which are used in some CO2 capture applications. The Tm was above 90 °C under all tested conditions. The enzyme was crystallized and the structure determined by molecular replacement, revealing a typical bacterial α-type CA non-covalent dimer, but not the disulphide mediated tetramer observed for the hyperthermophilic homologue used for molecular replacement, from Thermovibrio ammonificans. Structural comparison suggests that an increased secondary structure content, increased content of charges on the surface and ionic interactions compared to mesophilic enzymes, may be main structural sources of thermostability, as previously suggested for the homologue from Sulfurihydrogenibium yellowstonense.


Asunto(s)
Bacterias/enzimología , Proteínas Bacterianas/química , Anhidrasas Carbónicas/química , Respiraderos Hidrotermales/microbiología , Secuencia de Aminoácidos , Bacterias/genética , Bacterias/aislamiento & purificación , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Biocatálisis , Anhidrasas Carbónicas/genética , Anhidrasas Carbónicas/metabolismo , Dimerización , Estabilidad de Enzimas , Calor , Concentración de Iones de Hidrógeno , Cinética , Metagenoma , Alineación de Secuencia
16.
Acta Crystallogr F Struct Biol Commun ; 72(Pt 11): 846-852, 2016 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-27827356

RESUMEN

Bradyrhizobium japonicum sorbitol dehydrogenase is NADH-dependent and is active at elevated temperatures. The best substrate is D-glucitol (a synonym for D-sorbitol), although L-glucitol is also accepted, giving it particular potential in industrial applications. Crystallization led to a hexagonal crystal form, with crystals diffracting to 2.9 Šresolution. In attempts to phase the data, a molecular-replacement solution based upon PDB entry 4nbu (33% identical in sequence to the target) was found. The solution contained one molecule in the asymmetric unit, but a tetramer similar to that found in other short-chain dehydrogenases, including the search model, could be reconstructed by applying crystallographic symmetry operations. The active site contains electron density consistent with D-glucitol and phosphate, but there was not clear evidence for the binding of NADH. In a search for the features that determine the thermostability of the enzyme, the Tm for the orthologue from Rhodobacter sphaeroides, for which the structure was already known, was also determined, and this enzyme proved to be considerably less thermostable. A continuous ß-sheet is formed between two monomers in the tetramer of the B. japonicum enzyme, a feature not generally shared by short-chain dehydrogenases, and which may contribute to thermostability, as may an increased Pro/Gly ratio.


Asunto(s)
Proteínas Bacterianas/química , Bradyrhizobium/química , L-Iditol 2-Deshidrogenasa/química , Sorbitol/química , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Bradyrhizobium/enzimología , Dominio Catalítico , Clonación Molecular , Cristalografía por Rayos X , Estabilidad de Enzimas , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Calor , L-Iditol 2-Deshidrogenasa/genética , L-Iditol 2-Deshidrogenasa/metabolismo , Modelos Moleculares , Plásmidos/química , Plásmidos/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Multimerización de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Rhodobacter sphaeroides/química , Rhodobacter sphaeroides/enzimología , Sorbitol/metabolismo , Especificidad por Sustrato , Termodinámica
17.
J Biol Chem ; 291(38): 20220-31, 2016 09 16.
Artículo en Inglés | MEDLINE | ID: mdl-27502277

RESUMEN

The molecular details and impact of oligosaccharide uptake by distinct human gut microbiota (HGM) are currently not well understood. Non-digestible dietary galacto- and gluco-α-(1,6)-oligosaccharides from legumes and starch, respectively, are preferentially fermented by mainly bifidobacteria and lactobacilli in the human gut. Here we show that the solute binding protein (BlG16BP) associated with an ATP binding cassette (ABC) transporter from the probiotic Bifidobacterium animalis subsp. lactis Bl-04 binds α-(1,6)-linked glucosides and galactosides of varying size, linkage, and monosaccharide composition with preference for the trisaccharides raffinose and panose. This preference is also reflected in the α-(1,6)-galactoside uptake profile of the bacterium. Structures of BlG16BP in complex with raffinose and panose revealed the basis for the remarkable ligand binding plasticity of BlG16BP, which recognizes the non-reducing α-(1,6)-diglycoside in its ligands. BlG16BP homologues occur predominantly in bifidobacteria and a few Firmicutes but lack in other HGMs. Among seven bifidobacterial taxa, only those possessing this transporter displayed growth on α-(1,6)-glycosides. Competition assays revealed that the dominant HGM commensal Bacteroides ovatus was out-competed by B. animalis subsp. lactis Bl-04 in mixed cultures growing on raffinose, the preferred ligand for the BlG16BP. By comparison, B. ovatus mono-cultures grew very efficiently on this trisaccharide. These findings suggest that the ABC-mediated uptake of raffinose provides an important competitive advantage, particularly against dominant Bacteroides that lack glycan-specific ABC-transporters. This novel insight highlights the role of glycan transport in defining the metabolic specialization of gut bacteria.


Asunto(s)
Transportadoras de Casetes de Unión a ATP/metabolismo , Proteínas Bacterianas/metabolismo , Bifidobacterium animalis/crecimiento & desarrollo , Oligosacáridos/metabolismo , Transportadoras de Casetes de Unión a ATP/genética , Proteínas Bacterianas/genética , Bacteroides/genética , Bacteroides/crecimiento & desarrollo , Bifidobacterium animalis/genética , Humanos
18.
Mol Microbiol ; 2014 Oct 07.
Artículo en Inglés | MEDLINE | ID: mdl-25287704

RESUMEN

The Bifidobacterium genus harbours several health promoting members of the gut microbiota. Bifidobacteria display metabolic specialization by preferentially utilizing dietary or host-derived ß-galactosides. This study investigates the biochemistry and structure of a glycoside hydrolase family 42 (GH42) ß-galactosidase from the probiotic Bifidobacterium animalis subsp. lactis Bl-04 (BlGal42A). BlGal42A displays a preference for undecorated ß1-6 and ß1-3 linked galactosides and populates a phylogenetic cluster with close bifidobacterial homologues implicated in the utilization of N-acetyl substituted ß1-3 galactosides from human milk and mucin. A long loop containing an invariant tryptophan in GH42, proposed to bind substrate at subsite + 1, is identified here as specificity signature within this clade of bifidobacterial enzymes. Galactose binding at the subsite - 1 of the active site induced conformational changes resulting in an extra polar interaction and the ordering of a flexible loop that narrows the active site. The amino acid sequence of this loop provides an additional specificity signature within this GH42 clade. The phylogenetic relatedness of enzymes targeting ß1-6 and ß1-3 galactosides likely reflects structural differences between these substrates and ß1-4 galactosides, containing an axial galactosidic bond. These data advance our molecular understanding of the evolution of sub-specificities that support metabolic specialization in the gut niche.

19.
Mol Microbiol ; 90(5): 1100-12, 2013 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-24279727

RESUMEN

Glycan utilization plays a key role in modulating the composition of the gut microbiota, but molecular insight into oligosaccharide uptake by this microbial community is lacking. Arabinoxylo-oligosaccharides (AXOS) are abundant in the diet, and are selectively fermented by probiotic bifidobacteria in the colon. Here we show how selectivity for AXOS uptake is established by the probiotic strain Bifidobacterium animalis subsp. lactis Bl-04. The binding protein BlAXBP, which is associated with an ATP-binding cassette (ABC) transporter that mediates the uptake of AXOS, displays an exceptionally broad specificity for arabinosyl-decorated and undecorated xylo-oligosaccharides, with preference for tri- and tetra-saccharides. Crystal structures of BlAXBP in complex with four different ligands revealed the basis for this versatility. Uniquely, the protein was able to recognize oligosaccharides in two opposite orientations, which facilitates the optimization of interactions with the various ligands. Broad substrate specificity was further enhanced by a spacious binding pocket accommodating decorations at different mainchain positions and conformational flexibility of a lid-like loop. Phylogenetic and genetic analyses show that BlAXBP is highly conserved within Bifidobacterium, but is lacking in other gut microbiota members. These data indicate niche adaptation within Bifidobacterium and highlight the metabolic syntrophy (cross-feeding) among the gut microbiota.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Bifidobacterium/química , Bifidobacterium/metabolismo , Oligosacáridos/metabolismo , Proteínas Bacterianas/genética , Bifidobacterium/genética , Sitios de Unión , Clonación Molecular , Evolución Molecular , Genes Bacterianos , Humanos , Ligandos , Modelos Moleculares , Filogenia , Probióticos , Unión Proteica , Conformación Proteica , Estructura Terciaria de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Espectrometría de Fluorescencia , Especificidad por Sustrato , Resonancia por Plasmón de Superficie , Xilanos/metabolismo
20.
J Synchrotron Radiat ; 20(Pt 4): 648-53, 2013 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-23765310

RESUMEN

The macromolecular crystallography beamline I911-3, part of the Cassiopeia/I911 suite of beamlines, is based on a superconducting wiggler at the MAX II ring of the MAX IV Laboratory in Lund, Sweden. The beamline is energy-tunable within a range between 6 and 18 keV. I911-3 opened for users in 2005. In 2010-2011 the experimental station was completely rebuilt and refurbished such that it has become a state-of-the-art experimental station with better possibilities for rapid throughput, crystal screening and work with smaller samples. This paper describes the complete I911-3 beamline and how it is embedded in the Cassiopeia suite of beamlines.

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