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Pickens TL, Cockburn DW. Clostridium butyricum Prazmowski can degrade and utilize resistant starch via a set of synergistically acting enzymes. mSphere 2024; 9:e0056623. [PMID: 38131665 PMCID: PMC10826348 DOI: 10.1128/msphere.00566-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Resistant starch is a prebiotic fiber that is best known for its ability to increase butyrate production by the gut microbiota. This butyrate then plays an important role in modulating the immune system and inflammation. However, the ability to use this resistant starch appears to be a rare trait within the gut microbiota, with only a few species such as Ruminococcus bromii and Bifidobacterium adolescentis having been demonstrated to possess this ability. Furthermore, these bacteria do not directly produce butyrate themselves, rather they rely on cross-feeding interactions with other gut bacteria for its production. Here, we demonstrate that the often-used probiotic organism Clostridium butyricum also possesses the ability to utilize resistant starch from a number of sources, with direct production of butyrate. We further explore the enzymes responsible for this trait, demonstrating that they exhibit significant synergy, though with different enzymes exhibiting more or less importance depending on the source of the resistant starch. Thus, the co-administration of Clostridium butyricum may have the ability to improve the beneficial effects of resistant starch.IMPORTANCEClostridium butyricum is seeing increased use as a probiotic, due to potential health benefits tied to its ability to produce butyrate. Here, we demonstrate that this organism can use a variety of resistant starch sources and characterize the enzymes it uses to accomplish this. Given the relative rarity of resistant starch utilizing ability within the gut and the health benefits tied to resistant starch, the combined use of this organism with resistant starch in synbiotic formulations may prove beneficial.
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Affiliation(s)
- Tara L. Pickens
- Department of Food Science, The Pennsylvania State University, State College, Pennsylvania, USA
- The One Health Microbiome Center, Huck Institute of the Life Sciences, The Pennsylvania State University, State College, Pennsylvania, USA
| | - Darrell W. Cockburn
- Department of Food Science, The Pennsylvania State University, State College, Pennsylvania, USA
- The One Health Microbiome Center, Huck Institute of the Life Sciences, The Pennsylvania State University, State College, Pennsylvania, USA
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2
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Ledley AJ, Ziegler GR, Elias RJ, Cockburn DW. Microscopic assessment of the degradation of millet starch granules by endogenous and exogenous enzymes during mashing. Carbohydr Polym 2023; 314:120935. [PMID: 37173011 DOI: 10.1016/j.carbpol.2023.120935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/21/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
The high gelatinization temperature (GT) of millet starch prevents the usage of infusion or step mashes as an effective means to generate fermentable sugars (FS) in brewing because the malt amylases lack thermostability at GT. Here, we investigate processing modifications to determine if millet starch can be efficiently degraded below GT. We determined that producing finer grists through milling did not introduce enough granule damage to markedly change gelatinization characteristics, though there was improved liberation of the endogenous enzymes. Alternatively, exogenous enzyme preparations were added to investigate their ability to degrade intact granules. At the recommended dosages (0.625 μL/g malt), significant FS concentrations were observed, although at lower concentrations and with a much-altered profile than possible with a typical wort. When exogenous enzymes were introduced at high (10×) addition rates, significant losses of granule birefringence and granule hollowing were observed well below GT, suggesting these exogenous enzymes can be utilized to digest millet malt starch below GT. The exogenous maltogenic α-amylase appears to drive the loss of birefringence, but more research is needed to understand the observed predominate glucose production.
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Affiliation(s)
- Andrew J Ledley
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gregory R Ziegler
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ryan J Elias
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Darrell W Cockburn
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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3
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Ledley AJ, Elias RJ, Cockburn DW. Impact of mashing protocol on the formation of fermentable sugars from millet in gluten-free brewing. Food Chem 2023; 405:134758. [PMID: 36334456 DOI: 10.1016/j.foodchem.2022.134758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/14/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022]
Abstract
The production of fermentable sugars (FS) in gluten-free (GF) brewing is hindered by the high starch gelatinization temperatures of GF malts and lower diastatic power compared to barley malt. Our previous work has demonstrated that starch gelatinization was the primary hurdle, and when decoupled from a single mash phase, high concentrations of FS could be produced. However, more research was required to improve the applicability of GF brewing. In this study, millet was used as a model GF malt demonstrating that despite the low α-amylase and β-amylase activities compared to barley malt ∼ 90 % of the FS (∼110 g/L) could be produced within 40 min. Limitations to enzyme extraction and separation due to coarse milling and lautering initially limited FS by ∼ 30 g/L, requiring additional processing or exogenous enzyme supplements that improved fermentable sugar generation by ∼ 20 g/L. Overall, millet is a promising brewing ingredient, provided appropriate mashing procedures are implemented.
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Affiliation(s)
- Andrew J Ledley
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ryan J Elias
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Darrell W Cockburn
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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4
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Møller MS, Cockburn DW, Wilkens C. Surface Plasmon Resonance Analysis for Quantifying Protein-Carbohydrate Interactions. Methods Mol Biol 2023; 2657:141-150. [PMID: 37149528 DOI: 10.1007/978-1-0716-3151-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
During the past two decades, surface plasmon resonance (SPR) analysis has emerged as an important tool for studying protein-carbohydrate interactions, with several commercial instruments available. Binding affinities in the nM to mM range can be determined; however, there are pitfalls that require careful experimental design to avoid. Here we give an overview of each step in the SPR analysis from immobilization to data analysis, providing key points of consideration that will allow practitioners to achieve reliable and reproducible results.
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Affiliation(s)
- Marie Sofie Møller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Darrell W Cockburn
- Department of Food Science, The Pennsylvania State University, University Park, PA, USA
| | - Casper Wilkens
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark.
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Paff A, Cockburn DW. Evaluating the efficacy of non-thermal microbial load reduction treatments of heat labile food components for in vitro fermentation experiments. PLoS One 2023; 18:e0283287. [PMID: 36943858 PMCID: PMC10030034 DOI: 10.1371/journal.pone.0283287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Increasingly, in vitro simulated colon fermentations are being used as a pre-clinical step to assess the impacts of foods and drugs on the gut microbiota in a cost-effective manner. One challenge in such systems is that they are potentially susceptible to the influences of contaminating microbes in test materials. Simulated gastric and intestinal digestion can relieve some of these concerns, however, live microbes may remain that can confound analysis. Autoclave treatment of test materials is the surest way to eliminate these microbes but presents problems when using heat labile components such as resistant starch. In this study, liquid chemical sterilant alternatives to moist heat sterilization were explored for treating pulse flours for use during in vitro simulated colon fermentation. Key attributes considered in chemical selection were accessibility, impact on treated food components, and effectiveness of the treatments for reducing microbial load. Three chemicals were selected for evaluation, bleach, alcohol, and hydrogen peroxide, at varying concentrations. Flours chosen for testing were from green lentil, field pea, chickpea, or sprouted green lentil. All treatments significantly reduced microbial loads, though there were still detectable levels of microbes after alcohol treatments. Furthermore, in vitro simulated colon fermentations of the treated pulses showed minimal difference from the untreated control both in terms of microbial composition and short chain fatty acid production. Scanning electron microscopy showed minimal impact of sterilization treatments on the gross structure of the pulse flours. Together these results suggest that bleach and hydrogen peroxide treatments can be effective nonthermal treatments to eliminate contaminating microbes in pulse flours without causing significant damage to starch and other fermentable substrates. This is thus also a promising treatment method for other starchy food substrates, though further testing is required.
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Affiliation(s)
- Andrew Paff
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Darrell W Cockburn
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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Abstract
Affinity electrophoresis has long been used to study the interaction between proteins and large soluble ligands. The technique has been found to have great utility for the examination of polysaccharide binding by proteins, particularly carbohydrate-binding modules (CBMs). In recent years carbohydrate surface binding sites of proteins, mostly enzymes, have also been investigated by this method. Here we describe a protocol for identifying binding interactions between enzyme catalytic modules and a variety of carbohydrate ligands.
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Affiliation(s)
- Darrell W Cockburn
- Department of Food Science, The Pennsylvania State University, University Park, PA, USA.
| | - Casper Wilkens
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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Weikart DK, Indukuri VV, Racine KC, Coleman KM, Kovac J, Cockburn DW, Hopfer H, Neilson AP, Lambert JD. Effect of processing on the anti-inflammatory efficacy of cocoa in a high fat diet-induced mouse model of obesity. J Nutr Biochem 2022; 109:109117. [DOI: 10.1016/j.jnutbio.2022.109117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/16/2022] [Accepted: 06/24/2022] [Indexed: 10/31/2022]
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DeMartino P, Johnston EA, Petersen KS, Kris-Etherton PM, Cockburn DW. Additional Resistant Starch from One Potato Side Dish per Day Alters the Gut Microbiota but Not Fecal Short-Chain Fatty Acid Concentrations. Nutrients 2022; 14:nu14030721. [PMID: 35277080 PMCID: PMC8840755 DOI: 10.3390/nu14030721] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 01/11/2023] Open
Abstract
The composition of the gut microbiota and their metabolites are associated with cardiometabolic health and disease risk. Intake of dietary fibers, including resistant starch (RS), has been shown to favorably affect the health of the gut microbiome. The aim of this research was to measure changes in the gut microbiota and fecal short-chain fatty acids as part of a randomized, crossover supplemental feeding study. Fifty participants (68% female, aged 40 ± 13 years, BMI 24.5 ± 3.6 kg/m2) completed this study. Potato dishes (POT) contained more RS than refined grain dishes (REF) (POT: 1.31% wet basis (95% CI: 0.94, 1.71); REF: 0.73% wet basis (95% CI: 0.34, 1.14); p = 0.03). Overall, potato dish consumption decreased alpha diversity, but beta diversity was not impacted. Potato dish consumption was found to increase the abundance of Hungatella xylanolytica, as well as that of the butyrate producing Roseburia faecis, though fecal butyrate levels were unchanged. Intake of one potato-based side dish per day resulted in modest changes in gut microbiota composition and diversity, compared to isocaloric intake of refined grains in healthy adults. Studies examining foods naturally higher in RS are needed to understand microbiota changes in response to dietary intake of RS and associated health effects.
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Affiliation(s)
- Peter DeMartino
- Department of Food Science, Pennsylvania State University, University Park, PA 16802, USA;
| | - Emily A. Johnston
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA 16802, USA; (E.A.J.); (K.S.P.); (P.M.K.-E.)
| | - Kristina S. Petersen
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA 16802, USA; (E.A.J.); (K.S.P.); (P.M.K.-E.)
- Department of Nutritional Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Penny M. Kris-Etherton
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA 16802, USA; (E.A.J.); (K.S.P.); (P.M.K.-E.)
| | - Darrell W. Cockburn
- Department of Food Science, Pennsylvania State University, University Park, PA 16802, USA;
- Correspondence: ; Tel.: +1-814-863-2950
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9
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Cockburn DW, Kibler R, Brown HA, Duvall R, Moraïs S, Bayer E, Koropatkin NM. Structure and substrate recognition by the Ruminococcus bromii amylosome pullulanases. J Struct Biol 2021; 213:107765. [PMID: 34186214 DOI: 10.1016/j.jsb.2021.107765] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/11/2021] [Accepted: 06/23/2021] [Indexed: 01/15/2023]
Abstract
Pullulanases are glycoside hydrolase family 13 (GH13) enzymes that target α1,6 glucosidic linkages within starch and aid in the degradation of the α1,4- and α1,6- linked glucans pullulan, glycogen and amylopectin. The human gut bacterium Ruminococcus bromii synthesizes two extracellular pullulanases, Amy10 and Amy12, that are incorporated into the multiprotein amylosome complex that enables the digestion of granular resistant starch from the diet. Here we provide a comparative biochemical analysis of these pullulanases and the x-ray crystal structures of the wild type and the nucleophile mutant D392A of Amy12 complexed with maltoheptaose and 63-α-D glucosyl-maltotriose. While Amy10 displays higher catalytic efficiency on pullulan and cleaves only α1,6 linkages, Amy12 has some activity on α1,4 linkages suggesting that these enzymes are not redundant within the amylosome. Our structures of Amy12 include a mucin-binding protein (MucBP) domain that follows the C-domain of the GH13 fold, an atypical feature of these enzymes. The wild type Amy12 structure with maltoheptaose captured two oligosaccharides in the active site arranged as expected following catalysis of an α1,6 branch point in amylopectin. The nucleophile mutant D392A complexed with maltoheptaose or 63-α-D glucosyl-maltotriose captured β-glucose at the reducing end in the -1 subsite, facilitated by the truncation of the active site aspartate and stabilized by stacking with Y279. The core interface between the co-crystallized ligands and Amy12 occurs within the -2 through + 1 subsites, which may allow for flexible recognition of α1,6 linkages within a variety of starch structures.
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Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Ryan Kibler
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Rebecca Duvall
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Sarah Moraïs
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Edward Bayer
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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10
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Teichmann J, Cockburn DW. In vitro Fermentation Reveals Changes in Butyrate Production Dependent on Resistant Starch Source and Microbiome Composition. Front Microbiol 2021; 12:640253. [PMID: 33995299 PMCID: PMC8117019 DOI: 10.3389/fmicb.2021.640253] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/06/2021] [Indexed: 12/31/2022] Open
Abstract
One of the primary benefits associated with dietary resistant starch (RS) is the production of butyrate by the gut microbiome during fermentation of this fiber in the large intestine. The ability to degrade RS is a relatively rare trait among microbes in the gut, seemingly confined to only a few species, none of which are butyrate producing organisms. Thus, production of butyrate during RS fermentation requires a network of interactions between RS degraders and butyrate producers. This is further complicated by the fact that there are multiple types of RS that differ in their structural properties and impacts on the microbiome. Human dietary intervention trials with RS have shown increases in fecal butyrate levels at the population level but with individual to individual differences. This suggests that interindividual differences in microbiome composition dictate butyrate response, but the factors driving this are still unknown. Furthermore, it is unknown whether a lack of increase in butyrate production upon supplementation with one RS is indicative of a lack of butyrate production with any RS. To shed some light on these issues we have undertaken an in vitro fermentation approach in an attempt to mimic RS fermentation in the colon. Fecal samples from 10 individuals were used as the inoculum for fermentation with 10 different starch sources. Butyrate production was heterogeneous across both fecal inocula and starch source, suggesting that a given microbiome is best suited to produce butyrate only from a subset of RS sources that differs between individuals. Interestingly, neither the total amount of RS degraders nor butyrate producers seemed to be limiting for any individual, rather the membership of these sub-populations was more important. While none of the RS degrading organisms were correlated with butyrate levels, Ruminococcus bromii was strongly positively correlated with many of the most important butyrate producers in the gut, though total butyrate production was strongly influenced by factors such as pH and lactate levels. Together these results suggest that the membership of the RS degrader and butyrate producer communities rather than their abundances determine the RS sources that will increase butyrate levels for a given microbiome.
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Affiliation(s)
- June Teichmann
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
| | - Darrell W Cockburn
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
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11
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Wang HL, Hopfer H, Cockburn DW, Wee J. Characterization of Microbial Dynamics and Volatile Metabolome Changes During Fermentation of Chambourcin Hybrid Grapes From Two Pennsylvania Regions. Front Microbiol 2021; 11:614278. [PMID: 33505380 PMCID: PMC7829364 DOI: 10.3389/fmicb.2020.614278] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/14/2020] [Indexed: 12/24/2022] Open
Abstract
Microbial diversity present on grapes in wineries, and throughout fermentation has been associated with important metabolites for final wine quality. Although microbiome-metabolome associations have been well characterized and could be used as indicators of wine quality, the impact of regionality on the microbiome and metabolome is not well known. Additionally, studies between microbiome and metabolome have been conducted on single species grape such as Vitis vinifera instead of other species and interspecific hybrids. Although the Pennsylvania wine industry is relatively young compared to California, the industry has been experiencing rapid growth over the past decade and is expected to continue to grow in the future. Pennsylvania's climate of cold winters and high levels of rainfall throughout the growing season favors cultivation of interspecific hybrid grapes such as Vitis ssp. Chambourcin, one of the most commonly grown hybrid varieties in the state. Chambourcin is a prime candidate for studying the impact of regionality on microbiome-metabolome interactions as interspecific hybrid varieties could shape the future of winemaking. Here, we identify for the first time the regional distribution of microbial communities and their interactions with volatile metabolome during fermentation (0-20 days) by integrating high throughput Illumina sequencing (16S and ITS) and headspace-solid phase microextraction-gas chromatography-mass spectrometry. Analyzing 88 samples from nine wineries in the Central and East Pennsylvania regions, we observed high microbial diversity during early stages of fermentation (1-4 days) where non-Saccharomyces yeasts such as Starmerella and Aureobasidium and non-Oenococcus bacteria, Sphingomonas, likely contribute to microbial terroir to the resulting wines. Furthermore, key differentiators between two regions in Pennsylvania, as identified by LEfSe analysis, include the fungal genera Cladosporium and Kazachstania and the bacterial genera Lactococcus and Microbacterium. Moreover, 29 volatile fermentation metabolites were discriminated significantly (variable importance in projection > 1) between the two regions as shown by Partial Least Squares-Discriminant Analysis. Finally, Spearman's correlation identified regional differences of microbial-metabolite associations throughout fermentation that could be used for targeted microbiome manipulation to improve wine quality and preserve regionality. In summary, these results demonstrate the microbial signatures during fermentation and differential microorganisms and metabolites further support impact of regionality on Chambourcin wines in Pennsylvania.
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Affiliation(s)
- Hung Li Wang
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
| | - Helene Hopfer
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
- Sensory Evaluation Center, The Pennsylvania State University, State College, PA, United States
| | - Darrell W. Cockburn
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
- Microbiome Center, HUCK Institute for Life Sciences, The Pennsylvania State University, State College, PA, United States
| | - Josephine Wee
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
- Microbiome Center, HUCK Institute for Life Sciences, The Pennsylvania State University, State College, PA, United States
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12
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Cockburn DW, Cerqueira FM, Bahr C, Koropatkin NM. The structures of the GH13_36 amylases from Eubacterium rectale and Ruminococcus bromii reveal subsite architectures that favor maltose production. ACTA ACUST UNITED AC 2020. [DOI: 10.1515/amylase-2020-0003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractBacteria in the human gut including Ruminococcus bromii and Eubacterium rectale encode starch-active enzymes that dictate how these bacteria interact with starch to initiate a metabolic cascade that leads to increased butyrate. Here, we determined the structures of two predicted secreted glycoside hydrolase 13 subfamily 36 (GH13_36) enzymes: ErAmy13B complexed with maltotetraose from E. rectale and RbAmy5 from R. bromii. The structures show a limited binding pocket extending from –2 through +2 subsites with limited possibilities for substrate interaction beyond this, which contributes to the propensity for members of this family to produce maltose as their main product. The enzyme structures reveal subtle differences in the +1/+2 subsites that may restrict the recognition of larger starch polymers by ErAmy13B. Our bioinformatic analysis of the biochemically characterized members of the GH13_36 subfamily, which includes the cell-surface GH13 SusG from Bacteroides thetaiotaomicron, suggests that these maltogenic amylases (EC 3.2.1.133) are usually localized to the outside of the cell, display a range of substrate preferences, and most likely contribute to maltose liberation at the cell surface during growth on starch. A broader comparison between GH13_36 and other maltogenic amylase subfamilies explain how the activity profiles of these enzymes are influenced by their structures.
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Affiliation(s)
- Darrell W. Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Food Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Filipe M. Cerqueira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Constance Bahr
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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13
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Arnal G, Cockburn DW, Brumer H, Koropatkin NM. Structural basis for the flexible recognition of α-glucan substrates by Bacteroides thetaiotaomicron SusG. Protein Sci 2018; 27:1093-1101. [PMID: 29603462 PMCID: PMC5980535 DOI: 10.1002/pro.3410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/15/2018] [Accepted: 03/21/2018] [Indexed: 11/09/2022]
Abstract
Bacteria that reside in the mammalian intestinal tract efficiently hydrolyze dietary carbohydrates, including starch, that escape digestion in the small intestine. Starch is an abundant dietary carbohydrate comprised of α1,4 and α1,6 linked glucose, yet mammalian intestinal glucoamylases cannot effectively hydrolyze starch that has frequent α1,6 branching as these structures hinder recognition and processing by α1,4-specific amylases. Here we present the structure of the cell surface amylase SusG from Bacteroides thetaiotaomicron complexed with a mixed linkage amylosaccharide generated from transglycosylation during crystallization. Although SusG is specific for α1,4 glucosidic bonds, binding of this new oligosaccharide at the active site demonstrates that SusG can accommodate α1,6 branch points at subsite -3 to -2, and also at subsite+1 adjacent to the site of hydrolysis, explaining how this enzyme may be able to process a wide range of limit dextrins in the intestinal environment. These data suggest that B. thetaiotaomicron and related organisms may have a selective advantage for amylosaccharide scavenging in the gut.
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Affiliation(s)
- Gregory Arnal
- Michael Smith Laboratories, University of British Columbia, 2185 East MallVancouverBritish ColumbiaV6T 1Z4Canada
| | - Darrell W. Cockburn
- Department of Microbiology and ImmunologyUniversity of Michigan Medical School, 1150 W Medical Center DriveAnn ArborMichigan
- Present address:
Department of Food SciencePennsylvania State UniversityUniversity ParkPennsylvania
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East MallVancouverBritish ColumbiaV6T 1Z4Canada
- Department of ChemistryUniversity of British Columbia, 2036 Main MallVancouverBritish ColumbiaV6T 1Z1Canada
- Department of Biochemistry and Molecular BiologyUniversity of British Columbia, 2350 Health Sciences MallVancouverBritish ColumbiaV6T 1Z3Canada
| | - Nicole M. Koropatkin
- Department of Microbiology and ImmunologyUniversity of Michigan Medical School, 1150 W Medical Center DriveAnn ArborMichigan
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14
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Cockburn DW, Suh C, Medina KP, Duvall RM, Wawrzak Z, Henrissat B, Koropatkin NM. Novel carbohydrate binding modules in the surface anchored α-amylase of Eubacterium rectale provide a molecular rationale for the range of starches used by this organism in the human gut. Mol Microbiol 2017; 107:249-264. [PMID: 29139580 PMCID: PMC6939882 DOI: 10.1111/mmi.13881] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2017] [Indexed: 12/30/2022]
Abstract
Gut bacteria recognize accessible glycan substrates within a complex environment. Carbohydrate binding modules (CBMs) of cell surface glycoside hydrolases often drive binding to the target substrate. Eubacterium rectale, an important butyrate-producing organism in the gut, consumes a limited range of substrates, including starch. Host consumption of resistant starch increases the abundance of E. rectale in the intestine, likely because it successfully captures the products of resistant starch degradation by other bacteria. Here, we demonstrate that the cell wall anchored starch-degrading α-amylase, Amy13K of E. rectale harbors five CBMs that all target starch with differing specificities. Intriguingly these CBMs efficiently bind to both regular and high amylose corn starch (a type of resistant starch), but have almost no affinity for potato starch (another type of resistant starch). Removal of these CBMs from Amy13K reduces the activity level of the enzyme toward corn starches by ∼40-fold, down to the level of activity toward potato starch, suggesting that the CBMs facilitate activity on corn starch and allow its utilization in vivo. The specificity of the Amy13K CBMs provides a molecular rationale for why E. rectale is able to only use certain starch types without the aid of other organisms.
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Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Food Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Carolyn Suh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Krizia Perez Medina
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rebecca M Duvall
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zdzislaw Wawrzak
- Life Sciences Collaborative Access Team (LS-CAT), Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL, 60439, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, F-13288, France.,Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, F-13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Moraïs S, Cockburn DW, Ben-David Y, Koropatkin NM, Martens EC, Duncan SH, Flint HJ, Mizrahi I, Bayer EA. Lysozyme activity of theRuminococcus champanellensiscellulosome. Environ Microbiol 2016; 18:5112-5122. [DOI: 10.1111/1462-2920.13501] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 08/16/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah Moraïs
- Biomolecular Sciences Department; The Weizmann Institute of Science; Rehovot Israel
| | - Darrell W. Cockburn
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor MI 48109 USA
| | - Yonit Ben-David
- Biomolecular Sciences Department; The Weizmann Institute of Science; Rehovot Israel
| | - Nicole M. Koropatkin
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor MI 48109 USA
| | - Eric C. Martens
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor MI 48109 USA
| | - Sylvia H. Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen; Aberdeen UK
| | - Harry J. Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen; Aberdeen UK
| | - Itzhak Mizrahi
- The Department of Life Sciences & the National Institute for Biotechnology in the Negev; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Edward A. Bayer
- Biomolecular Sciences Department; The Weizmann Institute of Science; Rehovot Israel
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16
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Cockburn DW, Koropatkin NM. Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease. J Mol Biol 2016; 428:3230-3252. [PMID: 27393306 DOI: 10.1016/j.jmb.2016.06.021] [Citation(s) in RCA: 316] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 02/06/2023]
Abstract
Carbohydrates comprise a large fraction of the typical diet, yet humans are only able to directly process some types of starch and simple sugars. The remainder transits the large intestine where it becomes food for the commensal bacterial community. This is an environment of not only intense competition but also impressive cooperation for available glycans, as these bacteria work to maximize their energy harvest from these carbohydrates during their limited transit time through the gut. The species within the gut microbiota use a variety of strategies to process and scavenge both dietary and host-produced glycans such as mucins. Some act as generalists that are able to degrade a wide range of polysaccharides, while others are specialists that are only able to target a few select glycans. All are members of a metabolic network where substantial cross-feeding takes place, as by-products of one organism serve as important resources for another. Much of this metabolic activity influences host physiology, as secondary metabolites and fermentation end products are absorbed either by the epithelial layer or by transit via the portal vein to the liver where they can have additional effects. These microbially derived compounds influence cell proliferation and apoptosis, modulate the immune response, and can alter host metabolism. This review summarizes the molecular underpinnings of these polysaccharide degradation processes, their impact on human health, and how we can manipulate them through the use of prebiotics.
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Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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17
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Foley MH, Cockburn DW, Koropatkin NM. The Sus operon: a model system for starch uptake by the human gut Bacteroidetes. Cell Mol Life Sci 2016; 73:2603-17. [PMID: 27137179 PMCID: PMC4924478 DOI: 10.1007/s00018-016-2242-x] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/16/2022]
Abstract
Resident bacteria in the densely populated human intestinal tract must efficiently compete for carbohydrate nutrition. The Bacteroidetes, a dominant bacterial phylum in the mammalian gut, encode a plethora of discrete polysaccharide utilization loci (PULs) that are selectively activated to facilitate glycan capture at the cell surface. The most well-studied PUL-encoded glycan-uptake system is the starch utilization system (Sus) of Bacteroides thetaiotaomicron. The Sus includes the requisite proteins for binding and degrading starch at the surface of the cell preceding oligosaccharide transport across the outer membrane for further depolymerization to glucose in the periplasm. All mammalian gut Bacteroidetes possess analogous Sus-like systems that target numerous diverse glycans. In this review, we discuss what is known about the eight Sus proteins of B. thetaiotaomicron that define the Sus-like paradigm of nutrient acquisition that is exclusive to the Gram-negative Bacteroidetes. We emphasize the well-characterized outer membrane proteins SusDEF and the α-amylase SusG, each of which have unique structural features that allow them to interact with starch on the cell surface. Despite the apparent redundancy in starch-binding sites among these proteins, each has a distinct role during starch catabolism. Additionally, we consider what is known about how these proteins dynamically interact and cooperate in the membrane and propose a model for the formation of the Sus outer membrane complex.
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Affiliation(s)
- Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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18
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Cockburn DW, Orlovsky NI, Foley MH, Kwiatkowski KJ, Bahr CM, Maynard M, Demeler B, Koropatkin NM. Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale. Mol Microbiol 2015; 95:209-30. [PMID: 25388295 PMCID: PMC4437465 DOI: 10.1111/mmi.12859] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2014] [Indexed: 01/07/2023]
Abstract
Eubacterium rectale is a prominent human gut symbiont yet little is known about the molecular strategies this bacterium has developed to acquire nutrients within the competitive gut ecosystem. Starch is one of the most abundant glycans in the human diet, and E. rectale increases in vivo when the host consumes a diet rich in resistant starch, although it is not a primary degrader of this glycan. Here we present the results of a quantitative proteomics study in which we identify two glycoside hydrolase 13 family enzymes, and three ABC transporter solute-binding proteins that are abundant during growth on starch and, we hypothesize, work together at the cell surface to degrade starch and capture the released maltooligosaccharides. EUR_21100 is a multidomain cell wall anchored amylase that preferentially targets starch polysaccharides, liberating maltotetraose, whereas the membrane-associated maltogenic amylase EUR_01860 breaks down maltooligosaccharides longer than maltotriose. The three solute-binding proteins display a range of glycan-binding specificities that ensure the capture of glucose through maltoheptaose and some α1,6-branched glycans. Taken together, we describe a pathway for starch utilization by E. rectale DSM 17629 that may be conserved among other starch-degrading Clostridium cluster XIVa organisms in the human gut.
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Affiliation(s)
- Darrell W. Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Nicole I. Orlovsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Matthew H. Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Kurt J. Kwiatkowski
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Constance M. Bahr
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Mallory Maynard
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229
| | - Nicole M. Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
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Cockburn DW, Vandenende C, Clarke AJ. Modulating the pH−Activity Profile of Cellulase by Substitution: Replacing the General Base Catalyst Aspartate with Cysteinesulfinate in Cellulase A from Cellulomonas fimi. Biochemistry 2010; 49:2042-50. [DOI: 10.1021/bi1000596] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Darrell W. Cockburn
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Chris Vandenende
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Anthony J. Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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