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Dagher SF, Vaishnav A, Stanley CB, Meilleur F, Edwards BFP, Bruno-Bárcena JM. Structural analysis and functional evaluation of the disordered ß-hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis. Front Bioeng Biotechnol 2023; 11:1291245. [PMID: 38162180 PMCID: PMC10755861 DOI: 10.3389/fbioe.2023.1291245] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024] Open
Abstract
Hamamotoa (Sporobolomyces) singularis codes for an industrially important membrane bound ß-hexosyltransferase (BHT), (BglA, UniprotKB: Q564N5) that has applications in the production of natural fibers such as galacto-oligosaccharides (GOS) and natural sugars found in human milk. When heterologously expressed by Komagataella phaffii GS115, BHT is found both membrane bound and soluble secreted into the culture medium. In silico structural predictions and crystal structures support a glycosylated homodimeric enzyme and the presence of an intrinsically disordered region (IDR) with membrane binding potential within its novel N-terminal region (1-110 amino acids). Additional in silico analysis showed that the IDR may not be essential for stable homodimerization. Thus, we performed progressive deletion analyses targeting segments within the suspected disordered region, to determine the N-terminal disorder region's impact on the ratio of membrane-bound to secreted soluble enzyme and its contribution to enzyme activity. The ratio of the soluble secreted to membrane-bound enzyme shifted from 40% to 53% after the disordered N-terminal region was completely removed, while the specific activity was unaffected. Furthermore, functional analysis of each glycosylation site found within the C-terminal domain revealed reduced total secreted protein activity by 58%-97% in both the presence and absence of the IDR, indicating that glycosylation at all four locations is required by the host for the secretion of active enzyme and independent of the removed disordered N-terminal region. Overall, the data provides evidence that the disordered region only partially influences the secretion and membrane localization of BHT.
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Affiliation(s)
- Suzanne F. Dagher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States
| | | | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Brian F. P. Edwards
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States
| | - José M. Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Arnold JW, Whittington HD, Dagher SF, Roach J, Azcarate-Peril MA, Bruno-Barcena JM. Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome. Front Nutr 2021; 8:640100. [PMID: 33898497 PMCID: PMC8058378 DOI: 10.3389/fnut.2021.640100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/11/2021] [Indexed: 01/14/2023] Open
Abstract
Complex dietary carbohydrate structures including β(1-4) galacto-oligosaccharides (GOS) are resistant to digestion in the upper gastrointestinal (GI) tract and arrive intact to the colon where they benefit the host by selectively stimulating microbial growth. Studies have reported the beneficial impact of GOS (alone or in combination with other prebiotics) by serving as metabolic substrates for modulating the assembly of the infant gut microbiome while reducing GI infections. N-Acetyl-D-lactosamine (LacNAc, Galβ1,4GlcNAc) is found in breast milk as a free disaccharide. This compound is also found as a component of human milk oligosaccharides (HMOs), which have repeating and variably branched lactose and/or LacNAc units, often attached to sialic acid and fucose monosaccharides. Human glycosyl-hydrolases do not degrade most HMOs, indicating that these structures have evolved as natural prebiotics to drive the proper assembly of the infant healthy gut microbiota. Here, we sought to develop a novel enzymatic method for generating LacNAc-enriched GOS, which we refer to as humanized GOS (hGOS). We showed that the membrane-bound β-hexosyl transferase (rBHT) from Hamamotoa (Sporobolomyces) singularis was able to generate GOS and hGOS from lactose and N-Acetyl-glucosamine (GlcNAc). The enzyme catalyzed the regio-selective, repeated addition of galactose from lactose to GlcNAc forming the β-galactosyl linkage at the 4-position of the GlcNAc and at the 1-position of D-galactose generating, in addition to GOS, LacNAc, and Galactosyl-LacNAc trisaccharides which were produced by two sequential transgalactosylations. Humanized GOS is chemically distinct from HMOs, and its effects in vivo have yet to be determined. Thus, we evaluated its safety and demonstrated the prebiotic's ability to modulate the gut microbiome in 6-week-old C57BL/6J mice. Longitudinal analysis of gut microbiome composition of stool samples collected from mice fed a diet containing hGOS for 5 weeks showed a transient reduction in alpha diversity. Differences in microbiome community composition mostly within the Firmicutes phylum were observed between hGOS and GOS, compared to control-fed animals. In sum, our study demonstrated the biological synthesis of hGOS, and signaled its safety and ability to modulate the gut microbiome in vivo, promoting the growth of beneficial microorganisms, including Bifidobacterium and Akkermansia.
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Affiliation(s)
- Jason W. Arnold
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Hunter D. Whittington
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Suzanne F. Dagher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Jeffery Roach
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Information Technology Services and Research Computing, University of North Carolina, Chapel Hill, NC, United States
| | - M. Andrea Azcarate-Peril
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Jose M. Bruno-Barcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Dagher SF, Bruno-Bárcena JM. A novel N-terminal region of the membrane β-hexosyltransferase: its role in secretion of soluble protein by Pichia pastoris. Microbiology (Reading) 2016; 162:23-34. [PMID: 26552922 PMCID: PMC5974927 DOI: 10.1099/mic.0.000211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/05/2015] [Indexed: 11/18/2022]
Abstract
The β-hexosyltransferase (BHT) from Sporobolomyces singularis is a membrane-bound enzyme that catalyses transgalactosylation reactions to synthesize galacto-oligosaccharides (GOSs). To increase the secretion of the active soluble version of this protein, we examined the uncharacterized novel N-terminal region (amino acids 1-110), which included two predicted endogenous structural domains. The first domain (amino acids 1-22) may act as a classical leader while a non-classical signal was located within the remaining region (amino acids 23-110). A functional analysis of these domains was performed by evaluating the amounts of the rBHT forms secreted by recombinant P. pastoris strains carrying combinations of the predicted structural domains and the α mating factor (MFα) from Saccharomyces cerevisiae as positive control. Upon replacement of the leader domain (amino acids 1-22) by MFα (MFα-rBht(23-594)), protein secretion increased and activity of both soluble and membrane-bound enzymes was improved 53- and 14-fold, respectively. Leader interference was demonstrated when MFα preceded the putative classical rBHT(1-22) leader (amino acids 1-22), explaining the limited secretion of soluble protein by P. pastoris (GS115 : : MFα-rBht(1-594)). To validate the role of the N-terminal domains in promoting protein secretion, we tested the domains using a non-secreted protein, the anti-β-galactosidase single-chain variable antibody fragment scFv13R4. The recombinants carrying chimeras of the N-terminal 1-110 regions of rBHT preceding scFv13R4 correlated with the secretion strength of soluble protein observed with the rBHT recombinants. Finally, soluble bioactive HIS-tagged and non-tagged rBHT (purified to homogeneity) obtained from the most efficient recombinants (GS115 : : MFα-rBht(23-594)-HIS and GS115 : : MFα-rBht(23-594)) showed comparable activity rates of GOS generation.
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Affiliation(s)
- Suzanne F. Dagher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7615, USA
| | - José M. Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7615, USA
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Dagher SF, Azcarate-Peril MA, Bruno-Bárcena JM. Heterologous expression of a bioactive β-hexosyltransferase, an enzyme producer of prebiotics, from Sporobolomyces singularis. Appl Environ Microbiol 2013; 79:1241-9. [PMID: 23241974 PMCID: PMC3568590 DOI: 10.1128/aem.03491-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 11/15/2012] [Indexed: 11/20/2022] Open
Abstract
Galacto-oligosaccharides (GOS) are indigestible dietary fibers that are able to reach the lower gastrointestinal tract to be selectively fermented by health-promoting bacteria. In this report, we describe the heterologous expression of an optimized synthetically produced version of the β-hexosyltransferase gene (Bht) from Sporobolomyces singularis. The Bht gene encodes a glycosyl hydrolase (EC 3.2.1.21) that acts as galactosyltransferase, able to catalyze a one-step conversion of lactose to GOS. Expression of the enzyme in Escherichia coli yielded an inactive insoluble protein, while the methylotrophic yeast Pichia pastoris GS115 produced a bioactive β-hexosyltransferase (rBHT). The enzyme exhibited faster kinetics at pHs between 3.5 and 6 and at temperatures between 40 and 50°C. Enzyme stability improved at temperatures lower than 40°C, and glucose was found to be a competitive inhibitor of enzymatic activity. P. pastoris secreted a fraction of the bioactive rBHT into the fermentation broth, while the majority of the enzyme remained associated with the outer membrane. Both the secreted and the membrane-associated forms were able to efficiently convert lactose to GOS. Additionally, resting cells with membrane-bound enzyme converted 90% of the initial lactose into GOS at 68% yield (g/g) (the maximum theoretical is 75%) with no secondary residual (glucose or galactose) products. This is the first report of a bioactive BHT from S. singularis that has been heterologously expressed.
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Affiliation(s)
- Suzanne F. Dagher
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina, USA
| | - M. Andrea Azcarate-Peril
- Department of Cell Biology and Physiology, School of Medicine and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - José M. Bruno-Bárcena
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina, USA
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Dagher SF, Ragout AL, Siñeriz F, Bruno-Bárcena JM. Cell immobilization for production of lactic acid biofilms do it naturally. Adv Appl Microbiol 2010; 71:113-48. [PMID: 20378053 DOI: 10.1016/s0065-2164(10)71005-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Interest in natural cell immobilization or biofilms for lactic acid fermentation has developed considerably over the last few decades. Many studies report the benefits associated with biofilms as industrial methods for food production and for wastewater treatment, since the formation represents a protective means of microbial growth offering survival advantages to cells in toxic environments. The formation of biofilms is a natural process in which microbial cells adsorb to a support without chemicals or polymers that entrap the cells and is dependent on the reactor environment, microorganism, and characteristics of the support. These unique characteristics enable biofilms to cause chronic infections, disease, food spoilage, and devastating effects as in microbial corrosion. Their distinct resistance to toxicity, high biomass potential, and improved stability over cells in suspension make biofilms a good tool for improving the industrial economics of biological lactic acid production. Lactic acid bacteria and specific filamentous fungi are the main sources of biological lactic acid. Over the past two decades, studies have focused on improving the lactic acid volumetric productivity through reactor design development, new support materials, and improvements in microbial production strains. To illustrate the operational designs applied to the natural immobilization of lactic acid producing microorganisms, this chapter presents the results of a search for optimum parameters and how they are affected by the physical, chemical, and biological variables of the process. We will place particular emphasis upon the relationship between lactic acid productivity attained by various types of reactors, supports, media formulations, and lactic acid producing microorganisms.
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Affiliation(s)
- Suzanne F Dagher
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina, USA
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Abstract
The SRPK family of kinases is specific for RS domain-containing splicing factors and known to play a critical role in protein-protein interaction and intracellular distribution of their substrates in both yeast and mammalian cells. However, the function of these kinases in pre-mRNA splicing remains unclear. Here we report that SKY1, a SRPK family member in Saccharomyces cerevisiae, genetically interacts with PRP8 and PRP17/SLU4, both of which are involved in splice site selection during pre-mRNA splicing. Prp8 is essential for splicing and is known to interact with both 5' and 3' splice sites in the spliceosomal catalytic center, whereas Prp17/Slu4 is nonessential and is required only for efficient recognition of the 3' splice site. Interestingly, deletion of SKY1 was synthetically lethal with all prp17 mutants tested, but only with specific prp8 alleles in a domain implicated in governing fidelity of 3'AG recognition. Indeed, deletion of SKY1 specifically suppressed 3'AG mutations in ACT1-CUP1 splicing reporters. These results suggest for the first time that 3' AG recognition may be subject to phosphorylation regulation by Sky1p during pre-mRNA splicing.
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Affiliation(s)
- S F Dagher
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla 92093-0651, USA
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Abstract
Galectins are a family of beta-galactoside-binding proteins that contain characteristic amino acid sequences in the carbohydrate recognition domain (CRD) of the polypeptide. The polypeptide of galectin-1 contains a single domain, the CRD. The polypeptide of galectin-3 has two domains, a carboxyl-terminal CRD fused onto a proline- and glycine-rich amino-terminal domain. In previous studies, we showed that galectin-3 is a required factor in the splicing of nuclear pre-mRNA, assayed in a cell-free system. We now document that (i) nuclear extracts derived from HeLa cells contain both galectins-1 and -3; (ii) depletion of both galectins from the nuclear extract either by lactose affinity adsorption or by double-antibody adsorption results in a concomitant loss of splicing activity; (iii) depletion of either galectin-1 or galectin-3 by specific antibody adsorption fails to remove all of the splicing activity, and the residual splicing activity is still saccharide inhibitable; (iv) either galectin-1 or galectin-3 alone is sufficient to reconstitute, at least partially, the splicing activity of nuclear extracts depleted of both galectins; and (v) although the carbohydrate recognition domain of galectin-3 (or galectin-1) is sufficient to restore splicing activity to a galectin-depleted nuclear extract, the concentration required for reconstitution is greater than that of the full-length galectin-3 polypeptide. Consistent with these functional results, double-immunofluorescence analyses show that within the nucleus, galectin-3 colocalizes with the speckled structures observed with splicing factor SC35. Similar results are also obtained with galectin-1, although in this case, there are areas of galectin-1 devoid of SC35 and vice versa. Thus, nuclear galectins exhibit functional redundancy in their splicing activity and partition, at least partially, in the nucleoplasm with another known splicing factor.
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Affiliation(s)
- A Vyakarnam
- Department of Biochemistry, Michigan State University, East Lansing 48824, USA
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Abstract
Galectin-3 (M(r) approximately 35,000) is a galactose/lactose-specific lectin found in association with ribonucleoprotein complexes in many animal cells. Cell-free-splicing assays have been carried out to study the requirement for galectin-3 in RNA processing by HeLa cell nuclear extracts by using 32P-labeled MINX as the pre-mRNA substrate. Addition of saccharides that bind galectin-3 with high affinity inhibited product formation in the splicing assay, while addition of carbohydrates that do not bind to the lectin did not inhibit product formation. Nuclear extracts depleted of galectin-3 by affinity adsorption on a lactose-agarose column were deficient in splicing activity. Extracts subjected to parallel adsorption on control cellobiose-agarose retained splicing activity. The activity of the galectin-3-depleted extract could be reconstituted by the addition of purified recombinant galectin-3, whereas the addition of other lectins, either with a similar saccharide binding specificity (soybean agglutinin) or with a different specificity (wheat germ agglutinin), did not restore splicing activity. The formation of splicing complexes was also sensitive to galectin-3 depletion and reconstitution. Together, these results define a requirement for galectin-3 in pre-mRNA splicing and identify it as a splicing factor.
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Affiliation(s)
- S F Dagher
- Genetics Program, Michigan State University, East Lansing 48824
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Abstract
The ability to phenotypically rescue a mutant (Rat-3, thymidine kinase-deficient) cell line by electroporation of functional TK enzyme has been investigated. Extracts of electroporated cells showed a 35-fold increase in TK enzyme levels under conditions where greater than 90% of the cells remained viable. The electroporated enzyme was intracellular, as demonstrated by the fact that cells were able to utilize exogenous [3H]thymidine for DNA synthesis. By in situ autoradiography, 82% of electroporated cells contained functional enzyme and incorporated [3H]thymidine into DNA. Thus, this technique can efficiently provide a missing metabolic function to cultured mammalian cells.
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Affiliation(s)
- S F Dagher
- Graduate Program in Genetics, Michigan State University, East Lansing 48824-1101
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