1
|
Curci N, Iacono R, Segura DR, Cillo M, Cobucci-Ponzano B, Strazzulli A, Leonardi A, Giger L, Moracci M. Novel GH109 enzymes for bioconversion of group A red blood cells to the universal donor group O. N Biotechnol 2023; 77:130-138. [PMID: 37643666 DOI: 10.1016/j.nbt.2023.08.002] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 08/31/2023]
Abstract
Glycoside hydrolases (GHs) have been employed for industrial and biotechnological purposes and often play an important role in new applications. The red blood cell (RBC) antigen system depends on the composition of oligosaccharides on the surface of erythrocytes, thus defining the ABO blood type classification. Incorrect blood transfusions may lead to fatal consequences, making the availability of the correct blood group critical. In this regard, it has been demonstrated that some GHs may be helpful in the conversion of groups A and B blood types to produce group O universal donor blood. GHs belonging to the GH109 family are of particular interest for this application due to their ability to convert blood from group A to group O. This work describes the biochemical characterisation of three novel GH109 enzymes (NAg68, NAg69 and NAg71) and the exploration of their ability to produce enzymatically converted RBCs (ECO-RBC). The three enzymes showed superior specificity on pNP-α-N-acetylgalactosamine compared to previously reported GH109 enzymes. These novel enzymes were able to act on purified antigen-A trisaccharides and produce ECO-RBC from human donor blood. NAg71 converted type A RBC to group O with increased efficiency in the presence of dextran compared to a commercially available GH109, previously used for this application.
Collapse
Affiliation(s)
- Nicola Curci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cinthia 21, Naples 80126, Italy; Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples 80131, Italy
| | - Roberta Iacono
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cinthia 21, Naples 80126, Italy
| | | | - Michele Cillo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Via Sergio Pansini, 5, Naples 80131, Italy
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples 80131, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cinthia 21, Naples 80126, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy
| | - Antonio Leonardi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Via Sergio Pansini, 5, Naples 80131, Italy
| | - Lars Giger
- Novozymes A/S, Biologiens vej 2, 2800 Kgs. Lyngby, Denmark
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cinthia 21, Naples 80126, Italy; Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples 80131, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy.
| |
Collapse
|
2
|
Awala SI, Gwak JH, Kim Y, Seo C, Strazzulli A, Kim SG, Rhee SK. Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37791995 DOI: 10.1099/ijsem.0.006085] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Strain IT6T, a thermoacidophilic and facultative methane-oxidizing bacterium, was isolated from a mud-water mixture collected from Pisciarelli hot spring in Pozzuoli, Italy. The novel strain is white when grown in liquid or solid media and forms Gram-negative rod-shaped, non-flagellated, non-motile cells. It conserves energy by aerobically oxidizing methane and hydrogen while deriving carbon from carbon dioxide fixation. Strain IT6T had three complete pmoCAB operons encoding particulate methane monooxygenase and genes encoding group 1d and 3b [NiFe] hydrogenases. Simple carbon-carbon substrates such as ethanol, 2-propanol, acetone, acetol and propane-1,2-diol were used as alternative electron donors and carbon sources. Optimal growth occurred at 50-55°C and between pH 2.0-3.0. The major fatty acids were C18 : 0, C15 : 0 anteiso, C14 : 0 iso, C16 : 0 and C14 : 0, and the main polar lipids were phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, some unidentified phospholipids and glycolipids, and other unknown polar lipids. Strain IT6T has a genome size of 2.19 Mbp and a G+C content of 40.70 mol%. Relative evolutionary divergence using 120 conserved single-copy marker genes (bac120) and phylogenetic analyses based on bac120 and 16S rRNA gene sequences showed that strain IT6T is affiliated with members of the proposed order 'Methylacidiphilales' of the class Verrucomicrobiia in the phylum Verrucomicrobiota. It shared a 16S rRNA gene sequence identity of >96 % with cultivated isolates in the genus 'Methylacidiphilum' of the family 'Methylacidiphilaceae', which are thermoacidophilic methane-oxidizing bacteria. 'Methylacidiphilum sp.' Phi (100 %), 'Methylacidiphilum infernorum' V4 (99.02 %) and 'Methylacidiphilum sp.' RTK17.1 (99.02 %) were its closest relatives. Its physiological and genomic properties were consistent with those of other isolated 'Methylacidiphilum' species. Based on these results, we propose the name Methylacidiphilum caldifontis gen. nov., sp. nov. to accommodate strain IT6T (=KCTC 92103T=JCM 39288T). We also formally propose that the names Methylacidiphilaceae fam. nov. and Methylacidiphilales ord. nov. to accommodate the genus Methylacidiphilum gen. nov.
Collapse
Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Yongman Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Chanmee Seo
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126, Naples, Italy
| | - Song-Gun Kim
- University of Science and Technology, Yuseong-gu, Daejeon 305-850, Republic of Korea
- Biological Resource Center/ Korean Collection for Type Culture (KCTC), Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| |
Collapse
|
3
|
Iacono R, De Lise F, Moracci M, Cobucci-Ponzano B, Strazzulli A. Glycoside hydrolases from (hyper)thermophilic archaea: structure, function, and applications. Essays Biochem 2023; 67:731-751. [PMID: 37341134 DOI: 10.1042/ebc20220196] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/19/2023] [Accepted: 05/31/2023] [Indexed: 06/22/2023]
Abstract
(Hyper)thermophilic archaeal glycosidases are enzymes that catalyze the hydrolysis of glycosidic bonds to break down complex sugars and polysaccharides at high temperatures. These enzymes have an unique structure that allows them to remain stable and functional in extreme environments such as hot springs and hydrothermal vents. This review provides an overview of the current knowledge and milestones on the structures and functions of (hyper)thermophilic archaeal glycosidases and their potential applications in various fields. In particular, this review focuses on the structural characteristics of these enzymes and how these features relate to their catalytic activity by discussing different types of (hyper)thermophilic archaeal glycosidases, including β-glucosidases, chitinase, cellulases and α-amylases, describing their molecular structures, active sites, and mechanisms of action, including their role in the hydrolysis of carbohydrates. By providing a comprehensive overview of (hyper)thermophilic archaeal glycosidases, this review aims to stimulate further research into these fascinating enzymes.
Collapse
Affiliation(s)
- Roberta Iacono
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, Naples, 80126, Italy
| | - Federica De Lise
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples, 80131, Italy
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, Naples, 80126, Italy
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples, 80131, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, Naples, 80131, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, Naples, 80126, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| |
Collapse
|
4
|
Awala SI, Gwak JH, Kim YM, Kim SJ, Strazzulli A, Dunfield PF, Yoon H, Kim GJ, Rhee SK. Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone. ISME J 2021; 15:3636-3647. [PMID: 34158629 PMCID: PMC8630023 DOI: 10.1038/s41396-021-01037-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 11/26/2022]
Abstract
Short-chain alkanes (SCA; C2-C4) emitted from geological sources contribute to photochemical pollution and ozone production in the atmosphere. Microorganisms that oxidize SCA and thereby mitigate their release from geothermal environments have rarely been studied. In this study, propane-oxidizing cultures could not be grown from acidic geothermal samples by enrichment on propane alone, but instead required methane addition, indicating that propane was co-oxidized by methanotrophs. “Methylacidiphilum” isolates from these enrichments did not grow on propane as a sole energy source but unexpectedly did grow on C3 compounds such as 2-propanol, acetone, and acetol. A gene cluster encoding the pathway of 2-propanol oxidation to pyruvate via acetol was upregulated during growth on 2-propanol. Surprisingly, this cluster included one of three genomic operons (pmoCAB3) encoding particulate methane monooxygenase (PMO), and several physiological tests indicated that the encoded PMO3 enzyme mediates the oxidation of acetone to acetol. Acetone-grown resting cells oxidized acetone and butanone but not methane or propane, implicating a strict substrate specificity of PMO3 to ketones instead of alkanes. Another PMO-encoding operon, pmoCAB2, was induced only in methane-grown cells, and the encoded PMO2 could be responsible for co-metabolic oxidation of propane to 2-propanol. In nature, propane probably serves primarily as a supplemental growth substrate for these bacteria when growing on methane.
Collapse
Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Yong-Man Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126, Naples, Italy
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hyeokjun Yoon
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea.
| |
Collapse
|
5
|
De Lise F, Strazzulli A, Iacono R, Curci N, Di Fenza M, Maurelli L, Moracci M, Cobucci-Ponzano B. Programmed Deviations of Ribosomes From Standard Decoding in Archaea. Front Microbiol 2021; 12:688061. [PMID: 34149676 PMCID: PMC8211752 DOI: 10.3389/fmicb.2021.688061] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.
Collapse
Affiliation(s)
- Federica De Lise
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Roberta Iacono
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Nicola Curci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Marco Moracci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | | |
Collapse
|
6
|
Curci N, Strazzulli A, Iacono R, De Lise F, Maurelli L, Di Fenza M, Cobucci-Ponzano B, Moracci M. Xyloglucan Oligosaccharides Hydrolysis by Exo-Acting Glycoside Hydrolases from Hyperthermophilic Microorganism Saccharolobus solfataricus. Int J Mol Sci 2021; 22:3325. [PMID: 33805072 PMCID: PMC8037949 DOI: 10.3390/ijms22073325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
In the field of biocatalysis and the development of a bio-based economy, hemicellulases have attracted great interest for various applications in industrial processes. However, the study of the catalytic activity of the lignocellulose-degrading enzymes needs to be improved to achieve the efficient hydrolysis of plant biomasses. In this framework, hemicellulases from hyperthermophilic archaea show interesting features as biocatalysts and provide many advantages in industrial applications thanks to their stability in the harsh conditions encountered during the pretreatment process. However, the hemicellulases from archaea are less studied compared to their bacterial counterpart, and the activity of most of them has been barely tested on natural substrates. Here, we investigated the hydrolysis of xyloglucan oligosaccharides from two different plants by using, both synergistically and individually, three glycoside hydrolases from Saccharolobus solfataricus: a GH1 β-gluco-/β-galactosidase, a α-fucosidase belonging to GH29, and a α-xylosidase from GH31. The results showed that the three enzymes were able to release monosaccharides from xyloglucan oligosaccharides after incubation at 65 °C. The concerted actions of β-gluco-/β-galactosidase and the α-xylosidase on both xyloglucan oligosaccharides have been observed, while the α-fucosidase was capable of releasing all α-linked fucose units from xyloglucan from apple pomace, representing the first GH29 enzyme belonging to subfamily A that is active on xyloglucan.
Collapse
Affiliation(s)
- Nicola Curci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - Roberta Iacono
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
| | - Federica De Lise
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Luisa Maurelli
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Marco Moracci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| |
Collapse
|
7
|
Aulitto M, Strazzulli A, Sansone F, Cozzolino F, Monti M, Moracci M, Fiorentino G, Limauro D, Bartolucci S, Contursi P. Prebiotic properties of Bacillus coagulans MA-13: production of galactoside hydrolyzing enzymes and characterization of the transglycosylation properties of a GH42 β-galactosidase. Microb Cell Fact 2021; 20:71. [PMID: 33736637 PMCID: PMC7977261 DOI: 10.1186/s12934-021-01553-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 01/04/2021] [Accepted: 02/25/2021] [Indexed: 01/18/2023] Open
Abstract
Background The spore-forming lactic acid bacterium Bacillus coagulans MA-13 has been isolated from canned beans manufacturing and successfully employed for the sustainable production of lactic acid from lignocellulosic biomass. Among lactic acid bacteria, B. coagulans strains are generally recognized as safe (GRAS) for human consumption. Low-cost microbial production of industrially valuable products such as lactic acid and various enzymes devoted to the hydrolysis of oligosaccharides and lactose, is of great importance to the food industry. Specifically, α- and β-galactosidases are attractive for their ability to hydrolyze not-digestible galactosides present in the food matrix as well as in the human gastrointestinal tract. Results In this work we have explored the potential of B. coagulans MA-13 as a source of metabolites and enzymes to improve the digestibility and the nutritional value of food. A combination of mass spectrometry analysis with conventional biochemical approaches has been employed to unveil the intra- and extra- cellular glycosyl hydrolase (GH) repertoire of B. coagulans MA-13 under diverse growth conditions. The highest enzymatic activity was detected on β-1,4 and α-1,6-glycosidic linkages and the enzymes responsible for these activities were unambiguously identified as β-galactosidase (GH42) and α-galactosidase (GH36), respectively. Whilst the former has been found only in the cytosol, the latter is localized also extracellularly. The export of this enzyme may occur through a not yet identified secretion mechanism, since a typical signal peptide is missing in the α-galactosidase sequence. A full biochemical characterization of the recombinant β-galactosidase has been carried out and the ability of this enzyme to perform homo- and hetero-condensation reactions to produce galacto-oligosaccharides, has been demonstrated. Conclusions Probiotics which are safe for human use and are capable of producing high levels of both α-galactosidase and β-galactosidase are of great importance to the food industry. In this work we have proven the ability of B. coagulans MA-13 to over-produce these two enzymes thus paving the way for its potential use in treatment of gastrointestinal diseases. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01553-y.
Collapse
Affiliation(s)
- Martina Aulitto
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.,Task Force On Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Ferdinando Sansone
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.,CEINGE Advanced Biotechnologies, University of Naples Federico II, 80145, Naples, Italy
| | - Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.,CEINGE Advanced Biotechnologies, University of Naples Federico II, 80145, Naples, Italy
| | - Marco Moracci
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.,Task Force On Microbiome Studies, University of Naples Federico II, Naples, Italy.,Institute of Biosciences and BioResources-National Research Council of Italy, Naples, Italy
| | - Gabriella Fiorentino
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.,BAT Center-Interuniversity Center for Studies On Bioinspired Agro-Environmental Technology, University of Napoli Federico II, Portici, NA, Italy
| | - Danila Limauro
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy.,BAT Center-Interuniversity Center for Studies On Bioinspired Agro-Environmental Technology, University of Napoli Federico II, Portici, NA, Italy
| | | | - Patrizia Contursi
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy. .,Task Force On Microbiome Studies, University of Naples Federico II, Naples, Italy. .,BAT Center-Interuniversity Center for Studies On Bioinspired Agro-Environmental Technology, University of Napoli Federico II, Portici, NA, Italy.
| |
Collapse
|
8
|
Strazzulli A, Cobucci-Ponzano B, Iacono R, Giglio R, Maurelli L, Curci N, Schiano-di-Cola C, Santangelo A, Contursi P, Lombard V, Henrissat B, Lauro FM, Fontes CMGA, Moracci M. Discovery of hyperstable carbohydrate-active enzymes through metagenomics of extreme environments. FEBS J 2019; 287:1116-1137. [PMID: 31595646 DOI: 10.1111/febs.15080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 05/24/2019] [Revised: 07/23/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022]
Abstract
The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy), to discover hyperthermophilic carbohydrate-active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here, we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T = 85 °C and pH 5.5; T = 92 °C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in silico analysis led to 14 934 and 17 652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarchaeota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~ 2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β-mannanase/β-1,3-glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD+ -dependent GH109 with a previously unreported β-N-acetylglucosaminide/β-glucoside specificity. DATABASES: The sequencing reads are available in the NCBI Sequence Read Archive (SRA) database under the accession numbers SRR7545549 (Pool1) and SRR7545550 (Pool2). The sequences of GH5_Pool2 and GH109_Pool2 are available in GenBank database under the accession numbers MK869723 and MK86972, respectively. The environmental data relative to Pool1 and Pool2 (NCBI BioProject PRJNA481947) are available in the Biosamples database under the accession numbers SAMN09692669 (Pool1) and SAMN09692670 (Pool2).
Collapse
Affiliation(s)
- Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Italy
| | | | - Roberta Iacono
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Rosa Giglio
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Nicola Curci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Corinna Schiano-di-Cola
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Annalisa Santangelo
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Patrizia Contursi
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Italy
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, INRA, AFMB, USC 1408, Aix Marseille Univ, France
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique, INRA, AFMB, USC 1408, Aix Marseille Univ, France.,Department Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Federico M Lauro
- Asian School of the Environment, Nanyang Technological University, Singapore City, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
| | - Carlos M G A Fontes
- NZYTech LDA, Estrada Do Paco Do Lumiar, Lisbon, Portugal.,CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Portugal
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Italy.,Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| |
Collapse
|
9
|
Strazzulli A, Perugino G, Mazzone M, Rossi M, Withers SG, Moracci M. Probing the role of an invariant active site His in family GH1 β-glycosidases. J Enzyme Inhib Med Chem 2019; 34:973-980. [PMID: 31072150 PMCID: PMC6522968 DOI: 10.1080/14756366.2019.1608198] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The reaction mechanism of glycoside hydrolases belonging to family 1 (GH1) of carbohydrate-active enzymes classification, hydrolysing β-O-glycosidic bonds, is well characterised. This family includes several thousands of enzymes with more than 20 different EC numbers depending on the sugar glycone recognised as substrate. Most GH1 β-glycosidases bind their substrates with similar specificity through invariant amino acid residues. Despite extensive studies, the clear identification of the roles played by each of these residues in the recognition of different glycones is not always possible. We demonstrated here that a histidine residue, completely conserved in the active site of the enzymes of this family, interacts with the C2-OH of the substrate in addition to the C3-OH as previously shown by 3 D-structure determination.
Collapse
Affiliation(s)
- Andrea Strazzulli
- a Department of Biology , University of Naples "Federico II", Complesso Universitario di Monte S. Angelo , Napoli , Italy.,b Task Force on Microbiome Studies, University of Naples Federico II , Naples , Italy
| | - Giuseppe Perugino
- c Institute of Biosciences and BioResources - National Research Council of Italy , Naples , Italy
| | - Marialuisa Mazzone
- c Institute of Biosciences and BioResources - National Research Council of Italy , Naples , Italy
| | - Mosè Rossi
- c Institute of Biosciences and BioResources - National Research Council of Italy , Naples , Italy
| | - Stephen G Withers
- d Department of Chemistry , University of British Columbia , Vancouver , Canada
| | - Marco Moracci
- a Department of Biology , University of Naples "Federico II", Complesso Universitario di Monte S. Angelo , Napoli , Italy.,b Task Force on Microbiome Studies, University of Naples Federico II , Naples , Italy.,c Institute of Biosciences and BioResources - National Research Council of Italy , Naples , Italy
| |
Collapse
|
10
|
Mensitieri F, De Lise F, Strazzulli A, Moracci M, Notomista E, Cafaro V, Bedini E, Sazinsky MH, Trifuoggi M, Di Donato A, Izzo V. Structural and functional insights into RHA-P, a bacterial GH106 α-L-rhamnosidase from Novosphingobium sp. PP1Y. Arch Biochem Biophys 2018; 648:1-11. [PMID: 29678627 DOI: 10.1016/j.abb.2018.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 02/13/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 11/29/2022]
Abstract
α-L-Rhamnosidases (α-RHAs, EC 3.2.1.40) are glycosyl hydrolases (GHs) hydrolyzing terminal α-l-rhamnose residues from different substrates such as heteropolysaccharides, glycosylated proteins and natural flavonoids. Although the possibility to hydrolyze rhamnose from natural flavonoids has boosted the use of these enzymes in several biotechnological applications over the past decades, to date only few bacterial rhamnosidases have been fully characterized and only one crystal structure of a rhamnosidase of the GH106 family has been described. In our previous work, an α-l-rhamnosidase belonging to this family, named RHA-P, was isolated from the marine microorganism Novosphingobium sp. PP1Y. The initial biochemical characterization highlighted the biotechnological potential of RHA-P for bioconversion applications. In this work, further functional and structural characterization of the enzyme is provided. The recombinant protein was obtained fused to a C-terminal His-tag and, starting from the periplasmic fractions of induced recombinant cells of E. coli strain BL21(DE3), was purified through a single step purification protocol. Homology modeling of RHA-P in combination with a site directed mutagenesis analysis confirmed the function of residues D503, E506, E644, likely located at the catalytic site of RHA-P. In addition, a kinetic characterization of the enzyme on natural flavonoids such as naringin, rutin, hesperidin and quercitrin was performed. RHA-P showed activity on all flavonoids tested, with a catalytic efficiency comparable or even higher than other bacterial α-RHAs described in literature. The results confirm that RHA-P is able to hydrolyze both α-1,2 and α-1,6 glycosidic linkages, and suggest that the enzyme may locate different polyphenolic aromatic moities in the active site.
Collapse
Affiliation(s)
- Francesca Mensitieri
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Federica De Lise
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Marco Moracci
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy; Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Valeria Cafaro
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Emiliano Bedini
- Department of Chemical Sciences, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Matthew Howard Sazinsky
- Department of Chemistry, Pomona College, Sumner Hall, 333 N College Way, Claremont, CA, 91711, United States
| | - Marco Trifuoggi
- Department of Chemical Sciences, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Alberto Di Donato
- Department of Biology, University Federico II of Naples, Via Cinthia 26, 80127, Naples, Italy
| | - Viviana Izzo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Via S. Allende 2, 84131, Salerno, Italy.
| |
Collapse
|
11
|
Vecchio G, Parascandolo A, Allocca C, Ugolini C, Basolo F, Moracci M, Strazzulli A, Cobucci-Ponzano B, Laukkanen MO, Castellone MD, Tsuchida N. Human a-L-fucosidase-1 attenuates the invasive properties of thyroid cancer. Oncotarget 2018; 8:27075-27092. [PMID: 28404918 PMCID: PMC5432319 DOI: 10.18632/oncotarget.15635] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 11/24/2016] [Accepted: 01/24/2017] [Indexed: 12/19/2022] Open
Abstract
Glycans containing α-L-fucose participate in diverse interactions between cells and extracellular matrix. High glycan expression on cell surface is often associated with neoplastic progression. The lysosomal exoenzyme, α-L-fucosidase-1 (FUCA-1) removes fucose residues from glycans. The FUCA-1 gene is down-regulated in highly aggressive and metastatic human tumors. However, the role of FUCA-1 in tumor progression remains unclear. It is speculated that its inactivation perturbs glycosylation of proteins involved in cell adhesion and promotes cancer. FUCA-1 expression of various thyroid normal and cancer tissues assayed by immunohistochemical (IHC) staining was high in normal thyroids and papillary thyroid carcinomas (PTC), whereas it progressively decreased in poorly differentiated, metastatic and anaplastic thyroid carcinomas (ATC). FUCA-1 mRNA expression from tissue samples and cell lines and protein expression levels and enzyme activity in thyroid cancer cell lines paralleled those of IHC staining. Furthermore, ATC-derived 8505C cells adhesion to human E-selectin and HUVEC cells was inhibited by bovine α-L-fucosidase or Lewis antigens, thus pointing to an essential role of fucose residues in the adhesive phenotype of this cancer cell line. Finally, 8505C cells transfected with a FUCA-1 containing plasmid displayed a less invasive phenotype versus the parental 8505C. These results demonstrate that FUCA-1 is down-regulated in ATC compared to PTC and normal thyroid tissues and cell lines. As shown for other human cancers, the down-regulation of FUCA-1 correlates with increased aggressiveness of the cancer type. This is the first report indicating that the down-regulation of FUCA-1 is related to the increased aggressiveness of thyroid cancer.
Collapse
Affiliation(s)
- Giancarlo Vecchio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini, 5, Naples, Italy.,Istituto Superiore di Oncologia, Via Sergio Pansini, 5, Naples and Via Balbi 5, Genoa, Italy
| | | | - Chiara Allocca
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini, 5, Naples, Italy
| | - Clara Ugolini
- Dipartimento di Medicina di Laboratorio, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Fulvio Basolo
- Dipartimento di Patologia Chirurgica, Medica, Molecolare e dell'Area Critica, University of Pisa, Italy
| | - Marco Moracci
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), Via P. Castellino, 111, Naples, Italy.,Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Andrea Strazzulli
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), Via P. Castellino, 111, Naples, Italy.,Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), Via P. Castellino, 111, Naples, Italy
| | | | | | - Nobuo Tsuchida
- Graduate School of Medical and Dental Sciences Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
12
|
Strazzulli A, Cobucci-Ponzano B, Carillo S, Bedini E, Corsaro MM, Pocsfalvi G, Withers SG, Rossi M, Moracci M. Introducing transgalactosylation activity into a family 42 β-galactosidase. Glycobiology 2017; 27:425-437. [DOI: 10.1093/glycob/cwx013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/27/2017] [Indexed: 12/14/2022] Open
Affiliation(s)
- Andrea Strazzulli
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy
- Department of Biology, University of Naples “Federico II”, Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Napoli, Italy
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy
| | - Sara Carillo
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Napoli, Italy
| | - Emiliano Bedini
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Napoli, Italy
| | - Maria Michela Corsaro
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Napoli, Italy
| | - Gabriella Pocsfalvi
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy
| | - Marco Moracci
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy
- Department of Biology, University of Naples “Federico II”, Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Napoli, Italy
| |
Collapse
|
13
|
Tshililo NO, Strazzulli A, Cobucci-Ponzano B, Maurelli L, Iacono R, Bedini E, Corsaro MM, Strauss E, Moracci M. The α-Thioglycoligase Derived from a GH89 α-N-Acetylglucosaminidase Synthesises α-N-Acetylglucosamine-Based Glycosides of Biomedical Interest. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201601091] [Citation(s) in RCA: 13] [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] [Indexed: 11/12/2022]
Affiliation(s)
- Ndivhuwo Olga Tshililo
- Department of Biochemistry; Stellenbosch University; Private Bag X1 7602 Matieland South Africa
| | - Andrea Strazzulli
- Institute of Biosciences and Bioresources - National Research Council of Italy; Via P. Castellino 111 80131 Naples Italy
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and Bioresources - National Research Council of Italy; Via P. Castellino 111 80131 Naples Italy
| | - Luisa Maurelli
- Institute of Biosciences and Bioresources - National Research Council of Italy; Via P. Castellino 111 80131 Naples Italy
| | - Roberta Iacono
- Institute of Biosciences and Bioresources - National Research Council of Italy; Via P. Castellino 111 80131 Naples Italy
| | - Emiliano Bedini
- Department of Chemical Sciences; University of Naples “Federico II”, Complesso Universitario di Monte S. Angelo; Via Cupa Nuova Cinthia 21 80126 Napoli Italy
| | - Maria Michela Corsaro
- Department of Chemical Sciences; University of Naples “Federico II”, Complesso Universitario di Monte S. Angelo; Via Cupa Nuova Cinthia 21 80126 Napoli Italy
| | - Erick Strauss
- Department of Biochemistry; Stellenbosch University; Private Bag X1 7602 Matieland South Africa
| | - Marco Moracci
- Institute of Biosciences and Bioresources - National Research Council of Italy; Via P. Castellino 111 80131 Naples Italy
- Department of Biology; University of Naples “Federico II”, Complesso Universitario di Monte S. Angelo; Via Cupa Nuova Cinthia 21 80126 Napoli Italy
| |
Collapse
|
14
|
Cobucci-Ponzano B, Strazzulli A, Iacono R, Masturzo G, Giglio R, Rossi M, Moracci M. Novel thermophilic hemicellulases for the conversion of lignocellulose for second generation biorefineries. Enzyme Microb Technol 2015. [PMID: 26215346 DOI: 10.1016/j.enzmictec.2015.06.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 12/21/2022]
Abstract
The biotransformation of lignocellulose biomasses into fermentable sugars is a very complex procedure including, as one of the most critical steps, the (hemi) cellulose hydrolysis by specific enzymatic cocktails. We explored here, the potential of stable glycoside hydrolases from thermophilic organisms, so far not used in commercial enzymatic preparations, for the conversion of glucuronoxylan, the major hemicellulose of several energy crops. Searches in the genomes of thermophilic bacteria led to the identification, efficient production, and detailed characterization of novel xylanase and α-glucuronidase from Alicyclobacillus acidocaldarius (GH10-XA and GH67-GA, respectively) and a α-glucuronidase from Caldicellulosiruptor saccharolyticus (GH67-GC). Remarkably, GH10-XA, if compared to other thermophilic xylanases from this family, coupled good specificity on beechwood xylan and the best stability at 65 °C (3.5 days). In addition, GH67-GC was the most stable α-glucuronidases from this family and the first able to hydrolyse both aldouronic acid and aryl-α-glucuronic acid substrates. These enzymes, led to the very efficient hydrolysis of beechwood xylan by using 7- to 9-fold less protein (concentrations <0.3 μM) and in much less reaction time (2h vs 12h) if compared to other known biotransformations catalyzed by thermophilic enzymes. In addition, remarkably, together with a thermophilic β-xylosidase, they catalyzed the production of xylose from the smart cooking pre-treated biomass of one of the most promising energy crops for second generation biorefineries. We demonstrated that search by the CAZy Data Bank of currently available genomes and detailed enzymatic characterization of recombinant enzymes allow the identification of glycoside hydrolases with novel and interesting properties and applications.
Collapse
Affiliation(s)
- Beatrice Cobucci-Ponzano
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Andrea Strazzulli
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Roberta Iacono
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Giuseppe Masturzo
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Rosa Giglio
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| | - Marco Moracci
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy.
| |
Collapse
|
15
|
Sirec T, Strazzulli A, Isticato R, De Felice M, Moracci M, Ricca E. Adsorption of β-galactosidase of Alicyclobacillus acidocaldarius on wild type and mutants spores of Bacillus subtilis. Microb Cell Fact 2012; 11:100. [PMID: 22863452 PMCID: PMC3465195 DOI: 10.1186/1475-2859-11-100] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 07/28/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Bacillus subtilis spore has long been used as a surface display system with potential applications in a variety of fields ranging from mucosal vaccine delivery, bioremediation and biocatalyst development. More recently, a non-recombinant approach of spore display has been proposed and heterologous proteins adsorbed on the spore surface. We used the well-characterized β-galactosidase from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius as a model to study enzyme adsorption, to analyze whether and how spore-adsorption affects the properties of the enzyme and to improve the efficiency of the process. RESULTS We report that purified β-galactosidase molecules were adsorbed to purified spores of a wild type strain of B. subtilis retaining ca. 50% of their enzymatic activity. Optimal pH and temperature of the enzyme were not altered by the presence of the spore, that protected the adsorbed β-galactosidase from exposure to acidic pH conditions. A collection of mutant strains of B. subtilis lacking a single or several spore coat proteins was compared to the isogenic parental strain for the adsorption efficiency. Mutants with an altered outermost spore layer (crust) were able to adsorb 60-80% of the enzyme, while mutants with a severely altered or totally lacking outer coat adsorbed 100% of the β-galactosidase molecules present in the adsorption reaction. CONCLUSION Our results indicate that the spore surface structures, the crust and the outer coat layer, have an negative effect on the adhesion of the β-galactosidase. Electrostatic forces, previously suggested as main determinants of spore adsorption, do not seem to play an essential role in the spore-β-galactosidase interaction. The analysis of mutants with altered spore surface has shown that the process of spore adsorption can be improved and has suggested that such improvement has to be based on a better understanding of the spore surface structure. Although the molecular details of spore adsorption have not been fully elucidated, the efficiency of the process and the pH-stability of the adsorbed molecules, together with the well documented robustness and safety of spores of B. subtilis, propose the spore as a novel, non-recombinant system for enzyme display.
Collapse
Affiliation(s)
- Teja Sirec
- Department of Structural and Functional Biology, Federico II University of Naples, Naples, Italy
| | | | | | | | | | | |
Collapse
|
16
|
Cobucci-Ponzano B, Zorzetti C, Strazzulli A, Bedini E, Corsaro MM, Sulzenbacher G, Rossi M, Moracci M. Exploitation of β-glycosyl azides for the preparation of α-glycosynthases. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.679814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
17
|
|
18
|
|
19
|
|
20
|
Cobucci-Ponzano B, Zorzetti C, Strazzulli A, Carillo S, Bedini E, Corsaro MM, Comfort DA, Kelly RM, Rossi M, Moracci M. A novel α-d-galactosynthase from Thermotoga maritima converts β-d-galactopyranosyl azide to α-galacto-oligosaccharides. Glycobiology 2010; 21:448-56. [DOI: 10.1093/glycob/cwq177] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
21
|
Cobucci-Ponzano B, Conte F, Strazzulli A, Capasso C, Fiume I, Pocsfalvi G, Rossi M, Moracci M. The molecular characterization of a novel GH38 α-mannosidase from the crenarchaeon Sulfolobus solfataricus revealed its ability in de-mannosylating glycoproteins. Biochimie 2010; 92:1895-907. [PMID: 20696204 DOI: 10.1016/j.biochi.2010.07.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 07/29/2010] [Indexed: 02/03/2023]
Abstract
α-Mannosidases, important enzymes in the N-glycan processing and degradation in Eukaryotes, are frequently found in the genome of Bacteria and Archaea in which their function is still largely unknown. The α-mannosidase from the hyperthermophilic Crenarchaeon Sulfolobus solfataricus has been identified and purified from cellular extracts and its gene has been cloned and expressed in Escherichia coli. The gene, belonging to retaining GH38 mannosidases of the carbohydrate active enzyme classification, is abundantly expressed in this Archaeon. The purified α-mannosidase activity depends on a single Zn(2+) ion per subunit is inhibited by swainsonine with an IC(50) of 0.2 mM. The molecular characterization of the native and recombinant enzyme, named Ssα-man, showed that it is highly specific for α-mannosides and α(1,2), α(1,3), and α(1,6)-D-mannobioses. In addition, the enzyme is able to demannosylate Man(3)GlcNAc(2) and Man(7)GlcNAc(2) oligosaccharides commonly found in N-glycosylated proteins. More interestingly, Ssα-man removes mannose residues from the glycosidic moiety of the bovine pancreatic ribonuclease B, suggesting that it could process mannosylated proteins also in vivo. This is the first evidence that archaeal glycosidases are involved in the direct modification of glycoproteins.
Collapse
Affiliation(s)
- Beatrice Cobucci-Ponzano
- Institute of Protein Biochemistry - Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Cobucci-Ponzano B, Aurilia V, Riccio G, Henrissat B, Coutinho PM, Strazzulli A, Padula A, Corsaro MM, Pieretti G, Pocsfalvi G, Fiume I, Cannio R, Rossi M, Moracci M. A new archaeal beta-glycosidase from Sulfolobus solfataricus: seeding a novel retaining beta-glycan-specific glycoside hydrolase family along with the human non-lysosomal glucosylceramidase GBA2. J Biol Chem 2010; 285:20691-703. [PMID: 20427274 DOI: 10.1074/jbc.m109.086470] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbohydrate active enzymes (CAZymes) are a large class of enzymes, which build and breakdown the complex carbohydrates of the cell. On the basis of their amino acid sequences they are classified in families and clans that show conserved catalytic mechanism, structure, and active site residues, but may vary in substrate specificity. We report here the identification and the detailed molecular characterization of a novel glycoside hydrolase encoded from the gene sso1353 of the hyperthermophilic archaeon Sulfolobus solfataricus. This enzyme hydrolyzes aryl beta-gluco- and beta-xylosides and the observation of transxylosylation reactions products demonstrates that SSO1353 operates via a retaining reaction mechanism. The catalytic nucleophile (Glu-335) was identified through trapping of the 2-deoxy-2-fluoroglucosyl enzyme intermediate and subsequent peptide mapping, while the general acid/base was identified as Asp-462 through detailed mechanistic analysis of a mutant at that position, including azide rescue experiments. SSO1353 has detectable homologs of unknown specificity among Archaea, Bacteria, and Eukarya and shows distant similarity to the non-lysosomal bile acid beta-glucosidase GBA2 also known as glucocerebrosidase. On the basis of our findings we propose that SSO1353 and its homologs are classified in a new CAZy family, named GH116, which so far includes beta-glucosidases (EC 3.2.1.21), beta-xylosidases (EC 3.2.1.37), and glucocerebrosidases (EC 3.2.1.45) as known enzyme activities.
Collapse
|
23
|
Di Lauro B, Strazzulli A, Perugino G, La Cara F, Bedini E, Corsaro MM, Rossi M, Moracci M. Isolation and characterization of a new family 42 beta-galactosidase from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius: identification of the active site residues. Biochim Biophys Acta 2007; 1784:292-301. [PMID: 18068682 DOI: 10.1016/j.bbapap.2007.10.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 10/22/2007] [Accepted: 10/29/2007] [Indexed: 10/22/2022]
Abstract
The thermoacidophilic bacterium Alicyclobacillus acidocaldarius is a rich source of glycoside hydrolases enabling its growth on several di- and polysaccharides. We report here the purification and the characterization of a beta-galactosidase from this source, the cloning of its gene, and the expression and the characterization of the recombinant enzyme (Aabeta-gal). The enzyme was purified 46-fold from A. acidocaldarius extracts; the gene for Aabeta-gal encoded a new member of the glycoside hydrolase family 42 (GH42) and it is flanked by a putative AraC/XylS regulator, however, the two genes were transcribed independently. The recombinant Aabeta-gal was characterized in detail revealing that it is optimally active and stable at 65 degrees C. Aabeta-gal is very specific for glycosides with an axial C4-OH at their non-reducing end, with kcat/KM values of 484, 186, and 332 s(-1) mM(-1) for 2-nitrophenyl-beta-d-galactoside, -fucoside, and 4-nitrophenyl-alpha-l-arabinoside, respectively. Finally, the characterization of the site-directed mutants Glu157Gly and Glu313Gly confirmed the latter as the nucleophile of the reaction and gave experimental evidence, for the first time in GH42, of the role of Glu157 as the acid/base of the catalyzed reaction.
Collapse
Affiliation(s)
- Barbara Di Lauro
- Institute of Protein Biochemistry, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131, Naples, Italy
| | | | | | | | | | | | | | | |
Collapse
|