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Maresca E, Aulitto M, Contursi P. Harnessing the dual nature of Bacillus (Weizmannia) coagulans for sustainable production of biomaterials and development of functional food. Microb Biotechnol 2024; 17:e14449. [PMID: 38593329 PMCID: PMC11003712 DOI: 10.1111/1751-7915.14449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024] Open
Abstract
Bacillus coagulans, recently renamed Weizmannia coagulans, is a spore-forming bacterium that has garnered significant interest across various research fields, ranging from health to industrial applications. The probiotic properties of W. coagulans enhance intestinal digestion, by releasing prebiotic molecules including enzymes that facilitate the breakdown of not-digestible carbohydrates. Notably, some enzymes from W. coagulans extend beyond digestive functions, serving as valuable biotechnological tools and contributing to more sustainable and efficient manufacturing processes. Furthermore, the homofermentative thermophilic nature of W. coagulans renders it an exceptional candidate for fermenting foods and lignocellulosic residues into L-(+)-lactic acid. In this review, we provide an overview of the dual nature of W. coagulans, in functional foods and for the development of bio-based materials.
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Affiliation(s)
- Emanuela Maresca
- Department of BiologyUniversity of Naples “Federico II”NaplesItaly
| | - Martina Aulitto
- Department of BiologyUniversity of Naples “Federico II”NaplesItaly
- Institute for Polymers, Composites and Biomaterials—IPCB, National Research Council of Italy (CNR)PozzuoliItaly
| | - Patrizia Contursi
- Department of BiologyUniversity of Naples “Federico II”NaplesItaly
- NBFC, National Biodiversity Future CenterPalermoItaly
- BAT Center—Interuniversity Center for Studies on Bioinspired Agro‐Environmental TechnologyUniversity of Naples “Federico II”PorticiItaly
- Task Force on Microbiome StudiesUniversity of Naples “Federico II”NaplesItaly
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2
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Aulitto M, Martinez-Alvarez L, Fusco S, She Q, Bartolucci S, Peng X, Contursi P. Genomics, Transcriptomics, and Proteomics of SSV1 and Related Fusellovirus: A Minireview. Viruses 2022; 14:v14102082. [PMID: 36298638 PMCID: PMC9608457 DOI: 10.3390/v14102082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Saccharolobus spindle-shaped virus 1 (SSV1) was one of the first viruses identified in the archaeal kingdom. Originally isolated from a Japanese species of Saccharolobus back in 1984, it has been extensively used as a model system for genomic, transcriptomic, and proteomic studies, as well as to unveil the molecular mechanisms governing the host–virus interaction. The purpose of this mini review is to supply a compendium of four decades of research on the SSV1 virus.
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Affiliation(s)
- Martina Aulitto
- Dipartimento di Biologia, University of Naples Federico II, 80126 Naples, Italy
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA 94720, USA
| | - Laura Martinez-Alvarez
- Archaea Centre, Department of Biology, University of Copenhagen, DK-1165 Copenhagen, Denmark
| | - Salvatore Fusco
- Biochemistry and Industrial Biotechnology Laboratory, Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 250100, China
| | | | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, DK-1165 Copenhagen, Denmark
- Correspondence: (X.P.); (P.C.)
| | - Patrizia Contursi
- Dipartimento di Biologia, University of Naples Federico II, 80126 Naples, Italy
- BAT Center—Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples Federico II, 80055 Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80126 Naples, Italy
- Correspondence: (X.P.); (P.C.)
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3
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Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
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Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
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4
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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] [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.
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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.
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5
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Fusco S, Aulitto M, Iacobucci I, Crocamo G, Pucci P, Bartolucci S, Monti M, Contursi P. The interaction between the F55 virus-encoded transcription regulator and the RadA host recombinase reveals a common strategy in Archaea and Bacteria to sense the UV-induced damage to the host DNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194493. [PMID: 32014611 DOI: 10.1016/j.bbagrm.2020.194493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/09/2020] [Accepted: 01/29/2020] [Indexed: 01/28/2023]
Abstract
Sulfolobus spindle-shaped virus 1 is the only UV-inducible member of the virus family Fuselloviridae. Originally isolated from Saccharolobus shibatae B12, it can also infect Saccharolobus solfataricus. Like the CI repressor of the bacteriophage λ, the SSV1-encoded F55 transcription repressor acts as a key regulator for the maintenance of the SSV1 carrier state. In particular, F55 binds to tandem repeat sequences located within the promoters of the early and UV-inducible transcripts. Upon exposure to UV light, a temporally coordinated pattern of gene expression is triggered. In the case of the better characterized bacteriophage λ, the switch from lysogenic to lytic development is regulated by a crosstalk between the virus encoded CI repressor and the host RecA, which regulates also the SOS response. For SSV1, instead, the regulatory mechanisms governing the switch from the carrier to the induced state have not been completely unravelled. In this study we have applied an integrated biochemical approach based on a variant of the EMSA assay coupled to mass spectrometry analyses to identify the proteins associated with F55 when bound to its specific DNA promoter sequences. Among the putative F55 interactors, we identified RadA and showed that the archaeal molecular components F55 and RadA are functional homologs of bacteriophage λ (factor CI) and Escherichia coli (RecA) system.
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Affiliation(s)
- Salvatore Fusco
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Martina Aulitto
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ilaria Iacobucci
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, University of Naples Federico II, 80145 Naples, Italy
| | - Giulio Crocamo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Pietro Pucci
- 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.
| | - Patrizia Contursi
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy.
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6
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Negative regulation of bleomycins biosynthesis by ArsR/SmtB family repressor BlmR in Streptomyces verticillus. Appl Microbiol Biotechnol 2019; 103:6629-6644. [PMID: 31187208 DOI: 10.1007/s00253-019-09923-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 12/12/2022]
Abstract
Bleomycin, a broad-spectrum antibiotic, has been widely used for various tumor treatments. However, its poor fermentation yield is not satisfactory for industrial production. Here, the ArsR/SmtB family regulator BlmR was characterized as a repressor of bleomycin production. As an autoregulator, BlmR was found to bind to a 12-2-12 imperfect palindrome sequence in its own promoter, and deletion of blmR led to a 34% increase of bleomycin B2 production compared with the wild-type strain. Using reverse transcription and quantitative PCR (RT-qPCR), blmT, which encoded a putative transporter, was identified as the target gene regulated by BlmR. Therefore, high-production strain was constructed by blmT overexpression in a blmR deletion strain, and the bleomycin B2 titer reached to 80 mg/L, which was 1.9-fold higher than the wild-type strain. Moreover, electrophoretic mobility shift assay (EMSA) showed neither metal-binding motifs nor redox switches in BlmR. In order to elucidate the regulatory mechanism, a model of BlmR was constructed by homology modeling and protein-protein docking. The BlmR-DNA complex was generated by protein-DNA docking with the assistance of site-directed mutagenesis and molecular dynamic (MD) simulation, which directly revealed several key amino acid residues needed for the maintenance and stabilization of the interface between BlmR and target DNA. The interface information could provide the configuration reference and seek the potential effectors that could interact with BlmR, thereby extending the regulation role of ArsR/SmtB family members on the improvement of antibiotic production.
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7
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Pirone L, Di Gaetano S, Rizzarelli E, Bellia F, Pedone E. Focusing on the functional characterization of the anserinase from Oreochromis niloticus. Int J Biol Macromol 2019; 130:158-165. [PMID: 30797810 DOI: 10.1016/j.ijbiomac.2019.02.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 12/24/2022]
Abstract
Carnosine, anserine and homocarnosine are the three most representative compounds of the histidine dipeptides family, widely distributed in mammals in different amounts depending on the species and the tissue considered. Histidine dipeptides are mainly degraded by two different carnosinase homologues: a highly specific metal-ion dependent carnosinase (CN1) located in serum and brain and a non-specific cytosolic form (CN2). The hydrolysis of such dipeptides in prokaryotes and eukaryotes is also catalyzed by the anserinase (ANSN). Such naturally occurring dipeptides represent an interesting topic because they seem to have numerous biological roles such as potential neuroprotective and neurotransmitter functions in the brain and therefore ANSN results to be a very interesting target of study. We here report, for the first time, cloning, expression of ANSN from the fish Oreochromis niloticus both in a mammalian and in a prokaryotic system, in order to perform deep functional studies by enzymatic assays in the presence of different metals and substrates. Furthermore, by means of a mass spectrometry-based proteomic approach, we analysed protein sequence and the potential presence of post-translational modifications in the mammalian recombinant protein. Finally, a preliminary structural characterization was carried out on ANSN produced in Escherichia coli.
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Affiliation(s)
- L Pirone
- Institute of Biostructure and Bioimaging, CNR, Napoli, Italy
| | - S Di Gaetano
- Institute of Biostructure and Bioimaging, CNR, Napoli, Italy
| | - E Rizzarelli
- Institute of Biostructure and Bioimaging, CNR, Catania, Italy; Department of Chemical Sciences, University of Catania, Catania, Italy
| | - F Bellia
- Institute of Biostructure and Bioimaging, CNR, Catania, Italy.
| | - E Pedone
- Institute of Biostructure and Bioimaging, CNR, Napoli, Italy.
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8
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Tsika AC, Melekis E, Tsatsouli SA, Papageorgiou N, Maté MJ, Canard B, Coutard B, Bentrop D, Spyroulias GA. Deciphering the Nucleotide and RNA Binding Selectivity of the Mayaro Virus Macro Domain. J Mol Biol 2019; 431:2283-2297. [PMID: 30998933 PMCID: PMC7094482 DOI: 10.1016/j.jmb.2019.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/01/2019] [Accepted: 04/08/2019] [Indexed: 12/25/2022]
Abstract
Mayaro virus (MAYV) is a member of Togaviridae family, which also includes Chikungunya virus as a notorious member. MAYV recently emerged in urban areas of the Americas, and this emergence emphasized the current paucity of knowledge about its replication cycle. The macro domain (MD) of MAYV belongs to the N-terminal region of its non-structural protein 3, part of the replication complex. Here, we report the first structural and dynamical characterization of a previously unexplored Alphavirus MD investigated through high-resolution NMR spectroscopy, along with data on its ligand selectivity and binding properties. The structural analysis of MAYV MD reveals a typical "macro" (ββαββαβαβα) fold for this polypeptide, while NMR-driven interaction studies provide in-depth insights into MAYV MD-ligand adducts. NMR data in concert with thermodynamics and biochemical studies provide convincing experimental evidence for preferential binding of adenosine diphosphate ribose (ADP-r) and adenine-rich RNAs to MAYV MD, thus shedding light on the structure-function relationship of a previously unexplored viral MD. The emerging differences with any other related MD are expected to enlighten distinct functions.
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Affiliation(s)
| | | | | | | | - Maria J Maté
- AFMB, UMR7257 CNRS/Aix Marseille Université, Marseille, CEDEX 9, France
| | - Bruno Canard
- AFMB, UMR7257 CNRS/Aix Marseille Université, Marseille, CEDEX 9, France
| | - Bruno Coutard
- UVE: Aix-Marseille Univ-IRD 190-Inserm 27-IHU Méditerranée Infection, Marseille, France.
| | - Detlef Bentrop
- Institute of Physiology II, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
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9
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Pirone L, Caldinelli L, Di Lascio S, Di Girolamo R, Di Gaetano S, Fornasari D, Pollegioni L, Benfante R, Pedone E. Molecular insights into the role of the polyalanine region in mediating PHOX2B aggregation. FEBS J 2019; 286:2505-2521. [PMID: 30955232 DOI: 10.1111/febs.14841] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/27/2019] [Accepted: 04/04/2019] [Indexed: 11/26/2022]
Abstract
About 90% of congenital central hypoventilation syndrome (CCHS) patients show polyalanine triplet expansions in the coding region of transcription factor PHOX2B, which renders this protein an intriguing target to understand the insurgence of this syndrome and for the design of a novel therapeutical approach. Consistently with the role of PHOX2B as a transcriptional regulator, it is reasonable that a general transcriptional dysregulation caused by the polyalanine expansion might represent an important mechanism underlying CCHS pathogenesis. Therefore, this study focused on the biochemical characterization of different PHOX2B variants, such as a variant containing the correct C-terminal (20 alanines) stretch, one of the most frequent polyalanine expansions (+7 alanines), and a variant lacking the complete alanine stretch (0 alanines). Comparison of the different variants by a multidisciplinary approach based on different methodologies (including circular dichroism, spectrofluorimetry, light scattering, and Atomic Force Microscopy studies) highlighted the propensity to aggregate for the PHOX2B variant containing the polyalanine expansion (+7-alanines), especially in the presence of DNA, while the 0-alanines variant resembled the protein with the correct polyalanine length. Moreover, and unexpectedly, the formation of fibrils was revealed only for the pathological variant, suggesting a plausible role of such fibrils in the insurgence of CCHS.
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Affiliation(s)
- Luciano Pirone
- Institute of Biostructure and Bioimaging, CNR, Napoli, Italy
| | - Laura Caldinelli
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, Varese, Italy
| | - Simona Di Lascio
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Italy
| | - Rocco Di Girolamo
- Department of Chemical Sciences, University of Naples Federico II, Italy
| | | | - Diego Fornasari
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, Varese, Italy
| | - Roberta Benfante
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Italy
- CNR- Neuroscience Institute, Milan, Italy
| | - Emilia Pedone
- Institute of Biostructure and Bioimaging, CNR, Napoli, Italy
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10
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Aulitto M, Fusco S, Limauro D, Fiorentino G, Bartolucci S, Contursi P. Galactomannan degradation by thermophilic enzymes: a hot topic for biotechnological applications. World J Microbiol Biotechnol 2019; 35:32. [DOI: 10.1007/s11274-019-2591-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/10/2019] [Indexed: 01/06/2023]
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11
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Roscetto E, Contursi P, Vollaro A, Fusco S, Notomista E, Catania MR. Antifungal and anti-biofilm activity of the first cryptic antimicrobial peptide from an archaeal protein against Candida spp. clinical isolates. Sci Rep 2018; 8:17570. [PMID: 30514888 PMCID: PMC6279838 DOI: 10.1038/s41598-018-35530-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/29/2018] [Indexed: 01/20/2023] Open
Abstract
Candida species cause cutaneous and systemic infections with a high mortality rate, especially in immunocompromised patients. The emergence of resistance to the most common antifungal drugs, also due to biofilm formation, requires the development of alternative antifungal agents. The antimicrobial peptide VLL-28, isolated from an archaeal transcription factor, shows comparable antifungal activity against 10 clinical isolates of Candida spp. Using a fluoresceinated derivative of this peptide, we found that VLL-28 binds to the surface of planktonic cells. This observation suggested that it could exert its antifungal activity by damaging the cell wall. In addition, analyses performed on biofilms via confocal microscopy revealed that VLL-28 is differentially active on all the strains tested, with C. albicans and C. parapsilosis being the most sensitive ones. Notably, VLL-28 is the first example of an archaeal antimicrobial peptide that is active towards Candida spp. Thus, this points to archaeal microorganisms as a possible reservoir of novel antifungal agents.
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Affiliation(s)
- Emanuela Roscetto
- Section of Clinical Microbiology, Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131, Naples, Italy
| | - Patrizia Contursi
- Department of Biology, University of Naples Federico II, Campus of Monte S. Angelo, Via Cinthia, 80126, Naples, Italy.
| | - Adriana Vollaro
- Section of Clinical Microbiology, Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131, Naples, Italy
| | - Salvatore Fusco
- Department of Biology, University of Naples Federico II, Campus of Monte S. Angelo, Via Cinthia, 80126, Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, Campus of Monte S. Angelo, Via Cinthia, 80126, Naples, Italy
| | - Maria Rosaria Catania
- Section of Clinical Microbiology, Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131, Naples, Italy
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Baglivo I, Pirone L, Pedone EM, Pitzer JE, Muscariello L, Marino MM, Malgieri G, Freschi A, Chambery A, Roop Ii RM, Pedone PV. Ml proteins from Mesorhizobium loti and MucR from Brucella abortus: an AT-rich core DNA-target site and oligomerization ability. Sci Rep 2017; 7:15805. [PMID: 29150637 PMCID: PMC5693944 DOI: 10.1038/s41598-017-16127-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/07/2017] [Indexed: 11/09/2022] Open
Abstract
Mesorhizobium loti contains ten genes coding for proteins sharing high amino acid sequence identity with members of the Ros/MucR transcription factor family. Five of these Ros/MucR family members from Mesorhizobium loti (Ml proteins) have been recently structurally and functionally characterized demonstrating that Ml proteins are DNA-binding proteins. However, the DNA-binding studies were performed using the Ros DNA-binding site with the Ml proteins. Currently, there is no evidence as to when the Ml proteins are expressed during the Mesorhizobium lo ti life cycle as well as no information concerning their natural DNA-binding site. In this study, we examine the ml genes expression profile in Mesorhizobium loti and show that ml1, ml2, ml3 and ml5 are expressed during planktonic growth and in biofilms. DNA-binding experiments show that the Ml proteins studied bind a conserved AT-rich site in the promoter region of the exoY gene from Mesorhizobium loti and that the proteins make important contacts with the minor groove of DNA. Moreover, we demonstrate that the Ml proteins studied form higher-order oligomers through their N-terminal region and that the same AT-rich site is recognized by MucR from Brucella abortus using a similar mechanism involving contacts with the minor groove of DNA and oligomerization.
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Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy.
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, C.N.R., Naples, 80134, Italy
| | | | - Joshua Edison Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Lidia Muscariello
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Maria Michela Marino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Andrea Freschi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy
| | - Roy-Martin Roop Ii
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy.
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Gaglione R, Pirone L, Farina B, Fusco S, Smaldone G, Aulitto M, Dell'Olmo E, Roscetto E, Del Gatto A, Fattorusso R, Notomista E, Zaccaro L, Arciello A, Pedone E, Contursi P. Insights into the anticancer properties of the first antimicrobial peptide from Archaea. Biochim Biophys Acta Gen Subj 2017. [DOI: 10.1016/j.bbagen.2017.06.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Pirone L, Ripoll-Rozada J, Leone M, Ronca R, Lombardo F, Fiorentino G, Andersen JF, Pereira PJB, Arcà B, Pedone E. Functional analyses yield detailed insight into the mechanism of thrombin inhibition by the antihemostatic salivary protein cE5 from Anopheles gambiae. J Biol Chem 2017; 292:12632-12642. [PMID: 28592490 DOI: 10.1074/jbc.m117.788042] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/23/2017] [Indexed: 11/06/2022] Open
Abstract
Saliva of blood-feeding arthropods carries several antihemostatic compounds whose physiological role is to facilitate successful acquisition of blood. The identification of novel natural anticoagulants and the understanding of their mechanism of action may offer opportunities for designing new antithrombotics disrupting blood clotting. We report here an in-depth structural and functional analysis of the anophelin family member cE5, a salivary protein from the major African malaria vector Anopheles gambiae that specifically, tightly, and quickly binds and inhibits thrombin. Using calorimetry, functional assays, and complementary structural techniques, we show that the central region of the protein, encompassing amino acids Asp-31-Arg-62, is the region mainly responsible for α-thrombin binding and inhibition. As previously reported for the Anopheles albimanus orthologue anophelin, cE5 binds both thrombin exosite I with segment Glu-35-Asp-47 and the catalytic site with the region Pro-49-Arg-56, which includes the highly conserved DPGR tetrapeptide. Moreover, the N-terminal Ala-1-Ser-30 region of cE5 (which includes an RGD tripeptide) and the additional C-terminal serine-rich Asn-63-Glu-82 region (absent in orthologues from anophelines of the New World species A. albimanus and Anopheles darlingi) also played some functionally relevant role. Indeed, we observed decreased thrombin binding and inhibitory properties even when using the central cE5 fragment (Asp-31-Arg-62) alone. In summary, these results shed additional light on the mechanism of thrombin binding and inhibition by this family of salivary anticoagulants from anopheline mosquitoes.
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Affiliation(s)
- Luciano Pirone
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy
| | - Jorge Ripoll-Rozada
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy
| | - Raffaele Ronca
- Department of Biology, Universita' degli Studi di Napoli Federico II, Via Cinthia, 80126 Naples, Italy
| | - Fabrizio Lombardo
- Department of Public Health and Infectious Diseases, Division of Parasitology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Gabriella Fiorentino
- Department of Biology, Universita' degli Studi di Napoli Federico II, Via Cinthia, 80126 Naples, Italy
| | - John F Andersen
- Laboratory of Malaria and Vector Research, NIAID, National Institutes of Health, Rockville, Maryland 20852
| | - Pedro José Barbosa Pereira
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Bruno Arcà
- Department of Public Health and Infectious Diseases, Division of Parasitology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy.
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Di Giuseppe AM, Russo L, Russo R, Ragucci S, Caso JV, Isernia C, Chambery A, Di Maro A. Molecular characterization of myoglobin from Sciurus vulgaris meridionalis : Primary structure, kinetics and spectroscopic studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:499-509. [DOI: 10.1016/j.bbapap.2017.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/18/2017] [Accepted: 02/14/2017] [Indexed: 10/20/2022]
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Pane K, Durante L, Crescenzi O, Cafaro V, Pizzo E, Varcamonti M, Zanfardino A, Izzo V, Di Donato A, Notomista E. Antimicrobial potency of cationic antimicrobial peptides can be predicted from their amino acid composition: Application to the detection of “cryptic” antimicrobial peptides. J Theor Biol 2017; 419:254-265. [DOI: 10.1016/j.jtbi.2017.02.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 01/23/2017] [Accepted: 02/11/2017] [Indexed: 10/20/2022]
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Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea. SCIENCE CHINA-LIFE SCIENCES 2017; 60:370-385. [DOI: 10.1007/s11427-016-0355-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/18/2016] [Indexed: 12/26/2022]
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Thermus thermophilus as source of thermozymes for biotechnological applications: homologous expression and biochemical characterization of an α-galactosidase. Microb Cell Fact 2017; 16:28. [PMID: 28193276 PMCID: PMC5307791 DOI: 10.1186/s12934-017-0638-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/25/2017] [Indexed: 11/17/2022] Open
Abstract
Background The genus Thermus, which has been considered for a long time as a fruitful source of biotechnological relevant enzymes, has emerged more recently as suitable host to overproduce thermozymes. Among these, α-galactosidases are widely used in several industrial bioprocesses that require high working temperatures and for which thermostable variants offer considerable advantages over their thermolabile counterparts. Results Thermus thermophilus HB27 strain was used for the homologous expression of the TTP0072 gene encoding for an α-galactosidase (TtGalA). Interestingly, a soluble and active histidine-tagged enzyme was produced in larger amounts (5 mg/L) in this thermophilic host than in Escherichia coli (0.5 mg/L). The purified recombinant enzyme showed an optimal activity at 90 °C and retained more than 40% of activity over a broad range of pH (from 5 to 8). Conclusions TtGalA is among the most thermoactive and thermostable α-galactosidases discovered so far, thus pointing to T. thermophilus as cell factory for the recombinant production of biocatalysts active at temperature values over 90 °C. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0638-4) contains supplementary material, which is available to authorized users.
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Fusco S, Liguori R, Limauro D, Bartolucci S, She Q, Contursi P. Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system. Biochimie 2015; 118:322-32. [DOI: 10.1016/j.biochi.2015.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/08/2015] [Indexed: 11/26/2022]
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Notomista E, Falanga A, Fusco S, Pirone L, Zanfardino A, Galdiero S, Varcamonti M, Pedone E, Contursi P. The identification of a novel Sulfolobus islandicus CAMP-like peptide points to archaeal microorganisms as cell factories for the production of antimicrobial molecules. Microb Cell Fact 2015; 14:126. [PMID: 26338197 PMCID: PMC4559164 DOI: 10.1186/s12934-015-0302-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/22/2015] [Indexed: 12/03/2022] Open
Abstract
Background Pathogenic bacteria easily develop resistance to c
onventional antibiotics so that even relatively new molecules are quickly losing efficacy. This strongly encourages the quest of new antimicrobials especially for the treatment of chronic infections. Cationic antimicrobial peptides (CAMPs) are small positively charged peptides with an amphipathic structure, active against Gram-positive and Gram-negative bacteria, fungi, as well as protozoa. Results A novel (CAMP)-like peptide (VLL-28) was identified in the primary structure of a transcription factor, Stf76, encoded by pSSVx, a hybrid plasmid–virus from the archaeon Sulfolobus islandicus. VLL-28 displays chemical, physical and functional properties typical of CAMPs. Indeed, it has a broad-spectrum antibacterial activity and acquires a defined structure in the presence of membrane mimetics. Furthermore, it exhibits selective leakage and fusogenic capability on vesicles with a lipid composition similar to that of bacterial membranes. VLL-28 localizes not only on the cell membrane but also in the cytoplasm of Escherichia coli and retains the ability to bind nucleic acids. These findings suggest that this CAMP-like peptide could exert its antimicrobial activity both on membrane and intra cellular targets. Conclusions VLL-28 is the first CAMP-like peptide identified in the archaeal kingdom, thus pointing to archaeal microorganisms as cell factories to produce antimicrobial molecules of biotechnological interest. Furthermore, results from this work show that DNA/RNA-binding proteins could be used as sources of CAMPs. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0302-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eugenio Notomista
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126, Naples, Italy.
| | - Annarita Falanga
- Istituto di Biostrutture Bioimmagini, CNR, 80134, Naples, Italy.
| | - Salvatore Fusco
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126, Naples, Italy.
| | - Luciano Pirone
- Istituto di Biostrutture Bioimmagini, CNR, 80134, Naples, Italy. .,C.I.R.C.M.S.B. (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici), via Celso Ulpiani, 27, 70125, Bari, Italy.
| | - Anna Zanfardino
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126, Naples, Italy.
| | - Stefania Galdiero
- Istituto di Biostrutture Bioimmagini, CNR, 80134, Naples, Italy. .,Department of Pharmacy and CiRPEB, University of Naples Federico II, 80100, Naples, Italy.
| | - Mario Varcamonti
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126, Naples, Italy.
| | - Emilia Pedone
- Istituto di Biostrutture Bioimmagini, CNR, 80134, Naples, Italy.
| | - Patrizia Contursi
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, 80126, Naples, Italy.
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Abstract
SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade.
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A standardized protocol for the UV induction of Sulfolobus spindle-shaped virus 1. Extremophiles 2014; 19:539-46. [PMID: 25479832 DOI: 10.1007/s00792-014-0717-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/26/2014] [Indexed: 10/24/2022]
Abstract
The Fuselloviridae prototype member Sulfolobus spindle-shaped virus 1 is a model of UV-inducible viruses infecting Crenarchaeota. Previous works on SSV1 UV induction were bases on empirically determined parameters that have not yet been standardized. Thus, in many peer reviewed literature, it is not clear how the fluence and irradiance have been determined. Here, we describe a protocol for the UV induction of SSV1 replication, which is based on the combination of the following instrumentally monitored parameters: (1) the fluence; (2) the irradiance; (3) the exposure time, and (4) the exposure distance. With the aim of finding a good balance between the viral replication induction and the host cells viability, UV-irradiated cultures were monitored for their ability to recover in the aftermath of the UV exposure. This UV irradiation procedure has been set up using the well-characterized Sulfolobus solfataricus P2 strain as model system to study host-virus interaction.
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