1
|
Garcia Gonzalez J, Hernandez FJ. Nuclease activity: an exploitable biomarker in bacterial infections. Expert Rev Mol Diagn 2022; 22:265-294. [PMID: 35240900 DOI: 10.1080/14737159.2022.2049249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION In the increasingly challenging field of clinical microbiology, diagnosis is a cornerstone whose accuracy and timing are crucial for the successful management, therapy, and outcome of infectious diseases. Currently employed biomarkers of infectious diseases define the scope and limitations of diagnostic techniques. As such, expanding the biomarker catalog is crucial to address unmet needs and bring about novel diagnostic functionalities and applications. AREAS COVERED This review describes the extracellular nucleases of 15 relevant bacterial pathogens and discusses the potential use of nuclease activity as a diagnostic biomarker. Articles were searched for in PubMed using terms: "nuclease", "bacteria", "nuclease activity" or "biomarker". For overview sections, original and review articles between 2000 and 2019 were searched for using terms: "infections", "diagnosis", "bacterial", "burden", "challenges". Informative articles were selected. EXPERT OPINION Using the catalytic activity of nucleases offers new possibilities compared to established biomarkers. Nucleic acid activatable reporters in combination with different transduction platforms and delivery methods can be used to detect disease-associated nuclease activity patterns in vitro and in vivo for prognostic and diagnostic applications. Even when these patterns are not obvious or of unknown etiology, screening platforms could be used to identify new disease reporters.
Collapse
Affiliation(s)
- Javier Garcia Gonzalez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
| | - Frank J Hernandez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
| |
Collapse
|
2
|
Tuan VP, Yahara K, Dung HDQ, Binh TT, Huu Tung P, Tri TD, Thuan NPM, Khien VV, Trang TTH, Phuc BH, Tshibangu-Kabamba E, Matsumoto T, Akada J, Suzuki R, Okimoto T, Kodama M, Murakami K, Yano H, Fukuyo M, Takahashi N, Kato M, Nishiumi S, Azuma T, Ogura Y, Hayashi T, Toyoda A, Kobayashi I, Yamaoka Y. Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates. Microb Genom 2021; 7. [PMID: 34846284 PMCID: PMC8743543 DOI: 10.1099/mgen.0.000680] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWASs) can reveal genetic variations associated with a phenotype in the absence of any hypothesis of candidate genes. The problem of false-positive sites linked with the responsible site might be bypassed in bacteria with a high homologous recombination rate, such as Helicobacter pylori, which causes gastric cancer. We conducted a small-sample GWAS (125 gastric cancer cases and 115 controls) followed by prediction of gastric cancer and control (duodenal ulcer) H. pylori strains. We identified 11 single nucleotide polymorphisms (eight amino acid changes) and three DNA motifs that, combined, allowed effective disease discrimination. They were often informative of the underlying molecular mechanisms, such as electric charge alteration at the ligand-binding pocket, alteration in subunit interaction, and mode-switching of DNA methylation. We also identified three novel virulence factors/oncoprotein candidates. These results provide both defined targets for further informatic and experimental analyses to gain insights into gastric cancer pathogenesis and a basis for identifying a set of biomarkers for distinguishing these H. pylori-related diseases.
Collapse
Affiliation(s)
- Vo Phuoc Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Koji Yahara
- Antimicrobial Resistance ResearchCenter, National Institute of Infectious Diseases, Tokyo, Japan
- *Correspondence: Koji Yahara,
| | | | - Tran Thanh Binh
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Pham Huu Tung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Tran Dinh Tri
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | | | - Vu Van Khien
- Department of GI Endoscopy, 108 Central Hospital, Hanoi, Vietnam
| | | | - Bui Hoang Phuc
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
- Department of Microbiology, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | | | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Tadayoshi Okimoto
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Masaaki Kodama
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Hirokazu Yano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masaki Fukuyo
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Molecular Oncology, Chiba University, Chiba, Japan
| | - Noriko Takahashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases, Kyorin University School of Medicine, Mitaka City, Tokyo, Japan
| | - Mototsugu Kato
- Division of Endoscopy, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Department of Gastroenterology, National Hospital Organization Hakodate Hospital, Hakodate, Hokkaido, Japan
| | - Shin Nishiumi
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo, Japan
- Department of Omics Medicine, Hyogo College of Medicine, Hyogo, Japan
| | - Takashi Azuma
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Advanced GenomicsCenter, National Institute of Genetics, Shizuoka, Japan
| | - Ichizo Kobayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases, Kyorin University School of Medicine, Mitaka City, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
- *Correspondence: Ichizo Kobayashi, ;
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
- Department of Medicine, gastroenterology section, Baylor College of Medicine, Houston TX, USA
- *Correspondence: Yoshio Yamaoka,
| |
Collapse
|
3
|
Molecular coevolution of nuclear and nucleolar localization signals inside basic domain of HIV-1 Tat. J Virol 2021; 96:e0150521. [PMID: 34613791 DOI: 10.1128/jvi.01505-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
During evolution, viruses had to adapt to an increasingly complex environment of eukaryotic cells. Viral proteins that need to enter the cell nucleus or associate with nucleoli possess nuclear localization signals (NLSs) and nucleolar localization signals (NoLSs) for nuclear and nucleolar accumulation, respectively. As viral proteins are relatively small, acquisition of novel sequences seems to be a more complicated task for viruses than for eukaryotes. Here, we carried out a comprehensive analysis of the basic domain (BD) of HIV-1 Tat to show how viral proteins might evolve with NLSs and NoLSs without an increase in protein size. The HIV-1 Tat BD is involved in several functions, the most important being the transactivation of viral transcription. The BD also functions as an NLS, although it is substantially longer than a typical NLS. It seems that different regions in the BD could function as NLSs due to its enrichment with positively charged amino acids. Additionally, the high positive net charge inevitably causes the BD to function as an NoLS through a charge-specific mechanism. The integration of NLSs and NoLSs into functional domains enriched with positively charged amino acids might be a mechanism that allows the condensation of different functional sequences in small protein regions and, as a result, to reduce protein size, influencing the origin and evolution of NLSs and NoLSs in viruses. IMPORTANCE Here, we investigated the molecular mechanism of NLS and NoLS integration into the basic domain of HIV-1 Tat (49RKKRRQRRR57), and found that these two supplementary functions (i.e., function of NLS and NoLS) are embedded in the basic domain amino acid sequence. The integration of NLSs and NoLSs into functional domains of viral proteins enriched with positively charged amino acids is a mechanism that allows the concentration of different functions within small protein regions. Integration of NLS and NoLS into functional protein domains might have influenced the viral evolution, as this could prevent an increase in the protein size.
Collapse
|
4
|
Grahl MVC, Uberti AF, Broll V, Bacaicoa-Caruso P, Meirelles EF, Carlini CR. Proteus mirabilis Urease: Unsuspected Non-Enzymatic Properties Relevant to Pathogenicity. Int J Mol Sci 2021; 22:ijms22137205. [PMID: 34281258 PMCID: PMC8268090 DOI: 10.3390/ijms22137205] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/22/2022] Open
Abstract
Infection by Proteus mirabilis causes urinary stones and catheter incrustation due to ammonia formed by urease (PMU), one of its virulence factors. Non-enzymatic properties, such as pro-inflammatory and neurotoxic activities, were previously reported for distinct ureases, including that of the gastric pathogen Helicobacter pylori. Here, PMU was assayed on isolated cells to evaluate its non-enzymatic properties. Purified PMU (nanomolar range) was tested in human (platelets, HEK293 and SH-SY5Y) cells, and in murine microglia (BV-2). PMU promoted platelet aggregation. It did not affect cellular viability and no ammonia was detected in the cultures’ supernatants. PMU-treated HEK293 cells acquired a pro-inflammatory phenotype, producing reactive oxygen species (ROS) and cytokines IL-1β and TNF-α. SH-SY5Y cells stimulated with PMU showed high levels of intracellular Ca2+ and ROS production, but unlike BV-2 cells, SH-SY5Y did not synthesize TNF-α and IL-1β. Texas Red-labeled PMU was found in the cytoplasm and in the nucleus of all cell types. Bioinformatic analysis revealed two bipartite nuclear localization sequences in PMU. We have shown that PMU, besides urinary stone formation, can potentially contribute in other ways to pathogenesis. Our data suggest that PMU triggers pro-inflammatory effects and may affect cells beyond the renal system, indicating a possible role in extra-urinary diseases.
Collapse
Affiliation(s)
- Matheus V. C. Grahl
- Laboratory of Neurotoxins, Brain Institute of Rio Grande do Sul (BRAINS) and Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil; (M.V.C.G.); (A.F.U.)
| | - Augusto F. Uberti
- Laboratory of Neurotoxins, Brain Institute of Rio Grande do Sul (BRAINS) and Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil; (M.V.C.G.); (A.F.U.)
| | - Valquiria Broll
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil;
| | - Paula Bacaicoa-Caruso
- Laboratory of Neurotoxins, Brain Institute of Rio Grande do Sul (BRAINS) and Graduate Program in Cellular and Molecular Biology, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil;
| | - Evelin F. Meirelles
- Laboratory of Neurotoxins, Brain Institute of Rio Grande do Sul (BRAINS), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil;
| | - Celia R. Carlini
- Laboratory of Neurotoxins, Brain Institute of Rio Grande do Sul (BRAINS) and School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil
- Correspondence: ; Tel.: +55-51-33205986
| |
Collapse
|
5
|
Machicado C, Soto MP, La Chira LF, Torres J, Mendoza C, Marcos LA. In silico prediction of secretory proteins of Opisthorchis viverrini, Clonorchis sinensis and Fasciola hepatica that target the host cell nucleus. Heliyon 2021; 7:e07204. [PMID: 34337171 PMCID: PMC8318992 DOI: 10.1016/j.heliyon.2021.e07204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/21/2021] [Accepted: 05/31/2021] [Indexed: 12/01/2022] Open
Abstract
Liver flukes Fasciola hepatica, Opisthorchis viverrini and Clonorchis sinensis are causing agents of liver and hepatobiliary diseases. A remarkable difference between such worms is the fact that O. viverrini and C. sinensis are carcinogenic organisms whereas F. hepatica is not carcinogenic. The release of secretory factors by carcinogenic flukes seems to contribute to cancer development however if some of these target the host cell nuclei is unknown. We investigated the existence of O. viverrini and C. sinensis secretory proteins that target the nucleus of host cells and compared these with the corresponding proteins predicted in F. hepatica. Here we applied an algorithm composed by in silico approaches that screened and analyzed the potential genes predicted from genomes of liver flukes. We found 31 and 22 secretory proteins that target the nucleus of host cells in O. viverrini and C. sinensis, respectively, and that have no homologs in F. hepatica. These polypeptides have enriched the transcription initiation process and nucleic acid binding in O. viverrini and C. sinensis, respectively. In addition, other 11 secretory proteins of O. viverrini and C. sinensis, that target the nucleus of host cells, had F. hepatica homologs, have enriched RNA processing function. In conclusion, O. viverrini and C. sinensis have 31 and 22 genes, respectively, that may be involved in their carcinogenic action through a direct targeting on the host cell nuclei.
Collapse
Affiliation(s)
- Claudia Machicado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Honorio Delgado 430, Lima 31, Peru.,Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, Spain
| | - Maria Pia Soto
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Honorio Delgado 430, Lima 31, Peru.,Laboratorio de Investigación en Biología Molecular y Farmacología Experimental, Universidad Católica de Santa María, Urb. San José, San Jose s/n, Arequipa, Peru
| | - Luis Felipe La Chira
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Honorio Delgado 430, Lima 31, Peru
| | - Joel Torres
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Cercado de Lima, Peru
| | - Carlos Mendoza
- Facultad de Ciencias Biológicas, Universidad Nacional de Trujillo, Av. Juan Pablo II, Trujillo, 13011, Peru
| | - Luis A Marcos
- Department of Medicine (Division of Infectious Diseases), Department of Microbiology and Immunology, State University of New York at Stony Brook, NY, Stony Brook, USA
| |
Collapse
|
6
|
Le LHM, Ying L, Ferrero RL. Nuclear trafficking of bacterial effector proteins. Cell Microbiol 2021; 23:e13320. [PMID: 33600054 DOI: 10.1111/cmi.13320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Bacterial pathogens can subvert host responses by producing effector proteins that directly target the nucleus of eukaryotic cells in animals and plants. Nuclear-targeting proteins are categorised as either: "nucleomodulins," which have epigenetic-modulating activities; or "cyclomodulins," which specifically interfere with the host cell cycle. Bacteria can deliver these effector proteins to eukaryotic cells via a range of strategies. Despite an increasing number of reports describing the effects of bacterial effector proteins on nuclear processes in host cells, the intracellular pathways used by these proteins to traffic to the nucleus have yet to be fully elucidated. This review will describe current knowledge about how nucleomodulins and cyclomodulins enter eukaryotic cells, exploit endocytic pathways and translocate to the nucleus. We will also discuss the secretion of nuclear-targeting proteins or their release in bacterial membrane vesicles and the trafficking pathways employed by each of these forms. Besides their importance for bacterial pathogenesis, some nuclear-targeting proteins have been implicated in the development of chronic diseases and even cancer. A greater understanding of nuclear-targeting proteins and their actions will provide new insights into the pathogenesis of infectious diseases, as well as contribute to advances in the development of novel therapies against bacterial infections and possibly cancer.
Collapse
Affiliation(s)
- Lena Hoang My Le
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Le Ying
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Richard L Ferrero
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne, Victoria, Australia
| |
Collapse
|
7
|
Lisitsyna OM, Kurnaeva MA, Arifulin EA, Shubina MY, Musinova YR, Mironov AA, Sheval EV. Origin of the nuclear proteome on the basis of pre-existing nuclear localization signals in prokaryotic proteins. Biol Direct 2020; 15:9. [PMID: 32345340 PMCID: PMC7189692 DOI: 10.1186/s13062-020-00263-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
Background The origin of the selective nuclear protein import machinery, which consists of nuclear pore complexes and adaptor molecules interacting with the nuclear localization signals (NLSs) of cargo molecules, is one of the most important events in the evolution of eukaryotic cells. How proteins were selected for import into the forming nucleus remains an open question. Results Here, we demonstrate that functional NLSs may be integrated in the nucleotide-binding domains of both eukaryotic and prokaryotic proteins and may coevolve with these domains. Conclusion The presence of sequences similar to NLSs in the DNA-binding domains of prokaryotic proteins might have created an advantage for nuclear accumulation of these proteins during evolution of the nuclear-cytoplasmic barrier, influencing which proteins accumulated and became compartmentalized inside the forming nucleus (i.e., the content of the nuclear proteome). Reviewers This article was reviewed by Sergey Melnikov and Igor Rogozin. Open peer review Reviewed by Sergey Melnikov and Igor Rogozin. For the full reviews, please go to the Reviewers’ comments section.
Collapse
Affiliation(s)
- Olga M Lisitsyna
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Margarita A Kurnaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Eugene A Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Maria Y Shubina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Yana R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334, Moscow, Russia.,Skobelkin State Scientific Center of Laser Medicine FMBA, 121099, Moscow, Russia
| | - Andrey A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia.,Skolkovo Institute of Science and Technology, 121205, Moscow, Russia.,Institute for Information Transmission Problems, Russian Academy of Sciences, 127051, Moscow, Russia.,Faculty of Computer Science, National Research University Higher School of Economics, 101000, Moscow, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia. .,Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia. .,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France.
| |
Collapse
|
8
|
Kappaun K, Piovesan AR, Carlini CR, Ligabue-Braun R. Ureases: Historical aspects, catalytic, and non-catalytic properties - A review. J Adv Res 2018; 13:3-17. [PMID: 30094078 PMCID: PMC6077230 DOI: 10.1016/j.jare.2018.05.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 12/11/2022] Open
Abstract
Urease (urea amidohydrolase, EC 3.5.1.5) is a nickel-containing enzyme produced by plants, fungi, and bacteria that catalyzes the hydrolysis of urea into ammonia and carbamate. Urease is of historical importance in Biochemistry as it was the first enzyme ever to be crystallized (1926). Finding nickel in urease's active site (1975) was the first indication of a biological role for this metal. In this review, historical and structural features, kinetics aspects, activation of the metallocenter and inhibitors of the urea hydrolyzing activity of ureases are discussed. The review also deals with the non-enzymatic biological properties, whose discovery 40 years ago started a new chapter in the study of ureases. Well recognized as virulence factors due to the production of ammonia and alkalinization in diseases by urease-positive microorganisms, ureases have pro-inflammatory, endocytosis-inducing and neurotoxic activities that do not require ureolysis. Particularly relevant in plants, ureases exert insecticidal and fungitoxic effects. Data on the jack bean urease and on jaburetox, a recombinant urease-derived peptide, have indicated that interactions with cell membrane lipids may be the basis of the non-enzymatic biological properties of ureases. Altogether, with this review we wanted to invite the readers to take a second look at ureases, very versatile proteins that happen also to catalyze the breakdown of urea into ammonia and carbamate.
Collapse
Affiliation(s)
- Karine Kappaun
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Medicine and Health Sciences, School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Angela Regina Piovesan
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Celia Regina Carlini
- Brain Institute (InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6690, Prédio 63, Porto Alegre, RS CEP 90610-000, Brazil
- Graduate Program in Medicine and Health Sciences, School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Rodrigo Ligabue-Braun
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| |
Collapse
|
9
|
Scopel-Guerra A, Olivera-Severo D, Staniscuaski F, Uberti AF, Callai-Silva N, Jaeger N, Porto BN, Carlini CR. The Impact of Helicobacter pylori Urease upon Platelets and Consequent Contributions to Inflammation. Front Microbiol 2017; 8:2447. [PMID: 29312166 PMCID: PMC5733092 DOI: 10.3389/fmicb.2017.02447] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/24/2017] [Indexed: 12/22/2022] Open
Abstract
Gastric infection by Helicobacter pylori is considered a risk factor for gastric and duodenal cancer, and extragastric diseases. Previous data have shown that, in a non-enzymatic way, H. pylori urease (HPU) activates neutrophils to produce ROS and also induces platelet aggregation, requiring ADP secretion modulated by the 12-lipoxygenase pathway, a signaling cascade also triggered by the physiological agonist collagen. Here we investigated further the effects on platelets of recombinant versions of the holoenzyme HPU, and of its two subunits (HpUreA and HpUreB). Although HpUreA had no aggregating activity on platelets, it partially inhibited collagen-induced aggregation. HpUreB induced platelet aggregation in the nanomolar range, and also interfered dose-dependently on both collagen- and ADP-induced platelet aggregation. HPU-induced platelet aggregation was inhibited by antibodies against glycoprotein VI (GPVI), the main collagen receptor in platelets. Flow cytometry analysis revealed exposure of P-selectin in HPU-activated platelets. Anti-glycoprotein IIbIIIa (GPIIbIIIa) antibodies increased the binding of FITC-labeled HPU to activated platelets, whereas anti-GPVI did not. Evaluation of post-transcriptional events in HPU-activated platelets revealed modifications in the pre-mRNA processing of pro-inflammatory proteins, with increased levels of mRNAs encoding IL-1β and CD14. We concluded that HPU activates platelets probably through its HpUreB subunit. Activation of platelets by HPU turns these cells into a pro-inflammatory phenotype. Altogether, our data suggest that H. pylori urease, besides allowing bacterial survival within the gastric mucosa, may have an important, and so far overlooked, role in gastric inflammation mediated by urease-activated neutrophils and platelets.
Collapse
Affiliation(s)
- Adriele Scopel-Guerra
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Deiber Olivera-Severo
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Department of Biology, Universidade Regional Integrada do Alto Uruguai e das Missões, São Luiz Gonzaga, Brazil
| | - Fernanda Staniscuaski
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Department of Molecular Biology and Biotechnology, Institute of Biosciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Augusto F Uberti
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Institute of Biology, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Natália Callai-Silva
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Natália Jaeger
- Institute of Biomedical Research, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Bárbara N Porto
- Institute of Biomedical Research, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Celia R Carlini
- Brain Institute (BRAINS-InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| |
Collapse
|
10
|
Olivera-Severo D, Uberti AF, Marques MS, Pinto MT, Gomez-Lazaro M, Figueiredo C, Leite M, Carlini CR. A New Role for Helicobacter pylori Urease: Contributions to Angiogenesis. Front Microbiol 2017; 8:1883. [PMID: 29021786 PMCID: PMC5623709 DOI: 10.3389/fmicb.2017.01883] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/14/2017] [Indexed: 12/29/2022] Open
Abstract
Helicobacter pylori is a pathogen involved in gastric diseases such as ulcers and carcinomas. H. pylori's urease is an important virulence factor produced in large amounts by this bacterium. In previous studies, we have shown that this protein is able to activate several cell types like neutrophils, monocytes, platelets, endothelial cells, and gastric epithelial cells. Angiogenesis is a physiological process implicated in growth, invasion and metastization of tumors. Here, we have analyzed the angiogenic potential of H. pylori urease (HPU) in gastric epithelial cells. No cytotoxicity was observed in AGS, Kato-III, and MKN28 gastric cell lines treated with 300 nM HPU, as evaluated by the 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. As we previously reported in neutrophils, treatment with 300 nM HPU also had an anti-apoptotic effect in gastric epithelial cells leading to a 2.2-fold increase in the levels of Bcl-XL after 6 h, and a decrease of 80% in the content of BAD, after 48 h, two mitochondrial proteins involved in regulation of apoptosis. Within 10 min of exposure, HPU is rapidly internalized by gastric epithelial cells. Treatment of the gastric cells with methyl-β-cyclodextrin abolished HPU internalization suggesting a cholesterol-dependent process. HPU induces the expression of pro-angiogenic factors and the decrease of expression of anti-angiogenic factors by AGS cells. The angiogenic activity of HPU was analyzed using in vitro and in vivo models. HPU induced formation of tube-like structures by human umbilical vascular endothelial cells in a 9 h experiment. In the chicken embryo chorioallantoic membrane model, HPU induced intense neo-vascularization after 3 days. In conclusion, our results indicate that besides allowing bacterial colonization of the gastric mucosa, H. pylori's urease triggers processes that initiate pro-angiogenic responses in different cellular models. Thus, this bacterial urease, a major virulence factor, may also play a role in gastric carcinoma development.
Collapse
Affiliation(s)
- Deiber Olivera-Severo
- Center of Biotechnology, Universidade Federal Rio Grande do Sul, Porto Alegre, Brazil.,Biology Department, Universidade Regional Integrada do Alto Uruguai e das Missões, São Luiz Gonzaga, Brazil
| | - Augusto F Uberti
- Center of Biotechnology, Universidade Federal Rio Grande do Sul, Porto Alegre, Brazil.,Institute of Biology, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Miguel S Marques
- i3S, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Ipatimup-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Marta T Pinto
- i3S, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Ipatimup-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Maria Gomez-Lazaro
- i3S, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,INEB - Instituto Nacional de Engenharia Biomédica, University of Porto, Porto, Portugal
| | - Céu Figueiredo
- i3S, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Ipatimup-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Marina Leite
- i3S, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Ipatimup-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Célia R Carlini
- Center of Biotechnology, Universidade Federal Rio Grande do Sul, Porto Alegre, Brazil.,Brain Institute (BRAINS-InsCer), Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| |
Collapse
|
11
|
Whitmore LC, Weems MN, Allen LAH. Cutting Edge: Helicobacter pylori Induces Nuclear Hypersegmentation and Subtype Differentiation of Human Neutrophils In Vitro. THE JOURNAL OF IMMUNOLOGY 2017; 198:1793-1797. [PMID: 28148734 DOI: 10.4049/jimmunol.1601292] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/07/2017] [Indexed: 12/20/2022]
Abstract
Helicobacter pylori infects the human stomach and causes a spectrum of disease that includes gastritis, peptic ulcers, and gastric adenocarcinoma. A chronic, neutrophil-rich inflammatory response characterizes this infection. It is established that H. pylori stimulates neutrophil chemotaxis and a robust respiratory burst, but other aspects of this interaction are incompletely defined. We demonstrate here that H. pylori induces N1-like subtype differentiation of human neutrophils as indicated by profound nuclear hypersegmentation, a CD62Ldim, CD16bright, CD11bbright, CD66bbright, CD63bright surface phenotype, proinflammatory cytokine secretion, and cytotoxicity. Hypersegmentation requires direct neutrophil-H. pylori contact as well as transcription and both host and bacterial protein synthesis, but not urease, NapA, VacA, CagA, or CagT. The concept of neutrophil plasticity is new and, to our knowledge, these data are the first evidence that neutrophils can undergo subtype differentiation in vitro in response to bacterial pathogen infection. We hypothesize that these changes favor H. pylori persistence and disease.
Collapse
Affiliation(s)
- Laura C Whitmore
- Inflammation Program, University of Iowa, Iowa City, IA 52242.,Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| | - Megan N Weems
- Inflammation Program, University of Iowa, Iowa City, IA 52242.,Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| | - Lee-Ann H Allen
- Inflammation Program, University of Iowa, Iowa City, IA 52242; .,Department of Internal Medicine, University of Iowa, Iowa City, IA 52242.,Department of Microbiology, University of Iowa, Iowa City, IA 52242; and.,Iowa City VA Health Care System, Iowa City, IA 52246
| |
Collapse
|
12
|
Kim JM, Choe MH, Asaithambi K, Song JY, Lee YS, Lee JC, Seo JH, Kang HL, Lee KH, Lee WK, Cho MJ, Rhee KH, Youn HS, Baik SC. Helicobacter pylori HP0425 Targets the Nucleus with DNase I-Like Activity. Helicobacter 2016; 21:218-25. [PMID: 26395879 DOI: 10.1111/hel.12271] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND AND AIMS Nuclear targeting of bacterial proteins has a significant impact on host cell pathology. Helicobacter pylori have many nuclear targeting proteins that translocate into the nucleus of host cells. H. pylori HP0425, annotated as hypothetical, has a nuclear localization signal (NLS) sequence, but its function has not been demonstrated. The aim of this experiment was to address the nuclear translocation of HP0425 and determine the effect of HP0425 pathology on host cells. MATERIALS AND METHODS To investigate the nuclear localization of HP0425, it was expressed in AGS and MKN-1 cells as a GFP fusion protein (pEGFP-HP0425), and its localization was analyzed by confocal microscopy. Recombinant HP0425 (rHP0425) protein was overproduced as a GST fusion protein in Escherichia coli and purified by glutathione-affinity column chromatography. Purified rHP0425 was examined for cytotoxicity and DNase activity. RESULTS The pEGFP-HP0425 fluorescence was expressed in the nucleus and cytosol fraction of cells, while it was localized in the cytoplasm in the negative control. This protein exhibited DNase activity under various conditions, with the highest DNase activity in the presence of manganese. In addition, the rHP0425 protein efficiently decreased cell viability in a concentration-dependent manner. CONCLUSIONS These results suggest that HP0425 carrying a nuclear localization signal sequence translocates into the nucleus of host cells and degrades genomic DNA by DNase I-like enzymatic activity, which is a new pathogenic strategy of H. pylori in the host.
Collapse
Affiliation(s)
- Jung-Min Kim
- Department of Microbiology, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Min-Ho Choe
- Department of Microbiology, Gyeongsang National University School of Medicine, Jinju, Korea
| | | | - Jae-Young Song
- Department of Microbiology, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Korea
| | - Je Chul Lee
- Department of Microbiology, Kyungpook National University School of Medicine, Daegu, Korea
| | - Ji-Hyun Seo
- Department of Pediatrics, Gyeongsang Institute of Health Science, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Hyung-Lyun Kang
- Department of Microbiology, Gyeongsang National University School of Medicine, Jinju, Korea.,Research Institute of Life Science, Gyeongsang National University, Jinju, Korea
| | - Kon Ho Lee
- Department of Microbiology, Gyeongsang National University School of Medicine, Jinju, Korea.,Research Institute of Life Science, Gyeongsang National University, Jinju, Korea
| | - Woo-Kon Lee
- Department of Microbiology, Gyeongsang National University School of Medicine, Jinju, Korea.,Research Institute of Life Science, Gyeongsang National University, Jinju, Korea
| | - Myung-Je Cho
- Department of Microbiology, Gyeongsang National University School of Medicine, Jinju, Korea.,Research Institute of Life Science, Gyeongsang National University, Jinju, Korea
| | - Kwang-Ho Rhee
- Department of Microbiology, Gyeongsang National University School of Medicine, Jinju, Korea.,Research Institute of Life Science, Gyeongsang National University, Jinju, Korea
| | - Hee-Shang Youn
- Department of Pediatrics, Gyeongsang Institute of Health Science, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Seung-Chul Baik
- Department of Microbiology, Gyeongsang National University School of Medicine, Jinju, Korea.,Research Institute of Life Science, Gyeongsang National University, Jinju, Korea
| |
Collapse
|
13
|
Kwon YC, Kim S, Lee YS, Lee JC, Cho MJ, Lee WK, Kang HL, Song JY, Baik SC, Ro HS. Novel nuclear targeting coiled-coil protein of Helicobacter pylori showing Ca2+-independent, Mg2+-dependent DNase I activity. J Microbiol 2016; 54:387-95. [DOI: 10.1007/s12275-016-5631-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/30/2016] [Accepted: 03/30/2016] [Indexed: 01/02/2023]
|
14
|
Morphological changes in human gastric epithelial cells induced by nuclear targeting of Helicobacter pylori urease subunit A. J Microbiol 2015; 53:406-14. [PMID: 26025173 DOI: 10.1007/s12275-015-5085-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 12/20/2022]
Abstract
Nuclear targeting of bacterial proteins and their pathological effects on host cells are an emerging pathogenic mechanism in bacteria. We have previously reported that urease subunit A (UreA) of Helicobacter pylori targets the nuclei of COS-7 cells through nuclear localization signals (NLSs). This study further investigated whether UreA of H. pylori targets the nuclei of gastric epithelial cells and then induces molecular and cellular changes in the host cells. H. pylori 26695 strain produced and secreted outer membrane vesicles (OMVs). UreA was translocated into gastric epithelial AGS cells through outer membrane vesicles (OMVs) and then targeted the nuclei of AGS cells. Nuclear targeting of rUreA did not induce host cell death, but resulted in morphological changes, such as cellular elongation, in AGS cells. In contrast, AGS cells treated with rUreA?NLS proteins did not show this morphological change. Next generation sequencing revealed that nuclear targeting of UreA differentially regulated 102 morphogenesis- related genes, of which 67 and 35 were up-regulated and down-regulated, respectively. Our results suggest that nuclear targeting of H. pylori UreA induces both molecular and cellular changes in gastric epithelial cells.
Collapse
|