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Moreira SM, Chyou TY, Wade JT, Brown CM. Diversification of the Rho transcription termination factor in bacteria. Nucleic Acids Res 2024:gkae582. [PMID: 38966992 DOI: 10.1093/nar/gkae582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
Correct termination of transcription is essential for gene expression. In bacteria, factor-dependent termination relies on the Rho factor, that classically has three conserved domains. Some bacteria also have a functional insertion region. However, the variation in Rho structure among bacteria has not been analyzed in detail. This study determines the distribution, sequence conservation, and predicted features of Rho factors with diverse domain architectures by analyzing 2730 bacterial genomes. About half (49.8%) of the species analyzed have the typical Escherichia coli like Rho while most of the other species (39.8%) have diverse, atypical forms of Rho. Besides conservation of the main domains, we describe a duplicated RNA-binding domain present in specific species and novel variations in the bicyclomycin binding pocket. The additional regions observed in Rho proteins exhibit remarkable diversity. Commonly, however, they have exceptional amino acid compositions and are predicted to be intrinsically disordered, to undergo phase separation, or have prion-like behavior. Phase separation has recently been shown to play roles in Rho function and bacterial fitness during harsh conditions in one species and this study suggests a more widespread role. In conclusion, diverse atypical Rho factors are broadly distributed among bacteria, suggesting additional cellular roles.
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Affiliation(s)
- Sofia M Moreira
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| | - Te-Yuan Chyou
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY 12222, USA
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, Otago 9054, New Zealand
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2
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Aslam S, Aljawdah HM, Murshed M, Serrano GE. Pharmacophore modelling based virtual screening and molecular dynamics identified the novel inhibitors and drug targets against Waddlia chondrophila. Sci Rep 2024; 14:13472. [PMID: 38866811 PMCID: PMC11169463 DOI: 10.1038/s41598-024-63555-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Waddlia chondrophila is a possible cause of fetal death in humans. This Chlamydia-related bacterium is an emergent pathogen that causes human miscarriages and ruminant abortions, which results in financial losses. Despite the years of efforts, the underlying mechanism behind the pathogenesis of W. chondrophila is little known which hindered the development of novel treatment options. In the framework of current study, computational approaches were used to identify novel inhibitors (phytocompounds) and drug targets against W. chondrophila. At first, RNA polymerase sigma factor SigA and 3-deoxy-D-manno-octulosonic acid transferase were identified through subtractive proteomics pipeline. Afterwards, extensive docking and simulation analyses were conducted to optimize potentially novel phytocompounds by assessing their binding affinity to target proteins. A 100ns molecular dynamics simulation well complimented the compound's binding affinity and indicated strong stability of predicted compounds at the docked site. The calculation of binding free energies with MMGBSA corroborated the significant binding affinity between phytocompounds and target protein binding sites. The proposed phytocompounds may be a viable treatment option for patients infected with W. chondrophila; however, further research is required to ensure their safety.
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Affiliation(s)
- Sidra Aslam
- Banner Sun Health Research Institute, Sun City, AZ, USA.
| | - Hossam M Aljawdah
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Mutee Murshed
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
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3
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Xu J, Yu L, Ye S, Ye Z, Yang L, Xu X. Oral microbiota-host interaction: the chief culprit of alveolar bone resorption. Front Immunol 2024; 15:1254516. [PMID: 38455060 PMCID: PMC10918469 DOI: 10.3389/fimmu.2024.1254516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
There exists a bidirectional relationship between oral health and general well-being, with an imbalance in oral symbiotic flora posing a threat to overall human health. Disruptions in the commensal flora can lead to oral diseases, while systemic illnesses can also impact the oral cavity, resulting in the development of oral diseases and disorders. Porphyromonas gingivalis and Fusobacterium nucleatum, known as pathogenic bacteria associated with periodontitis, play a crucial role in linking periodontitis to accompanying systemic diseases. In periodontal tissues, these bacteria, along with their virulence factors, can excessively activate the host immune system through local diffusion, lymphatic circulation, and blood transmission. This immune response disruption contributes to an imbalance in osteoimmune mechanisms, alveolar bone resorption, and potential systemic inflammation. To restore local homeostasis, a deeper understanding of microbiota-host interactions and the immune network phenotype in local tissues is imperative. Defining the immune network phenotype in periodontal tissues offers a promising avenue for investigating the complex characteristics of oral plaque biofilms and exploring the potential relationship between periodontitis and associated systemic diseases. This review aims to provide an overview of the mechanisms underlying Porphyromonas gingivalis- and Fusobacterium nucleatum-induced alveolar bone resorption, as well as the immunophenotypes observed in host periodontal tissues during pathological conditions.
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Affiliation(s)
- Jingyu Xu
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Ling Yu
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Surong Ye
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Zitong Ye
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Luyi Yang
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Xiaoxi Xu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
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4
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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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5
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Rauthan K, Joshi S, Kumar L, Goel D, Kumar S. Functional annotation of uncharacterized proteins from Fusobacterium nucleatum: identification of virulence factors. Genomics Inform 2023; 21:e21. [PMID: 37415454 PMCID: PMC10326533 DOI: 10.5808/gi.22065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 07/08/2023] Open
Abstract
Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as "Uncharacterized." Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.
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Affiliation(s)
- Kanchan Rauthan
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Saranya Joshi
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Lokesh Kumar
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Divya Goel
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Sudhir Kumar
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
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6
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Fan Z, Tang P, Li C, Yang Q, Xu Y, Su C, Li L. Fusobacterium nucleatum and its associated systemic diseases: epidemiologic studies and possible mechanisms. J Oral Microbiol 2023; 15:2145729. [PMID: 36407281 PMCID: PMC9673791 DOI: 10.1080/20002297.2022.2145729] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Fusobacterium nucleatum (F. nucleatum) is an anaerobic oral commensal and the major coaggregation bridge organism linking early and late colonisers. In recent years, a large number of studies suggest that F. nucleatum is closely related to the development of various systemic diseases, such as cardiovascular diseases, adverse pregnancy outcomes, inflammatory bowel diseases, cancer, Alzheimer's disease, respiratory infection, rheumatoid arthritis, etc. Objective To review the effect of F. nucleatum on systemic diseases and its possible pathogenesis and to open new avenues for prevention and treatment of F. nucleatum-associated systemic diseases. Design The research included every article published up to July 2022 featuring the keywords 'Systemic diseases' OR 'Atherosclerotic cardiovascular diseases' OR 'Atherosclerosis' OR 'Adverse pregnancy outcomes' OR 'Inflammatory bowel disease' OR 'Ulcerative colitis' OR 'Crohn’s disease' OR 'Cancers' OR 'Oral squamous cell carcinomas' OR 'Gastrointestinal cancers' OR 'Colorectal cancer' OR 'Breast cancer' OR 'Genitourinary cancers' OR 'Alzheimer’s disease ' OR 'Rheumatoid arthritis' OR 'Respiratory diseases' AND 'Fusobacterium nucleatum' OR 'Periodontal pathogen' OR 'Oral microbiota' OR 'Porphyromonas gingivalis' and was conducted in the major medical databases. Results F. nucleatum can induce immune response and inflammation in the body through direct or indirect pathways, and thus affect the occurrence and development of systemic diseases. Only by continuing to investigate the pathogenic lifestyles of F. nucleatum will we discover the divergent pathways that may be leveraged for diagnostic, preventive and therapeutic purposes.
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Affiliation(s)
- Zixin Fan
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Pengzhou Tang
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cheng Li
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Qi Yang
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yan Xu
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chuan Su
- State KeyLaboratory of Reproductive Medicine, Jiangsu Key Laboratory of Pathogen Biology, Department of Pathogen Biology and Immunology, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lu Li
- Department of Periodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Shanghai road 1, Nanjing, Jiangsu, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
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Islam J, Sarkar H, Hoque H, Hasan MN, Jewel GNA. In-silico approach of identifying novel therapeutic targets against Yersinia pestis using pan and subtractive genomic analysis. Comput Biol Chem 2022; 101:107784. [DOI: 10.1016/j.compbiolchem.2022.107784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
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8
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He S, Chen Y, Wang L, Bai X, Bu T, Zhang J, Lu M, Ha NC, Quan C, Nam KH, Xu Y. Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS from Fusobacterium nucleatum. Molecules 2022; 27:molecules27154781. [PMID: 35897955 PMCID: PMC9332261 DOI: 10.3390/molecules27154781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP) is the active form of vitamin B6, but it is highly reactive and poisonous in its free form. YggS is a PLP-binding protein found in bacteria and humans that mediates PLP homeostasis by delivering PLP to target enzymes or by performing a protective function. Several biochemical and structural studies of YggS have been reported, but the mechanism by which YggS recognizes PLP has not been fully elucidated. Here, we report a functional and structural analysis of YggS from Fusobacterium nucleatum (FnYggS). The PLP molecule could bind to native FnYggS, but no PLP binding was observed for selenomethionine (SeMet)-derivatized FnYggS. The crystal structure of FnYggS showed a type III TIM barrel fold, exhibiting structural homology with several other PLP-dependent enzymes. Although FnYggS exhibited low (<35%) amino acid sequence similarity with previously studied YggS proteins, its overall structure and PLP-binding site were highly conserved. In the PLP-binding site of FnYggS, the sulfate ion was coordinated by the conserved residues Ser201, Gly218, and Thr219, which were positioned to provide the binding moiety for the phosphate group of PLP. The mutagenesis study showed that the conserved Ser201 residue in FnYggS was the key residue for PLP binding. These results will expand the knowledge of the molecular properties and function of the YggS family.
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Affiliation(s)
- Shanru He
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China; (S.H.); (Y.C.); (L.W.); (X.B.); (T.B.); (J.Z.)
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Yuanyuan Chen
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China; (S.H.); (Y.C.); (L.W.); (X.B.); (T.B.); (J.Z.)
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Lulu Wang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China; (S.H.); (Y.C.); (L.W.); (X.B.); (T.B.); (J.Z.)
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
| | - Xue Bai
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China; (S.H.); (Y.C.); (L.W.); (X.B.); (T.B.); (J.Z.)
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Tingting Bu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China; (S.H.); (Y.C.); (L.W.); (X.B.); (T.B.); (J.Z.)
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Jie Zhang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China; (S.H.); (Y.C.); (L.W.); (X.B.); (T.B.); (J.Z.)
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Ming Lu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuel, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China;
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 00826, Korea;
| | - Chunshan Quan
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China; (S.H.); (Y.C.); (L.W.); (X.B.); (T.B.); (J.Z.)
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Correspondence: (C.Q.); (K.H.N.); (Y.X.)
| | - Ki Hyun Nam
- Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Korea
- POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 37673, Korea
- Correspondence: (C.Q.); (K.H.N.); (Y.X.)
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China; (S.H.); (Y.C.); (L.W.); (X.B.); (T.B.); (J.Z.)
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Correspondence: (C.Q.); (K.H.N.); (Y.X.)
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9
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Zhang X, Wang R, Xie X, Hu Y, Wang J, Sun Q, Feng X, Lin W, Tong S, Yan W, Wen H, Wang M, Zhai S, Sun C, Wang F, Niu Q, Kropinski A, Cui Y, Jiang X, Peng S, Li S, Tong Y. Mining bacterial NGS data vastly expands the complete genomes of temperate phages. NAR Genom Bioinform 2022; 4:lqac057. [PMID: 35937545 PMCID: PMC9346568 DOI: 10.1093/nargab/lqac057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 06/13/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to their lysogenicity, curbing their identification and characterization. Existing bioinformatics tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes. This study proposes a novel computational temperate phage detection method (TemPhD) mining both the integrated active prophages and their spontaneously induced forms (temperate phages) from next-generation sequencing raw data. Applying the method to the available dataset resulted in 192 326 complete temperate phage genomes with different host species, expanding the existing number of complete temperate phage genomes by more than 100-fold. The wet-lab experiments demonstrated that TemPhD can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites, outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the microbial evolution by (i) cross-infecting different bacterial host species; (ii) transferring antibiotic resistance and virulence genes and (iii) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensively complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.
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Affiliation(s)
- Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
| | - Ruohan Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Xiangcheng Xie
- College of Computer, National University of Defense Technology , Changsha 410073, People's Republic of China
| | - Yunjia Hu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
- School of Medicine, Shanghai University , Shanghai 200444, People's Republic of China
| | - Jianping Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Qiang Sun
- The 964th Hospital , Changchun 130021, People's Republic of China
| | - Xikang Feng
- School of Software, Northwestern Polytechnical University , Xi’an 710072, People's Republic of China
| | - Wei Lin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Shanwei Tong
- Bioinformatics Graduate Program, University of British Columbia , Vancouver BC V6T 1Z4, Canada
- Faculty of Health Sciences, Simon Fraser University , Burnaby , BC V5A 1S6, Canada
| | - Wei Yan
- National Library of Medicine, National Institutes of Health , Bethesda , MD 20894, USA
| | - Huiqi Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Mengyao Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Shixiang Zhai
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences , Yantai 264003, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
- Center for Ocean Mega-Science, Chinese Academy of Sciences , Qingdao 266071, People's Republic of China
| | - Cheng Sun
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Fangyi Wang
- Department of Statistics, the Ohio State University , Columbus, OH 43210, USA
| | - Qi Niu
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Andrew M Kropinski
- Departments of Food Science, and Pathobiology, University of Guelph , Guelph , ON N1G 2W1 , Canada
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing 100071, People's Republic of China
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health , Bethesda , MD 20894, USA
| | - Shaoliang Peng
- School of Computer Science and Electronic Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong , Hong Kong 999077, People's Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
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Chen SJ, Bi YH, Zhang LH. Systematic analysis of the potential off-target activities of osimertinib by computational target fishing. Anticancer Drugs 2022; 33:e434-e443. [PMID: 34459459 DOI: 10.1097/cad.0000000000001229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Osimertinib is a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor used to treat non-small cell lung cancer. However, its off-targets are obscure, and systematic analysis of off-target activities remains to be performed. Here, we identified the off-targets of osimertinib using PharmMapper and DRAR-CPI and analyzed the intersected targets using the GeneMANIA and DAVID servers. A drug-target-pathway network was constructed to visualize the associations. The results showed that osimertinib is associated with 31 off-targets, 40 Kyoto Encyclopedia of Genes and Genomes pathways, and 9 diseases. Network analysis revealed that the targets were involved in cancer and other physiological processes. In addition to EGFR, molecular docking analysis showed that seven proteins, namely Janus kinase 3, peroxisome proliferator-activated receptor alpha, renin, mitogen-activated protein kinases, lymphocyte-specific protein tyrosine kinase, cell division protein kinase 2 and proto-oncogene tyrosine-protein kinase Src, could also be potential targets of osimertinib. In conclusion, osimertinib is predicted to target multiple proteins and pathways, resulting in the formation of an action network via which it exerts systematic pharmacological effects.
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Affiliation(s)
- Shao-Jun Chen
- Department of Traditional Chinese Medicine, Zhejiang Pharmaceutical College, Ningbo
| | - Yan-Hua Bi
- The Children's Hospital, Zhejiang University School of Medicine, National clinical research center for child health, Hangzhou
| | - Li-Hua Zhang
- Department of Food Science, Faculty of Food Science, Zhejiang Pharmaceutical College, Ningbo, China
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Wang Y, Wang H, Hu L, Chen L. Leptin Gene Protects Against Cold Stress in Antarctic Toothfish. Front Physiol 2021; 12:740806. [PMID: 34975517 PMCID: PMC8715755 DOI: 10.3389/fphys.2021.740806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Leptin is a cytokine-like peptide, predominantly biosynthesized in adipose tissue, which plays an important role in regulating food intake, energy balance and reproduction in mammals. However, how it may have been modified to enable life in the chronic cold is unclear. Here, we identified a leptin-a gene (lepa) in the cold-adapted and neutrally buoyant Antarctic toothfish Dissostichus mawsoni that encodes a polypeptide carrying four α-helices and two cysteine residues forming in-chain disulfide bonds, structures shared by most vertebrate leptins. Quantitative RT-PCR confirmed that mRNA levels of the leptin-a gene of D. mawsoni (DM-lepa) were highest in muscle, followed by kidney and liver; detection levels were low in the gill, brain, intestine, and ovary tissues. Compared with leptin-a genes of fishes living in warmer waters, DM-lepa underwent rapid evolution and was subjected to positive selection. Over-expression of DM-lepa in the zebrafish cell line ZFL resulted in signal accumulation in the cytoplasm and significantly increased cell proliferation both at the normal culture temperature and under cold treatment. DM-lepa over-expression also reduced apoptosis under low-temperature stress and activated the STAT3 signaling pathway, in turn upregulating the anti-apoptotic proteins bcl2l1, bcl2a, myca and mdm2 while downregulating the pro-apoptotic baxa, p53 and caspase-3. These results demonstrate that DM-lepa, through STAT3 signaling, plays a protective role in cold stress by preventing apoptotic damage. Our study reveals a new role of lepa in polar fish.
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Affiliation(s)
- Ying Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Huamin Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Linghong Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
- *Correspondence: Liangbiao Chen,
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In Silico Core Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors against Streptococcus pyogenes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111355. [PMID: 34769873 PMCID: PMC8582943 DOI: 10.3390/ijerph182111355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 12/18/2022]
Abstract
Streptococcus pyogenes is a significant pathogen that causes skin and upper respiratory tract infections and non-suppurative complications, such as acute rheumatic fever and post-strep glomerulonephritis. Multidrug resistance has emerged in S. pyogenes strains, making them more dangerous and pathogenic. Hence, it is necessary to identify and develop therapeutic methods that would present novel approaches to S. pyogenes infections. In the current study, a subtractive proteomics approach was employed to core proteomes of four strains of S. pyogenes using several bioinformatic software tools and servers. The core proteome consists of 1324 proteins, and 302 essential proteins were predicted from them. These essential proteins were analyzed using BLASTp against human proteome, and the number of potential targets was reduced to 145. Based on subcellular localization prediction, 46 proteins with cytoplasmic localization were chosen for metabolic pathway analysis. Only two cytoplasmic proteins, i.e., chromosomal replication initiator protein DnaA and two-component response regulator (TCR), were discovered to have the potential to be novel drug target candidates. Three-dimensional (3D) structure prediction of target proteins was carried out via the Swiss Model server. Molecular docking approach was employed to screen the library of 1000 phytochemicals against the interacting residues of the target proteins through the MOE software. Further, the docking studies were validated by running molecular dynamics simulation and highly popular binding free energy approaches of MM-GBSA and MM-PBSA. The findings revealed a promising candidate as a novel target against S. pyogenes infections.
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Ali Mohammed MM, Pettersen VK, Nerland AH, Wiker HG, Bakken V. Label-free quantitative proteomic analysis of the oral bacteria Fusobacterium nucleatum and Porphyromonas gingivalis to identify protein features relevant in biofilm formation. Anaerobe 2021; 72:102449. [PMID: 34543761 DOI: 10.1016/j.anaerobe.2021.102449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/24/2021] [Accepted: 09/14/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The opportunistic pathogens Fusobacterium nucleatum and Porphyromonas gingivalis are Gram-negative bacteria associated with oral biofilm and periodontal disease. This study investigated interactions between F. nucleatum and P. gingivalis proteomes with the objective to identify proteins relevant in biofilm formation. METHODS We applied liquid chromatography-tandem mass spectrometry to determine the expressed proteome of F. nucleatum and P. gingivalis cells grown in biofilm or planktonic culture, and as mono- and dual-species models. The detected proteins were classified into functional categories and their label-free quantitative (LFQ) intensities statistically compared. RESULTS The proteomic analyses detected 1,322 F. nucleatum and 966 P. gingivalis proteins, including abundant virulence factors. Using univariate statistics, we identified significant changes between biofilm and planktonic culture (p-value ≤0.05) in 0,4% F. nucleatum, 7% P. gingivalis, and 14% of all proteins in the dual-species model. For both species, proteins involved in vitamin B2 (riboflavin) metabolism had significantly increased levels in biofilm. In both mono- and dual-species biofilms, P. gingivalis increased the production of proteins for translation, oxidation-reduction, and amino acid metabolism compared to planktonic cultures. However, when we compared LFQ intensities between mono- and dual-species, over 90% of the significantly changed P. gingivalis proteins had their levels reduced in biofilm and planktonic settings of the dual-species model. CONCLUSIONS The findings suggest that P. gingivalis reduces the production of multiple proteins because of the F. nucleatum presence. The results highlight the complex interactions of bacteria contributing to oral biofilms, which need to be considered in the design of prevention strategies.
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Affiliation(s)
| | | | - Audun H Nerland
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Harald G Wiker
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Vidar Bakken
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.
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14
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Ponath F, Tawk C, Zhu Y, Barquist L, Faber F, Vogel J. RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum. Nat Microbiol 2021; 6:1007-1020. [PMID: 34239075 DOI: 10.1038/s41564-021-00927-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 05/24/2021] [Indexed: 12/14/2022]
Abstract
Fusobacterium nucleatum, long known as a constituent of the oral microflora, has recently garnered renewed attention for its association with several different human cancers. The growing interest in this emerging cancer-associated bacterium contrasts with a paucity of knowledge about its basic gene expression features and physiological responses. As fusobacteria lack all established small RNA-associated proteins, post-transcriptional networks in these bacteria are also unknown. In the present study, using differential RNA-sequencing, we generate high-resolution global RNA maps for five clinically relevant fusobacterial strains-F. nucleatum subspecies nucleatum, animalis, polymorphum and vincentii, as well as F. periodonticum-for early, mid-exponential growth and early stationary phase. These data are made available in an online browser, and we use these to uncover fundamental aspects of fusobacterial gene expression architecture and a suite of non-coding RNAs. Developing a vector for functional analysis of fusobacterial genes, we discover a conserved fusobacterial oxygen-induced small RNA, FoxI, which serves as a post-transcriptional repressor of the major outer membrane porin FomA. Our findings provide a crucial step towards delineating the regulatory networks enabling F. nucleatum adaptation to different environments, which may elucidate how these bacteria colonize different compartments of the human body.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Caroline Tawk
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Yan Zhu
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Franziska Faber
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany. .,Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany. .,Faculty of Medicine, University of Würzburg, Würzburg, Germany.
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15
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Dadashi M, Hajikhani B, Faghihloo E, Owlia P, Yaslianifard S, Goudarzi M, Nasiri MJ, Fallah F. Proliferative Effect of FadA Recombinant Protein from Fusobacterium nucleatum on SW480 Colorectal Cancer Cell Line. Infect Disord Drug Targets 2021; 21:623-628. [PMID: 32691717 DOI: 10.2174/1871526520666200720113004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/15/2020] [Accepted: 06/01/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND AND AIM Colorectal Cancer (CRC) is one of the most frequent cancers diagnosed in both men and women worldwide. Fusobacterium nucleatum adhesin A (FadA) has an important potential factor in the development or progression of CRC. The aim of the present study was to evaluate the proliferative effect of recombinant FadA on SW480 colorectal cancer cell line. MATERIALS AND METHODS The recombinant pET21(b)-fadA plasmid was synthesized and transformed into competent E.coli DH5α. In the next step, induction and expression of recombinant FadA were carried out in E. coli BL21 (DE3) competent cells. Expression and purification of protein were successfully done and it was analyzed and confirmed by SDS-PAGE and western blotting. The proliferative effect of purified FadA on SW480 CRC cell line was evaluated using MTT assay and cell counting methods. RESULTS Visualization of the specific band isolated from the linear plasmid on the agarose gel confirmed the presence of the desired gene. After electrophoresis and Coomassie blue staining, the protein of interest with an approximate molecular weight of 13KDa was detected. The MTT assay, similar to cell counting methods, revealed that FadA dose and time-dependently promoted SW480 cell growth and proliferation in 24, 48 and 72 hours. CONCLUSION The results showed that FadA stimulates proliferation of SW480 colorectal cancer cell line with a dose and time-dependent manner.
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Affiliation(s)
- Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parviz Owlia
- Molecular Microbiology Research Center, Shahed University, Tehran, Iran
| | - Somayeh Yaslianifard
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Fallah
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Levine M, Lohinai ZM. Resolving the Contradictory Functions of Lysine Decarboxylase and Butyrate in Periodontal and Intestinal Diseases. J Clin Med 2021; 10:jcm10112360. [PMID: 34072136 PMCID: PMC8198195 DOI: 10.3390/jcm10112360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
Periodontal disease is a common, bacterially mediated health problem worldwide. Mastication (chewing) repeatedly traumatizes the gingiva and periodontium, causing traces of inflammatory exudate, gingival crevicular fluid (GCF), to appear in crevices between the teeth and gingiva. Inadequate tooth cleaning causes a dentally adherent microbial biofilm composed of commensal salivary bacteria to appear around these crevices where many bacteria grow better on GCF than in saliva. We reported that lysine decarboxylase (Ldc) from Eikenella corrodens depletes the GCF of lysine by converting it to cadaverine and carbon dioxide. Lysine is an amino acid essential for the integrity and continuous renewal of dentally attached epithelium acting as a barrier to microbial products. Unless removed regularly by oral hygiene, bacterial products invade the lysine-deprived dental attachment where they stimulate inflammation that enhances GCF exudation. Cadaverine increases and supports the development of a butyrate-producing microbiome that utilizes the increased GCF substrates to slowly destroy the periodontium (dysbiosis). A long-standing paradox is that acid-induced Ldc and butyrate production support a commensal (probiotic) microbiome in the intestine. Here, we describe how the different physiologies of the respective tissues explain how the different Ldc and butyrate functions impact the progression and control of these two chronic diseases.
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Affiliation(s)
- Martin Levine
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Correspondence:
| | - Zsolt M. Lohinai
- Department of Conservative Dentistry, Semmelweis University, H-1088 Budapest, Hungary;
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17
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Khor B, Snow M, Herrman E, Ray N, Mansukhani K, Patel KA, Said-Al-Naief N, Maier T, Machida CA. Interconnections Between the Oral and Gut Microbiomes: Reversal of Microbial Dysbiosis and the Balance Between Systemic Health and Disease. Microorganisms 2021; 9:microorganisms9030496. [PMID: 33652903 PMCID: PMC7996936 DOI: 10.3390/microorganisms9030496] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
The human microbiota represents a complex array of microbial species that influence the balance between the health and pathology of their surrounding environment. These microorganisms impart important biological benefits to their host, such as immune regulation and resistance to pathogen colonization. Dysbiosis of microbial communities in the gut and mouth precede many oral and systemic diseases such as cancer, autoimmune-related conditions, and inflammatory states, and can involve the breakdown of innate barriers, immune dysregulation, pro-inflammatory signaling, and molecular mimicry. Emerging evidence suggests that periodontitis-associated pathogens can translocate to distant sites to elicit severe local and systemic pathologies, which necessitates research into future therapies. Fecal microbiota transplantation, probiotics, prebiotics, and synbiotics represent current modes of treatment to reverse microbial dysbiosis through the introduction of health-related bacterial species and substrates. Furthermore, the emerging field of precision medicine has been shown to be an effective method in modulating host immune response through targeting molecular biomarkers and inflammatory mediators. Although connections between the human microbiome, immune system, and systemic disease are becoming more apparent, the complex interplay and future innovations in treatment modalities will become elucidated through continued research and cross-disciplinary collaboration.
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Affiliation(s)
- Brandon Khor
- Academic DMD Program, Oregon Health & Science University, 2730 SW Moody Avenue, Portland, OR 97201, USA; (B.K.); (M.S.); (E.H.); (N.R.); (K.M.); (K.A.P.)
| | - Michael Snow
- Academic DMD Program, Oregon Health & Science University, 2730 SW Moody Avenue, Portland, OR 97201, USA; (B.K.); (M.S.); (E.H.); (N.R.); (K.M.); (K.A.P.)
| | - Elisa Herrman
- Academic DMD Program, Oregon Health & Science University, 2730 SW Moody Avenue, Portland, OR 97201, USA; (B.K.); (M.S.); (E.H.); (N.R.); (K.M.); (K.A.P.)
| | - Nicholas Ray
- Academic DMD Program, Oregon Health & Science University, 2730 SW Moody Avenue, Portland, OR 97201, USA; (B.K.); (M.S.); (E.H.); (N.R.); (K.M.); (K.A.P.)
| | - Kunal Mansukhani
- Academic DMD Program, Oregon Health & Science University, 2730 SW Moody Avenue, Portland, OR 97201, USA; (B.K.); (M.S.); (E.H.); (N.R.); (K.M.); (K.A.P.)
| | - Karan A. Patel
- Academic DMD Program, Oregon Health & Science University, 2730 SW Moody Avenue, Portland, OR 97201, USA; (B.K.); (M.S.); (E.H.); (N.R.); (K.M.); (K.A.P.)
| | - Nasser Said-Al-Naief
- Department of Integrative Biomedical and Diagnostic Sciences, School of Dentistry, Oregon Health & Science University 2730 SW Moody Avenue, Portland, OR 97201, USA; (N.S.-A.-N.); (T.M.)
| | - Tom Maier
- Department of Integrative Biomedical and Diagnostic Sciences, School of Dentistry, Oregon Health & Science University 2730 SW Moody Avenue, Portland, OR 97201, USA; (N.S.-A.-N.); (T.M.)
| | - Curtis A. Machida
- Department of Integrative Biomedical and Diagnostic Sciences, School of Dentistry, Oregon Health & Science University 2730 SW Moody Avenue, Portland, OR 97201, USA; (N.S.-A.-N.); (T.M.)
- Correspondence:
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18
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Mukherjee S, Kundu I, Askari M, Barai RS, Venkatesh KV, Idicula-Thomas S. Exploring the druggable proteome of Candida species through comprehensive computational analysis. Genomics 2021; 113:728-739. [PMID: 33484798 DOI: 10.1016/j.ygeno.2020.12.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022]
Abstract
Candida albicans and non-albicans Candida spp. are major cause of systemic mycoses. Antifungal drugs such as azoles and polyenes are not efficient to successfully eradicate Candida infection owing to their fungistatic nature or low bioavailability. Here, we have adopted a comprehensive computational workflow for identification, prioritization and validation of targets from proteomes of Candida albicans and Candida tropicalis. The protocol involves identification of essential drug-target candidates using subtractive genomics, protein-protein interaction network properties and systems biology based methods. The essentiality of the novel metabolic and non-metabolic targets was established by performing in silico gene knockouts, under aerobic as well as anaerobic conditions, and in vitro drug inhibition assays respectively. Deletion of twelve genes that are involved in amino acid, secondary metabolite, and carbon metabolism showed zero growth in metabolic model under simulated conditions. The algorithm, used in this study, can be downloaded from http://pbit.bicnirrh.res.in/offline.php and executed locally.
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Affiliation(s)
- Shuvechha Mukherjee
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Indra Kundu
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Mehdi Askari
- Department of Bioinformatics, Guru Nanak Khalsa College, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India
| | - Ram Shankar Barai
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - K V Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, Maharashtra, India.
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India.
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19
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Deciphering the role of sulfonamides and molecular basis of thioredoxin domain dynamics through comparative simulations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Rodriguez RM, Khadka VS, Menor M, Hernandez BY, Deng Y. Tissue-associated microbial detection in cancer using human sequencing data. BMC Bioinformatics 2020; 21:523. [PMID: 33272199 PMCID: PMC7713026 DOI: 10.1186/s12859-020-03831-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/19/2022] Open
Abstract
Cancer is one of the leading causes of morbidity and mortality in the globe. Microbiological infections account for up to 20% of the total global cancer burden. The human microbiota within each organ system is distinct, and their compositional variation and interactions with the human host have been known to attribute detrimental and beneficial effects on tumor progression. With the advent of next generation sequencing (NGS) technologies, data generated from NGS is being used for pathogen detection in cancer. Numerous bioinformatics computational frameworks have been developed to study viral information from host-sequencing data and can be adapted to bacterial studies. This review highlights existing popular computational frameworks that utilize NGS data as input to decipher microbial composition, which output can predict functional compositional differences with clinically relevant applicability in the development of treatment and prevention strategies.
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Affiliation(s)
- Rebecca M. Rodriguez
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Mānoa, Honolulu, HI USA
- Population Sciences in the Pacific Program-Cancer Epidemiology, Honolulu, HI USA
- NIDDK Central Repository, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, USA
| | - Vedbar S. Khadka
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Mānoa, Honolulu, HI USA
| | - Mark Menor
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Mānoa, Honolulu, HI USA
| | - Brenda Y. Hernandez
- Epidemiology, University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI USA
- Population Sciences in the Pacific Program-Cancer Epidemiology, Honolulu, HI USA
| | - Youping Deng
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Mānoa, Honolulu, HI USA
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Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients. Cardiol Res Pract 2020; 2020:1957843. [PMID: 33294219 PMCID: PMC7700061 DOI: 10.1155/2020/1957843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/06/2020] [Accepted: 10/19/2020] [Indexed: 01/11/2023] Open
Abstract
Indigenous animals show unique gut microbiota (GM) in the Tibetan plateau. However, it is unknown whether the hypertensive indigenous people in plateau also have the distinct gut bacteria, different from those living in plains. We sequenced the V3-V4 region of the gut bacteria 16S ribosomal RNA (rRNA) gene of feces samples among hypertensive patients (HPs) and healthy individuals (HIs) from 3 distinct altitudes: Tibetans from high altitude (3600-4500 m, n = 38 and 34), Hans from middle altitude (2260 m, n = 49 and 35), and Hans from low altitude (13 m, n = 34 and 35) and then analyzed the GM composition among hypertensive and healthy subgroups using the bioinformatics analysis, respectively. The GM of high-altitude Tibetan and middle-altitude Han HPs presented greater α- and β-diversities, lower ratio of Firmicutes/Bacteroidetes (F/B), and higher abundance of beneficial Verrucomicrobia and Akkermansia than the low-altitudes HPs did. The GM of high-altitude Tibetan and middle-altitude HIs showed greater α-diversity and lower ratio of F/B than the low-altitudes HIs did. But, β-diversity and abundance of Verrucomicrobia and Akkermansia among different subgroups of HIs did not show any differences. Conclusively, the high-altitude Tibetan and middle-altitude Han HPs have a distinct feature of GM, which may be important in their adaptation to hypertension in the plateau environments.
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Shahid F, Ashfaq UA, Saeed S, Munir S, Almatroudi A, Khurshid M. In Silico Subtractive Proteomics Approach for Identification of Potential Drug Targets in Staphylococcus saprophyticus. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17103644. [PMID: 32455889 PMCID: PMC7277342 DOI: 10.3390/ijerph17103644] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 11/16/2022]
Abstract
Staphylococcus saprophyticus is a uropathogenic bacteria responsible for acute urinary tract infections (UTIs) mainly in young female patients. Patients suffering from urinary catheterization, pregnant patients, the elderly as well as those with nosocomial UTIs are at greater risk of the colonizing S. saprophyticus infection. The causative factors include benign prostatic hyperplasia, indwelling catheter, neurogenic bladder, pregnancy, and history of frequent UTIs. Recent findings have exhibited that S. saprophyticus is resistant to several antimicrobial agents. Moreover, there is a global concern regarding the increasing level of antimicrobial resistance, which leads to treatment failure and reduced effectiveness of broad-spectrum antimicrobials. Therefore, a novel approach is being utilized to combat resistant microbes since the past few years. Subtractive proteome analysis has been performed with the entire proteome of S. saprophyticus strain American Type Culture Collection (ATCC) 15305 using several bioinformatics servers and software. The proteins that were non-homologous to humans and bacteria were identified for metabolic pathway analysis. Only four cytoplasmic proteins were found possessing the potential of novel drug target candidates. The development of innovative therapeutic agents by targeting the inhibition of any essential proteins may disrupt the metabolic pathways specific to the pathogen, thus causing destruction as well as eradication of the pathogen from a particular host. The identified targets can facilitate in designing novel and potent drugs against S. saprophyticus strain ATCC 15305.
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Affiliation(s)
- Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Punjab 38000, Pakistan; (F.S.); (S.S.); (S.M.)
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Punjab 38000, Pakistan; (F.S.); (S.S.); (S.M.)
- Correspondence:
| | - Sania Saeed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Punjab 38000, Pakistan; (F.S.); (S.S.); (S.M.)
| | - Samman Munir
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Punjab 38000, Pakistan; (F.S.); (S.S.); (S.M.)
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad, Punjab 38000, Pakistan;
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de Leeuw MA, Duval MX. The Presence of Periodontal Pathogens in Gastric Cancer. EXPLORATORY RESEARCH AND HYPOTHESIS IN MEDICINE 2020; 000:1-10. [DOI: 10.14218/erhm.2020.00024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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24
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Rodriguez RM, Hernandez BY, Menor M, Deng Y, Khadka VS. The landscape of bacterial presence in tumor and adjacent normal tissue across 9 major cancer types using TCGA exome sequencing. Comput Struct Biotechnol J 2020; 18:631-641. [PMID: 32257046 PMCID: PMC7109368 DOI: 10.1016/j.csbj.2020.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/26/2022] Open
Abstract
Identification of microbial composition directly from tumor tissue permits studying the relationship between microbial changes and cancer pathogenesis. We interrogated bacterial presence in tumor and adjacent normal tissue strictly in pairs utilizing human whole exome sequencing to generate microbial profiles. Profiles were generated for 813 cases from stomach, liver, colon, rectal, lung, head & neck, cervical and bladder TCGA cohorts. Core microbiota examination revealed twelve taxa to be common across the nine cancer types at all classification levels. Paired analyses demonstrated significant differences in bacterial shifts between tumor and adjacent normal tissue across stomach, colon, lung squamous cell, and head & neck cohorts, whereas little or no differences were evident in liver, rectal, lung adenocarcinoma, cervical and bladder cancer cohorts in adjusted models. Helicobacter pylori in stomach and Bacteroides vulgatus in colon were found to be significantly higher in adjacent normal compared to tumor tissue after false discovery rate correction. Computational results were validated with tissue from an independent population by species-specific qPCR showing similar patterns of co-occurrence among Fusobacterium nucleatum and Selenomonas sputigena in gastric samples. This study demonstrates the ability to identify bacteria differential composition derived from human tissue whole exome sequences. Taken together our results suggest the microbial profiles shift with advanced disease and that the microbial composition of the adjacent tissue can be indicative of cancer stage disease progression.
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Key Words
- BLCA, bladder carcinoma
- CESC, cervical & endocervical squamous cell carcinomas
- COAD, colon adenocarcinoma
- COREAD, colon and rectal adenocarcinoma TCGA cohorts
- Cancer microbiome
- Exome sequencing
- HNSC, head & neck squamous cell carcinoma
- L2FC, log 2 fold change
- LIHC, liver hepatocellular carcinoma
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- Microbial landscape
- READ, rectal adenocarcinoma
- STAD, stomach adenocarcinoma
- TCGA
- TCGA, The Cancer Genome Atlas
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Affiliation(s)
- Rebecca M. Rodriguez
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
- Population Sciences in the Pacific Program-Cancer Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, United States
| | - Brenda Y. Hernandez
- Epidemiology, University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, United States
- Population Sciences in the Pacific Program-Cancer Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, United States
| | - Mark Menor
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
| | - Youping Deng
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
| | - Vedbar S. Khadka
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
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25
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Cao P, Chen Y, Guo X, Chen Y, Su W, Zhan N, Dong W. Fusobacterium nucleatum Activates Endoplasmic Reticulum Stress to Promote Crohn's Disease Development via the Upregulation of CARD3 Expression. Front Pharmacol 2020; 11:106. [PMID: 32153411 PMCID: PMC7047714 DOI: 10.3389/fphar.2020.00106] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/28/2020] [Indexed: 12/26/2022] Open
Abstract
There is increasing evidence that members of the gut microbiota, especially Fusobacterium nucleatum (F. nucleatum), are associated with Crohn’s disease (CD), but the specific mechanism by which F. nucleatum promotes CD development is unclear. Here, we first examined the abundance of F. nucleatum and its effects on CD disease activity and explored whether F. nucleatum aggravated intestinal inflammation and promoted intestinal mucosal barrier damage in vitro and in vivo. Our data showed that F. nucleatum was enriched in 41.21% of CD tissues from patients and was correlated with the clinical course, clinical activity, and refractory behavior of CD (P < 0.05). In addition, we found that F. nucleatum infection is involved in activating the endoplasmic reticulum stress (ERS) pathway during CD development to promote intestinal mucosal barrier destruction. Mechanistically, F. nucleatum targeted caspase activation and recruitment domain 3 (CARD3) to activate the ERS pathway and promote F. nucleatum-mediated mucosal barrier damage in vivo and in vitro. Thus, F. nucleatum coordinates a molecular network involving CARD3 and ERS to control the CD process. Measuring and targeting F. nucleatum and its associated pathways will provide valuable insight into the prevention and treatment of CD.
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Affiliation(s)
- Pan Cao
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yongyu Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xufeng Guo
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yan Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenhao Su
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China.,Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Na Zhan
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China.,Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weiguo Dong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
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26
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Cesur MF, Siraj B, Uddin R, Durmuş S, Çakır T. Network-Based Metabolism-Centered Screening of Potential Drug Targets in Klebsiella pneumoniae at Genome Scale. Front Cell Infect Microbiol 2020; 9:447. [PMID: 31993376 PMCID: PMC6970976 DOI: 10.3389/fcimb.2019.00447] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 12/12/2019] [Indexed: 01/28/2023] Open
Abstract
Klebsiella pneumoniae is an opportunistic bacterial pathogen leading to life-threatening nosocomial infections. Emergence of highly resistant strains poses a major challenge in the management of the infections by healthcare-associated K. pneumoniae isolates. Thus, despite intensive efforts, the current treatment strategies remain insufficient to eradicate such infections. Failure of the conventional infection-prevention and treatment efforts explicitly indicates the requirement of new therapeutic approaches. This prompted us to systematically analyze the K. pneumoniae metabolism to investigate drug targets. Genome-scale metabolic networks (GMNs) facilitating the systematic analysis of the metabolism are promising platforms. Thus, we used a GMN of K. pneumoniae MGH 78578 to determine putative targets through gene- and metabolite-centric approaches. To develop more realistic infection models, we performed the bacterial growth simulations within different host-mimicking media, using an improved biomass formation reaction. We selected more suitable targets based on several property-based prioritization procedures. KdsA was identified as the high-ranked putative target satisfying most of the target prioritization criteria specified under the gene-centric approach. Through a structure-based virtual screening protocol, we identified potential KdsA inhibitors. In addition, the metabolite-centric approach extended the drug target list based on synthetic lethality. This revealed the importance of combined metabolic analyses for a better understanding of the metabolism. To our knowledge, this is the first comprehensive effort on the investigation of the K. pneumoniae metabolism for drug target prediction through the constraint-based analysis of its GMN in conjunction with several bioinformatic approaches. This study can guide the researchers for the future drug designs by providing initial findings regarding crucial components of the Klebsiella metabolism.
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Affiliation(s)
- Müberra Fatma Cesur
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Turkey
| | - Bushra Siraj
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Turkey
| | - Tunahan Çakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Turkey
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27
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Yang Z, Ji G. Fusobacterium nucleatum-positive colorectal cancer. Oncol Lett 2019; 18:975-982. [PMID: 31423156 PMCID: PMC6607099 DOI: 10.3892/ol.2019.10433] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is an important threat to human health and the fourth leading cause of mortality worldwide. Accumulating evidence indicates that the composition of the intestinal flora is associated with the occurrence of CRC. Fusobacterium nucleatum (Fn), one of the highly enriched bacteria in CRC tissues, invades the mucosa with adhesion factors and virulence proteins, interacts with the host immune system and promotes the occurrence and development of CRC and chemoresistance. Fn infection is prevalent in human colorectal carcinoma, although the infection rate varies in different regions. Fn may be used as a prognostic indicator of CRC. It is important to understand the multi-pathway carcinogenic mechanisms associated with CRC in order to develop novel antibacterial drugs against Fn. The current review summarizes the role of Fn and relevant research concerning CRC published in recent years, focusing on Fn infection in CRC, pathogenesis of Fn, Fn-positive CRC treatment, screening and prevention strategies against Fn-positive CRC.
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Affiliation(s)
- Zhenhua Yang
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, P.R. China.,Department of Digestive Endoscopy, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, P.R. China
| | - Guang Ji
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, P.R. China
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28
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De Witte C, Demeyere K, De Bruyckere S, Taminiau B, Daube G, Ducatelle R, Meyer E, Haesebrouck F. Characterization of the non-glandular gastric region microbiota in Helicobacter suis-infected versus non-infected pigs identifies a potential role for Fusobacterium gastrosuis in gastric ulceration. Vet Res 2019; 50:39. [PMID: 31126330 PMCID: PMC6534906 DOI: 10.1186/s13567-019-0656-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/08/2019] [Indexed: 02/08/2023] Open
Abstract
Helicobacter suis has been associated with development of gastric ulcers in the non-glandular part of the porcine stomach, possibly by affecting gastric acid secretion and altering the gastric microbiota. Fusobacterium gastrosuis is highly abundant in the gastric microbiota of H. suis-infected pigs and it was hypothesized that this micro-organism could play a role in the development of gastric ulceration. The aim of this study was to obtain further insights in the influence of a naturally acquired H. suis infection on the microbiota of the non-glandular part of the porcine stomach and in the pathogenic potential of F. gastrosuis. Infection with H. suis influenced the relative abundance of several taxa at phylum, family, genus and species level. H. suis-infected pigs showed a significantly higher colonization rate of F. gastrosuis in the non-glandular gastric region compared to non-infected pigs. In vitro, viable F. gastrosuis strains as well as their lysate induced death of both gastric and oesophageal epithelial cell lines. These gastric cell death inducing bacterial components were heat-labile. Genomic analysis revealed that genes are present in the F. gastrosuis genome with sequence similarity to genes described in other Fusobacterium spp. that encode factors involved in adhesion, invasion and induction of cell death as well as in immune evasion. We hypothesize that, in a gastric environment altered by H. suis, colonization and invasion of the non-glandular porcine stomach region and production of epithelial cell death inducing metabolites by F. gastrosuis, play a role in gastric ulceration.
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Affiliation(s)
- Chloë De Witte
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Kristel Demeyere
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Sofie De Bruyckere
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bernard Taminiau
- Department of Food Sciences, FARAH, University of Liège, Liège, Belgium
| | - Georges Daube
- Department of Food Sciences, FARAH, University of Liège, Liège, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evelyne Meyer
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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29
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Mothersole RG, Macdonald M, Kolesnikov M, Murphy MEP, Wolthers KR. Structural insight into the high reduction potentials observed for Fusobacterium nucleatum flavodoxin. Protein Sci 2019; 28:1460-1472. [PMID: 31116469 DOI: 10.1002/pro.3661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/17/2019] [Accepted: 05/20/2019] [Indexed: 11/08/2022]
Abstract
Flavodoxins are small flavin mononucleotide (FMN)-containing proteins that mediate a variety of electron transfer processes. The primary sequence of flavodoxin from Fusobacterium nucleatum, a pathogenic oral bacterium, is marked with a number of distinct features including a glycine to lysine (K13) substitution in the highly conserved phosphate-binding loop (T/S-X-T-G-X-T), variation in the aromatic residues that sandwich the FMN cofactor, and a more even distribution of acidic and basic residues. The Eox/sq (oxidized/semiquinone; -43 mV) and Esq/hq (semiquinone/hydroquinone; -256 mV) are the highest recorded reduction potentials of known long-chain flavodoxins. These more electropositive values are a consequence of the apoprotein binding to the FMN hydroquinone anion with ~70-fold greater affinity compared to the oxidized form of the cofactor. Inspection of the FnFld crystal structure revealed the absence of a hydrogen bond between the protein and the oxidized FMN N5 atom, which likely accounts for the more electropositive Eox/sq . The more electropositive Esq/hq is likely attributed to only one negatively charged group positioned within 12 Å of the FMN N1. We show that natural substitutions of highly conserved residues partially account for these more electropositive reduction potentials.
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Affiliation(s)
- Robert G Mothersole
- Department of Chemistry, University at the British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
| | - Marta Macdonald
- Department of Chemistry, University at the British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
| | - Maxim Kolesnikov
- Department of Microbiology and Immunology, University at the British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, University at the British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Kirsten R Wolthers
- Department of Chemistry, University at the British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
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30
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Wang G, Yu Y, Wang YZ, Wang JJ, Guan R, Sun Y, Shi F, Gao J, Fu XL. Role of SCFAs in gut microbiome and glycolysis for colorectal cancer therapy. J Cell Physiol 2019; 234:17023-17049. [PMID: 30888065 DOI: 10.1002/jcp.28436] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 02/02/2019] [Accepted: 02/14/2019] [Indexed: 12/19/2022]
Abstract
Increased risk of colorectal cancer (CRC) is associated with altered intestinal microbiota as well as short-chain fatty acids (SCFAs) reduction of output The energy source of colon cells relies mainly on three SCFAs, namely butyrate (BT), propionate, and acetate, while CRC transformed cells rely mainly on aerobic glycolysis to provide energy. This review summarizes recent research results for dysregulated glucose metabolism of SCFAs, which could be initiated by gut microbiome of CRC. Moreover, the relationship between SCFA transporters and glycolysis, which may correlate with the initiation and progression of CRC, are also discussed. Additionally, this review explores the linkage of BT to transport of SCFAs expressions between normal and cancerous colonocyte cell growth for tumorigenesis inhibition in CRC. Furthermore, the link between gut microbiota and SCFAs in the metabolism of CRC, in addition, the proteins and genes related to SCFAs-mediated signaling pathways, coupled with their correlation with the initiation and progression of CRC are also discussed. Therefore, targeting the SCFA transporters to regulate lactate generation and export of BT, as well as applying SCFAs or gut microbiota and natural compounds for chemoprevention may be clinically useful for CRCs treatment. Future research should focus on the combination these therapeutic agents with metabolic inhibitors to effectively target the tumor SCFAs and regulate the bacterial ecology for activation of potent anticancer effect, which may provide more effective application prospect for CRC therapy.
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Affiliation(s)
- Gang Wang
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
| | - Yang Yu
- Department of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yu-Zhu Wang
- Department of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jun-Jie Wang
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
| | - Rui Guan
- Information Resources Department, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yan Sun
- Information Resources Department, Hubei University of Medicine, Shiyan, Hubei, China
| | - Feng Shi
- Department of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jing Gao
- Department of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xing-Li Fu
- Department of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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31
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Liu Y, Baba Y, Ishimoto T, Iwatsuki M, Hiyoshi Y, Miyamoto Y, Yoshida N, Wu R, Baba H. Progress in characterizing the linkage between Fusobacterium nucleatum and gastrointestinal cancer. J Gastroenterol 2019; 54:33-41. [PMID: 30244399 DOI: 10.1007/s00535-018-1512-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/12/2018] [Indexed: 02/04/2023]
Abstract
Microbiome research is a rapidly advancing field in human cancers. Fusobacterium nucleatum is an oral bacterium, indigenous to the human oral cavity, that plays a role in periodontal disease. Recent studies have found that F. nucleatum can promote gastrointestinal tumor progression and affect the prognosis of the disease. In addition, F. nucleatum may contribute to the chemo-resistance of gastrointestinal cancers. This review summarizes recent progress in the pathogenesis of F. nucleatum and its impact on gastrointestinal cancer.
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Affiliation(s)
- Yang Liu
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan.,Second Oncology Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110022, China
| | - Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Takatsugu Ishimoto
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan.,International Research Center for Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Masaaki Iwatsuki
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Yukiharu Hiyoshi
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Yuji Miyamoto
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Rong Wu
- Second Oncology Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110022, China
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan.
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32
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Parvaiz N, Abbasi SW, Uddin R, Azam SS. Targeting isoprenoid biosynthesis pathway in Staphylococcus lugdunensis: Comparative docking and simulation studies of conventional and allosteric sites. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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33
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Gawade P, Ghosh P. Genomics driven approach for identification of novel therapeutic targets in Salmonella enterica. Gene 2018; 668:211-220. [DOI: 10.1016/j.gene.2018.05.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 05/13/2018] [Accepted: 05/16/2018] [Indexed: 02/06/2023]
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34
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Zhang S, Cai S, Ma Y. Association between Fusobacterium nucleatum and colorectal cancer: Progress and future directions. J Cancer 2018; 9:1652-1659. [PMID: 29760804 PMCID: PMC5950595 DOI: 10.7150/jca.24048] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/06/2018] [Indexed: 02/06/2023] Open
Abstract
The initiation and progression of colorectal cancer (CRC) involves genetic and epigenetic alterations influenced by dietary and environmental factors. Increasing evidence has linked the intestinal microbiota and colorectal cancer. More recently, Fusobacterium nucleatum (Fn), an opportunistic commensal anaerobe in the oral cavity, has been associated with CRC. Several research teams have reported an overabundance of Fn in human CRC and have elucidated the possible mechanisms by which Fn is involved in colorectal carcinogenesis in vitro and in mouse models. However, the mechanisms by which Fn promotes colorectal carcinogenesis remain unclear. To provide new perspectives for early diagnosis, the identification of high risk populations and treatment for colorectal cancer, this review will summarize the relative research progresses regarding the relationship between Fn and colorectal cancer.
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Affiliation(s)
- Sheng Zhang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
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35
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Hussan H, Clinton SK, Roberts K, Bailey MT. Fusobacterium's link to colorectal neoplasia sequenced: A systematic review and future insights. World J Gastroenterol 2017; 23:8626-8650. [PMID: 29358871 PMCID: PMC5752723 DOI: 10.3748/wjg.v23.i48.8626] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/09/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To critically evaluate previous scientific evidence on Fusobacterium's role in colorectal neoplasia development. METHODS Two independent investigators systematically reviewed all original scientific articles published between January, 2000, and July, 2017, using PubMed, EMBASE, and MEDLINE. A total of 355 articles were screened at the abstract level. Of these, only original scientific human, animal, and in vitro studies investigating Fusobacterium and its relationship with colorectal cancer (CRC) were included in the analysis. Abstracts, review articles, studies investigating other colonic diseases, and studies written in other languages than English were excluded from our analysis. Ninety articles were included after removing duplicates, resolving disagreements between the two reviewers, and applying the above criteria. RESULTS Studies have consistently identified positive associations between Fusobacterium, especially Fusobacterium nucleatum (F. nucleatum), and CRC. Stronger associations were seen in CRCs proximal to the splenic flexure and CpG island methylator phenotype (CIMP)-high CRCs. There was evidence of temporality and a biological gradient, with increased F. nucleatum DNA detection and quantity along the traditional adenoma-carcinoma sequence and in CIMP-high CRC precursors. Diet may have a differential impact on colonic F. nucleatum enrichment; evidence suggests that high fiber diet may reduce the risk of a subset of CRCs that are F. nucleatum DNA-positive. Data also suggest shorter CRC and disease-specific survival with increased amount of F. nucleatum DNA in CRC tissue. The pathophysiology of enrichment of F. nucleatum and other Fusobacterium species in colonic tissue is unclear; however, the virulence factors and changes to the local colonic environment with disruption of the protective mucus layer may contribute. The presence of a host lectin (Gal-GalNAc) in the colonic epithelium may also mediate F. nucleatum attachment to CRC and precursors through interaction with an F. nucleatum protein, fibroblast activation protein 2 (FAP2). The clinical significance of detection or enrichment of Fusobacterium in colorectal neoplasia is ambiguous, but data suggest a procarcinogenic effect of F. nucleatum, likely due to activation of oncogenic and inflammatory pathways and modulation of the tumor immune environment. This is hypothesized to be mediated by certain F. nucleatum strains carrying invasive properties and virulence factors such as FadA and FAP. CONCLUSION Evidence suggests a potential active role of Fusobacterium, specifically F. nucleatum, in CRC. Future prospective and experimental human studies would fill an important gap in this literature.
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Affiliation(s)
- Hisham Hussan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Steven K Clinton
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Kristen Roberts
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Michael T Bailey
- Department of Pediatrics, OSU College of Medicine And Center for Microbial Pathogenesis, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, United States
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Zanzoni A, Spinelli L, Braham S, Brun C. Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins. MICROBIOME 2017; 5:89. [PMID: 28793925 PMCID: PMC5551000 DOI: 10.1186/s40168-017-0307-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 07/13/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Fusobacterium nucleatum is a gram-negative anaerobic species residing in the oral cavity and implicated in several inflammatory processes in the human body. Although F. nucleatum abundance is increased in inflammatory bowel disease subjects and is prevalent in colorectal cancer patients, the causal role of the bacterium in gastrointestinal disorders and the mechanistic details of host cell functions subversion are not fully understood. RESULTS We devised a computational strategy to identify putative secreted F. nucleatum proteins (FusoSecretome) and to infer their interactions with human proteins based on the presence of host molecular mimicry elements. FusoSecretome proteins share similar features with known bacterial virulence factors thereby highlighting their pathogenic potential. We show that they interact with human proteins that participate in infection-related cellular processes and localize in established cellular districts of the host-pathogen interface. Our network-based analysis identified 31 functional modules in the human interactome preferentially targeted by 138 FusoSecretome proteins, among which we selected 26 as main candidate virulence proteins, representing both putative and known virulence proteins. Finally, six of the preferentially targeted functional modules are implicated in the onset and progression of inflammatory bowel diseases and colorectal cancer. CONCLUSIONS Overall, our computational analysis identified candidate virulence proteins potentially involved in the F. nucleatum-human cross-talk in the context of gastrointestinal diseases.
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Affiliation(s)
- Andreas Zanzoni
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France.
| | - Lionel Spinelli
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France
| | - Shérazade Braham
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France
| | - Christine Brun
- Aix-Marseille Université, Inserm, TAGC UMR_S1090, Marseille, France
- CNRS, Marseille, France
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Mima K, Ogino S, Nakagawa S, Sawayama H, Kinoshita K, Krashima R, Ishimoto T, Imai K, Iwatsuki M, Hashimoto D, Baba Y, Sakamoto Y, Yamashita YI, Yoshida N, Chikamoto A, Ishiko T, Baba H. The role of intestinal bacteria in the development and progression of gastrointestinal tract neoplasms. Surg Oncol 2017; 26:368-376. [PMID: 29113654 DOI: 10.1016/j.suronc.2017.07.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 07/09/2017] [Accepted: 07/20/2017] [Indexed: 12/12/2022]
Abstract
More than 100 trillion microorganisms inhabit the human intestinal tract and play important roles in health conditions and diseases, including cancer. Accumulating evidence demonstrates that specific bacteria and bacterial dysbiosis in the gastrointestinal tract can potentiate the development and progression of gastrointestinal tract neoplasms by damaging DNA, activating oncogenic signaling pathways, producing tumor-promoting metabolites such as secondary bile acids, and suppressing antitumor immunity. Other bacterial species have been shown to produce short-chain fatty acids such as butyrate, which can suppress inflammation and carcinogenesis in the gastrointestinal tract. Consistent with these lines of evidence, clinical studies using metagenomic analyses have shown associations of specific bacteria and bacterial dysbiosis with gastrointestinal tract cancers, including esophageal, gastric, and colorectal cancers. Emerging data demonstrate that intestinal bacteria can modulate the efficacy of cancer chemotherapies and novel targeted immunotherapies such as anti-CTLA4 and anti-CD274 therapies, the process of absorption, and the occurrence of complications after gastrointestinal surgery. A better understanding of the mechanisms by which the gut microbiota influence tumor development and progression in the intestine would provide opportunities to develop new prevention and treatment strategies for patients with gastrointestinal tract cancers by targeting the intestinal microflora.
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Affiliation(s)
- Kosuke Mima
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Shuji Ogino
- Division of MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shigeki Nakagawa
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Hiroshi Sawayama
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Koichi Kinoshita
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Ryuichi Krashima
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Takatsugu Ishimoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Katsunori Imai
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Masaaki Iwatsuki
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Daisuke Hashimoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Yasuo Sakamoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Yo-Ichi Yamashita
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Akira Chikamoto
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Takatoshi Ishiko
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan.
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Kumar A, Saranathan R, Prashanth K, Tiwary BK, Krishna R. Inhibition of the MurA enzyme in Fusobacterium nucleatum by potential inhibitors identified through computational and in vitro approaches. MOLECULAR BIOSYSTEMS 2017; 13:939-954. [DOI: 10.1039/c7mb00074j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Inhibition of MurA in open conformation by orientin and in closed conformation by quercetin-3-O-d-glucuronide with efficient inhibitory constant values.
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Affiliation(s)
- Amit Kumar
- Centre for Bioinformatics
- Pondicherry University
- Puducherry-605014
- India
| | | | - K. Prashanth
- Department of Biotechnology
- Pondicherry University
- Puducherry-605014
- India
| | - Basant K. Tiwary
- Centre for Bioinformatics
- Pondicherry University
- Puducherry-605014
- India
| | - Ramadas Krishna
- Centre for Bioinformatics
- Pondicherry University
- Puducherry-605014
- India
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