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Valadbeigi H, Khoshnood S, Negahdari B, Maleki A, Mohammadinejat M, Haddadi MH. Mixed oral biofilms are controlled by the interspecies interactions of Fusobacterium nucleatum. Oral Dis 2024; 30:3582-3590. [PMID: 38009960 DOI: 10.1111/odi.14822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/10/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Fusobacterium nucleatum (F. nucleatum) is an integral component of supra- and subgingival biofilms, especially more prevalent in subgingival areas during both periodontal health and disease. AIMS In this review, we explore the physical, metabolic, and genetic interactions that influence the role of F. nucleatum in the formation of mixed oral biofilms. The role of F. nucleatum in antibiotic resistance in oral biofilms was discussed and some therapeutic strategies were proposed. METHODS PubMed, Scopus, Google Scholar, and the Web of Science were extensively searched for English-language reports. RESULTS F. nucleatum-derived proteins such as RadD, Fap2, FomA, and CmpA are involved in direct interactions contributing to biofilm formation, while autoinducer-2 and putrescine are involved in metabolic interactions. Both groups are essential for the formation and persistence of oral biofilms. This study highlights the clinical relevance of targeted interactions of F. nucleatum in supra- and subgingival oral biofilms. CONCLUSIONS By focusing on these interactions, researchers and clinicians can develop more effective strategies to prevent biofilm-related disease and reduce the spread of antibiotic resistance. Further research in this area is warranted to explore the potential therapeutic interventions that can be derived from understanding the interactions of F. nucleatum in oral biofilm dynamics.
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Affiliation(s)
- Hassan Valadbeigi
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Babak Negahdari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Maleki
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Medya Mohammadinejat
- Department of Medicinal Chemistry, Faculty of Chemistry, North-Tehran Branch, Islamic Azad University, Tehran, Iran
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Zhang L, Leng XX, Qi J, Wang N, Han JX, Tao ZH, Zhuang ZY, Ren Y, Xie YL, Jiang SS, Li JL, Chen H, Zhou CB, Cui Y, Chen X, Wang Z, Zhang ZZ, Hong J, Chen HY, Jiang W, Chen YX, Zhao X, Yu J, Fang JY. The adhesin RadD enhances Fusobacterium nucleatum tumour colonization and colorectal carcinogenesis. Nat Microbiol 2024; 9:2292-2307. [PMID: 39169124 DOI: 10.1038/s41564-024-01784-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 07/15/2024] [Indexed: 08/23/2024]
Abstract
Fusobacterium nucleatum can bind to host cells and potentiate intestinal tumorigenesis. Here we used a genome-wide screen to identify an adhesin, RadD, which facilitates the attachment of F. nucleatum to colorectal cancer (CRC) cells in vitro. RadD directly binds to CD147, a receptor overexpressed on CRC cell surfaces, which initiated a PI3K-AKT-NF-κB-MMP9 cascade, subsequently enhancing tumorigenesis in mice. Clinical specimen analysis showed that elevated radD gene levels in CRC tissues correlated positively with activated oncogenic signalling and poor patient outcomes. Finally, blockade of the interaction between RadD and CD147 in mice effectively impaired F. nucleatum attachment and attenuated F. nucleatum-induced oncogenic response. Together, our study provides insights into an oncogenic mechanism driven by F. nucleatum RadD and suggests that the RadD-CD147 interaction could be a potential therapeutic target for CRC.
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Affiliation(s)
- Lu Zhang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Xu Leng
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ni Wang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ji-Xuan Han
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Hang Tao
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zi-Yan Zhuang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yimeng Ren
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Le Xie
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shan-Shan Jiang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Lu Li
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huimin Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng-Bei Zhou
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Cui
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyu Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zheng Wang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zi-Zhen Zhang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hong
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao-Yan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Weihong Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Zhou P, Bibek GC, Hu B, Wu C. Development of SacB-based Counterselection for Efficient Allelic Exchange in Fusobacterium nucleatum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.16.608263. [PMID: 39229080 PMCID: PMC11370447 DOI: 10.1101/2024.08.16.608263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Fusobacterium nucleatum , prevalent in the oral cavity, is significantly linked to overall human health. Our molecular comprehension of its role in oral biofilm formation and its interactions with the host under various pathological circumstances has seen considerable advancements in recent years, primarily due to the development of various genetic tools for DNA manipulation in this bacterium. Of these, counterselection-based unmarked in-frame mutation methods have proved notably effective. Under suitable growth conditions, cells carrying a counterselectable gene die, enabling efficient selection of rare defined allelic exchange mutants. The sacB gene from Bacillus subtilis , encoding levansucrase, is a widely used counterselective marker partly due to the easy availability of sucrose. Yet, its potential application in F. nucleatum genetic study remains untested. We demonstrated that F. nucleatum cells expressing sacB in either a shuttle or suicide plasmid exhibit a lethal sensitivity to supplemental sucrose. Utilizing sucrose counterselection, we created an in-frame deletion of the F. nucleatum tonB gene, a critical gene for energy-dependent transport processes in Gram-negative bacteria, and a precise knockin of the luciferase gene immediately following the stop codon of the hslO gene, the last gene of a five-gene operon possible related to the natural competence of F. nucleatum . Post counterselection with 5% sucrose, chromosomal plasmid loss occurred in all colonies, leading to gene alternations in half of the screened isolates. This sacB -based counterselection technique provides a reliable method for isolating unmarked gene mutations in wild-type F. nucleatum , enriching the toolkit for fusobacterial research. IMPORTANCE Investigations into Fusobacterium nucleatum 's role in related diseases significantly benefit from the strategies of creating unmarked gene mutations, which hinge on using a counterselective marker. Previously, the galk -based allelic exchange method, while effective, faced an inherent limitation - the need for a modified host. This study aims to surmount this limitation by substituting galK with sacB for gene modification in F. nucleatum . Our application of the sacB -based methodology successfully yielded a tonB in-frame deletion mutant and a luciferase gene knockin at the precise chromosomal location in the wild-type background. The new method augments the existing toolkit for F. nucleatum research and has far-reaching implications due to the easy accessibility to the counterselection compound sucrose. We anticipate its broader adoption in further exploration, thereby reinforcing its critical role in propelling our understanding of F. nucleatum .
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Rutherford J, Avad K, Dureja C, Norseeda K, GC B, Wu C, Sun D, Hevener KE, Hurdle JG. Evaluation of Fusobacterium nucleatum Enoyl-ACP Reductase (FabK) as a Narrow-Spectrum Drug Target. ACS Infect Dis 2024; 10:1612-1623. [PMID: 38597503 PMCID: PMC11091888 DOI: 10.1021/acsinfecdis.3c00710] [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: 12/20/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
Fusobacterium nucleatum, a pathobiont inhabiting the oral cavity, contributes to opportunistic diseases, such as periodontal diseases and gastrointestinal cancers, which involve microbiota imbalance. Broad-spectrum antimicrobial agents, while effective against F. nucleatum infections, can exacerbate dysbiosis. This necessitates the discovery of more targeted narrow-spectrum antimicrobial agents. We therefore investigated the potential for the fusobacterial enoyl-ACP reductase II (ENR II) isoenzyme FnFabK (C4N14_ 04250) as a narrow-spectrum drug target. ENRs catalyze the rate-limiting step in the bacterial fatty acid synthesis pathway. Bioinformatics revealed that of the four distinct bacterial ENR isoforms, F. nucleatum specifically encodes FnFabK. Genetic studies revealed that fabK was indispensable for F. nucleatum growth, as the gene could not be deleted, and silencing of its mRNA inhibited growth under the test conditions. Remarkably, exogenous fatty acids failed to rescue growth inhibition caused by the silencing of fabK. Screening of synthetic phenylimidazole analogues of a known FabK inhibitor identified an inhibitor (i.e., 681) of FnFabK enzymatic activity and F. nucleatum growth, with an IC50 of 2.1 μM (1.0 μg/mL) and a MIC of 0.4 μg/mL, respectively. Exogenous fatty acids did not attenuate the activity of 681 against F. nucleatum. Furthermore, FnFabK was confirmed as the intracellular target of 681 based on the overexpression of FnFabK shifting MICs and 681-resistant mutants having amino acid substitutions in FnFabK or mutations in other genetic loci affecting fatty acid biosynthesis. 681 had minimal activity against a range of commensal flora, and it was less active against streptococci in physiologic fatty acids. Taken together, FnFabK is an essential enzyme that is amenable to drug targeting for the discovery and development of narrow-spectrum antimicrobial agents.
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Affiliation(s)
- Jacob
T. Rutherford
- Center
for Infectious and Inflammatory Diseases, Institute of Biosciences
and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
| | - Kristiana Avad
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Chetna Dureja
- Center
for Infectious and Inflammatory Diseases, Institute of Biosciences
and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
| | - Krissada Norseeda
- Department
of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii 96720, United States
| | - Bibek GC
- Department
of Microbiology & Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Chenggang Wu
- Department
of Microbiology & Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Dianqing Sun
- Department
of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii 96720, United States
| | - Kirk E. Hevener
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Julian G. Hurdle
- Center
for Infectious and Inflammatory Diseases, Institute of Biosciences
and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
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5
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Ponath F, Zhu Y, Vogel J. Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σ E-dependent small RNA with unusual mRNA activation activity. mBio 2024; 15:e0353623. [PMID: 38436569 PMCID: PMC11005410 DOI: 10.1128/mbio.03536-23] [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: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 03/05/2024] Open
Abstract
The oral commensal Fusobacterium nucleatum can spread to extra-oral sites, where it is associated with diverse pathologies, including pre-term birth and cancer. Due to the evolutionary distance of F. nucleatum to other model bacteria, we lack a deeper understanding of the RNA regulatory networks that allow this bacterium to adapt to its various niches. As a first step in that direction, we recently showed that F. nucleatum harbors a global stress response governed by the extracytoplasmic function sigma factor, σE, which displays a striking functional conservation with Proteobacteria and includes a noncoding arm in the form of a regulatory small RNA (sRNA), FoxI. To search for putative additional σE-dependent sRNAs, we comprehensively mapped the 5' and 3' ends of transcripts in the model strain ATCC 23726. This enabled the discovery of FoxJ, a ~156-nucleotide sRNA previously misannotated as the 5' untranslated region (UTR) of ylmH. FoxJ is tightly controlled by σE and activated by the same stress conditions as is FoxI. Both sRNAs act as mRNA repressors of the abundant porin FomA, but FoxJ also regulates genes that are distinct from the target suite of FoxI. Moreover, FoxJ differs from other σE-dependent sRNAs in that it also positively regulates genes at the post-transcriptional level. We provide preliminary evidence for a new mode of sRNA-mediated mRNA activation, which involves the targeting of intra-operonic terminators. Overall, our study provides an important resource through the comprehensive annotation of 5' and 3' UTRs in F. nucleatum and expands our understanding of the σE response in this evolutionarily distant bacterium.IMPORTANCEThe oral microbe Fusobacterium nucleatum can colonize secondary sites, including cancer tissue, and likely deploys complex regulatory systems to adapt to these new environments. These systems are largely unknown, partly due to the phylogenetic distance of F. nucleatum to other model organisms. Previously, we identified a global stress response mediated by σE that displays functional conservation with the envelope stress response in Proteobacteria, comprising a coding and noncoding regulatory arm. Through global identification of transcriptional start and stop sites, we uncovered the small RNA (sRNA) FoxJ as a novel component of the noncoding arm of the σE response in F. nucleatum. Together with its companion sRNA FoxI, FoxJ post-transcriptionally modulates the synthesis of envelope proteins, revealing a conserved function for σE-dependent sRNAs between Fusobacteriota and Proteobacteria. Moreover, FoxJ activates the gene expression for several targets, which is a mode of regulation previously unseen in the noncoding arm of the σE response.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Yan Zhu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
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Pena MM, Martins TZ, Teper D, Zamuner C, Alves HA, Ferreira H, Wang N, Ferro MIT, Ferro JA. EnvC Homolog Encoded by Xanthomonas citri subsp. citri Is Necessary for Cell Division and Virulence. Microorganisms 2024; 12:691. [PMID: 38674634 PMCID: PMC11051873 DOI: 10.3390/microorganisms12040691] [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: 10/09/2023] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Peptidoglycan hydrolases are enzymes responsible for breaking the peptidoglycan present in the bacterial cell wall, facilitating cell growth, cell division and peptidoglycan turnover. Xanthomonas citri subsp. citri (X. citri), the causal agent of citrus canker, encodes an Escherichia coli M23 peptidase EnvC homolog. EnvC is a LytM factor essential for cleaving the septal peptidoglycan, thereby facilitating the separation of daughter cells. In this study, the investigation focused on EnvC contribution to the virulence and cell separation of X. citri. It was observed that disruption of the X. citri envC gene (ΔenvC) led to a reduction in virulence. Upon inoculation into leaves of Rangpur lime (Citrus limonia Osbeck), the X. citri ΔenvC exhibited a delayed onset of citrus canker symptoms compared with the wild-type X. citri. Mutant complementation restored the wild-type phenotype. Sub-cellular localization confirmed that X. citri EnvC is a periplasmic protein. Moreover, the X. citri ΔenvC mutant exhibited elongated cells, indicating a defect in cell division. These findings support the role of EnvC in the regulation of cell wall organization, cell division, and they clarify the role of this peptidase in X. citri virulence.
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Affiliation(s)
- Michelle M. Pena
- Agricultural and Livestock Microbiology Graduation Program, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil; (M.M.P.); (T.Z.M.)
| | - Thaisa Z. Martins
- Agricultural and Livestock Microbiology Graduation Program, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil; (M.M.P.); (T.Z.M.)
| | - Doron Teper
- Department of Plant Pathology and Weed Research, Institute of Plant Protection Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion 7505101, Israel;
| | - Caio Zamuner
- Biochemistry Building, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro 13506-900, SP, Brazil; (C.Z.); (H.F.)
| | - Helen A. Alves
- Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil; (H.A.A.); (M.I.T.F.)
| | - Henrique Ferreira
- Biochemistry Building, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro 13506-900, SP, Brazil; (C.Z.); (H.F.)
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, USA;
| | - Maria Inês T. Ferro
- Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil; (H.A.A.); (M.I.T.F.)
| | - Jesus A. Ferro
- Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil; (H.A.A.); (M.I.T.F.)
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7
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Zhou P, G. C. B, Stolte F, Wu C. Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum. Appl Environ Microbiol 2024; 90:e0166523. [PMID: 38185820 PMCID: PMC10880640 DOI: 10.1128/aem.01665-23] [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: 09/19/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Gene inactivation by creating in-frame deletion mutations in Fusobacterium nucleatum is time consuming, and most fusobacterial strains are genetically intractable. Addressing these problems, we introduced a riboswitch-based inducible CRISPR interference (CRISPRi) system. This system employs the nuclease-inactive Streptococcus pyogenes Cas9 protein (dCas9), specifically guided to the gene of interest by a constantly expressed single-guide RNA (sgRNA). Mechanistically, this dCas9-sgRNA complex serves as an insurmountable roadblock for RNA polymerase, thus repressing the target gene transcription. Leveraging this system, we first examined two non-essential genes, ftsX and radD, which are pivotal for fusobacterial cytokinesis and coaggregation. Upon adding the inducer, theophylline, ftsX suppression caused filamentous cell formation akin to chromosomal ftsX deletion, while targeting radD significantly reduced RadD protein levels, abolishing RadD-mediated coaggregation. The system was then extended to probe essential genes bamA and ftsZ, which are vital for outer membrane biogenesis and cell division. Impressively, bamA suppression disrupted membrane integrity and bacterial separation, stalling growth, while ftsZ targeting yielded elongated cells in broth with compromised agar growth. Further studies on F. nucleatum clinical strain CTI-2 and Fusobacterium periodonticum revealed reduced indole synthesis when targeting tnaA. Moreover, silencing clpB in F. periodonticum decreased ClpB, increasing thermal sensitivity. In summary, our CRISPRi system streamlines gene inactivation across various fusobacterial strains.IMPORTANCEHow can we effectively investigate the gene functions in Fusobacterium nucleatum, given the dual challenges of gene inactivation and the inherent genetic resistance of many strains? Traditional methods have been cumbersome and often inadequate. Addressing this, our work introduces a novel inducible CRISPR interference (CRISPRi) system in which dCas9 expression is controlled at the translation level by a theophylline-responsive riboswitch unit, and single-guide RNA expression is driven by the robust, constitutive rpsJ promoter. This approach simplifies gene inactivation in the model organism (ATCC 23726) and extends its application to previously considered genetically intractable strains like CTI-2 and Fusobacterium periodonticum. With CRISPRi's potential, it is a pivotal tool for in-depth genetic studies into fusobacterial pathogenesis, potentially unlocking targeted therapeutic strategies.
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Affiliation(s)
- Peng Zhou
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Bibek G. C.
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Flynn Stolte
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
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8
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Britton TA, Wu C, Chen YW, Franklin D, Chen Y, Camacho MI, Luong TT, Das A, Ton-That H. The respiratory enzyme complex Rnf is vital for metabolic adaptation and virulence in Fusobacterium nucleatum. mBio 2024; 15:e0175123. [PMID: 38059640 PMCID: PMC10790702 DOI: 10.1128/mbio.01751-23] [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: 07/06/2023] [Accepted: 10/20/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE This paper illuminates the significant question of how the oral commensal Fusobacterium nucleatum adapts to the metabolically changing environments of several extra-oral sites such as placenta and colon to promote various diseases as an opportunistic pathogen. We demonstrate here that the highly conserved Rhodobacter nitrogen-fixation complex, commonly known as Rnf complex, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of this Rnf complex causes global defects in polymicrobial interaction, biofilm formation, cell growth and morphology, hydrogen sulfide production, and ATP synthesis. Targeted metabolomic profiling demonstrates that the loss of this respiratory enzyme significantly diminishes catabolism of numerous amino acids, which negatively impacts fusobacterial virulence as tested in a preterm birth model in mice.
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Affiliation(s)
- Timmie A. Britton
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, University of Texas McGovern Medical School, Houston, Texas, USA
| | - Yi-Wei Chen
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Dana Franklin
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Yimin Chen
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Martha I. Camacho
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Truc T. Luong
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
| | - Asis Das
- Department of Medicine, Neag Comprehensive Cancer Center, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Hung Ton-That
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Division of Oral & Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, California, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, California, USA
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9
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Chen Z, Jin W, Hoover A, Chao Y, Ma Y. Decoding the microbiome: advances in genetic manipulation for gut bacteria. Trends Microbiol 2023; 31:1143-1161. [PMID: 37394299 DOI: 10.1016/j.tim.2023.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 07/04/2023]
Abstract
Studies of the gut microbiota have revealed associations between specific bacterial species or community compositions with health and disease, yet the causal mechanisms underlying microbiota gene-host interactions remain poorly understood. This is partly due to limited genetic manipulation (GM) tools for gut bacteria. Here, we review current advances and challenges in the development of GM approaches, including clustered regularly interspaced short palindromic repeats (CRISPR)-Cas and transposase-based systems in either model or non-model gut bacteria. By overcoming barriers to 'taming' the gut microbiome, GM tools allow molecular understanding of host-microbiome associations and accelerate microbiome engineering for clinical treatment of cancer and metabolic disorders. Finally, we provide perspectives on the future development of GM for gut microbiome species, where more effort should be placed on assembling a generalized GM pipeline to accelerate the application of groundbreaking GM tools in non-model gut bacteria towards both basic understanding and clinical translation.
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Affiliation(s)
- Ziying Chen
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200031, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200031, China; The Center for Microbes, Development and Health (CMDH), CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenbing Jin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Alex Hoover
- Ben May Department for Cancer Research, the University of Chicago, Chicago, IL, USA
| | - Yanjie Chao
- The Center for Microbes, Development and Health (CMDH), CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200031, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200031, China.
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Monteith W, Pascoe B, Mourkas E, Clark J, Hakim M, Hitchings MD, McCarthy N, Yahara K, Asakura H, Sheppard SK. Contrasting genes conferring short- and long-term biofilm adaptation in Listeria. Microb Genom 2023; 9:001114. [PMID: 37850975 PMCID: PMC10634452 DOI: 10.1099/mgen.0.001114] [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: 06/22/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Listeria monocytogenes is an opportunistic food-borne bacterium that is capable of infecting humans with high rates of hospitalization and mortality. Natural populations are genotypically and phenotypically variable, with some lineages being responsible for most human infections. The success of L. monocytogenes is linked to its capacity to persist on food and in the environment. Biofilms are an important feature that allow these bacteria to persist and infect humans, so understanding the genetic basis of biofilm formation is key to understanding transmission. We sought to investigate the biofilm-forming ability of L. monocytogenes by identifying genetic variation that underlies biofilm formation in natural populations using genome-wide association studies (GWAS). Changes in gene expression of specific strains during biofilm formation were then investigated using RNA sequencing (RNA-seq). Genetic variation associated with enhanced biofilm formation was identified in 273 genes by GWAS and differential expression in 220 genes by RNA-seq. Statistical analyses show that the number of overlapping genes flagged by either type of experiment is less than expected by random sampling. This novel finding is consistent with an evolutionary scenario where rapid adaptation is driven by variation in gene expression of pioneer genes, and this is followed by slower adaptation driven by nucleotide changes within the core genome.
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Affiliation(s)
- William Monteith
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biology, University of Bath, Claverton Down, Bath, UK
| | - Ben Pascoe
- Department of Biology, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | | | - Jack Clark
- Department of Genetics, University of Leicester, University Road, Leicester, UK
| | - Maliha Hakim
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Matthew D. Hitchings
- Swasnsea University Medical School, Swansea University, Singleton Campus, Swansea, UK
| | - Noel McCarthy
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, Tonomachi 3-25-26, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
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11
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G C B, Zhou P, Naha A, Gu J, Wu C. Development of a xylose-inducible promoter and riboswitch combination system for manipulating gene expression in Fusobacterium nucleatum. Appl Environ Microbiol 2023; 89:e0066723. [PMID: 37695289 PMCID: PMC10537658 DOI: 10.1128/aem.00667-23] [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: 04/21/2023] [Accepted: 07/05/2023] [Indexed: 09/12/2023] Open
Abstract
Inducible gene expression systems are important for studying bacterial gene function, yet most exhibit leakage. In this study, we engineered a leakage-free hybrid system for precise gene expression controls in Fusobacterium nucleatum by integrating the xylose-inducible expression system with the theophylline-responsive riboswitch. This innovative method enables concurrent control of target gene expression at both transcription and translation initiation levels. Using luciferase and the indole-producing enzyme tryptophanase (TnaA) as reporters, we demonstrated that the hybrid system displays virtually no observable signal in the absence of inducers. We employed this system to express FtsX, a protein related to fusobacterial cytokinesis, in an ftsX mutant strain, unveiling a dose-dependent manner in FtsX production. Without inducers, cells form long filaments, while increasing FtsX levels by increasing inducer concentrations led to a gradual reduction in cell length until normal morphology was restored. Crucially, this system facilitated essential gene investigation, identifying the signal peptidase lepB gene as vital for F. nucleatum. LepB's essentiality stems from depletion, affecting outer membrane biogenesis and cell division. This novel hybrid system holds the potential for advancing research on essential genes and accurate gene regulation in F. nucleatum. IMPORTANCE Fusobacterium nucleatum, an anaerobic bacterium prevalent in the human oral cavity, is strongly linked to periodontitis and can colonize areas beyond the oral cavity, such as the placenta and gastrointestinal tract, causing adverse pregnancy outcomes and promoting colorectal cancer growth. Given F. nucleatum's clinical significance, research is underway to develop targeted therapies to inhibit its growth or eradicate the bacterium specifically. Essential genes, crucial for bacterial survival, growth, and reproduction, are promising drug targets. A leak-free-inducible gene expression system is needed for studying these genes, enabling conditional gene knockouts and elucidating the importance of those essential genes. Our study identified lepB as the essential gene by first generating a conditional gene mutation in F. nucleatum. Combining a xylose-inducible system with a riboswitch facilitated the analysis of essential genes in F. nucleatum, paving the way for potential drug development targeting this bacterium for various clinical applications.
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Affiliation(s)
- Bibek G C
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Peng Zhou
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Arindam Naha
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Jianhua Gu
- Houston Methodist Hospital Research Institute, Houston, Texas, USA
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
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12
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Zhou P, G C B, Stolte F, Wu C. Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558491. [PMID: 37781593 PMCID: PMC10541141 DOI: 10.1101/2023.09.19.558491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Gene inactivation via creating in-frame deletion mutations in Fusobacterium nucleatum is time-consuming, and most fusobacterial strains are genetically intractable. Addressing these problems, we introduced a riboswitch-based inducible CRISPRi system. This system employs the nuclease-inactive Streptococcus pyogenes Cas9 protein (dCas9), specifically guided to the gene of interest by a constantly expressed single guide RNA (sgRNA). Mechanistically, this dCas9-sgRNA complex serves as an insurmountable roadblock for RNA polymerase, thus repressing the target gene transcription. Leveraging this system, we first examined two non-essential genes, ftsX, and radD , pivotal for fusobacterial cytokinesis and coaggregation. Upon adding the inducer, theophylline, ftsX suppression caused filamentous cell formation akin to chromosomal ftsX deletion, while targeting radD significantly reduced RadD protein levels, abolishing coaggregation. The system was then extended to probe essential genes bamA and ftsZ , vital for outer membrane biogenesis and cell division. Impressively, bamA suppression disrupted membrane integrity and bacterial separation, stalling growth, while ftsZ- targeting yielded elongated cells in broth with compromised agar growth. Further studies on F. nucleatum clinical strain CTI-2 and Fusobacterium periodonticum revealed reduced indole synthesis when targeting tnaA . Moreover, silencing clpB in F. periodonticum decreased ClpB, increasing thermal sensitivity. In summary, our CRISPRi system streamlines gene inactivation across various fusobacterial strains. IMPORTANCE How can we effectively investigate the gene functions in Fusobacterium nucleatum , given the dual challenges of gene inactivation and the inherent genetic resistance of many strains? Traditional methods have been cumbersome and often inadequate. Addressing this, our work introduces a novel inducible CRISPRi system in which dCas9 expression is controlled at the translation level by a theophylline-responsive riboswitch unit, and sgRNA expression is driven by the robust, constitutive rpsJ promoter. This approach simplifies gene inactivation in the model organism (ATCC 23726) and extends its application to previously considered resistant strains like CTI-2 and Fusobacterium periodontium . With CRISPRi's potential, it is a pivotal tool for in-depth genetic studies into fusobacterial pathogenesis, potentially unlocking targeted therapeutic strategies.
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13
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GC B, Zhou P, Wu C. HicA Toxin-Based Counterselection Marker for Allelic Exchange Mutations in Fusobacterium nucleatum. Appl Environ Microbiol 2023; 89:e0009123. [PMID: 37039662 PMCID: PMC10132090 DOI: 10.1128/aem.00091-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/20/2023] [Indexed: 04/12/2023] Open
Abstract
The study of fusobacterial virulence factors has dramatically benefited from the creation of various genetic tools for DNA manipulation, including galK-based counterselection for in-frame deletion mutagenesis in Fusobacterium nucleatum, which was recently developed. However, this method requires a host lacking the galK gene, which is an inherent limitation. To circumvent this limitation, we explored the possibility of using the hicA gene that encodes a toxin consisting of a HicAB toxin-antitoxin module in Fusobacterium periodonticum as a new counterselective marker. Interestingly, the full-length hicA gene is not toxic in F. nucleatum, but a truncated hicA gene version lacking the first six amino acids is functional as a toxin. The toxin expression is driven by an rpsJ promoter and is controlled at its translational level by using a theophylline-responsive riboswitch unit. As a proof of concept, we created markerless in-frame deletions in the fusobacterial adhesin radD gene within the F. nucleatum rad operon and the tnaA gene that encodes the tryptophanase for indole production. After vector integration, plasmid excision after counterselection appeared to have occurred in 100% of colonies grown on theophylline-added plates and resulted in in-frame deletions in 50% of the screened isolates. This hicA-based counterselection system provides a robust and reliable counterselection in wild-type background F. nucleatum and should also be adapted for use in other bacteria. IMPORTANCE Fusobacterium nucleatum is an indole-producing human oral anaerobe associated with periodontal diseases, preterm birth, and several cancers. Little is known about the mechanisms of fusobacterial pathogenesis and associated factors, mainly due to the lack of robust genetic tools for this organism. Here, we showed that a mutated hicA gene from Fusobacterium periodonticum expresses an active toxin and was used as a counterselection marker. This hicA-based in-frame deletion system efficiently creates in-frame deletion mutations in the wild-type background of F. nucleatum. This is the first report to use the hicA gene as a counterselection marker in a bacterial genetic study.
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Affiliation(s)
- Bibek GC
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Peng Zhou
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Chenggang Wu
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
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14
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Bibek GC, Zhou P, Naha A, Gu J, Wu C. Development of a Xylose-Inducible Promoter and Riboswitch Combination System for Manipulating Gene Expression in Fusobacterium nucleatum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538132. [PMID: 37163003 PMCID: PMC10168284 DOI: 10.1101/2023.04.24.538132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Inducible gene expression systems are important for studying bacterial gene function, yet most exhibit leakage. In this study, we engineered a leakage-free hybrid system for precise gene expression controls in Fusobacterium nucleatum by integrating the xylose-inducible expression system with the theophylline-responsive riboswitch. This innovative method enables concurrent control of target gene expression at both transcription and translation initiation levels. Using luciferase and the indole-producing enzyme tryptophanase (TnaA) as reporters, we demonstrated that the hybrid system displays virtually no observable signal in the absence of inducers. We employed this system to express FtsX, a protein related to fusobacterial cytokinesis, in an ftsX mutant strain, unveiling a dose-dependent manner in FtsX production. Without inducers, cells form long filaments, while increasing FtsX levels by increasing inducers concentrations led to a gradual reduction in cell length until normal morphology was restored. Crucially, this system facilitated essential gene investigation, identifying the signal peptidase lepB gene as vital for F. nucleatum . LepB's essentiality stems from depletion, affecting outer membrane biogenesis and cell division. This novel hybrid system holds the potential for advancing research on essential genes and accurate gene regulation in F. nucleatum .
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15
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Enhanced Fusobacterium nucleatum Genetics Using Host DNA Methyltransferases To Bypass Restriction-Modification Systems. J Bacteriol 2022; 204:e0027922. [PMID: 36326270 PMCID: PMC9764991 DOI: 10.1128/jb.00279-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial restriction-modification (R-M) systems are a first-line immune defense against foreign DNA from viruses and other bacteria. While R-M systems are critical in maintaining genome integrity, R-M nucleases unfortunately present significant barriers to targeted genetic modification. Bacteria of the genus Fusobacterium are oral, Gram-negative, anaerobic, opportunistic pathogens that are implicated in the progression and severity of multiple cancers and tissue infections, yet our understanding of their direct roles in disease have been severely hindered by their genetic recalcitrance. Here, we demonstrate a path to overcome these barriers in Fusobacterium by using native DNA methylation as a host mimicry strategy to bypass R-M system cleavage of transformed plasmid DNA. We report the identification, characterization, and successful use of Fusobacterium nucleatum type II and III DNA methyltransferase (MTase) enzymes to produce a multifold increase in gene knockout efficiency in the strain Fusobacterium nucleatum subsp. nucleatum 23726, as well as the first system for efficient gene knockouts and complementations in F. nucleatum subsp. nucleatum 25586. We show plasmid protection can be accomplished in vitro with purified enzymes, as well as in vivo in an Escherichia coli host that constitutively expresses F. nucleatum subsp. nucleatum MTase enzymes. In summary, this proof-of-concept study characterizes specific MTases that are critical for bypassing R-M systems and has enhanced our understanding of enzyme combinations that could be used to genetically modify clinical isolates of Fusobacterium that have thus far been inaccessible to molecular characterization. IMPORTANCE Fusobacterium nucleatum is an oral opportunistic pathogen associated with diseases that include cancer and preterm birth. Our understanding of how this bacterium modulates human disease has been hindered by a lack of genetic systems. Here, we show that F. nucleatum DNA methyltransferase-modified plasmid DNA overcomes the transformation barrier and has allowed the development of a genetic system in a previously inaccessible strain. We present a strategy that could potentially be expanded to enable the genetic modification of highly recalcitrant strains, thereby fostering investigational studies to uncover novel host-pathogen interactions in Fusobacterium.
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Ponath F, Zhu Y, Cosi V, Vogel J. Expanding the genetic toolkit helps dissect a global stress response in the early-branching species Fusobacterium nucleatum. Proc Natl Acad Sci U S A 2022; 119:e2201460119. [PMID: 36161895 PMCID: PMC9546586 DOI: 10.1073/pnas.2201460119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/13/2022] [Indexed: 11/18/2022] Open
Abstract
Fusobacterium nucleatum, long known as a common oral microbe, has recently garnered attention for its ability to colonize tissues and tumors elsewhere in the human body. Clinical and epidemiological research has now firmly established F. nucleatum as an oncomicrobe associated with several major cancer types. However, with the current research focus on host associations, little is known about gene regulation in F. nucleatum itself, including global stress-response pathways that typically ensure the survival of bacteria outside their primary niche. This is due to the phylogenetic distance of Fusobacteriota to most model bacteria, their limited genetic tractability, and paucity of known gene functions. Here, we characterize a global transcriptional stress-response network governed by the extracytoplasmic function sigma factor, σE. To this aim, we developed several genetic tools for this anaerobic bacterium, including four different fluorescent marker proteins, inducible gene expression, scarless gene deletion, and transcriptional and translational reporter systems. Using these tools, we identified a σE response partly reminiscent of phylogenetically distant Proteobacteria but induced by exposure to oxygen. Although F. nucleatum lacks canonical RNA chaperones, such as Hfq, we uncovered conservation of the noncoding arm of the σE response in form of the noncoding RNA FoxI. This regulatory small RNA acts as an mRNA repressor of several membrane proteins, thereby supporting the function of σE. In addition to the characterization of a global stress response in F. nucleatum, the genetic tools developed here will enable further discoveries and dissection of regulatory networks in this early-branching bacterium.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, D-97080 Germany
| | - Yan Zhu
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, D-97080 Germany
| | - Valentina Cosi
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, D-97080 Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, D-97080 Germany
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, D-97080 Germany
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Al Mamun AAM, Wu C, Chang C, Sanchez BC, Das A, Ton-That H. A cell wall-anchored glycoprotein confers resistance to cation stress in Actinomyces oris biofilms. Mol Oral Microbiol 2022; 37:206-217. [PMID: 35289506 PMCID: PMC9474737 DOI: 10.1111/omi.12365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/27/2022] [Accepted: 03/11/2022] [Indexed: 11/26/2022]
Abstract
Actinomyces oris plays an important role in oral biofilm development. Like many gram-positive bacteria, A. oris produces a sizable number of surface proteins that are anchored to bacterial peptidoglycan by a conserved transpeptidase named the housekeeping sortase SrtA; however, the biological role of many A. oris surface proteins in biofilm formation is largely unknown. Here, we report that the glycoprotein GspA-a genetic suppressor of srtA deletion lethality-not only promotes biofilm formation but also maintains cell membrane integrity under cation stress. In comparison to wild-type cells, under elevated concentrations of mono- and divalent cations the formation of mono- and multi-species biofilms by mutant cells devoid of gspA was significantly diminished, although planktonic growth of both cell types in the presence of cations was indistinguishable. Because gspA overexpression is lethal to cells lacking gspA and srtA, we performed a genetic screen to identify GspA determinants involving cell viability. DNA sequencing and biochemical characterizations of viable clones revealed that mutations of two critical cysteine residues and a serine residue severely affected GspA glycosylation and biofilm formation. Furthermore, mutant cells lacking gspA were markedly sensitive to sodium dodecyl sulfate, a detergent that solubilizes the cytoplasmic membranes, suggesting the cell envelope of the gspA mutant was altered. Consistent with this observation, the gspA mutant exhibited increased membrane permeability, independent of GspA glycosylation, compared to the wild-type strain. Altogether, the results support the notion that the cell wall-anchored glycoprotein GspA provides a defense mechanism against cation stress in biofilm development promoted by A. oris.
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Affiliation(s)
- Abu Amar M. Al Mamun
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Chungyu Chang
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Belkys C. Sanchez
- Department of Microbiology & Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - Asis Das
- Department of Medicine, Neag Comprehensive Cancer Center, University of Connecticut Health Center, Farmington, CT, USA
| | - Hung Ton-That
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
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18
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Genetic Determinants of Hydrogen Sulfide Biosynthesis in Fusobacterium nucleatum Are Required for Bacterial Fitness, Antibiotic Sensitivity, and Virulence. mBio 2022; 13:e0193622. [PMID: 36073813 PMCID: PMC9600241 DOI: 10.1128/mbio.01936-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gram-negative anaerobe Fusobacterium nucleatum is a major producer of hydrogen sulfide (H2S), a volatile sulfur compound that causes halitosis. Here, we dissected the genetic determinants of H2S production and its role in bacterial fitness and virulence in this important member of the oral microbiome. F. nucleatum possesses four enzymes, CysK1, CysK2, Hly, and MegL, that presumably metabolize l-cysteine to H2S, and CysK1 was previously shown to account for most H2S production in vitro, based on correlations of enzymatic activities with gene expression at mid-log phase. Our molecular studies showed that cysK1 and megL were highly expressed at the late exponential growth phase, concomitant with high-level H2S production, while the expression levels of the other genes remained substantially lower during all growth phases. Although the genetic deletion of cysK1 without supplementation with a CysK1-catalyzed product, lanthionine, caused cell death, the conditional ΔcysK1 mutant and a mutant lacking hly were highly proficient in H2S production. In contrast, a mutant devoid of megL showed drastically reduced H2S production, and a cysK2 mutant showed only minor deficiencies. Intriguingly, the exposure of these mutants to various antibiotics revealed that only the megL mutant displayed altered susceptibility compared to the parental strain: partial sensitivity to nalidixic acid and resistance to kanamycin. Most significantly, the megL mutant was attenuated in virulence in a mouse model of preterm birth, with considerable defects in the spread to amniotic fluid and the colonization of the placenta and fetus. Evidently, the l-methionine γ-lyase MegL is a major H2S-producing enzyme in fusobacterial cells that significantly contributes to fusobacterial virulence and antibiotic susceptibility.
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Huo RX, Wang YJ, Hou SB, Wang W, Zhang CZ, Wan XH. Gut mucosal microbiota profiles linked to colorectal cancer recurrence. World J Gastroenterol 2022; 28:1946-1964. [PMID: 35664963 PMCID: PMC9150055 DOI: 10.3748/wjg.v28.i18.1946] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/01/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Emerging evidence links gut microbiota to various human diseases including colorectal cancer (CRC) initiation and development. However, gut microbiota profiles associated with CRC recurrence and patient prognosis are not completely understood yet, especially in a Chinese cohort. AIM To investigate the relationship between gut mucosal microbiota profiles and CRC recurrence and patient prognosis. METHODS We obtained the composition and structure of gut microbiota collected from 75 patients diagnosed with CRC and 26 healthy controls. The patients were followed up by regular examination to determine whether tumors recurred. Triplet-paired samples from on-tumor, adjacent-tumor and off-tumor sites of patients diagnosed with/without CRC recurrence were analyzed to assess spatial-specific patterns of gut mucosal microbiota by 16S ribosomal RNA sequencing. Next, we carried out bioinformatic analyses, Kaplan-Meier survival analyses and Cox regression analyses to determine the relationship between gut mucosal microbiota profiles and CRC recurrence and patient prognosis. RESULTS We observed spatial-specific patterns of gut mucosal microbiota profiles linked to CRC recurrence and patient prognosis. A total of 17 bacterial genera/families were identified as potential biomarkers for CRC recurrence and patient prognosis, including Anaerotruncus, Bacteroidales, Coriobacteriaceae, Dialister, Eubacterium, Fusobacterium, Filifactor, Gemella, Haemophilus, Mogibacteriazeae, Pyramidobacter, Parvimonas, Porphyromonadaceae, Slackia, Schwartzia, TG5 and Treponema. CONCLUSION Our work suggests that intestinal microbiota can serve as biomarkers to predict the risk of CRC recurrence and patient death.
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Affiliation(s)
- Rui-Xue Huo
- Department of Oncology, Tianjin Union Medical Center, Nankai University, Tianjin 300121, China
| | - Yi-Jia Wang
- Laboratory of Oncologic Molecular Medicine, Tianjin Union Medical Center, Nankai University, Tianjin 300121, China
| | - Shao-Bin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii at Manoa, Honolulu, HI 96822, United States
| | - Wei Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Chun-Ze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Nankai University, Tianjin 300121, China
- Tianjin Institute of Coloproctology, Tianjin 300121, China
| | - Xue-Hua Wan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
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The Fused Methionine Sulfoxide Reductase MsrAB Promotes Oxidative Stress Defense and Bacterial Virulence in Fusobacterium nucleatum. mBio 2022; 13:e0302221. [PMID: 35420473 PMCID: PMC9239216 DOI: 10.1128/mbio.03022-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Fusobacterium nucleatum, an anaerobic Gram-negative bacterium frequently found in the human oral cavity and some extra-oral sites, is implicated in several important diseases: periodontitis, adverse pregnancy outcomes, and colorectal cancer. To date, how this obligate anaerobe copes with oxidative stress and host immunity within multiple human tissues remains unknown. Here, we uncovered a critical role in this process of a multigene locus encoding a single, fused methionine sulfoxide reductase (MsrAB), a two-component signal transduction system (ModRS), and thioredoxin (Trx)- and cytochrome c (CcdA)-like proteins, which are induced when fusobacterial cells are exposed to hydrogen peroxide. Comparative transcriptome analysis revealed that the response regulator ModR regulates a large regulon that includes trx, ccdA, and many metabolic genes. Significantly, specific mutants of the msrAB locus, including msrAB, are sensitive to reactive oxygen species and defective in adherence/invasion of colorectal epithelial cells. Strikingly, the msrAB mutant is also defective in survival in macrophages, and it is severely attenuated in virulence in a mouse model of preterm birth, consistent with its failure to spread to the amniotic fluid and colonize the placenta. Clearly, the MsrAB system regulated by the two-component system ModRS represents a major oxidative stress defense pathway that protects fusobacteria against oxidative damage in immune cells and confers virulence by enabling attachment and invasion of multiple target tissues. IMPORTANCE F. nucleatum colonizes various human tissues, including oral cavity, placenta, and colon. How this obligate anaerobe withstands oxidative stress in host immune cells has not been described. We report here that F. nucleatum possesses a five-gene locus encoding a fused methionine sulfoxide reductase (MsrAB), a two-component signal transduction system (ModRS), and thioredoxin- and cytochrome c-like proteins. Regulated by ModRS, MsrAB is essential for resistance to reactive oxygen species, adherence/invasion of colorectal epithelial cells, and survival in macrophage. Unable to colonize placenta and spread to amniotic fluid, the msrAB mutant failed to induce preterm birth in a murine model.
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21
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Abstract
Accumulating evidence demonstrates that the oral pathobiont Fusobacterium nucleatum is involved in the progression of an increasing number of tumors types. Thus far, the mechanisms underlying tumor exacerbation by F. nucleatum include the enhancement of proliferation, establishment of a tumor‐promoting immune environment, induction of chemoresistance, and the activation of immune checkpoints. This review focuses on the mechanisms that mediate tumor‐specific colonization by fusobacteria. Elucidating the mechanisms mediating fusobacterial tumor tropism and promotion might provide new insights for the development of novel approaches for tumor detection and treatment.
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Affiliation(s)
- Tamar Alon-Maimon
- The Institute of Dental Sciences, The Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Ofer Mandelboim
- The Concern Foundation Laboratories, Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research, Institute for Medical Research Israel Canada (IMRIC), Faculty of Medicine, The Hebrew University Medical School, Jerusalem, Israel
| | - Gilad Bachrach
- The Institute of Dental Sciences, The Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
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22
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Alcorlo M, Martínez-Caballero S, Molina R, Hermoso JA. Regulation of Lytic Machineries by the FtsEX Complex in the Bacterial Divisome. Subcell Biochem 2022; 99:285-315. [PMID: 36151380 DOI: 10.1007/978-3-031-00793-4_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The essential membrane complex FtsE/FtsX (FtsEX), belonging to the ABC transporter superfamily and widespread among bacteria, plays a relevant function in some crucial cell wall remodeling processes such as cell division, elongation, or sporulation. FtsEX plays a double role by recruiting proteins to the divisome apparatus and by regulating lytic activity of the cell wall hydrolases required for daughter cell separation. Interestingly, FtsEX does not act as a transporter but uses the ATPase activity of FtsE to mechanically transmit a signal from the cytosol, through the membrane, to the periplasm that activates the attached hydrolases. While the complete molecular details of such mechanism are not yet known, evidence has been recently reported that clarify essential aspects of this complex system. In this chapter we will present recent structural advances on this topic. The three-dimensional structure of FtsE, FtsX, and some of the lytic enzymes or their cognate regulators revealed an unexpected scenario in which a delicate set of intermolecular interactions, conserved among different bacterial genera, could be at the core of this regulatory mechanism providing exquisite control in both space and time of this central process to assist bacterial survival.
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Affiliation(s)
- Martín Alcorlo
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, Madrid, Spain
| | - Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, Madrid, Spain
- Department of Chemistry of Biomacromolecules, Universidade Nacional Autonoma de Mexico, Ciudad de México, Mexico
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, Madrid, Spain.
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23
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Zhang M, Lv Y, Hou S, Liu Y, Wang Y, Wan X. Differential Mucosal Microbiome Profiles across Stages of Human Colorectal Cancer. Life (Basel) 2021; 11:831. [PMID: 34440574 PMCID: PMC8401903 DOI: 10.3390/life11080831] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 02/06/2023] Open
Abstract
Emerging evidences link gut microbiota to colorectal cancer (CRC) initiation and development. However, the CRC stage- and spatial-specific bacterial taxa were less investigated, especially in a Chinese cohort, leading to our incomplete understanding of the functional roles of gut microbiota in promoting CRC progression and recurrence. Here, we report the composition and structure of gut microbiota across CRC stages I, II and III, by analyzing the gut mucosal microbiomes of 75 triplet-paired samples collected from on-tumor, adjacent-tumor and off-tumor sites and 26 healthy controls. We observed tumor-specific pattern of mucosal microbiome profiles as CRC progressed and identified ten bacterial taxa with high abundances (>1%) as potential biomarkers for tumor initiation and development. Peptostreptococcus and Parvimonas can serve as biomarkers for CRC stage I. Fusobacterium, Streptococcus, Parvimonas, Burkholderiales, Caulobacteraceae, Delftia and Oxalobacteraceae can serve as biomarkers for CRC stage II, while Fusobacterium, Burkholderiales, Caulobacteraceae, Oxalobacteraceae, Faecalibacterium and Sutterella can serve as biomarkers for CRC stage III. These biomarkers classified CRC stages I, II and III distinguished from each other with an area under the receiver-operating curve (AUC) > 0.5. Moreover, co-occurrence and co-excluding network analysis of these genera showed strong correlations in CRC stage I, which were subsequently reduced in CRC stages II and III. Our findings provide a reference index for stage-specific CRC diagnosis and suggest stage-specific roles of Peptostreptococcus, Fusobacterium, Streptococcus and Parvimonas in driving CRC progression.
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Affiliation(s)
- Mingqing Zhang
- Nankai University School of Medicine, Nankai University, Tianjin 300071, China;
- Tianjin Union Medical Center, Nankai University, Tianjin 300121, China; (Y.L.); (Y.L.)
| | - Yongming Lv
- Tianjin Union Medical Center, Nankai University, Tianjin 300121, China; (Y.L.); (Y.L.)
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI 96822, USA;
| | - Yanfei Liu
- Tianjin Union Medical Center, Nankai University, Tianjin 300121, China; (Y.L.); (Y.L.)
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yijia Wang
- Tianjin Union Medical Center, Nankai University, Tianjin 300121, China; (Y.L.); (Y.L.)
| | - Xuehua Wan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300071, China
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24
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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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25
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Genetic and molecular determinants of polymicrobial interactions in Fusobacterium nucleatum. Proc Natl Acad Sci U S A 2021; 118:2006482118. [PMID: 34074747 DOI: 10.1073/pnas.2006482118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A gram-negative colonizer of the oral cavity, Fusobacterium nucleatum not only interacts with many pathogens in the oral microbiome but also has the ability to spread to extraoral sites including placenta and amniotic fluid, promoting preterm birth. To date, however, the molecular mechanism of interspecies interactions-termed coaggregation-by F. nucleatum and how coaggregation affects bacterial virulence remain poorly defined. Here, we employed genome-wide transposon mutagenesis to uncover fusobacterial coaggregation factors, revealing the intertwined function of a two-component signal transduction system (TCS), named CarRS, and a lysine metabolic pathway in regulating the critical coaggregation factor RadD. Transcriptome analysis shows that CarR modulates a large regulon including radD and lysine metabolic genes, such as kamA and kamD, the expression of which are highly up-regulated in the ΔcarR mutant. Significantly, the native culture medium of ΔkamA or ΔkamD mutants builds up abundant amounts of free lysine, which blocks fusobacterial coaggregation with streptococci. Our demonstration that lysine-conjugated beads trap RadD from the membrane lysates suggests that lysine utilizes RadD as its receptor to act as a metabolic inhibitor of coaggregation. Lastly, using a mouse model of preterm birth, we show that fusobacterial virulence is significantly attenuated with the ΔkamA and ΔcarR mutants, in contrast to the enhanced virulence phenotype observed upon diminishing RadD (ΔradD or ΔcarS mutant). Evidently, F. nucleatum employs the TCS CarRS and environmental lysine to modulate RadD-mediated interspecies interaction, virulence, and nutrient acquisition to thrive in the adverse environment of oral biofilms and extraoral sites.
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26
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Peluso EA, Scheible M, Ton-That H, Wu C. Genetic Manipulation and Virulence Assessment of Fusobacterium nucleatum. ACTA ACUST UNITED AC 2021; 57:e104. [PMID: 32539234 DOI: 10.1002/cpmc.104] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Considered a commensal, the Gram-negative anaerobe Fusobacterium nucleatum is a key member of the oral microbiome due to its wide range of interactions with many oral microbes. While the periodontal pathogenic properties of this organism have widely been examined, its connotation with extra-oral infections, including preterm birth and colorectal cancer, has now become apparent. Nonetheless, little is known about the mechanisms of pathogenicity and the associated virulence factors of F. nucleatum, most likely due to limited genetic tools and facile methodology. Here, we describe molecular techniques for the genetic manipulation of F. nucleatum, including markerless, nonpolar gene deletion, complementation, and Tn5 transposon mutagenesis. Further, we provide methodology to assess virulence potential of F. nucleatum using a mouse model of preterm birth. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Generation of a galK mutant strain Basic Protocol 2: Complementation of a mutant strain Basic Protocol 3: Tn5 transposon mutagenesis of F. nucleatum Basic Protocol 4: Mouse model of preterm birth.
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Affiliation(s)
- Emily A Peluso
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, California
| | - Matthew Scheible
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, California
| | - Hung Ton-That
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, California
| | - Chenggang Wu
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School, Houston, Texas
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27
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Li Q, Wang H, Tan L, Zhang S, Lin L, Tang X, Pan Y. Oral Pathogen Fusobacterium nucleatum Coaggregates With Pseudomonas aeruginosa to Modulate the Inflammatory Cytotoxicity of Pulmonary Epithelial Cells. Front Cell Infect Microbiol 2021; 11:643913. [PMID: 33816348 PMCID: PMC8017200 DOI: 10.3389/fcimb.2021.643913] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/02/2021] [Indexed: 12/22/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is the third leading cause of mortality worldwide, and inflammatory damage induced by bacterial infections is an important contributor to the etiology of COPD. Fusobacterium nucleatum, a recognized periodontal pathogen, is considered as a biomarker of lung function deterioration of COPD patients coinfected with Pseudomonas aerugionsa, but the underlying mechanism is still unclear. This study established single- and dual-species infection models, bacterial simultaneous and sequential infection models, and found that F. nucleatum could coaggregate with P. aeruginosa to synergistically invade into pulmonary epithelial cells and transiently resist P. aeruginosa-induced cytotoxic damage to amplify IL-6 and TNF-α associated inflammation in pulmonary epithelial cells simultaneously infected with P. aeruginosa and F. nucleatum. Furthermore, F. nucleatum pretreatment or subsequential infection could maintain or even aggravate P. aeruginosa-induced inflammatory cytotoxicity of pulmonary epithelial cells. These results indicate that oral pathogen F. nucleatum coaggregates with P. aeruginosa to facilitate bacterial invasion and modulates the inflammatory cytotoxicity of pulmonary epithelial cells, which may contribute to lung function deterioration of COPD patients accompanied with P. aeruginosa and F. nucleatum coinfection.
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Affiliation(s)
- Qian Li
- Liaoning Provincial Key Laboratory of Oral Diseases, Department of Oral Biology, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Hongyan Wang
- Liaoning Provincial Key Laboratory of Oral Diseases, Department of Periodontics, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Lisi Tan
- Liaoning Provincial Key Laboratory of Oral Diseases, Department of Periodontics, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Shuwei Zhang
- Liaoning Provincial Key Laboratory of Oral Diseases, Department of Periodontics, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Li Lin
- Liaoning Provincial Key Laboratory of Oral Diseases, Department of Periodontics, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Xiaolin Tang
- Liaoning Provincial Key Laboratory of Oral Diseases, Department of Periodontics, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Yaping Pan
- Liaoning Provincial Key Laboratory of Oral Diseases, Department of Oral Biology, School and Hospital of Stomatology, China Medical University, Shenyang, China.,Liaoning Provincial Key Laboratory of Oral Diseases, Department of Periodontics, School and Hospital of Stomatology, China Medical University, Shenyang, China
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28
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Arenas J, Zomer A, Harders-Westerveen J, Bootsma HJ, De Jonge MI, Stockhofe-Zurwieden N, Smith HE, De Greeff A. Identification of conditionally essential genes for Streptococcus suis infection in pigs. Virulence 2021; 11:446-464. [PMID: 32419603 PMCID: PMC7239030 DOI: 10.1080/21505594.2020.1764173] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Streptococcus suis is a Gram-positive bacterium and zoonotic pathogen that causes meningitis and sepsis in pigs and humans. The aim of this study was to identify genes required for S. suis infection. We created Tn-Seq libraries in a virulent S. suis strain 10, which was used to inoculate pigs in an intrathecal experimental infection. Comparative analysis of the relative abundance of mutants recovered from different sites of infection (blood, cerebrospinal fluid, and meninges of the brain) identified 361 conditionally essential genes, i.e. required for infection, which is about 18% of the genome. The conditionally essential genes were primarily involved in metabolic and transport processes, regulation, ribosomal structure and biogenesis, transcription, and cell wall membrane and envelope biogenesis, stress defenses, and immune evasion. Directed mutants were created in a set of 10 genes of different genetic ontologies and their role was determined in ex vivo models. Mutants showed different levels of sensitivity to survival in whole blood, serum, cerebrospinal fluid, thermic shock, and stress conditions, as compared to the wild type. Additionally, the role of three selected mutants was validated in co-infection experiments in which pigs were infected with both wild type and isogenic mutant strains. The genetic determinants of infection identified in this work contribute to novel insights in S. suis pathogenesis and could serve as targets for novel vaccines or antimicrobial drugs.
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Affiliation(s)
- Jesús Arenas
- Department of Infection Biology, Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands.,Unit of Microbiology and Immunology, Faculty of Veterinary, University of Zaragoza, Zaragoza, Spain
| | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud, Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Jose Harders-Westerveen
- Department of Infection Biology, Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Hester J Bootsma
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud, Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Marien I De Jonge
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud, Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | | | - Hilde E Smith
- Department of Infection Biology, Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Astrid De Greeff
- Department of Infection Biology, Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
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29
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Koike R, Cueno ME, Nodomi K, Tamura M, Kamio N, Tanaka H, Kotani A, Imai K. Heat-Killed Fusobacterium nucleatum Triggers Varying Heme-Related Inflammatory and Stress Responses Depending on Primary Human Respiratory Epithelial Cell Type. Molecules 2020; 25:molecules25173839. [PMID: 32847022 PMCID: PMC7504371 DOI: 10.3390/molecules25173839] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/14/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023] Open
Abstract
Fusobacterium nucleatum (Fn) is generally an opportunistic oral pathogen that adheres to mammalian mucosal sites, triggering a host inflammatory response. In general, Fn is normally found within the human oral cavity; however, it was previously reported that Fn is a risk factor for certain respiratory diseases. Surprisingly, this was never fully elucidated. Here, we investigated the virulence potential of heat-killed Fn on primary human tracheal, bronchial, and alveolar epithelial cells. In this study, we measured the secretion of inflammatory- (IL-8 and IL-6), stress- (total heme and hydrogen peroxide), and cell death-related (caspase-1 and caspase-3) signals. We established that the inflammatory response mechanism varies in each epithelial cell type: (1) along tracheal cells, possible Fn adherence would trigger increased heme secretion and regulated inflammatory response; (2) along bronchial cells, potential Fn adherence would simultaneously initiate an increase in secreted H2O2 and inflammatory response (ascribable to decreased secreted heme amounts); and (3) along alveolar cells, putative Fn adherence would instigate the increased secretion of inflammatory responses attributable to a decrease in secreted heme levels. Moreover, regardless of the epithelial cell-specific inflammatory mechanism, we believe these are putative, not harmful. Taken together, we propose that any potential Fn-driven inflammation along the respiratory tract would be initiated by differing epithelial cell-specific inflammatory mechanisms that are collectively dependent on secreted heme.
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Affiliation(s)
- Ryo Koike
- Division of Oral Structural and Functional Biology, Nihon University Graduate School of Dentistry, Tokyo 101-8310, Japan;
| | - Marni E. Cueno
- Department of Microbiology, Nihon University School of Dentistry, Tokyo 101-8310, Japan; (K.N.); (M.T.); (N.K.); (H.T.)
- Correspondence: (M.E.C.); (K.I.)
| | - Keiko Nodomi
- Department of Microbiology, Nihon University School of Dentistry, Tokyo 101-8310, Japan; (K.N.); (M.T.); (N.K.); (H.T.)
| | - Muneaki Tamura
- Department of Microbiology, Nihon University School of Dentistry, Tokyo 101-8310, Japan; (K.N.); (M.T.); (N.K.); (H.T.)
| | - Noriaki Kamio
- Department of Microbiology, Nihon University School of Dentistry, Tokyo 101-8310, Japan; (K.N.); (M.T.); (N.K.); (H.T.)
| | - Hajime Tanaka
- Department of Microbiology, Nihon University School of Dentistry, Tokyo 101-8310, Japan; (K.N.); (M.T.); (N.K.); (H.T.)
| | - Ai Kotani
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Kanagawa 259-1193, Japan;
| | - Kenichi Imai
- Department of Microbiology, Nihon University School of Dentistry, Tokyo 101-8310, Japan; (K.N.); (M.T.); (N.K.); (H.T.)
- Correspondence: (M.E.C.); (K.I.)
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30
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Abstract
The oral bacterium Fusobacterium nucleatum is often found in colorectal cancer (CRC). In the 21 July 2020 issue of Science Signaling, Casasanta et al show that CRC cell-resident F. nucleatum promotes cytokine secretion that may potentiate tumor growth and metastatic progression in patients.
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Affiliation(s)
- Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Departments of Genetics and Medicine, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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31
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Casasanta MA, Yoo CC, Udayasuryan B, Sanders BE, Umaña A, Zhang Y, Peng H, Duncan AJ, Wang Y, Li L, Verbridge SS, Slade DJ. Fusobacterium nucleatum host-cell binding and invasion induces IL-8 and CXCL1 secretion that drives colorectal cancer cell migration. Sci Signal 2020; 13:13/641/eaba9157. [PMID: 32694172 DOI: 10.1126/scisignal.aba9157] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fusobacterium nucleatum is implicated in accelerating colorectal cancer (CRC) and is found within metastatic CRC cells in patient biopsies. Here, we found that bacterial invasion of CRC cells and cocultured immune cells induced a differential cytokine secretion that may contribute to CRC metastasis. We used a modified galactose kinase markerless gene deletion approach and found that F. nucleatum invaded cultured HCT116 CRC cells through the bacterial surface adhesin Fap2. In turn, Fap2-dependent invasion induced the secretion of the proinflammatory cytokines IL-8 and CXCL1, which are associated with CRC progression and promoted HCT116 cell migration. Conditioned medium from F. nucleatum-infected HCT116 cells caused naïve cells to migrate, which was blocked by depleting CXCL1 and IL-8 from the conditioned medium. Cytokine secretion from HCT116 cells and cellular migration were attenuated by inhibiting F. nucleatum host-cell binding and entry using galactose sugars, l-arginine, neutralizing membrane protein antibodies, or fap2 deletion. F. nucleatum also induces the mobilization of immune cells in the tumor microenvironment. However, in neutrophils and macrophages, the bacterial-induced secretion of cytokines was Fap2 independent. Thus, our findings show that F. nucleatum both directly and indirectly modulates immune and cancer cell signaling and migration. Because increased IL-8 and CXCL1 production in tumors is associated with increased metastatic potential and cell seeding, poor prognosis, and enhanced recruitment of tumor-associated macrophages and fibroblasts, we propose that inhibition of host-cell binding and invasion, potentially through vaccination or novel galactoside compounds, could be an effective strategy for reducing F. nucleatum-associated CRC metastasis.
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Affiliation(s)
- Michael A Casasanta
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Christopher C Yoo
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Barath Udayasuryan
- Laboratory of Integrative Tumor Ecology, and Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Blacksburg, VA 24061, USA
| | - Blake E Sanders
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Ariana Umaña
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Yao Zhang
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Huaiyao Peng
- Laboratory of Integrative Tumor Ecology, and Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Blacksburg, VA 24061, USA
| | - Alison J Duncan
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Yueying Wang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Liwu Li
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Scott S Verbridge
- Laboratory of Integrative Tumor Ecology, and Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Blacksburg, VA 24061, USA
| | - Daniel J Slade
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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32
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Brennan CA, Garrett WS. Fusobacterium nucleatum - symbiont, opportunist and oncobacterium. Nat Rev Microbiol 2020; 17:156-166. [PMID: 30546113 DOI: 10.1038/s41579-018-0129-6] [Citation(s) in RCA: 592] [Impact Index Per Article: 148.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fusobacterium nucleatum has long been found to cause opportunistic infections and has recently been implicated in colorectal cancer; however, it is a common member of the oral microbiota and can have a symbiotic relationship with its hosts. To address this dissonance, we explore the diversity and niches of fusobacteria and reconsider historic fusobacterial taxonomy in the context of current technology. We also undertake a critical reappraisal of fusobacteria with a focus on F. nucleatum as a mutualist, infectious agent and oncogenic microorganism. In this Review, we delve into recent insights and future directions for fusobacterial research, including the current genetic toolkit, our evolving understanding of its mechanistic role in promoting colorectal cancer and the challenges of developing diagnostics and therapeutics for F. nucleatum.
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Affiliation(s)
| | - Wendy S Garrett
- Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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Baffy G. Gut Microbiota and Cancer of the Host: Colliding Interests. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1219:93-107. [PMID: 32130695 DOI: 10.1007/978-3-030-34025-4_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cancer develops in multicellular organisms from cells that ignore the rules of cooperation and escape the mechanisms of anti-cancer surveillance. Tumorigenesis is jointly encountered by the host and microbiota, a vast collection of microorganisms that live on the external and internal epithelial surfaces of the body. The largest community of human microbiota resides in the gastrointestinal tract where commensal, symbiotic and pathogenic microorganisms interact with the intestinal barrier and gut mucosal lymphoid tissue, creating a tumor microenvironment in which cancer cells thrive or perish. Aberrant composition and function of the gut microbiota (dysbiosis) has been associated with tumorigenesis by inducing inflammation, promoting cell growth and proliferation, weakening immunosurveillance, and altering food and drug metabolism or other biochemical functions of the host. However, recent research has also identified several mechanisms through which gut microbiota support the host in the fight against cancer. These mechanisms include the use of antigenic mimicry, biotransformation of chemotherapeutic agents, and other mechanisms to boost anti-cancer immune responses and improve the efficacy of cancer immunotherapy. Further research in this rapidly advancing field is expected to identify additional microbial metabolites with tumor suppressing properties, map the complex interactions of host-microbe 'transkingdom network' with cancer cells, and elucidate cellular and molecular pathways underlying the impact of specific intestinal microbial configurations on immune checkpoint inhibitor therapy.
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Affiliation(s)
- Gyorgy Baffy
- Department of Medicine, VA Boston Healthcare System and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Utilizing Whole Fusobacterium Genomes To Identify, Correct, and Characterize Potential Virulence Protein Families. J Bacteriol 2019; 201:JB.00273-19. [PMID: 31501282 DOI: 10.1128/jb.00273-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022] Open
Abstract
Fusobacterium spp. are Gram-negative, anaerobic, opportunistic pathogens involved in multiple diseases, including a link between the oral pathogen Fusobacterium nucleatum and the progression and severity of colorectal cancer. The identification and characterization of virulence factors in the genus Fusobacterium has been greatly hindered by a lack of properly assembled and annotated genomes. Using newly completed genomes from nine strains and seven species of Fusobacterium, we report the identification and corrected annotation of verified and potential virulence factors from the type 5 secreted autotransporter, FadA, and MORN2 protein families, with a focus on the genetically tractable strain F. nucleatum subsp. nucleatum ATCC 23726 and type strain F. nucleatum subsp. nucleatum ATCC 25586. Within the autotransporters, we used sequence similarity networks to identify protein subsets and show a clear differentiation between the prediction of outer membrane adhesins, serine proteases, and proteins with unknown function. These data have identified unique subsets of type 5a autotransporters, which are key proteins associated with virulence in F. nucleatum However, we coupled our bioinformatic data with bacterial binding assays to show that a predicted weakly invasive strain of F. necrophorum that lacks a Fap2 autotransporter adhesin strongly binds human colonocytes. These analyses confirm a gap in our understanding of how autotransporters, MORN2 domain proteins, and FadA adhesins contribute to host interactions and invasion. In summary, we identify candidate virulence genes in Fusobacterium, and caution that experimental validation of host-microbe interactions should complement bioinformatic predictions to increase our understanding of virulence protein contributions in Fusobacterium infections and disease.IMPORTANCE Fusobacterium spp. are emerging pathogens that contribute to mammalian and human diseases, including colorectal cancer. Despite a validated connection with disease, few proteins have been characterized that define a direct molecular mechanism for Fusobacterium pathogenesis. We report a comprehensive examination of virulence-associated protein families in multiple Fusobacterium species and show that complete genomes facilitate the correction and identification of multiple, large type 5a secreted autotransporter genes in previously misannotated or fragmented genomes. In addition, we use protein sequence similarity networks and human cell interaction experiments to show that previously predicted noninvasive strains can indeed bind to and potentially invade human cells and that this could be due to the expansion of specific virulence proteins that drive Fusobacterium infections and disease.
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Pichoff S, Du S, Lutkenhaus J. Roles of FtsEX in cell division. Res Microbiol 2019; 170:374-380. [PMID: 31376483 PMCID: PMC6899183 DOI: 10.1016/j.resmic.2019.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 02/04/2023]
Abstract
FtsEX is a member of a small subclass of ABC transporters that uses mechano-transmission to perform work in the periplasm. FtsEX controls periplasmic peptidoglycan (PG) hydrolase activities in many Gram negative and positive organisms to ensure the safe separation of daughter cells during division. In these organisms FtsEX localizes to the Z ring and uses its ATPase activity to regulate its periplasmic effectors. In Escherichia coli, FtsEX also participates in building the divisome and coordinates PG synthesis with PG hydrolysis. This review discusses studies that are beginning to elucidate the mechanisms of FtsEX's various roles in cell division.
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Affiliation(s)
- Sebastien Pichoff
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Shishen Du
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Joe Lutkenhaus
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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Shields RC, Jensen PA. The bare necessities: Uncovering essential and condition-critical genes with transposon sequencing. Mol Oral Microbiol 2019; 34:39-50. [PMID: 30739386 DOI: 10.1111/omi.12256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/18/2019] [Accepted: 02/06/2019] [Indexed: 12/11/2022]
Abstract
Querying gene function in bacteria has been greatly accelerated by the advent of transposon sequencing (Tn-seq) technologies (related Tn-seq strategies are known as TraDIS, INSeq, RB-TnSeq, and HITS). Pooled populations of transposon mutants are cultured in an environment and next-generation sequencing tools are used to determine areas of the genome that are important for bacterial fitness. In this review we provide an overview of Tn-seq methodologies and discuss how Tn-seq has been applied, or could be applied, to the study of oral microbiology. These applications include studying the essential genome as a means to rationally design therapeutic agents. Tn-seq has also contributed to our understanding of well-studied biological processes in oral bacteria. Other important applications include in vivo pathogenesis studies and use of Tn-seq to probe the molecular basis of microbial interactions. We also highlight recent advancements in techniques that act in synergy with Tn-seq such as clustered regularly interspaced short palindromic repeats (CRISPR) interference and microfluidic chip platforms.
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Affiliation(s)
- Robert C Shields
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida
| | - Paul A Jensen
- Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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