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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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Samal A, Chan HL, Wang IC, Webber L, Gallagher S, Majzoub J, Barootchi S, Mazzocco J, Betancourt AR, Castilho R, Masotti M, Kripfgans OD. Use of High-Frequency Ultrasound for the Correlation of Epithelial Rete Peg Variation. ULTRASOUND IN MEDICINE & BIOLOGY 2024:S0301-5629(24)00236-9. [PMID: 39142939 DOI: 10.1016/j.ultrasmedbio.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 05/23/2024] [Accepted: 06/07/2024] [Indexed: 08/16/2024]
Abstract
OBJECTIVE Rete pegs are projections of the oral epithelium into connective tissue. Their dimensions change during pathological conditions and may correlate with wound-healing status. Non-invasive, high-frequency ultrasound (US) may be able to capture these changes and aid in early detection of histopathological changes. The aim of this preclinical study is to correlate US images with histology and quantify epithelial layers at different tooth sites. METHODS Sagittal B-mode images of mid-facial and interproximal oral soft tissue sites were recorded in a preclinical minipig model using a linear array in second harmonic mode (12/24 MHz). Histology samples from the same locations were stained (hematoxylin and eosin), digitized and registered with US images. Manual annotations were used to measure distances D1 (thickness of epithelium on histology vs. hyperechoic zone on US) and D2 (sum of epithelial thickness and length of rete pegs on histology vs. sum of hyperechoic and hypoechoic zone on US) to statistically analyze them. RESULTS Ultrasonic-derived dimensions yielded a mean bias of -0.64 (55% coefficient of variance [COV]: -180 to +180 µm) and -12 µm (39% COV: -260 to +240 µm) for D1 and D2, respectively. Individualized analysis of D1 and D2 by tooth type showed similar tends in the ability to differentiate between epithelium at different tooth locations, on both histology and US. CONCLUSION Assessing soft tissue dimensions on a sub-millimeter scale using clinical imaging hardware is still a developing area. Future research might open doors for diagnosis of oral pathologies and abnormal wound healing, and may limit false-positive indications for biopsies.
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Affiliation(s)
- Ankita Samal
- Department of Radiology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Periodontology, University of Iowa College of Dentistry and Dental Clinics, Iowa City, IA, USA
| | - Hsun-Liang Chan
- Department of Periodontology and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA; Department of Periodontology, Ohio State University College of Dentistry, Columbus, OH, USA
| | - I-Ching Wang
- Department of Periodontology, University of Iowa College of Dentistry and Dental Clinics, Iowa City, IA, USA; Department of Periodontology and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Liana Webber
- Department of Periodontology and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Sarah Gallagher
- Department of Radiology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jad Majzoub
- Department of Periodontology and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Shayan Barootchi
- Department of Periodontology and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - John Mazzocco
- Department of Periodontology and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Amanda Rodriguez Betancourt
- Department of Periodontology and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA; Department of Periodontology, University of Illinois Chicago College of Dentistry, Chicago, IL, USA
| | - Rogerio Castilho
- Department of Periodontology and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Maria Masotti
- Department of Radiology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Oliver D Kripfgans
- Department of Radiology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA.
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Schwarz C, Mathieu J, Laverde Gomez J, Miller MR, Tikhonova M, Hamor C, Alvarez PJJ. Isolation and Characterization of Six Novel Fusobacterium necrophorum Phages. PHAGE (NEW ROCHELLE, N.Y.) 2024; 5:63-75. [PMID: 39119211 PMCID: PMC11304844 DOI: 10.1089/phage.2023.0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Introduction Fusobacterium necrophorum, a human and animal pathogen, is the primary etiologic agent of bovine liver abscesses and a driving factor for prophylactic antibiotic use in the fed cattle industry. Considering calls to reduce agricultural antibiotic use, we isolated phages capable of killing F. necrophorum as an alternative or complementary biocontrol strategy. Methods Six novel phages (φFN37, φRTG5, φKSUM, φHugo, φPaco, and φBB) were isolated from rumen fluid or ruminal F. necrophorum isolates and subjected to host range testing on both F. necrophorum subspecies. Four F. necrophorum subspecies, necrophorum phages, were tested for cross-resistance and host growth inhibition individually and in pairs. Additionally, genomic sequencing, annotation, and analysis were performed.s. Results Four of six isolated phages were able to form lysogens, although all six contained lysogeny-related genes. φKSUM and φBB, did not form lysogens and were able to infect both subspecies. Four phages could infect F. necrophorum 8L1 (a liver abscess model challenge strain) in vitro. Genomic analysis showed that these phages belong to class Caudoviricetes with genome sizes ranging from 35 kbp to 111 kbp and GC values ranging from 26% to 36% and have extremely limited similarity to other deposited phage genomes infecting Fusobacterium or other genera. Conclusions Although all phages isolated contained sequences bearing similarities to genes implicated in lysogeny, the four selected for use in cocktails showed potential in inhibiting host growth, with several demonstrating promising attributes for biocontrol and therapeutic applications. Phage cocktails that may offer enhanced antibacterial activity were also identified, indicating the potential of some lysogenic phages to be adapted for biocontrol or therapeutic purposes when lytic phages are difficult to obtain.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
| | | | - Megan R. Miller
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | | | - Clark Hamor
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Pedro J. J. Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
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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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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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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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Bibek GC, Zhou P, Wu C. A New Method for Gene Deletion to Investigate Cell Wall Biogenesis in Fusobacterium nucleatum. Methods Mol Biol 2024; 2727:69-82. [PMID: 37815709 DOI: 10.1007/978-1-0716-3491-2_6] [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] [Indexed: 10/11/2023]
Abstract
Controlled septal peptidoglycan hydrolysis is vital for bacterial cell division, preserving cellular integrity and facilitating proper daughter cell separation. In Escherichia coli, the FtsEX ABC system governs cell wall hydrolase activation by regulating the EnvC activator. However, the processes underlying cell division in the Gram-negative oral bacterium Fusobacterium nucleatum are poorly understood, mainly due to its well-known genetic intractability. Herein, we provide a step-by-step procedure for a new gene deletion method in F. nucleatum, focusing on the ftsX gene as a target. This novel approach exploits the HicAB toxin-antitoxin system, using HicA as a counter-selective marker to enable efficient and precise gene deletion. By implementing this technique, we successfully demonstrated its applicability in F. nucleatum, providing new insights into this important microorganism's cell division process. Furthermore, this advanced gene deletion technique offers a valuable resource for future investigation into the functional characterization of genes involved in cell wall biogenesis in F. nucleatum and other genetically intractable microorganisms.
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Affiliation(s)
- G C Bibek
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, TX, USA
| | - Peng Zhou
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, TX, USA
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, TX, USA.
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Merritt J, Kreth J. Illuminating the oral microbiome and its host interactions: tools and approaches for molecular microbiology studies. FEMS Microbiol Rev 2023; 47:fuac050. [PMID: 36549660 PMCID: PMC10719069 DOI: 10.1093/femsre/fuac050] [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: 08/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Advancements in DNA sequencing technologies within the last decade have stimulated an unprecedented interest in the human microbiome, largely due the broad diversity of human diseases found to correlate with microbiome dysbiosis. As a direct consequence of these studies, a vast number of understudied and uncharacterized microbes have been identified as potential drivers of mucosal health and disease. The looming challenge in the field is to transition these observations into defined molecular mechanistic studies of symbiosis and dysbiosis. In order to meet this challenge, many of these newly identified microbes will need to be adapted for use in experimental models. Consequently, this review presents a comprehensive overview of the molecular microbiology tools and techniques that have played crucial roles in genetic studies of the bacteria found within the human oral microbiota. Here, we will use specific examples from the oral microbiome literature to illustrate the biology supporting these techniques, why they are needed in the field, and how such technologies have been implemented. It is hoped that this information can serve as a useful reference guide to help catalyze molecular microbiology studies of the many new understudied and uncharacterized species identified at different mucosal sites in the body.
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Affiliation(s)
- Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, United States
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, United States
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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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10
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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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11
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544113. [PMID: 37398403 PMCID: PMC10312631 DOI: 10.1101/2023.06.13.544113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
A prominent oral commensal and opportunistic pathogen, Fusobacterium nucleatum can traverse to extra-oral sites such as placenta and colon, promoting adverse pregnancy outcomes and colorectal cancer, respectively. How this anaerobe sustains many metabolically changing environments enabling its virulence potential remains unclear. Informed by our genome-wide transposon mutagenesis, we report here that the highly conserved Rnf complex, encoded by the rnfCDGEAB gene cluster, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of the Rnf complex via non-polar, in-frame deletion of rnfC (Δ rnfC ) abrogates polymicrobial interaction (or coaggregation) associated with adhesin RadD and biofilm formation. The defect in coaggregation is not due to reduced cell surface of RadD, but rather an increased level of extracellular lysine, which binds RadD and inhibits coaggregation. Indeed, removal of extracellular lysine via washing Δ rnfC cells restores coaggregation, while addition of lysine inhibits this process. These phenotypes mirror that of a mutant (Δ kamAΔ ) that fails to metabolize extracellular lysine. Strikingly, the Δ rnfC mutant is defective in ATP production, cell growth, cell morphology, and expression of the enzyme MegL that produces hydrogen sulfide from cysteine. Targeted metabolic profiling demonstrated that catabolism of many amino acids, including histidine and lysine, is altered in Δ rnfC cells, thereby reducing production of ATP and metabolites including H2S and butyrate. Most importantly, we show that the Δ rnfC mutant is severely attenuated in a mouse model of preterm birth. The indispensable function of Rnf complex in fusobacterial pathogenesis via modulation of bacterial metabolism makes it an attractive target for developing therapeutic intervention.
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Jiang SS, Xie YL, Xiao XY, Kang ZR, Lin XL, Zhang L, Li CS, Qian Y, Xu PP, Leng XX, Wang LW, Tu SP, Zhong M, Zhao G, Chen JX, Wang Z, Liu Q, Hong J, Chen HY, Chen YX, Fang JY. Fusobacterium nucleatum-derived succinic acid induces tumor resistance to immunotherapy in colorectal cancer. Cell Host Microbe 2023; 31:781-797.e9. [PMID: 37130518 DOI: 10.1016/j.chom.2023.04.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/05/2022] [Accepted: 04/06/2023] [Indexed: 05/04/2023]
Abstract
Immune checkpoint blockade therapy with anti-PD-1 monoclonal antibody (mAb) is a treatment for colorectal cancer (CRC). However, some patients remain unresponsive to PD-1 blockade. The gut microbiota has been linked to immunotherapy resistance through unclear mechanisms. We found that patients with metastatic CRC who fail to respond to immunotherapy had a greater abundance of Fusobacterium nucleatum and increased succinic acid. Fecal microbiota transfer from responders with low F. nucleatum, but not F. nucleatum-high non-responders, conferred sensitivity to anti-PD-1 mAb in mice. Mechanistically, F. nucleatum-derived succinic acid suppressed the cGAS-interferon-β pathway, consequently dampening the antitumor response by limiting CD8+ T cell trafficking to the tumor microenvironment (TME) in vivo. Treatment with the antibiotic metronidazole reduced intestinal F. nucleatum abundance, thereby decreasing serum succinic acid levels and resensitizing tumors to immunotherapy in vivo. These findings indicate that F. nucleatum and succinic acid induce tumor resistance to immunotherapy, offering insights into microbiota-metabolite-immune crosstalk in CRC.
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Affiliation(s)
- Shan-Shan Jiang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Yi-Le Xie
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Xiu-Ying Xiao
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zi-Ran Kang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Xiao-Lin Lin
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Zhang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Chu-Shu Li
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Yun Qian
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Ping-Ping Xu
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Xiao-Xu Leng
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Li-Wei Wang
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shui-Ping Tu
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ming Zhong
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Gang Zhao
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jin-Xian Chen
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zheng Wang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qiang Liu
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jie Hong
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Hao-Yan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China.
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China.
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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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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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Schwarz C, Mathieu J, Gomez JL, Miller MR, Tikhonova M, Nagaraja T, Alvarez PJJ. Unexpected finding of Fusobacterium varium as the dominant Fusobacterium species in cattle rumen: potential implications for liver abscess etiology and interventions. J Anim Sci 2023; 101:skad130. [PMID: 37104065 PMCID: PMC10195197 DOI: 10.1093/jas/skad130] [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: 02/21/2023] [Accepted: 04/25/2023] [Indexed: 04/28/2023] Open
Abstract
Fusobacterium varium has been generally overlooked in cattle rumen microbiome studies relative to the presumably more abundant liver abscess-causing Fusobacterium necrophorum. However, F. varium was found to be more abundant in the rumen fluid of cattle and under culture conditions tailored to enrich F. necrophorum. Using near-full length 16S ribosomal ribonucleic acid sequencing, we demonstrate that F. varium grows under restrictive conditions commonly used to enumerate F. necrophorum, suggesting that previous F. necrophorum abundance assessment may have been inaccurate and that F. varium may be an underestimated member of the ruminal bacterial community. Fusobacterium varium were not as susceptible as F. necrophorum to in-feed antibiotics conventionally used in feedlots. Exposure to tylosin, the current gold standard for liver abscess reduction strategies in cattle, consistently hindered growth of the F. necrophorum strains tested by over 67% (P < 0.05) relative to the unexposed control. In contrast, F. varium strains were totally or highly resistant (0%-13% reduction in maximum yield, P < 0.05). Monensin, an ionophore antibiotic, had greater inhibitory activity against F. necrophorum than F. varium. Finally, preliminary genomic analysis of two F. varium isolates from the rumen revealed the presence of virulence genes related to those of pathogenic human F. varium isolates associated with active invasion of mammalian cells. The data presented here encourage further investigation into the ecological role of F. varium within the bovine rumen and potential role in liver abscess development, and proactive interventions.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
- Sentinel Environmental Group, LLC, Houston, TX 77082, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
- Sentinel Environmental Group, LLC, Houston, TX 77082, USA
| | | | - Megan R Miller
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | | | - Tiruvoor.G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
- Sentinel Environmental Group, LLC, Houston, TX 77082, USA
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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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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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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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Abstract
The importance of the microbiota in the development of colorectal cancer (CRC) is increasingly evident, but identifying specific microbial features that influence CRC initiation and progression remains a central task for investigators. Studies determining the microbial mechanisms that directly contribute to CRC development or progression are revealing bacterial factors such as toxins that contribute to colorectal carcinogenesis. However, even when investigators have identified bacteria that express toxins, questions remain about the host determinants of a toxin's cancer-potentiating effects. For other cancer-correlating bacteria that lack toxins, the challenge is to define cancer-relevant virulence factors. Herein, we evaluate three CRC-correlating bacteria, colibactin-producing Escherichia coli, enterotoxigenic Bacteroides fragilis, and Fusobacterium nucleatum, for their virulence features relevant to CRC. We also consider the beneficial bioactivity of gut microbes by highlighting a microbial metabolite that may enhance CRC antitumor immunity. In doing so, we aim to elucidate unique and shared mechanisms underlying the microbiota's contributions to CRC and to accelerate investigation from target validation to CRC therapeutic discovery.
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Affiliation(s)
- Slater L. Clay
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
| | - Diogo Fonseca-Pereira
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
| | - Wendy S. Garrett
- Department of Immunology and Infectious Diseases and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Jin WB, Li TT, Huo D, Qu S, Li XV, Arifuzzaman M, Lima SF, Shi HQ, Wang A, Putzel GG, Longman RS, Artis D, Guo CJ. Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome. Cell 2022; 185:547-562.e22. [PMID: 35051369 PMCID: PMC8919858 DOI: 10.1016/j.cell.2021.12.035] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/01/2021] [Accepted: 12/21/2021] [Indexed: 02/05/2023]
Abstract
Hundreds of microbiota genes are associated with host biology/disease. Unraveling the causal contribution of a microbiota gene to host biology remains difficult because many are encoded by nonmodel gut commensals and not genetically targetable. A general approach to identify their gene transfer methodology and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. We developed a pipeline that identifies the gene transfer methods for multiple nonmodel microbes spanning five phyla, and we demonstrated the utility of their genetic tools by modulating microbiome-derived short-chain fatty acids and bile acids in vitro and in the host. In a proof-of-principle study, by deleting a commensal gene for bile acid synthesis in a complex microbiome, we discovered an intriguing role of this gene in regulating colon inflammation. This technology will enable genetically engineering the nonmodel gut microbiome and facilitate mechanistic dissection of microbiota-host interactions.
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Affiliation(s)
- Wen-Bing 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
| | - Ting-Ting Li
- 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
| | - Da Huo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Sophia Qu
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Xin V Li
- 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; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Mohammad Arifuzzaman
- 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; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Svetlana F Lima
- 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
| | - Hui-Qing Shi
- 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
| | - Aolin Wang
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Gregory G Putzel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Randy S Longman
- 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; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - David Artis
- 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; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Chun-Jun Guo
- 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; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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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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