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Ren JY, Yu HQ, Xu S, Zhou WJ, Liu ZH. Putative pathogenic factors underlying Streptococcus oralis opportunistic infections. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024:S1684-1182(24)00159-2. [PMID: 39261123 DOI: 10.1016/j.jmii.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 08/08/2024] [Accepted: 09/03/2024] [Indexed: 09/13/2024]
Abstract
Streptococcus oralis, belonging to the viridans group streptococci (VGS), has been considered a component of the normal flora predominantly inhabiting the oral cavity. In recent years, a growing body of literature has revealed that dental procedures or daily tooth brushing activities can cause the spread of S. oralis from the oral cavity into various body sites leading to life-threatening opportunistic infections such as infective endocarditis (IE) and meningitis. However, very little is currently known about the pathogenicity of S. oralis. Thus, the aim of this review is to update the current understanding of the pathogenic potential of S. oralis to pave the way for the prevention and treatment of S. oralis opportunistic infections.
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Affiliation(s)
- Jing-Yi Ren
- Department of Implantology, Yantai Stomatological Hospital Affiliated to Binzhou Medical University, Yantai, China; School of Stomatology, Binzhou Medical University, Yantai, China
| | - Hong-Qiang Yu
- Department of Stomatology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sheng Xu
- Department of Implantology, Yantai Stomatological Hospital Affiliated to Binzhou Medical University, Yantai, China
| | - Wen-Juan Zhou
- Department of Implantology, Yantai Stomatological Hospital Affiliated to Binzhou Medical University, Yantai, China; Yantai Engineering Research Center for Digital Technology of Stomatology, Yantai, China; Characteristic Laboratories of Colleges and Universities in Shandong Province for Digital Stomatology, Yantai, China.
| | - Zhong-Hao Liu
- Department of Implantology, Yantai Stomatological Hospital Affiliated to Binzhou Medical University, Yantai, China; School of Stomatology, Binzhou Medical University, Yantai, China; Yantai Engineering Research Center for Digital Technology of Stomatology, Yantai, China; Characteristic Laboratories of Colleges and Universities in Shandong Province for Digital Stomatology, Yantai, China
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Quaiyum S, Yuan Y, Sun G, Ratnayake RMMN, Hutinet G, Dedon PC, Minnick MF, de Crécy-Lagard V. Queuosine salvage in Bartonella henselae Houston 1: a unique evolutionary path. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39234940 DOI: 10.1099/mic.0.001490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Queuosine (Q) stands out as the sole tRNA modification that can be synthesized via salvage pathways. Comparative genomic analyses identified specific bacteria that showed a discrepancy between the projected Q salvage route and the predicted substrate specificities of the two identified salvage proteins: (1) the distinctive enzyme tRNA guanine-34 transglycosylase (bacterial TGT, or bTGT), responsible for inserting precursor bases into target tRNAs; and (2) queuosine precursor transporter (QPTR), a transporter protein that imports Q precursors. Organisms such as the facultative intracellular pathogen Bartonella henselae, which possess only bTGT and QPTR but lack predicted enzymes for converting preQ1 to Q, would be expected to salvage the queuine (q) base, mirroring the scenario for the obligate intracellular pathogen Chlamydia trachomatis. However, sequence analyses indicate that the substrate-specificity residues of their bTGTs resemble those of enzymes inserting preQ1 rather than q. Intriguingly, MS analyses of tRNA modification profiles in B. henselae reveal trace amounts of preQ1, previously not observed in a natural context. Complementation analysis demonstrates that B. henselae bTGT and QPTR not only utilize preQ1, akin to their Escherichia coli counterparts, but can also process q when provided at elevated concentrations. The experimental and phylogenomic analyses suggest that the Q pathway in B. henselae could represent an evolutionary transition among intracellular pathogens - from ancestors that synthesized Q de novo to a state prioritizing the salvage of q. Another possibility that will require further investigations is that the insertion of preQ1 confers fitness advantages when B. henselae is growing outside a mammalian host.
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Affiliation(s)
- Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - R M Madhushi N Ratnayake
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- Present address: Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Present address: Department of Biology, Haverford College, 370 Lancaster Ave., Haverford, PA, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael F Minnick
- Division of Biological Sciences, University of Montana, Missoula, Montana, MT 59812, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Genetic Institute, University of Florida, FL 32611, USA
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Jin LX, Fang YP, Xia CM, Cai TW, Li QQ, Wang YY, Yan HF, Chen X. Helicobacter pylori infection alters gastric microbiota structure and biological functions in patients with gastric ulcer or duodenal ulcer. World J Gastroenterol 2024; 30:3076-3085. [PMID: 38983956 PMCID: PMC11230059 DOI: 10.3748/wjg.v30.i24.3076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/21/2024] [Accepted: 05/31/2024] [Indexed: 06/25/2024] Open
Abstract
BACKGROUND Helicobacter pylori (H. pylori) infection is closely associated with gastrointestinal diseases. Our preliminary studies have indicated that H. pylori infection had a significant impact on the mucosal microbiome structure in patients with gastric ulcer (GU) or duodenal ulcer (DU). AIM To investigate the contributions of H. pylori infection and the mucosal microbiome to the pathogenesis and progression of ulcerative diseases. METHODS Patients with H. pylori infection and either GU or DU, and healthy individuals without H. pylori infection were included. Gastric or duodenal mucosal samples was obtained and subjected to metagenomic sequencing. The compositions of the microbial communities and their metabolic functions in the mucosal tissues were analyzed. RESULTS Compared with that in the healthy individuals, the gastric mucosal microbiota in the H. pylori-positive patients with GU was dominated by H. pylori, with significantly reduced biodiversity. The intergroup differential functions, which were enriched in the H. pylori-positive GU patients, were all derived from H. pylori, particularly those concerning transfer RNA queuosine-modification and the synthesis of demethylmenaquinones or menaquinones. A significant enrichment of the uibE gene was detected in the synthesis pathway. There was no significant difference in microbial diversity between the H. pylori-positive DU patients and healthy controls. CONCLUSION H. pylori infection significantly alters the gastric microbiota structure, diversity, and biological functions, which may be important contributing factors for GU.
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Affiliation(s)
- Ling-Xiao Jin
- Department of Gastroenterology, Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Wenling 317500, Zhejiang Province, China
| | - Yu-Peng Fang
- Department of Gastroenterology, Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Wenling 317500, Zhejiang Province, China
| | - Chen-Mei Xia
- Department of Gastroenterology, Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Wenling 317500, Zhejiang Province, China
| | - Teng-Wei Cai
- Department of Gastroenterology, Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Wenling 317500, Zhejiang Province, China
| | - Qian-Qian Li
- Department of Gastroenterology, Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Wenling 317500, Zhejiang Province, China
| | - Yu-Yin Wang
- Department of Gastroenterology, Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Wenling 317500, Zhejiang Province, China
| | - Hai-Fan Yan
- Department of Gastroenterology, Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Wenling 317500, Zhejiang Province, China
| | - Xia Chen
- Department of Gastroenterology, Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Wenling 317500, Zhejiang Province, China
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Quaiyum S, Yuan Y, Kuipers PJ, Martinelli M, Jaroch M, de Crécy-Lagard V. Deciphering the Diversity in Bacterial Transporters That Salvage Queuosine Precursors. EPIGENOMES 2024; 8:16. [PMID: 38804365 PMCID: PMC11130926 DOI: 10.3390/epigenomes8020016] [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: 03/05/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 05/29/2024] Open
Abstract
Queuosine (Q) is a modification of the wobble base of tRNA harboring GUN anticodons with roles in decoding accuracy and efficiency. Its synthesis is complex with multiple enzymatic steps, and several pathway intermediates can be salvaged. The only two transporter families known to salvage Q precursors are QPTR/COG1738 and QrtT/QueT. Analyses of the distribution of known Q synthesis and salvage genes in human gut and oral microbiota genomes have suggested that more transporter families remain to be found and that Q precursor exchanges must occur within the structured microenvironments of the mammalian host. Using physical clustering and fusion-based association with Q salvage genes, candidate genes for missing transporters were identified and five were tested experimentally by complementation assays in Escherichia coli. Three genes encoding transporters from three different Pfam families, a ureide permease (PF07168) from Acidobacteriota bacterium, a hemolysin III family protein (PF03006) from Bifidobacterium breve, and a Major Facilitator Superfamily protein (PF07690) from Bartonella henselae, were found to allow the transport of both preQ0 and preQ1 in this heterologous system. This work suggests that many transporter families can evolve to transport Q precursors, reinforcing the concept of transporter plasticity.
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Affiliation(s)
- Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
| | - Paul J. Kuipers
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
| | - Maria Martinelli
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
- eSTEAMed Learning Inc., Maitland, FL 32751, USA
| | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (S.Q.); (Y.Y.); (P.J.K.)
- Genetic Institute, University of Florida, Gainesville, FL 32611, USA
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Quaiyum S, Yuan Y, Sun G, Ratnayake RMMN, Hutinet G, Dedon PC, Minnick MF, de Crécy-Lagard V. Queuosine Salvage in Bartonella henselae Houston 1: A Unique Evolutionary Path. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.05.570228. [PMID: 38106016 PMCID: PMC10723273 DOI: 10.1101/2023.12.05.570228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Queuosine (Q) stands out as the sole tRNA modification that can be synthesized via salvage pathways. Comparative genomic analyses identified specific bacteria that showed a discrepancy between the projected Q salvage route and the predicted substrate specificities of the two identified salvage proteins: 1) the distinctive enzyme tRNA guanine-34 transglycosylase (bacterial TGT, or bTGT), responsible for inserting precursor bases into target tRNAs; and 2) Queuosine Precursor Transporter (QPTR), a transporter protein that imports Q precursors. Organisms like the facultative intracellular pathogen Bartonella henselae, which possess only bTGT and QPTR but lack predicted enzymes for converting preQ1 to Q, would be expected to salvage the queuine (q) base, mirroring the scenario for the obligate intracellular pathogen Chlamydia trachomatis. However, sequence analyses indicate that the substrate-specificity residues of their bTGTs resemble those of enzymes inserting preQ1 rather than q. Intriguingly, mass spectrometry analyses of tRNA modification profiles in B. henselae reveal trace amounts of preQ1, previously not observed in a natural context. Complementation analysis demonstrates that B. henselae bTGT and QPTR not only utilize preQ1, akin to their Escherichia coli counterparts, but can also process q when provided at elevated concentrations. The experimental and phylogenomic analyses suggest that the Q pathway in B. henselae could represent an evolutionary transition among intracellular pathogens-from ancestors that synthesized Q de novo to a state prioritizing the salvage of q. Another possibility that will require further investigations is that the insertion of preQ1 has fitness advantages when B. henselae is growing outside a mammalian host.
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Affiliation(s)
- Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael F. Minnick
- Division of Biological Sciences, University of Montana, Missoula, Montana, MT 59812
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
- Genetic Institute, University of Florida, FL 32611
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de Crécy-Lagard V, Hutinet G, Cediel-Becerra JDD, Yuan Y, Zallot R, Chevrette MG, Ratnayake RMMN, Jaroch M, Quaiyum S, Bruner S. Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages. Microbiol Mol Biol Rev 2024; 88:e0019923. [PMID: 38421302 PMCID: PMC10966956 DOI: 10.1128/mmbr.00199-23] [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] [Indexed: 03/02/2024] Open
Abstract
SUMMARYDeazaguanine modifications play multifaceted roles in the molecular biology of DNA and tRNA, shaping diverse yet essential biological processes, including the nuanced fine-tuning of translation efficiency and the intricate modulation of codon-anticodon interactions. Beyond their roles in translation, deazaguanine modifications contribute to cellular stress resistance, self-nonself discrimination mechanisms, and host evasion defenses, directly modulating the adaptability of living organisms. Deazaguanine moieties extend beyond nucleic acid modifications, manifesting in the structural diversity of biologically active natural products. Their roles in fundamental cellular processes and their presence in biologically active natural products underscore their versatility and pivotal contributions to the intricate web of molecular interactions within living organisms. Here, we discuss the current understanding of the biosynthesis and multifaceted functions of deazaguanines, shedding light on their diverse and dynamic roles in the molecular landscape of life.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
| | - Geoffrey Hutinet
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | | | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Rémi Zallot
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | | | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Steven Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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Czajkowski R, Krzyżanowska DM, Sokolova D, Rąbalski Ł, Kosiński M, Jafra S, Królicka A. Genetic Loci of Plant Pathogenic Dickeya solani IPO 2222 Expressed in Contact with Weed-Host Bittersweet Nightshade ( Solanum dulcamara L.) Plants. Int J Mol Sci 2024; 25:2794. [PMID: 38474041 DOI: 10.3390/ijms25052794] [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: 02/01/2024] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Dickeya solani, belonging to the Soft Rot Pectobacteriaceae, are aggressive necrotrophs, exhibiting both a wide geographic distribution and a wide host range that includes many angiosperm orders, both dicot and monocot plants, cultivated under all climatic conditions. Little is known about the infection strategies D. solani employs to infect hosts other than potato (Solanum tuberosum L.). Our earlier study identified D. solani Tn5 mutants induced exclusively by the presence of the weed host S. dulcamara. The current study assessed the identity and virulence contribution of the selected genes mutated by the Tn5 insertions and induced by the presence of S. dulcamara. These genes encode proteins with functions linked to polyketide antibiotics and polysaccharide synthesis, membrane transport, stress response, and sugar and amino acid metabolism. Eight of these genes, encoding UvrY (GacA), tRNA guanosine transglycosylase Tgt, LPS-related WbeA, capsular biosynthesis protein VpsM, DltB alanine export protein, glycosyltransferase, putative transcription regulator YheO/PAS domain-containing protein, and a hypothetical protein, were required for virulence on S. dulcamara plants. The implications of D. solani interaction with a weed host, S. dulcamara, are discussed.
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Affiliation(s)
- Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology of UG and MUG, University of Gdansk, A. Abrahama 58, 80-307 Gdansk, Poland
| | - Dorota M Krzyżanowska
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology of UG and MUG, University of Gdansk, A. Abrahama 58, 80-307 Gdansk, Poland
| | - Daryna Sokolova
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology of UG and MUG, University of Gdansk, A. Abrahama 58, 80-307 Gdansk, Poland
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, 148 Academika Zabolotnoho St., 03143 Kyiv, Ukraine
| | - Łukasz Rąbalski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307 Gdansk, Poland
| | - Maciej Kosiński
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307 Gdansk, Poland
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of UG and MUG, University of Gdansk, A. Abrahama 58, 80-307 Gdansk, Poland
| | - Aleksandra Królicka
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology of UG and MUG, University of Gdansk, A. Abrahama 58, 80-307 Gdansk, Poland
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