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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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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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Yan D, Li G, Zhang H, Xue Q, Zhou C, Jiang Y, Yin J, Wang Z, Zhao W, Han W. Metagenomic Sequencing Revealed Differences in the Composition of Cecal Microbes in Different Breeds of Chickens. Animals (Basel) 2023; 14:28. [PMID: 38200759 PMCID: PMC10778133 DOI: 10.3390/ani14010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/16/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
Intestinal microorganisms are closely related to the health, development, and production performance of animals and can also provide basic information for us to fully understand and explore the germplasm characteristics and traits of local chicken breeds. In this experiment, we used five local Chinese chicken breeds as research materials; metagenomic sequencing technology was used to explore the differences in the composition of intestinal microorganisms in different breeds, and it was found that each local chicken breed had unique unigenes, of which Silkies had the most, with a total of 12,948. GO and KEGG analyses found that the biological processes most enriched by differential functional genes include genetic coding, macromolecular transport, protein synthesis, and molecular functions such as glycoprotein binding, protein hydrolysis, etc. Each breed is enriched with specific pathways, such as Anyi tile-like gray chickens, which are enriched with pathways related to disease resistance, while Gamecocks' enrichment is related to amino acid metabolism. Random Forest and LEfSe analyses revealed specific species of intestinal microorganisms in the cecum of different breeds, such as Exiguobacterium, which is associated with melanin deposition in Silkies. Therefore, we infer that gut microorganisms are closely related to the formation of chicken breed characteristics, and the results of this experiment can provide a theoretical basis for the discovery of high-quality traits and the improvement of feeding conditions in the future.
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Affiliation(s)
- Dan Yan
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Guohui Li
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Huiyong Zhang
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Qian Xue
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Chenghao Zhou
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Yixiu Jiang
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Jianmei Yin
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Wenming Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Wei Han
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
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