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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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Qian M, Li C, Zhang M, Zhan Y, Zhu B, Wang L, Shen Q, Yue L, Chen H, Cheng Y. Blood metagenomics next-generation sequencing has advantages in detecting difficult-to-cultivate pathogens, and mixed infections: results from a real-world cohort. Front Cell Infect Microbiol 2023; 13:1268281. [PMID: 38188631 PMCID: PMC10768086 DOI: 10.3389/fcimb.2023.1268281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Background Blood is a common sample source for metagenomics next-generation sequencing (mNGS) in clinical practice. In this study, we aimed to detect the diagnostic value of blood mNGS in a large real-world cohorts. Methods Blood mNGS results of 1,046 cases were collected and analyzed along with other laboratory tests. The capabilities and accuracy of blood mNGS were compared with other conventional approaches. Results Both the surgical department and the intensive care unit had a positive rate of over 80% in blood mNGS. The positive rate of mNGS was consistent with clinical manifestations. Among the 739 positive samples, 532 were detected as mixed infections. Compared to pathogen cultures, the negative predictive value of blood mNGS for bacteria and fungi detection was 98.9% [95%CI, 96.9%-100%], with an accuracy rate of 89.39%. When compared with polymer chain reaction, the consistency rates of blood mNGS for virus identification were remarkably high. Conclusions Blood mNGS have significant advantages in detecting difficult-to-cultivate bacteria or fungi, viruses, and mixed infections, which benefits patients of surgery department the most. Samples other than blood are recommended for mNGS test if a specific infection is suspected. The reporting threshold and reporting criteria of blood mNGS need to be optimized.
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Affiliation(s)
- Mengjia Qian
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chang Li
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miaomiao Zhang
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanxia Zhan
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bijun Zhu
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingyan Wang
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qi Shen
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lei Yue
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hao Chen
- Department of Thoracic Surgery, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Yunfeng Cheng
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
- Department of Hematology, Zhongshan Hospital Qingpu Branch, Fudan University, Shanghai, China
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Deng T, Zheng H, Zhu Y, Liu M, He G, Li Y, Liu Y, Wu J, Cheng H. Emerging Trends and Focus in Human Skin Microbiome Over the Last Decade: A Bibliometric Analysis and Literature Review. Clin Cosmet Investig Dermatol 2023; 16:2153-2173. [PMID: 37583484 PMCID: PMC10424697 DOI: 10.2147/ccid.s420386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/29/2023] [Indexed: 08/17/2023]
Abstract
Background Human skin microbiome is the first barrier against exogenous attack and is associated with various skin disease pathogenesis and progression. Advancements in high-throughput sequencing technologies have paved the way for a deeper understanding of this field. Based on the bibliometric analysis, this investigation aimed to identify the hotspots and future research trends associated with human skin microbiomes studied over the past decade. Methods The published research on skin microbiome from January 2013 to January 2023 was retrieved from the Web of Science Core Collection. Data cleaning processes to ensure robust data and the bibliometrix packages R, CiteSpace, VOSviewer, Origin, and Scimago Graphica for bibliometric and visual analyses were utilized. Results A total of 1629 published documents were analyzed. The overall publication trend steadily increased, with relatively fast growth in 2017 and 2020. The United States of America has the highest number of publications and citations and shows close collaborations with China and Germany. The University of California, San Diego, indicated a higher number of publications than other institutions and the fastest growth rate. The top three most publishing journals on this topic are Microorganisms, Frontiers in Microbiology, and Experimental dermatology. Gallo RL is the most influential author with the highest h- and g-index and most publications in skin microecology, followed by Grice EA and Kong HH. The top 10 most frequently used keywords in recent years included skin microbiome, microbiome, staphylococcus aureus, diversity, atopic dermatitis, skin, bacteria, infections, gut microbiota, and disease. Conclusion The skin microbiome is an area of research that requires continuous analysis, and even with much-achieved progress, future research will further be aided as technology develops.
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Affiliation(s)
- Tinghan Deng
- Department of Dermatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, 610075, People’s Republic of China
| | - Huilan Zheng
- Department of Dermatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, 610075, People’s Republic of China
| | - Ying Zhu
- Department of Gynecology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, 610075, People’s Republic of China
| | - Ming Liu
- Department of Medical Oncology/Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, People’s Republic of China
| | - Guanjin He
- Department of Dermatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, 610075, People’s Republic of China
| | - Ya Li
- Department of Dermatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, 610075, People’s Republic of China
| | - Yichen Liu
- Department of Dermatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, 610075, People’s Republic of China
| | - Jingping Wu
- Department of Medical Cosmetology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, 610075, People’s Republic of China
| | - Hongbin Cheng
- Department of Dermatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, 610075, People’s Republic of China
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Caliskan M, Poschmann G, Gudzuhn M, Waldera-Lupa D, Molitor R, Strunk CH, Streit WR, Jaeger KE, Stühler K, Kovacic F. Pseudomonas aeruginosa responds to altered membrane phospholipid composition by adjusting the production of two-component systems, proteases and iron uptake proteins. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159317. [PMID: 37054907 DOI: 10.1016/j.bbalip.2023.159317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 04/15/2023]
Abstract
Membrane protein and phospholipid (PL) composition changes in response to environmental cues and during infections. To achieve these, bacteria use adaptation mechanisms involving covalent modification and remodelling of the acyl chain length of PLs. However, little is known about bacterial pathways regulated by PLs. Here, we investigated proteomic changes in the biofilm of P. aeruginosa phospholipase mutant (∆plaF) with altered membrane PL composition. The results revealed profound alterations in the abundance of many biofilm-related two-component systems (TCSs), including accumulation of PprAB, a key regulator of the transition to biofilm. Furthermore, a unique phosphorylation pattern of transcriptional regulators, transporters and metabolic enzymes, as well as differential production of several proteases, in ∆plaF, indicate that PlaF-mediated virulence adaptation involves complex transcriptional and posttranscriptional response. Moreover, proteomics and biochemical assays revealed the depletion of pyoverdine-mediated iron uptake pathway proteins in ∆plaF, while proteins from alternative iron-uptake systems were accumulated. These suggest that PlaF may function as a switch between different iron-acquisition pathways. The observation that PL-acyl chain modifying and PL synthesis enzymes were overproduced in ∆plaF reveals the interconnection of degradation, synthesis and modification of PLs for proper membrane homeostasis. Although the precise mechanism by which PlaF simultaneously affects multiple pathways remains to be elucidated, we suggest that alteration of PL composition in ∆plaF plays a role for the global adaptive response in P. aeruginosa mediated by TCSs and proteases. Our study revealed the global regulation of virulence and biofilm by PlaF and suggests that targeting this enzyme may have therapeutic potential.
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Affiliation(s)
- Muttalip Caliskan
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mirja Gudzuhn
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Daniel Waldera-Lupa
- Institute of Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rebecka Molitor
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | | | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany; Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Kai Stühler
- Institute of Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum, Heinrich-Heine-University, Düsseldorf, Düsseldorf, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany.
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Karnwal A, Shrivastava S, Al-Tawaha ARMS, Kumar G, Singh R, Kumar A, Mohan A, Malik T. Microbial Biosurfactant as an Alternate to Chemical Surfactants for Application in Cosmetics Industries in Personal and Skin Care Products: A Critical Review. BIOMED RESEARCH INTERNATIONAL 2023; 2023:2375223. [PMID: 37090190 PMCID: PMC10118887 DOI: 10.1155/2023/2375223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 04/25/2023]
Abstract
Cosmetics and personal care items are used worldwide and administered straight to the skin. The hazardous nature of the chemical surfactant utilized in the production of cosmetics has caused alarm on a global scale. Therefore, bacterial biosurfactants (BS) are becoming increasingly popular in industrial product production as a biocompatible, low-toxic alternative surfactant. Chemical surfactants can induce allergic responses and skin irritations; thus, they should be replaced with less harmful substances for skin health. The cosmetic industry seeks novel biological alternatives to replace chemical compounds and improve product qualities. Most of these chemicals have a biological origin and can be obtained from plant, bacterial, fungal, and algal sources. Various biological molecules have intriguing capabilities, such as biosurfactants, vitamins, antioxidants, pigments, enzymes, and peptides. These are safe, biodegradable, and environmentally friendly than chemical options. Plant-based biosurfactants, such as saponins, offer numerous advantages over synthetic surfactants, i.e., biodegradable, nontoxic, and environmentally friendly nature. Saponins are a promising source of natural biosurfactants for various industrial and academic applications. However, microbial glycolipids and lipopeptides have been used in biotechnology and cosmetics due to their multifunctional character, including detergency, emulsifying, foaming, and skin moisturizing capabilities. In addition, some of them have the potential to be used as antibacterial agents. In this review, we like to enlighten the application of microbial biosurfactants for replacing chemical surfactants in existing cosmetic and personal skincare pharmaceutical formulations due to their antibacterial, skin surface moisturizing, and low toxicity characteristics.
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Affiliation(s)
- Arun Karnwal
- Department of Microbiology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Seweta Shrivastava
- Department of Plant Pathology, School of Agriculture, Lovely Professional University, Phagwara, Punjab, India
| | | | - Gaurav Kumar
- Department of Microbiology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Rattandeep Singh
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Anupam Kumar
- Department of Biotechnology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Anand Mohan
- Department of Biotechnology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Tabarak Malik
- Department of Biomedical Sciences, Institute of Health, Jimma University, Ethiopia
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