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Wakchaure PD, Ganguly B. Exploring the structure, function of thiamine pyrophosphate riboswitch, and designing small molecules for antibacterial activity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1774. [PMID: 36594112 DOI: 10.1002/wrna.1774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023]
Abstract
During the last decade, riboswitches emerged as new small-molecule sensing RNA in bacteria. Thiamine pyrophosphate (TPP) riboswitch is widely distributed and occurs in plants, bacteria, fungi, and archaea. Extensive biochemical, structural, and genetic studies have been carried out to elucidate the recognition mechanism of TPP riboswitches. However, a comprehensive report summarizing all information on recognition principles and newly designed ligands for TPP riboswitch is scarce in the literature. This review gives a comprehensive understanding of the TPP riboswitch's structure, mechanism, and methods applied to design ligands for the TPP riboswitch. The ligand-bound TPP riboswitch was studied with various experimental and theoretical techniques to elucidate the conformational dynamics. The mutation studies shed light on the significance of pyrimidine sensing helix for the binding of ligands. Further, the structure-activity relationship study and fragment-based approach lead to the development of ligands with Kd values at the sub-micromolar level. However, there is a need to design more potent inhibitors for TPP riboswitch for therapeutic applications. The recent advancements in ligand design highlight the TPP riboswitch as a promising target for developing new antibiotics. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Riboswitches Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Padmaja D Wakchaure
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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Berrios L. Examining the genomic features of human and plant-associated Burkholderia strains. Arch Microbiol 2022; 204:335. [PMID: 35587294 DOI: 10.1007/s00203-022-02953-3] [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: 06/14/2021] [Revised: 04/01/2022] [Accepted: 05/02/2022] [Indexed: 11/28/2022]
Abstract
Humans and plants have evolved in the near omnipresence of a microbial milieu, and the factors that govern host-microbe interactions continue to require scientific exploration. To better understand if and to what degree patterns between microbial genomic features and host association (i.e., human and plant) exist, I analyzed the genomes of select Burkholderia strains-a bacterial genus comprised of both human and plant-associated strains-that were isolated from either humans or plants. To this end, I uncovered host-specific, genomic patterns related to metabolic pathway potentials in addition to convergent features that may be related to pathogenic overlap between hosts. Together, these findings detail the genomic associations of human and plant-associated Burkholderia strains and provide a framework for future investigations that seek to link host-host transmission potentials.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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Liu X, Wang X, Sun B, Sun L. The Involvement of Thiamine Uptake in the Virulence of Edwardsiella piscicida. Pathogens 2022; 11:464. [PMID: 35456139 PMCID: PMC9026889 DOI: 10.3390/pathogens11040464] [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: 03/03/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
Edwardsiella piscicida is a pathogenic bacterium, which can infect a number of fish species and cause a disease termed edwardsiellosis, threatening global fish farming with high prevalence and mortality. Thiamine (Vitamin B1), functioning in the form of thiamine pyrophosphate (TPP), is essential for almost all organisms. Bacteria acquire TPP by biosynthesis or by transportation of exogenous thiamine. TPP availability has been associated with bacterial pathogenicity, but the underlying mechanisms remain to be discovered. The role of thiamine in the pathogenicity of E. piscicida is unknown. In this study, we characterized a thiamine transporter (TT) operon in E. piscicida. The deletion of the TT operon resulted in an intracellular TPP lacking situation, which led to attenuated overall pathogenicity, impaired abilities associated with motility and host cell adhesion, as well as decreased expression of certain flagellar and adhesion genes. Moreover, TPP starvation led to intracellular c-di-GMP reduction, and introducing into the TPP-suppressed mutant strain an exogenous diguanylate cyclase for c-di-GMP synthesis restored the virulence loss. Taken together, this work reveals the involvement of thiamine uptake in the virulence regulation of E. piscicida, with c-di-GMP implicated in the process. These finding could be employed to explore potential drug targets against E. piscicida.
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Affiliation(s)
- Xin Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (X.L.); (X.W.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinhui Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (X.L.); (X.W.)
| | - Boguang Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (X.L.); (X.W.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (X.L.); (X.W.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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The emerging role of bacterial regulatory RNAs in disease. Trends Microbiol 2022; 30:959-972. [DOI: 10.1016/j.tim.2022.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 02/02/2023]
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Spoerry C, Karlsson J, Aschtgen MS, Loh E. Neisseria meningitidis IgA1-specific serine protease exhibits novel cleavage activity against IgG3. Virulence 2021; 12:389-403. [PMID: 33459578 PMCID: PMC7834093 DOI: 10.1080/21505594.2021.1871822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 11/16/2022] Open
Abstract
Neisseria meningitidis (meningococcus) is a common bacterial colonizer of the human nasopharynx but can occasionally cause very severe systemic infections with rapid onset. Meningococci are able to degrade IgA encountered during colonization of mucosal membranes using their IgA1-specific serine protease. During systemic infection, specific IgG can induce complement-mediated lysis of the bacterium. However, meningococcal immune evasion mechanisms in thwarting IgG remain undescribed. In this study, we report for the first time that the meningococcal IgA1-specific serine protease is able to degrade IgG3 in addition to IgA. The IgG3 heavy chain is specifically cleaved in the lower hinge region thereby separating the antigen binding part from its effector binding part. Through molecular characterization, we demonstrate that meningococcal IgA1-specific serine protease of cleavage type 1 degrades both IgG3 and IgA, whereas cleavage type 2 only degrades IgA. Epidemiological analysis of 7581 clinical meningococcal isolates shows a significant higher proportion of cleavage type 1 among isolates from invasive cases compared to carrier cases, regardless of serogroup. Notably, serogroup W cc11 which is an increasing cause of invasive meningococcal disease globally harbors almost exclusively cleavage type 1 protease. Our study also shows an increasing prevalence of meningococcal isolates encoding IgA1P cleavage type 1 compared to cleavage type 2 during the observed decade (2010-2019). Altogether, our work describes a novel mechanism of IgG3 degradation by meningococci and its association to invasive meningococcal disease.
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Affiliation(s)
- Christian Spoerry
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Jens Karlsson
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Marie-Stephanie Aschtgen
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Edmund Loh
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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Novel hypercapsulation RNA thermosensor variants in Neisseria meningitidis and their association with invasive meningococcal disease: a genetic and phenotypic investigation and molecular epidemiological study. THE LANCET MICROBE 2020; 1:e319-e327. [DOI: 10.1016/s2666-5247(20)30146-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/12/2020] [Accepted: 08/20/2020] [Indexed: 01/13/2023] Open
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