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Chandran S, Gibson KE. Utilizing Zebrafish Embryos for Replication of Tulane Virus: A Human Norovirus Surrogate. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09610-6. [PMID: 39179704 DOI: 10.1007/s12560-024-09610-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 08/15/2024] [Indexed: 08/26/2024]
Abstract
The zebrafish larvae/embryo model has been shown to support the replication of seven strains (G1.7[P7], GII.2[P16], GII.3[P16], GII.4[P4], GII.4[P16], GII.6[P7], and GII.17[P13]) of human norovirus (HuNoV). However, due to challenges in consistently obtaining HuNoV-positive stool samples from clinical sources, evaluating HuNoV surrogates in this model is highly valuable. This study assesses the potential of zebrafish embryos and larvae as a model for Tulane virus (TuV) replication. Three infection methods were examined: microinjection, immersion, and feeding. Droplet digital PCR was used to quantify viral RNA across all three infection methods. Microinjection of 3 nL of TuV into zebrafish embryos (< 6-h post-fertilization) resulted in significant replication, with viral RNA levels reaching 6.22 logs at 4-day post-infection. In contrast, the immersion method showed no replication after immersing 4-day post-fertilization (dpf) larvae in TuV suspension for 6 h. Similarly, no replication was observed with the feeding method, where Paramecium caudatum loaded with TuV were fed to 4 dpf larvae. The findings indicate that the zebrafish embryo model supports TuV replication through the microinjection method, suggesting that TuV may serve as a useful surrogate for studying HuNoV pathogenesis. Additionally, TuV can be utilized in place of HuNoV in method optimization studies using the zebrafish embryo model, circumventing the limited availability of HuNoV.
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Affiliation(s)
- Sahaana Chandran
- Department of Food Science, Center for Food Safety, University of Arkansas System Division of Agriculture, Fayetteville, AR, 72704, USA
| | - Kristen E Gibson
- Department of Food Science, Center for Food Safety, University of Arkansas System Division of Agriculture, Fayetteville, AR, 72704, USA.
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2
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Chandran S, Gibson KE. Improving the Detection and Understanding of Infectious Human Norovirus in Food and Water Matrices: A Review of Methods and Emerging Models. Viruses 2024; 16:776. [PMID: 38793656 PMCID: PMC11125872 DOI: 10.3390/v16050776] [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: 03/23/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Human norovirus (HuNoV) is a leading global cause of viral gastroenteritis, contributing to numerous outbreaks and illnesses annually. However, conventional cell culture systems cannot support the cultivation of infectious HuNoV, making its detection and study in food and water matrices particularly challenging. Recent advancements in HuNoV research, including the emergence of models such as human intestinal enteroids (HIEs) and zebrafish larvae/embryo, have significantly enhanced our understanding of HuNoV pathogenesis. This review provides an overview of current methods employed for HuNoV detection in food and water, along with their associated limitations. Furthermore, it explores the potential applications of the HIE and zebrafish larvae/embryo models in detecting infectious HuNoV within food and water matrices. Finally, this review also highlights the need for further optimization and exploration of these models and detection methods to improve our understanding of HuNoV and its presence in different matrices, ultimately contributing to improved intervention strategies and public health outcomes.
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Affiliation(s)
| | - Kristen E. Gibson
- Department of Food Science, Center for Food Safety, University of Arkansas System Division of Agriculture, Fayetteville, AR 72704, USA;
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3
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Lyu Z, Ling Y, van Hoof A, Ling J. Inactivation of the ribosome assembly factor RimP causes streptomycin resistance and impairs motility in Salmonella. Antimicrob Agents Chemother 2024:e0000224. [PMID: 38629858 DOI: 10.1128/aac.00002-24] [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: 01/02/2024] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
The ribosome is the central hub for protein synthesis and the target of many antibiotics. Although the majority of ribosome-targeting antibiotics inhibit protein synthesis and are bacteriostatic, aminoglycosides promote protein mistranslation and are bactericidal. Understanding the resistance mechanisms of bacteria against aminoglycosides is not only vital for improving the efficacy of this critically important group of antibiotics but also crucial for studying the molecular basis of translational fidelity. In this work, we analyzed Salmonella mutants evolved in the presence of the aminoglycoside streptomycin (Str) and identified a novel gene rimP to be involved in Str resistance. RimP is a ribosome assembly factor critical for the maturation of the 30S small subunit that binds Str. Deficiency in RimP increases resistance against Str and facilitates the development of even higher resistance. Deleting rimP decreases mistranslation and cellular uptake of Str and further impairs flagellar motility. Our work thus highlights a previously unknown mechanism of aminoglycoside resistance via defective ribosome assembly.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, USA
| | - Yunyi Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, USA
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4
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Hinnu M, Putrinš M, Kogermann K, Kaldalu N, Tenson T. Fluorescent reporters give new insights into antibiotics-induced nonsense and frameshift mistranslation. Sci Rep 2024; 14:6883. [PMID: 38519558 PMCID: PMC10959953 DOI: 10.1038/s41598-024-57597-8] [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: 11/15/2023] [Accepted: 03/20/2024] [Indexed: 03/25/2024] Open
Abstract
We developed a reporter system based on simultaneous expression of two fluorescent proteins: GFP as a reporter of the capacity of protein synthesis and mutated mScarlet-I as a reporter of translational errors. Because of the unique stop codons or frameshift mutations introduced into the mScarlet-I gene, red fluorescence was produced only after a mistranslation event. These reporters allowed us to estimate mistranslation at a single cell level using either flow cytometry or fluorescence microscopy. We found that laboratory strains of Escherichia coli are more prone to mistranslation compared to the clinical isolates. As relevant for uropathogenic E. coli, growth in human urine elevated translational frameshifting compared to standard laboratory media, whereas different standard media had a small effect on translational fidelity. Antibiotic-induced mistranslation was studied by using amikacin (aminoglycoside family) and azithromycin (macrolide family). Bactericidal amikacin induced preferably stop-codon readthrough at a moderate level. Bacteriostatic azithromycin on the other hand induced both frameshifting and stop-codon readthrough at much higher level. Single cell analysis revealed that fluorescent reporter-protein signal can be lost due to leakage from a fraction of bacteria in the presence of antibiotics, demonstrating the complexity of the antimicrobial activity.
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Affiliation(s)
- Mariliis Hinnu
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia.
| | - Marta Putrinš
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
- Institute of Pharmacy, University of Tartu, 50411, Tartu, Estonia
| | - Karin Kogermann
- Institute of Pharmacy, University of Tartu, 50411, Tartu, Estonia
| | - Niilo Kaldalu
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
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5
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Shuster M, Lyu Z, Augenstreich J, Mathur S, Ganesh A, Ling J, Briken V. Salmonella Typhimurium infection inhibits macrophage IFNβ signaling in a TLR4-dependent manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583530. [PMID: 38496427 PMCID: PMC10942315 DOI: 10.1101/2024.03.05.583530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Type I Interferons (IFNs) generally have a protective role during viral infections, but their function during bacterial infections is dependent on the bacterial species. Legionella pneumophila, Shigella sonnei and Mycobacterium tuberculosis can inhibit type I IFN signaling. Here we examined the role of type I IFN, specifically IFNβ, in the context of Salmonella enterica serovar Typhimurium (STm) macrophage infections and the capacity of STm to inhibit type I IFN signaling. We demonstrate that IFNβ has no effect on the intracellular growth of STm in infected bone marrow derived macrophages (BMDMs) derived from C57BL/6 mice. STm infection inhibits IFNβ signaling but not IFNγ signaling in a murine macrophage cell line. We show that this inhibition is independent of the type III and type VI secretion systems expressed by STm and is also independent of bacterial phagocytosis. The inhibition is Toll-like receptor 4 (TLR4)-dependent as the TLR4 ligand, lipopolysaccharide (LPS), alone is sufficient to inhibit IFNβ-mediated signaling and STm-infected, TLR4-deficient BMDMs do not exhibit inhibited IFNβ signaling. In summary, we show that macrophages exposed to STm have reduced IFNβ signaling via crosstalk with TLR4 signaling, and that IFNβ signaling does not affect cell autonomous host defense against STm.
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Affiliation(s)
- Michael Shuster
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Jacques Augenstreich
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Shrestha Mathur
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Akshaya Ganesh
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
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6
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Augenstreich J, Shuster M, Fan Y, Lyu Z, Ling J, Briken V. BBQ methods: streamlined workflows for bacterial burden quantification in infected cells by confocal microscopy. Biol Open 2024; 13:bio060189. [PMID: 38156988 PMCID: PMC10836645 DOI: 10.1242/bio.060189] [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: 10/31/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
Accurate quantification of bacterial burden within macrophages, termed bacterial burden quantification (BBQ), is crucial for understanding host-pathogen interactions. Various methods have been employed, each with strengths and weaknesses. This article addresses limitations in existing techniques and introduces two novel, automated methods for BBQ within macrophages based on confocal microscopy data analysis. The first method refines total fluorescence quantification by incorporating filtering steps to exclude uninfected cells, while the second method calculates total bacterial volume per cell to mitigate potential biases in fluorescence-based readouts. These workflows utilize PyImageJ and Cellpose software, providing reliable, unbiased, and rapid quantification of bacterial load. The proposed workflows were validated using Salmonella enterica serovar Typhimurium and Mycobacterium tuberculosis models, demonstrating their effectiveness in accurately assessing bacterial burden. These automated workflows offer valuable tools for studying bacterial interactions within host cells and provide insights for various research applications.
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Affiliation(s)
- Jacques Augenstreich
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Michael Shuster
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Yongqiang Fan
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Lyu Z, Ling Y, van Hoof A, Ling J. Deficiency in ribosome biogenesis causes streptomycin resistance and impairs motility in Salmonella. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574728. [PMID: 38260697 PMCID: PMC10802465 DOI: 10.1101/2024.01.08.574728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The ribosome is the central hub for protein synthesis and the target of many antibiotics. Whereas the majority of ribosome-targeting antibiotics inhibit protein synthesis and are bacteriostatic, aminoglycosides promote protein mistranslation and are bactericidal. Understanding the resistance mechanisms of bacteria against aminoglycosides is not only vital for improving the efficacy of this critically important group of antibiotics but also crucial for studying the molecular basis of translational fidelity. In this work, we analyzed Salmonella mutants evolved in the presence of the aminoglycoside streptomycin (Str) and identified a novel gene rimP to be involved in Str resistance. RimP is a ribosome assembly factor critical for the maturation of the 30S small subunit that binds Str. Deficiency in RimP increases resistance against Str and facilitates the development of even higher resistance. Deleting rimP decreases mistranslation and cellular uptake of Str, and further impairs flagellar motility. Our work thus highlights a previously unknown mechanism of aminoglycoside resistance via defective ribosome assembly.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Yunyi Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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8
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Lee SM, Le HT, Taizhanova A, Nong LK, Park JY, Lee EJ, Palsson BO, Kim D. Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution. Front Microbiol 2024; 14:1271121. [PMID: 38239730 PMCID: PMC10794520 DOI: 10.3389/fmicb.2023.1271121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/01/2023] [Indexed: 01/22/2024] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq. However, validation using ChIP-exo, which exhibits higher-resolution performance compared to conventional ChIP, has not been conducted to date. In this study, using the representative strain S. Typhimurium LT2 (LT2), the ChIP-exo experiment was conducted to accurately determine the binding sites of catalytic RNA polymerase subunit RpoB and major sigma factors (RpoD, RpoN, RpoS, and RpoE) during exponential phase. Integrated with the results of RNA-Seq, promoters and sigmulons for the sigma factors and their association with RpoB have been discovered. Notably, the overlapping regions among binding sites of each alternative sigma factor were found. Furthermore, comparative analysis with Escherichia coli str. K-12 substr. MG1655 (MG1655) revealed conserved binding sites of RpoD and RpoN across different species. In the case of small RNAs (sRNAs), 50 sRNAs observed their expression during the exponential growth of LT2. Collectively, the integration of ChIP-exo and RNA-Seq enables genome-scale promoter mapping with high resolution and facilitates the characterization of binding events of alternative sigma factors, enabling a comprehensive understanding of the bacterial sigma factor network and condition-specific active promoters.
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Affiliation(s)
- Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Hoa Thi Le
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Assiya Taizhanova
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Eun-Jin Lee
- Department of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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9
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Flores E, Dutta S, Bosserman R, van Hoof A, Krachler AM. Colonization of larval zebrafish ( Danio rerio) with adherent-invasive Escherichia coli prevents recovery of the intestinal mucosa from drug-induced enterocolitis. mSphere 2023; 8:e0051223. [PMID: 37971273 PMCID: PMC10732064 DOI: 10.1128/msphere.00512-23] [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: 09/05/2023] [Accepted: 10/07/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Although inflammatory bowel diseases are on the rise, what factors influence IBD risk and severity, and the underlying mechanisms remain to be fully understood. Although host genetics, microbiome, and environmental factors have all been shown to correlate with the development of IBD, cause and effect are difficult to disentangle in this context. For example, AIEC is a known pathobiont found in IBD patients, but it remains unclear if gut inflammation during IBD facilitates colonization with AIEC, or if AIEC colonization makes the host more susceptible to pro-inflammatory stimuli. It is critical to understand the mechanisms that contribute to AIEC infections in a susceptible host in order to develop successful therapeutics. Here, we show that the larval zebrafish model recapitulates key features of AIEC infections in other animal models and can be utilized to address these gaps in knowledge.
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Affiliation(s)
- Erika Flores
- Microbiology and Infectious Diseases Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Soumita Dutta
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Rachel Bosserman
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ambro van Hoof
- Microbiology and Infectious Diseases Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Anne-Marie Krachler
- Microbiology and Infectious Diseases Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
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10
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Ni J, Li S, Lai Y, Wang Z, Wang D, Tan Y, Fan Y, Lu J, Yao YF. Global profiling of ribosomal protein acetylation reveals essentiality of acetylation homeostasis in maintaining ribosome assembly and function. Nucleic Acids Res 2023; 51:10411-10427. [PMID: 37742082 PMCID: PMC10602876 DOI: 10.1093/nar/gkad768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Acetylation is a global post-translational modification that regulates various cellular processes. Bacterial acetylomic studies have revealed extensive acetylation of ribosomal proteins. However, the role of acetylation in regulating ribosome function remains poorly understood. In this study, we systematically profiled ribosomal protein acetylation and identified a total of 289 acetylated lysine residues in 52 ribosomal proteins (r-proteins) from Salmonella Typhimurium. The majority of acetylated lysine residues of r-proteins were found to be regulated by both acetyltransferase Pat and metabolic intermediate acetyl phosphate. Our results show that acetylation plays a critical role in the assembly of the mature 70S ribosome complex by modulating r-proteins binding to rRNA. Moreover, appropriate acetylation is important for the interactions between elongation factors and polysomes, as well as regulating ribosome translation efficiency and fidelity. Dysregulation of acetylation could alter bacterial sensitivity to ribosome-targeting antibiotics. Collectively, our data suggest that the acetylation homeostasis of ribosomes is crucial for their assembly and function. Furthermore, this mechanism may represent a universal response to environmental signals across different cell types.
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Affiliation(s)
- Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shuxian Li
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yanan Lai
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zuoqiang Wang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yongcong Tan
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yongqiang Fan
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - Jie Lu
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
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11
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Lyu Z, Villanueva P, O’Malley L, Murphy P, Augenstreich J, Briken V, Singh A, Ling J. Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP. Nucleic Acids Res 2023; 51:9905-9919. [PMID: 37670559 PMCID: PMC10570021 DOI: 10.1093/nar/gkad725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/12/2023] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
Translational fidelity is critical for microbial fitness, survival and stress responses. Much remains unknown about the genetic and environmental control of translational fidelity and its single-cell heterogeneity. In this study, we used a high-throughput fluorescence-based assay to screen a knock-out library of Escherichia coli and identified over 20 genes critical for stop-codon readthrough. Most of these identified genes were not previously known to affect translational fidelity. Intriguingly, we show that several genes controlling metabolism, including cyaA and crp, enhance stop-codon readthrough. CyaA catalyzes the synthesis of cyclic adenosine monophosphate (cAMP). Combining RNA sequencing, metabolomics and biochemical analyses, we show that deleting cyaA impairs amino acid catabolism and production of ATP, thus repressing the transcription of rRNAs and tRNAs to decrease readthrough. Single-cell analyses further show that cAMP is a major driver of heterogeneity in stop-codon readthrough and rRNA expression. Our results highlight that carbon metabolism is tightly coupled with stop-codon readthrough.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Patricia Villanueva
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Liam O’Malley
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Parker Murphy
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Jacques Augenstreich
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering and Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
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12
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Augenstreich J, Shuster M, Fan Y, Lyu Z, Ling J, Briken V. BBQ methods: Streamlined workflows for Bacterial Burden Quantification in infected cells by confocal microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.01.560379. [PMID: 37873092 PMCID: PMC10592879 DOI: 10.1101/2023.10.01.560379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Accurate quantification of bacterial burden within macrophages, termed Bacterial Burden Quantification (BBQ), is crucial for understanding host-pathogen interactions. Various methods have been employed, each with strengths and weaknesses. This article addresses limitations in existing techniques and introduces two novel automated methods for BBQ within macrophages based on confocal microscopy data analysis. The first method refines total fluorescence quantification by incorporating filtering steps to exclude uninfected cells, while the second method calculates total bacterial volume per cell to mitigate potential biases in fluorescence-based readouts. These workflows utilize PyImageJ and Cellpose software, providing reliable, unbiased, and rapid quantification of bacterial load. The proposed workflows were validated using Salmonella enterica serovar Typhimurium and Mycobacterium tuberculosis models, demonstrating their effectiveness in accurately assessing bacterial burden. These automated workflows offer valuable tools for studying bacterial interactions within host cells and provide insights for various research applications.
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Affiliation(s)
- Jacques Augenstreich
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Michael Shuster
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Yongqiang Fan
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
- Current affiliation: College of Life and Health Sciences, Northeastern University, Shenyang 110819, People’s Republic of China
| | - Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
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13
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Majdalani N, Chattopadhyay M, Keller C, Gottesman S. Lack of polyamines leads to cotranslational degradation of the general stress factor RpoS in Escherichia coli. J Biol Chem 2023; 299:104943. [PMID: 37343699 PMCID: PMC10372455 DOI: 10.1016/j.jbc.2023.104943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
The specialized sigma factor RpoS mediates a general stress response in Escherichia coli and related bacteria, activating promoters that allow cells to survive stationary phase and many stresses. RpoS synthesis and stability are regulated at multiple levels. Translation of RpoS is positively regulated by multiple small RNAs in response to stress. Degradation of RpoS, dependent upon the adaptor protein RssB, is rapid during exponential growth and ceases upon starvation or other stresses, increasing accumulation of RpoS. E. coli carrying mutations that block the synthesis of polyamines were previously found to have low levels of RpoS, while levels increased rapidly when polyamines were added. We have used a series of reporters to examine the basis for the lack of RpoS in polyamine-deficient cells. The polyamine requirement was independent of small RNA-mediated positive regulation of RpoS translation. Mutations in rssB stabilize RpoS and significantly bypassed the polyamine deficit, suggesting that lack of polyamines might lead to rapid RpoS degradation. However, rates of degradation of mature RpoS were unaffected by polyamine availability. Codon optimization in rpoS partially relieved the polyamine dependence, suggesting a defect in RpoS translation in the absence of polyamines. Consistent with this, a hyperproofreading allele of ribosomal protein S12, encoded by rpsL, showed a decrease in RpoS levels, and this decrease was also suppressed by either codon optimization or blocking RpoS degradation. We suggest that rpoS codon usage leads it to be particularly sensitive to slowed translation, due to either lack of polyamines or hyperproofreading, leading to cotranslational degradation. We dedicate this study to Herb Tabor and his foundational work on polyamines, including the basis for this study.
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Affiliation(s)
- Nadim Majdalani
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Manas Chattopadhyay
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bethesda, Maryland, USA
| | - Christopher Keller
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bethesda, Maryland, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA.
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14
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Patel P, Nandi A, Verma SK, Kaushik N, Suar M, Choi EH, Kaushik NK. Zebrafish-based platform for emerging bio-contaminants and virus inactivation research. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162197. [PMID: 36781138 PMCID: PMC9922160 DOI: 10.1016/j.scitotenv.2023.162197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 02/08/2023] [Indexed: 05/27/2023]
Abstract
Emerging bio-contaminants such as viruses have affected health and environment settings of every country. Viruses are the minuscule entities resulting in severe contagious diseases like SARS, MERS, Ebola, and avian influenza. Recent epidemic like the SARS-CoV-2, the virus has undergone mutations strengthen them and allowing to escape from the remedies. Comprehensive knowledge of viruses is essential for the development of targeted therapeutic and vaccination treatments. Animal models mimicking human biology like non-human primates, rats, mice, and rabbits offer competitive advantage to assess risk of viral infections, chemical toxins, nanoparticles, and microbes. However, their economic maintenance has always been an issue. Furthermore, the redundancy of experimental results due to aforementioned aspects is also in examine. Hence, exploration for the alternative animal models is crucial for risk assessments. The current review examines zebrafish traits and explores the possibilities to monitor emerging bio-contaminants. Additionally, a comprehensive picture of the bio contaminant and virus particle invasion and abatement mechanisms in zebrafish and human cells is presented. Moreover, a zebrafish model to investigate the emerging viruses such as coronaviridae and poxviridae has been suggested.
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Affiliation(s)
- Paritosh Patel
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea
| | - Aditya Nandi
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Suresh K Verma
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India; Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, 18323 Hwaseong, Republic of Korea
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea.
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15
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Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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16
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Lyu Z, Wilson C, Ling J. Translational Fidelity during Bacterial Stresses and Host Interactions. Pathogens 2023; 12:383. [PMID: 36986305 PMCID: PMC10057733 DOI: 10.3390/pathogens12030383] [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: 01/25/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Translational fidelity refers to accuracy during protein synthesis and is maintained in all three domains of life. Translational errors occur at base levels during normal conditions and may rise due to mutations or stress conditions. In this article, we review our current understanding of how translational fidelity is perturbed by various environmental stresses that bacterial pathogens encounter during host interactions. We discuss how oxidative stress, metabolic stresses, and antibiotics affect various types of translational errors and the resulting effects on stress adaption and fitness. We also discuss the roles of translational fidelity during pathogen-host interactions and the underlying mechanisms. Many of the studies covered in this review will be based on work with Salmonella enterica and Escherichia coli, but other bacterial pathogens will also be discussed.
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Affiliation(s)
| | | | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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17
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Lyu Z, Ling J. Increase in Ribosomal Fidelity Benefits Salmonella upon Bile Salt Exposure. Genes (Basel) 2022; 13:184. [PMID: 35205229 PMCID: PMC8872077 DOI: 10.3390/genes13020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Translational fidelity is maintained by multiple quality control steps in all three domains of life. Increased translational errors (mistranslation) occur due to genetic mutations and external stresses. Severe mistranslation is generally harmful, but moderate levels of mistranslation may be favored under certain conditions. To date, little is known about the link between translational fidelity and host-pathogen interactions. Salmonella enterica can survive in the gall bladder during systemic or chronic infections due to bile resistance. Here we show that increased translational fidelity contributes to the fitness of Salmonella upon bile salt exposure, and the improved fitness depends on an increased level of intracellular adenosine triphosphate (ATP). Our work thus reveals a previously unknown linkage between translational fidelity and bacterial fitness under bile stress.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
- Molecular and Cellular Biology, Bilogical Sciences Graduate Program, The University of Maryland, College Park, MD 20742, USA
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18
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Abstract
Phenotypic heterogeneity among single cells in a genetically identical population leads to diverse environmental adaptation. The human and animal pathogen Salmonella enterica serovar Typhimurium exhibits heterogeneous expression of virulence genes, including flagellar and Salmonella pathogenicity island (SPI) genes. Little is known about how the differential expression of flagellar genes among single cells affects bacterial adaptation to stresses. Here, we have developed a triple-fluorescence reporter to simultaneously monitor the expression of flagellar and SPI-1 pathways. We show that the two pathways cross talk at the single-cell level. Intriguingly, cells expressing flagella (fliC-ON) exhibit decreased tolerance to antibiotics compared to fliC-OFF cells. Such variation depends on TolC-dependent efflux pumps. We further show that fliC-ON cells contain higher intracellular proton concentrations. This suggests that the assembly and rotation of flagella consume the proton motive force and decrease the efflux activity, resulting in antibiotic sensitivity. Such a trade-off between motility and efflux highlights a novel mechanism of antibiotic tolerance.
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19
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The E. coli transcription factor GrlA is regulated by subcellular compartmentalization and activated in response to mechanical stimuli. Proc Natl Acad Sci U S A 2020; 117:9519-9528. [PMID: 32277032 DOI: 10.1073/pnas.1917500117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is a foodborne pathogen that colonizes the gastrointestinal tract and has evolved intricate mechanisms to sense and respond to the host environment. Upon the sensation of chemical and physical cues specific to the host's intestinal environment, locus of enterocyte effacement (LEE)-encoded virulence genes are activated and promote intestinal colonization. The LEE transcriptional activator GrlA mediates EHEC's response to mechanical cues characteristic of the intestinal niche, including adhesive force that results from bacterial adherence to epithelial cells and fluid shear that results from intestinal motility and transit. GrlA expression and release from its inhibitor GrlR was not sufficient to induce virulence gene transcription; mechanical stimuli were required for GrlA activation. The exact mechanism of GrlA activation, however, remained unknown. We isolated GrlA mutants that activate LEE transcription, independent of applied mechanical stimuli. In nonstimulated EHEC, wild-type GrlA associates with cardiolipin membrane domains via a patch of basic C-terminal residues, and this membrane sequestration is disrupted in EHEC that expresses constitutively active GrlA mutants. GrlA transitions from an inactive, membrane-associated state and relocalizes to the cytoplasm in response to mechanical stimuli, allowing GrlA to bind and activate the LEE1 promoter. GrlA expression and its relocalization in response to mechanical stimuli are required for optimal virulence regulation and colonization of the host intestinal tract during infection. These data suggest a posttranslational regulatory mechanism of the mechanosensor GrlA, whereby virulence gene expression can be rapidly fine-tuned in response to the highly dynamic spatiotemporal mechanical profile of the gastrointestinal tract.
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20
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Flores EM, Nguyen AT, Odem MA, Eisenhoffer GT, Krachler AM. The zebrafish as a model for gastrointestinal tract-microbe interactions. Cell Microbiol 2020; 22:e13152. [PMID: 31872937 DOI: 10.1111/cmi.13152] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/07/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023]
Abstract
The zebrafish (Danio rerio) has become a widely used vertebrate model for bacterial, fungal, viral, and protozoan infections. Due to its genetic tractability, large clutch sizes, ease of manipulation, and optical transparency during early life stages, it is a particularly useful model to address questions about the cellular microbiology of host-microbe interactions. Although its use as a model for systemic infections, as well as infections localised to the hindbrain and swimbladder having been thoroughly reviewed, studies focusing on host-microbe interactions in the zebrafish gastrointestinal tract have been neglected. Here, we summarise recent findings regarding the developmental and immune biology of the gastrointestinal tract, drawing parallels to mammalian systems. We discuss the use of adult and larval zebrafish as models for gastrointestinal infections, and more generally, for studies of host-microbe interactions in the gut.
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Affiliation(s)
- Erika M Flores
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.,M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas
| | - Anh T Nguyen
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.,M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas
| | - Max A Odem
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - George T Eisenhoffer
- M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas.,Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anne Marie Krachler
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.,M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas
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