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Sałamaszyńska-Guz A, Murawska M, Bącal P, Ostrowska A, Kwiecień E, Stefańska I, Douthwaite S. Increased Motility in Campylobacter jejuni and Changes in Its Virulence, Fitness, and Morphology Following Protein Expression on Ribosomes with Altered RsmA Methylation. Int J Mol Sci 2024; 25:9797. [PMID: 39337285 DOI: 10.3390/ijms25189797] [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: 08/01/2024] [Revised: 09/05/2024] [Accepted: 09/07/2024] [Indexed: 09/30/2024] Open
Abstract
Infection with Campylobacter jejuni is the major cause of human gastroenteritis in the United States and Europe, leading to debilitating autoimmune sequelae in many cases. While considerable progress has been made in detailing the infectious cycle of C. jejuni, a full understanding of the molecular mechanisms responsible for virulence remains to be elucidated. Here, we apply a novel approach by modulating protein expression on the pathogen's ribosomes by inactivating a highly conserved rRNA methyltransferase. Loss of the RsmA methyltransferase results in a more motile strain with greater adhesive and cell-invasive properties. These phenotypical effects correlate with enhanced expression of specific proteins related to flagellar formation and function, together with enzymes involved in cell wall/membrane and amino acid synthesis. Despite the enhancement of certain virulent traits, the null strain grows poorly on minimal media and is rapidly out-competed by the wild-type strain. Complementation with an active copy of the rsmA gene rescues most of the traits changed in the mutant. However, the complemented strain overexpresses rsmA and displays new flaws, including loss of the spiral cell shape, which is distinctive for C. jejuni. Proteins linked with altered virulence and morphology are identified here by mass spectrometry proteomic analyses of the strains.
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Affiliation(s)
- Agnieszka Sałamaszyńska-Guz
- Division of Microbiology, Department of Pre-Clinical Sciences, Institute of Veterinary Medicine, Warsaw University of Live Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Małgorzata Murawska
- Division of Microbiology, Department of Pre-Clinical Sciences, Institute of Veterinary Medicine, Warsaw University of Live Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Paweł Bącal
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00-818 Warsaw, Poland
| | - Agnieszka Ostrowska
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Live Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Ewelina Kwiecień
- Division of Microbiology, Department of Pre-Clinical Sciences, Institute of Veterinary Medicine, Warsaw University of Live Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Ilona Stefańska
- Division of Microbiology, Department of Pre-Clinical Sciences, Institute of Veterinary Medicine, Warsaw University of Live Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Stephen Douthwaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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Sun J, Kinman LF, Jahagirdar D, Ortega J, Davis JH. KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion. Nat Struct Mol Biol 2023; 30:1468-1480. [PMID: 37653244 PMCID: PMC10710901 DOI: 10.1038/s41594-023-01078-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
Abstract
Ribosome assembly is orchestrated by many assembly factors, including ribosomal RNA methyltransferases, whose precise role is poorly understood. Here, we leverage the power of cryo-EM and machine learning to discover that the E. coli methyltransferase KsgA performs a 'proofreading' function in the assembly of the small ribosomal subunit by recognizing and partially disassembling particles that have matured but are not competent for translation. We propose that this activity allows inactive particles an opportunity to reassemble into an active state, thereby increasing overall assembly fidelity. Detailed structural quantifications in our datasets additionally enabled the expansion of the Nomura assembly map to highlight rRNA helix and r-protein interdependencies, detailing how the binding and docking of these elements are tightly coupled. These results have wide-ranging implications for our understanding of the quality-control mechanisms governing ribosome biogenesis and showcase the power of heterogeneity analysis in cryo-EM to unveil functionally relevant information in biological systems.
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Affiliation(s)
- Jingyu Sun
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Laurel F Kinman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Dushyant Jahagirdar
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada.
- Centre for Structural Biology, McGill University, Montreal, Quebec, Canada.
| | - Joseph H Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA.
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3
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Hayashi Y, Funakoshi M, Hirosawa K, Zhang-Akiyama QM. The H2TH-like motif of the Escherichia coli multifunctional protein KsgA is required for DNA binding involved in DNA repair and the suppression of mutation frequencies. Genes Environ 2023; 45:13. [PMID: 37041652 PMCID: PMC10091538 DOI: 10.1186/s41021-023-00266-5] [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: 06/18/2022] [Accepted: 02/23/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND DNA oxidatively damaged by reactive oxygen species is repaired by base excision repair (BER) pathway proteins, with DNA glycosylases removing damaged or mismatched bases in the first step of BER. KsgA is a multifunctional protein that exhibits the activities of two enzymes, DNA glycosylase and rRNA dimethyltransferase. The structure-function relationship of the KsgA protein in cellular DNA repair remains unclear because the domains required for KsgA to recognize DNA have not been identified. PURPOSE To clarify the mechanisms by which KsgA recognizes damaged DNA and to identify the DNA-binding site, which exists in KsgA. METHODS A structural analysis and in vitro DNA-protein binding assay were performed. The C-terminal function of the KsgA protein was investigated in vitro and in vivo. RESULTS The 3D conformations of KsgA, MutM, and Nei were compared at UCSF Chimera. The root mean square deviation of KsgA (214-273) and MutM (148-212) and that of KsgA (214-273) and Nei (145-212) were 1.067 and 1.188 Å, both less than 2 Å, suggesting that the C terminal of KsgA is spatially similar to the H2TH domains of MutM and Nei. The full-length KsgA protein and KsgA lacking 1-8 or 214-273 amino acids were purified and used in gel mobility shift assays. KsgA exhibited DNA-binding activity, which was lost in the C-terminally deleted KsgA protein. Spontaneous mutation frequency was measured using a mutM mutY ksgA-deficient strain, and the results obtained showed that the mutation frequency was not suppressed by KsgA lacking the C-terminal region, whereas it was in KsgA. To assess dimethyltransferase activity, kasugamycin sensitivity was assessed in wild-type and ksgA-deficient strains. Plasmids carrying the full-length ksgA gene and C-terminal deletion gene were introduced into ksgA-deficient strains. KsgA lacking the C terminus restored dimethyltransferase activity in the ksgA-deficient strain as well as KsgA. CONCLUSION The present results confirmed that one enzyme exhibited two activities and revealed that the C-terminal (214-273) amino acids of KsgA were highly similar to the H2TH structural domain, exhibited DNA-binding activity, and inhibited spontaneous mutations. This site is not essential for dimethyltransferase activity.
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Affiliation(s)
- Yuichiro Hayashi
- Laboratory of Stress Response Biology, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Takara Bio Inc., Nojihigashi, Kusatsu-shi, Shiga, 525-0058, Japan
| | - Masafumi Funakoshi
- Laboratory of Stress Response Biology, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, 606-8507, Japan
| | - Kaname Hirosawa
- Laboratory of Stress Response Biology, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Qiu-Mei Zhang-Akiyama
- Laboratory of Stress Response Biology, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
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Ponzetti M, Rucci N, Falone S. RNA methylation and cellular response to oxidative stress-promoting anticancer agents. Cell Cycle 2023; 22:870-905. [PMID: 36648057 PMCID: PMC10054233 DOI: 10.1080/15384101.2023.2165632] [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: 10/28/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Disruption of the complex network that regulates redox homeostasis often underlies resistant phenotypes, which hinder effective and long-lasting cancer eradication. In addition, the RNA methylome-dependent control of gene expression also critically affects traits of cellular resistance to anti-cancer agents. However, few investigations aimed at establishing whether the epitranscriptome-directed adaptations underlying acquired and/or innate resistance traits in cancer could be implemented through the involvement of redox-dependent or -responsive signaling pathways. This is unexpected mainly because: i) the effectiveness of many anti-cancer approaches relies on their capacity to promote oxidative stress (OS); ii) altered redox milieu and reprogramming of mitochondrial function have been acknowledged as critical mediators of the RNA methylome-mediated response to OS. Here we summarize the current state of understanding on this topic, as well as we offer new perspectives that might lead to original approaches and strategies to delay or prevent the problem of refractory cancer and tumor recurrence.
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Affiliation(s)
- Marco Ponzetti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Nadia Rucci
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Stefano Falone
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
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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: 6] [Impact Index Per Article: 6.0] [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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Nigo F, Nakagawa R, Hirai Y, Imai L, Suzuki Y, Furuta K, Kaito C. Staphylococcus aureus MazG hydrolyzes oxidized guanine nucleotides and contributes to oxidative stress resistance. Biochimie 2023; 209:52-60. [PMID: 36746255 DOI: 10.1016/j.biochi.2023.02.001] [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: 11/23/2022] [Revised: 01/23/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
We previously reported that knockout of the mazG (SA1292) gene decreases Staphylococcus aureus killing activity against silkworms. S. aureus MazG (SaMazG) has a nucleotide pyrophosphatase domain conserved among MazG family proteins, but its biochemical characteristics are unknown. In the present study, we purified recombinant N-terminal His-tagged SaMazG protein and examined its biochemical activity. SaMazG hydrolyzed GTP, UTP, dGTP, and TTP into nucleoside monophosphates. Hydrolytic activity of SaMazG against ATP, CTP, dATP, and dCTP was low or not detected. SaMazG exhibited high hydrolytic activity against 8-oxo-GTP and 8-oxo-dGTP, oxidized guanine nucleotides, with a Vmax/Km ratio more than 15-fold that of GTP. Furthermore, the S. aureus mazG knockout mutant was sensitive to hydrogen peroxide compared with the parent strain. These results suggest that SaMazG is a nucleotide pyrophosphatase hydrolyzing oxidized guanine nucleotides that contributes to the oxidative stress resistance of S. aureus.
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Affiliation(s)
- Fuki Nigo
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
| | - Ryosuke Nakagawa
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
| | - Yuuki Hirai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Lina Imai
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
| | - Kazuyuki Furuta
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
| | - Chikara Kaito
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
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7
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Salaikumaran MR, Badiger VP, Burra VLSP. 16S rRNA Methyltransferases as Novel Drug Targets Against Tuberculosis. Protein J 2022; 41:97-130. [PMID: 35112243 DOI: 10.1007/s10930-021-10029-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) is an airborne infectious disease caused by Mycobacterium tuberculosis (M.tb) whose natural history traces back to 70,000 years. TB remains a major global health burden. Methylation is a type of post-replication, post-transcriptional and post-translational epi-genetic modification involved in transcription, translation, replication, tissue specific expression, embryonic development, genomic imprinting, genome stability and chromatin structure, protein protein interactions and signal transduction indicating its indispensable role in survival of a pathogen like M.tb. The pathogens use this epigenetic mechanism to develop resistance against certain drug molecules and survive the lethality. Drug resistance has become a major challenge to tackle and also a major concern raised by WHO. Methyltransferases are enzymes that catalyze the methylation of various substrates. None of the current TB targets belong to methyltransferases which provides therapeutic opportunities to develop novel drugs through studying methyltransferases as potential novel targets against TB. Targeting 16S rRNA methyltransferases serves two purposes simultaneously: a) translation inhibition and b) simultaneous elimination of the ability to methylate its substrates hence stopping the emergence of drug resistance strains. There are ~ 40 different rRNA methyltransferases and 13 different 16S rRNA specific methyltransferases which are unexplored and provide a huge opportunity for treatment of TB.
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Affiliation(s)
- M R Salaikumaran
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed To Be) University, Vaddeswaram, Andhra Pradesh, 522 502, India
| | - Veena P Badiger
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed To Be) University, Vaddeswaram, Andhra Pradesh, 522 502, India
| | - V L S Prasad Burra
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed To Be) University, Vaddeswaram, Andhra Pradesh, 522 502, India.
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8
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MdaB and NfrA, two novel reductases important in the survival and persistence of the major enteropathogen Campylobacter jejuni. J Bacteriol 2021; 204:e0042121. [PMID: 34606373 PMCID: PMC8765430 DOI: 10.1128/jb.00421-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The paralogues RrpA and RrpB, which are members of the MarR family of DNA binding proteins, are important for the survival of the global bacterial foodborne pathogen Campylobacter jejuni under redox stress. We report that RrpA is a positive regulator of mdaB, encoding a flavin-dependent quinone reductase that contributes to the protection from redox stress mediated by structurally diverse quinones, while RrpB negatively regulates the expression of cj1555c (renamed nfrA for NADPH-flavin reductase A), encoding a flavin reductase. NfrA reduces riboflavin at a greater rate than its derivatives, suggesting that exogenous free flavins are the natural substrate. MdaB and NfrA both prefer NADPH as an electron donor. Cysteine substitution and posttranslational modification analyses indicated that RrpA and RrpB employ a cysteine-based redox switch. Complete genome sequence analyses revealed that mdaB is frequently found in Campylobacter and related Helicobacter spp., while nfrA is predominant in C. jejuni strains. Quinones and flavins are redox cycling agents secreted by a wide range of cell types that can form damaging superoxide by one-electron reactions. We propose a model for stress adaptation where MdaB and NfrA facilitate a two-electron reduction mechanism to the less toxic hydroquinones, thus aiding survival and persistence of this major pathogen. IMPORTANCE Changes in cellular redox potential result in alteration in the oxidation state of intracellular metabolites and enzymes; consequently, cells make adjustments that favor growth and survival. The work we present here answers some of the many questions that have remained elusive over the years of investigation into the enigmatic microaerophile bacterium Campylobacter jejuni. We employed molecular approaches to understand the regulation mechanisms and functional analyses to reveal the roles of two novel quinone and flavin reductases; both serve as major pools of cellular redox-active molecules. This work extends our knowledge on bacterial redox sensing mechanisms and the significance of hemostasis.
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Kaito C, Murakami K, Imai L, Furuta K. Animal infection models using non-mammals. Microbiol Immunol 2020; 64:585-592. [PMID: 32757288 PMCID: PMC7590188 DOI: 10.1111/1348-0421.12834] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 12/31/2022]
Abstract
The use of non-human animal models for infection experiments is important for investigating the infectious processes of human pathogenic bacteria at the molecular level. Mammals, such as mice and rabbits, are also utilized as animal infection models, but large numbers of animals are needed for these experiments, which is costly, and fraught with ethical issues. Various non-mammalian animal infection models have been used to investigate the molecular mechanisms of various human pathogenic bacteria, including Staphylococcus aureus, Streptococcus pyogenes, and Pseudomonas aeruginosa. This review discusses the desirable characteristics of non-mammalian infection models and describes recent non-mammalian infection models that utilize Caenorhabditis elegans, silkworm, fruit fly, zebrafish, two-spotted cricket, hornworm, and waxworm.
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Affiliation(s)
- Chikara Kaito
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Kanade Murakami
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Lina Imai
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Kazuyuki Furuta
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Sharma H, Anand B. Ribosome assembly defects subvert initiation Factor3 mediated scrutiny of bona fide start signal. Nucleic Acids Res 2020; 47:11368-11386. [PMID: 31586395 PMCID: PMC6868393 DOI: 10.1093/nar/gkz825] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/17/2019] [Accepted: 10/03/2019] [Indexed: 12/02/2022] Open
Abstract
In bacteria, the assembly factors tightly orchestrate the maturation of ribosomes whose competency for protein synthesis is validated by translation machinery at various stages of translation cycle. However, what transpires to the quality control measures when the ribosomes are produced with assembly defects remains enigmatic. In Escherichia coli, we show that 30S ribosomes that harbour assembly defects due to the lack of assembly factors such as RbfA and KsgA display suboptimal initiation codon recognition and bypass the critical codon–anticodon proofreading steps during translation initiation. These premature ribosomes on entering the translation cycle compromise the fidelity of decoding that gives rise to errors during initiation and elongation. We show that the assembly defects compromise the binding of initiation factor 3 (IF3), which in turn appears to license the rapid transition of 30S (pre) initiation complex to 70S initiation complex by tempering the validation of codon–anticodon interaction during translation initiation. This suggests that the premature ribosomes harbouring the assembly defects subvert the IF3 mediated proofreading of cognate initiation codon to enter the translation cycle.
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Affiliation(s)
- Himanshu Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - B Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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Díaz-Riaño J, Posada L, Acosta IC, Ruíz-Pérez C, García-Castillo C, Reyes A, Zambrano MM. Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems. PLoS One 2019; 14:e0221540. [PMID: 31790419 PMCID: PMC6886795 DOI: 10.1371/journal.pone.0221540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023] Open
Abstract
Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m2 of UVR (with >95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the immediate radiation response of D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions.
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Affiliation(s)
- Jorge Díaz-Riaño
- Corporación Corpogen Research Center, Bogotá D.C, Colombia
- Research group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de Los Andes, Bogotá D.C, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá D.C, Colombia
| | | | | | - Carlos Ruíz-Pérez
- Research group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de Los Andes, Bogotá D.C, Colombia
| | - Catalina García-Castillo
- Research group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de Los Andes, Bogotá D.C, Colombia
| | - Alejandro Reyes
- Research group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de Los Andes, Bogotá D.C, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá D.C, Colombia
- Center of Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, United States of America
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12
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Staphylococcus aureus aggregation in the plasma fraction of silkworm hemolymph. PLoS One 2019; 14:e0217517. [PMID: 31145754 PMCID: PMC6542516 DOI: 10.1371/journal.pone.0217517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/13/2019] [Indexed: 11/19/2022] Open
Abstract
Staphylococcus aureus formed bacterial aggregates in the plasma fraction of the hemolymph of silkworm, the larva of Bombyx mori, in a growth-dependent manner. The addition of arabinose or galactose inhibited the formation of S. aureus aggregates in the silkworm plasma. Formation of the bacterial aggregates depended on S. aureus genes required for the synthesis of bacterial surface polysaccharides–ypfP and ltaA, which are involved in lipoteichoic acid synthesis, and the tagO gene, which is involved in wall teichoic acid synthesis. These findings suggest that S. aureus forms bacterial aggregates in the silkworm plasma via bacterial surface teichoic acids.
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Matsumoto Y, Sekimizu K. Silkworm as an experimental animal for research on fungal infections. Microbiol Immunol 2019; 63:41-50. [PMID: 30666711 PMCID: PMC6594098 DOI: 10.1111/1348-0421.12668] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/04/2019] [Accepted: 01/13/2019] [Indexed: 12/26/2022]
Abstract
Silkworm, Bombyx mori, has various advantages as an experimental animal, such as the low cost for rearing and fewer ethical problems. Models utilizing silkworms of infection with pathogenic bacteria have been established for identification of genes encoding virulence factors by large-scale in vivo screening. In this review, we describe recent progress in the study of silkworm infection models for elucidating the mechanisms of fungi infection. Silkworm infection models have been established for Candida albicans, Candida tropicalis, Candida glabrata and Cryptococcus neoformans, which are yeast type fungi, and Aspergillus fumigatus, Arthroderma vanbreuseghemii, Arthroderma benhamiae, Microsporum canis, Trichophyton rubrum, and Rhizopus oryzae, which are filamentous fungi. Novel genes encoding virulence factors in C. albicans and C. glabrata have been identified by using the silkworm infection models. We here outline the benefits of using silkworm infection models and a strategy for identifying the genes responsible for pathogenicity of microorganisms such as fungi. © 2019 The Authors. Microbiology and Immunology Published by The Societies and John Wiley & Sons Australia, Ltd.
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Affiliation(s)
- Yasuhiko Matsumoto
- Teikyo University Institute of Medical Mycology359 OtsukaHachiojiTokyo 192‐0395Japan
| | - Kazuhisa Sekimizu
- Teikyo University Institute of Medical Mycology359 OtsukaHachiojiTokyo 192‐0395Japan
- Genome Pharmaceuticals Institute102 Next Building, 3‐24‐17 HongoBunkyo‐kuTokyo 113‐0033Japan
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Studies on Aminoglycoside Susceptibility Identify a Novel Function of KsgA To Secure Translational Fidelity during Antibiotic Stress. Antimicrob Agents Chemother 2018; 62:AAC.00853-18. [PMID: 30082289 DOI: 10.1128/aac.00853-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance has become a global crisis. Studies on the mechanism of bacterial tolerance to antibiotics will not only increase our conceptual understanding of bacterial death but also provide potential targets for novel inhibitors. We screened a mutant library containing a full set of in-frame deletion mutants of Escherichia coli K-12 and identified 140 genes that possibly contribute to gentamicin tolerance. The deletion of ksgA increased the inhibition and killing potency against mid-log-phase bacteria by aminoglycosides. Initially identified as a 16S rRNA methyltransferase, KsgA also has additional functions as a ribosomal biogenesis factor and a DNA glycosylase. We found that the methyltransferase activity of KsgA is responsible for the tolerance, as demonstrated by a site-directed mutagenesis analysis. In contrast to the mechanism for cold sensitivity, the decreased tolerance to aminoglycoside is not related to the failure of ribosomal biogenesis. Furthermore, the DNA glycosylase activity of KsgA contributes minimally to kanamycin tolerance. Importantly, we discovered that KsgA secures protein translational fidelity upon kanamycin killing, in contrast to its role during cold stress and kasugamycin treatment. The results suggest that the compromise in protein translational fidelity in the absence of KsgA is the root cause of an increased sensitivity to a bactericidal aminoglycoside. In addition, KsgA in the pathogenic Acinetobacter baumannii contributes not only to the tolerance against aminoglycoside killing but also to virulence in the host, warranting its potential application as a target for inhibitors that potentiate aminoglycoside therapeutic killing as well as disarm bacterial virulence simultaneously.
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Errors during Gene Expression: Single-Cell Heterogeneity, Stress Resistance, and Microbe-Host Interactions. mBio 2018; 9:mBio.01018-18. [PMID: 29970467 PMCID: PMC6030554 DOI: 10.1128/mbio.01018-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Gene expression has been considered a highly accurate process, and deviation from such fidelity has been shown previously to be detrimental for the cell. More recently, increasing evidence has supported the notion that the accuracy of gene expression is indeed flexibly variable. The levels of errors during gene expression differ from condition to condition and even from cell to cell within genetically identical populations grown under the same conditions. The different levels of errors resulting from inaccurate gene expression are now known to play key roles in regulating microbial stress responses and host interactions. This minireview summarizes the recent development in understanding the level, regulation, and physiological impact of errors during gene expression. Gene expression has been considered a highly accurate process, and deviation from such fidelity has been shown previously to be detrimental for the cell. More recently, increasing evidence has supported the notion that the accuracy of gene expression is indeed flexibly variable.
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Protein tyrosine kinase, PtkA, is required for Mycobacterium tuberculosis growth in macrophages. Sci Rep 2018; 8:155. [PMID: 29317718 PMCID: PMC5760654 DOI: 10.1038/s41598-017-18547-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/13/2017] [Indexed: 01/08/2023] Open
Abstract
Protein phosphorylation plays a key role in Mycobacterium tuberculosis (Mtb) physiology and pathogenesis. We have previously shown that a secreted protein tyrosine phosphatase, PtpA, is essential for Mtb inhibition of host macrophage acidification and maturation, and is a substrate of the protein tyrosine kinase, PtkA, encoded in the same operon. In this study, we constructed a ∆ptkA deletion mutant in Mtb and found that the mutant exhibited impaired intracellular survival in the THP-1 macrophage infection model, correlated with the strain's inability to inhibit macrophage phagosome acidification. By contrast, the mutant displayed increased resistance to oxidative stress in vitro. Proteomic and transcriptional analyses revealed upregulation of ptpA, and increased secretion of TrxB2, in the ΔptkA mutant. Kinase and protein-protein interaction studies demonstrated that TrxB2 is a substrate of PtkA phosphorylation. Taken together these studies establish a central role for the ptkA-ptpA operon in Mtb pathogenesis.
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Kochi Y, Matsumoto Y, Sekimizu K, Kaito C. Two-spotted cricket as an animal infection model of human pathogenic fungi. Drug Discov Ther 2017; 11:259-266. [PMID: 29081438 DOI: 10.5582/ddt.2017.01052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Invertebrate infection models that can be evaluated at human body temperature are limited. In this study, we utilized the two-spotted cricket, a heat-tolerant insect, as an animal infection model of human pathogenic fungi. Injection of human pathogenic fungi, including Candida albicans, Candida glabrata, and Cryptococcus neoformans killed crickets within 48 h at both 27˚C and 37˚C. The median lethal dose values (LD50 values) of C. albicans and C. glabrata against crickets were decreased at 37˚C compared to that at 27˚C, whereas the LD50 value of C. neoformans was not different between 27˚C and 37˚C. Heat-killed cells of the three different fungi also killed crickets, but the LD50 value of the heat-killed cells was higher than 5-fold that of live fungal cells in the respective species. C. neoformans gene-knockout strains of cna1, gpa1, and pka1, which are required for virulence in mammals, had greater LD50 values than the parent strain in crickets. These findings suggest that the two-spotted cricket is a valuable infection model of human pathogenic fungi that can be used to evaluate fungal virulence at variable temperatures, including 37˚C, and that the killing abilities of C. albicans and C. glabrata against animals are increased at 37˚C.
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Affiliation(s)
- Yuto Kochi
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | | | | | - Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo
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Imae K, Saito Y, Kizaki H, Ryuno H, Mao H, Miyashita A, Suzuki Y, Sekimizu K, Kaito C. Novel Nucleoside Diphosphatase Contributes to Staphylococcus aureus Virulence. J Biol Chem 2016; 291:18608-18619. [PMID: 27422825 DOI: 10.1074/jbc.m116.721845] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Indexed: 11/06/2022] Open
Abstract
We identified SA1684 as a Staphylococcus aureus virulence gene using a silkworm infection model. The SA1684 gene product carried the DUF402 domain, which is found in RNA-binding proteins, and had amino acid sequence similarity with a nucleoside diphosphatase, Streptomyces coelicolor SC4828 protein. The SA1684-deletion mutant exhibited drastically decreased virulence, in which the LD50 against silkworms was more than 10 times that of the parent strain. The SA1684-deletion mutant also exhibited decreased exotoxin production and colony-spreading ability. Purified SA1684 protein had Mn(2+)- or Co(2+)-dependent hydrolyzing activity against nucleoside diphosphates. Alanine substitutions of Tyr-88, Asp-106, and Asp-123/Glu-124, which are conserved between SA1684 and SC4828, diminished the nucleoside diphosphatase activity. Introduction of the wild-type SA1684 gene restored the hemolysin production of the SA1684-deletion mutant, whereas none of the alanine-substituted SA1684 mutant genes restored the hemolysin production. RNA sequence analysis revealed that SA1684 is required for the expression of the virulence regulatory genes agr, sarZ, and sarX, as well as metabolic genes involved in glycolysis and fermentation pathways. These findings suggest that the novel nucleoside diphosphatase SA1684 links metabolic pathways and virulence gene expression and plays an important role in S. aureus virulence.
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Affiliation(s)
- Kenta Imae
- From the Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-Chome, Hongo, Bunkyo-ku, Tokyo 113-0033 and
| | - Yuki Saito
- From the Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-Chome, Hongo, Bunkyo-ku, Tokyo 113-0033 and
| | - Hayato Kizaki
- From the Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-Chome, Hongo, Bunkyo-ku, Tokyo 113-0033 and
| | - Hiroki Ryuno
- From the Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-Chome, Hongo, Bunkyo-ku, Tokyo 113-0033 and
| | - Han Mao
- From the Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-Chome, Hongo, Bunkyo-ku, Tokyo 113-0033 and
| | - Atsushi Miyashita
- From the Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-Chome, Hongo, Bunkyo-ku, Tokyo 113-0033 and
| | - Yutaka Suzuki
- the Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Kazuhisa Sekimizu
- From the Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-Chome, Hongo, Bunkyo-ku, Tokyo 113-0033 and
| | - Chikara Kaito
- From the Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-Chome, Hongo, Bunkyo-ku, Tokyo 113-0033 and
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Kaito C. Understanding of bacterial virulence using the silkworm infection model. Drug Discov Ther 2016; 10:30-3. [DOI: 10.5582/ddt.2016.01020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo
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