1
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Barlow VL, Tsai YH. Acetylation at Lysine 86 of Escherichia coli HUβ Modulates the DNA-Binding Capability of the Protein. Front Microbiol 2022; 12:809030. [PMID: 35185833 PMCID: PMC8854993 DOI: 10.3389/fmicb.2021.809030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
DNA-binding protein HU is highly conserved in bacteria and has been implicated in a range of cellular processes and phenotypes. Like eukaryotic histones, HU is subjected to post-translational modifications. Specifically, acetylation of several lysine residues have been reported in both homologs of Escherichia coli HU. Here, we investigated the effect of acetylation at Lys67 and Lys86, located in the DNA binding-loop and interface of E. coli HUβ, respectively. Using the technique of genetic code expansion, homogeneous HUβ(K67ac) and HUβ(K86ac) protein units were obtained. Acetylation at Lys86 seemed to have negligible effects on protein secondary structure and thermal stability. Nevertheless, we found that this site-specific acetylation can regulate DNA binding by the HU homodimer but not the heterodimer. Intriguingly, while Lys86 acetylation reduced the interaction of the HU homodimer with short double-stranded DNA containing a 2-nucleotide gap or nick, it enhanced the interaction with longer DNA fragments and had minimal effect on a short, fully complementary DNA fragment. These results demonstrate the complexity of post-translational modifications in functional regulation, as well as indicating the role of lysine acetylation in tuning bacterial gene transcription and epigenetic regulation.
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Affiliation(s)
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- *Correspondence: Yu-Hsuan Tsai,
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2
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Extracellular DNA (eDNA). A Major Ubiquitous Element of the Bacterial Biofilm Architecture. Int J Mol Sci 2021; 22:ijms22169100. [PMID: 34445806 PMCID: PMC8396552 DOI: 10.3390/ijms22169100] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/22/2022] Open
Abstract
After the first ancient studies on microbial slime (the name by which the biofilm matrix was initially indicated), multitudes of studies on the morphology, composition and physiology of biofilms have arisen. The emergence of the role that biofilms play in the pathogenesis of recalcitrant and persistent clinical infections, such as periprosthetic orthopedic infections, has reinforced scientific interest. Extracellular DNA (eDNA) is a recently uncovered component that is proving to be almost omnipresent in the extracellular polymeric substance (EPS) of biofilm. This macromolecule is eliciting unprecedented consideration for the critical impact on the pathogenesis of chronic clinical infections. After a systematic review of the literature, an updated description of eDNA in biofilms is presented, with a special focus on the latest findings regarding its fundamental structural role and the contribution it makes to the complex architecture of bacterial biofilms through interactions with a variety of other molecular components of the biofilm matrix.
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3
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The Pathogenic Factors from Oral Streptococci for Systemic Diseases. Int J Mol Sci 2019; 20:ijms20184571. [PMID: 31540175 PMCID: PMC6770522 DOI: 10.3390/ijms20184571] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 02/06/2023] Open
Abstract
The oral cavity is suggested as the reservoir of bacterial infection, and the oral and pharyngeal biofilms formed by oral bacterial flora, which is comprised of over 700 microbial species, have been found to be associated with systemic conditions. Almost all oral microorganisms are non-pathogenic opportunistic commensals to maintain oral health condition and defend against pathogenic microorganisms. However, oral Streptococci, the first microorganisms to colonize oral surfaces and the dominant microorganisms in the human mouth, has recently gained attention as the pathogens of various systemic diseases, such as infective endocarditis, purulent infections, brain hemorrhage, intestinal inflammation, and autoimmune diseases, as well as bacteremia. As pathogenic factors from oral Streptococci, extracellular polymeric substances, toxins, proteins and nucleic acids as well as vesicles, which secrete these components outside of bacterial cells in biofilm, have been reported. Therefore, it is necessary to consider that the relevance of these pathogenic factors to systemic diseases and also vaccine candidates to protect infectious diseases caused by Streptococci. This review article focuses on the mechanistic links among pathogenic factors from oral Streptococci, inflammation, and systemic diseases to provide the current understanding of oral biofilm infections based on biofilm and widespread systemic diseases.
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4
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Conforte VP, Malamud F, Yaryura PM, Toum Terrones L, Torres PS, De Pino V, Chazarreta CN, Gudesblat GE, Castagnaro AP, R. Marano M, Vojnov AA. The histone-like protein HupB influences biofilm formation and virulence in Xanthomonas citri ssp. citri through the regulation of flagellar biosynthesis. MOLECULAR PLANT PATHOLOGY 2019; 20:589-598. [PMID: 30537413 PMCID: PMC6637892 DOI: 10.1111/mpp.12777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Citrus canker is an important disease of citrus, whose causal agent is the bacterium Xanthomonas citri ssp. citri (Xcc). In previous studies, we found a group of Xcc mutants, generated by the insertion of the Tn5 transposon, which showed impaired ability to attach to an abiotic substrate. One of these mutants carries the Tn5 insertion in hupB, a gene encoding a bacterial histone-like protein, homologue to the β-subunit of the Heat-Unstable (HU) nucleoid protein of Escherichia coli. These types of protein are necessary to maintain the bacterial nucleoid organization and the global regulation of gene expression. Here, we characterized the influence of the mutation in hupB regarding Xcc biofilm formation and virulence. The mutant strain hupB was incapable of swimming in soft agar, whereas its complemented strain partially recovered this phenotype. Electron microscope imaging revealed that impaired motility of hupB was a consequence of the absence of the flagellum. Comparison of the expression of flagellar genes between the wild-type strain and hupB showed that the mutant exhibited decreased expression of fliC (encoding flagellin). The hupB mutant also displayed reduced virulence compared with the wild-type strain when they were used to infect Citrus lemon plants using different infection methods. Our results therefore show that the histone-like protein HupB plays an essential role in the pathogenesis of Xcc through the regulation of biofilm formation and biosynthesis of the flagellum.
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Affiliation(s)
- Valeria P. Conforte
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICETSaladillo 2468Ciudad de Buenos AiresC1440FFXArgentina
| | - Florencia Malamud
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San MartínCampus Migueletes, 25 de Mayo y FranciaGeneral San MartínB1650HMN Provincia de Buenos AiresArgentina
| | - Pablo M. Yaryura
- Centro de Investigaciones y Transferencia de Villa María CONICETUniversidad de Villa MaríaCarlos Pellegrini 211Villa María, X5900FSECórdobaArgentina
| | - Laila Toum Terrones
- Departamento de FisiologíaBiología Molecular y Celular, Instituto de Biodiversidad y Biología Experimental y Aplicada, CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos AiresIntendente Güiraldes 2160Buenos AiresC1428EGAArgentina
| | - Pablo S. Torres
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICETSaladillo 2468Ciudad de Buenos AiresC1440FFXArgentina
| | - Verónica De Pino
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICETSaladillo 2468Ciudad de Buenos AiresC1440FFXArgentina
| | - Cristian N. Chazarreta
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICETSaladillo 2468Ciudad de Buenos AiresC1440FFXArgentina
| | - Gustavo E. Gudesblat
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Av. William Cross 3150Las TalitasC.P. T4101XACTucumánArgentina
| | - Atilio P. Castagnaro
- Departamento de FisiologíaBiología Molecular y Celular, Instituto de Biodiversidad y Biología Experimental y Aplicada, CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos AiresIntendente Güiraldes 2160Buenos AiresC1428EGAArgentina
| | - María R. Marano
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias, Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioSuipacha 531RosarioS2002LRKSanta FéArgentina
| | - Adrian A. Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICETSaladillo 2468Ciudad de Buenos AiresC1440FFXArgentina
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5
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Guan Z, Wang Y, Gao L, Zhang W, Lu X. Effects of the histone-like protein HU on cellulose degradation and biofilm formation of Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2018; 102:6593-6611. [PMID: 29876607 DOI: 10.1007/s00253-018-9071-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/26/2018] [Accepted: 04/29/2018] [Indexed: 01/23/2023]
Abstract
Cytophaga hutchinsonii, belonging to Bacteroidetes, is speculated to use a novel cell-contact mode to digest cellulose. In this study, we identified a histone-like protein HU, CHU_2750, in C. hutchinsonii, whose transcription could be induced by crystalline but not amorphous cellulose. We constructed a CHU_2750-deleted mutant and expressed CHU_2750 in Escherichia coli to study the gene's functions. Our results showed that although the deletion of CHU_2750 was not lethal to C. hutchinsonii, the mutant displayed an abnormal filamentous morphology, loose nucleoid, and obvious defects in the degradation of crystalline cellulose and cell motility. Further study indicated that the mutant displayed significantly decreased cell surface and intracellular endoglucanase activities but with β-glucosidase activities similar to the wild-type strain. Analyses by real-time quantitative PCR revealed that the transcription levels of many genes involved in cellulose degradation and/or cell motility were significantly downregulated in the mutant. In addition, we found that CHU_2750 was important for biofilm formation of C. hutchinsonii. The main extracellular components of the biofilm were analyzed, and the results showed that the mutant yielded significantly less exopolysaccharide but more extracellular DNA and protein than the wild-type strain. Collectively, our findings demonstrated that CHU_2750 is important for cellulose degradation, cell motility, and biofilm formation of C. hutchinsonii by modulating transcription of certain related genes, and it is the first identified transcriptional regulator in these processes of C. hutchinsonii. Our study shed more light on the mechanisms of cellulose degradation, cell motility, and biofilm formation by C. hutchinsonii.
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Affiliation(s)
- Zhiwei Guan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.,School of Life Science, Qilu Normal University, Jinan, 250200, China
| | - Ying Wang
- Central Laboratory, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China
| | - Lijuan Gao
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
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6
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Ferrándiz MJ, Carreño D, Ayora S, de la Campa AG. HU of Streptococcus pneumoniae Is Essential for the Preservation of DNA Supercoiling. Front Microbiol 2018; 9:493. [PMID: 29662473 PMCID: PMC5890176 DOI: 10.3389/fmicb.2018.00493] [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] [Received: 12/05/2017] [Accepted: 03/02/2018] [Indexed: 01/11/2023] Open
Abstract
The histone-like protein HU is a conserved nucleoid-associated protein that is involved in the maintenance of the bacterial chromosome architecture. It is the only known nucleoid-associated protein in Streptococcus pneumoniae, but it has not been studied. The pneumococcal gene encoding this protein, hlp, is shown herein to be essential for cell viability. Its disruption was only possible either when it was duplicated in the chromosome and its expression induced from the P Zn promoter, or when hlp was cloned into a plasmid under the control of the inducible P mal promoter. In vitro assays indicated that pneumococcal HU shows a preference for binding to supercoiled DNA rather than to linear or nicked DNA. In vivo experiments in which the amount of HU was manipulated showed a relationship between the amount of HU and the level of DNA supercoiling. A twofold reduction in the amount of HU triggered a 21% increase in DNA relaxation in untreated cells. However, in cells treated with novobiocin, a drug that relaxes DNA by inhibiting DNA gyrase, a 35% increase in DNA relaxation was observed, instead of the expected 20% in cells with a constitutive HU amount. Conversely, a fourfold HU increase caused only 14% of DNA relaxation in the presence of novobiocin. Taken together, these results support an essential role for HU in the maintenance of DNA supercoiling in S. pneumoniae.
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Affiliation(s)
- María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - David Carreño
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Ayora
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Adela G de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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7
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Liao JH, Tsai CH, Patel SG, Yang JT, Tu IF, Lo Cicero M, Lipka-Lloyd M, Wu WL, Shen WJ, Ho MR, Chou CC, Sharma GR, Okanishi H, Luk LYP, Tsai YH, Wu SH. Acetylome of Acinetobacter baumannii SK17 Reveals a Highly-Conserved Modification of Histone-Like Protein HU. Front Mol Biosci 2017; 4:77. [PMID: 29230394 PMCID: PMC5711770 DOI: 10.3389/fmolb.2017.00077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/06/2017] [Indexed: 12/27/2022] Open
Abstract
Lysine acetylation is a prevalent post-translational modification in both eukaryotes and prokaryotes. Whereas this modification is known to play pivotal roles in eukaryotes, the function and extent of this modification in prokaryotic cells remain largely unexplored. Here we report the acetylome of a pair of antibiotic-sensitive and -resistant nosocomial pathogen Acinetobacter baumannii SK17-S and SK17-R. A total of 145 lysine acetylation sites on 125 proteins was identified, and there are 23 acetylated proteins found in both strains, including histone-like protein HU which was found to be acetylated at Lys13. HU is a dimeric DNA-binding protein critical for maintaining chromosomal architecture and other DNA-dependent functions. To analyze the effects of site-specific acetylation, homogenously Lys13-acetylated HU protein, HU(K13ac) was prepared by genetic code expansion. Whilst not exerting an obvious effect on the oligomeric state, Lys13 acetylation alters both the thermal stability and DNA binding kinetics of HU. Accordingly, this modification likely destabilizes the chromosome structure and regulates bacterial gene transcription. This work indicates that acetyllysine plays an important role in bacterial epigenetics.
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Affiliation(s)
- Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Han Tsai
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Sanjay G Patel
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Jhih-Tian Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Ph.D. Program in Microbial Genomics, National Chung Hsing University, Academia Sinica, Taipei, Taiwan
| | - I-Fan Tu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Matteo Lo Cicero
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | | | - Wan-Ling Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Wen-Jie Shen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Garima R Sharma
- School of Chemistry, Cardiff University, Cardiff, United Kingdom.,Republic Polytechnic, Singapore, Singapore
| | - Hiroki Okanishi
- Department of Tumor Genetics and Biology, Kumamoto University, Kumamoto, Japan
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.,Department of Chemistry, National Taiwan University, Taipei, Taiwan
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8
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Abebe AH, Aranovich A, Fishov I. HU content and dynamics in Escherichia coli during the cell cycle and at different growth rates. FEMS Microbiol Lett 2017; 364:4157278. [PMID: 28961819 DOI: 10.1093/femsle/fnx195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/11/2017] [Indexed: 11/12/2022] Open
Abstract
DNA-binding proteins play an important role in maintaining bacterial chromosome structure and functions. Heat-unstable (HU) histone-like protein is one of the most abundant of these proteins and participates in all major chromosome-related activities. Owing to its low sequence specificity, HU fusions with fluorescent proteins were used for general staining of the nucleoid, aiming to reveal its morphology and dynamics. We have exploited a single chromosomal copy of hupA-egfp fusion under the native promoter and used quantitative microscopy imaging to investigate the amount and dynamics of HUα in Escherichia coli cells. We found that in steady-state growing populations the cellular HUα content is proportional to the cell size, whereas its concentration is size independent. Single-cell live microscopy imaging confirmed that the amount of HUα exponentially increases during the cell cycle, but its concentration is maintained constant. This supports the existence of an auto-regulatory mechanism underlying the HUα cellular level, in addition to reflecting the gene copy number. Both the HUα amount and concentration strongly increase with the cell growth rate in different culture media. Unexpectedly, the HU/DNA stoichiometry also remarkably increases with the growth rate. This last finding may be attributed to a higher requirement for maintaining the chromosome structure in nucleoids with higher complexity.
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Affiliation(s)
- Anteneh Hailu Abebe
- Department of Life Sciences, Ben-Gurion University of the Negev, PO Box 653, Beer-Sheva 8410501, Israel.,Medical Biotechnology Unit, Institute of Biotechnology, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Alexander Aranovich
- Department of Life Sciences, Ben-Gurion University of the Negev, PO Box 653, Beer-Sheva 8410501, Israel
| | - Itzhak Fishov
- Department of Life Sciences, Ben-Gurion University of the Negev, PO Box 653, Beer-Sheva 8410501, Israel
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9
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HU histone-like DNA-binding protein from Thermus thermophilus: structural and evolutionary analyses. Extremophiles 2016; 20:695-709. [DOI: 10.1007/s00792-016-0859-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/14/2016] [Indexed: 10/21/2022]
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10
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O’Neil P, Lovell S, Mehzabeen N, Battaile K, Biswas I. Crystal structure of histone-like protein from Streptococcus mutans refined to 1.9 Å resolution. Acta Crystallogr F Struct Biol Commun 2016; 72:257-62. [PMID: 27050257 PMCID: PMC4822980 DOI: 10.1107/s2053230x1600217x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/04/2016] [Indexed: 12/18/2022] Open
Abstract
Nucleoid-associated proteins (NAPs) in prokaryotes play an important architectural role in DNA bending, supercoiling and DNA compaction. In addition to architectural roles, some NAPs also play regulatory roles in DNA replication and repair, and act as global transcriptional regulators in many bacteria. Bacteria encode multiple NAPs and some of them are even essential for survival. Streptococcus mutans, a dental pathogen, encodes one such essential NAP called histone-like protein (HLP). Here, the three-dimensional structure of S. mutans HLP has been determined to 1.9 Å resolution. The HLP structure is a dimer and shares a high degree of similarity with other bacterial NAPs, including HU. Since HLPs are essential for the survival of pathogenic streptococci, this structure determination is potentially beneficial for future drug development against these pathogens.
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Affiliation(s)
- Pierce O’Neil
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Kansas City, KS 66047, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Kansas City, KS 66047, USA
| | - Kevin Battaile
- IMCA-CAT, Hauptman–Woodward Medical Research Institute, APS, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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11
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Domenech M, Ruiz S, Moscoso M, García E. In vitro biofilm development of Streptococcus pneumoniae and formation of choline-binding protein-DNA complexes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:715-727. [PMID: 25950767 DOI: 10.1111/1758-2229.12295] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/08/2015] [Indexed: 06/04/2023]
Abstract
Extracellular deoxyribonucleic acid (eDNA) is an essential component of bacterial biofilm matrices, and is required in their formation and maintenance. Extracellular DNA binds to exopolysaccharides or extracellular proteins, affording biofilms greater structural integrity. Recently, we reported evidence of intercellular eDNA-LytC complexes in pneumococcal biofilms. The LytC lysozyme is a member of the choline-binding family of proteins (CBPs) located on the pneumococcal surface. The present work shows that other CBPs, i.e. LytA, LytB, Pce, PspC and CbpF, which have a pI between 5 and 6, can bind DNA in vitro. This process requires the presence of divalent cations other than Mg(2+). This DNA binding capacity of CBPs appears to be independent of their enzymatic activity and, at least in the case of LytA, does not require the choline-binding domain characteristic of CBPs. Positively charged, surface-exposed, 25 amino acid-long peptides derived from the catalytic domain of LytB, were also found capable of DNA binding through electrostatic interactions. Confocal laser scanning microcopy revealed the existence of cell-associated LytB-eDNA complexes in Streptococcus pneumoniae biofilms. These and other findings suggest that these surface-located proteins of S. pneumoniae could play roles of varying importance in the colonization and/or invasion of human host where different environmental conditions exist.
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Affiliation(s)
- Mirian Domenech
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, 28040, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Susana Ruiz
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Miriam Moscoso
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, 28040, Spain
| | - Ernesto García
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, 28040, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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12
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Wang S, Liu K, Xiao L, Yang L, Li H, Zhang F, Lei L, Li S, Feng X, Li A, He J. Characterization of a novel DNA glycosylase from S. sahachiroi involved in the reduction and repair of azinomycin B induced DNA damage. Nucleic Acids Res 2015; 44:187-97. [PMID: 26400161 PMCID: PMC4705692 DOI: 10.1093/nar/gkv949] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/13/2015] [Indexed: 01/27/2023] Open
Abstract
Azinomycin B is a hybrid polyketide/nonribosomal peptide natural product and possesses antitumor activity by interacting covalently with duplex DNA and inducing interstrand crosslinks. In the biosynthetic study of azinomycin B, a gene (orf1) adjacent to the azinomycin B gene cluster was found to be essential for the survival of the producer, Streptomyces sahachiroi ATCC33158. Sequence analyses revealed that Orf1 belongs to the HTH_42 superfamily of conserved bacterial proteins which are widely distributed in pathogenic and antibiotic-producing bacteria with unknown functions. The protein exhibits a protective effect against azinomycin B when heterologously expressed in azinomycin-sensitive strains. EMSA assays showed its sequence nonspecific binding to DNA and structure-specific binding to azinomycin B-adducted sites, and ChIP assays revealed extensive association of Orf1 with chromatin in vivo. Interestingly, Orf1 not only protects target sites by protein–DNA interaction but is also capable of repairing azinomycin B-mediated DNA cross-linking. It possesses the DNA glycosylase-like activity and specifically repairs DNA damage induced by azinomycin B through removal of both adducted nitrogenous bases in the cross-link. This bifunctional protein massively binds to genomic DNA to reduce drug attack risk as a novel DNA binding protein and triggers the base excision repair system as a novel DNA glycosylase.
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Affiliation(s)
- Shan Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Le Xiao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - LiYuan Yang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - FeiXue Zhang
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Lei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - ShengQing Li
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - AiYing Li
- State Key Laboratory of Microbial Technology, Shandong University Helmholtz Joint Institute of Biotechnology, School of Life Science, Shandong University, Jinan 250100, China
| | - Jing He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Bacterial histone-like proteins: roles in stress resistance. Curr Genet 2015; 61:489-92. [DOI: 10.1007/s00294-015-0478-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 12/16/2022]
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14
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A novel DNA-binding protein plays an important role in Helicobacter pylori stress tolerance and survival in the host. J Bacteriol 2014; 197:973-82. [PMID: 25535274 DOI: 10.1128/jb.02489-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The gastric pathogen Helicobacter pylori must combat chronic acid and oxidative stress. It does so via many mechanisms, including macromolecule repair and gene regulation. Mitomycin C-sensitive clones from a transposon mutagenesis library were screened. One sensitive strain contained the insertion element at the locus of hp119, a hypothetical gene. No homologous gene exists in any (non-H. pylori) organism. Nevertheless, the predicted protein has some features characteristic of histone-like proteins, and we showed that purified HP119 protein is a DNA-binding protein. A Δhp119 strain was markedly more sensitive (viability loss) to acid or to air exposure, and these phenotypes were restored to wild-type (WT) attributes upon complementation of the mutant with the wild-type version of hp119 at a separate chromosomal locus. The mutant strain was approximately 10-fold more sensitive to macrophage-mediated killing than the parent or the complemented strain. Of 12 mice inoculated with the wild type, all contained H. pylori, whereas 5 of 12 mice contained the mutant strain; the mean colonization numbers were 158-fold less for the mutant strain. A proteomic (two-dimensional PAGE with mass spectrometric analysis) comparison between the Δhp119 mutant and the WT strain under oxidative stress conditions revealed a number of important antioxidant protein differences; SodB, Tpx, TrxR, and NapA, as well as the peptidoglycan deacetylase PgdA, were significantly less expressed in the Δhp119 mutant than in the WT strain. This study identified HP119 as a putative histone-like DNA-binding protein and showed that it plays an important role in Helicobacter pylori stress tolerance and survival in the host.
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Bright fluorescent Streptococcus pneumoniae for live-cell imaging of host-pathogen interactions. J Bacteriol 2014; 197:807-18. [PMID: 25512311 DOI: 10.1128/jb.02221-14] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Streptococcus pneumoniae is a common nasopharyngeal resident in healthy people but, at the same time, one of the major causes of infectious diseases such as pneumonia, meningitis, and sepsis. The shift from commensal to pathogen and its interaction with host cells are poorly understood. One of the major limitations for research on pneumococcal-host interactions is the lack of suitable tools for live-cell imaging. To address this issue, we developed a generally applicable strategy to create genetically stable, highly fluorescent bacteria. Our strategy relies on fusing superfolder green fluorescent protein (GFP) or a far-red fluorescent protein (RFP) to the abundant histone-like protein HlpA. Due to efficient translation and limited cellular diffusion of these fusions, the cells are 25-fold brighter than those of the currently best available imaging S. pneumoniae strain. These novel bright pneumococcal strains are fully virulent, and the GFP reporter can be used for in situ imaging in mouse tissue. We used our reporter strains to study the effect of the polysaccharide capsule, a major pneumococcal virulence factor, on different stages of infection. By dual-color live-cell imaging experiments, we show that unencapsulated pneumococci adhere significantly better to human lung epithelial cells than encapsulated strains, in line with previous data obtained by classical approaches. We also confirm with live-cell imaging that the capsule protects pneumococci from neutrophil phagocytosis, demonstrating the versatility and usability of our reporters. The described imaging tools will pave the way for live-cell imaging of pneumococcal infection and help further understanding of the mechanisms of pneumococcal pathogenesis.
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Kjos M, Veening JW. Tracking of chromosome dynamics in liveStreptococcus pneumoniaereveals that transcription promotes chromosome segregation. Mol Microbiol 2014; 91:1088-105. [DOI: 10.1111/mmi.12517] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Morten Kjos
- Molecular Genetics Group; Groningen Biomolecular Sciences and Biotechnology Institute; Centre for Synthetic Biology; University of Groningen; Nijenborgh 7 Groningen 9747 AG The Netherlands
| | - Jan-Willem Veening
- Molecular Genetics Group; Groningen Biomolecular Sciences and Biotechnology Institute; Centre for Synthetic Biology; University of Groningen; Nijenborgh 7 Groningen 9747 AG The Netherlands
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Nur A, Hirota K, Yumoto H, Hirao K, Liu D, Takahashi K, Murakami K, Matsuo T, Shu R, Miyake Y. Effects of extracellular DNA and DNA-binding protein on the development of a Streptococcus intermedius biofilm. J Appl Microbiol 2013; 115:260-70. [PMID: 23551549 DOI: 10.1111/jam.12202] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/13/2013] [Accepted: 03/22/2013] [Indexed: 02/01/2023]
Abstract
AIMS The aim of this study was to clarify the effects of homologous and heterologous extracellular DNAs (eDNAs) and histone-like DNA-binding protein (HLP) on Streptococcus intermedius biofilm development and rigidity. METHODS AND RESULTS Formed biofilm mass was measured with 0·1% crystal violet staining method and observed with a scanning electron microscope. The localizations of eDNA and extracellular HLP (eHLP) in formed biofilm were detected by staining with 7-hydoxyl-9H-(1,3-dichloro-9,9-dimethylacridin-2-one) and anti-HLP antibody without fixation, respectively. DNase I treatment (200 U ml(-1)) markedly decreased biofilm formation and cell density in biofilms. Colocalization of eHLP and eDNA in biofilm was confirmed. The addition of eDNA (up to 1 μg ml(-1)) purified from Strep. intermedius, other Gram-positive bacteria, Gram-negative bacteria, or human KB cells into the Strep. intermedius culture increased the biofilm mass of all tested strains of Strep. intermedius, wild-type, HLP-downregulated strain and control strains. In contrast, the addition of eDNA (>1 μg ml(-1)) decreased the biofilm mass of all Strep. intermedius strains. CONCLUSIONS These findings demonstrated that eDNA and eHLP play crucial roles in biofilm development and its rigidity. SIGNIFICANCE AND IMPACT OF THE STUDY eDNA- and HLP-targeting strategies may be applicable to novel treatments for bacterial biofilm-related infectious diseases.
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Affiliation(s)
- A Nur
- Department of Oral Microbiology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
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A histone-like protein of Helicobacter pylori protects DNA from stress damage and aids host colonization. DNA Repair (Amst) 2012; 11:733-40. [PMID: 22776439 DOI: 10.1016/j.dnarep.2012.06.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/16/2012] [Accepted: 06/18/2012] [Indexed: 02/06/2023]
Abstract
Genomic DNA in a bacterial cell is folded into a compact structure called a nucleoid, and nucleoid-associated proteins are responsible for proper assembly of active higher-order genome structures. The human gastric pathogen Helicobacter pylori express a nucleoid-associated protein encoded by the hup gene, which is the homolog to the Escherichia coli histone-like protein HU. An H. pylori hup mutant strain (X47 hup:cat) showed a defect in stationary phase survival. The X47 hup:cat mutant was more sensitive to the DNA damaging agent mitomycin C, and displayed a decreased frequency of DNA recombination, indicating Hup plays a significant role in facilitating DNA recombinational repair. The X47 hup:cat mutant was also sensitive to both oxidative and acid stress, conditions that H. pylori commonly encounters in the host. The hup mutant cells survived significantly (7-fold) less upon exposure to macrophages than the wild type strain. In a mouse infection model, the hup mutant strain displayed a greatly reduced ability to colonize host stomachs. The geometric means of colonization number for the wild type and hup mutant were 6×10(5) and 1.5×10(4)CFU/g stomachs, respectively. Complementation of the hup strain by chromosomal insertion of a functional hup gene restored oxidative stress resistance, DNA transformation frequency, and mouse colonization ability to the wild type level. We directly demonstrated that the purified His-tagged H. pylori Hup protein can protect (in vitro) an H. pylori-derived DNA fragment from oxidative damage.
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CovR alleviates transcriptional silencing by a nucleoid-associated histone-like protein in Streptococcus mutans. J Bacteriol 2012; 194:2050-61. [PMID: 22343292 DOI: 10.1128/jb.06812-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Streptococcus mutans, the global response regulator CovR plays an important role in biofilm formation, stress tolerance response, and caries production. We have previously demonstrated that CovR activates a large gene cluster, which is a part of a genomic island, TnSmu2. In this article, we have further characterized CovR at the molecular level to understand the gene activation mechanism. Toward this end, we mapped the transcription start site of the operon that lies upstream of the SMU.1348 gene (P(SMU.1348)), the first gene of the cluster. We constructed a transcriptional reporter fusion and showed that CovR induces expression from P(SMU.1348). We also demonstrated that purified CovR protects the sequence surrounding the -10 region of P(SMU.1348). In an in vitro transcription assay, we showed that histone-like protein (HLP), a homologue of Escherichia coli HU protein, represses transcription from P(SMU.1348). In vivo overexpression of HLP in trans also represses transcription from P(SMU.1348). Addition of CovR to the HLP-repressed P(SMU.1348) resulted in increased transcription from the promoter, suggesting a role for CovR in countering HLP silencing. Moreover, addition of SMU.1349, a transcriptional activator of the operon, to the in vitro assay further stimulated the transcription. Based on our in vivo and in vitro results, we propose a model for transcriptional activation of the operon.
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20
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Anuchin AM, Goncharenko AV, Demidenok OI, Kaprelyants AS. Histone-like proteins of bacteria (review). APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683811060020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Serine/threonine protein kinase Stk is required for virulence, stress response, and penicillin tolerance in Streptococcus pyogenes. Infect Immun 2011; 79:4201-9. [PMID: 21788381 DOI: 10.1128/iai.05360-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Genes encoding one or more Ser/Thr protein kinases have been identified recently in many bacteria, including one (stk) in the human pathogen Streptococcus pyogenes (group A streptococcus [GAS]). We report that in GAS, stk is required to produce disease in a murine myositis model of infection. Using microarray and quantitative reverse transcription-PCR (qRT-PCR) studies, we found that Stk activates genes for virulence factors, osmoregulation, metabolism of α-glucans, and fatty acid biosynthesis, as well as genes affecting cell wall synthesis. Confirming these transcription studies, we determined that the stk deletion mutant is more sensitive to osmotic stress and to penicillin than the wild type. We discuss several possible Stk phosphorylation targets that might explain Stk regulation of expression of specific operons and the possible role of Stk in resuscitation from quiescence.
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The histone-like protein Hlp is essential for growth of Streptococcus pyogenes: comparison of genetic approaches to study essential genes. Appl Environ Microbiol 2011; 77:4422-8. [PMID: 21531823 DOI: 10.1128/aem.00554-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Selection of possible targets for vaccine and drug development requires an understanding of the physiology of bacterial pathogens, for which the ability to manipulate expression of essential genes is critical. For Streptococcus pyogenes (the group A streptococcus [GAS]), an important human pathogen, the lack of genetic tools for such studies has seriously hampered research. To address this problem, we characterized variants of the inducible Ptet cassette, in both sense and antisense contexts, as tools to regulate transcription from GAS genes. We found that although the three-operator Ptet construct [Ptet(O)3] had low uninduced expression, its induction level was low, while the two-operator construct [Ptet(O)2] was inducible to a high level but showed significant constitutive expression. Use of Ptet(O)3 in the chromosome allowed us to demonstrate previously that RNases J1 and J2 are required for growth of GAS. Here we report that the uninduced level from the chromosomally inserted Ptet(O)2 construct was too high for us to observe differential growth. For the highly expressed histone-like protein (Hlp) of GAS, neither chromosomal insertion of Ptet(O)2 or Ptet(O)3 nor their use on a high-copy-number plasmid to produce antisense RNA specific to hlp resulted in adequate differential expression. However, by replacing the ribosome binding site of hlp with an engineered riboswitch to control translation of Hlp, we demonstrated for the first time that this protein is essential for GAS growth.
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Long-term bacterial exposure can trigger nonsuppurative destructive cholangitis associated with multifocal epithelial inflammation. J Transl Med 2010; 90:577-88. [PMID: 20142809 DOI: 10.1038/labinvest.2010.40] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Bacterial infection has become a focus of attention in the pathogenesis of primary biliary cirrhosis (PBC). We earlier reported that the bacterial lipoteichoic acid was detected at the sites of inflammation around damaged bile ducts in the livers of PBC, and PBC patients' sera showed high titers against streptococcal histone-like protein. Here, we investigated whether chronic bacterial exposure could trigger PBC-like epithelial cell damage in normal mouse. BALB/c mice were repeatedly inoculated with various bacteria for 8 weeks. At 1 week (Group 1) and 3, 4, or 20 months (long term; Group 2) after the final inoculation, mice were killed to obtain samples. In the livers of the Streptococcus intermedius (S.i.)-inoculated mice in Group 1, cellular infiltration was predominantly observed around the bile ducts over the hepatic parenchyma. In the S.i.-inoculated mice in Group 2, portal but not parenchymal inflammation was observed in the livers, and periductal cellular infiltrates were detected in the salivary glands. Both S.i.-inoculated Groups 1 and 2 BALB/c mice sera had antibodies against HuCCT1 biliary epithelial cells, anti-nuclear antibodies, and anti-gp210 antibodies, but not anti-mitochondrial antibodies. Immunoreactivity to histone-like DNA-binding protein of S.i. (S.i.-HLP) was detectable around the sites of chronic nonsuppurative destructive cholangitis in the portal area in the livers of both S.i.-inoculated Groups 1 and 2 BALB/c mice. Furthermore, anti-S.i.-HLP antibody bound to synthetic gp210 peptide, as well. Bacteria triggered PBC-like cholangitis, multifocal epithelial inflammation, and autoantibody production. Bacteria are likely involved in the pathogenesis of PBC and of associated multifocal epithelial inflammation.
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Liu D, Yumoto H, Murakami K, Hirota K, Kayama S, Taniguchi T, Yamamoto A, Ono T, Matsuo T, Miyake Y. Heterologous expression ofa histone-like protein from Streptococcus intermedius in Escherichia coli alters the nucleoid structure and inhibits the growth of E. coli. FEMS Microbiol Lett 2008; 288:68-75. [PMID: 18761672 DOI: 10.1111/j.1574-6968.2008.01327.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Escherichia coli failed to survive after transformation with a Streptococcus intermedius histone-like protein gene (Si-hlp) and its promoter-harbored plasmid. The promoter function of Si-hlp in E. coli was determined using enhanced green fluorescence protein (egfp) gene as a reporter. The inhibitory effect of Si-HLP on E. coli viability was verified by a tetracycline-inducible gene expression system. Further study suggested that Si-HLP may alter the bacterial nucleoid structure, leading to the growth inhibition of E. coli.
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