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The Major Chromosome Condensation Factors Smc, HBsu, and Gyrase in Bacillus subtilis Operate via Strikingly Different Patterns of Motion. mSphere 2020; 5:5/5/e00817-20. [PMID: 32907955 PMCID: PMC7485690 DOI: 10.1128/msphere.00817-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
All types of cells need to compact their chromosomes containing their genomic information several-thousand-fold in order to fit into the cell. In eukaryotes, histones achieve a major degree of compaction and bind very tightly to DNA such that they need to be actively removed to allow access of polymerases to the DNA. Bacteria have evolved a basic, highly dynamic system of DNA compaction, accommodating rapid adaptability to changes in environmental conditions. We show that the Bacillus subtilis histone-like protein HBsu exchanges on DNA on a millisecond scale and moves through the entire nucleoid containing the genome as a slow-mobility fraction and a dynamic fraction, both having short dwell times. Thus, HBsu achieves compaction via short and transient DNA binding, thereby allowing rapid access of DNA replication or transcription factors to DNA. Topoisomerase gyrase and B. subtilis Smc show different interactions with DNA in vivo, displaying continuous loading or unloading from DNA, or using two fractions, one moving through the genome and one statically bound on a time scale of minutes, respectively, revealing three different modes of DNA compaction in vivo. Although DNA-compacting proteins have been extensively characterized in vitro, knowledge of their DNA binding dynamics in vivo is greatly lacking. We have employed single-molecule tracking to characterize the motion of the three major chromosome compaction factors in Bacillus subtilis, Smc (structural maintenance of chromosomes) proteins, topoisomerase DNA gyrase, and histone-like protein HBsu. We show that these three proteins display strikingly different patterns of interaction with DNA; while Smc displays two mobility fractions, one static and one moving through the chromosome in a constrained manner, gyrase operates as a single slow-mobility fraction, suggesting that all gyrase molecules are catalytically actively engaged in DNA binding. Conversely, bacterial histone-like protein HBsu moves through the nucleoid as a larger, slow-mobility fraction and a smaller, high-mobility fraction, with both fractions having relatively short dwell times. Turnover within the SMC complex that makes up the static fraction is shown to be important for its function in chromosome compaction. Our report reveals that chromosome compaction in bacteria can occur via fast, transient interactions in vivo, avoiding clashes with RNA and DNA polymerases. IMPORTANCE All types of cells need to compact their chromosomes containing their genomic information several-thousand-fold in order to fit into the cell. In eukaryotes, histones achieve a major degree of compaction and bind very tightly to DNA such that they need to be actively removed to allow access of polymerases to the DNA. Bacteria have evolved a basic, highly dynamic system of DNA compaction, accommodating rapid adaptability to changes in environmental conditions. We show that the Bacillus subtilis histone-like protein HBsu exchanges on DNA on a millisecond scale and moves through the entire nucleoid containing the genome as a slow-mobility fraction and a dynamic fraction, both having short dwell times. Thus, HBsu achieves compaction via short and transient DNA binding, thereby allowing rapid access of DNA replication or transcription factors to DNA. Topoisomerase gyrase and B. subtilis Smc show different interactions with DNA in vivo, displaying continuous loading or unloading from DNA, or using two fractions, one moving through the genome and one statically bound on a time scale of minutes, respectively, revealing three different modes of DNA compaction in vivo.
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Liu YC, Han LL, Chen TY, Lu YB, Feng H. Characterization of a Protease Hyper-Productive Mutant of Bacillus pumilus by Comparative Genomic and Transcriptomic Analysis. Curr Microbiol 2020; 77:3612-3622. [PMID: 32749522 DOI: 10.1007/s00284-020-02154-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/28/2020] [Indexed: 01/06/2023]
Abstract
Bacillus pumilus BA06 has great potential for the production of alkaline proteases. To improve the protease yield, classical mutagenesis to combine the physical and chemical mutagens was performed to obtain a protease hyper-productive mutant SCU11. The full genome sequences of BA06 and SCU11 strains were assembled through DNA sequencing using the PacBio sequencing platform. By comparative genomics analysis, 147 SNPs and 15 InDels were found between these two genomes, which lead to alternation of coding sequence in 15 genes. Noticeable, the gene (kinA) encoding sporulation kinase A is interrupted by introducing a stop codon in its coding region in BA06. Interestedly, this gene is reversely corrected in SCU11. Furthermore, comparative transcriptome analysis revealed that kinA and two positive regulatory genes (DegU and Spo0A) were upregulated in transcription in SCU11. In terms of the transcriptional data, upregulation of a phosphorylation cascade starting with KinA may enhance Spo0A phosphorylation, and thus activate expression of the gene aprE (encoding major extracellular protease) through repression of AbrB (a repressor of aprE) and activation of SinI, an antagonist of SinR (a repressor of aprE). In addition, the other genes involved in various metabolic pathways, especially of membrane transport and sporulation, were altered in transcription between these two strains. Conclusively, our transcriptome data suggested that upregulation degU and spo0A, as well as kinA, may at least partially contribute to the high production of alkaline protease in SCU11.
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Affiliation(s)
- Yong-Cheng Liu
- College of Life Sciences, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Lin-Li Han
- College of Life Sciences, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Tian-Yu Chen
- College of Life Sciences, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Yan-Bing Lu
- College of Life Sciences, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Hong Feng
- College of Life Sciences, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China.
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Novotny LA, Goodman SD, Bakaletz LO. Redirecting the immune response towards immunoprotective domains of a DNABII protein resolves experimental otitis media. NPJ Vaccines 2019; 4:43. [PMID: 31632744 PMCID: PMC6791836 DOI: 10.1038/s41541-019-0137-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/13/2019] [Indexed: 12/18/2022] Open
Abstract
The chronicity and recurrence of many bacterial diseases is largely attributable to the presence of a biofilm, and eradication of these structures is confounded by an extracellular DNA-rich matrix. DNABII proteins, including integration host factor (IHF), are critical components of the matrix formed by all human pathogens tested to date. Whereas the natural adaptive immune response to IHF is against non-protective epitopes within the carboxyl-terminal region, antibodies against the DNA-binding “tips” induce biofilm collapse. We designed a “tip-chimer” immunogen to mimic the DNA-binding regions within the α-subunit and β-subunit of IHF from nontypeable Haemophilus influenzae (IHFNTHi). Re-direction of the natural adaptive immune response toward immunoprotective domains disrupted NTHi biofilms in vitro and in an experimental model of otitis media. Our data support the rational design of a powerful therapeutic approach, and also that of a DNABII-directed vaccine antigen that would avoid augmentation of any pre-existing natural, but nonprotective, immune response. Bacterial biofilms are characterized by the presence of a protective extracellular polymeric substance (EPS) that incorporates both eDNA and members of the DNABII family of bacterial DNA-binding proteins. Antibodies against the “tips” of these DNA binding-domains can cause biofilm collapse, but these epitopes are masked from the host adaptive immune system when bound to eDNA, making biofilm eradication difficult. Here, the team led by Lauren Bakaletz used a chimeric peptide to generate tip-specific antibodies against nontypeable Haemophilus influenzae to treat biofilms in vitro and in vivo. The “tip-chimer” contained the immunoprotective domains from the DNA-binding tips of a DNABII protein, integration host factor (IHF), expressed by nontypeable Haemophilus influenzae. The consequent antibodies disrupted H. influenzae biofilms in vitro and were used to treat a chinchilla model of experimental otitis media when inoculated directly into the middle ear, resulting in reduced bacterial load and clearance of already established mucosal biofilms. These findings suggest that redirecting the host adaptive immune response towards the immunoprotective tips of DNABII proteins could provide a strategy to eradicate biofilms caused by various pathogens that produce these proteins.
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Affiliation(s)
- L A Novotny
- 1Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205 USA
| | - S D Goodman
- 1Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205 USA.,2The Ohio State University College of Medicine, Columbus, OH 43210 USA
| | - L O Bakaletz
- 1Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205 USA.,2The Ohio State University College of Medicine, Columbus, OH 43210 USA
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Brantl S, Müller P. Toxin⁻Antitoxin Systems in Bacillus subtilis. Toxins (Basel) 2019; 11:toxins11050262. [PMID: 31075979 PMCID: PMC6562991 DOI: 10.3390/toxins11050262] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/30/2019] [Accepted: 05/07/2019] [Indexed: 12/31/2022] Open
Abstract
Toxin-antitoxin (TA) systems were originally discovered as plasmid maintenance systems in a multitude of free-living bacteria, but were afterwards found to also be widespread in bacterial chromosomes. TA loci comprise two genes, one coding for a stable toxin whose overexpression kills the cell or causes growth stasis, and the other coding for an unstable antitoxin that counteracts toxin action. Of the currently known six types of TA systems, in Bacillus subtilis, so far only type I and type II TA systems were found, all encoded on the chromosome. Here, we review our present knowledge of these systems, the mechanisms of antitoxin and toxin action, and the regulation of their expression, and we discuss their evolution and possible physiological role.
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Affiliation(s)
- Sabine Brantl
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany.
| | - Peter Müller
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany.
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Schneider JP, Basler M. Shedding light on biology of bacterial cells. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0499. [PMID: 27672150 PMCID: PMC5052743 DOI: 10.1098/rstb.2015.0499] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2016] [Indexed: 12/11/2022] Open
Abstract
To understand basic principles of living organisms one has to know many different properties of all cellular components, their mutual interactions but also their amounts and spatial organization. Live-cell imaging is one possible approach to obtain such data. To get multiple snapshots of a cellular process, the imaging approach has to be gentle enough to not disrupt basic functions of the cell but also have high temporal and spatial resolution to detect and describe the changes. Light microscopy has become a method of choice and since its early development over 300 years ago revolutionized our understanding of living organisms. As most cellular components are indistinguishable from the rest of the cellular contents, the second revolution came from a discovery of specific labelling techniques, such as fusions to fluorescent proteins that allowed specific tracking of a component of interest. Currently, several different tags can be tracked independently and this allows us to simultaneously monitor the dynamics of several cellular components and from the correlation of their dynamics to infer their respective functions. It is, therefore, not surprising that live-cell fluorescence microscopy significantly advanced our understanding of basic cellular processes. Current cameras are fast enough to detect changes with millisecond time resolution and are sensitive enough to detect even a few photons per pixel. Together with constant improvement of properties of fluorescent tags, it is now possible to track single molecules in living cells over an extended period of time with a great temporal resolution. The parallel development of new illumination and detection techniques allowed breaking the diffraction barrier and thus further pushed the resolution limit of light microscopy. In this review, we would like to cover recent advances in live-cell imaging technology relevant to bacterial cells and provide a few examples of research that has been possible due to imaging. This article is part of the themed issue ‘The new bacteriology’.
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Affiliation(s)
- Johannes P Schneider
- Focal Area Infection Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Marek Basler
- Focal Area Infection Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
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A widespread family of polymorphic toxins encoded by temperate phages. BMC Biol 2017; 15:75. [PMID: 28851366 PMCID: PMC5576092 DOI: 10.1186/s12915-017-0415-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/07/2017] [Indexed: 12/21/2022] Open
Abstract
Background Polymorphic toxins (PTs) are multi-domain bacterial exotoxins belonging to distinct families that share common features in terms of domain organization. PTs are found in all major bacterial clades, including many toxic effectors of type V and type VI secretion systems. PTs modulate the dynamics of microbial communities by killing or inhibiting the growth of bacterial competitors lacking protective immunity proteins. Results In this work, we identified a novel widespread family of PTs, named MuF toxins, which were exclusively encoded within temperate phages and their prophages. By analyzing the predicted proteomes of 1845 bacteriophages and 2464 bacterial genomes, we found that MuF-containing proteins were frequently part of the DNA packaging module of tailed phages. Interestingly, MuF toxins were abundant in the human gut microbiome. Conclusions Our results uncovered the presence of the MuF toxin family in the temperate phages of Firmicutes. The MuF toxin family is likely to play an important role in the ecology of the human microbiota where pathogens and commensal species belonging to the Firmicutes are abundant. We propose that MuF toxins could be delivered by phages into host bacteria and either influence the lysogeny decision or serve as bacterial weapons by inhibiting the growth of competing bacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0415-1) contains supplementary material, which is available to authorized users.
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Jurcisek JA, Brockman KL, Novotny LA, Goodman SD, Bakaletz LO. Nontypeable Haemophilus influenzae releases DNA and DNABII proteins via a T4SS-like complex and ComE of the type IV pilus machinery. Proc Natl Acad Sci U S A 2017; 114:E6632-E6641. [PMID: 28696280 PMCID: PMC5559034 DOI: 10.1073/pnas.1705508114] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Biofilms formed by nontypeable Haemophilus influenzae (NTHI) are central to the chronicity, recurrence, and resistance to treatment of multiple human respiratory tract diseases including otitis media, chronic rhinosinusitis, and exacerbations of both cystic fibrosis and chronic obstructive pulmonary disease. Extracellular DNA (eDNA) and associated DNABII proteins are essential to the overall architecture and structural integrity of biofilms formed by NTHI and all other bacterial pathogens tested to date. Although cell lysis and outer-membrane vesicle extrusion are possible means by which these canonically intracellular components might be released into the extracellular environment for incorporation into the biofilm matrix, we hypothesized that NTHI additionally used a mechanism of active DNA release. Herein, we describe a mechanism whereby DNA and associated DNABII proteins transit from the bacterial cytoplasm to the periplasm via an inner-membrane pore complex (TraC and TraG) with homology to type IV secretion-like systems. These components exit the bacterial cell through the ComE pore through which the NTHI type IV pilus is expressed. The described mechanism is independent of explosive cell lysis or cell death, and the release of DNA is confined to a discrete subpolar location, which suggests a novel form of DNA release from viable NTHI. Identification of the mechanisms and determination of the kinetics by which critical biofilm matrix-stabilizing components are released will aid in the design of novel biofilm-targeted therapeutic and preventative strategies for diseases caused by NTHI and many other human pathogens known to integrate eDNA and DNABII proteins into their biofilm matrix.
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Affiliation(s)
- Joseph A Jurcisek
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205
| | - Kenneth L Brockman
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210
| | - Laura A Novotny
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205
| | - Steven D Goodman
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205;
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210
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Acquisition of Phage Sensitivity by Bacteria through Exchange of Phage Receptors. Cell 2017; 168:186-199.e12. [DOI: 10.1016/j.cell.2016.12.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/29/2016] [Accepted: 12/01/2016] [Indexed: 12/14/2022]
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Bloom-Ackermann Z, Steinberg N, Rosenberg G, Oppenheimer-Shaanan Y, Pollack D, Ely S, Storzi N, Levy A, Kolodkin-Gal I. Toxin-Antitoxin systems eliminate defective cells and preserve symmetry in Bacillus subtilis biofilms. Environ Microbiol 2016; 18:5032-5047. [PMID: 27450630 DOI: 10.1111/1462-2920.13471] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/07/2016] [Accepted: 07/20/2016] [Indexed: 01/02/2023]
Abstract
Toxin-antitoxin modules are gene pairs encoding a toxin and its antitoxin, and are found on the chromosomes of many bacteria, including pathogens. Here, we characterize the specific contribution of the TxpA and YqcG toxins in elimination of defective cells from developing Bacillus subtilis biofilms. On nutrient limitation, defective cells accumulated in the biofilm breaking its symmetry. Deletion of the toxins resulted in accumulation of morphologically abnormal cells, and interfered with the proper development of the multicellular community. Dual physiological responses are of significance for TxpA and YqcG activation: nitrogen deprivation enhances the transcription of both TxpA and YqcG toxins, and simultaneously sensitizes the biofilm cells to their activity. Furthermore, we demonstrate that while both toxins when overexpressed affect the morphology of the developing biofilm, the toxin TxpA can act to lyse and dissolve pre-established B. subtilis biofilms.
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Affiliation(s)
- Zohar Bloom-Ackermann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nitai Steinberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gili Rosenberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | | | - Dan Pollack
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shir Ely
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nimrod Storzi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Asaf Levy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
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