1
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Mikucki A, Kahler CM. Microevolution and Its Impact on Hypervirulence, Antimicrobial Resistance, and Vaccine Escape in Neisseria meningitidis. Microorganisms 2023; 11:3005. [PMID: 38138149 PMCID: PMC10745880 DOI: 10.3390/microorganisms11123005] [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: 11/06/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Neisseria meningitidis is commensal of the human pharynx and occasionally invades the host, causing the life-threatening illness invasive meningococcal disease. The meningococcus is a highly diverse and adaptable organism thanks to natural competence, a propensity for recombination, and a highly repetitive genome. These mechanisms together result in a high level of antigenic variation to invade diverse human hosts and evade their innate and adaptive immune responses. This review explores the ways in which this diversity contributes to the evolutionary history and population structure of the meningococcus, with a particular focus on microevolution. It examines studies on meningococcal microevolution in the context of within-host evolution and persistent carriage; microevolution in the context of meningococcal outbreaks and epidemics; and the potential of microevolution to contribute to antimicrobial resistance and vaccine escape. A persistent theme is the idea that the process of microevolution contributes to the development of new hyperinvasive meningococcal variants. As such, microevolution in this species has significant potential to drive future public health threats in the form of hypervirulent, antibiotic-resistant, vaccine-escape variants. The implications of this on current vaccination strategies are explored.
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Affiliation(s)
- August Mikucki
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
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2
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Seow VY, Tsygelnytska O, Biais N. Multisite transformation in Neisseria gonorrhoeae: insights on transformations mechanisms and new genetic modification protocols. Front Microbiol 2023; 14:1178128. [PMID: 37408636 PMCID: PMC10319059 DOI: 10.3389/fmicb.2023.1178128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023] Open
Abstract
Natural transformation, or the uptake of naked DNA from the external milieu by bacteria, holds a unique place in the history of biology. This is both the beginning of the realization of the correct chemical nature of genes and the first technical step to the molecular biology revolution that sees us today able to modify genomes almost at will. Yet the mechanistic understanding of bacterial transformation still presents many blind spots and many bacterial systems lag behind power horse model systems like Escherichia coli in terms of ease of genetic modification. Using Neisseria gonorrhoeae as a model system and using transformation with multiple DNA molecules, we tackle in this paper both some aspects of the mechanistic nature of bacterial transformation and the presentation of new molecular biology techniques for this organism. We show that similarly to what has been demonstrated in other naturally competent bacteria, Neisseria gonorrhoeae can incorporate, at the same time, different DNA molecules modifying DNA at different loci within its genome. In particular, co-transformation of a DNA molecule bearing an antibiotic selection cassette and another non-selected DNA piece can lead to the integration of both molecules in the genome while selecting only through the selective cassette at percentages above 70%. We also show that successive selections with two selection markers at the same genetic locus can drastically reduce the number of genetic markers needed to do multisite genetic modifications in Neisseria gonorrhoeae. Despite public health interest heightened with the recent rise in antibiotic resistance, the causative agent of gonorrhea still does not possess a plethora of molecular techniques. This paper will extend the techniques available to the Neisseria community while providing some insights into the mechanisms behind bacterial transformation in Neisseria gonorrhoeae. We are providing a suite of new techniques to quickly obtain modifications of genes and genomes in the Neisserial naturally competent bacteria.
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Affiliation(s)
- Vui Yin Seow
- Brooklyn College of the City University of New York, Brooklyn, NY, United States
- The Graduate Center of the City University of New York, New York, NY, United States
- Laboratoire Jean Perrin, UMR8237, Sorbonne Université, Paris, France
| | - Olga Tsygelnytska
- Brooklyn College of the City University of New York, Brooklyn, NY, United States
| | - Nicolas Biais
- Brooklyn College of the City University of New York, Brooklyn, NY, United States
- The Graduate Center of the City University of New York, New York, NY, United States
- Laboratoire Jean Perrin, UMR8237, Sorbonne Université, Paris, France
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3
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Cheng YY, Zhou Z, Papadopoulos JM, Zuke JD, Falbel TG, Anantharaman K, Burton BM, Venturelli OS. Efficient plasmid transfer via natural competence in a microbial co-culture. Mol Syst Biol 2023; 19:e11406. [PMID: 36714980 PMCID: PMC9996237 DOI: 10.15252/msb.202211406] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/21/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species growth, and HGT efficiency over time. In the co-culture, plasmid release and HGT efficiency are significantly enhanced than in the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released in high concentrations, enabling efficient HGT. However, HGT is reduced in response to high donor lysis rates. HGT is independent of the donor viability state as both live and dead cells transfer the plasmid with high efficiency. In sum, plasmid HGT via natural transformation depends on the interplay of plasmid properties, donor stress responses and lysis rates, and interspecies interactions.
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Affiliation(s)
- Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - James M Papadopoulos
- Department of Chemical & Biological Engineering, University of Wisconsin, Madison, WI, USA
| | - Jason D Zuke
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Tanya G Falbel
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | | | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin, Madison, WI, USA.,Department of Chemical & Biological Engineering, University of Wisconsin, Madison, WI, USA
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4
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Biochemical Properties and Roles of DprA Protein in Bacterial Natural Transformation, Virulence, and Pilin Variation. J Bacteriol 2023; 205:e0046522. [PMID: 36695594 PMCID: PMC9945497 DOI: 10.1128/jb.00465-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Natural transformation enables bacteria to acquire DNA from the environment and contributes to genetic diversity, DNA repair, and nutritional requirements. DNA processing protein A (DprA) receives incoming single-stranded DNA and assists RecA loading for homology-directed natural chromosomal transformation and DNA strand annealing during plasmid transformation. The dprA gene occurs in the genomes of all known bacteria, irrespective of their natural transformation status. The DprA protein has been characterized by its molecular, cellular, biochemical, and biophysical properties in several bacteria. This review summarizes different aspects of DprA biology, collectively describing its biochemical properties, molecular interaction with DNA, and function interaction with bacterial RecA during natural transformation. Furthermore, the roles of DprA in natural transformation, bacterial virulence, and pilin variation are discussed.
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5
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Merfa MV, Zhu X, Shantharaj D, Gomez LM, Naranjo E, Potnis N, Cobine PA, De La Fuente L. Complete functional analysis of type IV pilus components of a reemergent plant pathogen reveals neofunctionalization of paralog genes. PLoS Pathog 2023; 19:e1011154. [PMID: 36780566 PMCID: PMC9956873 DOI: 10.1371/journal.ppat.1011154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/24/2023] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
Type IV pilus (TFP) is a multifunctional bacterial structure involved in twitching motility, adhesion, biofilm formation, as well as natural competence. Here, by site-directed mutagenesis and functional analysis, we determined the phenotype conferred by each of the 38 genes known to be required for TFP biosynthesis and regulation in the reemergent plant pathogenic fastidious prokaryote Xylella fastidiosa. This pathogen infects > 650 plant species and causes devastating diseases worldwide in olives, grapes, blueberries, and almonds, among others. This xylem-limited, insect-transmitted pathogen lives constantly under flow conditions and therefore is highly dependent on TFP for host colonization. In addition, TFP-mediated natural transformation is a process that impacts genomic diversity and environmental fitness. Phenotypic characterization of the mutants showed that ten genes were essential for both movement and natural competence. Interestingly, seven sets of paralogs exist, and mutations showed opposing phenotypes, indicating evolutionary neofunctionalization of subunits within TFP. The minor pilin FimT3 was the only protein exclusively required for natural competence. By combining approaches of molecular microbiology, structural biology, and biochemistry, we determined that the minor pilin FimT3 (but not the other two FimT paralogs) is the DNA receptor in TFP of X. fastidiosa and constitutes an example of neofunctionalization. FimT3 is conserved among X. fastidiosa strains and binds DNA non-specifically via an electropositive surface identified by homolog modeling. This protein surface includes two arginine residues that were exchanged with alanine and shown to be involved in DNA binding. Among plant pathogens, fimT3 was found in ~ 10% of the available genomes of the plant associated Xanthomonadaceae family, which are yet to be assessed for natural competence (besides X. fastidiosa). Overall, we highlight here the complex regulation of TFP in X. fastidiosa, providing a blueprint to understand TFP in other bacteria living under flow conditions.
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Affiliation(s)
- Marcus V. Merfa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Xinyu Zhu
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Deepak Shantharaj
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Laura M. Gomez
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Eber Naranjo
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Paul A. Cobine
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
- * E-mail:
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6
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Shao Y, Chen M, Luo J, Li D, Yuan L, Yang X, Wang M, Chen M, Guo Q. Serogroup Y Clonal Complex 23 Meningococcus in China Acquiring Penicillin Resistance from Commensal Neisseria lactamica Species. Antimicrob Agents Chemother 2022; 66:e0238321. [PMID: 35652645 PMCID: PMC9211434 DOI: 10.1128/aac.02383-21] [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: 12/21/2021] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis (NmY) is rare in China; recently, an invasive NmY isolate, Nm512, was discovered in Shanghai with decreased susceptibility to penicillin (PenNS). Here, we investigated the epidemiology of NmY isolates in Shanghai and explored the potential commensal Neisseria lactamica donor of the PenNS NmY isolate. A total of 491 N. meningitidis and 724 commensal Neisseria spp. isolates were collected. Eleven NmY isolates were discovered from IMD (n = 1) and carriers (n = 10), including two PenNS isolates with five-key-mutation-harboring (F504L-A510V-I515V-H541N-I566V) penA genes. Five of the eight ST-175 complex (CC175) isolates had a genotype [Y:P1.5-1,2-2:F5-8:ST-175(CC175)] identical to that of the predominant invasive clone found in South Africa. Only one invasive NmY CC23 isolate (Nm512) was discovered; this isolate carried a novel PenNSpenA832 allele, which was identified in commensal N. lactamica isolates locally. Recombination analysis and transformation of the penA allele highlighted that N. meningitidis Nm512 may acquire resistance from its commensal donor; this was supported by the similar distribution of transformation-required DNA uptake sequence variants and the highly cognate receptor ComP between N. meningitidis and N. lactamica. In 2,309 NmY CC23 genomes from the PubMLST database, isolates with key-mutation-harboring penA genes comprised 12% and have been increasing since the 1990s, accompanied by recruitment of the blaROB-1 and/or quinolone resistance allele. Moreover, penA22 was predominant among genomes without key mutations in penA. These results strongly suggest that Nm512 is a descendant of the penA22-harboring CC23 isolate from Europe and acquired its penicillin resistance locally from commensal N. lactamica species by natural transformation.
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Affiliation(s)
- Youxing Shao
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People’s Republic of China, Shanghai, People’s Republic of China
| | - Mingliang Chen
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
- Department of Microbiology, Shanghai Institutes of Preventive Medicine, Shanghai, People’s Republic of China
| | - Jiayuan Luo
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Dan Li
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Lingyue Yuan
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Xiaoying Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People’s Republic of China, Shanghai, People’s Republic of China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People’s Republic of China, Shanghai, People’s Republic of China
| | - Min Chen
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Qinglan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People’s Republic of China, Shanghai, People’s Republic of China
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7
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Rhodes KA, Ma MC, Rendón MA, So M. Neisseria genes required for persistence identified via in vivo screening of a transposon mutant library. PLoS Pathog 2022; 18:e1010497. [PMID: 35580146 PMCID: PMC9140248 DOI: 10.1371/journal.ppat.1010497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/27/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
The mechanisms used by human adapted commensal Neisseria to shape and maintain a niche in their host are poorly defined. These organisms are common members of the mucosal microbiota and share many putative host interaction factors with Neisseria meningitidis and Neisseria gonorrhoeae. Evaluating the role of these shared factors during host carriage may provide insight into bacterial mechanisms driving both commensalism and asymptomatic infection across the genus. We identified host interaction factors required for niche development and maintenance through in vivo screening of a transposon mutant library of Neisseria musculi, a commensal of wild-caught mice which persistently and asymptomatically colonizes the oral cavity and gut of CAST/EiJ and A/J mice. Approximately 500 candidate genes involved in long-term host interaction were identified. These included homologs of putative N. meningitidis and N. gonorrhoeae virulence factors which have been shown to modulate host interactions in vitro. Importantly, many candidate genes have no assigned function, illustrating how much remains to be learned about Neisseria persistence. Many genes of unknown function are conserved in human adapted Neisseria species; they are likely to provide a gateway for understanding the mechanisms allowing pathogenic and commensal Neisseria to establish and maintain a niche in their natural hosts. Validation of a subset of candidate genes confirmed a role for a polysaccharide capsule in N. musculi persistence but not colonization. Our findings highlight the potential utility of the Neisseria musculi-mouse model as a tool for studying the pathogenic Neisseria; our work represents a first step towards the identification of novel host interaction factors conserved across the genus. The Neisseria genus contains many genetically related commensals of animals and humans, and two human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. The mechanisms allowing commensal Neisseria to maintain a niche in their host is little understood. To identify genes required for persistence, we screened a library of transposon mutants of Neisseria musculi, a commensal of wild-caught mice, in CAST/EiJ mice, which persistently and asymptomatically colonizes. Approximately 500 candidate host interaction genes were identified. A subset of these are homologs of N. meningitidis and N. gonorrhoeae genes known to modulate pathogen-host interactions in vitro. Many candidate genes have no known function, demonstrating how much remains to be learned about N. musculi niche maintenance. As many genes of unknown function are conserved in human adapted Neisseria, they provide a gateway for understanding Neisseria persistence mechanisms in general.
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Affiliation(s)
- Katherine A. Rhodes
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
| | - Man Cheong Ma
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - María A. Rendón
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Magdalene So
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
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Bender N, Hennes M, Maier B. Mobility of extracellular DNA within gonococcal colonies. Biofilm 2022; 4:100078. [PMID: 35647521 PMCID: PMC9136125 DOI: 10.1016/j.bioflm.2022.100078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022] Open
Abstract
Transformation enables bacteria to acquire genetic information from extracellular DNA (eDNA). Close proximity between bacteria in colonies and biofilms may inhibit escape of eDNA from the colony but it also hinders its diffusion between donor and recipient. In this study, we investigate the mobility of DNA within colonies formed by Neisseria gonorrhoeae, and relate it to transformation efficiency. We characterize the penetration dynamics of fluorescent DNA into the colony at a time scale of hours and find that 300 bp fragments diffuse through the colony without hindrance. For DNA length exceeding 3 kbp, a concentration gradient between the edge and the center of the colony develops, indicating hindered diffusion. Accumulation of DNA within the colony increases with increasing DNA length. The presence of the gonococcal DNA uptake sequence (DUS), which mediates specific binding to type 4 pili (T4P) and uptake into the cell, steepens the radial concentration gradient within the colony, suggesting that the DUS reduces DNA mobility. In particular, DNA of N. gonorrhoeae containing multiple DUS is trapped at the periphery. Under conditions, where DUS containing DNA fragments readily enter the colony center, we investigate the efficiency of transformation. We show that despite rapid diffusion of DNA, the transformation is limited to the edge of young colonies. We conclude that DNA mobility depends on DNA length and specific binding mediated by the DUS, resulting in restricted mobility of gonococcal DNA. Yet gonococcal colonies accumulate DNA, and may therefore act as a reservoir for eDNA. DNA fragments encompassing the length of a typical operon efficiently penetrate bacterial colonies. Bacterial colonies accumulate eDNA with an efficiency that depends on the length and the DNA uptake sequence. Genomic DNA from a distinct species spreads efficiently through gonococcal colonies, while gonococcal DNA and DNA from a closely related species are trapped. Transformation is most efficient at the periphery of freshly assembled gonococcal colonies.
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9
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de Block T, González N, Abdellati S, Laumen JGE, Van Dijck C, De Baetselier I, Van den Bossche D, Manoharan-Basil SS, Kenyon C. Successful Intra- but Not Inter-species Recombination of msr(D) in Neisseria subflava. Front Microbiol 2022; 13:855482. [PMID: 35432273 PMCID: PMC9007320 DOI: 10.3389/fmicb.2022.855482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
Resistance acquisition via natural transformation is a common process in the Neisseria genus. Transformation has played an important role in the emergence of resistance to many antimicrobials in Neisseria gonorrhoeae and Neisseria meningitidis. In a previous study, we found that currently circulating isolates of Neisseria subflava had acquired an msr(D) gene that has been found to result in macrolide resistance in other bacteria but never found in Neisseria species before. To determine if this resistance mechanism is transferable among Neisseria species, we assessed if we could transform the msr(D) gene into other commensal and pathogenic Neisseria under low dose azithromycin pressure. Intraspecies recombination in commensal N. subflava was confirmed with PCR and resulted in high-level macrolide resistance. Whole-genome sequencing of these transformed strains identified the complete uptake of the msr(D) integration fragment. Sequence analysis showed that a large fragment of DNA (5 and 12 kb) was transferred through a single horizontal gene transfer event. Furthermore, uptake of the msr(D) gene had no apparent fitness cost. Interspecies transformation of msr(D) from N. subflava to N. gonorrhoeae was, however, not successful.
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Affiliation(s)
- Tessa de Block
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Natalia González
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Medicine, University of Cape Town, Cape Town, South Africa
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10
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The molecular basis of FimT-mediated DNA uptake during bacterial natural transformation. Nat Commun 2022; 13:1065. [PMID: 35246533 PMCID: PMC8897410 DOI: 10.1038/s41467-022-28690-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/08/2022] [Indexed: 01/05/2023] Open
Abstract
Naturally competent bacteria encode sophisticated protein machinery for the uptake and translocation of exogenous DNA into the cell. If this DNA is integrated into the bacterial genome, the bacterium is said to be naturally transformed. Most competent bacterial species utilise type IV pili for the initial DNA uptake step. These proteinaceous cell-surface structures are composed of thousands of pilus subunits (pilins), designated as major or minor according to their relative abundance in the pilus. Here, we show that the minor pilin FimT plays an important role in the natural transformation of Legionella pneumophila. We use NMR spectroscopy, in vitro DNA binding assays and in vivo transformation assays to understand the molecular basis of FimT's role in this process. FimT binds to DNA via an electropositive patch, rich in arginines, several of which are well-conserved and located in a conformationally flexible C-terminal tail. FimT orthologues from other Gammaproteobacteria share the ability to bind to DNA. Our results suggest that FimT plays an important role in DNA uptake in a wide range of competent species.
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11
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Ailloud F, Estibariz I, Suerbaum S. Evolved to vary: genome and epigenome variation in the human pathogen Helicobacter pylori. FEMS Microbiol Rev 2021; 45:5900976. [PMID: 32880636 DOI: 10.1093/femsre/fuaa042] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/31/2020] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori is a Gram-negative, spiral shaped bacterium that selectively and chronically infects the gastric mucosa of humans. The clinical course of this infection can range from lifelong asymptomatic infection to severe disease, including peptic ulcers or gastric cancer. The high mutation rate and natural competence typical of this species are responsible for massive inter-strain genetic variation exceeding that observed in all other bacterial human pathogens. The adaptive value of such a plastic genome is thought to derive from a rapid exploration of the fitness landscape resulting in fast adaptation to the changing conditions of the gastric environment. Nevertheless, diversity is also lost through recurrent bottlenecks and H. pylori's lifestyle is thus a perpetual race to maintain an appropriate pool of standing genetic variation able to withstand selection events. Another aspect of H. pylori's diversity is a large and variable repertoire of restriction-modification systems. While not yet completely understood, methylome evolution could generate enough transcriptomic variation to provide another intricate layer of adaptive potential. This review provides an up to date synopsis of this rapidly emerging area of H. pylori research that has been enabled by the ever-increasing throughput of Omics technologies and a multitude of other technological advances.
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Affiliation(s)
- Florent Ailloud
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Iratxe Estibariz
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Sebastian Suerbaum
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany.,DZIF Deutsches Zentrum für Infektionsforschung, Partner Site Munich, Pettenkoferstr. 9a, 80336 München, Germany.,National Reference Center for Helicobacter pylori, Pettenkoferstr. 9a, 80336 München, Germany
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12
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Dos Santos Souza I, Ziveri J, Bouzinba-Segard H, Morand P, Bourdoulous S. Meningococcus, this famous unknown. C R Biol 2021; 344:127-143. [PMID: 34213851 DOI: 10.5802/crbiol.56] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 01/04/2023]
Abstract
Neisseria meningitidis (meningococcus) is a Gram-negative bacterium responsible for two devastating forms of invasive diseases: purpura fulminans and meningitis. Since the first description of the epidemic nature of the illness at the dawn of the nineteenth century, the scientific knowledge of meningococcal infection has increased greatly. Major advances have been made in the management of the disease with the advent of antimicrobial therapy and the implementation of meningococcal vaccines. More recently, an extensive knowledge has been accumulated on meningococcal interaction with its human host, revealing key processes involved in disease progression and new promising therapeutic approaches.
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Affiliation(s)
- Isabel Dos Santos Souza
- CNRS, UMR8104, Paris, France.,Inserm, U1016, Institut Cochin, Paris, France.,Université de Paris, Faculté de Santé, France
| | - Jason Ziveri
- Inserm, U1016, Institut Cochin, Paris, France.,Inserm, U1016, Institut Cochin, Paris, France.,Université de Paris, Faculté de Santé, France
| | - Haniaa Bouzinba-Segard
- Inserm, U1016, Institut Cochin, Paris, France.,Inserm, U1016, Institut Cochin, Paris, France.,Université de Paris, Faculté de Santé, France
| | - Philippe Morand
- Inserm, U1016, Institut Cochin, Paris, France.,Inserm, U1016, Institut Cochin, Paris, France.,Université de Paris, Faculté de Santé, France
| | - Sandrine Bourdoulous
- Inserm, U1016, Institut Cochin, Paris, France.,Inserm, U1016, Institut Cochin, Paris, France.,Université de Paris, Faculté de Santé, France
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13
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Bakkali M. A cross-species genome-wide analysis of sequences similar to those involved in DNA uptake bias in the Pastuerellaceae and Neisseriaceae families of pathogenic bacteria. Genomics 2021; 113:2800-2811. [PMID: 34157405 DOI: 10.1016/j.ygeno.2021.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/22/2021] [Accepted: 06/14/2021] [Indexed: 11/19/2022]
Abstract
Acquiring new DNA allows the emergence of drug resistance in bacteria. Some Pasteurellaceae and Neisseriaceae species preferentially take up specific sequence tags. The study of such sequences is therefore relevant. They are over-represented in the genomes of the corresponding species. I found similar sequences to be present only in, but not in all, the genomes of the Pasteurellaceae and Neisseriaceae families. The genomic densities of these sequences are different both between species and between families. Interestingly, the family whose genomes harbor more of such sequences also shows more sequence types. A phylogenetic analysis allowed inferring the possible ancestral Neisseriacean sequence and a nucleotide-by-nucleotide analysis allowed inferring the potential ancestral Pasteurellacean sequence based on its genomic footprint. The method used for this work could be applied to other sequences, including transcription factor binding and repeated DNAs.
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Affiliation(s)
- M Bakkali
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
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14
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Dos Santos Souza I, Maïssa N, Ziveri J, Morand PC, Coureuil M, Nassif X, Bourdoulous S. Meningococcal disease: A paradigm of type-IV pilus dependent pathogenesis. Cell Microbiol 2021; 22:e13185. [PMID: 32185901 DOI: 10.1111/cmi.13185] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 01/11/2023]
Abstract
Neisseria meningitidis (meningococcus) is a Gram-negative bacterium responsible for two devastating forms of invasive diseases: purpura fulminans and meningitis. Interaction with both peripheral and cerebral microvascular endothelial cells is at the heart of meningococcal pathogenesis. During the last two decades, an essential role for meningococcal type IV pili in vascular colonisation and disease progression has been unravelled. This review summarises 20 years of research on meningococcal type IV pilus-dependent virulence mechanisms, up to the identification of promising anti-virulence compounds that target type IV pili.
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Affiliation(s)
- Isabel Dos Santos Souza
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Faculté de Santé, Université de Paris, Paris, France
| | - Nawal Maïssa
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Faculté de Santé, Université de Paris, Paris, France
| | - Jason Ziveri
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Faculté de Santé, Université de Paris, Paris, France
| | - Philippe C Morand
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Faculté de Santé, Université de Paris, Paris, France
| | - Mathieu Coureuil
- Faculté de Santé, Université de Paris, Paris, France.,Inserm, U1151, Institut-Necker-Enfants-Malades, Paris, France.,CNRS, UMR 8253, Paris, France
| | - Xavier Nassif
- Faculté de Santé, Université de Paris, Paris, France.,Inserm, U1151, Institut-Necker-Enfants-Malades, Paris, France.,CNRS, UMR 8253, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Necker Enfants Malades, Paris, France
| | - Sandrine Bourdoulous
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Faculté de Santé, Université de Paris, Paris, France
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15
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Huang L, Liu M, Zhu D, Xie L, Huang M, Xiang C, Biville F, Jia R, Chen S, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Wang M, Cheng A. Natural Transformation of Riemerella columbina and Its Determinants. Front Microbiol 2021; 12:634895. [PMID: 33746928 PMCID: PMC7965970 DOI: 10.3389/fmicb.2021.634895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/12/2021] [Indexed: 12/17/2022] Open
Abstract
In a previous study, it was shown that Riemerella anatipestifer, a member of Flavobacteriaceae, is naturally competent. However, whether natural competence is universal in Flavobacteriaceae remains unknown. In this study, it was shown for the first time that Riemerella columbina was naturally competent in the laboratory condition; however, Flavobacterium johnsoniae was not naturally competent under the same conditions. The competence of R. columbina was maintained throughout the growth phases, and the transformation frequency was highest during the logarithmic phase. A competition assay revealed that R. columbina preferentially took up its own genomic DNA over heterologous DNA. The natural transformation frequency of R. columbina was significantly increased in GCB medium without peptone or phosphate. Furthermore, natural transformation of R. columbina was inhibited by 0.5 mM EDTA, but could be restored by the addition of CaCl2, MgCl2, ZnCl2, and MnCl2, suggesting that these divalent cations promote the natural transformation of R. columbina. Overall, this study revealed that natural competence is not universal in Flavobacteriaceae members and triggering of competence differs from species to species.
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Affiliation(s)
- Li Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Dekang Zhu
- Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Li Xie
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Chen Xiang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Francis Biville
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
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16
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Barnier JP, Euphrasie D, Join-Lambert O, Audry M, Schonherr-Hellec S, Schmitt T, Bourdoulous S, Coureuil M, Nassif X, El Behi M. Type IV pilus retraction enables sustained bacteremia and plays a key role in the outcome of meningococcal sepsis in a humanized mouse model. PLoS Pathog 2021; 17:e1009299. [PMID: 33592056 PMCID: PMC7909687 DOI: 10.1371/journal.ppat.1009299] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/26/2021] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
Neisseria meningitidis (the meningococcus) remains a major cause of bacterial meningitis and fatal sepsis. This commensal bacterium of the human nasopharynx can cause invasive diseases when it leaves its niche and reaches the bloodstream. Blood-borne meningococci have the ability to adhere to human endothelial cells and rapidly colonize microvessels. This crucial step enables dissemination into tissues and promotes deregulated inflammation and coagulation, leading to extensive necrotic purpura in the most severe cases. Adhesion to blood vessels relies on type IV pili (TFP). These long filamentous structures are highly dynamic as they can rapidly elongate and retract by the antagonistic action of two ATPases, PilF and PilT. However, the consequences of TFP dynamics on the pathophysiology and the outcome of meningococcal sepsis in vivo have been poorly studied. Here, we show that human graft microvessels are replicative niches for meningococci, that seed the bloodstream and promote sustained bacteremia and lethality in a humanized mouse model. Intriguingly, although pilus-retraction deficient N. meningitidis strain (ΔpilT) efficiently colonizes human graft tissue, this mutant did not promote sustained bacteremia nor induce mouse lethality. This effect was not due to a decreased inflammatory response, nor defects in bacterial clearance by the innate immune system. Rather, TFP-retraction was necessary to promote the release of TFP-dependent contacts between bacteria and, in turn, the detachment from colonized microvessels. The resulting sustained bacteremia was directly correlated with lethality. Altogether, these results demonstrate that pilus retraction plays a key role in the occurrence and outcome of meningococcal sepsis by supporting sustained bacteremia. These findings open new perspectives on the role of circulating bacteria in the pathological alterations leading to lethal sepsis.
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Affiliation(s)
- Jean-Philippe Barnier
- Université de Paris, Faculté de Médecine, Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, Paris, France
- Service de microbiologie, Assistance Publique–Hôpitaux de Paris. Centre–Université de Paris, Hôpital Necker Enfants Malades, Paris, France
| | - Daniel Euphrasie
- Université de Paris, Faculté de Médecine, Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, Paris, France
| | - Olivier Join-Lambert
- Université de Paris, Faculté de Médecine, Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, Paris, France
- Service de microbiologie, Assistance Publique–Hôpitaux de Paris. Centre–Université de Paris, Hôpital Necker Enfants Malades, Paris, France
| | - Mathilde Audry
- Université de Paris, Faculté de Médecine, Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, Paris, France
| | - Sophia Schonherr-Hellec
- Université de Paris, Faculté de Médecine, Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, Paris, France
| | - Taliah Schmitt
- Service de chirurgie reconstructrice et plastique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Sandrine Bourdoulous
- Université de Paris, Faculté de Médecine, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris, France
| | - Mathieu Coureuil
- Université de Paris, Faculté de Médecine, Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, Paris, France
| | - Xavier Nassif
- Université de Paris, Faculté de Médecine, Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, Paris, France
- Service de microbiologie, Assistance Publique–Hôpitaux de Paris. Centre–Université de Paris, Hôpital Necker Enfants Malades, Paris, France
| | - Mohamed El Behi
- Université de Paris, Faculté de Médecine, Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, Paris, France
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17
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Muir A, Gurung I, Cehovin A, Bazin A, Vallenet D, Pelicic V. Construction of a complete set of Neisseria meningitidis mutants and its use for the phenotypic profiling of this human pathogen. Nat Commun 2020; 11:5541. [PMID: 33139723 PMCID: PMC7606547 DOI: 10.1038/s41467-020-19347-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/05/2020] [Indexed: 01/29/2023] Open
Abstract
The bacterium Neisseria meningitidis causes life-threatening meningitis and sepsis. Here, we construct a complete collection of defined mutants in protein-coding genes of this organism, identifying all genes that are essential under laboratory conditions. The collection, named NeMeSys 2.0, consists of individual mutants in 1584 non-essential genes. We identify 391 essential genes, which are associated with basic functions such as expression and preservation of genome information, cell membrane structure and function, and metabolism. We use this collection to shed light on the functions of diverse genes, including a gene encoding a member of a previously unrecognised class of histidinol-phosphatases; a set of 20 genes required for type IV pili function; and several conditionally essential genes encoding antitoxins and/or immunity proteins. We expect that NeMeSys 2.0 will facilitate the phenotypic profiling of a major human bacterial pathogen.
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Affiliation(s)
- Alastair Muir
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Ishwori Gurung
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Ana Cehovin
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Adelme Bazin
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Evry, Université Paris-Saclay, CNRS, Evry, France
| | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Evry, Université Paris-Saclay, CNRS, Evry, France
| | - Vladimir Pelicic
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.
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18
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All living cells are cognitive. Biochem Biophys Res Commun 2020; 564:134-149. [PMID: 32972747 DOI: 10.1016/j.bbrc.2020.08.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/28/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022]
Abstract
All living cells sense and respond to changes in external or internal conditions. Without that cognitive capacity, they could not obtain nutrition essential for growth, survive inevitable ecological changes, or correct accidents in the complex processes of reproduction. Wherever examined, even the smallest living cells (prokaryotes) display sophisticated regulatory networks establishing appropriate adaptations to stress conditions that maximize the probability of survival. Supposedly "simple" prokaryotic organisms also display remarkable capabilities for intercellular signalling and multicellular coordination. These observations indicate that all living cells are cognitive.
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19
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Calder A, Menkiti CJ, Çağdaş A, Lisboa Santos J, Streich R, Wong A, Avini AH, Bojang E, Yogamanoharan K, Sivanesan N, Ali B, Ashrafi M, Issa A, Kaur T, Latif A, Mohamed HAS, Maqsood A, Tamang L, Swager E, Stringer AJ, Snyder LAS. Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire. Microb Genom 2020; 6. [PMID: 32845827 PMCID: PMC7643975 DOI: 10.1099/mgen.0.000423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Commensal non-pathogenic Neisseria spp. live within the human host alongside the pathogenic Neisseria meningitidis and Neisseria gonorrhoeae and due to natural competence, horizontal gene transfer within the genus is possible and has been observed. Four distinct Neisseria spp. isolates taken from the throats of two human volunteers have been assessed here using a combination of microbiological and bioinformatics techniques. Three of the isolates have been identified as Neisseria subflava biovar perflava and one as Neisseria cinerea. Specific gene clusters have been identified within these commensal isolate genome sequences that are believed to encode a Type VI Secretion System, a newly identified CRISPR system, a Type IV Secretion System unlike that in other Neisseria spp., a hemin transporter, and a haem acquisition and utilization system. This investigation is the first to investigate these systems in either the non-pathogenic or pathogenic Neisseria spp. In addition, the N. subflava biovar perflava possess previously unreported capsule loci and sequences have been identified in all four isolates that are similar to genes seen within the pathogens that are associated with virulence. These data from the four commensal isolates provide further evidence for a Neisseria spp. gene pool and highlight the presence of systems within the commensals with functions still to be explored.
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Affiliation(s)
- Alan Calder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Chukwuma Jude Menkiti
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Aylin Çağdaş
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Jefferson Lisboa Santos
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Ricarda Streich
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Alice Wong
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Amir H Avini
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Ebrima Bojang
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Karththeepan Yogamanoharan
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Nivetha Sivanesan
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Besma Ali
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Mariam Ashrafi
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Abdirizak Issa
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Tajinder Kaur
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Aisha Latif
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Hani A Sheik Mohamed
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Atifa Maqsood
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Laxmi Tamang
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Emily Swager
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Alex J Stringer
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Lori A S Snyder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
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20
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Hughes-Games A, Roberts AP, Davis SA, Hill DJ. Identification of integrative and conjugative elements in pathogenic and commensal Neisseriaceae species via genomic distributions of DNA uptake sequence dialects. Microb Genom 2020; 6:e000372. [PMID: 32375974 PMCID: PMC7371117 DOI: 10.1099/mgen.0.000372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/13/2020] [Indexed: 02/02/2023] Open
Abstract
Mobile genetic elements (MGEs) are key factors responsible for dissemination of virulence determinants and antimicrobial-resistance genes amongst pathogenic bacteria. Conjugative MGEs are notable for their high gene loads donated per transfer event, broad host ranges and phylogenetic ubiquity amongst prokaryotes, with the subclass of chromosomally inserted integrative and conjugative elements (ICEs) being particularly abundant. The focus on a small number of model systems has biased the study of ICEs towards those conferring readily selectable phenotypes to host cells, whereas the identification and characterization of integrated cryptic elements remains challenging. Even though antimicrobial resistance and horizontally acquired virulence genes are major factors aggravating neisserial infection, conjugative MGEs of Neisseria gonorrhoeae and Neisseria meningitidis remain poorly characterized. Using a phenotype-independent approach based on atypical distributions of DNA uptake sequences (DUSs) in MGEs relative to the chromosomal background, we have identified two groups of chromosomally integrated conjugative elements in Neisseria: one found almost exclusively in pathogenic species possibly deriving from the genus Kingella, the other belonging to a group of Neisseria mucosa-like commensals. The former element appears to enable transfer of traditionally gonococcal-specific loci such as the virulence-associated toxin-antitoxin system fitAB to N. meningitidis chromosomes, whilst the circular form of the latter possesses a unique attachment site (attP) sequence seemingly adapted to exploit DUS motifs as chromosomal integration sites. In addition to validating the use of DUS distributions in Neisseriaceae MGE identification, the >170 identified ICE sequences provide a valuable resource for future studies of ICE evolution and host adaptation.
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Affiliation(s)
- Alex Hughes-Games
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, University of Bristol, Bristol, UK
| | - Adam P. Roberts
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sean A. Davis
- School of Chemistry, University of Bristol, Bristol, UK
| | - Darryl J. Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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21
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The circadian clock and darkness control natural competence in cyanobacteria. Nat Commun 2020; 11:1688. [PMID: 32245943 PMCID: PMC7125226 DOI: 10.1038/s41467-020-15384-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 03/05/2020] [Indexed: 11/15/2022] Open
Abstract
The cyanobacterium Synechococcus elongatus is a model organism for the study of circadian rhythms. It is naturally competent for transformation—that is, it takes up DNA from the environment, but the underlying mechanisms are unclear. Here, we use a genome-wide screen to identify genes required for natural transformation in S. elongatus, including genes encoding a conserved Type IV pilus, genes known to be associated with competence in other bacteria, and others. Pilus biogenesis occurs daily in the morning, while natural transformation is maximal when the onset of darkness coincides with the dusk circadian peak. Thus, the competence state in cyanobacteria is regulated by the circadian clock and can adapt to seasonal changes of day length. The cyanobacterium Synechococcus elongatus is a model organism for the study of circadian rhythms, and is naturally competent for transformation. Here, Taton et al. identify genes required for natural transformation in this organism, and show that the coincidence of circadian dusk and darkness regulates the competence state in different day lengths.
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22
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Abstract
The bacterium Neisseria gonorrhoeae causes the sexually transmitted infection (STI) gonorrhoea, which has an estimated global annual incidence of 86.9 million adults. Gonorrhoea can present as urethritis in men, cervicitis or urethritis in women, and in extragenital sites (pharynx, rectum, conjunctiva and, rarely, systemically) in both sexes. Confirmation of diagnosis requires microscopy of Gram-stained samples, bacterial culture or nucleic acid amplification tests. As no gonococcal vaccine is available, prevention relies on promoting safe sexual behaviours and reducing STI-associated stigma, which hinders timely diagnosis and treatment thereby increasing transmission. Single-dose systemic therapy (usually injectable ceftriaxone plus oral azithromycin) is the recommended first-line treatment. However, a major public health concern globally is that N. gonorrhoeae is evolving high levels of antimicrobial resistance (AMR), which threatens the effectiveness of the available gonorrhoea treatments. Improved global surveillance of the emergence, evolution, fitness, and geographical and temporal spread of AMR in N. gonorrhoeae, and improved understanding of the pharmacokinetics and pharmacodynamics for current and future antimicrobials in the treatment of urogenital and extragenital gonorrhoea, are essential to inform treatment guidelines. Key priorities for gonorrhoea control include strengthening prevention, early diagnosis, and treatment of patients and their partners; decreasing stigma; expanding surveillance of AMR and treatment failures; and promoting responsible antimicrobial use and stewardship. To achieve these goals, the development of rapid and affordable point-of-care diagnostic tests that can simultaneously detect AMR, novel therapeutic antimicrobials and gonococcal vaccine(s) in particular is crucial.
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Fleming BA, Mulvey MA. Commensal Strains of Neisseria Use DNA to Poison Their Pathogenic Rivals. Cell Host Microbe 2019; 26:156-158. [PMID: 31415746 DOI: 10.1016/j.chom.2019.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Commensal bacteria can interfere with colonization of the host by infiltrating pathogens. In this issue of Cell Host & Microbe, Kim et al. (2019) describe an intriguing mechanism of colonization resistance driven by the mismatching of methylation patterns following uptake of commensal-derived DNA by pathogenic strains of Neisseria.
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Affiliation(s)
- Brittany A Fleming
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112-0565, USA
| | - Matthew A Mulvey
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112-0565, USA.
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Kim WJ, Higashi D, Goytia M, Rendón MA, Pilligua-Lucas M, Bronnimann M, McLean JA, Duncan J, Trees D, Jerse AE, So M. Commensal Neisseria Kill Neisseria gonorrhoeae through a DNA-Dependent Mechanism. Cell Host Microbe 2019; 26:228-239.e8. [PMID: 31378677 DOI: 10.1016/j.chom.2019.07.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/25/2019] [Accepted: 07/11/2019] [Indexed: 12/13/2022]
Abstract
The mucosa is colonized with commensal Neisseria. Some of these niches are sites of infection for the STD pathogen Neisseria gonorrhoeae (Ngo). Given the antagonistic behavior of commensal bacteria toward their pathogenic relatives, we hypothesized that commensal Neisseria may negatively affect Ngo colonization. Here, we report that commensal species of Neisseria kill Ngo through a mechanism based on genetic competence and DNA methylation state. Specifically, commensal-triggered killing occurs when the pathogen takes up commensal DNA containing a methylation pattern that it does not recognize. Indeed, any DNA will kill Ngo if it can enter the cell, is differentially methylated, and has homology to the pathogen genome. Consistent with these findings, commensal Neisseria elongata accelerates Ngo clearance from the mouse in a DNA-uptake-dependent manner. Collectively, we propose that commensal Neisseria antagonizes Ngo infection through a DNA-mediated mechanism and that DNA is a potential microbicide against this highly drug-resistant pathogen.
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Affiliation(s)
- Won Jong Kim
- Department of Immunobiology and the BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Dustin Higashi
- Department of Immunobiology and the BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Maira Goytia
- Department of Biology, Spelman College, Atlanta, GA 30314, USA
| | - Maria A Rendón
- Department of Immunobiology and the BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michelle Pilligua-Lucas
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA
| | - Matthew Bronnimann
- Department of Immunobiology and the BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Jeanine A McLean
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joseph Duncan
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David Trees
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Ann E Jerse
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814, USA
| | - Magdalene So
- Department of Immunobiology and the BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA.
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Structure and Properties of a Natural Competence-Associated Pilin Suggest a Unique Pilus Tip-Associated DNA Receptor. mBio 2019; 10:mBio.00614-19. [PMID: 31186316 PMCID: PMC6561018 DOI: 10.1128/mbio.00614-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Natural competence is the term used to describe the uptake of "naked" extracellular DNA by bacteria; it plays a significant role in horizontal genetic exchange. It is associated with type IV pili, and specialized competence pili mediate DNA uptake. Here, we show that the crystal structure of a competence-associated protein from Thermus thermophilus, ComZ, consists of a type II secretion pseudopilin-like domain, with a large β-solenoid domain inserted into the β-sheet of the pilin-like fold. ComZ binds with high affinity to another competence-associated pilin, PilA2, which lies adjacent to the comZ gene in the genome. The crystal structure of PilA2 revealed a similar type II secretion pseudopilin-like fold, with a small subdomain; docking simulations predicted that PilA2 binds between the pseudopilin-like and β-solenoid domains of ComZ. Electrophoretic shift analysis and DNase protection studies were used to show that ComZ alone and the ComZ/PilA2 complex are able to bind DNA. Protection against reductive dimethylation was used in combination with mass spectrometry and site-directed mutagenesis to identify two lysine residues in ComZ which are involved in DNA binding. They are located between the two domains in ComZ, on the opposite side from the predicted PilA2 binding site. These results suggest a model in which PilA2 assists ComZ in forming the competence pilus tip and DNA binds to the side of the fiber. The results demonstrate how a type IV pilin can be adapted to a specific function by domain insertion and provide the first structural insights into a tip-located competence pilin.IMPORTANCE Thermus thermophilus is a thermophilic bacterium which is capable of natural transformation, the uptake of external DNA with high efficiency. DNA uptake is thought to be mediated by a competence-associated pilus, which binds the DNA substrate and mediates its transfer across the outer membrane and periplasm. Here, we describe the structural and functional analysis of two pilins which are known to be essential for DNA uptake, ComZ and PilA2. ComZ adopts an unusual structure, incorporating a large β-solenoid domain into the pilin structural framework. We argue on structural grounds that this structure cannot readily be accommodated into the competence pilus fiber unless it is at the tip. We also show that ComZ binds DNA and identify two lysine residues which appear to be important for DNA binding. These results suggest a model in which ComZ and PilA2 form a tip-associated DNA receptor which mediates DNA uptake.
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Abstract
Laboratory techniques for transformation of the pathogenic Neisseria are well developed, and take advantage of the natural transformability of these species. More recently, these techniques have been successfully applied to some nonpathogenic species of Neisseria as well. This chapter provides foundational information on the mechanism of Neisseria transformation, considerations for DNA transformation substrate design, two methods for transforming Neisseria in the laboratory, and guidelines for identifying successful transformants.
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Affiliation(s)
- Melanie M Callaghan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Joseph P Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.
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27
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Leong CG, Bloomfield RA, Boyd CA, Dornbusch AJ, Lieber L, Liu F, Owen A, Slay E, Lang KM, Lostroh CP. The role of core and accessory type IV pilus genes in natural transformation and twitching motility in the bacterium Acinetobacter baylyi. PLoS One 2017; 12:e0182139. [PMID: 28771515 PMCID: PMC5542475 DOI: 10.1371/journal.pone.0182139] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/12/2017] [Indexed: 11/21/2022] Open
Abstract
Here we present an examination of type IV pilus genes associated with competence and twitching in the bacterium Acinetobacter baylyi (strain ADP1, BD413). We used bioinformatics to identify potential competence and twitching genes and their operons. We measured the competence and twitching phenotypes of the bioinformatically-identified genes. These results demonstrate that competence and twitching in A. baylyi both rely upon a core of the same type IV pilus proteins. The core includes the inner membrane assembly platform (PilC), a periplasmic assemblage connecting the inner membrane assembly platform to the secretin (ComM), a secretin (ComQ) and its associated pilotin (PilF) that assists with secretin assembly and localization, both cytoplasmic pilus retraction ATPases (PilU, PilT), and pilins (ComP, ComB, PilX). Proteins not needed for both competence and twitching are instead found to specialize in either of the two traits. The pilins are varied in their specialization with some required for either competence (FimT) and others for twitching (ComE). The protein that transports DNA across the inner membrane (ComA) specializes in competence, while signal transduction proteins (PilG, PilS, and PilR) specialize in twitching. Taken together our results suggest that the function of accessory proteins should not be based on homology alone. In addition the results suggest that in A. baylyi the mechanisms of natural transformation and twitching are mediated by the same set of core Type IV pilus proteins with distinct specialized proteins required for each phenotype. Finally, since competence requires multiple pilins as well as both pilus retraction motors PilU and PilT, this suggests that A. baylyi employs a pilus in natural transformation.
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Affiliation(s)
- Colleen G. Leong
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Rebecca A. Bloomfield
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Caroline A. Boyd
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Amber J. Dornbusch
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Leah Lieber
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Flora Liu
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Amie Owen
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Erin Slay
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Kristine M. Lang
- Department of Physics, Colorado College, Colorado Springs, Colorado, United States of America
| | - C. Phoebe Lostroh
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
- * E-mail:
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Beyene GT, Kalayou S, Riaz T, Tonjum T. Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis. BMC Microbiol 2017; 17:96. [PMID: 28431522 PMCID: PMC5399837 DOI: 10.1186/s12866-017-1004-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/08/2017] [Indexed: 11/10/2022] Open
Abstract
Background DNA processing chain A (DprA) is a DNA binding protein which is ubiquitous in bacteria, and is required for DNA transformation to various extents among bacterial species. However, the interaction of DprA with competence and recombination proteins is poorly understood. Therefore, the proteomes of whole Neisseria meningitidis (Nm) wildtype and dprA mutant cells were compared. Such a comparative proteomic analysis increases our understanding of the interactions of DprA with other Nm components and may elucidate its potential role beyond DNA processing in transformation. Results Using label-free quantitative proteomics, a total of 1057 unique Nm proteins were identified, out of which 100 were quantified as differentially abundant (P ≤ 0.05 and fold change ≥ |2|) in the dprA null mutant. Proteins involved in homologous recombination (RecA, UvrD and HolA), pilus biogenesis (PilG, PilT1, PilT2, PilM, PilO, PilQ, PilF and PilE), cell division, including core energy metabolism, and response to oxidative stress were downregulated in the Nm dprA null mutant. The mass spectrometry data are available via ProteomeXchange with identifier PXD006121. Immunoblotting and co-immunoprecipitation were employed to validate the association of DprA with PilG. The analysis revealed reduced amounts of PilG in the dprA null mutant and reduced amounts of DprA in the Nm pilG null mutant. Moreover, a number of pilus biogenesis proteins were shown to interact with DprA and /or PilG. Conclusions DprA interacts with proteins essential for Nm DNA recombination in transformation, pilus biogenesis, and other functions associated with the inner membrane. Inverse downregulation of Nm DprA and PilG expression in the corresponding mutants indicates a link between DNA processing and pilus biogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1004-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Getachew Tesfaye Beyene
- Department of Microbiology, University of Oslo, Oslo, Norway.,Present address: College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Shewit Kalayou
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Mekelle University College of Veterinary Medicine, Mekelle, Ethiopia
| | - Tahira Riaz
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tonjum
- Department of Microbiology, University of Oslo, Oslo, Norway. .,Department of Microbiology, Oslo University Hospital, Oslo, Norway.
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Duffin PM, Barber DA. DprA is required for natural transformation and affects pilin variation in Neisseria gonorrhoeae. Microbiology (Reading) 2016; 162:1620-1628. [DOI: 10.1099/mic.0.000343] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Paul M. Duffin
- Division of Natural Sciences and Mathematics, Transylvania University, Lexington, KY, USA
| | - Daniel A. Barber
- Division of Natural Sciences and Mathematics, Transylvania University, Lexington, KY, USA
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30
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Single-Stranded DNA Uptake during Gonococcal Transformation. J Bacteriol 2016; 198:2515-23. [PMID: 27381919 DOI: 10.1128/jb.00464-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 06/30/2016] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED Neisseria gonorrhoeae is naturally competent for transformation. The first step of the transformation process is the uptake of DNA from the environment into the cell. This transport step is driven by a powerful molecular machine. Here, we addressed the question whether this machine imports single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) at similar rates. The fluorescence signal associated with the uptake of short DNA fragments labeled with a single fluorescent marker molecule was quantified. We found that ssDNA with a double-stranded DNA uptake sequence (DUS) was taken up with a similar efficiency as dsDNA. Imported ssDNA was degraded rapidly, and the thermonuclease Nuc was required for degradation. In a nuc deletion background, dsDNA and ssDNA with a double-stranded DUS were imported and used as the substrates for transformation, whereas the import and transformation efficiencies of ssDNA with single-stranded DUS were below the detection limits. We conclude that the DNA uptake machine requires a double-stranded DUS for efficient DNA recognition and transports ssDNA and dsDNA with comparable efficiencies. IMPORTANCE Bacterial transformation enables bacteria to exchange genetic information. It can speed up adaptive evolution and enhances the potential of DNA repair. The transport of DNA through the outer membrane is the first step of transformation in Gram-negative species. It is driven by a powerful molecular machine whose mechanism remains elusive. Here, we show for Neisseria gonorrhoeae that the machine transports single- and double-stranded DNA at comparable rates, provided that the species-specific DNA uptake sequence is double stranded. Moreover, we found that single-stranded DNA taken up into the periplasm is rapidly degraded by the thermonuclease Nuc. We conclude that the secondary structure of transforming DNA is important for the recognition of self DNA but not for the process of transport through the outer membrane.
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31
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Spencer-Smith R, Roberts S, Gurung N, Snyder LAS. DNA uptake sequences in Neisseria gonorrhoeae as intrinsic transcriptional terminators and markers of horizontal gene transfer. Microb Genom 2016; 2:e000069. [PMID: 28348864 DOI: 10.1099/mgen.0.000069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/24/2016] [Indexed: 01/24/2023] Open
Abstract
DNA uptake sequences are widespread throughout the Neisseria gonorrhoeae genome. These short, conserved sequences facilitate the exchange of endogenous DNA between members of the genus Neisseria. Often the DNA uptake sequences are present as inverted repeats that are able to form hairpin structures. It has been suggested previously that DNA uptake sequence inverted repeats present 3' of genes play a role in rho-independent termination and attenuation. However, there is conflicting experimental evidence to support this role. The aim of this study was to determine the role of DNA uptake sequences in transcriptional termination. Both bioinformatics predictions, conducted using TransTermHP, and experimental evidence, from RNA-seq data, were used to determine which inverted repeat DNA uptake sequences are transcriptional terminators and in which direction. Here we show that DNA uptake sequences in the inverted repeat configuration occur in N. gonorrhoeae both where the DNA uptake sequence precedes the inverted version of the sequence and also, albeit less frequently, in reverse order. Due to their symmetrical configuration, inverted repeat DNA uptake sequences can potentially act as bi-directional terminators, therefore affecting transcription on both DNA strands. This work also provides evidence that gaps in DNA uptake sequence density in the gonococcal genome coincide with areas of DNA that are foreign in origin, such as prophage. This study differentiates for the first time, to our knowledge, between DNA uptake sequences that form intrinsic transcriptional terminators and those that do not, providing characteristic features within the flanking inverted repeat that can be identified.
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Affiliation(s)
- Russell Spencer-Smith
- 1School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK.,2Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Sabrina Roberts
- 1School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
| | - Neesha Gurung
- 1School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
| | - Lori A S Snyder
- 1School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
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32
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Krüger NJ, Knüver MT, Zawilak-Pawlik A, Appel B, Stingl K. Genetic Diversity as Consequence of a Microaerobic and Neutrophilic Lifestyle. PLoS Pathog 2016; 12:e1005626. [PMID: 27166672 PMCID: PMC4864210 DOI: 10.1371/journal.ppat.1005626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/21/2016] [Indexed: 01/10/2023] Open
Abstract
As a neutrophilic bacterium, Helicobacter pylori is growth deficient under extreme acidic conditions. The gastric pathogen is equipped with an acid survival kit, regulating urease activity by a pH-gated urea channel, opening below pH 6.5. After overcoming acid stress, the bacterium’s multiplication site is situated at the gastric mucosa with near neutral pH. The pathogen exhibits exceptional genetic variability, mainly due to its capability of natural transformation, termed competence. Using single cell analysis, we show here that competence is highly regulated in H. pylori. DNA uptake complex activity was reversibly shut down below pH 6.5. pH values above 6.5 opened a competence window, in which competence development was triggered by the combination of pH increase and oxidative stress. In contrast, addition of sublethal concentrations of the DNA-damaging agents ciprofloxacin or mitomycin C did not trigger competence development under our conditions. An oxygen-sensitive mutant lacking superoxide dismutase (sodB) displayed a higher competent fraction of cells than the wild type under comparable conditions. In addition, the sodB mutant was dependent on adenine for growth in broth and turned into non-cultivable coccoid forms in its absence, indicating that adenine had radical quenching capacity. Quantification of periplasmically located DNA in competent wild type cells revealed outstanding median imported DNA amounts of around 350 kb per cell within 10 min of import, with maximally a chromosomal equivalent (1.6 Mb) in individual cells, far exceeding previous amounts detected in other Gram-negative bacteria. We conclude that the pathogen’s high genetic diversity is a consequence of its enormous DNA uptake capacity, triggered by intrinsic and extrinsic oxidative stress once a neutral pH at the site of chronic host colonization allows competence development. Natural transformation, i.e. the capacity to take up DNA from the environment, is one of the crucial means for horizontal gene transfer and genetic diversity in bacteria. The human gastric pathogen Helicobacter pylori is confronted with acid stress before entering its multiplication site, the gastric mucosa. The bacterium causes lifelong chronic gastritis and is perfectly adapted to the human host, crucially by displaying unusual genetic diversity. Using a single cell approach and well-controlled conditions, we show here that the amount of imported DNA in competent H. pylori is outstanding, far exceeding previous measurement with other Gram-negative bacteria. Furthermore, DNA uptake activity was tightly regulated and limited to pH above 6.5, conditions thought to be met in close contact with the gastric mucosa. In addition, we show that within this pH competence window, competence development was triggered by an increase in pH in combination with the level of oxidative stress. Our data provide explanations for the extraordinary high genetic diversity, often referred to as genome plasticity of this unusual microaerobic pathogen.
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Affiliation(s)
- Nora-Johanna Krüger
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Marie-Theres Knüver
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Anna Zawilak-Pawlik
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Department of Microbiology, Wroclaw, Poland
| | - Bernd Appel
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Kerstin Stingl
- Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
- * E-mail:
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Berry JL, Xu Y, Ward PN, Lea SM, Matthews SJ, Pelicic V. A Comparative Structure/Function Analysis of Two Type IV Pilin DNA Receptors Defines a Novel Mode of DNA Binding. Structure 2016; 24:926-34. [PMID: 27161979 PMCID: PMC4906244 DOI: 10.1016/j.str.2016.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/19/2016] [Accepted: 04/04/2016] [Indexed: 11/29/2022]
Abstract
DNA transformation is a widespread process allowing bacteria to capture free DNA by using filamentous nano-machines composed of type IV pilins. These proteins can act as DNA receptors as demonstrated by the finding that Neisseria meningitidis ComP minor pilin has intrinsic DNA-binding ability. ComP binds DNA better when it contains the DNA-uptake sequence (DUS) motif abundant in this species genome, playing a role in its trademark ability to selectively take up its own DNA. Here, we report high-resolution structures for meningococcal ComP and Neisseria subflava ComPsub, which recognize different DUS motifs. We show that they are structurally identical type IV pilins that pack readily into filament models and display a unique DD region delimited by two disulfide bonds. Functional analysis of ComPsub defines a new mode of DNA binding involving the DD region, adapted for exported DNA receptors.
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Affiliation(s)
- Jamie-Lee Berry
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Yingqi Xu
- Centre for Structural Biology, Imperial College London, London SW7 2AZ, UK
| | - Philip N Ward
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Stephen J Matthews
- Centre for Structural Biology, Imperial College London, London SW7 2AZ, UK.
| | - Vladimir Pelicic
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
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34
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Abstract
The genus Neisseria contains two pathogenic species of prominant public health concern: Neisseria gonorrhoeae and Neisseria meningitidis. These pathogens display a notable ability to undergo frequent programmed recombination events. The recombination-mediated pathways of transformation and pilin antigenic variation in the Neisseria are well-studied systems that are critical for pathogenesis. Here we will detail the conserved and unique aspects of transformation and antigenic variation in the Neisseria. Transformation will be followed from initial DNA binding through recombination into the genome with consideration to the factors necessary at each step. Additional focus is paid to the unique type IV secretion system that mediates donation of transforming DNA in the pathogenic Neisseria. The pilin antigenic variation system uses programmed recombinations to alter a major surface determinant, which allows immune avoidance and promotes infection. We discuss the trans- and cis- acting factors which facilitate pilin antigenic variation and present the current understanding of the mechanisms involved in the process.
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35
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Frye SA, Lång E, Beyene GT, Balasingham SV, Homberset H, Rowe AD, Ambur OH, Tønjum T. The Inner Membrane Protein PilG Interacts with DNA and the Secretin PilQ in Transformation. PLoS One 2015; 10:e0134954. [PMID: 26248334 PMCID: PMC4527729 DOI: 10.1371/journal.pone.0134954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/15/2015] [Indexed: 11/19/2022] Open
Abstract
Expression of type IV pili (Tfp), filamentous appendages emanating from the bacterial surface, is indispensable for efficient neisserial transformation. Tfp pass through the secretin pore consisting of the membrane protein PilQ. PilG is a polytopic membrane protein, conserved in Gram-positive and Gram-negative bacteria, that is required for the biogenesis of neisserial Tfp. PilG null mutants are devoid of pili and non-competent for transformation. Here, recombinant full-length, truncated and mutated variants of meningococcal PilG were overexpressed, purified and characterized. We report that meningococcal PilG directly binds DNA in vitro, detected by both an electromobility shift analysis and a solid phase overlay assay. PilG DNA binding activity was independent of the presence of the consensus DNA uptake sequence. PilG-mediated DNA binding affinity was mapped to the N-terminus and was inactivated by mutation of residues 43 to 45. Notably, reduced meningococcal transformation of DNA in vivo was observed when PilG residues 43 to 45 were substituted by alanine in situ, defining a biologically significant DNA binding domain. N-terminal PilG also interacted with the N-terminal region of PilQ, which previously was shown to bind DNA. Collectively, these data suggest that PilG and PilQ in concert bind DNA during Tfp-mediated transformation.
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Affiliation(s)
- Stephan A. Frye
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Emma Lång
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | | | | | | | - Ole Herman Ambur
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Department of Microbiology, University of Oslo, Oslo, Norway
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36
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Sequence-specific transport of oligonucleotides into human endothelial cells. Russ Chem Bull 2015. [DOI: 10.1007/s11172-015-1033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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37
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Affiliation(s)
- Alain Filloux
- Alain Filloux, MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; E-mail:
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Jung J, Park W. Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives. Appl Microbiol Biotechnol 2015; 99:2533-48. [PMID: 25693672 DOI: 10.1007/s00253-015-6439-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 01/11/2023]
Abstract
Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.
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Affiliation(s)
- Jaejoon Jung
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
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Berry JL, Pelicic V. Exceptionally widespread nanomachines composed of type IV pilins: the prokaryotic Swiss Army knives. FEMS Microbiol Rev 2014; 39:134-54. [PMID: 25793961 PMCID: PMC4471445 DOI: 10.1093/femsre/fuu001] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Prokaryotes have engineered sophisticated surface nanomachines that have allowed them to colonize Earth and thrive even in extreme environments. Filamentous machineries composed of type IV pilins, which are associated with an amazing array of properties ranging from motility to electric conductance, are arguably the most widespread since distinctive proteins dedicated to their biogenesis are found in most known species of prokaryotes. Several decades of investigations, starting with type IV pili and then a variety of related systems both in bacteria and archaea, have outlined common molecular and structural bases for these nanomachines. Using type IV pili as a paradigm, we will highlight in this review common aspects and key biological differences of this group of filamentous structures. Using type IV pili as a paradigm, we review common genetic, structural and mechanistic features (many) as well as differences (few) of the exceptionally widespread and functionally versatile prokaryotic nano-machines composed of type IV pilins.
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Affiliation(s)
- Jamie-Lee Berry
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Vladimir Pelicic
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
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Abstract
Neisseria gonorrhoeae and Neisseria meningitidis are closely related organisms that cause the sexually transmitted infection gonorrhea and serious bacterial meningitis and septicemia, respectively. Both species possess multiple mechanisms to alter the expression of surface-exposed proteins through the processes of phase and antigenic variation. This potential for wide variability in surface-exposed structures allows the organisms to always have subpopulations of divergent antigenic types to avoid immune surveillance and to contribute to functional variation. Additionally, the Neisseria are naturally competent for DNA transformation, which is their main means of genetic exchange. Although bacteriophages and plasmids are present in this genus, they are not as effective as DNA transformation for horizontal genetic exchange. There are barriers to genetic transfer, such as restriction-modification systems and CRISPR loci, that limit particular types of exchange. These host-restricted pathogens illustrate the rich complexity of genetics that can help define the similarities and differences of closely related organisms.
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Affiliation(s)
- Ella Rotman
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611; ,
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Abstract
Many bacteria are naturally competent, able to actively transport environmental DNA fragments across their cell envelope and into their cytoplasm. Because incoming DNA fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular DNA. This review starts with an introductory overview of competence and continues with a detailed consideration of the DNA uptake specificity of competent proteobacteria in the Pasteurellaceae and Neisseriaceae. Species in these distantly related families exhibit strong preferences for genomic DNA from close relatives, a self-specificity arising from the combined effects of biases in the uptake machinery and genomic overrepresentation of the sequences this machinery prefers. Other competent species tested lack obvious uptake bias or uptake sequences, suggesting that strong convergent evolutionary forces have acted on these two families. Recent results show that uptake sequences have multiple "dialects," with clades within each family preferring distinct sequence variants and having corresponding variants enriched in their genomes. Although the genomic consensus uptake sequences are 12 and 29 to 34 bp, uptake assays have found that only central cores of 3 to 4 bp, conserved across dialects, are crucial for uptake. The other bases, which differ between dialects, make weaker individual contributions but have important cooperative interactions. Together, these results make predictions about the mechanism of DNA uptake across the outer membrane, supporting a model for the evolutionary accumulation and stability of uptake sequences and suggesting that uptake biases may be more widespread than currently thought.
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