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Parker CT, Villafuerte DA, Miller WG, Huynh S, Chapman MH, Hanafy Z, Jackson JH, Miller MA, Kathariou S. Genomic Analysis Points to Multiple Genetic Mechanisms for Non-Transformable Campylobacter jejuni ST-50. Microorganisms 2024; 12:327. [PMID: 38399730 PMCID: PMC10893306 DOI: 10.3390/microorganisms12020327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Campylobacter jejuni and Campylobacter coli are well known for their natural competence, i.e., their capacity for the uptake of naked DNA with subsequent transformation. This study identifies non-transformable C. jejuni and C. coli strains from domestic animals and employs genomic analysis to investigate the strain genotypes and their associated genetic mechanisms. The results reveal genetic associations leading to a non-transformable state, including functional DNase genes from bacteriophages and mutations within the cts-encoded DNA-uptake system, which impact the initial steps of the DNA uptake during natural transformation. Interestingly, all 38 tested C. jejuni ST-50 strains from the United States exhibit a high prevalence of non-transformability, and the strains harbor a variety of these genetic markers. This research emphasizes the role of these genetic markers in hindering the transfer of antimicrobial resistance (AMR) determinants, providing valuable insights into the genetic diversity of Campylobacter. As ST-50 is a major clone of C. jejuni globally, we additionally determined the prevalence of the genetic markers for non-transformability among C. jejuni ST-50 from different regions of the world, revealing distinct patterns of evolution and a strong selective pressure on the loss of competence in ST-50 strains, particularly in the agricultural environment in the United States. Our findings contribute to a comprehensive understanding of genetic exchange mechanisms within Campylobacter strains, and their implications for antimicrobial resistance dissemination and evolutionary pathways within specific lineages.
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Affiliation(s)
- Craig T. Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA; (W.G.M.)
| | - David A. Villafuerte
- Department of Food, Nutrition and Bioprocessing Sciences, North Carolina State University, Raleigh, NC 27695, USA; (D.A.V.); (Z.H.); (J.H.J.III); (M.A.M.)
| | - William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA; (W.G.M.)
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA; (W.G.M.)
| | - Mary H. Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA; (W.G.M.)
| | - Zahra Hanafy
- Department of Food, Nutrition and Bioprocessing Sciences, North Carolina State University, Raleigh, NC 27695, USA; (D.A.V.); (Z.H.); (J.H.J.III); (M.A.M.)
| | - James H. Jackson
- Department of Food, Nutrition and Bioprocessing Sciences, North Carolina State University, Raleigh, NC 27695, USA; (D.A.V.); (Z.H.); (J.H.J.III); (M.A.M.)
| | - Morgan A. Miller
- Department of Food, Nutrition and Bioprocessing Sciences, North Carolina State University, Raleigh, NC 27695, USA; (D.A.V.); (Z.H.); (J.H.J.III); (M.A.M.)
| | - Sophia Kathariou
- Department of Food, Nutrition and Bioprocessing Sciences, North Carolina State University, Raleigh, NC 27695, USA; (D.A.V.); (Z.H.); (J.H.J.III); (M.A.M.)
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Cj0683 Is a Competence Protein Essential for Efficient Initialization of DNA Uptake in Campylobacter jejuni. Biomolecules 2023; 13:biom13030514. [PMID: 36979449 PMCID: PMC10046745 DOI: 10.3390/biom13030514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/10/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
C. jejuni is an important food-borne pathogen displaying high genetic diversity, substantially based on natural transformation. The mechanism of DNA uptake from the environment depends on a type II secretion/type IV pilus system, whose components are partially known. Here, we quantified DNA uptake in C. jejuni at the single cell level and observed median transport capacities of approximately 30 kb per uptake location. The process appeared to be limited by the initialization of DNA uptake, was finite, and, finalized within 30 min of contact to DNA. Mutants lacking either the outer membrane pore PilQ or the inner membrane channel ComEC were deficient in natural transformation. The periplasmic DNA binding protein ComE was negligible for DNA uptake, which is in contrast to its proposed function. Intriguingly, a mutant lacking the unique periplasmic protein Cj0683 displayed rare but fully functional DNA uptake events. We conclude that Cj0683 was essential for the efficient initialization of DNA uptake, consistent with the putative function as a competence pilus protein. Unravelling features important in natural transformation might lead to target identification, reducing the adaptive potential of pathogens.
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Gabbert AD, Mydosh JL, Talukdar PK, Gloss LM, McDermott JE, Cooper KK, Clair GC, Konkel ME. The Missing Pieces: The Role of Secretion Systems in Campylobacter jejuni Virulence. Biomolecules 2023; 13:135. [PMID: 36671522 PMCID: PMC9856085 DOI: 10.3390/biom13010135] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 12/29/2022] [Accepted: 01/05/2023] [Indexed: 01/10/2023] Open
Abstract
Campylobacter jejuni is likely the most common bacterial cause of gastroenteritis worldwide, responsible for millions of cases of inflammatory diarrhea characterized by severe abdominal cramps and blood in the stool. Further, C. jejuni infections are associated with post-infection sequelae in developed countries and malnutrition and growth-stunting in low- and middle-income countries. Despite the increasing prevalence of the disease, campylobacteriosis, and the recognition that this pathogen is a serious health threat, our understanding of C. jejuni pathogenesis remains incomplete. In this review, we focus on the Campylobacter secretion systems proposed to contribute to host-cell interactions and survival in the host. Moreover, we have applied a genomics approach to defining the structural and mechanistic features of C. jejuni type III, IV, and VI secretion systems. Special attention is focused on the flagellar type III secretion system and the prediction of putative effectors, given that the proteins exported via this system are essential for host cell invasion and the inflammatory response. We conclude that C. jejuni does not possess a type IV secretion system and relies on the type III and type VI secretion systems to establish a niche and potentiate disease.
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Affiliation(s)
- Amber D. Gabbert
- School of Molecular Biosciences, College of Veterinary Sciences, Washington State University, Pullman, WA 99164, USA
| | - Jennifer L. Mydosh
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721, USA
| | - Prabhat K. Talukdar
- School of Molecular Biosciences, College of Veterinary Sciences, Washington State University, Pullman, WA 99164, USA
| | - Lisa M. Gloss
- School of Molecular Biosciences, College of Veterinary Sciences, Washington State University, Pullman, WA 99164, USA
| | - Jason E. McDermott
- Integrative Omics, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kerry K. Cooper
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721, USA
| | - Geremy C. Clair
- Integrative Omics, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Michael E. Konkel
- School of Molecular Biosciences, College of Veterinary Sciences, Washington State University, Pullman, WA 99164, USA
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Benoit SL, Maier RJ. Copper toxicity towards Campylobacter jejuni is enhanced by the nickel chelator dimethylglyoxime. Metallomics 2021; 14:6486457. [PMID: 34963007 DOI: 10.1093/mtomcs/mfab076] [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: 09/01/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022]
Abstract
The nickel (Ni)-chelator dimethylglyoxime (DMG) was found to be bacteriostatic towards Campylobacter jejuni. Supplementation of nickel to DMG-containing media restored bacterial growth, whereas supplementation of cobalt or zinc had no effect on the growth inhibition. Unexpectedly, the combination of millimolar levels of DMG with micromolar levels of copper (Cu) was bactericidal, an effect not seen in select Gram-negative pathogenic bacteria. Both the cytoplasmic Ni-binding chaperone SlyD and the twin arginine translocation (Tat)-dependent periplasmic copper oxidase CueO were found to play a central role in the Cu-DMG hypersensitivity phenotype. Ni-replete SlyD is needed for Tat-dependent CueO translocation to the periplasm, whereas Ni-depleted (DMG-treated) SlyD is unable to interact with the CueO Tat signal peptide, leading to mislocalization of CueO and increased copper sensitivity. In support of this model, C. jejuni ΔslyD and ΔcueO mutants were more sensitive to copper than the wild-type (WT); CueO was less abundant in the periplasmic fraction of ΔslyD or DMG-grown WT cells, compared to WT cells grown on plain medium; SlyD binds the CueO signal sequence peptide, with DMG inhibiting and nickel enhancing the binding, respectively. Injection of Cu-DMG into Galleria mellonella before C. jejuni inoculation significantly increased the insect survival rate compared to the control group. In chickens, oral administration of DMG or Cu-DMG decreased and even abolished C. jejuni colonization in some cases, compared to both water-only and Cu-only control groups. The latter finding is important, since campylobacteriosis is the leading bacterial foodborne infection, and chicken meat constitutes the major foodborne source.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology.,Center for Metalloenzyme Studies, The University of Georgia, Athens, Georgia, 30602
| | - Robert J Maier
- Department of Microbiology.,Center for Metalloenzyme Studies, The University of Georgia, Athens, Georgia, 30602
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"Take It or Leave It"-Factors Regulating Competence Development and DNA Uptake in Campylobacter jejuni. Int J Mol Sci 2021; 22:ijms221810169. [PMID: 34576332 PMCID: PMC8468864 DOI: 10.3390/ijms221810169] [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: 08/17/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/21/2022] Open
Abstract
Campylobacter jejuni has a large adaptive potential due to enormous genetic exchange. Factors regulating natural transformation in this food-borne pathogen are largely unknown but of interest for the application of sustained reduction strategies in the food-processing industry. Using a single cell DNA uptake assay, we visualized that recognition of methylated C. jejuni DNA was essential for the first step of DNA uptake into a DNase resistant state. Transformation rates using a resistance marker correlated with the fraction of competent bacteria, harboring one to maximally four locations of active DNA uptake, not necessarily being located at the cell pole. Competence developed with rising pH between 6.5 and 7.5 under microaerobic conditions and was nearly insensitive towards growth temperatures between 32 °C and 42 °C, CO2 concentrations ranging from 0 to 50% and growth rates. However, competence development was abolished at pH 5 or under aerobic stress conditions, in which the bacteria ceased growth but fully survived. The DNA uptake machinery in competent bacteria shut down at slightly acidic pH and was reversibly switched on upon neutralization. It was dependent on the proton motive force and, in contrast to competence development, slightly enhanced under aerobic conditions. The results suggest that natural transformation in C. jejuni occurs in the neutral and microaerobic intestinal environment for enhanced genetic diversity and pre-adaption before host switch. In addition, highly competent bacteria might be shed into the environment, still able to acquire genetic material for increased survival.
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Bonifácio M, Mateus C, Alves AR, Maldonado E, Duarte AP, Domingues F, Oleastro M, Ferreira S. Natural Transformation as a Mechanism of Horizontal Gene Transfer in Aliarcobacter butzleri. Pathogens 2021; 10:pathogens10070909. [PMID: 34358059 PMCID: PMC8308473 DOI: 10.3390/pathogens10070909] [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: 05/14/2021] [Revised: 06/30/2021] [Accepted: 07/15/2021] [Indexed: 12/16/2022] Open
Abstract
Aliarcobacter butzleri is an emergent enteropathogen, showing high genetic diversity, which likely contributes to its adaptive capacity to different environments. Whether natural transformation can be a mechanism that generates genetic diversity in A. butzleri is still unknown. In the present study, we aimed to establish if A. butzleri is naturally competent for transformation and to investigate the factors influencing this process. Two different transformation procedures were tested using exogenous and isogenic DNA containing antibiotic resistance markers, and different external conditions influencing the process were evaluated. The highest number of transformable A. butzleri strains were obtained with the agar transformation method when compared to the biphasic system (65% versus 47%). A. butzleri was able to uptake isogenic chromosomal DNA at different growth phases, and the competence state was maintained from the exponential to the stationary phases. Overall, the optimal conditions for transformation with the biphasic system were the use of 1 μg of isogenic DNA and incubation at 30 °C under a microaerobic atmosphere, resulting in a transformation frequency ~8 × 10−6 transformants/CFU. We also observed that A. butzleri favored the transformation with the genetic material of its own strain/species, with the DNA incorporation process occurring promptly after the addition of genomic material. In addition, we observed that A. butzleri strains could exchange genetic material in co-culture assays. The presence of homologs of well-known genes involved in the competence in the A. butzleri genome corroborates the natural competence of this species. In conclusion, our results show that A. butzleri is a naturally transformable species, suggesting that horizontal gene transfer mediated by natural transformation is one of the processes contributing to its genetic diversity. In addition, natural transformation can be used as a tool for genetic studies of this species.
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Affiliation(s)
- Marina Bonifácio
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (M.B.); (C.M.); (A.R.A.); (A.P.D.); (F.D.)
| | - Cristiana Mateus
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (M.B.); (C.M.); (A.R.A.); (A.P.D.); (F.D.)
| | - Ana R. Alves
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (M.B.); (C.M.); (A.R.A.); (A.P.D.); (F.D.)
| | - Emanuel Maldonado
- C4-UBI-Cloud Computing Competence Centre, University of Beira Interior, 6200-284 Covilhã, Portugal;
| | - Ana P. Duarte
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (M.B.); (C.M.); (A.R.A.); (A.P.D.); (F.D.)
- C4-UBI-Cloud Computing Competence Centre, University of Beira Interior, 6200-284 Covilhã, Portugal;
| | - Fernanda Domingues
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (M.B.); (C.M.); (A.R.A.); (A.P.D.); (F.D.)
| | - Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal;
| | - Susana Ferreira
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (M.B.); (C.M.); (A.R.A.); (A.P.D.); (F.D.)
- Correspondence:
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Abstract
Thermophilic Campylobacter, in particular Campylobacter jejuni, C. coli and C. lari are the main relevant Campylobacter species for human infections. Due to their high capacity of genetic exchange by horizontal gene transfer (HGT), rapid adaptation to changing environmental and host conditions contribute to successful spreading and persistence of these foodborne pathogens. However, extensive HGT can exert dangerous side effects for the bacterium, such as the incorporation of gene fragments leading to disturbed gene functions. Here we discuss mechanisms of HGT, notably natural transformation, conjugation and bacteriophage transduction and limiting regulatory strategies of gene transfer. In particular, we summarize the current knowledge on how the DNA macromolecule is exchanged between single cells. Mechanisms to stimulate and to limit HGT obviously coevolved and maintained an optimal balance. Chromosomal rearrangements and incorporation of harmful mutations are risk factors for survival and can result in drastic loss of fitness. In Campylobacter, the restricted recognition and preferential uptake of free DNA from relatives are mediated by a short methylated DNA pattern and not by a classical DNA uptake sequence as found in other bacteria. A class two CRISPR-Cas system is present but also other DNases and restriction-modification systems appear to be important for Campylobacter genome integrity. Several lytic and integrated bacteriophages have been identified, which contribute to genome diversity. Furthermore, we focus on the impact of gene transfer on the spread of antibiotic resistance genes (resistome) and persistence factors. We discuss remaining open questions in the HGT field, supposed to be answered in the future by current technologies like whole-genome sequencing and single-cell approaches.
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Affiliation(s)
- Julia Carolin Golz
- Department of Biological Safety, National Reference Laboratory for Campylobacter, German Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Kerstin Stingl
- Department of Biological Safety, National Reference Laboratory for Campylobacter, German Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, 12277, Berlin, Germany.
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Burnham PM, Hendrixson DR. Campylobacter jejuni: collective components promoting a successful enteric lifestyle. Nat Rev Microbiol 2019; 16:551-565. [PMID: 29892020 DOI: 10.1038/s41579-018-0037-9] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Campylobacter jejuni is the leading cause of bacterial diarrhoeal disease in many areas of the world. The high incidence of sporadic cases of disease in humans is largely due to its prevalence as a zoonotic agent in animals, both in agriculture and in the wild. Compared with many other enteric bacterial pathogens, C. jejuni has strict growth and nutritional requirements and lacks many virulence and colonization determinants that are typically used by bacterial pathogens to infect hosts. Instead, C. jejuni has a different collection of factors and pathways not typically associated together in enteric pathogens to establish commensalism in many animal hosts and to promote diarrhoeal disease in the human population. In this Review, we discuss the cellular architecture and structure of C. jejuni, intraspecies genotypic variation, the multiple roles of the flagellum, specific nutritional and environmental growth requirements and how these factors contribute to in vivo growth in human and avian hosts, persistent colonization and pathogenesis of diarrhoeal disease.
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Affiliation(s)
- Peter M Burnham
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David R Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Stingl K, Koraimann G. Prokaryotic Information Games: How and When to Take up and Secrete DNA. Curr Top Microbiol Immunol 2019. [PMID: 29536355 DOI: 10.1007/978-3-319-75241-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Besides transduction via bacteriophages natural transformation and bacterial conjugation are the most important mechanisms driving bacterial evolution and horizontal gene spread. Conjugation systems have evolved in eubacteria and archaea. In Gram-positive and Gram-negative bacteria, cell-to-cell DNA transport is typically facilitated by a type IV secretion system (T4SS). T4SSs also mediate uptake of free DNA in Helicobacter pylori, while most transformable bacteria use a type II secretion/type IV pilus system. In this chapter, we focus on how and when bacteria "decide" that such a DNA transport apparatus is to be expressed and assembled in a cell that becomes competent. Development of DNA uptake competence and DNA transfer competence is driven by a variety of stimuli and often involves intricate regulatory networks leading to dramatic changes in gene expression patterns and bacterial physiology. In both cases, genetically homogeneous populations generate a distinct subpopulation that is competent for DNA uptake or DNA transfer or might uniformly switch into competent state. Phenotypic conversion from one state to the other can rely on bistable genetic networks that are activated stochastically with the integration of external signaling molecules. In addition, we discuss principles of DNA uptake processes in naturally transformable bacteria and intend to understand the exceptional use of a T4SS for DNA import in the gastric pathogen H. pylori. Realizing the events that trigger developmental transformation into competence within a bacterial population will eventually help to create novel and effective therapies against the transmission of antibiotic resistances among pathogens.
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Affiliation(s)
- Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, 12277, Berlin, Germany.
| | - Günther Koraimann
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.
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Methylation-dependent DNA discrimination in natural transformation of Campylobacter jejuni. Proc Natl Acad Sci U S A 2017; 114:E8053-E8061. [PMID: 28855338 DOI: 10.1073/pnas.1703331114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Campylobacter jejuni, a leading cause of bacterial gastroenteritis, is naturally competent. Like many competent organisms, C. jejuni restricts the DNA that can be used for transformation to minimize undesirable changes in the chromosome. Although C. jejuni can be transformed by C. jejuni-derived DNA, it is poorly transformed by the same DNA propagated in Escherichia coli or produced with PCR. Our work indicates that methylation plays an important role in marking DNA for transformation. We have identified a highly conserved DNA methyltransferase, which we term Campylobacter transformation system methyltransferase (ctsM), which methylates an overrepresented 6-bp sequence in the chromosome. DNA derived from a ctsM mutant transforms C. jejuni significantly less well than DNA derived from ctsM+ (parental) cells. The ctsM mutation itself does not affect transformation efficiency when parental DNA is used, suggesting that CtsM is important for marking transforming DNA, but not for transformation itself. The mutant has no growth defect, arguing against ongoing restriction of its own DNA. We further show that E. coli plasmid and PCR-derived DNA can efficiently transform C. jejuni when only a subset of the CtsM sites are methylated in vitro. A single methylation event 1 kb upstream of the DNA involved in homologous recombination is sufficient to transform C. jejuni, whereas otherwise identical unmethylated DNA is not. Methylation influences DNA uptake, with a slight effect also seen on DNA binding. This mechanism of DNA discrimination in C. jejuni is distinct from the DNA discrimination described in other competent bacteria.
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