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Price CTD, Hanford HE, Al-Quadan T, Santic M, Shin CJ, Da'as MSJ, Abu Kwaik Y. Amoebae as training grounds for microbial pathogens. mBio 2024; 15:e0082724. [PMID: 38975782 PMCID: PMC11323580 DOI: 10.1128/mbio.00827-24] [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] [Indexed: 07/09/2024] Open
Abstract
Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.
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Affiliation(s)
- Christopher T. D. Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Hannah E. Hanford
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Tasneem Al-Quadan
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | | | - Cheon J. Shin
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Manal S. J. Da'as
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, Kentucky, USA
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Seibert BA, Keel MK, Kelly TR, Nilsen RA, Ciembor P, Pesti D, Gregory CR, Ritchie BW, Hawkins MG. Chlamydia buteonis in birds of prey presented to California wildlife rehabilitation facilities. PLoS One 2021; 16:e0258500. [PMID: 34644359 PMCID: PMC8513822 DOI: 10.1371/journal.pone.0258500] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Chlamydial infections, caused by a group of obligate, intracellular, gram-negative bacteria, have health implications for animals and humans. Due to their highly infectious nature and zoonotic potential, staff at wildlife rehabilitation centers should be educated on the clinical manifestations, prevalence, and risk factors associated with Chlamydia spp. infections in raptors. The objectives of this study were to document the prevalence of chlamydial DNA shedding and anti-chlamydial antibodies in raptors admitted to five wildlife rehabilitation centers in California over a one-year period. Chlamydial prevalence was estimated in raptors for each center and potential risk factors associated with infection were evaluated, including location, species, season, and age class. Plasma samples and conjunctiva/choana/cloaca swabs were collected for serology and qPCR from a subset of 263 birds of prey, representing 18 species. Serologic assays identified both anti-C. buteonis IgM and anti-chlamydial IgY antibodies. Chlamydial DNA and anti-chlamydial antibodies were detected in 4.18% (11/263) and 3.14% (6/191) of patients, respectively. Chamydial DNA was identified in raptors from the families Accipitridae and Strigidae while anti-C.buteonis IgM was identified in birds identified in Accipitridae, Falconidae, Strigidae, and Cathartidae. Two of the chlamydial DNA positive birds (one Swainson’s hawk (Buteo swainsoni) and one red-tailed hawk (Buteo jamaicensis)) were necropsied, and tissues were collected for culture. Sequencing of the cultured elementary bodies revealed a chlamydial DNA sequence with 99.97% average nucleotide identity to the recently described Chlamydia buteonis. Spatial clusters of seropositive raptors and raptors positive for chlamydial DNA were detected in northern California. Infections were most prevalent during the winter season. Furthermore, while the proportion of raptors testing positive for chlamydial DNA was similar across age classes, seroprevalence was highest in adults. This study questions the current knowledge on C. buteonis host range and highlights the importance of further studies to evaluate the diversity and epidemiology of Chlamydia spp. infecting raptor populations.
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Affiliation(s)
- Brittany A. Seibert
- Department of Avian Science, University of California, Davis, California, United States of America
| | - Michael K. Keel
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Terra R. Kelly
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Roger A. Nilsen
- Infectious Disease Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Paula Ciembor
- Infectious Disease Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Denise Pesti
- Infectious Disease Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Christopher R. Gregory
- Infectious Disease Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Branson W. Ritchie
- Infectious Disease Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Michelle G. Hawkins
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, United States of America
- * E-mail:
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Ravindranath BS, Vishnu Vinayak S, Chandra Mohan V. RNR inhibitor binding studies of Chlamydia felis: insights from in silico molecular modeling, docking, and simulation studies. J Biomol Struct Dyn 2021; 40:9416-9428. [PMID: 34032189 DOI: 10.1080/07391102.2021.1930160] [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] [Indexed: 12/14/2022]
Abstract
Chlamydia felis is the primary cause of chronic conjunctivitis without respiratory infections in cats, making conjunctiva as its primary target. It is a Gram-negative obligate intracellular bacterium that cannot survive outside the host cell. C. felis can be found worldwide and its zoonotic potential is a known phenomenon. The scope of zoonoses, its scale, and their impact experiencing today has no historical precedence. Among the identified 1415 human pathogens 868 have a zoonotic origin making it to 61%. Although with appropriate drug administration there are instances of re-occurrence of chlamydial infections, the emergence of heterotypic antimicrobial resistance to antibiotics targeting rRNA due to mutations has further complicated the diagnosis and treatment of chlamydial infections. Ribonucleotide-diphosphate reductase subunit beta (RNR) is one of the crucial target proteins of the bacterial pathogens essential in the synthesis of deoxyribonucleotides. Our current study primarily focuses on modeling the target structure through homology modeling. Further, the validated model is complexed with the specific inhibitor Cladribine through sequence-based ligand search. Docking of the identified ligand was performed to identify the different modes of interactions with amino acids present in the prioritized binding pockets. Validation of the binding modes is carried out through molecular dynamics (MD) simulations for the best binding pose with a high binding score. MD simulation study demonstrated the stability of the docked complex considered in this study. The findings from this study may be helpful in drug repurposing and novel drug research in the scenario of resistance to currently practiced antibiotics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B S Ravindranath
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - S Vishnu Vinayak
- Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vivek Chandra Mohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka, India
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Bugalhão JN, Mota LJ. The multiple functions of the numerous Chlamydia trachomatis secreted proteins: the tip of the iceberg. MICROBIAL CELL 2019; 6:414-449. [PMID: 31528632 PMCID: PMC6717882 DOI: 10.15698/mic2019.09.691] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chlamydia trachomatis serovars are obligate intracellular bacterial pathogens mainly causing ocular and urogenital infections that affect millions of people worldwide and which can lead to blindness or sterility. They reside and multiply intracellularly within a membrane-bound vacuolar compartment, known as inclusion, and are characterized by a developmental cycle involving two morphologically and physiologically distinct chlamydial forms. Completion of the developmental cycle involves the secretion of > 70 C. trachomatis proteins that function in the host cell cytoplasm and nucleus, in the inclusion membrane and lumen, and in the extracellular milieu. These proteins can, for example, interfere with the host cell cytoskeleton, vesicular and non-vesicular transport, metabolism, and immune signalling. Generally, this promotes C. trachomatis invasion into, and escape from, host cells, the acquisition of nutrients by the chlamydiae, and evasion of cell-autonomous, humoral and cellular innate immunity. Here, we present an in-depth review on the current knowledge and outstanding questions about these C. trachomatis secreted proteins.
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Affiliation(s)
- Joana N Bugalhão
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Luís Jaime Mota
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae. Int J Mol Sci 2018; 19:ijms19124010. [PMID: 30545112 PMCID: PMC6321445 DOI: 10.3390/ijms19124010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023] Open
Abstract
The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.
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