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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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Tekle YI, Tefera H. A Small Genome amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba. Genome Biol Evol 2024; 16:evae058. [PMID: 38504610 PMCID: PMC10980511 DOI: 10.1093/gbe/evae058] [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: 12/04/2023] [Revised: 01/22/2024] [Accepted: 03/14/2024] [Indexed: 03/21/2024] Open
Abstract
This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. Additionally, our investigation into noncoding and repetitive elements sheds light on the evolution of genome size in amoebae, with E. silvestris distinguished by low percentage of repetitive elements. Furthermore, the analysis reveals that E. silvestris has the lowest mean number of introns per gene among the species studied, providing further support for its observed compact genome. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic data sets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.
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Affiliation(s)
- Yonas I Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Hanna Tefera
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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Tekle YI, Tefera H. A Small Genome Amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570689. [PMID: 38106205 PMCID: PMC10723436 DOI: 10.1101/2023.12.07.570689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
This study investigates the genomic characteristics of Echinamoeba silvestris , a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce . E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. The investigation delves into genomic structural evidence, including gene content and repetitive elements, illuminating the distinctive genomic traits of E. silvestris and providing reinforcement for its compact genome size. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic datasets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.
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Tekle YI, Tran H, Wang F, Singla M, Udu I. Omics of an Enigmatic Marine Amoeba Uncovers Unprecedented Gene Trafficking from Giant Viruses and Provides Insights into Its Complex Life Cycle. MICROBIOLOGY RESEARCH 2023; 14:656-672. [PMID: 37752971 PMCID: PMC10521059 DOI: 10.3390/microbiolres14020047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Amoebozoa include lineages of diverse ecology, behavior, and morphology. They are assumed to encompass members with the largest genome sizes of all living things, yet genomic studies in the group are limited. Trichosphaerium, a polymorphic, multinucleate, marine amoeba with a complicated life cycle, has puzzled experts for over a century. In an effort to explore the genomic diversity and investigate extraordinary behavior observed among the Amoebozoa, we used integrated omics approaches to study this enigmatic marine amoeba. Omics data, including single-cell transcriptomics and cytological data, demonstrate that Trichosphaerium sp. possesses the complete meiosis toolkit genes. These genes are expressed in life stages of the amoeba including medium and large cells. The life cycle of Trichosphaerium sp. involves asexual processes via binary fission and multiple fragmentation of giant cells, as well as sexual-like processes involving genes implicated in sexual reproduction and polyploidization. These findings are in stark contrast to a life cycle previously reported for this amoeba. Despite the extreme morphological plasticity observed in Trichosphaerium, our genomic data showed that populations maintain a species-level intragenomic variation. A draft genome of Trichosphaerium indicates elevated lateral gene transfer (LGT) from bacteria and giant viruses. Gene trafficking in Trichosphaerium is the highest within Amoebozoa and among the highest in microbial eukaryotes.
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Affiliation(s)
- Yonas I. Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Hanh Tran
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Fang Wang
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Mandakini Singla
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Isimeme Udu
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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Erdozain S, Barrionuevo E, Ripoll L, Mier P, Andrade-Navarro MA. Protein repeats evolve and emerge in giant viruses. J Struct Biol 2023; 215:107962. [PMID: 37031868 DOI: 10.1016/j.jsb.2023.107962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/21/2023] [Accepted: 04/04/2023] [Indexed: 04/11/2023]
Abstract
Nucleocytoplasmatic large DNA viruses (NCLDVs or giant viruses) stand out because of their relatively large genomes encoding hundreds of proteins. These species give us an unprecedented opportunity to study the emergence and evolution of repeats in protein sequences. On the one hand, as viruses, these species have a restricted set of functions, which can help us better define the functional landscape of repeats. On the other hand, given the particular use of the genetic machinery of the host, it is worth asking whether this allows the variations of genetic material that lead to repeats in non-viral species. To support research in the characterization of repeat protein evolution and function, we present here an analysis focused on the repeat proteins of giant viruses, namely tandem repeats (TRs), short repeats (SRs), and homorepeats (polyX). Proteins with large and short repeats are not very frequent in non-eukaryotic organisms because of the difficulties that their folding may entail; however, their presence in giant viruses remarks their advantage for performance in the protein environment of the eukaryotic host. The heterogeneous content of these TRs, SRs and polyX in some viruses hints at diverse needs. Comparisons to homologs suggest that the mechanisms that generate these repeats are extensively used by some of these viruses, but also their capacity to adopt genes with repeats. Giant viruses could be very good models for the study of the emergence and evolution of protein repeats.
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Affiliation(s)
- Sofía Erdozain
- Instituto de Biotecnología y Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Argentina
| | - Emilia Barrionuevo
- Laboratory of Bioactive Research and Development, Faculty of Exact Sciences, National University of La Plata, Argentina
| | - Lucas Ripoll
- Laboratory of Genetic Engineering, Cell, and Molecular Biology, National University of Quilmes, Argentina
| | - Pablo Mier
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
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Distribution and Current State of Molecular Genetic Characterization in Pathogenic Free-Living Amoebae. Pathogens 2022; 11:pathogens11101199. [PMID: 36297255 PMCID: PMC9612019 DOI: 10.3390/pathogens11101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/03/2022] [Accepted: 10/15/2022] [Indexed: 11/17/2022] Open
Abstract
Free-living amoebae (FLA) are protozoa widely distributed in the environment, found in a great diversity of terrestrial biomes. Some genera of FLA are linked to human infections. The genus Acanthamoeba is currently classified into 23 genotypes (T1-T23), and of these some (T1, T2, T4, T5, T10, T12, and T18) are known to be capable of causing granulomatous amoebic encephalitis (GAE) mainly in immunocompromised patients while other genotypes (T2, T3, T4, T5, T6, T10, T11, T12, and T15) cause Acanthamoeba keratitis mainly in otherwise healthy patients. Meanwhile, Naegleria fowleri is the causative agent of an acute infection called primary amoebic meningoencephalitis (PAM), while Balamuthia mandrillaris, like some Acanthamoeba genotypes, causes GAE, differing from the latter in the description of numerous cases in patients immunocompetent. Finally, other FLA related to the pathologies mentioned above have been reported; Sappinia sp. is responsible for one case of amoebic encephalitis; Vermamoeba vermiformis has been found in cases of ocular damage, and its extraordinary capacity as endocytobiont for microorganisms of public health importance such as Legionella pneumophila, Bacillus anthracis, and Pseudomonas aeruginosa, among others. This review addressed issues related to epidemiology, updating their geographic distribution and cases reported in recent years for pathogenic FLA.
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Acosta-Pérez VJ, Ángeles-Hernández JC, Vega-Sánchez V, Zepeda-Velázquez AP, Añorve-Morga J, Ponce-Noguez JB, Reyes-Rodríguez NE, De-La-Rosa-Arana JL, Ramírez-Paredes JG, Gómez-De-Anda FR. Prevalence of Parasitic Infections with Zoonotic Potential in Tilapia: A Systematic Review and Meta-Analysis. Animals (Basel) 2022; 12:ani12202800. [PMID: 36290186 PMCID: PMC9597807 DOI: 10.3390/ani12202800] [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: 08/09/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 12/01/2022] Open
Abstract
Tilapia has a high socioeconomic value in many countries worldwide. However, it has been identified as a zoonotic parasite reservoir. A systematic literature search and meta-analysis were carried out in order to estimate the global prevalence of zoonotic parasites that affect tilapia. The search was performed by three field experts to avoid reviewer bias. Polled prevalence was estimated using a logistic-normal random-effect regression model in the R software. We dealt with the heterogeneity among studies through subgroup analysis, taking into account the continent, country, genus of the host, parasite taxonomic group, sample origin, and type of diagnostic test as moderator variables. Fifty-two eligible articles were identified covering five tilapia genera with a pooled prevalence of 0.14 (95% CI: 0.10−0.20) showed significant heterogeneity (I2 = 98.4; p < 0.001). The subgroup analysis revealed that the most affected host was Sarotherodon, with a prevalence of 0.42 (95% CI: 0.22−0.65). Cestode was the taxonomic group with the largest prevalence (0.40; 95% CI:0.32−0.48), followed by amoeba (0.24; 95% CI: 0.16−0.35) and nematode (0.22; 95% CI: 0.11−0.38), among which, Schyzocotyle spp., Opistorchis spp., Gnathostoma spp. and Vermamoeba spp. have an impact on public health. Significant differences (p < 0.004) were found among continents and countries, with the highest value of prevalence detected in the African continent (0.28; 95% CI: 0.20−0.37), specifically in Tanzania (0.56; 95% CI: 0.22−0.87) and Egypt (0.43; 95% CI: 0.20−0.55). The origin of samples had a significant effect (p < 0.0001) on the detected prevalence, especially from those that showed the highest prevalence (0.24; 95% CI: 0.17−0.33). Finally, there were no differences in prevalence according to the diagnostic test (p = 0.97). Our results provide useful information on the development of epidemiological programs for the control of zoonoses associated with parasites in tilapia and in the design, planning, and implementation of future research.
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Affiliation(s)
- Víctor Johan Acosta-Pérez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Tulancingo de Bravo 43600, Mexico
| | - Juan Carlos Ángeles-Hernández
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Tulancingo de Bravo 43600, Mexico
- Correspondence: (J.C.Á.-H.); (F.R.G.-D.-A.); Tel.: +52-77-2106-7438 (J.C.Á.-H.); +52-55-3745-2556 (F.R.G.-D.-A.)
| | - Vicente Vega-Sánchez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Tulancingo de Bravo 43600, Mexico
| | - Andrea Paloma Zepeda-Velázquez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Tulancingo de Bravo 43600, Mexico
| | - Javier Añorve-Morga
- Área Académica de Química, Instituto de Ciencias Básica e Ingeniería, Kilometro 4.5 Carretera Pachuca—Tulancingo, Col. Carbonera Mineral de la Reforma, Hidalgo 42082, Mexico
| | | | - Nydia Edith Reyes-Rodríguez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Tulancingo de Bravo 43600, Mexico
| | - Jorge Luis De-La-Rosa-Arana
- Microbiología en Salud Humana, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuahutitlan Izcalli, Estado de Mexico 54743, Mexico
| | - José Gustavo Ramírez-Paredes
- Ridgeway Biologicals Ltd., a Ceva Santé Animale Company, Units 1–3 Old Station Business Park, Compton RG20 6NE, UK
| | - Fabián Ricardo Gómez-De-Anda
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Tulancingo de Bravo 43600, Mexico
- Correspondence: (J.C.Á.-H.); (F.R.G.-D.-A.); Tel.: +52-77-2106-7438 (J.C.Á.-H.); +52-55-3745-2556 (F.R.G.-D.-A.)
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Schulz F, Abergel C, Woyke T. Giant virus biology and diversity in the era of genome-resolved metagenomics. Nat Rev Microbiol 2022; 20:721-736. [PMID: 35902763 DOI: 10.1038/s41579-022-00754-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/09/2022]
Abstract
The discovery of giant viruses, with capsids as large as some bacteria, megabase-range genomes and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. Until recently, most of our knowledge of giant viruses came from ~100 species-level isolates for which genome sequences were available. However, these isolates were primarily derived from laboratory-based co-cultivation with few cultured protists and algae and, thus, did not reflect the true diversity of giant viruses. Although virus co-cultures enabled valuable insights into giant virus biology, many questions regarding their origin, evolution and ecological importance remain unanswered. With advances in sequencing technologies and bioinformatics, our understanding of giant viruses has drastically expanded. In this Review, we summarize our understanding of giant virus diversity and biology based on viral isolates as laboratory cultivation has enabled extensive insights into viral morphology and infection strategies. We then explore how cultivation-independent approaches have heightened our understanding of the coding potential and diversity of the Nucleocytoviricota. We discuss how metagenomics has revolutionized our perspective of giant viruses by revealing their distribution across our planet's biomes, where they impact the biology and ecology of a wide range of eukaryotic hosts and ultimately affect global nutrient cycles.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Chantal Abergel
- Aix Marseille University, CNRS, IGS UMR7256, IMM FR3479, IM2B, IO, Marseille, France
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California Merced, Merced, CA, USA.
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Tekle YI, Wang F, Tran H, Hayes TD, Ryan JF. The draft genome of Cochliopodium minus reveals a complete meiosis toolkit and provides insight into the evolution of sexual mechanisms in Amoebozoa. Sci Rep 2022; 12:9841. [PMID: 35701521 PMCID: PMC9198077 DOI: 10.1038/s41598-022-14131-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/06/2022] [Indexed: 11/23/2022] Open
Abstract
To date, genomic analyses in amoebozoans have been mostly limited to model organisms or medically important lineages. Consequently, the vast diversity of Amoebozoa genomes remain unexplored. A draft genome of Cochliopodium minus, an amoeba characterized by extensive cellular and nuclear fusions, is presented. C. minus has been a subject of recent investigation for its unusual sexual behavior. Cochliopodium's sexual activity occurs during vegetative stage making it an ideal model for studying sexual development, which is sorely lacking in the group. Here we generate a C. minus draft genome assembly. From this genome, we detect a substantial number of lateral gene transfer (LGT) instances from bacteria (15%), archaea (0.9%) and viruses (0.7%) the majority of which are detected in our transcriptome data. We identify the complete meiosis toolkit genes in the C. minus genome, as well as the absence of several key genes involved in plasmogamy and karyogamy. Comparative genomics of amoebozoans reveals variation in sexual mechanism exist in the group. Similar to complex eukaryotes, C. minus (some amoebae) possesses Tyrosine kinases and duplicate copies of SPO11. We report a first example of alternative splicing in a key meiosis gene and draw important insights on molecular mechanism of sex in C. minus using genomic and transcriptomic data.
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Affiliation(s)
- Yonas I Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA.
| | - Fang Wang
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
| | - Hanh Tran
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
| | - T Danielle Hayes
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Iowa State University, Ames, IA, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
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Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease. Clin Microbiol Rev 2022; 35:e0014021. [PMID: 35658516 DOI: 10.1128/cmr.00140-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm3 and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.
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Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation. Microbiol Spectr 2021; 9:e0106921. [PMID: 35007432 PMCID: PMC8694215 DOI: 10.1128/spectrum.01069-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, the candidate phyla radiation (CPR) group has been recognized as representing a large proportion of the microbial kingdom (>26%). CPR are characterized by their obligate symbiotic or exoparasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the coculture of CPR with a suitable bacterial host. Based on various sputum samples, we tried to enrich CPR (Saccharibacteria members) and to cocultivate them with pure hosts (Schaalia odontolytica). This protocol was monitored by TaqMan real-time quantitative PCR (qPCR) using a system specific for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in coculturing and sequencing the complete genomes of two new Saccharibacteria species, "Candidatus Minimicrobia naudis" and "Candidatus Minimicrobia vallesae." In addition, we noticed a decrease in the CT values of Saccharibacteria and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members, and in the future, their currently unknown characteristics may be revealed. IMPORTANCE In this study, the first TaqMan real-time quantitative PCR (qPCR) system, targeting Saccharibacteria phylum, has been developed. This technique can specifically quantify Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific, and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol facilitates subsequent studies of the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.
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Giglione C, Meinnel T. Mapping the myristoylome through a complete understanding of protein myristoylation biochemistry. Prog Lipid Res 2021; 85:101139. [PMID: 34793862 DOI: 10.1016/j.plipres.2021.101139] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/22/2022]
Abstract
Protein myristoylation is a C14 fatty acid modification found in all living organisms. Myristoylation tags either the N-terminal alpha groups of cysteine or glycine residues through amide bonds or lysine and cysteine side chains directly or indirectly via glycerol thioester and ester linkages. Before transfer to proteins, myristate must be activated into myristoyl coenzyme A in eukaryotes or, in bacteria, to derivatives like phosphatidylethanolamine. Myristate originates through de novo biosynthesis (e.g., plants), from external uptake (e.g., human tissues), or from mixed origins (e.g., unicellular organisms). Myristate usually serves as a molecular anchor, allowing tagged proteins to be targeted to membranes and travel across endomembrane networks in eukaryotes. In this review, we describe and discuss the metabolic origins of protein-bound myristate. We review strategies for in vivo protein labeling that take advantage of click-chemistry with reactive analogs, and we discuss new approaches to the proteome-wide discovery of myristate-containing proteins. The machineries of myristoylation are described, along with how protein targets can be generated directly from translating precursors or from processed proteins. Few myristoylation catalysts are currently described, with only N-myristoyltransferase described to date in eukaryotes. Finally, we describe how viruses and bacteria hijack and exploit myristoylation for their pathogenicity.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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Amaro F, Martín-González A. Microbial warfare in the wild-the impact of protists on the evolution and virulence of bacterial pathogens. Int Microbiol 2021; 24:559-571. [PMID: 34365574 DOI: 10.1007/s10123-021-00192-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/03/2021] [Accepted: 06/28/2021] [Indexed: 01/01/2023]
Abstract
During the long history of co-evolution with protists, bacteria have evolved defense strategies to avoid grazing and survive phagocytosis. These mechanisms allow bacteria to exploit phagocytic cells as a protective niche in which to escape from environmental stress and even replicate. Importantly, these anti-grazing mechanisms can function as virulence factors when bacteria infect humans. Here, we discuss how protozoan predation exerts a selective pressure driving bacterial virulence and shaping their genomes, and how bacteria-protist interactions might contribute to the spread of antibiotic resistance as well. We provide examples to demonstrate that besides being voracious bacterial predators, protozoa can serve as melting pots where intracellular organisms exchange genetic information, or even "training grounds" where some pathogens become hypervirulent after passing through. In this special issue, we would like to emphasize the tremendous impact of bacteria-protist interactions on human health and the potential of amoebae as model systems to study biology and evolution of a variety of pathogens. Besides, a better understanding of bacteria-protist relationships will help us expand our current understanding of bacterial virulence and, likely, how pathogens emerge.
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Affiliation(s)
- Francisco Amaro
- Department of Genetics, Physiology and Microbiology, School of Biology, Complutense University of Madrid, 28040, Madrid, Spain.
| | - Ana Martín-González
- Department of Genetics, Physiology and Microbiology, School of Biology, Complutense University of Madrid, 28040, Madrid, Spain
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14
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Ibrahim A, Colson P, Merhej V, Zgheib R, Maatouk M, Naud S, Bittar F, Raoult D. Rhizomal Reclassification of Living Organisms. Int J Mol Sci 2021; 22:5643. [PMID: 34073251 PMCID: PMC8199106 DOI: 10.3390/ijms22115643] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/14/2021] [Accepted: 05/23/2021] [Indexed: 12/11/2022] Open
Abstract
Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant viruses and candidate phyla radiation (CPR). Here, we tried to provide an updated classification, which integrates 216 representative genomes of the current described organisms. The reclassification was expressed through a genetic network based on the total genomic content, not on a single gene to represent the tree of life. This rhizomal exploration represents, more accurately, the evolutionary relationships among the studied species. Our analyses show a separated branch named fifth TRUC (Things Resisting Uncompleted Classifications). This taxon groups CPRs together, independently from Bacteria, Archaea (which regrouped also Nanoarchaeota and Asgard members), Eukarya, and the giant viruses (recognized recently as fourth TRUC). Finally, the broadening of analysis methods will lead to the discovery of new organisms, which justify the importance of updating the classification at every opportunity. In this perspective, our pragmatic representation could be adjusted along with the progress of evolutionary studies.
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Affiliation(s)
- Ahmad Ibrahim
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Vicky Merhej
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Rita Zgheib
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, 13005 Marseille, France
| | - Mohamad Maatouk
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Sabrina Naud
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Fadi Bittar
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
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15
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Siddiqui R, Makhlouf Z, Khan NA. The Increasing Importance of Vermamoeba vermiformis. J Eukaryot Microbiol 2021; 68:e12857. [PMID: 33987951 DOI: 10.1111/jeu.12857] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Vermamoeba vermiformis are one of the most prevalent free-living amoebae. These amoebae are ubiquitous and also thermotolerant. Of concern, V. vermiformis have been found in hospital water networks. Furthermore, associations between V. vermiformis and pathogenic bacteria have been reported, such as Legionella pneumophila. Moreover, V. vermiformis are well known to host viruses, bacteria, and other microorganisms and cases of keratitis due to V. vermiformis in conjunction with other amoebae have been reported. Despite the preceding, the medical importance of V. vermiformis is still an ongoing discussion and its genome has been only recently sequenced. Herein, we present a review of the current understanding of the biology and pathogenesis pertaining to V. vermiformis, as well as its' role as an etiological agent and trojan horse. An approach known as theranostics which combines both diagnosis and therapy could be utilized to eradicate and diagnose keratitis cases caused by such amoebae. Given the rise in global warming, it is imperative to investigate these rarely studied amoebae and to understand their importance in human health.
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Affiliation(s)
- Ruqaiyyah Siddiqui
- College of Arts and Sciences, American University of Sharjah, Sharjah, UAE
| | - Zinb Makhlouf
- College of Arts and Sciences, American University of Sharjah, Sharjah, UAE
| | - Naveed Ahmed Khan
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE.,Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
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Proteomics and Lipidomics Investigations to Decipher the Behavior of Willaertia magna C2c Maky According to Different Culture Modes. Microorganisms 2020; 8:microorganisms8111791. [PMID: 33207645 PMCID: PMC7696429 DOI: 10.3390/microorganisms8111791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 11/17/2022] Open
Abstract
Willaertia magna C2c Maky is a free-living amoeba that has demonstrated its ability to inhibit the intracellular multiplication of some Legionella pneumophila strains, which are pathogenic bacteria inhabiting the aquatic environment. The Amoeba, an industry involved in the treatment of microbiological risk in the water and plant protection sectors, has developed a natural biocide based on the property of W. magna to manage the proliferation of the pathogen in cooling towers. In axenic liquid medium, amoebas are usually cultivated in adhesion on culture flask. However, we implemented a liquid culture in suspension using bioreactors in order to produce large quantities of W. magna. In order to investigate the culture condition effects on W. magna, we conducted a study based on microscopic, proteomics and lipidomics analyzes. According to the culture condition, amoeba exhibited two different phenotypes. The differential proteomics study showed that amoebas seemed to promote the lipid metabolism pathway in suspension culture, whereas we observed an upregulation of the carbohydrate pathway in adherent culture. Furthermore, we observed an over-regulation of proteins related to the cytoskeleton for W. magna cells grown in adhesion. Regarding the lipid analysis, suspension and adhesion cell growth showed comparable lipid class compositions. However, the differential lipid analysis revealed differences that confirmed cell phenotype differences observed by microscopy and predicted by proteomics. Overall, this study provides us with a better insight into the biology and molecular processes of W. magna in different culture lifestyles.
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Hasni I, Decloquement P, Demanèche S, Mameri RM, Abbe O, Colson P, La Scola B. Insight into the Lifestyle of Amoeba Willaertia magna during Bioreactor Growth Using Transcriptomics and Proteomics. Microorganisms 2020; 8:microorganisms8050771. [PMID: 32455615 PMCID: PMC7285305 DOI: 10.3390/microorganisms8050771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
Willaertia magna C2c maky is a thermophilic free-living amoeba strain that showed ability to eliminate Legionella pneumophila, a pathogenic bacterium living in the aquatic environment. The amoeba industry has proposed the use of Willaertia magna as a natural biocide to control L. pneumophila proliferation in cooling towers. Here, transcriptomic and proteomic studies were carried out in order to expand knowledge on W. magna produced in a bioreactor. Illumina RNA-seq generated 217 million raw reads. A total of 8790 transcripts were identified, of which 6179 and 5341 were assigned a function through comparisons with National Center of Biotechnology Information (NCBI) reference sequence and the Clusters of Orthologous Groups of proteins (COG) databases, respectively. To corroborate these transcriptomic data, we analyzed the W. magna proteome using LC–MS/MS. A total of 3561 proteins were identified. The results of transcriptome and proteome analyses were highly congruent. Metabolism study showed that W. magna preferentially consumed carbohydrates and fatty acids to grow. Finally, an in-depth analysis has shown that W. magna produces several enzymes that are probably involved in the metabolism of secondary metabolites. Overall, our multi-omic study of W. magna opens the way to a better understanding of the genetics and biology of this amoeba.
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Affiliation(s)
- Issam Hasni
- Aix-Marseille University, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), UM63, 13005 Marseille, France; (I.H.); (P.D.); (P.C.)
- R&D Department, Amoéba, 69680 Chassieu, France; (S.D.); (R.M.M.); (O.A.)
- Institut Hospitalo-Universitaire (IHU)—Méditerranée Infection, 13005 Marseille, France
| | - Philippe Decloquement
- Aix-Marseille University, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), UM63, 13005 Marseille, France; (I.H.); (P.D.); (P.C.)
| | - Sandrine Demanèche
- R&D Department, Amoéba, 69680 Chassieu, France; (S.D.); (R.M.M.); (O.A.)
| | - Rayane Mouh Mameri
- R&D Department, Amoéba, 69680 Chassieu, France; (S.D.); (R.M.M.); (O.A.)
| | - Olivier Abbe
- R&D Department, Amoéba, 69680 Chassieu, France; (S.D.); (R.M.M.); (O.A.)
| | - Philippe Colson
- Aix-Marseille University, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), UM63, 13005 Marseille, France; (I.H.); (P.D.); (P.C.)
- Institut Hospitalo-Universitaire (IHU)—Méditerranée Infection, 13005 Marseille, France
| | - Bernard La Scola
- Aix-Marseille University, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), UM63, 13005 Marseille, France; (I.H.); (P.D.); (P.C.)
- Institut Hospitalo-Universitaire (IHU)—Méditerranée Infection, 13005 Marseille, France
- Correspondence: ; Tel.: +33-4-9132-4375; Fax: +33-4-9138-7772
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