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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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Martyn JE, Gomez-Valero L, Buchrieser C. The evolution and role of eukaryotic-like domains in environmental intracellular bacteria: the battle with a eukaryotic cell. FEMS Microbiol Rev 2022; 46:6529235. [DOI: 10.1093/femsre/fuac012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Intracellular pathogens that are able to thrive in different environments, such as Legionella spp. which preferentially live in protozoa in aquatic environments or environmental Chlamydiae which replicate either within protozoa or a range of animals, possess a plethora of cellular biology tools to influence their eukaryotic host. The host manipulation tools that evolved in the interaction with protozoa, confer these bacteria the capacity to also infect phylogenetically distinct eukaryotic cells, such as macrophages and thus they can also be human pathogens. To manipulate the host cell, bacteria use protein secretion systems and molecular effectors. Although these molecular effectors are encoded in bacteria, they are expressed and function in a eukaryotic context often mimicking or inhibiting eukaryotic proteins. Indeed, many of these effectors have eukaryotic-like domains. In this review we propose that the main pathways environmental intracellular bacteria need to subvert in order to establish the host eukaryotic cell as a replication niche are chromatin remodelling, ubiquitination signalling, and modulation of protein-protein interactions via tandem repeat domains. We then provide mechanistic insight into how these proteins might have evolved as molecular weapons. Finally, we highlight that in environmental intracellular bacteria the number of eukaryotic-like domains and proteins is considerably higher than in intracellular bacteria specialised to an isolated niche, such as obligate intracellular human pathogens. As mimics of eukaryotic proteins are critical components of host pathogen interactions, this distribution of eukaryotic-like domains suggests that the environment has selected them.
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Affiliation(s)
- Jessica E Martyn
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, Paris, France
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Nelson DR, Hazzouri KM, Lauersen KJ, Jaiswal A, Chaiboonchoe A, Mystikou A, Fu W, Daakour S, Dohai B, Alzahmi A, Nobles D, Hurd M, Sexton J, Preston MJ, Blanchette J, Lomas MW, Amiri KMA, Salehi-Ashtiani K. Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution. Cell Host Microbe 2021; 29:250-266.e8. [PMID: 33434515 DOI: 10.1016/j.chom.2020.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/08/2020] [Accepted: 11/18/2020] [Indexed: 01/08/2023]
Abstract
Being integral primary producers in diverse ecosystems, microalgal genomes could be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar and cellular membrane functions. Further, marine species contained significantly more viral families in their genomes (p = 8e-4). Sequences from Chlorovirus, Coccolithovirus, Pandoravirus, Marseillevirus, Tupanvirus, and other viruses were found integrated into the genomes of algal from marine environments. These viral-origin sequences were found to be expressed and code for a wide variety of functions. Together, this study comprehensively defines the expanse of protein-coding and viral elements in microalgal genomes and posits a unified adaptive strategy for algal halotolerance.
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Affiliation(s)
- David R Nelson
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Khaled M Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Al Ain, Abu Dhabi, UAE; Biology Department, College of Science, UAE University, Al Ain, Abu Dhabi, UAE
| | - Kyle J Lauersen
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Alexandra Mystikou
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Weiqi Fu
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Bushra Dohai
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Amnah Alzahmi
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - David Nobles
- UTEX Culture Collection of Algae at the University of Texas at Austin, Austin, TX, USA
| | - Mark Hurd
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Julie Sexton
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Michael J Preston
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Joan Blanchette
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Al Ain, Abu Dhabi, UAE; Biology Department, College of Science, UAE University, Al Ain, Abu Dhabi, UAE
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE; Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
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Collingro A, Köstlbacher S, Horn M. Chlamydiae in the Environment. Trends Microbiol 2020; 28:877-888. [PMID: 32591108 DOI: 10.1016/j.tim.2020.05.020] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Chlamydiae have been known for more than a century as major pathogens of humans. Yet they are also found ubiquitously in the environment where they thrive within protists and in an unmatched wide range of animals. This review summarizes recent advances in understanding chlamydial diversity and distribution in nature. Studying these environmental chlamydiae provides a novel perspective on basic chlamydial biology and evolution. A picture is beginning to emerge with chlamydiae representing one of the evolutionarily most ancient and successful groups of obligate intracellular bacteria.
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Affiliation(s)
- Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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Brandes N, Linial M. Giant Viruses-Big Surprises. Viruses 2019; 11:v11050404. [PMID: 31052218 PMCID: PMC6563228 DOI: 10.3390/v11050404] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Viruses are the most prevalent infectious agents, populating almost every ecosystem on earth. Most viruses carry only a handful of genes supporting their replication and the production of capsids. It came as a great surprise in 2003 when the first giant virus was discovered and found to have a >1 Mbp genome encoding almost a thousand proteins. Following this first discovery, dozens of giant virus strains across several viral families have been reported. Here, we provide an updated quantitative and qualitative view on giant viruses and elaborate on their shared and variable features. We review the complexity of giant viral proteomes, which include functions traditionally associated only with cellular organisms. These unprecedented functions include components of the translation machinery, DNA maintenance, and metabolic enzymes. We discuss the possible underlying evolutionary processes and mechanisms that might have shaped the diversity of giant viruses and their genomes, highlighting their remarkable capacity to hijack genes and genomic sequences from their hosts and environments. This leads us to examine prominent theories regarding the origin of giant viruses. Finally, we present the emerging ecological view of giant viruses, found across widespread habitats and ecological systems, with respect to the environment and human health.
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Affiliation(s)
- Nadav Brandes
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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