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Ore A, Angelastro JM, Giulivi C. Integrating Mitochondrial Biology into Innovative Cell Therapies for Neurodegenerative Diseases. Brain Sci 2024; 14:899. [PMID: 39335395 PMCID: PMC11429837 DOI: 10.3390/brainsci14090899] [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: 08/08/2024] [Revised: 08/31/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
The role of mitochondria in neurodegenerative diseases is crucial, and recent developments have highlighted its significance in cell therapy. Mitochondrial dysfunction has been implicated in various neurodegenerative disorders, including Alzheimer's, Parkinson's, amyotrophic lateral sclerosis, and Huntington's diseases. Understanding the impact of mitochondrial biology on these conditions can provide valuable insights for developing targeted cell therapies. This mini-review refocuses on mitochondria and emphasizes the potential of therapies leveraging mesenchymal stem cells, embryonic stem cells, induced pluripotent stem cells, stem cell-derived secretions, and extracellular vesicles. Mesenchymal stem cell-mediated mitochondria transfer is highlighted for restoring mitochondrial health in cells with dysfunctional mitochondria. Additionally, attention is paid to gene-editing techniques such as mito-CRISPR, mitoTALENs, mito-ZNFs, and DdCBEs to ensure the safety and efficacy of stem cell treatments. Challenges and future directions are also discussed, including the possible tumorigenic effects of stem cells, off-target effects, disease targeting, immune rejection, and ethical issues.
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Affiliation(s)
- Adaleiz Ore
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.O.); (J.M.A.)
- Department of Chemical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
| | - James M. Angelastro
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.O.); (J.M.A.)
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.O.); (J.M.A.)
- University of California Medical Investigations of Neurodevelopmental Disorders Institute (MIND Institute), University of California Health, Sacramento, CA 95817, USA
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2
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Castelli M, Nardi T, Giovannini M, Sassera D. Addictive manipulation: a perspective on the role of reproductive parasitism in the evolution of bacteria-eukaryote symbioses. Biol Lett 2024; 20:20240310. [PMID: 39288812 DOI: 10.1098/rsbl.2024.0310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/09/2024] [Accepted: 07/26/2024] [Indexed: 09/19/2024] Open
Abstract
Wolbachia bacteria encompass noteworthy reproductive manipulators of their arthropod hosts. which influence host reproduction to favour their own transmission, also exploiting toxin-antitoxin systems. Recently, multiple other bacterial symbionts of arthropods have been shown to display comparable manipulative capabilities. Here, we wonder whether such phenomena are truly restricted to arthropod hosts. We focused on protists, primary models for evolutionary investigations on eukaryotes due to their diversity and antiquity, but still overall under-investigated. After a thorough re-examination of the literature on bacterial-protist interactions with this question in mind, we conclude that such bacterial 'addictive manipulators' of protists do exist, are probably widespread, and have been overlooked until now as a consequence of the fact that investigations are commonly host-centred, thus ineffective to detect such behaviour. Additionally, we posit that toxin-antitoxin systems are crucial in these phenomena of addictive manipulation of protists, as a result of recurrent evolutionary repurposing. This indicates intriguing functional analogy and molecular homology with plasmid-bacterial interplays. Finally, we remark that multiple addictive manipulators are affiliated with specific bacterial lineages with ancient associations with diverse eukaryotes. This suggests a possible role of addictive manipulation of protists in paving the way to the evolution of bacteria associated with multicellular organisms.
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Affiliation(s)
- Michele Castelli
- Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | - Tiago Nardi
- Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | - Michele Giovannini
- Department of Biology, University of Pisa , Pisa, Italy
- Department of Biology, University of Florence , Florence, Italy
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
- IRCCS Policlinico San Matteo , Pavia, Italy
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3
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Vosseberg J, van Hooff JJE, Köstlbacher S, Panagiotou K, Tamarit D, Ettema TJG. The emerging view on the origin and early evolution of eukaryotic cells. Nature 2024; 633:295-305. [PMID: 39261613 DOI: 10.1038/s41586-024-07677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 06/05/2024] [Indexed: 09/13/2024]
Abstract
The origin of the eukaryotic cell, with its compartmentalized nature and generally large size compared with bacterial and archaeal cells, represents a cornerstone event in the evolution of complex life on Earth. In a process referred to as eukaryogenesis, the eukaryotic cell is believed to have evolved between approximately 1.8 and 2.7 billion years ago from its archaeal ancestors, with a symbiosis with a bacterial (proto-mitochondrial) partner being a key event. In the tree of life, the branch separating the first from the last common ancestor of all eukaryotes is long and lacks evolutionary intermediates. As a result, the timing and driving forces of the emergence of complex eukaryotic features remain poorly understood. During the past decade, environmental and comparative genomic studies have revealed vital details about the identity and nature of the host cell and the proto-mitochondrial endosymbiont, enabling a critical reappraisal of hypotheses underlying the symbiotic origin of the eukaryotic cell. Here we outline our current understanding of the key players and events underlying the emergence of cellular complexity during the prokaryote-to-eukaryote transition and discuss potential avenues of future research that might provide new insights into the enigmatic origin of the eukaryotic cell.
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Affiliation(s)
- Julian Vosseberg
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Jolien J E van Hooff
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Stephan Köstlbacher
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Kassiani Panagiotou
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Daniel Tamarit
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
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4
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Bontemps Z, Paranjape K, Guy L. Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts. FEMS Microbiol Rev 2024; 48:fuae021. [PMID: 39081075 PMCID: PMC11338181 DOI: 10.1093/femsre/fuae021] [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: 12/15/2023] [Revised: 07/22/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024] Open
Abstract
Interactions between eukaryotic hosts and their bacterial symbionts drive key ecological and evolutionary processes, from regulating ecosystems to the evolution of complex molecular machines and processes. Over time, endosymbionts generally evolve reduced genomes, and their relationship with their host tends to stabilize. However, host-bacteria relationships may be heavily influenced by environmental changes. Here, we review these effects on one of the most ancient and diverse endosymbiotic groups, formed by-among others-Legionellales, Francisellaceae, and Piscirickettsiaceae. This group is referred to as Deep-branching Intracellular Gammaproteobacteria (DIG), whose last common ancestor presumably emerged about 2 Ga ago. We show that DIGs are globally distributed, but generally at very low abundance, and are mainly identified in aquatic biomes. Most DIGs harbour a type IVB secretion system, critical for host-adaptation, but its structure and composition vary. Finally, we review the different types of microbial interactions that can occur in diverse environments, with direct or indirect effects on DIG populations. The increased use of omics technologies on environmental samples will allow a better understanding of host-bacterial interactions and help unravel the definition of DIGs as a group from an ecological, molecular, and evolutionary perspective.
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Affiliation(s)
- Zélia Bontemps
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75237 Uppsala, Sweden
| | - Kiran Paranjape
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75237 Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75237 Uppsala, Sweden
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5
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Lanzoni O, Szokoli F, Schrallhammer M, Sabaneyeva E, Krenek S, Doak TG, Verni F, Berendonk TU, Castelli M, Petroni G. "Candidatus Intestinibacterium parameciiphilum"-member of the "Candidatus Paracaedibacteraceae" family (Alphaproteobacteria, Holosporales) inhabiting the ciliated protist Paramecium. Int Microbiol 2024; 27:659-671. [PMID: 37615902 PMCID: PMC11144129 DOI: 10.1007/s10123-023-00414-5] [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: 05/13/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023]
Abstract
Protists frequently host diverse bacterial symbionts, in particular those affiliated with the order Holosporales (Alphaproteobacteria). All characterised members of this bacterial lineage have been retrieved in obligate association with a wide range of eukaryotes, especially multiple protist lineages (e.g. amoebozoans, ciliates, cercozoans, euglenids, and nucleariids), as well as some metazoans (especially arthropods and related ecdysozoans). While the genus Paramecium and other ciliates have been deeply investigated for the presence of symbionts, known members of the family "Candidatus Paracaedibacteraceae" (Holosporales) are currently underrepresented in such hosts. Herein, we report the description of "Candidatus Intestinibacterium parameciiphilum" within the family "Candidatus Paracaedibacteraceae", inhabiting the cytoplasm of Paramecium biaurelia. This novel bacterium is almost twice as big as its relative "Candidatus Intestinibacterium nucleariae" from the opisthokont Nuclearia and does not present a surrounding halo. Based on phylogenetic analyses of 16S rRNA gene sequences, we identified six further potential species-level lineages within the genus. Based on the provenance of the respective samples, we investigated the environmental distribution of the representatives of "Candidatus Intestinibacterium" species. Obtained results are consistent with an obligate endosymbiotic lifestyle, with protists, in particular freshwater ones, as hosts. Thus, available data suggest that association with freshwater protists could be the ancestral condition for the members of the "Candidatus Intestinibacterium" genus.
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Affiliation(s)
| | - Franziska Szokoli
- Department of Biology, University of Pisa, Pisa, Italy
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Martina Schrallhammer
- Mikrobiologie, Institut für Biologie II, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Elena Sabaneyeva
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Sascha Krenek
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | | | - Franco Verni
- Department of Biology, University of Pisa, Pisa, Italy
| | - Thomas U Berendonk
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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6
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Lehman SS, Verhoeve VI, Driscoll TP, Beckmann JF, Gillespie JJ. Metagenome diversity illuminates the origins of pathogen effectors. mBio 2024; 15:e0075923. [PMID: 38564675 PMCID: PMC11077975 DOI: 10.1128/mbio.00759-23] [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: 03/27/2023] [Accepted: 02/12/2024] [Indexed: 04/04/2024] Open
Abstract
Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity for the genus Rickettsia and delineated a sister lineage (the novel genus Tisiphia) that stands to inform on the emergence of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages illuminates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, indicating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role in shaping the rvh effector landscape, as evinced by the discovery of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can yield insight into pathogen effector origins, particularly how effector architectures might become tailored to the discrete host cell functions of different eukaryotic hosts.IMPORTANCEWhile rickettsioses are deadly vector-borne human diseases, factors distinguishing Rickettsia pathogens from the innumerable bevy of environmental rickettsial endosymbionts remain lacking. Recent metagenome-assembled genome (MAG) studies revealed evolutionary timepoints for rickettsial transitions to host dependency. The rvh type IV secretion system was likely repurposed from congener killing in basal extracellular species to parasitizing host cells in later-evolving pathogens. Our analysis of MAG diversity for over two dozen rvh effectors unearthed their presence in some non-pathogens. However, most effectors were found in multiple divergent forms with variable architectures, indicating gene duplication and recombination-fashioned effector repertoires of Rickettsia pathogens. Lateral gene transfer substantially shaped pathogen effector arsenals, evinced by the discovery of effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchanges between Rickettsia and Legionella species. Our study exemplifies how MAGs yield insight into pathogen effector origins and evolutionary processes tailoring effectors to eukaryotic host cell biology.
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Affiliation(s)
- Stephanie S. Lehman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Victoria I. Verhoeve
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Timothy P. Driscoll
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - John F. Beckmann
- Department of Microbiology and Immunology, University of South Alabama, Mobile, Alabama, USA
| | - Joseph J. Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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7
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Liao T, Wang S, Zhang H, Stüeken EE, Luo H. Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils. Mol Biol Evol 2024; 41:msae096. [PMID: 38776415 PMCID: PMC11135946 DOI: 10.1093/molbev/msae096] [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: 01/09/2024] [Revised: 04/21/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Evolution of a complete nitrogen (N) cycle relies on the onset of ammonia oxidation, which aerobically converts ammonia to nitrogen oxides. However, accurate estimation of the antiquity of ammonia-oxidizing bacteria (AOB) remains challenging because AOB-specific fossils are absent and bacterial fossils amenable to calibrate molecular clocks are rare. Leveraging the ancient endosymbiosis of mitochondria and plastid, as well as using state-of-the-art Bayesian sequential dating approach, we obtained a timeline of AOB evolution calibrated largely by eukaryotic fossils. We show that the first AOB evolved in marine Gammaproteobacteria (Gamma-AOB) and emerged between 2.1 and 1.9 billion years ago (Ga), thus postdating the Great Oxidation Event (GOE; 2.4 to 2.32 Ga). To reconcile the sedimentary N isotopic signatures of ammonia oxidation occurring near the GOE, we propose that ammonia oxidation likely occurred at the common ancestor of Gamma-AOB and Gammaproteobacterial methanotrophs, or the actinobacterial/verrucomicrobial methanotrophs which are known to have ammonia oxidation activities. It is also likely that nitrite was transported from the terrestrial habitats where ammonia oxidation by archaea took place. Further, we show that the Gamma-AOB predated the anaerobic ammonia-oxidizing (anammox) bacteria, implying that the emergence of anammox was constrained by the availability of dedicated ammonia oxidizers which produce nitrite to fuel anammox. Our work supports a new hypothesis that N redox cycle involving nitrogen oxides evolved rather late in the ocean.
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Affiliation(s)
- Tianhua Liao
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Sishuo Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Eva E Stüeken
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, Queen's Terrace, KY16 9TS, UK
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Earth and Environmental Sciences Programme, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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8
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Kim M, Kim W, Park Y, Jung J, Park W. Lineage-specific evolution of Aquibium, a close relative of Mesorhizobium, during habitat adaptation. Appl Environ Microbiol 2024; 90:e0209123. [PMID: 38412007 PMCID: PMC10952388 DOI: 10.1128/aem.02091-23] [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: 11/17/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
The novel genus Aquibium that lacks nitrogenase was recently reclassified from the Mesorhizobium genus. The genomes of Aquibium species isolated from water were smaller and had higher GC contents than those of Mesorhizobium species. Six Mesorhizobium species lacking nitrogenase were found to exhibit low similarity in the average nucleotide identity values to the other 24 Mesorhizobium species. Therefore, they were classified as the non-N2-fixing Mesorhizobium lineage (N-ML), an evolutionary intermediate species. The results of our phylogenomic analyses and the loss of Rhizobiales-specific fur/mur indicated that Mesorhizobium species may have evolved from Aquibium species through an ecological transition. Halotolerant and alkali-resistant Aquibium and Mesorhizobium microcysteis belonging to N-ML possessed many tripartite ATP-independent periplasmic transporter and sodium/proton antiporter subunits composed of seven genes (mrpABCDEFG). These genes were not present in the N2-fixing Mesorhizobium lineage (ML), suggesting that genes acquired for adaptation to highly saline and alkaline environments were lost during the evolution of ML as the habitat changed to soil. Land-to-water habitat changes in Aquibium species, close relatives of Mesorhizobium species, could have influenced their genomic evolution by the gain and loss of genes. Our study indicated that lineage-specific evolution could have played a significant role in shaping their genome architecture and conferring their ability to thrive in different habitats.IMPORTANCEPhylogenetic analyses revealed that the Aquibium lineage (AL) and non-N2-fixing Mesorhizobium lineage (N-ML) were monophyletically grouped into distinct clusters separate from the N2-fixing Mesorhizobium lineage (ML). The N-ML, an evolutionary intermediate species having characteristics of both ancestral and descendant species, could provide a genomic snapshot of the genetic changes that occur during adaptation. Genomic analyses of AL, N-ML, and ML revealed that changes in the levels of genes related to transporters, chemotaxis, and nitrogen fixation likely reflect adaptations to different environmental conditions. Our study sheds light on the complex and dynamic nature of the evolution of rhizobia in response to changes in their environment and highlights the crucial role of genomic analysis in understanding these processes.
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Affiliation(s)
- Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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Castelli M, Nardi T, Gammuto L, Bellinzona G, Sabaneyeva E, Potekhin A, Serra V, Petroni G, Sassera D. Host association and intracellularity evolved multiple times independently in the Rickettsiales. Nat Commun 2024; 15:1093. [PMID: 38321113 PMCID: PMC10847448 DOI: 10.1038/s41467-024-45351-7] [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: 12/14/2022] [Accepted: 01/18/2024] [Indexed: 02/08/2024] Open
Abstract
The order Rickettsiales (Alphaproteobacteria) encompasses multiple diverse lineages of host-associated bacteria, including pathogens, reproductive manipulators, and mutualists. Here, in order to understand how intracellularity and host association originated in this order, and whether they are ancestral or convergently evolved characteristics, we built a large and phylogenetically-balanced dataset that includes de novo sequenced genomes and a selection of published genomic and metagenomic assemblies. We perform detailed functional reconstructions that clearly indicates "late" and parallel evolution of obligate host-association in different Rickettsiales lineages. According to the depicted scenario, multiple independent horizontal acquisitions of transporters led to the progressive loss of biosynthesis of nucleotides, amino acids and other metabolites, producing distinct conditions of host-dependence. Each clade experienced a different pattern of evolution of the ancestral arsenal of interaction apparatuses, including development of specialised effectors involved in the lineage-specific mechanisms of host cell adhesion and/or invasion.
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Affiliation(s)
- Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Tiago Nardi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | | | - Greta Bellinzona
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Elena Sabaneyeva
- Department of Cytology and Histology, Saint Petersburg State University, Petersburg, Russia
| | - Alexey Potekhin
- Department of Microbiology, Saint Petersburg State University, Petersburg, Russia
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | | | | | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
- IRCCS Policlinico San Matteo, Pavia, Italy.
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10
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Giovannini M, Petroni G, Castelli M. Novel evolutionary insights on the interactions of the Holosporales (Alphaproteobacteria) with eukaryotic hosts from comparative genomics. Environ Microbiol 2024; 26:e16562. [PMID: 38173299 DOI: 10.1111/1462-2920.16562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Holosporales are an alphaproteobacterial order engaging in obligate and complex associations with eukaryotes, in particular protists. The functional and evolutionary features of those interactions are still largely undisclosed. Here, we sequenced the genomes of two members of the species Bealeia paramacronuclearis (Holosporales, Holosporaceae) intracellularly associated with the ciliate protist Paramecium, which resulted in high correspondence. Consistent with the short-branched early-divergent phylogenetic position, Bealeia presents a larger functional repertoire than other Holosporaceae, comparable to those of other Holosporales families, particularly for energy metabolism and motility. Our analyses indicate that different Holosporales likely experienced at least partly autonomous genome reduction and adaptation to host interactions, for example regarding dependence on host biotin driven by multiple independent horizontal acquisitions of transporters. Among Alphaproteobacteria, this is reminiscent of the convergently evolved Rickettsiales, which however appear more diverse, possibly due to a probably more ancient origin. We identified in Bealeia and other Holosporales the plasmid-encoded putative genetic determinants of R-bodies, which may be involved in a killer trait towards symbiont-free hosts. While it is not clear whether these genes are ancestral or recently horizontally acquired, an intriguing and peculiar role of R-bodies is suggested in the evolution of the interactions of multiple Holosporales with their hosts.
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Affiliation(s)
| | | | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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11
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Anda M, Yamanouchi S, Cosentino S, Sakamoto M, Ohkuma M, Takashima M, Toyoda A, Iwasaki W. Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years. Nat Commun 2023; 14:7232. [PMID: 37963895 PMCID: PMC10645730 DOI: 10.1038/s41467-023-42681-w] [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: 02/13/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
It is generally assumed that all bacteria must have at least one rRNA operon (rrn operon) on the chromosome, but some strains of the genera Aureimonas and Oecophyllibacter carry their sole rrn operon on a plasmid. However, other related strains and species have chromosomal rrn loci, suggesting that the exclusive presence of rrn operons on a plasmid is rare and unlikely to be stably maintained over long evolutionary periods. Here, we report the results of a systematic search for additional bacteria without chromosomal rrn operons. We find that at least four bacterial clades in the phyla Bacteroidota, Spirochaetota, and Pseudomonadota (Proteobacteria) lost chromosomal rrn operons independently. Remarkably, Persicobacteraceae have apparently maintained this peculiar genome organization for hundreds of millions of years. In our study, all the rrn-carrying plasmids in bacteria lacking chromosomal rrn loci possess replication initiator genes of the Rep_3 family. Furthermore, the lack of chromosomal rrn operons is associated with differences in copy numbers of rrn operons, plasmids, and chromosomal tRNA genes. Thus, our findings indicate that the absence of rrn loci in bacterial chromosomes can be stably maintained over long evolutionary periods.
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Affiliation(s)
- Mizue Anda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Shun Yamanouchi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Salvatore Cosentino
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Masako Takashima
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Atmosphere and Ocean Research Institute, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Institute for Quantitative Biosciences, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
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12
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Vos M, Padfield D, Quince C, Vos R. Adaptive radiations in natural populations of prokaryotes: innovation is key. FEMS Microbiol Ecol 2023; 99:fiad154. [PMID: 37996397 PMCID: PMC10710302 DOI: 10.1093/femsec/fiad154] [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: 09/13/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Rutger Vos
- Naturalis Biodiversity Center, Understanding Evolution, Darwinweg 2, Leiden 2333 CR, the Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, the Netherlands
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13
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Yang Z, Ma X, Wang Q, Tian X, Sun J, Zhang Z, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae. Nat Commun 2023; 14:5542. [PMID: 37696791 PMCID: PMC10495350 DOI: 10.1038/s41467-023-41137-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of these lineages, Prasinodermophyta, which is previously grouped with prasinophytes, has been identified as the sister lineage to both Chlorophyta and Streptophyta. Resolving the deep relationships among green plants is crucial for understanding the historical impact of green algal diversity on marine ecology and geochemistry, but has been proven difficult given the ancient timing of the diversification events. Through extensive taxon and gene sampling, we conduct large-scale phylogenomic analyses to resolve deep relationships and reveal the Prasinodermophyta as the lineage sister to Chlorophyta, raising questions about the necessity of classifying the Prasinodermophyta as a distinct phylum. We unveil that incomplete lineage sorting is the main cause of discordance regarding the placement of Prasinodermophyta. Molecular dating analyses suggest that crown-group green plants and crown-group Prasinodermophyta date back to the Paleoproterozoic-Mesoproterozoic. Our study establishes a plausible link between oxygen levels in the Paleoproterozoic-Mesoproterozoic and the origin of Viridiplantae.
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Affiliation(s)
- Zhiping Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolin Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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14
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Craig JM, Kumar S, Hedges SB. The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen. FRONTIERS IN BIOINFORMATICS 2023; 3:1233281. [PMID: 37727796 PMCID: PMC10505794 DOI: 10.3389/fbinf.2023.1233281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/07/2023] [Indexed: 09/21/2023] Open
Abstract
The origin of eukaryotes was among the most important events in the history of life, spawning a new evolutionary lineage that led to all complex multicellular organisms. However, the timing of this event, crucial for understanding its environmental context, has been difficult to establish. The fossil and biomarker records are sparse and molecular clocks have thus far not reached a consensus, with dates spanning 2.1-0.91 billion years ago (Ga) for critical nodes. Notably, molecular time estimates for the last common ancestor of eukaryotes are typically hundreds of millions of years younger than the Great Oxidation Event (GOE, 2.43-2.22 Ga), leading researchers to question the presumptive link between eukaryotes and oxygen. We obtained a new time estimate for the origin of eukaryotes using genetic data of both archaeal and bacterial origin, the latter rarely used in past studies. We also avoided potential calibration biases that may have affected earlier studies. We obtained a conservative interval of 2.2-1.5 Ga, with an even narrower core interval of 2.0-1.8 Ga, for the origin of eukaryotes, a period closely aligned with the rise in oxygen. We further reconstructed the history of biological complexity across the tree of life using three universal measures: cell types, genes, and genome size. We found that the rise in complexity was temporally consistent with and followed a pattern similar to the rise in oxygen. This suggests a causal relationship stemming from the increased energy needs of complex life fulfilled by oxygen.
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Affiliation(s)
- Jack M. Craig
- Center for Biodiversity, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Sudhir Kumar
- Center for Biodiversity, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - S. Blair Hedges
- Center for Biodiversity, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
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15
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Geiger O, Sanchez-Flores A, Padilla-Gomez J, Degli Esposti M. Multiple approaches of cellular metabolism define the bacterial ancestry of mitochondria. SCIENCE ADVANCES 2023; 9:eadh0066. [PMID: 37556552 PMCID: PMC10411912 DOI: 10.1126/sciadv.adh0066] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/11/2023] [Indexed: 08/11/2023]
Abstract
We breathe at the molecular level when mitochondria in our cells consume oxygen to extract energy from nutrients. Mitochondria are characteristic cellular organelles that derive from aerobic bacteria and carry out oxidative phosphorylation and other key metabolic pathways in eukaryotic cells. The precise bacterial origin of mitochondria and, consequently, the ancestry of the aerobic metabolism of our cells remain controversial despite the vast genomic information that is now available. Here, we use multiple approaches to define the most likely living relatives of the ancestral bacteria from which mitochondria originated. These bacteria live in marine environments and exhibit the highest frequency of aerobic traits and genes for the metabolism of fundamental lipids that are present in the membranes of eukaryotes, sphingolipids, and cardiolipin.
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Affiliation(s)
- Otto Geiger
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, México
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformatica, Institute of Biotechnology, UNAM, Cuernavaca, México
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16
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Hardies SC, Cho BC, Jang GI, Wang Z, Hwang CY. Identification of Structural and Morphogenesis Genes of Sulfitobacter Phage ΦGT1 and Placement within the Evolutionary History of the Podoviruses. Viruses 2023; 15:1475. [PMID: 37515163 PMCID: PMC10386132 DOI: 10.3390/v15071475] [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: 05/11/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
ΦGT1 is a lytic podovirus of an alphaproteobacterial Sulfitobacter species, with few closely matching sequences among characterized phages, thus defying a useful description by simple sequence clustering methods. The history of the ΦGT1 core structure module was reconstructed using timetrees, including numerous related prospective prophages, to flesh out the evolutionary lineages spanning from the origin of the ejectosomal podovirus >3.2 Gya to the present genes of ΦGT1 and its closest relatives. A peculiarity of the ΦGT1 structural proteome is that it contains two paralogous tubular tail A (tubeA) proteins. The origin of the dual tubeA arrangement was traced to a recombination between two more ancient podoviral lineages occurring ~0.7 Gya in the alphaproteobacterial order Rhizobiales. Descendants of the ancestral dual A recombinant were tracked forward forming both temperate and lytic phage clusters and exhibiting both vertical transmission with patchy persistence and horizontal transfer with respect to host taxonomy. The two ancestral lineages were traced backward, making junctions with a major metagenomic podoviral family, the LUZ24-like gammaproteobacterial phages, and Myxococcal phage Mx8, and finally joining near the origin of podoviruses with P22. With these most conservative among phage genes, deviations from uncomplicated vertical and nonrecombinant descent are numerous but countable. The use of timetrees allowed conceptualization of the phage's evolution in the context of a sequence of ancestors spanning the time of life on Earth.
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Affiliation(s)
- Stephen C Hardies
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
- Saemangeum Environmental Research Center, Kunsan National University, Gunsan 54150, Republic of Korea
| | - Gwang Il Jang
- Aquatic Disease Control Division, National Fishery Products Quality Management Service, Busan 46083, Republic of Korea
| | - Zhiqing Wang
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Chung Yeon Hwang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
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17
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Degli Esposti M. The bacterial origin of mitochondria: Incorrect phylogenies and the importance of metabolic traits. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 374:1-35. [PMID: 36858653 DOI: 10.1016/bs.ircmb.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This article provides an updated review on the evolution of mitochondria from bacteria, which were likely related to extant alphaproteobacteria. Particular attention is given to the timeline of oxygen history on Earth and the entwined phases of eukaryotic evolution that produced the animals that still populate our planet. Mitochondria of early-branching unicellular eukaryotes and plants appear to retain partial or vestigial traits that were directly inherited from the alphaproteobacterial ancestors of the organelles. Most of such traits define the current aerobic physiology of mitochondria. Conversely, the anaerobic traits that would be essential in the syntrophic associations postulated for the evolution of eukaryotic cells are scantly present in extant alphaproteobacteria, and therefore cannot help defining from which bacterial lineage the ancestors of mitochondria originated. This question has recently been addressed quantitatively, reaching the novel conclusion that marine bacteria related to Iodidimonas may be the living relatives of protomitochondria. Additional evidence is presented that either support or does not contrast this novel view of the bacterial origin of mitochondria.
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18
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Liao T, Wang S, Stüeken EE, Luo H. Phylogenomic Evidence for the Origin of Obligate Anaerobic Anammox Bacteria Around the Great Oxidation Event. Mol Biol Evol 2022; 39:msac170. [PMID: 35920138 PMCID: PMC9387917 DOI: 10.1093/molbev/msac170] [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] [Indexed: 11/29/2022] Open
Abstract
The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remain enigmatic. Here, we performed a comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which include implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32-2.5 Ga) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics, and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.
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Affiliation(s)
- Tianhua Liao
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Sishuo Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Eva E Stüeken
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, Bute Building, Queen’s Terrace KY16 9TS, United Kingdom
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
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19
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Schön ME, Martijn J, Vosseberg J, Köstlbacher S, Ettema TJG. The evolutionary origin of host association in the Rickettsiales. Nat Microbiol 2022; 7:1189-1199. [PMID: 35798888 PMCID: PMC9352585 DOI: 10.1038/s41564-022-01169-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/30/2022] [Indexed: 12/14/2022]
Abstract
The evolution of obligate host-association of bacterial symbionts and pathogens remains poorly understood. The Rickettsiales are an alphaproteobacterial order of obligate endosymbionts and parasites that infect a wide variety of eukaryotic hosts, including humans, livestock, insects and protists. Induced by their host-associated lifestyle, Rickettsiales genomes have undergone reductive evolution, leading to small, AT-rich genomes with limited metabolic capacities. Here we uncover eleven deep-branching alphaproteobacterial metagenome assembled genomes from aquatic environments, including data from the Tara Oceans initiative and other publicly available datasets, distributed over three previously undescribed Rickettsiales-related clades. Phylogenomic analyses reveal that two of these clades, Mitibacteraceae and Athabascaceae, branch sister to all previously sampled Rickettsiales. The third clade, Gamibacteraceae, branch sister to the recently identified ectosymbiotic ‘Candidatus Deianiraea vastatrix’. Comparative analyses indicate that the gene complement of Mitibacteraceae and Athabascaceae is reminiscent of that of free-living and biofilm-associated bacteria. Ancestral genome content reconstruction across the Rickettsiales species tree further suggests that the evolution of host association in Rickettsiales was a gradual process that may have involved the repurposing of a type IV secretion system. Phylogenomic analyses reveal novel environmental clades of Rickettsiales providing insights into their evolution from free-living to host-associated lifestyle.
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Affiliation(s)
- Max E Schön
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Julian Vosseberg
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Stephan Köstlbacher
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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20
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Nocedal I, Laub MT. Ancestral reconstruction of duplicated signaling proteins reveals the evolution of signaling specificity. eLife 2022; 11:e77346. [PMID: 35686729 PMCID: PMC9208753 DOI: 10.7554/elife.77346] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/27/2022] [Indexed: 01/30/2023] Open
Abstract
Gene duplication is crucial to generating novel signaling pathways during evolution. However, it remains unclear how the redundant proteins produced by gene duplication ultimately acquire new interaction specificities to establish insulated paralogous signaling pathways. Here, we used ancestral sequence reconstruction to resurrect and characterize a bacterial two-component signaling system that duplicated in α-proteobacteria. We determined the interaction specificities of the signaling proteins that existed before and immediately after this duplication event and then identified key mutations responsible for establishing specificity in the two systems. Just three mutations, in only two of the four interacting proteins, were sufficient to establish specificity of the extant systems. Some of these mutations weakened interactions between paralogous systems to limit crosstalk. However, others strengthened interactions within a system, indicating that the ancestral interaction, although functional, had the potential to be strengthened. Our work suggests that protein-protein interactions with such latent potential may be highly amenable to duplication and divergence.
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Affiliation(s)
- Isabel Nocedal
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
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21
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Cevallos MA, Degli Esposti M. New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient. Microorganisms 2022; 10:455. [PMID: 35208909 PMCID: PMC8879329 DOI: 10.3390/microorganisms10020455] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in their taxonomic position within Alphaproteobacteria. The traditional classification of NCBI taxonomy is increasingly complemented by the Genome Taxonomy Database (GTDB), but the two taxonomies differ considerably in the classification of several Alphaproteobacteria, especially from ocean metagenomes. We analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism. Using protein markers such as NuoL, the largest membrane subunit of complex I, we have identified new clades of Alphaproteobacteria that are specific to marine niches with steep oxygen gradients (oxycline). These bacteria have relatives among MAGs found in anoxic strata of Lake Tanganyika and together define a lineage that is distinct from either Rhodospirillales or Sneathiellales. We characterized in particular the new 'oxycline' clade. Our analysis of Alphaproteobacteria also reveals new clues regarding the ancestry of mitochondria, which likely evolved in oxycline marine environments.
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Affiliation(s)
| | - Mauro Degli Esposti
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico;
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22
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Wang S, Luo H. Estimating the Divergence Times of Alphaproteobacteria Based on Mitochondrial Endosymbiosis and Eukaryotic Fossils. Methods Mol Biol 2022; 2569:95-116. [PMID: 36083445 DOI: 10.1007/978-1-0716-2691-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Alphaproteobacteria is one of the most abundant bacterial lineages that successfully colonize diverse marine and terrestrial environments on Earth. In addition, many alphaproteobacterial lineages have established close association with eukaryotes. This makes Alphaproteobacteria a promising system to test the link between the emergence of ecologically important bacteria and related geological events and the co-evolution between symbiotic bacteria and their hosts. Understanding the timescale of evolution of Alphaproteobacteria is key to testing these hypotheses, which is limited by the scarcity of bacterial fossils, however. Based on the mitochondrial endosymbiosis which posits that the mitochondrion originated from an alphaproteobacterial lineage, we propose a new strategy to estimate the divergence times of lineages within the Alphaproteobacteria by leveraging the fossil records of eukaryotes. In this chapter, we describe the workflow of the mitochondria-based method to date Alphaproteobacteria evolution by detailing the software, methods, and commands used for each step. Visualization of data and results is also described. We also provide related notes with background information and alternative options. All codes used to build this protocol are made available to the public, and we strive to make this protocol user-friendly in particular to microbiologists with limited practical skills in bioinformatics.
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Affiliation(s)
- Sishuo Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Haiwei Luo
- School of Life Sciences, Earth and Environmental Sciences Programme, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
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23
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Singh LN, Kao SH, Wallace DC. Unlocking the Complexity of Mitochondrial DNA: A Key to Understanding Neurodegenerative Disease Caused by Injury. Cells 2021; 10:cells10123460. [PMID: 34943968 PMCID: PMC8715673 DOI: 10.3390/cells10123460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative disorders that are triggered by injury typically have variable and unpredictable outcomes due to the complex and multifactorial cascade of events following the injury and during recovery. Hence, several factors beyond the initial injury likely contribute to the disease progression and pathology, and among these are genetic factors. Genetics is a recognized factor in determining the outcome of common neurodegenerative diseases. The role of mitochondrial genetics and function in traditional neurodegenerative diseases, such as Alzheimer’s and Parkinson’s diseases, is well-established. Much less is known about mitochondrial genetics, however, regarding neurodegenerative diseases that result from injuries such as traumatic brain injury and ischaemic stroke. We discuss the potential role of mitochondrial DNA genetics in the progression and outcome of injury-related neurodegenerative diseases. We present a guide for understanding mitochondrial genetic variation, along with the nuances of quantifying mitochondrial DNA variation. Evidence supporting a role for mitochondrial DNA as a risk factor for neurodegenerative disease is also reviewed and examined. Further research into the impact of mitochondrial DNA on neurodegenerative disease resulting from injury will likely offer key insights into the genetic factors that determine the outcome of these diseases together with potential targets for treatment.
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Affiliation(s)
- Larry N. Singh
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
- Correspondence:
| | - Shih-Han Kao
- Resuscitation Science Center, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Douglas C. Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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