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Jain K, Panigrahi M, Nayak SS, Rajawat D, Sharma A, Sahoo SP, Bhushan B, Dutt T. The evolution of contemporary livestock species: Insights from mitochondrial genome. Gene 2024; 927:148728. [PMID: 38944163 DOI: 10.1016/j.gene.2024.148728] [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: 04/16/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.
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Affiliation(s)
- Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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2
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Quaiyum S, Yuan Y, Sun G, Ratnayake RMMN, Hutinet G, Dedon PC, Minnick MF, de Crécy-Lagard V. Queuosine salvage in Bartonella henselae Houston 1: a unique evolutionary path. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39234940 DOI: 10.1099/mic.0.001490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Queuosine (Q) stands out as the sole tRNA modification that can be synthesized via salvage pathways. Comparative genomic analyses identified specific bacteria that showed a discrepancy between the projected Q salvage route and the predicted substrate specificities of the two identified salvage proteins: (1) the distinctive enzyme tRNA guanine-34 transglycosylase (bacterial TGT, or bTGT), responsible for inserting precursor bases into target tRNAs; and (2) queuosine precursor transporter (QPTR), a transporter protein that imports Q precursors. Organisms such as the facultative intracellular pathogen Bartonella henselae, which possess only bTGT and QPTR but lack predicted enzymes for converting preQ1 to Q, would be expected to salvage the queuine (q) base, mirroring the scenario for the obligate intracellular pathogen Chlamydia trachomatis. However, sequence analyses indicate that the substrate-specificity residues of their bTGTs resemble those of enzymes inserting preQ1 rather than q. Intriguingly, MS analyses of tRNA modification profiles in B. henselae reveal trace amounts of preQ1, previously not observed in a natural context. Complementation analysis demonstrates that B. henselae bTGT and QPTR not only utilize preQ1, akin to their Escherichia coli counterparts, but can also process q when provided at elevated concentrations. The experimental and phylogenomic analyses suggest that the Q pathway in B. henselae could represent an evolutionary transition among intracellular pathogens - from ancestors that synthesized Q de novo to a state prioritizing the salvage of q. Another possibility that will require further investigations is that the insertion of preQ1 confers fitness advantages when B. henselae is growing outside a mammalian host.
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Affiliation(s)
- Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - R M Madhushi N Ratnayake
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- Present address: Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Present address: Department of Biology, Haverford College, 370 Lancaster Ave., Haverford, PA, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael F Minnick
- Division of Biological Sciences, University of Montana, Missoula, Montana, MT 59812, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Genetic Institute, University of Florida, FL 32611, USA
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3
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Quaiyum S, Yuan Y, Sun G, Ratnayake RMMN, Hutinet G, Dedon PC, Minnick MF, de Crécy-Lagard V. Queuosine Salvage in Bartonella henselae Houston 1: A Unique Evolutionary Path. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.05.570228. [PMID: 38106016 PMCID: PMC10723273 DOI: 10.1101/2023.12.05.570228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Queuosine (Q) stands out as the sole tRNA modification that can be synthesized via salvage pathways. Comparative genomic analyses identified specific bacteria that showed a discrepancy between the projected Q salvage route and the predicted substrate specificities of the two identified salvage proteins: 1) the distinctive enzyme tRNA guanine-34 transglycosylase (bacterial TGT, or bTGT), responsible for inserting precursor bases into target tRNAs; and 2) Queuosine Precursor Transporter (QPTR), a transporter protein that imports Q precursors. Organisms like the facultative intracellular pathogen Bartonella henselae, which possess only bTGT and QPTR but lack predicted enzymes for converting preQ1 to Q, would be expected to salvage the queuine (q) base, mirroring the scenario for the obligate intracellular pathogen Chlamydia trachomatis. However, sequence analyses indicate that the substrate-specificity residues of their bTGTs resemble those of enzymes inserting preQ1 rather than q. Intriguingly, mass spectrometry analyses of tRNA modification profiles in B. henselae reveal trace amounts of preQ1, previously not observed in a natural context. Complementation analysis demonstrates that B. henselae bTGT and QPTR not only utilize preQ1, akin to their Escherichia coli counterparts, but can also process q when provided at elevated concentrations. The experimental and phylogenomic analyses suggest that the Q pathway in B. henselae could represent an evolutionary transition among intracellular pathogens-from ancestors that synthesized Q de novo to a state prioritizing the salvage of q. Another possibility that will require further investigations is that the insertion of preQ1 has fitness advantages when B. henselae is growing outside a mammalian host.
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Affiliation(s)
- Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael F. Minnick
- Division of Biological Sciences, University of Montana, Missoula, Montana, MT 59812
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
- Genetic Institute, University of Florida, FL 32611
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4
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Hyde JR, Armond T, Herring JA, Hope S, Grose JH, Breakwell DP, Pickett BE. Diversity and conservation of the genome architecture of phages infecting the Alphaproteobacteria. Microbiol Spectr 2024; 12:e0282723. [PMID: 37991376 PMCID: PMC10783043 DOI: 10.1128/spectrum.02827-23] [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: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE This study reports the results of the largest analysis of genome sequences from phages that infect the Alphaproteobacteria class of bacterial hosts. We analyzed over 100 whole genome sequences of phages to construct dotplots, categorize them into genetically distinct clusters, generate a bootstrapped phylogenetic tree, compute protein orthologs, and predict packaging strategies. We determined that the phage sequences primarily cluster by the bacterial host family, phage morphotype, and genome size. We expect that the findings reported in this seminal study will facilitate future analyses that will improve our knowledge of the phages that infect these hosts.
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Affiliation(s)
- Jonathan R. Hyde
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Thomas Armond
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jacob A. Herring
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P. Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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5
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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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Lanclos VC, Rasmussen AN, Kojima CY, Cheng C, Henson MW, Faircloth BC, Francis CA, Thrash JC. Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa. THE ISME JOURNAL 2023; 17:620-629. [PMID: 36739346 PMCID: PMC10030771 DOI: 10.1038/s41396-023-01376-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/06/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.
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Affiliation(s)
- V Celeste Lanclos
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Anna N Rasmussen
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Conner Y Kojima
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Chuankai Cheng
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | | | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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7
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Dittmer J, Bredon M, Moumen B, Raimond M, Grève P, Bouchon D. The terrestrial isopod symbiont 'Candidatus Hepatincola porcellionum' is a potential nutrient scavenger related to Holosporales symbionts of protists. ISME COMMUNICATIONS 2023; 3:18. [PMID: 36882494 PMCID: PMC9992710 DOI: 10.1038/s43705-023-00224-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/09/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
The order Holosporales (Alphaproteobacteria) encompasses obligate intracellular bacterial symbionts of diverse Eukaryotes. These bacteria have highly streamlined genomes and can have negative fitness effects on the host. Herein, we present a comparative analysis of the first genome sequences of 'Ca. Hepatincola porcellionum', a facultative symbiont occurring extracellularly in the midgut glands of terrestrial isopods. Using a combination of long-read and short-read sequencing, we obtained the complete circular genomes of two Hepatincola strains and an additional metagenome-assembled draft genome. Phylogenomic analysis validated its phylogenetic position as an early-branching family-level clade relative to all other established Holosporales families associated with protists. A 16S rRNA gene survey revealed that this new family encompasses diverse bacteria associated with both marine and terrestrial host species, which expands the host range of Holosporales bacteria from protists to several phyla of the Ecdysozoa (Arthropoda and Priapulida). Hepatincola has a highly streamlined genome with reduced metabolic and biosynthetic capacities as well as a large repertoire of transmembrane transporters. This suggests that this symbiont is rather a nutrient scavenger than a nutrient provider for the host, likely benefitting from a nutrient-rich environment to import all necessary metabolites and precursors. Hepatincola further possesses a different set of bacterial secretion systems compared to protist-associated Holosporales, suggesting different host-symbiont interactions depending on the host organism.
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Affiliation(s)
- Jessica Dittmer
- Dipartimento di Scienze Agrarie e Ambientali (DISAA), Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy.
- UMR 1345, Université d'Angers, Institut Agro, INRAE, IRHS, SFR Quasav, 42 Rue Georges Morel, 49070, Beaucouzé, France.
| | - Marius Bredon
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, 3 Rue Jacques Fort, 86073, Poitiers, France
- Université Paris-Sorbonne, Centre de Recherche Saint-Antoine, Equipe Microbiote, Intestin et Inflammation, 27 Rue Chaligny, 75012, Paris, France
| | - Bouziane Moumen
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, 3 Rue Jacques Fort, 86073, Poitiers, France
| | - Maryline Raimond
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, 3 Rue Jacques Fort, 86073, Poitiers, France
| | - Pierre Grève
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, 3 Rue Jacques Fort, 86073, Poitiers, France
| | - Didier Bouchon
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, 3 Rue Jacques Fort, 86073, Poitiers, France.
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8
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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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9
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Borges DGF, Carvalho DS, Bomfim GC, Ramos PIP, Brzozowski J, Góes-Neto A, F. S. Andrade R, El-Hani C. On the origin of mitochondria: a multilayer network approach. PeerJ 2023; 11:e14571. [PMID: 36632145 PMCID: PMC9828282 DOI: 10.7717/peerj.14571] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/28/2022] [Indexed: 01/08/2023] Open
Abstract
Backgound The endosymbiotic theory is widely accepted to explain the origin of mitochondria from a bacterial ancestor. While ample evidence supports the intimate connection of Alphaproteobacteria to the mitochondrial ancestor, pinpointing its closest relative within sampled Alphaproteobacteria is still an open evolutionary debate. Many different phylogenetic methods and approaches have been used to answer this challenging question, further compounded by the heterogeneity of sampled taxa, varying evolutionary rates of mitochondrial proteins, and the inherent biases in each method, all factors that can produce phylogenetic artifacts. By harnessing the simplicity and interpretability of protein similarity networks, herein we re-evaluated the origin of mitochondria within an enhanced multilayer framework, which is an extension and improvement of a previously developed method. Methods We used a dataset of eight proteins found in mitochondria (N = 6 organisms) and bacteria (N = 80 organisms). The sequences were aligned and resulting identity matrices were combined to generate an eight-layer multiplex network. Each layer corresponded to a protein network, where nodes represented organisms and edges were placed following mutual sequence identity. The Multi-Newman-Girvan algorithm was applied to evaluate community structure, and bifurcation events linked to network partition allowed to trace patterns of divergence between studied taxa. Results In our network-based analysis, we first examined the topology of the 8-layer multiplex when mitochondrial sequences disconnected from the main alphaproteobacterial cluster. The resulting topology lent firm support toward an Alphaproteobacteria-sister placement for mitochondria, reinforcing the hypothesis that mitochondria diverged from the common ancestor of all Alphaproteobacteria. Additionally, we observed that the divergence of Rickettsiales was an early event in the evolutionary history of alphaproteobacterial clades. Conclusion By leveraging complex networks methods to the challenging question of circumscribing mitochondrial origin, we suggest that the entire Alphaproteobacteria clade is the closest relative to mitochondria (Alphaproteobacterial-sister hypothesis), echoing recent findings based on different datasets and methodologies.
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Affiliation(s)
| | - Daniel S. Carvalho
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gilberto C. Bomfim
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | - Jerzy Brzozowski
- Philosophy Department, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil,Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roberto F. S. Andrade
- Institute of Physics, Federal University of Bahia, Salvador, Bahia, Brazil,National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Salvador, Bahia, Brazil
| | - Charbel El-Hani
- Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil,National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Salvador, Bahia, Brazil
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Fan L, Wu D, Goremykin V, Trost K, Knopp M, Zhang C, Martin WF, Zhu R. Reply to: Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact. Nat Ecol Evol 2022; 6:1832-1835. [PMID: 36280779 DOI: 10.1038/s41559-022-01896-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 09/01/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Lu Fan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Dingfeng Wu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Vadim Goremykin
- Research and Innovation Centre, Fondazione E. Mach, San Michele all'Adige, Italy
| | - Katharina Trost
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Michael Knopp
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - William F Martin
- Institute of Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany.
| | - Ruixin Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
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11
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Bolaños LM, Tait K, Somerfield PJ, Parsons RJ, Giovannoni SJ, Smyth T, Temperton B. Influence of short and long term processes on SAR11 communities in open ocean and coastal systems. ISME COMMUNICATIONS 2022; 2:116. [PMID: 37938786 PMCID: PMC9723719 DOI: 10.1038/s43705-022-00198-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/21/2022] [Accepted: 11/01/2022] [Indexed: 07/18/2023]
Abstract
SAR11 bacteria dominate the surface ocean and are major players in converting fixed carbon back to atmospheric carbon dioxide. The SAR11 clade is comprised of niche-specialized ecotypes that display distinctive spatiotemporal transitions. We analyzed SAR11 ecotype seasonality in two long-term 16S rRNA amplicon time series representing different North Atlantic regimes: the Sargasso Sea (subtropical ocean-gyre; BATS) and the temperate coastal Western English Channel (WEC). Using phylogenetically resolved amplicon sequence variants (ASVs), we evaluated seasonal environmental constraints on SAR11 ecotype periodicity. Despite large differences in temperature and nutrient availability between the two sites, at both SAR11 succession was defined by summer and winter clusters of ASVs. The summer cluster was dominated by ecotype Ia.3 in both sites. Winter clusters were dominated by ecotypes Ib and IIa.A at BATS and Ia.1 and IIa.B at WEC. A 2-year weekly analysis within the WEC time series showed that the response of SAR11 communities to short-term environmental fluctuations was variable. In 2016, community shifts were abrupt and synchronized to environmental shifts. However, in 2015, changes were gradual and decoupled from environmental fluctuations, likely due to increased mixing from strong winds. We demonstrate that interannual weather variability disturb the pace of SAR11 seasonal progression.
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Affiliation(s)
- Luis M Bolaños
- School of Biosciences, University of Exeter, Exeter, UK.
| | - Karen Tait
- Plymouth Marine Laboratory, Plymouth, UK
| | | | | | | | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK.
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12
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Hargitai D, Kenéz L, Al-Lami M, Szenczi G, Lőrincz P, Juhász G. Autophagy controls Wolbachia infection upon bacterial damage and in aging Drosophila. Front Cell Dev Biol 2022; 10:976882. [PMID: 36299486 PMCID: PMC9589277 DOI: 10.3389/fcell.2022.976882] [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: 06/23/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Autophagy is a conserved catabolic process in eukaryotic cells that degrades intracellular components in lysosomes, often in an organelle-specific selective manner (mitophagy, ERphagy, etc). Cells also use autophagy as a defense mechanism, eliminating intracellular pathogens via selective degradation known as xenophagy. Wolbachia pipientis is a Gram-negative intracellular bacterium, which is one of the most common parasites on Earth affecting approximately half of terrestrial arthropods. Interestingly, infection grants the host resistance against other pathogens and modulates lifespan, so this bacterium resembles an endosymbiont. Here we demonstrate that Drosophila somatic cells normally degrade a subset of these bacterial cells, and autophagy is required for selective elimination of Wolbachia upon antibiotic damage. In line with these, Wolbachia overpopulates in autophagy-compromised animals during aging while its presence fails to affect host lifespan unlike in case of control flies. The autophagic degradation of Wolbachia thus represents a novel antibacterial mechanism that controls the propagation of this unique bacterium, behaving both as parasite and endosymbiont at the same time.
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Affiliation(s)
- Dávid Hargitai
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Lili Kenéz
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Muna Al-Lami
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Győző Szenczi
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Péter Lőrincz
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
- *Correspondence: Péter Lőrincz, ; Gábor Juhász,
| | - Gábor Juhász
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
- *Correspondence: Péter Lőrincz, ; Gábor Juhász,
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13
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Lakey BD, Myers KS, Alberge F, Mettert EL, Kiley PJ, Noguera DR, Donohue TJ. The essential Rhodobacter sphaeroides CenKR two-component system regulates cell division and envelope biosynthesis. PLoS Genet 2022; 18:e1010270. [PMID: 35767559 PMCID: PMC9275681 DOI: 10.1371/journal.pgen.1010270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/12/2022] [Accepted: 05/20/2022] [Indexed: 12/13/2022] Open
Abstract
Bacterial two-component systems (TCSs) often function through the detection of an extracytoplasmic stimulus and the transduction of a signal by a transmembrane sensory histidine kinase. This kinase then initiates a series of reversible phosphorylation modifications to regulate the activity of a cognate, cytoplasmic response regulator as a transcription factor. Several TCSs have been implicated in the regulation of cell cycle dynamics, cell envelope integrity, or cell wall development in Escherichia coli and other well-studied Gram-negative model organisms. However, many α-proteobacteria lack homologs to these regulators, so an understanding of how α-proteobacteria orchestrate extracytoplasmic events is lacking. In this work we identify an essential TCS, CenKR (Cell envelope Kinase and Regulator), in the α-proteobacterium Rhodobacter sphaeroides and show that modulation of its activity results in major morphological changes. Using genetic and biochemical approaches, we dissect the requirements for the phosphotransfer event between CenK and CenR, use this information to manipulate the activity of this TCS in vivo, and identify genes that are directly and indirectly controlled by CenKR in Rb. sphaeroides. Combining ChIP-seq and RNA-seq, we show that the CenKR TCS plays a direct role in maintenance of the cell envelope, regulates the expression of subunits of the Tol-Pal outer membrane division complex, and indirectly modulates the expression of peptidoglycan biosynthetic genes. CenKR represents the first TCS reported to directly control the expression of Tol-Pal machinery genes in Gram-negative bacteria, and we predict that homologs of this TCS serve a similar function in other closely related organisms. We propose that Rb. sphaeroides genes of unknown function that are directly regulated by CenKR play unknown roles in cell envelope biosynthesis, assembly, and/or remodeling in this and other α-proteobacteria.
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Affiliation(s)
- Bryan D. Lakey
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kevin S. Myers
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - François Alberge
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Erin L. Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Patricia J. Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Daniel R. Noguera
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Timothy J. Donohue
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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14
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Castelli M, Lanzoni O, Giovannini M, Lebedeva N, Gammuto L, Sassera D, Melekhin M, Potekhin A, Fokin S, Petroni G. 'Candidatus Gromoviella agglomerans', a novel intracellular Holosporaceae parasite of the ciliate Paramecium showing marked genome reduction. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:34-49. [PMID: 34766443 DOI: 10.1111/1758-2229.13021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Holosporales are an alphaproteobacterial lineage encompassing bacteria obligatorily associated with multiple diverse eukaryotes. For most representatives, little is known on the interactions with their hosts. In this study, we characterized a novel Holosporales symbiont of the ciliate Paramecium polycaryum. This bacterium inhabits the host cytoplasm, frequently forming quite large aggregates. Possibly due to such aggregates, host cells sometimes displayed lethal division defects. The symbiont was also able to experimentally stably infect another Paramecium polycaryum strain. The bacterium is phylogenetically related with symbionts of other ciliates and diplonemids, forming a putatively fast-evolving clade within the family Holosporaceae. Similarly to many close relatives, it presents a very small genome (<600 kbp), and, accordingly, a limited predicted metabolism, implying a heavy dependence on Paramecium, thanks also to some specialized membrane transporters. Characterized features, including the presence of specific secretion systems, are overall suggestive of a mild parasitic effect on the host. From an evolutionary perspective, a potential ancestral trend towards pronounced genome reduction and possibly linked to parasitism could be inferred, at least among fast-evolving Holosporaceae, with some lineage-specific traits. Interestingly, similar convergent features could be observed in other host-associated lineages, in particular Rickettsiales among Alphaproteobacteria.
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Affiliation(s)
- Michele Castelli
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Olivia Lanzoni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | | | - Natalia Lebedeva
- Centre of Core Facilities "Culture Collections of Microorganisms", Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Davide Sassera
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Maksim Melekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Sergei Fokin
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
- Department of Invertebrate Zoology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Giulio Petroni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
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15
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Muñoz-Gómez SA, Susko E, Williamson K, Eme L, Slamovits CH, Moreira D, López-García P, Roger AJ. Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria. Nat Ecol Evol 2022; 6:253-262. [PMID: 35027725 DOI: 10.1038/s41559-021-01638-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/29/2021] [Indexed: 01/01/2023]
Abstract
Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kelsey Williamson
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | | | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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16
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Vera-Ruiz VA, Robinson J, Jermiin LS. A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process retained in Recoded DNA? Syst Biol 2021; 71:660-675. [PMID: 34498090 DOI: 10.1093/sysbio/syab074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/19/2021] [Accepted: 08/27/2021] [Indexed: 11/12/2022] Open
Abstract
In molecular phylogenetics, it is typically assumed that the evolutionary process for DNA can be approximated by independent and identically distributed Markovian processes at the variable sites and that these processes diverge over the edges of a rooted bifurcating tree. Sometimes the nucleotides are transformed from a 4-state alphabet to a 3- or 2-state alphabet by a procedure that is called recoding, lumping, or grouping of states. Here, we introduce a likelihood-ratio test for lumpability for DNA that has diverged under different Markovian conditions, which assesses the assumption that the Markovian property of the evolutionary process over each edge is retained after recoding of the nucleotides. The test is derived and validated numerically on simulated data. To demonstrate the insights that can be gained by using the test, we assessed two published data sets, one of mitochondrial DNA from a phylogenetic study of the ratites (Syst. Biol. 59:90-107 [2010]) and the other of nuclear DNA from a phylogenetic study of yeast (Mol. Biol. Evol. 21:1455-1458 [2004]). Our analysis of these data sets revealed that recoding of the DNA eliminated some of the compositional heterogeneity detected over the sequences. However, the Markovian property of the original evolutionary process was not retained by the recoding, leading to some significant distortions of edge lengths in reconstructed trees.
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Affiliation(s)
- Victor A Vera-Ruiz
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia.,Department of Mathematics and Statistics, University of Nevada, Reno, NV 89557, USA
| | - John Robinson
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia
| | - Lars S Jermiin
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.,School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.,Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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17
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Pearson SA, Cowan JA. Glutathione-coordinated metal complexes as substrates for cellular transporters. Metallomics 2021; 13:mfab015. [PMID: 33770183 PMCID: PMC8086996 DOI: 10.1093/mtomcs/mfab015] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/15/2021] [Indexed: 11/15/2022]
Abstract
Glutathione is the major thiol-containing species in both prokaryotes and eukaryotes and plays a wide variety of roles, including detoxification of metals by sequestration, reduction, and efflux. ABC transporters such as MRP1 and MRP2 detoxify the cell from certain metals by exporting the cations as a metal-glutathione complex. The ability of the bacterial Atm1 protein to efflux metal-glutathione complexes appears to have evolved over time to become the ABCB7 transporter in mammals, located in the inner mitochondrial membrane. No longer needed for the role of cellular detoxification, ABCB7 appears to be used to transport glutathione-coordinated iron-sulfur clusters from mitochondria to the cytosol.
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Affiliation(s)
- Stephen A Pearson
- The Ohio State University Biophysics Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - J A Cowan
- The Ohio State University Biophysics Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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18
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Stavru F, Riemer J, Jex A, Sassera D. When bacteria meet mitochondria: The strange case of the tick symbiont Midichloria mitochondrii †. Cell Microbiol 2021; 22:e13189. [PMID: 32185904 DOI: 10.1111/cmi.13189] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 12/28/2022]
Abstract
Mitochondria are key eukaryotic organelles that perform several essential functions. Not surprisingly, many intracellular bacteria directly or indirectly target mitochondria, interfering with innate immunity, energy production or apoptosis, to make the host cell a more hospitable niche for bacterial replication. The alphaproteobacterium Midichloria mitochondrii has taken mitochondrial targeting to another level by physically colonising mitochondria, as shown by transmission electron micrographs of bacteria residing in the mitochondrial intermembrane space. This unique localization provokes a number of questions around the mechanisms allowing, and reasons driving intramitochondrial tropism. We suggest possible scenarios that could lead to this peculiar localization and hypothesize potential costs and benefits of mitochondrial colonisation for the bacterium and its host.
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Affiliation(s)
- Fabrizia Stavru
- Unité de Biologie Evolutive de la Cellule Microbienne, Institut Pasteur, Paris, France.,CNRS ERL6002, Paris, France
| | - Jan Riemer
- Department for Chemistry, Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Aaron Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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19
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Adhikari S, Erill I, Curtis PD. Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria. PLoS Genet 2021; 17:e1009433. [PMID: 33705385 PMCID: PMC7987155 DOI: 10.1371/journal.pgen.1009433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 03/23/2021] [Accepted: 02/19/2021] [Indexed: 01/14/2023] Open
Abstract
Transcriptional rewiring is the regulation of different target genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. These regulators are well-conserved across Alphaproteobacteria, but the extent to which their regulatory targets are conserved is not known. In this study, the regulatory targets of GcrA and CcrM were analyzed by SMRT-seq, RNA-seq, and ChIP-seq technologies in the Alphaproteobacterium Brevundimonas subvibrioides, and then compared to those of its close relative C. crescentus that inhabits the same environment. Although the regulators themselves are highly conserved, the genes they regulate are vastly different. GcrA directly regulates 204 genes in C. crescentus, and though B. subvibrioides has orthologs to 147 of those genes, only 48 genes retained GcrA binding in their promoter regions. Additionally, only 12 of those 48 genes demonstrated significant transcriptional change in a gcrA mutant, suggesting extensive transcriptional rewiring between these organisms. Similarly, out of hundreds of genes CcrM regulates in each of these organisms, only 2 genes were found in common. When multiple Alphaproteobacterial genomes were analyzed bioinformatically for potential GcrA regulatory targets, the regulation of genes involved in DNA replication and cell division was well conserved across the Caulobacterales but not outside this order. This work suggests that significant transcriptional rewiring can occur in cell cycle regulatory systems even over short evolutionary distances. The degree to which genetic or physiological systems evolve over evolutionary distance is often untested. One can assume that the same system in different organisms will change very little if 1) the evolutionary distance between the organisms is small, 2) the systems perform critical functions, and 3) the organisms have been under similar selective pressures (i.e. the organisms inhabited the same ecological niche). The Alphaproteobacteria offer an excellent opportunity to test this assertion as several critical global transcriptional regulators are conserved throughout this clade. In this study, the regulons of two such global regulators, GcrA and CcrM, in two closely related Alphaproteobacteria that inhabit the same ecological niche were compared and it was found that they regulate vastly different genes. In many cases, genes were present in both organisms, but targeted by a regulator in one organism and not in the other. These results suggest that significant transcriptional rewiring can occur even in a core regulatory system over small evolutionary distances and indicate that conservation of genes and genetic regulators may not be a complete indicator of their physiological function in an organism.
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Affiliation(s)
- Satish Adhikari
- Department of Biology, University of Mississippi, University, Mississippi, United States of America
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - Patrick D. Curtis
- Department of Biology, University of Mississippi, University, Mississippi, United States of America
- * E-mail:
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20
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Arrais RC, Paula RC, Martins TF, Nieri-Bastos FA, Marcili A, Labruna MB. Survey of ticks and tick-borne agents in maned wolves (Chrysocyon brachyurus) from a natural landscape in Brazil. Ticks Tick Borne Dis 2020; 12:101639. [PMID: 33360385 DOI: 10.1016/j.ttbdis.2020.101639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/31/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022]
Abstract
This study evaluated ticks and tick-borne agents in 104 captures of the maned wolf Chrysocyon brachyurus (50 different individuals and 54 recaptures) in the Serra da Canastra National Park (SCNP), a Cerrado preserved area in southeastern Brazil, from 2005 to 2012. From the 104 capture events, a total of 1,206 ticks were collected on 94 occasions (90.4 %), and identified into five species: Amblyomma tigrinum (77.3 % of all collected ticks), Amblyomma sculptum (16.6 %), Amblyomma ovale (0.1 %), Amblyomma brasiliense (0.1 %), Rhipicephalus microplus (0.1 %), and Amblyomma spp. larvae (5.8 %). Molecular analyses of A. tigrinum adult ticks revealed the presence of 'Candidatus Rickettsia andeanae', Rickettsia parkeri sensu stricto, two different haplotypes of 'Ca. Midichloria sp.', and a Hepatozoon canis haplotype. Molecular analyses of maned wolf blood samples revealed two distinct haplotypes of Hepatozoon spp., one identical to the H. canis genotype that was detected in the A. tigrinum ticks, and a Hepatozoon americanum-like haplotype. None tick or blood samples yielded amplicons through PCR assays targeting the genera Ehrlichia, Anaplasma, Babesia, Rangelia, Cytauxzoon, and Theileria. Maned wolf serum samples were tested by immunofluorescence assay against antigens of five Rickettsia species (R. parkeri, R. rickettsii, R. amblyommatis, R. rhipicephali, and R. bellii) and Ehrlichia canis. Among 78 serum samples (45 captures plus 33 recaptures), 74 (95 %) were reactive to at least one Rickettsia species, with R. parkeri eliciting the highest endpoint titers. Some maned wolves that were recaptured during the study were shown to seroconvert to R. parkeri. Serum-reactiveness to E. canis was detected in 36 % (16/45) maned wolves. During the study, general clinical signs of tick-borne diseases were not found in any of the captured animals, indicating that they were under a good health status in the SCNP, despite of been exposed to ticks (mostly A. tigrinum) and some tick-borne agents (Rickettsia, Hepatozoon, Ehrlichia). The results of the present study might represent baseline data for the conservation of the maned wolf in its natural habitat, which should be used to interpret further studies about ticks and tick-borne diseases in maned wolves within human-modified landscapes.
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Affiliation(s)
- Ricardo C Arrais
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Rogério C Paula
- Centro Nacional de Pesquisa e Conservação de Mamíferos Carnívoros, Instituto Chico Mendes de Conservação da Biodiversidade, Ministério do Meio Ambiente, Atibaia, SP, Brazil
| | - Thiago F Martins
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil; Departamento de Laboratórios Especializados, Superintendência de Controle de Endemias, Secretaria de Estado da Saúde de São Paulo, São Paulo, SP, Brazil
| | - Fernanda A Nieri-Bastos
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Arlei Marcili
- Programa de Pós-graduação em Medicina e Bem-Estar Animal e Saúde Única, Universidade Santo Amaro, R. Prof. Enéas de Siqueira Neto, 340 - Jardim das Imbuias, São Paulo, SP, 04829-300, Brazil
| | - Marcelo B Labruna
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil.
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21
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Jiao J, Tian CF. Ancestral zinc-finger bearing protein MucR in alpha-proteobacteria: A novel xenogeneic silencer? Comput Struct Biotechnol J 2020; 18:3623-3631. [PMID: 33304460 PMCID: PMC7710501 DOI: 10.1016/j.csbj.2020.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
The MucR/Ros family protein is conserved in alpha-proteobacteria and characterized by its zinc-finger motif that has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure evolved. In the past decades, accumulated evidences have revealed MucR as a pleiotropic transcriptional regulator that integrating multiple functions such as virulence, symbiosis, cell cycle and various physiological processes. Scattered reports indicate that MucR mainly acts as a repressor, through oligomerization and binding to multiple sites of AT-rich target promoters. The N-terminal region and zinc-finger bearing C-terminal region of MucR mediate oligomerization and DNA-binding, respectively. These features are convergent to those of xenogeneic silencers such as H-NS, MvaT, Lsr2 and Rok, which are mainly found in other lineages. Phylogenetic analysis of MucR homologs suggests an ancestral origin of MucR in alpha- and delta-proteobacteria. Multiple independent duplication and lateral gene transfer events contribute to the diversity and phyletic distribution of MucR. Finally, we posed questions which remain unexplored regarding the putative roles of MucR as a xenogeneic silencer and a general manager in balancing adaptation and regulatory integration in the pangenome context.
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Affiliation(s)
- Jian Jiao
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.,MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.,MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University, Beijing, China
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22
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De R, Mazumder S, Bandyopadhyay U. Mediators of mitophagy that regulate mitochondrial quality control play crucial role in diverse pathophysiology. Cell Biol Toxicol 2020; 37:333-366. [PMID: 33067701 DOI: 10.1007/s10565-020-09561-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023]
Abstract
Mitochondria are double membrane-bound cellular work-horses constantly functioning to regulate vital aspects of cellular metabolism, bioenergetics, proliferation and death. Biogenesis, homeostasis and regulated turnover of mitochondria are stringently regulated to meet the bioenergetic requirements. Diverse external and internal stimuli including oxidative stress, diseases, xenobiotics and even age profoundly affect mitochondrial integrity. Damaged mitochondria need immediate segregation and selective culling to maintain physiological homeostasis. Mitophagy is a specialised form of macroautophagy that constantly checks mitochondrial quality followed by elimination of rogue mitochondria by lysosomal targeting through multiple pathways tightly regulated and activated in context-specific manners. Mitophagy is implicated in diverse oxidative stress-associated metabolic, proliferating and degenerative disorders owing to the centrality of mitopathology in diseases as well as the common mandate to eliminate damaged mitochondria for restoring physiological homeostasis. With improved health care and growing demand for precision medicine, specifically targeting the keystone factors in pathogenesis, more exploratory studies are focused on mitochondrial quality control as underlying guardian of cellular pathophysiology. In this context, mitophagy emerged as a promising area to focus biomedical research for identifying novel therapeutic targets against diseases linked with physiological redox perturbation. The present review provides a comprehensive account of the recent developments on mitophagy along with precise discussion on its impact on major diseases and possibilities of therapeutic modulation.
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Affiliation(s)
- Rudranil De
- Amity Institute of Biotechnology, Amity University, Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, West Bengal, 700135, India
| | - Somnath Mazumder
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, West Bengal, 700032, India
- Department of Zoology, Raja Peary Mohan College, 1 Acharya Dhruba Pal Road, Uttarpara, West Bengal, 712258, India
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, West Bengal, 700032, India.
- Division of Molecular Medicine, Bose Institute, P-1/12, CIT Rd, Scheme VIIM, Kankurgachi, Kolkata, West Bengal, 700054, India.
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23
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Two Metagenome-Assembled Genome Sequences of Magnetotactic Bacteria in the Order Magnetococcales. Microbiol Resour Announc 2020; 9:9/35/e00363-20. [PMID: 32855242 PMCID: PMC7453278 DOI: 10.1128/mra.00363-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Magnetotactic bacteria represent a valuable model system for the study of microbial biomineralization and magnetotaxis. Here, we report two metagenome-assembled genome sequences of uncultivated magnetotactic bacteria belonging to the order Magnetococcales. These genomes contain nearly complete magnetosome gene clusters responsible for magnetosome biomineralization. Magnetotactic bacteria represent a valuable model system for the study of microbial biomineralization and magnetotaxis. Here, we report two metagenome-assembled genome sequences of uncultivated magnetotactic bacteria belonging to the order Magnetococcales. These genomes contain nearly complete magnetosome gene clusters responsible for magnetosome biomineralization.
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24
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Zlotnik G, Vansintjan A. Storage of Information and Its Implications for Human Development: A Dialectic Approach. Front Psychol 2020; 11:1715. [PMID: 32765380 PMCID: PMC7378732 DOI: 10.3389/fpsyg.2020.01715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/22/2020] [Indexed: 11/23/2022] Open
Abstract
How has the storage of information shaped human cognition? We bring together current advances in cognitive science, the neurobiology of memory, and archeology to explore how storage of information affects consciousness. These fields strongly suggest that the increase in storage of information in the environment - which we call exosomatic storage of information - may have led to changes in human consciousness and human neurophysiology over time. To bring these findings together conceptually, we develop what we call a dialectical model of the relationship between storage of information and the development of human consciousness. Using the system of dialectic philosophy, we put forward that (a) environmental changes, consciousness, and neurophysiology develop together, (b) these changes were irreversible, (c) quantitative increases in exosomatic storage of information may have led to qualitative changes in human consciousness and neurophysiology, (d) these changes in turn affected how we see ourselves. Indeed, our capacity to store information exosomatically distinguishes us from other animals, and may be a key attribute of our self-awareness and therefore self-consciousness. Because metaphors are central to human thought and can help structure scientific inquiry, we illustrate our model using a metaphor of drops of silver on the back of a glass, eventually making a mirror - where successive quantitative change leads to an irreversible qualitative development in human consciousness. The dialectic model can offer new insights into the co-evolution of material culture and human beings through its broader philosophical foundations and explanatory power.
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Affiliation(s)
| | - Aaron Vansintjan
- Department of Film, Media, and Cultural Studies, Birkbeck, University of London, London, United Kingdom
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25
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Takeshita K, Yamada T, Kawahara Y, Narihiro T, Ito M, Kamagata Y, Shinzato N. Tripartite Symbiosis of an Anaerobic Scuticociliate with Two Hydrogenosome-Associated Endosymbionts, a Holospora-Related Alphaproteobacterium and a Methanogenic Archaeon. Appl Environ Microbiol 2019; 85:e00854-19. [PMID: 31585988 PMCID: PMC6881808 DOI: 10.1128/aem.00854-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/17/2019] [Indexed: 11/20/2022] Open
Abstract
A number of anaerobic ciliates, unicellular eukaryotes, intracellularly possess methanogenic archaea and bacteria as symbiotic partners. Although this tripartite relationship is of interest in terms of the fact that each participant is from a different domain, the difficulty in culture and maintenance of those host species with symbiotic partners has disturbed both ecological and functional studies so far. In this study, we obtained a stable culture of a small anaerobic scuticociliate, strain GW7. By transmission electron microscopic observation and fluorescent in situ hybridization with domain-specific probes, we demonstrate that GW7 possesses both archaeal and bacterial endosymbionts in its cytoplasm. These endosymbionts are in dependently associated with hydrogenosomes, which are organelle producing hydrogen and ATP under anaerobic conditions. Clone library analyses targeting prokaryotic 16S rRNA genes, fluorescent in situ hybridization with endosymbiont-specific probes, and molecular phylogenetic analyses revealed the phylogenetic affiliations and intracellular localizations of these endosymbionts. The endosymbiotic archaeon is a methanogen belonging to the genus Methanoregula (order Methanomicrobiales); a member of this genus has previously been described as the endosymbiont of an anaerobic ciliate from the genus Metopus (class Armophorea), which is only distantly related to strain GW7 (class Oligohymenophorea). The endosymbiotic bacterium belongs to the family Holosporaceae of the class Alphaproteobacteria, which also comprises several endosymbionts of various aerobic ciliates. For this endosymbiotic bacterium, we propose a novel candidate genus and species, "Candidatus Hydrogenosomobacter endosymbioticus."IMPORTANCE Tripartite symbioses between anaerobic ciliated protists and their intracellular archaeal and bacterial symbionts are not uncommon, but most reports have been based mainly on microscopic observations. Deeper insights into the function, ecology, and evolution of these fascinating symbioses involving partners from all three domains of life have been hampered by the difficulties of culturing anaerobic ciliates in the laboratory and the frequent loss of their prokaryotic partners during long-term cultivation. In the present study, we report the isolation of an anaerobic scuticociliate, strain GW7, which has been stably maintained in our laboratory for more than 3 years without losing either of its endosymbionts. Unexpectedly, molecular characterization of the endosymbionts revealed that the bacterial partner of GW7 is phylogenetically related to intranuclear endosymbionts of aerobic ciliates. This strain will enable future genomic, transcriptomic, and proteomic analyses of the interactions in this tripartite symbiosis and a comparison with endosymbioses in aerobic ciliates.
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Affiliation(s)
- Kazutaka Takeshita
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Takanori Yamada
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Yuto Kawahara
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Michihiro Ito
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Naoya Shinzato
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
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26
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Igloi GL. Molecular evidence for the evolution of the eukaryotic mitochondrial arginyl-tRNA synthetase from the prokaryotic suborder Cystobacterineae. FEBS Lett 2019; 594:951-957. [PMID: 31705651 DOI: 10.1002/1873-3468.13665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 02/01/2023]
Abstract
The evolutionary origin of the family of eukaryotic aminoacyl-tRNA synthetases that are essential to all living organisms is a matter of debate. In order to shed molecular light on the ancient source of arginyl-tRNA synthetase, a total of 1347 eukaryotic arginyl-tRNA synthetase sequences were mined from databases and analyzed. Their multiple sequence alignment reveals a signature sequence that is characteristic of the nuclear-encoded enzyme, which is imported into mitochondria. Using this molecular beacon, the origins of this gene can be traced to modern prokaryotes. In this way, a previous phylogenetic analysis linking Myxococcus to the emergence of the eukaryotic mitochondrial arginyl-tRNA synthetase is supported by the unique existence of the molecular signature within the suborder Cystobacterineae that includes Myxococcus.
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Affiliation(s)
- Gabor L Igloi
- Institute of Biology, University of Freiburg, Germany
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27
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Zlotnik G, Vansintjan A. Memory: An Extended Definition. Front Psychol 2019; 10:2523. [PMID: 31787916 PMCID: PMC6853990 DOI: 10.3389/fpsyg.2019.02523] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/24/2019] [Indexed: 11/13/2022] Open
Abstract
Recent developments in science and technology point to the need to unify, and extend, the definition of memory. On the one hand, molecular neurobiology has shown that memory is largely a neuro-chemical process, which includes conditioning and any form of stored experience. On the other hand, information technology has led many to claim that cognition is also extended, that is, memory may be stored outside of the brain. In this paper, we review these advances and describe an extended definition of memory. This definition is largely accepted in neuroscience but not explicitly stated. In the extended definition, memory is the capacity to store and retrieve information. Does this new definition of memory mean that everything is now a form of memory? We stress that memory still requires incorporation, that is, in corpore. It is a relationship - where one biological or chemical process is incorporated into another, and changes both in a permanent way. Looking at natural and biological processes of incorporation can help us think of how incorporation of internal and external memory occurs in cognition. We further argue that, if we accept that there is such a thing as the storage of information outside the brain - and that this organic, dynamic process can also be called "memory" - then we open the door to a very different world. The mind is not static. The brain, and the memory it uses, is a work in progress; we are not now who we were then.
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Affiliation(s)
| | - Aaron Vansintjan
- Department of Film, Media and Cultural Studies, Birkbeck, University of London, London, United Kingdom
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28
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Delmont TO, Kiefl E, Kilinc O, Esen OC, Uysal I, Rappé MS, Giovannoni S, Eren AM. Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade. eLife 2019; 8:46497. [PMID: 31478833 PMCID: PMC6721796 DOI: 10.7554/elife.46497] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022] Open
Abstract
Members of the SAR11 order Pelagibacterales dominate the surface oceans. Their extensive diversity challenges emerging operational boundaries defined for microbial 'species' and complicates efforts of population genetics to study their evolution. Here, we employed single-amino acid variants (SAAVs) to investigate ecological and evolutionary forces that maintain the genomic heterogeneity within ubiquitous SAR11 populations we accessed through metagenomic read recruitment using a single isolate genome. Integrating amino acid and protein biochemistry with metagenomics revealed that systematic purifying selection against deleterious variants governs non-synonymous variation among very closely related populations of SAR11. SAAVs partitioned metagenomes into two main groups matching large-scale oceanic current temperatures, and six finer proteotypes that connect distant oceanic regions. These findings suggest that environmentally-mediated selection plays a critical role in the journey of cosmopolitan surface ocean microbial populations, and the idea 'everything is everywhere but the environment selects' has credence even at the finest resolutions.
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Affiliation(s)
- Tom O Delmont
- Department of Medicine, The University of Chicago, Chicago, United States
| | - Evan Kiefl
- Department of Medicine, The University of Chicago, Chicago, United States.,Graduate Program in Biophysical Sciences, University of Chicago, Chicago, United States
| | - Ozsel Kilinc
- Department of Electrical Engineering, University of South Florida, Tampa, United States
| | - Ozcan C Esen
- Department of Medicine, The University of Chicago, Chicago, United States
| | - Ismail Uysal
- Department of Electrical Engineering, University of South Florida, Tampa, United States
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, United States
| | - Steven Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, United States
| | - A Murat Eren
- Department of Medicine, The University of Chicago, Chicago, United States.,Marine Biological Laboratory, Woods Hole, United States
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29
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Castelli M, Sabaneyeva E, Lanzoni O, Lebedeva N, Floriano AM, Gaiarsa S, Benken K, Modeo L, Bandi C, Potekhin A, Sassera D, Petroni G. Deianiraea, an extracellular bacterium associated with the ciliate Paramecium, suggests an alternative scenario for the evolution of Rickettsiales. THE ISME JOURNAL 2019; 13:2280-2294. [PMID: 31073215 PMCID: PMC6776064 DOI: 10.1038/s41396-019-0433-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/19/2019] [Accepted: 04/10/2019] [Indexed: 12/28/2022]
Abstract
Rickettsiales are a lineage of obligate intracellular Alphaproteobacteria, encompassing important human pathogens, manipulators of host reproduction, and mutualists. Here we report the discovery of a novel Rickettsiales bacterium associated with Paramecium, displaying a unique extracellular lifestyle, including the ability to replicate outside host cells. Genomic analyses show that the bacterium possesses a higher capability to synthesise amino acids, compared to all investigated Rickettsiales. Considering these observations, phylogenetic and phylogenomic reconstructions, and re-evaluating the different means of interaction of Rickettsiales bacteria with eukaryotic cells, we propose an alternative scenario for the evolution of intracellularity in Rickettsiales. According to our reconstruction, the Rickettsiales ancestor would have been an extracellular and metabolically versatile bacterium, while obligate intracellularity would have evolved later, in parallel and independently, in different sub-lineages. The proposed new scenario could impact on the open debate on the lifestyle of the last common ancestor of mitochondria within Alphaproteobacteria.
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Affiliation(s)
- Michele Castelli
- Centro Romeo ed Enrica Invernizzi Ricerca Pediatrica, Dipartimento di Bioscienze, Università degli studi di Milano, Milan, Italy
| | - Elena Sabaneyeva
- Department of Cytology and Histology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Olivia Lanzoni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Natalia Lebedeva
- Centre of Core Facilities "Culture Collections of Microorganisms", Saint Petersburg State University, Saint Petersburg, Russia
| | - Anna Maria Floriano
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Stefano Gaiarsa
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Konstantin Benken
- Core Facility Center for Microscopy and Microanalysis, Saint Petersburg State University, Saint Petersburg, Russia
| | - Letizia Modeo
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Claudio Bandi
- Centro Romeo ed Enrica Invernizzi Ricerca Pediatrica, Dipartimento di Bioscienze, Università degli studi di Milano, Milan, Italy
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Davide Sassera
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy.
| | - Giulio Petroni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy.
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30
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Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res 2019; 46:D624-D632. [PMID: 29145643 PMCID: PMC5753285 DOI: 10.1093/nar/gkx1134] [Citation(s) in RCA: 1003] [Impact Index Per Article: 200.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/30/2017] [Indexed: 12/15/2022] Open
Abstract
The MEROPS database (http://www.ebi.ac.uk/merops/) is an integrated source of information about peptidases, their substrates and inhibitors. The hierarchical classification is: protein-species, family, clan, with an identifier at each level. The MEROPS website moved to the EMBL-EBI in 2017, requiring refactoring of the code-base and services provided. The interface to sequence searching has changed and the MEROPS protein sequence libraries can be searched at the EMBL-EBI with HMMER, FastA and BLASTP. Cross-references have been established between MEROPS and the PANTHER database at both the family and protein-species level, which will help to improve curation and coverage between the resources. Because of the increasing size of the MEROPS sequence collection, in future only sequences of characterized proteins, and from completely sequenced genomes of organisms of evolutionary, medical or commercial significance will be added. As an example, peptidase homologues in four proteomes from the Asgard superphylum of Archaea have been identified and compared to other archaean, bacterial and eukaryote proteomes. This has given insights into the origins and evolution of peptidase families, including an expansion in the number of proteasome components in Asgard archaeotes and as organisms increase in complexity. Novel structures for proteasome complexes in archaea are postulated.
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Affiliation(s)
- Neil D Rawlings
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alan J Barrett
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, 1450 Biggy St, NRT 2502, Los Angeles, CA 90033, USA
| | - Xiaosong Huang
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, 1450 Biggy St, NRT 2502, Los Angeles, CA 90033, USA
| | - Alex Bateman
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Robert D Finn
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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31
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Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov. ISME JOURNAL 2019; 13:2938-2953. [PMID: 31384012 PMCID: PMC6863919 DOI: 10.1038/s41396-019-0482-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 07/10/2019] [Accepted: 07/13/2019] [Indexed: 12/14/2022]
Abstract
Bacterial symbionts are integral to the health and homeostasis of invertebrate hosts. Notably, members of the Rickettsiales genus Wolbachia influence several aspects of the fitness and evolution of their terrestrial hosts, but few analogous partnerships have been found in marine systems. We report here the genome, phylogenetics, and biogeography of a ubiquitous and novel Rickettsiales species that primarily associates with marine organisms. We previously showed that this bacterium was found in scleractinian corals, responds to nutrient exposure, and is associated with reduced host growth and increased mortality. This bacterium, like other Rickettsiales, has a reduced genome indicative of a parasitic lifestyle. Phylogenetic analysis places this Rickettsiales within a new genus we define as “Candidatus Aquarickettsia.” Using data from the Earth Microbiome Project and SRA databases, we also demonstrate that members of “Ca. Aquarickettsia” are found globally in dozens of invertebrate lineages. The coral-associated “Candidatus A. rohweri” is the first finished genome in this new clade. “Ca. A. rohweri” lacks genes to synthesize most sugars and amino acids but possesses several genes linked to pathogenicity including Tlc, an antiporter that exchanges host ATP for ADP, and a complete Type IV secretion system. Despite its inability to metabolize nitrogen, “Ca. A. rohweri” possesses the NtrY-NtrX two-component system involved in sensing and responding to extracellular nitrogen. Given these data, along with visualization of the parasite in host tissues, we hypothesize that “Ca. A. rohweri” reduces coral health by consuming host nutrients and energy, thus weakening and eventually killing host cells. Last, we hypothesize that nutrient enrichment, which is increasingly common on coral reefs, encourages unrestricted growth of “Ca. A. rohweri” in its host by providing abundant N-rich metabolites to be scavenged.
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32
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Moore KR, Magnabosco C, Momper L, Gold DA, Bosak T, Fournier GP. An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids. Front Microbiol 2019; 10:1612. [PMID: 31354692 PMCID: PMC6640209 DOI: 10.3389/fmicb.2019.01612] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/27/2019] [Indexed: 01/16/2023] Open
Abstract
The phylum Cyanobacteria includes free-living bacteria and plastids, the descendants of cyanobacteria that were engulfed by the ancestral lineage of the major photosynthetic eukaryotic group Archaeplastida. Endosymbiotic events that followed this primary endosymbiosis spread plastids across diverse eukaryotic groups. The remnants of the ancestral cyanobacterial genome present in all modern plastids, enable the placement of plastids within Cyanobacteria using sequence-based phylogenetic analyses. To date, such phylogenetic studies have produced conflicting results and two competing hypotheses: (1) plastids diverge relatively recently in cyanobacterial evolution and are most closely related to nitrogen-fixing cyanobacteria, or (2) plastids diverge early in the evolutionary history of cyanobacteria, before the divergence of most cyanobacterial lineages. Here, we use phylogenetic analysis of ribosomal proteins from an expanded data set of cyanobacterial and representative plastid genomes to infer a deep placement for the divergence of the plastid ancestor lineage. We recover plastids as sister to Gloeomargarita and show that the group diverges from other cyanobacterial groups before Pseudanabaena, a previously unreported placement. The tree topologies and phylogenetic distances in our study have implications for future molecular clock studies that aim to model accurate divergence times, especially with respect to groups containing fossil calibrations. The newly sequenced cyanobacterial groups included here will also enable the use of novel cyanobacterial microfossil calibrations.
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Affiliation(s)
- Kelsey R Moore
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Cara Magnabosco
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, United States
| | - Lily Momper
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - David A Gold
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, CA, United States
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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33
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Martijn J, Lind AE, Schön ME, Spiertz I, Juzokaite L, Bunikis I, Pettersson OV, Ettema TJG. Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon. Environ Microbiol 2019; 21:2485-2498. [PMID: 31012228 PMCID: PMC6849856 DOI: 10.1111/1462-2920.14636] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 11/30/2022]
Abstract
Amplicon sequencing of the 16S rRNA gene is the predominant method to quantify microbial compositions and to discover novel lineages. However, traditional short amplicons often do not contain enough information to confidently resolve their phylogeny. Here we present a cost-effective protocol that amplifies a large part of the rRNA operon and sequences the amplicons with PacBio technology. We tested our method on a mock community and developed a read-curation pipeline that reduces the overall read error rate to 0.18%. Applying our method on four environmental samples, we captured near full-length rRNA operon amplicons from a large diversity of prokaryotes. The method operated at moderately high-throughput (22286-37,850 raw ccs reads) and generated a large amount of putative novel archaeal 23S rRNA gene sequences compared to the archaeal SILVA database. These long amplicons allowed for higher resolution during taxonomic classification by means of long (∼1000 bp) 16S rRNA gene fragments and for substantially more confident phylogenies by means of combined near full-length 16S and 23S rRNA gene sequences, compared to shorter traditional amplicons (250 bp of the 16S rRNA gene). We recommend our method to those who wish to cost-effectively and confidently estimate the phylogenetic diversity of prokaryotes in environmental samples at high throughput.
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Affiliation(s)
- Joran Martijn
- Department of Cell and Molecular Biology, Science for Life LaboratoryUppsala UniversitySE‐75123, UppsalaSweden
| | - Anders E. Lind
- Department of Cell and Molecular Biology, Science for Life LaboratoryUppsala UniversitySE‐75123, UppsalaSweden
| | - Max E. Schön
- Department of Cell and Molecular Biology, Science for Life LaboratoryUppsala UniversitySE‐75123, UppsalaSweden
| | - Ian Spiertz
- Department of Cell and Molecular Biology, Science for Life LaboratoryUppsala UniversitySE‐75123, UppsalaSweden
| | - Lina Juzokaite
- Department of Cell and Molecular Biology, Science for Life LaboratoryUppsala UniversitySE‐75123, UppsalaSweden
| | - Ignas Bunikis
- Science for Life LaboratoryUppsala UniversitySE‐75185, UppsalaSweden
| | | | - Thijs J. G. Ettema
- Department of Cell and Molecular Biology, Science for Life LaboratoryUppsala UniversitySE‐75123, UppsalaSweden
- Laboratory of Microbiology, Department of Agrotechnology and Food SciencesWageningen UniversityStippeneng 4, 6708WE, WageningenThe Netherlands
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34
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Petrov AS, Wood EC, Bernier CR, Norris AM, Brown A, Amunts A. Structural Patching Fosters Divergence of Mitochondrial Ribosomes. Mol Biol Evol 2019; 36:207-219. [PMID: 30517740 PMCID: PMC6367999 DOI: 10.1093/molbev/msy221] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data. We generate a map of the acquisition of structural variation and reconstruct the fundamental stages that shaped the evolution of the mitoribosomal large subunit and led to this diversity. Our analysis suggests a critical role for ablation and expansion of rapidly evolving mt-rRNA. These changes cause structural instabilities that are “patched” by the acquisition of pre-existing compensatory elements, thus providing opportunities for rapid evolution. This mechanism underlies the incorporation of mt-tRNA into the central protuberance of the mammalian mitoribosome, and the altered path of the polypeptide exit tunnel of the yeast mitoribosome. We propose that since the toolkits of elements utilized for structural patching differ between mitochondria of different species, it fosters the growing divergence of mitoribosomes.
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Affiliation(s)
- Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Elizabeth C Wood
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Chad R Bernier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Ashlyn M Norris
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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35
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Scheid AD, Beadnell TC, Welch DR. The second genome: Effects of the mitochondrial genome on cancer progression. Adv Cancer Res 2019; 142:63-105. [PMID: 30885364 DOI: 10.1016/bs.acr.2019.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The role of genetics in cancer has been recognized for centuries, but most studies elucidating genetic contributions to cancer have understandably focused on the nuclear genome. Mitochondrial contributions to cancer pathogenesis have been documented for decades, but how mitochondrial DNA (mtDNA) influences cancer progression and metastasis remains poorly understood. This lack of understanding stems from difficulty isolating the nuclear and mitochondrial genomes as experimental variables, which is critical for investigating direct mtDNA contributions to disease given extensive crosstalk exists between both genomes. Several in vitro and in vivo models have isolated mtDNA as an independent variable from the nuclear genome. This review compares and contrasts different models, their advantages and disadvantages for studying mtDNA contributions to cancer, focusing on the mitochondrial-nuclear exchange (MNX) mouse model and findings regarding tumor progression, metastasis, and other complex cancer-related phenotypes.
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Affiliation(s)
- Adam D Scheid
- Department of Cancer Biology, The University of Kansas Medical Center, and The University of Kansas Cancer Center, Kansas City, KS, United States
| | - Thomas C Beadnell
- Department of Cancer Biology, The University of Kansas Medical Center, and The University of Kansas Cancer Center, Kansas City, KS, United States
| | - Danny R Welch
- Department of Cancer Biology, The University of Kansas Medical Center, and The University of Kansas Cancer Center, Kansas City, KS, United States.
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36
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Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife 2019; 8:e42535. [PMID: 30789345 PMCID: PMC6447387 DOI: 10.7554/elife.42535] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/21/2019] [Indexed: 11/13/2022] Open
Abstract
The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
| | - Sebastian Hess
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
- Institute of ZoologyUniversity of CologneCologneGermany
| | - Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and GenomicsUniversité de MontréalMontrealCanada
| | - B Franz Lang
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and GenomicsUniversité de MontréalMontrealCanada
| | - Edward Susko
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
- Department of Mathematics and StatisticsDalhousie UniversityHalifaxCanada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
| | - Andrew J Roger
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
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37
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Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife 2019; 8. [PMID: 30789345 DOI: 10.7554/elife.42535.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/21/2019] [Indexed: 05/20/2023] Open
Abstract
The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Sebastian Hess
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - B Franz Lang
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Edward Susko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
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38
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Han B, Lin CCJ, Hu G, Wang MC. 'Inside Out'- a dialogue between mitochondria and bacteria. FEBS J 2018; 286:630-641. [PMID: 30390412 DOI: 10.1111/febs.14692] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/05/2018] [Accepted: 11/02/2018] [Indexed: 12/28/2022]
Abstract
Mitochondria play crucial roles in regulating metabolism and longevity. A body of recent evidences reveals that the gut microbiome can also exert significant effects on these activities in the host. Here, by summarizing the currently known mechanisms underlying these regulations, and by comparing mitochondrial fission-fusion dynamics with bacterial interactions such as quorum sensing, we hypothesize that the microbiome impacts the host by communicating with their intracellular relatives, mitochondria. We highlight recent discoveries supporting this model, and these new findings reveal that metabolite molecules derived from bacteria can fine-tune mitochondrial dynamics in intestinal cells and hence influence host metabolic fitness and longevity. This perspective mode of chemical communication between bacteria and mitochondria may help us understand complex and dynamic environment-microbiome-host interactions regarding their vital impacts on health and diseases.
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Affiliation(s)
- Bing Han
- Children's Hospital, Fudan University, Minhang, Shanghai, China.,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Chih-Chun Janet Lin
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Guo Hu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Meng C Wang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
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39
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Chan LL, Mak JW, Ambu S, Chong PY. Identification and ultrastructural characterization of Acanthamoeba bacterial endocytobionts belonging to the Alphaproteobacteria class. PLoS One 2018; 13:e0204732. [PMID: 30356282 PMCID: PMC6200196 DOI: 10.1371/journal.pone.0204732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 09/13/2018] [Indexed: 12/17/2022] Open
Abstract
The detection and identification of two endocytobiotic bacterial strains, one affiliated to the “Candidatus Caedibacter acanthamoebae”/“Ca. Paracaedimonas acanthamoeba”, and another to the endosymbiont of Acanthamoeba UWC8 and “Ca. Jidaibacter acanthamoeba” are described. For endocytobiont screening, we developed a PCR method with a set of broad-range bacterial 16S rRNA primers to substitute the commonly used but technically demanding fluorescent in situ hybridization technique. Our PCR test alone without sequencing failed to discriminate the endocytobiont-containing and endocytobiont-free Acanthamoeba sp. due to the presence of mismatched primers to host mitochondrial DNA. We highlighted the need to perform bacterial primer checking against the Acanthamoeba genome to avoid false positive detection in PCR. Although the genetic aspect of “Ca. Caedibacter acanthamoebae”/“Ca. Paracaedimonas acanthamoeba” and the endosymbiont of Acanthamoeba UWC8/“Ca. Jidaibacter acanthamoeba” are well studied, knowledge pertaining to their morphologies are quite vague. Hence, we used transmission electron microscopy to examine our endocytobionts which are affiliated to previously described intracellular bacteria of Acanthamoeba sp. We used good-quality TEM images for the localization and the fate of the current endocytobionts inside different life stages of the hosts. Furthermore, to the best of our knowledge, our TEM findings are the first to provide morphological evidence for the clearance of defective Acanthamoeba endocytobionts via an autophagic-like process.
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Affiliation(s)
- Li Li Chan
- Pathology Division, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
- * E-mail:
| | - Joon Wah Mak
- Pathology Division, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
- School of Postgraduate Studies and Research, International Medical University, Kuala Lumpur, Malaysia
| | - Stephen Ambu
- Pathology Division, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
- School of Postgraduate Studies and Research, International Medical University, Kuala Lumpur, Malaysia
| | - Pei Yee Chong
- Medical Sciences, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
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40
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Zhang B, Lv Z, Li Z, Wang W, Li G, Guo Y. Dietary l-arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut Microbiota in Broiler Chickens Challenged by Clostridium perfringens. Front Microbiol 2018; 9:1716. [PMID: 30108569 PMCID: PMC6080643 DOI: 10.3389/fmicb.2018.01716] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/10/2018] [Indexed: 12/19/2022] Open
Abstract
Our previous reports suggested that Dietary l-arginine supplementation attenuated gut injury of broiler chickens infected with Clostridium perfringens by enhancing intestinal immune responses, absorption and barrier function, but its effect on the gut microbiome of broiler chickens remains unclear. This experiment aimed at evaluating the effects of Dietary l-arginine supplementation on the gut bacterial community composition and function of broiler chickens challenged with C. perfringens. In total, 105 1-day-old male Arbor Acres broiler chickens were assigned to three groups: Control (CTL), C. perfringens-challenged (CP), and C. perfringens-challenged and fed diet supplemented with 0.3% l-arginine (ARGCP) groups. The challenge led to macroscopic and histomorphological gut lesions, decreased villus height and increased the number of Observed species, Shannon, Chao1 and ACE indices of ileal microbiota, whereas l-arginine addition reversed these changes. Moreover, the three treatments harbored distinct microbial communities (ANOSIM, P < 0.05). At the genus level, 24 taxa (e.g., Nitrosomonas spp., Coxiella spp., Ruegeria spp., and Thauera spp.) were significantly more abundant in CP group than in CTL group (P < 0.05), whereas the levels of 23 genera of them were significantly decreased by l-arginine supplementation (P < 0.05). The abundances of only 3 genera were different between CTL and ARGCP groups (P < 0.05). At the species level, the challenge promoted the relative abundance of Nitrospira sp. enrichment culture clone M1-9, Bradyrhizobium elkanii, Nitrospira bacterium SG8-3, and Pseudomonas veronii, which was reversed by l-arginine supplementation (P < 0.05). Furthermore, the challenge decreased the levels of Lactobacillus gasseri (P < 0.05). Predictive functional profiling of microbial communities by PICRUSt showed that compared with CP group, ARGCP group had enriched pathways relating to membrane transport, replication and repair, translation and nucleotide metabolism and suppressed functions corresponding to amino acid and lipid metabolisms (P < 0.05). The relative abundances of KEGG pathways in l-arginine-fed broilers were almost equal to those of the controls. In conclusion, l-arginine alleviated the gut injury and normalized the ileal microbiota of C. perfringens-challenged chickens to resemble that of unchallenged controls in terms of microbial composition and functionality.
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Affiliation(s)
- Beibei Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zengpeng Lv
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhui Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Weiwei Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guang Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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41
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Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature 2018; 557:101-105. [DOI: 10.1038/s41586-018-0059-5] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 03/02/2018] [Indexed: 11/08/2022]
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42
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Garushyants SK, Beliavskaia AY, Malko DB, Logacheva MD, Rautian MS, Gelfand MS. Comparative Genomic Analysis of Holospora spp., Intranuclear Symbionts of Paramecia. Front Microbiol 2018; 9:738. [PMID: 29713316 PMCID: PMC5911502 DOI: 10.3389/fmicb.2018.00738] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/29/2018] [Indexed: 11/16/2022] Open
Abstract
While most endosymbiotic bacteria are transmitted only vertically, Holospora spp., an alphaproteobacterium from the Rickettsiales order, can desert its host and invade a new one. All bacteria from the genus Holospora are intranuclear symbionts of ciliates Paramecium spp. with strict species and nuclear specificity. Comparative metabolic reconstruction based on the newly sequenced genome of Holospora curviuscula, a macronuclear symbiont of Paramecium bursaria, and known genomes of other Holospora species shows that even though all Holospora spp. can persist outside the host, they cannot synthesize most of the essential small molecules, such as amino acids, and lack some central energy metabolic pathways, including glycolysis and the citric acid cycle. As the main energy source, Holospora spp. likely rely on nucleotides pirated from the host. Holospora-specific genes absent from other Rickettsiales are possibly involved in the lifestyle switch from the infectious to the reproductive form and in cell invasion.
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Affiliation(s)
- Sofya K Garushyants
- Skolkovo Institute of Science and Technology, Moscow, Russia.,Kharkevitch Institute for Information Transmission Problems, Moscow, Russia
| | - Alexandra Y Beliavskaia
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Maria D Logacheva
- Skolkovo Institute of Science and Technology, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Maria S Rautian
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia.,Kharkevitch Institute for Information Transmission Problems, Moscow, Russia.,National Research Center for Hematology, Moscow, Russia.,National Research University Higher School of Economics, Moscow, Russia
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43
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Lin W, Zhang W, Zhao X, Roberts AP, Paterson GA, Bazylinski DA, Pan Y. Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution. ISME JOURNAL 2018; 12:1508-1519. [PMID: 29581530 PMCID: PMC5955933 DOI: 10.1038/s41396-018-0098-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 11/09/2022]
Abstract
The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth's magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3O4) or greigite (Fe3S4) called magnetosomes. Magnetosomes are responsible for magnetotaxis in MTB. Here we report the first large-scale metagenomic survey of MTB from both northern and southern hemispheres combined with 28 genomes from uncultivated MTB. These genomes expand greatly the coverage of MTB in the Proteobacteria, Nitrospirae, and Omnitrophica phyla, and provide the first genomic evidence of MTB belonging to the Zetaproteobacteria and "Candidatus Lambdaproteobacteria" classes. The gene content and organization of magnetosome gene clusters, which are physically grouped genes that encode proteins for magnetosome biosynthesis and organization, are more conserved within phylogenetically similar groups than between different taxonomic lineages. Moreover, the phylogenies of core magnetosome proteins form monophyletic clades. Together, these results suggest a common ancient origin of iron-based (Fe3O4 and Fe3S4) magnetotaxis in the domain Bacteria that underwent lineage-specific evolution, shedding new light on the origin and evolution of biomineralization and magnetotaxis, and expanding significantly the phylogenomic representation of MTB.
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Affiliation(s)
- Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China. .,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China. .,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Wensi Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Zhao
- Research School of Earth Sciences, Australian National University, Canberra, ACT, 2601, Australia
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, Canberra, ACT, 2601, Australia
| | - Greig A Paterson
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China.,Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZE, UK
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China. .,Institutions of Earth Science, Chinese Academy of Sciences, Beijing, 100029, China. .,France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing, 100029, China. .,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Tashyreva D, Prokopchuk G, Votýpka J, Yabuki A, Horák A, Lukeš J. Life Cycle, Ultrastructure, and Phylogeny of New Diplonemids and Their Endosymbiotic Bacteria. mBio 2018; 9:e02447-17. [PMID: 29511084 PMCID: PMC5845003 DOI: 10.1128/mbio.02447-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/31/2018] [Indexed: 11/20/2022] Open
Abstract
Diplonemids represent a hyperdiverse and abundant yet poorly studied group of marine protists. Here we describe two new members of the genus Diplonema (Diplonemea, Euglenozoa), Diplonema japonicum sp. nov. and Diplonema aggregatum sp. nov., based on life cycle, morphology, and 18S rRNA gene sequences. Along with euglenozoan apomorphies, they contain several unique features. Their life cycle is complex, consisting of a trophic stage that is, following the depletion of nutrients, transformed into a sessile stage and subsequently into a swimming stage. The latter two stages are characterized by the presence of tubular extrusomes and the emergence of a paraflagellar rod, the supportive structure of the flagellum, which is prominently lacking in the trophic stage. These two stages also differ dramatically in motility and flagellar size. Both diplonemid species host endosymbiotic bacteria that are closely related to each other and constitute a novel branch within Holosporales, for which a new genus, "Candidatus Cytomitobacter" gen. nov., has been established. Remarkably, the number of endosymbionts in the cytoplasm varies significantly, as does their localization within the cell, where they seem to penetrate the mitochondrion, a rare occurrence.IMPORTANCE We describe the morphology, behavior, and life cycle of two new Diplonema species that established a relationship with two Holospora-like bacteria in the first report of an endosymbiosis in diplonemids. Both endosymbionts reside in the cytoplasm and the mitochondrion, which establishes an extremely rare case. Within their life cycle, the diplonemids undergo transformation from a trophic to a sessile and eventually a highly motile swimming stage. These stages differ in several features, such as the presence or absence of tubular extrusomes and a paraflagellar rod, along with the length of the flagella. These morphological and behavioral interstage differences possibly reflect distinct functions in dispersion and invasion of the host and/or prey and may provide novel insight into the virtually unknown function of diplonemids in the oceanic ecosystem.
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Affiliation(s)
- Daria Tashyreva
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Galina Prokopchuk
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Jan Votýpka
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Akinori Yabuki
- Department of Marine Diversity, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Aleš Horák
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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45
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Shakya M, Soucy SM, Zhaxybayeva O. Insights into origin and evolution of α-proteobacterial gene transfer agents. Virus Evol 2017; 3:vex036. [PMID: 29250433 PMCID: PMC5721377 DOI: 10.1093/ve/vex036] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several bacterial and archaeal lineages produce nanostructures that morphologically resemble small tailed viruses, but, unlike most viruses, contain apparently random pieces of the host genome. Since these elements can deliver the packaged DNA to other cells, they were dubbed gene transfer agents (GTAs). Because many genes involved in GTA production have viral homologs, it has been hypothesized that the GTA ancestor was a virus. Whether GTAs represent an atypical virus, a defective virus, or a virus co-opted by the prokaryotes for some function, remains to be elucidated. To evaluate these possibilities, we examined the distribution and evolutionary histories of genes that encode a GTA in the α-proteobacterium Rhodobacter capsulatus (RcGTA). We report that although homologs of many individual RcGTA genes are abundant across bacteria and their viruses, RcGTA-like genomes are mainly found in one subclade of α-proteobacteria. When compared with the viral homologs, genes of the RcGTA-like genomes evolve significantly slower, and do not have higher %A+T nucleotides than their host chromosomes. Moreover, they appear to reside in stable regions of the bacterial chromosomes that are generally conserved across taxonomic orders. These findings argue against RcGTA being an atypical or a defective virus. Our phylogenetic analyses suggest that RcGTA ancestor likely originated in the lineage that gave rise to contemporary α-proteobacterial orders Rhizobiales, Rhodobacterales, Caulobacterales, Parvularculales, and Sphingomonadales, and since that time the RcGTA-like element has co-evolved with its host chromosomes. Such evolutionary history is compatible with maintenance of these elements by bacteria due to some selective advantage. As for many other prokaryotic traits, horizontal gene transfer played a substantial role in the evolution of RcGTA-like elements, not only in shaping its genome components within the orders, but also in occasional dissemination of RcGTA-like regions across the orders and even to different bacterial phyla.
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Affiliation(s)
- Migun Shakya
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Shannon M Soucy
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA.,Department of Computer Science, Dartmouth College, 6211 Sudikoff Lab, Hanover, NH 03755, USA
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Karlsen C, Ottem KF, Brevik ØJ, Davey M, Sørum H, Winther-Larsen HC. The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders. JOURNAL OF FISH DISEASES 2017; 40:1645-1663. [PMID: 28449237 DOI: 10.1111/jfd.12632] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/10/2017] [Accepted: 02/12/2017] [Indexed: 06/07/2023]
Abstract
The Norwegian aquaculture of Atlantic salmon (Salmo salar L.) is hampered by ulcerative disorders associated with bacterial infections. Chronic ulceration may provide microenvironments that disturb the normal microbial biodiversity of external surfaces. Studying the composition of microbial communities in skin ulcers will enhance our understanding of ulcer aetiology. To achieve this, we tested marine farmed Atlantic salmon and sampled the base and edge of ulcers at the end of winter (April) and end of summer (September), in addition to skin mucus of healthy individuals. In order to assess microbiota associated with the host and obtain insight into the environmental ecology, we also sampled sea water, the sediment layer underneath the farm facility and the distal intestine of Atlantic salmon. The skin microbiota of Atlantic salmon was different from that of the surrounding water. Residential Tenacibaculum and Arcobacter species persistently dominated the cutaneous skin and ulcer mucus surfaces of Atlantic salmon during both winter and summer periods. The intestinal microbiota was dominated by Mycoplasma with an increase in Aliivibrio and Alcaligenes abundance in the intestine of fish with ulcerative disorder at the end of winter. These findings suggest the presence of resilient microbes in the mucus surfaces of Atlantic salmon.
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Affiliation(s)
- C Karlsen
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences (NMBU), Oslo, Norway
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, Center of Integrative Microbial Evolution (CIME), School of Pharmacy, University of Oslo, Oslo, Norway
| | | | | | - M Davey
- Department of Biological Sciences, University of Oslo, Oslo, Norway
| | - H Sørum
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - H C Winther-Larsen
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, Center of Integrative Microbial Evolution (CIME), School of Pharmacy, University of Oslo, Oslo, Norway
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47
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Calvo AY, Manrique JM, Jones LR. Rare unclassified 16S rRNA operational taxonomic units from the uncharted Engaño Bay (Argentinean Patagonia). Can J Microbiol 2017; 64:91-96. [PMID: 29078061 DOI: 10.1139/cjm-2017-0342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rare microbes make up most of the diversity of marine microbiomes, and recent works have highlighted their importance for microbial community dynamics and in fragmented habitats. Rare taxa have been infrequently studied in comparison with abundant groups, and rare unclassified sequences are common in culture-independent studies. Here, we describe a detailed analysis of nonclassifiable sequences from the Chubut river estuary at the Argentinean Patagonia. Standard taxonomic assignments of environmental 16S rRNA sequences resulted in about 13% unclassified operational taxonomic units (OTUs). The potential affiliations of these OTUs could be narrowed by mapping the classification software assignments on a phylogeny obtained directly from our environmental sequence data. Customized BLAST analyses were remarkably consistent with these phylogenetic assignments, especially when the unclassified OTUs were blasted against sequences from cultured and type microorganisms. In addition, our BLAST analyses revealed significant similarities between several unclassified OTUs and a plethora of unclassified sequences from around the world. Further phylogenetic comparisons with 6194 carefully selected reference sequences showed that these unclassified sequences may correspond to 5 unnamed groups, possibly encompassing ranks from subclass to family inside the Alphaproteobacteria, and to an unknown Gracilibacteria lineage. Overall, these results demonstrate the value of straight phylogenetic analysis, customized BLAST searches, and comparisons with sequences from type material, for the systematic study of rare unclassified sequences.
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Affiliation(s)
- Andrea Y Calvo
- Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales y Ciencias de la Salud (FCNyCS), Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), 9 de Julio y Belgrano s/n (9100), Trelew, Chubut, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Rivadavia 1917 (C1083ACA) Buenos Aires, Argentina.,Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales y Ciencias de la Salud (FCNyCS), Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), 9 de Julio y Belgrano s/n (9100), Trelew, Chubut, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Rivadavia 1917 (C1083ACA) Buenos Aires, Argentina
| | - Julieta M Manrique
- Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales y Ciencias de la Salud (FCNyCS), Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), 9 de Julio y Belgrano s/n (9100), Trelew, Chubut, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Rivadavia 1917 (C1083ACA) Buenos Aires, Argentina.,Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales y Ciencias de la Salud (FCNyCS), Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), 9 de Julio y Belgrano s/n (9100), Trelew, Chubut, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Rivadavia 1917 (C1083ACA) Buenos Aires, Argentina
| | - Leandro R Jones
- Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales y Ciencias de la Salud (FCNyCS), Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), 9 de Julio y Belgrano s/n (9100), Trelew, Chubut, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Rivadavia 1917 (C1083ACA) Buenos Aires, Argentina.,Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales y Ciencias de la Salud (FCNyCS), Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), 9 de Julio y Belgrano s/n (9100), Trelew, Chubut, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Rivadavia 1917 (C1083ACA) Buenos Aires, Argentina
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48
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Zachar I, Szathmáry E. Breath-giving cooperation: critical review of origin of mitochondria hypotheses : Major unanswered questions point to the importance of early ecology. Biol Direct 2017; 12:19. [PMID: 28806979 PMCID: PMC5557255 DOI: 10.1186/s13062-017-0190-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/20/2017] [Indexed: 02/08/2023] Open
Abstract
The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address. We have objectively compared contending hypotheses under these questions to find the most plausible course of events and to draw insight on missing pieces of the puzzle. Since endosymbiosis borders evolution and ecology, and since a realistic theory has to comply with both domains' constraints, the conclusion is that the most important aspect to clarify is the initial ecological relationship of partners. Metabolic benefits are largely irrelevant at this initial phase, where ecological costs could be more disruptive. There is no single theory capable of answering all questions indicating a severe lack of ecological considerations. A new theory, compliant with recent phylogenomic results, should adhere to these criteria. REVIEWERS This article was reviewed by Michael W. Gray, William F. Martin and Purificación López-García.
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Affiliation(s)
- István Zachar
- Eötvös Loránd University, Department of Plant Systematics, Ecology and Theoretical Biology, Pázmány P. sétány 1/C, Budapest, 1117, Hungary.
- Evolutionary Systems Research Group, MTA, Centre for Ecological Research, Hungarian Academy of Sciences, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary.
| | - Eörs Szathmáry
- Eötvös Loránd University, Department of Plant Systematics, Ecology and Theoretical Biology, Pázmány P. sétány 1/C, Budapest, 1117, Hungary
- Evolutionary Systems Research Group, MTA, Centre for Ecological Research, Hungarian Academy of Sciences, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary
- Parmenides Foundation, Kirchplatz 1, 82049 Pullach/Munich, Munich, Germany
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Timmermans ML, Paudel YP, Ross AC. Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies. Mar Drugs 2017; 15:E235. [PMID: 28762997 PMCID: PMC5577590 DOI: 10.3390/md15080235] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023] Open
Abstract
The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.
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Affiliation(s)
| | - Yagya P Paudel
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
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50
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Ferla MP, Brewster JL, Hall KR, Evans GB, Patrick WM. Primordial‐like enzymes from bacteria with reduced genomes. Mol Microbiol 2017. [DOI: 10.1111/mmi.13737] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Matteo P. Ferla
- Department of BiochemistryUniversity of OtagoDunedin New Zealand
| | - Jodi L. Brewster
- Department of BiochemistryUniversity of OtagoDunedin New Zealand
| | - Kelsi R. Hall
- Department of BiochemistryUniversity of OtagoDunedin New Zealand
| | - Gary B. Evans
- Ferrier Research InstituteVictoria UniversityLower Hutt New Zealand
| | - Wayne M. Patrick
- Department of BiochemistryUniversity of OtagoDunedin New Zealand
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