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Willemin MS, Armand F, Hamelin R, Maillard J, Holliger C. Conditional essentiality of the 11-subunit complex I-like enzyme in strict anaerobes: the case of Desulfitobacterium hafniense strain DCB-2. Front Microbiol 2024; 15:1388961. [PMID: 38993499 PMCID: PMC11238625 DOI: 10.3389/fmicb.2024.1388961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/28/2024] [Indexed: 07/13/2024] Open
Abstract
In oxidative phosphorylation, respiratory complex I serves as an entry point in the electron transport chain for electrons generated in catabolic processes in the form of NADH. An ancestral version of the complex, lacking the NADH-oxidising module, is encoded in a significant number of bacterial genomes. Amongst them is Desulfitobacterium hafniense, a strict anaerobe capable of conserving energy via organohalide respiration. This study investigates the role of the complex I-like enzyme in D. hafniense energy metabolism using rotenone as a specific complex I inhibitor under different growth conditions. The investigation revealed that the complex I-like enzyme was essential for growth with lactate and pyruvate but not in conditions involving H2 as an electron donor. In addition, a previously published proteomic dataset of strain DCB-2 was analysed to reveal the predominance of the complex under different growth conditions and to identify potential redox partners. This approach revealed seven candidates with expression patterns similar to Nuo homologues, suggesting the use of diverse electron sources. Based on these results, we propose a model where the complex I-like enzyme serves as an electron entry point into the respiratory chain for substrates delivering electrons within the cytoplasm, such as lactate or pyruvate, with ferredoxins shuttling electrons to the complex.
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Affiliation(s)
- Mathilde Stéphanie Willemin
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Armand
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Romain Hamelin
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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2
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Lettl C, Schindele F, Mehdipour AR, Steiner T, Ring D, Brack-Werner R, Stecher B, Eisenreich W, Bilitewski U, Hummer G, Witschel M, Fischer W, Haas R. Selective killing of the human gastric pathogen Helicobacter pylori by mitochondrial respiratory complex I inhibitors. Cell Chem Biol 2023; 30:499-512.e5. [PMID: 37100053 DOI: 10.1016/j.chembiol.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/16/2023] [Accepted: 04/05/2023] [Indexed: 04/28/2023]
Abstract
Respiratory complex I is a multicomponent enzyme conserved between eukaryotic cells and many bacteria, which couples oxidation of electron donors and quinone reduction with proton pumping. Here, we report that protein transport via the Cag type IV secretion system, a major virulence factor of the Gram-negative bacterial pathogen Helicobacter pylori, is efficiently impeded by respiratory inhibition. Mitochondrial complex I inhibitors, including well-established insecticidal compounds, selectively kill H. pylori, while other Gram-negative or Gram-positive bacteria, such as the close relative Campylobacter jejuni or representative gut microbiota species, are not affected. Using a combination of different phenotypic assays, selection of resistance-inducing mutations, and molecular modeling approaches, we demonstrate that the unique composition of the H. pylori complex I quinone-binding pocket is the basis for this hypersensitivity. Comprehensive targeted mutagenesis and compound optimization studies highlight the potential to develop complex I inhibitors as narrow-spectrum antimicrobial agents against this pathogen.
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Affiliation(s)
- Clara Lettl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Franziska Schindele
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Ahmad Reza Mehdipour
- Center for Molecular Modeling, Ghent University, 9052 Zwijnaarde, Belgium; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Thomas Steiner
- Bavarian NMR Center-Structural Membrane Biochemistry, Department of Chemistry, Technical University Munich, 85748 Garching, Germany
| | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany
| | - Ruth Brack-Werner
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany; German Research Center for Environmental Health, Institute of Virology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Wolfgang Eisenreich
- Bavarian NMR Center-Structural Membrane Biochemistry, Department of Chemistry, Technical University Munich, 85748 Garching, Germany
| | - Ursula Bilitewski
- Helmholtz Center for Infection Research, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover/Braunschweig, Braunschweig, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | | | - Wolfgang Fischer
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
| | - Rainer Haas
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstrasse 9a, 80336 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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3
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Glass JB, Elbon CE, Williams LD. Something old, something new, something borrowed, something blue: the anaerobic microbial ancestry of aerobic respiration. Trends Microbiol 2023; 31:135-141. [PMID: 36058785 DOI: 10.1016/j.tim.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 01/27/2023]
Abstract
Aerobic respiration evolved by bricolage, with modules cobbled together as microbial biochemistry coevolved with Earth's geochemistry. The mitochondrial electron transport chain represents a patchwork of respiratory modules inherited from microbial methanogenesis, iron oxidation, anoxygenic photosynthesis, and denitrification pathways, and preserves a biochemical record of Earth's redox environment over its four-billion-year history. Imprints of the anoxic early Earth are recognizable in Complex I's numerous iron-sulfur cofactors and vestigial binding sites for ferredoxin, nickel-iron, and molybdopterin, whereas the more recent advent of oxygen as a terminal electron acceptor necessitated use of heme and copper cofactors by Complex IV. Bricolage of respiratory complexes resulted in supercomplexes for improved electron transfer efficiency in some bacteria and archaea, and in many eukaryotes. Accessory subunits evolved to wrap mitochondrial supercomplexes for improved assembly and stability. Environmental microbes with 'fossil' proteins that are similar to ancestral forms of the respiratory complexes deserve further scrutiny and may reveal new insights on the evolution of aerobic respiration.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Claire E Elbon
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
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4
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Musiani F, Rigobello L, Iommarini L, Carelli V, Degli Esposti M, Ghelli AM. New Insights on Rotenone Resistance of Complex I Induced by the m.11778G>A/ MT-ND4 Mutation Associated with Leber's Hereditary Optic Neuropathy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041341. [PMID: 35209128 PMCID: PMC8876992 DOI: 10.3390/molecules27041341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 11/16/2022]
Abstract
The finding that the most common mitochondrial DNA mutation m.11778G>A/MT-ND4 (p.R340H) associated with Leber's hereditary optic neuropathy (LHON) induces rotenone resistance has produced a long-standing debate, because it contrasts structural evidence showing that the ND4 subunit is far away from the quinone-reaction site in complex I, where rotenone acts. However, recent cryo-electron microscopy data revealed that rotenone also binds to the ND4 subunit. We investigated the possible structural modifications induced by the LHON mutation and found that its amino acid replacement would disrupt a possible hydrogen bond between native R340 and Q139 in ND4, thereby destabilizing rotenone binding. Our analysis thus explains rotenone resistance in LHON patients as a biochemical signature of its pathogenic effect on complex I.
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Affiliation(s)
- Francesco Musiani
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, I-40126 Bologna, Italy; (F.M.); (L.R.); (L.I.)
| | - Laura Rigobello
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, I-40126 Bologna, Italy; (F.M.); (L.R.); (L.I.)
| | - Luisa Iommarini
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, I-40126 Bologna, Italy; (F.M.); (L.R.); (L.I.)
| | - Valerio Carelli
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università di Bologna, I-40100 Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, I-40139 Bologna, Italy
- Correspondence: (V.C.); (A.M.G.)
| | - Mauro Degli Esposti
- Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM), Cuernavaca 62210, Mexico;
| | - Anna Maria Ghelli
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, I-40126 Bologna, Italy; (F.M.); (L.R.); (L.I.)
- Correspondence: (V.C.); (A.M.G.)
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5
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Cevallos MA, Degli Esposti M. New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient. Microorganisms 2022; 10:455. [PMID: 35208909 PMCID: PMC8879329 DOI: 10.3390/microorganisms10020455] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in their taxonomic position within Alphaproteobacteria. The traditional classification of NCBI taxonomy is increasingly complemented by the Genome Taxonomy Database (GTDB), but the two taxonomies differ considerably in the classification of several Alphaproteobacteria, especially from ocean metagenomes. We analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism. Using protein markers such as NuoL, the largest membrane subunit of complex I, we have identified new clades of Alphaproteobacteria that are specific to marine niches with steep oxygen gradients (oxycline). These bacteria have relatives among MAGs found in anoxic strata of Lake Tanganyika and together define a lineage that is distinct from either Rhodospirillales or Sneathiellales. We characterized in particular the new 'oxycline' clade. Our analysis of Alphaproteobacteria also reveals new clues regarding the ancestry of mitochondria, which likely evolved in oxycline marine environments.
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Affiliation(s)
| | - Mauro Degli Esposti
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico;
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6
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Abstract
Respiratory complex I (NADH:ubiquinone oxidoreductase) captures the free energy from oxidising NADH and reducing ubiquinone to drive protons across the mitochondrial inner membrane and power oxidative phosphorylation. Recent cryo-EM analyses have produced near-complete models of the mammalian complex, but leave the molecular principles of its long-range energy coupling mechanism open to debate. Here, we describe the 3.0-Å resolution cryo-EM structure of complex I from mouse heart mitochondria with a substrate-like inhibitor, piericidin A, bound in the ubiquinone-binding active site. We combine our structural analyses with both functional and computational studies to demonstrate competitive inhibitor binding poses and provide evidence that two inhibitor molecules bind end-to-end in the long substrate binding channel. Our findings reveal information about the mechanisms of inhibition and substrate reduction that are central for understanding the principles of energy transduction in mammalian complex I. The respiratory complex I (NADH:ubiquinone oxidoreductase) is a large redox-driven proton pump that initiates respiration in mitochondria. Here, the authors present the 3.0 Å cryo-EM structure of complex I from mouse heart mitochondria with the ubiquinone-analogue inhibitor piericidin A bound in the active site and with kinetic measurements and MD simulations they further show that this inhibitor acts competitively against the native ubiquinone-10 substrate.
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7
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Lindström K, Mousavi SA. Effectiveness of nitrogen fixation in rhizobia. Microb Biotechnol 2020; 13:1314-1335. [PMID: 31797528 PMCID: PMC7415380 DOI: 10.1111/1751-7915.13517] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/01/2022] Open
Abstract
Biological nitrogen fixation in rhizobia occurs primarily in root or stem nodules and is induced by the bacteria present in legume plants. This symbiotic process has fascinated researchers for over a century, and the positive effects of legumes on soils and their food and feed value have been recognized for thousands of years. Symbiotic nitrogen fixation uses solar energy to reduce the inert N2 gas to ammonia at normal temperature and pressure, and is thus today, especially, important for sustainable food production. Increased productivity through improved effectiveness of the process is seen as a major research and development goal. The interaction between rhizobia and their legume hosts has thus been dissected at agronomic, plant physiological, microbiological and molecular levels to produce ample information about processes involved, but identification of major bottlenecks regarding efficiency of nitrogen fixation has proven to be complex. We review processes and results that contributed to the current understanding of this fascinating system, with focus on effectiveness of nitrogen fixation in rhizobia.
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Affiliation(s)
- Kristina Lindström
- Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiFI‐00014HelsinkiFinland
| | - Seyed Abdollah Mousavi
- Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiFI‐00014HelsinkiFinland
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8
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Chen Y, Bendix C, Lewis JD. Comparative Genomics Screen Identifies Microbe-Associated Molecular Patterns from ' Candidatus Liberibacter' spp. That Elicit Immune Responses in Plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:539-552. [PMID: 31790346 DOI: 10.1094/mpmi-11-19-0309-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Citrus huanglongbing (HLB), caused by phloem-limited 'Candidatus Liberibacter' bacteria, is a destructive disease threatening the worldwide citrus industry. The mechanisms of pathogenesis are poorly understood and no efficient strategy is available to control HLB. Here, we used a comparative genomics screen to identify candidate microbe-associated molecular patterns (MAMPs) from 'Ca. Liberibacter' spp. We identified the core genome from multiple 'Ca. Liberibacter' pathogens, and searched for core genes with signatures of positive selection. We hypothesized that genes encoding putative MAMPs would evolve to reduce recognition by the plant immune system, while retaining their essential functions. To efficiently screen candidate MAMP peptides, we established a high-throughput microtiter plate-based screening assay, particularly for citrus, that measured reactive oxygen species (ROS) production, which is a common immune response in plants. We found that two peptides could elicit ROS production in Arabidopsis and Nicotiana benthamiana. One of these peptides elicited ROS production and defense gene expression in HLB-tolerant citrus genotypes, and induced MAMP-triggered immunity against the bacterial pathogen Pseudomonas syringae. Our findings identify MAMPs that boost immunity in citrus and could help prevent or reduce HLB infection.
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Affiliation(s)
- Yuan Chen
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service and Department of Plant and Microbial Biology, University of California-Berkeley, 800 Buchanan Street, Albany, CA 94710, U.S.A
| | - Claire Bendix
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service and Department of Plant and Microbial Biology, University of California-Berkeley, 800 Buchanan Street, Albany, CA 94710, U.S.A
| | - Jennifer D Lewis
- Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service and Department of Plant and Microbial Biology, University of California-Berkeley, 800 Buchanan Street, Albany, CA 94710, U.S.A
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9
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Otero L, Martínez-Rosales C, Barrera E, Pantano S, Salinas G. Complex I and II Subunit Gene Duplications Provide Increased Fitness to Worms. Front Genet 2019; 10:1043. [PMID: 31781156 PMCID: PMC6859908 DOI: 10.3389/fgene.2019.01043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/30/2019] [Indexed: 11/20/2022] Open
Abstract
Helminths use an alternative mitochondrial electron transport chain (ETC) under hypoxic conditions, such as those found in the gastrointestinal tract. In this alternative ETC, fumarate is the final electron acceptor and rhodoquinone (RQ) serves as an electron carrier. RQ receives electrons from reduced nicotinamide adenine dinucleotide through complex I and donates electrons to fumarate through complex II. In this latter reaction, complex II functions in the opposite direction to the conventional ETC (i.e., as fumarate reductase instead of succinate dehydrogenase). Studies in Ascaris suum indicate that this is possible due to changes in complex II, involving alternative succinate dehydrogenase (SDH) subunits SDHA and SDHD, derived from duplicated genes. We analyzed helminth genomes and found that distinct lineages have different gene duplications of complex II subunits (SDHA, SDHB, SDHC, and SDHD). Similarly, we found lineage-specific duplications in genes encoding complex I subunits that interact with quinones (NDUF2 and NDUF7). The phylogenetic analysis of ETC subunits revealed a complex history with independent evolutionary events involving gene duplications and losses. Our results indicated that there is not a common evolutionary event related to ETC subunit genes linked to RQ. The free-living nematode Caenorhabditis elegans uses RQ and has two genes encoding SDHA (sdha-1 and sdha-2) and two genes encoding NDUF2 (nduf2-1 and nduf2-2). sdha-1 and nduf2-1 are essential genes and have a similar expression pattern during C. elegans lifecycle. Using knockout strains, we found that sdha-2 and nduf2-2 are not essential, even in hypoxia. Yet, sdha-2 and nduf2-2 expression is increased in the early embryo and in dauer larvae, stages where there is low oxygen tension. Strikingly, sdha-1 and sdha-2 as well as nduf2-1 and nduf2-2 showed inverted expression profiles during the C. elegans life cycle. Finally, we found that sdha-2 and nduf2-2 knockout mutant strain progeny is affected. Our results indicate that different complex I and II subunit gene duplications provide increased fitness to worms.
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Affiliation(s)
- Lucía Otero
- Laboratorio de Biología de Gusanos, Unidad Mixta Departamento de Biociencias, Facultad de Química, Universidad de la República–Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Cecilia Martínez-Rosales
- Laboratorio de Biología de Gusanos, Unidad Mixta Departamento de Biociencias, Facultad de Química, Universidad de la República–Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Exequiel Barrera
- Laboratorio de Simulaciones Biomoleculares, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Sergio Pantano
- Laboratorio de Simulaciones Biomoleculares, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Gustavo Salinas
- Laboratorio de Biología de Gusanos, Unidad Mixta Departamento de Biociencias, Facultad de Química, Universidad de la República–Institut Pasteur de Montevideo, Montevideo, Uruguay
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Trost BM, Gholami H. Propene as an Atom-Economical Linchpin for Concise Total Synthesis of Polyenes: Piericidin A. J Am Chem Soc 2018; 140:11623-11626. [DOI: 10.1021/jacs.8b08974] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Barry M. Trost
- Department of Chemistry, Stanford University, Stanford, California 94305-5580, United States
| | - Hadi Gholami
- Department of Chemistry, Stanford University, Stanford, California 94305-5580, United States
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11
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Degli Esposti M, Martinez Romero E. The functional microbiome of arthropods. PLoS One 2017; 12:e0176573. [PMID: 28475624 PMCID: PMC5419562 DOI: 10.1371/journal.pone.0176573] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
Many studies on the microbiome of animals have been reported but a comprehensive analysis is lacking. Here we present a meta-analysis on the microbiomes of arthropods and their terrestrial habitat, focusing on the functional profile of bacterial communities derived from metabolic traits that are essential for microbial life. We report a detailed analysis of probably the largest set of biochemically defined functional traits ever examined in microbiome studies. This work deals with the phylum proteobacteria, which is usually dominant in marine and terrestrial environments and covers all functions associated with microbiomes. The considerable variation in the distribution and abundance of proteobacteria in microbiomes has remained fundamentally unexplained. This analysis reveals discrete functional groups characteristic for adaptation to anaerobic conditions, which appear to be defined by environmental filtering of taxonomically related taxa. The biochemical diversification of the functional groups suggests an evolutionary trajectory in the structure of arthropods' microbiome, from metabolically versatile to specialized proteobacterial organisms that are adapted to complex environments such as the gut of social insects. Bacterial distribution in arthropods' microbiomes also shows taxonomic clusters that do not correspond to functional groups and may derive from other factors, including common contaminants of soil and reagents.
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Affiliation(s)
- Mauro Degli Esposti
- Italian Institute of Technology, Genoa, Italy
- Center for Genomic Sciences, UNAM Campus of Cuernavaca, Cuernavaca, Morelos, Mexico
- * E-mail:
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12
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Plazzi F, Puccio G, Passamonti M. Burrowers from the Past: Mitochondrial Signatures of Ordovician Bivalve Infaunalization. Genome Biol Evol 2017; 9:956-967. [PMID: 28338965 PMCID: PMC5393379 DOI: 10.1093/gbe/evx051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2017] [Indexed: 12/20/2022] Open
Abstract
Bivalves and gastropods are the two largest classes of extant molluscs. Despite sharing a huge number of features, they do not share a key ecological one: gastropods are essentially epibenthic, although most bivalves are infaunal. However, this is not the ancestral bivalve condition; Cambrian forms were surface crawlers and only during the Ordovician a fundamental infaunalization process took place, leading to bivalves as we currently know them. This major ecological shift is linked to the exposure to a different redox environoments (hypoxic or anoxic) and with the Lower Devonian oxygenation event. We investigated selective signatures on bivalve and gastropod mitochondrial genomes with respect to a time calibrated mitochondrial phylogeny by means of dN/dS ratios. We were able to detect 1) a major signal of directional selection between the Ordovician and the Lower Devonian for bivalve mitochondrial Complex I, and 2) an overall higher directional selective pressure on bivalve Complex V with respect to gastropods. These and other minor dN/dS patterns and timings are discussed, showing that the Ordovician infaunalization event left heavy traces in bivalve mitochondrial genomes.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
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13
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Degli Esposti M, Cortez D, Lozano L, Rasmussen S, Nielsen HB, Martinez Romero E. Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes. Biol Direct 2016; 11:34. [PMID: 27473689 PMCID: PMC4967309 DOI: 10.1186/s13062-016-0136-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/21/2016] [Indexed: 11/10/2022] Open
Abstract
Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α proteobacteria, subsequently evolving into the mitochondrial organelle of our cells. The consensus is based upon genetic and metabolic similarities between mitochondria and aerobic α proteobacteria but fails to explain the origin of several enzymes found in the mitochondria-derived organelles of anaerobic eukaryotes such as Trichomonas and Entamoeba. These enzymes are thought to derive from bacterial lineages other than α proteobacteria, e.g., Clostridium - an obligate anaerobe. [FeFe]-hydrogenase constitues the characteristic enzyme of this anaerobic metabolism and is present in different types also in Entamoeba and other anaerobic eukaryotes. Here we show that α proteobacteria derived from metagenomic studies possess both the cytosolic and organellar type of [FeFe]-hydrogenase, as well as all the proteins required for hydrogenase maturation. These organisms are related to cultivated members of the Rhodospirillales order previously suggested to be close relatives of mitochondrial ancestors. For the first time, our evidence supports an α proteobacterial ancestry for both the anaerobic and the aerobic metabolism of eukaryotes. Reviewers: This article was reviewed by William Martin and Nick Lane, both suggested by the Authors.
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Affiliation(s)
- Mauro Degli Esposti
- Italian Institute of Technology, Via Morego 30, 16136, Genoa, Italy. .,Center for Genomic Sciences, UNAM Cuernavaca, Cuernavaca, Mexico.
| | - Diego Cortez
- Center for Genomic Sciences, UNAM Cuernavaca, Cuernavaca, Mexico
| | - Luis Lozano
- Center for Genomic Sciences, UNAM Cuernavaca, Cuernavaca, Mexico
| | - Simon Rasmussen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, 2800, Kongens Lyngby, Denmark
| | - Henrik Bjørn Nielsen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, 2800, Kongens Lyngby, Denmark
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Degli Esposti M, Martinez Romero E. A survey of the energy metabolism of nodulating symbionts reveals a new form of respiratory complex I. FEMS Microbiol Ecol 2016; 92:fiw084. [DOI: 10.1093/femsec/fiw084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2016] [Indexed: 01/18/2023] Open
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