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Sigal N, Lichtenstein-Wolfheim R, Schlussel S, Azulay G, Borovok I, Holdengraber V, Elad N, Wolf SG, Zalk R, Zarivach R, Frank GA, Herskovits AA. Specialized Listeria monocytogenes produce tailocins to provide a population-level competitive growth advantage. Nat Microbiol 2024; 9:2727-2737. [PMID: 39300324 DOI: 10.1038/s41564-024-01793-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 07/23/2024] [Indexed: 09/22/2024]
Abstract
Tailocins are phage tail-like bacteriocins produced by various bacterial species to kill kin competitors. Given that tailocin release is dependent upon cell lysis, regulation of tailocin production at the single-cell and population level remains unclear. Here we used flow cytometry, competition assays and structural characterization of tailocin production in a human bacterial pathogen, Listeria monocytogenes. We revealed that a specialized subpopulation, constituting less than 1% of the total bacterial population, differentiates to produce, assemble and store thousands of tailocin particles. Tailocins are packed in a highly ordered manner, clustered in a liquid crystalline phase that occupies a substantial volume of the cell. Tailocin production confers a competitive growth advantage for the rest of the population. This study provides molecular insights into tailocin production as a form of altruism, showing how cell specialization within bacterial populations can confer competitive advantages at the population level.
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Affiliation(s)
- Nadejda Sigal
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rotem Lichtenstein-Wolfheim
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shai Schlussel
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Gil Azulay
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ilya Borovok
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Nadav Elad
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Ran Zalk
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Gabriel A Frank
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anat A Herskovits
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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2
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Hird C, Jékely G, Williams EA. Microalgal biofilm induces larval settlement in the model marine worm Platynereis dumerilii. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240274. [PMID: 39295916 PMCID: PMC11407872 DOI: 10.1098/rsos.240274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/17/2024] [Accepted: 08/12/2024] [Indexed: 09/21/2024]
Abstract
A free-swimming larval stage features in many marine invertebrate life cycles. To transition to a seafloor-dwelling juvenile stage, larvae need to settle out of the plankton, guided by specific environmental cues that lead them to an ideal habitat for their future life on the seafloor. Although the marine annelid Platynereis dumerilii has been cultured in research laboratories since the 1950s and has a free-swimming larval stage, specific environmental cues that induce settlement in this nereid worm are yet to be identified. Here, we demonstrate that microalgal biofilm is a key settlement cue for P. dumerilii larvae, inducing earlier onset of settlement and enhancing subsequent juvenile growth as a primary food source. We tested the settlement response of P. dumerilii to 40 different strains of microalgae, predominantly diatom species, finding that P. dumerilii have species-specific preferences in their choice of settlement substrate. The most effective diatom species for inducing P. dumerilii larval settlement were benthic pennate species including Grammatophora marina, Achnanthes brevipes and Nitzschia ovalis. The identification of specific environmental cues for P. dumerilii settlement enables a link between its ecology and the sensory and nervous system signalling that regulates larval behaviour and development. Incorporation of diatoms into P. dumerilii culture practices will improve the husbandry of this marine invertebrate model.
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Affiliation(s)
- Cameron Hird
- Scymaris Ltd, Brixham Laboratory, Freshwater Quarry, Brixham, Devon TQ5 8BA, UK
- University of Exeter, Biosciences, Faculty of Health and Life Sciences, Streatham Campus, Exeter EX4 4QD, UK
| | - Gáspár Jékely
- University of Heidelberg, Centre for Organismal Studies, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
- University of Exeter Living Systems Institute, Streatham Campus, Exeter EX4 4QD, UK
| | - Elizabeth A Williams
- University of Exeter, Biosciences, Faculty of Health and Life Sciences, Streatham Campus, Exeter EX4 4QD, UK
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3
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Danov A, Pollin I, Moon E, Ho M, Wilson BA, Papathanos PA, Kaplan T, Levy A. Identification of novel toxins associated with the extracellular contractile injection system using machine learning. Mol Syst Biol 2024; 20:859-879. [PMID: 39069594 PMCID: PMC11297309 DOI: 10.1038/s44320-024-00053-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/06/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
Secretion systems play a crucial role in microbe-microbe or host-microbe interactions. Among these systems, the extracellular contractile injection system (eCIS) is a unique bacterial and archaeal extracellular secretion system that injects protein toxins into target organisms. However, the specific proteins that eCISs inject into target cells and their functions remain largely unknown. Here, we developed a machine learning classifier to identify eCIS-associated toxins (EATs). The classifier combines genetic and biochemical features to identify EATs. We also developed a score for the eCIS N-terminal signal peptide to predict EAT loading. Using the classifier we classified 2,194 genes from 950 genomes as putative EATs. We validated four new EATs, EAT14-17, showing toxicity in bacterial and eukaryotic cells, and identified residues of their respective active sites that are critical for toxicity. Finally, we show that EAT14 inhibits mitogenic signaling in human cells. Our study provides insights into the diversity and functions of EATs and demonstrates machine learning capability of identifying novel toxins. The toxins can be employed in various applications dependently or independently of eCIS.
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Affiliation(s)
- Aleks Danov
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Inbal Pollin
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Eric Moon
- Department of Microbiology, University of Illinois Urbana-Champaign, 601 South Goodwin Ave, Urbana, 61801, IL, USA
| | - Mengfei Ho
- Department of Microbiology, University of Illinois Urbana-Champaign, 601 South Goodwin Ave, Urbana, 61801, IL, USA
| | - Brenda A Wilson
- Department of Microbiology, University of Illinois Urbana-Champaign, 601 South Goodwin Ave, Urbana, 61801, IL, USA
| | - Philippos A Papathanos
- Department of Entomology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
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Freckelton ML, Nedved BT, Hadfield MG. Bacterial envelope polysaccharide cues settlement and metamorphosis in the biofouling tubeworm Hydroides elegans. Commun Biol 2024; 7:883. [PMID: 39030323 PMCID: PMC11271524 DOI: 10.1038/s42003-024-06585-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 07/15/2024] [Indexed: 07/21/2024] Open
Abstract
Metamorphosis for many marine invertebrates is triggered by external cues, commonly produced by bacteria. For larvae of Hydroides elegans, lipopolysaccharide (LPS) from the biofilm-dwelling bacterium Cellulophaga lytica induces metamorphosis. To determine whether bacterial LPS is a common metamorphosis-inducing factor for this species, we compare larval responses to LPS from 3 additional inductive Gram-negative marine biofilm bacteria with commercially available LPS from 3 bacteria not known to induce metamorphosis. LPS from all the inductive bacteria trigger metamorphosis, while LPS from non-inductive isolated marine bacteria do not. We then ask, which part of the LPS is the inductive element, the lipid (Lipid-A) or the polysaccharide (O-antigen), and find it is the latter for all four inductive bacteria. Finally, we examine the LPS subunits from two strains of the same bacterial species, one inductive and the other not, and find the LPS and O-antigen to be inductive from only the inductive bacterial strain.
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Affiliation(s)
| | - Brian T Nedved
- Kewalo Marine Laboratory, University of Hawai'i, Honolulu, HI, 96813, USA
| | - Michael G Hadfield
- Kewalo Marine Laboratory, University of Hawai'i, Honolulu, HI, 96813, USA.
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5
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Liang Y, Carrillo-Baltodano AM, Martín-Durán JM. Emerging trends in the study of spiralian larvae. Evol Dev 2024; 26:e12459. [PMID: 37787615 DOI: 10.1111/ede.12459] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023]
Abstract
Many animals undergo indirect development, where their embryogenesis produces an intermediate life stage, or larva, that is often free-living and later metamorphoses into an adult. As their adult counterparts, larvae can have unique and diverse morphologies and occupy various ecological niches. Given their broad phylogenetic distribution, larvae have been central to hypotheses about animal evolution. However, the evolution of these intermediate forms and the developmental mechanisms diversifying animal life cycles are still debated. This review focuses on Spiralia, a large and diverse clade of bilaterally symmetrical animals with a fascinating array of larval forms, most notably the archetypical trochophore larva. We explore how classic research and modern advances have improved our understanding of spiralian larvae, their development, and evolution. Specifically, we examine three morphological features of spiralian larvae: the anterior neural system, the ciliary bands, and the posterior hyposphere. The combination of molecular and developmental evidence with modern high-throughput techniques, such as comparative genomics, single-cell transcriptomics, and epigenomics, is a promising strategy that will lead to new testable hypotheses about the mechanisms behind the evolution of larvae and life cycles in Spiralia and animals in general. We predict that the increasing number of available genomes for Spiralia and the optimization of genome-wide and single-cell approaches will unlock the study of many emerging spiralian taxa, transforming our views of the evolution of this animal group and their larvae.
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Affiliation(s)
- Yan Liang
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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6
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Videau P, Shlafstein MD, Oline DK, Givan SA, Chapman LF, Strangman WK, Hahnke RL, Saw JH, Ushijima B. Genome-based taxonomic analysis of the genus Pseudoalteromonas reveals heterotypic synonyms. Environ Microbiol 2024; 26:e16672. [PMID: 39040020 DOI: 10.1111/1462-2920.16672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/31/2024] [Indexed: 07/24/2024]
Abstract
The Pseudoalteromonas genus comprises members that have been demonstrated to play significant ecological roles and produce enzymes, natural products, and activities that are beneficial to the environment and economy. A comprehensive evaluation of the genus revealed that the genomes of several Pseudoalteromonas species are highly similar to each other, exceeding species cutoff values. This evaluation involved determining and comparing the average nucleotide identity, in silico DNA-DNA hybridization, average amino acid identity, and the difference in G + C% between Pseudoalteromonas type strains with publicly available genomes. The genome of the Pseudoalteromonas elyakovii type strain was further assessed through additional sequencing and genomic comparisons to historical sequences. These findings suggest that six Pseudoalteromonas species, namely P. mariniglutinosa, P. donghaensis, P. maricaloris, P. elyakovii, P. profundi, and P. issachenkonii, should be reclassified as later heterotypic synonyms of the following validly published species: P. haloplanktis, P. lipolytica, P. flavipulchra, P. distincta, P. gelatinilytica, and P. tetraodonis. Furthermore, two names without valid standing, 'P. telluritireducens' and 'P. spiralis', should be associated with the validly published Pseudoalteromonas species P. agarivorans and P. tetraodonis, respectively.
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Affiliation(s)
- Patrick Videau
- Department of Biology, Southern Oregon University, Ashland, Oregon, USA
| | | | - David K Oline
- Department of Biology, Southern Oregon University, Ashland, Oregon, USA
| | - Scott A Givan
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Linda Fleet Chapman
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Wendy K Strangman
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Richard L Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jimmy H Saw
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
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7
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Hu XM, Peng L, Wang Y, Ma F, Tao Y, Liang X, Yang JL. Bacterial c-di-GMP triggers metamorphosis of mussel larvae through a STING receptor. NPJ Biofilms Microbiomes 2024; 10:51. [PMID: 38902226 PMCID: PMC11190208 DOI: 10.1038/s41522-024-00523-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
Bacteria induced metamorphosis observed in nearly all marine invertebrates. However, the mechanism of bacteria regulating the larvae-juvenile metamorphosis remains unknown. Here, we test the hypothesis that c-di-GMP, a ubiquitous bacterial second-messenger molecule, directly triggers the mollusc Mytilus coruscus larval metamorphosis via the stimulator of interferon genes (STING) receptor. We determined that the deletion of c-di-GMP synthesis genes resulted in reduced c-di-GMP levels and biofilm-inducing activity on larval metamorphosis, accompanied by alterations in extracellular polymeric substances. Additionally, c-di-GMP extracted from tested varying marine bacteria all exhibited inducing activity on larval metamorphosis. Simultaneously, through pharmacological and molecular experiments, we demonstrated that M. coruscus STING (McSTING) participates in larval metamorphosis by binding with c-di-GMP. Our findings reveal that new role of bacterial c-di-GMP that triggers mussel larval metamorphosis transition, and extend knowledge in the interaction of bacteria and host development in marine ecosystems.
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Affiliation(s)
- Xiao-Meng Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China
| | - Lihua Peng
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China
| | - Yuyi Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China
| | - Fan Ma
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China
| | - Yu Tao
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China
| | - Xiao Liang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China.
| | - Jin-Long Yang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China.
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8
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Lin L. The expanding universe of contractile injection systems in bacteria. Curr Opin Microbiol 2024; 79:102465. [PMID: 38520915 DOI: 10.1016/j.mib.2024.102465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
Contractile injection systems (CISs) are phage tail-like machineries found in a wide range of bacteria. They are often deployed by bacteria to translocate effectors into the extracellular space or into target cells. CISs are classified into intracellular type VI secretion systems (T6SSs) and extracellular CIS (eCISs). eCISs are assembled in cytoplasm and released into the extracellular milieu upon cell lysis, while T6SSs are the secretion systems widespread among Gram-negative bacteria and actively translocate effectors into the environment or into the adjacent cell, without lysis of T6SS-producing cells. Recently, several noncanonical CISs that exhibit distinct characteristics have been discovered. This review will provide an overview on these noncanonical CISs and their unique features, as well as new advances in reprogramming CISs for therapeutic protein delivery.
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Affiliation(s)
- Lin Lin
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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9
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Nagakubo T, Nishiyama T, Yamamoto T, Nomura N, Toyofuku M. Contractile injection systems facilitate sporogenic differentiation of Streptomyces davawensis through the action of a phage tapemeasure protein-related effector. Nat Commun 2024; 15:4442. [PMID: 38789435 PMCID: PMC11126660 DOI: 10.1038/s41467-024-48834-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Contractile injection systems (CISs) are prokaryotic phage tail-like nanostructures loading effector proteins that mediate various biological processes. Although CIS functions have been diversified through evolution and hold the great potential as protein delivery systems, the functional characterisation of CISs and their effectors is currently limited to a few CIS lineages. Here, we show that the CISs of Streptomyces davawensis belong to a unique group of bacterial CISs distributed across distant phyla and facilitate sporogenic differentiation of this bacterium. CIS loss results in decreases in extracellular DNA release, biomass accumulation, and spore formation in S. davawensis. CISs load an effector, which is a remote homolog of phage tapemeasure proteins, and its C-terminal domain has endonuclease activity responsible for the CIS-associated phenotypes. Our findings illustrate that CISs can contribute to the reproduction of bacteria through the action of the effector and suggest an evolutionary link between CIS effectors and viral cargos.
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Affiliation(s)
- Toshiki Nagakubo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan.
| | - Tatsuya Nishiyama
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Chiyoda, Japan
| | - Tatsuya Yamamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
- Life Science Center for Survival Dynamics, University of Tsukuba, Tsukuba, Japan
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan.
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Hu XM, Peng L, Wu J, Wu G, Liang X, Yang JL. Bacterial c-di-GMP signaling gene affects mussel larval metamorphosis through outer membrane vesicles and lipopolysaccharides. NPJ Biofilms Microbiomes 2024; 10:38. [PMID: 38575604 PMCID: PMC10994910 DOI: 10.1038/s41522-024-00508-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
Biofilms serve as crucial cues for settlement and metamorphosis in marine invertebrates. Within bacterial systems, c-di-GMP functions as a pivotal signaling molecule regulating both biofilm formation and dispersion. However, the molecular mechanism of how c-di-GMP modulates biofilm-induced larval metamorphosis remains elusive. Our study reveals that the deletion of a c-di-GMP related gene in Pseudoalteromonas marina led to an increase in the level of bacterial c-di-GMP by knockout technique, and the mutant strain had an enhanced ability to produce more outer membrane vesicles (OMVs) and lipopolysaccharides (LPS). The mutant biofilms had higher induction activity for larval metamorphosis in mussels Mytilus coruscus, and OMVs play a major role in the induction activity. We further explored the function of LPS in OMVs. Extracted LPS induced high larval metamorphosis rate, and LPS content were subject to c-di-GMP and LPS-biosynthesis gene. Thus, we postulate that the impact of c-di-GMP on biofilm-induced metamorphosis is mediated through OMVs and LPS.
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Affiliation(s)
- Xiao-Meng Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China
| | - Lihua Peng
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China
| | - Jingxian Wu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China
| | - Guanju Wu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China
| | - Xiao Liang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China.
| | - Jin-Long Yang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai, 201306, China.
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11
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Yang Z, Zhang L, Zhang W, Tian X, Lai W, Lin D, Feng Y, Jiang W, Zhang Z, Zhang Z. Identification of the principal neuropeptide MIP and its action pathway in larval settlement of the echiuran worm Urechis unicinctus. BMC Genomics 2024; 25:337. [PMID: 38641568 PMCID: PMC11027379 DOI: 10.1186/s12864-024-10228-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/15/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Larval settlement and metamorphosis represent critical events in the life history of marine benthic animals. Myoinhibitory peptide (MIP) plays a pivotal role in larval settlement of marine invertebrates. However, the molecular mechanisms of MIP involved in this process are not well understood. RESULTS In this study, we evaluated the effects of thirteen MIP mature peptides on triggering the larval settlement of Urechis unicinctus (Xenopneusta, Urechidae), and determined that MIP2 was the principal neuropeptide. Transcriptomic analysis was employed to identify differentially expressed genes (DEGs) between the MIP2-treated larvae and normal early-segmentation larvae. Both cAMP and calcium signaling pathways were enriched in the DEGs of the MIP2-treated larvae, and two neuropeptide receptor genes (Spr, Fmrfar) were up-regulated in the MIP2-treated larvae. The activation of the SPR-cAMP pathway by MIP2 was experimentally validated in HEK293T cells. Furthermore, fourteen cilia-related genes, including Tctex1d2, Cfap45, Ift43, Ift74, Ift22, Cav1 and Mns1, etc. exhibited down-regulated expression in the MIP2-treated larvae. Whole-mount in situ hybridization identified two selected ciliary genes, Tctex1d2 and Cfap45, were specially expressed in circumoral ciliary cells of the early-segmentation larvae. Knocking down Tctex1d2 mRNA levels by in vivo RNA interference significantly increased the larval settlement rate. CONCLUSION Our findings suggest that MIP2 inhibits the function of the cilia-related genes, such as Tctex1d2, through the SPR-cAMP-PKA pathway, thereby inducing larval settlement in U. unicinctus. The study contributes important data to the understanding of neuropeptide regulation in larval settlement.
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Affiliation(s)
- Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya, China
| | - Long Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya, China
| | - Wenqing Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya, China
| | - Xinhua Tian
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya, China
| | - Wenyuan Lai
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Dawei Lin
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya, China
| | - Yuxin Feng
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya, China
| | - Wenwen Jiang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya, China
| | - Zhengrui Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
| | - Zhifeng Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya, China.
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
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12
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Feldmüller M, Ericson CF, Afanasyev P, Lien YW, Weiss GL, Wollweber F, Schoof M, Hurst M, Pilhofer M. Stepwise assembly and release of Tc toxins from Yersinia entomophaga. Nat Microbiol 2024; 9:405-420. [PMID: 38316932 PMCID: PMC10847046 DOI: 10.1038/s41564-024-01611-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Tc toxins are virulence factors of bacterial pathogens. Although their structure and intoxication mechanism are well understood, it remains elusive where this large macromolecular complex is assembled and how it is released. Here we show by an integrative multiscale imaging approach that Yersinia entomophaga Tc (YenTc) toxin components are expressed only in a subpopulation of cells that are 'primed' with several other potential virulence factors, including filaments of the protease M66/StcE. A phage-like lysis cassette is required for YenTc release; however, before resulting in complete cell lysis, the lysis cassette generates intermediate 'ghost' cells, which may serve as assembly compartments and become packed with assembled YenTc holotoxins. We hypothesize that this stepwise mechanism evolved to minimize the number of cells that need to be killed. The occurrence of similar lysis cassettes in diverse organisms indicates a conserved mechanism for Tc toxin release that may apply to other extracellular macromolecular machines.
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Affiliation(s)
- Miki Feldmüller
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Charles F Ericson
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | | | - Yun-Wei Lien
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Gregor L Weiss
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Florian Wollweber
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Marion Schoof
- Bio-Protection Research Centre, Lincoln University, Lincoln, Christchurch, New Zealand
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Christchurch, New Zealand
| | - Mark Hurst
- Bio-Protection Research Centre, Lincoln University, Lincoln, Christchurch, New Zealand
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Christchurch, New Zealand
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland.
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13
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Sonani RR, Palmer LK, Esteves NC, Horton AA, Sebastian AL, Kelly RJ, Wang F, Kreutzberger MAB, Russell WK, Leiman PG, Scharf BE, Egelman EH. An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano. Nat Commun 2024; 15:756. [PMID: 38272938 PMCID: PMC10811340 DOI: 10.1038/s41467-024-44959-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, contraction of an external sheath powers the motion of an inner tube through the membrane. The structure, energetics, and mechanism of the machinery imply rigidity and straightness. The contractile tail of Agrobacterium tumefaciens bacteriophage Milano is flexible and bent to varying degrees, which sets it apart from other contractile tail-like systems. Here, we report structures of the Milano tail including the sheath-tube complex, baseplate, and putative receptor-binding proteins. The flexible-to-rigid transformation of the Milano tail upon contraction can be explained by unique electrostatic properties of the tail tube and sheath. All components of the Milano tail, including sheath subunits, are crosslinked by disulfides, some of which must be reduced for contraction to occur. The putative receptor-binding complex of Milano contains a tailspike, a tail fiber, and at least two small proteins that form a garland around the distal ends of the tailspikes and tail fibers. Despite being flagellotropic, Milano lacks thread-like tail filaments that can wrap around the flagellum, and is thus likely to employ a different binding mechanism.
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Affiliation(s)
- Ravi R Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Lee K Palmer
- Mass Spectrometry Facility, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Nathaniel C Esteves
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Abigail A Horton
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Amanda L Sebastian
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Rebecca J Kelly
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - William K Russell
- Mass Spectrometry Facility, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA.
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14
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Almeda R, Rist S, Christensen AM, Antoniou E, Parinos C, Olsson M, Young CM. Crude Oil and Its Burnt Residues Induce Metamorphosis in Marine Invertebrates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19304-19315. [PMID: 37963269 DOI: 10.1021/acs.est.3c05194] [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: 11/16/2023]
Abstract
Metamorphosis is a critical process in the life cycle of most marine benthic invertebrates, determining their transition from plankton to benthos. It affects dispersal and settlement and therefore decisively influences the dynamics of marine invertebrate populations. An extended period of metamorphic competence is an adaptive feature of numerous invertebrate species that increases the likelihood of finding a habitat suitable for settlement and survival. We found that crude oil and residues of burnt oil rapidly induce metamorphosis in two different marine invertebrate larvae, a previously unknown sublethal effect of oil pollution. When exposed to environmentally realistic oil concentrations, up to 84% of tested echinoderm larvae responded by undergoing metamorphosis. Similarly, up to 87% of gastropod larvae metamorphosed in response to burnt oil residues. This study demonstrates that crude oil and its burned residues can act as metamorphic inducers in marine planktonic larvae, short-circuiting adaptive metamorphic delay. Future studies on molecular pathways and oil-bacteria-metamorphosis interactions are needed to fully understand the direct or indirect mechanisms of oil-induced metamorphosis in marine invertebrates. With 90% of chronic oiling occurring in coastal areas, this previously undescribed impact of crude oil on planktonic larvae may have global implications for marine invertebrate populations and biodiversity.
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Affiliation(s)
- Rodrigo Almeda
- EOMAR-ECOAQUA, University of Las Palmas de Gran Canaria, 35017 Tafira Baja, Las Palmas, Spain
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby ,Denmark
| | - Sinja Rist
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby ,Denmark
- Oregon Institute of Marine Biology, University of Oregon, Charleston, Oregon 97420,United States
| | - Anette M Christensen
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby ,Denmark
| | - Eleftheria Antoniou
- School of Chemical and Environmental Engineering, Technical University of Crete, 73100 Chania, Greece
- School of Mineral Resources Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Constantine Parinos
- Hellenic Centre for Marine Research (HCMR), Institute of Oceanography, 19013 Anavyssos, Attiki, Greece
| | - Mikael Olsson
- DTU Sustain, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Craig M Young
- Oregon Institute of Marine Biology, University of Oregon, Charleston, Oregon 97420,United States
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15
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Nesbit KT, Shikuma NJ. Future research directions of the model marine tubeworm Hydroides elegans and synthesis of developmental staging of the complete life cycle. Dev Dyn 2023; 252:1391-1400. [PMID: 37227089 PMCID: PMC10674040 DOI: 10.1002/dvdy.628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The biofouling marine tube worm, Hydroides elegans, is an indirect developing polychaete with significance as a model organism for questions in developmental biology and the evolution of host-microbe interactions. However, a complete description of the life cycle from fertilization through sexual maturity remains scattered in the literature, and lacks standardization. RESULTS AND DISCUSSION Here, we present a unified staging scheme synthesizing the major morphological changes that occur during the entire life cycle of the animal. These data represent a complete record of the life cycle, and serve as a foundation for connecting molecular changes with morphology. CONCLUSIONS The present synthesis and associated staging scheme are especially timely as this system gains traction within research communities. Characterizing the Hydroides life cycle is essential for investigating the molecular mechanisms that drive major developmental transitions, like metamorphosis, in response to bacteria.
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Affiliation(s)
- Katherine T. Nesbit
- Molecular Biology Division, San Diego State University, 5500 Campanile Drive, San Diego CA, 92182
| | - Nicholas J. Shikuma
- Molecular Biology Division, San Diego State University, 5500 Campanile Drive, San Diego CA, 92182
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16
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Nadolski EM, Moczek AP. Promises and limits of an agency perspective in evolutionary developmental biology. Evol Dev 2023; 25:371-392. [PMID: 37038309 DOI: 10.1111/ede.12432] [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: 09/20/2022] [Revised: 01/23/2023] [Accepted: 03/02/2023] [Indexed: 04/12/2023]
Abstract
An agent-based perspective in the study of complex systems is well established in diverse disciplines, yet is only beginning to be applied to evolutionary developmental biology. In this essay, we begin by defining agency and associated terminology formally. We then explore the assumptions and predictions of an agency perspective, apply these to select processes and key concept areas relevant to practitioners of evolutionary developmental biology, and consider the potential epistemic roles that an agency perspective might play in evo devo. Throughout, we discuss evidence supportive of agential dynamics in biological systems relevant to evo devo and explore where agency thinking may enrich the explanatory reach of research efforts in evolutionary developmental biology.
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Affiliation(s)
- Erica M Nadolski
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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17
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Heiman CM, Vacheron J, Keel C. Evolutionary and ecological role of extracellular contractile injection systems: from threat to weapon. Front Microbiol 2023; 14:1264877. [PMID: 37886057 PMCID: PMC10598620 DOI: 10.3389/fmicb.2023.1264877] [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: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Contractile injection systems (CISs) are phage tail-related structures that are encoded in many bacterial genomes. These devices encompass the cell-based type VI secretion systems (T6SSs) as well as extracellular CISs (eCISs). The eCISs comprise the R-tailocins produced by various bacterial species as well as related phage tail-like structures such as the antifeeding prophages (Afps) of Serratia entomophila, the Photorhabdus virulence cassettes (PVCs), and the metamorphosis-associated contractile structures (MACs) of Pseudoalteromonas luteoviolacea. These contractile structures are released into the extracellular environment upon suicidal lysis of the producer cell and play important roles in bacterial ecology and evolution. In this review, we specifically portray the eCISs with a focus on the R-tailocins, sketch the history of their discovery and provide insights into their evolution within the bacterial host, their structures and how they are assembled and released. We then highlight ecological and evolutionary roles of eCISs and conceptualize how they can influence and shape bacterial communities. Finally, we point to their potential for biotechnological applications in medicine and agriculture.
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Affiliation(s)
- Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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18
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Murali R, Yu H, Speth DR, Wu F, Metcalfe KS, Crémière A, Laso-Pèrez R, Malmstrom RR, Goudeau D, Woyke T, Hatzenpichler R, Chadwick GL, Connon SA, Orphan VJ. Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea. PLoS Biol 2023; 21:e3002292. [PMID: 37747940 PMCID: PMC10553843 DOI: 10.1371/journal.pbio.3002292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 10/05/2023] [Accepted: 08/08/2023] [Indexed: 09/27/2023] Open
Abstract
Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.
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Affiliation(s)
- Ranjani Murali
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, United States of America
| | - Daan R. Speth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Fabai Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Kyle S. Metcalfe
- Department of Plant and Molecular Biology, University of California, Berkeley. Berkeley, California, United States of America
| | - Antoine Crémière
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
| | - Rafael Laso-Pèrez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Rex R. Malmstrom
- DOE Joint Genome Institute, Department of Energy, Berkeley, California, United States of America
| | - Danielle Goudeau
- DOE Joint Genome Institute, Department of Energy, Berkeley, California, United States of America
| | - Tanja Woyke
- DOE Joint Genome Institute, Department of Energy, Berkeley, California, United States of America
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
- Department of Plant and Molecular Biology, University of California, Berkeley. Berkeley, California, United States of America
| | - Stephanie A. Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
| | - Victoria J. Orphan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
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19
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Alker AT, Farrell MV, Aspiras AE, Dunbar TL, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine bacteria reveals functional insights during bacteria-stimulated metamorphosis. mBio 2023; 14:e0150223. [PMID: 37530556 PMCID: PMC10470607 DOI: 10.1128/mbio.01502-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 08/03/2023] Open
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea, which stimulates the metamorphosis of the model tubeworm, Hydroides elegans. Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for testing the genetic tractability of marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts resulted in the successful conjugation of 12 marine strains from the Alphaproteobacteria and Gammaproteobacteria classes. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with potential implications for environmental restoration and biotechnology. IMPORTANCE Marine Proteobacteria are attractive targets for genetic engineering due to their ability to produce a diversity of bioactive metabolites and their involvement in host-microbe symbioses. Modular cloning toolkits have become a standard for engineering model microbes, such as Escherichia coli, because they enable innumerable mix-and-match DNA assembly and engineering options. However, such modular tools have not yet been applied to most marine bacterial species. In this work, we adapt a modular plasmid toolkit for use in a set of 12 marine bacteria from the Gammaproteobacteria and Alphaproteobacteria classes. We demonstrate the utility of this genetic toolkit by engineering a marine Pseudoalteromonas bacterium to study their association with its host animal Hydroides elegans. This work provides a proof of concept that modular genetic tools can be applied to diverse marine bacteria to address basic science questions and for biotechnology innovations.
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Affiliation(s)
- Amanda T. Alker
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Morgan V. Farrell
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Alpher E. Aspiras
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Tiffany L. Dunbar
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Andriy Fedoriouk
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Jeffrey E. Jones
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Sama R. Mikhail
- Department of Biology, San Diego State University, San Diego, California, USA
| | | | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
| | - Nicholas J. Shikuma
- Department of Biology, San Diego State University, San Diego, California, USA
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20
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Jensen N, Weiland-Bräuer N, Joel S, Chibani CM, Schmitz RA. The Life Cycle of Aurelia aurita Depends on the Presence of a Microbiome in Polyps Prior to Onset of Strobilation. Microbiol Spectr 2023; 11:e0026223. [PMID: 37378516 PMCID: PMC10433978 DOI: 10.1128/spectrum.00262-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Aurelia aurita's intricate life cycle alternates between benthic polyp and pelagic medusa stages. The strobilation process, a critical asexual reproduction mechanism in this jellyfish, is severely compromised in the absence of the natural polyp microbiome, with limited production and release of ephyrae. Yet, the recolonization of sterile polyps with a native polyp microbiome can correct this defect. Here, we investigated the precise timing necessary for recolonization as well as the host-associated molecular processes involved. We deciphered that a natural microbiota had to be present in polyps prior to the onset of strobilation to ensure normal asexual reproduction and a successful polyp-to-medusa transition. Providing the native microbiota to sterile polyps after the onset of strobilation failed to restore the normal strobilation process. The absence of a microbiome was associated with decreased transcription of developmental and strobilation genes as monitored by reverse transcription-quantitative PCR. Transcription of these genes was exclusively observed for native polyps and sterile polyps that were recolonized before the initiation of strobilation. We further propose that direct cell contact between the host and its associated bacteria is required for the normal production of offspring. Overall, our findings indicate that the presence of a native microbiome at the polyp stage prior to the onset of strobilation is essential to ensure a normal polyp-to-medusa transition. IMPORTANCE All multicellular organisms are associated with microorganisms that play fundamental roles in the health and fitness of the host. Notably, the native microbiome of the Cnidarian Aurelia aurita is crucial for the asexual reproduction by strobilation. Sterile polyps display malformed strobilae and a halt of ephyrae release, which is restored by recolonizing sterile polyps with a native microbiota. Despite that, little is known about the microbial impact on the strobilation process's timing and molecular consequences. The present study shows that A. aurita's life cycle depends on the presence of the native microbiome at the polyp stage prior to the onset of strobilation to ensure the polyp-to-medusa transition. Moreover, sterile individuals correlate with reduced transcription levels of developmental and strobilation genes, evidencing the microbiome's impact on strobilation on the molecular level. Transcription of strobilation genes was exclusively detected in native polyps and those recolonized before initiating strobilation, suggesting microbiota-dependent gene regulation.
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Affiliation(s)
- Nadin Jensen
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Nancy Weiland-Bräuer
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Shindhuja Joel
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Cynthia Maria Chibani
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Ruth Anne Schmitz
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
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21
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Ohdera A, Attarwala K, Wu V, Henry R, Laird H, Hofmann DK, Fitt WK, Medina M. Comparative Genomic Insights into Bacterial Induction of Larval Settlement and Metamorphosis in the Upside-Down Jellyfish Cassiopea. mSphere 2023:e0031522. [PMID: 37154768 DOI: 10.1128/msphere.00315-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Bacteria are important mediators of the larval transition from pelagic to benthic environments for marine organisms. Bacteria can therefore dictate species distribution and success of an individual. Despite the importance of marine bacteria to animal ecology, the identity of inductive microbes for many invertebrates are unknown. Here, we report the first successful isolation of bacteria from natural substrates capable of inducing settlement and metamorphosis of the planula larvae stage of a true jellyfish, the upside-down jellyfish Cassiopea xamachana. Inductive bacteria belonged to multiple phyla, with various capacity to induce settlement and metamorphosis. The most inductive isolates belonged to the genus Pseudoalteromonas, a marine bacterium known to induce the pelago-benthic transition in other marine invertebrates. In sequencing the genome of the isolated Pseudoalteromonas and a semiinductive Vibrio, we found biosynthetic pathways previously implicated in larval settlement were absent in Cassiopea inducing taxa. We instead identified other candidate biosynthetic gene clusters involved in larval metamorphosis. These findings could provide hints to the ecological success of C. xamachana compared to sympatric congeneric species within mangrove environments and provide avenues to investigate the evolution of animal-microbe interactions. IMPORTANCE The pelagic to benthic transition for the larvae of many marine invertebrate species are thought to be triggered by microbial cues. The microbial species and exact cue that initiates this transition remains unknown for many animals. Here, we identify two bacterial species, a Pseudoalteromonas and a Vibrio, isolated from natural substrate that induce settlement and metamorphosis of the upside-down jellyfish Cassiopea xamachana. Genomic sequencing revealed both isolates lacked genes known to induce the life history transition in other marine invertebrates. Instead, we identified other gene clusters that may be important for jellyfish settlement and metamorphosis. This study is the first step to identifying the bacterial cue for C. xamachana, an ecologically important species to coastal ecosystems and an emerging model system. Understanding the bacterial cues provides insight into marine invertebrate ecology and evolution of animal-microbe interactions.
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Affiliation(s)
- Aki Ohdera
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
- National Museum of Natural History, Smithsonian Institute, Washington, DC, USA
| | - Khushboo Attarwala
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Victoria Wu
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Rubain Henry
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Henry Laird
- University of Wisconsin, Madison, Wisconsin, USA
| | | | - William K Fitt
- Odum School of Ecology, University of Georgia, Athens, Georgia, USA
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
- Smithsonian Tropical Research Institute, Smithsonian Institute, Washington, DC, USA
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22
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Ericson CF, Pilhofer M. Mix-and-match tools for protein injection into cells. Nature 2023; 616:254-255. [PMID: 36991045 DOI: 10.1038/d41586-023-00847-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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23
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Kreitz J, Friedrich MJ, Guru A, Lash B, Saito M, Macrae RK, Zhang F. Programmable protein delivery with a bacterial contractile injection system. Nature 2023; 616:357-364. [PMID: 36991127 PMCID: PMC10097599 DOI: 10.1038/s41586-023-05870-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/21/2023] [Indexed: 03/31/2023]
Abstract
Endosymbiotic bacteria have evolved intricate delivery systems that enable these organisms to interface with host biology. One example, the extracellular contractile injection systems (eCISs), are syringe-like macromolecular complexes that inject protein payloads into eukaryotic cells by driving a spike through the cellular membrane. Recently, eCISs have been found to target mouse cells1-3, raising the possibility that these systems could be harnessed for therapeutic protein delivery. However, whether eCISs can function in human cells remains unknown, and the mechanism by which these systems recognize target cells is poorly understood. Here we show that target selection by the Photorhabdus virulence cassette (PVC)-an eCIS from the entomopathogenic bacterium Photorhabdus asymbiotica-is mediated by specific recognition of a target receptor by a distal binding element of the PVC tail fibre. Furthermore, using in silico structure-guided engineering of the tail fibre, we show that PVCs can be reprogrammed to target organisms not natively targeted by these systems-including human cells and mice-with efficiencies approaching 100%. Finally, we show that PVCs can load diverse protein payloads, including Cas9, base editors and toxins, and can functionally deliver them into human cells. Our results demonstrate that PVCs are programmable protein delivery devices with possible applications in gene therapy, cancer therapy and biocontrol.
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Affiliation(s)
- Joseph Kreitz
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mirco J Friedrich
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akash Guru
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Blake Lash
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Makoto Saito
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rhiannon K Macrae
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Vladimirov M, Zhang RX, Mak S, Nodwell JR, Davidson AR. A contractile injection system is required for developmentally regulated cell death in Streptomyces coelicolor. Nat Commun 2023; 14:1469. [PMID: 36927736 PMCID: PMC10020575 DOI: 10.1038/s41467-023-37087-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
Diverse bacterial species produce extracellular contractile injection systems (eCISs). Although closely related to contractile phage tails, eCISs can inject toxic proteins into eukaryotic cells. Thus, these systems are commonly viewed as cytotoxic defense mechanisms that are not central to other aspects of bacterial biology. Here, we provide evidence that eCISs appear to participate in the complex developmental process of the bacterium Streptomyces coelicolor. In particular, we show that S. coelicolor produces eCIS particles during its normal growth cycle, and that strains lacking functional eCIS particles exhibit pronounced alterations in their developmental program. Furthermore, eCIS-deficient mutants display reduced levels of cell death and altered morphology during growth in liquid media. Our results suggest that the main role of eCISs in S. coelicolor is to modulate the developmental switch that leads to aerial hyphae formation and sporulation, rather than to attack other species.
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Affiliation(s)
- Maria Vladimirov
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ruo Xi Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Stefanie Mak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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25
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Cytoplasmic contractile injection systems mediate cell death in Streptomyces. Nat Microbiol 2023; 8:711-726. [PMID: 36894633 PMCID: PMC10066040 DOI: 10.1038/s41564-023-01341-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023]
Abstract
Contractile injection systems (CIS) are bacteriophage tail-like structures that mediate bacterial cell-cell interactions. While CIS are highly abundant across diverse bacterial phyla, representative gene clusters in Gram-positive organisms remain poorly studied. Here we characterize a CIS in the Gram-positive multicellular model organism Streptomyces coelicolor and show that, in contrast to most other CIS, S. coelicolor CIS (CISSc) mediate cell death in response to stress and impact cellular development. CISSc are expressed in the cytoplasm of vegetative hyphae and are not released into the medium. Our cryo-electron microscopy structure enabled the engineering of non-contractile and fluorescently tagged CISSc assemblies. Cryo-electron tomography showed that CISSc contraction is linked to reduced cellular integrity. Fluorescence light microscopy furthermore revealed that functional CISSc mediate cell death upon encountering different types of stress. The absence of functional CISSc had an impact on hyphal differentiation and secondary metabolite production. Finally, we identified three putative effector proteins, which when absent, phenocopied other CISSc mutants. Our results provide new functional insights into CIS in Gram-positive organisms and a framework for studying novel intracellular roles, including regulated cell death and life-cycle progression in multicellular bacteria.
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26
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Abstract
Developmental processes in animals are influenced by colonization and/or signaling from microbial symbionts. Here, we show that bacteria from the environment are linked to development of a symbiotic organ that houses a bacterial consortium in female Hawaiian bobtail squid, Euprymna scolopes. In addition to the well-characterized light organ association with the bioluminescent bacterium Vibrio fischeri, female E. scolopes house a simple bacterial community in a reproductive organ, the accessory nidamental gland (ANG). In order to understand the influences of bacteria on ANG development, squid were raised in the laboratory under conditions where exposure to environmental microorganisms was experimentally manipulated. Under conditions where hosts were exposed to depleted environmental bacteria, ANGs were completely absent or stunted, a result independent of the presence of the light organ symbiont V. fischeri. When squid were raised in the laboratory with substrate from the host's natural environment containing the native microbiota, normal ANG development was observed, and the bacterial communities were similar to wild-caught animals. Analysis of the bacterial communities from ANGs and substrates of wild-caught and laboratory-raised animals suggests that certain bacterial groups, namely, the Verrucomicrobia, are linked to ANG development. The ANG community composition was also experimentally manipulated. Squid raised with natural substrate supplemented with a specific ANG bacterial strain, Leisingera sp. JC1, had high proportions of this strain in the ANG, suggesting that once ANG development is initiated, specific strains can be introduced and subsequently colonize the organ. Overall, these data suggest that environmental bacteria are required for development of the ANG in E. scolopes. IMPORTANCE Microbiota have profound effects on animal and plant development. Hosts raised axenically or without symbionts often suffer negative outcomes resulting in developmental defects or reduced organ function. Using defined experimental conditions, we demonstrate that environmental bacteria are required for the formation of a female-specific symbiotic organ in the Hawaiian bobtail squid, Euprymna scolopes. Although nascent tissues from this organ that are involved with bacterial recruitment formed initially, the mature organ failed to develop and was absent or severely reduced in sexually mature animals that were not exposed to microbiota from the host's natural environment. This is the first example of complete organ development relying on exposure to symbiotic bacteria in an animal host. This study broadens the use of E. scolopes as a model organism for studying the influence of beneficial bacteria on animal development.
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27
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Alker AT, Aspiras AE, Dunbar TL, Farrell MV, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526474. [PMID: 36778221 PMCID: PMC9915575 DOI: 10.1101/2023.01.31.526474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea , which stimulates the metamorphosis of the model tubeworm, Hydroides elegans . Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for rapidly creating and iteratively testing genetic tractability by modifying marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts enabled the successful transformation of twelve marine strains across two Proteobacteria classes, four orders and ten genera. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with broader implications for environmental restoration and biotechnology.
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28
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Fine structure and assembly pattern of a minimal myophage Pam3. Proc Natl Acad Sci U S A 2023; 120:e2213727120. [PMID: 36656854 PMCID: PMC9942802 DOI: 10.1073/pnas.2213727120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater Myoviridae cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology.
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29
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Seasonal dynamics of a complex cheilostome bryozoan symbiosis: vertical transfer challenged. Sci Rep 2023; 13:375. [PMID: 36611035 PMCID: PMC9825505 DOI: 10.1038/s41598-022-26251-6] [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: 08/10/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Symbiotic associations are dynamic systems influenced by both intrinsic and extrinsic factors. Here we describe for the first time the developmental and seasonal changes of the funicular bodies in the bryozoan Dendrobeania fruticosa, which are unique temporary organs of cheilostome bryozoans containing prokaryotic symbionts. Histological and ultrastructural studies showed that these organs undergo strong seasonal modification in the White Sea during the ice-free period. Initially (in June) they play a trophic function and support the development of a large population of bacteria. From June to September, both funicular bodies and bacteria show signs of degradation accompanied by development of presumed virus-like particles (VLPs); these self-organize to hollow spheres inside bacteria and are also detected outside of them. Although the destruction of bacteria coincides with the development of VLPs and spheres, the general picture differs considerably from the known instances of bacteriophagy in bryozoans. We broadly discuss potential routes of bacterial infection in Bryozoa and question the hypothesis of vertical transfer, which, although widely accepted in the literature, is contradicted by molecular, morphological and ecological evidence.
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30
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Abstract
The gut epithelia of virtually all animals harbor complex microbial communities that play an important role in maintaining immune and cellular homeostasis. Gut microbiota have evolutionarily adapted to the host gut environment, serving as key regulators of intestinal stem cells to promote a healthy gut barrier and modulate epithelial self-renewal. Disruption of these populations has been associated with inflammatory disorders or cancerous lesions of the intestine. However, the molecular mechanisms controlling gut-microbe interactions are only partially understood due to the high diversity and biologically dynamic nature of these microorganisms. This article reviews the current knowledge on Drosophila gut microbiota and its role in signaling pathways that are crucial for the induction of distinct homeostatic and immune responses. Thanks to the genetic tractability of Drosophila and its cultivable and simple microbiota, this association model offers new efficient tools for investigating the crosstalk between a host and its microbiota while providing a framework for a better understanding of the ecological and evolutionary roles of the microbiome.
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Affiliation(s)
- Ghada Tafesh-Edwards
- Infection and Innate Immunity Laboratory, Department of Biological Sciences, The George Washington University, Washington DC, USA
| | - Ioannis Eleftherianos
- Infection and Innate Immunity Laboratory, Department of Biological Sciences, The George Washington University, Washington DC, USA
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31
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Parish AJ, Rice DW, Tanquary VM, Tennessen JM, Newton ILG. Honey bee symbiont buffers larvae against nutritional stress and supplements lysine. THE ISME JOURNAL 2022; 16:2160-2168. [PMID: 35726020 PMCID: PMC9381588 DOI: 10.1038/s41396-022-01268-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/17/2022] [Accepted: 06/07/2022] [Indexed: 02/07/2023]
Abstract
Honey bees have suffered dramatic losses in recent years, largely due to multiple stressors underpinned by poor nutrition [1]. Nutritional stress especially harms larvae, who mature into workers unable to meet the needs of their colony [2]. In this study, we characterize the metabolic capabilities of a honey bee larvae-associated bacterium, Bombella apis (formerly Parasaccharibacter apium), and its effects on the nutritional resilience of larvae. We found that B. apis is the only bacterium associated with larvae that can withstand the antimicrobial larval diet. Further, we found that B. apis can synthesize all essential amino acids and significantly alters the amino acid content of synthetic larval diet, largely by supplying the essential amino acid lysine. Analyses of gene gain/loss across the phylogeny suggest that four amino acid transporters were gained in recent B. apis ancestors. In addition, the transporter LysE is conserved across all sequenced strains of B. apis. Finally, we tested the impact of B. apis on developing honey bee larvae subjected to nutritional stress and found that larvae supplemented with B. apis are bolstered against mass reduction despite limited nutrition. Together, these data suggest a novel role of B. apis as a nutritional mutualist of honey bee larvae.
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Affiliation(s)
- Audrey J Parish
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Danny W Rice
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Vicki M Tanquary
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Jason M Tennessen
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Irene L G Newton
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
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32
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Discovery of a Novel Inner Membrane-Associated Bacterial Structure Related to the Flagellar Type III Secretion System. J Bacteriol 2022; 204:e0014422. [PMID: 35862756 PMCID: PMC9380563 DOI: 10.1128/jb.00144-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The bacterial flagellar type III secretion system (fT3SS) is a suite of membrane-embedded and cytoplasmic proteins responsible for building the flagellar motility machinery. Homologous nonflagellar (NF-T3SS) proteins form the injectisome machinery that bacteria use to deliver effector proteins into eukaryotic cells, and other family members were recently reported to be involved in the formation of membrane nanotubes. Here, we describe a novel, evolutionarily widespread, hat-shaped structure embedded in the inner membranes of bacteria, of yet-unidentified function, that is present in species containing fT3SS. Mutant analysis suggests a relationship between this novel structure and the fT3SS, but not the NF-T3SS. While the function of this novel structure remains unknown, we hypothesize that either some of the fT3SS proteins assemble within the hat-like structure, perhaps including the fT3SS core complex, or that fT3SS components regulate other proteins that form part of this novel structure. IMPORTANCE The type III secretion system (T3SS) is a fascinating suite of proteins involved in building diverse macromolecular systems, including the bacterial flagellar motility machine, the injectisome machinery that bacteria use to inject effector proteins into host cells, and probably membrane nanotubes which connect bacterial cells. Here, we accidentally discovered a novel inner membrane-associated complex related to the flagellar T3SS. Examining our lab database, which is comprised of more than 40,000 cryo-tomograms of dozens of species, we discovered that this novel structure is both ubiquitous and ancient, being present in highly divergent classes of bacteria. Discovering a novel, widespread structure related to what are among the best-studied molecular machines in bacteria will open new venues for research aiming at understanding the function and evolution of T3SS proteins.
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33
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Rischer M, Guo H, Beemelmanns C. Signalling molecules inducing metamorphosis in marine organisms. Nat Prod Rep 2022; 39:1833-1855. [PMID: 35822257 DOI: 10.1039/d1np00073j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: findings from early 1980s until early 2022Microbial-derived cues of marine biofilms induce settlement and metamorphosis of marine organisms, a process responsible for the emergence of diverse flora and fauna in marine habitats. Although this phenomenon is known for more than 80 years, the research field has only recently gained much momentum. Here, we summarize the currently existing biochemical and microbial knowledge about microbial signalling molecules, con-specific signals, and synthetic compounds that induce or prevent recruitment, settlement, and metamorphosis in invertebrate larvae. We discuss the possible modes of action and conclude with perspectives for future research directions in the field of marine chemical ecology.
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Affiliation(s)
- Maja Rischer
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany.
| | - Huijuan Guo
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany.
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany. .,Biochemistry of Microbial Metabolism, Institute of Biochemistry, Leipzig University, Johannisallee 21-23, Leipzig 04103, Germany
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34
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Abstract
Animal development is an inherently complex process that is regulated by highly conserved genomic networks, and the resulting phenotype may remain plastic in response to environmental signals. Despite development having been studied in a more natural setting for the past few decades, this framework often precludes the role of microbial prokaryotes in these processes. Here, we address how microbial symbioses impact animal development from the onset of gametogenesis through adulthood. We then provide a first assessment of which developmental processes may or may not be influenced by microbial symbioses and, in doing so, provide a holistic view of the budding discipline of developmental symbiosis.
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Affiliation(s)
- Tyler J Carrier
- GEOMAR Helmholtz Centre for Ocean Research, Kiel 24105, Germany.,Zoological Institute, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Thomas C G Bosch
- Zoological Institute, Christian-Albrechts University of Kiel, Kiel 24118, Germany
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35
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George EE, Tashyreva D, Kwong WK, Okamoto N, Horák A, Husnik F, Lukeš J, Keeling PJ. Gene Transfer Agents in Bacterial Endosymbionts of Microbial Eukaryotes. Genome Biol Evol 2022; 14:6615375. [PMID: 35738252 PMCID: PMC9254644 DOI: 10.1093/gbe/evac099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/14/2022] Open
Abstract
Gene transfer agents (GTAs) are virus-like structures that package and transfer prokaryotic DNA from donor to recipient prokaryotic cells. Here, we describe widespread GTA gene clusters in the highly reduced genomes of bacterial endosymbionts from microbial eukaryotes (protists). Homologs of the GTA capsid and portal complexes were initially found to be present in several highly reduced alphaproteobacterial endosymbionts of diplonemid protists (Rickettsiales and Rhodospirillales). Evidence of GTA expression was found in polyA-enriched metatranscriptomes of the diplonemid hosts and their endosymbionts, but due to biases in the polyA-enrichment methods, levels of GTA expression could not be determined. Examining the genomes of closely related bacteria revealed that the pattern of retained GTA head/capsid complexes with missing tail components was common across Rickettsiales and Holosporaceae (Rhodospirillales), all obligate symbionts with a wide variety of eukaryotic hosts. A dN/dS analysis of Rickettsiales and Holosporaceae symbionts revealed that purifying selection is likely the main driver of GTA evolution in symbionts, suggesting they remain functional, but the ecological function of GTAs in bacterial symbionts is unknown. In particular, it is unclear how increasing horizontal gene transfer in small, largely clonal endosymbiont populations can explain GTA retention, and, therefore, the structures may have been repurposed in endosymbionts for host interactions. Either way, their widespread retention and conservation in endosymbionts of diverse eukaryotes suggests an important role in symbiosis.
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Affiliation(s)
- Emma E George
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada
| | - Daria Tashyreva
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Waldan K Kwong
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Instituto Gulbenkian de Ciência, 6, 2780-156 Oeiras, Portugal
| | - Noriko Okamoto
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Hakai Institute, Quadra Island, British Columbia, Canada
| | - Aleš Horák
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.,University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Filip Husnik
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.,University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Patrick J Keeling
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada
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36
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Abstract
Marine biofilms are ubiquitous in the marine environment. These complex microbial communities rapidly respond to environmental changes and encompass hugely diverse microbial structures, functions and metabolisms. Nevertheless, knowledge is limited on the microbial community structures and functions of natural marine biofilms and their influence on global geochemical cycles. Microbial cues, including secondary metabolites and microbial structures, regulate interactions between microorganisms, with their environment and with other benthic organisms, which affects their community succession and metamorphosis. Furthermore, marine biofilms are key mediators of marine biofouling, which greatly affect marine industries. In this Review, we discuss marine biofilm dynamics, including their diversity, abundance and functions. We also highlight knowledge gaps, areas for future research and potential biotechnological applications of marine biofilms.
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37
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Carrier TJ, Maldonado M, Schmittmann L, Pita L, Bosch TCG, Hentschel U. Symbiont transmission in marine sponges: reproduction, development, and metamorphosis. BMC Biol 2022; 20:100. [PMID: 35524305 PMCID: PMC9077847 DOI: 10.1186/s12915-022-01291-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 04/07/2022] [Indexed: 11/10/2022] Open
Abstract
Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission is widespread but not universal, that microbes are vertically transmitted during a select developmental window, and that properties of the developmental microbiome depends on whether a species is a high or low microbial abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships form remains the central and elusive tenet of these developmental symbioses.
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Affiliation(s)
- Tyler J Carrier
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
- Zoological Institute, University of Kiel, Kiel, Germany.
| | - Manuel Maldonado
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | | | - Lucía Pita
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | | | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Zoological Institute, University of Kiel, Kiel, Germany
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38
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Freckelton ML, Nedved BT, Cai YS, Cao S, Turano H, Alegado RA, Hadfield MG. Bacterial lipopolysaccharide induces settlement and metamorphosis in a marine larva. Proc Natl Acad Sci U S A 2022; 119:e2200795119. [PMID: 35467986 PMCID: PMC9651628 DOI: 10.1073/pnas.2200795119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/16/2022] [Indexed: 08/09/2023] Open
Abstract
How larvae of the many phyla of marine invertebrates find places appropriate for settlement, metamorphosis, growth, and reproduction is an enduring question in marine science. Biofilm-induced metamorphosis has been observed in marine invertebrate larvae from nearly every major marine phylum. Despite the widespread nature of this phenomenon, the mechanism of induction remains poorly understood. The serpulid polychaete Hydroides elegans is a well established model for investigating bacteria-induced larval development. A broad range of biofilm bacterial species elicit larval metamorphosis in H. elegans via at least two mechanisms, including outer membrane vesicles (OMVs) and complexes of phage-tail bacteriocins. We investigated the interaction between larvae of H. elegans and the inductive bacterium Cellulophaga lytica, which produces an abundance of OMVs but not phage-tail bacteriocins. We asked whether the OMVs of C. lytica induce larval settlement due to cell membrane components or through delivery of specific cargo. Employing a biochemical structure–function approach with a strong ecological focus, the cells and OMVs produced by C. lytica were interrogated to determine the class of the inductive compounds. Here, we report that larvae of H. elegans are induced to metamorphose by lipopolysaccharide produced by C. lytica. The widespread prevalence of lipopolysaccharide and its associated taxonomic and structural variability suggest it may be a broadly employed cue for bacterially induced larval settlement of marine invertebrates.
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Affiliation(s)
| | - Brian T. Nedved
- Kewalo Marine Laboratory, University of Hawaiʻi, Honolulu, HI 96813
| | - You-Sheng Cai
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawaiʻi at Hilo, Hilo, HI 96720
- Department of Nephrology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People’s Republic of China
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawaiʻi at Hilo, Hilo, HI 96720
| | - Helen Turano
- Department of Oceanography, University of Hawaiʻi Mānoa, Honolulu, HI 96813
| | - Rosanna A. Alegado
- Department of Oceanography, University of Hawaiʻi Mānoa, Honolulu, HI 96813
- Sea Grant College Program, University of Hawaiʻi Mānoa, Honolulu, HI 96813
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Diacylglycerol, PKC and MAPK signaling initiate tubeworm metamorphosis in response to bacteria. Dev Biol 2022; 487:99-109. [DOI: 10.1016/j.ydbio.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 11/21/2022]
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40
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Dong Y, Feng D, Song GL, Su P, Zheng D. The effect of a biofilm-forming bacterium Tenacibaculum mesophilum D-6 on the passive film of stainless steel in the marine environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152909. [PMID: 34998779 DOI: 10.1016/j.scitotenv.2021.152909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/27/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
The microbiologically influenced corrosion of 304 stainless steel in the presence of a marine biofilm-forming bacterium Tenacibaculum mesophilum D-6 was systematically investigated by means of electrochemical techniques and surface analyses to reveal the effect of the selective attachment and adsorption of the biofilms on the passivity breakdown of the stainless steel. It was found that the T. mesophilum D-6 was electroactive and could oxidize low valent cations and metal, facilitating the local dissolution of the passive film and the substrate in the film defects, nearly doubling the surface roughness. The biofilms of T. mesophilum D-6 with mucopolysaccharide secreta and chloride ions tended to preferentially adsorb at the defects of the passive film on the steel, yielding non-homogeneous microbial aggregates and local Cl- enrichment there. The adsorption of the bacteria and chloride ions reduced the thickness of passive film by 23.9%, and generate more active sites for pitting corrosion on the passive film and more semiconducting carrier acceptors in the film. The maximum current density of the 304 SS in the presence of T. mesophilum D-6 was over one order of magnitude higher than that in the sterile medium, and the largest pit was deepened 3 times.
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Affiliation(s)
- Yuqiao Dong
- Center for Marine Materials Corrosion and Protection, College of Materials, Xiamen University, Xiamen 361005, China
| | - Danqing Feng
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Guang-Ling Song
- Center for Marine Materials Corrosion and Protection, College of Materials, Xiamen University, Xiamen 361005, China; Department of Ocean Science and Engineering, Southern University of Science and Technology, China; The University of Queensland, School of Mechanical and Mining Engineering, Division of Materials Engineering, St Lucia, Qld 4072, Australia.
| | - Pei Su
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Dajiang Zheng
- Center for Marine Materials Corrosion and Protection, College of Materials, Xiamen University, Xiamen 361005, China
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41
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Weiss GL, Eisenstein F, Kieninger AK, Xu J, Minas HA, Gerber M, Feldmüller M, Maldener I, Forchhammer K, Pilhofer M. Structure of a thylakoid-anchored contractile injection system in multicellular cyanobacteria. Nat Microbiol 2022; 7:386-396. [PMID: 35165386 PMCID: PMC8894136 DOI: 10.1038/s41564-021-01055-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/20/2021] [Indexed: 01/10/2023]
Abstract
Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 secretion systems (T6SSs) are attached to the cytoplasmic membrane and function upon cell-cell contact. Here, we characterized a CIS in the multicellular cyanobacterium Anabaena, with features distinct from extracellular CISs and T6SSs. Cryo-electron tomography of focused ion beam-milled cells revealed that CISs were anchored in thylakoid membrane stacks, facing the cell periphery. Single particle cryo-electron microscopy showed that this unique in situ localization was mediated by extensions of tail fibre and baseplate components. On stress, cyanobacteria induced the formation of ghost cells, presenting thylakoid-anchored CISs to the environment. Functional assays suggest that these CISs may mediate ghost cell formation and/or interactions of ghost cells with other organisms. Collectively, these data provide a framework for understanding the evolutionary re-engineering of CISs and potential roles of these CISs in cyanobacterial programmed cell death.
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Affiliation(s)
- Gregor L Weiss
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Fabian Eisenstein
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Ann-Katrin Kieninger
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Jingwei Xu
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Hannah A Minas
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Milena Gerber
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Miki Feldmüller
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Iris Maldener
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland.
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Nagakubo T. Biological Functions and Applications of Virus-Related Bacterial Nanoparticles: A Review. Int J Mol Sci 2022; 23:ijms23052595. [PMID: 35269736 PMCID: PMC8910223 DOI: 10.3390/ijms23052595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/25/2022] Open
Abstract
Accumulating evidence suggests that microorganisms produce various nanoparticles that exhibit a variety of biological functions. The structure of these bacterial nanoparticles ranges from membrane vesicles composed of membrane lipids to multicomponent proteinaceous machines. Of bacterial nanoparticles, bacterial phage tail-like nanoparticles, associated with virus-related genes, are found in bacteria from various environments and have diverse functions. Extracellular contractile injection systems (eCISs), a type of bacterial phage tail-like nanostructure, have diverse biological functions that mediate the interactions between the producer bacteria and target eukaryote. Known gram-negative bacterial eCISs can act as protein translocation systems and inject effector proteins that modulate eukaryotic cellular processes by attaching to the target cells. Further investigation of the functions of eCISs will facilitate the application of these nanomachines as nano-sized syringes in the field of nanomedicine and vaccine development. This review summarises the recent progress in elucidating the structures and biological functions of nanoparticles that resemble the tail components of phages that infect bacteria and discusses directions for future research to improve the clinical applicability of virus-related bacterial nanoparticles.
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Affiliation(s)
- Toshiki Nagakubo
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan;
- Microbiology Research Centre for Sustainability (MiCS), University of Tsukuba, Tsukuba 305-8577, Japan
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Xu J, Ericson CF, Lien YW, Rutaganira FUN, Eisenstein F, Feldmüller M, King N, Pilhofer M. Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis. Nat Microbiol 2022; 7:397-410. [PMID: 35165385 PMCID: PMC8894135 DOI: 10.1038/s41564-022-01059-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/05/2022] [Indexed: 12/11/2022]
Abstract
Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell–cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a ‘cap adaptor’ located at the distal end, a ‘plug’ exposed to the tube lumen, and a ‘cage’ formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re−engineering CISs. The characterization of an extracellular contractile injection system (eCIS) from the marine bacterium Algoriphagus machipongonensis (AlgoCIS) reveals structural features linked to the assembly and function of this nanomachine.
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44
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Coral-microbe interactions: their importance to reef function and survival. Emerg Top Life Sci 2022; 6:33-44. [PMID: 35119475 DOI: 10.1042/etls20210229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
Many different microorganisms associate with the coral host in a single entity known as the holobiont, and their interactions with the host contribute to coral health, thereby making them a fundamental part of reef function, survival, and conservation. As corals continue to be susceptible to bleaching due to environmental stress, coral-associated bacteria may have a potential role in alleviating bleaching. This review provides a synthesis of the various roles bacteria have in coral physiology and development, and explores the possibility that changes in the microbiome with environmental stress could have major implications in how corals acclimatize and survive. Recent studies on the interactions between the coral's algal and bacterial symbionts elucidate how bacteria may stabilize algal health and, therefore, mitigate bleaching. A summary of the innovative tools and experiments to examine host-microbe interactions in other cnidarians (a temperate coral, a jellyfish, two anemones, and a freshwater hydroid) is offered in this review to delineate our current knowledge of mechanisms underlying microbial establishment and maintenance in the animal host. A better understanding of these mechanisms may enhance the success of maintaining probiotics long-term in corals as a conservation strategy.
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45
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Tran TD, Ali MA, Lee D, Félix MA, Luallen RJ. Bacterial filamentation as a mechanism for cell-to-cell spread within an animal host. Nat Commun 2022; 13:693. [PMID: 35121734 PMCID: PMC8816909 DOI: 10.1038/s41467-022-28297-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
Intracellular pathogens are challenged with limited space and resources while replicating in a single host cell. Mechanisms for direct invasion of neighboring host cells have been discovered in cell culture, but we lack an understanding of how bacteria directly spread between host cells in vivo. Here, we describe the discovery of intracellular bacteria that use filamentation for spreading between the intestinal epithelial cells of a natural host, the rhabditid nematode Oscheius tipulae. The bacteria, which belong to the new species Bordetella atropi, can infect the nematodes following a fecal-oral route, and reduce host life span and fecundity. Filamentation requires UDP-glucose biosynthesis and sensing, a highly conserved pathway that is used by other bacteria to detect rich conditions and inhibit cell division. Our results indicate that B. atropi uses a pathway that normally regulates bacterial cell size to trigger filamentation inside host cells, thus facilitating cell-to-cell dissemination. Some intracellular pathogens can directly invade neighboring host cells in cell culture, but it is unclear how this happens in vivo. Here, Tran et al. describe an intracellular bacterium that forms filaments to spread between intestinal epithelial cells in its host nematode, in a process regulated by a conserved nutrient-sensing pathway.
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46
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Selberherr E, Penz T, König L, Conrady B, Siegl A, Horn M, Schmitz-Esser S. The life cycle-dependent transcriptional profile of the obligate intracellular amoeba symbiont Amoebophilus asiaticus. FEMS Microbiol Ecol 2022; 98:6499296. [PMID: 34999767 PMCID: PMC8831229 DOI: 10.1093/femsec/fiac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Free-living amoebae often harbor obligate intracellular bacterial symbionts. Amoebophilus (A.) asiaticus is a representative of a lineage of amoeba symbionts in the phylum Bacteroidota. Here, we analyse the transcriptome of A. asiaticus strain 5a2 at four time points during its infection cycle and replication within the Acanthamoeba host using RNA sequencing. Our results reveal a dynamic transcriptional landscape throughout different A. asiaticus life cycle stages. Many intracellular bacteria and pathogens utilize eukaryotic-like proteins (ELPs) for host cell interaction and the A. asiaticus 5a2 genome shows a particularly high abundance of ELPs. We show the expression of all genes encoding ELPs and found many ELPs to be differentially expressed. At the replicative stage of A. asiaticus, ankyrin repeat proteins and tetratricopeptide/Sel1-like repeat proteins were upregulated. At the later time points, high expression levels of a type 6 secretion system that likely prepares for a new infection cycle after lysing its host, were found. This study reveals comprehensive insights into the intracellular lifestyle of A. asiaticus and highlights candidate genes for host cell interaction. The results from this study have implications for other intracellular bacteria such as other amoeba-associated bacteria and the arthropod symbionts Cardinium forming the sister lineage of A. asiaticus.
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Affiliation(s)
- E Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - T Penz
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,current affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - L König
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - B Conrady
- Department of Veterinary and Animal Science, University of Copenhagen, Denmark
| | - A Siegl
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - M Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - S Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, USA
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47
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Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, Boetius A, Orphan VJ. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol 2022; 20:e3001508. [PMID: 34986141 PMCID: PMC9012536 DOI: 10.1371/journal.pbio.3001508] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/15/2022] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor. A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.
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Affiliation(s)
- Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andy O. Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Daan R. Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Danielle Goudeau
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex Malmstrom
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, British Columbia, Canada
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
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Abstract
Protein toxins secreted by prokaryotes have been found to affect the pathogenicity of pathogens or directly mediate antagonistic interactions between prokaryotes. PAAR proteins are important carriers of toxic effectors and are located at the forefront of either the type VI secretion system (T6SS) or the extracellular contractile injection system (eCIS). This study systematically investigated PAAR homologues and related toxic effectors. We found that PAAR homologues were divided into 8 types and 16 subtypes and distributed in 23.1% of bacterial genomes and 7.8% of archaeal genomes. PAAR proteins of all types fold into a highly similar conical structure, even from relatively diverse underlying sequences. PAAR homologues associated with different secretion systems display a mixed phylogenetic relationship, indicating that PAAR proteins from such a subtype can be assembled on either a T6SS or an eCIS. More than 1,300 PAAR-related toxic effector genes were identified; one PAAR subtype can be associated with toxins of over 40 families, and toxins from one family can be associated with more than 10 PAAR subtypes. A large-scale comparison of Earth Microbiome Project data and prokaryotic genomes revealed that prokaryotes encoding PAAR genes are widely present in diverse environments worldwide, and taxa encoding multiple PAAR gene copies exhibit a wider distribution in environments than other taxa. Overall, our studies highlighted that PAAR proteins are versatile clips loaded with antimicrobial toxin bullets for secretion weapons (T6SS and eCIS), greatly enriching the weapon arsenal of prokaryotes, which, often together with VgrG, help prokaryotes fight for survival advantages in crowded environments. IMPORTANCE Infectious diseases caused by microbial pathogens are severe threats to human health and economic development. To respond to these threats, it is necessary to understand how microorganisms survive in and adapt to complex environments. Microorganic toxins, which are widely distributed in nature, are the key weapons in life domain interactions. PAAR proteins are important carriers of prokaryotic toxic effectors. We reveal the versatility of PAAR proteins between secretory systems and the massive diversity of toxic effectors carried by PAAR proteins, which helps prokaryotes enrich their arsenal and expand their ability to attack their neighbors. A large number of PAAR homologues and related toxic effectors enhance the survival competitiveness of prokaryotic populations. In conclusion, our work provides an example for large-scale analysis of the global distribution and ecological functions of prokaryotic functional genes.
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49
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Nagakubo T, Yamamoto T, Asamizu S, Toyofuku M, Nomura N, Onaka H. Phage tail-like nanostructures affect microbial interactions between Streptomyces and fungi. Sci Rep 2021; 11:20116. [PMID: 34635733 PMCID: PMC8505568 DOI: 10.1038/s41598-021-99490-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular contractile injection systems (eCISs) are structurally similar to headless phages and are versatile nanomachines conserved among diverse classes of bacteria. Herein, Streptomyces species, which comprise filamentous Gram-positive bacteria and are ubiquitous in soil, were shown to produce Streptomyces phage tail-like particles (SLPs) from eCIS-related genes that are widely conserved among Streptomyces species. In some Streptomyces species, these eCIS-related genes are regulated by a key regulatory gene, which is essential for Streptomyces life cycle and is involved in morphological differentiation and antibiotic production. Deletion mutants of S. lividans of the eCIS-related genes appeared phenotypically normal in terms of morphological differentiation and antibiotic production, suggesting that SLPs are involved in other aspects of Streptomyces life cycle. Using co-culture method, we found that colonies of SLP-deficient mutants of S. lividans were more severely invaded by fungi, including Saccharomyces cerevisiae and Schizosaccharomyces pombe. In addition, microscopic and transcriptional analyses demonstrated that SLP expression was elevated upon co-culture with the fungi. In contrast, co-culture with Bacillus subtilis markedly decreased SLP expression and increased antibiotic production. Our findings demonstrate that in Streptomyces, eCIS-related genes affect microbial competition, and the patterns of SLP expression can differ depending on the competitor species.
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Affiliation(s)
- Toshiki Nagakubo
- Graduate School of Agricultural and Life Sciences, Department of Biotechnology, The University of Tokyo, Tokyo, Japan.
| | - Tatsuya Yamamoto
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, Department of Biotechnology, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Masanori Toyofuku
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, Department of Biotechnology, The University of Tokyo, Tokyo, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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50
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Zhang Y, Zhang Y, Yang Q, Ling J, Tang X, Zhang W, Dong J. Complete genome sequence of Metabacillus sp. cB07, a bacterium inducing settlement and metamorphosis of coral larvae. Mar Genomics 2021; 60:100877. [PMID: 34627550 DOI: 10.1016/j.margen.2021.100877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 10/21/2022]
Abstract
The settlement and metamorphosis of coral larvae are the bottleneck of coral recruitment. They are critical for the extension of coral population, which is the basis of the restoration of degraded coral reef ecosystem. In this study, we described the genomic characteristics of Metabacillus sp. cB07, which can efficiently induce larvae settlement and metamorphosis of coral Pocillopora damicornis. This function is first reported in the genus Metabacillus. Strain cB07 was isolated from the coral Porites pukoensis, and comprised one circular chromosome of 4,148,576 bp (44.14 mol% G + C content), containing 4148 protein coding sequences. To explore the potential mechanism of coral larvae settlement and metamorphosis induced by Metabacillus sp. cB07, we predicted that numerous genes related to the bacterial inductive ability. The genome of Metabacillus sp. cB07 will be helpful for further insights into the mechanism of bacterial induction of settlement and metamorphosis of coral larvae.
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Affiliation(s)
- Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences & Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanying Zhang
- Ocean School, Yantai University, Yantai 264005, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xiaoyu Tang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences & Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya 572000, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China.
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