1
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Moreland RT, Zhang S, Barreira SN, Ryan JF, Baxevanis AD. An AI-generated proteome-scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi. Proteomics 2024; 24:e2300397. [PMID: 38329168 PMCID: PMC11296891 DOI: 10.1002/pmic.202300397] [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: 10/19/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
This Dataset Brief describes the computational prediction of protein structures for the ctenophore Mnemiopsis leidyi. Here, we report the proteome-scale generation of 15,333 protein structure predictions using AlphaFold, as well as an updated implementation of publicly available search, manipulation, and visualization tools for these protein structure predictions through the Mnemiopsis Genome Project Portal (https://research.nhgri.nih.gov/mnemiopsis). The utility of these predictions is demonstrated by highlighting comparisons to experimentally determined structures for the light-sensitive protein mnemiopsin 1 and the ionotropic glutamate receptor (iGluR). The application of these novel protein structure prediction methods will serve to further position non-bilaterian species such as Mnemiopsis as powerful model systems for the study of early animal evolution and human health.
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Affiliation(s)
- R. Travis Moreland
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Suiyuan Zhang
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Sofia N. Barreira
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Joseph F. Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, U.S.A
| | - Andreas D. Baxevanis
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, U.S.A
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2
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Vargas A, DeBiasse M, Dykes L, Edgar A, Hayes T, Groso D, Babonis L, Martindale M, Ryan J. Morphological and dietary changes encoded in the genome of Beroe ovata, a ctenophore-eating ctenophore. NAR Genom Bioinform 2024; 6:lqae072. [PMID: 38895105 PMCID: PMC11184263 DOI: 10.1093/nargab/lqae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/03/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
As the sister group to all other animals, ctenophores (comb jellies) are important for understanding the emergence and diversification of numerous animal traits. Efforts to explore the evolutionary processes that promoted diversification within Ctenophora are hindered by undersampling genomic diversity within this clade. To address this gap, we present the sequence, assembly and initial annotation of the genome of Beroe ovata. Beroe possess unique morphology, behavior, ecology and development. Unlike their generalist carnivorous kin, beroid ctenophores feed exclusively on other ctenophores. Accordingly, our analyses revealed a loss of chitinase, an enzyme critical for the digestion of most non-ctenophore prey, but superfluous for ctenophorivores. Broadly, our genomic analysis revealed that extensive gene loss and changes in gene regulation have shaped the unique biology of B. ovata. Despite the gene losses in B. ovata, our phylogenetic analyses on photosensitive opsins and several early developmental regulatory genes show that these genes are conserved in B. ovata. This additional sampling contributes to a more complete reconstruction of the ctenophore ancestor and points to the need for extensive comparisons within this ancient and diverse clade of animals. To promote further exploration of these data, we present BovaDB (http://ryanlab.whitney.ufl.edu/bovadb/), a portal for the B. ovata genome.
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Affiliation(s)
- Alexandra M Vargas
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, Radford University, Radford, VA 24142, USA
| | - Lana L Dykes
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - T Danielle Hayes
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Daniel J Groso
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Leslie S Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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3
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Boohar RT, Vandepas LE, Traylor-Knowles N, Browne WE. Phylogenetic and Protein Structure Analyses Provide Insight into the Evolution and Diversification of the CD36 Domain "Apex" among Scavenger Receptor Class B Proteins across Eukarya. Genome Biol Evol 2023; 15:evad218. [PMID: 38035778 PMCID: PMC10715195 DOI: 10.1093/gbe/evad218] [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: 12/27/2022] [Revised: 11/07/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023] Open
Abstract
The cluster of differentiation 36 (CD36) domain defines the characteristic ectodomain associated with class B scavenger receptor (SR-B) proteins. In bilaterians, SR-Bs play critical roles in diverse biological processes including innate immunity functions such as pathogen recognition and apoptotic cell clearance, as well as metabolic sensing associated with fatty acid uptake and cholesterol transport. Although previous studies suggest this protein family is ancient, SR-B diversity across Eukarya has not been robustly characterized. We analyzed SR-B homologs identified from the genomes and transcriptomes of 165 diverse eukaryotic species. The presence of highly conserved amino acid motifs across major eukaryotic supergroups supports the presence of a SR-B homolog in the last eukaryotic common ancestor. Our comparative analyses of SR-B protein structure identify the retention of a canonical asymmetric beta barrel tertiary structure within the CD36 ectodomain across Eukarya. We also identify multiple instances of independent lineage-specific sequence expansions in the apex region of the CD36 ectodomain-a region functionally associated with ligand-sensing. We hypothesize that a combination of both sequence expansion and structural variation in the CD36 apex region may reflect the evolution of SR-B ligand-sensing specificity between diverse eukaryotic clades.
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Affiliation(s)
- Reed T Boohar
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Lauren E Vandepas
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida, USA
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, Florida, USA
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4
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Ladewig L, Gloy L, Langfeldt D, Pinnow N, Weiland-Bräuer N, Schmitz RA. Antimicrobial Peptides Originating from Expression Libraries of Aurelia aurita and Mnemiopsis leidyi Prevent Biofilm Formation of Opportunistic Pathogens. Microorganisms 2023; 11:2184. [PMID: 37764028 PMCID: PMC10537229 DOI: 10.3390/microorganisms11092184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
The demand for novel antimicrobial compounds is rapidly growing due to the rising appearance of antibiotic resistance in bacteria; accordingly, alternative approaches are urgently needed. Antimicrobial peptides (AMPs) are promising, since they are a naturally occurring part of the innate immune system and display remarkable broad-spectrum activity and high selectivity against various microbes. Marine invertebrates are a primary resource of natural AMPs. Consequently, cDNA expression (EST) libraries from the Cnidarian moon jellyfish Aurelia aurita and the Ctenophore comb jelly Mnemiopsis leidyi were constructed in Escherichia coli. Cell-free size-fractionated cell extracts (<3 kDa) of the two libraries (each with 29,952 clones) were consecutively screened for peptides preventing the biofilm formation of opportunistic pathogens using the crystal violet assay. The 3 kDa fraction of ten individual clones demonstrated promising biofilm-preventing activities against Klebsiella oxytoca and Staphylococcus epidermidis. Sequencing the respective activity-conferring inserts allowed for the identification of small ORFs encoding peptides (10-22 aa), which were subsequently chemically synthesized to validate their inhibitory potential. Although the peptides are likely artificial products from a random translation of EST inserts, the biofilm-preventing effects against K. oxytoca, Pseudomonas aeruginosa, S. epidermidis, and S. aureus were verified for five synthetic peptides in a concentration-dependent manner, with peptide BiP_Aa_5 showing the strongest effects. The impact of BiP_Aa_2, BiP_Aa_5, and BiP_Aa_6 on the dynamic biofilm formation of K. oxytoca was further validated in microfluidic flow cells, demonstrating a significant reduction in biofilm thickness and volume by BiP_Aa_2 and BiP_Aa_5. Overall, the structural characteristics of the marine invertebrate-derived AMPs, their physicochemical properties, and their promising antibiofilm effects highlight them as attractive candidates for discovering new antimicrobials.
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Affiliation(s)
- Lisa Ladewig
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Leon Gloy
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Daniela Langfeldt
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
- Institute of Clinical Molecular Biology (IKMB), Kiel University, Am Botanischen Garten 11, 24118 Kiel, Germany
| | - Nicole Pinnow
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Nancy Weiland-Bräuer
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Ruth A. Schmitz
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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5
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Rouhana L, Edgar A, Hugosson F, Dountcheva V, Martindale MQ, Ryan JF. Cytoplasmic Polyadenylation Is an Ancestral Hallmark of Early Development in Animals. Mol Biol Evol 2023; 40:msad137. [PMID: 37288606 PMCID: PMC10284499 DOI: 10.1093/molbev/msad137] [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: 12/02/2022] [Revised: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 06/09/2023] Open
Abstract
Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3'-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element-Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in nonanimal lineages. Whether cytoplasmic polyadenylation is present in non-bilaterian animals (i.e., sponges, ctenophores, placozoans, and cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs, and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life.
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Affiliation(s)
- Labib Rouhana
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Fredrik Hugosson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Valeria Dountcheva
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
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6
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Jokura K, Sato Y, Shiba K, Inaba K. Two distinct compartments of a ctenophore comb plate provide structural and functional integrity for the motility of giant multicilia. Curr Biol 2022; 32:5144-5152.e6. [PMID: 36272402 DOI: 10.1016/j.cub.2022.09.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/12/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022]
Abstract
Comb plates are large ciliary structures uniquely seen in comb jellies (ctenophores).1,2,3 A comb plate is constructed from tens of thousands of cilia that are bundled together by structures called compartmenting lamellae (CLs).4,5,6 We previously reported the first component of the CL, CTENO64, and found that it was specifically found in ctenophores and was essential for the determination of ciliary orientation.3 However, CTENO64 is localized only in the proximal region of the CL; therefore, the molecular architecture of the CL over the entire length of a comb plate has not been elucidated. Here, we identified a second CL component, CTENO189. This ctenophore-specific protein was present in the distal region of comb plates, with a localization clearly segregated from CTENO64. Knockdown of the CTENO189 gene using morpholino antisense oligonucleotides resulted in complete loss of CLs in the distal region of comb plates but did not affect the formation of comb plates or the orientation of each cilium. However, the hexagonal distribution of cilia was disarranged, and the metachronal coordination of comb plates along a comb row was lost in the CTENO189 morphants. The morphant comb plate showed asymmetric ciliary-type movement in normal seawater, and in a high-viscosity solution, it could not maintain the normal waveforms but showed a symmetric flagellar-type movement. Our findings demonstrated two distinct compartments of a comb plate: the proximal CL as the building foundation that rigidly fixes the ciliary orientation, and the distal CL that reinforces the elastic connection among cilia to overcome the hydrodynamic drag of giant multiciliary plates.
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Affiliation(s)
- Kei Jokura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Yu Sato
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Kogiku Shiba
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan.
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7
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Multigenerational laboratory culture of pelagic ctenophores and CRISPR-Cas9 genome editing in the lobate Mnemiopsis leidyi. Nat Protoc 2022; 17:1868-1900. [PMID: 35697825 DOI: 10.1038/s41596-022-00702-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 03/23/2022] [Indexed: 11/08/2022]
Abstract
Despite long-standing experimental interest in ctenophores due to their unique biology, ecological influence and evolutionary status, previous work has largely been constrained by the periodic seasonal availability of wild-caught animals and difficulty in reliably closing the life cycle. To address this problem, we have developed straightforward protocols that can be easily implemented to establish long-term multigenerational cultures for biological experimentation in the laboratory. In this protocol, we describe the continuous culture of the Atlantic lobate ctenophore Mnemiopsis leidyi. A rapid 3-week egg-to-egg generation time makes Mnemiopsis suitable for a wide range of experimental genetic, cellular, embryological, physiological, developmental, ecological and evolutionary studies. We provide recommendations for general husbandry to close the life cycle of Mnemiopsis in the laboratory, including feeding requirements, light-induced spawning, collection of embryos and rearing of juveniles to adults. These protocols have been successfully applied to maintain long-term multigenerational cultures of several species of pelagic ctenophores, and can be utilized by laboratories lacking easy access to the ocean. We also provide protocols for targeted genome editing via microinjection with CRISPR-Cas9 that can be completed within ~2 weeks, including single-guide RNA synthesis, early embryo microinjection, phenotype assessment and sequence validation of genome edits. These protocols provide a foundation for using Mnemiopsis as a model organism for functional genomic analyses in ctenophores.
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8
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Simonetti B, Guo Q, Giménez-Andrés M, Chen KE, Moody ERR, Evans AJ, Chandra M, Danson CM, Williams TA, Collins BM, Cullen PJ. SNX27-Retromer directly binds ESCPE-1 to transfer cargo proteins during endosomal recycling. PLoS Biol 2022; 20:e3001601. [PMID: 35417450 PMCID: PMC9038204 DOI: 10.1371/journal.pbio.3001601] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/25/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022] Open
Abstract
Coat complexes coordinate cargo recognition through cargo adaptors with biogenesis of transport carriers during integral membrane protein trafficking. Here, we combine biochemical, structural, and cellular analyses to establish the mechanistic basis through which SNX27-Retromer, a major endosomal cargo adaptor, couples to the membrane remodeling endosomal SNX-BAR sorting complex for promoting exit 1 (ESCPE-1). In showing that the SNX27 FERM (4.1/ezrin/radixin/moesin) domain directly binds acidic-Asp-Leu-Phe (aDLF) motifs in the SNX1/SNX2 subunits of ESCPE-1, we propose a handover model where SNX27-Retromer captured cargo proteins are transferred into ESCPE-1 transport carriers to promote endosome-to-plasma membrane recycling. By revealing that assembly of the SNX27:Retromer:ESCPE-1 coat evolved in a stepwise manner during early metazoan evolution, likely reflecting the increasing complexity of endosome-to-plasma membrane recycling from the ancestral opisthokont to modern animals, we provide further evidence of the functional diversification of yeast pentameric Retromer in the recycling of hundreds of integral membrane proteins in metazoans.
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Affiliation(s)
- Boris Simonetti
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Qian Guo
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Manuel Giménez-Andrés
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Edmund R. R. Moody
- School of Biological Sciences, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Ashley J. Evans
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Mintu Chandra
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Chris M. Danson
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Peter J. Cullen
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
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9
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Neuropeptide repertoire and 3D anatomy of the ctenophore nervous system. Curr Biol 2021; 31:5274-5285.e6. [PMID: 34587474 DOI: 10.1016/j.cub.2021.09.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 07/20/2021] [Accepted: 09/02/2021] [Indexed: 11/24/2022]
Abstract
Ctenophores are gelatinous marine animals famous for locomotion by ciliary combs. Due to the uncertainties of the phylogenetic placement of ctenophores and the absence of some key bilaterian neuronal genes, it has been hypothesized that their neurons evolved independently. Additionally, recent whole-body, single-cell RNA sequencing (scRNA-seq) analysis failed to identify ctenophore neurons using any of the known neuronal molecular markers. To reveal the molecular machinery of ctenophore neurons, we have characterized the neuropeptide repertoire of the ctenophore Mnemiopsis leidyi. Using the machine learning NeuroPID tool, we predicted 129 new putative neuropeptide precursors. Sixteen of them were localized to the subepithelial nerve net (SNN), sensory aboral organ (AO), and epithelial sensory cells (ESCs), providing evidence that they are neuropeptide precursors. Four of these putative neuropeptides had a behavioral effect and increased the animals' swimming speed. Intriguingly, these putative neuropeptides finally allowed us to identify neuronal cell types in single-cell transcriptomic data and reveal the molecular identity of ctenophore neurons. High-resolution electron microscopy and 3D reconstructions of the nerve net underlying the comb plates confirmed a more than 100-year-old hypothesis of anastomoses between neurites of the same cell in ctenophores and revealed that they occur through a continuous membrane. Our work demonstrates the unique ultrastructure of the peptidergic nerve net and a rich neuropeptide repertoire of ctenophores, supporting the hypothesis that the first nervous system(s) evolved as nets of peptidergic cells.
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10
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Presnell JS, Browne WE. Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing. Development 2021; 148:272041. [PMID: 34373891 DOI: 10.1242/dev.199771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022]
Abstract
The Krüppel-like factor (Klf) gene family encodes transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation and development in bilaterians. Although Klf genes have been shown to specify functionally various cell types in non-bilaterian animals, their role in early-diverging animal lineages has not been assessed. Thus, the ancestral activity of these transcription factors in animal development is not well understood. The ctenophore Mnemiopsis leidyi has emerged as an important non-bilaterian model system for understanding early animal evolution. Here, we characterize the expression and functional role of Klf genes during M. leidyi embryogenesis. Zygotic Klf gene function was assessed with both CRISPR/Cas9-mediated genome editing and splice-blocking morpholino oligonucleotide knockdown approaches. Abrogation of zygotic Klf expression during M. leidyi embryogenesis resulted in abnormal development of several organs, including the pharynx, tentacle bulbs and apical organ. Our data suggest an ancient role for Klf genes in regulating endodermal patterning, possibly through regulation of cell proliferation.
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Affiliation(s)
- Jason S Presnell
- Department of Biology, University of Miami, Cox Science Center, 1301 Memorial Drive, Miami, FL 33146, USA
| | - William E Browne
- Department of Biology, University of Miami, Cox Science Center, 1301 Memorial Drive, Miami, FL 33146, USA
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11
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Edgar A, Mitchell DG, Martindale MQ. Whole-Body Regeneration in the Lobate Ctenophore Mnemiopsis leidyi. Genes (Basel) 2021; 12:genes12060867. [PMID: 34198839 PMCID: PMC8228598 DOI: 10.3390/genes12060867] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 01/28/2023] Open
Abstract
Ctenophores (a.k.a. comb jellies) are one of the earliest branching extant metazoan phyla. Adult regenerative ability varies greatly within the group, with platyctenes undergoing both sexual and asexual reproduction by fission while others in the genus Beroe having completely lost the ability to replace missing body parts. We focus on the unique regenerative aspects of the lobate ctenophore, Mnemiopsis leidyi, which has become a popular model for its rapid wound healing and tissue replacement, optical clarity, and sequenced genome. M. leidyi’s highly mosaic, stereotyped development has been leveraged to reveal the polar coordinate system that directs whole-body regeneration as well as lineage restriction of replacement cells in various regenerating organs. Several cell signaling pathways known to function in regeneration in other animals are absent from the ctenophore’s genome. Further research will either reveal ancient principles of the regenerative process common to all animals or reveal novel solutions to the stability of cell fates and whole-body regeneration.
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12
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Moreland RT, Nguyen AD, Ryan JF, Baxevanis AD. The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5834871. [PMID: 32386298 DOI: 10.1093/database/baaa029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 03/22/2020] [Indexed: 11/13/2022]
Abstract
Following the completion of the genome sequencing and gene prediction of Mnemiopsis leidyi, a lobate ctenophore that is native to the coastal waters of the western Atlantic Ocean, we developed and implemented the Mnemiopsis Genome Project Portal (MGP Portal), a comprehensive Web-based data portal for navigating the genome sequence and gene annotations. In the years following the first release of the MGP Portal, it has become evident that the inclusion of data from significant published studies on Mnemiopsis has been critical to its adoption as the centralized resource for this emerging model organism. With this most recent update, the Portal has significantly expanded to include in situ images, temporal developmental expression profiles and single-cell expression data. Recent enhancements also include implementations of an updated BLAST interface, new graphical visualization tools and updates to gene pages that integrate all new data types. Database URL: https://research.nhgri.nih.gov/mnemiopsis/.
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Affiliation(s)
- R Travis Moreland
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anh-Dao Nguyen
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA.,Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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13
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Traylor-Knowles N, Vandepas LE, Browne WE. Still Enigmatic: Innate Immunity in the Ctenophore Mnemiopsis leidyi. Integr Comp Biol 2020; 59:811-818. [PMID: 31251332 DOI: 10.1093/icb/icz116] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Innate immunity is an ancient physiological response critical for protecting metazoans from invading pathogens. It is the primary pathogen defense mechanism among invertebrates. While innate immunity has been studied extensively in diverse invertebrate taxa, including mollusks, crustaceans, and cnidarians, this system has not been well characterized in ctenophores. The ctenophores comprise an exclusively marine, non-bilaterian lineage that diverged early during metazoan diversification. The phylogenetic position of ctenophore lineage suggests that characterization of the ctenophore innate immune system will reveal important features associated with the early evolution of the metazoan innate immune system. Here, we review current understanding of the ctenophore immune repertoire and identify innate immunity genes recovered from three ctenophore species. We also isolate and characterize Mnemiopsis leidyi cells that display macrophage-like behavior when challenged with bacteria. Our results indicate that ctenophores possess cells capable of phagocytosing microbes and that two distantly related ctenophores, M. leidyi and Hormiphora californiensis, possess many candidate innate immunity proteins.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, FL 33149, USA
| | - Lauren E Vandepas
- Benaroya Research Institute, 1201 9th Avenue, Seattle, WA 98101, USA.,Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - William E Browne
- Department of Biology, University of Miami, Cox Science Building, 1301 Memorial Drive, Miami, FL 33146, USA
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14
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Hammond MJ, Wang T, Cummins SF. Characterisation of early metazoan secretion through associated signal peptidase complex subunits, prohormone convertases and carboxypeptidases of the marine sponge (Amphimedon queenslandica). PLoS One 2019; 14:e0225227. [PMID: 31714927 PMCID: PMC6850559 DOI: 10.1371/journal.pone.0225227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/30/2019] [Indexed: 01/31/2023] Open
Abstract
Efficient communication between cells requires the ability to process precursor proteins into their mature and biologically active forms, prior to secretion into the extracellular space. Eukaryotic cells achieve this via a suite of enzymes that involve a signal peptidase complex, prohormone convertases and carboxypeptidases. Using genome and transcriptome data of the demosponge Amphimedon queenslandica, a universal ancestor to metazoan multicellularity, we endeavour to bridge the evolution of precursor processing machinery from single-celled eukaryotic ancestors through to the complex multicellular organisms that compromise Metazoa. The precursor processing repertoire as defined in this study of A. queenslandica consists of 3 defined signal peptidase subunits, 6 prohormone convertases and 1 carboxypeptidase, with 2 putative duplicates identified for signal peptidase complex subunits. Analysis of their gene expression levels throughout the sponge development enabled us to predict levels of activity. Some A. queenslandica precursor processing components belong to established functional clades while others were identified as having novel, yet to be discovered roles. These findings have clarified the presence of precursor processing machinery in the poriferans, showing the necessary machinery for the removal of precursor sequences, a critical post-translational modification required by multicellular organisms, and further sets a foundation towards understanding the molecular mechanism for ancient protein processing.
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Affiliation(s)
- Michael J. Hammond
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore Dc, Queensland, Australia
| | - Tianfang Wang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore Dc, Queensland, Australia
| | - Scott F. Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore Dc, Queensland, Australia
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15
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Bastin BR, Schneider SQ. Taxon-specific expansion and loss of tektins inform metazoan ciliary diversity. BMC Evol Biol 2019; 19:40. [PMID: 30704394 PMCID: PMC6357514 DOI: 10.1186/s12862-019-1360-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 01/14/2019] [Indexed: 11/15/2022] Open
Abstract
Background Cilia and flagella are complex cellular structures thought to have first evolved in a last ciliated eukaryotic ancestor due to the conserved 9 + 2 microtubule doublet structure of the axoneme and associated proteins. The Tektin family of coiled-coil domain containing proteins was previously identified in cilia of organisms as diverse as green algae and sea urchin. While studies have shown that some Tektins are necessary for ciliary function, there has been no comprehensive phylogenetic survey of tektin genes. To fill this gap, we sampled tektin sequences broadly among metazoan and unicellular lineages in order to determine how the tektin gene complements evolved in over 100 different extant species. Results Using Bayesian and Maximum Likelihood analyses, we have ascertained with high confidence that all metazoan tektins arose from a single ancestral tektin gene in the last common ancestor of metazoans and choanoflagellates. Gene duplications gave rise to two tektin genes in the metazoan ancestor, and a subsequent expansion to three and four tektin genes in early bilaterian ancestors. While all four tektin genes remained highly conserved in most deuterostome and spiralian species surveyed, most tektin genes in ecdysozoans are highly derived with extensive gene loss in several lineages including nematodes and some crustaceans. In addition, while tektin-1, − 2, and − 4 have remained as single copy genes in most lineages, tektin-3/5 has been duplicated independently several times, notably at the base of the spiralian, vertebrate and hymenopteran (Ecdysozoa) clades. Conclusions We provide a solid description of tektin evolution supporting one, two, three, and four ancestral tektin genes in a holozoan, metazoan, bilaterian, and nephrozoan ancestor, respectively. The isolated presence of tektin in a cryptophyte and a chlorophyte branch invokes events of horizontal gene transfer, and that the last common ciliated eukaryotic ancestor lacked a tektin gene. Reconstructing the evolutionary history of the tektin complement in each extant metazoan species enabled us to pinpoint lineage specific expansions and losses. Our analysis will help to direct future studies on Tektin function, and how gain and loss of tektin genes might have contributed to the evolution of various types of cilia and flagella. Electronic supplementary material The online version of this article (10.1186/s12862-019-1360-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin R Bastin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Stephan Q Schneider
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA. .,Present Address: Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan.
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16
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Hernandez AM, Ryan JF. Horizontally transferred genes in the ctenophore Mnemiopsis leidyi. PeerJ 2018; 6:e5067. [PMID: 29922518 PMCID: PMC6005172 DOI: 10.7717/peerj.5067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
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17
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Abstract
In bilaterian animals the 3′ ends of microRNAs (miRNAs) are frequently modified by tailing and trimming. These modifications affect miRNA-mediated gene regulation by modulating miRNA stability. Here, we analyzed data from three nonbilaterian animals: two cnidarians (Nematostella vectensis and Hydra magnipapillata) and one poriferan (Amphimedon queenslandica). Our analysis revealed that nonbilaterian miRNAs frequently undergo modifications like the bilaterian counterparts: the majority are expressed as different length isoforms and frequent modifications of the 3′ end by mono U or mono A tailing are observed. Moreover, as the factors regulating miRNA modifications are largely uncharacterized in nonbilaterian animal phyla, in present study, we investigated the evolution of 3′ terminal uridylyl transferases (TUTases) that are known to involved in miRNA 3′ nontemplated modifications in Bilateria. Phylogenetic analysis on TUTases showed that TUTase1 and TUTase6 are a result of duplication in bilaterians and that TUTase7 and TUTase4 are the result of a vertebrate-specific duplication. We also find an unexpected number of Drosophila-specific gene duplications and domain losses in most of the investigated gene families. Overall, our findings shed new light on the evolutionary history of TUTases in Metazoa, as they reveal that this core set of enzymes already existed in the last common ancestor of all animals and was probably involved in modifying small RNAs in a similar fashion to its present activity in bilaterians.
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Affiliation(s)
- Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
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18
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Davidson PL, Koch BJ, Schnitzler CE, Henry JQ, Martindale MQ, Baxevanis AD, Browne WE. The maternal-zygotic transition and zygotic activation of the Mnemiopsis leidyi genome occurs within the first three cleavage cycles. Mol Reprod Dev 2017; 84:1218-1229. [PMID: 29068507 DOI: 10.1002/mrd.22926] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/03/2017] [Indexed: 12/20/2022]
Abstract
The maternal-zygotic transition (MZT) describes the developmental reprogramming of gene expression marked by the degradation of maternally supplied gene products and activation of the zygotic genome. While the timing and duration of the MZT vary among taxa, little is known about early-stage transcriptional dynamics in the non-bilaterian phylum Ctenophora. We sought to better understand the extent of maternal mRNA loading and subsequent differential transcript abundance during the earliest stages of development by performing comprehensive RNA-sequencing-based analyses of mRNA abundance in single- and eight-cell stage embryos in the lobate ctenophore Mnemiopsis leidyi. We found 1,908 contigs with significant differential abundance between single- and eight-cell stages, of which 1,208 contigs were more abundant at the single-cell stage and 700 contigs were more abundant at the eight-cell stage. Of the differentially abundant contigs, 267 were exclusively present in the eight-cell samples, providing strong evidence that both the MZT and zygotic genome activation (ZGA) have commenced by the eight-cell stage. Many highly abundant transcripts encode genes involved in molecular mechanisms critical to the MZT, such as maternal transcript degradation, serine/threonine kinase activity, and chromatin remodeling. Our results suggest that chromosomal restructuring, which is critical to ZGA and the initiation of transcriptional regulation necessary for normal development, begins by the third cleavage within 1.5 hr post-fertilization in M. leidyi.
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Affiliation(s)
| | - Bernard J Koch
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Christine E Schnitzler
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, Florida.,Department of Biology, University of Florida, Gainesville, Florida
| | - Jonathan Q Henry
- Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois
| | - Mark Q Martindale
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, Florida.,Department of Biology, University of Florida, Gainesville, Florida
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, Florida
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19
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Sasson DA, Ryan JF. The sex lives of ctenophores: the influence of light, body size, and self-fertilization on the reproductive output of the sea walnut, Mnemiopsis leidyi. PeerJ 2016; 4:e1846. [PMID: 27042395 PMCID: PMC4811168 DOI: 10.7717/peerj.1846] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/03/2016] [Indexed: 12/31/2022] Open
Abstract
Ctenophores (comb jellies) are emerging as important animals for investigating fundamental questions across numerous branches of biology (e.g., evodevo, neuroscience and biogeography). A few ctenophore species including, most notably, Mnemiopsis leidyi, are considered as invasive species, adding to the significance of studying ctenophore ecology. Despite the growing interest in ctenophore biology, relatively little is known about their reproduction. Like most ctenophores, M. leidyi is a simultaneous hermaphrodite capable of self-fertilization. In this study, we assess the influence of light on spawning, the effect of body size on spawning likelihood and reproductive output, and the cost of self-fertilization on egg viability in M. leidyi. Our results suggest that M. leidyi spawning is more strongly influenced by circadian rhythms than specific light cues and that body size significantly impacts spawning and reproductive output. Mnemiopsis leidyi adults that spawned alone produced a lower percentage of viable embryos versus those that spawned in pairs, suggesting that self-fertilization may be costly in this species. These results provide insight into the reproductive ecology of M. leidyi and provide a fundamental resource for researchers working with them in the laboratory.
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Affiliation(s)
- Daniel A Sasson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, United States of America; Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, United States of America; Department of Biology, University of Florida, Gainesville, Florida, United States of America
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20
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Gaiti F, Fernandez-Valverde SL, Nakanishi N, Calcino AD, Yanai I, Tanurdzic M, Degnan BM. Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity. Mol Biol Evol 2015; 32:2367-82. [PMID: 25976353 PMCID: PMC4540969 DOI: 10.1093/molbev/msv117] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are important developmental regulators in bilaterian animals. A correlation has been claimed between the lncRNA repertoire expansion and morphological complexity in vertebrate evolution. However, this claim has not been tested by examining morphologically simple animals. Here, we undertake a systematic investigation of lncRNAs in the demosponge Amphimedon queenslandica, a morphologically simple, early-branching metazoan. We combine RNA-Seq data across multiple developmental stages of Amphimedon with a filtering pipeline to conservatively predict 2,935 lncRNAs. These include intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, long intergenic nonprotein coding RNAs, and precursors for small RNAs. Sponge lncRNAs are remarkably similar to their bilaterian counterparts in being relatively short with few exons and having low primary sequence conservation relative to protein-coding genes. As in bilaterians, a majority of sponge lncRNAs exhibit typical hallmarks of regulatory molecules, including high temporal specificity and dynamic developmental expression. Specific lncRNA expression profiles correlate tightly with conserved protein-coding genes likely involved in a range of developmental and physiological processes, such as the Wnt signaling pathway. Although the majority of Amphimedon lncRNAs appears to be taxonomically restricted with no identifiable orthologs, we find a few cases of conservation between demosponges in lncRNAs that are antisense to coding sequences. Based on the high similarity in the structure, organization, and dynamic expression of sponge lncRNAs to their bilaterian counterparts, we propose that these noncoding RNAs are an ancient feature of the metazoan genome. These results are consistent with lncRNAs regulating the development of animals, regardless of their level of morphological complexity.
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Affiliation(s)
- Federico Gaiti
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | | | - Nagayasu Nakanishi
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Andrew D Calcino
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Itai Yanai
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Milos Tanurdzic
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
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