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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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Bonacolta AM, Connelly MT, M Rosales S, Del Campo J, Traylor-Knowles N. The starlet sea anemone, Nematostella vectensis, possesses body region-specific bacterial associations with spirochetes dominating the capitulum. FEMS Microbiol Lett 2021; 368:6070651. [PMID: 33417693 DOI: 10.1093/femsle/fnab002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Sampling of different body regions can reveal highly specialized bacterial associations within the holobiont and facilitate identification of core microbial symbionts that would otherwise be overlooked by bulk sampling methods. Here, we characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphology into three distinct microhabitats. This sampling design allowed us to uncover a capitulum-specific dominance of spirochetes within N. vectensis. Bacteria from the family Spirochaetaceae made up 66% of the community in the capitulum, while only representing 1.2% and 0.1% of the communities in the mesenteries and physa, respectively. A phylogenetic analysis of the predominant spirochete sequence recovered from N. vectensis showed a close relation to spirochetes previously recovered from wild N. vectensis. These sequences clustered closer to the recently described genus Oceanispirochaeta, rather than Spirochaeta perfilievii, supporting them as members of this clade. This suggests a prevalent and yet uncharacterized association between N. vectensis and spirochetes from the order Spirochaetales.
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Affiliation(s)
- Anthony M Bonacolta
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Michael T Connelly
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Stephanie M Rosales
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA.,Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, FL 33149, USA
| | - Javier Del Campo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
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Har JY, Helbig T, Lim JH, Fernando SC, Reitzel AM, Penn K, Thompson JR. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression. Front Microbiol 2015; 6:818. [PMID: 26388838 PMCID: PMC4557100 DOI: 10.3389/fmicb.2015.00818] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/27/2015] [Indexed: 01/08/2023] Open
Abstract
We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing <85% identity with cultivated strains, and two γ-Proteobacterial ribotypes sharing >99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat.
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Affiliation(s)
- Jia Y Har
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Tim Helbig
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Ju H Lim
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Samodha C Fernando
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte Charlotte, NC, USA
| | - Kevin Penn
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Janelle R Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
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Maxwell EK, Schnitzler CE, Havlak P, Putnam NH, Nguyen AD, Moreland RT, Baxevanis AD. Evolutionary profiling reveals the heterogeneous origins of classes of human disease genes: implications for modeling disease genetics in animals. BMC Evol Biol 2014; 14:212. [PMID: 25281000 PMCID: PMC4219131 DOI: 10.1186/s12862-014-0212-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/25/2014] [Indexed: 12/17/2022] Open
Abstract
Background The recent expansion of whole-genome sequence data available from diverse animal lineages provides an opportunity to investigate the evolutionary origins of specific classes of human disease genes. Previous studies have observed that human disease genes are of particularly ancient origin. While this suggests that many animal species have the potential to serve as feasible models for research on genes responsible for human disease, it is unclear whether this pattern has meaningful implications and whether it prevails for every class of human disease. Results We used a comparative genomics approach encompassing a broad phylogenetic range of animals with sequenced genomes to determine the evolutionary patterns exhibited by human genes associated with different classes of disease. Our results support previous claims that most human disease genes are of ancient origin but, more importantly, we also demonstrate that several specific disease classes have a significantly large proportion of genes that emerged relatively recently within the metazoans and/or vertebrates. An independent assessment of the synonymous to non-synonymous substitution rates of human disease genes found in mammals reveals that disease classes that arose more recently also display unexpected rates of purifying selection between their mammalian and human counterparts. Conclusions Our results reveal the heterogeneity underlying the evolutionary origins of (and selective pressures on) different classes of human disease genes. For example, some disease gene classes appear to be of uncommonly recent (i.e., vertebrate-specific) origin and, as a whole, have been evolving at a faster rate within mammals than the majority of disease classes having more ancient origins. The novel patterns that we have identified may provide new insight into cases where studies using traditional animal models were unable to produce results that translated to humans. Conversely, we note that the larger set of disease classes do have ancient origins, suggesting that many non-traditional animal models have the potential to be useful for studying many human disease genes. Taken together, these findings emphasize why model organism selection should be done on a disease-by-disease basis, with evolutionary profiles in mind. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0212-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evan K Maxwell
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research, National Institutes of Health, Bethesda, MD, 20892, USA. .,Bioinformatics Program, Boston University, Boston, MA, 02215, USA.
| | - Christine E Schnitzler
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Paul Havlak
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, 77005, USA. .,Biomedical Informatics Core, College of Medicine, Texas A&M Health Science Center, Houston, Texas, 77030, USA.
| | - Nicholas H Putnam
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, 77005, USA.
| | - Anh-Dao Nguyen
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - R Travis Moreland
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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Tarrant AM, Gilmore TD, Reitzel AM, Levy O, Technau U, Martindale MQ. Current directions and future perspectives from the third Nematostella research conference. ZOOLOGY 2014; 118:135-40. [PMID: 25450665 DOI: 10.1016/j.zool.2014.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 12/16/2022]
Abstract
The third Nematostella vectensis Research Conference took place in December 2013 in Eilat, Israel, as a satellite to the 8th International Conference on Coelenterate Biology. The starlet sea anemone, N. vectensis, has emerged as a powerful cnidarian model, in large part due to the extensive genomic and transcriptomic resources and molecular approaches that are becoming available for Nematostella, which were the focus of several presentations. In addition, research was presented highlighting the broader utility of this species for studies of development, circadian rhythms, signal transduction, and gene-environment interactions.
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Affiliation(s)
- Ann M Tarrant
- Biology Department, Woods Hole Oceanographic Institution, 45 Water Street, Woods Hole, MA 02543, USA.
| | - Thomas D Gilmore
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Adam M Reitzel
- Department of Biological Sciences, The University of North Carolina at Charlotte, Woodward Hall 245, Charlotte, NC 28223, USA
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
| | - Ulrich Technau
- Department of Molecular Evolution and Development, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL 32136, USA
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Collecting, rearing, spawning and inducing regeneration of the starlet sea anemone, Nematostella vectensis. Nat Protoc 2013; 8:916-23. [PMID: 23579780 DOI: 10.1038/nprot.2013.044] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Over the past 20 years, the starlet sea anemone, Nematostella vectensis, a small estuarine animal, has emerged as a powerful model system for field and laboratory studies of development, evolution, genomics, molecular biology and toxicology. Here we describe how to collect Nematostella, culture it through its entire sexual life cycle and induce regeneration for the production of clonal stocks. In less than 1 h at a suitable field site, a researcher on foot can collect hundreds of individual anemones. In a few months, it is possible to establish a laboratory colony that will be reliable in generating hundreds or thousands of fertilized eggs on a roughly weekly schedule. By inducing regeneration roughly every 2 weeks, in less than 6 months, one can establish a clonal stock consisting of hundreds of genetically identical anemones. These results can be achieved very inexpensively and without specialized equipment.
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Stefanik DJ, Wolenski FS, Friedman LE, Gilmore TD, Finnerty JR. Isolation of DNA, RNA and protein from the starlet sea anemone Nematostella vectensis. Nat Protoc 2013; 8:892-9. [PMID: 23579778 DOI: 10.1038/nprot.2012.151] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Among marine invertebrates, the starlet sea anemone Nematostella vectensis has emerged as an important laboratory model system. One advantage of working with this species relative to many other marine invertebrates is the ease of isolating relatively pure DNA, RNA and protein. Nematostella can be raised at high densities, under clean culture conditions, and it lacks integumentary or skeletal structures that can impede the recovery of DNA, RNA or protein. Here we describe methods used in our lab to isolate DNA, RNA and protein from Nematostella embryos, larvae and adults. The methods described here are less expensive than commercial kits and are more easily scalable to larger tissue amounts. Preparation of DNA can be completed in ∼7 h, RNA preparation in ∼1.5 h and protein preparation in ∼1 h.
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Affiliation(s)
- Derek J Stefanik
- Department of Biology, Boston University, Boston, Massachusetts, USA
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