1
|
Melo Clavijo J, Drews F, Pirritano M, Simon M, Salhab A, Donath A, Frankenbach S, Serôdio J, Bleidißel S, Preisfeld A, Christa G. The complete mitochondrial genome of the photosymbiotic sea slug Berghia stephanieae (Valdés, 2005) (Gastropoda, Nudibranchia). Mitochondrial DNA B Resour 2021; 6:2281-2284. [PMID: 34291161 PMCID: PMC8279152 DOI: 10.1080/23802359.2021.1914211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Berghia stephanieae (Nudibranchia, Cladobranchia) is a photosymbiotic sea slug that feeds exclusively on sea anemones from the genus Exaiptasia. It then specifically incorporates dinoflagellates belonging to the Symbiodiniaceae obtained from their prey. Here, we present the complete mitochondrial genome sequence of B. stephanieae combining Oxford Nanopore long read and Illumina short-read sequencing data. The mitochondrial genome has a total length of 14,786 bp, it contains the 13 protein-encoding genes, 23 tRNAs, and two rRNAs and is similar to other nudibranchs except for the presence of a duplicated tRNA-Ser 1.
Collapse
Affiliation(s)
- Jenny Melo Clavijo
- Bergische Universität Wuppertal, Fakultät für Mathematik und Naturwissenschaften, Zoologie und Biologiedidaktik, Wuppertal, Germany
| | - Franziska Drews
- Bergische Universität Wuppertal, Fakultät für Mathematik und Naturwissenschaften, Chemie und Biologie, Molekulare Zellbiologie und Mikrobiologie, Wuppertal, Germany
| | - Marcello Pirritano
- Bergische Universität Wuppertal, Fakultät für Mathematik und Naturwissenschaften, Chemie und Biologie, Molekulare Zellbiologie und Mikrobiologie, Wuppertal, Germany
| | - Martin Simon
- Bergische Universität Wuppertal, Fakultät für Mathematik und Naturwissenschaften, Chemie und Biologie, Molekulare Zellbiologie und Mikrobiologie, Wuppertal, Germany
| | | | - Alexander Donath
- Zoologisches Forschungsinstitut und Museum Alexander Koenig, Bonn, Germany
| | - Silja Frankenbach
- Department of Biology and CESAM, Centre for Environmental and Marine Studies, University of Aveiro, Aveiro, Portugal
| | - João Serôdio
- Department of Biology and CESAM, Centre for Environmental and Marine Studies, University of Aveiro, Aveiro, Portugal
| | - Sabrina Bleidißel
- Bergische Universität Wuppertal, Fakultät für Mathematik und Naturwissenschaften, Zoologie und Biologiedidaktik, Wuppertal, Germany
| | - Angelika Preisfeld
- Bergische Universität Wuppertal, Fakultät für Mathematik und Naturwissenschaften, Zoologie und Biologiedidaktik, Wuppertal, Germany
| | - Gregor Christa
- Bergische Universität Wuppertal, Fakultät für Mathematik und Naturwissenschaften, Zoologie und Biologiedidaktik, Wuppertal, Germany
| |
Collapse
|
2
|
Torres JP, Lin Z, Winter JM, Krug PJ, Schmidt EW. Animal biosynthesis of complex polyketides in a photosynthetic partnership. Nat Commun 2020; 11:2882. [PMID: 32513940 PMCID: PMC7280274 DOI: 10.1038/s41467-020-16376-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/29/2020] [Indexed: 11/09/2022] Open
Abstract
Complex polyketides are typically associated with microbial metabolism. Here, we report that animals also make complex, microbe-like polyketides. We show there is a widespread branch of fatty acid synthase- (FAS)-like polyketide synthase (PKS) proteins, which sacoglossan animals use to synthesize complex products. The purified sacogolassan protein EcPKS1 uses only methylmalonyl-CoA as a substrate, otherwise unknown in animal lipid metabolism. Sacoglossans are sea slugs, some of which eat algae, digesting the cells but maintaining functional chloroplasts. Here, we provide evidence that polyketides support this unusual photosynthetic partnership. The FAS-like PKS family represents an uncharacterized branch of polyketide and fatty acid metabolism, encoding a large diversity of biomedically relevant animal enzymes and chemicals awaiting discovery. The biochemical characterization of an intact animal polyketide biosynthetic enzyme opens the door to understanding the immense untapped metabolic potential of metazoans. Complex polyketides are usually produced by microbes, whereas the origin of polyketides found in animals remained unknown. This study shows that sacoglossan animals, such as sea slugs, employ fatty acid synthase-like proteins to produce microbe-like polyketides.
Collapse
Affiliation(s)
- Joshua P Torres
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jaclyn M Winter
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA.
| |
Collapse
|
3
|
Ganley JG, Derbyshire ER. Linking Genes to Molecules in Eukaryotic Sources: An Endeavor to Expand Our Biosynthetic Repertoire. Molecules 2020; 25:E625. [PMID: 32023950 PMCID: PMC7036892 DOI: 10.3390/molecules25030625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
The discovery of natural products continues to interest chemists and biologists for their utility in medicine as well as facilitating our understanding of signaling, pathogenesis, and evolution. Despite an attenuation in the discovery rate of new molecules, the current genomics and transcriptomics revolution has illuminated the untapped biosynthetic potential of many diverse organisms. Today, natural product discovery can be driven by biosynthetic gene cluster (BGC) analysis, which is capable of predicting enzymes that catalyze novel reactions and organisms that synthesize new chemical structures. This approach has been particularly effective in mining bacterial and fungal genomes where it has facilitated the discovery of new molecules, increased the understanding of metabolite assembly, and in some instances uncovered enzymes with intriguing synthetic utility. While relatively less is known about the biosynthetic potential of non-fungal eukaryotes, there is compelling evidence to suggest many encode biosynthetic enzymes that produce molecules with unique bioactivities. In this review, we highlight how the advances in genomics and transcriptomics have aided natural product discovery in sources from eukaryotic lineages. We summarize work that has successfully connected genes to previously identified molecules and how advancing these techniques can lead to genetics-guided discovery of novel chemical structures and reactions distributed throughout the tree of life. Ultimately, we discuss the advantage of increasing the known biosynthetic space to ease access to complex natural and non-natural small molecules.
Collapse
Affiliation(s)
- Jack G Ganley
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0346, USA
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0346, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
| |
Collapse
|
4
|
Yang T, Xu G, Gu B, Shi Y, Mzuka HL, Shen H. The Complete Mitochondrial Genome Sequences of the Philomycus bilineatus (Stylommatophora: Philomycidae) and Phylogenetic Analysis. Genes (Basel) 2019; 10:E198. [PMID: 30841657 PMCID: PMC6471268 DOI: 10.3390/genes10030198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 01/22/2023] Open
Abstract
The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (A + T-rich region). There were 15 overlap locations and 18 intergenic spacer regions found throughout the mitogenome of P. bilineatus. The A + T content in the mitogenome was 72.11%. All PCGs used a standard ATN as a start codon, with the exception of cytochrome c oxidase 1 (cox1) and ATP synthase F0 subunit 8 (atp8) with TTG and GTG. Additionally, TAA or TAG was identified as the typical stop codon. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except for trnS1 (AGC), trnS2 (TCA), and trnK (TTT). A phylogenetic analysis with another 37 species of gastropods was performed using Bayesian inference, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that P. bilineatus shares a close ancestry with Meghimatium bilineatum. It seems more appropriate to reclassify it as Arionoidea rather than Limacoidea, as previously thought. Our research may provide a new meaningful insight into the evolution of P. bilineatus.
Collapse
Affiliation(s)
- Tiezhu Yang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Guolyu Xu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Bingning Gu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Yanmei Shi
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Hellen Lucas Mzuka
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Heding Shen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| |
Collapse
|
5
|
Vieira GA, Prosdocimi F. Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data. PeerJ 2019; 7:e6271. [PMID: 30697483 PMCID: PMC6348091 DOI: 10.7717/peerj.6271] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/10/2018] [Indexed: 11/20/2022] Open
Abstract
The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the "no budget mitogenomics" approach ideal for comprehensive molecular studies, especially for subsampled taxa.
Collapse
Affiliation(s)
- Gabriel A. Vieira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Francisco Prosdocimi
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|