1
|
Salisbury JP, Sîrbulescu RF, Moran BM, Auclair JR, Zupanc GKH, Agar JN. The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation. BMC Genomics 2015; 16:166. [PMID: 25879418 PMCID: PMC4424500 DOI: 10.1186/s12864-015-1354-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background The brown ghost knifefish (Apteronotus leptorhynchus) is a weakly electric teleost fish of particular interest as a versatile model system for a variety of research areas in neuroscience and biology. The comprehensive information available on the neurophysiology and neuroanatomy of this organism has enabled significant advances in such areas as the study of the neural basis of behavior, the development of adult-born neurons in the central nervous system and their involvement in the regeneration of nervous tissue, as well as brain aging and senescence. Despite substantial scientific interest in this species, no genomic resources are currently available. Results Here, we report the de novo assembly and annotation of the A. leptorhynchus transcriptome. After evaluating several trimming and transcript reconstruction strategies, de novo assembly using Trinity uncovered 42,459 unique contigs containing at least a partial protein-coding sequence based on alignment to a reference set of known Actinopterygii sequences. As many as 11,847 of these contigs contained full or near-full length protein sequences, providing broad coverage of the proteome. A variety of non-coding RNA sequences were also identified and annotated, including conserved long intergenic non-coding RNA and other long non-coding RNA observed previously to be expressed in adult zebrafish (Danio rerio) brain, as well as a variety of miRNA, snRNA, and snoRNA. Shotgun proteomics confirmed translation of open reading frames from over 2,000 transcripts, including alternative splice variants. Assignment of tandem mass spectra was greatly improved by use of the assembly compared to databases of sequences from closely related organisms. The assembly and raw reads have been deposited at DDBJ/EMBL/GenBank under the accession number GBKR00000000. Tandem mass spectrometry data is available via ProteomeXchange with identifier PXD001285. Conclusions Presented here is the first release of an annotated de novo transcriptome assembly from Apteronotus leptorhynchus, providing a broad overview of RNA expressed in central nervous system tissue. The assembly, which includes substantial coverage of a wide variety of both protein coding and non-coding transcripts, will allow the development of better tools to understand the mechanisms underlying unique characteristics of the knifefish model system, such as their tremendous regenerative capacity and negligible brain senescence. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1354-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Joseph P Salisbury
- Barnett Institute, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 412 TF, Boston, MA, 02115, USA.
| | - Ruxandra F Sîrbulescu
- Laboratory of Neurobiology, Department of Biology, Northeastern University, 360 Huntington Avenue, 134 Mugar Life Sciences, Boston, MA, 02115, USA.
| | - Benjamin M Moran
- Laboratory of Neurobiology, Department of Biology, Northeastern University, 360 Huntington Avenue, 134 Mugar Life Sciences, Boston, MA, 02115, USA.
| | - Jared R Auclair
- Barnett Institute, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 412 TF, Boston, MA, 02115, USA.
| | - Günther K H Zupanc
- Laboratory of Neurobiology, Department of Biology, Northeastern University, 360 Huntington Avenue, 134 Mugar Life Sciences, Boston, MA, 02115, USA.
| | - Jeffrey N Agar
- Barnett Institute, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 412 TF, Boston, MA, 02115, USA. .,Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, 412 TF, Boston, MA, 02115, USA.
| |
Collapse
|
2
|
Leon DR, Ytterberg AJ, Boontheung P, Kim U, Loo JA, Gunsalus RP, Ogorzalek Loo RR. Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1. Front Microbiol 2015; 6:149. [PMID: 25798134 PMCID: PMC4350412 DOI: 10.3389/fmicb.2015.00149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 02/09/2015] [Indexed: 12/11/2022] Open
Abstract
Proteomic tools identify constituents of complex mixtures, often delivering long lists of identified proteins. The high-throughput methods excel at matching tandem mass spectrometry data to spectra predicted from sequence databases. Unassigned mass spectra are ignored, but could, in principle, provide valuable information on unanticipated modifications and improve protein annotations while consuming limited quantities of material. Strategies to "mine" information from these discards are presented, along with discussion of features that, when present, provide strong support for modifications. In this study we mined LC-MS/MS datasets of proteolytically-digested concanavalin A pull down fractions from Methanosarcina mazei Gö1 cell lysates. Analyses identified 154 proteins. Many of the observed proteins displayed post-translationally modified forms, including O-formylated and methyl-esterified segments that appear biologically relevant (i.e., not artifacts of sample handling). Interesting cleavages and modifications (e.g., S-cyanylation and trimethylation) were observed near catalytic sites of methanogenesis enzymes. Of 31 Methanosarcina protein N-termini recovered by concanavalin A binding or from a previous study, only M. mazei S-layer protein MM1976 and its M. acetivorans C2A orthologue, MA0829, underwent signal peptide excision. Experimental results contrast with predictions from algorithms SignalP 3.0 and Exprot, which were found to over-predict the presence of signal peptides. Proteins MM0002, MM0716, MM1364, and MM1976 were found to be glycosylated, and employing chromatography tailored specifically for glycopeptides will likely reveal more. This study supplements limited, existing experimental datasets of mature archaeal N-termini, including presence or absence of signal peptides, translation initiation sites, and other processing. Methanosarcina surface and membrane proteins are richly modified.
Collapse
Affiliation(s)
- Deborah R Leon
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles, CA, USA
| | - A Jimmy Ytterberg
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles, CA, USA
| | - Pinmanee Boontheung
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles, CA, USA
| | - Unmi Kim
- Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles Los Angeles, CA, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles, CA, USA ; Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles Los Angeles, CA, USA ; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles Los Angeles, CA, USA
| | - Robert P Gunsalus
- Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles Los Angeles, CA, USA ; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles Los Angeles, CA, USA
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles Los Angeles, CA, USA ; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles Los Angeles, CA, USA
| |
Collapse
|
3
|
Förster F, Lasker K, Nickell S, Sali A, Baumeister W. Toward an integrated structural model of the 26S proteasome. Mol Cell Proteomics 2010; 9:1666-77. [PMID: 20467039 PMCID: PMC2938054 DOI: 10.1074/mcp.r000002-mcp201] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/26/2010] [Indexed: 11/06/2022] Open
Abstract
The 26S proteasome is the end point of the ubiquitin-proteasome pathway and degrades ubiquitylated substrates. It is composed of the 20S core particle (CP), where degradation occurs, and the 19S regulatory particle (RP), which ensures substrate specificity of degradation. Whereas the CP is resolved to atomic resolution, the architecture of the RP is largely unknown. We provide a comprehensive analysis of the current structural knowledge on the RP, including structures of the RP subunits, physical protein-protein interactions, and cryoelectron microscopy data. These data allowed us to compute an atomic model for the CP-AAA-ATPase subcomplex. In addition to this atomic model, further subunits can be mapped approximately, which lets us hypothesize on the substrate path during its degradation.
Collapse
Affiliation(s)
- Friedrich Förster
- From the ‡Department of Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Keren Lasker
- ¶Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, California 94158, and
- ‖Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stephan Nickell
- From the ‡Department of Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Andrej Sali
- ¶Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, California 94158, and
| | - Wolfgang Baumeister
- From the ‡Department of Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| |
Collapse
|