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Jeanne F, Bernay B, Sourdaine P. Comparative Proteome Analysis of Four Stages of Spermatogenesis in the Small-Spotted Catshark ( Scyliorhinus canicula), Using High-Resolution NanoLC-ESI-MS/MS. J Proteome Res 2023. [PMID: 37290099 DOI: 10.1021/acs.jproteome.3c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spermatogenesis is a highly specialized process of cell proliferation and differentiation leading to the production of spermatozoa from spermatogonial stem cells. Due to its testicular anatomy, Scyliorhinus canicula is an interesting model to explore stage-based changes in proteins during spermatogenesis. The proteomes of four testicular zones corresponding to the germinative niche and to spermatocysts (cysts) with spermatogonia (zone A), cysts with spermatocytes (zone B), cysts with young spermatids (zone C), and cysts with late spermatids (zone D) have been analyzed by nanoLC-ESI-MS/MS. Gene ontology and KEGG annotations were also performed. A total of 3346 multiple protein groups were identified. Zone-specific protein analyses highlighted RNA-processing, chromosome-related processes, cilium organization, and cilium activity in zones A, D, C, and D, respectively. Analyses of proteins with zone-dependent abundance revealed processes related to cellular stress, ubiquitin-dependent degradation by the proteasome, post-transcriptional regulation, and regulation of cellular homeostasis. Our results also suggest that the roles of some proteins, such as ceruloplasmin, optineurin, the pregnancy zone protein, PA28β or the Culling-RING ligase 5 complex, as well as some uncharacterized proteins, during spermatogenesis could be further explored. Finally, the study of this shark species allows one to integrate these data in an evolutionary context of the regulation of spermatogenesis. Mass spectrometry data are freely accessible via iProX-integrated Proteome resources (https://www.iprox.cn/) for reuse purposes.
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Affiliation(s)
- Fabian Jeanne
- Université de Caen Normandie, MNHN, SU, UA, CNRS, IRD, Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), UMR 8067, 14032 Caen cedex 5, France
| | - Benoît Bernay
- Université de Caen Normandie - Plateforme PROTEOGEN, US EMerode, 14032 Caen cedex 5, France
| | - Pascal Sourdaine
- Université de Caen Normandie, MNHN, SU, UA, CNRS, IRD, Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), UMR 8067, 14032 Caen cedex 5, France
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Stavrianakou M, Perez R, Wu C, Sachs MS, Aramayo R, Harlow M. Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ. BMC Genomics 2017; 18:611. [PMID: 28806931 PMCID: PMC5557070 DOI: 10.1186/s12864-017-3890-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 06/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background The electric organ of Tetronarce californica (an electric ray formerly known as Torpedo californica) is a classic preparation for biochemical studies of cholinergic neurotransmission. To broaden the usefulness of this preparation, we have performed a transcriptome assembly of the presynaptic component of the electric organ (the electric lobe). We combined our assembled transcriptome with a previous transcriptome of the postsynaptic electric organ, to define a MetaProteome containing pre- and post-synaptic components of the electric organ. Results Sequencing yielded 102 million paired-end 100 bp reads. De novo Trinity assembly was performed at Kmer 25 (default) and Kmers 27, 29, and 31. Trinity, generated around 103,000 transcripts, and 78,000 genes per assembly. Assemblies were evaluated based on the number of bases/transcripts assembled, RSEM-EVAL scores and informational content and completeness. We found that different assemblies scored differently according to the evaluation criteria used, and that while each individual assembly contained unique information, much of the assembly information was shared by all assemblies. To generate the presynaptic transcriptome (electric lobe), while capturing all information, assemblies were first clustered and then combined with postsynaptic transcripts (electric organ) downloaded from NCBI. The completness of the resulting clustered predicted MetaProteome was rigorously evaluated by comparing its information against the predicted proteomes from Homo sapiens, Callorhinchus milli, and the Transporter Classification Database (TCDB). Conclusions In summary, we obtained a MetaProteome containing 92%, 88.5%, and 66% of the expected set of ultra-conserved sequences (i.e., BUSCOs), expected to be found for Eukaryotes, Metazoa, and Vertebrata, respectively. We cross-annotated the conserved set of proteins shared between the T. californica MetaProteome and the proteomes of H. sapiens and C. milli, using the H. sapiens genome as a reference. This information was used to predict the position in human pathways of the conserved members of the T. californica MetaProteome. We found proteins not detected before in T. californica, corresponding to processes involved in synaptic vesicle biology. Finally, we identified 42 transporter proteins in TCDB that were detected by the T. californica MetaProteome (electric fish) and not selected by a control proteome consisting of the combined proteomes of 12 widely diverse non-electric fishes by Reverse-Blast-Hit Blast. Combined, the information provided here is not only a unique tool for the study of cholinergic neurotransmission, but it is also a starting point for understanding the evolution of early vertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3890-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Stavrianakou
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, 77843-3258, USA
| | - Ricardo Perez
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, 77843-3258, USA
| | - Cheng Wu
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, 77843-3258, USA
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, 77843-3258, USA
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, 77843-3258, USA.
| | - Mark Harlow
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, 77843-3258, USA.
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Traeger LL, Sabat G, Barrett-Wilt GA, Wells GB, Sussman MR. A tail of two voltages: Proteomic comparison of the three electric organs of the electric eel. SCIENCE ADVANCES 2017; 3:e1700523. [PMID: 28695212 PMCID: PMC5498108 DOI: 10.1126/sciadv.1700523] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/19/2017] [Indexed: 05/22/2023]
Abstract
The electric eel (Electrophorus electricus) is unusual among electric fishes because it has three pairs of electric organs that serve multiple biological functions: For navigation and communication, it emits continuous pulses of weak electric discharge (<1 V), but for predation and defense, it intermittently emits lethal strong electric discharges (10 to 600 V). We hypothesized that these two electrogenic outputs have different energetic demands reflected by differences in their proteome and phosphoproteome. We report the use of isotope-assisted quantitative mass spectrometry to test this hypothesis. We observed novel phosphorylation sites in sodium transporters and identified a potassium channel with unique differences in protein concentration among the electric organs. In addition, we found transcription factors and protein kinases that show differential abundance in the strong versus weak electric organs. Our findings support the hypothesis that proteomic differences among electric organs underlie differences in energetic needs, reflecting a trade-off between generating weak voltages continuously and strong voltages intermittently.
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Affiliation(s)
- Lindsay L. Traeger
- Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Gregg B. Wells
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Michael R. Sussman
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Corresponding author.
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Pitchers WR, Constantinou SJ, Losilla M, Gallant JR. Electric fish genomics: Progress, prospects, and new tools for neuroethology. ACTA ACUST UNITED AC 2016; 110:259-272. [PMID: 27769923 DOI: 10.1016/j.jphysparis.2016.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/06/2016] [Accepted: 10/16/2016] [Indexed: 01/01/2023]
Abstract
Electric fish have served as a model system in biology since the 18th century, providing deep insight into the nature of bioelectrogenesis, the molecular structure of the synapse, and brain circuitry underlying complex behavior. Neuroethologists have collected extensive phenotypic data that span biological levels of analysis from molecules to ecosystems. This phenotypic data, together with genomic resources obtained over the past decades, have motivated new and exciting hypotheses that position the weakly electric fish model to address fundamental 21st century biological questions. This review article considers the molecular data collected for weakly electric fish over the past three decades, and the insights that data of this nature has motivated. For readers relatively new to molecular genetics techniques, we also provide a table of terminology aimed at clarifying the numerous acronyms and techniques that accompany this field. Next, we pose a research agenda for expanding genomic resources for electric fish research over the next 10years. We conclude by considering some of the exciting research prospects for neuroethology that electric fish genomics may offer over the coming decades, if the electric fish community is successful in these endeavors.
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Affiliation(s)
- William R Pitchers
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA.
| | - Savvas J Constantinou
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA
| | - Mauricio Losilla
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA
| | - Jason R Gallant
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA.
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Traeger LL, Volkening JD, Moffett H, Gallant JR, Chen PH, Novina CD, Phillips GN, Anand R, Wells GB, Pinch M, Güth R, Unguez GA, Albert JS, Zakon H, Sussman MR, Samanta MP. Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus). BMC Genomics 2015; 16:243. [PMID: 25887781 PMCID: PMC4393597 DOI: 10.1186/s12864-015-1288-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/26/2015] [Indexed: 11/10/2022] Open
Abstract
Background With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. Remarkably little is understood about the molecular nature of its electric organs. Results We present an in-depth analysis of the genome of E. electricus, including the transcriptomes of eight mature tissues: brain, spinal cord, kidney, heart, skeletal muscle, Sachs’ electric organ, main electric organ, and Hunter’s electric organ. A gene set enrichment analysis based on gene ontology reveals enriched functions in all three electric organs related to transmembrane transport, androgen binding, and signaling. This study also represents the first analysis of miRNA in electric fish. It identified a number of miRNAs displaying electric organ-specific expression patterns, including one novel miRNA highly over-expressed in all three electric organs of E. electricus. All three electric organ tissues also express three conserved miRNAs that have been reported to inhibit muscle development in mammals, suggesting that miRNA-dependent regulation of gene expression might play an important role in specifying an electric organ identity from its muscle precursor. These miRNA data were supported using another complete miRNA profile from muscle and electric organ tissues of a second gymnotiform species. Conclusions Our work on the E. electricus genome and eight tissue-specific gene expression profiles will greatly facilitate future research on determining the coding and regulatory sequences that specify the function, development, and evolution of electric organs. Moreover, these data and future studies will be informed by the first comprehensive analysis of miRNA expression in an electric fish presented here. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1288-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lindsay L Traeger
- Department of Genetics, University of Wisconsin, Madison, WI, 53706, USA. .,Biotechnology Center, University of Wisconsin, Madison, WI, 53706, USA.
| | - Jeremy D Volkening
- Biotechnology Center, University of Wisconsin, Madison, WI, 53706, USA. .,Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA.
| | - Howell Moffett
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Jason R Gallant
- Department of Zoology, Michigan State University, East Lansing, MI, 48824, USA. .,BEACON Center for the Study of Evolution in Action, Lansing, USA.
| | - Po-Hao Chen
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02141, USA.
| | - Carl D Novina
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02141, USA.
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX, 77005, USA.
| | - Rene Anand
- Department of Pharmacology and Department of Neuroscience, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA.
| | - Gregg B Wells
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, 77483, USA.
| | - Matthew Pinch
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Robert Güth
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Graciela A Unguez
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - James S Albert
- Department of Biology, University of Louisiana, Lafayette, LA, 70503, USA.
| | - Harold Zakon
- BEACON Center for the Study of Evolution in Action, Lansing, USA. .,University of Texas, Austin, TX, 78712, USA. .,The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, The Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
| | - Michael R Sussman
- Biotechnology Center, University of Wisconsin, Madison, WI, 53706, USA. .,Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA.
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Rhee JS, Lee JS. Whole genome data for omics-based research on the self-fertilizing fish Kryptolebias marmoratus. MARINE POLLUTION BULLETIN 2014; 85:532-541. [PMID: 24759509 DOI: 10.1016/j.marpolbul.2014.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 03/24/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
Genome resources have advantages for understanding diverse areas such as biological patterns and functioning of organisms. Omics platforms are useful approaches for the study of organs and organisms. These approaches can be powerful screening tools for whole genome, proteome, and metabolome profiling, and can be used to understand molecular changes in response to internal and external stimuli. This methodology has been applied successfully in freshwater model fish such as the zebrafish Danio rerio and the Japanese medaka Oryzias latipes in research areas such as basic physiology, developmental biology, genetics, and environmental biology. However, information is still scarce about model fish that inhabit brackish water or seawater. To develop the self-fertilizing killifish Kryptolebias marmoratus as a potential model species with unique characteristics and research merits, we obtained genomic information about K. marmoratus. We address ways to use these data for genome-based molecular mechanistic studies. We review the current state of genome information on K. marmoratus to initiate omics approaches. We evaluate the potential applications of integrated omics platforms for future studies in environmental science, developmental biology, and biomedical research. We conclude that information about the K. marmoratus genome will provide a better understanding of the molecular functions of genes, proteins, and metabolites that are involved in the biological functions of this species. Omics platforms, particularly combined technologies that make effective use of bioinformatics, will provide powerful tools for hypothesis-driven investigations and discovery-driven discussions on diverse aspects of this species and on fish and vertebrates in general.
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Affiliation(s)
- Jae-Sung Rhee
- Department of Marine Science, College of Natural Science, Incheon National University, Incheon 406-772, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
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Mate SE, Brown KJ, Hoffman EP. Integrated genomics and proteomics of the Torpedo californica electric organ: concordance with the mammalian neuromuscular junction. Skelet Muscle 2011; 1:20. [PMID: 21798097 PMCID: PMC3156643 DOI: 10.1186/2044-5040-1-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 05/04/2011] [Indexed: 11/25/2022] Open
Abstract
Background During development, the branchial mesoderm of Torpedo californica transdifferentiates into an electric organ capable of generating high voltage discharges to stun fish. The organ contains a high density of cholinergic synapses and has served as a biochemical model for the membrane specialization of myofibers, the neuromuscular junction (NMJ). We studied the genome and proteome of the electric organ to gain insight into its composition, to determine if there is concordance with skeletal muscle and the NMJ, and to identify novel synaptic proteins. Results Of 435 proteins identified, 300 mapped to Torpedo cDNA sequences with ≥2 peptides. We identified 14 uncharacterized proteins in the electric organ that are known to play a role in acetylcholine receptor clustering or signal transduction. In addition, two human open reading frames, C1orf123 and C6orf130, showed high sequence similarity to electric organ proteins. Our profile lists several proteins that are highly expressed in skeletal muscle or are muscle specific. Synaptic proteins such as acetylcholinesterase, acetylcholine receptor subunits, and rapsyn were present in the electric organ proteome but absent in the skeletal muscle proteome. Conclusions Our integrated genomic and proteomic analysis supports research describing a muscle-like profile of the organ. We show that it is a repository of NMJ proteins but we present limitations on its use as a comprehensive model of the NMJ. Finally, we identified several proteins that may become candidates for signaling proteins not previously characterized as components of the NMJ.
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Affiliation(s)
- Suzanne E Mate
- Department of Biochemistry and Molecular Genetics, IBS, George Washington University, Washington DC, USA
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Nazarian J, Berry DL, Sanjari S, Razvi M, Brown K, Hathout Y, Vertes A, Dadgar S, Hoffman EP. Evolution and comparative genomics of subcellular specializations: EST sequencing of Torpedo electric organ. Mar Genomics 2011; 4:33-40. [PMID: 21429463 DOI: 10.1016/j.margen.2010.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 12/09/2010] [Accepted: 12/13/2010] [Indexed: 02/04/2023]
Abstract
Uncharacterized open reading frames (ORFs) in human genomic sequence often show a high degree of evolutionary conservation, yet have little or no tissue EST or protein data suggestive of protein product function. The encoded proteins may have highly restricted expression in specialized cells, subcellular specializations, and/or narrow windows during development. One such highly specialized and minute subcellular compartment is the neuromuscular junction (NMJ), where motorneurons contact muscle fibers. The electric Torpedo ray has evolved to expand the NMJ structure to the size of a large organ (electroplax organ), and we hypothesized that Torpedo electroplax proteins would be candidates for human ESTs expressed at the human NMJ. A total of 9719 primary electroplax cDNA clones were sequenced. We identified 44 human ORFs showing high (>63%) amino acid identity to Torpedo electroplax transcripts with enrichment for mRNA splicing motifs (SH2 and pre-mRNA splicing domains), an observation potentially important for the strict nuclear domains maintained by myonuclei underlying the NMJ. We generated antibodies against two uncharacterized human genes (C19orf29 [Drosophila cactin] and C15orf24) and showed that these were indeed expressed at the murine NMJ. Cactin, a member of the Rel transcription factor family in Drosophila, localized to the postsynaptic cytosol of the NMJ and nuclear membrane. C15orf24 protein localized to the murine postsynaptic sarcolemma. We show a novel approach towards identifying proteins expressed at a subcellular specialization using evolutionary diversity of organ function and cross-species mapping.
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Affiliation(s)
- Javad Nazarian
- Research Center for Genetic Medicine, Children's National Medical Center, Department of Integrative Systems Biology, The George Washington University School of Medicine & Health Sciences, Washington, DC 20010, United States
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Heiny JA, Kravtsova VV, Mandel F, Radzyukevich TL, Benziane B, Prokofiev AV, Pedersen SE, Chibalin AV, Krivoi II. The nicotinic acetylcholine receptor and the Na,K-ATPase alpha2 isoform interact to regulate membrane electrogenesis in skeletal muscle. J Biol Chem 2010; 285:28614-26. [PMID: 20595385 DOI: 10.1074/jbc.m110.150961] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nicotinic acetylcholine receptor (nAChR) and the Na,K-ATPase functionally interact in skeletal muscle (Krivoi, I. I., Drabkina, T. M., Kravtsova, V. V., Vasiliev, A. N., Eaton, M. J., Skatchkov, S. N., and Mandel, F. (2006) Pflugers Arch. 452, 756-765; Krivoi, I., Vasiliev, A., Kravtsova, V., Dobretsov, M., and Mandel, F. (2003) Ann. N.Y. Acad. Sci. 986, 639-641). In this interaction, the specific binding of nanomolar concentrations of nicotinic agonists to the nAChR stimulates electrogenic transport by the Na,K-ATPase alpha2 isozyme, causing membrane hyperpolarization. This study examines the molecular nature and membrane localization of this interaction. Stimulation of Na,K-ATPase activity by the nAChR does not require ion flow through open nAChRs. It can be induced by nAChR desensitization alone, in the absence of nicotinic agonist, and saturates when the nAChR is fully desensitized. It is enhanced by noncompetitive blockers of the nAChR (proadifen, QX-222), which promote non-conducting or desensitized states; and retarded by tetracaine, which stabilizes the resting nAChR conformation. The interaction operates at the neuromuscular junction as well as on extrajunctional sarcolemma. The Na,K-ATPase alpha2 isozyme is enriched at the postsynaptic neuromuscular junction and co-localizes with nAChRs. The nAChR and Na,K-ATPase alpha subunits specifically coimmunoprecipitate with each other, phospholemman, and caveolin-3. In a purified membrane preparation from Torpedo californica enriched in nAChRs and the Na,K-ATPase, a ouabain-induced conformational change of the Na,K-ATPase enhances a conformational transition of the nAChR to a desensitized state. These results suggest a mechanism by which the nAChR in a desensitized state with high apparent affinity for agonist interacts with the Na,K-ATPase to stimulate active transport. The interaction utilizes a membrane-delimited complex involving protein-protein interactions, either directly or through additional protein partners. This interaction is expected to enhance neuromuscular transmission and muscle excitation.
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Affiliation(s)
- Judith A Heiny
- Department of General Physiology, St. Petersburg State University, St. Petersburg 199034, Russia
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Ketterer C, Zeiger U, Budak MT, Rubinstein NA, Khurana TS. Identification of the neuromuscular junction transcriptome of extraocular muscle by laser capture microdissection. Invest Ophthalmol Vis Sci 2010; 51:4589-99. [PMID: 20393109 DOI: 10.1167/iovs.09-4893] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To examine and characterize the profile of genes expressed at the synapses or neuromuscular junctions (NMJs) of extraocular muscles (EOMs) compared with those expressed at the tibialis anterior (TA). METHODS Adult rat eyeballs with rectus EOMs attached and TAs were dissected, snap frozen, serially sectioned, and stained for acetylcholinesterase (AChE) to identify the NMJs. Approximately 6000 NMJs for rectus EOM (EOMsyn), 6000 NMJs for TA (TAsyn), equal amounts of NMJ-free fiber regions (EOMfib, TAfib), and underlying myonuclei and RNAs were captured by laser capture microdissection (LCM). RNA was processed for microarray-based expression profiling. Expression profiles and interaction lists were generated for genes differentially expressed at synaptic and nonsynaptic regions of EOM (EOMsyn versus EOMfib) and TA (TAsyn versus TAfib). Profiles were validated by using real-time quantitative polymerase chain reaction (qPCR). RESULTS The regional transcriptomes associated with NMJs of EOMs and TAs were identified. Two hundred seventy-five genes were preferentially expressed in EOMsyn (compared with EOMfib), 230 in TAsyn (compared with TAfib), and 288 additional transcripts expressed in both synapses. Identified genes included novel genes as well as well-known, evolutionarily conserved synaptic markers (e.g., nicotinic acetylcholine receptor (AChR) alpha (Chrna) and epsilon (Chrne) subunits and nestin (Nes). CONCLUSIONS Transcriptome level differences exist between EOM synaptic regions and TA synaptic regions. The definition of the synaptic transcriptome provides insight into the mechanism of formation and functioning of the unique synapses of EOM and their differential involvement in diseases noted in the EOM allotype.
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Affiliation(s)
- Caroline Ketterer
- Department of Cell and Developmental Biology, Pennsylvania Muscle Institute, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Forné I, Abián J, Cerdà J. Fish proteome analysis: Model organisms and non-sequenced species. Proteomics 2009; 10:858-72. [DOI: 10.1002/pmic.200900609] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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De Souza AG, MacCormack TJ, Wang N, Li L, Goss GG. Large-Scale Proteome Profile of the Zebrafish (Danio rerio) Gill for Physiological and Biomarker Discovery Studies. Zebrafish 2009; 6:229-38. [DOI: 10.1089/zeb.2009.0591] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Andrea G. De Souza
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Tyson J. MacCormack
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Nan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Greg G. Goss
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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