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Jaiswal S, Nandi S, Iquebal MA, Jasrotia RS, Patra S, Mishra G, Udit UK, Sahu DK, Angadi UB, Meher PK, Routray P, Sundaray JK, Verma DK, Das P, Jayasankar P, Rai A, Kumar D. Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing. BMC Genomics 2021; 22:685. [PMID: 34548034 PMCID: PMC8456608 DOI: 10.1186/s12864-021-08001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/26/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. RESULT A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. CONCLUSION This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Samiran Nandi
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunita Patra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Gayatri Mishra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Uday Kumar Udit
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Dinesh Kumar Sahu
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prem Kumar Meher
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Padmanav Routray
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | | | - Paramananda Das
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Chen MH, Fang C, Wu NY, Xia YH, Zeng YJ, Ouyang W. Genetic variation of rs12918566 affects GRIN2A expression and is associated with spontaneous movement response during sevoflurane anesthesia induction. Brain Behav 2021; 11:e02165. [PMID: 34291608 PMCID: PMC8413822 DOI: 10.1002/brb3.2165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/02/2021] [Accepted: 04/11/2021] [Indexed: 11/09/2022] Open
Abstract
N-methyl-D-aspartate (NMDA) receptors mediate excitatory neurotransmission in the nervous system and are preferentially inhibited by general anesthetics such as sevoflurane. Spontaneous movement is a common complication during sevoflurane anesthesia induction and seriously affects operations. In this study, we investigated the relationship between NMDA polymorphisms and spontaneous movement during sevoflurane induction. This prospective clinical study enrolled 393 patients undergoing sevoflurane anesthesia as part of their surgical routine. In the GRIN1, GRIN2A, and GRIN2B genes, 13 polymorphisms that form a heteromeric complex as part of the NMDA receptor were selected using Haploview and genotyped using matrix-assisted laser desorption ionization-time of flight mass spectrometry MassARRAY. Both RNAfold and Genotype-Tissue Expression portals were used to identify gene expression profiles. Our data showed that 35.8% of subjects exhibited spontaneous movement. The GRIN2A rs12918566 polymorphism was associated with spontaneous movement during sevoflurane induction. A logistic regression analysis of additive, dominant, and recessive models indicated a significant association (odds ratio [OR] (95% confidence limit [CI]): 0.58 (0.42-0.80), p = .00086; OR (95% CI): 0.51 (0.31-0.84), p = .0075, and OR (95% CI): 0.47 (0.27-0.81), p = .0060, respectively). After false discovery rate (FDR) correction, the additive model was still significant with a PFDR =0.010. Bioinformatics demonstrated that the rs12918566 genomic variation affected GRIN2A expression in brain tissue. We also revealed that GRIN2A rs12918566 was significantly associated with spontaneous movement during sevoflurane induction. We believe the NMDA receptor plays an important role in regulating the anesthetic effects of sevoflurane.
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Affiliation(s)
- Ming-Hua Chen
- Department of Anesthesiology, Third Xiangya Hospital of Central South University, Changsha, China
| | - Chao Fang
- Department of Anesthesiology, Third Xiangya Hospital of Central South University, Changsha, China.,Postdoctoral Research Station of Clinical Medicine, Third Xiangya Hospital of Central South University, Changsha, China
| | - Na-Yiyuan Wu
- Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Yu-Hao Xia
- Department of Anesthesiology, Third Xiangya Hospital of Central South University, Changsha, China
| | - You-Jie Zeng
- Department of Anesthesiology, Third Xiangya Hospital of Central South University, Changsha, China
| | - Wen Ouyang
- Department of Anesthesiology, Third Xiangya Hospital of Central South University, Changsha, China
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3
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Astrocytic contribution to glutamate-related central respiratory chemoreception in vertebrates. Respir Physiol Neurobiol 2021; 294:103744. [PMID: 34302992 DOI: 10.1016/j.resp.2021.103744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/01/2021] [Accepted: 07/18/2021] [Indexed: 12/24/2022]
Abstract
Central respiratory chemoreceptors play a key role in the respiratory homeostasis by sensing CO2 and H+ in brain and activating the respiratory neural network. This ability of specific brain regions to respond to acidosis and hypercapnia is based on neuronal and glial mechanisms. Several decades ago, glutamatergic transmission was proposed to be involved as a main mechanism in central chemoreception. However, a complete identification of mechanism has been elusive. At the rostral medulla, chemosensitive neurons of the retrotrapezoid nucleus (RTN) are glutamatergic and they are stimulated by ATP released by RTN astrocytes in response to hypercapnia. In addition, recent findings show that caudal medullary astrocytes in brainstem can also contribute as CO2 and H+ sensors that release D-serine and glutamate, both gliotransmitters able to activate the respiratory neural network. In this review, we describe the mammalian astrocytic glutamatergic contribution to the central respiratory chemoreception trying to trace in vertebrates the emergence of several components involved in this process.
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4
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Ramos-Vicente D, Grant SG, Bayés À. Metazoan evolution and diversity of glutamate receptors and their auxiliary subunits. Neuropharmacology 2021; 195:108640. [PMID: 34116111 DOI: 10.1016/j.neuropharm.2021.108640] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 01/18/2023]
Abstract
Glutamate is the major excitatory neurotransmitter in vertebrate and invertebrate nervous systems. Proteins involved in glutamatergic neurotransmission, and chiefly glutamate receptors and their auxiliary subunits, play key roles in nervous system function. Thus, understanding their evolution and uncovering their diversity is essential to comprehend how nervous systems evolved, shaping cognitive function. Comprehensive phylogenetic analysis of these proteins across metazoans have revealed that their evolution is much more complex than what can be anticipated from vertebrate genomes. This is particularly true for ionotropic glutamate receptors (iGluRs), as their current classification into 6 classes (AMPA, Kainate, Delta, NMDA1, NMDA2 and NMDA3) would be largely incomplete. New work proposes a classification of iGluRs into 4 subfamilies that encompass 10 classes. Vertebrate AMPA, Kainate and Delta receptors would belong to one of these subfamilies, named AKDF, the NMDA subunits would constitute another subfamily and non-vertebrate iGluRs would be organised into the previously unreported Epsilon and Lambda subfamilies. Similarly, the animal evolution of metabotropic glutamate receptors has resulted in the formation of four classes of these receptors, instead of the three currently recognised. Here we review our current knowledge on the animal evolution of glutamate receptors and their auxiliary subunits. This article is part of the special issue on 'Glutamate Receptors - Orphan iGluRs'.
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Affiliation(s)
- David Ramos-Vicente
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Seth Gn Grant
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, EH16 4SB, UK; Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Àlex Bayés
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain.
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5
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Fjelldal MF, Freyd T, Evenseth LM, Sylte I, Ring A, Paulsen RE. Exploring the overlapping binding sites of ifenprodil and EVT-101 in GluN2B-containing NMDA receptors using novel chicken embryo forebrain cultures and molecular modeling. Pharmacol Res Perspect 2019; 7:e00480. [PMID: 31164987 PMCID: PMC6543015 DOI: 10.1002/prp2.480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
N-methyl-d-aspartate receptors (NMDAR) are widely expressed in the brain. GluN2B subunit-containing NMDARs has recently attracted significant attention as potential pharmacological targets, with emphasis on the functional properties of allosteric antagonists. We used primary cultures from chicken embryo forebrain (E10), expressing native GluN2B-containing NMDA receptors as a novel model system. Comparing the inhibition of calcium influx by well-known GluN2B subunit-specific allosteric antagonists, the following rank order of potency was found: EVT-101 (EC 50 22 ± 8 nmol/L) > Ro 25-6981 (EC 50 60 ± 30 nmol/L) > ifenprodil (EC 50 100 ± 40 nmol/L) > eliprodil (EC 50 1300 ± 700 nmol/L), similar to previous observations in rat cortical cultures and cell lines overexpressing chimeric receptors. The less explored Ro 04-5595 had an EC 50 of 186 ± 32 nmol/L. Venturing to explain the differences in potency, binding properties were further studied by in silico docking and molecular dynamics simulations using x-ray crystal structures of GluN1/GluN2B amino terminal domain. We found that Ro 04-5595 was predicted to bind the recently discovered EVT-101 binding site, not the ifenprodil-binding site. The EVT-101 binding pocket appears to accommodate more structurally different ligands than the ifenprodil-binding site, and contains residues essential in ligand interactions necessary for calcium influx inhibition. For the ifenprodil site, the less effective antagonist (eliprodil) fails to interact with key residues, while in the EVT-101 pocket, difference in potency might be explained by differences in ligand-receptor interaction patterns.
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Affiliation(s)
- Marthe F. Fjelldal
- Department of Pharmaceutical BiosciencesSchool of PharmacyUniversity of OsloOsloNorway
- Norwegian Defence Research EstablishmentKjellerNorway
- Realomics Strategic Research InitiativeOsloNorway
| | - Thibaud Freyd
- Molecular Pharmacology and ToxicologyDepartment of Medical BiologyUniversity of Tromsø—The Arctic University of NorwayTromsøNorway
- Department of ChemistryHylleraas Centre for Quantum Molecular SciencesUniversity of OsloOsloNorway
| | - Linn M. Evenseth
- Molecular Pharmacology and ToxicologyDepartment of Medical BiologyUniversity of Tromsø—The Arctic University of NorwayTromsøNorway
| | - Ingebrigt Sylte
- Molecular Pharmacology and ToxicologyDepartment of Medical BiologyUniversity of Tromsø—The Arctic University of NorwayTromsøNorway
| | - Avi Ring
- Norwegian Defence Research EstablishmentKjellerNorway
| | - Ragnhild E. Paulsen
- Department of Pharmaceutical BiosciencesSchool of PharmacyUniversity of OsloOsloNorway
- Realomics Strategic Research InitiativeOsloNorway
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6
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Swanger SA, Traynelis SF. Synaptic Receptor Diversity Revealed Across Space and Time. Trends Neurosci 2018; 41:486-488. [DOI: 10.1016/j.tins.2018.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 12/20/2022]
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7
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Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP. Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence. Mol Biol Evol 2018; 34:3006-3022. [PMID: 28962009 DOI: 10.1093/molbev/msx213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Numerous approaches have been developed to infer natural selection based on the comparison of polymorphism within species and divergence between species. These methods are especially powerful for the detection of uniform selection operating across a gene. However, empirical analyses have demonstrated that regions of protein-coding genes exhibiting clusters of amino acid substitutions are subject to different levels of selection relative to other regions of the same gene. To quantify this heterogeneity of selection within coding sequences, we developed Model Averaged Site Selection via Poisson Random Field (MASS-PRF). MASS-PRF identifies an ensemble of intragenic clustering models for polymorphic and divergent sites. This ensemble of models is used within the Poisson Random Field framework to estimate selection intensity on a site-by-site basis. Using simulations, we demonstrate that MASS-PRF has high power to detect clusters of amino acid variants in small genic regions, can reliably estimate the probability of a variant occurring at each nucleotide site in sequence data and is robust to historical demographic trends and recombination. We applied MASS-PRF to human gene polymorphism derived from the 1,000 Genomes Project and divergence data from the common chimpanzee. On the basis of this analysis, we discovered striking regional variation in selection intensity, indicative of positive or negative selection, in well-defined domains of genes that have previously been associated with neurological processing, immunity, and reproduction. We suggest that amino acid-altering substitutions within these regions likely are or have been selectively advantageous in the human lineage, playing important roles in protein function.
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Affiliation(s)
- Zi-Ming Zhao
- Department of Biostatistics, Yale University, New Haven, CT
| | - Michael C Campbell
- Department of Biostatistics, Yale University, New Haven, CT.,Department of Biology, Howard University, Washington, DC
| | - Ning Li
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Daniel S W Lee
- Department of Biostatistics, Yale University, New Haven, CT
| | - Zhang Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University, New Haven, CT.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
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8
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Greer JB, Khuri S, Fieber LA. Phylogenetic analysis of ionotropic L-glutamate receptor genes in the Bilateria, with special notes on Aplysia californica. BMC Evol Biol 2017; 17:11. [PMID: 28077092 PMCID: PMC5225553 DOI: 10.1186/s12862-016-0871-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 12/22/2016] [Indexed: 01/17/2023] Open
Abstract
Background The neurotransmitter L-Glutamate (L-Glu) acting at ionotropic L-Glu receptors (iGluR) conveys fast excitatory signal transmission in the nervous systems of all animals. iGluR-dependent neurotransmission is a key component of the synaptic plasticity that underlies learning and memory. During learning, two subtypes of iGluR, α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPAR) and N-methyl-D-aspartate receptors (NMDAR), are dynamically regulated postsynaptically in vertebrates. Invertebrate organisms such as Aplysia californica (Aplysia) are well-studied models for iGluR-mediated function, yet no studies to date have analyzed the evolutionary relationships between iGluR genes in these species and those in vertebrates, to identify genes that may mediate plasticity. We conducted a thorough phylogenetic analysis spanning Bilateria to elucidate these relationships. The expression status of iGluR genes in the Aplysia nervous system was also examined. Results Our analysis shows that ancestral genes for both NMDAR and AMPAR subtypes were present in the common bilaterian ancestor. NMDAR genes show very high conservation in motifs responsible for forming the conductance pore of the ion channel. The number of NMDAR subunits is greater in vertebrates due to an increased number of splice variants and an increased number of genes, likely due to gene duplication events. AMPAR subunits form an orthologous group, and there is high variability in the number of AMPAR genes in each species due to extensive taxon specific gene gain and loss. qPCR results show that all 12 Aplysia iGluR subunits are expressed in all nervous system ganglia. Conclusions Orthologous NMDAR subunits in all species studied suggests conserved function across Bilateria, and potentially a conserved mechanism of neuroplasticity and learning. Vertebrates display an increased number of NMDAR genes and splice variants, which may play a role in their greater diversity of physiological responses. Extensive gene gain and loss of AMPAR genes may result in different physiological properties that are taxon specific. Our results suggest a significant role for L-Glu mediated responses throughout the Aplysia nervous system, consistent with L-Glu’s role as the primary excitatory neurotransmitter. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0871-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Justin B Greer
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA.
| | - Sawsan Khuri
- Center for Computational Science, University of Miami, 1320 S. Dixie Highway, Coral Gables, FL, 33146, USA.,Department of Computer Science, University of Miami, P.O. Box 248154, Coral Gables, FL, 33124, USA
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
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9
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Glutamate and ATP at the Interface Between Signaling and Metabolism in Astroglia: Examples from Pathology. Neurochem Res 2016; 42:19-34. [PMID: 26915104 DOI: 10.1007/s11064-016-1848-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 12/17/2022]
Abstract
Glutamate is the main excitatory transmitter in the brain, while ATP represents the most important energy currency in any living cell. Yet, these chemicals play an important role in both processes, enabling them with dual-acting functions in metabolic and intercellular signaling pathways. Glutamate can fuel ATP production, while ATP can act as a transmitter in intercellular signaling. We discuss the interface between glutamate and ATP in signaling and metabolism of astrocytes. Not only do glutamate and ATP cross each other's paths in physiology of the brain, but they also do so in its pathology. We present the fabric of this process in (patho)physiology through the discussion of synthesis and metabolism of ATP and glutamate in astrocytes as well as by providing a general description of astroglial receptors for these molecules along with the downstream signaling pathways that may be activated. It is astroglial receptors for these dual-acting molecules that could hold a key for medical intervention in pathological conditions. We focus on two examples disclosing the role of activation of astroglial ATP and glutamate receptors in pathology of two kinds of brain tissue, gray matter and white matter, respectively. Interventions at the interface of metabolism and signaling show promise for translational medicine.
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10
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Liu C, Hu J, Qu C, Wang L, Huang G, Niu P, Zhong Z, Hong F, Wang G, Postlethwait JH, Wang H. Molecular evolution and functional divergence of zebrafish (Danio rerio) cryptochrome genes. Sci Rep 2015; 5:8113. [PMID: 25630924 PMCID: PMC4558521 DOI: 10.1038/srep08113] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 01/07/2015] [Indexed: 01/04/2023] Open
Abstract
Cryptochromes function in animal circadian regulation. Zebrafish are known to have six cryptochrome (cry) genes but their evolutionary relationships are not yet fully resolved. Here, comparative genomic analyses revealed that a local duplication of ancestral chordate Cry occurred likely before the first round of vertebrate genome duplication (VGD); following two successive rounds of VGD and subsequent gene losses, coelacanths retained cry1a, cry1b, cry2 and cry3; and following the third-round teleost genome duplication (TGD) and subsequent gene losses, zebrafish retained six cry genes, renamed as cry1aa (zcry1a in the old nomenclature), cry1ab (zcry1b), cry1ba (zcry2a), cry1bb (zcry2b), cry2 (zcry3) and cry3 (zcry4). Molecular evolutionary analyses suggested that zebrafish cry genes have evolved divergent functions, which is further supported by their distinct and rhythmic expression patterns as shown by both in situ hybridization and quantitative real-time PCR. Systematic cell transfection assays divided six Cry proteins into repressive Cry1aa, Cry1ab, Cry1ba and Cry1bb, and non-repressive Cry2 and Cry3. Cry2 is non-repressive because it lacks an effective protein-protein interaction domain although it does possess a nuclear localization signal (NLS) motif, whilst Cry3 lacks both an NLS motif and a protein-protein interaction domain. These findings provide a better understanding of evolution of zebrafish cry genes.
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Affiliation(s)
- Chao Liu
- 1] Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China [2] School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Jia Hu
- 1] Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China [2] School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Chunxiang Qu
- School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Lin Wang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China
| | - Guodong Huang
- 1] Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China [2] School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Pengfei Niu
- 1] Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China [2] School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Zhaomin Zhong
- 1] Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China [2] School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Fashui Hong
- School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Guanghui Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, Jiangsu, China
| | | | - Han Wang
- 1] Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China [2] School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
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11
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Evolution, functional divergence and conserved exon–intron structure of bHLH/PAS gene family. Mol Genet Genomics 2013; 289:25-36. [DOI: 10.1007/s00438-013-0786-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/09/2013] [Accepted: 10/15/2013] [Indexed: 10/26/2022]
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12
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Chandrasekar R. Alcohol and NMDA receptor: current research and future direction. Front Mol Neurosci 2013; 6:14. [PMID: 23754976 PMCID: PMC3664776 DOI: 10.3389/fnmol.2013.00014] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/07/2013] [Indexed: 01/05/2023] Open
Abstract
The brain is one of the major targets of alcohol actions. Most of the excitatory synaptic transmission in the central nervous system is mediated by N-methyl-D-aspartate (NMDA) receptors. However, one of the most devastating effects of alcohol leads to brain shrinkage, loss of nerve cells at specific regions through a mechanism involving excitotoxicity, oxidative stress. Earlier studies have indicated that chronic exposure to ethanol both in vivo and in vitro, increases NR1 and NR2B gene expression and their polypeptide levels. The effect of alcohol and molecular changes on the regulatory process, which modulates NMDAR functions including factors altering transcription, translation, post-translational modifications, and protein expression, as well as those influencing their interactions with different regulatory proteins (downstream effectors) are incessantly increasing at the cellular level. Further, I discuss the various genetically altered mice approaches that have been used to study NMDA receptor subunits and their functional implication. In a recent countable review, epigenetic dimension (i.e., histone modification-induced chromatin remodeling and DNA methylation, in the process of alcohol related neuroadaptation) is one of the key molecular mechanisms in alcohol mediated NMDAR alteration. Here, I provide a recount on what has already been achieved, current trends and how the future research/studies of the NMDA receptor might lead to even greater engagement with many possible new insights into the neurobiology and treatment of alcoholism.
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Affiliation(s)
- Raman Chandrasekar
- Department of Biochemistry and Biotechnology Core Facility, Kansas State University Manhattan, KS, USA
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13
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GluN2A versus GluN2B: twins, but quite different. Neurosci Bull 2013; 29:761-72. [PMID: 23604599 DOI: 10.1007/s12264-013-1336-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 11/15/2012] [Indexed: 10/26/2022] Open
Abstract
N-Methyl-D-aspartate receptors (NMDARs) play vital roles in the central nervous system, as they are primary mediators of Ca(2+) influx during synaptic activity. The subunits that compose NMDARs share similar topological structures but are distinct in distribution and pharmacological properties, as well as physiological and pathological functions, which make the NMDAR one of the most complex and elusive ionotropic glutamate receptors. In this review, we focus on GluN2A and GluN2B, the primary NMDAR subunits in the cortex and hippocampus, and discuss their differences in developmental expression, brain distribution, trafficking, and functional properties during neuronal activity.
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14
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Genome-wide identification and divergent transcriptional expression of StAR-related lipid transfer (START) genes in teleosts. Gene 2013; 519:18-25. [DOI: 10.1016/j.gene.2013.01.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/28/2013] [Accepted: 01/30/2013] [Indexed: 12/20/2022]
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15
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Parpura V, Verkhratsky A. Astroglial amino acid-based transmitter receptors. Amino Acids 2013; 44:1151-8. [DOI: 10.1007/s00726-013-1458-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022]
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