1
|
Southey BR, Romanova EV, Rodriguez-Zas SL, Sweedler JV. Bioinformatics for Prohormone and Neuropeptide Discovery. Methods Mol Biol 2024; 2758:151-178. [PMID: 38549013 PMCID: PMC11045269 DOI: 10.1007/978-1-0716-3646-6_8] [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] [Indexed: 04/02/2024]
Abstract
Neuropeptides and peptide hormones are signaling molecules produced via complex posttranslational modifications of precursor proteins known as prohormones. Neuropeptides activate specific receptors and are associated with the regulation of physiological systems and behaviors. The identification of prohormones-and the neuropeptides created by these prohormones-from genomic assemblies has become essential to support the annotation and use of the rapidly growing number of sequenced genomes. Here we describe a well-validated methodology for identifying the prohormone complement from genomic assemblies that employs widely available public toolsets and databases. The uncovered prohormone sequences can then be screened for putative neuropeptides to enable accurate proteomic discovery and validation.
Collapse
Affiliation(s)
- Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Elena V Romanova
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sandra L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
2
|
Changes in Neuropeptide Prohormone Genes among Cetartiodactyla Livestock and Wild Species Associated with Evolution and Domestication. Vet Sci 2022; 9:vetsci9050247. [PMID: 35622775 PMCID: PMC9144646 DOI: 10.3390/vetsci9050247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022] Open
Abstract
The impact of evolution and domestication processes on the sequences of neuropeptide prohormone genes that participate in cell–cell signaling influences multiple biological process that involve neuropeptide signaling. This information is important to understand the physiological differences between Cetartiodactyla domesticated species such as cow, pig, and llama and wild species such as hippopotamus, giraffes, and whales. Systematic analysis of changes associated with evolutionary and domestication forces in neuropeptide prohormone protein sequences that are processed into neuropeptides was undertaken. The genomes from 118 Cetartiodactyla genomes representing 22 families were mined for 98 neuropeptide prohormone genes. Compared to other Cetartiodactyla suborders, Ruminantia preserved PYY2 and lost RLN1. Changes in GNRH2, IAPP, INSL6, POMC, PRLH, and TAC4 protein sequences could result in the loss of some bioactive neuropeptides in some families. An evolutionary model suggested that most neuropeptide prohormone genes disfavor sequence changes that incorporate large and hydrophobic amino acids. A compelling finding was that differences between domestic and wild species are associated with the molecular system underlying ‘fight or flight’ responses. Overall, the results demonstrate the importance of simultaneously comparing the neuropeptide prohormone gene complement from close and distant-related species. These findings broaden the foundation for empirical studies about the function of the neuropeptidome associated with health, behavior, and food production.
Collapse
|
3
|
Southey BR, Zhang P, Keever MR, Rymut HE, Johnson RW, Sweedler JV, Rodriguez-Zas SL. Effects of maternal immune activation in porcine transcript isoforms of neuropeptide and receptor genes. J Integr Neurosci 2021; 20:21-31. [PMID: 33834688 PMCID: PMC8103820 DOI: 10.31083/j.jin.2021.01.332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/11/2020] [Accepted: 02/09/2021] [Indexed: 12/17/2022] Open
Abstract
The prolonged effects of maternal immune activation in response stressors during gestation on the offspring's molecular pathways after birth are beginning to be understood. An association between maternal immune activation and neurodevelopmental and behavior disorders such as autism and schizophrenia spectrum disorders has been detected in long-term gene dysregulation. The incidence of alternative splicing among neuropeptides and neuropeptide receptor genes, critical cell-cell signaling molecules, associated with behavior may compromise the replicability of reported maternal immune activation effects at the gene level. This study aims to advance the understanding of the effect of maternal immune activation on transcript isoforms of the neuropeptide system (including neuropeptide, receptor and connecting pathway genes) underlying behavior disorders later in life. Recognizing the wide range of bioactive peptides and functional receptors stemming from alternative splicing, we studied the effects of maternal immune activation at the transcript isoform level on the hippocampus and amygdala of three-week-old pigs exposed to maternal immune activation due to viral infection during gestation. In the hippocampus and amygdala, 29 and 9 transcript isoforms, respectively, had maternal immune activation effects (P-value < 0.01). We demonstrated that the study of the effect of maternal immune activation on neuropeptide systems at the isoform level is necessary to expose opposite effects among transcript isoforms from the same gene. Genes were maternal immune activation effects have also been associated with neurodevelopmental and behavior disorders. The characterization of maternal immune activation effects at the transcript isoform level advances the understanding of neurodevelopmental disorders and identifies precise therapeutic targets.
Collapse
Affiliation(s)
- Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Pan Zhang
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Marissa R Keever
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Haley E Rymut
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Rodney W Johnson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Jonathan V Sweedler
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| | - Sandra L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA.,Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA.,Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, 61801 IL, USA
| |
Collapse
|
4
|
Southey BR, Rodriguez-Zas SL, Rhodes JS, Sweedler JV. Characterization of the prohormone complement in Amphiprion and related fish species integrating genome and transcriptome assemblies. PLoS One 2020; 15:e0228562. [PMID: 32163422 PMCID: PMC7067429 DOI: 10.1371/journal.pone.0228562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 01/19/2020] [Indexed: 12/31/2022] Open
Abstract
The Amphiprion (anemonefish or clownfish) family of teleost fish, which is not a common model species, exhibits multiple unique characteristics, including social control of body size and protandrous sex change. The social changes in sex and body size are modulated by neuropeptide signaling pathways. These neuropeptides are formed from complex processing from larger prohormone proteins; understanding the neuropeptide complement requires information on complete prohormones sequences. Genome and transcriptome information within and across 22 teleost fish species, including 11 Amphiprion species, were assembled and integrated to achieve the first comprehensive survey of their prohormone genes. This information enabled the identification of 175 prohormone isoforms from 159 prohormone proteins across all species. This included identification of 9 CART prepropeptide genes and the loss of insulin-like 5B and tachykinin precursor 1B genes in Pomacentridae species. Transcriptome assemblies generally detected most prohormone genes but provided fewer prohormone genes than genome assemblies due to the lack of expression of prohormone genes or specific isoforms and tissue sampled. Comparisons between duplicate genes indicated that subfunctionalization, degradation, and neofunctionalization may be occurring between all copies. Characterization of the prohormone complement lays the foundation for future peptidomic investigation of the molecular basis of social physiology and behavior in the teleost fish.
Collapse
Affiliation(s)
- Bruce R. Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Sandra L. Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Justin S. Rhodes
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Psychology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States of America
| | - Jonathan V. Sweedler
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States of America
| |
Collapse
|
5
|
Southey BR, Romanova EV, Rodriguez-Zas SL, Sweedler JV. Bioinformatics for Prohormone and Neuropeptide Discovery. Methods Mol Biol 2018; 1719:71-96. [PMID: 29476505 DOI: 10.1007/978-1-4939-7537-2_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Neuropeptides and peptide hormones are signaling molecules produced via complex post-translational modifications of precursor proteins known as prohormones. Neuropeptides activate specific receptors and are associated with the regulation of physiological systems and behaviors. The identification of prohormones-and the neuropeptides created by these prohormones-from genomic assemblies has become essential to support the annotation and use of the rapidly growing number of sequenced genomes. Here we describe a methodology for identifying the prohormone complement from genomic assemblies that employs widely available public toolsets and databases. The uncovered prohormone sequences can then be screened for putative neuropeptides to enable accurate proteomic discovery and validation.
Collapse
Affiliation(s)
- Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Elena V Romanova
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sandra L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
6
|
Gan L, Yang B, Mei H. The effect of iron dextran on the transcriptome of pig hippocampus. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0469-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
7
|
Gan L, Xie L, Zuo F, Xiang Z, He N. Transcriptomic analysis of Rongchang pig brains and livers. Gene 2015; 560:96-106. [PMID: 25637719 DOI: 10.1016/j.gene.2015.01.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/31/2014] [Accepted: 01/26/2015] [Indexed: 01/01/2023]
Abstract
Recent developments in high-throughput RNA sequencing (RNA-seq) technology have led to a dramatic impact on our understanding of the structure and expression profiles of the mammalian transcriptome. To gain insights into the usefulness of swine production and biomedical model, the transcriptome profiling of Rongchang pig brains and livers was characterized using RNA-seq technology to uncover functional candidate molecules. In the study, total RNAs from brains and livers of Rongchang pig were sequenced and 8.6Gb sequencing data was obtained. This analysis revealed tissue specificity through the identification of 5575 and 4600 differentially expressed genes (DEGs) in brains and livers, respectively and the functional analysis of DEGs. Furthermore, 83 neuropeptide gene transcripts, 69 neuropeptide receptor gene transcripts, 10 pro-neuropeptide convertase gene transcripts and many other neuropeptide related protein gene transcripts were identified. Totally, the major characteristics of the transcriptional profiles of Rongchang pig brains and livers were present.
Collapse
Affiliation(s)
- Ling Gan
- The Department of Veterinary Medicine, Rongchang Campus, Southwest University, Rongchang, Chongqing 402460, China.
| | - Liwei Xie
- Center of Molecular Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Fuyuan Zuo
- The Department of Animal Husbandry, Rongchang Campus, Southwest University, Rongchang, Chongqing 402460, China.
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing 400715, China.
| |
Collapse
|
8
|
Wang F, Xiao J, Cong W, Li A, Wei F, Xu J, Zhang C, Fan Z, He J, Wang S. Stage-specific differential gene expression profiling and functional network analysis during morphogenesis of diphyodont dentition in miniature pigs, Sus Scrofa. BMC Genomics 2014; 15:103. [PMID: 24498892 PMCID: PMC3937075 DOI: 10.1186/1471-2164-15-103] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 01/28/2014] [Indexed: 12/11/2022] Open
Abstract
Background Our current knowledge of tooth development derives mainly from studies in mice, which have only one set of non-replaced teeth, compared with the diphyodont dentition in humans. The miniature pig is also diphyodont, making it a valuable alternative model for understanding human tooth development and replacement. However, little is known about gene expression and function during swine odontogenesis. The goal of this study is to undertake the survey of differential gene expression profiling and functional network analysis during morphogenesis of diphyodont dentition in miniature pigs. The identification of genes related to diphyodont development should lead to a better understanding of morphogenetic patterns and the mechanisms of diphyodont replacement in large animal models and humans. Results The temporal gene expression profiles during early diphyodont development in miniature pigs were detected with the Affymetrix Porcine GeneChip. The gene expression data were further evaluated by ANOVA as well as pathway and STC analyses. A total of 2,053 genes were detected with differential expression. Several signal pathways and 151 genes were then identified through the construction of pathway and signal networks. Conclusions The gene expression profiles indicated that spatio-temporal down-regulation patterns of gene expression were predominant; while, both dynamic activation and inhibition of pathways occurred during the morphogenesis of diphyodont dentition. Our study offers a mechanistic framework for understanding dynamic gene regulation of early diphyodont development and provides a molecular basis for studying teeth development, replacement, and regeneration in miniature pigs.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Songlin Wang
- Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Tian Tan Xi Li No,4, Beijing 100050, PR China.
| |
Collapse
|