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Reis HBD, Carvalho ME, Espigolan R, Poleti MD, Ambrizi DR, Berton MP, Ferraz JBS, de Mattos Oliveira EC, Eler JP. Genome-Wide Association (GWAS) Applied to Carcass and Meat Traits of Nellore Cattle. Metabolites 2023; 14:6. [PMID: 38276296 PMCID: PMC10818672 DOI: 10.3390/metabo14010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 01/27/2024] Open
Abstract
The meat market has enormous importance for the world economy, and the quality of the product offered to the consumer is fundamental for the success of the sector. In this study, we analyzed a database which contained information on 2470 animals from a commercial farm in the state of São Paulo, Brazil. Of this total, 2181 animals were genotyped, using 777,962 single-nucleotide polymorphisms (SNPs). After quality control analysis, 468,321 SNPs provided information on the number of genotyped animals. Genome-wide association analyses (GWAS) were performed for the characteristics of the rib eye area (REA), subcutaneous fat thickness (SFT), shear force at 7 days' ageing (SF7), and intramuscular fat (IMF), with the aid of the single-step genomic best linear unbiased prediction (ssGBLUP) method, with the purpose of identifying possible genomic windows (~1 Mb) responsible for explaining at least 0.5% of the genetic variance of the traits under analysis (≥0.5%). These genomic regions were used in a gene search and enrichment analyses using MeSH terms. The distributed heritability coefficients were 0.14, 0.20, 0.18, and 0.21 for REA, SFT, SF7, and IMF, respectively. The GWAS results indicated significant genomic windows for the traits of interest in a total of 17 chromosomes. Enrichment analyses showed the following significant terms (FDR ≤ 0.05) associated with the characteristics under study: for the REA, heat stress disorders and life cycle stages; for SFT, insulin and nonesterified fatty acids; for SF7, apoptosis and heat shock proteins (HSP27); and for IMF, metalloproteinase 2. In addition, KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis allowed us to highlight important metabolic pathways related to the studied phenotypes, such as the growth hormone synthesis, insulin-signaling, fatty acid metabolism, and ABC transporter pathways. The results obtained provide a better understanding of the molecular processes involved in the expression of the studied characteristics and may contribute to the design of selection strategies and future studies aimed at improving the productivity of Nellore cattle.
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Affiliation(s)
- Hugo Borges Dos Reis
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Minos Esperândio Carvalho
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Rafael Espigolan
- Department of Animal Science and Biological Sciences, Federal University of Santa Maria (UFSM), Av. Independencia, 3751, Palmeira das Missões 98300-000, RS, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Dewison Ricardo Ambrizi
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Mariana Piatto Berton
- School of Agricultural and Veterinary Studies (FCAV), São Paulo State University, Jaboticabal 14884-900, SP, Brazil;
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Elisângela Chicaroni de Mattos Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Joanir Pereira Eler
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
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2
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Chau KD, Shamekh M, Huisken J, Rehan SM. The effects of maternal care on the developmental transcriptome and metatranscriptome of a wild bee. Commun Biol 2023; 6:904. [PMID: 37709905 PMCID: PMC10502028 DOI: 10.1038/s42003-023-05275-2] [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] [Received: 03/24/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023] Open
Abstract
Maternal care acts as a strong environmental stimulus that can induce phenotypic plasticity in animals and may also alter their microbial communities through development. Here, we characterize the developmental metatranscriptome of the small carpenter bee, Ceratina calcarata, across developmental stages and in the presence or absence of mothers. Maternal care had the most influence during early development, with the greatest number and magnitude of differentially expressed genes between maternal care treatments, and enrichment for transcription factors regulating immune response in motherless early larvae. Metatranscriptomic data revealed fungi to be the most abundant group in the microbiome, with Aspergillus the most abundant in early larvae raised without mothers. Finally, integrative analysis between host transcriptome and metatranscriptome highlights several fungi correlating with developmental and immunity genes. Our results provide characterizations of the influence of maternal care on gene expression and the microbiome through development in a wild bee.
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Affiliation(s)
| | | | - Jesse Huisken
- Department of Biology, York University, Toronto, Canada
| | - Sandra M Rehan
- Department of Biology, York University, Toronto, Canada.
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3
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Quddusi DM, Bajcinca N. Identification of genomic biomarkers and their pathway crosstalks for deciphering mechanistic links in glioblastoma. IET Syst Biol 2023; 17:143-161. [PMID: 37277696 PMCID: PMC10439498 DOI: 10.1049/syb2.12066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 04/22/2023] [Accepted: 05/03/2023] [Indexed: 06/07/2023] Open
Abstract
Glioblastoma is a grade IV pernicious neoplasm occurring in the supratentorial region of brain. As its causes are largely unknown, it is essential to understand its dynamics at the molecular level. This necessitates the identification of better diagnostic and prognostic molecular candidates. Blood-based liquid biopsies are emerging as a novel tool for cancer biomarker discovery, guiding the treatment and improving its early detection based on their tumour origin. There exist previous studies focusing on the identification of tumour-based biomarkers for glioblastoma. However, these biomarkers inadequately represent the underlying pathological state and incompletely illustrate the tumour because of non-recursive nature of this approach to monitor the disease. Also, contrary to the tumour biopsies, liquid biopsies are non-invasive and can be performed at any interval during the disease span to surveil the disease. Therefore, in this study, a unique dataset of blood-based liquid biopsies obtained primarily from tumour-educated blood platelets (TEP) is utilised. This RNA-seq data from ArrayExpress is acquired comprising human cohort with 39 glioblastoma subjects and 43 healthy subjects. Canonical and machine learning approaches are applied for identification of the genomic biomarkers for glioblastoma and their crosstalks. In our study, 97 genes appeared enriched in 7 oncogenic pathways (RAF-MAPK, P53, PRC2-EZH2, YAP conserved, MEK-MAPK, ErbB2 and STK33 signalling pathways) using GSEA, out of which 17 have been identified participating actively in crosstalks. Using PCA, 42 genes are found enriched in 7 pathways (cytoplasmic ribosomal proteins, translation factors, electron transport chain, ribosome, Huntington's disease, primary immunodeficiency pathways, and interferon type I signalling pathway) harbouring tumour when altered, out of which 25 actively participate in crosstalks. All the 14 pathways foster well-known cancer hallmarks and the identified DEGs can serve as genomic biomarkers, not only for the diagnosis and prognosis of Glioblastoma but also in providing a molecular foothold for oncogenic decision making in order to fathom the disease dynamics. Moreover, SNP analysis for the identified DEGs is performed to investigate their roles in disease dynamics in an elaborated manner. These results suggest that TEPs are capable of providing disease insights just like tumour cells with an advantage of being extracted anytime during the course of disease in order to monitor it.
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Affiliation(s)
- Darrak Moin Quddusi
- Chair of Mechatronics in the Faculty of Mechanical and Process EngineeringRheinland‐Pfälzische Technische Universität Kaiserslautern‐LandauKaiserslauternGermany
| | - Naim Bajcinca
- Chair of Mechatronics in the Faculty of Mechanical and Process EngineeringRheinland‐Pfälzische Technische Universität Kaiserslautern‐LandauKaiserslauternGermany
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4
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Zhang G, Mou Z, Wang H, Liu H. Comprehensive proteomic analysis of the main liver
and attached liver of <i>Glyptosternum maculatum</i> on the basis
of data-independent mass spectrometry acquisition. JOURNAL OF ANIMAL AND FEED SCIENCES 2022. [DOI: 10.22358/jafs/154070/2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Ercc2/Xpd deficiency results in failure of digestive organ growth in zebrafish with elevated nucleolar stress. iScience 2022; 25:104957. [PMID: 36065184 PMCID: PMC9440294 DOI: 10.1016/j.isci.2022.104957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/23/2022] [Accepted: 08/12/2022] [Indexed: 12/09/2022] Open
Abstract
Mutations in ERCC2/XPD helicase, an important component of the TFIIH complex, cause distinct human genetic disorders which exhibit various pathological features. However, the molecular mechanisms underlying many symptoms remain elusive. Here, we have shown that Ercc2/Xpd deficiency in zebrafish resulted in hypoplastic digestive organs with normal bud initiation but later failed to grow. The proliferation of intestinal endothelial cells was impaired in ercc2/xpd mutants, and mitochondrial abnormalities, autophagy, and inflammation were highly induced. Further studies revealed that these abnormalities were associated with the perturbation of rRNA synthesis and nucleolar stress in a p53-independent manner. As TFIIH has only been implicated in RNA polymerase I-dependent transcription in vitro, our results provide the first evidence for the connection between Ercc2/Xpd and rRNA synthesis in an animal model that recapitulates certain key characteristics of ERCC2/XPD-related human genetic disorders, and will greatly advance our understanding of the molecular pathogenesis of these diseases. Ercc2/Xpd deficiency results in failure of digestive organ growth in zebrafish Ercc2/Xpd-deficient intestinal endothelial cells exhibit impaired proliferation Mitochondrial abnormalities, autophagy, and inflammation are highly induced rRNA synthesis perturbation leads to nucleolar stress in a p53-independent manner
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Transcriptome Sequencing and Bioinformatics Analysis of Ovarian Tissues from Pomacea canaliculata in Guangdong and Hunan. Mediators Inflamm 2022; 2022:3917036. [PMID: 35431656 PMCID: PMC9007660 DOI: 10.1155/2022/3917036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/04/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022] Open
Abstract
In this study, the fecundity of Pomacea canaliculata was studied by collecting egg masses from Guangdong and Hunan using field egg collection and indoor propagation. Through high-throughput RNA sequencing (RNA-seq), we analyzed the ovarian tissue of the snails in Guangdong (G_O) and those in Hunan (H_O) using comparative analysis of transcription. Moreover, we used bioinformatics methods to screen the key pathways and genes that affect the fecundity of snails from the two locations. Results. The results showed that the absolute fecundity and weight-relative fecundity of Pomacea canaliculata in Guangdong were significantly higher than those in Hunan. We found 1,546 differential genes through differential gene screening (528 genes upregulated in snails from Guangdong and 1018 in snails from Hunan). The ribosomal signaling pathway and rpl23a, uba52 are critical pathways and essential genes that affect the fecundity of snails. Conclusions. The 27 differential genes in the ribosome signaling pathway, collected from H_O, were all downregulated. As a result, ovarian tissue protein synthesis is impaired, which is an important mechanism that affects snails' ability to reproduce.
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Luan Y, Tang N, Yang J, Liu S, Cheng C, Wang Y, Chen C, Guo YN, Wang H, Zhao W, Zhao Q, Li W, Xiang M, Ju R, Xie Z. Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells. Nucleic Acids Res 2022; 50:6601-6617. [PMID: 35137207 PMCID: PMC9262593 DOI: 10.1093/nar/gkac053] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 01/13/2022] [Accepted: 02/03/2022] [Indexed: 01/05/2023] Open
Abstract
Human ribosomes have long been thought to be uniform factories with little regulatory function. Accumulating evidence emphasizes the heterogeneity of ribosomal protein (RP) expression in specific cellular functions and development. However, a systematic understanding of functional relevance of RPs is lacking. Here, we surveyed translational and transcriptional changes after individual knockdown of 75 RPs, 44 from the large subunit (60S) and 31 from the small subunit (40S), by Ribo-seq and RNA-seq analyses. Deficiency of individual RPs altered specific subsets of genes transcriptionally and translationally. RP genes were under cotranslational regulation upon ribosomal stress, and deficiency of the 60S RPs and the 40S RPs had opposite effects. RP deficiency altered the expression of genes related to eight major functional classes, including the cell cycle, cellular metabolism, signal transduction and development. 60S RP deficiency led to greater inhibitory effects on cell growth than did 40S RP deficiency, through P53 signaling. Particularly, we showed that eS8/RPS8 deficiency stimulated apoptosis while eL13/RPL13 or eL18/RPL18 deficiency promoted senescence. We also validated the phenotypic impacts of uL5/RPL11 and eL15/RPL15 deficiency on retina development and angiogenesis, respectively. Overall, our study provides a valuable resource for and novel insights into ribosome regulation in cellular activities, development and diseases.
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Affiliation(s)
- Yizhao Luan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Nan Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jiaqi Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shuting Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Chichi Cheng
- School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Yan Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Congying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Ya-Nan Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenxue Zhao
- School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR 999077, China
| | - Wei Li
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Rong Ju
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China
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8
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Zhang C, Huang R, Ma X, Chen J, Han X, Li L, Luo L, Ruan H, Huang H. The Ribosome Biogenesis Factor Ltv1 Is Essential for Digestive Organ Development and Definitive Hematopoiesis in Zebrafish. Front Cell Dev Biol 2021; 9:704730. [PMID: 34692673 PMCID: PMC8528963 DOI: 10.3389/fcell.2021.704730] [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: 05/03/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Ribosome biogenesis is a fundamental activity in cells. Ribosomal dysfunction underlies a category of diseases called ribosomopathies in humans. The symptomatic characteristics of ribosomopathies often include abnormalities in craniofacial skeletons, digestive organs, and hematopoiesis. Consistently, disruptions of ribosome biogenesis in animals are deleterious to embryonic development with hypoplasia of digestive organs and/or impaired hematopoiesis. In this study, ltv1, a gene involved in the small ribosomal subunit assembly, was knocked out in zebrafish by clustered regularly interspaced short palindromic repeats (CRISPRs)/CRISPR associated protein 9 (Cas9) technology. The recessive lethal mutation resulted in disrupted ribosome biogenesis, and ltv1 Δ14/Δ14 embryos displayed hypoplastic craniofacial cartilage, digestive organs, and hematopoiesis. In addition, we showed that the impaired cell proliferation, instead of apoptosis, led to the defects in exocrine pancreas and hematopoietic stem and progenitor cells (HSPCs) in ltv1 Δ14/Δ14 embryos. It was reported that loss of function of genes associated with ribosome biogenesis often caused phenotypes in a P53-dependent manner. In ltv1 Δ14/Δ14 embryos, both P53 protein level and the expression of p53 target genes, Δ113p53 and p21, were upregulated. However, knockdown of p53 failed to rescue the phenotypes in ltv1 Δ14/Δ14 larvae. Taken together, our data demonstrate that LTV1 ribosome biogenesis factor (Ltv1) plays an essential role in digestive organs and hematopoiesis development in zebrafish in a P53-independent manner.
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Affiliation(s)
- Chong Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Rui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Xirui Ma
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Jiehui Chen
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Xinlu Han
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Li Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Lingfei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Hua Ruan
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Honghui Huang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environments and Bio-Resources of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
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Selvaraju S, Swathi D, Ramya L, Lavanya M, Archana SS, Sivaram M. Orchestrating the expression levels of sperm mRNAs reveals CCDC174 as an important determinant of semen quality and bull fertility. Syst Biol Reprod Med 2020; 67:89-101. [PMID: 33190538 DOI: 10.1080/19396368.2020.1836286] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Bulls with acceptable semen quality vary in actual field fertility and this can be elucidated by studying the expression levels of mRNAs in the sperm. The present study aimed at assessing the variations in the sperm gene expression levels of PRM1, CCDC174, RPL36A, TMCO2, SWI5 and OIT3 in bulls differing in fertility status. Frozen semen samples from Holstein-Friesian bulls were classified into high-fertile (n = 8, average field conception rate = 46.1 ± 0.51, p < 0.001) and sub-fertile (n = 7, average field conception rate = 39.4 ± 0.69) groups. In the post-thaw semen samples, sperm kinematics, structural and functional membrane integrities, mitochondrial membrane potential and chromatin distribution were analyzed. The sperm total RNA was subjected to gene expression studies by Real-Time PCR. Multivariate regression analysis was performed using gene expression levels and conception rates. The sperm functional attributes did not differ significantly between the groups. The relative mRNA levels (fold change) of CCDC174 (6.20), RPL36A (4.66), SWI5 (1.86) and OIT3 (1.53) were higher in high-fertile bulls. Further, the expression level of the CCDC174 gene was significantly (p = 0.02) up-regulated in high-fertile bulls. The fertility prediction multivariate model with genes, CCDC174, RPL36A, TMCO2 and OIT3 had the maximum coefficient of determination (R2 = 0.68) with the field conception rate. This model had 93.3% bull fertility prediction accuracy with 100% sensitivity and 87.5% specificity. The study suggests that the expression level of CCDC174 can be used as a potential marker for assessing bull fertility.
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Affiliation(s)
- Sellappan Selvaraju
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru-560030, India
| | - Divakar Swathi
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru-560030, India
| | - Laxman Ramya
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru-560030, India
| | - Maharajan Lavanya
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru-560030, India.,Division of Animal Reproduction, Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, India
| | - Santhanahalli Siddalingappa Archana
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru-560030, India
| | - Muniandy Sivaram
- Southern Regional Station, ICAR-National Dairy Research Institute, Bengaluru-560030, India
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Farhadian M, Rafat SA, Panahi B, Ebrahimie E. Transcriptome signature of two lactation stages in Ghezel sheep identifies using RNA-Sequencing. Anim Biotechnol 2020; 33:223-233. [PMID: 32633600 DOI: 10.1080/10495398.2020.1784185] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The expression of genes and their regulation during lactation in Ghezel sheep breed remains less understood. To explore the underlying molecular mechanism of the lactation process in the mammary gland, transcriptome profiles of Iranian fat-tailed Ghezel sheep breed milk at two stages, before (BF) and after peak (AF) stages of lactation were investigated. Functional impacts of differentially expressed genes (DEGs) between BF and AF stages were surveyed using Gene Ontology (GO) and Protein-Protein Interaction (PPI) network analysis. Totally, 75 DEGs were identified between BF and AF stages of lactation. The RNA-Seq results were validated by Q-RT-PCR. Gene ontology of DEGs mainly enriched in metabolic process and oxidative phosphorylation. PPI network analysis also highlighted the contribution of peroxisome proliferator-activated receptors (PPAR) signaling, oxidative phosphorylation and metabolic pathways in the lactation process. Intriguingly, the genes involved in fat metabolism dominantly down-regulated at AF stage. Our results provide new insight into transcriptional changes and add to growing body of knowledge on the lactation process in fat-tailed sheep breeds.
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Affiliation(s)
- Mohammad Farhadian
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Seyed Aabbas Rafat
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Bahman Panahi
- Department of Genomics, Branch for Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia.,School of Animal and Veterinary Sciences, The University of Adelaide, South Australia, Australia
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11
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The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules. Int J Mol Sci 2019; 20:ijms20010140. [PMID: 30609737 PMCID: PMC6337102 DOI: 10.3390/ijms20010140] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/18/2022] Open
Abstract
We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.
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12
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Choi J, Saraf A, Florens L, Washburn MP, Busino L. PTPN14 regulates Roquin2 stability by tyrosine dephosphorylation. Cell Cycle 2018; 17:2243-2255. [PMID: 30209976 DOI: 10.1080/15384101.2018.1522912] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein phosphorylation regulates a variety of cellular signaling pathways and fundamental mechanisms in cells. In this paper, we demonstrate that the mRNA decay factor Roquin2 is phosphorylated at tyrosine residue in position 691 in vivo. This phosphorylation disrupts the interaction with KLHL6, the E3 ligase for Roquin2. Furthermore, we establish that the tyrosine phosphatase PTPN14 specifically interacts with Roquin2 through its phosphatase domain and dephosphorylates Roquin2 tyrosine 691. Overexpression of PTPN14 promotes Roquin2 degradation in a KLHL6-dependant manner by promoting interaction with KLHL6. Collectively, our findings reveal that PTPN14 negatively regulates the protein stability of Roquin2, thereby adding a new layer of regulation to the KLHL6-Roquin2 axis.
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Affiliation(s)
- Jaewoo Choi
- a Department of Cancer Biology, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Anita Saraf
- b The Stowers Institute of Medical Research , Kansas , MO , USA
| | | | - Michael P Washburn
- b The Stowers Institute of Medical Research , Kansas , MO , USA.,c Department of Pathology and Laboratory Medicine , The University of Kansas Medical Center , Kansas , KS , USA
| | - Luca Busino
- a Department of Cancer Biology, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
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Lin HD, Hsu LS, Chien CC, Chen SC. Proteomic analysis of ametryn toxicity in zebrafish embryos. ENVIRONMENTAL TOXICOLOGY 2018; 33:579-586. [PMID: 29427468 DOI: 10.1002/tox.22546] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 01/19/2018] [Accepted: 01/27/2018] [Indexed: 06/08/2023]
Abstract
Ametrym (AMT) is the most widely used herbicide and frequently detected in the aquatic environment. AMT also represent a potential health risk to aquatic organisms and animals, including humans. However, little data are available on their toxicity to zebrafish (Danio rerio). The aim of the present study was to evaluate the toxicological effects of AMT exposure on zebrafish embryos. In the acute toxicity test, 6 hpf embryos were exposed to various concentrations of AMT for 24 or 48 h. The results indicated that AMT induced malformation in larvae. To investigate the toxicological mechanism on the protein expression level. A proteomic approach was employed to investigate the proteome alterations of zebra fish embryos exposed to 20 mg/L AMT for 48 h. Among 2925 unique proteins identified, 298 differential proteins (> or <1.3-fold, P < 0.05) were detected in the treated embryos as compared to the corresponding proteins in the untreated embryos. Gene ontology analysis showed that these up-regulated proteins were most involved in glycolysis, lipid transport, protein polymerization, and nucleotide binding, and the down-regulated proteins were related to microtubule-based process, protein polymerization, oxygen transport. Moreover, KEGG pathway analysis indicated that tight junction, ribosome, and oxidative phosphorylation were inhibited in the treated embryos. These findings provide new insight into the mechanisms of toxicity induced by AMT.
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Affiliation(s)
- Heng-Dao Lin
- Department of Life Sciences, National Central University, Jhongli, Taiwan
| | - Li-Sung Hsu
- Institute of Biochemistry, Microbiology, and Immunology, Chung Shan Medical University, Taichung, Taiwan
- Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chih-Ching Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Jhongli, Taiwan
| | - Ssu-Ching Chen
- Department of Life Sciences, National Central University, Jhongli, Taiwan
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14
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He J, Yang Y, Zhang J, Chen J, Wei X, He J, Luo L. Ribosome biogenesis protein Urb1 acts downstream of mTOR complex 1 to modulate digestive organ development in zebrafish. J Genet Genomics 2017; 44:567-576. [DOI: 10.1016/j.jgg.2017.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 12/23/2022]
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15
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Arnold N, Messaoudi I. Simian varicella virus causes robust transcriptional changes in T cells that support viral replication. Virus Res 2017; 238:226-235. [PMID: 28698046 PMCID: PMC7114558 DOI: 10.1016/j.virusres.2017.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 05/24/2017] [Accepted: 07/04/2017] [Indexed: 12/13/2022]
Abstract
T cells play a major role in varicella viruses dissemination to ganglia and skin. SVV infection of T cells increases the expression of cell cycle genes. SVV infection downregulates genes important for antigen presentation in T cells. SVV T cell infection disrupts expression of genes vital for metabolism and immunity.
Varicella zoster virus (VZV) causes varicella (chickenpox) during acute infection. Several studies have shown that T cells are early and preferential targets of VZV infection that play a critical role in disseminating VZV in to the skin and ganglia. However, the transcriptional changes that occur in VZV-infected T cells remain unclear due to limited access to clinical samples and robust translational animal models. In this study, we used a nonhuman primate model of VZV infection where rhesus macaques are infected with the closely related Simian Varicella Virus (SVV) to provide novel insights into VZV-T cell interactions. RNA sequencing of bronchial alveolar lavage-resident T cells isolated from infected rhesus macaques show that SVV infection alters expression of genes important for regulation of gene expression, cell cycle progression, metabolism, and antiviral immunity. These data provide insight into cellular processes that may support viral replication, facilitate SVV dissemination, and evade host defense.
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Affiliation(s)
- Nicole Arnold
- Graduate Program in Microbiology, University of California, Riverside, CA, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, CA, 92697, USA.
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16
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Selenoprotein H is an essential regulator of redox homeostasis that cooperates with p53 in development and tumorigenesis. Proc Natl Acad Sci U S A 2016; 113:E5562-71. [PMID: 27588899 DOI: 10.1073/pnas.1600204113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Selenium, an essential micronutrient known for its cancer prevention properties, is incorporated into a class of selenocysteine-containing proteins (selenoproteins). Selenoprotein H (SepH) is a recently identified nucleolar oxidoreductase whose function is not well understood. Here we report that seph is an essential gene regulating organ development in zebrafish. Metabolite profiling by targeted LC-MS/MS demonstrated that SepH deficiency impairs redox balance by reducing the levels of ascorbate and methionine, while increasing methionine sulfoxide. Transcriptome analysis revealed that SepH deficiency induces an inflammatory response and activates the p53 pathway. Consequently, loss of seph renders larvae susceptible to oxidative stress and DNA damage. Finally, we demonstrate that seph interacts with p53 deficiency in adulthood to accelerate gastrointestinal tumor development. Overall, our findings establish that seph regulates redox homeostasis and suppresses DNA damage. We hypothesize that SepH deficiency may contribute to the increased cancer risk observed in cohorts with low selenium levels.
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Bielczyk-Maczyńska E, Lam Hung L, Ferreira L, Fleischmann T, Weis F, Fernández-Pevida A, Harvey SA, Wali N, Warren AJ, Barroso I, Stemple DL, Cvejic A. The Ribosome Biogenesis Protein Nol9 Is Essential for Definitive Hematopoiesis and Pancreas Morphogenesis in Zebrafish. PLoS Genet 2015; 11:e1005677. [PMID: 26624285 PMCID: PMC4666468 DOI: 10.1371/journal.pgen.1005677] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/26/2015] [Indexed: 12/27/2022] Open
Abstract
Ribosome biogenesis is a ubiquitous and essential process in cells. Defects in ribosome biogenesis and function result in a group of human disorders, collectively known as ribosomopathies. In this study, we describe a zebrafish mutant with a loss-of-function mutation in nol9, a gene that encodes a non-ribosomal protein involved in rRNA processing. nol9sa1022/sa1022 mutants have a defect in 28S rRNA processing. The nol9sa1022/sa1022 larvae display hypoplastic pancreas, liver and intestine and have decreased numbers of hematopoietic stem and progenitor cells (HSPCs), as well as definitive erythrocytes and lymphocytes. In addition, ultrastructural analysis revealed signs of pathological processes occurring in endothelial cells of the caudal vein, emphasizing the complexity of the phenotype observed in nol9sa1022/sa1022 larvae. We further show that both the pancreatic and hematopoietic deficiencies in nol9sa1022/sa1022 embryos were due to impaired cell proliferation of respective progenitor cells. Interestingly, genetic loss of Tp53 rescued the HSPCs but not the pancreatic defects. In contrast, activation of mRNA translation via the mTOR pathway by L-Leucine treatment did not revert the erythroid or pancreatic defects. Together, we present the nol9sa1022/sa1022 mutant, a novel zebrafish ribosomopathy model, which recapitulates key human disease characteristics. The use of this genetically tractable model will enhance our understanding of the tissue-specific mechanisms following impaired ribosome biogenesis in the context of an intact vertebrate.
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Affiliation(s)
- Ewa Bielczyk-Maczyńska
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Laure Lam Hung
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lauren Ferreira
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Tobias Fleischmann
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Félix Weis
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Antonio Fernández-Pevida
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Steven A. Harvey
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Neha Wali
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alan J. Warren
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ana Cvejic
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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18
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Tourlakis ME, Zhang S, Ball HL, Gandhi R, Liu H, Zhong J, Yuan JS, Guidos CJ, Durie PR, Rommens JM. In Vivo Senescence in the Sbds-Deficient Murine Pancreas: Cell-Type Specific Consequences of Translation Insufficiency. PLoS Genet 2015; 11:e1005288. [PMID: 26057580 PMCID: PMC4461263 DOI: 10.1371/journal.pgen.1005288] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/18/2015] [Indexed: 01/01/2023] Open
Abstract
Genetic models of ribosome dysfunction show selective organ failure, highlighting a gap in our understanding of cell-type specific responses to translation insufficiency. Translation defects underlie a growing list of inherited and acquired cancer-predisposition syndromes referred to as ribosomopathies. We sought to identify molecular mechanisms underlying organ failure in a recessive ribosomopathy, with particular emphasis on the pancreas, an organ with a high and reiterative requirement for protein synthesis. Biallelic loss of function mutations in SBDS are associated with the ribosomopathy Shwachman-Diamond syndrome, which is typified by pancreatic dysfunction, bone marrow failure, skeletal abnormalities and neurological phenotypes. Targeted disruption of Sbds in the murine pancreas resulted in p53 stabilization early in the postnatal period, specifically in acinar cells. Decreased Myc expression was observed and atrophy of the adult SDS pancreas could be explained by the senescence of acinar cells, characterized by induction of Tgfβ, p15Ink4b and components of the senescence-associated secretory program. This is the first report of senescence, a tumour suppression mechanism, in association with SDS or in response to a ribosomopathy. Genetic ablation of p53 largely resolved digestive enzyme synthesis and acinar compartment hypoplasia, but resulted in decreased cell size, a hallmark of decreased translation capacity. Moreover, p53 ablation resulted in expression of acinar dedifferentiation markers and extensive apoptosis. Our findings indicate a protective role for p53 and senescence in response to Sbds ablation in the pancreas. In contrast to the pancreas, the Tgfβ molecular signature was not detected in fetal bone marrow, liver or brain of mouse models with constitutive Sbds ablation. Nevertheless, as observed with the adult pancreas phenotype, disease phenotypes of embryonic tissues, including marked neuronal cell death due to apoptosis, were determined to be p53-dependent. Our findings therefore point to cell/tissue-specific responses to p53-activation that include distinction between apoptosis and senescence pathways, in the context of translation disruption. Growth of all living things relies on protein synthesis. Failure of components of the complex protein synthesis machinery underlies a growing list of inherited and acquired multi—organ syndromes referred to as ribosomopathies. While ribosomes, the critical working components of the protein synthesis machinery, are required in all cell types to translate the genetic code, only certain organs manifest clinical symptoms in ribosomopathies, indicating specific cell-type features of protein synthesis control. Further, many of these diseases result in cancer despite an inherent deficit in growth. Here we report a range of consequences of protein synthesis insufficiency with loss of a broadly expressed ribosome factor, leading to growth impairment and cell cycle arrest at different stages. Apparent induction of p53-dependent cell death and arrest pathways included apoptosis in the fetal brain and senescence in the mature exocrine pancreas. The senescence, considered a tumour suppression mechanism, was accompanied by the expression of biomarkers associated with early stages of malignant transformation. These findings inform how cancer may initiate when growth is compromised and provide new insights into cell-type specific consequences of protein synthesis insufficiency.
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Affiliation(s)
- Marina E. Tourlakis
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Siyi Zhang
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Heather L. Ball
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Rikesh Gandhi
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Hongrui Liu
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jian Zhong
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Julie S. Yuan
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Department of Immunology, University of Toronto, Toronto, Canada
| | - Cynthia J. Guidos
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Department of Immunology, University of Toronto, Toronto, Canada
| | - Peter R. Durie
- Program in Physiology & Experimental Medicine, Research Institute, Division of Gastroenterology & Nutrition, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Johanna M. Rommens
- Program in Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- * E-mail:
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Zhou X, Liao WJ, Liao JM, Liao P, Lu H. Ribosomal proteins: functions beyond the ribosome. J Mol Cell Biol 2015; 7:92-104. [PMID: 25735597 DOI: 10.1093/jmcb/mjv014] [Citation(s) in RCA: 427] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/05/2014] [Indexed: 01/05/2023] Open
Abstract
Although ribosomal proteins are known for playing an essential role in ribosome assembly and protein translation, their ribosome-independent functions have also been greatly appreciated. Over the past decade, more than a dozen of ribosomal proteins have been found to activate the tumor suppressor p53 pathway in response to ribosomal stress. In addition, these ribosomal proteins are involved in various physiological and pathological processes. This review is composed to overview the current understanding of how ribosomal stress provokes the accumulation of ribosome-free ribosomal proteins, as well as the ribosome-independent functions of ribosomal proteins in tumorigenesis, immune signaling, and development. We also propose the potential of applying these pieces of knowledge to the development of ribosomal stress-based cancer therapeutics.
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Affiliation(s)
- Xiang Zhou
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Wen-Juan Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jun-Ming Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Peng Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
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20
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Wang W, Nag S, Zhang X, Wang MH, Wang H, Zhou J, Zhang R. Ribosomal proteins and human diseases: pathogenesis, molecular mechanisms, and therapeutic implications. Med Res Rev 2014; 35:225-85. [PMID: 25164622 DOI: 10.1002/med.21327] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ribosomes are essential components of the protein synthesis machinery. The process of ribosome biogenesis is well organized and tightly regulated. Recent studies have shown that ribosomal proteins (RPs) have extraribosomal functions that are involved in cell proliferation, differentiation, apoptosis, DNA repair, and other cellular processes. The dysfunction of RPs has been linked to the development and progression of hematological, metabolic, and cardiovascular diseases and cancer. Perturbation of ribosome biogenesis results in ribosomal stress, which triggers activation of the p53 signaling pathway through RPs-MDM2 interactions, resulting in p53-dependent cell cycle arrest and apoptosis. RPs also regulate cellular functions through p53-independent mechanisms. We herein review the recent advances in several forefronts of RP research, including the understanding of their biological features and roles in regulating cellular functions, maintaining cell homeostasis, and their involvement in the pathogenesis of human diseases. We also highlight the translational potential of this research for the identification of molecular biomarkers, and in the discovery and development of novel treatments for human diseases.
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Affiliation(s)
- Wei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, 79106; Cancer Biology Center, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, 79106
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21
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Qin W, Chen Z, Zhang Y, Yan R, Yan G, Li S, Zhong H, Lin S. Nom1 mediates pancreas development by regulating ribosome biogenesis in zebrafish. PLoS One 2014; 9:e100796. [PMID: 24967912 PMCID: PMC4072693 DOI: 10.1371/journal.pone.0100796] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/29/2014] [Indexed: 11/18/2022] Open
Abstract
Ribosome biogenesis is an important biological process for proper cellular function and development. Defects leading to improper ribosome biogenesis can cause diseases such as Diamond-Blackfan anemia and Shwachman-Bodian-Diamond syndrome. Nucleolar proteins are a large family of proteins and are involved in many cellular processes, including the regulation of ribosome biogenesis. Through a forward genetic screen and positional cloning, we identified and characterized a zebrafish line carrying mutation in nucleolar protein with MIF4G domain 1 (nom1), which encodes a conserved nulceolar protein with a role in pre-rRNA processing. Zebrafish nom1 mutants exhibit major defects in endoderm development, especially in exocrine pancreas. Further studies revealed that impaired proliferation of ptf1a-expressing pancreatic progenitor cells mainly contributed to the phenotype. RNA-seq and molecular analysis showed that ribosome biogenesis and pre-mRNA splicing were both affected in the mutant embryos. Several defects of ribosome assembly have been shown to have a p53-dependent mechanism. In the nom1 mutant, loss of p53 did not rescue the pancreatic defect, suggesting a p53-independent role. Further studies indicate that protein phosphatase 1 alpha, an interacting protein to Nom1, could partially rescue the pancreatic defect in nom1 morphants if a human nucleolar localization signal sequence was artificially added. This suggests that targeting Pp1α into the nucleolus by Nom1 is important for pancreatic proliferation. Altogether, our studies revealed a new mechanism involving Nom1 in controlling vertebrate exocrine pancreas formation.
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Affiliation(s)
- Wei Qin
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Zelin Chen
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yihan Zhang
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Ruibin Yan
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Guanrong Yan
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Song Li
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Hanbing Zhong
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, China
| | - Shuo Lin
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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