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Qadir MMF, Elgamal RM, Song K, Kudtarkar P, Sakamuri SS, Katakam PV, El-Dahr SS, Kolls JK, Gaulton KJ, Mauvais-Jarvis F. Single cell regulatory architecture of human pancreatic islets suggests sex differences in β cell function and the pathogenesis of type 2 diabetes. RESEARCH SQUARE 2024:rs.3.rs-4607352. [PMID: 39011095 PMCID: PMC11247939 DOI: 10.21203/rs.3.rs-4607352/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Type 2 and type 1 diabetes (T2D, T1D) exhibit sex differences in insulin secretion, the mechanisms of which are unknown. We examined sex differences in human pancreatic islets from 52 donors with and without T2D combining single cell RNA-seq (scRNA-seq), single nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), hormone secretion, and bioenergetics. In nondiabetic (ND) donors, sex differences in islet cells gene accessibility and expression predominantly involved sex chromosomes. Islets from T2D donors exhibited similar sex differences in sex chromosomes differentially expressed genes (DEGs), but also exhibited sex differences in autosomal genes. Comparing β cells from T2D vs. ND donors, gene enrichment of female β cells showed suppression in mitochondrial respiration, while male β cells exhibited suppressed insulin secretion. Thus, although sex differences in gene accessibility and expression of ND β cells predominantly affect sex chromosomes, the transition to T2D reveals sex differences in autosomes highlighting mitochondrial failure in females.
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Affiliation(s)
- Mirza Muhammad Fahd Qadir
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
| | - Ruth M. Elgamal
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Keijing Song
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Siva S.V.P Sakamuri
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Prasad V. Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Samir S. El-Dahr
- Department of Pediatrics, Tulane University, School of Medicine, New Orleans, LA, USA
| | - Jay K. Kolls
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Franck Mauvais-Jarvis
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
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Qadir MMF, Elgamal RM, Song K, Kudtarkar P, Sakamuri SS, Katakam PV, El-Dahr S, Kolls J, Gaulton KJ, Mauvais-Jarvis F. Single cell regulatory architecture of human pancreatic islets suggests sex differences in β cell function and the pathogenesis of type 2 diabetes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589096. [PMID: 38645001 PMCID: PMC11030320 DOI: 10.1101/2024.04.11.589096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Biological sex affects the pathogenesis of type 2 and type 1 diabetes (T2D, T1D) including the development of β cell failure observed more often in males. The mechanisms that drive sex differences in β cell failure is unknown. Studying sex differences in islet regulation and function represent a unique avenue to understand the sex-specific heterogeneity in β cell failure in diabetes. Here, we examined sex and race differences in human pancreatic islets from up to 52 donors with and without T2D (including 37 donors from the Human Pancreas Analysis Program [HPAP] dataset) using an orthogonal series of experiments including single cell RNA-seq (scRNA-seq), single nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), dynamic hormone secretion, and bioenergetics. In cultured islets from nondiabetic (ND) donors, in the absence of the in vivo hormonal environment, sex differences in islet cell type gene accessibility and expression predominantly involved sex chromosomes. Of particular interest were sex differences in the X-linked KDM6A and Y-linked KDM5D chromatin remodelers in female and male islet cells respectively. Islets from T2D donors exhibited similar sex differences in differentially expressed genes (DEGs) from sex chromosomes. However, in contrast to islets from ND donors, islets from T2D donors exhibited major sex differences in DEGs from autosomes. Comparing β cells from T2D and ND donors revealed that females had more DEGs from autosomes compared to male β cells. Gene set enrichment analysis of female β cell DEGs showed a suppression of oxidative phosphorylation and electron transport chain pathways, while male β cell had suppressed insulin secretion pathways. Thus, although sex-specific differences in gene accessibility and expression of cultured ND human islets predominantly affect sex chromosome genes, major differences in autosomal gene expression between sexes appear during the transition to T2D and which highlight mitochondrial failure in female β cells.
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Affiliation(s)
- Mirza Muhammad Fahd Qadir
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
| | - Ruth M. Elgamal
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Keijing Song
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Siva S.V.P Sakamuri
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Prasad V. Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Samir El-Dahr
- Department of Pediatrics, Tulane University, School of Medicine, New Orleans, LA, USA
| | - Jay Kolls
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Franck Mauvais-Jarvis
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
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Zhao J, Wang C, Zhang L, Lei A, Wang L, Niu L, Zhan S, Guo J, Cao J, Li L, Zhang H, Zhong T. Genome-Wide Identification of Reference Genes for Reverse-Transcription Quantitative PCR in Goat Rumen. Animals (Basel) 2021; 11:ani11113137. [PMID: 34827869 PMCID: PMC8614340 DOI: 10.3390/ani11113137] [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: 10/08/2021] [Revised: 10/30/2021] [Accepted: 10/30/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary The rumen plays an essential role as a digestive organ and serves as the primary site of energy substrate absorption for the productive ruminants. Understanding gene expression profiles is necessary to explore the intrinsic regulatory mechanisms of rumen development in goats. The selection of suitable reference genes (RGs) was the primary assay before the real-time quantitative PCR (RT-qPCR). We identified sixteen genome-wide candidate RGs for normalization of gene expression assessments in goat rumen tissues. We demonstrate that the RGs selected (RPS4X and RPS6) were more stably expressed than the commonly used HKGs (ACTB and GAPDH) in goat rumen tissues, suggesting that the ribosomal protein gene family may be another source for the RG pool. Abstract As the largest chamber of the ruminant stomach, the rumen not only serves as the principal absorptive surface and nutrient transport pathway from the lumen into the animal, but also plays an important short-chain fatty acid (SCFA) metabolic role in addition to protective functions. Accurate characterization of the gene expression profiles of genes of interest is essential to the exploration of the intrinsic regulatory mechanisms of rumen development in goats. Thus, the selection of suitable reference genes (RGs) is an important prerequisite for real-time quantitative PCR (RT-qPCR). In the present study, 16 candidate RGs were identified from our previous transcriptome sequencing of caprine rumen tissues. The quantitative expressions of the candidate RGs were measured using the RT-qPCR method, and the expression stability of the RGs was assessed using the geNorm, NormFinder, and BestKeeper programs. GeNorm analysis showed that the M values were less than 0.5 for all the RGs except GAPT4, indicating that they were stably expressed in the rumen tissues throughout development. RPS4X and RPS6 were the two most stable RGs. Furthermore, the expressions of two randomly selected target genes (IGF1 and TOP2A), normalized by the selected most stable RGs (RPS4X and RPS6), were consistent with the results of RNA sequencing, while the use of GAPDH and ACTB as RGs resulted in altered profiles. Overall, RPS4X and RPS6 showed the highest expression stability and the lowest coefficients of variation, and could be used as the optimal reference combination for quantifying gene expression in rumen tissues via RT-qPCR analysis.
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Affiliation(s)
- Juan Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Cheng Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Aiai Lei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxue Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Development of a Specific Monoclonal Antibody to Detect Male Cells Expressing the RPS4Y1 Protein. Int J Mol Sci 2021; 22:ijms22042001. [PMID: 33670450 PMCID: PMC7921920 DOI: 10.3390/ijms22042001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/24/2022] Open
Abstract
Hemophilia is an X-linked recessive bleeding disorder. In pregnant women carrier of hemophilia, the fetal sex can be determined by non-invasive analysis of fetal DNA circulating in the maternal blood. However, in case of a male fetus, conventional invasive procedures are required for the diagnosis of hemophilia. Fetal cells, circulating in the maternal bloodstream, are an ideal target for a safe non-invasive prenatal diagnosis. Nevertheless, the small number of cells and the lack of specific fetal markers have been the most limiting factors for their isolation. We aimed to develop monoclonal antibodies (mAbs) against the ribosomal protein RPS4Y1 expressed in male cells. By Western blotting, immunoprecipitation and immunofluorescence analyses performed on cell lysates from male human hepatoma (HepG2) and female human embryonic kidney (HEK293) we developed and characterized a specific monoclonal antibody against the native form of the male RPS4Y1 protein that can distinguish male from female cells. The availability of the RPS4Y1-targeting monoclonal antibody should facilitate the development of novel methods for the reliable isolation of male fetal cells from the maternal blood and their future use for non-invasive prenatal diagnosis of X-linked inherited disease such as hemophilia.
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Reindl-Schwaighofer R, Heinzel A, Gualdoni GA, Mesnard L, Claas FHJ, Oberbauer R. Novel insights into non-HLA alloimmunity in kidney transplantation. Transpl Int 2019; 33:5-17. [PMID: 31650645 PMCID: PMC6972536 DOI: 10.1111/tri.13546] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/26/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022]
Abstract
Recognition of non‐self structures on donor cells represents the main immunological barrier in solid organ transplantation. The human leukocyte antigens (HLA) are considered the most important non‐self (allo)antigens in transplantation. Long‐term graft attrition is mainly caused by the formation of alloreactive antibodies that are directed against non‐self structures (i.e., epitopes) on cell surface proteins. Recently published data provided evidence for a similar importance of non‐HLA mismatches between donors and recipients in acute rejection as well as long‐term kidney allograft survival. These data suggest a broader concept of immunological non‐self that goes beyond HLA incompatibility and expands the current concept of polymorphic non‐self epitopes on cell surface molecules from HLA to non‐HLA targets. Amino acid substitutions caused by single nucleotide variants in protein‐coding genes or complete loss of gene expression represent the basis for polymorphic residues in both HLA and non‐HLA molecules. To better understand these novel insights in non‐HLA alloimmunity, we will first review basic principles of the alloimmune response with a focus on the HLA epitope concept in donor‐specific antibody formation before discussing key publications on non‐HLA antibodies.
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Affiliation(s)
- Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Guido A Gualdoni
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Laurent Mesnard
- Sorbonne Université, Urgences Néphrologiques et Transplantation Rénale, Assistance Publique-Hôpitaux de Paris (APHP), Hôpital Tenon, Paris, France
| | - Frans H J Claas
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
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6
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Parthiban K, Perera RL, Sattar M, Huang Y, Mayle S, Masters E, Griffiths D, Surade S, Leah R, Dyson MR, McCafferty J. A comprehensive search of functional sequence space using large mammalian display libraries created by gene editing. MAbs 2019; 11:884-898. [PMID: 31107136 PMCID: PMC6601556 DOI: 10.1080/19420862.2019.1618673] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The construction of large libraries in mammalian cells allows the direct screening of millions of molecular variants for binding properties in a cell type relevant for screening or production. We have created mammalian cell libraries of up to 10 million clones displaying a repertoire of IgG-formatted antibodies on the cell surface. TALE nucleases or CRISPR/Cas9 were used to direct the integration of the antibody genes into a single genomic locus, thereby rapidly achieving stable expression and transcriptional normalization. The utility of the system is illustrated by the affinity maturation of a PD-1-blocking antibody through the systematic mutation and functional survey of 4-mer variants within a 16 amino acid paratope region. Mutating VH CDR3 only, we identified a dominant "solution" involving substitution of a central tyrosine to histidine. This appears to be a local affinity maximum, and this variant was surpassed by a lysine substitution when light chain variants were introduced. We achieve this comprehensive and quantitative interrogation of sequence space by combining high-throughput oligonucleotide synthesis with mammalian display and flow cytometry operating at the multi-million scale.
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7
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Zhou Q, Wang T, Leng L, Zheng W, Huang J, Fang F, Yang L, Chen F, Lin G, Wang WJ, Kristiansen K. Single-cell RNA-seq reveals distinct dynamic behavior of sex chromosomes during early human embryogenesis. Mol Reprod Dev 2019; 86:871-882. [PMID: 31094050 DOI: 10.1002/mrd.23162] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/21/2019] [Accepted: 04/11/2019] [Indexed: 12/20/2022]
Abstract
Several animal and human studies have demonstrated that sex affects kinetics and metabolism during early embryo development. However, the mechanism governing these differences at the molecular level before the expression of the sex-determining gene SRY is unknown. We performed a systematic profiling of gene expression comparing male and female embryos using available single-cell RNA-sequencing data of 1607 individual cells from 99 human preimplantation embryos, covering development stages from 4-cell to late blastocyst. We observed consistent chromosome-wide transcription of autosomes, whereas expression from sex chromosomes exhibits significant differences after embryonic genome activation (EGA). Activation of the Y chromosome is initiated by expression of two genes, RPS4Y1 and DDX3Y, whereas the X chromosome is widely activated, with both copies in females being activated after EGA. In contrast to the stable activation of the Y chromosome, expression of X-linked genes in females declines at the late blastocyst stage, especially in trophectoderm cells, revealing a rapid process of dosage compensation. This dynamic behavior results in a dosage imbalance between male and female embryos, which influences genes involved in cell cycle, protein translation and metabolism. Our results reveal the dynamics of sex chromosomes expression and silencing during early embryogenesis. Studying sex differences during human embryogenesis, as well as understanding the process of X chromosome inactivation and their effects on the sex bias development of in vitro fertilized embryos, will expand the capabilities of assisted reproductive technology and possibly improve the treatment of infertility and enhance reproductive health.
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Affiliation(s)
- Qing Zhou
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Taifu Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Lizhi Leng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China
| | - Wei Zheng
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Jinrong Huang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Fang Fang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ling Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China.,Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Wen-Jing Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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8
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Ferretti MB, Karbstein K. Does functional specialization of ribosomes really exist? RNA (NEW YORK, N.Y.) 2019; 25:521-538. [PMID: 30733326 PMCID: PMC6467006 DOI: 10.1261/rna.069823.118] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
It has recently become clear that ribosomes are much more heterogeneous than previously thought, with diversity arising from rRNA sequence and modifications, ribosomal protein (RP) content and posttranslational modifications (PTMs), as well as bound nonribosomal proteins. In some cases, the existence of these diverse ribosome populations has been verified by biochemical or structural methods. Furthermore, knockout or knockdown of RPs can diversify ribosome populations, while also affecting the translation of some mRNAs (but not others) with biological consequences. However, the effects on translation arising from depletion of diverse proteins can be highly similar, suggesting that there may be a more general defect in ribosome function or stability, perhaps arising from reduced ribosome numbers. Consistently, overall reduced ribosome numbers can differentially affect subclasses of mRNAs, necessitating controls for specificity. Moreover, in order to study the functional consequences of ribosome diversity, perturbations including affinity tags and knockouts are introduced, which can also affect the outcome of the experiment. Here we review the available literature to carefully evaluate whether the published data support functional diversification, defined as diverse ribosome populations differentially affecting translation of distinct mRNA (classes). Based on these observations and the commonly observed cellular responses to perturbations in the system, we suggest a set of important controls to validate functional diversity, which should include gain-of-function assays and the demonstration of inducibility under physiological conditions.
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Affiliation(s)
- Max B Ferretti
- Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA
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9
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Peeters SB, Korecki AJ, Baldry SEL, Yang C, Tosefsky K, Balaton BP, Simpson EM, Brown CJ. How do genes that escape from X-chromosome inactivation contribute to Turner syndrome? AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:28-35. [PMID: 30779428 DOI: 10.1002/ajmg.c.31672] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/09/2018] [Indexed: 12/30/2022]
Abstract
X-chromosome inactivation generally results in dosage equivalence for expression of X-linked genes between 46,XY males and 46,XX females. The 20-30% of genes that escape silencing are thus candidates for having a role in the phenotype of Turner syndrome. Understanding which genes escape from silencing, and how they avoid this chromosome-wide inactivation is therefore an important step toward understanding Turner Syndrome. We have examined the mechanism of escape using a previously reported knock-in of a BAC containing the human escape gene RPS4X in mouse. We now demonstrate that escape from inactivation for RPS4X is already established by embryonic Day 9.5, and that both silencing and escape are faithfully maintained across the lifespan. No overt abnormalities were observed for transgenic mice up to 1 year of age despite robust transcription of the human RPS4X gene with no detectable downregulation of the mouse homolog. However, there was no significant increase in protein levels, suggesting translational compensation in the mouse. Finally, while many of the protein-coding genes have been assessed for their inactivation status, less is known about the X-linked RNA genes, and we propose that for many microRNA genes their inactivation status can be predicted as they are intronic to genes for which the inactivation status is known.
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Affiliation(s)
- Samantha B Peeters
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Sarah E L Baldry
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Christine Yang
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Kira Tosefsky
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Bradley P Balaton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Elizabeth M Simpson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
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10
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Davegårdh C, Hall Wedin E, Broholm C, Henriksen TI, Pedersen M, Pedersen BK, Scheele C, Ling C. Sex influences DNA methylation and gene expression in human skeletal muscle myoblasts and myotubes. Stem Cell Res Ther 2019; 10:26. [PMID: 30646953 PMCID: PMC6332625 DOI: 10.1186/s13287-018-1118-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/07/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022] Open
Abstract
Background Sex differences are known to impact muscle phenotypes, metabolism, and disease risk. Skeletal muscle stem cells (satellite cells) are important for muscle repair and to maintain functional skeletal muscle. Here we studied, for the first time, effects of sex on DNA methylation and gene expression in primary human myoblasts (activated satellite cells) before and after differentiation into myotubes. Method We used an array-based approach to analyse genome-wide DNA methylation and gene expression in myoblasts and myotubes from 13 women and 13 men. The results were followed up with a reporter gene assay. Results Genome-wide DNA methylation and gene expression differences between the sexes were detected in both myoblasts and myotubes, on the autosomes as well as the X-chromosome, despite lack of exposure to sex hormones and other factors that differ between sexes. Pathway analysis revealed higher expression of oxidative phosphorylation and other metabolic pathways in myoblasts from women compared to men. Oxidative phosphorylation was also enriched among genes with higher expression in myotubes from women. Forty genes in myoblasts and 9 in myotubes had differences in both DNA methylation and gene expression between the sexes, including LAMP2 and SIRT1 in myoblasts and KDM6A in myotubes. Furthermore, increased DNA methylation of LAMP2 promoter had negative effects on reporter gene expression. Five genes (CREB5, RPS4X, SYAP1, XIST, and ZRSR2) showed differential DNA methylation and gene expression between the sexes in both myoblasts and myotubes. Interestingly, differences in DNA methylation and expression between women and men were also found during differentiation (myoblasts versus myotubes), e.g., in genes involved in energy metabolism. Interestingly, more DNA methylation changes occur in women compared to men on autosomes. Conclusion All together, we show that epigenetic and transcriptional differences exist in human myoblasts and myotubes as well as during differentiation between women and men. We believe that these intrinsic differences might contribute to sex dependent differences in muscular phenotypes. Electronic supplementary material The online version of this article (10.1186/s13287-018-1118-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cajsa Davegårdh
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 20502, Malmö, Sweden.
| | - Elin Hall Wedin
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 20502, Malmö, Sweden
| | - Christa Broholm
- Department of Endocrinology, Rigshospitalet, 2100, Copenhagen, Denmark.,The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Tora Ida Henriksen
- Department of Endocrinology, Rigshospitalet, 2100, Copenhagen, Denmark.,The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bente Klarlund Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Scheele
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center, Section for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 20502, Malmö, Sweden.
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Reindl-Schwaighofer R, Heinzel A, Signorini L, Thaunat O, Oberbauer R. Mechanisms underlying human genetic diversity: consequence for antigraft antibody responses. Transpl Int 2017; 31:239-250. [DOI: 10.1111/tri.13059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 07/28/2017] [Accepted: 08/30/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis; Department of Internal Medicine III; Medical University of Vienna; Vienna Austria
| | - Andreas Heinzel
- Division of Nephrology and Dialysis; Department of Internal Medicine III; Medical University of Vienna; Vienna Austria
| | - Lorenzo Signorini
- Renal and Dialysis Unit; Department of Medicine; University of Verona; Verona Italy
| | - Olivier Thaunat
- Hospices Civils de Lyon; Hôpital Edouard Herriot; Service de Transplantation; Néphrologie et Immunologie Clinique; INSERM U1111; Université Lyon-I; Lyon France
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis; Department of Internal Medicine III; Medical University of Vienna; Vienna Austria
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12
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Kuang J, Li QY, Fan F, Shen NJ, Zhan YJ, Tang ZH, Yu WL. Overexpression of the X-linked ribosomal protein S4 predicts poor prognosis in patients with intrahepatic cholangiocarcinoma. Oncol Lett 2017; 14:41-46. [PMID: 28693133 PMCID: PMC5494819 DOI: 10.3892/ol.2017.6137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/11/2017] [Indexed: 12/27/2022] Open
Abstract
X-linked ribosomal protein S4 (RPS4X) has previously been reported to be associated with cisplatin resistance and clinical outcome in bladder and ovarian cancer. However, the value of RPS4X as a diagnostic and prognostic marker in intrahepatic cholangiocarcinoma (ICC) has not yet been investigated. The present study evaluated the expression pattern, and diagnostic and prognostic value of RPS4X in patients with ICC. Retrospective analysis was performed for a total of 201 patients with intrahepatic cholangiocarcinoma, and 8 patients with inflammation of the bile duct. Immunohistochemistry was performed using tissue microarrays to characterize the expression profile of RPS4X. Receiver operating characteristic (ROC) curves, the Kaplan-Meier estimator and Cox regression analysis were applied to evaluate the potential diagnostic and prognostic value of RPS4X in ICC. RPS4X was significantly upregulated in ICC tissues compared with the inflamed bile duct tissues. When differentiating ICC from normal controls, ROC analysis of RPS4X gave an area under the curve value of 0.9030 (sensitivity, 82.59%; specificity, 100%). RPS4X expression was significantly positively correlated with serum alkaline phosphatase levels. Survival analysis demonstrated that RPS4X expression levels were an independent prognostic factor for overall survival. Therefore, RPS4X expression levels may serve as a novel diagnostic and prognostic marker in ICC.
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Affiliation(s)
- Jie Kuang
- Department of Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
| | - Qin-Yu Li
- Department of Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
| | - Fei Fan
- Department II of Biliary Tract Surgery, Eastern Hepatobiliary Hospital, Shanghai 200438, P.R. China
| | - Ning-Jia Shen
- Department II of Biliary Tract Surgery, Eastern Hepatobiliary Hospital, Shanghai 200438, P.R. China
| | - Yong-Jie Zhan
- Department II of Biliary Tract Surgery, Eastern Hepatobiliary Hospital, Shanghai 200438, P.R. China
| | - Zhao-Hui Tang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
| | - Wen-Long Yu
- Department II of Biliary Tract Surgery, Eastern Hepatobiliary Hospital, Shanghai 200438, P.R. China
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Loss of RPS41 but not its paralog RPS42 results in altered growth, filamentation and transcriptome changes in Candida albicans. Fungal Genet Biol 2015; 80:31-42. [DOI: 10.1016/j.fgb.2015.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/23/2015] [Accepted: 03/31/2015] [Indexed: 11/22/2022]
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Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus. J Virol 2014; 89:1389-403. [PMID: 25392223 DOI: 10.1128/jvi.02019-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Since 1998, cyclic mortality events in common eiders (Somateria mollissima), numbering in the hundreds to thousands of dead birds, have been documented along the coast of Cape Cod, MA, USA. Although longitudinal disease investigations have uncovered potential contributing factors responsible for these outbreaks, detecting a primary etiological agent has proven enigmatic. Here, we identify a novel orthomyxovirus, tentatively named Wellfleet Bay virus (WFBV), as a potential causative agent of these outbreaks. Genomic analysis of WFBV revealed that it is most closely related to members of the Quaranjavirus genus within the family Orthomyxoviridae. Similar to other members of the genus, WFBV contains an alphabaculovirus gp64-like glycoprotein that was demonstrated to have fusion activity; this also tentatively suggests that ticks (and/or insects) may vector the virus in nature. However, in addition to the six RNA segments encoding the prototypical structural proteins identified in other quaranjaviruses, a previously unknown RNA segment (segment 7) encoding a novel protein designated VP7 was discovered in WFBV. Although WFBV shows low to moderate levels of sequence similarity to Quaranfil virus and Johnston Atoll virus, the original members of the Quaranjavirus genus, additional antigenic and genetic analyses demonstrated that it is closely related to the recently identified Cygnet River virus (CyRV) from South Australia, suggesting that WFBV and CyRV may be geographic variants of the same virus. Although the identification of WFBV in part may resolve the enigma of these mass mortality events, the details of the ecology and epidemiology of the virus remain to be determined. IMPORTANCE The emergence or reemergence of viral pathogens resulting in large-scale outbreaks of disease in humans and/or animals is one of the most important challenges facing biomedicine. For example, understanding how orthomyxoviruses such as novel influenza A virus reassortants and/or mutants emerge to cause epidemic or pandemic disease is at the forefront of current global health concerns. Here, we describe the emergence of a novel orthomyxovirus, Wellfleet Bay virus (WFBV), which has been associated with cyclic large-scale bird die-offs in the northeastern United States. This initial characterization study provides a foundation for further research into the evolution, epidemiology, and ecology of newly emerging orthomyxoviruses, such as WFBV, and their potential impacts on animal and/or human health.
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Cysteine endoprotease activity of human ribosomal protein S4 is entirely due to the C-terminal domain, and is consistent with Michaelis–Menten mechanism. Biochim Biophys Acta Gen Subj 2013; 1830:5342-9. [DOI: 10.1016/j.bbagen.2013.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/10/2013] [Accepted: 06/09/2013] [Indexed: 11/20/2022]
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16
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Sudhamalla B, Kumar M, Kumar RS, Sashi P, Yasin UM, Ramakrishna D, Rao PN, Bhuyan AK. Enzyme dimension of the ribosomal protein S4 across plant and animal kingdoms. Biochim Biophys Acta Gen Subj 2013; 1830:5335-41. [PMID: 23791937 DOI: 10.1016/j.bbagen.2013.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/10/2013] [Accepted: 06/09/2013] [Indexed: 01/28/2023]
Abstract
BACKGROUND The protein S4 of the smaller ribosomal subunit is centrally important for its anchorage role in ribosome assembly and rRNA binding. Eubacterial S4 also facilitates synthesis of rRNA, and restrains translation of ribosomal proteins of the same polycistronic mRNA. Eukaryotic S4 has no homolog in eubacterial kingdom, nor are such extraribosomal functions of S4 known in plants and animals even as genetic evidence suggests that deficiency of S4X isoform in 46,XX human females may produce Turner syndrome (45,XO). METHODS Recombinant human S4X and rice S4 were used to determine their enzymatic action in the cleavage of synthetic peptide substrates and natural proteins. We also studied autoproteolysis of the recombinant S4 proteins, and examined the growth and proliferation of S4-transfected human embryonic kidney cells. RESULTS Extraribosomal enzyme nature of eukaryotic S4 is described. Both human S4X and rice S4 are cysteine proteases capable of hydrolyzing a wide spectrum of peptides and natural proteins of diverse origin. Whereas rice S4 also cleaves the -XXXD↓- consensus sequence assumed to be specific for caspase-9 and granzyme B, human S4 does not. Curiously, both human and rice S4 show multiple-site autoproteolysis leading to self-annihilation. Overexpression of human S4 blocks the growth and proliferation of transfected embryonic kidney cells, presumably due to the extraribosomal enzyme trait reported. CONCLUSIONS The S4 proteins of humans and rice, prototypes of eukaryota, are non-specific cysteine proteases in the extraribosomal milieu. GENERAL SIGNIFICANCE The enzyme nature of S4 is relevant toward understanding not only the origin of ribosomal proteins, but also processes in cell biology and diseases.
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Affiliation(s)
- Babu Sudhamalla
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
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17
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Identification and expression of an autosomal paralogue of ribosomal protein S4, X-linked, in mice: Potential involvement of testis-specific ribosomal proteins in translation and spermatogenesis. Gene 2013; 521:91-9. [DOI: 10.1016/j.gene.2013.02.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 02/25/2013] [Accepted: 02/28/2013] [Indexed: 11/24/2022]
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18
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Yadaiah M, Sudhamalla B, Rao PN, Roy KR, Ramakrishna D, Hussain Syed G, Ramaiah KVA, Bhuyan AK. Arrested cell proliferation through cysteine protease activity of eukaryotic ribosomal protein S4. FASEB J 2012; 27:803-10. [PMID: 23118024 DOI: 10.1096/fj.12-217752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
S4 is an integral protein of the smaller subunit of cytosolic ribosome. In prokaryotes, it regulates the synthesis of ribosomal proteins by feedback inhibition of the α-operon gene expression, and it facilitates ribosomal RNA synthesis by direct binding to RNA polymerase. However, functional roles of S4 in eukaryotes are poorly understood, although its deficiency in humans is thought to produce Turner syndrome. We report here that wheat S4 is a cysteine protease capable of abrogating total protein synthesis in an actively translating cell-free system of rabbit reticulocytes. The translation-blocked medium, imaged by atomic force microscopy, scanning electron microscopy, and transmission electron microscopy, shows dispersed polysomes, and the disbanded polyribosome elements aggregate to form larger bodies. We also show that human embryonic kidney cells transfected with recombinant wheat S4 are unable to grow and proliferate. The mutant S4 protein, where the putative active site residue Cys 41 is replaced by a phenylalanine, can neither suppress protein synthesis nor arrest cell proliferation, suggesting that the observed phenomenon arises from the cysteine protease attribute of S4. The results also inspire many questions concerning in vivo significance of extraribosomal roles of eukaryotic S4 performed through its protease activity.
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Affiliation(s)
- Madasu Yadaiah
- School of Chemistry, University of Hyderabad, Hyderabad, India
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Sudhamalla B, Yadaiah M, Ramakrishna D, Bhuyan AK. Cysteine protease attribute of eukaryotic ribosomal protein S4. Biochim Biophys Acta Gen Subj 2012; 1820:1535-42. [PMID: 22579920 DOI: 10.1016/j.bbagen.2012.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/25/2012] [Accepted: 05/03/2012] [Indexed: 12/29/2022]
Abstract
BACKGROUND Ribosomal proteins often carry out extraribosomal functions. The protein S4 from the smaller subunit of Escherichia coli, for instance, regulates self synthesis and acts as a transcription factor. In humans, S4 might be involved in Turner syndrome. Recent studies also associate many ribosomal proteins with malignancy, and cell death and survival. The list of extraribosomal functions of ribosomal proteins thus continues to grow. METHODS Enzymatic action of recombinant wheat S4 on fluorogenic peptide substrates Ac-XEXD↓-AFC (N-acetyl-residue-Glu-residue-Asp-7-amino-4-trifluoromethylcoumarin) and Z-FR↓-AMC (N-CBZ-Phe-Arg-aminomethylcoumarin) as well as proteins has been examined under a variety of solution conditions. RESULTS Eukaryotic ribosomal protein S4 is an endoprotease exhibiting all characteristics of cysteine proteases. The K(m) value for the cleavage of Z-FR↓-AMC by a cysteine mutant (C41F) is about 70-fold higher relative to that for the wild-type protein under identical conditions, implying that S4 is indeed a cysteine protease. Interestingly, activity responses of the S4 protein and caspases toward environmental parameters, including pH, temperature, ionic strength, and Mg(2+) and Zn(2+) concentrations, are quite similar. Respective kinetic constants for their cleavage action on Ac-LEHD↓-AFC are also similar. However, S4 cannot be a caspase, because unlike the latter it also hydrolyzes the cathepsin substrate Z-FR↓-AMC. GENERAL SIGNIFICANCE The eukaryotic S4 is a generic cysteine protease capable of hydrolyzing a broad spectrum of synthetic substrates and proteins. The enzyme attribute of eukaryotic ribosomal protein S4 is a new phenomenon. Its possible involvement in cell growth and proliferations are presented in the light of known extraribosomal roles of ribosomal proteins.
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Affiliation(s)
- Babu Sudhamalla
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
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Cloning, Escherichia coli expression, purification, characterization, and enzyme assay of the ribosomal protein S4 from wheat seedlings (Triticum vulgare). Protein Expr Purif 2011; 81:55-62. [PMID: 21945701 DOI: 10.1016/j.pep.2011.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 09/06/2011] [Accepted: 09/07/2011] [Indexed: 12/19/2022]
Abstract
S4 is a paradigm of ribosomal proteins involved in multifarious activities both within and outside the ribosome. For a detailed biochemical and structural investigations of eukaryotic S4, the wheat S4 gene has been cloned and expressed in Escherichia coli, and the protein purified to a high degree of homogeneity. The 285-residue recombinant protein containing an N-terminal His(6) tag along with fourteen additional residues derived from the cloning vector is characterized by a molecular mass of 31981.24 Da. The actual sequence of 265 amino acids having a molecular mass of 29931 Da completely defines the primary structure of wheat S4. Homology modeling shows a bi-lobed protein topology arising from folding of the polypeptide into two domains, consistent with the fold topology of prokaryotic S4. The purified protein is stable and folded since it can be reversibly unfolded in guanidinium hydrochloride, and is capable of hydrolyzing cysteine protease-specific peptide-based fluorescence substrates, including Ac-DEVD-AFC (N-acetyl-Asp-Glu-Val-Asp-7-amino-4-trifluoromethylcoumarin) and Z-FR-AMC (N-CBZ-Phe-Arg-aminomethylcoumarin).
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21
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Xie Y, Li F, Wang B, Li S, Wang D, Jiang H, Zhang C, Yu K, Xiang J. Screening of genes related to ovary development in Chinese shrimp Fenneropenaeus chinensis by suppression subtractive hybridization. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 5:98-104. [PMID: 20403774 DOI: 10.1016/j.cbd.2010.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 02/01/2010] [Accepted: 02/01/2010] [Indexed: 11/16/2022]
Abstract
The ovary of triploid shrimp Fenneropenaeus chinensis was apparently impaired compared to that of the diploid shrimp at the same age. Therefore triploid shrimp ovary is possible to be taken as a model to understand the mechanism of ovary development of shrimp compared to that of the ovary of diploid shrimp at the same age. In the present study, a suppression subtractive hybridization (SSH) technique was applied to identify differentially expressed genes in the ovary between diploid and triploid shrimp. For the forward library (RNA from the ovary of triploid shrimp as the tester), 54 genes were identified. For the reverse library (RNA from the ovary of diploid shrimp as the tester), 16 genes were identified. The identified genes encoded proteins with multiple functions, including extracellular matrix components, cytoskeleton, cell growth and death, metabolism, genetic information processing, signal transduction/transport or immunity related proteins. Eleven differentially expressed genes were selected to be confirmed in the ovaries of triploid and diploid shrimp by semi-quantitative RT-PCR. Genes encoding spermatogonial stem-cell renewal factor, cytochrome c oxidase subunits I and II, clottable protein, antimicrobial peptide and transposase showed up-regulated expressions in the ovary of triploid shrimp. Genes encoding tubulin, cellular apoptosis susceptibility protein, farnesoic acid O-methyltransferase, thrombospondin and heat shock protein 90 genes showed higher expressions in the ovary of diploid shrimp. The differential expressions of the above genes are suggested to be related to the ovary development of shrimp. It will provide a new clue to uncover the molecular mechanisms underlying the ovarian development in penaeid shrimp.
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Affiliation(s)
- Yusu Xie
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
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Yao C, Wang Z, Zhou Y, Xu W, Li Q, Ma D, Wang L, Qiao Z. A study of Y chromosome gene mRNA in human ejaculated spermatozoa. Mol Reprod Dev 2009; 77:158-66. [DOI: 10.1002/mrd.21116] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Andrés O, Kellermann T, López-Giráldez F, Rozas J, Domingo-Roura X, Bosch M. RPS4Y gene family evolution in primates. BMC Evol Biol 2008; 8:142. [PMID: 18477388 PMCID: PMC2397393 DOI: 10.1186/1471-2148-8-142] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 05/13/2008] [Indexed: 01/31/2023] Open
Abstract
Backgound The RPS4 gene codifies for ribosomal protein S4, a very well-conserved protein present in all kingdoms. In primates, RPS4 is codified by two functional genes located on both sex chromosomes: the RPS4X and RPS4Y genes. In humans, RPS4Y is duplicated and the Y chromosome therefore carries a third functional paralog: RPS4Y2, which presents a testis-specific expression pattern. Results DNA sequence analysis of the intronic and cDNA regions of RPS4Y genes from species covering the entire primate phylogeny showed that the duplication event leading to the second Y-linked copy occurred after the divergence of New World monkeys, about 35 million years ago. Maximum likelihood analyses of the synonymous and non-synonymous substitutions revealed that positive selection was acting on RPS4Y2 gene in the human lineage, which represents the first evidence of positive selection on a ribosomal protein gene. Putative positive amino acid replacements affected the three domains of the protein: one of these changes is located in the KOW protein domain and affects the unique invariable position of this motif, and might thus have a dramatic effect on the protein function. Conclusion Here, we shed new light on the evolutionary history of RPS4Y gene family, especially on that of RPS4Y2. The results point that the RPS4Y1 gene might be maintained to compensate gene dosage between sexes, while RPS4Y2 might have acquired a new function, at least in the lineage leading to humans.
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Affiliation(s)
- Olga Andrés
- Genètica de Conservació Animal, Institut de Recerca i Tecnologia Agroalimentàries, Crta, de Cabrils km2, 08348 Cabrils, Spain.
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Nino-Soto MI, Basrur PK, King WA. Impact of in vitro production techniques on the expression of X-linked genes in bovine (bos taurus) oocytes and pre-attachment embryos. Mol Reprod Dev 2007; 74:144-53. [PMID: 16998849 DOI: 10.1002/mrd.20575] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Our previous studies showed that expression patterns of X-linked genes in cultured cells are different from those of their tissues of origin. This investigation analyses the transcription pattern of the X-linked genes BIRC4, GAB3, MECP2, RPS4X, SLC25A6, and XIST in bovine in vitro matured oocytes and in vitro fertilized embryos, and their in vivo counterparts. In vitro-derived pools of mature oocytes and pre-attachment embryos were obtained by: (a) TCM-199/serum with bovine oviductal epithelial cells as co-culture, and (b) synthetic oviductal fluid/BSA. Pools of in vivo-derived morulae and blastocysts were provided by a commercial embryo transfer operation. Total RNA was extracted for quantification of gene-specific transcript levels using real-time quantitative PCR. Statistical analysis was performed using a mixed model factorial ANOVA with alpha = 0.05. The effect of the in vitro environmental conditions on X-linked gene transcription was most evident during the fourth cell cycle, at the period of activation of the embryonic genome, and seemed to be less pronounced at later developmental stages, with the exception of BIRC4. The levels of X-linked genes transcripts in in vivo-derived embryos were lower relative to their in vitro counterparts for all genes tested. Finally, the pattern of expression of XIST in bovine oocytes and embryos was similar to that reported in humans. These results highlight the possibility that X-linked gene expression analysis is a useful tool to monitor the impact of reproductive biotechnologies on the developmental potential of embryos and aid in their improvement.
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Affiliation(s)
- Maria I Nino-Soto
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Nino-Soto MI, Nuber UA, Basrur PK, Ropers HH, King WA. Differences in the pattern of X-linked gene expression between fetal bovine muscle and fibroblast cultures derived from the same muscle biopsies. Cytogenet Genome Res 2005; 111:57-64. [PMID: 16093722 DOI: 10.1159/000085671] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2004] [Accepted: 10/22/2004] [Indexed: 11/19/2022] Open
Abstract
The sex determination system in mammals creates an imbalance between males and females in the number of X chromosomes. This imbalance is compensated through transcriptional silencing of one of the two X chromosomes in female diploid cells by epigenetic modifications. Although common for mammals, X inactivation shows marked species-specific differences in mechanisms and end results, and provides a unique opportunity to study epigenetic regulation of gene expression. The aim of the present study was to establish the expression pattern of selected X-linked genes in bovine fetal muscle tissue and muscle fibroblast cultures in order to follow possible modifications at the transcriptional level attributable to in vitro culture. We used heterologous cDNA microarray hybridization and quantitative real-time PCR to study the pattern of expression of X-linked genes including SLC25A6, GAB3, MECP2, RPS4X, JARID1C, UBE1, BIRC4 and SLC16A2. Quantitative real-time PCR analysis in fetal bovine muscle showed higher transcript levels in females for all X-linked genes tested with the exception of SLC25A6, with differences being significant for RPS4X, JARID1C and UBE1. The expression in fibroblast cultures derived from the same samples differed, with significantly higher levels for UBE1, GAB3 and BIRC4, while the rest of the panel of X-linked genes remained unchanged. The changed expression pattern in vitro, probably reflecting modifications in the epigenetic mechanisms that regulate transcriptional activity and gene silencing in X inactivation, has important implications for the advancement of new biotechnologies such as somatic cell nuclear transfer and stem cell therapy.
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Affiliation(s)
- M I Nino-Soto
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
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Ivanov R, Aarts T, Hol S, Doornenbal A, Hagenbeek A, Petersen E, Ebeling S. Identification of a 40S Ribosomal Protein S4–Derived H-Y Epitope Able to Elicit a Lymphoblast-Specific Cytotoxic T Lymphocyte Response. Clin Cancer Res 2005; 11:1694-703. [PMID: 15755990 DOI: 10.1158/1078-0432.ccr-04-1772] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The superior graft-versus-leukemia (GVL) effect of the female-to-male stem cell transplantation is partially independent from the concomitant graft-versus-host reactivity. However, the antigenic basis of this selective GVL response remains enigmatic, because no H-Y antigens with hematopoietic-restricted expression were identified. In this study, we report a novel H-Y epitope that is preferentially recognized on activated proliferating lymphocytes. EXPERIMENTAL DESIGN We generated a CTL clone YKIII.8 that showed reactivity toward male B*5201+ CD40-activated B cells, EBV-lymphoblastoid cell lines, and phytohemagglutinin-activated T-cell blasts but little or no reactivity toward fibroblasts, CD14+ cells, or unstimulated B and T cells. The antigen recognized by YKIII.8 was identified by screening of a cDNA expression library, and its pattern of expression was investigated. RESULTS cDNA of the male isoform of 40S ribosomal protein S4 was found to encode the antigenic peptide TIRYPDPVI, which was recognized by YKIII.8. Western blot analysis showed that rapidly proliferating cells overexpress the RPS4 protein in comparison with nonrecognized cell subsets. Retroviral transfer of YKIII.8 T-cell receptor resulted in preservation of the lymphoblast-specific reactivity pattern. CONCLUSION Our findings suggest that CTL specific to certain epitopes of ubiquitously expressed H-Y antigens may specifically target lymphoblasts, contributing to the selective GVL effect of female-to-male stem cell transplantation.
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Affiliation(s)
- Roman Ivanov
- Jordan Laboratory for Hemato-oncology, Department of Hematology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
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Patterson A, Karsi A, Feng J, Liu Z. Translational machinery of channel catfish: II. Complementary DNA and expression of the complete set of 47 60S ribosomal proteins. Gene 2003; 305:151-60. [PMID: 12609735 DOI: 10.1016/s0378-1119(02)01183-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Ribosomal protein genes have become widely used as markers for phylogenetic studies and comparative genomics, but they have not been available in fish. We have cloned and sequenced a complete set of all 47 60S ribosomal protein cDNAs from channel catfish (Ictalurus punctatus), of which 43 included the complete protein encoding regions. Most ribosomal protein mRNAs in channel catfish are highly similar to their mammalian counterparts. However, L4, L14, and L29 are significantly shorter in channel catfish than in mammals due to deletions in the 3' end of the gene. Two distantly related L5 cDNAs, L5a and L5b, were found in channel catfish. L5a is more similar to L5 in other vertebrates, while L5b showed significant levels of divergence, suggesting independent evolution of the two L5-encoding genes. The 47 ribosomal protein genes are generally highly expressed and together account for 11-14% of overall gene expression, depending on the tissues. Expression levels were highly variable both within a single tissue among different ribosomal protein genes, and among tissues with regard to a single ribosomal protein gene. Strong tissue preference expression was also observed for some ribosomal proteins. This set of ribosomal protein gene sequences represents one of the most complete sets from any single organism and will aid in fish phylogenetic and comparative genomic studies.
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Affiliation(s)
- Andrea Patterson
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, 203, Swingle Hall, Auburn, AL 36849, USA
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Gueydan C, Wauquier C, De Mees C, Huez G, Kruys V. Identification of ribosomal proteins specific to higher eukaryotic organisms. J Biol Chem 2002; 277:45034-40. [PMID: 12202495 DOI: 10.1074/jbc.m208551200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This report describes the identification of a novel protein named PS1D (Genbank accession number ), which is composed of an S1-like RNA-binding domain, a (cysteine)x3-(histidine) CCCH-zinc finger, and a very basic carboxyl domain. PS1D is expressed as two isoforms, probably resulting from the alternative splicing of mRNA. The long PS1D isoform differs from the short one by the presence of 48 additional amino acids at its amino-terminal extremity. Analysis of PS1D subcellular distribution by cell fractionation reveals that this protein belongs to the core of the eukaryotic 60S ribosomal subunit. Interestingly, PS1D protein is a highly conserved protein among mammalians as murine, human, and simian PS1D homologues share more than 95% identity. In contrast, no homologous protein is found in lower eukaryotes such as yeast and Caenorhabditis elegans. These observations indicate that PS1D is the first eukaryotic ribosomal protein that is specific to higher eukaryotes.
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Affiliation(s)
- Cyril Gueydan
- Laboratoire de Chimie Biologique, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 12 rue des Profs. Jeener et Brachet, 6041 Gosselies, Belgium.
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Karsi A, Patterson A, Feng J, Liu Z. Translational machinery of channel catfish: I. A transcriptomic approach to the analysis of 32 40S ribosomal protein genes and their expression. Gene 2002; 291:177-86. [PMID: 12095691 DOI: 10.1016/s0378-1119(02)00595-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Ribosomal protein (RP) genes have become widely used as markers for phylogenetic studies and comparative genomics. However, they have not been available for evolutionary studies in fish although teleosts are the largest group of vertebrates with more than 23,000 species. Using a transcriptomic approach, we have cloned and sequenced 32 40S RP complementary DNAs (cDNAs) from channel catfish (Ictalurus punctatus), making them one of the most complete sets of 40S RP gene sequences from a single organism. Most 40S RPs in channel catfish are highly similar to their orthologues in mammalian species, but S19, S21, and S25 are highly divergent. Only one type of cDNA was found for all RP genes except S26 and S27, for which two cDNAs were found in channel catfish. Alternatively spliced transcripts for the S3 and alternatively polyadenylated transcripts for S19 and S21 were found. The 32 40S RP genes are generally highly expressed and together they account for 5.33-11.42% of expression depending on the tissues. Expression levels of the RP genes were highly variable both within a single tissue among different RP genes and among tissues with regard to a single RP gene. Taken together, these data strongly suggest post-transcriptional regulation of RP gene expression, particularly in consideration of the stoichiometry of their representation in ribosomes.
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Affiliation(s)
- Attila Karsi
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, 201 Swingle Hall, Auburn, AL 36849, USA
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30
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Abstract
Comparisons between species reveal when and how SRY, the testis-determining gene, evolved. SRY is younger than the Y chromosome, and so was probably not the original mammal sex-determining gene that defined the Y. SRY is typical of genes on the Y chromosome. It arose from a gene on the proto-sex chromosome pair with a function (possibly brain-determination) in both sexes. It has been buffeted in evolution, and shows variation in copy number, structure and expression. And it is dispensable, having been lost at least twice independently in different rodent lineages. At the observed rate of attrition, the human Y chromosome will be gone in 5-10 million years. This could lead to the extinction of our species or to a burst of hominid speciation.
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31
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Yoshihama M, Uechi T, Asakawa S, Kawasaki K, Kato S, Higa S, Maeda N, Minoshima S, Tanaka T, Shimizu N, Kenmochi N. The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. Genome Res 2002; 12:379-90. [PMID: 11875025 PMCID: PMC155282 DOI: 10.1101/gr.214202] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ribosome, as a catalyst for protein synthesis, is universal and essential for all organisms. Here we describe the structure of the genes encoding human ribosomal proteins (RPs) and compare this class of genes among several eukaryotes. Using genomic and full-length cDNA sequences, we characterized 73 RP genes and found that (1) transcription starts at a C residue within a characteristic oligopyrimidine tract; (2) the promoter region is GC rich, but often has a TATA box or similar sequence element; (3) the genes are small (4.4 kb), but have as many as 5.6 exons on average; (4) the initiator ATG is in the first or second exon and is within plus minus 5 bp of the first intron boundaries in about half of cases; and (5) 5'- and 3'-UTRs are significantly smaller (42 bp and 56 bp, respectively) than the genome average. Comparison of RP genes from humans, Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae revealed the coding sequences to be highly conserved (63% homology on average), although gene size and the number of exons vary. The positions of the introns are also conserved among these species as follows: 44% of human introns are present at the same position in either D. melanogaster or C. elegans, suggesting RP genes are highly suitable for studying the evolution of introns.
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Affiliation(s)
- Maki Yoshihama
- Department of Biochemistry, School of Medicine, University of the Ryukyus, Nishihara, Okinawa 903-0215, Japan
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32
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Wang YH, McWilliam SM, Barendse W, Kata SR, Womack JE, Moore SS, Lehnert SA. Mapping of 12 bovine ribosomal protein genes using a bovine radiation hybrid panel. Anim Genet 2001; 32:269-73. [PMID: 11683713 DOI: 10.1046/j.1365-2052.2001.00791.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Twelve bovine ribosomal protein genes, for which sequence data had been acquired from complementary deoxyribonucleic acid (cDNA) clones isolated from a cattle skin cDNA library, were mapped. As ribosomal protein genes are a group of highly conserved house keeping genes, specific primers were designed to span the intron-exon splice sites and to amplify intronic sequences, in order to obtain bovine-specific polymerase chain reaction (PCR) products. Two of 12 ribosomal protein genes were genotyped in this way and the remaining 10 were mapped using additional primers designed from within the intron. Eleven previously unmapped ribosomal protein genes were localized and one previously reported ribosomal protein gene localization was confirmed. The 12 ribosomal protein genes mapped in this study are spread over 10 chromosomes, including the X chromosome. The locations show conservation of comparative map position in cattle and human.
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Affiliation(s)
- Y H Wang
- CSIRO Livestock Industries, Molecular Animal Genetics Centre, Gehrmann Laboratories, Brisbane, Australia.
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33
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Chrast R, Scott HS, Papasavvas MP, Rossier C, Antonarakis ES, Barras C, Davisson MT, Schmidt C, Estivill X, Dierssen M, Pritchard M, Antonarakis SE. The Mouse Brain Transcriptome by SAGE: Differences in Gene Expression between P30 Brains of the Partial Trisomy 16 Mouse Model of Down Syndrome (Ts65Dn) and Normals. Genome Res 2000. [DOI: 10.1101/gr.158500] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Trisomy 21, or Down syndrome (DS), is the most common genetic cause of mental retardation. Changes in the neuropathology, neurochemistry, neurophysiology, and neuropharmacology of DS patients' brains indicate that there is probably abnormal development and maintenance of central nervous system structure and function. The segmental trisomy mouse (Ts65Dn) is a model of DS that shows analogous neurobehavioral defects. We have studied the global gene expression profiles of normal and Ts65Dn male and normal female mice brains (P30) using the serial analysis of gene expression (SAGE) technique. From the combined sample we collected a total of 152,791 RNA tags and observed 45,856 unique tags in the mouse brain transcriptome. There are 14 ribosomal protein genes (nine underexpressed) among the 330 statistically significant differences between normal male and Ts65Dn male brains, which possibly implies abnormal ribosomal biogenesis in the development and maintenance of DS phenotypes. This study contributes to the establishment of a mouse brain transcriptome and provides the first overall analysis of the differences in gene expression in aneuploid versus normal mammalian brain cells.
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34
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Cloning and characterization of the gene for the human ribosomal protein S21. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2000. [DOI: 10.1007/bf02759289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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35
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Kirschner LS, Stratakis CA. Structure of the human ubiquitin fusion gene Uba80 (RPS27a) and one of its pseudogenes. Biochem Biophys Res Commun 2000; 270:1106-10. [PMID: 10772958 DOI: 10.1006/bbrc.2000.2568] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Ubiquitin is a highly conserved 76 amino acid protein that is generated in the cell by proteolysis of larger proteins containing either polyubiquitin chains or ubiquitin fused to carboxyl extension proteins (CEPs). In humans, the two human ubiquitin-CEP genes are Uba80 and Uba52, which code for ubiquitin fused to ribosomal protein S27a and L40, respectively. Working from a recently generated physical map of human chromosome 2p16, we determined the genetic and physical location and the genomic structure of the Uba80 gene in its entirety. A comparison of Uba80 to Uba52 revealed that the two genes share a conserved 5'-end structure, but that the structure of the ubiquitin coding regions was not conserved. Analysis of 400 bp of the promoter of Uba80 revealed strong similarity not only to the Uba52 promoter, but also to the other known human ribosomal gene promoters that have been identified to date. Homology searches also detected the presence of a pseudogene for Uba80, and the structure of this sequence feature is also reported.
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Affiliation(s)
- L S Kirschner
- Unit on Genetics and Endocrinology, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA.
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36
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Lambertsson A. The minute genes in Drosophila and their molecular functions. ADVANCES IN GENETICS 1998; 38:69-134. [PMID: 9677706 DOI: 10.1016/s0065-2660(08)60142-x] [Citation(s) in RCA: 198] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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37
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Abstract
Turner syndrome was one of the first human genetic disorders ascribed to haploinsufficiency but the identification of specific genes responsible for the phenotype has been problematic. Recent data point to several candidate genes, some new and some old, for specific aspects of the phenotype associated with monosomy X in humans.
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Affiliation(s)
- A R Zinn
- University of Texas Southwestern Medical School, Dallas, Texas 75235-8591, USA.
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38
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Kenmochi N, Kawaguchi T, Rozen S, Davis E, Goodman N, Hudson TJ, Tanaka T, Page DC. A map of 75 human ribosomal protein genes. Genome Res 1998; 8:509-23. [PMID: 9582194 DOI: 10.1101/gr.8.5.509] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We mapped 75 genes that collectively encode >90% of the proteins found in human ribosomes. Because localization of ribosomal protein genes (rp genes) is complicated by the existence of processed pseudogenes, multiple strategies were devised to identify PCR-detectable sequence-tagged sites (STSs) at introns. In some cases we exploited specific, pre-existing information about the intron/exon structure of a given human rp gene or its homolog in another vertebrate. When such information was unavailable, selection of PCR primer pairs was guided by general insights gleaned from analysis of all mammalian rp genes whose intron/exon structures have been published. For many genes, PCR amplification of introns was facilitated by use of YAC pool DNAs rather than total human genomic DNA as templates. We then assigned the rp gene STSs to individual human chromosomes by typing human-rodent hybrid cell lines. The genes were placed more precisely on the physical map of the human genome by typing of radiation hybrids or screening YAC libraries. Fifty-one previously unmapped rp genes were localized, and 24 previously reported rp gene localizations were confirmed, refined, or corrected. Though functionally related and coordinately expressed, the 75 mapped genes are widely dispersed: Both sex chromosomes and at least 20 of the 22 autosomes carry one or more rp genes. Chromosome 19, known to have a high gene density, contains an unusually large number of rp genes (12). This map provides a foundation for the study of the possible roles of ribosomal protein deficiencies in chromosomal and Mendelian disorders.
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Affiliation(s)
- N Kenmochi
- Howard Hughes Medical Institute, Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.
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39
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Fisher EM. The contribution of the mouse to advances in human genetics. ADVANCES IN GENETICS 1997; 35:155-205. [PMID: 9348648 DOI: 10.1016/s0065-2660(08)60450-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- E M Fisher
- Neurogenetics Unit, Imperial College School of Medicine at St. Mary's, London, United Kingdom
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40
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Klein H. Hamster ribosomal protein S24 multigene family: genomic organization and molecular structure of two pseudogenes. Biochem Cell Biol 1997. [DOI: 10.1139/o97-034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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41
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Avni D, Biberman Y, Meyuhas O. The 5' terminal oligopyrimidine tract confers translational control on TOP mRNAs in a cell type- and sequence context-dependent manner. Nucleic Acids Res 1997; 25:995-1001. [PMID: 9023110 PMCID: PMC146534 DOI: 10.1093/nar/25.5.995] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
TOP mRNAs are vertebrate transcripts which contain a 5'terminal oligopyrimidine tract (5'TOP), encode for ribosomal proteins and elongation factors 1alpha and 2, and are candidates for growth-dependent translational control mediated through their 5'TOP. In the present study we show that elongation factor 2 (EF2) mRNA is translationally regulated in a growth-dependent manner in cells of hematopoietic origin, but not in any of three different non-hematopoietic cell lines studied. Human beta1-tubulin mRNA is a new member of the family which contains all the hallmarks of a typical TOP mRNA, yet its translation is refractory to growth arrest of any of the examined cell lines. Transfection experiments indicate that the first 29 and 53 nucleotides of the mRNAs encoding EF2 and beta1-tubulin, respectively, contain all the translational cis-regulatory elements sufficient for ubiquitously conferring growth-dependent translational control on a reporter mRNA. These results suggest that the distinct translational regulation of TOP mRNAs reflects downstream sequences which can override the regulatory features of the 5'TOP in a cell type-specific manner. This notion is further supported by the fact that mutations within the region immediately downstream of the 5'TOP of rpS16 mRNA confer onto the resulting transcripts growth-dependent translational control with a cell type specificity similar to that displayed by EF2 mRNA.
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Affiliation(s)
- D Avni
- Department of Biochemistry, The Hebrew University Hadassah Medical School, PO Box 12272, Jerusalem 91120, Israel
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42
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Samollow PB, Cherry LM, Witte SM, Rogers J. Interspecific variation at the Y-linked RPS4Y locus in hominoids: implications for phylogeny. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1996; 101:333-43. [PMID: 8922180 DOI: 10.1002/(sici)1096-8644(199611)101:3<333::aid-ajpa3>3.0.co;2-#] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Within- and between-species variation in restriction endonuclease recognition sites was examined at the Y-linked RPS4Y locus of six hominoid species: human (Homo sapiens), gorilla (Gorilla gorilla), chimpanzee (Pan troglodytes), bonobo (Pan paniscus), orangutan (Pongo pygmaeus), and gibbon (Hylobates lar). RPS4Y is an expressed gene that maps to the non-recombining region of the Y chromosome. An approximately 1,490 base pair fragment of the RPS4Y gene, including all of intron 3, was amplified by PCR from DNA extracted from each of the six species. Forty-seven restriction sites were identified on the six-species composite map derived from double-digest restriction analyses of the amplified fragment. As expected, maximum parsimony analysis indicated that chimpanzee and bonobo are the two most closely related living hominoids. The same analysis suggested that the closest living relative of Homo is Gorilla, not Pan, although support for this relationship was relatively weak. These results disagree with recently published phylogenies based on analyses of mtDNA sequences (Horai et al. [1995] Proc. Natl. Acad. Sci. U.S.A. 88:7401-7404) and the Y-linked ZFY locus (Dorit et al. [1995] Science 268:1183-1185). A combined data set derived from three distinct Y-linked loci-RPS4Y, SRY, and ZFY-was also analyzed. The maximum parsimony topology for the combined data provided only weak support for a shared common ancestor for Homo and Pan subsequent to divergence from the Gorilla lineage. Taken together, the data from the Y chromosome do not provide unequivocal support for any single, dichotomously branching species tree linking Homo, Pan, and Gorilla.
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Affiliation(s)
- P B Samollow
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas 78245-0549, USA
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43
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Abstract
The gene encoding mouse ribosomal protein (r-protein) S6 is 2.7 kb in length, and is composed of five exons. The intron positions of the mouse S6 (Rps6) coincide exactly to those of the homologous human S6 (RPS6), but the last intron present in the human is absent in the mouse gene. The latter displays higher G + C content than the RPS6, both in the overall sequenced region and at the 3rd codon position. The promoter area is highly conserved between mouse and human, and contains several putative cis-acting elements. Comparison of the intronic sequences of both genes revealed surprisingly a high degree of identity (63%) within 350 bp of the first intron. Besides the single-copy Rsp6 there are up to 15 S6 family members, most likely processed pseudogenes. Characterization of the Rps6 provides a basis to study the functions of the mammalian S6 by gene targeting.
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Affiliation(s)
- I Pata
- Institute of Molecular and Cell Biology, Tartu University, Estonian Biocentre, Estonia
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44
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Nanda I, Tanaka T, Schmid M. The intron-containing ribosomal protein-encoding genes L5, L7a and L37a are unlinked in chicken. Gene 1996; 170:159-64. [PMID: 8666239 DOI: 10.1016/0378-1119(95)00828-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Chicken ribosomal protein (rp)-encoding genes are currently being studied at the nucleotide level and three independent recombinant phages have been isolated from chicken genomic libraries using cloned cDNA probes. Each of these was shown to include an intron-containing rp gene of chicken (L5, L7a, L37a). In this study the chromosomal location of these three intron-containing rp from the large subunit of the chicken ribosome was determined by fluorescence in situ hybridization. L7a mapped to a microchromosome, whereas L5 and L37a mapped to macrochromosomes 8 and 7, respectively. The results demonstrate that these functionally related genes are widely dispersed in the genome. Furthermore, as in the case of many other evolutionarily advanced eukaryotes, there is no apparent linkage of rp and rRNA genes.
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Affiliation(s)
- I Nanda
- Department of Human Genetics, University of Würzburg, Germany
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45
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Nolte D, Taimor G, Kalff-Suske M, Seifart KH. The human S3a ribosomal protein: sequence, location and cell-free transcription of the functional gene. Gene 1996; 169:179-85. [PMID: 8647443 DOI: 10.1016/0378-1119(95)00708-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The intron-containing gene encoding human ribosomal protein S3a (hRPS3a) was isolated by utilizing a PCR-based strategy to detect a gene-specific intron which was subsequently used as a probe for cloning of the entire gene. The hRPS3a gene is composed of six exons and five introns spanning 5013 bp. As described for other hRP-encoding genes, the promoter lacks a canonical TATA sequence and a defined CAAT box. Primer extension experiments, as well as cell-free transcription, revealed that a cytosine functions as the major transcription start point in a polypyrimidine region, but a guanosine at position -1 was also able to initiate transcription. Hybridization analysis of chromosomal DNA from a panel of human-rodent somatic cell hybrids revealed that hRPS3a is encoded by a single locus in the human genome, present on chromosome 4.
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Affiliation(s)
- D Nolte
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Germany
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46
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Mazuruk K, Schoen TJ, Chader GJ, Iwata T, Rodriguez IR. Structural organization and chromosomal localization of the human ribosomal protein L9 gene. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1305:151-62. [PMID: 8597601 DOI: 10.1016/0167-4781(95)00201-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The intron-containing gene for the human ribosomal protein L9 has been cloned, sequenced and localized. The gene is approximately 5.5 kb in length and contains 8 exons. Splice sites follow the AG/GT consensus rule. The message for human rpL9 is 712 nt in length and is detected in all tissues examined. In the adult, expression is highest in retina and liver while brain shows highest expression among the fetal tissues tested. The transcription start site contains an oligopyrimidine tract, TTCTTTCTT, similar to those found in other ribosomal protein genes. As in other previously characterized ribosomal protein genes, a TATA box is absent from the 5' flanking region but a number of elements recognized by common transcription factors are present including Sp1 sites, CACCC boxes, inverted CCAAT boxes, and GATA elements. Another possible element of interest in the rpL9 5' flanking region is RFX1 also found in the well characterized rat rpL30 promoter. The gene was mapped by fluorescent in situ hybridization to band 13p of chromosome 4. At least 8 possible pseudogenes are present in the human genome, one of which is on Xp. As assessed by Southern 'Zoo-blot' analysis and direct cDNA sequence comparison, the human ribosomal protein L9 gene, like other ribosomal protein genes, is highly conserved among mammals.
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Affiliation(s)
- K Mazuruk
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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47
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Geerkens C, Just W, Held KR, Vogel W. Ullrich-Turner syndrome is not caused by haploinsufficiency of RPS4X. Hum Genet 1996; 97:39-44. [PMID: 8557258 DOI: 10.1007/bf00218830] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ullrich-Turner syndrome (UTS) is frequently associated with monosomy X but may also occur with structural aberrations of the X and the Y chromosomes. It has been hypothesized that the ribosomal protein genes RPS4X and RPS4Y play a critical role in the prevention of UTS. Individual patients with a 46,X,i(Xq) karyotype cannot be differentiated phenotypically from 45,X UTS patients and carry three gene copies of RPS4X. Since haploinsufficiency of one or several gene(s) is thought to cause the UTS phenotype, direct assessment of RPS4X expression levels in these patients should establish whether RPS4X is involved in UTS. We have investigated fibroblasts of four 46,X,i(Xq) UTS patients with typical symptoms and a non-mosaic chromosome complement, and have found significantly increased RPS4X mRNA levels in all patients. Based on our results, we conclude that haploinsufficiency of RPS4X is not the cause of UTS.
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Affiliation(s)
- C Geerkens
- Abteilung Medizinische Genetik, Universität Ulm, Germany
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48
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Wool IG, Chan YL, Glück A. Structure and evolution of mammalian ribosomal proteins. Biochem Cell Biol 1995; 73:933-47. [PMID: 8722009 DOI: 10.1139/o95-101] [Citation(s) in RCA: 245] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mammalian (rat) ribosomes have 80 proteins; the sequence of amino acids in 75 have been determined. What has been learned of the structure of the rat ribosomal proteins is reviewed with particular attention to their evolution and to amino acid sequence motifs. The latter include: clusters of basic or acidic residues; sequence repeats or shared sequences; zinc finger domains; bZIP elements; and nuclear localization signals. The occurrence and the possible significance of phosphorylated residues and of ubiquitin extensions is noted. The characteristics of the mRNAs that encode the proteins are summarized. The relationship of the rat ribosomal proteins to the proteins in ribosomes from humans, yeast, archaebacteria, and Escherichia coli is collated.
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Affiliation(s)
- I G Wool
- Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA
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Annilo T, Laan M, Stahl J, Metspalu A. The human ribosomal protein S7-encoding gene: isolation, structure and localization in 2p25. Gene 1995. [DOI: 10.1016/0378-1119(95)00576-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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