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Deryusheva EI, Machulin AV, Galzitskaya OV. Diversity and features of proteins with structural repeats. Biophys Rev 2023; 15:1159-1169. [PMID: 37974986 PMCID: PMC10643770 DOI: 10.1007/s12551-023-01130-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/28/2023] [Indexed: 11/19/2023] Open
Abstract
The review provides information on proteins with structural repeats, including their classification, characteristics, functions, and relevance in disease development. It explores methods for identifying structural repeats and specialized databases. The review also highlights the potential use of repeat proteins as drug design scaffolds and discusses their evolutionary mechanisms.
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Affiliation(s)
- Evgeniya I. Deryusheva
- Institute for Biological Instrumentation, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
| | - Andrey V. Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics of the Russian Academy of Sciences, Pushchino, Russia
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Molecular Characterization, Expression Profile, and A 21-bp Indel within the ASB9 Gene and Its Associations with Chicken Production Traits. Genes (Basel) 2023; 14:genes14020339. [PMID: 36833266 PMCID: PMC9957280 DOI: 10.3390/genes14020339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
A growing number of studies have shown that members of the ankyrin repeat and suppressors of cytokine signaling (SOCS) box-containing protein (ASB) family are extensively involved in biological processes such as cell growth, tissue development, insulin signaling, ubiquitination, protein degradation, and skeletal muscle membrane protein formation, while the specific biological role of ankyrin-repeat and SOCS box protein 9 (ASB9) remains unclear. In this study, a 21 bp indel in the intron of ASB9 was identified for the first time in 2641 individuals from 11 different breeds and an F2 resource population, and differences were observed among individuals with different genotypes (II, ID, and DD). An association study of a cross-designed F2 resource population revealed that the 21-bp indel was significantly related to growth and carcass traits. The significantly associated growth traits were body weight (BW) at 4, 6, 8, 10, and 12 weeks of age; sternal length (SL) at 4, 8, and 12 weeks of age; body slope length (BSL) at 4, 8, and 12 weeks of age; shank girth (SG) at 4 and 12 weeks of age; tibia length (TL) at 12 weeks of age; and pelvic width (PW) at 4 weeks of age (p < 0.05). This indel was also significantly correlated with carcass traits including semievisceration weight (SEW), evisceration weight (EW), claw weight (CLW), breast muscle weight (BMW), leg weight (LeW), leg muscle weight (LMW), claw rate (CLR), and shedding weight (ShW) (p < 0.05). In commercial broilers, the II genotype was the dominant genotype and underwent extensive selection. Interestingly, the ASB9 gene was expressed at significantly higher levels in the leg muscles of Arbor Acres broilers than those of Lushi chickens, while the opposite was true for the breast muscles. In summary, the 21-bp indel in the ASB9 gene significantly influenced the expression of the ASB9 gene in muscle tissue and was associated with multiple growth and carcass traits in the F2 resource population. These findings suggested that the 21-bp indel within the ASB9 gene could be used in marker-assisted selection breeding for traits related to chicken growth.
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Deryusheva EI, Machulin AV, Galzitskaya OV. Structural, Functional, and Evolutionary Characteristics of Proteins with Repeats. Mol Biol 2021. [DOI: 10.1134/s0026893321040038] [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]
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Steele-Ogus MC, Johnson RS, MacCoss MJ, Paredez AR. Identification of Actin Filament-Associated Proteins in Giardia lamblia. Microbiol Spectr 2021; 9:e0055821. [PMID: 34287056 PMCID: PMC8552679 DOI: 10.1128/spectrum.00558-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
The deep-branching protozoan parasite Giardia lamblia is the causative agent of the intestinal disease giardiasis. Consistent with its proposed evolutionary position, many pathways are minimalistic or divergent, including its actin cytoskeleton. Giardia is the only eukaryote known to lack all canonical actin-binding proteins. Previously, our lab identified a number of noncanonical Giardia lamblia actin (GlActin) interactors; however, these proteins appeared to interact only with monomeric or globular actin (G-actin) rather than with filamentous actin (F-actin). To identify F-actin interactors, we used a chemical cross-linker to preserve native interactions followed by an anti-GlActin antibody, protein A affinity chromatography, and liquid chromatography coupled to mass spectrometry. We found 46 putative actin interactors enriched under the conditions favoring F-actin. Data are available via ProteomeXchange with identifier PXD026067. None of the proteins identified contain known actin-interacting motifs, and many lacked conserved domains. Each potential interactor was then tagged with the fluorescent protein mNeonGreen and visualized in live cells. We categorized the proteins based on their primary localization; localizations included ventral disc, marginal plate, nuclei, flagella, plasma membrane, and internal membranes. One protein from each of the six categories was colocalized with GlActin using immunofluorescence microscopy. We also co-immunoprecipitated one protein from each category and confirmed three of the six potential interactions. Most of the localization patterns are consistent with previously demonstrated GlActin functions, but the ventral disc represents a new category of actin interactor localization. These results suggest a role for GlActin in ventral disc function, which has previously been controversial. IMPORTANCE Giardia lamblia is an intestinal parasite that colonizes the small intestine and causes diarrhea, which can lead to dehydration and malnutrition. Giardia actin (GlActin) has a conserved role in Giardia cells, despite being a highly divergent protein with none of the conserved regulators found in model organisms. Here, we identify and localize 46 interactors of polymerized actin. These putative interactors localize to a number of places in the cell, underlining GlActin's importance in multiple cellular processes. Surprisingly, eight of these proteins localize to the ventral disc, Giardia's host attachment organelle. Since host attachment is required for infection, proteins involved in this process are an appealing target for new drugs. While treatments for Giardia exist, drug resistance is becoming more common, resulting in a need for new treatments. Giardia and human systems are highly dissimilar, thus drugs specifically tailored to Giardia proteins would be less likely to have side effects.
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Affiliation(s)
| | - Richard S. Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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Sarnowski C, Chen H, Biggs ML, Wassertheil-Smoller S, Bressler J, Irvin MR, Ryan KA, Karasik D, Arnett DK, Cupples LA, Fardo DW, Gogarten SM, Heavner BD, Jain D, Kang HM, Kooperberg C, Mainous AG, Mitchell BD, Morrison AC, O’Connell JR, Psaty BM, Rice K, Smith AV, Vasan RS, Windham BG, Kiel DP, Murabito JM, Lunetta KL. Identification of novel and rare variants associated with handgrip strength using whole genome sequence data from the NHLBI Trans-Omics in Precision Medicine (TOPMed) Program. PLoS One 2021; 16:e0253611. [PMID: 34214102 PMCID: PMC8253404 DOI: 10.1371/journal.pone.0253611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/08/2021] [Indexed: 12/15/2022] Open
Abstract
Handgrip strength is a widely used measure of muscle strength and a predictor of a range of morbidities including cardiovascular diseases and all-cause mortality. Previous genome-wide association studies of handgrip strength have focused on common variants primarily in persons of European descent. We aimed to identify rare and ancestry-specific genetic variants associated with handgrip strength by conducting whole-genome sequence association analyses using 13,552 participants from six studies representing diverse population groups from the Trans-Omics in Precision Medicine (TOPMed) Program. By leveraging multiple handgrip strength measures performed in study participants over time, we increased our effective sample size by 7-12%. Single-variant analyses identified ten handgrip strength loci among African-Americans: four rare variants, five low-frequency variants, and one common variant. One significant and four suggestive genes were identified associated with handgrip strength when aggregating rare and functional variants; all associations were ancestry-specific. We additionally leveraged the different ancestries available in the UK Biobank to further explore the ancestry-specific association signals from the single-variant association analyses. In conclusion, our study identified 11 new loci associated with handgrip strength with rare and/or ancestry-specific genetic variations, highlighting the added value of whole-genome sequencing in diverse samples. Several of the associations identified using single-variant or aggregate analyses lie in genes with a function relevant to the brain or muscle or were reported to be associated with muscle or age-related traits. Further studies in samples with sequence data and diverse ancestries are needed to confirm these findings.
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Affiliation(s)
- Chloé Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States of America
- Center for Precision Health, School of Public Health and School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Mary L. Biggs
- Cardiovascular Health Unit, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Sylvia Wassertheil-Smoller
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Jan Bressler
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, United States of America
| | - Kathleen A. Ryan
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - David Karasik
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, United States of America
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Donna K. Arnett
- University of Kentucky, College of Public Health, Lexington, KY, United States of America
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
- National Heart Lung and Blood Institute and Boston University’s Framingham Heart Study, Framingham, MA, United States of America
| | - David W. Fardo
- Department of Biostatistics and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States of America
| | - Stephanie M. Gogarten
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Benjamin D. Heavner
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Arch G. Mainous
- Department of Health Services Research, Management and Policy, University of Florida, Gainesville, FL, United States of America
| | - Braxton D. Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, United States of America
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Jeffrey R. O’Connell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Bruce M. Psaty
- Cardiovascular Health Unit, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Departments of Epidemiology and Health Services, University of Washington, Seattle, WA, United States of America
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, United States of America
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Albert V. Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States of America
| | - Ramachandran S. Vasan
- National Heart Lung and Blood Institute and Boston University’s Framingham Heart Study, Framingham, MA, United States of America
- Section of Preventive Medicine and Epidemiology, Evans Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
- Whitaker Cardiovascular Institute and Cardiology Section, Evans Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
| | - B. Gwen Windham
- The MIND Center, University of Mississippi Medical Center, Jackson, MS, United States of America
| | - Douglas P. Kiel
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, United States of America
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States of America
- Broad Institute of Harvard & MIT, Cambridge, MA, United States of America
| | - Joanne M. Murabito
- National Heart Lung and Blood Institute and Boston University’s Framingham Heart Study, Framingham, MA, United States of America
- Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
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Liu Y, Li X, He Y, Wang H, Gao M, Han L, Qiu D, Ling L, Liu H, Gu L. ASB7 Is a Novel Regulator of Cytoskeletal Organization During Oocyte Maturation. Front Cell Dev Biol 2020; 8:595917. [PMID: 33251222 PMCID: PMC7674779 DOI: 10.3389/fcell.2020.595917] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/12/2020] [Indexed: 11/30/2022] Open
Abstract
Ankyrin repeat and SOCS box (ASB) family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence of variable repeats. To date, the roles of ASB family members remain largely unknown. In the present study, by employing knockdown analysis, we investigated the effects of ASB7 on mouse oocyte meiosis. We show that specific depletion of ASB7 disrupts maturational progression and meiotic apparatus. In particular, abnormal spindle, misaligned chromosomes, and loss of cortical actin cap are frequently observed in ASB7-abated oocytes. Consistent with this observation, incidence of aneuploidy is increased in these oocytes. Meanwhile, confocal scanning reveals that loss of ASB7 impairs kinetochore–microtubule interaction and provokes the spindle assembly checkpoint during oocyte meiosis. Furthermore, we find a significant reduction of ASB7 protein in oocytes from aged mice. Importantly, increasing ASB7 expression is capable of partially rescuing the maternal age-induced meiotic defects in oocytes. Together, our data identify ASB7 as a novel player in regulating cytoskeletal organization and discover the potential effects of ASB7 on quality control of aging oocytes.
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Affiliation(s)
- Yuan Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyan Li
- Jinling Hospital Department Reproductive Medical Center, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Yongfu He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hengjie Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Min Gao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Longsen Han
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Danhong Qiu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Li Ling
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ling Gu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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Blondelle J, Biju A, Lange S. The Role of Cullin-RING Ligases in Striated Muscle Development, Function, and Disease. Int J Mol Sci 2020; 21:E7936. [PMID: 33114658 PMCID: PMC7672578 DOI: 10.3390/ijms21217936] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
The well-orchestrated turnover of proteins in cross-striated muscles is one of the fundamental processes required for muscle cell function and survival. Dysfunction of the intricate protein degradation machinery is often associated with development of cardiac and skeletal muscle myopathies. Most muscle proteins are degraded by the ubiquitin-proteasome system (UPS). The UPS involves a number of enzymes, including E3-ligases, which tightly control which protein substrates are marked for degradation by the proteasome. Recent data reveal that E3-ligases of the cullin family play more diverse and crucial roles in cross striated muscles than previously anticipated. This review highlights some of the findings on the multifaceted functions of cullin-RING E3-ligases, their substrate adapters, muscle protein substrates, and regulatory proteins, such as the Cop9 signalosome, for the development of cross striated muscles, and their roles in the etiology of myopathies.
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Affiliation(s)
- Jordan Blondelle
- Department of Medicine, University of California, La Jolla, CA 92093, USA
| | - Andrea Biju
- Department of Medicine, University of California, La Jolla, CA 92093, USA
| | - Stephan Lange
- Department of Medicine, University of California, La Jolla, CA 92093, USA
- Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden
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Ehrlich KC, Lacey M, Ehrlich M. Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families. EPIGENOMES 2020; 4:1. [PMID: 34968235 PMCID: PMC8594701 DOI: 10.3390/epigenomes4010001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/21/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
Much remains to be discovered about the intersection of tissue-specific transcription control and the epigenetics of skeletal muscle (SkM), a very complex and dynamic organ. From four gene families, Leucine-Rich Repeat Containing (LRRC), Oxysterol Binding Protein Like (OSBPL), Ankyrin Repeat and Socs Box (ASB), and Transmembrane Protein (TMEM), we chose 21 genes that are preferentially expressed in human SkM relative to 52 other tissue types and analyzed relationships between their tissue-specific epigenetics and expression. We also compared their genetics, proteomics, and descriptions in the literature. For this study, we identified genes with little or no previous descriptions of SkM functionality (ASB4, ASB8, ASB10, ASB12, ASB16, LRRC14B, LRRC20, LRRC30, TMEM52, TMEM233, OSBPL6/ORP6, and OSBPL11/ORP11) and included genes whose SkM functions had been previously addressed (ASB2, ASB5, ASB11, ASB15, LRRC2, LRRC38, LRRC39, TMEM38A/TRIC-A, and TMEM38B/TRIC-B). Some of these genes have associations with SkM or heart disease, cancer, bone disease, or other diseases. Among the transcription-related SkM epigenetic features that we identified were: super-enhancers, promoter DNA hypomethylation, lengthening of constitutive low-methylated promoter regions, and SkM-related enhancers for one gene embedded in a neighboring gene (e.g., ASB8-PFKM, LRRC39-DBT, and LRRC14B-PLEKHG4B gene-pairs). In addition, highly or lowly co-expressed long non-coding RNA (lncRNA) genes probably regulate several of these genes. Our findings give insights into tissue-specific epigenetic patterns and functionality of related genes in a gene family and can elucidate normal and disease-related regulation of gene expression in SkM.
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Affiliation(s)
- Kenneth C. Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA;
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Melanie Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA;
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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Chagula DB, Rechciński T, Rudnicka K, Chmiela M. Ankyrins in human health and disease - an update of recent experimental findings. Arch Med Sci 2020; 16:715-726. [PMID: 32542072 PMCID: PMC7286341 DOI: 10.5114/aoms.2019.89836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/25/2018] [Indexed: 12/17/2022] Open
Abstract
Ankyrins are adaptor molecules that in eukaryotic cells form complexes with ion channel proteins, cell adhesion and signalling molecules and components of the cytoskeleton. They play a pivotal role as scaffolding proteins, in the structural anchoring to the muscle membrane, in muscle development, neurogenesis and synapse formation. Dysfunction of ankyrins is implicated in numerous diseases such as hereditary spherocytosis, neurodegeneration of Purkinje cells, cardiac arrhythmia, Brugada syndrome, bipolar disorders and schizophrenia, congenital myopathies and congenital heart disease as well as cancers. Detecting either down- or over-expression of ankyrins and ergo their use as biomarkers can provide a new paradigm in the diagnosis of these diseases. This paper provides an outline of knowledge about the structure of ankyrins, and by making use of recent experimental research studies critically discusses their role in several health disorders. Moreover, therapeutic options utilizing engineered ankyrins, designed ankyrin repeat proteins (DARPins), are discussed.
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Affiliation(s)
- Damian B. Chagula
- Laboratory of Gastroimmunology, Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Tomasz Rechciński
- Department of Cardiology, Bieganski Regional Speciality Hospital, Medical University of Lodz, Lodz, Poland
| | - Karolina Rudnicka
- Laboratory of Gastroimmunology, Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Magdalena Chmiela
- Laboratory of Gastroimmunology, Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
- Corresponding author: Prof. Magdalena Chmiela Laboratory of Gastroimmunology, Department of Immmunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St, 90-237 Lodz, Poland, E-mail:
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Mukund K, Subramaniam S. Skeletal muscle: A review of molecular structure and function, in health and disease. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1462. [PMID: 31407867 PMCID: PMC6916202 DOI: 10.1002/wsbm.1462] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/03/2019] [Accepted: 07/03/2019] [Indexed: 12/11/2022]
Abstract
Decades of research in skeletal muscle physiology have provided multiscale insights into the structural and functional complexity of this important anatomical tissue, designed to accomplish the task of generating contraction, force and movement. Skeletal muscle can be viewed as a biomechanical device with various interacting components including the autonomic nerves for impulse transmission, vasculature for efficient oxygenation, and embedded regulatory and metabolic machinery for maintaining cellular homeostasis. The "omics" revolution has propelled a new era in muscle research, allowing us to discern minute details of molecular cross-talk required for effective coordination between the myriad interacting components for efficient muscle function. The objective of this review is to provide a systems-level, comprehensive mapping the molecular mechanisms underlying skeletal muscle structure and function, in health and disease. We begin this review with a focus on molecular mechanisms underlying muscle tissue development (myogenesis), with an emphasis on satellite cells and muscle regeneration. We next review the molecular structure and mechanisms underlying the many structural components of the muscle: neuromuscular junction, sarcomere, cytoskeleton, extracellular matrix, and vasculature surrounding muscle. We highlight aberrant molecular mechanisms and their possible clinical or pathophysiological relevance. We particularly emphasize the impact of environmental stressors (inflammation and oxidative stress) in contributing to muscle pathophysiology including atrophy, hypertrophy, and fibrosis. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Developmental Biology > Developmental Processes in Health and Disease Models of Systems Properties and Processes > Cellular Models.
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Affiliation(s)
- Kavitha Mukund
- Department of BioengineeringUniversity of CaliforniaSan DiegoCalifornia
| | - Shankar Subramaniam
- Department of Bioengineering, Bioinformatics & Systems BiologyUniversity of CaliforniaSan DiegoCalifornia
- Department of Computer Science and EngineeringUniversity of CaliforniaSan DiegoCalifornia
- Department of Cellular and Molecular Medicine and NanoengineeringUniversity of CaliforniaSan DiegoCalifornia
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Purfield DC, Evans RD, Carthy TR, Berry DP. Genomic Regions Associated With Gestation Length Detected Using Whole-Genome Sequence Data Differ Between Dairy and Beef Cattle. Front Genet 2019; 10:1068. [PMID: 31749838 PMCID: PMC6848454 DOI: 10.3389/fgene.2019.01068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/04/2019] [Indexed: 12/17/2022] Open
Abstract
While many association studies exist that have attempted to relate genomic markers to phenotypic performance in cattle, very few have considered gestation length as a phenotype, and of those that did, none used whole genome sequence data from multiple breeds. The objective of the present study was therefore to relate imputed whole genome sequence data to estimated breeding values for gestation length using 22,566 sires (representing 2,262,706 progeny) of multiple breeds [Angus (AA), Charolais (CH), Holstein-Friesian (HF), and Limousin (LM)]. The associations were undertaken within breed using linear mixed models that accounted for genomic relatedness among sires; a separate association analysis was undertaken with all breeds analysed together but with breed included as a fixed effect in the model. Furthermore, the genome was divided into 500 kb segments and whether or not segments harboured a single nucleotide polymorphism (SNP) with a P ≤ 1 × 10-4 common to different combinations of breeds was determined. Putative quantitative trait loci (QTL) regions associated with gestation length were detected in all breeds; significant associations with gestation length were only detected in the HF population and in the across-breed analysis of all 22,566 sires. Twenty-five SNPs were significantly associated (P ≤ 5 × 10-8) with gestation length in the HF population. Of the 25 significant SNPs, 18 were located within three QTLs on Bos taurus autosome number (BTA) 18, six were in two QTL on BTA19, and one was located within a QTL on BTA7. The strongest association was rs381577268, a downstream variant of ZNF613 located within a QTL spanning from 58.06 to 58.19 Mb on BTA18; it accounted for 1.37% of the genetic variance in gestation length. Overall there were 11 HF animals within the edited dataset that were homozygous for the T allele at rs381577268 and these had a 3.3 day longer (P < 0.0001) estimated breeding value (EBV) for gestation length than the heterozygous animals and a 4.7 day longer (P < 0.0001) EBV for gestation length than the homozygous CC animals. The majority of the 500 kb windows harboring a SNP with a P ≤ 1 × 10-4 were unique to a single breed and no window was shared among all four breeds for gestation length, suggesting any QTLs identified are breed-specific associations.
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Affiliation(s)
- Deirdre C Purfield
- Animal & Grassland Research and Innovation Centre, Teagasc, Cork, Ireland
| | | | - Tara R Carthy
- Animal & Grassland Research and Innovation Centre, Teagasc, Cork, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Cork, Ireland
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Pierantozzi E, Szentesi P, Al-Gaadi D, Oláh T, Dienes B, Sztretye M, Rossi D, Sorrentino V, Csernoch L. Calcium Homeostasis Is Modified in Skeletal Muscle Fibers of Small Ankyrin1 Knockout Mice. Int J Mol Sci 2019; 20:ijms20133361. [PMID: 31323924 PMCID: PMC6651408 DOI: 10.3390/ijms20133361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 11/16/2022] Open
Abstract
Small Ankyrins (sAnk1) are muscle-specific isoforms generated by the Ank1 gene that participate in the organization of the sarcoplasmic reticulum (SR) of striated muscles. Accordingly, the volume of SR tubules localized around the myofibrils is strongly reduced in skeletal muscle fibers of 4- and 10-month-old sAnk1 knockout (KO) mice, while additional structural alterations only develop with aging. To verify whether the lack of sAnk1 also alters intracellular Ca2+ handling, cytosolic Ca2+ levels were analyzed in stimulated skeletal muscle fibers from 4- and 10-month-old sAnk1 KO mice. The SR Ca2+ content was reduced in sAnk1 KO mice regardless of age. The amplitude of the Ca2+ transients induced by depolarizing pulses was decreased in myofibers of sAnk1 KO with respect to wild type (WT) fibers, while their voltage dependence was not affected. Furthermore, analysis of spontaneous Ca2+ release events (sparks) on saponin-permeabilized muscle fibers indicated that the frequency of sparks was significantly lower in fibers from 4-month-old KO mice compared to WT. Furthermore, both the amplitude and spatial spread of sparks were significantly smaller in muscle fibers from both 4- and 10-month-old KO mice compared to WT. These data suggest that the absence of sAnk1 results in an impairment of SR Ca2+ release, likely as a consequence of a decreased Ca2+ store due to the reduction of the SR volume in sAnk1 KO muscle fibers.
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Affiliation(s)
- Enrico Pierantozzi
- Department of Molecular and Developmental Medicine, Molecular Medicine Section, University of Siena, 53100 Siena, Italy
| | - Péter Szentesi
- Department of Physiology, Medical Faculty, University of Debrecen, H-4002 Debrecen, Hungary
| | - Dána Al-Gaadi
- Department of Physiology, Medical Faculty, University of Debrecen, H-4002 Debrecen, Hungary
- Doctoral School of Molecular Medicine, University of Debrecen, H-4002 Debrecen, Hungary
| | - Tamás Oláh
- Department of Physiology, Medical Faculty, University of Debrecen, H-4002 Debrecen, Hungary
| | - Beatrix Dienes
- Department of Physiology, Medical Faculty, University of Debrecen, H-4002 Debrecen, Hungary
| | - Mónika Sztretye
- Department of Physiology, Medical Faculty, University of Debrecen, H-4002 Debrecen, Hungary
| | - Daniela Rossi
- Department of Molecular and Developmental Medicine, Molecular Medicine Section, University of Siena, 53100 Siena, Italy
| | - Vincenzo Sorrentino
- Department of Molecular and Developmental Medicine, Molecular Medicine Section, University of Siena, 53100 Siena, Italy
| | - László Csernoch
- Department of Physiology, Medical Faculty, University of Debrecen, H-4002 Debrecen, Hungary.
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Yang Q, Liu H, Li Z, Wang Y, Liu W. Purification and mutagenesis studies of TANC1 ankyrin repeats domain provide clues to understand mis-sense variants from diseases. Biochem Biophys Res Commun 2019; 514:358-364. [PMID: 31040020 DOI: 10.1016/j.bbrc.2019.04.151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 04/22/2019] [Indexed: 12/26/2022]
Abstract
TANC1 and its close relative TANC2 are two important synaptic scaffold proteins which play critical roles in regulating densities of synaptic spines and excitatory synapse strength. Recent studies indicated TANC1 and TANC2 are candidate genes of several neurodevelopmental disorders (NDD). So far, the biochemical properties of TANC1/2 proteins remain largely unknown. In this study, Ankyrin-repeats (AR) domain of TANC1 was expressed and purified using Escherichia coli. (E. coli.) cells, which showed low solubility and stability after removing the maltose binding protein (MBP) tag. Sequence analysis revealed that the TANC1 AR domain is lack of canonical N, C-capping units. By introducing two point mutations in the C-capping unit and replacing the N-capping unit, monomeric and well-folded TANC1 AR domain was purified and characterized by size exclusion chromatography coupled with multi-angle static light scattering (SEC-MALS) and circular dichroism spectroscopy (CD). In addition, mutations from intellectual disability (ID) patients and cancer patients were imported into the TANC1 AR domain. The ID mutant exhibited marginal effects in terms of conformation and protein folding stability changes. By contrast, the cancer mutants dramatically decreased protein solubility. Combined with structural prediction, we speculated that mis-sense variants tested in this study may either affect protein folding or disrupt the interaction between TANC1/2 AR domains and their binding partners.
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Affiliation(s)
- Qingqing Yang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong province, China
| | - Haiyang Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong province, China; Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Zhiwei Li
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong province, China
| | - Yue Wang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong province, China
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong province, China.
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Liu P, Verhaar AP, Peppelenbosch MP. Signaling Size: Ankyrin and SOCS Box-Containing ASB E3 Ligases in Action. Trends Biochem Sci 2018; 44:64-74. [PMID: 30446376 DOI: 10.1016/j.tibs.2018.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 12/14/2022]
Abstract
Ankyrin repeat and suppressor of cytokine signaling (SOCS) box (Asb) proteins are ubiquitin E3 ligases. The subfamily of six-ankyrin repeat domain-containing Asb proteins (Asb5, Asb9, Asb11, and Asb13) is of specific interest because they display unusual strong evolutionary conservation (e.g., urochordate and human ASB11 are >49% similar at the amino acid level) and mediate compartment size expansion, regulating, for instance, the size of the brain and muscle compartment. Thus, they may be involved in the explanation of the differences in brain size between humans and apes. Mechanistically, many questions remain, but it has become clear that regulation of canonical Notch signaling and also mitochondrial function are important effectors. Here, we review the action and function of six ankyrin repeat domain-containing Asb proteins in physiology and pathophysiology.
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Affiliation(s)
- Pengyu Liu
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Auke P Verhaar
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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Ortega A, Tarazón E, Gil-Cayuela C, Martínez-Dolz L, Lago F, González-Juanatey JR, Sandoval J, Portolés M, Roselló-Lletí E, Rivera M. ASB1 differential methylation in ischaemic cardiomyopathy: relationship with left ventricular performance in end-stage heart failure patients. ESC Heart Fail 2018; 5:732-737. [PMID: 29667349 PMCID: PMC6073036 DOI: 10.1002/ehf2.12289] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 01/11/2018] [Accepted: 03/10/2018] [Indexed: 12/15/2022] Open
Abstract
Aims Ischaemic cardiomyopathy (ICM) leads to impaired contraction and ventricular dysfunction, causing high rates of morbidity and mortality. Epigenomics allows the identification of epigenetic signatures in human diseases. We analyse the differential epigenetic patterns of the ASB gene family in ICM patients and relate these alterations to their haemodynamic and functional status. Methods and results Epigenomic analysis was carried out using 16 left ventricular (LV) tissue samples, eight from ICM patients undergoing heart transplantation and eight from control (CNT) subjects without cardiac disease. We increased the sample size up to 13 ICM and 10 CNT for RNA sequencing and to 14 ICM for pyrosequencing analyses. We found a hypermethylated profile (cg11189868) in the ASB1 gene that showed a differential methylation of 0.26Δβ (P = 0.016). This result was validated by a pyrosequencing technique (0.23Δβ, P = 0.048). Notably, the methylation pattern was strongly related to LV ejection fraction (r = −0.849, P = 0.008), stroke volume (r = −0.929, P = 0.001), and end‐systolic and diastolic LV diameters (r = −0.743, P = 0.035 for both). ASB1 showed a down‐regulation in messenger RNA levels (−1.2‐fold, P = 0.039). Conclusions Our findings link a specific ASB1 methylation pattern to LV structure and performance in end‐stage ICM, opening new therapeutic opportunities and providing new insights regarding which is the functionally relevant genome in the ischaemic failing myocardium.
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Affiliation(s)
- Ana Ortega
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Avd. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Estefanía Tarazón
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Avd. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Carolina Gil-Cayuela
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Avd. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Luis Martínez-Dolz
- Heart Failure and Transplantation Unit, Cardiology Department, University and Polytechnic La Fe Hospital, Valencia, Spain
| | - Francisca Lago
- Cellular and Molecular Cardiology Research Unit, Department of Cardiology and Institute of Biomedical Research, University Clinical Hospital, Santiago de Compostela, Spain
| | - José Ramón González-Juanatey
- Cellular and Molecular Cardiology Research Unit, Department of Cardiology and Institute of Biomedical Research, University Clinical Hospital, Santiago de Compostela, Spain
| | - Juan Sandoval
- Epigenomic Unit, Health Research Institute La Fe, Valencia, Spain
| | - Manuel Portolés
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Avd. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Esther Roselló-Lletí
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Avd. Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Miguel Rivera
- Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital (IIS La Fe), Avd. Fernando Abril Martorell, 106, 46026, Valencia, Spain
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Wang YC, Li ZJ, Han RL, Xu CL, Wang SH, Sun GR, Wang SH, Wu JP, Kang XT. Promoter analysis and tissue expression of the chicken ASB15 gene. Br Poult Sci 2016; 58:26-31. [PMID: 27844487 DOI: 10.1080/00071668.2016.1236363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
1. This study was conducted to explore the promoter region of the chicken ASB15 gene by detecting the activities of the dual luciferase reporter gene and to assess expression profiles of the ASB15 gene in 10 different tissues from Gushi chickens. 2. Five dual luciferase reporter gene vectors were constructed and transfected into DF1 cells. The activities of recombined plasmids were measured and the core promoter was confirmed by bioinformatic analysis. Total RNA was extracted and the relative expression of the ASB15 gene was examined. 3. Data analysis indicated that the promoter was located from -955 to -212 bp. Results showed that the chicken ASB15 gene was expressed in heart, breast muscle and leg muscle. 4. This study has confirmed the promoter region and the expression profile of the chicken ASB15 gene, which provides a foundation for further exploring its transcriptional regulation and function.
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Affiliation(s)
- Y C Wang
- b Department of Animal Science , College of Animal Science and Technology, Gansu Agricultural University , Lanzhou , P. R. China
| | - Z J Li
- a Department of Animal Science , College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou , P. R. China
| | - R L Han
- a Department of Animal Science , College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou , P. R. China
| | - C L Xu
- a Department of Animal Science , College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou , P. R. China
| | - S H Wang
- a Department of Animal Science , College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou , P. R. China
| | - G R Sun
- a Department of Animal Science , College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou , P. R. China
| | - S H Wang
- a Department of Animal Science , College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou , P. R. China
| | - J P Wu
- b Department of Animal Science , College of Animal Science and Technology, Gansu Agricultural University , Lanzhou , P. R. China
| | - X T Kang
- a Department of Animal Science , College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou , P. R. China
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18
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Wang YC, Han RL, Li ZJ, Geng J, Tian YD, Jiang RR, Wu JP, Kang XT. Polymorphisms of Flanking Region of the ASB15 Gene and Their Associations with Performance Traits in Chicken. Anim Biotechnol 2016; 28:53-60. [PMID: 27736301 DOI: 10.1080/10495398.2016.1200986] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Research on the identity of genes and their relationship with traits of economic importance in chickens could assist in the selection of poultry. In this study, an F2 resource population of Gushi chickens crossed with Anka broilers was used to detect single-nucleotide polymorphisms (SNPs) in the flanking region of the ASB15 gene by DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). One SNP of -1271 C>T in 5' flanking region of the chicken ASB15 gene and two SNPs of the 10618 A>G and 10716 G>A in 3' flanking region were identified. Furthermore, the 10618 A>G and 10716 G>A in 3' flanking region were in complete linkage. Association analysis results showed that -1271 C>T was not associated with performance traits, while the 10618 A>G and 10716 G>A were significantly associated with BW2, 4, 6, 8, 10, 12, SL12, CD8, CW4, 8, 12, BSL4, 8, 12, and SEW, EW, WW, BMW, LW, CW, SFT. Our results suggest that the ASB15 gene profoundly affects chicken performance traits.
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Affiliation(s)
- Y C Wang
- a College of Animal Science and Veterinary Medicine , Henan Agricultural University , Zhengzhou , P. R. China.,b College of Animal Science and Technology , Gansu Agricultural University , Lanzhou , P. R. China
| | - R L Han
- a College of Animal Science and Veterinary Medicine , Henan Agricultural University , Zhengzhou , P. R. China
| | - Z J Li
- a College of Animal Science and Veterinary Medicine , Henan Agricultural University , Zhengzhou , P. R. China
| | - J Geng
- a College of Animal Science and Veterinary Medicine , Henan Agricultural University , Zhengzhou , P. R. China
| | - Y D Tian
- a College of Animal Science and Veterinary Medicine , Henan Agricultural University , Zhengzhou , P. R. China
| | - R R Jiang
- a College of Animal Science and Veterinary Medicine , Henan Agricultural University , Zhengzhou , P. R. China
| | - J P Wu
- b College of Animal Science and Technology , Gansu Agricultural University , Lanzhou , P. R. China
| | - X T Kang
- a College of Animal Science and Veterinary Medicine , Henan Agricultural University , Zhengzhou , P. R. China
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Israel E, Lasky-Su J, Markezich A, Damask A, Szefler SJ, Schuemann B, Klanderman B, Sylvia J, Kazani S, Wu R, Martinez F, Boushey HA, Chinchilli VM, Mauger D, Weiss ST, Tantisira KG. Genome-wide association study of short-acting β2-agonists. A novel genome-wide significant locus on chromosome 2 near ASB3. Am J Respir Crit Care Med 2015; 191:530-7. [PMID: 25562107 DOI: 10.1164/rccm.201408-1426oc] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE β2-Agonists are the most common form of treatment of asthma, but there is significant variability in response to these medications. A significant proportion of this responsiveness may be heritable. OBJECTIVES To investigate whether a genome-wide association study (GWAS) could identify novel pharmacogenetic loci in asthma. METHODS We performed a GWAS of acute bronchodilator response (BDR) to inhaled β2-agonists. A total of 444,088 single-nucleotide polymorphisms (SNPs) were examined in 724 individuals from the SNP Health Association Resource (SHARe) Asthma Resource Project (SHARP). The top 50 SNPs were carried forward to replication in a population of 444 individuals. MEASUREMENTS AND MAIN RESULTS The combined P value for four SNPs reached statistical genome-wide significance aftercorrecting for multiple comparisons. Combined P values for rs350729, rs1840321, rs1384918, and rs1319797 were 2.21 × 10(-10), 5.75 × 10(-8), 9.3 × 10(-8), and 3.95 × 10(-8), respectively. The significant variants all map to a novel genetic region on chromosome 2 near the ASB3 gene, a region associated with smooth muscle proliferation. As compared with the wild type, the presence of the minor alleles reduced the degree of BDR by 20% in the original population and by a similar percentage in the confirmatory population. CONCLUSIONS These GWAS findings for BDR in subjects with asthma suggest that a gene associated with smooth muscle proliferation may influence a proportion of the smooth muscle relaxation that occurs in asthma.
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Affiliation(s)
- Elliot Israel
- 1 Division of Pulmonary and Critical Care Medicine and
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Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle. BMC Genomics 2015; 16:50. [PMID: 25651817 PMCID: PMC4328970 DOI: 10.1186/s12864-015-1238-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/12/2015] [Indexed: 01/12/2023] Open
Abstract
Background Domestication of the wild pig has led to obese and lean phenotype breeds, and evolutionary genome research has sought to identify the regulatory mechanisms underlying this phenotypic diversity. However, revealing the molecular mechanisms underlying muscle phenotype variation based on differentially expressed genes has proved to be difficult. To characterize the mechanisms regulating muscle phenotype variation under artificial selection, we aimed to provide an integrated view of genome organization by weighted gene coexpression network analysis. Results Our analysis was based on 20 publicly available next-generation sequencing datasets of lean and obese pig muscle generated from 10 developmental stages. The evolution of the constructed coexpression modules was examined using the genome resequencing data of 37 domestic pigs and 11 wild boars. Our results showed the regulation of muscle development might be more complex than had been previously acknowledged, and is regulated by the coordinated action of muscle, nerve and immunity related genes. Breed-specific modules that regulated muscle phenotype divergence were identified, and hundreds of hub genes with major roles in muscle development were determined to be responsible for key functional distinctions between breeds. Our evolutionary analysis showed that the role of changes in the coding sequence under positive selection in muscle phenotype divergence was minor. Conclusions Muscle phenotype divergence was found to be regulated by the divergence of coexpression network modules under artificial selection, and not by changes in the coding sequence of genes. Our results present multiple lines of evidence suggesting links between modules and muscle phenotypes, and provide insights into the molecular bases of genome organization in muscle development and phenotype variation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1238-5) contains supplementary material, which is available to authorized users.
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Jasnic-Savovic J, Nestorovic A, Savic S, Karasek S, Vitulo N, Valle G, Faulkner G, Radojkovic D, Kojic S. Profiling of skeletal muscle Ankrd2 protein in human cardiac tissue and neonatal rat cardiomyocytes. Histochem Cell Biol 2015; 143:583-97. [PMID: 25585647 DOI: 10.1007/s00418-015-1307-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/26/2014] [Indexed: 10/24/2022]
Abstract
Muscle-specific mechanosensors Ankrd2/Arpp (ankyrin repeat protein 2) and Ankrd1/CARP (cardiac ankyrin repeat protein) have an important role in transcriptional regulation, myofibrillar assembly, cardiogenesis and myogenesis. In skeletal muscle myofibrils, Ankrd2 has a structural role as a component of a titin associated stretch-sensing complex, while in the nucleus it exerts regulatory function as transcriptional co-factor. It is also involved in myogenic differentiation and coordination of myoblast proliferation. Although expressed in the heart, the role of Ankrd2 in the cardiac muscle is completely unknown. Recently, we have shown that hypertrophic and dilated cardiomyopathy pathways are altered upon Ankrd2 silencing suggesting the importance of this protein in cardiac tissue. Here we provide the underlying basis for the functional investigation of Ankrd2 in the heart. We confirmed reduced Ankrd2 expression levels in human heart in comparison with Ankrd1 using RNAseq and Western blot. For the first time we demonstrated that, apart from the sarcomere and nucleus, both proteins are localized to the intercalated disks of human cardiomyocytes. We further tested the expression and localization of endogenous Ankrd2 in rat neonatal cardiomyocytes, a well-established model for studying cardiac-specific proteins. Ankrd2 was found to be expressed in both the cytoplasm and nucleus, independently from maturation status of cardiomyocytes. In contrast to Ankrd1, it is not responsive to the cardiotoxic drug Doxorubicin, suggesting that different mechanisms govern their expression in cardiac cells.
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Affiliation(s)
- Jovana Jasnic-Savovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, PO Box 23, 11010, Belgrade, Serbia
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Meira CT, Fortes MR, Farah MM, Porto-Neto LR, Kelly M, Moore SS, Pereira GL, Chardulo LAL, Curi RA. Speed Index in the Racing Quarter Horse: A Genome-wide Association Study. J Equine Vet Sci 2014. [DOI: 10.1016/j.jevs.2014.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Qian X, Mruk DD, Cheng YH, Cheng CY. RAI14 (retinoic acid induced protein 14) is an F-actin regulator: Lesson from the testis. SPERMATOGENESIS 2014; 3:e24824. [PMID: 23885305 PMCID: PMC3710223 DOI: 10.4161/spmg.24824] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 04/22/2013] [Accepted: 04/25/2013] [Indexed: 12/20/2022]
Abstract
RAI14 (retinoic acid induced protein 14) is an actin-binding protein first identified in the liver. In the testis, RAI14 is expressed by both Sertoli and germ cells in the seminiferous epithelium. Besides binding to actin in the testis, RAI14 is also a binding protein for palladin, an actin cross-linking and bundling protein. A recent report has shown that RAI14 displays stage-specific and spatiotemporal expression at the ES [ectoplasmic specialization, a testis-specific filamentous (F)-actin-rich adherens junction] in the seminiferous epithelium of adult rat testes during the epithelial cycle of spermatogenesis, illustrating its likely involvement in F-actin organization at the ES. Functional studies in which RAI14 was knocked down by RNAi in Sertoli cells in vitro and also in testicular cells in vivo have illustrated its role in conferring the integrity of actin filament bundles at the ES, perturbing the Sertoli cell tight junction (TJ)-pemeability barrier function in vitro, and also spermatid polarity and adhesion in vivo, thereby regulating spermatid transport at spermiation. Herein, we critically evaluate these earlier findings and also provide a likely hypothetic model based on the functional role of RAI14 at the ES, and how RAI14 is working with palladin and other actin regulatory proteins in the testis to regulate the transport of (1) spermatids and (2) preleptotene spermatocytes across the seminiferous epithelium and the blood-testis barrier (BTB), respectively, during spermatogenesis. This model should serve as a framework upon which functional experiments can be designed to better understand the biology of RAI14 and other actin-binding and regulatory proteins in the testis.
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Affiliation(s)
- Xiaojing Qian
- The Mary M. Wohlford Laboratory for Male Contraceptive Research; Center for Biomedical Research; Population Council; New York NY USA ; Department of Anatomy, Histology and Embryology; School of Basic Medicine; Peking Union Medical College; Beijing, China
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Woo JS, Lee KJ, Huang M, Cho CH, Lee EH. Heteromeric TRPC3 with TRPC1 formed via its ankyrin repeats regulates the resting cytosolic Ca2+ levels in skeletal muscle. Biochem Biophys Res Commun 2014; 446:454-9. [PMID: 24613381 DOI: 10.1016/j.bbrc.2014.02.127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 02/26/2014] [Indexed: 01/05/2023]
Abstract
The main tasks of skeletal muscle are muscle contraction and relaxation, which are mediated by changes in cytosolic Ca(2+) levels. Canonical-type transient receptor potential 3 (TRPC3) contains an ankyrin repeat (AR) region at the N-terminus (38-188 amino acids) and forms extracellular Ca(2+)-entry channels by homo or heteromerization with other TRP subtypes in various cells including skeletal myotubes. However, previous research has not determined which region(s) of TRPC3 is responsible for the heteromerization, whether the AR region participates in the heteromerizations, or what is the role of heteromeric TRPC3s in skeletal muscle. In the present study, the heteromerization of TRPC3 with TRPC1 was first examined by GST pull-down assays of TRPC3 portions with TRPC1. The portion containing the AR region of TRPC3 was bound to the TRPC1, but the binding was inhibited by the very end sub-region of the TRPC3 (1-37 amino acids). In-silico studies have suggested that the very end sub-region possibly induces a structural change in the AR region. Second, the very end sub-region of TRPC3 was expressed in mouse primary skeletal myotubes, resulting in a dominant-negative inhibition of heteromeric TRPC3/1 formation. In addition, the skeletal myotubes expressing the very end sub-region showed a decrease in resting cytosolic Ca(2+) levels. These results suggest that the AR region of TRPC3 could mediate the heteromeric TRPC3/1 formation, and the heteromeric TRPC3/1 could participate in regulating the resting cytosolic Ca(2+) levels in skeletal muscle.
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Affiliation(s)
- Jin Seok Woo
- Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Keon Jin Lee
- Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Mei Huang
- Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Chung-Hyun Cho
- Department of Pharmacology and Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea
| | - Eun Hui Lee
- Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea.
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Blandin G, Marchand S, Charton K, Danièle N, Gicquel E, Boucheteil JB, Bentaib A, Barrault L, Stockholm D, Bartoli M, Richard I. A human skeletal muscle interactome centered on proteins involved in muscular dystrophies: LGMD interactome. Skelet Muscle 2013; 3:3. [PMID: 23414517 PMCID: PMC3610214 DOI: 10.1186/2044-5040-3-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 02/07/2013] [Indexed: 02/01/2023] Open
Abstract
Background The complexity of the skeletal muscle and the identification of numerous human disease-causing mutations in its constitutive proteins make it an interesting tissue for proteomic studies aimed at understanding functional relationships of interacting proteins in both health and diseases. Method We undertook a large-scale study using two-hybrid screens and a human skeletal-muscle cDNA library to establish a proteome-scale map of protein-protein interactions centered on proteins involved in limb-girdle muscular dystrophies (LGMD). LGMD is a group of more than 20 different neuromuscular disorders that principally affect the proximal pelvic and shoulder girdle muscles. Results and conclusion The interaction network we unraveled incorporates 1018 proteins connected by 1492 direct binary interactions and includes 1420 novel protein-protein interactions. Computational, experimental and literature-based analyses were performed to assess the overall quality of this network. Interestingly, LGMD proteins were shown to be highly interconnected, in particular indirectly through sarcomeric proteins. In-depth mining of the LGMD-centered interactome identified new candidate genes for orphan LGMDs and other neuromuscular disorders. The data also suggest the existence of functional links between LGMD2B/dysferlin and gene regulation, between LGMD2C/γ-sarcoglycan and energy control and between LGMD2G/telethonin and maintenance of genome integrity. This dataset represents a valuable resource for future functional investigations.
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Affiliation(s)
- Gaëlle Blandin
- Généthon CNRS UMR8587, 1, rue de l'Internationale, Evry 91000, France.
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Transcriptional response of bovine monocyte-derived macrophages after the infection with different Argentinean Mycobacterium bovis isolates. BIOMED RESEARCH INTERNATIONAL 2013; 2013:458278. [PMID: 23484118 PMCID: PMC3581155 DOI: 10.1155/2013/458278] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 11/13/2012] [Accepted: 11/27/2012] [Indexed: 12/03/2022]
Abstract
Infection of bovines with Mycobacterium bovis causes important financial hardship in many countries presenting also a risk for humans. M. bovis is known to be adapted to survive and thrive within the intramacrophage environment. In spite of its relevance, at present the information about macrophage expression patterns is scarce, particularly regarding the bovine host. In this study, transcriptomic analysis was used to detect genes differentially expressed in macrophages derived from peripheral blood mononuclear cells at early stages of infection with two Argentinean strains of M. bovis, a virulent and an attenuated strains. The results showed that the number of differentially expressed genes in the cells infected with the virulent strain (5) was significantly lower than those in the cells infected with the attenuated strain (172). Several genes were more strongly expressed in infected macrophages. Among them, we detected encoding transcription factors, anthrax toxin receptor, cell division and apoptosis regulator, ankyrin proteins, cytoskeleton proteins, protein of cell differentiation, and regulators of endocytic traffic of membrane. Quantitative real-time PCR of a selected group of differentially expressed genes confirmed the microarrays results. Altogether, the present results contribute to understanding the mechanisms involved in the early interaction of M. bovis with the bovine macrophage.
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Innate immune messenger 2-5A tethers human RNase L into active high-order complexes. Cell Rep 2012; 2:902-13. [PMID: 23084743 DOI: 10.1016/j.celrep.2012.09.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 07/23/2012] [Accepted: 09/07/2012] [Indexed: 11/23/2022] Open
Abstract
2',5'-linked oligoadenylates (2-5As) serve as conserved messengers of pathogen presence in the mammalian innate immune system. 2-5As induce self-association and activation of RNase L, which cleaves cytosolic RNA and promotes the production of interferons (IFNs) and cytokines driven by the transcription factors IRF-3 and NF-κB. We report that human RNase L is activated by forming high-order complexes, reminiscent of the mode of activation of the phylogenetically related transmembrane kinase/RNase Ire1 in the unfolded protein response. We describe crystal structures determined at 2.4 Å and 2.8 Å resolution, which show that two molecules of 2-5A at a time tether RNase L monomers via the ankyrin-repeat (ANK) domain. Each ANK domain harbors two distinct sites for 2-5A recognition that reside 50 Å apart. These data reveal a function for the ANK domain as a 2-5A-sensing homo-oligomerization device and describe a nonlinear, ultrasensitive regulation in the 2-5A/RNase L system poised for amplification of the IFN response.
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28
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Tee JM, Sartori da Silva MA, Rygiel AM, Muncan V, Bink R, van den Brink GR, van Tijn P, Zivkovic D, Kodach LL, Guardavaccaro D, Diks SH, Peppelenbosch MP. asb11 is a regulator of embryonic and adult regenerative myogenesis. Stem Cells Dev 2012; 21:3091-103. [PMID: 22512762 DOI: 10.1089/scd.2012.0123] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The specific molecular determinants that govern progenitor expansion and final compartment size in the myogenic lineage, either during gestation or during regenerative myogenesis, remain largely obscure. Recently, we retrieved d-asb11 from a zebrafish screen designed to identify gene products that are downregulated during embryogenesis upon terminal differentiation and identified it as a potential regulator of compartment size in the ectodermal lineage. A role in mesodermal derivatives remained, however, unexplored. Here we report pan-vertebrate expression of Asb11 in muscle compartments, where it highly specifically localizes to the Pax7(+) muscle satellite cell compartment. Forced expression of d-asb11 impaired terminal differentiation and caused enhanced proliferation in the myogenic progenitor compartment both in in vivo and in vitro model systems. Conversely, introduction of a germline hypomorphic mutation in the zebrafish d-asb11 gene produced premature differentiation of the muscle progenitors and delayed regenerative responses in adult injured muscle. Thus, the expression of d-asb11 is necessary for muscle progenitor expansion, whereas its downregulation marks the onset of terminal differentiation. Hence, we provide evidence that d-asb11 is a principal regulator of embryonic as well as adult regenerative myogenesis.
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Affiliation(s)
- Jin-Ming Tee
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
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Kojic S, Radojkovic D, Faulkner G. Muscle ankyrin repeat proteins: their role in striated muscle function in health and disease. Crit Rev Clin Lab Sci 2011; 48:269-94. [DOI: 10.3109/10408363.2011.643857] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Current world literature. Curr Opin Organ Transplant 2011; 16:650-60. [PMID: 22068023 DOI: 10.1097/mot.0b013e32834dd969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wang L, Wang Y. Molecular characterization, expression patterns and subcellular localization of Myotrophin (MTPN) gene in porcine skeletal muscle. Mol Biol Rep 2011; 39:2733-8. [PMID: 21667249 DOI: 10.1007/s11033-011-1028-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 06/03/2011] [Indexed: 11/24/2022]
Abstract
Myotrophin (MTPN) is an effective growth factor in promoting skeletal muscle growth in vitro and vivo and has been purified from porcine skeletal muscle. However, in pigs, the information on MTPN gene is very limited. In this study, we cloned cDNA sequences and analyzed the genomic structure of porcine MTPN gene. The deduced amino acid sequence of porcine MTPN contains two the ankyrin repeat domains. RT-PCR analysis revealed that porcine MTPN gene was widely expressed in many tissues, a high expression level was observed in the spleen, liver and uterus, and transient transfection indicated that porcine MTPN proteins was located in cytoplasms within Pig Kidney Epithelial cells (PK15). Quantitative real-time PCR (qRT-PCR) analyses showed that MTPN expression peaked at embryonic 65 day post conception (dpc). During postnatal muscle development, MTPN expression was down-regulated from the 3 day to the 180 day in Yorkshire pigs. This result suggests that the MTPN gene may be important gene for skeletal muscle growth and provides useful information for further studies on its roles in porcine skeletal muscle.
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Affiliation(s)
- Linjie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China.
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