1
|
Bonchuk AN, Georgiev PG. C2H2 proteins: Evolutionary aspects of domain architecture and diversification. Bioessays 2024; 46:e2400052. [PMID: 38873893 DOI: 10.1002/bies.202400052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2-type zinc finger domains that specifically bind to DNA. Few well-studied C2H2 proteins, however, demonstrate their key role in the control of gene expression and chromosome architecture. Here we review the features of the domain architecture of C2H2 proteins and the likely origin of C2H2 zinc fingers. A comprehensive investigation of proteomes for the presence of proteins with multiple clustered C2H2 domains has revealed a key difference between groups of organisms. Unlike plants, transcription factors in metazoans contain clusters of C2H2 domains typically separated by a linker with the TGEKP consensus sequence. The average size of C2H2 clusters varies substantially, even between genomes of higher metazoans, and with a tendency to increase in combination with SCAN, and especially KRAB domains, reflecting the increasing complexity of gene regulatory networks.
Collapse
Affiliation(s)
- Artem N Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel G Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
2
|
Malik F, Surrey LF, Zhang PJ. ISLET-1 expression in soft tissue neoplasms reveals high sensitivity but moderate specificity for desmoplastic small round cell tumors and potential utility as a diagnostic biomarker. Pathol Res Pract 2024; 260:155469. [PMID: 39018925 DOI: 10.1016/j.prp.2024.155469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
ISLET-1 (ISL1) is a LIM-homeodomain transcription factor. Selective ISL1 expression is shown in neuroendocrine, non-neuroendocrine, and some soft tissue tumors including desmoplastic small round cell tumor (DSRCT). We assessed the specificity of ISL1 (clone EP283, 1:500, Cell Marque) in 288 soft tissue tumors, which included 17 DSRCTs and other histologic mimics. Positive staining threshold for ISL1 was set to >10 % of neoplastic cell nuclei at moderate intensity. ISL1 IHC was positive in 15/16 (94 %) DSRCTs with 75 % showing diffuse (>50 %) expression. ISL1 was positive in 1/10 (10 %) Ewing sarcomas (EWS), 7/13 (54 %) alveolar rhabdomyosarcoma (RMS), 14/22 (63 %) embryonal RMS, 7/14 (50 %) synovial sarcomas, 15/16 (93 %) neuroblastoma, 1/5 (20 %) Wilms tumor, 2/4 (50 %) olfactory neuroblastoma, and all 9 Merkel cell carcinomas. Other tumors, including all CIC::DUX4 sarcomas, were negative except 3/27 leiomyosarcomas, and 1 each of angiosarcoma, myxoid liposarcomas, inflammatory myofibroblastic tumor, malignant peripheral nerve sheath tumor, tenosynovial giant cell tumor, dedifferentiated LPS, and 1 ectomesenchymoma. In summary, among the soft tissue tumors tested, ISL1 is a highly sensitive but moderately specific marker for DSRCT and may be useful to distinguish from round cell mimics including EWS and CIC::DUX4 sarcomas. The oncogenic role of ISL1 in these tumors warrants further investigation.
Collapse
Affiliation(s)
- Faizan Malik
- Department of Pathology St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Lea F Surrey
- Department of Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, 5NW-26, Philadelphia, PA 19104, USA.
| | - Paul J Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine Hospital of the University of Pennsylvania, 3400 Spruce Street, 6 Founders, Philadelphia, PA 19104, USA.
| |
Collapse
|
3
|
Zhang J, Zhang R, Liu C, Ge X, Wang Y, Jiang F, Zhuang L, Li T, Zhu Q, Jiang Y, Chen Y, Lu M, Wang Y, Jiang M, Liu Y, Liu L. Missense mutation of ISL1 (E283D) is associated with the development of type 2 diabetes. Diabetologia 2024:10.1007/s00125-024-06186-5. [PMID: 38819467 DOI: 10.1007/s00125-024-06186-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 03/25/2024] [Indexed: 06/01/2024]
Abstract
AIMS/HYPOTHESIS Mutations in Isl1, encoding the insulin enhancer-binding protein islet-1 (ISL1), may contribute to attenuated insulin secretion in type 2 diabetes mellitus. We made an Isl1E283D mouse model to investigate the disease-causing mechanism of diabetes mellitus. METHODS The ISL1E283D mutation (c. 849A>T) was identified by whole exome sequencing on an early-onset type 2 diabetes family and then the Isl1E283D knockin (KI) mouse model was created and an IPGTT and IPITT were conducted. Glucose-stimulated insulin secretion (GSIS), expression of Ins2 and other ISL1 target genes and interacting proteins were evaluated in isolated pancreas islets. Transcriptional activity of Isl1E283D was evaluated by cell-based luciferase reporter assay and electrophoretic mobility shift assay, and the expression levels of Ins2 driven by Isl1 wild-type (Isl1WT) and Isl1E283D mutation in rat INS-1 cells were determined by RT-PCR and western blotting. RESULTS Impaired GSIS and elevated glucose level were observed in Isl1E283D KI mice while expression of Ins2 and other ISL1 target genes Mafa, Pdx1, Slc2a2 and the interacting protein NeuroD1 were downregulated in isolated islets. Transcriptional activity of the Isl1E283D mutation for Ins2 was reduced by 59.3%, and resulted in a marked downregulation of Ins2 expression when it was overexpressed in INS-1 cells, while overexpression of Isl1WT led to an upregulation of Ins2 expression. CONCLUSIONS/INTERPRETATION Isl1E283D mutation reduces insulin expression and secretion by regulating insulin and other target genes, as well as its interacting proteins such as NeuroD1, leading to the development of glucose intolerance in the KI mice, which recapitulated the human diabetic phenotype. This study identified and highlighted the Isl1E283D mutation as a novel causative factor for type 2 diabetes, and suggested that targeting transcription factor ISL1 could offer an innovative avenue for the precise treatment of human type 2 diabetes.
Collapse
Affiliation(s)
- Juan Zhang
- Shanghai Diabetes Institute, Department of Endocrinology & Metabolism, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Medicine, Huanghuai University, Henan, China
| | - Rong Zhang
- Shanghai Diabetes Institute, Department of Endocrinology & Metabolism, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chanwei Liu
- Shanghai Diabetes Institute, Department of Endocrinology & Metabolism, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoxu Ge
- Department of Endocrinology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Wang
- Department of Pediatrics, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Fusong Jiang
- Shanghai Diabetes Institute, Department of Endocrinology & Metabolism, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Langen Zhuang
- Department of Endocrinology, the First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Tiantian Li
- Shanghai Diabetes Institute, Department of Endocrinology & Metabolism, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qihan Zhu
- Department of Endocrinology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanyan Jiang
- Shanghai Diabetes Institute, Department of Endocrinology & Metabolism, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yating Chen
- Shanghai Diabetes Institute, Department of Endocrinology & Metabolism, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Lu
- Department of Endocrinology & Metabolism, Putuo Hospital Attached to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yanzhong Wang
- School of Population Health and Environmental Science, King's College London, London, UK
| | - Meisheng Jiang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Yanjun Liu
- Department of Pediatrics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Limei Liu
- Shanghai Diabetes Institute, Department of Endocrinology & Metabolism, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
4
|
Masuda A, Nishida K, Ajima R, Saga Y, Bakhtan M, Klar A, Hirata T, Zhu Y. A global gene regulatory program and its region-specific regulator partition neurons into commissural and ipsilateral projection types. SCIENCE ADVANCES 2024; 10:eadk2149. [PMID: 38781326 PMCID: PMC11114196 DOI: 10.1126/sciadv.adk2149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Understanding the genetic programs that drive neuronal diversification into classes and subclasses is key to understand nervous system development. All neurons can be classified into two types: commissural and ipsilateral, based on whether their axons cross the midline or not. However, the gene regulatory program underlying this binary division is poorly understood. We identified a pair of basic helix-loop-helix transcription factors, Nhlh1 and Nhlh2, as a global transcriptional mechanism that controls the laterality of all floor plate-crossing commissural axons in mice. Mechanistically, Nhlh1/2 play an essential role in the expression of Robo3, the key guidance molecule for commissural axon projections. This genetic program appears to be evolutionarily conserved in chick. We further discovered that Isl1, primarily expressed in ipsilateral neurons within neural tubes, negatively regulates the Robo3 induction by Nhlh1/2. Our findings elucidate a gene regulatory strategy where a conserved global mechanism intersects with neuron class-specific regulators to control the partitioning of neurons based on axon laterality.
Collapse
Affiliation(s)
- Aki Masuda
- National Institute of Genetics, Graduate University for Advanced Studies, Sokendai, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiko Nishida
- Department of Medical Chemistry, Kansai Medical University, Hirakata, Osaka 573-1010, Japan
| | - Rieko Ajima
- National Institute of Genetics, Graduate University for Advanced Studies, Sokendai, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yumiko Saga
- National Institute of Genetics, Graduate University for Advanced Studies, Sokendai, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Marah Bakhtan
- Department of Medical Neurobiology, IMRIC, Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Avihu Klar
- Department of Medical Neurobiology, IMRIC, Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Tatsumi Hirata
- National Institute of Genetics, Graduate University for Advanced Studies, Sokendai, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yan Zhu
- National Institute of Genetics, Graduate University for Advanced Studies, Sokendai, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| |
Collapse
|
5
|
Bogatkevich GS, Atanelishvili I, Bogatkevich AM, Silver RM. Critical Role of LMCD1 in Promoting Profibrotic Characteristics of Lung Myofibroblasts in Experimental and Scleroderma-Associated Lung Fibrosis. Arthritis Rheumatol 2023; 75:438-448. [PMID: 36103378 PMCID: PMC9998340 DOI: 10.1002/art.42344] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 07/15/2022] [Accepted: 08/31/2022] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Interstitial lung disease (ILD) is a serious complication and leading cause of mortality in patients with systemic sclerosis (SSc). In this study, we explored the role of LIM and cysteine-rich domains protein 1 (LMCD1) as a novel factor in the pathogenesis of SSc-related ILD (SSc-ILD). METHODS The expression and effects of LMCD1 were studied in lung tissue samples and fibroblasts from SSc-ILD patients and control subjects as well as in lung tissue samples from animal models. RESULTS LMCD1 was consistently elevated in lung tissue samples and in fibroblasts isolated from SSc-ILD patients as compared to controls. Additionally, LMCD1 was found to be highly expressed in the lung in the fibroblast-specific protein (FSP)-driven, constitutively active transforming growth factor β receptor type I (TGFβR1) transgenic mouse model of ILD and the bleomycin-induced mouse model of ILD. In lung fibroblasts from SSc-ILD patients, LMCD1 is an essential factor for the TGFβ-induced generation of type I collagen, fibronectin, and α-smooth muscle actin (α-SMA). Depletion of LMCD1 by small interfering RNA reduced the expression of extracellular matrix proteins and lowered transcriptional activity and expression of α-SMA, as well as decreased the proliferation and contractile activity of SSc-ILD lung fibroblasts. In dense fibrotic areas of affected lung tissue, lung LMCD1 colocalized with α-SMA. In cultured scleroderma lung fibroblasts, LMCD1 colocalized and interacted with serum response factor which mediates LMCD1-induced contractile activity of lung fibroblasts. CONCLUSION Our study identifies LMCD1 as a profibrotic molecule contributing to the activation of myofibroblasts and the persistent fibroproliferation observed in SSc-ILD. Thus, LMCD1 may be a potential novel therapeutic target for patients with SSc-ILD.
Collapse
Affiliation(s)
- Galina S Bogatkevich
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston
| | - Ilia Atanelishvili
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston
| | - Andrew M Bogatkevich
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, and College of Charleston (BSc Student), Charleston, South Carolina
| | - Richard M Silver
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston
| |
Collapse
|
6
|
Wang YS, Huang YS, Chiu CC, Wu TY, Zhou JQ, Liang SR, Tai MH, Wu CY. Interaction of transcription factors Islet2 and Nr2f1b to control vascular patterning during zebrafish development. Biochem Biophys Res Commun 2022; 604:123-129. [PMID: 35303678 DOI: 10.1016/j.bbrc.2022.03.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 11/25/2022]
Abstract
Many regulators controlling arterial identity are well described; however, transcription factors that promote vein identity and vascular patterning have remained largely unknown. We previously identified the transcription factors Islet2 (Isl2) and Nr2f1b required for specification of the vein and tip cell identity mediated by notch pathway in zebrafish. However, the interaction between Isl2 and Nr2f1b is not known. In this study, we report that Nr2f2 plays minor roles on vein and intersegmental vessels (ISV) growth and dissect the genetic interactions among the three transcription factors Isl2, Nr2f1b, and Nr2f2 using a combinatorial knockdown strategy. The double knockdown of isl2/nr2f1b, isl2/nr2f2, and nr2f1b/nr2f2 showed the enhanced defects in vasculature including less completed ISV, reduced veins, and ISV cells. We further tested the genetic relationship among these three transcription factors. We found isl2 can regulate the expression of nr2f1b and nr2f2, suggesting a model where Isl2 functions upstream of Nr2f1b and Nr2f2. We hypothsized that Isl2 and Nr2f1b can function together through cis-regulatory binding motifs. In-vitro luciferase assay results, we showed that Isl2 and Nr2f1b can cooperatively enhance gene expression. Moreover, co-immunoprecipitation results indicated that Isl2 and Nr2f1b interact physically. Together, we showed that the interaction of the Nr2f1b and Nr2f2 transcription factors in combination with the Islet2 play coordinated roles in the vascular development of zebrafish.
Collapse
Affiliation(s)
- Yi-Shan Wang
- Department of Biological Sciences, National Sun Yat-sen University, Taiwan; Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan; Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
| | - Yi-Shan Huang
- Department of Biological Sciences, National Sun Yat-sen University, Taiwan; Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chien-Chih Chiu
- Department of Biological Sciences, National Sun Yat-sen University, Taiwan; Department of Biotechnology, Kaohsiung Medical University, Taiwan
| | - Ting-Yun Wu
- Department of Biological Sciences, National Sun Yat-sen University, Taiwan
| | - Jun-Qing Zhou
- Department of Biological Sciences, National Sun Yat-sen University, Taiwan
| | - Shuo-Rong Liang
- Department of Biological Sciences, National Sun Yat-sen University, Taiwan
| | - Ming-Hong Tai
- Department of Biological Sciences, National Sun Yat-sen University, Taiwan; Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan; Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan; Institute of Biomedical Sciences, National Sun Yat-sen University, Taiwan
| | - Chang-Yi Wu
- Department of Biological Sciences, National Sun Yat-sen University, Taiwan; Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan; Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan; Department of Biotechnology, Kaohsiung Medical University, Taiwan; Institute of Medical Science and Technology, National Sun Yat-sen University, Taiwan.
| |
Collapse
|
7
|
A BMP4-p38 MAPK signaling axis controls ISL1 protein stability and activity during cardiogenesis. Stem Cell Reports 2021; 16:1894-1905. [PMID: 34329593 PMCID: PMC8365108 DOI: 10.1016/j.stemcr.2021.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 12/03/2022] Open
Abstract
During development, cells respond rapidly to intra- and intercellular signals, which induce signaling cascades regulating the activity of transcription factors at the transcriptional and/or post-translational level. The transcription factor ISL1 plays a key role in second heart field development and cardiac differentiation, and its mRNA levels are tightly regulated during cardiogenesis. Here, we show that a BMP-p38 MAPK signaling axis controls ISL1 protein function at the post-translational level. BMP-mediated activation of p38 MAPK leads to ISL1 phosphorylation at S269 by p38, which prevents ISL1 degradation and ensures its transcriptional activity during cardiogenesis. Interfering with p38 MAPK signaling leads to the degradation of ISL1 by the proteasome, resulting in defects in cardiomyocyte differentiation and impaired zebrafish and mouse heart morphogenesis and function. Given the critical role of the tight control of ISL1 activity during cardiac lineage diversification, modulation of BMP4-p38 MAPK signaling could direct differentiation into specific cardiac cell subpopulations. ISL1 is phosphorylated by p38 MAPK at serine 269 A BMP4-p38 MAPK signaling axis controls ISL1 protein stability Phosphorylation of ISL1 by p38 regulates its activity during cardiogenesis p38 Inhibition in vivo results in ISL1 degradation and second heart field defects
Collapse
|
8
|
Abstract
The field of molecular embryology started around 1990 by identifying new genes and analyzing their functions in early vertebrate embryogenesis. Those genes encode transcription factors, signaling molecules, their regulators, etc. Most of those genes are relatively highly expressed in specific regions or exhibit dramatic phenotypes when ectopically expressed or mutated. This review focuses on one of those genes, Lim1/Lhx1, which encodes a transcription factor. Lim1/Lhx1 is a member of the LIM homeodomain (LIM-HD) protein family, and its intimate partner, Ldb1/NLI, binds to two tandem LIM domains of LIM-HDs. The most ancient LIM-HD protein and its partnership with Ldb1 were innovated in the metazoan ancestor by gene fusion combining LIM domains and a homeodomain and by creating the LIM domain-interacting domain (LID) in ancestral Ldb, respectively. The LIM domain has multiple interacting interphases, and Ldb1 has a dimerization domain (DD), the LID, and other interacting domains that bind to Ssbp2/3/4 and the boundary factor, CTCF. By means of these domains, LIM-HD-Ldb1 functions as a hub protein complex, enabling more intricate and elaborate gene regulation. The common, ancestral role of LIM-HD proteins is neuron cell-type specification. Additionally, Lim1/Lhx1 serves crucial roles in the gastrula organizer and in kidney development. Recent studies using Xenopus embryos have revealed Lim1/Lhx1 functions and regulatory mechanisms during development and regeneration, providing insight into evolutionary developmental biology, functional genomics, gene regulatory networks, and regenerative medicine. In this review, we also discuss recent progress at unraveling participation of Ldb1, Ssbp, and CTCF in enhanceosomes, long-distance enhancer-promoter interactions, and trans-interactions between chromosomes.
Collapse
Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Masanori Taira
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan.
| |
Collapse
|
9
|
Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins. Int J Mol Sci 2021; 22:ijms22052647. [PMID: 33808029 PMCID: PMC7961639 DOI: 10.3390/ijms22052647] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share similarities with transcriptional regulators and have positively charged electrostatic patches, which may indicate that they have previously unanticipated nucleic acid binding properties. Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3. Furthermore, we analyzed protein expression and mutational frequency in various malignancies, as well as mapped protein-protein interaction networks they are involved in. Overall, our comprehensive bioinformatic analysis suggests that these proteins may play important roles in mediating protein-protein and protein-nucleic acid interactions.
Collapse
|
10
|
Smith NC, Wilkinson-White LE, Kwan AHY, Trewhella J, Matthews JM. Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification. JOURNAL OF STRUCTURAL BIOLOGY-X 2021; 5:100043. [PMID: 33458649 PMCID: PMC7797366 DOI: 10.1016/j.yjsbx.2020.100043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 11/29/2022]
Abstract
The mechanisms by which ISL1 and LHX3 specify neuronal cell identity are unknown. EMSA/SPR data show ISL1 and LHX3 have markedly different DNA-binding behaviours. SAXS shows ISL1/LHX3:DNA complexes are flexible in nature. ISL1 binds DNA poorly but appears to modulate the DNA-binding specificity of LHX3.
The roles of ISL1 and LHX3 in the development of spinal motor neurons have been well established. Whereas LHX3 triggers differentiation into interneurons, the additional expression of ISL1 in developing neuronal cells is sufficient to redirect their developmental trajectory towards spinal motor neurons. However, the underlying mechanism of this action by these transcription factors is less well understood. Here, we used electrophoretic mobility shift assays (EMSAs) and surface plasmon resonance (SPR) to probe the different DNA-binding behaviours of these two proteins, both alone and in complexes mimicking those found in developing neurons, and found that ISL1 shows markedly different binding properties to LHX3. We used small angle X-ray scattering (SAXS) to structurally characterise DNA-bound species containing ISL1 and LHX3. Taken together, these results have allowed us to develop a model of how these two DNA-binding modules coordinate to regulate gene expression and direct development of spinal motor neurons.
Collapse
Affiliation(s)
- Ngaio C Smith
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | | | - Ann H Y Kwan
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, University of Sydney, NSW 2006, Australia
| | - Jill Trewhella
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| |
Collapse
|
11
|
Pavlinkova G. Molecular Aspects of the Development and Function of Auditory Neurons. Int J Mol Sci 2020; 22:ijms22010131. [PMID: 33374462 PMCID: PMC7796308 DOI: 10.3390/ijms22010131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 01/08/2023] Open
Abstract
This review provides an up-to-date source of information on the primary auditory neurons or spiral ganglion neurons in the cochlea. These neurons transmit auditory information in the form of electric signals from sensory hair cells to the first auditory nuclei of the brain stem, the cochlear nuclei. Congenital and acquired neurosensory hearing loss affects millions of people worldwide. An increasing body of evidence suggest that the primary auditory neurons degenerate due to noise exposure and aging more readily than sensory cells, and thus, auditory neurons are a primary target for regenerative therapy. A better understanding of the development and function of these neurons is the ultimate goal for long-term maintenance, regeneration, and stem cell replacement therapy. In this review, we provide an overview of the key molecular factors responsible for the function and neurogenesis of the primary auditory neurons, as well as a brief introduction to stem cell research focused on the replacement and generation of auditory neurons.
Collapse
Affiliation(s)
- Gabriela Pavlinkova
- BIOCEV, Institute of Biotechnology of the Czech Academy of Sciences, 25250 Vestec, Czech Republic
| |
Collapse
|
12
|
Abstract
Cellular reprogramming experiments from somatic cell types have demonstrated the plasticity of terminally differentiated cell states. Recent efforts in understanding the mechanisms of cellular reprogramming have begun to elucidate the differentiation trajectories along the reprogramming processes. In this review, we focus mainly on direct reprogramming strategies by transcription factors and highlight the variables that contribute to cell fate conversion outcomes. We review key studies that shed light on the cellular and molecular mechanisms by investigating differentiation trajectories and alternative cell states as well as transcription factor regulatory activities during cell fate reprogramming. Finally, we highlight a few concepts that we believe require attention, particularly when measuring the success of cell reprogramming experiments.
Collapse
Affiliation(s)
- Begüm Aydin
- Department of Biology, New York University, New York, NY 10003, USA; .,Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
| | - Esteban O Mazzoni
- Department of Biology, New York University, New York, NY 10003, USA; .,Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
| |
Collapse
|
13
|
Enhancer long-range contacts: The multi-adaptor protein LDB1 is the tie that binds. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:625-633. [DOI: 10.1016/j.bbagrm.2019.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/20/2022]
|
14
|
Schrauwen I, Melegh BI, Chakchouk I, Acharya A, Nasir A, Poston A, Cornejo-Sanchez DM, Szabo Z, Karosi T, Bene J, Melegh B, Leal SM. Hearing impairment locus heterogeneity and identification of PLS1 as a new autosomal dominant gene in Hungarian Roma. Eur J Hum Genet 2019; 27:869-878. [PMID: 30872814 PMCID: PMC6777543 DOI: 10.1038/s41431-019-0372-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/24/2019] [Accepted: 02/08/2019] [Indexed: 01/07/2023] Open
Abstract
Roma are a socially and culturally distinct isolated population with genetically divergent subisolates, residing mainly across Central, Southern, and Eastern Europe. We evaluated the genetic etiology of hearing impairment (HI) in 15 Hungarian Roma families through exome sequencing. A family with autosomal dominant non-syndromic HI segregating a rare variant in the Calponin-homology 2 domain of PLS1, or Plastin 1 [p.(Leu363Phe)] was identified. Young adult Pls1 knockout mice have progressive HI and show morphological defects to their inner hair cells. There is evidence that PLS1 is important in the preservation of adult stereocilia and normal hearing. Four families segregated the European ancestral variant c.35delG [p.(Gly12fs)] in GJB2, and one family was homozygous for p.(Trp24*), an Indian subcontinent ancestral variant which is common amongst Roma from Slovakia, Czech Republic, and Spain. We also observed variants in known HI genes USH1G, USH2A, MYH9, MYO7A, and a splice site variant in MANBA (c.2158-2A>G) in a family with HI, intellectual disability, behavioral problems, and respiratory inflammation, which was previously reported in a Czech Roma family with similar features. Lastly, using multidimensional scaling and ADMIXTURE analyses, we delineate the degree of Asian/European admixture in the HI families understudy, and show that Roma individuals carrying the GJB2 p.(Trp24*) and MANBA c.2158-2A>G variants have a more pronounced South Asian background, whereas the other hearing-impaired Roma display an ancestral background similar to Europeans. We demonstrate a diverse genetic HI etiology in the Hungarian Roma and identify a new gene PLS1, for autosomal dominant human non-syndromic HI.
Collapse
Affiliation(s)
- Isabelle Schrauwen
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Béla I Melegh
- Department of Medical Genetics, University of Pecs, Medical School, and Szentagothai Research Centre, Pecs, Hungary
| | - Imen Chakchouk
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Anushree Acharya
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, South Korea
| | - Alexis Poston
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Diana M Cornejo-Sanchez
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX, USA
- Grupo Mapeo Genético, Facultad de Medicina, Universidad de Antioquia. Medellín, 050010470, Antioquia, Colombia
| | - Zsolt Szabo
- Department of Otolaryngology and Head and Neck Surgery, B-A-Z County Central Hospital and University Teaching Hospital, Miskolc, Hungary
| | - Tamás Karosi
- Department of Otolaryngology and Head and Neck Surgery, B-A-Z County Central Hospital and University Teaching Hospital, Miskolc, Hungary
| | - Judit Bene
- Department of Medical Genetics, University of Pecs, Medical School, and Szentagothai Research Centre, Pecs, Hungary
| | - Béla Melegh
- Department of Medical Genetics, University of Pecs, Medical School, and Szentagothai Research Centre, Pecs, Hungary
| | - Suzanne M Leal
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
15
|
Stokes PH, Robertson NO, Silva APG, Estephan T, Trewhella J, Guss JM, Matthews JM. Mutation in a flexible linker modulates binding affinity for modular complexes. Proteins 2019; 87:425-429. [PMID: 30788856 DOI: 10.1002/prot.25675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/05/2019] [Accepted: 02/17/2019] [Indexed: 11/11/2022]
Abstract
Tandem beta zippers are modular complexes formed between repeated linear motifs and tandemly arrayed domains of partner proteins in which β-strands form upon binding. Studies of such complexes, formed by LIM domain proteins and linear motifs in their intrinsically disordered partners, revealed spacer regions between the linear motifs that are relatively flexible but may affect the overall orientation of the binding modules. We demonstrate that mutation of a solvent exposed side chain in the spacer region of an LHX4-ISL2 complex has no significant effect on the structure of the complex, but decreases binding affinity, apparently by increasing flexibility of the linker.
Collapse
Affiliation(s)
- Philippa H Stokes
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neil O Robertson
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tanya Estephan
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Jill Trewhella
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - J Mitchell Guss
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
16
|
Bethea M, Liu Y, Wade AK, Mullen R, Gupta R, Gelfanov V, DiMarchi R, Bhatnagar S, Behringer R, Habegger KM, Hunter CS. The islet-expressed Lhx1 transcription factor interacts with Islet-1 and contributes to glucose homeostasis. Am J Physiol Endocrinol Metab 2019; 316:E397-E409. [PMID: 30620636 PMCID: PMC6415717 DOI: 10.1152/ajpendo.00235.2018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The LIM-homeodomain (LIM-HD) transcription factor Islet-1 (Isl1) interacts with the LIM domain-binding protein 1 (Ldb1) coregulator to control expression of key pancreatic β-cell genes. However, Ldb1 also has Isl1-independent effects, supporting that another LIM-HD factor interacts with Ldb1 to impact β-cell development and/or function. LIM homeobox 1 (Lhx1) is an Isl1-related LIM-HD transcription factor that appears to be expressed in the developing mouse pancreas and in adult islets. However, roles for this factor in the pancreas are unknown. This study aimed to determine Lhx1 interactions and elucidate gene regulatory and physiological roles in the pancreas. Co-immunoprecipitation using β-cell extracts demonstrated an interaction between Lhx1 and Isl1, and thus we hypothesized that Lhx1 and Isl1 regulate similar target genes. To test this, we employed siRNA-mediated Lhx1 knockdown in β-cell lines and discovered reduced Glp1R mRNA. Chromatin immunoprecipitation revealed Lhx1 occupancy at a domain also known to be occupied by Isl1 and Ldb1. Through development of a pancreas-wide knockout mouse model ( Lhx1∆Panc), we demonstrate that aged Lhx1∆Panc mice have elevated fasting blood glucose levels, altered intraperitoneal and oral glucose tolerance, and significantly upregulated glucagon, somatostatin, pancreatic polypeptide, MafB, and Arx islet mRNAs. Additionally, Lhx1∆Panc mice exhibit significantly reduced Glp1R, an mRNA encoding the insulinotropic receptor for glucagon-like peptide 1 along with a concomitant dampened Glp1 response and mild glucose intolerance in mice challenged with oral glucose. These data are the first to reveal that the Lhx1 transcription factor contributes to normal glucose homeostasis and Glp1 responses.
Collapse
Affiliation(s)
- Maigen Bethea
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham , Birmingham, Alabama
| | - Yanping Liu
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham , Birmingham, Alabama
| | - Alexa K Wade
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham , Birmingham, Alabama
| | - Rachel Mullen
- Department of Genetics, The University of Texas MD Anderson Cancer Center , Houston, Texas
| | - Rajesh Gupta
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham , Birmingham, Alabama
| | - Vasily Gelfanov
- Department of Chemistry, Indiana University , Bloomington, Indiana
| | - Richard DiMarchi
- Department of Chemistry, Indiana University , Bloomington, Indiana
| | - Sushant Bhatnagar
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham , Birmingham, Alabama
| | - Richard Behringer
- Department of Genetics, The University of Texas MD Anderson Cancer Center , Houston, Texas
| | - Kirk M Habegger
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham , Birmingham, Alabama
| | - Chad S Hunter
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham , Birmingham, Alabama
| |
Collapse
|
17
|
Jiang M, Pei Z, Fan X, Jiang J, Wang Q, Zhang Z. Function Analysis of Human Protein Interactions Based on a Novel Minimal Loop Algorithm. Curr Bioinform 2019. [DOI: 10.2174/1574893613666180906103946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background:
Various properties of Protein-Protein Interaction (PPI) network have been
widely exploited to discover the topological organizing principle and the crucial function motifs
involving specific biological pathway or disease process. The current motifs of PPI network are
either detected by the topology-based coarse grain algorithms, i.e. community discovering, or
depended on the limited-accessible protein annotation data derived precise algorithms. However,
the identified network motifs are hardly compatible with the well-defined biological functions
according to those two types of methods.
Method:
In this paper, we proposed a minimal protein loop finding method to explore the
elementary structural motifs of human PPI network. Initially, an improved article exchange model
was designed to search all the independent shortest protein loops of PPI network. Furthermore,
Gene Ontology (GO) based function clustering analysis was implemented to identify the biological
functions of the shortest protein loops. Additionally, the disease process associated shortest protein
loops were considered as the potential drug targets.
</P><P>
Result: Our proposed method presents the lowest computational complexity and the highest
functional consistency, compared to the three other methods. The functional enrichment and
clustering analysis for the identified minimal protein loops revealed the high correlation between
the protein loops and the corresponding biological functions, particularly, statistical analysis
presenting the protein loops with the length less than 4 is closely connected with some disease
process, suggesting the potential drug target.
Conclusion:
Our minimal protein loop method provides a novel manner to precisely define the
functional motif of PPI network, which extends the current knowledge about the cooperating
mechanisms and topological properties of protein modules composed of the short loops.
Collapse
Affiliation(s)
- Mingyang Jiang
- Inner Mongolia Engineering Research Center of Personalized Medicine, College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Zhili Pei
- Inner Mongolia Engineering Research Center of Personalized Medicine, College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Xiaojing Fan
- College of Mechanical Engineering, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Jingqing Jiang
- Inner Mongolia Engineering Research Center of Personalized Medicine, College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Qinghu Wang
- Inner Mongolia Engineering Research Center of Personalized Medicine, College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Zhifeng Zhang
- Inner Mongolia Engineering Research Center of Personalized Medicine, College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| |
Collapse
|
18
|
Schrauwen I, Chakchouk I, Liaqat K, Jan A, Nasir A, Hussain S, Nickerson DA, Bamshad MJ, Ullah A, Ahmad W, Leal SM. A variant in LMX1A causes autosomal recessive severe-to-profound hearing impairment. Hum Genet 2018; 137:471-478. [PMID: 29971487 PMCID: PMC6094940 DOI: 10.1007/s00439-018-1899-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
Abstract
Hereditary hearing impairment is a common sensory disorder that is genetically and phenotypically heterogeneous. In this study, we used a homozygosity mapping and exome sequencing strategy to study a consanguineous Pakistani family with autosomal recessive severe-to-profound hearing impairment. This led to the identification of a missense variant (p.Ile369Thr) in the LMX1A gene affecting a conserved residue in the C-terminus of the protein, which was predicted damaging by an in silico bioinformatics analysis. The p.Ile369Thr variant disrupts several C-terminal and homeodomain residue interactions, including an interaction with homeodomain residue p.Val241 that was previously found to be involved in autosomal dominant progressive HI. LIM-homeodomain factor Lmx1a is expressed in the inner ear through development, shows a progressive restriction to non-sensory epithelia, and is important in the separation of the sensory and non-sensory domains in the inner ear. Homozygous Lmx1a mutant mice (Dreher) are deaf with dysmorphic ears with an abnormal morphogenesis and fused and misshapen sensory organs; however, computed tomography performed on a hearing-impaired family member did not reveal any cochleovestibular malformations. Our results suggest that LMX1A is involved in both human autosomal recessive and dominant sensorineural hearing impairment.
Collapse
Affiliation(s)
- Isabelle Schrauwen
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, One Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Imen Chakchouk
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, One Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Khurram Liaqat
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abid Jan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, South Korea
| | - Shabir Hussain
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Asmat Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Suzanne M Leal
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, One Baylor Plaza 700D, Houston, TX, 77030, USA.
| |
Collapse
|
19
|
Disparate binding kinetics by an intrinsically disordered domain enables temporal regulation of transcriptional complex formation. Proc Natl Acad Sci U S A 2018; 115:4643-4648. [PMID: 29666277 DOI: 10.1073/pnas.1714646115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered regions are highly represented among mammalian transcription factors, where they often contribute to the formation of multiprotein complexes that regulate gene expression. An example of this occurs with LIM-homeodomain (LIM-HD) proteins in the developing spinal cord. The LIM-HD protein LHX3 and the LIM-HD cofactor LDB1 form a binary complex that gives rise to interneurons, whereas in adjacent cell populations, LHX3 and LDB1 form a rearranged ternary complex with the LIM-HD protein ISL1, resulting in motor neurons. The protein-protein interactions within these complexes are mediated by ordered LIM domains in the LIM-HD proteins and intrinsically disordered LIM interaction domains (LIDs) in LDB1 and ISL1; however, little is known about how the strength or rates of binding contribute to complex assemblies. We have measured the interactions of LIM:LID complexes using FRET-based protein-protein interaction studies and EMSAs and used these data to model population distributions of complexes. The protein-protein interactions within the ternary complexes are much weaker than those in the binary complex, yet surprisingly slow LDB1:ISL1 dissociation kinetics and a substantial increase in DNA binding affinity promote formation of the ternary complex over the binary complex in motor neurons. We have used mutational and protein engineering approaches to show that allostery and modular binding by tandem LIM domains contribute to the LDB1LID binding kinetics. The data indicate that a single intrinsically disordered region can achieve highly disparate binding kinetics, which may provide a mechanism to regulate the timing of transcriptional complex assembly.
Collapse
|
20
|
Bhati M, Llamosas E, Jacques DA, Jeffries CM, Dastmalchi S, Ripin N, Nicholas HR, Matthews JM. Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans. Sci Rep 2017; 7:4579. [PMID: 28676648 PMCID: PMC5496915 DOI: 10.1038/s41598-017-04587-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
LIM-Homeodomain (LIM-HD) transcription factors are highly conserved in animals where they are thought to act in a transcriptional ‘LIM code’ that specifies cell types, particularly in the central nervous system. In chick and mammals the interaction between two LIM-HD proteins, LHX3 and Islet1 (ISL1), is essential for the development of motor neurons. Using yeast two-hybrid analysis we showed that the Caenorhabditis elegans orthologs of LHX3 and ISL1, CEH-14 and LIM-7 can physically interact. Structural characterisation of a complex comprising the LIM domains from CEH-14 and a LIM-interaction domain from LIM-7 showed that these nematode proteins assemble to form a structure that closely resembles that of their vertebrate counterparts. However, mutagenic analysis across the interface indicates some differences in the mechanisms of binding. We also demonstrate, using fluorescent reporter constructs, that the two C. elegans proteins are co-expressed in a small subset of neurons. These data show that the propensity for LHX3 and Islet proteins to interact is conserved from C. elegans to mammals, raising the possibility that orthologous cell specific LIM-HD-containing transcription factor complexes play similar roles in the development of neuronal cells across diverse species.
Collapse
Affiliation(s)
- Mugdha Bhati
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,Teva Pharmaceuticals Australia Pty Ltd, Macquarie Park, NSW, 2113, Australia
| | - Estelle Llamosas
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,School of Women's and Children's Health, University of New South Wales, NSW, Australia
| | - David A Jacques
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,iThree Institute, University of Technology, NSW, 2007, Australia
| | - Cy M Jeffries
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Siavoush Dastmalchi
- Biotechnology Research Center and School of Pharmacy, Tabritz Univeristy of Medical Science, Tabritz, Iran
| | - Nina Ripin
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.,Department of Biology, ETH, Zurich, 8093, Switzerland
| | - Hannah R Nicholas
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Australia.
| |
Collapse
|
21
|
The Isl1-Lhx3 Complex Promotes Motor Neuron Specification by Activating Transcriptional Pathways that Enhance Its Own Expression and Formation. eNeuro 2017; 4:eN-NWR-0349-16. [PMID: 28451636 PMCID: PMC5394944 DOI: 10.1523/eneuro.0349-16.2017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/27/2017] [Accepted: 03/11/2017] [Indexed: 01/27/2023] Open
Abstract
Motor neuron (MN) progenitor cells rapidly induce high expression of the transcription factors Islet-1 (Isl1), LIM-homeobox 3 (Lhx3), and the transcriptional regulator LMO4, as they differentiate. While these factors are critical for MN specification, the mechanisms regulating their precise temporal and spatial expression patterns are not well characterized. Isl1 and Lhx3 form the Isl1-Lhx3 complex, which induces the transcription of genes critical for MN specification and maturation. Here, we report that Isl1, Lhx3, and Lmo4 are direct target genes of the Isl1-Lhx3 complex. Our results show that specific genomic loci associated with these genes recruit the Isl1-Lhx3 complex to activate the transcription of Isl1, Lhx3, and Lmo4 in embryonic MNs of chick and mouse. These findings support a model in which the Isl1-Lhx3 complex amplifies its own expression through a potent autoregulatory feedback loop and simultaneously enhances the transcription of Lmo4. LMO4 blocks the formation of the V2 interneuron-specifying Lhx3 complex. In developing MNs, this action inhibits the expression of V2 interneuron genes and increases the pool of unbound Lhx3 available to incorporate into the Isl1-Lhx3 complex. Identifying the pathways that regulate the expression of these key factors provides important insights into the genetic strategies utilized to promote MN differentiation and maturation.
Collapse
|
22
|
Ramzan K, Bin-Abbas B, Al-Jomaa L, Allam R, Al-Owain M, Imtiaz F. Two novel LHX3 mutations in patients with combined pituitary hormone deficiency including cervical rigidity and sensorineural hearing loss. BMC Endocr Disord 2017; 17:17. [PMID: 28302169 PMCID: PMC5356396 DOI: 10.1186/s12902-017-0164-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/22/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Congenital combined pituitary hormone deficiency (CPHD) is a rare heterogeneous group of conditions. CPHD-type 3 (CPHD3; MIM# 221750) is caused by recessive mutations in LHX3, a LIM-homeodomain transcription factor gene. The isoforms of LHX3 are critical for pituitary gland formation and specification of the anterior pituitary hormone-secreting cell types. They also play distinct roles in the development of neuroendocrine and auditory systems. CASE PRESENTATION Here, we summarize the clinical, endocrinological, radiological and molecular features of three patients from two unrelated families. Clinical evaluation revealed severe CPHD coupled with cervical vertebral malformations (rigid neck, scoliosis), mild developmental delay and moderate sensorineural hearing loss (SNHL). The patients were diagnosed with CPHD3 based on the array of hormone deficiencies and other associated syndromic symptoms, suggestive of targeted LHX3 gene sequencing. A novel missense mutation c.437G > T (p. Cys146Phe) and a novel nonsense mutation c.466C > T (p. Arg156Ter), both in homozygous forms, were found. The altered Cys146 resides in the LIM2 domain of the encoded protein and is a phylogenetically conserved residue, which mediates LHX3 transcription factor binding with a zinc cation. The p. Arg156Ter is predicted to result in a severely truncated protein, lacking the DNA binding homeodomain. CONCLUSIONS Considering genotype/phenotype correlation, we suggest that the presence of SNHL and limited neck rotation should be considered in the differential diagnosis of CPHD3 to facilitate molecular diagnosis. This report describes the first LHX3 mutations from Saudi patients and highlights the importance of combining molecular diagnosis with the clinical findings. In addition, it also expands the knowledge of LHX3-related CPHD3 phenotype and the allelic spectrum for this gene.
Collapse
Affiliation(s)
- Khushnooda Ramzan
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O.Box 3354, Riyadh, 11211 Saudi Arabia
| | - Bassam Bin-Abbas
- Department of Pediatrics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Lolwa Al-Jomaa
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O.Box 3354, Riyadh, 11211 Saudi Arabia
| | - Rabab Allam
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O.Box 3354, Riyadh, 11211 Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Faiqa Imtiaz
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, P.O.Box 3354, Riyadh, 11211 Saudi Arabia
| |
Collapse
|
23
|
Protein Inhibitor of Activated STAT Y (PIASy) Regulates Insulin Secretion by Interacting with LIM Homeodomain Transcription Factor Isl1. Sci Rep 2016; 6:39308. [PMID: 28000708 PMCID: PMC5175275 DOI: 10.1038/srep39308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/22/2016] [Indexed: 11/26/2022] Open
Abstract
It is known that the LIM homeodomain transcription factor Isl1 is highly expressed in all pancreatic endocrine cells and functions in regulating pancreatic development and insulin secretion. The Isl1 mutation has been found to be associated with type 2 diabetes, but the mechanism responsible for Isl1 regulation of insulin synthesis and secretion still needs to be elucidated. In the present study, the protein inhibitor of activated STAT Y (PIASy) was identified as a novel Isl1-interacting protein with a yeast two-hybrid system, and its interaction with Isl1 was further confirmed by a co-immunoprecipitation experiment. PIASy and Isl1 colocalize in human and mouse pancreas and NIT beta cells. Furthermore, PIASy and Isl1 upregulate insulin gene expression and insulin secretion in a dose-dependent manner by activating the insulin promoter. PIASy and Isl1 mRNA expression levels were also increased in type 2 diabetic db/db mice. In addition, our results demonstrate that PIASy and Isl1 cooperate to activate the insulin promoter through the Isl1 homeodomain and PIASy ring domain. These data suggest that that PIASy regulates insulin synthesis and secretion by interacting with Isl1 and provide new insight into insulin regulation, although the detailed molecular mechanism needs to be clarified in future studies.
Collapse
|
24
|
Robertson NO, Shah M, Matthews JM. A Quantitative Fluorescence-Based Assay for Assessing LIM Domain-Peptide Interactions. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Neil O. Robertson
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
| | - Manan Shah
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
| | | |
Collapse
|
25
|
Robertson NO, Shah M, Matthews JM. A Quantitative Fluorescence-Based Assay for Assessing LIM Domain-Peptide Interactions. Angew Chem Int Ed Engl 2016; 55:13236-13239. [DOI: 10.1002/anie.201605964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Neil O. Robertson
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
| | - Manan Shah
- School of Life and Environmental Sciences; The University of Sydney; NSW 2006 Australia
| | | |
Collapse
|
26
|
Gueta K, David A, Cohen T, Menuchin-Lasowski Y, Nobel H, Narkis G, Li L, Love P, de Melo J, Blackshaw S, Westphal H, Ashery-Padan R. The stage-dependent roles of Ldb1 and functional redundancy with Ldb2 in mammalian retinogenesis. Development 2016; 143:4182-4192. [PMID: 27697904 DOI: 10.1242/dev.129734] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/20/2016] [Indexed: 12/26/2022]
Abstract
The Lim domain-binding proteins are key co-factor proteins that assemble with LIM domains of the LMO/LIM-HD family to form functional complexes that regulate cell proliferation and differentiation. Using conditional mutagenesis and comparative phenotypic analysis, we analyze the function of Ldb1 and Ldb2 in mouse retinal development, and demonstrate overlapping and specific functions of both proteins. Ldb1 interacts with Lhx2 in the embryonic retina and both Ldb1 and Ldb2 play a key role in maintaining the pool of retinal progenitor cells. This is accomplished by controlling the expression of the Vsx2 and Rax, and components of the Notch and Hedgehog signaling pathways. Furthermore, the Ldb1/Ldb2-mediated complex is essential for generation of early-born photoreceptors through the regulation of Rax and Crx. Finally, we demonstrate functional redundancy between Ldb1 and Ldb2. Ldb1 can fully compensate the loss of Ldb2 during all phases of retinal development, whereas Ldb2 alone is sufficient to sustain activity of Lhx2 in both early- and late-stage RPCs and in Müller glia. By contrast, loss of Ldb1 disrupts activity of the LIM domain factors in neuronal precursors. An intricate regulatory network exists that is mediated by Ldb1 and Ldb2, and promotes RPC proliferation and multipotency; it also controls specification of mammalian retina cells.
Collapse
Affiliation(s)
- Keren Gueta
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ahuvit David
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tsadok Cohen
- Mammalian Genes and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yotam Menuchin-Lasowski
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hila Nobel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ginat Narkis
- Mammalian Genes and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - LiQi Li
- Program on Genomics of Differentiation, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Love
- Program on Genomics of Differentiation, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jimmy de Melo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Heiner Westphal
- Mammalian Genes and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
27
|
Smith NC, Matthews JM. Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors. Curr Opin Struct Biol 2016; 38:68-74. [PMID: 27295424 DOI: 10.1016/j.sbi.2016.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
Abstract
Eukaryotic transcription factors up-regulate and down-regulate the expression of genes in a very controlled manner. The DNA-binding domains of these proteins have quite well established mechanisms for binding to DNA, but a surprisingly poor intrinsic ability to discriminate target and variant non-target DNA sequences. Here, we summarise established mechanisms of protein-DNA recognition, as specified by both macromolecules. We also review recent advances in the fields of genome binding, molecular dynamics and biomolecular interaction studies that bring us close to a full understanding of how eukaryotic transcription factors find and target DNA in vivo to form functional centres of gene regulation through networks of protein-protein and protein-DNA interactions.
Collapse
Affiliation(s)
- Ngaio C Smith
- School of Life and Environmental Science, The University of Sydney, NSW 2006, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Science, The University of Sydney, NSW 2006, Australia.
| |
Collapse
|
28
|
Martín-Partido G, Francisco-Morcillo J. The role of Islet-1 in cell specification, differentiation, and maintenance of phenotypes in the vertebrate neural retina. Neural Regen Res 2016; 10:1951-2. [PMID: 26889183 PMCID: PMC4730819 DOI: 10.4103/1673-5374.165301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Gervasio Martín-Partido
- Departamento de Biología Celular, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Spain
| | | |
Collapse
|
29
|
Bery A, Mérot Y, Rétaux S. Genes expressed in mouse cortical progenitors are enriched in Pax, Lhx, and Sox transcription factor putative binding sites. Brain Res 2015; 1633:37-51. [PMID: 26721689 DOI: 10.1016/j.brainres.2015.12.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 11/25/2015] [Accepted: 12/14/2015] [Indexed: 11/19/2022]
Abstract
Considerable progress has been made in the understanding of molecular and cellular mechanisms controlling the development of the mammalian cortex. The proliferative and neurogenic properties of cortical progenitors located in the ventricular germinal zone start being understood. Little is known however on the cis-regulatory control that finely tunes gene expression in these progenitors. Here, we undertook an in silico-based approach to address this question, followed by some functional validation. Using the Eurexpress database, we established a list of 30 genes specifically expressed in the cortical germinal zone, we selected mouse/human conserved non-coding elements (CNEs) around these genes and we performed motif-enrichment search in these CNEs. We found an over-representation of motifs corresponding to binding sites for Pax, Sox, and Lhx transcription factors, often found as pairs and located within 100bp windows. A small subset of CNEs (n=7) was tested for enhancer activity, by ex-vivo and in utero electroporation assays. Two showed strong enhancer activity in the germinal zone progenitors. Mutagenesis experiments on a selected CNE showed the functional importance of the Pax, Sox, and Lhx TFBS for conferring enhancer activity to the CNE. Overall, from a cis-regulatory viewpoint, our data suggest an input from Pax, Sox and Lhx transcription factors to orchestrate corticogenesis. These results are discussed with regards to the known functional roles of Pax6, Sox2 and Lhx2 in cortical development.
Collapse
Affiliation(s)
- Amandine Bery
- DECA Group, Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, 91198 Gif-sur-Yvette, France.
| | - Yohann Mérot
- DECA Group, Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, 91198 Gif-sur-Yvette, France
| | - Sylvie Rétaux
- DECA Group, Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, 91198 Gif-sur-Yvette, France.
| |
Collapse
|
30
|
Expression and function of the LIM-homeodomain transcription factor Islet-1 in the developing and mature vertebrate retina. Exp Eye Res 2015; 138:22-31. [DOI: 10.1016/j.exer.2015.06.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 11/19/2022]
|
31
|
Chumak T, Bohuslavova R, Macova I, Dodd N, Buckiova D, Fritzsch B, Syka J, Pavlinkova G. Deterioration of the Medial Olivocochlear Efferent System Accelerates Age-Related Hearing Loss in Pax2-Isl1 Transgenic Mice. Mol Neurobiol 2015; 53:2368-83. [PMID: 25990412 DOI: 10.1007/s12035-015-9215-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 05/07/2015] [Indexed: 11/28/2022]
Abstract
The development, maturation, and maintenance of the inner ear are governed by temporal and spatial expression cascades of transcription factors that form a gene regulatory network. ISLET1 (ISL1) may be one of the major players in this cascade, and in order to study its role in the regulation of inner ear development, we produced a transgenic mouse overexpressing Isl1 under the Pax2 promoter. Pax2-regulated ISL1 overexpression increases the embryonic ISL1(+) domain and induces accelerated nerve fiber extension and branching in E12.5 embryos. Despite these gains in early development, the overexpression of ISL1 impairs the maintenance and function of hair cells of the organ of Corti. Mutant mice exhibit hyperactivity, circling behavior, and progressive age-related decline in hearing functions, which is reflected in reduced otoacoustic emissions (DPOAEs) followed by elevated hearing thresholds. The reduction of the amplitude of DPOAEs in transgenic mice was first detected at 1 month of age. By 6-9 months of age, DPOAEs completely disappeared, suggesting a functional inefficiency of outer hair cells (OHCs). The timing of DPOAE reduction coincides with the onset of the deterioration of cochlear efferent terminals. In contrast to these effects on efferents, we only found a moderate loss of OHCs and spiral ganglion neurons. For the first time, our results show that the genetic alteration of the medial olivocochlear (MOC) efferent system induces an early onset of age-related hearing loss. Thus, the neurodegeneration of the MOC system could be a contributing factor to the pathology of age-related hearing loss.
Collapse
Affiliation(s)
- Tetyana Chumak
- Institute of Experimental Medicine, CAS, Prague, Czechia
| | - Romana Bohuslavova
- Laboratory of Molecular Pathogenetics, Institute of Biotechnology, CAS, Prague 4, CZ-142 20, Prague, Czechia
| | - Iva Macova
- Laboratory of Molecular Pathogenetics, Institute of Biotechnology, CAS, Prague 4, CZ-142 20, Prague, Czechia
| | - Nicole Dodd
- Laboratory of Molecular Pathogenetics, Institute of Biotechnology, CAS, Prague 4, CZ-142 20, Prague, Czechia
| | | | - Bernd Fritzsch
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Josef Syka
- Institute of Experimental Medicine, CAS, Prague, Czechia
| | - Gabriela Pavlinkova
- Laboratory of Molecular Pathogenetics, Institute of Biotechnology, CAS, Prague 4, CZ-142 20, Prague, Czechia.
| |
Collapse
|
32
|
Whitney IE, Kautzman AG, Reese BE. Alternative splicing of the LIM-homeodomain transcription factor Isl1 in the mouse retina. Mol Cell Neurosci 2015; 65:102-13. [PMID: 25752730 DOI: 10.1016/j.mcn.2015.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 02/12/2015] [Accepted: 03/05/2015] [Indexed: 11/25/2022] Open
Abstract
Islet-1 (Isl1) is a LIM-homeodomain (LIM-HD) transcription factor that functions in a combinatorial manner with other LIM-HD proteins to direct the differentiation of distinct cell types within the central nervous system and many other tissues. A study of pancreatic cell lines showed that Isl1 is alternatively spliced generating a second isoform, Isl1β, which is missing 23 amino acids within the C-terminal region. This study examines the expression of the canonical and alternative Isl1 transcripts across other tissues, in particular, within the retina, where Isl1 is required for the differentiation of multiple neuronal cell types. The alternative splicing of Isl1 is shown to occur in multiple tissues, but the relative abundance of Isl1α and Isl1β expression varies greatly across them. In most tissues, Isl1α is the more abundant transcript, but in others the transcripts are expressed equally, or the alternative splice variant is dominant. Within the retina, differential expression of the two Isl1 transcripts increases as a function of development, with dynamic changes in expression peaking at E16.5 and again at P10. At the cellular level, individual retinal ganglion cells vary in their expression, with a subset of small-to-medium sized cells expressing only the alternative isoform. The functional significance of the difference in protein sequence between the two Isl1 isoforms was also assessed using a luciferase assay, demonstrating that the alternative isoform forms a less effective transcriptional complex for activating gene expression. These results demonstrate the differential presence of the canonical and alternative isoforms of Isl1 amongst retinal ganglion cell classes. As Isl1 participates in the differentiation of multiple cell types within the CNS, the present results support a role for alternative splicing in the establishment of cellular diversity in the developing nervous system.
Collapse
Affiliation(s)
- Irene E Whitney
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, United States; Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106-9625, United States.
| | - Amanda G Kautzman
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, United States; Department of Psychological & Brain Sciences, University of California at Santa Barbara, Santa Barbara, CA 93106-9660, United States.
| | - Benjamin E Reese
- Neuroscience Research Institute, University of California at Santa Barbara, Santa Barbara, CA 93106-5060, United States; Department of Psychological & Brain Sciences, University of California at Santa Barbara, Santa Barbara, CA 93106-9660, United States.
| |
Collapse
|
33
|
Ediger BN, Du A, Liu J, Hunter CS, Walp ER, Schug J, Kaestner KH, Stein R, Stoffers DA, May CL. Islet-1 Is essential for pancreatic β-cell function. Diabetes 2014; 63:4206-17. [PMID: 25028525 PMCID: PMC4237994 DOI: 10.2337/db14-0096] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Islet-1 (Isl-1) is essential for the survival and ensuing differentiation of pancreatic endocrine progenitors. Isl-1 remains expressed in all adult pancreatic endocrine lineages; however, its specific function in the postnatal pancreas is unclear. Here we determine whether Isl-1 plays a distinct role in the postnatal β-cell by performing physiological and morphometric analyses of a tamoxifen-inducible, β-cell-specific Isl-1 loss-of-function mouse: Isl-1(L/L); Pdx1-CreER(Tm). Ablating Isl-1 in postnatal β-cells reduced glucose tolerance without significantly reducing β-cell mass or increasing β-cell apoptosis. Rather, islets from Isl-1(L/L); Pdx1-CreER(Tm) mice showed impaired insulin secretion. To identify direct targets of Isl-1, we integrated high-throughput gene expression and Isl-1 chromatin occupancy using islets from Isl-1(L/L); Pdx1-CreER(Tm) mice and βTC3 insulinoma cells, respectively. Ablating Isl-1 significantly affected the β-cell transcriptome, including known targets Insulin and MafA as well as novel targets Pdx1 and Slc2a2. Using chromatin immunoprecipitation sequencing and luciferase reporter assays, we found that Isl-1 directly occupies functional regulatory elements of Pdx1 and Slc2a2. Thus Isl-1 is essential for postnatal β-cell function, directly regulates Pdx1 and Slc2a2, and has a mature β-cell cistrome distinct from that of pancreatic endocrine progenitors.
Collapse
Affiliation(s)
- Benjamin N Ediger
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA Department of Medicine and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Aiping Du
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jingxuan Liu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Chad S Hunter
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN
| | - Erik R Walp
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jonathan Schug
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Roland Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN
| | - Doris A Stoffers
- Department of Medicine and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Catherine L May
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA Janssen Research & Development, Spring House, PA
| |
Collapse
|
34
|
Joseph S, Kwan AH, Stokes PH, Mackay JP, Cubeddu L, Matthews JM. The structure of an LIM-only protein 4 (LMO4) and Deformed epidermal autoregulatory factor-1 (DEAF1) complex reveals a common mode of binding to LMO4. PLoS One 2014; 9:e109108. [PMID: 25310299 PMCID: PMC4195752 DOI: 10.1371/journal.pone.0109108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/27/2014] [Indexed: 12/23/2022] Open
Abstract
LIM-domain only protein 4 (LMO4) is a widely expressed protein with important roles in embryonic development and breast cancer. It has been reported to bind many partners, including the transcription factor Deformed epidermal autoregulatory factor-1 (DEAF1), with which LMO4 shares many biological parallels. We used yeast two-hybrid assays to show that DEAF1 binds both LIM domains of LMO4 and that DEAF1 binds the same face on LMO4 as two other LMO4-binding partners, namely LIM domain binding protein 1 (LDB1) and C-terminal binding protein interacting protein (CtIP/RBBP8). Mutagenic screening analysed by the same method, indicates that the key residues in the interaction lie in LMO4LIM2 and the N-terminal half of the LMO4-binding domain in DEAF1. We generated a stable LMO4LIM2-DEAF1 complex and determined the solution structure of that complex. Although the LMO4-binding domain from DEAF1 is intrinsically disordered, it becomes structured on binding. The structure confirms that LDB1, CtIP and DEAF1 all bind to the same face on LMO4. LMO4 appears to form a hub in protein-protein interaction networks, linking numerous pathways within cells. Competitive binding for LMO4 therefore most likely provides a level of regulation between those different pathways.
Collapse
Affiliation(s)
- Soumya Joseph
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Ann H. Kwan
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Philippa H. Stokes
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Joel P. Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Liza Cubeddu
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
- School of Science and Health, University of Western Sydney, Campbelltown, NSW Australia
| | | |
Collapse
|
35
|
Biophysical properties of intrinsically disordered p130Cas substrate domain--implication in mechanosensing. PLoS Comput Biol 2014; 10:e1003532. [PMID: 24722239 PMCID: PMC3983058 DOI: 10.1371/journal.pcbi.1003532] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 02/05/2014] [Indexed: 02/06/2023] Open
Abstract
Mechanical stretch-induced tyrosine phosphorylation in the proline-rich 306-residue substrate domain (CasSD) of p130Cas (or BCAR1) has eluded an experimentally validated structural understanding. Cellular p130Cas tyrosine phosphorylation is shown to function in areas without internal actomyosin contractility, sensing force at the leading edge of cell migration. Circular dichroism shows CasSD is intrinsically disordered with dominant polyproline type II conformations. Strongly conserved in placental mammals, the proline-rich sequence exhibits a pseudo-repeat unit with variation hotspots 2–9 residues before substrate tyrosine residues. Atomic-force microscopy pulling experiments show CasSD requires minimal extension force and exhibits infrequent, random regions of weak stability. Proteolysis, light scattering and ultracentrifugation results show that a monomeric intrinsically disordered form persists for CasSD in solution with an expanded hydrodynamic radius. All-atom 3D conformer sampling with the TraDES package yields ensembles in agreement with experiment when coil-biased sampling is used, matching the experimental radius of gyration. Increasing β-sampling propensities increases the number of prolate conformers. Combining the results, we conclude that CasSD has no stable compact structure and is unlikely to efficiently autoinhibit phosphorylation. Taking into consideration the structural propensity of CasSD and the fact that it is known to bind to LIM domains, we propose a model of how CasSD and LIM domain family of transcription factor proteins may function together to regulate phosphorylation of CasSD and effect machanosensing. Mechanical stretching of cells causes the substrate domain of p130Cas (CasSD) to be phosphorylated on 15 tyrosine residues embedded along its length. CasSD is rich in proline and surprisingly well conserved in placental mammals. Stretching of CasSD by atomic force microscopy has identified that it requires far less force than normal folded proteins. Classical biophysical analyses have determined that CasSD is a typical intrinsically disordered protein, a difficult-to-study group of molecules covering about 30% of human proteins. The average size of CasSD is larger and elongated than folded globular proteins but smaller than chemically denatured proteins. We have simulated a large number of all-atom protein structures using a fast all-atom sampling method. The result is in good agreement with the experimental observation. As it is already known that stretching somehow exposes the tyrosine residues to phosphorylation, a mechanism is proposed where straightening of the p130Cas substrate domain backbone conformation through mechanical stretching can lead to dissociation of p130Cas-binding LIM domain proteins and exposure of CasSD tyrosine residues for phosphorylation. This study has led to a new model of a protein-based mechanism of force sensing at the leading edge of cells that allows the cells to feel their way as they move.
Collapse
|
36
|
Francius C, Clotman F. Generating spinal motor neuron diversity: a long quest for neuronal identity. Cell Mol Life Sci 2014; 71:813-29. [PMID: 23765105 PMCID: PMC11113339 DOI: 10.1007/s00018-013-1398-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/30/2013] [Accepted: 05/31/2013] [Indexed: 03/26/2023]
Abstract
Understanding how thousands of different neuronal types are generated in the CNS constitutes a major challenge for developmental neurobiologists and is a prerequisite before considering cell or gene therapies of nervous lesions or pathologies. During embryonic development, spinal motor neurons (MNs) segregate into distinct subpopulations that display specific characteristics and properties including molecular identity, migration pattern, allocation to specific motor columns, and innervation of defined target. Because of the facility to correlate these different characteristics, the diversification of spinal MNs has become the model of choice for studying the molecular and cellular mechanisms underlying the generation of multiple neuronal populations in the developing CNS. Therefore, how spinal motor neuron subpopulations are produced during development has been extensively studied during the last two decades. In this review article, we will provide a comprehensive overview of the genetic and molecular mechanisms that contribute to the diversification of spinal MNs.
Collapse
Affiliation(s)
- Cédric Francius
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Neural Differentiation, 55 Avenue Hippocrate, Box (B1.55.11), 1200 Brussels, Belgium
| | - Frédéric Clotman
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Neural Differentiation, 55 Avenue Hippocrate, Box (B1.55.11), 1200 Brussels, Belgium
| |
Collapse
|
37
|
Expression of LIM-homeodomain transcription factors in the developing and mature mouse retina. Gene Expr Patterns 2013; 14:1-8. [PMID: 24333658 DOI: 10.1016/j.gep.2013.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/26/2013] [Accepted: 12/03/2013] [Indexed: 01/08/2023]
Abstract
LIM-homeodomain (LIM-HD) transcription factors have been extensively studied for their role in the development of the central nervous system. Their function is key to several developmental events like cell proliferation, differentiation and subtype specification. However, their roles in retinal neurogenesis remain largely unknown. Here we report a detailed expression study of LIM-HD transcription factors LHX9 and LHX2, LHX3 and LHX4, and LHX6 in the developing and mature mouse retina using immunohistochemistry and in situ hybridization techniques. We show that LHX9 is expressed during the early stages of development in the retinal ganglion cell layer and the inner nuclear layer. We also show that LHX9 is expressed in a subset of amacrine cells in the adult retina. LHX2 is known to be expressed in retinal progenitor cells during development and in Müller glial cells and a subset of amacrine cells in the adult retina. We found that the LHX2 subset of amacrine cells is not cholinergic and that a very few of LHX2 amacrine cells express calretinin. LHX3 and LHX4 are expressed in a subset of bipolar cells in the adult retina. LHX6 is expressed in cells in the ganglion cell layer and the neuroblast layer starting at embryonic stage 13.5 (E13.5) and continues to be expressed in cells in the ganglion cell layer and inner nuclear layer, postnatally, suggesting its likely expression in amacrine cells or a subset thereof. Taken together, our comprehensive assay of expression patterns of LIM-HD transcription factors during mouse retinal development will help further studies elucidating their biological functions in the differentiation of retinal cell subtypes.
Collapse
|
38
|
Gadd MS, Jacques DA, Nisevic I, Craig VJ, Kwan AH, Guss JM, Matthews JM. A structural basis for the regulation of the LIM-homeodomain protein islet 1 (Isl1) by intra- and intermolecular interactions. J Biol Chem 2013; 288:21924-35. [PMID: 23750000 DOI: 10.1074/jbc.m113.478586] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Islet 1 (Isl1) is a transcription factor of the LIM-homeodomain (LIM-HD) protein family and is essential for many developmental processes. LIM-HD proteins all contain two protein-interacting LIM domains, a DNA-binding homeodomain (HD), and a C-terminal region. In Isl1, the C-terminal region also contains the LIM homeobox 3 (Lhx3)-binding domain (LBD), which interacts with the LIM domains of Lhx3. The LIM domains of Isl1 have been implicated in inhibition of DNA binding potentially through an intramolecular interaction with or close to the HD. Here we investigate the LBD as a candidate intramolecular interaction domain. Competitive yeast-two hybrid experiments indicate that the LIM domains and LBD from Isl1 can interact with apparently low affinity, consistent with no detection of an intermolecular interaction in the same system. Nuclear magnetic resonance studies show that the interaction is specific, whereas substitution of the LBD with peptides of the same amino acid composition but different sequence is not specific. We solved the crystal structure of a similar but higher affinity complex between the LIM domains of Isl1 and the LIM interaction domain from the LIM-HD cofactor protein LIM domain-binding protein 1 (Ldb1) and used these coordinates to generate a homology model of the intramolecular interaction that indicates poorer complementarity for the weak intramolecular interaction. The intramolecular interaction in Isl1 may provide protection against aggregation, minimize unproductive DNA binding, and facilitate cofactor exchange within the cell.
Collapse
Affiliation(s)
- Morgan S Gadd
- School of Molecular Bioscience, Building G08, University of Sydney, New South Wales 2006, Australia
| | | | | | | | | | | | | |
Collapse
|
39
|
Zhang Z, Gutierrez D, Li X, Bidlack F, Cao H, Wang J, Andrade K, Margolis HC, Amendt BA. The LIM homeodomain transcription factor LHX6: a transcriptional repressor that interacts with pituitary homeobox 2 (PITX2) to regulate odontogenesis. J Biol Chem 2013; 288:2485-500. [PMID: 23229549 PMCID: PMC3554917 DOI: 10.1074/jbc.m112.402933] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 11/29/2012] [Indexed: 11/06/2022] Open
Abstract
LHX6 is a LIM-homeobox transcription factor expressed during embryogenesis; however, the molecular mechanisms regulating LHX6 transcriptional activities are unknown. LHX6 and the PITX2 homeodomain transcription factor have overlapping expression patterns during tooth and craniofacial development, and in this report, we demonstrate new transcriptional mechanisms for these factors. PITX2 and LHX6 are co-expressed in the oral and dental epithelium and epithelial cell lines. Lhx6 expression is increased in Pitx2c transgenic mice and decreased in Pitx2 null mice. PITX2 activates endogenous Lhx6 expression and the Lhx6 promoter, whereas LHX6 represses its promoter activity. Chromatin immunoprecipitation experiments reveal endogenous PITX2 binding to the Lhx6 promoter. LHX6 directly interacts with PITX2 to inhibit PITX2 transcriptional activities and activation of multiple promoters. Bimolecular fluorescence complementation assays reveal an LHX6·PITX2 nuclear interaction in living cells. LHX6 has a dominant repressive effect on the PITX2 synergistic activation with LEF-1 and β-catenin co-factors. Thus, LHX6 acts as a transcriptional repressor and represses the expression of several genes involved in odontogenesis. We have identified specific defects in incisor, molar, mandible, bone, and root development and late stage enamel formation in Lhx6 null mice. Amelogenin and ameloblastin expression is reduced and/or delayed in the Lhx6 null mice, potentially resulting from defects in dentin deposition and ameloblast differentiation. Our results demonstrate that LHX6 regulates cell proliferation in the cervical loop and promotes cell differentiation in the anterior region of the incisor. We demonstrate new molecular mechanisms for LHX6 and an interaction with PITX2 for normal craniofacial and tooth development.
Collapse
Affiliation(s)
- Zichao Zhang
- From the Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A & M University Health Science Center, Houston, Texas 77030 and
| | - Diana Gutierrez
- From the Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A & M University Health Science Center, Houston, Texas 77030 and
| | - Xiao Li
- From the Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A & M University Health Science Center, Houston, Texas 77030 and
| | - Felicitas Bidlack
- the Department of Biomineralization, The Forsyth Institute, Boston, Massachusetts 02142
| | - Huojun Cao
- From the Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A & M University Health Science Center, Houston, Texas 77030 and
| | - Jianbo Wang
- From the Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A & M University Health Science Center, Houston, Texas 77030 and
| | - Kelsey Andrade
- From the Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A & M University Health Science Center, Houston, Texas 77030 and
| | - Henry C. Margolis
- the Department of Biomineralization, The Forsyth Institute, Boston, Massachusetts 02142
| | - Brad A. Amendt
- From the Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A & M University Health Science Center, Houston, Texas 77030 and
| |
Collapse
|
40
|
Stokes PH, Liew CW, Kwan AH, Foo P, Barker HE, Djamirze A, O'Reilly V, Visvader JE, Mackay JP, Matthews JM. Structural basis of the interaction of the breast cancer oncogene LMO4 with the tumour suppressor CtIP/RBBP8. J Mol Biol 2013; 425:1101-10. [PMID: 23353824 DOI: 10.1016/j.jmb.2013.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/12/2013] [Accepted: 01/15/2013] [Indexed: 12/14/2022]
Abstract
LIM-only protein 4 (LMO4) is strongly linked to the progression of breast cancer. Although the mechanisms underlying this phenomenon are not well understood, a role is emerging for LMO4 in regulation of the cell cycle. We determined the solution structure of LMO4 in complex with CtIP (C-terminal binding protein interacting protein)/RBBP8, a tumour suppressor protein that is involved in cell cycle progression, DNA repair and transcriptional regulation. Our data reveal that CtIP and the essential LMO cofactor LDB1 (LIM-domain binding protein 1) bind to the same face on LMO4 and cannot simultaneously bind to LMO4. We hypothesise that overexpression of LMO4 may disrupt some of the normal tumour suppressor activities of CtIP, thereby contributing to breast cancer progression.
Collapse
Affiliation(s)
- P H Stokes
- School of Molecular Bioscience, University of Sydney, NSW 2006, Australia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Matthews JM, Potts JR. The tandem β-zipper: Modular binding of tandem domains and linear motifs. FEBS Lett 2013; 587:1164-71. [DOI: 10.1016/j.febslet.2013.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/07/2013] [Accepted: 01/07/2013] [Indexed: 11/17/2022]
|
42
|
Reddy Chichili VP, Kumar V, Sivaraman J. Linkers in the structural biology of protein-protein interactions. Protein Sci 2013; 22:153-67. [PMID: 23225024 DOI: 10.1002/pro.2206] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/08/2012] [Accepted: 11/13/2012] [Indexed: 12/14/2022]
Abstract
Linkers or spacers are short amino acid sequences created in nature to separate multiple domains in a single protein. Most of them are rigid and function to prohibit unwanted interactions between the discrete domains. However, Gly-rich linkers are flexible, connecting various domains in a single protein without interfering with the function of each domain. The advent of recombinant DNA technology made it possible to fuse two interacting partners with the introduction of artificial linkers. Often, independent proteins may not exist as stable or structured proteins until they interact with their binding partner, following which they gain stability and the essential structural elements. Gly-rich linkers have been proven useful for these types of unstable interactions, particularly where the interaction is weak and transient, by creating a covalent link between the proteins to form a stable protein-protein complex. Gly-rich linkers are also employed to form stable covalently linked dimers, and to connect two independent domains that create a ligand-binding site or recognition sequence. The lengths of linkers vary from 2 to 31 amino acids, optimized for each condition so that the linker does not impose any constraints on the conformation or interactions of the linked partners. Various structures of covalently linked protein complexes have been described using X-ray crystallography, nuclear magnetic resonance and cryo-electron microscopy techniques. In this review, we evaluate several structural studies where linkers have been used to improve protein quality, to produce stable protein-protein complexes, and to obtain protein dimers.
Collapse
|
43
|
Dastmalchi S, Wilkinson-White L, Kwan AH, Gamsjaeger R, Mackay JP, Matthews JM. Solution structure of a tethered Lmo2(LIM2) /Ldb1(LID) complex. Protein Sci 2012; 21:1768-74. [PMID: 22936624 PMCID: PMC3527713 DOI: 10.1002/pro.2153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/21/2012] [Accepted: 08/24/2012] [Indexed: 11/05/2022]
Abstract
LIM-only protein 2, Lmo2, is a regulatory protein that is essential for hematopoietic development and inappropriate overexpression of Lmo2 in T-cells contributes to T-cell leukemia. It exerts its functions by mediating protein-protein interactions and nucleating multicomponent transcriptional complexes. Lmo2 interacts with LIM domain binding protein 1 (Ldb1) through the tandem LIM domains of Lmo2 and the LIM interaction domain (LID) of Ldb1. Here, we present the solution structure of the LIM2 domain of Lmo2 bound to Ldb1(LID) . The ordered regions of Ldb1 in this complex correspond well with binding hotspots previously defined by mutagenic studies. Comparisons of this Lmo2(LIM2) -Ldb1(LID) structure with previously determined structures of the Lmo2/Ldb1(LID) complexes lead to the conclusion that modular binding of tandem LIM domains in Lmo2 to tandem linear motifs in Ldb1 is accompanied by several disorder-to-order transitions and/or conformational changes in both proteins.
Collapse
Affiliation(s)
- Siavoush Dastmalchi
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
- Biotechnology Research Centre and School of Pharmacy, Tabriz University of Medical SciencesTabriz, Iran
| | - Lorna Wilkinson-White
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| | - Ann H Kwan
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| | - Roland Gamsjaeger
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
- School of Science and Health, University of Western SydneyPenrith, New South Wales 2751, Australia
| | - Joel P Mackay
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| | - Jacqueline M Matthews
- School of Molecular Bioscience, University of SydneySydney, New South Wales 2006, Australia
| |
Collapse
|
44
|
Gadd MS, Jacques DA, Guss JM, Matthews JM. Crystallization and diffraction of an Isl1-Ldb1 complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1398-401. [PMID: 23143258 DOI: 10.1107/s1744309112040031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 09/21/2012] [Indexed: 11/10/2022]
Abstract
A stable intramolecular complex comprising the LIM domains of the LIM-homeodomain protein Isl1 tethered to a peptide region of Ldb1 has been engineered, purified and crystallized. The orthorhombic crystals belonged to space group P222(1), with unit-cell parameters a=57.2, b=56.7, c=179.8 Å, and diffracted to 3.10 Å resolution.
Collapse
Affiliation(s)
- Morgan S Gadd
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia.
| | | | | | | |
Collapse
|
45
|
Bhati M, Lee C, Gadd MS, Jeffries CM, Kwan A, Whitten AE, Trewhella J, Mackay JP, Matthews JM. Solution structure of the LIM-homeodomain transcription factor complex Lhx3/Ldb1 and the effects of a pituitary mutation on key Lhx3 interactions. PLoS One 2012; 7:e40719. [PMID: 22848397 PMCID: PMC3405102 DOI: 10.1371/journal.pone.0040719] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 06/12/2012] [Indexed: 01/01/2023] Open
Abstract
Lhx3 is a LIM-homeodomain (LIM-HD) transcription factor that regulates neural cell subtype specification and pituitary development in vertebrates, and mutations in this protein cause combined pituitary hormone deficiency syndrome (CPHDS). The recently published structures of Lhx3 in complex with each of two key protein partners, Isl1 and Ldb1, provide an opportunity to understand the effect of mutations and posttranslational modifications on key protein-protein interactions. Here, we use small-angle X-ray scattering of an Ldb1-Lhx3 complex to confirm that in solution the protein is well represented by our previously determined NMR structure as an ensemble of conformers each comprising two well-defined halves (each made up of LIM domain from Lhx3 and the corresponding binding motif in Ldb1) with some flexibility between the two halves. NMR analysis of an Lhx3 mutant that causes CPHDS, Lhx3(Y114C), shows that the mutation does not alter the zinc-ligation properties of Lhx3, but appears to cause a structural rearrangement of the hydrophobic core of the LIM2 domain of Lhx3 that destabilises the domain and/or reduces the affinity of Lhx3 for both Ldb1 and Isl1. Thus the mutation would affect the formation of Lhx3-containing transcription factor complexes, particularly in the pituitary gland where these complexes are required for the production of multiple pituitary cell types and hormones.
Collapse
Affiliation(s)
- Mugdha Bhati
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Christopher Lee
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Morgan S. Gadd
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Cy M. Jeffries
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Ann Kwan
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Andrew E. Whitten
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Jill Trewhella
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P. Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Jacqueline M. Matthews
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
| |
Collapse
|
46
|
Cubeddu L, Joseph S, Richard DJ, Matthews JM. Contribution of DEAF1 structural domains to the interaction with the breast cancer oncogene LMO4. PLoS One 2012; 7:e39218. [PMID: 22723967 PMCID: PMC3378519 DOI: 10.1371/journal.pone.0039218] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/17/2012] [Indexed: 12/22/2022] Open
Abstract
The proteins LMO4 and DEAF1 contribute to the proliferation of mammary epithelial cells. During breast cancer LMO4 is upregulated, affecting its interaction with other protein partners. This may set cells on a path to tumour formation. LMO4 and DEAF1 interact, but it is unknown how they cooperate to regulate cell proliferation. In this study, we identify a specific LMO4-binding domain in DEAF1. This domain contains an unstructured region that directly contacts LMO4, and a coiled coil that contains the DEAF1 nuclear export signal (NES). The coiled coil region can form tetramers and has the typical properties of a coiled coil domain. Using a simple cell-based assay, we show that LMO4 modulates the activity of the DEAF NES, causing nuclear accumulation of a construct containing the LMO4-interaction region of DEAF1.
Collapse
Affiliation(s)
- Liza Cubeddu
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail: (LC); (JM)
| | - Soumya Joseph
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia
| | - Derek J. Richard
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | - Jacqueline M. Matthews
- School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail: (LC); (JM)
| |
Collapse
|
47
|
Chondrolectin mediates growth cone interactions of motor axons with an intermediate target. J Neurosci 2012; 32:4426-39. [PMID: 22457492 DOI: 10.1523/jneurosci.5179-11.2012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The C-type lectin chondrolectin (chodl) represents one of the major gene products dysregulated in spinal muscular atrophy models in mice. However, to date, no function has been determined for the gene. We have identified chodl and other novel genes potentially involved in motor axon differentiation, by expression profiling of transgenically labeled motor neurons in embryonic zebrafish. To enrich the profile for genes involved in differentiation of peripheral motor axons, we inhibited the function of LIM-HDs (LIM homeodomain factors) by overexpression of a dominant-negative cofactor, thereby rendering labeled axons unable to grow out of the spinal cord. Importantly, labeled cells still exhibited axon growth and most cells retained markers of motor neuron identity. Functional tests of chodl, by overexpression and knockdown, confirm crucial functions of this gene for motor axon growth in vivo. Indeed, knockdown of chodl induces arrest or stalling of motor axon growth at the horizontal myoseptum, an intermediate target and navigational choice point, and reduced muscle innervation at later developmental stages. This phenotype is rescued by chodl overexpression, suggesting that correct expression levels of chodl are important for interactions of growth cones of motor axons with the horizontal myoseptum. Combined, these results identify upstream regulators and downstream functions of chodl during motor axon growth.
Collapse
|
48
|
Sobrier ML, Brachet C, Vié-Luton MP, Perez C, Copin B, Legendre M, Heinrichs C, Amselem S. Symptomatic heterozygotes and prenatal diagnoses in a nonconsanguineous family with syndromic combined pituitary hormone deficiency resulting from two novel LHX3 mutations. J Clin Endocrinol Metab 2012; 97:E503-9. [PMID: 22238406 DOI: 10.1210/jc.2011-2095] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Only 11 mutations have been reported in the transcription factor LHX3, known to be important for the development of the pituitary and motor neurons. All patients were homozygous, with various syndromic forms of combined pituitary hormone deficiency (CPHD), hampering to allocate, in these consanguineous patients, the respective contribution of LHX3 and additional genes to each symptom. OBJECTIVE The aim of the study was to report the family history and the molecular basis of a nonconsanguineous patient with syndromic CPHD. PATIENT The patient, who presented at birth with respiratory distress, had a syndromic CPHD, including severe scoliosis, and normal intelligence. His father and paternal grandmother displayed limited head rotation. RESULTS Two new LHX3 defects were identified. The paternally inherited c.252-3C>G mutation, which disrupts an acceptor splice site, would lead to severely truncated proteins containing a single LIM domain, resembling LIM-only proteins. Coexpression studies revealed the dominant-negative effect of this LIM-only protein over the wild-type LHX3. The maternally inherited p.Cys118Tyr mutation results in partial loss of transcriptional activity and synergy with POU1F1. Given the severity of the patient's phenotype, two prenatal diagnoses were performed: the first led to pregnancy interruption, the second to the birth of a healthy boy. CONCLUSIONS This study of the first nonconsanguineous patient with LHX3 mutations demonstrates the pleiotropic roles of LHX3 during development and its full involvement in the complex disease phenotype. Isolated limitation of head rotation may exist in heterozygous carriers and would result from a dominant-negative effect. These data allowed the first prenatal diagnoses of this severe condition to be performed.
Collapse
Affiliation(s)
- Marie-Laure Sobrier
- Institut National de la Santé et de la Recherche Médicale Unité 933, Université Pierre et Marie Curie-Paris 6, Hôpital Armand Trousseau, 26 avenue du Docteur Arnold Netter, 75571 Paris, Cedex 12 France.
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Simmons DK, Pang K, Martindale MQ. Lim homeobox genes in the Ctenophore Mnemiopsis leidyi: the evolution of neural cell type specification. EvoDevo 2012; 3:2. [PMID: 22239757 PMCID: PMC3283466 DOI: 10.1186/2041-9139-3-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/13/2012] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Nervous systems are thought to be important to the evolutionary success and diversification of metazoans, yet little is known about the origin of simple nervous systems at the base of the animal tree. Recent data suggest that ctenophores, a group of macroscopic pelagic marine invertebrates, are the most ancient group of animals that possess a definitive nervous system consisting of a distributed nerve net and an apical statocyst. This study reports on details of the evolution of the neural cell type specifying transcription factor family of LIM homeobox containing genes (Lhx), which have highly conserved functions in neural specification in bilaterian animals. RESULTS Using next generation sequencing, the first draft of the genome of the ctenophore Mnemiopsis leidyi has been generated. The Lhx genes in all animals are represented by seven subfamilies (Lhx1/5, Lhx3/4, Lmx, Islet, Lhx2/9, Lhx6/8, and LMO) of which four were found to be represented in the ctenophore lineage (Lhx1/5, Lhx3/4, Lmx, and Islet). Interestingly, the ctenophore Lhx gene complement is more similar to the sponge complement (sponges do not possess neurons) than to either the cnidarian-bilaterian or placozoan Lhx complements. Using whole mount in situ hybridization, the Lhx gene expression patterns were examined and found to be expressed around the blastopore and in cells that give rise to the apical organ and putative neural sensory cells. CONCLUSION This research gives us a first look at neural cell type specification in the ctenophore M. leidyi. Within M. leidyi, Lhx genes are expressed in overlapping domains within proposed neural cellular and sensory cell territories. These data suggest that Lhx genes likely played a conserved role in the patterning of sensory cells in the ancestor of sponges and ctenophores, and may provide a link to the expression of Lhx orthologs in sponge larval photoreceptive cells. Lhx genes were later co-opted into patterning more diversified complements of neural and non-neural cell types in later evolving animals.
Collapse
Affiliation(s)
- David K Simmons
- Kewalo Marine Laboratory, Department of Zoology, University of Hawaii at Manoa, Honolulu, HI, USA, 96813
| | - Kevin Pang
- Sars, International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Mark Q Martindale
- Kewalo Marine Laboratory, Department of Zoology, University of Hawaii at Manoa, Honolulu, HI, USA, 96813
| |
Collapse
|
50
|
Gadd MS, Bhati M, Jeffries CM, Langley DB, Trewhella J, Guss JM, Matthews JM. Structural basis for partial redundancy in a class of transcription factors, the LIM homeodomain proteins, in neural cell type specification. J Biol Chem 2011; 286:42971-80. [PMID: 22025611 DOI: 10.1074/jbc.m111.248559] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Combinations of LIM homeodomain proteins form a transcriptional "LIM code" to direct the specification of neural cell types. Two paralogous pairs of LIM homeodomain proteins, LIM homeobox protein 3/4 (Lhx3/Lhx4) and Islet-1/2 (Isl1/Isl2), are expressed in developing ventral motor neurons. Lhx3 and Isl1 interact within a well characterized transcriptional complex that triggers motor neuron development, but it was not known whether Lhx4 and Isl2 could participate in equivalent complexes. We have identified an Lhx3-binding domain (LBD) in Isl2 based on sequence homology with the Isl1(LBD) and show that both Isl2(LBD) and Isl1(LBD) can bind each of Lhx3 and Lhx4. X-ray crystal- and small-angle x-ray scattering-derived solution structures of an Lhx4·Isl2 complex exhibit many similarities with that of Lhx3·Isl1; however, structural differences supported by mutagenic studies reveal differences in the mechanisms of binding. Differences in binding have implications for the mode of exchange of protein partners in transcriptional complexes and indicate a divergence in functions of Lhx3/4 and Isl1/2. The formation of weaker Lhx·Isl complexes would likely be masked by the availability of the other Lhx·Isl complexes in postmitotic motor neurons.
Collapse
Affiliation(s)
- Morgan S Gadd
- School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia
| | | | | | | | | | | | | |
Collapse
|