1
|
Generation of Human Stomach Cancer iPSC-Derived Organoids Induced by Helicobacter pylori Infection and Their Application to Gastric Cancer Research. Cells 2022; 11:cells11020184. [PMID: 35053302 PMCID: PMC8773924 DOI: 10.3390/cells11020184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 12/13/2022] Open
Abstract
There is considerable cellular diversity in the human stomach, which has helped to clarify cell plasticity in normal development and tumorigenesis. Thus, the stomach is an interesting model for understanding cellular plasticity and for developing prospective anticancer therapeutic agents. However, many questions remain regarding the development of cancers in vivo and in vitro in two- or three-dimensional (2D/3D) cultures, as well as the role of Helicobacter pylori (H. p.) infection. Here, we focus on the characteristics of cancer stem cells and their derived 3D organoids in culture, including the formation of stem cell niches. We define the conditions required for such organoid culture in vitro and examine the ability of such models for testing the use of anticancer agents. We also summarize the signaling cascades and the specific markers of stomach-cancer-derived organoids induced by H. p. infection, and their stem cell niches.
Collapse
|
2
|
Chen W, Zhou Y, Wu G, Sun P. CCNI2 promotes the progression of human gastric cancer through HDGF. Cancer Cell Int 2021; 21:661. [PMID: 34895232 PMCID: PMC8665640 DOI: 10.1186/s12935-021-02352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gastric cancer is a highly aggressive malignant tumor with heterogeneity and is still a global health problem. The present study aimed to investigate the role of Cyclin I-like (CCNI2) in the regulation of phenotype and tumorigenesis, as well as its underlying mechanisms. METHOD The expression profile of CCNI2 in gastric cancer was determined based on The Cancer Genome Atlas (TCGA) database and immunohistochemical staining. The effects of altered CCNI2 expression on the biological phenotypes such as proliferation, clone formation, apoptosis and migration of gastric cancer cell lines BGC-823 and SGC-7901 were investigated. Mice xenograft models were established to reveal the role of CCNI2 knockdown on tumorigenesis. The potential mechanism of CCNI2 regulating gastric cancer was preliminarily determined by RNA sequencing. RESULT CCNI2 was abundantly expressed in gastric cancer and was positively correlated with pathological stage. Knockdown of CCNI2 slowed down the malignant progression of gastric cancer by inhibiting tumor cell proliferation, increasing the susceptibility to apoptosis and suppressing migration. Moreover, downregulation of CCNI2 attenuated the ability of gastric cancer cells to form tumors in mice. Additionally, there was an interaction between CCNI2 and transcription factor hepatoma-derived growth factor (HDGF) in SGC-7901 cells. Knockdown of CCNI2 alleviated the promoting effects of HDGF overexpression in gastric cancer cells. CONCLUSIONS CCNI2 promoted the progression of human gastric cancer through HDGF, which drew further interest regarding its clinical application as a potential therapeutic target.
Collapse
Affiliation(s)
- Wenchao Chen
- Department of Gastrointestinal Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Yang Zhou
- Department of Gastrointestinal Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Gang Wu
- Department of Gastrointestinal Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China.
| | - Peichun Sun
- Department of Gastrointestinal Surgery, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China.
| |
Collapse
|
3
|
Yun HS, Lee J, Kim JY, Sim YJ, Lee CW, Park JK, Kim JS, Ahn J, Song JY, Baek JH, Hwang SG. A novel function of HRP-3 in regulating cell cycle progression via the HDAC-E2F1-Cyclin E pathway in lung cancer. Cancer Sci 2021; 113:145-155. [PMID: 34714604 PMCID: PMC8748221 DOI: 10.1111/cas.15183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022] Open
Abstract
To improve the poor survival rate of lung cancer patients, we investigated the role of HDGF‐related protein 3 (HRP‐3) as a potential biomarker for lung cancer. The expression of endogenous HRP‐3 in human lung cancer tissues and xenograft tumor models is indicative of its clinical relevance in lung cancer. Additionally, we demonstrated that HRP‐3 directly binds to the E2F1 promoter on chromatin. Interestingly, HRP‐3 depletion in A549 cells impedes the binding of HRP‐3 to the E2F1 promoter; this in turn hampers the interaction between Histone H3/H4 and HDAC1/2 on the E2F1 promoter, while concomitantly inducing Histone H3/H4 acetylation around the E2F1 promoter. The enhanced Histone H3/H4 acetylation on the E2F1 promoter through HRP‐3 depletion increases the transcription level of E2F1. Furthermore, the increased E2F1 transcription levels lead to the enhanced transcription of Cyclin E, known as the E2F1‐responsive gene, thus inducing S‐phase accumulation. Therefore, our study provides evidence for the utility of HRP‐3 as a biomarker for the prognosis and treatment of lung cancer. Furthermore, we delineated the capacity of HRP‐3 to regulate the E2F1 transcription level via histone deacetylation.
Collapse
Affiliation(s)
- Hong Shik Yun
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Janet Lee
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Ju-Young Kim
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Ye-Ji Sim
- Radiation Biology Research Team, Research Center, Dongnam Institute of Radiological and Medical Sciences, Busan, Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jong Kuk Park
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jae-Sung Kim
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jiyeon Ahn
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jie-Young Song
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jeong-Hwa Baek
- Radiation Biology Research Team, Research Center, Dongnam Institute of Radiological and Medical Sciences, Busan, Korea
| | - Sang-Gu Hwang
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| |
Collapse
|
4
|
Yang Y, Ma Y, Gao H, Peng T, Shi H, Tang Y, Li H, Chen L, Hu K, Han A. A novel HDGF-ALCAM axis promotes the metastasis of Ewing sarcoma via regulating the GTPases signaling pathway. Oncogene 2020; 40:731-745. [PMID: 33239755 DOI: 10.1038/s41388-020-01485-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 09/12/2020] [Accepted: 09/21/2020] [Indexed: 12/24/2022]
Abstract
Ewing sarcoma (ES) is a type of highly aggressive pediatric tumor in bones and soft tissues and its metastatic spread remains the most powerful predictor of poor outcome. We previously identified that the transcription factor hepatoma-derived growth factor (HDGF) promotes ES tumorigenesis. However, the mechanisms underlying ES metastasis remain unclear. Here, we show that HDGF drives ES metastasis in vitro and in vivo, and HDGF reduces metastasis-free survival (MFS) in two independent large cohorts of human ES patients. Integrative analyses of HDGF ChIP-seq and gene expression profiling in ES cells reveal that HDGF regulates multiple metastasis-associated genes, among which activated leukocyte cell adhesion molecule (ALCAM) emerges as a major HDGF target and a novel metastasis-suppressor in ES. HDGF down-regulates ALCAM, induces expression and activation of the downstream effectors Rho-GTPase Rac1 and Cdc42, and promotes actin cytoskeleton remodeling and cell-matrix adhesion. In addition, repression of ALCAM and activation of Rac1 and Cdc42 are required for the pro-metastatic functions of HDGF in vitro. Moreover, analyses in murine models with ES tumor orthotopic implantation and experimental metastasis, as well as in human ES samples, demonstrate the associations among HDGF, ALCAM, and GTPases expression levels. Furthermore, high HDGF/low ALCAM expression define a subgroup of patients harboring the worst MFS. These findings suggest that the HDGF/ALCAM/GTPases axis represents a promising therapeutic target for limiting ES metastasis.
Collapse
Affiliation(s)
- Yang Yang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, P.R. China
| | - Yuedong Ma
- Department of Cardiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, P.R. China
| | - Huabin Gao
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, P.R. China
| | - Tingsheng Peng
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, P.R. China
| | - Huijuan Shi
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, P.R. China
| | - Yunxiang Tang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, P.R. China
| | - Hui Li
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, P.R. China
| | - Lin Chen
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, P.R. China
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, P.R. China.
| | - Anjia Han
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, P.R. China.
| |
Collapse
|
5
|
Higuchi K, Yabuki T, Ito M, Kigawa T. Cold shock proteins improve
E. coli
cell‐free synthesis in terms of soluble yields of aggregation‐prone proteins. Biotechnol Bioeng 2020; 117:1628-1639. [DOI: 10.1002/bit.27326] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/05/2020] [Accepted: 03/08/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Kae Higuchi
- Laboratory for Cellular Structural BiologyRIKEN Center for Biosystems Dynamics Research Yokohama Kanagawa Japan
| | - Takashi Yabuki
- Laboratory for Cellular Structural BiologyRIKEN Center for Biosystems Dynamics Research Yokohama Kanagawa Japan
- SI Innovation Center, Taiyo Nippon Sanso Corporation Tama‐shi Tokyo Japan
| | - Masahiro Ito
- Laboratory for Cellular Structural BiologyRIKEN Center for Biosystems Dynamics Research Yokohama Kanagawa Japan
| | - Takanori Kigawa
- Laboratory for Cellular Structural BiologyRIKEN Center for Biosystems Dynamics Research Yokohama Kanagawa Japan
| |
Collapse
|
6
|
Tian W, Yan P, Xu N, Chakravorty A, Liefke R, Xi Q, Wang Z. The HRP3 PWWP domain recognizes the minor groove of double-stranded DNA and recruits HRP3 to chromatin. Nucleic Acids Res 2019; 47:5436-5448. [PMID: 31162607 PMCID: PMC6547440 DOI: 10.1093/nar/gkz294] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/12/2022] Open
Abstract
HDGF-related protein 3 (HRP3, also known as HDGFL3) belongs to the family of HDGF-related proteins (HRPs) and plays an essential role in hepatocellular carcinoma pathogenesis. All HRPs have a PWWP domain at the N-terminus that binds both histone and DNA substrates. Despite previous advances in PWWP domains, the molecular basis by which HRP3 interacts with chromatin is unclear. In this study, we solved the crystal structures of the HRP3 PWWP domain in complex with various double-stranded DNAs with/without bound histone peptides. We found that HRP3 PWWP bound to the phosphate backbone of the DNA minor groove and showed a preference for DNA molecules bearing a narrow minor groove width. In addition, HRP3 PWWP preferentially bound to histone peptides bearing the H3K36me3/2 modification. HRP3 PWWP uses two adjacent surfaces to bind both DNA and histone substrates simultaneously, enabling us to generate a model illustrating the recruitment of PWWP to H3K36me3-containing nucleosomes. Cell-based analysis indicated that both DNA and histone binding by the HRP3 PWWP domain is important for HRP3 recruitment to chromatin in vivo. Our work establishes that HRP3 PWWP is a new family of minor groove-specific DNA-binding proteins, which improves our understanding of HRP3 and other PWWP domain-containing proteins.
Collapse
Affiliation(s)
- Wei Tian
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Peiqiang Yan
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ning Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Arghya Chakravorty
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
- Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg, 35043 Marburg, Germany
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhanxin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| |
Collapse
|
7
|
Weaver TM, Morrison EA, Musselman CA. Reading More than Histones: The Prevalence of Nucleic Acid Binding among Reader Domains. Molecules 2018; 23:molecules23102614. [PMID: 30322003 PMCID: PMC6222470 DOI: 10.3390/molecules23102614] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/02/2018] [Accepted: 10/07/2018] [Indexed: 01/09/2023] Open
Abstract
The eukaryotic genome is packaged into the cell nucleus in the form of chromatin, a complex of genomic DNA and histone proteins. Chromatin structure regulation is critical for all DNA templated processes and involves, among many things, extensive post-translational modification of the histone proteins. These modifications can be “read out” by histone binding subdomains known as histone reader domains. A large number of reader domains have been identified and found to selectively recognize an array of histone post-translational modifications in order to target, retain, or regulate chromatin-modifying and remodeling complexes at their substrates. Interestingly, an increasing number of these histone reader domains are being identified as also harboring nucleic acid binding activity. In this review, we present a summary of the histone reader domains currently known to bind nucleic acids, with a focus on the molecular mechanisms of binding and the interplay between DNA and histone recognition. Additionally, we highlight the functional implications of nucleic acid binding in chromatin association and regulation. We propose that nucleic acid binding is as functionally important as histone binding, and that a significant portion of the as yet untested reader domains will emerge to have nucleic acid binding capabilities.
Collapse
Affiliation(s)
- Tyler M Weaver
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| |
Collapse
|
8
|
He H, Hu Z, Xiao H, Zhou F, Yang B. The tale of histone modifications and its role in multiple sclerosis. Hum Genomics 2018; 12:31. [PMID: 29933755 PMCID: PMC6013900 DOI: 10.1186/s40246-018-0163-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/08/2018] [Indexed: 02/08/2023] Open
Abstract
Epigenetics defines the persistent modifications of gene expression in a manner that does not involve the corresponding alterations in DNA sequences. It includes modifications of DNA nucleotides, nucleosomal remodeling, and post-translational modifications (PTMs). It is becoming evident that PTMs which act singly or in combination to form “histone codes” orchestrate the chromatin structure and dynamic functions. PTMs of histone tails have been demonstrated to influence numerous biological developments, as well as disease onset and progression. Multiple sclerosis (MS) is an autoimmune inflammatory demyelinating and neurodegenerative disease of the central nervous system, of which the precise pathophysiological mechanisms remain to be fully elucidated. There is a wealth of emerging evidence that epigenetic modifications may confer risk for MS, which provides new insights into MS. Histone PTMs, one of the key events that regulate gene activation, seem to play a prominent role in the epigenetic mechanism of MS. In this review, we summarize recent studies in our understanding of the epigenetic language encompassing histone, with special emphasis on histone acetylation and histone lysine methylation, two of the best characterized histone modifications. We also discuss how the current studies address histone acetylation and histone lysine methylation influencing pathophysiology of MS and how future studies could be designed to establish optimized therapeutic strategies for MS.
Collapse
Affiliation(s)
- Hui He
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Zhiping Hu
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Han Xiao
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Fangfang Zhou
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Binbin Yang
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China.
| |
Collapse
|
9
|
Nüße J, Mirastschijski U, Waespy M, Oetjen J, Brandes N, Rebello O, Paroni F, Kelm S, Dietz F. Two new isoforms of the human hepatoma-derived growth factor interact with components of the cytoskeleton. Biol Chem 2016; 397:417-36. [PMID: 26845719 DOI: 10.1515/hsz-2015-0273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/28/2016] [Indexed: 01/27/2023]
Abstract
Hepatoma-derived growth factor (HDGF) is involved in diverse, apparently unrelated processes, such as cell proliferation, apoptosis, DNA-repair, transcriptional control, ribosome biogenesis and cell migration. Most of the interactions of HDGF with diverse molecules has been assigned to the hath region of HDGF. In this study we describe two previously unknown HDGF isoforms, HDGF-B and HDGF-C, generated via alternative splicing with structurally unrelated N-terminal regions of their hath region, which is clearly different from the well described isoform, HDGF-A. In silico modeling revealed striking differences near the PHWP motif, an essential part of the binding site for glycosaminoglycans and DNA/RNA. This observation prompted the hypothesis that these isoforms would have distinct interaction patterns with correspondingly diverse roles on cellular processes. Indeed, we discovered specific associations of HDGF-B and HDGF-C with cytoskeleton elements, such as tubulin and dynein, suggesting previously unknown functions of HDGF in retrograde transport, site directed localization and/or cytoskeleton organization. In contrast, the main isoform HDGF-A does not interact directly with the cytoskeleton, but via RNA with messenger ribonucleoprotein (mRNP) complexes. In summary, the discovery of HDGF splice variants with their discrete binding activities and subcellular distributions opened new avenues for understanding its biological function and importance.
Collapse
|
10
|
Rona GB, Eleutherio ECA, Pinheiro AS. PWWP domains and their modes of sensing DNA and histone methylated lysines. Biophys Rev 2016; 8:63-74. [PMID: 28510146 DOI: 10.1007/s12551-015-0190-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/14/2015] [Indexed: 12/21/2022] Open
Abstract
Chromatin plays an important role in gene transcription control, cell cycle progression, recombination, DNA replication and repair. The fundamental unit of chromatin, the nucleosome, is formed by a DNA duplex wrapped around an octamer of histones. Histones are susceptible to various post-translational modifications, covalent alterations that change the chromatin status. Lysine methylation is one of the major post-translational modifications involved in the regulation of chromatin function. The PWWP domain is a member of the Royal superfamily that functions as a chromatin methylation reader by recognizing both DNA and histone methylated lysines. The PWWP domain three-dimensional structure is based on an N-terminal hydrophobic β-barrel responsible for histone methyl-lysine binding, and a C-terminal α-helical domain. In this review, we set out to discuss the most recent literature on PWWP domains, focusing on their structural features and the mechanisms by which they specifically recognize DNA and histone methylated lysines at the level of the nucleosome.
Collapse
Affiliation(s)
- Germana B Rona
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Elis C A Eleutherio
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil.
| |
Collapse
|
11
|
Impact of Chromatin on HIV Replication. Genes (Basel) 2015; 6:957-76. [PMID: 26437430 PMCID: PMC4690024 DOI: 10.3390/genes6040957] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/14/2015] [Accepted: 09/22/2015] [Indexed: 12/22/2022] Open
Abstract
Chromatin influences Human Immunodeficiency Virus (HIV) integration and replication. This review highlights critical host factors that influence chromatin structure and organization and that also impact HIV integration, transcriptional regulation and latency. Furthermore, recent attempts to target chromatin associated factors to reduce the HIV proviral load are discussed.
Collapse
|
12
|
Kenzior A, Folk WR. Arabidopsis thaliana MSI4/FVE associates with members of a novel family of plant specific PWWP/RRM domain proteins. PLANT MOLECULAR BIOLOGY 2015; 87:329-339. [PMID: 25600937 DOI: 10.1007/s11103-014-0280-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
AtMSI4/FVE/ACG1, one of five Arabidopsis thaliana genes encoding MSI1-like proteins, helps determine plant growth and development (including control of flowering), as well as responses to certain biotic and abiotic stresses. We reasoned that the product of this gene, AtMSI4, acts through protein partners, which we have co-immunopurified with AtMSI4 from A. thaliana suspension culture cells and identified by liquid chromatography-mass spectrometry (LC-MS). Many of the proteins associated with AtMSI4 have distinct RNA recognition motif (RRM) domains, which we determined to be responsible for association with AtMSI4; and most of the associated RRM domain proteins also contain PWWP domains that are specific to plants. We propose these novel ATMSI4-associated proteins help form nucleoprotein complexes that determine pleiotropic functional properties of AtMSI4/FVE/ACG1 involving plant development and responses to stress.
Collapse
Affiliation(s)
- Alexander Kenzior
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA,
| | | |
Collapse
|
13
|
Qin S, Min J. Structure and function of the nucleosome-binding PWWP domain. Trends Biochem Sci 2014; 39:536-47. [PMID: 25277115 DOI: 10.1016/j.tibs.2014.09.001] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/26/2014] [Accepted: 09/08/2014] [Indexed: 12/11/2022]
Abstract
PWWP domain-containing proteins are often involved in chromatin-associated biological processes, such as transcriptional regulation and DNA repair, and recent studies have shown that the PWWP domain specifies chromatin localization. Mutations in the PWWP domain, a 100-150 amino acid motif, have been linked to various human diseases, emphasizing its importance. Structural studies reveal that PWWP domains possess a conserved aromatic cage for histone methyl-lysine recognition, and synergistically bind both histone and DNA, which contributes to their nucleosome-binding ability and chromatin localization. Furthermore, the PWWP domain often cooperates with other histone and DNA 'reader' or 'modifier' domains to evoke crosstalk between various epigenetic marks. Here, we discuss these recent advances in understanding the structure and function of the PWWP domain.
Collapse
Affiliation(s)
- Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| |
Collapse
|
14
|
Dürr R, Keppler O, Christ F, Crespan E, Garbelli A, Maga G, Dietrich U. Targeting Cellular Cofactors in HIV Therapy. TOPICS IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1007/7355_2014_45] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
15
|
Morchikh M, Naughtin M, Di Nunzio F, Xavier J, Charneau P, Jacob Y, Lavigne M. TOX4 and NOVA1 proteins are partners of the LEDGF PWWP domain and affect HIV-1 replication. PLoS One 2013; 8:e81217. [PMID: 24312278 PMCID: PMC3842248 DOI: 10.1371/journal.pone.0081217] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 10/10/2013] [Indexed: 12/31/2022] Open
Abstract
PWWP domains are involved in the chromatin attachment of several proteins. They bind to both DNA and proteins and their interaction with specific histone methylation marks define them as a new class of histone code readers. The lens epithelium derived growth factor (LEDGF/p75) contains an N-terminal PWWP domain necessary for its interaction with chromatin but also a C-terminal domain which interacts with several proteins, such as lentiviral integrases. These two domains confer a chromatin-tethering function to LEDGF/p75 and in the case of lentiviral integrases, this tethering participates in the efficiency and site selectivity of integration. Although proteins interacting with LEDGF/p75 C-terminal domain have been extensively studied, no data exist about partners of its PWWP domain regulating its interaction with chromatin. In this study, we report the identification by yeast-two-hybrid of thirteen potential partners of the LEDGF PWWP domain. Five of these interactions were confirmed in mammalian cells, using both a protein complementation assay and co-immunoprecipitation approaches. Three of these partners interact with full length LEDGF/p75, they are specific for PWWP domains of the HDGF family and they require PWWP amino acids essential for the interaction with chromatin. Among them, the transcription activator TOX4 and the splicing cofactor NOVA1 were selected for a more extensive study. These two proteins or their PWWP interacting regions (PIR) colocalize with LEDGF/p75 in Hela cells and interact in vitro in the presence of DNA. Finally, single round VSV-G pseudotyped HIV-1 but not MLV infection is inhibited in cells overexpressing these two PIRs. The observed inhibition of infection can be attributed to a defect in the integration step. Our data suggest that a regulation of LEDGF interaction with chromatin by cellular partners of its PWWP domain could be involved in several processes linked to LEDGF tethering properties, such as lentiviral integration, DNA repair or transcriptional regulation.
Collapse
Affiliation(s)
- Mehdi Morchikh
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
- Institut Pasteur, Unité de Virologie Structurale, Centre National de la Recherche Scientifique, Unité de recherche associée, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Monica Naughtin
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
| | - Francesca Di Nunzio
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, Centre National de la Recherche Scientifique, Paris, France
| | - Johan Xavier
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
| | - Pierre Charneau
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, Centre National de la Recherche Scientifique, Paris, France
| | - Yves Jacob
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Centre National de la Recherche Scientifique, Paris, France
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Marc Lavigne
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
- Institut Pasteur, Unité de Virologie Structurale, Centre National de la Recherche Scientifique, Unité de recherche associée, Paris, France
- * E-mail:
| |
Collapse
|
16
|
Yang Y, Li H, Zhang F, Shi H, Zhen T, Dai S, Kang L, Liang Y, Wang J, Han A. Clinical and biological significance of hepatoma-derived growth factor in Ewing's sarcoma. J Pathol 2013; 231:323-34. [PMID: 23878072 DOI: 10.1002/path.4241] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 01/08/2023]
Abstract
We sought to investigate the clinicopathological significance and biological function of hepatoma-derived growth factor (HDGF) in Ewing's sarcoma. Our results showed that HDGF expression is up-regulated in Ewing's sarcoma. Nuclear HDGF expression is significantly associated with tumour volume (p < 0.001), metastases at diagnosis (p < 0.001), low overall survival rate (p < 0.001) and low disease-free survival rate (p < 0.001). HDGF knock-down results in significant reduction of Ewing's sarcoma cell growth, proliferation and enhances tumourigenesis, both in vitro and in vivo. Meanwhile, HDGF knock-down causes cell cycle arrest and enhanced sensitization to serum starvation-induced apoptosis. Furthermore, recombinant HDGF promotes proliferation and colony formation of Ewing's sarcoma cells. Ninety-eight candidate HDGF downstream genes were identified in Ewing's sarcoma cells using cDNA microarray analysis. In addition, we found that HDGF knock-down inhibited FLI1 expression in Ewing's sarcoma cells at the mRNA and protein levels. Our findings suggest that HDGF exhibits oncogenic properties and may be a novel prognostic factor in Ewing's sarcoma. Targeting HDGF might be a potential therapeutic strategy for Ewing's sarcoma.
Collapse
Affiliation(s)
- Yang Yang
- Department of Pathology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Li SZ, Zhao YB, Cao WD, Qu Y, Luo P, Zhen HN, Chen XY, Yan ZF, Fei Z. The expression of hepatoma-derived growth factor in primary central nervous system lymphoma and its correlation with angiogenesis, proliferation and clinical outcome. Med Oncol 2013; 30:622. [PMID: 23771798 DOI: 10.1007/s12032-013-0622-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 05/28/2013] [Indexed: 01/03/2023]
Abstract
Hepatoma-derived growth factor (HDGF), a potential predictive and prognostic marker in several human cancers, is the firstly reported member of the HDGF family of proteins containing a well-conserved N-terminal amino acid sequence. HDGF is implicated in tumorigenesis by direct angiogenic activity, and its expression is correlated with aggressive biological ability of cancer cells including proliferation and angiogenesis. So, we propose that HDGF may be a valuable factor in progression and prognosis for primary central nervous system lymphoma (PCNSL) through its angiogenic and proliferative activity. So, HDGF, CD31 and Ki67 expression in the specimens of 60 patients suffering from PCNSL was investigated by immunohistochemistry in this study. Their correlations with clinicopathologic features and prognosis were evaluated to determine whether HDGF, CD31 and Ki67 expression levels correlate with the prognosis of the 60 patients suffering from PCNSL. We found that all PCNSL specimens showed HDGF, CD31 and Ki67 expression with different expression levels. Statistical analysis showed that HDGF had a positive correlation with CD31, but not with Ki67. Patients with higher HDGF and CD31 expression level had poorer overall survival rates than those with lower expression levels of HDGF and CD31, while Ki67 expression level did not correlate with overall survival. Multivariate analysis revealed that postoperative adjuvant chemotherapy and high expression of HDGF was independent prognostic indicator of patient survival.
Collapse
Affiliation(s)
- San-Zhong Li
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Changle West Road 169#, Xi'an, 710032, China
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Eidahl JO, Crowe BL, North JA, McKee CJ, Shkriabai N, Feng L, Plumb M, Graham RL, Gorelick RJ, Hess S, Poirier MG, Foster MP, Kvaratskhelia M. Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes. Nucleic Acids Res 2013; 41:3924-36. [PMID: 23396443 PMCID: PMC3616739 DOI: 10.1093/nar/gkt074] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/27/2012] [Accepted: 01/18/2013] [Indexed: 01/19/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) tethers lentiviral preintegration complexes (PICs) to chromatin and is essential for effective HIV-1 replication. LEDGF/p75 interactions with lentiviral integrases are well characterized, but the structural basis for how LEDGF/p75 engages chromatin is unknown. We demonstrate that cellular LEDGF/p75 is tightly bound to mononucleosomes (MNs). Our proteomic experiments indicate that this interaction is direct and not mediated by other cellular factors. We determined the solution structure of LEDGF PWWP and monitored binding to the histone H3 tail containing trimethylated Lys36 (H3K36me3) and DNA by NMR. Results reveal two distinct functional interfaces of LEDGF PWWP: a well-defined hydrophobic cavity, which selectively interacts with the H3K36me3 peptide and adjacent basic surface, which non-specifically binds DNA. LEDGF PWWP exhibits nanomolar binding affinity to purified native MNs, but displays markedly lower affinities for the isolated H3K36me3 peptide and DNA. Furthermore, we show that LEDGF PWWP preferentially and tightly binds to in vitro reconstituted MNs containing a tri-methyl-lysine analogue at position 36 of H3 and not to their unmodified counterparts. We conclude that cooperative binding of the hydrophobic cavity and basic surface to the cognate histone peptide and DNA wrapped in MNs is essential for high-affinity binding to chromatin.
Collapse
Affiliation(s)
- Jocelyn O. Eidahl
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Brandon L. Crowe
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Justin A. North
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher J. McKee
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Nikoloz Shkriabai
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Lei Feng
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew Plumb
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert L. Graham
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert J. Gorelick
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sonja Hess
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Michael G. Poirier
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mark P. Foster
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mamuka Kvaratskhelia
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA, Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, Columbus, OH 43210, USA, Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA and AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| |
Collapse
|
19
|
Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC Evol Biol 2012; 12:101. [PMID: 22734652 PMCID: PMC3457860 DOI: 10.1186/1471-2148-12-101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 06/06/2012] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Conserved domains are recognized as the building blocks of eukaryotic proteins. Domains showing a tendency to occur in diverse combinations ('promiscuous' domains) are involved in versatile architectures in proteins with different functions. Current models, based on global-level analyses of domain combinations in multiple genomes, have suggested that the propensity of some domains to associate with other domains in high-level architectures increases with organismal complexity. Alternative models using domain-based phylogenetic trees propose that domains have become promiscuous independently in different lineages through convergent evolution and are, thus, random with no functional or structural preferences. Here we test whether complex protein architectures have occurred by accretion from simpler systems and whether the appearance of multidomain combinations parallels organismal complexity. As a model, we analyze the modular evolution of the PWWP domain and ask whether its appearance in combinations with other domains into multidomain architectures is linked with the occurrence of more complex life-forms. Whether high-level combinations of domains are conserved and transmitted as stable units (cassettes) through evolution is examined in the genomes of plant or metazoan species selected for their established position in the evolution of the respective lineages. RESULTS Using the domain-tree approach, we analyze the evolutionary origins and distribution patterns of the promiscuous PWWP domain to understand the principles of its modular evolution and its existence in combination with other domains in higher-level protein architectures. We found that as a single module the PWWP domain occurs only in proteins with a limited, mainly, species-specific distribution. Earlier, it was suggested that domain promiscuity is a fast-changing (volatile) feature shaped by natural selection and that only a few domains retain their promiscuity status throughout evolution. In contrast, our data show that most of the multidomain PWWP combinations in extant multicellular organisms (humans or land plants) are present in their unicellular ancestral relatives suggesting they have been transmitted through evolution as conserved linear arrangements ('cassettes'). Among the most interesting biologically relevant results is the finding that the genes of the two plant Trithorax family subgroups (ATX1/2 and ATX3/4/5) have different phylogenetic origins. The two subgroups occur together in the earliest land plants Physcomitrella patens and Selaginella moellendorffii. CONCLUSION Gain/loss of a single PWWP domain is observed throughout evolution reflecting dynamic lineage- or species-specific events. In contrast, higher-level protein architectures involving the PWWP domain have survived as stable arrangements driven by evolutionary descent. The association of PWWP domains with the DNA methyltransferases in O. tauri and in the metazoan lineage seems to have occurred independently consistent with convergent evolution. Our results do not support models wherein more complex protein architectures involving the PWWP domain occur with the appearance of more evolutionarily advanced life forms.
Collapse
Affiliation(s)
- Raúl Alvarez-Venegas
- Department of Genetic Engineering, Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Irapuato Gto., 36821, Mexico
| | | |
Collapse
|
20
|
Thakar K, Votteler I, Kelkar D, Shidore T, Gupta S, Kelm S, Dietz F. Interaction of HRP-2 isoforms with HDGF. Chromatin binding of a specific heteromer. FEBS J 2012; 279:737-51. [DOI: 10.1111/j.1742-4658.2011.08464.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
21
|
Zhao J, Yu H, Lin L, Tu J, Cai L, Chen Y, Zhong F, Lin C, He F, Yang P. Interactome study suggests multiple cellular functions of hepatoma-derived growth factor (HDGF). J Proteomics 2011; 75:588-602. [DOI: 10.1016/j.jprot.2011.08.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 08/14/2011] [Accepted: 08/25/2011] [Indexed: 02/05/2023]
|
22
|
Gijsbers R, Vets S, De Rijck J, Ocwieja KE, Ronen K, Malani N, Bushman FD, Debyser Z. Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting. J Biol Chem 2011; 286:41812-41826. [PMID: 21987578 DOI: 10.1074/jbc.m111.255711] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
LEDGF/p75 is a chromatin-interacting, cellular cofactor of HIV integrase that dictates lentiviral integration site preference. In this study we determined the role of the PWWP domain of LEDGF/p75 in tethering and targeting of the lentiviral pre-integration complex, employing potent knockdown cell lines allowing analysis in the absence of endogenous LEDGF/p75. Deletion of the PWWP domain resulted in a diffuse subnuclear distribution pattern, loss of interaction with condensed chromatin, and failure to rescue proviral integration, integration site distribution, and productive virus replication. Substitution of the PWWP domain of LEDGF/p75 with that of hepatoma-derived growth factor or HDGF-related protein-2 rescued viral replication and lentiviral integration site distribution in LEDGF/p75-depleted cells. Replacing all chromatin binding elements of LEDGF/p75 with full-length hepatoma-derived growth factor resulted in more integration in genes combined with a preference for CpG islands. In addition, we showed that any PWWP domain targets SMYD1-like sequences. Analysis of integration preferences of lentiviral vectors for epigenetic marks indicates that the PWWP domain is critical for interactions specifying the relationship of integration sites to regions enriched in specific histone post-translational modifications.
Collapse
Affiliation(s)
- Rik Gijsbers
- Division of Molecular Medicine, KU Leuven, 3000 Leuven, Belgium.
| | - Sofie Vets
- Division of Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Jan De Rijck
- Division of Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Karen E Ocwieja
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Keshet Ronen
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Nirav Malani
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Zeger Debyser
- Division of Molecular Medicine, KU Leuven, 3000 Leuven, Belgium.
| |
Collapse
|
23
|
Zhang J, Qi J, Guo Y, Guo Y, Fu W, Zhou B, Wu G, Han L, He A. [Aberrant expression of HDGF and its prognostic values in surgically resected non-small cell lung cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2011; 14:211-8. [PMID: 21426662 PMCID: PMC5999669 DOI: 10.3779/j.issn.1009-3419.2011.03.06] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND AND OBJECTIVE Our previous studies revealed that hepatoma-derived growth factor (HDGF) is highly expressed in non-small cell lung cancer (NSCLC) cells, playing important roles in promoting NSCLC cells growth and invasion. The aim of this study is to detect the expression of HDGF in 158 cases of surgically resected NSCLC and evaluate its clinical significance. METHODS Immunohistochemical SP method was used to detect the expression of HDGF in 158 NSCLC tissues and 12 normal control lung tissues. Survival analysis was further conducted. RESULTS HDGF was found significantly highly expressed in 158 NSCLC tissues compared with normal control lung tissues (P < 0.001). The 5-year survival rate was 38.2% in HDGF high expression cases, compared with 63.1% in HDGF low expression cases, the difference was statistically significant (P=0.009). Linear correlation analysis discovered a significantly negative correlation between HDGF expression and the survival time (r=-0.183, P=0.022). COX proportion hazard model analysis revealed that pathological stages and HDGF expression were independent prognostic factors for this group of 158 resected NSCLC cases. CONCLUSIONS HDGF is highly expressed in human NSCLC tissues, predicting worse prognosis in resected NSCLCs. It might be useful molecular biomarker for predicting the prognosis of resected NSCLCs.
Collapse
Affiliation(s)
- Jun Zhang
- China Medical University Lung Cancer Center, the First Hospital of China Medical University, Shenyang, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Cell surface heparan sulfates mediate internalization of the PWWP/HATH domain of HDGF via macropinocytosis to fine-tune cell signalling processes involved in fibroblast cell migration. Biochem J 2011; 433:127-38. [PMID: 20964630 DOI: 10.1042/bj20100589] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
HDGF (hepatoma-derived growth factor) stimulates cell proliferation by functioning on both sides of the plasma membrane as a ligand for membrane receptor binding to trigger cell signalling and as a stimulator for DNA synthesis in the nucleus. Although HDGF was initially identified as a secretory heparin-binding protein, the biological significance of its heparin-binding ability remains to be determined. In the present study we demonstrate that cells devoid of surface HS (heparan sulfate) were unable to internalize HDGF, HATH (N-terminal domain of HDGF consisting of amino acid residues 1-100, including the PWWP motif) and HATH(K96A) (single-site mutant form of HATH devoid of receptor binding activity), suggesting that the binding of HATH to surface HS is important for HDGF internalization. We further demonstrate that both HATH and HATH(K96A) could be internalized through macropinocytosis after binding to the cell surface HS. Interestingly, HS-mediated HATH(K96A) internalization is found to exhibit an inhibitory effect on cell migration and proliferation in contrast with that observed for HATH action on NIH 3T3 cells, suggesting that HDGF exploits the innate properties of both cell surface HS and membrane receptor via the HATH domain to affect related cell signalling processes. The present study indicates that MAPK (mitogen-activated protein kinase) signalling pathways could be affected by the HS-mediated HATH internalization to regulate cell migration in NIH 3T3 fibroblasts, as judged from the differential effect of HATH and HATH(K96A) treatment on the expression level of matrix metalloproteases.
Collapse
|
25
|
Thakar K, Kröcher T, Savant S, Gollnast D, Kelm S, Dietz F. Secretion of hepatoma-derived growth factor is regulated by N-terminal processing. Biol Chem 2010; 391:1401-10. [DOI: 10.1515/bc.2010.147] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Hepatoma-derived growth factor (HDGF) was first purified as a growth factor secreted by hepatoma cells. It promotes angiogenesis and has been related to tumorigenesis. To date, little is known about the molecular mechanisms of HDGF functions and especially its routes or regulation of secretion. Here we show that secretion of HDGF requires the N-terminal 10 amino acids and that this peptide can mediate secretion of other proteins, such as enhanced green fluorescent protein, if fused to their N-terminus. Our results further demonstrate that cysteine residues at positions 12 and 108 are linked via an intramolecular disulfide bridge. Surprisingly, phosphorylation of serine 165 in the C-terminal part of HDGF plays a critical role in the secretion process. If this serine is replaced by alanine, the N-terminus is truncated, the intramolecular disulfide bridge is not formed and the protein is not secreted. In summary, these observations provide a model of how phosphorylation, a disulfide bridge and proteolytic cleavage are involved in HDGF secretion.
Collapse
|
26
|
Yap KL, Zhou MM. Keeping it in the family: diverse histone recognition by conserved structural folds. Crit Rev Biochem Mol Biol 2010; 45:488-505. [PMID: 20923397 DOI: 10.3109/10409238.2010.512001] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epigenetic regulation of gene transcription relies on an array of recurring structural domains that have evolved to recognize post-translational modifications on histones. The roles of bromodomains, PHD fingers, and the Royal family domains in the recognition of histone modifications to direct transcription have been well characterized. However, only through recent structural studies has it been realized that these basic folds are capable of interacting with increasingly more complex histone modification landscapes, illuminating how nature has concocted a way to accomplish more with less. Here we review the recent biochemical and structural studies of several conserved folds that recognize modified as well as unmodified histone sequences, and discuss their implications on gene expression.
Collapse
Affiliation(s)
- Kyoko L Yap
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY, USA
| | | |
Collapse
|
27
|
Bueno MTD, Garcia-Rivera JA, Kugelman JR, Morales E, Rosas-Acosta G, Llano M. SUMOylation of the lens epithelium-derived growth factor/p75 attenuates its transcriptional activity on the heat shock protein 27 promoter. J Mol Biol 2010; 399:221-39. [PMID: 20382164 DOI: 10.1016/j.jmb.2010.03.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Revised: 03/28/2010] [Accepted: 03/30/2010] [Indexed: 10/19/2022]
Abstract
Lens epithelium-derived growth factor (LEDGF) proteins p75 and p52 are transcriptional coactivators that connect sequence-specific activators to the basal transcription machinery. We have found that these proteins are posttranslationally modified by SUMO (small ubiquitin-like modifier)-1 and SUMO-3. Three SUMOylation sites, K75, K250, and K254, were mapped on the shared N-terminal region of these molecules, while a fourth site, K364, was identified in the C-terminal part exclusive of LEDGF/p75. The N-terminal SUMO targets are located in evolutionarily conserved charge-rich regions that lack resemblance to the described consensus SUMOylation motif, whereas the C-terminal SUMO target is solvent exposed and situated in a typical consensus motif. SUMOylation did not affect the cellular localization of LEDGF proteins and was not necessary for their chromatin-binding ability, nor did it affect this activity. However, lysine to arginine mutations of the identified SUMO acceptor sites drastically inhibited LEDGF SUMOylation, extended the half-life of LEDGF/p75, and significantly increased its transcriptional activity on the heat shock protein 27 promoter, indicating a negative effect of SUMOylation on the transcriptional activity of LEDGF/p75. Considering that SUMOylation is known to negatively affect the transcriptional activity of all transcription factors known to transactivate heat shock protein 27 expression, these findings support the paradigm establishing SUMOylation as a global neutralizer of cellular processes upregulated upon cellular stress.
Collapse
Affiliation(s)
- Murilo T D Bueno
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, TX 79968, USA
| | | | | | | | | | | |
Collapse
|
28
|
Abstract
Chromatin is a highly regulated nucleoprotein complex through which genetic material is structured and maneuvered to elicit cellular processes, including transcription, cell division, differentiation, and DNA repair. In eukaryotes, the core of this structure is composed of nucleosomes, or repetitive histone octamer units typically enfolded by 147 base pairs of DNA. DNA is arranged and indexed through these nucleosomal structures to adjust local chromatin compaction and accessibility. Histones are subject to multiple covalent posttranslational modifications, some of which alter intrinsic chromatin properties, others of which present or hinder binding modules for non-histone, chromatin-modifying complexes. Although certain histone marks correlate with different biological outputs, we have yet to fully appreciate their effects on transcription and other cellular processes. Tremendous advancements over the past years have uncovered intriguing histone-related matters and raised important related questions. This review revisits past breakthroughs and discusses novel developments that pertain to histone posttranslational modifications and the affects they have on transcription and DNA packaging.
Collapse
Affiliation(s)
- Eric I Campos
- Department of Biochemistry, Howard Hughes Medical Institute, NYU School of Medicine, New York, New York 10016, USA
| | | |
Collapse
|
29
|
Wang Y, Reddy B, Thompson J, Wang H, Noma KI, Yates JR, Jia S. Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein. Mol Cell 2009; 33:428-37. [PMID: 19250904 DOI: 10.1016/j.molcel.2009.02.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 05/18/2008] [Accepted: 02/04/2009] [Indexed: 01/05/2023]
Abstract
Methylation of histone H4 lysine 20 (H4K20me) is essential for recruiting checkpoint proteins 53BP1/Crb2 to DNA lesions and subsequent activation of a DNA-damage checkpoint. In fission yeast, Set9 (spKMT5) catalyzes mono-, di-, and trimethylation of H4K20. However, the mechanisms that regulate Set9 function are poorly understood. Here, we identified a PWWP domain protein Pdp1 as a Set9-associated factor. Pdp1 binds to histones and is required for Set9 chromatin localization. Yeast cells without Pdp1 were deficient in all three states of H4K20me, sensitive to genotoxic treatments, and impaired in Crb2 recruitment. The PWWP domain of Pdp1 binds to H4K20me, and mutations within the PWWP domain that abrogated this interaction in vitro reduced both the association of Set9 with chromatin and the extent of H4K20me in vivo. These results demonstrate that the PWWP domain is a new methyl-lysine recognition motif that plays important roles in epigenetic regulation.
Collapse
Affiliation(s)
- Yu Wang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Hepatoma-derived growth factor represses SET and MYND domain containing 1 gene expression through interaction with C-terminal binding protein. J Mol Biol 2009; 386:938-50. [PMID: 19162039 DOI: 10.1016/j.jmb.2008.12.080] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 11/28/2008] [Accepted: 12/26/2008] [Indexed: 11/22/2022]
Abstract
Hepatoma-derived growth factor (HDGF) is a nuclear protein with both mitogenic and angiogenic activity that is highly expressed in the developing heart and vasculature. To date, the mechanism underlying the function of HDGF is unknown. Oligonucleotide microarray analysis was used to gain insights into HDGF function. Adenoviral expression of HDGF significantly (> or =2-fold) downregulated a large group (66) of genes, and increased expression of a relatively small number of genes (9). Two groups of target genes that are involved in cardiovascular development and transcriptional regulation, including the skeletal/cardiac muscle specific SET and MYND domain containing 1 (SMYD1) gene, were validated by real time PCR. This suggested that HDGF could function as a transcriptional repressor. In a one-hybrid system, GBD-HDGF significantly repressed reporter gene activity in a dose-dependent manner. This demonstrated that HDGF has transcriptional repressive activity. Moreover, in G-7 myoblast cells, over-expression of a GFP-HDGF fusion specifically downregulated SMYD1 mRNA expression and the activity of the human SMYD1 promoter. HDGF repressed SMYD1 gene transcription through interaction with a transcriptional corepressor C-terminal binding protein (CtBP). Over-expression of CtBP potentiated the trans-repressive activity of HDGF; on the other hand, knocking down CtBP attenuated the trans-repressive effect of HDGF. HDGF binds CtBP through a non-canonical binding motif (PKDLF) within the PWWP domain, as mutation of DL to AS abolished HDGF and CtBP interaction, and diminished the trans-repressive effect of HDGF without affecting DNA binding. Finally, fluorescent microscopy showed that HDGF induced the nuclear accumulation of CtBP, suggesting that HDGF forms a transcriptional complex with CtBP. Taken together, our data demonstrate that HDGF functions as a transcriptional repressor of the SMYD1 gene through interaction with the transcriptional corepressor CtBP. Because of moderate conservation of the CtBP binding motif in HDGF family members, trans-repressive activity mediated by CtBP may be a common function among HDGF proteins.
Collapse
|
31
|
Tsang TY, Tang WY, Tsang WP, Co NN, Kong SK, Kwok TT. Downregulation of hepatoma-derived growth factor activates the Bad-mediated apoptotic pathway in human cancer cells. Apoptosis 2008; 13:1135-47. [PMID: 18651222 DOI: 10.1007/s10495-008-0241-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Hepatoma-derived growth factor (HDGF) is highly expressed in human cancer and its expression is correlated with poor prognosis of cancer. The growth factor is known to stimulate cell growth while the underlying mechanism is however not clear. Transfection with HDGF cDNA stimulated while its specific antisense oligonucleotides repressed the growth of human hepatocellular carcinoma HepG2 cells. Furthermore, knock-down of HDGF by antisense oligos also induced apoptosis in HepG2 cells and in other human cancer cells, e.g. human squamous carcinoma A431 cells. HDGF knock-down was found to induce the expression of the pro-apoptotic protein Bad and also inactivate ERK and Akt, which in turn led to dephosphorylation of Bad at Ser-112, Ser-136, and activation of the intrinsic apoptotic pathway, i.e. depolarization of the mitochondrial membrane, release of mitochondrial cytochrome c, increase in the processing of caspase 9 and 3. As HDGF knock-down not only suppresses the growth but also induces apoptosis in human cancer cells, HDGF may therefore serve as a survival factor for human cancer cells and a potential target for cancer therapy.
Collapse
Affiliation(s)
- Tsun Yee Tsang
- Department of Biochemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | | | | | | | | | | |
Collapse
|
32
|
Brown-Bryan TA, Leoh LS, Ganapathy V, Pacheco FJ, Mediavilla-Varela M, Filippova M, Linkhart TA, Gijsbers R, Debyser Z, Casiano CA. Alternative splicing and caspase-mediated cleavage generate antagonistic variants of the stress oncoprotein LEDGF/p75. Mol Cancer Res 2008; 6:1293-307. [PMID: 18708362 DOI: 10.1158/1541-7786.mcr-08-0125] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
There is increasing evidence that an augmented state of cellular oxidative stress modulates the expression of stress genes implicated in diseases associated with health disparities such as certain cancers and diabetes. Lens epithelium-derived growth factor p75 (LEDGF/p75), also known as DFS70 autoantigen, is emerging as a survival oncoprotein that promotes resistance to oxidative stress-induced cell death and chemotherapy. We previously showed that LEDGF/p75 is targeted by autoantibodies in prostate cancer patients and is overexpressed in prostate tumors, and that its stress survival activity is abrogated during apoptosis. LEDGF/p75 has a COOH-terminally truncated splice variant, p52, whose role in stress survival and apoptosis has not been thoroughly investigated. We observed unbalanced expression of these proteins in a panel of tumor cell lines, with LEDGF/p75 generally expressed at higher levels. During apoptosis, caspase-3 cleaved p52 to generate a p38 fragment that lacked the NH(2)-terminal PWWP domain and failed to transactivate the Hsp27 promoter in reporter assays. However, p38 retained chromatin association properties and repressed the transactivation potential of LEDGF/p75. Overexpression of p52 or its variants with truncated PWWP domains in several tumor cell lines induced apoptosis, an activity that was linked to the presence of an intron-derived COOH-terminal sequence. These results implicate the PWWP domain of p52 in transcription function but not in chromatin association and proapoptotic activities. Consistent with their unbalanced expression in tumor cells, LEDGF/p75 and p52 seem to play antagonistic roles in the cellular stress response and could serve as targets for novel antitumor therapies.
Collapse
Affiliation(s)
- Terry A Brown-Bryan
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Identification and characterization of PWWP domain residues critical for LEDGF/p75 chromatin binding and human immunodeficiency virus type 1 infectivity. J Virol 2008; 82:11555-67. [PMID: 18799576 DOI: 10.1128/jvi.01561-08] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Lens epithelium-derived growth factor (LEDGF)/p75 functions as a bimodal tether during lentiviral DNA integration: its C-terminal integrase-binding domain interacts with the viral preintegration complex, whereas the N-terminal PWWP domain can bind to cellular chromatin. The molecular basis for the integrase-LEDGF/p75 interaction is understood, while the mechanism of chromatin binding is unknown. The PWWP domain is homologous to other protein interaction modules that together comprise the Tudor clan. Based on primary amino acid sequence and three-dimensional structural similarities, 24 residues of the LEDGF/p75 PWWP domain were mutagenized to garner essential details of its function during human immunodeficiency virus type 1 (HIV-1) infection. Mutating either Trp-21 or Ala-51, which line the inner wall of a hydrophobic cavity that is common to Tudor clan members, disrupts chromatin binding and virus infectivity. Consistent with a role for chromatin-associated LEDGF/p75 in stimulating integrase activity during infection, recombinant W21A protein is preferentially defective for enhancing integration into chromatinized target DNA in vitro. The A51P mutation corresponds to the S270P change in DNA methyltransferase 3B that causes human immunodeficiency, centromeric instability, and facial anomaly syndrome, revealing a critical role for this amino acid position in the chromatin binding functions of varied PWWP domains. Our results furthermore highlight the requirement for a conserved Glu in the hydrophobic core that mediates interactions between other Tudor clan members and their substrates. This initial systematic mutagenesis of a PWWP domain identifies amino acid residues critical for chromatin binding function and the consequences of their changes on HIV-1 integration and infection.
Collapse
|
34
|
Yokoyama A, Cleary ML. Menin critically links MLL proteins with LEDGF on cancer-associated target genes. Cancer Cell 2008; 14:36-46. [PMID: 18598942 PMCID: PMC2692591 DOI: 10.1016/j.ccr.2008.05.003] [Citation(s) in RCA: 398] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 05/15/2008] [Accepted: 05/15/2008] [Indexed: 12/15/2022]
Abstract
Menin displays the unique ability to either promote oncogenic function in the hematopoietic lineage or suppress tumorigenesis in the endocrine lineage; however, its molecular mechanism of action has not been defined. We demonstrate here that these discordant functions are unified by menin's ability to serve as a molecular adaptor that physically links the MLL (mixed-lineage leukemia) histone methyltransferase with LEDGF (lens epithelium-derived growth factor), a chromatin-associated protein previously implicated in leukemia, autoimmunity, and HIV-1 pathogenesis. LEDGF is required for both MLL-dependent transcription and leukemic transformation. Conversely, a subset of menin mutations in multiple endocrine neoplasia type 1 patients abrogate interaction with LEDGF while preserving MLL interaction but nevertheless compromise MLL/menin-dependent functions. Thus, LEDGF critically associates with MLL and menin at the nexus of transcriptional pathways that are recurrently targeted in diverse diseases.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Gene Expression Regulation, Leukemic
- HeLa Cells
- Histone Methyltransferases
- Histone-Lysine N-Methyltransferase/metabolism
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Leukemia/enzymology
- Leukemia/genetics
- Leukemia/metabolism
- Leukemia/pathology
- Mice
- Mice, Inbred C57BL
- Multiple Endocrine Neoplasia Type 1/genetics
- Multiple Endocrine Neoplasia Type 1/metabolism
- Mutation
- Myeloid Progenitor Cells/enzymology
- Myeloid Progenitor Cells/metabolism
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Protein Binding
- Protein Methyltransferases
- Protein Structure, Tertiary
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA Interference
- Time Factors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Transduction, Genetic
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
- U937 Cells
Collapse
Affiliation(s)
- Akihiko Yokoyama
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | | |
Collapse
|
35
|
Laguri C, Duband-Goulet I, Friedrich N, Axt M, Belin P, Callebaut I, Gilquin B, Zinn-Justin S, Couprie J. Human mismatch repair protein MSH6 contains a PWWP domain that targets double stranded DNA. Biochemistry 2008; 47:6199-207. [PMID: 18484749 DOI: 10.1021/bi7024639] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The eukaryotic mismatch repair (MMR) protein MSH6 exhibits a core region structurally and functionally similar to bacterial MutS. However, it possesses an additional N-terminal region (NTR), comprising a PCNA binding motif, a large region of unknown function and a nonspecific DNA binding fragment. Yeast NTR was recently described as an extended tether between PCNA and the core of MSH6 . In contrast, we show that human NTR presents a globular PWWP domain in the region of unknown function. We demonstrate that this PWWP domain binds double-stranded DNA, without any preference for mismatches or nicks, whereas its apparent affinity for single-stranded DNA is about 20 times lower. The S144I mutation, which in human MSH6 causes inherited somatic defects in MMR resulting in increased development of hereditary non polyposis colorectal cancer , is located in the DNA binding surface of the PWWP domain. However, it only moderately affects domain stability, and it does not perturb DNA binding in vitro.
Collapse
Affiliation(s)
- Cédric Laguri
- CEA Laboratoire de Biologie Structurale et Radiobiologie, iBiTec-Saclay, 91191 Gif sur Yvette, France
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Thakar K, Niedenthal R, Okaz E, Franken S, Jakobs A, Gupta S, Kelm S, Dietz F. SUMOylation of the hepatoma-derived growth factor negatively influences its binding to chromatin. FEBS J 2008; 275:1411-1426. [PMID: 18331345 DOI: 10.1111/j.1742-4658.2008.06303.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hepatoma-derived growth factor is a nuclear targeted mitogen containing a PWWP domain that mediates binding to DNA. To date, almost nothing is known about the molecular mechanisms of the functions of hepatoma-derived growth factor, its routes of secretion and internalization or post-translational modifications. In the present study, we show for the first time that hepatoma-derived growth factor is modified by the covalent attachment of small ubiquitin-related modifier 1 (SUMO-1), a post-translational modification with regulatory functions for an increasing number of proteins. Using a basal SUMOylation system in Escherichia coli followed by a MALDI-TOF-MS based peptide analysis, we identified the lysine residue SUMOylated located in the N-terminal part of the protein adjacent to the PWWP domain. Surprisingly, this lysine residue is not part of the consensus motif described for SUMOylation. With a series of hepatoma-derived growth factor mutants, we then confirmed that this unusual location is also used in mammalian cells and that SUMOylation of hepatoma-derived growth factor takes place in the nucleus. Finally, we demonstrate that SUMOylated hepatoma-derived growth factor is not binding to chromatin, in contrast to its unSUMOylated form. These observations potentially provide new perspectives for a better understanding of the functions of hepatoma-derived growth factor.
Collapse
Affiliation(s)
- Ketan Thakar
- Department of Biochemistry, Centre for Biomolecular Interactions Bremen (CBIB), University of Bremen, Germany
| | | | - Elwy Okaz
- Department of Biochemistry, Centre for Biomolecular Interactions Bremen (CBIB), University of Bremen, Germany
| | - Sebastian Franken
- Department of Physiological Chemistry, Rheinische-Friedrich-Wilhelm University of Bonn, Germany
| | - Astrid Jakobs
- Department of Biochemistry, Hannover Medical School, Germany
| | - Shivangi Gupta
- Department of Biochemistry, Centre for Biomolecular Interactions Bremen (CBIB), University of Bremen, Germany
| | - Sørge Kelm
- Department of Biochemistry, Centre for Biomolecular Interactions Bremen (CBIB), University of Bremen, Germany
| | - Frank Dietz
- Department of Biochemistry, Centre for Biomolecular Interactions Bremen (CBIB), University of Bremen, Germany
| |
Collapse
|
37
|
Yabuki T, Motoda Y, Hanada K, Nunokawa E, Saito M, Seki E, Inoue M, Kigawa T, Yokoyama S. A robust two-step PCR method of template DNA production for high-throughput cell-free protein synthesis. ACTA ACUST UNITED AC 2008; 8:173-91. [PMID: 18167031 DOI: 10.1007/s10969-007-9038-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Accepted: 10/29/2007] [Indexed: 12/01/2022]
Abstract
A two-step PCR method has been developed for the robust, high-throughput production of linear templates ready for cell-free protein synthesis. The construct made from the cDNA expresses a target protein region with N- and/or C-terminal tags. The procedure consists only of mixing, dilution, and PCR steps, and is free from cloning and purification steps. In the first step of the two-step PCR, a target region within the coding sequence is amplified using two gene-specific forward and reverse primers, which contain the linker sequences and the terminal sequences of the target region. The second PCR concatenates the first PCR product with the N- and C-terminal double-stranded fragments, which contain the linker sequences as well as the sequences for the tag(s) and the initiation and termination, respectively, for T7 transcription and ribosomal translation, and amplifies it with the universal primer. Proteins can be fused with a variety of tags, such as natural poly-histidine, glutathione-S-transferase, maltose-binding protein, and/or streptavidin-binding peptide. The two-step PCR method was successfully applied to 42 human target protein regions with various GC contents (38-77%). The robustness of the two-step PCR method against possible fluctuations of experimental conditions in practical use was explored. The second PCR product was obtained at 60-120 microg/ml, and was used without purification as a template at a concentration of 2-4 microg/ml in an Escherichia coli coupled transcription-translation system. This combination of two-step PCR with cell-free protein synthesis is suitable for the rapid production of proteins in milligram quantities for genome-scale studies.
Collapse
Affiliation(s)
- Takashi Yabuki
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Hepatoma-derived growth factor binds DNA through the N-terminal PWWP domain. BMC Mol Biol 2007; 8:101. [PMID: 17974029 PMCID: PMC2176068 DOI: 10.1186/1471-2199-8-101] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 10/31/2007] [Indexed: 11/16/2022] Open
Abstract
Background Hepatoma Derived Growth Factor (HDGF) is a nuclear protein with nuclear targeting required for mitogenic activity. Recently we demonstrated that HDGF is a transcriptional repressor, but whether HDGF binds DNA, the specificity of DNA binding and what protein domain is required are still unknown. In this study, we aimed to identify if HDGF is a DNA binding protein, map the functional DNA binding domain and DNA binding element for HDGF. Results Using chromatin immunoprecipitation (ChIP) of human DNA, we isolated 10 DNA sequences sharing a conserved ~200 bp element. Homology analysis identified the binding sequences as a motif within the promoter of the SMYD1 gene, a HDGF target gene. Electrophoretic Mobility Shift Assays (EMSA) confirmed the binding of HDGF to this conserved sequence. As a result, an 80 bp conserved sequence located in the SMYD1 promoter bound GST-HDGF tightly. The binding core sequence for HDGF was narrowed down to 37 bp using a deletion mapping strategy from both the 5' and 3' ends. Moreover, ChIP and DNase I footprinting analysis revealed that HDGF binds this 80 bp DNA fragment specifically. Functionally overexpression of HDGF represses a reporter gene which is controlled by an SV-40 promoter containing the 80 bp DNA element. Using serial truncations of GST-HDGF, we mapped the DNA binding domain of HDGF to the N-terminal PWWP domain. Conclusion HDGF is a DNA binding protein, binds DNA specifically, and prefers a minimum of 37 bp long DNA fragment. The N-terminal PWWP domain of HDGF is required for DNA binding. HDGF exerts its transcription repressive effect through binding to a conserved DNA element in the promoter of target genes.
Collapse
|
39
|
Bartholomeeusen K, De Rijck J, Busschots K, Desender L, Gijsbers R, Emiliani S, Benarous R, Debyser Z, Christ F. Differential interaction of HIV-1 integrase and JPO2 with the C terminus of LEDGF/p75. J Mol Biol 2007; 372:407-21. [PMID: 17669426 DOI: 10.1016/j.jmb.2007.06.090] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 06/27/2007] [Accepted: 06/29/2007] [Indexed: 11/28/2022]
Abstract
The transcriptional co-activator lens epithelium-derived growth factor (LEDGF) has been shown to protect cells against environmental stress. The protein has been implicated in auto-immunity and cancer, and is present in cells as the p52 or p75 splice variant. Recently, LEDGF/p75, but not p52, was identified as the prominent interaction partner of human immunodeficiency virus type 1 (HIV-1) integrase. This interaction of HIV-1 integrase with the C-terminal integrase-binding domain of LEDGF/p75 is crucial for HIV-1 replication. To gain insight into the cell biology of LEDGF/p75, we were interested in identifying cellular binding partners of its C-terminal domain. By yeast-two-hybrid screening with a CEMC7 cDNA-library, we were able to identify JPO2 as a binding partner of the C-terminal part of LEDGF/p75. The specific interaction between JPO2 and LEDGF/p75 was verified by pull-down, AlphaScreen, and co-immunoprecipitation. Competition assays using recombinant proteins show a mutually exclusive binding of either JPO2 or HIV-1 integrase to LEDGF/p75. However, differing mechanisms of binding were suggested by continuing interaction of JPO2 with some LEDGF/p75 mutants (I365A, D366A, F406A) that are totally defective for interaction with HIV-1 integrase. This finding is of significance for the development of specific inhibitors targeting only the interaction between LEDGF/p75 and HIV-1 integrase, without disturbing interaction with other cellular factors. Over-expression of JPO2 resulted in a modest but reproducible inhibition of HIV-1 replication, consistent with competition between integrase and JPO2 for binding to LEDGF/p75. Furthermore, JPO2 over-expression activated transcription from the HIV-1 LTR.
Collapse
|
40
|
Sue SC, Lee WT, Tien SC, Lee SC, Yu JG, Wu WJ, Wu WG, Huang TH. PWWP module of human hepatoma-derived growth factor forms a domain-swapped dimer with much higher affinity for heparin. J Mol Biol 2007; 367:456-72. [PMID: 17270212 DOI: 10.1016/j.jmb.2007.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2006] [Revised: 01/01/2007] [Accepted: 01/03/2007] [Indexed: 01/14/2023]
Abstract
Hepatoma-derived growth factor (hHDGF)-related proteins (HRPs) comprise a new growth factor family sharing a highly conserved and ordered N-terminal PWWP module (residues 1-100, previously referred to as a HATH domain) and a variable disordered C-terminal domain. We have shown that the PWWP module is responsible for heparin binding and have solved its structure in solution. Here, we show that under physiological conditions, both the PWWP module and hHDGF can form dimers. Surface plasmon resonance (SPR) studies revealed that the PWWP dimer binds to heparin with affinity that is two orders of magnitude higher (K(d)=13 nM) than that of the monomeric PWWP module (K(d)=1.2 microM). The monomer-dimer equilibrium properties and NMR structural data together suggest that the PWWP dimer is formed through a domain-swapping mechanism. The domain-swapped PWWP dimer structures were calculated on the basis of the NMR data. The results show that the two PWWP protomers exchange their N-terminal hairpin to form a domain-swapped dimer. The two monomers in a dimer are linked by the long flexible L2 loops, a feature supported by NMR relaxation data for the monomer and dimer. The enhanced heparin-binding affinity of the dimer can be rationalized in the framework of the dimer structure.
Collapse
Affiliation(s)
- Shih-Che Sue
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, R.O.C
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Llano M, Vanegas M, Hutchins N, Thompson D, Delgado S, Poeschla EM. Identification and characterization of the chromatin-binding domains of the HIV-1 integrase interactor LEDGF/p75. J Mol Biol 2006; 360:760-73. [PMID: 16793062 DOI: 10.1016/j.jmb.2006.04.073] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Revised: 04/19/2006] [Accepted: 04/30/2006] [Indexed: 10/24/2022]
Abstract
Depletion of the transcriptional co-activator LEDGF/p75 by RNA interference alters the genome-wide pattern of HIV-1 integration, reducing integration into active genes, reducing integration into LEDGF/p75-regulated genes, and increasing integration into G+C-rich sequences. LEDGF/p75 is also able to act as a molecular tether linking HIV-1 integrase protein to chromatin, a phenomenon likely to underlie the integration site distribution effects. The LEDGF/p75 integrase-binding domain has been established but the domain or domains responsible for the chromatin-binding component of tethering are unknown. Here, we identify and characterize these domains. Complementary methods were used to assess condensed and uncondensed chromatin, and to determine the stringency of chromatin binding. Immuno-localization analyses revealed that an N-terminal PWWP domain and its beta-barrel substructure are needed for binding to metaphase chromatin. However, the PWWP domain is insufficient to transfer metaphase chromatin binding to green fluorescent protein, which requires addition of a downstream charged region (CR1). Biochemical analysis showed that full-length LEDGF/p75 resists Triton X-100 extraction from chromatin. To transfer Triton-resistant chromatin binding to green fluorescent protein, PWWP-CR1 is necessary but not sufficient. Further inclusion of a tandem pair of AT-hooks in combination with at least one of two identified downstream charged regions (CR2 or CR3) is needed. Deletion of just the PWWP or the AT-hook domain from full-length LEDGF/p75 reduced Triton-resistant chromatin binding, while deletion of both elements abolished it, underscoring their dominant and cooperative role. The results establish a molecular mechanism for LEDGF/p75-mediated tethering of HIV-1 integrase to chromatin.
Collapse
Affiliation(s)
- Manuel Llano
- Molecular Medicine Program, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | | | | | | | | |
Collapse
|
42
|
Vandekerckhove L, Christ F, Van Maele B, De Rijck J, Gijsbers R, Van den Haute C, Witvrouw M, Debyser Z. Transient and stable knockdown of the integrase cofactor LEDGF/p75 reveals its role in the replication cycle of human immunodeficiency virus. J Virol 2006; 80:1886-96. [PMID: 16439544 PMCID: PMC1367129 DOI: 10.1128/jvi.80.4.1886-1896.2006] [Citation(s) in RCA: 170] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
After identifying the interaction between the transcriptional coactivator lens epithelium-derived growth factor (LEDGF/p75) and the human immunodeficiency virus type 1 (HIV-1) integrase (IN), we have now investigated the role of LEDGF/p75 during HIV replication. Transient small interfering RNA-mediated knockdown of LEDGF/p75 in HeLaP4 cells resulted in a three- to fivefold inhibition of HIV-1 (strain NL4.3) replication. Quantitative PCR was used to pinpoint the replication block to the integration step. Next, polyclonal and monoclonal HeLaP4-derived cell lines were selected with a stable knockdown of LEDGF/p75 mediated by a lentiviral vector (lentivector) encoding a short hairpin RNA (shRNA) targeting this protein. Cell lines stably transduced with a lentivector encoding an unrelated hairpin or a double-mismatch hairpin served as controls. Again, a two- to fourfold reduction of HIV-1 replication was observed. The extent of LEDGF/p75 knockdown closely correlated with the reduction of HIV-1 replication. After the back-complementation of LEDGF/p75 in the poly- and monoclonal knockdown cell lines using an shRNA-resistant expression plasmid, viral replication was restored to nearly wild-type levels. The Q168A mutation in integrase has been shown to interfere with the interaction with LEDGF/p75 without reducing the enzymatic activity. Transduction by HIV-1-derived lentivectors carrying the Q168A IN mutant was severely hampered, pointing again to a requirement for LEDGF/p75. Altogether, our data validate LEDGF/p75 as an important cellular cofactor for HIV integration and as a potential target for antiviral drug development.
Collapse
Affiliation(s)
- Linos Vandekerckhove
- Molecular Medicine, K.U.Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Lukasik SM, Cierpicki T, Borloz M, Grembecka J, Everett A, Bushweller JH. High resolution structure of the HDGF PWWP domain: a potential DNA binding domain. Protein Sci 2005; 15:314-23. [PMID: 16384999 PMCID: PMC2242466 DOI: 10.1110/ps.051751706] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Hepatoma Derived Growth Factor (HDGF) is an endogenous nuclear-targeted mitogen that is linked with human disease. HDGF is a member of the weakly conserved PWWP domain family. This 70-amino acid motif, originally identified from the WHSC1 gene, has been found in more than 60 eukaryotic proteins. In addition to the PWWP domain, many proteins in this class contain known chromatin remodeling domains, suggesting a role for HDGF in chromatin remodeling. We have determined the NMR structure of the HDGF PWWP domain to high resolution using a combination of NOEs, J-couplings, and dipolar couplings. Comparison of this structure to a previously determined structure of the HDGF PWWP domain shows a significant difference in the C-terminal region. Comparison to structures of other PWWP domains shows a high degree of similarity to the PWWP domain structures from Dnmt3b and mHRP. The results of selected and amplified binding assay and NMR titrations with DNA suggest that the HDGF PWWP domain may function as a nonspecific DNA-binding domain. Based on the NMR titrations, we propose a model of the interaction of the PWWP domain with DNA.
Collapse
Affiliation(s)
- Stephen M Lukasik
- Department of Chemistry, University of Virginia, Charlottesville, VA 22906, USA
| | | | | | | | | | | |
Collapse
|