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Li, Siyi, Zhulin Wu, Qiuyue Li, Qiting Liang, Hengli Zhou, Yafei Shi, Rong Zhang, and Huafeng Pan. "The Prognostic Value of AT-Rich Interaction Domain (ARID) Family Members in Patients with Hepatocellular Carcinoma." Evidence-Based Complementary and Alternative Medicine 2022 (August 18, 2022): 1–16. http://dx.doi.org/10.1155/2022/1150390.
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Objective. Hepatocellular carcinoma (HCC) is one of the most lethal malignancies with a poor prognosis. The AT-rich interaction domain (ARID) family plays an essential regulatory role in the pathogenesis and progression of cancers. This study aims to evaluate the prognostic value and clinical significance of human ARID family genes in HCC. Methods. ONCOMINE and The Cancer Genome Atlas (TCGA) databases were employed to retrieve ARIDs expression profile and clinicopathological information of HCC. Kaplan–Meier plotter and MethSurv were applied to the survival analysis of patients with HCC. CBioPortal was used to analyze genetic mutations of ARIDs. Gene Expression Profiling Interactive Analysis (GEPIA) and Metascape were used to perform hub gene identification and functional enrichment. Results. Expression levels of 11 ARIDs were upregulated in HCC, and 2 ARIDs were downregulated. Also, 4 ARIDs and 5 ARIDs were correlated with pathologic stages and histologic grades, respectively. Furthermore, higher expression of ARID1A, ARID1B, ARID2, ARID3A, ARID3B, ARID5B, KDM5A, KDM5B, KDM5C, and JARID2 was remarkably correlated with worse overall survival of patients with HCC, and the high ARID3C/KDM5D expression was related to longer overall survival. Multivariate Cox analysis indicated that ARID3A, KDM5C, and KDM5D were independent risk factors for HCC prognosis. Moreover, ARIDs mutations and 127 CpGs methylation in all ARIDs were observed to be significantly associated with the prognosis of HCC patients. Besides, our data showed that ARIDs could regulate tumor-related pathways and distinct immune cells in the HCC microenvironment. Conclusions. ARIDs present the potential prognostic value for HCC. Our findings suggest that ARID3A, KDM5C, and KDM5D may be the prognostic biomarkers for patients with HCC.
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Dallas, Peter B., Stephen Pacchione, Deborah Wilsker, Valerie Bowrin, Ryuji Kobayashi, and Elizabeth Moran. "The Human SWI-SNF Complex Protein p270 Is an ARID Family Member with Non-Sequence-Specific DNA Binding Activity." Molecular and Cellular Biology 20, no. 9 (May 1, 2000): 3137–46. http://dx.doi.org/10.1128/mcb.20.9.3137-3146.2000.
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ABSTRACT p270 is an integral member of human SWI-SNF complexes, first identified through its shared antigenic specificity with p300 and CREB binding protein. The deduced amino acid sequence of p270 reported here indicates that it is a member of an evolutionarily conserved family of proteins distinguished by the presence of a DNA binding motif termed ARID (AT-rich interactive domain). The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogastergene product required for normal development), and MRF-2 (which represses expression from the cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions.
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HURLSTONE, Adam F. L., Ivan A. OLAVE, Nick BARKER, Mascha van NOORT, and Hans CLEVERS. "Cloning and characterization of hELD/OSA1, a novel BRG1 interacting protein." Biochemical Journal 364, no. 1 (May 8, 2002): 255–64. http://dx.doi.org/10.1042/bj3640255.
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A highly conserved multisubunit enzymic complex, SWI/SNF, participates in the regulation of eukaryote gene expression through its ability to remodel chromatin. While a single component of SWI/SNF, Swi2 or a related protein, can perform this function in vitro, the other components appear to modulate the activity and specificity of the complex in vivo. Here we describe the cloning of hELD/OSA1, a 189KDa human homologue of Drosophila Eld/Osa protein, a constituent of Drosophila SWI/SNF. By comparing conserved peptide sequences in Eld/Osa homologues we define three domains common to all family members. A putative DNA binding domain, or ARID (AT-rich DNA-interacting domain), may function in targetting SWI/SNF to chromatin. Two other domains unique to Eld/Osa proteins, EHD1 and EHD2, map to the C-teminus. We show that EHD2 mediates binding to Brahma-related gene 1 (BRG1), a human homologue of yeast Swi2. EHD1 and EHD2 also appear capable of interacting with each other. Using an antibody raised against EHD2 of hELD/OSA1, we detected Eld/Osa1 in endogenous SWI/SNF complexes derived from mouse brain.
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Iwahara, J. "Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID)." EMBO Journal 18, no. 21 (November 1, 1999): 6084–94. http://dx.doi.org/10.1093/emboj/18.21.6084.
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Kusunoki, Hideki, Tsukasa Hasegawa, Chieko Komatsu, Takashi Takeuchi, and Toshiyuki Kohno. "1H, 13C and 15N Resonance Assignments of the AT-Rich Interaction Domain (ARID) of Jumonji." Journal of Biomolecular NMR 33, no. 1 (September 2005): 74. http://dx.doi.org/10.1007/s10858-005-1282-6.
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Hirose-Yotsuya, Lisa, Fumio Okamoto, Takahiro Yamakawa, Robert H. Whitson, Yoko Fujita-Yamaguchi, and Keiichi Itakura. "Knockdown of AT-rich interaction domain (ARID) 5B gene expression induced AMPKα2 activation in cardiac myocytes." BioScience Trends 9, no. 6 (2015): 377–85. http://dx.doi.org/10.5582/bst.2015.01159.
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Liu, Gaohua, Yuanpeng J. Huang, Rong Xiao, Dongyan Wang, Thomas B. Acton, and Gaetano T. Montelione. "Solution NMR structure of the ARID domain of human AT-rich interactive domain-containing protein 3A: A human cancer protein interaction network target." Proteins: Structure, Function, and Bioinformatics 78, no. 9 (March 18, 2010): 2170–75. http://dx.doi.org/10.1002/prot.22718.
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Roy, Adrita, Arkajyoti Dutta, Dipan Roy, Payel Ganguly, Ritesh Ghosh, Rajiv K. Kar, Anirban Bhunia, Jayanta Mukhobadhyay, and Shubho Chaudhuri. "Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana." Plant Molecular Biology 92, no. 3 (August 9, 2016): 371–88. http://dx.doi.org/10.1007/s11103-016-0519-y.
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Loesch, Robin, Linda Chenane, and Sabine Colnot. "ARID2 Chromatin Remodeler in Hepatocellular Carcinoma." Cells 9, no. 10 (September 23, 2020): 2152. http://dx.doi.org/10.3390/cells9102152.
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Chromatin remodelers are found highly mutated in cancer including hepatocellular carcinoma. These mutations frequently occur in ARID (AT-rich Interactive Domain) genes, encoding subunits of the ATP-dependent SWI/SNF remodelers. The increasingly prevalent complexity that surrounds the functions and specificities of the highly modular BAF (BG1/BRM-associated factors) and PBAF (polybromo-associated BAF) complexes, including ARID1A/B or ARID2, is baffling. The involvement of the SWI/SNF complexes in diverse tissues and processes, and especially in the regulation of gene expression, multiplies the specific outcomes of specific gene alterations. A better understanding of the molecular consequences of specific mutations impairing chromatin remodelers is needed. In this review, we summarize what we know about the tumor-modulating properties of ARID2 in hepatocellular carcinoma.
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Roy, Adrita, Arkajyoti Dutta, Dipan Roy, Payel Ganguly, Ritesh Ghosh, Rajiv K. Kar, Anirban Bhunia, Jayanta Mukhopadhyay, and Shubho Chaudhuri. "Erratum to: Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana." Plant Molecular Biology 92, no. 3 (September 5, 2016): 389–90. http://dx.doi.org/10.1007/s11103-016-0534-z.
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Kim, Suhkmann, Ziming Zhang, Sean Upchurch, Nancy Isern, and Yuan Chen. "Structure and DNA-binding Sites of the SWI1 AT-rich Interaction Domain (ARID) Suggest Determinants for Sequence-specific DNA Recognition." Journal of Biological Chemistry 279, no. 16 (January 13, 2004): 16670–76. http://dx.doi.org/10.1074/jbc.m312115200.
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Inoue, Hiroko, Stavros Giannakopoulos, Christopher N. Parkhurst, Tatsushi Matsumura, Evelyn A. Kono, Takako Furukawa, and Naoko Tanese. "Target genes of the largest human SWI/SNF complex subunit control cell growth." Biochemical Journal 434, no. 1 (January 27, 2011): 83–92. http://dx.doi.org/10.1042/bj20101358.
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The largest subunit of the mammalian SWI/SNF-A or BAF (BRG1-associated factor) chromatin-remodelling complex is encoded by two related cDNAs hOsa1/BAF250a and hOsa2/BAF250b that are unique to the BAF complex and absent in the related PBAF (Polybromo BAF). hOsa/BAF250 has been shown to interact with transcriptional activators and bind to DNA suggesting that it acts to target the remodelling complex to chromatin. To better understand the functions of hOsa2, we established inducible stable HeLa cell lines over-expressing FLAG–hOsa2 or a derivative lacking the ARID (AT-rich interactive domain) DNA-binding domain. Immunopurification of complexes containing hOsa2 that was followed by mass spectrometry and immunoblotting demonstrated the presence of BRG1 and known BAFs, but not hOsa1 or hBRM. Deletion of the ARID did not compromise the integrity of the complex. Induction of hOsa2 expression caused impaired cell growth and accumulation of cells in the G0/G1 cell cycle phase. Elevated levels of the p53 and p21 proteins were detected in these cells while c-Myc mRNA and protein levels were found to decrease. Chromatin immunoprecipitation and reporter assays suggested that hOsa2 had a direct effect on c-myc and p21 promoter activity. Thus hOsa2 plays an important role in controlling genes regulating the cell cycle.
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Iwahara, Junji, Robert D. Peterson, and Robert T. Clubb. "Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich interaction domain (ARID) binds DNA: A nitrogen-15 relaxation study." Protein Science 14, no. 5 (May 2005): 1140–50. http://dx.doi.org/10.1110/ps.041154405.
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Garin, Gwenaele, Kazem Zibara, Frederick Aguilar, Ming Lo, Adam Hurlstone, Robin Poston, and John L. Mcgregor. "6A3-5/Osa2 is an Early Activated Gene Implicated in the Control of Vascular Smooth Muscle Cell Functions." Journal of Biomedicine and Biotechnology 2006 (2006): 1–17. http://dx.doi.org/10.1155/jbb/2006/97287.
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Vascular smooth muscle cells (VSMC) growth plays a key role in the pathophysiology of vascular diseases. However, the molecular mechanisms controlling gene transcription in VSMC remain poorly understood. We previously identified, by differential display, a new gene (6A3-5) overexpressed in proliferating rat VSMC. In this study, we have cloned the full-length cDNA by screening a rat foetal brain cDNA library and investigated its functions. The 6A3-5 protein shows 4 putative conserved functional motifs: a DNA binding domain called ARID (AT-rich interaction domain), two recently described motifs (Osa Homology Domain), and a nuclear localization signal. The deduced protein sequence was observed to be 85% identical to the recently described human Osa2 gene. Immunolabelling, using an anti-6A3-5/Osa2 monoclonal antibody, showed a nuclear localization of the 6A3-5/Osa2 protein. In addition, PDGF upregulated 6A3-5/Osa2 expression at both the transcript and protein levels in a dose and time-dependent fashion. The pattern of upregulation by PDGF was reminiscent of the early responsive gene c-fos. The PDGF-induced upregulation of 6A3-5/Osa2 and proliferation of VSMC were significantly inhibited in a dose and sequence-dependent fashion by an antisense, but not by sense, scrambled or mismatched oligonucleotides directed against 6A3-5/Osa2. In VSMC of aortas derived from hypertensive (LH) rats, 6A3-5/Osa2 is overexpressed as compared to that in normotensive (LL) rats. The 6A3-5/Osa2-gene expression is downregulated by an ACE inhibitor and upregulated by exogenous AngiotensinII in LH rats. In summary, these results indicate that 6A3-5/Osa2 is an early activated gene that belongs to a new family of proteins involved in the control of VSMC growth.
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Ali, Asghar, Gerrit J. Bouma, Russell V. Anthony, and Quinton A. Winger. "The Role of LIN28-let-7-ARID3B Pathway in Placental Development." International Journal of Molecular Sciences 21, no. 10 (May 21, 2020): 3637. http://dx.doi.org/10.3390/ijms21103637.
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Placental disorders are a major cause of pregnancy loss in humans, and 40–60% of embryos are lost between fertilization and birth. Successful embryo implantation and placental development requires rapid proliferation, invasion, and migration of trophoblast cells. In recent years, microRNAs (miRNAs) have emerged as key regulators of molecular pathways involved in trophoblast function. A miRNA binds its target mRNA in the 3ʹ-untranslated region (3ʹ-UTR), causing its degradation or translational repression. Lethal-7 (let-7) miRNAs induce cell differentiation and reduce cell proliferation by targeting proliferation-associated genes. The oncoprotein LIN28 represses the biogenesis of mature let-7 miRNAs. Proliferating cells have high LIN28 and low let-7 miRNAs, whereas differentiating cells have low LIN28 and high let-7 miRNAs. In placenta, low LIN28 and high let-7 miRNAs can lead to reduced proliferation of trophoblast cells, resulting in abnormal placental development. In trophoblast cells, let-7 miRNAs reduce the expression of proliferation factors either directly by binding their mRNA in 3ʹ-UTR or indirectly by targeting the AT-rich interaction domain (ARID)3B complex, a transcription-activating complex comprised of ARID3A, ARID3B, and histone demethylase 4C (KDM4C). In this review, we discuss regulation of trophoblast function by miRNAs, focusing on the role of LIN28-let-7-ARID3B pathway in placental development.
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Nyati, Kishan K., Kazuya Masuda, Praveen Dubey, Mohammad Mahabub-Uz Zaman, and Tadamitsu Kishimoto. "NF-κB and MAPK signaling pathways regulate the IL6 mRNA stability under TLR4 by regulating the expression and degradation of Arid5a." Journal of Immunology 196, no. 1_Supplement (May 1, 2016): 59.5. http://dx.doi.org/10.4049/jimmunol.196.supp.59.5.
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Abstract AT-rich interactive domain (ARID) 5a controls the IL-6 mRNA stability by binding to its 3′UTR region and preventing it from degradation by Regnase-1. This mechanism was shown to contribute to the elevation of IL-6 levels, which causes the development of autoimmune diseases. However, almost nothing is known about the regulatory mechanisms of Arid5a mRNA and protein expression. In the present study, we have investigated the regulatory mechanisms of Arid5a at transcriptional, post-transcriptional and post-translational levels under TLR4 signaling. We found that in response to LPS stimulation NF-κB binds to the promoter region of Arid5a and induce its gene expression. After expression of Arid5a mRNA, MKP-1 signaling induces AUF-1 to translocate from the nucleus to the cytoplasm where it binds to the 3′UTR region of Arid5a and resulting in its destabilization. Inhibition of MKP-1 and AUF-1 results in the stabilization of Arid5a mRNA, which leads to higher expression of IL6, suggesting that this pathway has a significant role in regulating IL6 mRNA through Arid5a. We also show that during the late phase of LPS stimulation, p38 MAPK phosphorylates the Arid5a protein at Ser 253, 433 and 458 positions that lead to its ubiquitination at lysine 80 and 93 positions resulting in degradation. Inhibition of Arid5a phosphorylation and degradation causes the over-production IL6 mRNA further supports the importance of Arid5a in the regulation of IL6. Our data demonstrate that LPS signaling controls IL6 mRNA stability; therefore, its regulation through up-regulation of Arid5a by NF-κB at the early phase, and down-regulation of Arid5a at the mRNA and protein level by MKP-1-mediated AUF1 and P38 MAPK signaling, respectively at the later phase.
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Bluemn, Theresa, Jesse Schmitz, Yongwei Zheng, and Nan Zhu. "Both Arid1b and Arid2 Are Tumor Suppressors in MLL-AF9 Leukemogenesis." Blood 134, Supplement_1 (November 13, 2019): 1248. http://dx.doi.org/10.1182/blood-2019-127123.
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ATP-dependent chromatin remodeling complexes, including BAF (BRG1 associated factor) and PBAF (Polybromo-associated BRG1 associated factor), play major roles in development and disease. These complexes contain multiple subunits and utilize ATP to remodel nucleosomes and, as a result, affect downstream processes. Subunits of the BAF and PBAF complexes are frequently mutated in various cancers, including in acute myeloid leukemia. However, the role of distinct members of these complexes in leukemogenesis is poorly understood. BAF and PBAF complexes are distinguished from each other by unique AT-rich interacting domain (ARID) subunits, ARID1A/B and ARID2, respectively. Recently, Arid2 was suggested to have tumor suppressive functions in MLL-AF9 leukemogenesis, however the role of Arid1b is unknown. In this study, we further evaluated the tumor suppressor roles of Arid2 and Arid1b in MLL-AF9 leukemogenesis. To study the effect of the loss of Arid2 and Arid1b on MLL-AF9 leukemia in vitro, hematopoietic stem and progenitor cells from Arid1bfl/fl, Arid2fl/fl and wild type (control) mice were transformed by retroviral expression of MLL-AF9. Arid1b or Arid2 was then deleted by retroviral delivery of Cre-recombinase and cellular phenotypes were characterized by flow cytometry. In vitro characterization revealed Arid1b-/-and Arid2-/-MLL-AF9 cells have similar growth rates to control cells and no changes in cell cycle status and apoptosis. To study leukemogenesis in vivo, two hematopoietic specific conditional knockout mouse models, Vav1Cre, a constitutively active Cre-recombinase, and Mx1Cre, an inducible Cre-recombinase, were used. Primary and secondary transplant recipient mice were assessed for survival, disease burden, and leukemia stem cell frequency. In primary transplantation, leukemic initiation was not altered by the loss of the Arid2. Overall survival of primary recipients and disease burden in moribund mice (percentage of GFP positive MLL-AF9 cells in bone marrow/spleen and spleen weight) were similar to control counterparts. However, in limiting dilution secondary transplantation of Arid2fl/flVav1Cre (Arid2-/-) and wild type Vav1Cre (control) MLL-AF9, median survival of the Arid2-/- cohort decreased 1 to 2 weeks in comparison to the control cohort and there was a two-fold increase in leukemia initiating cell frequency upon deletion of Arid2. Together these results support the previous indication that Arid2 is a tumor suppressor in MLL-AF9 leukemic initiation. To gain insight into the function of Arid1b in MLL-AF9 leukemogenesis, we performed primary transplantation of Arid1bfl/flcells transduced with MLL-AF9. Our data showed that loss of Arid1b enhanced leukemic initiation in the MLL-AF9 leukemia model. One-month post induction with pIpC, Arid1bfl/fl Mx1Cre MLL-AF9 cells accumulated faster in the peripheral blood and primary recipients exhibited decreased median survival compared with wild type Mx1Cre controls. Percentage of GFP+ leukemia cells was higher in the spleen of moribund mice in the Arid1bfl/fl Mx1Cre cohort, compared with the control cohort. Taken together, our data suggests Arid1b, in addition to Arid2, acts as a potential novel tumor suppressor in MLL-AF9 leukemogenesis. To study the mechanism of Arid1b and Arid2's function in MLL-AF9 leukemogenesis, RNA-sequencing of leukemic bone marrow cells was conducted. Consistent with the previous study, Arid2 null leukemia cells had increased Gata2 expression and decreased p57 expression. Gene Set Enrichment Analysis of Arid1b null cells showed enrichment of oncogenic signatures including ATM, Cyclin D and macrophage development as potentially contributing to the underlying tumor suppressive mechanism of Arid1b. In summary, our study uncovered Arid1b, in addition to Arid2, as a potential novel tumor suppressor in MLL-AF9 leukemia. Our study, together with published studies on the requirement of other subunits (SMARCA4, SMARCD2 and DPF2) of the BAF and PBAF complexes in MLL-AF9 leukemia, reveal opposing roles of the components of the BAF and PBAF complexes in leukemogenesis, the mechanism of which require further investigation. Disclosures No relevant conflicts of interest to declare.
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Zhu, Lihuan, Zhizhong Chen, Tianxing Guo, Wenshu Chen, Lilan Zhao, Lingwen Guo, and Xiaojie Pan. "USP2 Inhibits Lung Cancer Pathogenesis by Reducing ARID2 Protein Degradation via Ubiquitination." BioMed Research International 2022 (December 15, 2022): 1–15. http://dx.doi.org/10.1155/2022/1525216.
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Background. Ubiquitination is an important regulator in physiological and pathological conditions. Ubiquitin-specific protease 2 (USP2), as a member of the USP family, exhibits oncogenic effects in multiple malignancies. However, the exact role of USP2 has not been well clarified in lung cancer pathogenesis and progression. Therefore, we aimed to further investigate the regulatory roles of USP2 in lung cancer in this study. Methods. Firstly, immunoprecipitation-Mass Spectrometry (IP-MS), Co-immunoprecipitation (Co-IP), combined with immunofluorescent colocalization method, was conducted for USP2 protein interaction analysis in lung cancer cell lines. qRT-PCR, Western blot, and immunohistochemistry assays explored the USP2 expression pattern and USP2/ARID2- (AT-rich interactive domain 2-) specific shRNAs and overexpression vectors. Co-IP assays were designed to validate USP2-ARID2 protein interaction. Further functional studies including CHX chase assay, transwell assay, and wound healing assay were subsequently applied to evaluate the impact of USP2 modulation on lung cancer cells. Results. USP2 suppression was characteristic in lung cancer cell line models and lung cancer samples. USP2 and ARID2 demonstrated protein-protein interaction and overlapping localization in cancer cell models. Functional experiments suggested USP2 inhibited lung cancer cell invasion and migration by reducing ARID2 protein degradation. Subsequent ubiquitination assays indicated ARID2 protein degradation via the ubiquitination was significantly reduced by USP2 interaction. Conclusions. Our study provided novel insight that USP2 might suppress lung cancer by reducing ARID2 protein degradation via ubiquitination.
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Iwahara, J. "The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA." EMBO Journal 21, no. 5 (March 1, 2002): 1197–209. http://dx.doi.org/10.1093/emboj/21.5.1197.
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Loeb, J. A., and G. D. Fischbach. "ARIA can be released from extracellular matrix through cleavage of a heparin-binding domain." Journal of Cell Biology 130, no. 1 (July 1, 1995): 127–35. http://dx.doi.org/10.1083/jcb.130.1.127.
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ARIA, or acetylcholine receptor-inducing activity, is a polypeptide that stimulates the synthesis of acetylcholine receptors in skeletal muscle. Here we demonstrate that the ability of ARIA to induce phosphorylation of its receptor in muscle is blocked by highly charged glycosaminoglycans. ARIA constructs lacking the NH2-terminal portion, containing an immunoglobulin-like domain, are fully active and are not inhibited by glycosaminoglycans. Limited proteolysis of ARIA with subtilisin blocks the glycosaminoglycan interaction by degrading this NH2-terminal portion, but preserves the active, EGF-like domain. We also show that ARIA can be released from freshly dissociated cells from embryonic chick spinal cord and cerebellum by either heparin, high salt or limited proteolysis with subtilisin, suggesting that ARIA is bound to the extracellular matrix through charged interactions. We present a model of how ARIA may be stored in extracellular matrix at developing synapses and how its release may be mediated by local proteolysis.
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Ma, Liqun, Ke Cheng, Jinyan Li, Zhiqi Deng, Chunjiao Zhang, and Hongliang Zhu. "Roles of Plant Glycine-Rich RNA-Binding Proteins in Development and Stress Responses." International Journal of Molecular Sciences 22, no. 11 (May 29, 2021): 5849. http://dx.doi.org/10.3390/ijms22115849.
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In recent years, much progress has been made in elucidating the functional roles of plant glycine-rich RNA-binding proteins (GR-RBPs) during development and stress responses. Canonical GR-RBPs contain an RNA recognition motif (RRM) or a cold-shock domain (CSD) at the N-terminus and a glycine-rich domain at the C-terminus, which have been associated with several different RNA processes, such as alternative splicing, mRNA export and RNA editing. However, many aspects of GR-RBP function, the targeting of their RNAs, interacting proteins and the consequences of the RNA target process are not well understood. Here, we discuss recent findings in the field, newly defined roles for GR-RBPs and the actions of GR-RBPs on target RNA metabolism.
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Saito, Kota, Koh Yamashiro, Yuki Ichikawa, Patrik Erlmann, Kenji Kontani, Vivek Malhotra, and Toshiaki Katada. "cTAGE5 mediates collagen secretion through interaction with TANGO1 at endoplasmic reticulum exit sites." Molecular Biology of the Cell 22, no. 13 (July 2011): 2301–8. http://dx.doi.org/10.1091/mbc.e11-02-0143.
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Cutaneous T-cell lymphoma-–associated antigen 5 (cTAGE5), an originally identified tumor antigen, is overexpressed in various cancer cell lines. The cDNA encodes an integral membrane protein containing two coiled-coil motifs and a proline-rich domain. We show that cTAGE5 specifically localizes to the endoplasmic reticulum (ER) exit sites. In addition, cTAGE5 forms a complex with TANGO1 (MIA3), a previously characterized cargo receptor for collagen VII, by the interaction of their coiled-coil motifs. Of interest, cTAGE5, as well as TANGO1, is capable of interacting with the inner-layer coatomer of COPII Sec23/24 complex through their C-terminal proline-rich domains and required for collagen VII secretion. We propose that cTAGE5 acts as a coreceptor of TANGO1 for collagen VII export from the ER.
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Yang, Yan-Lin, Fang Hu, Meng Xue, Yi-Jie Jia, Zong-Ji Zheng, Yang Li, and Yao-Ming Xue. "Early growth response protein-1 upregulates long noncoding RNA Arid2-IR to promote extracellular matrix production in diabetic kidney disease." American Journal of Physiology-Cell Physiology 316, no. 3 (March 1, 2019): C340—C352. http://dx.doi.org/10.1152/ajpcell.00167.2018.
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Diabetic kidney disease (DKD) has surpassed chronic glomerulonephritis as the leading cause of end-stage renal disease. Previously, we showed that early growth response protein-1 (Egr1) plays a key role in DKD by enhancing mesangial cell proliferation and extracellular matrix (ECM) production. The long noncoding RNA (lncRNA) AT-rich interactive domain 2-IR (Arid2-IR) has been identified as a mothers against decapentaplegic homolog 3 (Smad3)-associated lncRNA in unilateral ureteral obstructive kidney disease. However, the effect of Egr1 on Arid2-IR in the development of DKD is still unknown. In this study, we found that Arid2-IR was increased in mice with high-fat diet and streptozotocin-induced type 2 diabetes and in mouse mesangial cells cultured with high glucose to mimic diabetes. Knockdown of Arid2-IR in mouse mesangial cells reduced the high expression levels of collagen-α1(I) (Col1a1) and α-smooth muscle actin (α-SMA) induced by high glucose. Furthermore, Arid2-IR expression changed the increased expression of Col1a1 and α-SMA caused by overexpression of Egr1. Overall, these data suggest that increased Arid2-IR likely contributes to ECM production in DKD and that Egr1 promotes ECM production in DKD partly by upregulating Arid2-IR. Thus, Arid2-IR may be a new target in the treatment of DKD.
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Lai, Maria, Jack Lee, Xinxin Li, Chloe Kwok, Marc Chong, and Benny Zee. "Lifestyle Changes Reduced Estimated White Matter Hyperintensities Based on Retinal Image Analysis." International Journal of Environmental Research and Public Health 20, no. 4 (February 16, 2023): 3530. http://dx.doi.org/10.3390/ijerph20043530.
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This study evaluates if there is an association between lifestyle changes and the risk of small vessel disease (SVD) as measured by cerebral white matter hyperintensities (WMH) estimated by the automatic retinal image analysis (ARIA) method. We recruited 274 individuals into a community cohort study. Subjects were assessed at baseline and annually with the Health-Promoting Lifestyle Profile II Questionnaire (HPLP-II) and underwent a simple physical assessment. Retinal images were taken using a non-mydriatic digital fundus camera to evaluate the level of WMH estimated by ARIA (ARIA-WMH) to measure the risk of small vessel disease. We calculated the changes from baseline to one year for the six domains of HPLP-II and analysed the relationship with the ARIA-WMH change. A total of 193 (70%) participants completed both the HPLP-II and ARIA-WMH assessments. The mean age was 59.1 ± 9.4 years, and 76.2% (147) were women. HPLP-II was moderate (Baseline, 138.96 ± 20.93; One-year, 141.97 ± 21.85). We observed a significant difference in ARIA-WMH change between diabetes and non-diabetes subjects (0.03 vs. −0.008, respectively, p = 0.03). A multivariate analysis model showed a significant interaction between the health responsibility (HR) domain and diabetes (p = 0.005). For non-diabetes subgroups, those with improvement in the HR domain had significantly decreased in ARIA-WMH than those without HR improvement (−0.04 vs. 0.02, respectively, p = 0.003). The physical activity domain was negatively related to the change in ARIA-WMH (p = 0.02). In conclusion, this study confirms that there is a significant association between lifestyle changes and ARIA-WMH. Furthermore, increasing health responsibility for non-diabetes subjects reduces the risk of having severe white matter hyperintensities.
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Luo, Shuo, Yu Chen, Kwok-On Lai, Juan Carlos Arévalo, Stanley C. Froehner, Marvin E. Adams, Moses V. Chao, and Nancy Y. Ip. "α-Syntrophin regulates ARMS localization at the neuromuscular junction and enhances EphA4 signaling in an ARMS-dependent manner." Journal of Cell Biology 169, no. 5 (June 6, 2005): 813–24. http://dx.doi.org/10.1083/jcb.200412008.
Full textAbstract:
EphA4 signaling has recently been implicated in the regulation of synapse formation and plasticity. In this study, we show that ankyrin repeat-rich membrane spanning (ARMS; also known as a kinase D–interacting substrate of 220 kD), a substrate for ephrin and neurotrophin receptors, was expressed in developing muscle and was concentrated at the neuromuscular junction (NMJ). Using yeast two-hybrid screening, we identified a PDZ (PSD-95, Dlg, ZO-1) domain protein, α-syntrophin, as an ARMS-interacting protein in muscle. Overexpression of α-syntrophin induced ARMS clustering in a PDZ domain–dependent manner. Coexpression of ARMS enhanced EphA4 signaling, which was further augmented by the presence of α-syntrophin. Moreover, the ephrin-A1–induced tyrosine phosphorylation of EphA4 was reduced in C2C12 myotubes after the blockade of ARMS and α-syntrophin expression by RNA interference. Finally, α-syntrophin–null mice exhibited a disrupted localization of ARMS and EphA4 at the NMJ and a reduced expression of ARMS in muscle. Altogether, our findings suggest that ARMS may play an important role in regulating postsynaptic signal transduction through the syntrophin-mediated localization of receptor tyrosine kinases such as EphA4.
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Kalthoff, Christoph, Stephanie Groos, Rüdiger Kohl, Stefan Mahrhold, and Ernst J. Ungewickell. "Clint: A Novel Clathrin-binding ENTH-Domain Protein at the Golgi." Molecular Biology of the Cell 13, no. 11 (November 2002): 4060–73. http://dx.doi.org/10.1091/mbc.e02-03-0171.
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We have characterized a novel clathrin-binding 68-kDa epsin N-terminal homology domain (ENTH-domain) protein that we name clathrin interacting protein localized in the trans-Golgi region (Clint). It localizes predominantly to the Golgi region of epithelial cells as well as to more peripheral vesicular structures. Clint colocalizes with AP-1 and clathrin only in the perinuclear area. Recombinantly expressed Clint interacts directly with the γ-appendage domain of AP-1, with the clathrin N-terminal domain through the peptide motif 423LFDLM, with the γ-adaptin ear homology domain of Golgi-localizing, γ-adaptin ear homology domain 2, with the appendage domain of β2-adaptin and to a lesser extent with the appendage domain of α-adaptin. Moreover, the Clint ENTH-domain asssociates with phosphoinositide-containing liposomes. A significant amount of Clint copurifies with rat liver clathrin-coated vesicles. In rat kidney it is preferentially expressed in the apical region of epithelial cells that line the collecting duct. Clathrin and Clint also colocalize in the apical region of enterocytes along the villi of the small intestine. Apart from the ENTH-domain Clint has no similarities with the epsins AP180/CALM or Hip1/1R. A notable feature of Clint is a carboxyl-terminal methionine-rich domain (Met427-Met605), which contains >17% methionine. Our results suggest that Clint might participate in the formation of clathrin-coated vesicles at the level of thetrans-Golgi network and remains associated with the vesicles longer than clathrin and adaptors.
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Ren, Xiu-Rong, Quan-Sheng Du, Yang-Zhong Huang, Shi-Zhou Ao, Lin Mei, and Wen-Cheng Xiong. "Regulation of Cdc42 Gtpase by Proline-Rich Tyrosine Kinase 2 Interacting with Psgap, a Novel Pleckstrin Homology and Src Homology 3 Domain Containing Rhogap Protein." Journal of Cell Biology 152, no. 5 (March 5, 2001): 971–84. http://dx.doi.org/10.1083/jcb.152.5.971.
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Proline-rich tyrosine kinase 2 (PYK2), a tyrosine kinase structurally related to focal adhesion kinase (FAK), is implicated in regulating cytoskeletal organization. However, mechanisms by which PYK2 participates in and regulates cytoskeletal organization remain largely unknown. Here we report identification of PSGAP, a novel protein that interacts with PYK2 and FAK and contains multiple domains including a pleckstrin homology domain, a rhoGTPase-activating protein domain, and a Src homology 3 domain. PYK2 interacts with PSGAP Src homology 3 domain via the carboxyl-terminal proline-rich sequence. PSGAP is able to increase GTPase activity of CDC42 and RhoA in vitro and in vivo. Remarkably, PYK2, but not FAK, can activate CDC42 via inhibition of PSGAP-mediated GTP hydrolysis of CDC42. Moreover, PSGAP is localized at cell periphery in fibroblasts in a pleckstrin homology domain–dependent manner. Over expression of PSGAP in fibroblasts results in reorganization of cytoskeletal structures and changes of cellular morphology, which requires rhoGTPase-activating activity. Taken together, our results suggest that PSGAP is a signaling protein essential for PYK2 regulation of cytoskeletal organization via Rho family GTPases.
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Shepard, Jeremiah, Martin Reick, Sara Olson, and Brenton R. Graveley. "Characterization of U2AF6, a Splicing Factor Related to U2AF35." Molecular and Cellular Biology 22, no. 1 (January 1, 2002): 221–30. http://dx.doi.org/10.1128/mcb.22.1.221-230.2002.
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ABSTRACT The essential splicing factor U2AF (U2 auxiliary factor) is a heterodimer composed of 65-kDa (U2AF65) and 35-kDa (U2AF35) subunits. U2AF35 has multiple functions in pre-mRNA splicing. First, U2AF35 has been shown to function by directly interacting with the AG at the 3′ splice site. Second, U2AF35 is thought to play a role in the recruitment of U2AF65 by serine-arginine-rich (SR) proteins in enhancer-dependent splicing. It has been proposed that the physical interaction between the arginine-serine-rich (RS) domain of U2AF35 and SR proteins is important for this activity. However, other data suggest that this may not be the case. Here, we report the identification of a mammalian gene that encodes a 26-kDa protein bearing strong sequence similarity to U2AF35, designated U2AF26. The N-terminal 187 amino acids of U2AF35 and U2AF26 are nearly identical. However, the C-terminal domain of U2AF26 lacks many characteristics of the U2AF35 RS domain and, therefore, might be incapable of interacting with SR proteins. We show that U2AF26 can associate with U2AF65 and can functionally substitute for U2AF35 in both constitutive and enhancer-dependent splicing, demonstrating that the RS domain of the small U2AF subunit is not required for splicing enhancer function. Finally, we show that U2AF26 functions by enhancing the binding of U2AF65 to weak 3′ splice sites. These studies identify U2AF26 as a mammalian splicing factor and demonstrate that distinct U2AF complexes can participate in pre-mRNA splicing. Based on its sequence and functional similarity to U2AF35, U2AF26 may play a role in regulating alternative splicing.
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Doliana, Roberto, Simonetta Bot, Gabriella Mungiguerra, Anna Canton, Stefano Paron Cilli, and Alfonso Colombatti. "Isolation and Characterization of EMILIN-2, a New Component of the Growing EMILINs Family and a Member of the EMI Domain-containing Superfamily." Journal of Biological Chemistry 276, no. 15 (January 16, 2001): 12003–11. http://dx.doi.org/10.1074/jbc.m011591200.
Full textAbstract:
EMILIN (elastinmicrofibrilinterfaselocated Protein) is an elastic fiber-associated glycoprotein consisting of a self-interacting globular C1q domain at the C terminus, a short collagenous stalk, an extended region of potential coiled-coil structure, and an N-terminal cysteine-rich domain (EMI domain). Using the globular C1q domain as a bait in the yeast two-hybrid system, we have isolated a cDNA encoding a novel protein. Determination of the entire primary structure demonstrated that this EMILIN-binding polypeptide is highly homologous to EMILIN. The domain organization is superimposable, one important difference being a proline-rich (41%) segment of 56 residues between the potential coiled-coil region and the collagenous domain absent in EMILIN. The entire gene (localized on chromosome 18p11.3) was isolated from a BAC clone, and it is structurally almost identical to that of EMILIN (8 exons, 7 introns with identical phases at the exon/intron boundaries) but much larger (about 40versus8 kilobases) than that of EMILIN. Given these findings we propose to name the novel protein EMILIN-2 and the prototype member of this family EMILIN-1 (formerly EMILIN). The mRNA expression of EMILIN-2 is more restricted compared with that of EMILIN-1; highest levels are present in fetal heart and adult lung, whereas, differently from EMILIN-1, adult aorta, small intestine, and appendix show very low expression, and adult uterus and fetal kidney are negative. Finally, the EMILIN-2 protein is secreted extracellularly byin vitro-grown cells, and in accordance with the partial coexpression in fetal and adult tissues, the two proteins shown extensive but not absolute immunocolocalizationin vitro.
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DeJournett, Robert E., Ryuji Kobayashi, Shujuan Pan, Chuanfen Wu, Laurence D. Etkin, Richard B. Clark, Oliver Bögler, and Jian Kuang. "Phosphorylation of the proline-rich domain of Xp95 modulates Xp95 interaction with partner proteins." Biochemical Journal 401, no. 2 (December 21, 2006): 521–31. http://dx.doi.org/10.1042/bj20061287.
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The mammalian adaptor protein Alix [ALG-2 (apoptosis-linked-gene-2 product)-interacting protein X] belongs to a conserved family of proteins that have in common an N-terminal Bro1 domain and a C-terminal PRD (proline-rich domain), both of which mediate partner protein interactions. Following our previous finding that Xp95, the Xenopus orthologue of Alix, undergoes a phosphorylation-dependent gel mobility shift during progesteroneinduced oocyte meiotic maturation, we explored potential regulation of Xp95/Alix by protein phosphorylation in hormone-induced cell cycle re-entry or M-phase induction. By MALDI–TOF (matrix-assisted laser-desorption ionization–time-of-flight) MS analyses and gel mobility-shift assays, Xp95 is phosphorylated at multiple sites within the N-terminal half of the PRD during Xenopus oocyte maturation, and a similar region in Alix is phosphorylated in mitotically arrested but not serum-stimulated mammalian cells. By tandem MS, Thr745 within this region, which localizes in a conserved binding site to the adaptor protein SETA [SH3 (Src homology 3) domain-containing, expressed in tumorigenic astrocytes] CIN85 (α-cyano-4-hydroxycinnamate)/SH3KBP1 (SH3-domain kinase-binding protein 1), is one of the phosphorylation sites in Xp95. Results from GST (glutathione S-transferase)-pull down and peptide binding/competition assays further demonstrate that the Thr745 phosphorylation inhibits Xp95 interaction with the second SH3 domain of SETA. However, immunoprecipitates of Xp95 from extracts of M-phase-arrested mature oocytes contained additional partner proteins as compared with immunoprecipitates from extracts of G2-arrested immature oocytes. The deubiquitinase AMSH (associated molecule with the SH3 domain of signal transducing adaptor molecule) specifically interacts with phosphorylated Xp95 in M-phase cell lysates. These findings establish that Xp95/Alix is phosphorylated within the PRD during M-phase induction, and indicate that the phosphorylation may both positively and negatively modulate their interaction with partner proteins.
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He, Fan, Wade Borcherds, Tanjing Song, Xi Wei, Mousumi Das, Lihong Chen, Gary W. Daughdrill, and Jiandong Chen. "Interaction between p53 N terminus and core domain regulates specific and nonspecific DNA binding." Proceedings of the National Academy of Sciences 116, no. 18 (April 15, 2019): 8859–68. http://dx.doi.org/10.1073/pnas.1903077116.
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The p53 tumor suppressor is a sequence-specific DNA binding protein that activates gene transcription to regulate cell survival and proliferation. Dynamic control of p53 degradation and DNA binding in response to stress signals are critical for tumor suppression. The p53 N terminus (NT) contains two transactivation domains (TAD1 and TAD2), a proline-rich region (PRR), and multiple phosphorylation sites. Previous work revealed the p53 NT reduced DNA binding in vitro. Here, we show that TAD2 and the PRR inhibit DNA binding by directly interacting with the sequence-specific DNA binding domain (DBD). NMR spectroscopy revealed that TAD2 and the PRR interact with the DBD at or near the DNA binding surface, possibly acting as a nucleic acid mimetic to competitively block DNA binding. In vitro and in vivo DNA binding analyses showed that the NT reduced p53 DNA binding affinity but improved the ability of p53 to distinguish between specific and nonspecific sequences. MDMX inhibits p53 binding to specific target promoters but stimulates binding to nonspecific chromatin sites. The results suggest that the p53 NT regulates the affinity and specificity of DNA binding by the DBD. The p53 NT-interacting proteins and posttranslational modifications may regulate DNA binding, partly by modulating the NT–DBD interaction.
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Nerusheva, Olga O., and Bungo Akiyoshi. "Divergent polo box domains underpin the unique kinetoplastid kinetochore." Open Biology 6, no. 3 (March 2016): 150206. http://dx.doi.org/10.1098/rsob.150206.
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Kinetochores are macromolecular machines that drive eukaryotic chromosome segregation by interacting with centromeric DNA and spindle microtubules. While most eukaryotes possess conventional kinetochore proteins, evolutionarily distant kinetoplastid species have unconventional kinetochore proteins, composed of at least 19 proteins (KKT1–19). Polo-like kinase (PLK) is not a structural kinetochore component in either system. Here, we report the identification of an additional kinetochore protein, KKT20, in Trypanosoma brucei . KKT20 has sequence similarity with KKT2 and KKT3 in the Cys-rich region, and all three proteins have weak but significant similarity to the polo box domain (PBD) of PLK. These divergent PBDs of KKT2 and KKT20 are sufficient for kinetochore localization in vivo . We propose that the ancestral PLK acquired a Cys-rich region and then underwent gene duplication events to give rise to three structural kinetochore proteins in kinetoplastids.
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Komla-Soukha, Isabelle, and Camille Sureau. "A Tryptophan-Rich Motif in the Carboxyl Terminus of the Small Envelope Protein of Hepatitis B Virus Is Central to the Assembly of Hepatitis Delta Virus Particles." Journal of Virology 80, no. 10 (May 15, 2006): 4648–55. http://dx.doi.org/10.1128/jvi.80.10.4648-4655.2006.
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ABSTRACT The small hepatitis B virus surface antigen (S-HBsAg) is capable of driving the assembly and secretion of hepatitis delta virus (HDV) particles by interacting with the HDV ribonucleoprotein (RNP). Previously, a specific domain of the S-HBsAg protein carboxyl terminus, including a tryptophan residue at position 196 (W196), was proven essential for HDV maturation (S. Jenna and C. Sureau, J. Virol. 73: 3351-3358, 1999). Mutation of W196 to phenylalanine (W196F) was permissive for HBV subviral particle (SVP) secretion but deleterious to HDV virion assembly. Here, the W196F S-HBsAg deficiency was assigned to a loss of its ability for interaction with the large HDV antigen (L-HDAg), a major component of the RNP. Because the overall S-HBsAg carboxyl terminus is particularly rich in tryptophan, an amino acid frequently involved in protein-protein interactions, site-directed mutagenesis was conducted to investigate the function of the S-HBsAg Trp-rich domain in HDV assembly. Single substitutions of tryptophan between positions 163 and 201 with alanine or phenylalanine were tolerated for SVP secretion, but those affecting W196, W199, and W201 were detrimental for HDV assembly. This was proven to result from a reduced capacity of the mutants for interaction with L-HDAg. In addition, a W196S S-HBsAg mutant, which has been described in HBV strains that arose in a few cases of lamivudine-treated HBV-infected patients, was deficient for HDV assembly as a consequence of its impaired capacity for interacting with L-HDAg. Interestingly, the fact that even the most conservative substitution of phenylalanine for tryptophan at positions 196, 199, or 201 was sufficient to ablate interaction of S-HBsAg with L-HDAg suggests that W196, W199, and W201 are located at a binding interface that is central to HDV maturation.
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Gao, Weiqiang, Patricia J. Anderson, Elaine M. Majerus, Elodee A. Tuley, and J. Evan Sadler. "The C-Terminal α-Helix of von Willebrand Factor Domain A2 Interacts with ADAMTS13 C-Terminal Domains To Regulate Substrate Cleavage." Blood 106, no. 11 (November 16, 2005): 410. http://dx.doi.org/10.1182/blood.v106.11.410.410.
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Abstract ADAMTS13 is a member of the A Disintergrin And Metalloprotease with ThromboSpondin type I repeat family, and it cleaves the Tyr1605-Met1606 bond in the von Willebrand factor (VWF) central A2 domain, thereby decreasing platelet adhesion mediated by VWF. Recently a minimal substrate for ADAMTS13 was characterized that consists of GST linked to Asp1596-Arg1668 with a C-terminal 6×His tag (VWF73). Further removal of 9 amino acids that comprise a predicted C-terminal α-helix (VWF64) appeared to eliminate cleavage by plasma ADAMTS13, suggesting a critical role for this helix in substrate recognition. We obtained similar results, but VWF64 was cleaved significantly at long reaction times. For example, plasma ADAMTS13 (0.3 nM, one-tenth of normal plasma) cleaved 50% of 65 nM VWF73 in 2 hours and 50% of 62 nM VWF64 in 24 hours. Similar results were obtained in either 50 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl2, 0.1 μM ZnCl2, or 5 mM Tris-HCl, pH 8.0, 10 mM BaCl2. By amino acid sequencing, ADAMTS13 was shown to cleave the Tyr1605-Met1606 bond of VWF64. Truncation of ADAMTS13 after certain structural domains had different effects on substrate cleavage. Using 3 nM enzyme for 30 min, VWF73 was cleaved ~2-fold faster by ADAMTS13 truncated after the spacer domain (MDTCS) than by ADAMTS13 truncated after the cysteine-rich domain (MDTC). Conversely, VWF64 was cleaved ~3-fold faster by MDTC than by MDTCS. Also, in 30 min MDTCS cleaved 70% of VWF73 and <10% of VWF64, whereas MDTC cleaved 40% of VWF73 and 30% of VWF64. ADAMTS13 truncated after the first TSP1 repeat (MDT) or the disintegrin domain (MD) had markedly reduced activity, but with prolonged incubation (24 h) at increased concentration (30 nM) both enzymes cleaved most of VWF64 and VWF73 at the expected site. No aberrant cleavage products were detected by Western blotting. The metalloproteinase domain alone (M) was inactive. The selective effects of deleting the cysteine-rich or spacer domain suggest that the C-terminal α-helix of the VWF A2 domain is not essential but facilitates substrate recognition by interacting with specific C-terminal domains of ADAMTS13, particularly the cysteine-rich and spacer domains.
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Hu, Miaoqing, Luqin Li, Jianbing Chao, Yaqin Zhao, Zhiyun Zhang, and Aihua Liang. "The acidic ribosomal protein P2 from Euplotes octocarinatus is phosphorylated at its N-terminal domain." Biochemistry and Cell Biology 92, no. 1 (February 2014): 23–32. http://dx.doi.org/10.1139/bcb-2013-0063.
Full textAbstract:
The eukaryotic acid ribosomal P0, P1, and P2 proteins share a conserved flexible C-terminal tail that is rich in acidic residues, which are involved in the interaction with elongation factor 2 during protein synthesis. Our previous work suggested that the acidic ribosomal P proteins from Euplotes octocarinatus have a special C-terminal domain. To further understand this characteristic feature, both P2 and elongation factor 2 from E. octocarinatus were overexpressed, for the first time, in Escherichia coli in this study. GST pull-down assay indicated that P2 protein from E. octocarinatus (EoP2) interacted specifically with the N-terminal domain of elongation factor 2 from E. octocarinatus (EoEF-2) in vitro. The interacting part of EoP2 is in the C-terminal domains, consistent with the observation in other organisms. Phosphorylation of the recombinant EoP2 was performed in vitro using multiple methods such as 31P-NMR spectroscopy, native PAGE, and Phos-tagTM SDS-PAGE. Results showed that ribosomal protein EoP2 was phosphorylated by casein kinase II at serine 21 located at the N terminus. This phosphorylation site identified in EoP2 is quite different from that of P2 from other organisms, in which the phosphorylation site is located in the conserved C-terminal region.
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Wang, Qiang, Yi Xie, Quan-Sheng Du, Xiao-Jun Wu, Xu Feng, Lin Mei, Jay M. McDonald, and Wen-Cheng Xiong. "Regulation of the formation of osteoclastic actin rings by proline-rich tyrosine kinase 2 interacting with gelsolin." Journal of Cell Biology 160, no. 4 (February 10, 2003): 565–75. http://dx.doi.org/10.1083/jcb.200207036.
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Osteoclast activation is important for bone remodeling and is altered in multiple bone disorders. This process requires cell adhesion and extensive actin cytoskeletal reorganization. Proline-rich tyrosine kinase 2 (PYK2), a major cell adhesion–activated tyrosine kinase in osteoclasts, plays an important role in regulating this event. The mechanisms by which PYK2 regulates actin cytoskeletal organization and osteoclastic activation remain largely unknown. In this paper, we provide evidence that PYK2 directly interacts with gelsolin, an actin binding, severing, and capping protein essential for osteoclastic actin cytoskeletal organization. The interaction is mediated via the focal adhesion–targeting domain of PYK2 and an LD motif in gelsolin's COOH terminus. PYK2 phosphorylates gelsolin at tyrosine residues and regulates gelsolin bioactivity, including decreasing gelsolin binding to actin monomer and increasing gelsolin binding to phosphatidylinositol lipids. In addition, PYK2 increases actin polymerization at the fibroblastic cell periphery. Finally, PYK2 interacts with gelsolin in osteoclasts, where PYK2 activation is required for the formation of actin rings. Together, our results suggest that PYK2 is a regulator of gelsolin, revealing a novel PYK2–gelsolin pathway in regulating actin cytoskeletal organization in multiple cells, including osteoclasts.
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Li, Yang, Wei Xi, Jianfeng Hao, Li Zhang, Xingpeng Wen, Zhiguo Wu, and Yuxian Zhu. "A Novel Tandem Zinc Finger Protein in Gossypium hirsutum, GhTZF2, Interacts with GhMORF8 to Regulate Cotton Fiber Cell Development." Agronomy 13, no. 2 (February 11, 2023): 519. http://dx.doi.org/10.3390/agronomy13020519.
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Arginine-rich Tandem Zinc Finger (RR-TZF) proteins make up a plant-specific superfamily that participates in plant development, while their roles in cotton fiber development remain to be explored. In this study, we identified an RR-TZF protein-coding gene, GhTZF2, containing two CCCH domains (C-X7-C-X5-C-X3-H-X16-C-X5-C-X4-C-X3-H) and one RR domain at the N-terminus of the two CCCH domains, by comparing the differences of chromatin H3K4me3 modifications between wild-type upland cotton (WT) and the fuzzless-lintless mutant (fl) ovules. GhTZF2 was highly expressed in ovule cells near anthesis, and multiple experiments revealed that GhTZF2 could interact directly with GhMORF8. Homozygotic GhTZF2-knockout cotton lines produced significantly shorter fibers with thinner cell walls. Additionally, comparative transcriptome analysis confirmed that many differentially expressed transcripts contain adenine- and uridine-rich (AU-rich) elements (AREs) in their 3’ untranslated regions (UTR). Together, this study indicated that GhTZF2 may regulate cotton fiber cell development through interacting with GhMORF8, or may be involved in mRNA turnover.
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Schmid, Susanne I., and Patrick Hearing. "Cellular Components Interact with Adenovirus Type 5 Minimal DNA Packaging Domains." Journal of Virology 72, no. 8 (August 1, 1998): 6339–47. http://dx.doi.org/10.1128/jvi.72.8.6339-6347.1998.
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ABSTRACT Adenovirus type 5 DNA packaging is initiated from the left end of the viral genome and depends on the presence of acis-acting packaging domain located between nucleotides 194 and 380. Multiple redundant packaging elements (termed A repeats I through VII [AI through AVII]) are contained within this domain and display differential abilities to support DNA packaging in vivo. The functionally most important repeats, AI, AII, AV, and AVI, follow a bipartite consensus motif exhibiting AT-rich and CG-rich core sequences. Results from previous mutational analyses defined a fragment containing AV, AVI, and AVII as a minimal packaging domain in vivo, which supports a functional independence of the respectivecis-acting sequences. Here we describe multimeric versions of individual packaging elements as minimal packaging domains that can confer viability and packaging activity to viruses carrying gross truncations within their left end. These mutant viruses directly rate the functional role that different packaging elements play relative to each other. The A repeats are likely to be binding sites for limiting,trans-acting packaging factors of cellular and/or viral origin. We report here the characterization of two cellular binding activities interacting with all of the minimal packaging domains in vitro, an unknown binding activity termed P-complex, and the transcription factor chicken ovalbumin upstream promoter transcription factor. The binding of both activities is dependent on the integrity of the AT-rich, but not the CG-rich, consensus half site. In the case of P-complex, binding affinity for different minimal packaging domains in vitro correlates well with their abilities to support DNA packaging in vivo. Interestingly, P-complex interacts not only with packaging elements but also with the left terminus of the viral genome, the core origin of replication. Our data implicate cellular factors as components of the viral packaging machinery. The dual binding specificity of P-complex for packaging and replication sequences may further suggest a direct involvement of left-end replication sequences in viral DNA encapsidation.
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Shi, Xiaoli, Sandrine Opi, Adrien Lugari, Audrey Restouin, Thibault Coursindel, Isabelle Parrot, Javier Perez, et al. "Identification and biophysical assessment of the molecular recognition mechanisms between the human haemopoietic cell kinase Src homology domain 3 and ALG-2-interacting protein X." Biochemical Journal 431, no. 1 (September 14, 2010): 93–102. http://dx.doi.org/10.1042/bj20100314.
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SFKs (Src family kinases) are central regulators of many signalling pathways. Their functions are tightly regulated through SH (Src homology) domain-mediated protein–protein interactions. A yeast two-hybrid screen using SH3 domains as bait identified Alix [ALG-2 (apoptosis-linked gene 2)-interacting protein X] as a novel Hck (haemopoietic cell kinase) SH3 domain interactor. The Alix–Hck-SH3 interaction was confirmed in vitro by a GST (glutathione transferase) pull-down assay and in intact cells by a mammalian two-hybrid assay. Furthermore, the interaction was demonstrated to be biologically relevant in cells. Through biophysical experiments, we then identified the PRR (proline-rich region) motif of Alix that binds Hck-SH3 and determined a dissociation constant of 34.5 μM. Heteronuclear NMR spectroscopy experiments were used to map the Hck-SH3 residues that interact with an ALIX construct containing the V and PRR domains or with the minimum identified interacting motif. Finally, SAXS (small-angle X-ray scattering) analysis showed that the N-terminal PRR of Alix is unfolded, at least before Hck-SH3 recognition. These results indicate that residues outside the canonical PxxP motif of Alix enhance its affinity and selectivity towards Hck-SH3. The structural framework of the Hck–Alix interaction will help to clarify how Hck and Alix assist during virus budding and cell-surface receptor regulation.
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Li, Youjun, Kenneth Rogulski, Quansheng Zhou, Peter J. Sims, and Edward V. Prochownik. "The Negative c-Myc Target Onzin Affects Proliferation and Apoptosis via Its Obligate Interaction with Phospholipid Scramblase I." Molecular and Cellular Biology 26, no. 9 (May 1, 2006): 3401–13. http://dx.doi.org/10.1128/mcb.26.9.3401-3413.2006.
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ABSTRACT Onzin, the product of a negatively c-Myc-regulated target gene, is highly expressed in myeloid cells. As a result of its interaction with and activation of Akt1 and Mdm2, onzin down-regulates p53. The apoptotic sensitivity of several cell lines is thus directly related to onzin levels. We have conducted a search for additional onzin-interacting proteins and identified phospholipid scramblase 1 (PLSCR1), an endofacial membrane protein, which is proposed to mediate the bidirectional movement of plasma membrane phospholipids during proliferation and apoptosis. PLSCR1 interacts with the same cysteine-rich domain of onzin as do Akt1 and Mdm2, whereas the onzin-interacting domain of PLSCR1 centers around, but does not require, a previously identified palmitoylation signal. Depletion of endogenous PLSCR1 in myeloid cells leads to a phenotype that mimics that of onzin overexpression, providing evidence that PLSCR1 is a physiologic regulator of onzin. In contrast, PLSCR1 overexpression in fibroblasts, which normally do not express onzin, affects neither growth nor apoptosis unless onzin is coexpressed, in which case PLSCR1 completely abrogates onzin's positive effects on proliferation and survival. These findings demonstrate a functional interdependence between onzin and PLSCR1. They further suggest a contiguous link between the earliest events mediated by c-Myc and the latest ones, which culminate at the cell surface and lead to phospholipid reshuffling and cell death.
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Nile, Arti, Jisoo Shin, Juhyun Shin, Gyun Seok Park, Suhyun Lee, Ji-Ho Lee, Kyung-Woo Lee, et al. "Cinnamaldehyde-Rich Cinnamon Extract Induces Cell Death in Colon Cancer Cell Lines HCT 116 and HT-29." International Journal of Molecular Sciences 24, no. 9 (May 3, 2023): 8191. http://dx.doi.org/10.3390/ijms24098191.
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Cinnamon is a natural spice with a wide range of pharmacological functions, including anti-microbial, antioxidant, and anti-tumor activities. The aim of this study is to investigate the effects of cinnamaldehyde-rich cinnamon extract (CRCE) on the colorectal cancer cell lines HCT 116 and HT-29. The gas chromatography mass spectrometry analysis of a lipophilic extract of cinnamon revealed the dominance of trans-cinnamaldehyde. Cells treated with CRCE (10–60 µg/mL) showed significantly decreased cell viability in a time- and dose-dependent manner. We also observed that cell proliferation and migration capacity were inhibited in CRCE-treated cells. In addition, a remarkable increase in the number of sub-G1-phase cells was observed with arrest at the G2 phase by CRCE treatment. CRCE also induced mitochondrial stress, and finally, CRCE treatment resulted in activation of apoptotic proteins Caspase-3, -9, and PARP and decreased levels of mu-2-related death-inducing gene protein expression with BH3-interacting domain death agonist (BID) activation.
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Hoque, Mainul, Tara M. Young, Chee-Gun Lee, Ginette Serrero, Michael B. Mathews, and Tsafi Pe'ery. "The Growth Factor Granulin Interacts with Cyclin T1 and Modulates P-TEFb-Dependent Transcription." Molecular and Cellular Biology 23, no. 5 (March 1, 2003): 1688–702. http://dx.doi.org/10.1128/mcb.23.5.1688-1702.2003.
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ABSTRACT Cyclin T1, together with the kinase CDK9, is a component of the transcription elongation factor P-TEFb which binds the human immunodeficiency virus type 1 (HIV-1) transactivator Tat. P-TEFb facilitates transcription by phosphorylating the carboxy-terminal domain (CTD) of RNA polymerase II. Cyclin T1 is an exceptionally large cyclin and is therefore a candidate for interactions with regulatory proteins. We identified granulin as a cyclin T1-interacting protein that represses expression from the HIV-1 promoter in transfected cells. The granulins, mitogenic growth factors containing repeats of a cysteine-rich motif, were reported previously to interact with Tat. We show that granulin formed stable complexes in vivo and in vitro with cyclin T1 and Tat. Granulin bound to the histidine-rich domain of cyclin T1, which was recently found to bind to the CTD, but not to cyclin T2. Binding of granulin to P-TEFb inhibited the phosphorylation of a CTD peptide. Granulin expression inhibited Tat transactivation, and tethering experiments showed that this effect was due, at least in part, to a direct action on cyclin T1 in the absence of Tat. In addition, granulin was a substrate for CDK9 but not for the other transcription-related kinases CDK7 and CDK8. Thus, granulin is a cellular protein that interacts with cyclin T1 to inhibit transcription.
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Bou Zeidan, Marc, Lourdes Carmona, Severino Zara, and Jose F. Marcos. "FLO11Gene Is Involved in the Interaction of Flor Strains of Saccharomyces cerevisiae with a Biofilm-Promoting Synthetic Hexapeptide." Applied and Environmental Microbiology 79, no. 19 (July 26, 2013): 6023–32. http://dx.doi.org/10.1128/aem.01647-13.
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ABSTRACTSaccharomyces cerevisiae“flor” yeasts have the ability to form a buoyant biofilm at the air-liquid interface of wine. The formation of biofilm, also called velum, depends onFLO11gene length and expression.FLO11encodes a cell wall mucin-like glycoprotein with a highly O-glycosylated central domain and an N-terminal domain that mediates homotypic adhesion between cells. In the present study, we tested previously known antimicrobial peptides with different mechanisms of antimicrobial action for their effect on the viability and ability to form biofilm ofS. cerevisiaeflor strains. We found that PAF26, a synthetic tryptophan-rich cationic hexapeptide that belongs to the class of antimicrobial peptides with cell-penetrating properties, but not other antimicrobial peptides, enhanced biofilm formation without affecting cell viability in ethanol-rich medium. The PAF26 biofilm enhancement required a functionalFLO11but was not accompanied by increasedFLO11expression. Moreover, fluorescence microscopy and flow cytometry analyses showed that the PAF26 peptide binds flor yeast cells and that aflo11gene knockout mutant lost the ability to bind PAF26 but not P113, a different cell-penetrating antifungal peptide, demonstrating that theFLO11gene is selectively involved in the interaction of PAF26 with cells. Taken together, our data suggest that the cationic and hydrophobic PAF26 hexapeptide interacts with the hydrophobic and negatively charged cell wall, favoring Flo11p-mediated cell-to-cell adhesion and thus increasing biofilm biomass formation. The results are consistent with previous data that point to glycosylated mucin-like proteins at the fungal cell wall as potential interacting partners for antifungal peptides.
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Weighardt, F., F. Cobianchi, L. Cartegni, I. Chiodi, A. Villa, S. Riva, and G. Biamonti. "A novel hnRNP protein (HAP/SAF-B) enters a subset of hnRNP complexes and relocates in nuclear granules in response to heat shock." Journal of Cell Science 112, no. 10 (May 15, 1999): 1465–76. http://dx.doi.org/10.1242/jcs.112.10.1465.
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A two-hybrid screening in yeast for proteins interacting with the human hnRNP A1, yielded a nuclear protein of 917 amino acids that we termed hnRNP A1 associated protein (HAP). HAP contains an RNA binding domain (RBD) flanked by a negatively charged domain and by an S/K-R/E-rich region. In in vitro pull-down assays, HAP interacts with hnRNP A1, through its S/K-R/E-rich region, and with several other hnRNPs. HAP was found to be identical to the previously described Scaffold Attachment Factor B (SAF-B) and to HET, a transcriptional regulator of the Heat Shock Protein 27 gene. We show that HAP is a bona fide hnRNP protein, since anti-HAP antibodies immunoprecipitate from HeLa cell nucleoplasm the complete set of hnRNP proteins. Unlike most hnRNP proteins, the subnuclear distribution of HAP is profoundly modified in heat-shocked HeLa cells. Heat-shock treatment at 42 degrees C causes a transcription-dependent recruitment of HAP to a few large nuclear granules that exactly coincide with sites of accumulation of Heat Shock Factor 1 (HSF1). The recruitment of HAP to the granules is temporally delayed with respect to HSF1 and persists for a longer time during recovery at 37 degrees C. The hnRNP complexes immunoprecipitated from nucleoplasm of heat-shocked cells with anti-HAP antibodies have an altered protein composition with respect to canonical complexes. Altogether our results suggest an involvement of HAP in the cellular response to heat shock, possibly at the RNA metabolism level.
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Lavillette, Dimitri, Marielle Maurice, Catherine Roche, Stephen J. Russell, Marc Sitbon, and François-Loïc Cosset. "A Proline-Rich Motif Downstream of the Receptor Binding Domain Modulates Conformation and Fusogenicity of Murine Retroviral Envelopes." Journal of Virology 72, no. 12 (December 1, 1998): 9955–65. http://dx.doi.org/10.1128/jvi.72.12.9955-9965.1998.
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ABSTRACT The entry of retroviruses into cells depends on receptor recognition by the viral envelope surface subunit SU followed by membrane fusion, which is thought to be mediated by a fusion peptide located at the amino terminus of the envelope transmembrane subunit TM. Several fusion determinants have been previously identified in murine leukemia virus (MLV) envelopes, but their functional interrelationships as well as the processes involved in fusion activation upon retroviral receptor recognition remain unelucidated. Despite both structural and functional similarities of their envelope glycoproteins, ecotropic and amphotropic MLVs display two different postbinding properties: (i) while amphotropic MLVs fuse the cells at neutral pH, penetration of ecotropic MLVs is relatively acid pH dependent and (ii) ecotropic envelopes are more efficient than amphotropic envelopes in inducing cell-to-cell fusion and syncytium formation. By exploiting the latter characteristic in the analysis of chimeras of ecotropic and amphotropic MLV envelopes, we show here that substitution of the ecotropic MLV proline-rich region (PRR), located in the SU between the amino-terminal receptor binding domain and the TM-interacting SU carboxy-terminal domains, is sufficient to revert the amphotropic low-fusogenic phenotype into a high-fusogenic one. Furthermore, we have identified potential β-turns in the PRR that control the stability of SU-TM associations as well as the thresholds required to trigger either cell-to-cell or virus-to-cell fusion. These data, demonstrating that the PRR functions as a signal which induces envelope conformational changes leading to fusion, have enabled us to derive envelopes which can infect cells harboring low levels of available amphotropic receptors.
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Zhou, Xi, Jiali Si, Joe Corvera, Gary E. Gallick, and Jian Kuang. "Decoding the intrinsic mechanism that prohibits ALIX interaction with ESCRT and viral proteins." Biochemical Journal 432, no. 3 (November 25, 2010): 525–38. http://dx.doi.org/10.1042/bj20100862.
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The adaptor protein ALIX [ALG-2 (apoptosis-linked-gene-2 product)-interacting protein X] links retroviruses to ESCRT (endosomal sorting complex required for transport) machinery during retroviral budding. This function of ALIX requires its interaction with the ESCRT-III component CHMP4 (charged multivesicular body protein 4) at the N-terminal Bro1 domain and retroviral Gag proteins at the middle V domain. Since cytoplasmic or recombinant ALIX is unable to interact with CHMP4 or retroviral Gag proteins under non-denaturing conditions, we constructed ALIX truncations and mutations to define the intrinsic mechanism through which ALIX interactions with these partner proteins are prohibited. Our results demonstrate that an intramolecular interaction between Patch 2 in the Bro1 domain and the TSG101 (tumour susceptibility gene 101 protein)-docking site in the proline-rich domain locks ALIX into a closed conformation that renders ALIX unable to interact with CHMP4 and retroviral Gag proteins. Relieving the intramolecular interaction of ALIX, by ectopically expressing a binding partner for one of the intramolecular interaction sites or by deleting one of these sites, promotes ALIX interaction with these partner proteins and facilitates ALIX association with the membrane. Ectopic expression of a GFP (green fluorescent protein)–ALIX mutant with a constitutively open conformation, but not the wild-type protein, increases EIAV (equine infectious anaemia virus) budding from HEK (human embryonic kidney)-293 cells. These findings predict that relieving the autoinhibitory intramolecular interaction of ALIX is a critical step for ALIX to participate in retroviral budding.
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Haikonen, Tuuli, Minna-Liisa Rajamäki, and Jari P. T. Valkonen. "Interaction of the Microtubule-Associated Host Protein HIP2 with Viral Helper Component Proteinase Is Important in Infection with Potato virus A." Molecular Plant-Microbe Interactions® 26, no. 7 (July 2013): 734–44. http://dx.doi.org/10.1094/mpmi-01-13-0023-r.
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Microtubules (MT) outline and maintain the overall shape of cells and can reorganize cellular membranes to serve as sites of RNA virus replication. Here, we provide data on involvement of an MT-associated protein in infection of plants with a potyvirus, Potato virus A (PVA), representing the largest family of plant-infecting RNA viruses. Our results showed that helper-component proteinase (HCpro)-interacting protein 2 (HIP2) of potato (Solanum tuberosum) is an MT-associated protein similar to Arabidopsis SPR2. Virus-induced silencing of HIP2 in Nicotiana benthamiana resulted in a spiral-like growth phenotype, similar to the Arabidopsis spr2 mutant, and the spr2 phenotype in Arabidopsis was complemented with potato HIP2. HCpro of PVA interacted with HIP2 of potato and tobacco (Nicotiana tabacum). The interaction was detected by bimolecular fluorescence complementation in PVA-infected leaves on MT and MT intersections at the cell cortex. HIP2-HCpro interaction was determined by the C-proximal α-helix-rich domain of HIP2, whereas the N-proximal putative TOG domain and the central coiled-coil domain of HIP2 controlled HIP2 dimerization and binding to MT. Accumulation of PVA was significantly reduced in the HIP2-silenced leaves of N. benthamiana, which indicates that HIP2-HCpro interactions are important for virus infection.
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Melkumov, Georgy. "Recent results of strong interaction program from NA61/SHINE experiment at CERN SPS." EPJ Web of Conferences 204 (2019): 01010. http://dx.doi.org/10.1051/epjconf/201920401010.
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The NA61/SHINE experiment at the CERN SPS pursues a rich program of strong interactions. The main physics goals of this program are the study of properties of the onset of deconfinement and search for the signatures of the critical point of strongly interacting matter by performing the two-dimensional scan in a broad region of energy (beam momentum 13A-158A GeV/c) and system size (p+p, Be+Be, Ar+Sc and Xe+La). Recent NA61/SHINE results on particle spectra and event-by-event fluctuations in p+p, Be+Be and Ar+Sc collisions are shown with emphasis on the measurements of particle ratios, namely of pion a strangeness production, multiplicity fluctuations versus energy and the system size of colliding nuclei. It will be shown that the hadron production properties in heavy ion collisions which change rapidly in the low SPS energy domain and are interpreted as the beginning of quark-gluon plasma production – onset of deconfinement could be also the case in inelastic p+p interactions and probably in Be+Be collisions. The paper presents a selection of NA61/SHINE results on particle production properties discussed together with existing data from the NA49 collaboration. The evolution of non-monotonic structures in the pion and strangeness production as a function of the system size and energy is addressed. The rapid change of hadron production properties from p+p and Be+Be up to Ar+Sc and Pb+Pb collisions can be interpreted as the beginning of the large clusters formation of strongly interacting matter - the onset of fireball. The NA61/SHINE strong interaction programme is presented including the recent status on proton intermittency analysis and strongly intensive fluctuation observables of particle multiplicity and transverse momentum.
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Chakraborty, Animikha, Aswini Viswanath, Renuka Malipatil, Janani Semalaiyappan, Priya Shah, Swarna Ronanki, Abhishek Rathore, et al. "Identification of Candidate Genes Regulating Drought Tolerance in Pearl Millet." International Journal of Molecular Sciences 23, no. 13 (June 21, 2022): 6907. http://dx.doi.org/10.3390/ijms23136907.
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Pearl millet is an important crop of the arid and semi-arid ecologies to sustain food and fodder production. The greater tolerance to drought stress attracts us to examine its cellular and molecular mechanisms via functional genomics approaches to augment the grain yield. Here, we studied the drought response of 48 inbreds representing four different maturity groups at the flowering stage. A set of 74 drought-responsive genes were separated into five major phylogenic groups belonging to eight functional groups, namely ABA signaling, hormone signaling, ion and osmotic homeostasis, TF-mediated regulation, molecular adaptation, signal transduction, physiological adaptation, detoxification, which were comprehensively studied. Among the conserved motifs of the drought-responsive genes, the protein kinases and MYB domain proteins were the most conserved ones. Comparative in-silico analysis of the drought genes across millet crops showed foxtail millet had most orthologs with pearl millet. Of 698 haplotypes identified across millet crops, MyC2 and Myb4 had maximum haplotypes. The protein–protein interaction network identified ABI2, P5CS, CDPK, DREB, MYB, and CYP707A3 as major hub genes. The expression assay showed the presence of common as well as unique drought-responsive genes across maturity groups. Drought tolerant genotypes in respective maturity groups were identified from the expression pattern of genes. Among several gene families, ABA signaling, TFs, and signaling proteins were the prospective contributors to drought tolerance across maturity groups. The functionally validated genes could be used as promising candidates in backcross breeding, genomic selection, and gene-editing schemes in pearl millet and other millet crops to increase the yield in drought-prone arid and semi-arid ecologies.
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Li, He, Lawrence M. Schopfer, Patrick Masson, and Oksana Lockridge. "Lamellipodin proline rich peptides associated with native plasma butyrylcholinesterase tetramers." Biochemical Journal 411, no. 2 (March 27, 2008): 425–32. http://dx.doi.org/10.1042/bj20071551.
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BChE (butyrylcholinesterase) protects the cholinergic nervous system from organophosphorus nerve agents by scavenging these toxins. Recombinant human BChE produced from transgenic goat to treat nerve agent intoxication is currently under development. The therapeutic potential of BChE relies on its ability to stay in the circulation for a prolonged period, which in turn depends on maintaining tetrameric quaternary configuration. Native human plasma BChE consists of 98% tetramers and has a half-life (t½) of 11–14 days. BChE in the neuromuscular junctions and the central nervous system is anchored to membranes through interactions with ColQ (AChE-associated collagen tail protein) and PRiMA (proline-rich membrane anchor) proteins containing proline-rich domains. BChE prepared in cell culture is primarily monomeric, unless expressed in the presence of proline-rich peptides. We hypothesized that a poly-proline peptide is an intrinsic component of soluble plasma BChE tetramers, just as it is for membrane-bound BChE. We found that a series of proline-rich peptides was released from denatured human and horse plasma BChE. Eight peptides, with masses from 2072 to 2878 Da, were purified by HPLC and sequenced by electrospray ionization tandem MS and Edman degradation. All peptides derived from the same proline-rich core sequence PSPPLPPPPPPPPPPPPPPPPPPPPLP (mass 2663 Da) but varied in length at their N- and C-termini. The source of these peptides was identified through database searching as RAPH1 [Ras-associated and PH domains (pleckstrin homology domains)-containing protein 1; lamellipodin, gi:82581557]. A proline-rich peptide of 17 amino acids derived from lamellipodin drove the assembly of human BChE secreted from CHO (Chinese-hamster ovary) cells into tetramers. We propose that the proline-rich peptides organize the 4 subunits of BChE into a 340 kDa tetramer, by interacting with the C-terminal BChE tetramerization domain.