Association of theAgrobacteriumT-DNA–protein complex with plant nucleosomes

Agrobacteriumrepresents the only natural example of transkingdom transfer of genetic information, from bacteria to plants. Before the bacterial transferred DNA (T- DNA) can integrate into the plant genome, it should be targeted to and bind the host chromatin. However, the T-DNA association with the host chromatin has not been demonstrated. Here, we study T-DNA binding to plant nucleosomesin vitroand show that it is mediated by bacterial and host proteins associated with the T-DNA. The main factor that determines nucleosomal binding of the T-DNA is the cellular VirE2-interacting protein 1 (VIP1), which functions as a molecular link between the T-DNA-associated bacterial virulence protein VirE2 and core histones. The presence of both VIP1 and VirE2 is required for association of the T-DNA with mononucleosomes in which the DNA molecule exists as a tripartite complex DNA–VirE2–VIP1. Furthermore, this nucleosome-associated ternary complex can bind another bacterial virulence factor, VirF, which is an F-box protein known to target both VirE2 and VIP1 for proteasomal degradation and uncoat the T-DNA.

Download Full-text

Core Histones and HIRIP3, a Novel Histone-Binding Protein, Directly Interact with WD Repeat Protein HIRA

Molecular and Cellular Biology ◽

10.1128/mcb.18.9.5546 ◽

1998 ◽

Vol 18 (9) ◽

pp. 5546-5556 ◽

Cited By ~ 59

Author(s):

Stéphanie Lorain ◽

Jean-Pierre Quivy ◽

Frédérique Monier-Gavelle ◽

Christine Scamps ◽

Yann Lécluse ◽

...

Keyword(s):

Protein Interaction ◽

Developmental Disorders ◽

Core Histone ◽

Histone H4 ◽

Interacting Protein ◽

Amino Terminal ◽

Core Histones ◽

Α Helix ◽

Interaction Trap

ABSTRACT The human HIRA gene has been named after Hir1p and Hir2p, two corepressors which together appear to act on chromatin structure to control gene transcription in Saccharomyces cerevisiae. HIRA homologs are expressed in a regulated fashion during mouse and chicken embryogenesis, and the human gene is a major candidate for the DiGeorge syndrome and related developmental disorders caused by a reduction to single dose of a fragment of chromosome 22q. Western blot analysis and double-immunofluorescence experiments using a specific antiserum revealed a primary nuclear localization of HIRA. Similar to Hir1p, HIRA contains seven amino-terminal WD repeats and probably functions as part of a multiprotein complex. HIRA and core histone H2B were found to physically interact in a yeast double-hybrid protein interaction trap, in GST pull-down assays, and in coimmunoprecipitation experiments performed from cellular extracts. In vitro, HIRA also interacted with core histone H4. H2B- and H4-binding domains were overlapping but distinguishable in the carboxy-terminal region of HIRA, and the region for HIRA interaction was mapped to the amino-terminal tail of H2B and the second α helix of H4. HIRIP3 (HIRA-interacting protein 3) is a novel gene product that was identified from its HIRA-binding properties in the yeast protein interaction trap. In vitro, HIRIP3 directly interacted with HIRA but also with core histones H2B and H3, suggesting that a HIRA-HIRIP3-containing complex could function in some aspects of chromatin and histone metabolism. Insufficient production of HIRA, which we report elsewhere interacts with homeodomain-containing DNA-binding factors during mammalian embryogenesis, could perturb the stoichiometric assembly of multimolecular complexes required for normal embryonic development.

Download Full-text

Faculty Opinions recommendation of A bacterial virulence protein suppresses host innate immunity to cause plant disease.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1040109.489027 ◽

2006 ◽

Author(s):

Eric Lam

Keyword(s):

Innate Immunity ◽

Plant Disease ◽

Bacterial Virulence ◽

Virulence Protein ◽

Host Innate Immunity

Download Full-text

Faculty Opinions recommendation of Activation of a bacterial virulence protein by the GTPase RhoA.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1168123.630249 ◽

2009 ◽

Author(s):

Mitsuhiko Ikura ◽

Chris Marshall

Keyword(s):

Bacterial Virulence ◽

Virulence Protein

Download Full-text

Generation of High-Yield, Functional Oligodendrocytes from a c-myc Immortalized Neural Cell Line, Endowed with Staminal Properties

International Journal of Molecular Sciences ◽

10.3390/ijms22031124 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1124

Author(s):

Mafalda Giovanna Reccia ◽

Floriana Volpicelli ◽

Eirkiur Benedikz ◽

Åsa Fex Svenningsen ◽

Luca Colucci-D’Amato

Keyword(s):

Cell Line ◽

Low Cost ◽

Neural Cell ◽

New Drugs ◽

High Yield ◽

Time Saving ◽

Interacting Protein ◽

Neuronal Marker ◽

Differentiation Status

Neural stem cells represent a powerful tool to study molecules involved in pathophysiology of Nervous System and to discover new drugs. Although they can be cultured and expanded in vitro as a primary culture, their use is hampered by their heterogeneity and by the cost and time needed for their preparation. Here we report that mes-c-myc A1 cells (A1), a neural cell line, is endowed with staminal properties. Undifferentiated/proliferating and differentiated/non-proliferating A1 cells are able to generate neurospheres (Ns) in which gene expression parallels the original differentiation status. In fact, Ns derived from undifferentiated A1 cells express higher levels of Nestin, Kruppel-like factor 4 (Klf4) and glial fibrillary protein (GFAP), markers of stemness, while those obtained from differentiated A1 cells show higher levels of the neuronal marker beta III tubulin. Interestingly, Ns differentiation, by Epidermal Growth Factors (EGF) and Fibroblast Growth Factor 2 (bFGF) withdrawal, generates oligodendrocytes at high-yield as shown by the expression of markers, Galactosylceramidase (Gal-C) Neuron-Glial antigen 2 (NG2), Receptor-Interacting Protein (RIP) and Myelin Basic Protein (MBP). Finally, upon co-culture, Ns-A1-derived oligodendrocytes cause a redistribution of contactin-associated protein (Caspr/paranodin) protein on neuronal cells, as primary oligodendrocytes cultures, suggesting that they are able to form compact myelin. Thus, Ns-A1-derived oligodendrocytes may represent a time-saving and low-cost tool to study the pathophysiology of oligodendrocytes and to test new drugs.

Download Full-text

Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley

International Journal of Molecular Sciences ◽

10.3390/ijms22136783 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6783

Author(s):

Renata Orłowska ◽

Katarzyna A. Pachota ◽

Wioletta M. Dynkowska ◽

Agnieszka Niedziela ◽

Piotr T. Bednarek

Keyword(s):

Dna Methylation ◽

Transposable Elements ◽

Dna Sequence ◽

Sequence Variation ◽

Nuclear Dna ◽

Point Mutations ◽

Mobile Elements ◽

Dna Demethylation ◽

Plant Genome

A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.

Download Full-text

Restoration of Silencing in Saccharomyces cerevisiae by Tethering of a Novel Sir2-Interacting Protein, Esc8

Genetics ◽

10.1093/genetics/162.2.633 ◽

2002 ◽

Vol 162 (2) ◽

pp. 633-645 ◽

Cited By ~ 2

Author(s):

Guido Cuperus ◽

David Shore

Keyword(s):

Protein A ◽

Dominant Negative ◽

Class I ◽

Dominant Negative Effect ◽

Rna Pol Ii ◽

Interacting Protein ◽

Nucleosome Remodeling ◽

Negative Effect ◽

Close Homolog

Abstract We previously described two classes of SIR2 mutations specifically defective in either telomeric/HM silencing (class I) or rDNA silencing (class II) in S. cerevisiae. Here we report the identification of genes whose protein products, when either overexpressed or directly tethered to the locus in question, can establish silencing in SIR2 class I mutants. Elevated dosage of SCS2, previously implicated as a regulator of both inositol biosynthesis and telomeric silencing, suppressed the dominant-negative effect of a SIR2-143 mutation. In a genetic screen for proteins that restore silencing when tethered to a telomere, we isolated ESC2 and an uncharacterized gene, (YOL017w), which we call ESC8. Both Esc2p and Esc8p interact with Sir2p in two-hybrid assays, and the Esc8p-Sir2 interaction is detected in vitro. Interestingly, Esc8p has a single close homolog in yeast, the ISW1-complex factor Ioc3p, and has also been copurified with Isw1p, raising the possibility that Esc8p is a component of an Isw1p-containing nucleosome remodeling complex. Whereas esc2 and esc8 deletion mutants alone have only marginal silencing defects, cells lacking Isw1p show a strong silencing defect at HMR but not at telomeres. Finally, we show that Esc8p interacts with the Gal11 protein, a component of the RNA pol II mediator complex.

Download Full-text

Tick Importin-α Is Implicated in the Interactome and Regulome of the Cofactor Subolesin

Pathogens ◽

10.3390/pathogens10040457 ◽

2021 ◽

Vol 10 (4) ◽

pp. 457

Author(s):

Sara Artigas-Jerónimo ◽

Margarita Villar ◽

Alejandro Cabezas-Cruz ◽

Grégory Caignard ◽

Damien Vitour ◽

...

Keyword(s):

Rational Design ◽

Fat Body ◽

Animal Health ◽

Direct Interaction ◽

Vaccine Antigen ◽

Tick Feeding ◽

Interacting Protein ◽

Expression Levels ◽

Importin Α

Ticks and tick-borne diseases (TBDs) represent a burden for human and animal health worldwide. Currently, vaccines constitute the safest and most effective approach to control ticks and TBDs. Subolesin (SUB) has been identified as a vaccine antigen for the control of tick infestations and pathogen infection and transmission. The characterization of the molecular function of SUB and the identification of tick proteins interacting with SUB may provide the basis for the discovery of novel antigens and for the rational design of novel anti-tick vaccines. In the present study, we used the yeast two-hybrid system (Y2H) as an unbiased approach to identify tick SUB-interacting proteins in an Ixodes ricinus cDNA library, and studied the possible role of SUB as a chromatin remodeler through direct interaction with histones. The Y2H screening identified Importin-α as a potential SUB-interacting protein, which was confirmed in vitro in a protein pull-down assay. The sub gene expression levels in tick midgut and fat body were significantly higher in unfed than fed female ticks, however, the importin-α expression levels did not vary between unfed and fed ticks but tended to be higher in the ovary when compared to those in other organs. The effect of importin-α RNAi was characterized in I. ricinus under artificial feeding conditions. Both sub and importin-α gene knockdown was observed in all tick tissues and, while tick weight was significantly lower in sub RNAi-treated ticks than in controls, importin-α RNAi did not affect tick feeding or oviposition, suggesting that SUB is able to exert its function in the absence of Importin-α. Furthermore, SUB was shown to physically interact with histone 4, which was corroborated by protein pull-down and western blot analysis. These results confirm that by interacting with numerous tick proteins, SUB is a key cofactor of the tick interactome and regulome. Further studies are needed to elucidate the nature of the SUB-Importin-α interaction and the biological processes and functional implications that this interaction may have.

Download Full-text

Long non-coding RNA OIP5-AS1 aggravates acute lung injury by promoting inflammation and cell apoptosis via regulating the miR-26a-5p/TLR4 axis

BMC Pulmonary Medicine ◽

10.1186/s12890-021-01589-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Qingsong Sun ◽

Man Luo ◽

Zhiwei Gao ◽

Xiang Han ◽

Weiqin Wu ◽

...

Keyword(s):

Acute Lung Injury ◽

Lung Injury ◽

Inflammatory Response ◽

Cell Apoptosis ◽

Quantitative Polymerase Chain Reaction ◽

Luciferase Reporter ◽

Enzyme Linked Immunosorbent Assay ◽

Interacting Protein ◽

Wide Range

Abstract Background Acute lung injury (ALI) is a pulmonary disorder that leads to acute respiration failure and thereby results in a high mortality worldwide. Increasing studies have indicated that toll-like receptor 4 (TLR4) is a promoter in ALI, and we aimed to explore the underlying upstream mechanism of TLR4 in ALI. Methods We used lipopolysaccharide (LPS) to induce an acute inflammatory response in vitro model and a murine mouse model. A wide range of experiments including reverse transcription quantitative polymerase chain reaction, western blot, enzyme linked immunosorbent assay, flow cytometry, hematoxylin–eosin staining, RNA immunoprecipitation, luciferase activity and caspase-3 activity detection assays were conducted to figure out the expression status, specific role and potential upstream mechanism of TLR4 in ALI. Result TLR4 expression was upregulated in ALI mice and LPS-treated primary bronchial/tracheal epithelial cells. Moreover, miR-26a-5p was confirmed to target TLR4 according to results of luciferase reporter assay. In addition, miR-26a-5p overexpression decreased the contents of proinflammatory factors and inhibited cell apoptosis, while upregulation of TLR4 reversed these effects of miR-26a-5p mimics, implying that miR-26a-5p alleviated ALI by regulating TLR4. Afterwards, OPA interacting protein 5 antisense RNA 1 (OIP5-AS1) was identified to bind with miR-26a-5p. Functionally, OIP5-AS1 upregulation promoted the inflammation and miR-26a-5p overexpression counteracted the influence of OIP5-AS1 upregulation on cell inflammatory response and apoptosis. Conclusion OIP5-AS1 promotes ALI by regulating the miR-26a-5p/TLR4 axis in ALI mice and LPS-treated cells, which indicates a promising insight into diagnostics and therapeutics in ALI.

Download Full-text