Analysis of a new begomovirus unveils a composite element conserved in the CP gene promoters of several Geminiviridae genera: Clues to comprehend the complex regulation of late genes

ABSTRACTIn the beta- and gammaherpesviruses, a specialized complex of viral transcriptional activators (vTAs) coordinate to direct expression of virus-encoded late genes, which are critical for viral assembly and whose transcription initiates only after the onset of viral DNA replication. The vTAs in Kaposi’s sarcoma-associated herpesvirus (KSHV) are ORF18, ORF24, ORF30, ORF31, ORF34, and ORF66. While the general organization of the vTA complex has been mapped, the individual roles of these proteins and how they coordinate to activate late gene promoters remain largely unknown. Here, we performed a comprehensive mutational analysis of the conserved residues in ORF18, which is a highly interconnected vTA component. Surprisingly, the mutants were largely selective for disrupting the interaction with ORF30 but not the other three ORF18 binding partners. Furthermore, disrupting the ORF18-ORF30 interaction weakened the vTA complex as a whole, and an ORF18 point mutant that failed to bind ORF30 was unable to complement an ORF18 null virus. Thus, contacts between individual vTAs are critical as even small disruptions in this complex result in profound defects in KSHV late gene expression.IMPORTANCEKaposi’s sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi’s sarcoma and other B-cell cancers and remains a leading cause of death in immunocompromised individuals. A key step in the production of infectious virions is the transcription of viral late genes, which generates capsid and structural proteins and requires the coordination of six viral proteins that form a complex. The role of these proteins during transcription complex formation and the importance of protein-protein interactions are not well understood. Here, we focused on a central component of the complex, ORF18, and revealed that disruption of its interaction with even a single component of the complex (ORF30) prevents late gene expression and completion of the viral lifecycle. These findings underscore how individual interactions between the late gene transcription components are critical for both the stability and function of the complex.

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Conserved CxnC Motifs in Kaposi’s Sarcoma-Associated Herpesvirus ORF66 Are Required for Viral Late Gene Expression and Are Essential for Its Interaction with ORF34

Journal of Virology ◽

10.1128/jvi.01299-19 ◽

2019 ◽

Vol 94 (2) ◽

Cited By ~ 3

Author(s):

Allison L. Didychuk ◽

Angelica F. Castañeda ◽

Lola O. Kushnir ◽

Carolyn J. Huang ◽

Britt A. Glaunsinger

Keyword(s):

Gene Transcription ◽

Kaposi's Sarcoma ◽

Kaposi’S Sarcoma ◽

Late Gene ◽

Gene Promoters ◽

Preinitiation Complex ◽

Terminal Domain ◽

Late Genes ◽

Kaposi's Sarcoma Associated Herpesvirus ◽

Kaposi’S Sarcoma Associated Herpesvirus

ABSTRACT Late gene transcription in the beta- and gammaherpesviruses depends on a set of virally encoded transcriptional activators (vTAs) that hijack the host transcriptional machinery and direct it to a subset of viral genes that are required for completion of the viral replication cycle and capsid assembly. In Kaposi’s sarcoma-associated herpesvirus (KSHV), these vTAs are encoded by ORF18, ORF24, ORF30, ORF31, ORF34, and ORF66. Assembly of the vTAs into a complex is critical for late gene transcription, and thus, deciphering the architecture of the complex is central to understanding its transcriptional regulatory activity. Here, we generated an ORF66-null virus and confirmed that it fails to produce late genes and infectious virions. We show that ORF66 is incorporated into the vTA complex primarily through its interaction with ORF34, which is dependent upon a set of four conserved cysteine-rich motifs in the C-terminal domain of ORF66. While both ORF24 and ORF66 occupy the canonical K8.1 late gene promoter, their promoter occupancy requires the presence of the other vTAs, suggesting that sequence-specific, stable binding requires assembly of the entire complex on the promoter. Additionally, we found that ORF24 expression is impaired in the absence of a stable vTA complex. This work extends our knowledge about the architecture of the KSHV viral preinitiation complex and suggests that it functions as a complex to recognize late gene promoters. IMPORTANCE Kaposi’s sarcoma-associated herpesvirus (KSHV; human herpesvirus 8) is an oncogenic gammaherpesvirus that is the causative agent of multiple human cancers. The release of infectious virions requires the production of capsid proteins and other late genes, whose production is transcriptionally controlled by a complex of six virally encoded proteins that hijack the host transcription machinery. It is poorly understood how this complex assembles or what function five of its six components play in transcription. Here, we demonstrate that ORF66 is an essential component of this complex in KSHV and that its inclusion in the complex depends upon its C-terminal domain, which contains highly conserved cysteine-rich motifs reminiscent of zinc finger motifs. Additionally, we examined the assembly of the viral preinitiation complex at late gene promoters and found that while sequence-specific binding of late gene promoters requires ORF24, it additionally requires a fully assembled viral preinitiation complex.

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Conserved CxnC motifs in Kaposi’s sarcoma-associated herpesvirus ORF66 are required for viral late gene expression and mediate its interaction with ORF34

10.1101/728139 ◽

2019 ◽

Cited By ~ 1

Author(s):

Allison L. Didychuk ◽

Angelica F. Castañeda ◽

Lola O. Kushnir ◽

Carolyn J. Huang ◽

Britt A. Glaunsinger

Keyword(s):

Gene Transcription ◽

Kaposi's Sarcoma ◽

Kaposi’S Sarcoma ◽

Late Gene ◽

Gene Promoters ◽

Terminal Domain ◽

Late Genes ◽

Virally Encoded ◽

Kaposi's Sarcoma Associated Herpesvirus ◽

Kaposi’S Sarcoma Associated Herpesvirus

ABSTRACTLate gene transcription in the beta- and gammaherpesviruses depends on a set of virally-encoded transcriptional activators (vTAs) that hijack the host transcriptional machinery and direct it to a subset of viral genes that are required for completion of the viral replication cycle and capsid assembly. In Kaposi’s sarcoma-associated herpesvirus (KSHV), these vTAs are encoded by ORF18, ORF24, ORF30, ORF31, ORF34, ORF66. Assembly of the vTAs into a complex is critical for late gene transcription, and thus deciphering the architecture of the complex is central to understanding its transcriptional regulatory activity. Here, we generated an ORF66-null virus and confirmed that it fails to produce late genes and infectious virions. We show that ORF66 is incorporated into the vTA complex primarily through its interaction with ORF34, which is mediated by a set of four conserved cysteine-rich motifs in the C-terminal domain of ORF66. While both ORF24 and ORF66 occupy the canonical K8.1 late gene promoter, their promoter occupancy requires the presence of the other vTAs, suggesting that sequence-specific, stable binding requires assembly of the entire complex on the promoter. Additionally, we find that ORF24 expression is impaired in the absence of a stable vTA complex. This work extends our knowledge about the architecture of the KSHV vPIC and suggests that it functions as a complex to recognize late gene promoters.IMPORTANCEKaposi’s sarcoma-associated herpesvirus (KSHV; human herpesvirus 8) is an oncogenic gammaherpesvirus that is the causative agent of multiple human cancers. Release of infectious virions requires production of capsid proteins and other late genes, whose production are transcriptionally controlled by a complex of six virally-encoded proteins that hijack the host transcription machinery. It is poorly understood how this complex assembles or what function five of its six components play in transcription. Here, we demonstrate that ORF66 is an essential component of this complex in KSHV and that its inclusion in the complex is mediated through its C-terminal domain, which contains highly conserved cysteine-rich motifs reminiscent of zinc finger motifs. Additionally, we examine assembly of the viral pre-initiation complex at late gene promoters and find that while sequence-specific binding of late gene promoters requires ORF24, it additionally requires a fully assembled viral pre-initation complex.

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BDNF activates an NFI-dependent neurodevelopmental timing program by sequestering NFATc4

Molecular Biology of the Cell ◽

10.1091/mbc.e16-08-0595 ◽

2018 ◽

Vol 29 (8) ◽

pp. 975-987 ◽

Cited By ~ 2

Author(s):

Baojin Ding ◽

Paul R. Dobner ◽

Debra Mullikin-Kilpatrick ◽

Wei Wang ◽

Hong Zhu ◽

...

Keyword(s):

Gene Network ◽

Late Gene ◽

Dependent Manner ◽

Gene Promoters ◽

Granule Neurons ◽

Late Gene Expression ◽

Late Genes ◽

Nuclear Factor I ◽

Synaptic Maturation

How intrinsic and extrinsic signals are coordinated to regulate synaptic maturation and its timing is an important question for neurodevelopment and its disorders. We investigated the influence of the neurotrophin BDNF on the developmental timing of a dendrite/synapse-related gene program controlled by nuclear factor I (NFI) in maturing cerebellar granule neurons (CGNs). BDNF accelerated the onset of NFI-regulated late-gene expression and NFI temporal occupancy in CGN cultures in a MEK5/ERK5-dependent manner. BDNF and NFI occupancy were mutually regulating, with BDNF enhancing the temporal binding of NFI to the Bdnf4 promoter itself. Moreover, BDNF induced phosphorylation and accelerated the departure of the trans-repressor NFATc4 from NFI late-gene promoters, including Bdnf4, which is permissive for NFI binding. BDNF dismissal of NFATc4 from late genes was linked to MEK5/ERK5-dependent sequestration of NFATc4 in the cis–Golgi, an event mirrored in CGNs developing in vivo. These studies reveal an expanded autoregulatory gene network for NFI temporal occupancy involving BDNF and NFATc4 extranuclear sequestration. Based on these and earlier findings, NFATc4 integrates intrinsic developmental signaling from membrane potential/calcineurin and autocrine/paracrine BDNF/TrkB to control initiation of NFI occupancy in maturing CGNs. We also identify a local Bdnf/Etv1 gene circuit within the larger NFI autoregulatory network.

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The Dynamics of NO3− and NH4+ Uptake in Duckweed Are Coordinated with the Expression of Major Nitrogen Assimilation Genes

Plants ◽

10.3390/plants11010011 ◽

2021 ◽

Vol 11 (1) ◽

pp. 11

Author(s):

Yuzhen Zhou ◽

Olena Kishchenko ◽

Anton Stepanenko ◽

Guimin Chen ◽

Wei Wang ◽

...

Keyword(s):

Nitrogen Assimilation ◽

Lemna Minor ◽

Inorganic Nitrogen ◽

Gene Promoters ◽

Spirodela Polyrhiza ◽

Expression Of Genes ◽

G Quadruplex ◽

Genes Encoding ◽

Use Efficiency ◽

Complex Regulation

Duckweed plants play important roles in aquatic ecosystems worldwide. They rapidly accumulate biomass and have potential uses in bioremediation of water polluted by fertilizer runoff or other chemicals. Here we studied the assimilation of two major sources of inorganic nitrogen, nitrate (NO3−) and ammonium (NH4+), in six duckweed species: Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, Lemna turionifera, Lemna minor, and Wolffia globosa. All six duckweed species preferred NH4+ over NO3− and started using NO3− only when NH4+ was depleted. Using the available genome sequence, we analyzed the molecular structure and expression of eight key nitrogen assimilation genes in S. polyrhiza. The expression of genes encoding nitrate reductase and nitrite reductase increased about 10-fold when NO3− was supplied and decreased when NH4+ was supplied. NO3− and NH4+ induced the glutamine synthetase (GS) genes GS1;2 and the GS2 by 2- to 5-fold, respectively, but repressed GS1;1 and GS1;3. NH4+ and NO3− upregulated the genes encoding ferredoxin- and NADH-dependent glutamate synthases (Fd-GOGAT and NADH-GOGAT). A survey of nitrogen assimilation gene promoters suggested complex regulation, with major roles for NRE-like and GAATC/GATTC cis-elements, TATA-based enhancers, GA/CTn repeats, and G-quadruplex structures. These results will inform efforts to improve bioremediation and nitrogen use efficiency.

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THE ROLE OF THE GENETIC ABNORMALITIES, EPIGENETIC AND microRNA IN THE PROGNOSIS OF CHRONIC LYMPHOCYTIC LEUKEMIA

Experimental Oncology ◽

10.31768/2312-8852.2018.40(4):261-267 ◽

2018 ◽

Vol 40 (4) ◽

pp. 261-267 ◽

Cited By ~ 5

Author(s):

K Tari ◽

Z Shamsi ◽

H Reza Ghafari ◽

A Atashi ◽

M Shahjahani ◽

...

Keyword(s):

B Cells ◽

Chronic Lymphocytic Leukemia ◽

Kinase Inhibitors ◽

Bone Marrow Involvement ◽

P53 Mutation ◽

Lymphocytic Leukemia ◽

Gene Promoters ◽

Epigenetic Changes ◽

Genetic Changes ◽

Trisomy 12

Chronic lymphocytic leukemia (CLL) is increased proliferation of B-cells with peripheral blood and bone marrow involvement, which is usually observed in older people. Genetic mutations, epigenetic changes and miRs play a role in CLL pathogenesis. Del 11q, del l17q, del 6q, trisomy 12, p53 and IgVH mutations are the most important genetic changes in CLL. Deletion of miR-15a and miR-16a can increase bcl2 gene expression, miR-29 and miR-181 deletions decrease the expression of TCL1, and miR-146a deletion prevents tumor metastasis. Epigenetic changes such as hypo- and hypermethylation, ubiquitination, hypo- and hyperacetylation of gene promoters involved in CLL pathogenesis can also play a role in CLL. Expression of CD38 and ZAP70, presence or absence of mutation in IgVH and P53 mutation are among the factors involved in CLL prognosis. Use of monoclonal antibodies against surface markers of B-cells like anti-CD20 as well as tyrosine kinase inhibitors are the most important therapeutic approaches for CLL.

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Faculty Opinions recommendation of PIF3 regulates anthocyanin biosynthesis in an HY5-dependent manner with both factors directly binding anthocyanin biosynthetic gene promoters in Arabidopsis.

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

10.3410/f.1068720.521639 ◽

2007 ◽

Author(s):

Julin Maloof

Keyword(s):

Anthocyanin Biosynthesis ◽

Dependent Manner ◽

Gene Promoters ◽

Biosynthetic Gene

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Faculty Opinions recommendation of Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters.

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

10.3410/f.732604921.793545305 ◽

2018 ◽

Author(s):

Sandra Wolin ◽

Marco Boccitto

Keyword(s):

Dna Methylation ◽

Gene Promoters

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Genetic complementation by cloned bacteriophage T4 late genes.

Journal of Virology ◽

10.1128/jvi.39.1.31-45.1981 ◽

1981 ◽

Vol 39 (1) ◽

pp. 31-45 ◽

Cited By ~ 17

Author(s):

K A Jacobs ◽

L M Albright ◽

D K Shibata ◽

E P Geiduschek

Keyword(s):

Bacteriophage T4 ◽

Genetic Complementation ◽

Late Genes

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AP2M1 Supports TGF-β Signals to Promote Collagen Expression by Inhibiting Caveolin Expression

International Journal of Molecular Sciences ◽

10.3390/ijms22041639 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1639

Author(s):

Saerom Lee ◽

Ga-Eun Lim ◽

Yong-Nyun Kim ◽

Hyeon-Sook Koo ◽

Jaegal Shim

Keyword(s):

Rna Seq ◽

Gene Encoding ◽

Caveolin 1 ◽

Collagen Expression ◽

Disease States ◽

Tumor Growth Factor ◽

Complex Process ◽

Collagen Protein ◽

Complex Regulation ◽

Collagen Genes

The extracellular matrix (ECM) is important for normal development and disease states, including inflammation and fibrosis. To understand the complex regulation of ECM, we performed a suppressor screening using Caenorhabditis elegans expressing the mutant ROL-6 collagen protein. One cuticle mutant has a mutation in dpy-23 that encodes the μ2 adaptin (AP2M1) of clathrin-associated protein complex II (AP-2). The subsequent suppressor screening for dpy-23 revealed the lon-2 mutation. LON-2 functions to regulate body size through negative regulation of the tumor growth factor-beta (TGF-β) signaling pathway responsible for ECM production. RNA-seq analysis showed a dominant change in the expression of collagen genes and cuticle components. We noted an increase in the cav-1 gene encoding caveolin-1, which functions in clathrin-independent endocytosis. By knockdown of cav-1, the reduced TGF-β signal was significantly restored in the dpy-23 mutant. In conclusion, the dpy-23 mutation upregulated cav-1 expression in the hypodermis, and increased CAV-1 resulted in a decrease of TβRI. Finally, the reduction of collagen expression including rol-6 by the reduced TGF-β signal influenced the cuticle formation of the dpy-23 mutant. These findings could help us to understand the complex process of ECM regulation in organism development and disease conditions.

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