The HMG-box: a versatile protein domain occurring in a wide variety of DNA-binding proteins

Štros, Michal; Launholt, Dorte; Grasser, Klaus D.

doi:10.1007/s00018-007-7162-3

Cited by 252 publications

(258 citation statements)

References 123 publications

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“…It has no similarity to any PBCV-1-encoded protein. HMG box-containing proteins bind non-B-type DNA conformations with high affinity (44), and they are involved in the regulation of DNA-dependent processes, such as transcription, replication, and DNA repair, all of which require changing the conformation of chromatin (48). Thus, this host protein may be important in initiating PBCV-1 gene expression, which occurs within minutes of infection (64).…”

Section: Pbcv-1 Virion Proteomementioning

confidence: 99%

Paramecium bursaria Chlorella Virus 1 Proteome Reveals Novel Architectural and Regulatory Features of a Giant Virus

Dunigan

Cerny

Bauman³

et al. 2012

J Virol

104

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The 331-kbp chlorovirusParamecium bursariachlorella virus 1 (PBCV-1) genome was resequenced and annotated to correct errors in the original 15-year-old sequence; 40 codons was considered the minimum protein size of an open reading frame. PBCV-1 has 416 predicted protein-encoding sequences and 11 tRNAs. A proteome analysis was also conducted on highly purified PBCV-1 virions using two mass spectrometry-based protocols. The mass spectrometry-derived data were compared to PBCV-1 and its hostChlorella variabilisNC64A predicted proteomes. Combined, these analyses revealed 148 unique virus-encoded proteins associated with the virion (about 35% of the coding capacity of the virus) and 1 host protein. Some of these proteins appear to be structural/architectural, whereas others have enzymatic, chromatin modification, and signal transduction functions. Most (106) of the proteins have no known function or homologs in the existing gene databases except as orthologs with proteins of other chloroviruses, phycodnaviruses, and nuclear-cytoplasmic large DNA viruses. The genes encoding these proteins are dispersed throughout the virus genome, and most are transcribed late or early-late in the infection cycle, which is consistent with virion morphogenesis.

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Section: Pbcv-1 Virion Proteomementioning

confidence: 99%

Paramecium bursaria Chlorella Virus 1 Proteome Reveals Novel Architectural and Regulatory Features of a Giant Virus

Dunigan

Cerny

Bauman³

et al. 2012

J Virol

104

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“…Alternatively, one can keep the medium constant but impair nuclear localization of Cic. Although Cic does not have a canonical nuclear localization signal (NLS), it is known that other HMG box proteins contain a functional NLS within their HMG domains (Qin et al, 2003;Stros et al, 2007;Malki et al, 2010). A previous study established that deletion of the Cic HMG box not only abolishes its repressor activity but impairs nuclear localization (Astigarraga et al, 2007).…”

Section: Research Report Rtk-dependent Control Of Capicuamentioning

confidence: 99%

Torso RTK controls Capicua degradation by changing its subcellular localization

et al. 2012

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SUMMARYThe transcriptional repressor Capicua (Cic) controls multiple aspects of Drosophila embryogenesis and has been implicated in vertebrate development and human diseases. Receptor tyrosine kinases (RTKs) can antagonize Cic-dependent gene repression, but the mechanisms responsible for this effect are not fully understood. Based on genetic and imaging studies in the early Drosophila embryo, we found that Torso RTK signaling can increase the rate of Cic degradation by changing its subcellular localization. We propose that Cic is degraded predominantly in the cytoplasm and show that Torso reduces the stability of Cic by controlling the rates of its nucleocytoplasmic transport. This model accounts for the experimentally observed spatiotemporal dynamics of Cic in the early embryo and might explain RTK-dependent control of Cic in other developmental contexts. DEVELOPMENTprotein Dronpa (Ando et al., 2004) or the fluorescent protein Venus (Nagai et al., 2002) and controlled by the regulatory sequences of the cic gene (Fig. 1A). The spatial distributions of Cic resulting from either of these constructs mimic the distribution of endogenous Cic (supplementary material Fig. S1).Cic is first detected after the 9th nuclear division . At this stage, Cic predominantly localizes to nuclei and levels in the middle region of the embryo are already significantly higher than those at the poles. Levels of Cic in the central region drop during mitoses, reflecting protein dispersal into the cytoplasm. During the subsequent interphase, nuclear levels recover and eventually exceed those observed in the preceding mitosis. The levels within individual nuclei increase ~2.5-fold between cycles 10 and the beginning of cycle 14. By contrast, levels at the poles remain low from the first time Cic is detected and until the embryo reaches the cellularization stage. Torso increases the rate of Cic degradationStudies in mice suggest that Cic-target gene derepression depends on RTK-dependent reduction of Cic levels (Fryer et al., 2011). To explore this mechanism in the embryo, we examined the degradation rates of Cic at different levels of RTK signaling. Based on the pattern of double-phosphorylated ERK (dpERK), which serves as a reporter of Torso signaling, the central region and poles of the wild-type embryo correspond to zero and maximal levels of Torso activation, respectively. To generate an intermediate level of Torso activation, we used a gain-of-function allele of torso (Szabad et al., 1989) (Fig. 2A,B).If Torso reduces the stability of Cic, its lifetime should be inversely correlated with the level of ERK activation. To test this prediction, we measured the lifetime of Cic using an optical pulselabeling method, which relies on the photo-switchable fluorescent protein Dronpa. Dronpa is synthesized in a bright state, which can be reversibly converted to the dark state by brief illumination at 3963 RESEARCH REPORT RTK-dependent control of Capicua 496 nm. The dark state is optically stable, but it can be converted back to the bright state ...

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“…1D). Animal proteins containing HMG and ELM2 motifs have been implicated in DNA binding and transcription regulation (Ding et al, 2003;Stros et al, 2007). PHD-containing proteins are known to be involved in binding to methylated histone H3 (Ramon-Maiques et al, 2007).…”

Section: Characterization Of a Symrk-associated Proteinmentioning

confidence: 99%

A Novel ARID DNA-Binding Protein Interacts with SymRK and Is Expressed during Early Nodule Development in Lotus japonicus

et al. 2008

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During the establishment of symbiosis in legume roots, the rhizobial Nod factor signal is perceived by the host cells via receptorlike kinases, including SymRK. The NODULE INCEPTION (NIN) gene in Lotus japonicus is required for rhizobial entry into root cells and for nodule organogenesis. We describe here a novel DNA-binding protein from L. japonicus, referred to as SIP1, because it was identified as a SymRK-interacting protein. SIP1 contains a conserved AT-rich interaction domain (ARID) and represents a unique member of the ARID-containing proteins in plants. The C terminus of SIP1 was found to be responsible for its interaction with the kinase domain of SymRK and for homodimerization in the absence of DNA. SIP1 specifically binds to the promoter of LjNIN but not to that of LjCBP1 (a calcium-binding protein gene), both of which are known to be inducible by Nod factors. SIP1 recognizes two of the three AT-rich domains present in the NIN gene promoter. Deletion of one of the AT-rich domains at the NIN promoter diminishes the binding of SIP1 to the NIN promoter. The protein is localized to the nuclei when expressed as a red fluorescence fusion protein in the onion (Allium cepa) epidermal cells. The SIP1 gene is expressed constitutively in the uninfected roots, and its expression levels are elevated after infection by Mesorhizobium loti. It is proposed that SIP1 may be required for the expression of NIN and involved in the initial communications between the rhizobia and the host root cells.

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The HMG-box: a versatile protein domain occurring in a wide variety of DNA-binding proteins

Cited by 252 publications

References 123 publications

Paramecium bursaria Chlorella Virus 1 Proteome Reveals Novel Architectural and Regulatory Features of a Giant Virus

Paramecium bursaria Chlorella Virus 1 Proteome Reveals Novel Architectural and Regulatory Features of a Giant Virus

Torso RTK controls Capicua degradation by changing its subcellular localization

A Novel ARID DNA-Binding Protein Interacts with SymRK and Is Expressed during Early Nodule Development in Lotus japonicus

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