scholarly journals Tar DNA-binding protein-43 (TDP-43) regulates axon growth in vitro and in vivo

2014 ◽  
Vol 65 ◽  
pp. 25-34 ◽  
Author(s):  
Vineeta Bhasker Tripathi ◽  
Pranetha Baskaran ◽  
Christopher E. Shaw ◽  
Sarah Guthrie
Keyword(s):  
Dna Binding ◽  
Binding Protein ◽  
Axon Growth ◽  
Dna Binding Protein

scholarly journals The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Antoine Hocher ◽  
Maria Rojec ◽  
Jacob B Swadling ◽  
Alexander Esin ◽  
Tobias Warnecke
Keyword(s):  
Dna Binding ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Coli Strain ◽  
Micrococcal Nuclease ◽  
Thermoplasma Acidophilum ◽  
Chromatin Architecture ◽  
Archaeal Histone

Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are widespread but not universal: several lineages have lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we elucidate primary chromatin architecture in an archaeon without histones, Thermoplasma acidophilum, which harbors a HU family protein (HTa) that protects part of the genome from micrococcal nuclease digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa preferentially binds to GC-rich sequences, exhibits invariant positioning throughout the growth cycle, and shows archaeal histone-like oligomerization behavior. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

The DNA Binding Protein H-NS Binds to and Alters the Stability of RNA in vitro and in vivo

2004 ◽  
Vol 339 (3) ◽  
pp. 505-514 ◽  
Author(s):  
Cristin C Brescia ◽  
Meenakshi K Kaw ◽  
Darren D Sledjeski
Keyword(s):  
Dna Binding ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
The Stability

scholarly journals The Mycobacterium bovis BCG Cyclic AMP Receptor-Like Protein Is a Functional DNA Binding Protein In Vitro and In Vivo, but Its Activity Differs from That of Its M. tuberculosis Ortholog, Rv3676

2007 ◽  
Vol 75 (11) ◽  
pp. 5509-5517 ◽  
Author(s):  
Guangchun Bai ◽  
Michaela A. Gazdik ◽  
Damen D. Schaak ◽  
Kathleen A. McDonough
Keyword(s):  
Gene Regulation ◽  
Dna Binding ◽  
Cyclic Amp ◽  
Mycobacterium Bovis ◽  
Dna Sequences ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Mobility Shift

ABSTRACT Mycobacterium tuberculosis Rv3676 encodes a cyclic AMP (cAMP) receptor-like protein (CRPMt) that has been implicated in global gene regulation and may play an important role during tuberculosis infection. The CRPMt ortholog in Mycobacterium bovis BCG, CRPBCG, is dysfunctional in an Escherichia coli CRP competition assay and has been proposed as a potential source of M. bovis BCG's attenuation. We compared CRPBCG and CRPMt in vitro and in vivo, in M. bovis BCG and M. tuberculosis, to evaluate CRPBCG's potential function in a mycobacterial system. Both proteins formed dimers in mycobacterial lysates, bound to the same target DNA sequences, and were similarly affected by the presence of cAMP in DNA binding assays. However, CRPMt and CRPBCG differed in their relative affinities for specific DNA target sequences and in their susceptibilities to protease digestion. Surprisingly, CRPBCG DNA binding activity was stronger than that of CRPMt both in vitro and in vivo, as measured by electrophoretic mobility shift and chromatin immunoprecipitation assays. Nutrient starvation-associated regulation of several CRPMt regulon members also differed between M. bovis BCG and M. tuberculosis. We conclude that CRPBCG is a functional cAMP-responsive DNA binding protein with an in vivo DNA binding profile in M. bovis BCG similar to that of CRPMt in M. tuberculosis. However, biologically significant functional differences may exist between CRPBCG and CRPMt with respect to gene regulation, and this issue warrants further study.

Cell-penetrating DNA-binding protein as a safe and efficient naked DNA delivery carrier in vitro and in vivo

2010 ◽  
Vol 392 (1) ◽  
pp. 9-15 ◽  
Author(s):  
Eun-Sung Kim ◽  
Seung-Woo Yang ◽  
Dong-Ki Hong ◽  
Woo-Taek Kim ◽  
Ho-Guen Kim ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Protein ◽  
Dna Delivery ◽  
Dna Binding Protein ◽  
Naked Dna ◽  
Cell Penetrating

Translocation of a UV-damaged DNA binding protein into a tight association with chromatin after treatment of mammalian cells with UV light

1997 ◽  
Vol 110 (10) ◽  
pp. 1159-1168 ◽  
Author(s):  
V.R. Otrin ◽  
M. McLenigan ◽  
M. Takao ◽  
A.S. Levine ◽  
M. Protic
Keyword(s):  
Dna Binding ◽  
Genomic Dna ◽  
Mammalian Cells ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Uv Treatment ◽  
Tight Association ◽  
Damaged Dna

A UV-damaged DNA binding protein (UV-DDB) is the major source of UV-damaged DNA binding activity in mammalian cell extracts. This activity is defective in at least some xeroderma pigmentosum group E (XP-E) patients; microinjection of the UV-DDB protein into their fibroblasts corrects nucleotide excision repair (NER). In an in vitro reconstituted NER system, small amounts of UV-DDB stimulate repair synthesis a few fold. After exposure to UV, mammalian cells show an early dose-dependent inhibition of the extractable UV-DDB activity; this inhibition may reflect a tight association of the binding protein with UV-damaged genomic DNA. To investigate the dynamics and location of UV-DDB with respect to damaged chromatin in vivo, we utilized nuclear fractionation and specific antibodies and detected translocation of the p127 component of UV-DDB from a loose to a tight association with chromatinized DNA immediately after UV treatment. A similar redistribution was found for other NER proteins, i.e. XPA, RP-A and PCNA, suggesting their tighter association with genomic DNA after UV. These studies revealed a specific protein-protein interaction between UV-DDB/p127 and RP-A that appears to enhance binding of both proteins to UV-damaged DNA in vitro, providing evidence for the involvement of UV-DDB in the damage-recognition step of NER. Moreover, the kinetics of the reappearance of extractable UV-DDB activity after UV treatment of human cells with differing repair capacities positively correlate with the cell's capacity to repair 6–4 pyrimidine dimers (6–4 PD) in the whole genome, a result consistent with an in vivo role for UV-DDB in recognizing this type of UV lesion.

scholarly journals The U3 small nucleolar ribonucleoprotein component Imp4p is a telomeric DNA-binding protein

2007 ◽  
Vol 408 (3) ◽  
pp. 387-393 ◽  
Author(s):  
Yi-Ching Hsieh ◽  
Pei-Jung Tu ◽  
Ying-Yuan Lee ◽  
Chun-Chen Kuo ◽  
Yi-Chien Lin ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Binding Activity ◽  
Telomere Maintenance ◽  
Telomeric Dna ◽  
Mobility Shift ◽  
Telomere Function

Imp4p is a component of U3 snoRNP (small nucleolar ribonucleoprotein) involved in the maturation of 18S rRNA. We have shown that Imp4p interacts with Cdc13p, a single-stranded telomere-binding protein involved in telomere maintenance. To understand the role of Imp4p in telomeres, we purified recombinant Imp4p protein and tested its binding activity towards telomeric DNA using electrophoretic mobility-shift assays. Our results showed that Imp4p bound specifically to single-stranded telomeric DNA in vitro. The interaction of Imp4p to telomeres in vivo was also demonstrated by chromatin immunoprecipitation experiments. Significantly, the binding of Imp4p to telomeres was not limited to yeast proteins, since the hImp4 (human Imp4) also bound to vertebrate single-stranded telomeric DNA. Thus we conclude that Imp4p is a novel telomeric DNA-binding protein that, in addition to its role in rRNA processing, might participate in telomere function.

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