scholarly journals DNA-Binding Properties of YbaB, a Putative Nucleoid-Associated Protein From Caulobacter crescentus

2021 ◽  
Vol 12 ◽  
Author(s):  
Parul Pal ◽  
Malvika Modi ◽  
Shashank Ravichandran ◽  
Ragothaman M. Yennamalli ◽  
Richa Priyadarshini
Keyword(s):  
Gene Regulation ◽  
Dna Binding ◽  
Caulobacter Crescentus ◽  
Binding Protein ◽  
Bacterial Species ◽  
Physiological Role ◽  
Dna Binding Protein ◽  
Associated Proteins ◽  
Family Gene ◽  
Almost All

Nucleoid-associated proteins (NAPs) or histone-like proteins (HLPs) are DNA-binding proteins present in bacteria that play an important role in nucleoid architecture and gene regulation. NAPs affect bacterial nucleoid organization via DNA bending, bridging, or forming aggregates. EbfC is a nucleoid-associated protein identified first in Borrelia burgdorferi, belonging to YbaB/EbfC family of NAPs capable of binding and altering DNA conformation. YbaB, an ortholog of EbfC found in Escherichia coli and Haemophilus influenzae, also acts as a transcriptional regulator. YbaB has a novel tweezer-like structure and binds DNA as homodimers. The homologs of YbaB are found in almost all bacterial species, suggesting a conserved function, yet the physiological role of YbaB protein in many bacteria is not well understood. In this study, we characterized the YbaB/EbfC family DNA-binding protein in Caulobacter crescentus. C. crescentus has one YbaB/EbfC family gene annotated in the genome (YbaBCc) and it shares 41% sequence identity with YbaB/EbfC family NAPs. Computational modeling revealed tweezer-like structure of YbaBCc, a characteristic of YbaB/EbfC family of NAPs. N-terminal–CFP tagged YbaBCc localized with the nucleoid and is able to compact DNA. Unlike B. burgdorferi EbfC protein, YbaBCc protein is a non-specific DNA-binding protein in C. crescentus. Moreover, YbaBCc shields DNA against enzymatic degradation. Collectively, our findings reveal that YbaBCc is a small histone-like protein and may play a role in bacterial chromosome structuring and gene regulation in C. crescentus.

scholarly journals REB1, a yeast DNA-binding protein with many targets, is essential for growth and bears some resemblance to the oncogene myb.

1990 ◽  
Vol 10 (10) ◽  
pp. 5226-5234 ◽  
Author(s):  
Q D Ju ◽  
B E Morrow ◽  
J R Warner
Keyword(s):  
Amino Acids ◽  
Dna Binding ◽  
Rna Polymerase Ii ◽  
Essential Gene ◽  
Binding Protein ◽  
Consensus Sequence ◽  
Physiological Role ◽  
Dna Binding Protein ◽  
Reading Frame ◽  
Chromosome Ii

REB1 is a DNA-binding protein that recognizes sites within both the enhancer and the promoter of rRNA transcription as well as upstream of many genes transcribed by RNA polymerase II. We report here the cloning of the gene for REB1 by screening a yeast genomic lambda gt11 library with specific oligonucleotides containing the REB1 binding site consensus sequence. The REB1 gene was sequenced, revealing an open reading frame encoding 809 amino acids. The predicted protein was highly hydrophilic, with numerous OH-containing amino acids and glutamines, features common to many of the general DNA-binding proteins of Saccharomyces cerevisiae, such as ABF1, RAP1, GCN4, and HSF1. There was some homology between a portion of REB1 and the DNA-binding domain of the oncogene myb. REB1 is an essential gene that maps on chromosome II. However, the physiological role that it plays in the cell has yet to be established.

A locust DNA-binding protein involved in gene regulation by juvenile hormone

2002 ◽  
Vol 190 (1-2) ◽  
pp. 177-185 ◽  
Author(s):  
S. Zhou ◽  
J. Zhang ◽  
M. Hirai ◽  
Y. Chinzei ◽  
H. Kayser ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Dna Binding ◽  
Juvenile Hormone ◽  
Binding Protein ◽  
Dna Binding Protein

scholarly journals Switch-like control of helicase processivity by single-stranded DNA binding protein

2020 ◽  
Author(s):  
Barbara Stekas ◽  
Masayoshi Honda ◽  
Maria Spies ◽  
Yann R. Chemla
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Molecular Mechanisms ◽  
Binding Protein ◽  
Optical Trap ◽  
Dna Binding Protein ◽  
Single Stranded Dna ◽  
Associated Proteins ◽  
Underlying Mechanisms ◽  
Xpd Helicase

Helicases utilize the energy of NTP hydrolysis to translocate along single-stranded nucleic acids (NA) and unwind the duplex. In the cell, helicases function in the context of other NA-associated proteins which regulate helicase function. For example, single-stranded DNA binding proteins are known to enhance helicase activity, although the underlying mechanisms remain largely unknown. F. acidarmanus XPD helicase serves as a model for understanding the molecular mechanisms of Superfamily 2B helicases, and previous work has shown that its activity is enhanced by the cognate single-stranded DNA binding protein RPA2. Here, single-molecule optical trap measurements of the unwinding activity of a single XPD helicase in the presence of RPA2 reveal a mechanism in which XPD interconverts between two states with different processivities and transient RPA2 interactions stabilize the more processive state, activating a latent “processivity switch” in XPD. These findings provide new insights on mechanisms of helicase regulation by accessory proteins.

scholarly journals A Novel DNA-binding Protein Coordinates Asymmetric Chromosome Replication and Chromosome Partitioning

2016 ◽  
Author(s):  
James A. Taylor ◽  
Gaël Panis ◽  
Patrick H. Viollier ◽  
Gregory T. Marczynski
Keyword(s):  
Cell Cycle ◽  
Dna Binding ◽  
Replication Origin ◽  
Caulobacter Crescentus ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Chromosome Replication ◽  
Chromosome Partitioning ◽  
Chromosome Separation

AbstractBacterial chromosome replication is regulated from a single replication origin (ori) that receives cell cycle signals. Following replication, bacteria often use theparABSpartition system with a centromere-likeparSlocus to place the chromosomes into the daughter cells. Our knowledge of cell cycle regulation is incomplete and we searched for novel regulators of chromosome replication. Here we show that in the cell cycle modelCaulobacter crescentusa novel DNA-binding protein promotes both the initiation of chromosome replication and the earliest step of chromosome partitioning. We used biochemical fractionation to identify a protein (OpaA) that preferentially binds to mutatedoriDNA that also increasesori-plasmid replicationin vivo. OpaA represents a previously unknown class of DNA-binding proteins.opaAgene expression is essential and sufficient OpaA levels are required for the correct timing of chromosome replication. Whole genome ChIP-seq identified the genomic binding sites for OpaA, with the strongest associations at theparABSlocus nearori. Using molecular-genetic and fluorescence microscopy experiments, we showed that OpaA also promotes the first step of chromosome partitioning, the initial separation of the duplicatedparSloci followingorireplication. This separation occurs before theparABSmechanism and it coincides with the regulatory step that splits the symmetry of the chromosomes so that they are placed at distinct cell-poles which develop into replicating and non-replicating cell-types. We propose that OpaA coordinates replication with the poorly understood mechanism of early chromosome separation.opaAlethal suppressor and antibiotic experiments argue that future studies be focused on the mechanistic roles for transcription and translation at this critical step of the cell cycle.Author SummaryLike all organisms, bacteria must replicate their chromosomes and move them into the newly dividing cells. Eukaryotes use non-overlapping phases, first for chromosome replication (S-phase) followed by mitosis (M-phase) when the completely duplicated chromosomes are separated. However, bacteria combine both phases so chromosome replication and chromosome separation (termed chromosome “partitioning”) overlap. In many bacteria, includingCaulobacter crescentus, chromosome replication initiates from a single replication origin (ori) and the first duplicated regions of the chromosome immediately begin “partitioning” towards the cell poles long before the whole chromosome has finished replication. This partitioning movement uses the centromere-like DNA called“parS”that is located near theori. Here we identify a completely novel type of DNA-binding protein called OpaA and we show that it acts at bothoriandparS. The timing and coordination of overlapping chromosome replication and partitioning phases is a special regulatory problem for bacteria. We further demonstrate that OpaA is selectively required for the initiation of chromosome replication atoriand likewise that OpaA is selectively required for the initial partitioning ofparS. Therefore, we propose that OpaA is a novel regulator that coordinates chromosome replication with the poorly understood mechanism of early chromosome separation.

REB1, a yeast DNA-binding protein with many targets, is essential for growth and bears some resemblance to the oncogene myb

1990 ◽  
Vol 10 (10) ◽  
pp. 5226-5234
Author(s):  
Q D Ju ◽  
B E Morrow ◽  
J R Warner
Keyword(s):  
Amino Acids ◽  
Dna Binding ◽  
Rna Polymerase Ii ◽  
Essential Gene ◽  
Binding Protein ◽  
Consensus Sequence ◽  
Physiological Role ◽  
Dna Binding Protein ◽  
Reading Frame ◽  
Chromosome Ii

REB1 is a DNA-binding protein that recognizes sites within both the enhancer and the promoter of rRNA transcription as well as upstream of many genes transcribed by RNA polymerase II. We report here the cloning of the gene for REB1 by screening a yeast genomic lambda gt11 library with specific oligonucleotides containing the REB1 binding site consensus sequence. The REB1 gene was sequenced, revealing an open reading frame encoding 809 amino acids. The predicted protein was highly hydrophilic, with numerous OH-containing amino acids and glutamines, features common to many of the general DNA-binding proteins of Saccharomyces cerevisiae, such as ABF1, RAP1, GCN4, and HSF1. There was some homology between a portion of REB1 and the DNA-binding domain of the oncogene myb. REB1 is an essential gene that maps on chromosome II. However, the physiological role that it plays in the cell has yet to be established.

scholarly journals Epstein-Barr Virus Immediate-Early Protein Zta Co-Opts Mitochondrial Single-Stranded DNA Binding Protein To Promote Viral and Inhibit Mitochondrial DNA Replication

2008 ◽  
Vol 82 (9) ◽  
pp. 4647-4655 ◽  
Author(s):  
Andreas Wiedmer ◽  
Pu Wang ◽  
Jing Zhou ◽  
Andrew J. Rennekamp ◽  
Valeria Tiranti ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Binding ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Lytic Replication ◽  
Single Stranded Dna ◽  
Barr Virus ◽  
Early Protein ◽  
Associated Proteins ◽  
Epstein Barr

ABSTRACT Disruption of cellular metabolic processes and usurpation of host proteins are hallmarks of herpesvirus lytic infection. Epstein-Barr virus (EBV) lytic replication is initiated by the immediate-early protein Zta. Zta is a multifunctional DNA binding protein that stimulates viral gene transcription, nucleates a replication complex at the viral origin of lytic replication, and inhibits cell cycle proliferation. To better understand these functions and identify cellular collaborators of Zta, we purified an epitope-tagged version of Zta in cells capable of supporting lytic replication. FLAG-tagged Zta was purified from a nuclear fraction using FLAG antibody immunopurification and peptide elution. Zta-associated proteins were isolated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and identified by mass spectrometry. The Zta-associated proteins included members of the HSP70 family and various single-stranded DNA and RNA binding proteins. The nuclear replication protein A subunits (RPA70 and RPA32) and the human mitochondrial single-stranded DNA binding protein (mtSSB) were confirmed by Western blotting to be specifically enriched in the FLAG-Zta immunopurified complex. mtSSB coimmunoprecipitated with endogenous Zta during reactivation of EBV-positive Burkitt lymphoma and lymphoblastoid cell lines. Small interfering RNA depletion of mtSSB reduced Zta-induced lytic replication of EBV but had only a modest effect on transcription activation function. A point mutation in the Zta DNA binding domain (C189S), which is known to reduce lytic cycle replication, eliminated mtSSB association with Zta. The predominantly mitochondrial localization of mtSSB was shifted to partly nuclear localization in cells expressing Zta. Mitochondrial DNA synthesis and genome copy number were reduced by Zta-induced EBV lytic replication. We conclude that Zta interaction with mtSSB serves the dual function of facilitating viral and blocking mitochondrial DNA replication.

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.

scholarly journals Switch-like control of helicase processivity by single-stranded DNA binding protein

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Barbara Stekas ◽  
Steve Yeo ◽  
Alice Troitskaia ◽  
Masayoshi Honda ◽  
Sei Sho ◽  
...  
Keyword(s):  
Dna Binding ◽  
Molecular Mechanisms ◽  
Binding Protein ◽  
Optical Trap ◽  
Dna Binding Protein ◽  
Single Stranded Dna ◽  
Associated Proteins ◽  
Underlying Mechanisms ◽  
Regulatory Dna ◽  
Xpd Helicase

Helicases utilize NTP hydrolysis to translocate along single-stranded nucleic acids (NA) and unwind the duplex. In the cell, helicases function in the context of other NA-associated proteins such as single-stranded DNA binding proteins. Such encounters regulate helicase function, although the underlying mechanisms remain largely unknown. F. acidarmanus XPD helicase serves as a model for understanding the molecular mechanisms of Superfamily 2B helicases, and its activity is enhanced by the cognate single-stranded DNA binding protein RPA2. Here, optical trap measurements of the unwinding activity of a single XPD helicase in the presence of RPA2 reveal a mechanism in which XPD interconverts between two states with different processivities and transient RPA2 interactions stabilize the more processive state, activating a latent 'processivity switch' in XPD. A point mutation at a regulatory DNA binding site on XPD similarly activates this switch. These findings provide new insights on mechanisms of helicase regulation by accessory proteins.

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