scholarly journals The DNA Recognition Motif of GapR Has an Intrinsic DNA Binding Preference towards AT-rich DNA

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 5776
Author(s):  
Qian Huang ◽  
Bo Duan ◽  
Zhi Qu ◽  
Shilong Fan ◽  
Bin Xia
Keyword(s):  
Dna Binding ◽  
Caulobacter Crescentus ◽  
Structural Rearrangement ◽  
Replication Forks ◽  
Recognition Motif ◽  
Binding Preference ◽  
Highly Expressed Genes ◽  
Initial Binding ◽  
Structure In Solution ◽  
Phosphate Groups

The nucleoid-associated protein GapR found in Caulobacter crescentus is crucial for DNA replication, transcription, and cell division. Associated with overtwisted DNA in front of replication forks and the 3′ end of highly-expressed genes, GapR can stimulate gyrase and topo IV to relax (+) supercoils, thus facilitating the movement of the replication and transcription machines. GapR forms a dimer-of-dimers structure in solution that can exist in either an open or a closed conformation. It initially binds DNA through the open conformation and then undergoes structural rearrangement to form a closed tetramer, with DNA wrapped in the central channel. Here, we show that the DNA binding domain of GapR (residues 1–72, GapRΔC17) exists as a dimer in solution and adopts the same fold as the two dimer units in the full-length tetrameric protein. It binds DNA at the minor groove and reads the spatial distribution of DNA phosphate groups through a lysine/arginine network, with a preference towards AT-rich overtwisted DNA. These findings indicate that the dimer unit of GapR has an intrinsic DNA binding preference. Thus, at the initial binding step, the open tetramer of GapR with two relatively independent dimer units can be more efficiently recruited to overtwisted regions.

scholarly journals Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks

2014 ◽  
Vol 31 (10) ◽  
pp. 2672-2688 ◽  
Author(s):  
Alys M. Cheatle Jarvela ◽  
Lisa Brubaker ◽  
Anastasia Vedenko ◽  
Anisha Gupta ◽  
Bruce A. Armitage ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Modular Evolution ◽  
Binding Preference ◽  
Gene Regulatory

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 The Nucleoid-Associated Protein GapR Uses Conserved Structural Elements To Oligomerize and Bind DNA

mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Rogério F. Lourenço ◽  
Saumya Saurabh ◽  
Jonathan Herrmann ◽  
Soichi Wakatsuki ◽  
Lucy Shapiro
Keyword(s):  
Dna Binding ◽  
Caulobacter Crescentus ◽  
Genetic Material ◽  
Bacterial Cells ◽  
Structural Elements ◽  
Content Type ◽  
Time Dynamic ◽  
Associated Proteins ◽  
And Function

ABSTRACT Nucleoid-associated proteins (NAPs) are DNA binding proteins critical for the organization and function of the bacterial chromosome. A newly discovered NAP in Caulobacter crescentus, GapR, is thought to facilitate the movement of the replication and transcription machines along the chromosome by stimulating type II topoisomerases to remove positive supercoiling. Here, utilizing genetic, biochemical, and biophysical studies of GapR in light of a recently published DNA-bound crystal structure of GapR, we identified the structural elements involved in oligomerization and DNA binding. Moreover, we show that GapR is maintained as a tetramer upon its dissociation from DNA and that tetrameric GapR is capable of binding DNA molecules in vitro. Analysis of protein chimeras revealed that two helices of GapR are functionally conserved in H-NS, demonstrating that two evolutionarily distant NAPs with distinct mechanisms of action utilize conserved structural elements to oligomerize and bind DNA. IMPORTANCE Bacteria organize their genetic material in a structure called the nucleoid, which needs to be compact to fit inside the cell and, at the same time, dynamic to allow high rates of replication and transcription. Nucleoid-associated proteins (NAPs) play a pivotal role in this process, so their detailed characterization is crucial for our understanding of DNA organization into bacterial cells. Even though NAPs affect DNA-related processes differently, all of them have to oligomerize and bind DNA for their function. The significance of this study is the identification of structural elements involved in the oligomerization and DNA binding of a newly discovered NAP in C. crescentus and the demonstration that structural elements are conserved in evolutionarily distant and functionally distinct NAPs.

Determining the DNA Binding Preference of the Transcription Factor Optix in Heliconius Butterflies

2020 ◽  
Vol 34 (S1) ◽  
pp. 1-1
Author(s):  
Anthony Rafael Rivera Barreto ◽  
José Arcadio Rodríguez Martínez
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Binding Preference ◽  
Heliconius Butterflies

scholarly journals Sensory domain of the cell cycle kinase CckA inCaulobacter crescentusregulates the differential DNA binding activity of the master regulator CtrA

2018 ◽  
Author(s):  
Sharath Narayanan ◽  
Lokesh Kumar ◽  
Sunish Kumar Radhakrishnan
Keyword(s):  
Cell Cycle ◽  
Dna Binding ◽  
Caulobacter Crescentus ◽  
Point Mutations ◽  
Signal Transduction Pathway ◽  
Binding Activity ◽  
Cellular Damage ◽  
Bacterial Cells ◽  
Topoisomerase Iv ◽  
A Genome

Sophisticated signaling mechanisms allow bacterial cells to cope with environmental and intracellular challenges. Activation of specific pathways facilitates the cells to overcome cellular damage and thereby warrant integrity. Here we demonstrate the pliability of the CckA-CtrA two component signaling system in the freshwater bacteriumCaulobacter crescentus. Our forward genetic screen to analyse suppressor mutations that can negate the chromosome segregation block induced by the topoisomerase IV inhibitor, NstA, yielded various point mutations in the cell cycle histidine kinase, CckA. Notably, we identified a point mutation in the PAS-B domain of CckA, which resulted in increased levels of phosphorylated CtrA (CtrA~P), the master cell cycle regulator. Surprisingly, this increase in CtrA~P levels did not translate into a genome-wide increase in the DNA occupancy of CtrA, but specifically enriched its affinity to the chromosomal origin of replication, Cori, and a very small sub-set of CtrA regulated promoters. We show that through this enhanced binding of CtrA to the Cori, cells are able to overcome the toxic defects rendered by stable NstA through a possible slow down in the chromosome cycle. Taken together, our work opens up an unexplored and intriguing aspect of the CckA-CtrA signal transduction pathway. The distinctive DNA binding nature of CtrA and its regulation by CckA might also be crucial for pathogenesis because of the highly conserved nature of CckA-CtrA pathway in alphaproteobacteria.

Determination of the secondary structure in solution of the Escherichia coli DnaA DNA-binding domain

2002 ◽  
Vol 299 (1) ◽  
pp. 42-48 ◽  
Author(s):  
Takayuki Obita ◽  
Takafumi Iwura ◽  
Masayuki Su’etsugu ◽  
Yoichiro Yoshida ◽  
Yoshitsugu Tanaka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Secondary Structure ◽  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Structure In Solution

scholarly journals DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria

PLoS Genetics ◽  
2013 ◽  
Vol 9 (5) ◽  
pp. e1003541 ◽  
Author(s):  
Antonella Fioravanti ◽  
Coralie Fumeaux ◽  
Saswat S. Mohapatra ◽  
Coralie Bompard ◽  
Matteo Brilli ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Binding ◽  
Caulobacter Crescentus ◽  
Transcriptional Regulator

scholarly journals Cooperative-Binding and Splicing-Repressive Properties of hnRNP A1

2009 ◽  
Vol 29 (20) ◽  
pp. 5620-5631 ◽  
Author(s):  
Hazeem L. Okunola ◽  
Adrian R. Krainer
Keyword(s):  
Hnrnp A1 ◽  
Sr Protein ◽  
High Affinity ◽  
Splicing Silencer ◽  
Immunodeficiency Virus ◽  
Rna Hairpin ◽  
Initial Binding ◽  
Structure In Solution ◽  
Hiv 1

ABSTRACT hnRNP A1 binds to RNA in a cooperative manner. Initial hnRNP A1 binding to an exonic splicing silencer at the 3′ end of human immunodeficiency virus type 1 (HIV-1) tat exon 3, which is a high-affinity site, is followed by cooperative spreading in a 3′-to-5′ direction. As hnRNP A1 propagates toward the 5′ end of the exon, it antagonizes binding of a serine/arginine-rich (SR) protein to an exonic splicing enhancer, thereby inhibiting splicing at that exon's alternative 3′ splice site. tat exon 3 and the preceding intron of HIV-1 pre-mRNA can fold into an elaborate RNA secondary structure in solution, which could potentially influence hnRNP A1 binding. We report here that hnRNP A1 binding and splicing repression can occur on an unstructured RNA. Moreover, hnRNP A1 can effectively unwind an RNA hairpin upon binding, displacing a bound protein. We further show that hnRNP A1 can also spread in a 5′-to-3′ direction, although when initial binding takes place in the middle of an RNA, spreading preferentially proceeds in a 3′-to-5′ direction. Finally, when two distant high-affinity sites are present on the same RNA, they facilitate cooperative spreading of hnRNP A1 between the two sites.

Sign in / Sign up

Export Citation Format

Share Document