Roles for the AAA+ motifs of DnaA in the initiation of DNA replication

2008 ◽  
Vol 36 (1) ◽  
pp. 78-82 ◽  
Author(s):  
Tsutomu Katayama
Keyword(s):  
Bacterial Species ◽  
Replication Initiation ◽  
Chromosomal Replication ◽  
Aaa Atpase ◽  
Initiation Of Replication ◽  
Oric Region ◽  
Specific Proteins ◽  
Ordered Assembly ◽  
Related Proteins ◽  
Hydrolysis Of

The cell-cycle-co-ordinated initiation of chromosomal replication is highly regulated. The ordered assembly and conformational change of specific proteins at the replication origin are crucial to the process of replication initiation. In Escherichia coli, ATP–DnaA molecules form multimeric complexes with the chromosomal origin of replication (oriC), and unwind the duplex DNA within oriC, resulting in initiation of replication. DnaA is a common protein in bacterial species and plays a main and crucial role in the initiation of chromosomal replication. Unlike well-characterized AAA+ (ATPase associated with various cellular activities) proteins such as chaperons and proteases, DnaA molecules stably take on a monomeric form and form homomultimers in a manner dependent on binding to oriC. The oriC region carries several DnaA-binding sites with various affinities. Recent progress in the analysis of DnaA and related proteins has revealed specific roles for the AAA+ unique motifs of DnaA. These results suggest mechanisms for recognition of ATP bound to DnaA, the co-operative binding of ATP–DnaA molecules on oriC, the formation of an ATP–DnaA-specific oriC complex, an initiation complex and regulatory hydrolysis of DnaA-bound ATP.

scholarly journals DiaA, a Novel DnaA-binding Protein, Ensures the Timely Initiation ofEscherichia coliChromosome Replication

2004 ◽  
Vol 279 (44) ◽  
pp. 45546-45555 ◽  
Author(s):  
Takuma Ishida ◽  
Nobuyoshi Akimitsu ◽  
Tamami Kashioka ◽  
Masakazu Hatano ◽  
Toshio Kubota ◽  
...  
Keyword(s):  
Gel Filtration ◽  
Replication Initiation ◽  
Temperature Sensitive ◽  
Minichromosome Maintenance ◽  
Chromosomal Replication ◽  
Timely Initiation ◽  
Initiation Of Replication ◽  
Direct Binding ◽  
Cold Sensitive

The DnaA protein is the initiator ofEscherichia colichromosomal replication. In this study, we identify a novel DnaA-associating protein, DiaA, that is required for the timely initiation of replication during the cell cycle. DiaA promotes the growth of specific temperature-sensitivednaAmutants and ensures stable minichromosome maintenance, whereas DiaA does not decrease the cellular DnaA content. AdiaA::Tn5mutation suppresses the cold-sensitive growth of an overinitiation typednaAmutant independently of SeqA, a negative modulator of initiation. Flow cytometry analyses revealed that the timing of replication initiation is disrupted in thediaAmutant cells as well as wild-type cells with pBR322 expressing thediaAgene. Gel filtration and chemical cross-linking experiments showed that purified DiaA forms a stable homodimer. Immunoblotting analysis indicated that a single cell contains about 280 DiaA dimers. DiaA stimulates minichromosome replication in anin vitrosystem especially when the level of DnaA included is limited. Moreover, specific and direct binding between DnaA and DiaA was observed, which requires a DnaA N-terminal region. DiaA binds to both ATP- and ADP-bound forms of DnaA with a similar affinity. Thus, we conclude that DiaA is a novel DnaA-associating factor that is crucial to ensure the timely initiation of chromosomal replication.

scholarly journals Effects of the Chromosome Partitioning Protein Spo0J (ParB) on oriC Positioning and Replication Initiation in Bacillus subtilis

2003 ◽  
Vol 185 (4) ◽  
pp. 1326-1337 ◽  
Author(s):  
Philina S. Lee ◽  
Daniel Chi-Hong Lin ◽  
Shigeki Moriya ◽  
Alan D. Grossman
Keyword(s):  
Bacillus Subtilis ◽  
Binding Sites ◽  
Fluorescent Protein ◽  
Bacterial Species ◽  
Significant Proportion ◽  
Subcellular Location ◽  
Replication Initiation ◽  
Null Mutant ◽  
Protein Ratio ◽  
Chromosome Partitioning

ABSTRACT Spo0J (ParB) of Bacillus subtilis is a DNA-binding protein that belongs to a conserved family of proteins required for efficient plasmid and chromosome partitioning in many bacterial species. We found that Spo0J contributes to the positioning of the chromosomal oriC region, but probably not by recruiting the origin regions to specific subcellular locations. In wild-type cells during exponential growth, duplicated origin regions were generally positioned around the cell quarters. In a spo0J null mutant, sister origin regions were often closer together, nearer to midcell. We found, by using a Spo0J-green fluorescent protein [GFP] fusion, that the subcellular location of Spo0J was a consequence of the chromosomal positions of the Spo0J binding sites. When an array of binding sites (parS sites) were inserted at various chromosomal locations in the absence of six of the eight known parS sites, Spo0J-GFP was no longer found predominantly at the cell quarters, indicating that Spo0J is not sufficient to recruit chromosomal parS sites to the cell quarters. spo0J also affected chromosome positioning during sporulation. A spo0J null mutant showed an increase in the number of cells with some origin-distal regions located in the forespore. In addition, a spo0J null mutation caused an increase in the number of foci per cell of LacI-GFP bound to arrays of lac operators inserted in various positions in the chromosome, including the origin region, an increase in the DNA-protein ratio, and an increase in origins per cell, as determined by flow cytometry. These results indicate that the spo0J mutant produced a significant proportion of cells with increased chromosome content, probably due to increased and asynchronous initiation of DNA replication.

scholarly journals Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation

2006 ◽  
Vol 59 (1) ◽  
pp. 265-275 ◽  
Author(s):  
Tomotake Ote ◽  
Masayuki Hashimoto ◽  
Yoshiho Ikeuchi ◽  
Masayuki Su'etsugu ◽  
Tsutomu Suzuki ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Binding Protein ◽  
Replication Initiation ◽  
Rna Modification ◽  
Chromosomal Replication ◽  
Folate Binding Protein

scholarly journals Archaeal Orc1 protein interacts with T-rich single-stranded DNA

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Katarzyna Wegrzyn ◽  
Igor Konieczny
Keyword(s):  
Dna Replication ◽  
Replication Initiation ◽  
Single Stranded Dna ◽  
Dna Replication Initiation ◽  
Double Stranded Dna ◽  
Nucleoprotein Complexes ◽  
Eukaryotic Organisms ◽  
Replication Initiation Proteins ◽  
Hydrolysis Of ◽  
Replication Activity

Abstract Objective The ability to form nucleoprotein complexes is a fundamental activity of DNA replication initiation proteins. They bind within or nearby the region of replication origin what results in melting of a double-stranded DNA (dsDNA) and formation of single-stranded DNA (ssDNA) region where the replication machinery can assemble. For prokaryotic initiators it was shown that they interact with the formed ssDNA and that this interaction is required for the replication activity. The ability to interact with ssDNA was also shown for Saccharomyces cerevisiae replication initiation protein complex ORC. For Archaea, which combine features of both prokaryotic and eukaryotic organisms, there was no evidence whether DNA replication initiators can interact with ssDNA. We address this issue in this study. Results Using purified Orc1 protein from Aeropyrum pernix (ApOrc1) we analyzed its ability to interact with ssDNA containing sequence of an AT-rich region of the A. pernix origin Ori1 as well as with homopolymers of thymidine (polyT) and adenosine (polyA). The Bio-layer interferometry, surface plasmon resonance and microscale thermophoresis showed that the ApOrc1 can interact with ssDNA and it binds preferentially to T-rich ssDNA. The hydrolysis of ATP is not required for this interaction.

Anaerobic treatment of proteinaceous wastewater under mesophilic and thermophilic conditions

1999 ◽  
Vol 40 (1) ◽  
pp. 77-84 ◽  
Author(s):  
H. H. P. Fang ◽  
D. Wai-Chung Chung
Keyword(s):  
Bacterial Species ◽  
Oxygen Demand ◽  
Anaerobic Treatment ◽  
Upflow Anaerobic Sludge Blanket ◽  
Anaerobic Sludge ◽  
Loading Rates ◽  
Batch Tests ◽  
Thermophilic Conditions ◽  
Anaerobic Sludge Blanket ◽  
Hydrolysis Of

Experiments were conducted in two 2.8 liter UASB (upflow anaerobic sludge blanket) reactors treating proteinaceous wastewaters at 37° and 55°C with 9 hours of hydraulic retention. Results showed that the mesophilic reactor consistently removed 83.5-85.1% of COD (chemical oxygen demand) at loading rates ranging 8-22 g COD l−1 d−1 (corresponding to 3000-8250 mg l−1 of proteinaceous COD in wastewater), whereas the thermophilic reactor removed only 68.5-82.7%. At 32 g COD l−1 d−1 (i.e. 12000 mg COD l−1), the removal efficiencies were lowered to 75.7% in the mesophilic reactor and 65.1% in the thermophilic reactor. At 42 g COD l−1 d−1, severe sludge washout occurred in the mesophilic reactor; at the same loading rate, the thermophilic reactor removed only 53.8% of COD even though sludge washout was under control. The degradation rate in the both reactors was limited by the initial hydrolysis of proteins. However, batch tests showed that thermophilic sludge had slightly higher methanogenic activities than mesophilic sludge in treating proteins and intermediate acids, except propionate. The sludge yields in mesophilic and thermophilic reactors were 0.066 and 0.099 g VSS g COD−1, respectively. Observations by scanning electron microscopy indicated that both types of sludge granules were of irregular shape. There was little noticeable difference between the two granules; both had neither a layered microstructure nor a predominant bacterial species.

scholarly journals Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes

2020 ◽  
Vol 8 (1) ◽  
pp. 105 ◽  
Author(s):  
Adam Kawalek ◽  
Pawel Wawrzyniak ◽  
Aneta Agnieszka Bartosik ◽  
Grazyna Jagura-Burdzy
Keyword(s):  
Bacterial Species ◽  
Regulation Of Gene Expression ◽  
Replication Initiation ◽  
Bacterial Cells ◽  
Dna Segregation ◽  
Cellular Processes ◽  
Chromosome Partitioning ◽  
Structural Maintenance Of Chromosome ◽  
Dna Partitioning

The segregation of newly replicated chromosomes in bacterial cells is a highly coordinated spatiotemporal process. In the majority of bacterial species, a tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target(s) parS sequence(s), facilitates the initial steps of chromosome partitioning. ParB nucleates around parS(s) located in the vicinity of newly replicated oriCs to form large nucleoprotein complexes, which are subsequently relocated by ParA to distal cellular compartments. In this review, we describe the role of ParB in various processes within bacterial cells, pointing out interspecies differences. We outline recent progress in understanding the ParB nucleoprotein complex formation and its role in DNA segregation, including ori positioning and anchoring, DNA condensation, and loading of the structural maintenance of chromosome (SMC) proteins. The auxiliary roles of ParBs in the control of chromosome replication initiation and cell division, as well as the regulation of gene expression, are discussed. Moreover, we catalog ParB interacting proteins. Overall, this work highlights how different bacterial species adapt the DNA partitioning ParAB-parS system to meet their specific requirements.

scholarly journals The Chinese Hamster Dihydrofolate Reductase Replication Origin Decision Point Follows Activation of Transcription and Suppresses Initiation of Replication within Transcription Units

2006 ◽  
Vol 26 (3) ◽  
pp. 1051-1062 ◽  
Author(s):  
Takayo Sasaki ◽  
Sunita Ramanathan ◽  
Yukiko Okuno ◽  
Chiharu Kumagai ◽  
Seemab S. Shaikh ◽  
...  
Keyword(s):  
Dihydrofolate Reductase ◽  
Replication Origin ◽  
Chinese Hamster ◽  
Replication Initiation ◽  
Decision Point ◽  
Protein Synthesis Inhibitors ◽  
Initiation Of Replication ◽  
Activation Of Transcription ◽  
Egg Extracts ◽  
Active Transcription

ABSTRACT Chinese hamster ovary (CHO) cells select specific replication origin sites within the dihydrofolate reductase (DHFR) locus at a discrete point during G1 phase, the origin decision point (ODP). Origin selection is sensitive to transcription but not protein synthesis inhibitors, implicating a pretranslational role for transcription in origin specification. We have constructed a DNA array covering 121 kb surrounding the DHFR locus, to comprehensively investigate replication initiation and transcription in this region. When nuclei isolated within the first 3 h of G1 phase were stimulated to initiate replication in Xenopus egg extracts, replication initiated without any detectable preference for specific sites. At the ODP, initiation became suppressed from within the Msh3, DHFR, and 2BE2121 transcription units. Active transcription was mostly confined to these transcription units, and inhibition of transcription by alpha-amanitin resulted in the initiation of replication within transcription units, indicating that transcription is necessary to limit initiation events to the intergenic region. However, the resumption of DHFR transcription after mitosis took place prior to the ODP and so is not on its own sufficient to suppress initiation of replication. Together, these results demonstrate a remarkable flexibility in sequence selection for initiating replication and implicate transcription as one important component of origin specification at the ODP.

scholarly journals Regulation of chromosomal replication initiation by oriC-proximal DnaA-box clusters in Bacillus subtilis

2011 ◽  
Vol 40 (1) ◽  
pp. 220-234 ◽  
Author(s):  
Hajime Okumura ◽  
Mika Yoshimura ◽  
Mikako Ueki ◽  
Taku Oshima ◽  
Naotake Ogasawara ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Replication Initiation ◽  
Chromosomal Replication ◽  
Dnaa Box

scholarly journals DNA Replication Origins Fire Stochastically in Fission Yeast

2006 ◽  
Vol 17 (1) ◽  
pp. 308-316 ◽  
Author(s):  
Prasanta K. Patel ◽  
Benoit Arcangioli ◽  
Stephen P. Baker ◽  
Aaron Bensimon ◽  
Nicholas Rhind
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Replication Initiation ◽  
Epigenetic Mechanism ◽  
Replication Origins ◽  
Origin Firing ◽  
Cell Cycles ◽  
Initiation Of Replication ◽  
Dna Combing ◽  
Dna Replication Origins

DNA replication initiates at discrete origins along eukaryotic chromosomes. However, in most organisms, origin firing is not efficient; a specific origin will fire in some but not all cell cycles. This observation raises the question of how individual origins are selected to fire and whether origin firing is globally coordinated to ensure an even distribution of replication initiation across the genome. We have addressed these questions by determining the location of firing origins on individual fission yeast DNA molecules using DNA combing. We show that the firing of replication origins is stochastic, leading to a random distribution of replication initiation. Furthermore, origin firing is independent between cell cycles; there is no epigenetic mechanism causing an origin that fires in one cell cycle to preferentially fire in the next. Thus, the fission yeast strategy for the initiation of replication is different from models of eukaryotic replication that propose coordinated origin firing.

scholarly journals The Escherichia coli datA site promotes proper regulation of cell division

Microbiology ◽  
2014 ◽  
Vol 160 (4) ◽  
pp. 703-710 ◽  
Author(s):  
Morigen Morigen ◽  
Ingvild Flåtten ◽  
Kirsten Skarstad
Keyword(s):  
Escherichia Coli ◽  
Cell Division ◽  
Binding Sites ◽  
Replication Initiation ◽  
Permissive Temperature ◽  
Initiator Protein ◽  
Dnaa Protein ◽  
Daughter Cells ◽  
Initiation Of Replication ◽  
Replication Initiator

In Escherichia coli inhibition of replication leads to a block of cell division. This checkpoint mechanism ensures that no cell divides without having two complete copies of the genome to pass on to the two daughter cells. The chromosomal datA site is a 1 kb region that contains binding sites for the DnaA replication initiator protein, and which contributes to the inactivation of DnaA. An excess of datA sites provided on plasmids has been found to lead to both a delay in initiation of replication and in cell division during exponential growth. Here we have investigated the effect of datA on the cell division block that occurs upon inhibition of replication initiation in a dnaC2 mutant. We found that this checkpoint mechanism was aided by the presence of datA. In cells where datA was deleted or an excess of DnaA was provided, cell division occurred in the absence of replication and anucleate cells were formed. This finding indicates that loss of datA and/or excess of DnaA protein promote cell division. This conclusion was supported by the finding that the lethality of the division-compromised mutants ftsZ84 and ftsI23 was suppressed by deletion of datA, at the lowest non-permissive temperature. We propose that the cell division block that occurs upon inhibition of DNA replication is, at least in part, due to a drop in the concentration of the ATP–DnaA protein.

Sign in / Sign up

Export Citation Format

Share Document