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Genomics Analysis of Replicative Helicase DnaB Sequences in Proteobacteria.

Poggi S, Chandra SB - Acta Inform Med (2014)

Bottom Line: Our results were further supported, when we reanalyzed and reconstructed the phylogenetic tree after the inclusion of sequences from Actinobacteria and Firmicute phylum.In addition, Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria appear to share a closer common ancestor than from the other two subclasses.The Dot-plot analysis indicated that, the region between amino acid residues 320 to 400 was strongly conserved among all five subclasses.

View Article: PubMed Central - PubMed

Affiliation: Research Resources Centre, University of Illinois at Chicago, Chicago, USA.

ABSTRACT
Replicative Helicase DnaB interacts with DnaA, DnaC, DnaG, and DNA polymerase III to commence replication, increase the movement rate of the replication fork, and to assemble part of the primosome. The formation of the replication fork is limited by the ability to load DnaB to the DNA, thus DnaB has shown to be vital to a large extent. In the absence of DnaB, the replication fork is not maintained and in a state of inactivity the replication fork degrades and collapses. To further understand importance of this enzyme from an evolutionary perspective, a genomic analysis DnaB protein sequences, chosen from five Proteobacteria subclasses was performed. Our analysis indicates that, DnaB replicative helicases of Alphaproteobacteria and Epsilonproteobacteria have diverged at an earlier stage from Betaproteobacteria, Deltaproteobacteria and Gammaproteobacteria as well as from one another. Our results were further supported, when we reanalyzed and reconstructed the phylogenetic tree after the inclusion of sequences from Actinobacteria and Firmicute phylum. In addition, Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria appear to share a closer common ancestor than from the other two subclasses. The Dot-plot analysis indicated that, the region between amino acid residues 320 to 400 was strongly conserved among all five subclasses.

No MeSH data available.


Related in: MedlinePlus

The dot plot comparison of DnaB sequences between subclasses of proteobacteria showed some co-linearity, but resulted in a plot with numerous non- collinear fragments: (A) Beta/Alpha, (B) Delta/Gamma, (C) Epsilon/Delta, and (D) Beta/Gamma (E) Alpha/Epsilon [not shown in the figure], at threshold= 23 and window size= 10.
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Figure 2: The dot plot comparison of DnaB sequences between subclasses of proteobacteria showed some co-linearity, but resulted in a plot with numerous non- collinear fragments: (A) Beta/Alpha, (B) Delta/Gamma, (C) Epsilon/Delta, and (D) Beta/Gamma (E) Alpha/Epsilon [not shown in the figure], at threshold= 23 and window size= 10.

Mentions: Dot-plot analysis was carried to compare the protein sequences within and between the five subclasses using one organism per group. The Dot-plots for organisms within each sub-class, not surprisingly, exhibited a high degree of co-linearity; particularly for Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria (Figure 1). When comparing the sequences between each sub-class, the Dot-plot analysis revealed a short region of co-linearity between all subclasses from approximate amino acid position from 320 through 400 (Figure 2).


Genomics Analysis of Replicative Helicase DnaB Sequences in Proteobacteria.

Poggi S, Chandra SB - Acta Inform Med (2014)

The dot plot comparison of DnaB sequences between subclasses of proteobacteria showed some co-linearity, but resulted in a plot with numerous non- collinear fragments: (A) Beta/Alpha, (B) Delta/Gamma, (C) Epsilon/Delta, and (D) Beta/Gamma (E) Alpha/Epsilon [not shown in the figure], at threshold= 23 and window size= 10.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4216422&req=5

Figure 2: The dot plot comparison of DnaB sequences between subclasses of proteobacteria showed some co-linearity, but resulted in a plot with numerous non- collinear fragments: (A) Beta/Alpha, (B) Delta/Gamma, (C) Epsilon/Delta, and (D) Beta/Gamma (E) Alpha/Epsilon [not shown in the figure], at threshold= 23 and window size= 10.
Mentions: Dot-plot analysis was carried to compare the protein sequences within and between the five subclasses using one organism per group. The Dot-plots for organisms within each sub-class, not surprisingly, exhibited a high degree of co-linearity; particularly for Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria (Figure 1). When comparing the sequences between each sub-class, the Dot-plot analysis revealed a short region of co-linearity between all subclasses from approximate amino acid position from 320 through 400 (Figure 2).

Bottom Line: Our results were further supported, when we reanalyzed and reconstructed the phylogenetic tree after the inclusion of sequences from Actinobacteria and Firmicute phylum.In addition, Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria appear to share a closer common ancestor than from the other two subclasses.The Dot-plot analysis indicated that, the region between amino acid residues 320 to 400 was strongly conserved among all five subclasses.

View Article: PubMed Central - PubMed

Affiliation: Research Resources Centre, University of Illinois at Chicago, Chicago, USA.

ABSTRACT
Replicative Helicase DnaB interacts with DnaA, DnaC, DnaG, and DNA polymerase III to commence replication, increase the movement rate of the replication fork, and to assemble part of the primosome. The formation of the replication fork is limited by the ability to load DnaB to the DNA, thus DnaB has shown to be vital to a large extent. In the absence of DnaB, the replication fork is not maintained and in a state of inactivity the replication fork degrades and collapses. To further understand importance of this enzyme from an evolutionary perspective, a genomic analysis DnaB protein sequences, chosen from five Proteobacteria subclasses was performed. Our analysis indicates that, DnaB replicative helicases of Alphaproteobacteria and Epsilonproteobacteria have diverged at an earlier stage from Betaproteobacteria, Deltaproteobacteria and Gammaproteobacteria as well as from one another. Our results were further supported, when we reanalyzed and reconstructed the phylogenetic tree after the inclusion of sequences from Actinobacteria and Firmicute phylum. In addition, Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria appear to share a closer common ancestor than from the other two subclasses. The Dot-plot analysis indicated that, the region between amino acid residues 320 to 400 was strongly conserved among all five subclasses.

No MeSH data available.


Related in: MedlinePlus