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Comparative sequence analysis of acid sensitive/resistance proteins in Escherichia coli and Shigella flexneri.

Manikandan S, Balaji S, Kumar A, Kumar R - Bioinformation (2007)

Bottom Line: Here we found the molecular evidence that proved the relationship between E. coli and S. flexneri.It was observed that as the alignment approaches towards the C-terminal, the number of conserved residues decreases, indicating that the N-terminal region of this protein has much active role when compared to the carboxyl terminal.The gadC coded proteins are converged as a clade and diverged from other antiporters belongs to the amino acid-polyamine-organocation (APC) superfamily.

View Article: PubMed Central - PubMed

ABSTRACT
The molecular basis for the survival of bacteria under extreme conditions in which growth is inhibited is a question of great current interest. A preliminary study was carried out to determine residue pattern conservation among the antiporters of enteric bacteria, responsible for extreme acid sensitivity especially in Escherichia coli and Shigella flexneri. Here we found the molecular evidence that proved the relationship between E. coli and S. flexneri. Multiple sequence alignment of the gadC coded acid sensitive antiporter showed many conserved residue patterns at regular intervals at the N-terminal region. It was observed that as the alignment approaches towards the C-terminal, the number of conserved residues decreases, indicating that the N-terminal region of this protein has much active role when compared to the carboxyl terminal. The motif, FHLVFFLLLGG, is well conserved within the entire gadC coded protein at the amino terminal. The motif is also partially conserved among other antiporters (which are not coded by gadC) but involved in acid sensitive/resistance mechanism. Phylogenetic cluster analysis proves the relationship of Escherichia coli and Shigella flexneri. The gadC coded proteins are converged as a clade and diverged from other antiporters belongs to the amino acid-polyamine-organocation (APC) superfamily.

No MeSH data available.


Related in: MedlinePlus

Web logo (ver 2.8.2) was used to identify the consensus region of the N-terminal among the antiporter proteins not coded by gadC which is shown in box.
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Related In: Results  -  Collection


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Figure 5: Web logo (ver 2.8.2) was used to identify the consensus region of the N-terminal among the antiporter proteins not coded by gadC which is shown in box.

Mentions: We also extended our analysis to address the pattern conservation among the other antiporters (which are not coded by gadC) involved in acid sensitive/resistance mechanism. Amazingly we found that the pattern is still partially conserved for the acid sensitive/ resistance mechanism (Figure 5). This pattern conservation also depicts that the function is highly dependant on the pattern used for the acid resistance. The motif ‘FHLVFFLLLGG’ was well conserved with the entire gadC coded proteins at the amino terminal where the binding residue could be found with in the first and second transmembrane helices. [5] The partial conservation of this motif among the other antiporters (not coded by gadC) is due to the poor acid resistance. The strong motif conservation could be the reason for the extreme acid resistance of E. coli and S. flexneri. Our pattern analysis shows the relationship of Escherichia coli and Shigella flexneri. This can be correlated with the claims of Waterman and Small (2003) [19], for a strong-link between the possession of the gadC genes and the expression of stationary-phase acid resistance. This also correlates with the epidemiological data that associated these species with having a lower infective dose compared to other enteric pathogens and confirms the close evolutionary relationship between Escherichia coli and Shigella flexneri amongst the Enterobacteriaceae.


Comparative sequence analysis of acid sensitive/resistance proteins in Escherichia coli and Shigella flexneri.

Manikandan S, Balaji S, Kumar A, Kumar R - Bioinformation (2007)

Web logo (ver 2.8.2) was used to identify the consensus region of the N-terminal among the antiporter proteins not coded by gadC which is shown in box.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2255067&req=5

Figure 5: Web logo (ver 2.8.2) was used to identify the consensus region of the N-terminal among the antiporter proteins not coded by gadC which is shown in box.
Mentions: We also extended our analysis to address the pattern conservation among the other antiporters (which are not coded by gadC) involved in acid sensitive/resistance mechanism. Amazingly we found that the pattern is still partially conserved for the acid sensitive/ resistance mechanism (Figure 5). This pattern conservation also depicts that the function is highly dependant on the pattern used for the acid resistance. The motif ‘FHLVFFLLLGG’ was well conserved with the entire gadC coded proteins at the amino terminal where the binding residue could be found with in the first and second transmembrane helices. [5] The partial conservation of this motif among the other antiporters (not coded by gadC) is due to the poor acid resistance. The strong motif conservation could be the reason for the extreme acid resistance of E. coli and S. flexneri. Our pattern analysis shows the relationship of Escherichia coli and Shigella flexneri. This can be correlated with the claims of Waterman and Small (2003) [19], for a strong-link between the possession of the gadC genes and the expression of stationary-phase acid resistance. This also correlates with the epidemiological data that associated these species with having a lower infective dose compared to other enteric pathogens and confirms the close evolutionary relationship between Escherichia coli and Shigella flexneri amongst the Enterobacteriaceae.

Bottom Line: Here we found the molecular evidence that proved the relationship between E. coli and S. flexneri.It was observed that as the alignment approaches towards the C-terminal, the number of conserved residues decreases, indicating that the N-terminal region of this protein has much active role when compared to the carboxyl terminal.The gadC coded proteins are converged as a clade and diverged from other antiporters belongs to the amino acid-polyamine-organocation (APC) superfamily.

View Article: PubMed Central - PubMed

ABSTRACT
The molecular basis for the survival of bacteria under extreme conditions in which growth is inhibited is a question of great current interest. A preliminary study was carried out to determine residue pattern conservation among the antiporters of enteric bacteria, responsible for extreme acid sensitivity especially in Escherichia coli and Shigella flexneri. Here we found the molecular evidence that proved the relationship between E. coli and S. flexneri. Multiple sequence alignment of the gadC coded acid sensitive antiporter showed many conserved residue patterns at regular intervals at the N-terminal region. It was observed that as the alignment approaches towards the C-terminal, the number of conserved residues decreases, indicating that the N-terminal region of this protein has much active role when compared to the carboxyl terminal. The motif, FHLVFFLLLGG, is well conserved within the entire gadC coded protein at the amino terminal. The motif is also partially conserved among other antiporters (which are not coded by gadC) but involved in acid sensitive/resistance mechanism. Phylogenetic cluster analysis proves the relationship of Escherichia coli and Shigella flexneri. The gadC coded proteins are converged as a clade and diverged from other antiporters belongs to the amino acid-polyamine-organocation (APC) superfamily.

No MeSH data available.


Related in: MedlinePlus