A comparative analysis of three classes of bacterial non-specific Acid phosphatases and archaeal phosphoesterases: evolutionary perspective

Abstract

Introduction: Bacterial nonspecific acid phosphohydrolases (NSAPs) or phosphatases are group of enzymes secreted as soluble periplasmic proteins or retained as membrane bound lipoproteins that are usually able to dephosphorylate a broad array of structurally unrelated organic phosphoesters (nucleotides, sugar phosphates, phytic acid etc.) to acquire inorganic phosphate (Pi) and organic byproducts. They exhibit optimal catalytic activity at acidic to neutral pH values. On the basis of amino acid sequence relatedness, phosphatase are grouped into different molecular families namely Class A, Class B and Class C acid phosphatase respectively.

Results and discussion: In this article out of thirty three sequences, twenty six belonging to each of the three classes of bacterial acid phosphatase and seven belonging to archaeal phosphoesterases were analyzed using various tools of bioinformatics. Phylogenetic analysis, dot plot comparisons and motif analysis were done to identify a number of similarities and differences between three classes of bacterial acid phosphatases and archaeal phosphoesterases. In this research we have attempted to decipher evolutionary relationship between three classes of bacterial acid phosphatase and archaeal phosphoesterases using bioinformatics approach.

Keywords: NSAP; Non-specific acid phosphatase; archaeal phosphoesterase; evolution..

Figure 1a

The motifs present in all 33 sequences of the three classes of bacterial acid phosphatase and archaeal phosphoesterases are shown in above table. to the left are the names of all 26 bacterial species whose acid phosphatases and 7 archaeal species whose phosphoesterases sequences were taken for analysis. sequences 1 through 10 represent bacterial Class A acid phosphatases, sequences 11 through 17 represent bacterial Class B acid phosphatases, sequences 18 through 26 represent bacterial Class C acid phosphatases and sequences 27 through 33 represent archaeal phosphoesterases. thirteen different motifs are shown in 33 sequences. some of the sequences share some conserved sequence motifs whereas some of the motifs are uniquely present in each class of bacterial acid phosphatase and archaeal phosphoesterases. the height of the motif “block” is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.

Figure 1b

The sequences of motifs 1, 2, 3, 5, 7, 13 are shown in the figure above. The numbers to the left of each protein sequence corresponds with the number and name of the organism in table of Fig. 1a. The second number represents the sequence length of the enzyme acid phosphatase and phosphoesterase and third column shows the sequence with the motifs. For example in Motif 2, the first bacterium is number 15, Escherichia coli str. K-12 substr. MG1655 has a length of 80 amino acids which is shown in the sequence with its motif.

Figure 2a

The dot plot comparison of sequences belonging to same classes resulted in collinear diagonal fragment. the dot plots shown are within the same class of bacterial acid phosphatase ClassA/ClassA, ClassB/ClassB, ClassC/ClassC and archaeal phoshoesterases, Archaea/Archaea.

Figure 2b

The dot plot comparison of sequences belonging to different classes such as ClassA/ClassB, ClassB/ClassC, ClassC/ClassA, Archaea/ClassB resulted in a plot with non- collinear fragments.

Figure 3

A Phylogenetic tree constructed by using amino acid sequences belonging to all the tree classes of bacterial acid phosphatase and archaeal phosphoesterase. The name of the bacteria with the class it belongs to makes the first and second clade and archaea that makes the third clade is shown on the right hand side of the cladogram. The scores seen on the tree show the degree of sequence similarity between the sequences of each class. The names of bacteria and archaea along with the accession numbers in parentheses are as follows: The numbers 1 to10 represent Class A bacterial acid phosphatase. Numbers 11 to 17 represent Class B acid phosphatase, numbers 18 to 26 represent Class C acid phosphatase and number 27-33 represent Archaeal phosphoesterase. 1. Rahnella sp. Y9602 (ADW72173.1), 2. Zymomonas mobilis (AAA27700.1), 3. Salmonella enterica subsp. enterica serovar Typhi str. CT18 (NP _458615.1), 4. Salmonella enterica subsp. enterica serovar Typhimurium (CAA41760.1), 5. Providencia stuartii (CAA46032.1), 6. Enterobacter cloacae SCF1(YP _003942142.1), 7. Escherichia blattae (BAA84942.1) , 8. Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884 (ZP_06016217.1), 9. Raoultella planticola (BAB18918.1), 10. Enterobacter aerogenes (ABW37174.1), 11. Haemophilus influenza (CAA68889.1), 12. Morganella morganii (CAA55131.1), 13. Klebsiella pneumoniae (AAL59317.1), 14. Shigella boydii CDC 3083-94 (ACD06580.1), 15. Escherichia coli str. K-12 substr. MG1655 (CAA60534.1), 16. Salmonella enterica subsp. enterica serovar Typhimurium (AAW22868.1), 17. Salmonella enterica (CAB40974.1), 18. Streptococcus agalactiae 2603V/R (NP _688757.1), 19. Streptococcus pyogenes MGAS9429 (YP _597336.1), 20. Streptococcus dysgalactiae subsp. equisimilis GGS_124 (YP _002997631.1), 21. Streptococcus dysgalactiae subsp. equisimilis (CAA73175.1), 22. Bacillus sp. FR C_Y9-2(ABO69628.1), 23. Bacillus anthracis str. ‘Ames Ancestor’ (YP _021394.1), 24. Bacillus anthracis str. Ames (NP _846955.1), 25. Clostridium perfringens (ACB11490.1), 26. Pasteurella multocida (ACM68930.1), 27. Thermococcus gammatolerans EJ3 (YP _002960201.1), 28. Thermococcus kodakarensis KOD 1 (BAD84554.1), 29. Thermococcus sibiricus MM 739 (YP _002993470.1), 30. Thermococcus sp. AM4 (ZP_04880406.1), 31. Thermococcus gammatolerans EJ3 (YP _002959503.1), 32. Methanocaldococcus sp. FS 406-22 (YP _003458929.1), 33. Methanocaldococcus vulcanius M7 (YP _003247262.1).