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Phylogenetic and amino acid conservation analyses of bacterial L-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain.

Stuecker TN, Bramhacharya S, Hodge-Hanson KM, Suen G, Escalante-Semerena JC - BMC Res Notes (2015)

Bottom Line: This class is found exclusively in the Gammaproteobacteria.Class II L-aspartate-α-decarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla.Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583).

View Article: PubMed Central - PubMed

Affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA. BramhacharyaS@my.hiram.edu.

ABSTRACT

Background: All organisms must synthesize the enzymatic cofactor coenzyme A (CoA) from the precursor pantothenate. Most bacteria can synthesize pantothenate de novo by the condensation of pantoate and β-alanine. The synthesis of β-alanine is catalyzed by L-aspartate-α-decarboxylase (PanD), a pyruvoyl enzyme that is initially synthesized as a zymogen (pro-PanD). Active PanD is generated by self-cleavage of pro-PanD at Gly24-Ser25 creating the active-site pyruvoyl moiety. In Salmonella enterica, this cleavage requires PanM, an acetyl-CoA sensor related to the Gcn5-like N-acetyltransferases. PanM does not acetylate pro-PanD, but the recent publication of the three-dimensional crystal structure of the PanM homologue PanZ in complex with the PanD zymogen of Escherichia coli provides validation to our predictions and provides a framework in which to further examine the cleavage mechanism. In contrast, PanD from bacteria lacking PanM efficiently cleaved in the absence of PanM in vivo.

Results: Using phylogenetic analyses combined with in vivo phenotypic investigations, we showed that two classes of bacterial L-aspartate-α-decarboxylases exist. This classification is based on their posttranslational activation by self-cleavage of its zymogen. Class I L-aspartate-α-decarboxylase zymogens require the acetyl-CoA sensor PanM to be cleaved into active PanD. This class is found exclusively in the Gammaproteobacteria. Class II L-aspartate-α-decarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla. Several members of the Euryarchaeota and Crenarchaeota also contain Class II L-aspartate-α-decarboxylases. Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583). This conserved region represents a putative domain for interactions with L-aspartate-α-decarboxylase zymogens. This work may inform future biochemical and structural studies of pro-PanD-PanM interactions.

Conclusions: Experimental results indicate that S. enterica and C. glutamicum L-aspartate-α-decarboxylases represent two different classes of homologues of these enzymes. Class I homologues require PanM for activation, while Class II self cleave in the absence of PanM. Computer modeling of conserved amino acids using structure coordinates of PanM and L-aspartate-α-decarboxylase available in the protein data bank (RCSB PDB) revealed a putative site of interactions, which may help generate models to help understand the molecular details of the self-cleavage mechanism of L-aspartate-α-decarboxylases.

No MeSH data available.


Related in: MedlinePlus

l-Aspartate-α-decarboxylase (PanD) is predominantly found in Gammaproteobacteria. Results of maximum likelihood phylogenetic analysis of l-aspartate-α-decarboxylase homologues in the Proteobacteria are highlighted: teal Alphaproteobacteria; blue Betaproteobacteria; pink Epsilonproteobacteria; yellow Gammaproteobacteria. Archaeal l-aspartate-α-decarboxylase homologues are marked with an asterisk.
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Fig1: l-Aspartate-α-decarboxylase (PanD) is predominantly found in Gammaproteobacteria. Results of maximum likelihood phylogenetic analysis of l-aspartate-α-decarboxylase homologues in the Proteobacteria are highlighted: teal Alphaproteobacteria; blue Betaproteobacteria; pink Epsilonproteobacteria; yellow Gammaproteobacteria. Archaeal l-aspartate-α-decarboxylase homologues are marked with an asterisk.

Mentions: To gain insights into the evolutionary history of PanM and l-aspartate-α-decarboxylase, phylogenetic trees were constructed using alignments of all homologues for each protein. l-aspartate-α-decarboxylase was widely distributed amongst numerous bacterial phyla and two archaeal phyla (Fig. 1). Interestingly, the phylogeny of l-aspartate-α-decarboxylase did not follow standard 16S phylogenetic relationships. This was observed in the phylum Proteobacteria (Fig. 1), where l-aspartate-α-decarboxylase homologues from Gamma, Alpha, Beta, and Epsilonproteobacteria did not cluster as expected. In light of this information, we posited that horizontal gene transfer might have played a role in l-aspartate-α-decarboxylase evolution. In contrast, homologues of PanM were only found in genomes belonging to the Gammaproteobacteria (Fig. 2). However, not all gammaproteobacterial genomes contained a panM gene. Of the 216 gammaproteobacterial genomes encoding an l-aspartate-α-decarboxylase homologue, only 129 (~60 %) also encoded a PanM homologue. All bacterial genomes encoding a PanM homologue also encoded l-aspartate-α-decarboxylase, which supported the physiological role of PanM as a maturation factor of the l-aspartate-α-decarboxylase zymogen.Fig. 1


Phylogenetic and amino acid conservation analyses of bacterial L-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain.

Stuecker TN, Bramhacharya S, Hodge-Hanson KM, Suen G, Escalante-Semerena JC - BMC Res Notes (2015)

l-Aspartate-α-decarboxylase (PanD) is predominantly found in Gammaproteobacteria. Results of maximum likelihood phylogenetic analysis of l-aspartate-α-decarboxylase homologues in the Proteobacteria are highlighted: teal Alphaproteobacteria; blue Betaproteobacteria; pink Epsilonproteobacteria; yellow Gammaproteobacteria. Archaeal l-aspartate-α-decarboxylase homologues are marked with an asterisk.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4537548&req=5

Fig1: l-Aspartate-α-decarboxylase (PanD) is predominantly found in Gammaproteobacteria. Results of maximum likelihood phylogenetic analysis of l-aspartate-α-decarboxylase homologues in the Proteobacteria are highlighted: teal Alphaproteobacteria; blue Betaproteobacteria; pink Epsilonproteobacteria; yellow Gammaproteobacteria. Archaeal l-aspartate-α-decarboxylase homologues are marked with an asterisk.
Mentions: To gain insights into the evolutionary history of PanM and l-aspartate-α-decarboxylase, phylogenetic trees were constructed using alignments of all homologues for each protein. l-aspartate-α-decarboxylase was widely distributed amongst numerous bacterial phyla and two archaeal phyla (Fig. 1). Interestingly, the phylogeny of l-aspartate-α-decarboxylase did not follow standard 16S phylogenetic relationships. This was observed in the phylum Proteobacteria (Fig. 1), where l-aspartate-α-decarboxylase homologues from Gamma, Alpha, Beta, and Epsilonproteobacteria did not cluster as expected. In light of this information, we posited that horizontal gene transfer might have played a role in l-aspartate-α-decarboxylase evolution. In contrast, homologues of PanM were only found in genomes belonging to the Gammaproteobacteria (Fig. 2). However, not all gammaproteobacterial genomes contained a panM gene. Of the 216 gammaproteobacterial genomes encoding an l-aspartate-α-decarboxylase homologue, only 129 (~60 %) also encoded a PanM homologue. All bacterial genomes encoding a PanM homologue also encoded l-aspartate-α-decarboxylase, which supported the physiological role of PanM as a maturation factor of the l-aspartate-α-decarboxylase zymogen.Fig. 1

Bottom Line: This class is found exclusively in the Gammaproteobacteria.Class II L-aspartate-α-decarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla.Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583).

View Article: PubMed Central - PubMed

Affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA. BramhacharyaS@my.hiram.edu.

ABSTRACT

Background: All organisms must synthesize the enzymatic cofactor coenzyme A (CoA) from the precursor pantothenate. Most bacteria can synthesize pantothenate de novo by the condensation of pantoate and β-alanine. The synthesis of β-alanine is catalyzed by L-aspartate-α-decarboxylase (PanD), a pyruvoyl enzyme that is initially synthesized as a zymogen (pro-PanD). Active PanD is generated by self-cleavage of pro-PanD at Gly24-Ser25 creating the active-site pyruvoyl moiety. In Salmonella enterica, this cleavage requires PanM, an acetyl-CoA sensor related to the Gcn5-like N-acetyltransferases. PanM does not acetylate pro-PanD, but the recent publication of the three-dimensional crystal structure of the PanM homologue PanZ in complex with the PanD zymogen of Escherichia coli provides validation to our predictions and provides a framework in which to further examine the cleavage mechanism. In contrast, PanD from bacteria lacking PanM efficiently cleaved in the absence of PanM in vivo.

Results: Using phylogenetic analyses combined with in vivo phenotypic investigations, we showed that two classes of bacterial L-aspartate-α-decarboxylases exist. This classification is based on their posttranslational activation by self-cleavage of its zymogen. Class I L-aspartate-α-decarboxylase zymogens require the acetyl-CoA sensor PanM to be cleaved into active PanD. This class is found exclusively in the Gammaproteobacteria. Class II L-aspartate-α-decarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla. Several members of the Euryarchaeota and Crenarchaeota also contain Class II L-aspartate-α-decarboxylases. Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583). This conserved region represents a putative domain for interactions with L-aspartate-α-decarboxylase zymogens. This work may inform future biochemical and structural studies of pro-PanD-PanM interactions.

Conclusions: Experimental results indicate that S. enterica and C. glutamicum L-aspartate-α-decarboxylases represent two different classes of homologues of these enzymes. Class I homologues require PanM for activation, while Class II self cleave in the absence of PanM. Computer modeling of conserved amino acids using structure coordinates of PanM and L-aspartate-α-decarboxylase available in the protein data bank (RCSB PDB) revealed a putative site of interactions, which may help generate models to help understand the molecular details of the self-cleavage mechanism of L-aspartate-α-decarboxylases.

No MeSH data available.


Related in: MedlinePlus