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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

Growth of S. enterica ΔpanD (circles) or ΔpanM strains (triangles) on glycerol in the absence of exogenous β-alanine. Each strain expressed the wild-type panD allele from the bacterium indicated in the upper right corner of each panel.
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Fig3: Growth of S. enterica ΔpanD (circles) or ΔpanM strains (triangles) on glycerol in the absence of exogenous β-alanine. Each strain expressed the wild-type panD allele from the bacterium indicated in the upper right corner of each panel.

Mentions: To validate the phylogenetic results, panD genes were cloned from several bacteria that contained panM and several that lacked panM. Each panD gene was expressed ectopically in a ΔpanD S. enterica strain grown on minimal medium devoid of β-alanine to verify l-aspartate-α-decarboxylase function in vivo. To determine whether each l-aspartate-α-decarboxylase could mature in the absence of PanM, the panD genes were also expressed in a ΔpanM S. enterica strain. The S. entericapanD+ allele was used as control for a bona fidel-aspartate-α-decarboxylase that required PanM for maturation [10]. The C. glutamicum panD+ was included as a control of a gene encoding a l-aspartate-α-decarboxylase that did not require PanM for processing [10] (Fig. 3).Fig. 3


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)

Growth of S. enterica ΔpanD (circles) or ΔpanM strains (triangles) on glycerol in the absence of exogenous β-alanine. Each strain expressed the wild-type panD allele from the bacterium indicated in the upper right corner of each panel.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Growth of S. enterica ΔpanD (circles) or ΔpanM strains (triangles) on glycerol in the absence of exogenous β-alanine. Each strain expressed the wild-type panD allele from the bacterium indicated in the upper right corner of each panel.
Mentions: To validate the phylogenetic results, panD genes were cloned from several bacteria that contained panM and several that lacked panM. Each panD gene was expressed ectopically in a ΔpanD S. enterica strain grown on minimal medium devoid of β-alanine to verify l-aspartate-α-decarboxylase function in vivo. To determine whether each l-aspartate-α-decarboxylase could mature in the absence of PanM, the panD genes were also expressed in a ΔpanM S. enterica strain. The S. entericapanD+ allele was used as control for a bona fidel-aspartate-α-decarboxylase that required PanM for maturation [10]. The C. glutamicum panD+ was included as a control of a gene encoding a l-aspartate-α-decarboxylase that did not require PanM for processing [10] (Fig. 3).Fig. 3

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