contradiction may reflect the presence of noncanonical ACC deaminase enzymes
that are members of the amino hydrolase superfamily and are also able (albeit
sometimes inefficiently) to cleave ACC (Li et al. 2001). On the other hand, microbial
genera including Meiothermus and Phytophthora have been found to possess
sequences similar to acdS genes in their genomes; however, no experimental
evidence of enzyme activity has yet been documented (Nascimento et al. 2014).
Similarly, genomic and metagenomic database search-based studies revealed that
sequences similar to the acdS gene locus of Pseudomonas sp. UW4 are the most
prevalent in bacteria (485 individual strains) and include Acidovorax, Bordetella,
Brenneria, Burkholderia, Collimonas, Cupriavidus, Curvibacter, Dickeya,
Herbaspirillum, Halomonas, Lonsdalea, Methylibium, Pantoea, Phytophthora,
Polaromonas, Pseudomonas, Ralstonia, Serratia, Tatumella, Variovorax, and
Xenophilus. Within the domain Archaea, strains of Archaeoglobus fulgidus,
Pyrococcus abyssi, Pyrococcus furiosus, and Thermococcus nautili were found to
contain ACC deaminase genes; likewise, the fungal phyla Ascomycota and
Basidiomycota, and soybean, potato, maize, and castor oil in the kingdom Plantae
all appear to contain the acdS gene (Singh et al. 2015). However, some
misidentification of the presence of this enzyme in various bacteria has also been
reported. To avoid this sort of overestimation of the ACC deaminase positive strains
in any environment, Li et al. (2015) proposed a molecular tool for differentiating true
ACC deaminase-containing bacteria from its structural homologs. This tool is based
on consensus-degenerate hybrid oligonucleotide primers and is specific for picking
up key differences between ACC deaminase and its structural homologs, which are
found in amino acid sequences at E295 and L322 residues that are unique for ACC
deaminase, whereas ACC deaminase homologs can have any other amino acids at
those two positions (Todorovic and Glick 2008; Li et al. 2015). Using this approach,
some genes belonging to the bacterial genera Enterobacter, Klebsiella, and Bacillus
that were previously reported to be putatively positive for the presence of ACC
deaminase were found to be false positives (and are likely to be D-cysteine
sulfhydrase) based on their genomic structures (Nascimento et al. 2014; Li et al.
2015).
19.3 Phylogenetic Origin of ACC Deaminase
The structural gene responsible for ACC deaminase, acdS, is predominantly found
on bacterial chromosomal DNA, with a few bacteria containing the gene on their
plasmids. Protein sequence analysis of ACC deaminase from diverse bacterial
genera found that more than 60% of the amino acid residues were identical, even
for the most phylogenetically distinct sequences. It has been proposed that acdS
originated from a bacterial/Eukaryote ancestor (Nascimento et al. 2014) and most
likely is the product of mutation from some ancestral gene. Based on analysis of a
limited number of bacterial ACC deaminase protein sequences and 16S rRNA gene
analysis of the same bacterial genera (mainly Pseudomonas), it was hypothesized
368
S. Ali and B. R. Glick
that are members of the amino hydrolase superfamily and are also able (albeit
sometimes inefficiently) to cleave ACC (Li et al. 2001). On the other hand, microbial
genera including Meiothermus and Phytophthora have been found to possess
sequences similar to acdS genes in their genomes; however, no experimental
evidence of enzyme activity has yet been documented (Nascimento et al. 2014).
Similarly, genomic and metagenomic database search-based studies revealed that
sequences similar to the acdS gene locus of Pseudomonas sp. UW4 are the most
prevalent in bacteria (485 individual strains) and include Acidovorax, Bordetella,
Brenneria, Burkholderia, Collimonas, Cupriavidus, Curvibacter, Dickeya,
Herbaspirillum, Halomonas, Lonsdalea, Methylibium, Pantoea, Phytophthora,
Polaromonas, Pseudomonas, Ralstonia, Serratia, Tatumella, Variovorax, and
Xenophilus. Within the domain Archaea, strains of Archaeoglobus fulgidus,
Pyrococcus abyssi, Pyrococcus furiosus, and Thermococcus nautili were found to
contain ACC deaminase genes; likewise, the fungal phyla Ascomycota and
Basidiomycota, and soybean, potato, maize, and castor oil in the kingdom Plantae
all appear to contain the acdS gene (Singh et al. 2015). However, some
misidentification of the presence of this enzyme in various bacteria has also been
reported. To avoid this sort of overestimation of the ACC deaminase positive strains
in any environment, Li et al. (2015) proposed a molecular tool for differentiating true
ACC deaminase-containing bacteria from its structural homologs. This tool is based
on consensus-degenerate hybrid oligonucleotide primers and is specific for picking
up key differences between ACC deaminase and its structural homologs, which are
found in amino acid sequences at E295 and L322 residues that are unique for ACC
deaminase, whereas ACC deaminase homologs can have any other amino acids at
those two positions (Todorovic and Glick 2008; Li et al. 2015). Using this approach,
some genes belonging to the bacterial genera Enterobacter, Klebsiella, and Bacillus
that were previously reported to be putatively positive for the presence of ACC
deaminase were found to be false positives (and are likely to be D-cysteine
sulfhydrase) based on their genomic structures (Nascimento et al. 2014; Li et al.
2015).
19.3 Phylogenetic Origin of ACC Deaminase
The structural gene responsible for ACC deaminase, acdS, is predominantly found
on bacterial chromosomal DNA, with a few bacteria containing the gene on their
plasmids. Protein sequence analysis of ACC deaminase from diverse bacterial
genera found that more than 60% of the amino acid residues were identical, even
for the most phylogenetically distinct sequences. It has been proposed that acdS
originated from a bacterial/Eukaryote ancestor (Nascimento et al. 2014) and most
likely is the product of mutation from some ancestral gene. Based on analysis of a
limited number of bacterial ACC deaminase protein sequences and 16S rRNA gene
analysis of the same bacterial genera (mainly Pseudomonas), it was hypothesized
368
S. Ali and B. R. Glick