Differentiation of 1-aminocyclopropane-1-carboxylate (ACC) deaminase from its homologs is the key for identifying bacteria containing ACC deaminase

• Published in: FEMS microbiology ecology 2015-10, Vol.91 (10), p.fiv112
• Main Authors: Li, Zhengyi, Chang, Siping, Ye, Shuting, Chen, Mingyue, Lin, Li, Li, Yuanyuan, Li, Shuying, An, Qianli
• Format: Article
• Language: English
• Subjects: Actinobacteria - classification; Actinobacteria - enzymology; Actinobacteria - genetics; Amino Acid Sequence; Amplification; Bacteria; Carbon-Carbon Lyases - genetics; DNA Primers - genetics; Ecology; Ethylenes - metabolism; Gene sequencing; Genes; Homology; Horizontal transfer; Klebsiella; Microbiology; Molecular Sequence Data; Oligonucleotides; Phylogeny; Plant Development; Plant growth; Plants - microbiology; Polymerase Chain Reaction; Primers; Proteobacteria - classification; Proteobacteria - enzymology; Proteobacteria - genetics
• ISSN: 1574-6941; 0168-6496; 1574-6941
• DOI: 10.1093/femsec/fiv112

1-Aminocyclopropane-1-carboxylate (ACC) deaminase-mediated reduction of ethylene generation in plants under abiotic stresses is a key mechanism by which bacteria can promote plant growth. Misidentification of ACC deaminase and the ACC deaminase structure gene (acdS) can lead to overestimation of the number of bacteria containing ACC deaminase and their function in ecosystems. Previous non-specific amplification of acdS homologs has led to an overestimation of the horizontal transfer of acdS genes. Here, we designed consensus-degenerate hybrid oligonucleotide primers (acdSf3, acdSr3 and acdSr4) based on differentiating the key residues in ACC deaminases from those of homologs for specific amplification of partial acdS genes. PCR amplification, sequencing and phylogenetic analysis identified acdS genes from a wide range of proteobacteria and actinobacteria. PCR amplification and a genomic search did not find the acdS gene in bacteria belonging to Pseudomonas stutzeri or in the genera Enterobacter, Klebsiella or Bacillus. We showed that differentiating the acdS gene and ACC deaminase from their homologs was crucial for the molecular identification of bacteria containing ACC deaminase and for understanding the evolution of the acdS gene. We provide an effective method for screening and identifying bacteria containing ACC deaminase. We developed an efficient molecular method for identifying bacteria containing ACC deaminase and clarified previous misunderstandings regarding identification of bacteria containing ACC deaminase and horizontal transfer of acdS genes.