title: Differentiation of 1-aminocyclopropane-1-carboxylate (ACC) deaminase from its homologs is the key for identifying bacteria containing ACC deaminase.
abstract: 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.
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
authors.forename: Zhengyi
authors.initials: Z
authors.lastname: Li
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
authors.forename: Siping
authors.initials: S
authors.lastname: Chang
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
authors.forename: Shuting
authors.initials: S
authors.lastname: Ye
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
authors.forename: Mingyue
authors.initials: M
authors.lastname: Chen
authors.affiliation: Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
authors.forename: Li
authors.initials: L
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
authors.forename: Shuying
authors.initials: S
authors.lastname: Li
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China an@zju.edu.cn.
authors.forename: Qianli
authors.initials: Q
authors.lastname: An
mesh_terms: D039903:Actinobacteria / Q000145:classification* / Q000201:enzymology / Q000235:genetics; D000595:Amino Acid Sequence; D019755:Carbon-Carbon Lyases / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D005030:Ethylenes / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D063245:Plant Development; D010944:Plants / Q000382:microbiology*; D016133:Polymerase Chain Reaction; D020560:Proteobacteria / Q000145:classification* / Q000201:enzymology / Q000235:genetics
chemical_list: D017931:DNA Primers; D005030:Ethylenes; C036216:ethylene; C033634:1-aminocyclopropane-1-carboxylate deaminase; D019755:Carbon-Carbon Lyases
keywords: D-cysteine desulfhydrase; consensus-degenerate hybrid oligonucleotide primers; horizontal gene transfer; plant growth-promoting bacteria