Physical organization and phylogenetic analysis of acdR as leucine-responsive regulator of the 1-aminocyclopropane-1-carboxylate deaminase gene acdS in phytobeneficial Azospirillum lipoferum 4B and other Proteobacteria

• Published in: FEMS microbiology ecology Vol. 65; no. 2; pp. 202 - 219
• Main Authors: Prigent-Combaret, Claire, Blaha, Didier, Pothier, Joël F, Vial, Ludovic, Poirier, Marie-Andrée, Wisniewski-Dyé, Florence, Moënne-Loccoz, Yvan
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01.08.2008; Blackwell Publishing Ltd; Oxford University Press; Wiley-Blackwell
• Subjects: 1-aminocyclopropane-1-carboxylate; 1-Aminocyclopropane-1-carboxylate deaminase; ACC deaminase; acdR; Amino Acid Sequence; Amino Acids, Cyclic - metabolism; Azospirillum; Azospirillum lipoferum; Azospirillum lipoferum - enzymology; Azospirillum lipoferum - genetics; Azospirillum lipoferum - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Base Sequence; Binding sites; Carbon-Carbon Lyases - genetics; Carbon-Carbon Lyases - metabolism; Carboxylic acids; Deamination; Deoxyribonucleic acid; DNA; Ecology; Functional analysis; Gene Expression Regulation, Bacterial; Gene Expression Regulation, Enzymologic; Gene regulation; Gene sequencing; Genes; Homology; Leucine; Leucine - metabolism; Leucine-Responsive Regulatory Protein - chemistry; Leucine-Responsive Regulatory Protein - genetics; Leucine-Responsive Regulatory Protein - metabolism; Life Sciences; Microbiology; Molecular Sequence Data; NifH gene; Nitrate reduction; Nitrogen fixation; Nitrogenation; Nucleotide sequence; phase variation; Phenotype; Phenotypic variations; Phylogenetics; Phylogeny; Plant growth; Plasmids; Proteins; Proteobacteria; Proteobacteria - classification; Proteobacteria - enzymology; Proteobacteria - genetics; Proteobacteria - metabolism; Sequence Alignment; Synteny; Transcription; 1-aminocyclopropane-1-carboxylate; ACC deaminase; phase variation
• ISSN: 0168-6496; 1574-6941
• DOI: 10.1111/j.1574-6941.2008.00474.x

The phytostimulatory alphaproteobacterium Azospirillum lipoferum 4B exhibits the plant-beneficial gene acdS, which enables deamination of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Here, we show that acdS is in the vicinity of acdR, a homolog to leucine-responsive regulator lrp, in A. lipoferum 4B and most other acdS⁺Proteobacteria. Unlike in Beta- and Gammaproteobacteria, acdS (and acdR) is preferentially located on symbiotic islands and plasmids in Alphaproteobacteria. In A. lipoferum 4B, acdS was mapped on a 750-kb plasmid that is lost during phenotypic variation, whereas other phytobeneficial genes such as nifH (associative nitrogen fixation) are maintained. In Proteobacteria, the phylogenies of acdR and acdS were largely but not totally congruent, despite physical proximity of the genes, regardless of whether DNA or deduced protein sequences were used. Potential Lrp, cAMP receptor protein (CRP) and fumarate-nitrate reduction regulator (FNR) binding sites were evidenced in the acdS promoter regions of strain 4B and most of 46 other acdS⁺Proteobacteria. Indeed, transcriptional and enzymatic analyses done in vitro pointed to the involvement of Lrp- and FNR-like transcriptional up-regulation of ACC deaminase activity in A. lipoferum 4B. This is the first synteny, phylogenetic, and functional analysis of factors modulating acdS expression in Azospirillum plant growth-promoting rhizobacterium.