In silico identification and characterization of 1-aminocyclopropane-1-carboxylate deaminase from Phytophthora sojae

Singh, Nidhi; Kashyap, Sudhanshu

doi:10.1007/s00894-012-1389-0

Cited by 23 publications

(13 citation statements)

References 31 publications

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“…Putative acdS genes were also found many in members of Stramenopiles, mostly in Phytophthora . By computational analysis, Singh and Kashyap, [56] suggest that the acdS gene found in Phytophthora sojae encodes a functional ACC deaminase.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, the presence of a putative functional ACC deaminase in Phytophthora sojae [56] further emphasizes the notion that the current view of acdS phylogeny and evolution is somewhat incomplete. To address this, here we have undertaken a comprehensive study of the phylogeny of acdS and acdR and the results are discussed in terms of evolutionary and ecological implications of ACC deaminase production by diverse microorganisms.…”

Section: Introductionmentioning

confidence: 88%

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New Insights into 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Phylogeny, Evolution and Ecological Significance

et al. 2014

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The main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth–promoting microorganisms. The ACC deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis was conducted. Strain habitat, origin and ACC deaminase activity were taken into account when analyzing the results. In order to unveil ACC deaminase origin, evolution and relationships with other closely related pyridoxal phosphate (PLP) dependent enzymes a phylogenetic analysis was also performed. The data obtained show that ACC deaminase is mostly prevalent in some Bacteria, Fungi and members of Stramenopiles. Contrary to previous reports, we show that ACC deaminase genes are predominantly vertically inherited in various bacterial and fungal classes. Still, results suggest a considerable degree of horizontal gene transfer events, including interkingdom transfer events. A model for ACC deaminase origin and evolution is also proposed. This study also confirms the previous reports suggesting that the Lrp-like regulatory protein AcdR is a common mechanism regulating ACC deaminase expression in Proteobacteria, however, we also show that other regulatory mechanisms may be present in some Proteobacteria and other bacterial phyla. In this study we provide a more complete view of the role for ACC deaminase than was previously available. The results show that ACC deaminase may not only be related to plant growth promotion abilities, but may also play multiple roles in microorganism's developmental processes. Hence, exploring the origin and functioning of this enzyme may be the key in a variety of important agricultural and biotechnological applications.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 88%

New Insights into 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Phylogeny, Evolution and Ecological Significance

et al. 2014

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“…The ligand (PLP-ACC) which was used for docking purpose was retrieved from docked H. saturnus ACCD (HsACCD) (PDB: 1j0d) molecule, and the modelled ACC deaminase structures were used directly as a receptor. Enzyme-substrate docking was done using PatchDOCK server (http://bioinfo3d.cs.tau.ac.il/PatchDock) by keeping the clustering RMSD at 4 Å while all other parameters at default values [25]. The final docking pose results were obtained, and receptors binding in the docked structure were analysed using Accelrys Discovery Studio 3.5 Client software.…”

Section: Homology Modelling Of Acc Deaminasementioning

confidence: 99%

Studies on Plant Growth Promoting Properties of Fruit-Associated Bacteria from Elettaria cardamomum and Molecular Analysis of ACC Deaminase Gene

Jasim

Anish

Shimil

et al. 2015

Appl Biochem Biotechnol

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Endophytic microorganisms have been reported to have diverse plant growth promoting mechanisms including phosphate solubilization, N2 fixation, production of phyto-hormones and ACC (1-aminocyclopropane-1-carboxylate) deaminase and antiphyto-pathogenic properties. Among these, ACC deaminase production is very important because of its regulatory effect on ethylene which is a stress hormone with precise role in the control of fruit development and ripening. However, distribution of these properties among various endophytic bacteria associated with fruit tissue and its genetic basis is least investigated. In the current study, 11 endophytic bacteria were isolated and identified from the fruit tissue of Elettaria cardamomum and were studied in detail for various plant growth promoting properties especially ACC deaminase activity using both culture-based and PCR-based methods. PCR-based screening identified the isolates EcB 2 (Pantoea sp.), EcB 7 (Polaromonas sp.), EcB 9 (Pseudomonas sp.), EcB 10 (Pseudomonas sp.) and EcB 11 (Ralstonia sp.) as positive for ACC deaminase. The PCR products were further subjected to sequence analysis which proved the similarity of the sequences identified in the study with ACC deaminase sequences reported from other sources. The detailed bioinformatic analysis of the sequence including homology-based modelling and molecular docking confirmed the sequences to have ACC deaminase activity. The docking of the modelled proteins was done using patch dock, and the detailed scrutiny of the protein ligand interaction revealed conservation of key amino acids like Lys51, Ser78, Tyr268 and Tyr294 which play important role in the enzyme activity. These suggest the possible regulatory effect of these isolates on fruit physiology.

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“…The enzyme ACC deaminase (encoded by the acdS gene) is thought to be a key trait in the arsenal that PGPB use to promote plant growth. There are numerous literature reports describing this enzyme in taxonomically distinct bacteria, including PGPB, phytopathogens, opportunistic human pathogens (Blaha et al 2006 ;Nascimento et al 2014 ), and fungi (Jia et al 2000 ;Viterbo et al 2010 ;Singh and Kashyap 2012 ). In addition, based on sequence similarity, many microorganisms have putative ACC deaminase genes; however, whether all of these are bona fi de ACC deaminases remains to be determined.…”

Section: Introduction To Acc Deaminasementioning

confidence: 98%

Methods to Study 1-Aminocyclopropane-1-carboxylate (ACC) Deaminase in Plant Growth-Promoting Bacteria

Brı́gido

Duan

Glick

2015

Handbook for Azospirillum

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The lowering of plant ethylene levels by the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase is one of the key mechanisms employed by plant growth-promoting bacteria (PGPB) to facilitate plant growth. Since its discovery, it has been detected in both fungi and bacteria. It has been shown by a large number of workers in a wide range of bacteria that the activity of this enzyme in PGPB is important during normal plant development and also protects plants from the deleterious effects of a wide range of environmental stresses. ACC deaminase-containing PGPB bound to a plant act as a sink for ACC, thereby lowering ethylene levels in plant tissues. The result of the functioning of this enzyme is an increase in the growth of plant roots and shoots and a reduction of the inhibitory effects of ethylene synthesis especially during stressful conditions. This chapter briefl y summarizes the current knowledge of various ACC deaminases emphasizing the use of ACC deaminase-containing bacteria in promoting plant growth under diverse biotic and abiotic stresses, and describes methods for the isolation and study of ACC deaminase-containing bacteria.

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In silico identification and characterization of 1-aminocyclopropane-1-carboxylate deaminase from Phytophthora sojae

Cited by 23 publications

References 31 publications

New Insights into 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Phylogeny, Evolution and Ecological Significance

New Insights into 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Phylogeny, Evolution and Ecological Significance

Studies on Plant Growth Promoting Properties of Fruit-Associated Bacteria from Elettaria cardamomum and Molecular Analysis of ACC Deaminase Gene

Methods to Study 1-Aminocyclopropane-1-carboxylate (ACC) Deaminase in Plant Growth-Promoting Bacteria

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