scholarly journals The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis

2019 ◽  
Author(s):  
Pengfan Zhang ◽  
Tao Jin ◽  
Sunil Kumar Sahu ◽  
Jin Xu ◽  
Qiong Shi ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Large Scale ◽  
Growth Promotion ◽  
Plant Root ◽  
Genomic Analysis ◽  
Acid Synthesis ◽  
Metagenomic Data ◽  
Bacterial Genomes ◽  
Bacterial Phyla ◽  
Indole 3 Acetic Acid

Bacterial indole-3-acetic acid (IAA), an effector molecule in microbial physiology, plays an important role in plant growth-promotion. Here, we comprehensively analyzed about 7282 prokaryotic genomes representing diverse bacterial phyla, combined with root-associated metagenomic data to unravel the distribution of tryptophan-dependent IAA synthesis pathways and to quantify the IAA synthesis-related genes in the plant root environments. We found that 82.2% of the analyzed bacterial genomes were potentially capable of synthesizing IAA from tryptophan (Trp) or intermediates. Interestingly, several phylogenetically diverse bacteria showed a preferential tendency to utilize different pathways and tryptamine and indole-3-pyruvate pathways are most prevalent in bacteria. About 45.3% of the studied genomes displayed multiple coexisting pathways, constituting complex IAA synthesis systems. Furthermore, root-associated metagenomic analyses revealed that rhizobacteria mainly synthesize IAA via IAM and tryptamine (TMP) pathways and might possess stronger IAA synthesis abilities than bacteria colonizing other environments. The obtained results refurbished our understanding of bacterial IAA synthesis pathways and provided a faster and less labor-intensive alternative to physiological screening based on genome collections. The better understanding of IAA synthesis among bacterial communities could maximize the utilization of bacterial IAA to augment the crop growth and physiological function.

scholarly journals The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1411 ◽  
Author(s):  
Pengfan Zhang ◽  
Tao Jin ◽  
Sunil Kumar Sahu ◽  
Jin Xu ◽  
Qiong Shi ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Large Scale ◽  
Growth Promotion ◽  
Plant Root ◽  
Genomic Analysis ◽  
Acid Synthesis ◽  
Metagenomic Data ◽  
Bacterial Genomes ◽  
Bacterial Phyla ◽  
Indole 3 Acetic Acid

Bacterial indole-3-acetic acid (IAA), an effector molecule in microbial physiology, plays an important role in plant growth-promotion. Here, we comprehensively analyzed about 7282 prokaryotic genomes representing diverse bacterial phyla, combined with root-associated metagenomic data to unravel the distribution of tryptophan-dependent IAA synthesis pathways and to quantify the IAA synthesis-related genes in the plant root environments. We found that 82.2% of the analyzed bacterial genomes were potentially capable of synthesizing IAA from tryptophan (Trp) or intermediates. Interestingly, several phylogenetically diverse bacteria showed a preferential tendency to utilize different pathways and tryptamine and indole-3-pyruvate pathways are most prevalent in bacteria. About 45.3% of the studied genomes displayed multiple coexisting pathways, constituting complex IAA synthesis systems. Furthermore, root-associated metagenomic analyses revealed that rhizobacteria mainly synthesize IAA via indole-3-acetamide (IAM) and tryptamine (TMP) pathways and might possess stronger IAA synthesis abilities than bacteria colonizing other environments. The obtained results refurbished our understanding of bacterial IAA synthesis pathways and provided a faster and less labor-intensive alternative to physiological screening based on genome collections. The better understanding of IAA synthesis among bacterial communities could maximize the utilization of bacterial IAA to augment the crop growth and physiological function.

scholarly journals Highly Efficient Biosynthesis of Indole-3-acetic acid by Enterobacter xiangfangensis BHW6

2020 ◽  
Author(s):  
Bi-Xian Zhang ◽  
Ying-Ying Wang ◽  
Xiaomei Hu
Keyword(s):  
Acetic Acid ◽  
Economic Value ◽  
Pyruvate Decarboxylase ◽  
Genomic Analysis ◽  
Rrna Gene ◽  
H Nmr ◽  
Gene Coding ◽  
Key Enzyme ◽  
Indole 3 Acetic Acid ◽  
Iaa Biosynthesis

Abstract Background: Indole-3-acetic acid (IAA) plays an important role in the growth and development of plants. Various bacteria in the rhizosphere are capable to produce IAA that acts as a signaling molecule for the communication between plants and microbes to promote the plant growth. Due to the low IAA content and various interfering analogs, it is difficult to detect and isolate IAA from microbial secondary metabolites. Results: A predominant strain with a remarkable capability to secrete IAA was identified as Enterobacter xiangfangensis BHW6 based on 16S rRNA gene sequence, the determination of average nucleotide identity (ANI) and digital DDH (dDDH). The maximum IAA content (134-1129 μg/mL) was found with the addition of 0.2-15 g/L of L-tryptophan at pH 5 for 6 days, which was 4-40 fold higher than that in the absence of L-tryptophan. The highest yield of IAA was obtained at the stationary phase of bacterial growth. An acidic culture medium was preferred for the IAA biosynthesis of the strain. The strain was tolerant and stable to produce IAA in the presence 2.5%-5% (w/v) of NaCl. IAA was then isolated through column chromatography with a mobile phase of hexane/ethyl acetate (1/2, v/v) and characterized by 1H Nuclear Magnetic Resonance (1H NMR). Conclusions: A remarkable IAA production was obtained from E. xiangfangensis BHW6 that was tryptophan–dependent. According to genomic analysis, the ipdC gene coding for the key enzyme (indole-3-pyruvate decarboxylase) was identified indicating that IAA biosynthesis was mainly through the indole-3-pyruvia acid (IPyA) pathway, which was further confirmed by intermediate assay. E. xiangfangensis BHW6 with an important economic value has great prospect in agricultural and industrial application.

scholarly journals SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

2020 ◽  
Vol 16 (12) ◽  
pp. e1008439
Author(s):  
Jennifer Lu ◽  
Steven L. Salzberg
Keyword(s):  
Large Scale ◽  
Analysis Tool ◽  
Index Test ◽  
Bacterial Genomes ◽  
Phylogenetic Groups ◽  
Bacterial Phyla ◽  
Link Type ◽  
Gc Skew ◽  
A Genome ◽  
Web App

GC skew is a phenomenon observed in many bacterial genomes, wherein the two replication strands of the same chromosome contain different proportions of guanine and cytosine nucleotides. Here we demonstrate that this phenomenon, which was first discovered in the mid-1990s, can be used today as an analysis tool for the 15,000+ complete bacterial genomes in NCBI’s Refseq library. In order to analyze all 15,000+ genomes, we introduce a new method, SkewIT (Skew Index Test), that calculates a single metric representing the degree of GC skew for a genome. Using this metric, we demonstrate how GC skew patterns are conserved within certain bacterial phyla, e.g. Firmicutes, but show different patterns in other phylogenetic groups such as Actinobacteria. We also discovered that outlier values of SkewIT highlight potential bacterial mis-assemblies. Using our newly defined metric, we identify multiple mis-assembled chromosomal sequences in previously published complete bacterial genomes. We provide a SkewIT web app https://jenniferlu717.shinyapps.io/SkewIT/ that calculates SkewI for any user-provided bacterial sequence. The web app also provides an interactive interface for the data generated in this paper, allowing users to further investigate the SkewI values and thresholds of the Refseq-97 complete bacterial genomes. Individual scripts for analysis of bacterial genomes are provided in the following repository: https://github.com/jenniferlu717/SkewIT.

Rhizobium leguminosarum as a plant growth-promoting rhizobacterium: direct growth promotion of canola and lettuce

1996 ◽  
Vol 42 (3) ◽  
pp. 279-283 ◽  
Author(s):  
T. C. Noel ◽  
C. Sheng ◽  
C. K. Yost ◽  
R. P. Pharis ◽  
M. F. Hynes
Keyword(s):  
Acetic Acid ◽  
Plant Growth ◽  
Rhizobium Leguminosarum ◽  
Growth Promotion ◽  
Plant Growth Promoting Rhizobacteria ◽  
Plant Growth Promoting ◽  
Direct Growth ◽  
Early Seedling ◽  
Growth Promoting ◽  
Indole 3 Acetic Acid

Early seedling root growth of the nonlegumes canola (Brassica campestris cv. Tobin, Brassica napus cv. Westar) and lettuce (Lactuca saliva cv. Grand Rapids) was significantly promoted by inoculation of seeds with certain strains of Rhizobium leguminosarum, including nitrogen- and nonnitrogen-fixing derivatives under gnotobiotic conditions. The growfh-promotive effect appears to be direct, with possible involvement of the plant growth regulators indole-3-acetic acid and cytokinin. Auxotrophic Rhizobium mutants requiring tryptophan or adenosine (precursors for indole-3-acetic acid and cytokinin synthesis, respectively) did not promote growth to the extent of the parent strain. The findings of this study demonstrate a new facet of the Rhizobium–plant relationship and that Rhizobium leguminosarum can be considered a plant growth-promoting rhizobacterium (PGPR).Key words: Rhizobium, plant growth-promoting rhizobacteria, PGPR, indole-3-acetic acid, cytokinin, roots, auxotrophic mutants.

scholarly journals Quorum Sensing and Indole-3-Acetic Acid Degradation Play a Role in Colonization and Plant Growth Promotion of Arabidopsis thaliana by Burkholderia phytofirmans PsJN

2013 ◽  
Vol 26 (5) ◽  
pp. 546-553 ◽  
Author(s):  
Ana Zúñiga ◽  
María Josefina Poupin ◽  
Raúl Donoso ◽  
Thomas Ledger ◽  
Nicolás Guiliani ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Acetic Acid ◽  
Quorum Sensing ◽  
Plant Growth ◽  
Growth Promotion ◽  
Auxin Signaling ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Indole 3 Acetic Acid ◽  
Burkholderia Phytofirmans Psjn

Although not fully understood, molecular communication in the rhizosphere plays an important role regulating traits involved in plant–bacteria association. Burkholderia phytofirmans PsJN is a well-known plant-growth-promoting bacterium, which establishes rhizospheric and endophytic colonization in different plants. A competent colonization is essential for plant-growth-promoting effects produced by bacteria. Using appropriate mutant strains of B. phytofirmans, we obtained evidence for the importance of N-acyl homoserine lactone-mediated (quorum sensing) cell-to-cell communication in efficient colonization of Arabidopsis thaliana plants and the establishment of a beneficial interaction. We also observed that bacterial degradation of the auxin indole-3-acetic acid (IAA) plays a key role in plant-growth-promoting traits and is necessary for efficient rhizosphere colonization. Wildtype B. phytofirmans but not the iacC mutant in IAA mineralization is able to restore promotion effects in roots of A. thaliana in the presence of exogenously added IAA, indicating the importance of this trait for promoting primary root length. Using a transgenic A. thaliana line with suppressed auxin signaling (miR393) and analyzing the expression of auxin receptors in wild-type inoculated plants, we provide evidence that auxin signaling in plants is necessary for the growth promotion effects produced by B. phytofirmans. The interplay between ethylene and auxin signaling was also confirmed by the response of the plant to a 1-aminocyclopropane-1-carboxylate deaminase bacterial mutant strain.

The Route, Control and Compartmentation of Auxin Synthesis

1993 ◽  
Vol 20 (5) ◽  
pp. 527 ◽  
Author(s):  
HM Nonhebel ◽  
TP Cooney ◽  
R Simpson
Keyword(s):  
Amino Acids ◽  
Acetic Acid ◽  
Recent Work ◽  
Aspartate Aminotransferase ◽  
Acid Synthesis ◽  
Pea Seedlings ◽  
Auxin Synthesis ◽  
Aromatic Aminotransferase ◽  
Work Supports ◽  
Indole 3 Acetic Acid

The study of indole-3-acetic acid synthesis has undergone something of a revival recently in an attempt to understand the control of IAA levels. Results are, however, contradictory with three separate hypotheses emerging. Our own work supports older evidence for L-tryptophan as the IAA precursor and appears to simplify the metabolism of tryptophan to IAA. Work comparing incorporation of 2H from 2H2O into IAA, tryptophan, tryptamine and indole-3-pyruvate in tomato shoots showed that the indole-3-pyruvate became labelled at a rate compatible with it being the sole intermediate between tryptophan and indole-3-acetaldehyde. Results also showed that tryptamine was not involved in IAA synthesis although it was present. Indole-3-acetaldoxime was not detected in tomato shoots. An aromatic aminotransferase able to catalyse the synthesis of indole-3-pyruvate has been purified from mung beans. This enzyme was separated from aspartate aminotransferase and is fairly specific for aromatic L-amino acids. Other work, however, has implicated D-tryptophan as a more direct precursor than the L-enantiomer. A D-tryptophan aminotransferase has been isolated from dark grown pea seedlings. Finally, other recent work has indicated the existence of an alternative biosynthetic route to IAA which does not involve tryptophan. These results are reviewed in this paper and the apparent contradictions between them discussed.

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