Tryptophan catabolism to indolepyruvic and indoleacetic acids byRhizobium japonicum L-259 mutants

Anaerobic degradation of aromatic amino acids by the hyperthermophilic archaeon Ferroglobus placidus

Ferroglobus placidus was discovered to oxidize completely the aromatic amino acids tyrosine, phenylalanine and tryptophan when Fe(III) oxide was provided as an electron acceptor. This property had not been reported previously for a hyperthermophilic archaeon. It appeared that F. placidus follows a pathway for phenylalanine and tryptophan degradation similar to that of mesophilic nitrate-reducing bacteria, Thauera aromatica and Aromatoleum aromaticum EbN1. Phenylacetate, 4-hydroxyphenylacetate and indole-3-acetate were formed during anaerobic degradation of phenylalanine, tyrosine and tryptophan, respectively. Candidate genes for enzymes involved in the anaerobic oxidation of phenylalanine to phenylacetate (phenylalanine transaminase, phenylpyruvate decarboxylase and phenylacetaldehyde : ferredoxin oxidoreductase) were identified in the F. placidus genome. In addition, transcription of candidate genes for the anaerobic phenylacetate degradation, benzoyl-CoA degradation and glutaryl-CoA degradation pathways was significantly upregulated in microarray and quantitative real-time-PCR studies comparing phenylacetate-grown cells with acetate-grown cells. These results suggested that the general strategies for anaerobic degradation of aromatic amino acids are highly conserved amongst bacteria and archaea living in both mesophilic and hyperthermophilic environments. They also provided insights into the diverse metabolism of Archaeoglobaceae species living in hyperthermophilic environments.

Activity, distribution and function of indole-3-acetic acid biosynthetic pathways in bacteria

The capacity to produce the phytohormone indole-3-acetic acid (IAA) is widespread among bacteria that inhabit diverse environments such as soils, fresh and marine waters, and plant and animal hosts. Three major pathways for bacterial IAA synthesis have been characterized that remove the amino and carboxyl groups from the α-carbon of tryptophan via the intermediates indolepyruvate, indoleacetamide, or indoleacetonitrile; the oxidized end product IAA is typically secreted. The enzymes in these pathways often catabolize a broad range of substrates including aromatic amino acids and in some cases the branched chain amino acids. Moreover, expression of some of the genes encoding key IAA biosynthetic enzymes is induced by all three aromatic amino acids. The broad distribution and substrate specificity of the enzymes suggests a role for these pathways beyond plant-microbe interactions in which bacterial IAA has been best studied.

Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants

Plants grown at high densities perceive a decrease in the red to far-red (R:FR) ratio of incoming light, resulting from absorption of red light by canopy leaves and reflection of far-red light from neighboring plants. These changes in light quality trigger a series of responses known collectively as the shade avoidance syndrome. During shade avoidance, stems elongate at the expense of leaf and storage organ expansion, branching is inhibited, and flowering is accelerated. We identified several loci in Arabidopsis, mutations in which lead to plants defective in multiple shade avoidance responses. Here we describe TAA1, an aminotransferase, and show that TAA1 catalyzes the formation of indole-3-pyruvic acid (IPA) from L-tryptophan (L-Trp), the first step in a previously proposed, but uncharacterized, auxin biosynthetic pathway. This pathway is rapidly deployed to synthesize auxin at the high levels required to initiate the multiple changes in body plan associated with shade avoidance.

Biosynthesis of auxin by the gram-positive phytopathogen Rhodococcus fascians is controlled by compounds specific to infected plant tissues

The role and metabolism of indole-3-acetic acid in gram-negative bacteria is well documented, but little is known about indole-3-acetic acid biosynthesis and regulation in gram-positive bacteria. The phytopathogen Rhodococcus fascians, a gram-positive organism, incites diverse developmental alterations, such as leafy galls, on a wide range of plants. Phenotypic analysis of a leafy gall suggests that auxin may play an important role in the development of the symptoms. We show here for the first time that R. fascians produces and secretes the auxin indole-3-acetic acid. Interestingly, whereas noninfected-tobacco extracts have no effect, indole-3-acetic acid synthesis is highly induced in the presence of infected-tobacco extracts when tryptophan is not limiting. Indole-3-acetic acid production by a plasmid-free strain shows that the biosynthetic genes are located on the bacterial chromosome, although plasmid-encoded genes contribute to the kinetics and regulation of indole-3-acetic acid biosynthesis. The indole-3-acetic acid intermediates present in bacterial cells and secreted into the growth media show that the main biosynthetic route used by R. fascians is the indole-3-pyruvic acid pathway with a possible rate-limiting role for indole-3-ethanol. The relationship between indole-3-acetic acid production and the symptoms induced by R. fascians is discussed.

Bacterial biosynthesis of indole-3-acetic acid

Production of the phytohormone indole-3-acetic acid (IAA) is widespread among bacteria that inhabit the rhizosphere of plants. Several different IAA biosynthesis pathways are used by these bacteria, with a single bacterial strain sometimes containing more than one pathway. The level of expression of IAA depends on the biosynthesis pathway; the location of the genes involved, either on chromosomal or plasmid DNA, and their regulatory sequences; and the presence of enzymes that can convert active, free IAA into an inactive, conjugated form. The role of bacterial IAA in the stimulation of plant growth and phytopathogenesis is considered.

Catabolism of indole-3-acetic acid and 4- and 5-chloroindole-3-acetic acid in Bradyrhizobium japonicum

Some strains of Bradyrhizobium japonicum have the ability to catabolize indole-3-acetic acid. Indoleacetic acid (IAA), 4-chloro-IAA (4-Cl-IAA), and 5-Cl-IAA were metabolized to different extents by strains 61A24 and 110. Metabolites were isolated and analyzed by high-performance liquid chromatography and conventional mass spectrometry (MS) methods, including MS-mass spectroscopy, UV spectroscopy, and high-performance liquid chromatography-MS. The identified products indicate a novel metabolic pathway in which IAA is metabolized via dioxindole-3-acetic acid, dioxindole, isatin, and 2-aminophenyl glyoxylic acid (isatinic acid) to anthranilic acid, which is further metabolized. Degradation of 4-Cl-IAA apparently stops at the 4-Cl-dioxindole step in contrast to 5-Cl-IAA which is metabolized to 5-Cl-anthranilic acid.

Oleic acid transformations by selected strains of Sphingobacterium thalpophilum and Bacillus cereus from composted manure

In a survey of 186 randomly selected microbial strains isolated from composted manure, 63 transformed oleic acid into three types of products: hydroxy fatty acid, fatty amide, and less polar oleyl lipid. Selection of oleic acid-transforming microorganisms was enhanced in nutrient agar supplemented with 0.1% (vol/vol) oleic acid at pH 7.2. Most of the 63 diverse isolates elicited inconsistent and poorly reproduced transformations. However, strains 142b (NRRL B-14797) transformed oleic acid to 10-hydroxystearic acid consistently, and strain 229b (NRRL B-14812) produced an octadecenamide. Taxonomic studies indicated that NRRL strain B-14797, possessing 1,3-dihydroxy-2-amino-15-methylhexadecane and sphinganine bases, was closely related to Sphingobacterium thalpophilum, and NRRL B-14812 was identified as Bacillus cereus.

Synthesis of phytohormones by plant-associated bacteria

The plant hormones, auxins and cytokinins, are involved in several stages of plant growth and development such as cell elongation, cell division, tissue differentiation, and apical dominance. The biosynthesis and the underlying mechanism of auxins and cytokinins action are subjects of intense investigation. Not only plants but also microorganisms can synthesize auxins and cytokinins. The role of phytohormone biosynthesis by microorganisms is not fully elucidated: in several cases of pathogenic fungi and bacteria these compounds are involved in pathogenesis on plants; auxin and cytokinin production may also be involved in root growth stimulation by beneficial bacteria and associative symbiosis. The genetic mechanism of auxin biosynthesis and regulation by Pseudomonas, Agrobacterium, Rhizobium, Bradyrhizobium, and Azospirillum, are well studied; in these bacteria several physiological effects have been correlated to the bacterial phytohormones biosynthesis. The pathogenic bacteria Pseudomonas and Agrobacterium produce indole-3-acetic acid via the indole-3-acetamide pathway, for which the genes are plasmid borne. However, they do possess also the indole-3-pyruvic acid pathway, which is chromosomally encoded. In addition, they have genes that can conjugate free auxins or hydrolyze conjugated forms of auxins and cytokinins. In Agrobacterium there are also several genes, located near the auxin and cytokinin biosynthetic genes, that are involved in the regulation of auxins and cytokinins sensibility of the transformed plant tissue. Symbiotic bacteria Rhizobium and Bradyrhizobium synthesize indole-3-acetic acid via indole-3-pyruvic acid; also the genetic determinants for the indole-3-acetamide pathway have been detected, but their activity has not been demonstrated. In the plant growth-promoting bacterium Azospirillum, as in Agrobacterium and Pseudomonas, both the indole-3-pyruvic acid and the indole-3-acetamide pathways are present, although in Azospirillum the indole-3-pyruvic acid pathway is of major significance. In addition, biochemical evidence for a tryptophan-independent indole-3-acetic acid pathway in Azospirillum has been presented.

Enhanced Nodulation and Nitrogen Fixation by a Revertant of a Nodulation-Defective Bradyrhizobium japonicum Tryptophan Auxotroph

In greenhouse studies, the symbiotic properties of a prototrophic revertant (TA11 NOD + ) of a nodulation defective tryptophan auxotroph of Bradyrhizobium japonicum were compared with those of the normally nodulating wild-type strain, B. japonicum I-110 ARS. Strain I-110 ARS was the parent of auxotrophic mutant TA11. Plants inoculated with TA11 NOD + contained significantly more nitrogen per plant than did plants inoculated with wild-type bacteria (275.9 ± 35 versus 184 ± 18 mg). Also, plants that received the revertant were larger, averaging 8.4 ± 0.9 g (dry weight) versus 6.4 ± 0.6 g for those that received the wild-type bacterial strain. Additionally, plants that received the NOD + strain had 56% more nodules and 41% more nodule mass than did control plants. With both inocula, average nodule size and amount of nitrogen fixed per gram of nodule were about the same. These data indicated that the improvement in nitrogen fixation observed with the TA11 NOD + resulted from an increase in the overall nodule number. The physiological basis for this increase in nodulation is not known, but enhanced tryptophan catabolism does not appear to be involved.

Molecular cloning of a gene for indole-3-acetamide hydrolase from Bradyrhizobium japonicum

A pLAFR1 cosmid genomic library of wild-type Bradyrhizobium japonicum J1063 was constructed. A cosmid clone designated pBjJ4, containing a 26-kilobase (kb) DNA insert, was identified as being able to confer the ability to convert alpha-naphthaleneacetamide acid on B. japonicum J1B7 Rifr, which cannot perform this conversion. The gene coding for the enzyme that converts alpha-naphthaleneacetamide to alpha-naphthaleneacetic acid was localized in the 3.5-kb region of pBjJ4 by recloning in plasmid pSUP202. The gene coding for the enzyme was also mapped by Tn5 insertion mutagenesis to a region of ca. 2.3 kb. When the gene was placed behind the lacZ promoter and used to transform Escherichia coli, a high level of expression of indole-3-acetamide hydrolase activity was found. Since there have been no reports of this activity in E. coli, we have thus confirmed that the gene cloned here is a structural gene for indole-3-acetamide hydrolase and have designated it as the bam (Bradyrhizobium amidehydrolase) gene. Southern hybridization with the central region of the bam gene indicated that a high degree of similarity exists among the bam gene, the iaaH gene from Pseudomonas savastonoi, and the tms-2 gene from Agrobacterium tumefaciens. The result suggests that there is a common origin for the gene that encodes the enzyme that catalyzes the biosynthesis of indoleacetic acid.

Influence of 5-Methyltryptophan-Resistant Bradyrhizobium japonicum on Soybean Root Nodule Indole-3-Acetic Acid Content

Bradyrhizobium japonicum mutants resistant to 5-methyltryptophan were isolated. Some of these mutants were found to accumulate indole-3-acetic acid (IAA) and tryptophan in culture. In greenhouse studies, nodules from control plants inoculated with wild-type bradyrhizobia contained 0.04, 0.10, and 0.58 μg of free, ester-linked, and peptidyl IAA g (fresh weight) of nodules −1 , respectively. Nodules from plants inoculated with 5-methyltryptophan-resistant bradyrhizobia contained 0.94, 1.30, and 10.6 μg of free, ester-linked, and peptidyl IAA g (fresh weight) of nodules −1 , respectively. This manyfold increase in nodule IAA content indicates that the Bradyrhizobium inoculum can have a considerable influence on the endogenous IAA level of the nodule. Further, these data imply that much of the IAA that accumulated in the high-IAA-containing nodules was of bacterial rather than plant origin. These high-IAA-producing 5-methyltryptophan-resistant bacteria were poor symbiotic nitrogen fixers. Plants inoculated with these bacteria had a lower nodule mass and fixed less nitrogen per gram of nodule than did plants inoculated with wild-type bacteria.