Cloning and characterization of indolepyruvate decarboxylase from Methylobacterium extorquens AM1

AcdR protein is an activator of transcription of 1-aminocyclopropane-1-carboxylate deaminase in Methylobacterium radiotolerans JCM 2831

It has been previously shown that a number of plant associated methylotrophic bacteria contain an enzyme aminocyclopropane carboxylate (ACC) deaminase (AcdS) hydrolyzing ACC, the immediate precursor of ethylene in plants. The genome of the epiphytic methylotroph Methylobacterium radiotolerans JCM2831 contains an open reading frame encoding a protein homologous to transcriptional regulatory protein AcdR of the Lrp (leucine-responsive regulatory protein) family. The acdR gene of M. radiotolerans was heterologously expressed in Escherichia coli and purified. The results of gel retardation experiments have shown that AcdR specifically binds the DNA fragment containing the promoter-operator region of the acdS gene. ACC decreased electrophoretic mobility of the AcdR-DNA complex whereas leucine had no effect on the complex mobility. The mutant strains of M. radiotolerans obtained by insertion of a tetracycline cassette in the acdS or acdR gene lost the ACC-deaminase activity but the strains with complementation of the mutation recovered this function. The acdS^- mutant but not acdR^- strain expressed the xylE reporter gene under the control of acdS promoter region thus resulting in a catechol 2,3-dioxygenase activity. This suggested that AcdR in vivo functions as activator of transcription of the acdS gene. The results obtained in this study showed that in phytosymbiotic methylotroph Methylobacterium radiotolerans AcdR mediates activation of the acdS gene transcription in the presence of an inducer ACC or 2-aminoisobutyrate and the excess of the regulatory protein assists in transcription initiation even in the absence of the inducer. The model of regulation of acdS transcription in M. radiotolerans was proposed.

Plant Growth-Promoting Activity of Herbaspirillum aquaticum ZXN111 on the Zijuan Tea Plant (Camellia sinensis var. assamica)

Herbaspirillum aquaticum ZXN111 which was isolated from the tea plant Zijuan can produce indole-3-acetic acid (IAA) and contain abiotic-stress tolerance gene 1-aminocyclopropane-1-carboxylate deaminase (accd). In this study, ZXN111 PGP activity and the molecular mechanism were investigated. The result showed that ACCD activity of wild-type ZXN111 was 0.4505 mM α-KB/mg·Pro·h, but mutants Δacc and Δacc-tyrb did not showed ACCD activity. IAA production by ZXN111 within 48 hrs was 20.4 μg/mL, while mutants of Δtyrb and Δacc-tyrb were lower than 3.6 μg/mL, indicating that indole-3-pyruvic acid is the primary IAA synthesis pathway. Potting tests found that ZXN111 displayed significant PGP activity to the tea plant Zijuan, but Δtyrb and Δacc-tyrb did not show PGP activity, indicating that IAA is critical to PGP activity. In a salt-stress test, ZXN111 did not enhance the tea plant NaCl tolerance by gene accd. The results of this study indicated that strain ZXN111 has potential for biofertilizer development on tea plantation.

Methylobacterium populi VP2: plant growth-promoting bacterium isolated from a highly polluted environment for polycyclic aromatic hydrocarbon (PAH) biodegradation

The use of microorganisms to accelerate the natural detoxification processes of toxic substances in the soil represents an alternative ecofriendly and low-cost method of environmental remediation compared to harmful incineration and chemical treatments. Fourteen strains able to grow on minimal selective medium with a complex mixture of different classes of xenobiotic compounds as the sole carbon source were isolated from the soil of the ex-industrial site ACNA (Aziende Chimiche Nazionali Associate) in Cengio (Savona, Italy). The best putative degrading isolate, Methylobacterium populi VP2, was identified using a polyphasic approach on the basis of its phenotypic, biochemical, and molecular characterisation. Moreover, this strain also showed multiple plant growth promotion activities: it was able to produce indole-3-acetic acid (IAA) and siderophores, solubilise phosphate, and produce a biofilm in the presence of phenanthrene and alleviate phenanthrene stress in tomato seeds. This is the first report on the simultaneous occurrence of the PAH-degrading ability by Methylobacterium populi and its multiple plant growth-promoting activities. Therefore, the selected indigenous strain, which is naturally present in highly contaminated soils, is good candidate for plant growth promotion and is capable of biodegrading xenobiotic organic compounds to remediate contaminated soil alone and/or soil associated with plants.

Auxin production by the plant trypanosomatidPhytomonas serpensand auxin homoeostasis in infected tomato fruits

Previously we have characterized the complete gene encoding a pyruvate decarboxylase (PDC)/indolepyruvate decarboxylase (IPDC) ofPhytomonas serpens, a trypanosomatid highly abundant in tomato fruits. Phylogenetic analyses indicated that the clade that contains the trypanosomatid protein behaves as a sister group of IPDCs ofγ-proteobacteria. Since IPDCs are key enzymes in the biosynthesis of the plant hormone indole-3-acetic acid (IAA), the ability for IAA production byP. serpenswas investigated. Similar to many microorganisms, the production of IAA and related indolic compounds, quantified by high performance liquid chromatography, increased inP. serpensmedia in response to amounts of tryptophan. The auxin functionality was confirmed in the hypocotyl elongation assay. In tomato fruits inoculated withP. serpensthe concentration of free IAA had no significant variation, whereas increased levels of IAA-amide and IAA-ester conjugates were observed. The data suggest that the auxin produced by the flagellate is converted to IAA conjugates, keeping unaltered the concentration of free IAA. Ethanol also accumulated inP. serpens-conditioned media, as the result of a PDC activity. In the article we discuss the hypothesis of the bifunctionality ofP. serpensPDC/IPDC and provide a three-dimensional model of the enzyme.

Indole-3-acetic acid in plant-microbe interactions

Indole-3-acetic acid (IAA) is an important phytohormone with the capacity to control plant development in both beneficial and deleterious ways. The ability to synthesize IAA is an attribute that many bacteria including both plant growth-promoters and phytopathogens possess. There are three main pathways through which IAA is synthesized; the indole-3-pyruvic acid, indole-3-acetamide and indole-3-acetonitrile pathways. This chapter reviews the factors that effect the production of this phytohormone, the role of IAA in bacterial physiology and in plant-microbe interactions including phytostimulation and phytopathogenesis.

Dominant colonization and inheritance of Methylobacterium sp. strain OR01 on perilla plants

Pink-pigmented facultative methylotrophs (PPFMs) are major inhabitants of the phyllosphere. In a preceding study, we found that perilla plants harbor a dominant population of PPFMs on their leaves and seeds, and that the closest relative of PPFMs (Methylobacterium sp. strain OR01 as representative strain) isolated from red perilla seeds was M. fujisawaense DSM5686(T). In the present study, the specific interaction between red perilla and Methylobacterium species was investigated. All the PPFMs isolated from red perilla seeds harvested in the Ohara area of Kyoto, Japan in 2009, 2010, and 2011 and the PPFMs isolated from red perilla leaves planted at four geographically different places in Japan had 16S rRNA sequences identical to that of strain OR01. Direct transmission of PPFMs from seeds to leaves and the competitiveness of strain OR01 were confirmed. This report is the first step toward understanding the species-level specificity of the interaction between perilla plants and Methylobacterium species.

A simple method for simultaneous RP-HPLC determination of indolic compounds related to bacterial biosynthesis of indole-3-acetic acid

In this short technical report, we present a fast and simple procedure for sample preparation and a single-run Reversed Phase High Performance Liquid Chromatography (RP-HPLC) determination of seven indoles (indole-3-acetic acid, indole-3-acetamide, indole-3-acetonitrile, indole-3-ethanol, indole-3-lactic acid, tryptamine and tryptophan) in bacterial culture supernatants. The separation of the analytes, after a single centrifugal filtration clean-up step, was performed using a gradient elution on a symmetry C8 column followed by fluorimetric detection (λ_ex = 280/λ_em = 350 nm). The calibration curves were linear for all of the studied compounds over the concentration range of 0.0625–125 μg mL⁻¹ (r² ≥ 0.998) and the limits of detection were below 0.015 μg mL⁻¹. The applicability of the method was confirmed by analysis of Pseudomonasputida culture supernatants.

High-throughput identification and screening of novel Methylobacterium species using whole-cell MALDI-TOF/MS analysis

Methylobacterium species are ubiquitous α-proteobacteria that reside in the phyllosphere and are fed by methanol that is emitted from plants. In this study, we applied whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (WC-MS) to evaluate the diversity of Methylobacterium species collected from a variety of plants. The WC-MS spectrum was reproducible through two weeks of cultivation on different media. WC-MS spectrum peaks of M. extorquens strain AM1 cells were attributed to ribosomal proteins, but those were not were also found. We developed a simple method for rapid identification based on spectra similarity. Using all available type strains of Methylobacterium species, the method provided a certain threshold similarity value for species-level discrimination, although the genus contains some type strains that could not be easily discriminated solely by 16S rRNA gene sequence similarity. Next, we evaluated the WC-MS data of approximately 200 methylotrophs isolated from various plants with MALDI Biotyper software (Bruker Daltonics). Isolates representing each cluster were further identified by 16S rRNA gene sequencing. In most cases, the identification by WC-MS matched that by sequencing, and isolates with unique spectra represented possible novel species. The strains belonging to M. extorquens, M. adhaesivum, M. marchantiae, M. komagatae, M. brachiatum, M. radiotolerans, and novel lineages close to M. adhaesivum, many of which were isolated from bryophytes, were found to be the most frequent phyllospheric colonizers. The WC-MS technique provides emerging high-throughputness in the identification of known/novel species of bacteria, enabling the selection of novel species in a library and identification without 16S rRNA gene sequencing.

Practical application of methanol-mediated mutualistic symbiosis between Methylobacterium species and a roof greening moss, Racomitrium japonicum

Bryophytes, or mosses, are considered the most maintenance-free materials for roof greening. Racomitrium species are most often used due to their high tolerance to desiccation. Because they grow slowly, a technology for forcing their growth is desired. We succeeded in the efficient production of R. japonicum in liquid culture. The structure of the microbial community is crucial to stabilize the culture. A culture-independent technique revealed that the cultures contain methylotrophic bacteria. Using yeast cells that fluoresce in the presence of methanol, methanol emission from the moss was confirmed, suggesting that it is an important carbon and energy source for the bacteria. We isolated Methylobacterium species from the liquid culture and studied their characteristics. The isolates were able to strongly promote the growth of some mosses including R. japonicum and seed plants, but the plant-microbe combination was important, since growth promotion was not uniform across species. One of the isolates, strain 22A, was cultivated with R. japonicum in liquid culture and in a field experiment, resulting in strong growth promotion. Mutualistic symbiosis can thus be utilized for industrial moss production.