• indole-3-acetic acid;
  • plant–microorganism interactions;
  • microbial signaling


  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information

Diverse bacterial species possess the ability to produce the auxin phytohormone indole-3-acetic acid (IAA). Different biosynthesis pathways have been identified and redundancy for IAA biosynthesis is widespread among plant-associated bacteria. Interactions between IAA-producing bacteria and plants lead to diverse outcomes on the plant side, varying from pathogenesis to phytostimulation. Reviewing the role of bacterial IAA in different microorganism–plant interactions highlights the fact that bacteria use this phytohormone to interact with plants as part of their colonization strategy, including phytostimulation and circumvention of basal plant defense mechanisms. Moreover, several recent reports indicate that IAA can also be a signaling molecule in bacteria and therefore can have a direct effect on bacterial physiology. This review discusses past and recent data, and emerging views on IAA, a well-known phytohormone, as a microbial metabolic and signaling molecule.


  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information

In 1880 Charles Darwin proposed that some plant growth responses are regulated by ‘a matter which transmits its effects from one part of the plant to another’ (Darwin & Darwin, 1880). Several decades later, this ‘matter,’ termed auxin (from the Greek ‘auxein’ which means ‘to grow’), was identified as indole-3-acetic acid (IAA) (Kögl & Kostermans, 1934; Went & Thimann, 1937). IAA has since been implicated in virtually all aspects of plant growth and development (reviewed by Woodward & Bartel, 2005 and Teale et al., 2006).

Intriguingly, the discovery of IAA as a plant growth regulator coincided with the first indication of the molecular mechanisms involved in tumorigenesis induced by Agrobacterium. Agrobacterium-induced tumors were shown to be sources of IAA (Link & Eggers, 1941) and capable of growth in the absence of plant growth regulators, which are normally required to incite growth of callus from sterile plant tissues (White & Braun, 1941). It was later found that not only plants but also microorganisms including bacteria and fungi are able to synthesize IAA (Kaper & Veldstra, 1958; Gruen, 1959; Perley & Stowe, 1966; Libbert et al., 1970; Arshad & Frankenberger, 1991; Costacurta & Vanderleyden, 1995).

In recent years, advancement in understanding the IAA signaling pathway in plants has been truly spectacular. The role of IAA in bacteria has not thus far been investigated in such detail. Undoubtedly, the advancement in plant IAA signaling has also intensified research on the various aspects of bacterial IAA synthesis, including its role in bacteria–plant interactions.

As more bacterial species have been analyzed, the role of auxins in plant–microorganism interactions appears diverse. Molecular studies on the biochemical pathways of bacterial IAA synthesis and their regulation have provided some clues on the possible outcomes of the interactions between plants and IAA-producing bacteria, varying from pathogenesis to phytostimulation. Recently, a number of studies have clearly shown that IAA can be a signaling molecule in microorganisms, in both IAA-producing and IAA-nonproducing species. These findings raise new intriguing questions on the role of IAA in bacteria and their interaction with plants.

IAA biosynthesis pathways in bacteria

  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information

With the analysis of additional bacterial species, different bacterial pathways to synthesize IAA have been identified. A high degree of similarity between IAA biosynthesis pathways in plants and bacteria was observed. Here an overview of bacterial IAA biosynthesis pathways is given (Fig. 1), and the current status of related genes, proteins and intermediate metabolites is discussed. Where relevant, comparisons with plant IAA biosynthesis are made.


Figure 1.  Overview of the different pathways to synthesize IAA in bacteria. The intermediate referring to the name of the pathway or the pathway itself is underlined with a dashed line. IAAld, indole-3-acetaldehyde; IAM, indole-3-acetamide; IPDC, indole-3-pyruvate decarboxylase; Trp, tryptophan.

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Tryptophan has been identified as a main precursor for IAA biosynthesis pathways in bacteria. The identification of intermediates led to the identification of five different pathways using tryptophan as a precursor for IAA.

Indole-3-acetamide pathway

The indole-3-acetamide (IAM) pathway is the best characterized pathway in bacteria. In this two-step pathway tryptophan is first converted to IAM by the enzyme tryptophan-2-monooxygenase (IaaM), encoded by the iaaM gene. In the second step IAM is converted to IAA by an IAM hydrolase (IaaH), encoded by iaaH. The genes iaaM and iaaH have been cloned and characterized from various bacteria, such as Agrobacterium tumefaciens, Pseudomonas syringae, Pantoea agglomerans, Rhizobium and Bradyrhizobium (Sekine et al., 1989; Clark et al., 1993; Morris, 1995; Theunis et al., 2004). The IAM-related genes have been detected on the chromosome in different Pseudomonas species as well as on plasmids such as pPATH of Pa. agglomerans (Glickmann et al., 1998; Manulis et al., 1998).

The IAM pathway was described previously as a bacterial-specific pathway, as no evidence for this pathway could be found in plants. However, with an improved, highly sensitive method for the analysis of IAM using a combination of HPLC and GC-MS/MS techniques it was proven beyond doubt that IAM is an endogenous compound of Arabidopsis thaliana (Pollmann et al., 2002). Experiments described by Piotrowski et al. (2001) and Pollmann et al. (2003) further support the operation of the IAM pathway in Arabidopsis.

Indole-3-pyruvate pathway

The indole-3-pyruvate (IPyA) pathway is thought to be a major pathway for IAA biosynthesis in plants. However, the key genes/enzymes have not been identified yet in plants. In bacteria, IAA production via the IPyA pathway has been described in a broad range of bacteria, such as the pythopathogenic bacterium Pa. agglomerans, the beneficial bacteria Bradyrhizobium, Azospirillum, Rhizobium and Enterobacter cloacae, and cyanobacteria. The first step in this pathway is the conversion of tryptophan to IPyA by an aminotransferase (transamination). In the rate-limiting step, IPyA is decarboxylated to indole-3-acetaldehyde (IAAld) by indole-3-pyruvate decarboxylase (IPDC). In the last step IAAld is oxidized in IAA (Fig. 1). The gene, encoding for the key enzyme, IPDC, has been isolated and characterized from Azospirillum brasilense, En. cloacae, Pseudomonas putida and Pa. agglomerans (Koga et al., 1991; Costacurta et al., 1994; Brandl & Lindow, 1996; Patten & Glick, 2002b). In Azospirillum lipoferum, the ipdC gene is located on the chromosome (Blaha et al., 2005) but in most cases the genome localization of this gene has not been determined. In these organisms, insertional inactivation of the pathway resulted in a lower IAA production, up to 90% reduction in Az. brasilense (Prinsen et al., 1993), indicating the importance of the IPyA pathway in auxin production. However, no mutants completely abolished in IAA biosynthesis could be constructed, indicating redundancy for IAA biosynthesis pathways.

Tryptamine pathway

In bacteria, the tryptamine (TAM) pathway has been identified in Bacillus cereus by identification of tryptophan decarboxylase activity (Perley & Stowe, 1966) and in Azospirillum by detection of the conversion of exogenous tryptamine to IAA (Hartmann et al., 1983). In plants tryptamine was identified as an endogenous compound and genes encoding for tryptophan decarboxylases (catalyzing the decarboxylation of tryptophan to tryptamine) have been cloned and characterized from different plants, indicating an IAA biosynthetic pathway via tryptamine in plants. The rate-limiting step for this pathway in plants is probably catalyzed by a flavin monooxygenase-like protein (YUCCA) (conversion of tryptamine to N-hydroxyl-tryptamine). The presence of the intermediates, which are downstream of N-hydroxyl-tryptamine (presumably indole-3-acetaldoxime and indole-3-acetaldehyde), still needs to be confirmed (Bak et al., 2001; Zhao et al., 2001). The last step of this pathway in bacteria is different to that in plants: in bacteria TAM is directly converted to IAAld by an amine oxidase (Hartmann et al., 1983).

Tryptophan side-chain oxidase pathway

Tryptophan side-chain oxidase (TSO) activity has only been demonstrated in Pseudomonas fluorescens CHA0. In this pathway tryptophan is directly converted to IAAld bypassing IPyA, which can be oxidized to IAA (Oberhansli et al., 1991). There are no indications that this pathway exists in plants.

Indole-3-acetonitrile pathway

The biosynthesis of IAA via indole-3-acetonitrile (IAN) has been extensively studied in plants in recent years. The last step in this pathway – the conversion of IAN to IAA by a nitrilase – was identified by Bartling et al. (1992); the steps leading to the formation of IAN from tryptophan are still a matter of debate. Recently, two pathways were suggested for this formation: one via indolic glucosinolates (glucobrassicin) and another via indole-3-acetaldoxime (Bak et al., 2001; Zhao et al., 2001). A tryptophan-independent pathway for the biosynthesis of IAN in plants has been suggested, but not further examined (Normanly et al., 1993; Bartling et al., 1994). In bacteria such as Alcaligenes faecalis (Nagasawa et al., 1990; Kobayashi et al., 1993) nitrilases have been detected with specificity for indole-3-acetonitrile. In Ag. tumefaciens and Rhizobium spp., nitrile hydratase and amidase activity could be identified, indicating the conversion of IAN to IAA via IAM (Kobayashi et al., 1995).

Tryptophan-independent pathway

Analysis of knock-out mutants of Arabidopsis thaliana for tryptophan biosynthesis (defective in tryptophan synthase alpha and beta) revealed increased levels of IAA conjugates, which led to the proposal of a tryptophan-independent pathway for the biosynthesis of IAA (Last et al., 1991; Normanly et al., 1993). This pathway branches from indole-3-glycerolphosphate or indole. However, no enzyme of this pathway has been characterized. The importance (and existence) of the tryptophan-independent pathway has been questioned (Muller & Weiler, 2000).

A bacterial tryptophan-independent pathway could be demonstrated in Az. brasilense by feeding experiments with labeled precursors. This pathway is predominant in case no tryptophan is supplied to the medium: 90% of the IAA is synthesized via the tryptophan-independent pathway, while 0.1% is produced via the IAM pathway (Prinsen et al., 1993). As no specific enzymes of this pathway have yet been identified, the existence of this pathway is currently being reexamined.

Having described these pathways individually, it should be noted that some bacteria possess more than one pathway. In Pa. agglomerans for instance genes for the IAM as well as for the IPyA pathway have been identified (Manulis et al., 1998). Our present knowledge on IAA biosynthesis in bacteria dates back to the end of the last century, as reflected by the list of references. The use of improved analytical techniques for the detection and quantitation of intermediates as well as the rapid progress in functional genomics will undoubtedly provide a more detailed knowledge on the different IAA biosynthesis pathways present in bacteria.

IAA conjugation and storage

In plants most IAA is found in a conjugated form; only a small amount of free IAA is present. The role of these conjugates is diverse: IAA conjugates are involved in transport, storage and protection of IAA from enzymatic degradation. Furthermore, conjugates can control IAA levels in the cell (homeostatic mechanism) and these compounds can allow the catabolism of IAA (Cohen & Bandurski, 1982; Seidel et al., 2006).

The only characterized bacterial gene involved in IAA conjugation is the indole-3-acetic acid-lysine synthetase (iaaL) from Pseudomonas savastanoi pv. savastanoi. The gene product converts IAA to IAA-lysine via an ATP-dependent formation of an amide bond between the carboxyl group of IAA and the epsilon amino acid group of lysine. It is presumed that IAA is released through hydrolysis from its conjugated form inside the plant tissue by plant enzymes (Glass & Kosuge, 1986).

In bacteria some intermediates of IAA biosynthesis can be converted to storage compounds, e.g. the reduction of indole-3-pyruvate and indole-3-acetaldehyde to indole-3-lactic acid (ILA) and indole-3-ethanol or tryptophol respectively. The physiological function of these compounds remains unknown. ILA is inactive as a phytohormone but it can compete for auxin-binding sites in plants with IAA (Sprunck et al., 1995).

Genome-wide screening for key genes in IAA biosynthesis

  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information

It has been suggested that 80% of rhizosphere bacteria produce IAA (Patten & Glick, 1996; Khalid et al., 2004). However, studies on the identification and characterization of the key genes or proteins involved in IAA biosynthesis are few and have mostly been directed to one specific gene or protein of a biosynthetic pathway. Although a vast collection of IAA-producing strains are available, the identification of genes or proteins is restricted to a small group of ‘model organisms,’ e.g. Ag. tumefaciens, Azospirillum, Pa. agglomerans and En. cloacae. Even in these model organisms, attempts to generate mutants, completely impaired in IAA production, failed, indicating that IAA is synthesized via multiple pathways present in a single bacterial species.

To extend the overview of bacteria with the capacity to produce IAA, publicly available genomes were analyzed in silico for the presence of IAA biosynthetic genes. In a first stage well-characterized genes or proteins were selected to function as bait in a blast search (see Table 1). The genes or proteins involved in the tryptophan-independent and TSO pathway are unknown and therefore these pathways could not be searched for. Additionally, the IAN pathway was excluded from the analysis due to the lack of characterized genes or proteins of this pathway in bacteria. In the second phase of the blast algorithm (Altschul et al., 1997), the translated nucleotide sequence or protein sequence of the baits were used to identify similar proteins in the sequenced genomes. blast results are summarized and interpreted in Table 2, which shows the distribution of the different pathways among the annotated genomes. Of the 369 genomes sequenced (sequences retrieved from NCBI on 12 September 2006), 57 genome sequences (15.4%) contain genes necessary to synthesize IAA from tryptophan. The presence of IAA biosynthetic genes in the genome does not imply that the bacterium is capable of producing IAA: functional analysis of the genes is still needed to confirm a possible role in IAA production. The uncoupling between the presence of IAA biosynthetic genes and IAA biosynthesis is illustrated by the anaerobic aromatic-degrading denitrifying bacterium Azoarcus strain EbN1. The genome encodes a phenylpyruvate decarboxylase and other genes that form part of the IPyA pathway (Rabus et al., 2005). The bacterium, however, does not produce auxins (neither IAA nor phenylacetic acid) as such. The IAA biosynthesis genes are involved in the Ehrlich pathway (degradation of amino acids via transamination, decarboxylation and dehydrogenation), leading to phenylacetic acid, which can be further catalyzed into benzoyl-coenzyme A (CoA) or into 3-ketoadipyl-CoA via an aerobic degradation. Benzoyl-CoA is a central molecule that can be further metabolized (via aerobic β-oxidation to acetyl-CoA and succinyl-CoA, which can enter the tricarboxylic acid cycle; Rabus, 2005).

Table 1.   Selected proteins as bait for blast search
PathwayGeneOrganismAccession no.Cut-off blast E value
  • *

    Member of the Eukaryota; sequence data for the gene/protein are not available from Bacteria.

  • IAM, indole-3-acetamide; IPyA, indole-3-pyruvate; TAM, tryptamine.

IAMTryptophan monooxygenaseAgrobacterium tumefaciens C58AAD304891e-60
IAMIndole-3-acetamide hydrolaseAgrobacterium tumefaciens C58AAD304881e-50
IPyAIndole-3-pyruvate decarboxylaseEnterobacter cloacaeP232341e-75
IPyAPhenylpyruvate decarboxylaseAzospirillum brasilense Sp245P518521e-75
IPyA/TAMIndole-3-acetaldehyde dehydrogenaseUstilago maydis FB1*AAC495751e-75
TAMTryptophan decarboxylaseCatharanthus roseus*CAA478981e-50
TAMCopper amine/tyramine oxidaseKlebsiella aerogenesP492501e-75
Table 2.   Distribution of IAA biosynthetic pathways in publicly available annotated genomes of bacteria, including cyanobacteria
  • The number of publicly available genome sequences was 369 (NCBI database accession on 12 September 2006). Using the blast algorithm, the baits of Table 1 were used to identify similar genes, using the cut-off value indicated in Table 1. A biosynthetic pathway was present in a genome sequence when the E value of all biosynthetic genes leading from tryptophan to IAA was below the threshold. Using this method, possible IAA biosynthetic pathways could be identified in 57 bacterial species.

  • *

    The total number of IAA biosynthetic pathways is higher than the number of bacterial species due to redundancy in Burkholderia xenoverans LB400, Rhodopseudomonas palustris HaA2 and the cyanobacterium Anabaena variabilis ATCC 29413. All three organisms have the IPyA pathway in common, in addition to another pathway.

  • IAM, indole-3-acetamide; IPyA, indole-3-pyruvate; TAM, tryptamine.

Plant-associated bacteria2/52/51/5
 Plant pathogens2/20/20/2
 Beneficial bacteria0/32/31/3
Soil bacteria*2/53/51/5
Human pathogens0/2525/250/25

Among bacteria for which the genome is sequenced and available at NCBI, genes encoding for the IPyA pathway are most abundant, present in 89.5% of the putative IAA-producing strains. Even human pathogens possess genes encoding for IAA biosynthesis via IPyA. However, as described above for Azoarcus, it is likely that the genes in human pathogenic strains are not involved in IAA production. They are part of the Ehrlich pathway, leading to molecules that can enter different metabolic cycles as energy source. Similarly, ruminal bacteria and anaerobic bacteria from the human large intestine are able to metabolize tryptophan and phenylalanine to indolic and phenolic compounds such as IAA and phenylacetic acid (Amin & Onodera, 1997; Smith & Macfarlane, 1997; Mohammed et al., 2003).

In plant-associated bacteria, both the IAM and the IPyA pathway are distributed among the sequenced genomes. Phytopathogenic organisms tend to use the IAM pathway to produce IAA, whereas beneficial bacteria tend to use the IPyA pathway. As only five genomic sequences of plant-associated bacteria that have been annotated encode for one or more possible IAA biosynthetic pathways, this tendency needs further confirmation. The capacity to produce IAA is not as widespread as expected in plant-associated bacteria: 19.2% of the sequenced strains have one or more IAA biosynthetic pathways encoded in their genome. However, these data are biased owing to a high number of sequenced genomes of plant-associated Pseudomonas and Xanthomonas strains (46.2% of the plant-associated bacteria, for which the genome sequence is publicly available). Only the genome sequence of Ps. syringae pv. syringae B728a encodes for a possible IAA biosynthetic pathway.

A remarkable observation is the distribution of the TAM pathway (identified in 8.8% of the putative IAA-producing strains): genes encoding enzymes of the TAM pathway were found in cyanobacteria, and soil and plant-associated bacteria (Rhodopseudomonas and Mesorhizobium). Via feeding experiments, the intermediate TAM was identified in Azospirillum and Bacillus cereus (Hartmann et al., 1983). Proteins similar to tryptophan decarboxylase, involved in the first step of the TAM pathway, have not yet been identified and characterized in bacteria.

The production of IAA via IPyA has been described for cyanobacteria (Sergeeva et al., 2002). As cyanobacteria are the progenitors of chloroplasts, the evolutionary link between plant and bacterial IAA biosynthesis becomes relevant. In three cyanobacteria species possible key genes, involved in IAA biosynthesis, could be determined: both genes for the IPyA pathway, which is considered as a major IAA biosynthesis pathway detected in plants, as for the TAM pathway have been identified.

Factors that influence bacterial IAA biosynthesis

  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information

Reports describing factors that alter the level of IAA biosynthesis and/or the expression of IAA biosynthesis genes in bacteria are numerous. However, it is not yet possible to integrate these factors into a comprehensive regulatory scheme of IAA biosynthesis in bacteria. This is partly due to the diversity of IAA expression regulation across IAA biosynthesis pathways and across bacteria. Furthermore, there is a lack of integrated studies following IAA expression in different bacteria and different environments.

This part of the review gives an overview of the different factors that have been described thus far to modulate IAA biosynthesis and/or expression of genes involved in IAA biosynthesis and of the remaining gaps in our understanding of the regulation of IAA biosynthesis in bacteria.

Environmental factors modulating IAA biosynthesis

A first class of factors influencing IAA biosynthesis in diverse bacteria is related to environmental stress, including acidic pH, osmotic and matrix stress, and carbon limitation. In Az. brasilense IAA production and expression of the key gene ipdC have been shown to be increased under carbon limitation, during reduction in growth rate and under acidic pH (Ona et al., 2003, 2005; Vande Broek et al., 2005). Interestingly, carbon limitation and reduction in growth rate are both associated with the entry in the stationary phase, raising the question of the importance of population growth status in IAA biosynthesis and, vice versa, the importance of IAA in cell population behavior. The concerted action of these two factors is in agreement with the observation that overproduction of the stress-related stationary-phase sigma factor RpoS enhanced IAA production in En. cloacae and Ps. putida (Saleh & Glick, 2001; Patten & Glick, 2002a).

The pH inducibility of ipdC gene expression in Az. brasilense seems to be independent of other regulating environmental factors. This was shown using different deletions and mutations in the promoter of ipdC (Vande Broek et al., 2005). An alternative sigma factor, which is acid-regulated, was suggested to be responsible in passing on the pH response to ipdC expression (Ona et al., 2003; Vande Broek et al., 2005). In contrast to Azospirillum, the expression of the ipdC gene of Pa. agglomerans is not regulated by pH. In this bacterial species the ipdC gene was shown to be under control of other environmental stresses: expression increased 18-fold under low solute and matrix potentials (Brandl & Lindow, 1997). This effect was not observed for the expression of ipdC from Az. brasilense (Vande Broek et al., 2005).

Despite the diversity in stress factors modulating IAA expression in different bacteria, a common feature can be identified. The expression of genes involved in IAA biosynthesis is fine-tuned to encounter environmental stresses associated with the soil and plant environment. An acidic pH is typical for the rhizosphere environment due to proton extrusion through membranes of root cells. Matrix potential may be an important condition encountered in the environment of epiphytic bacteria on plant surfaces such as Pa. agglomerans.

A second class of factors altering bacterial IAA production contains plant extracts or specific compounds and/or the presence of plant surfaces. In the symbiotic bacterium Rhizobium sp. strain NGR234, flavonoids, which are produced by the host plant and accumulate in the rhizosphere, stimulate IAA production in a NodD1-, NodD2- and SyrM2-dependent manner. NodD1, NodD2 and SyrM2 form a regulatory cascade that coordinates the expression of genes under influence of flavonoids (Prinsen et al., 1991; Theunis et al., 2004). In Xanthomonas axonopodis IAA production is increased in the presence of plant leaf extracts from Citrus cinensis. The question as to which specific compound is responsible for this induction remains unclear (Costacurta et al., 1998). Similarly, in the phytopathogenic gram-positive bacterium Rhodococcus fascians IAA production is induced by plant extracts. Interestingly, only extracts from plant tissue infected with R. fascians, the so-called leavy galls, could upregulate IAA production in R. fascians. An extract from a mock-inoculated plant had no effect on IAA biosynthesis (Vandeputte et al., 2005).

The expression of the ipdC gene of Pa. agglomerans is very low in broth culture and independent from carbon source, pH, tryptophan availability and O2 availability, but increases dramatically when the bacterium is grown on plant surfaces, indicating that a signal from the plant surface is involved in transcriptional regulation and subsequent IAA production. The environmental cues altering ipdC expression in Pa. agglomerans allow the bacterium to modify its habitat and exploit plant surfaces (Brandl & Lindow, 1997). A later study on the spatial pattern of ipdC expression on plant leaves revealed a heterogeneous distribution of expression along the surface environment, suggesting that the leaf surface significantly varies over a small scale (Brandl et al., 2001). These results indicate that IAA production by bacteria can be remarkably different within a microenvironment.

An important molecule that can alter the level of IAA synthesis is the amino acid tryptophan, identified as the main precursor for IAA and thus expected to play a role in modulating the level of IAA biosynthesis. The application of exogenous tryptophan was shown to increase strongly the IAA production in various bacteria, for example Azospirillum, Pa. agglomerans, Ps. putida and Rhizobium (Prinsen et al., 1993; Brandl & Lindow, 1996; Patten & Glick, 2002b; Theunis et al., 2004). In both Az. brasilense Sp7 as in Ps. putida GR12-2 the presence of tryptophan increased the expression level of the key enzyme ipdC, three- to four-fold and five-fold, respectively (Zimmer et al., 1998; Patten & Glick, 2002b). In the rhizosphere tryptophan can originate from two sources: released from degrading root and microbial cells and from root exudates. Support for the first source is the observation that IAA is produced during the late exponential and stationary phase in Azospirillum (Omay et al., 1993). The amount of tryptophan in plant root exudates can vary strongly among plant species (Kravchenko et al., 2004). Although the amount of tryptophan in root exudates is rather low (Kravchenko et al., 1991), exogenous tryptophan can be efficiently absorbed by bacteria. As the Km value, an indicator of the affinity of the transporter for tryptophan, is low, the affinity of bacteria for tryptophan is high, which makes them good scavengers for tryptophan. This results in efficient transport into the cells, even at low concentration (Marlow & Kosuge, 1972).

Besides the role of the precursor tryptophan in the regulation of IAA production, IAA biosynthesis can also be modulated by the end-product IAA and by its intermediates. In Ps. savastanoi pv. savastanoi the activity of the first enzyme in the IAM pathway, IaaM, is controlled through feedback inhibition by IAM and IAA (Hutcheson & Kosuge, 1985). Curiously, while tryptophan stimulates IAA production in Azospirillum, anthranilate, a precursor for tryptophan, reduces IAA synthesis. By this mechanism IAA biosynthesis is fine-tuned because tryptophan inhibits anthranilate formation by a negative feedback regulation on the anthranilate synthase, resulting in an indirect induction of IAA production (Hartmann & Zimmer, 1994).

Interestingly, nitrile hydratase, which catalyzes the first step in the conversion of IAN to IAA in Ag. tumefaciens, is induced by its product IAM, indicating a positive feedback regulation in IAA biosynthesis (Kobayashi et al., 1995).

Another positive feedback mechanism has been described for Az. brasilense Sp245 by Vande Broek et al. (1999). The level of IAA production by Az. brasilense increases during growth, with highest levels of IAA production during the stationary phase (Prinsen et al., 1993). The expression of the key gene for IAA production in the presence of significant amounts of tryptophan, the indole-3-pyruvate decarboxylase gene, increases with the cell density and reaches its maximum at stationary phase. Cell density-dependent induction of genes can be mediated by small diffusible signal molecules. Surprisingly, in Az. brasilense Sp245 IAA itself is responsible for the increase in expression by induction of the ipdC gene (Vande Broek et al., 1999). Other auxins such as naphataleneacetic acid and phenylacetic acid (Somers et al., 2005) also upregulate the expression. Compounds that had no effect on the expression were IAA conjugates, indole-3-butyric acid and tryptophan, although IAA production is enhanced by tryptophan. In contrast to negative control of the transcription of biosynthetic genes by the end-product, the positive feedback regulation or autoinduction by IAA is rather unusual (Vande Broek et al., 1999). The ipdC gene of Az. brasilense was the first discovered bacterial gene that is induced by auxins, indicating that proteins responsible for IAA perception and signal transduction are present in bacteria.

Genetic factors

Different genetic factors have been described to affect the level of IAA biosynthesis in bacteria. Firstly, the location of auxin biosynthesis genes in the genome, either plasmid or chromosomal, has been shown to modulate the level of IAA production. Plasmids are generally present in various copies in the bacterial cell, providing a higher number of IAA biosynthesis genes that can be transcribed as compared with IAA biosynthesis genes that are located on the chromosome (Brandl & Lindow, 1996; Patten & Glick, 1996). In Ps. savastanoi pv. savastanoi the biosynthetic genes are located on a plasmid, whereas in Ps. syringae pv. syringae the homologous genes are encoded on the chromosomal DNA. In the latter species, a much smaller amount of IAA is produced. When this Pseudomonas strain is equipped with a low-copy plasmid, encoding the IAA operon, IAA production is increased four-fold (Mazzola & White, 1994), indicating the importance of either the location or the copy number or both of the encoding genes.

Secondly, the mode of expression, constitutive vs. induced, of IAA biosynthesis genes was observed to differ across biosynthesis pathways and across bacterial species. In Ag. tumefaciens and Agrobacterium rhizogenes the region of the Ti plasmid containing iaaM and iaaH is transferred and integrated into the plant genome. The genes are expressed under control of strong constitutive promoters, resulting in the production of high levels of IAA inside the plant tissue (reviewed by Costacurta & Vanderleyden, 1995). In Ps. fluorescens CHA0 the IPyA pathway is presumably constitutive, while the TSO pathway is only active during the stationary phase (Oberhansli et al., 1991).

Furthermore, two transcriptional regulators, RpoS – which regulates the transcription of genes in response to stress conditions and starvation – and the two-component system GacS/GacA – which controls the expression of genes of which many are induced during a late logarithmic growth phase and have a role in maintaining the competitiveness of the bacterium in the rhizosphere – have been shown to interact with the expression level of IAA biosynthesis genes. The ipdC genes show a typical stationary-phase-dependent expression. IAA production starts in the late logarithmic to early stationary phase and the promoter region of some ipdC genes contains a sequence similar to the consensus sequence recognized by RpoS. In Ps. putida GR12-2 and Pa. agglomerans ipdC expression is regulated by RpoS (Brandl et al., 2001; Patten & Glick, 2002a): the ipdC promoter region contains elements similar to the RpoS recognition sequence, and mutants, carrying constitutively expressed rpoS on a plasmid, produce IAA earlier at consistently elevated levels as compared with wild-type cells (Patten & Glick, 2002a). In Azospirillum species RpoS is not present (RpoS is not detected in Alphaproteobacteria). In this case alternative sigma factors, RpoN and possibly RpoH, regulate IAA expression (Gysegom, 2005).

In Pseudomonas chlororaphis, the GacS/GacA two-component system acts as a negative regulator of the tryptophan-dependent IAA biosynthesis (Haas & Keel, 2003; Kang et al., 2006). The involvement of RpoS and GacS in IAA production was further confirmed by overexpression of the rpoS and gacS genes of Ps. fluorescens in two En. cloacae strains (Saleh & Glick, 2001).

Bacterial IAA in plant–microorganism interactions

  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information

With the analysis of further bacterial species, the role of bacterial IAA in plant–microorganism interactions appears to be diverse. Previously, bacterial auxin production was mainly associated with pathogenesis, specifically with bacterial gall formation. However, it became apparent that many of the phytopathogenic (not only gall-inducing) as well as plant growth-promoting bacteria have the ability to synthesize IAA. The broad distribution of IAA biosynthesis genes across bacteria, the existence of different metabolic pathways and the diversity in outcomes on the plant side when IAA-synthesizing bacteria interact with plants, evoke the question as to why bacteria produce IAA. Except for a few cases, the link between IAA synthesis and plant, phenotype has not been demonstrated or at least remains ambiguous. This part of the review aims to give an insight into bacterial IAA production as one of different strategies to seduce the plant partner.

Factors steering the outcome of the interaction between IAA-producing bacteria and plants

IAA is the main auxin in plants, controlling many important physiological processes including cell enlargement and division, tissue differentiation, and responses to light and gravity (Taiz & Zeiger, 1998; Woodward & Bartel, 2005; Teale et al., 2006). Bacterial IAA producers interacting with plants have the potential to interfere with any of these processes by changing in a spatiotemporal way the plant auxin pool. The impact of exogenous auxin on plant development ranges from positive to negative effects. The consequence for the plant is usually a function of (1) the amount of IAA produced that is available to the plant and (2) the sensitivity of the plant tissue to changes in IAA concentration.

The optimal IAA concentration range for a given plant phenotype may be extremely narrow, as demonstrated by the isolation of a plant growth-promoting Ps. putida strain producing IAA and of a plant growth-inhibiting IAA overproducer mutant producing only four times the amount of IAA synthesized by the wild-type strain (Xie et al., 1996; Persello-Cartieaux et al., 2003). Similarly, inoculation with Pseudomonas thivervalensis, an IAA-producing strain, resulted in reproducible morphological changes of Arabidopsis roots without effects on plant growth when inoculated at a concentration of 105 CFU mL−1, and in inhibition of plant growth when inoculated at concentrations above 106 CFU mL−1 (Persello-Cartieaux et al., 2001). It cannot, however, be excluded that other factors (e.g. metabolites) than auxin production contribute to the inhibitory effect of highly concentrated inoculants. The use of mutant and transgenic strains and the analysis of inoculant supernatants are necessary to distinguish further the role of different bacterial factors in the diverse outcome on the plant side upon inoculation with increasing concentrations of bacterial cells.

The actual concentration of bacterial IAA available to the plant is, in part, contingent upon the physical relationship between the two organisms. Whereas bacterial phytopathogens infect their host plants and, in the peculiar case of agrobacteria transform plant cells, beneficial bacteria (symbionts excepted) appear to exert their effect predominantly while colonizing the external surface of a plant (Patten & Glick, 1996). However, as more plant tissues are analyzed for the presence of bacteria, an increasing number of IAA-producing plant growth-promoting rhizobacteria (PGPR) are detected inside the plant tissue (Rosenblueth & Martinez-Romero, 2006).

The pathway used by the plant-associated bacterial strain to synthesize IAA may further affect the outcome on the plant side. Phytopathogenetic symptoms are mostly linked to the IAM pathway, which is generally believed to be a specific microbial pathway (see above). However, as mentioned above, there is growing evidence for the presence of an IAM pathway in Arabidopsis thaliana (Piotrowski et al., 2001; Pollmann et al., 2002, 2003, 2006). As plants may not generally possess the metabolic intermediates or pools of this pathway, they may not be able to maintain IAA at nontoxic or physiologically appropriate levels in their tissues by feedback regulation (Persello-Cartieaux et al., 2003). In contrast, the biosynthesis of IAA via indole-3-pyruvic acid and indole-3-acetaldehyde is predominant in higher plants and is observed in pathogenic as well as in nonpathogenic bacteria. Most beneficial bacteria produce IAA via the IPyA pathway. This view of an IAM route linked to pathogenesis and an IPyA pathway involved in epiphytic and rhizosphere fitness of the bacteria has been supported through the generation of mutants of Pa. agglomerans pv. gypsophilae, a gall-inducing bacterium, in which the different biosynthetic pathways were disrupted individually or in combination. Inactivation of the IAM pathway caused the largest reduction in gall size whereas inactivation of the IPyA pathway caused a minor, nonsignificant decrease in pathogenicity. The reverse effect was observed for epiphytic fitness: inactivation of the IAM pathway did not affect colonization capacity whereas inactivation of the IPyA pathway did (Manulis et al., 1998). The difference in function of the two IAA biosynthesis pathways in Pa. agglomerans was associated with differences in expression profiles of the corresponding genes. The ipdC gene showed enhanced expression during colonization while iaaM was upregulated during later phases of the plant–microorganism interactions, including gall formation. However, it was also reported that cranberry stem gall is induced by multiple opportunistic bacteria, including Pa. agglomerans strains, which produce IAA exclusively through the IPyA pathway. These data indicate that pathogenesis is not necessarily associated with the IAM pathway for IAA biosynthesis (Vasanthakumar & McManus, 2004). Furthermore, some nonpathogenic symbiotic bacteria including Rhizobium synthesize IAA mainly through the IAM pathway (Theunis et al., 2004).

In addition to the amount of bacterial auxin produced, the contrasting effects of IAA on plant development are linked to the sensitivity of the host itself. The study of the effect of auxin-producing bacterial strains on wheat (Kucey, 1988), blackcurrant and sourcherry softwood (Dubeikovsky et al., 1993) highlights the cultivar specificity of the response of plants to bacteria. More extremely, auxin-resistant mutants of Arabidopsis are insensitive to Ps. thivervalensis colonization while the same inoculation on wild-type plants induces changes in root morphology (Persello-Cartieaux et al., 2001). The host plant can also take an active part in the regulation of microbial IAA biosynthesis. Transcription of ipdC in Pa. agglomerans pv. gypsophilae is induced in response to bean and tobacco compounds, the structure of which is not yet known (Brandl & Lindow, 1997). As the ability to produce auxins from tryptophan is common among soil organisms, it is tempting to assume that bacterial auxin is in part dependent upon plant-exuded tryptophan (Persello-Cartieaux et al., 2003). Bar and Okon proposed that IAA biosynthesis may contribute to bacterial survival in the rhizosphere by detoxification of plant-exuded tryptophan. They observed that addition of 10 mM (1.4 mg mL−1) or more of tryptophan strongly inhibited growth of Az. brasilense Sp7. Instability of tryptophan, variation in exudation across plant species and environments, and the lack of comprehensive studies on exudation in the rhizosphere complicate and currently impede linking this observation of microbial growth inhibition by tryptophan (Bar & Okon, 1992, 1993) with actual rhizosphere activities.

IAA in gall formation

Tumor- and gall-inducing bacteria were the first plant-associated bacteria in which IAA biosynthesis pathways were studied because of the suspected role of microbially released auxins in disturbing plant morphology and development (Morris, 1995). Agrobacterium tumefaciens, Ag. rhizogenes, Ps. savastanoi and Pa. agglomerans pv. gypsophilae all possess the IAM pathway, and the DNA sequence of the iaaM gene suggests a common evolutionary origin (Morris, 1995). In all of these bacteria, IAA is involved in pathogenesis. However, depending on the bacterial species, the mechanism of either gall or tumor formation and the role of IAA therein differ. Tumor formation induced by Ag. tumefaciens involves transfer of T-DNA from the bacteria into the host genome of infected cells. This T-DNA possesses genes (iaaM and iaaH) encoding the IAM pathway for IAA biosynthesis (Zambryski, 1992; Zupan et al., 2000). The overproduction of auxin and cytokinin by the transformed plant cells results in the typical crown gall or tumor. Other transferred genes encode enzymes involved in the synthesis of amino acid and sugar derivatives, the opines, which the strain of Agrobacterium that induces the tumor can use as a source of carbon, nitrogen and energy. Removing the Ti phytohormone biosynthesis genes from Agrobacterium abolishes tumor formation, demonstrating that the IAA as well as the cytokinins synthesized by the enzymes encoded by the transferred bacterial oncogenes are essential for tumor formation. It was proposed by Aloni et al. (1995) that the high IAA concentrations induced by the enzymes encoded by the T-DNA genes iaaM and iaaH stimulate ethylene synthesis in the crown gall. The tumor-induced ethylene would be the controlling signal that induces narrowing of the vessels in the host adjacent to the tumor, which, in turn, substantially limits water and nutrient supply to the shoot organs above the tumor (Aloni et al., 1995).

The mechanism of gall formation by Pa. agglomerans pv. gypsophilae on Gypsophila is fundamentally different from that by Ag. tumefaciens. Gall formation by Pa. agglomerans pv. gypsophilae does not involve transfer of DNA into host cells (Clark et al., 1989); therefore, it requires the constant presence of living bacteria, in contrast to the situation with Ag. tumefaciens. Pathogenic and nonpathogenic strains of Pa. agglomerans possess chromosomal genes encoding the IPyA pathway for IAA biosynthesis, whereas only pathogenic strains carry the genes encoding the IAM pathway on the pPATHPag plasmid (Clark et al., 1993; Brandl & Lindow, 1996; Manulis et al., 1998). Inactivation of the IPyA pathway in Pa. agglomerans pv. gypsophilae did not affect gall formation significantly, while mutations in genes of the IAM pathway substantially reduced the gall size but did not eliminate gall initiation (Clark et al., 1993; Manulis et al., 1998). This demonstrates that in Pa. agglomerans pv. gypsophilae bacterial IAA synthesized by the IAM pathway contributes to obtain optimal gall size but is not essential for gall induction. It has been shown that the translocation of effectors of the type III secretion system (TTSS) into the host cells is the key factor for gall induction by Pa. agglomerans pv. gypsophilae (Mor et al., 2001; Manulis & Barash, 2003; Nizan-Koren et al., 2003). Similar to tumor development induced by Ag. tumefaciens, an increase in ethylene is associated with bacterial IAA production in gall formation induced by Pa. agglomerans pv. gypsophilae (Chalupowicz et al., 2006).

IAA in plant growth-promoting rhizobacteria

For various PGPR, it has been demonstrated that enhanced root proliferation is related to bacterial IAA biosynthesis.

Studies with Azospirillum mutants altered in IAA production support the view that increased rooting is caused by Azospirillum IAA synthesis (Dobbelaere et al., 1999). This increased rooting enhances plant mineral uptake and root exudation, which in turn stimulates bacterial colonization and thus amplifies the inoculation effect (Dobbelaere et al., 1999; Lambrecht et al., 2000; Steenhoudt & Vanderleyden, 2000). Furthermore, the dose–response curve of roots to cultures with increasing concentrations of Azospirillum nicely fits the dose–response curve of roots to increasing concentrations of IAA (Fallik et al., 1994). However, in several studies it was shown that Azospirillum IAA biosynthesis alone cannot account for the overall plant growth-promoting effect observed. Therefore, the ‘additive hypothesis’ was suggested to explain growth and yield promotion with Azospirillum, postulating that growth promotion is the result of multiple mechanisms (phytohormone biosynthesis, nitrogen fixation, among others) working together (Bashan & Holguin, 1997).

Similarly, the capacity of Ps. putida GR12-2 to stimulate root elongation was shown to be related to its production of IAA but production of IAA alone does not account for growth promotion, as evidenced by a study with IAA-overproducing mutants (Xie et al., 1996). In their study transposon mutagenesis was used to isolate seven mutants that overproduced IAA in comparison with the wild-type. Interestingly, six of the seven mutants, including one which produced IAA at three times the rate of GR12-2, elicited root elongation at a level statistically equivalent to GR12-2. This finding demonstrates that for GR12-2 inoculation there is not a direct relationship between the level of IAA produced and the magnitude of root elongation. One mutant that produced IAA at four times the rate of GR12-2 lost root elongation activity. This was explained by the interaction of IAA with the enzyme 1-aminocyclopropane-1-carboxylate (ACC) synthase. Large amounts of IAA produced by bacteria together with endogenously produced plant IAA activate ACC synthase, leading to production of ACC, a precursor for ethylene. Ethylene is an inhibitor of root growth especially reducing the primary root length (Glick et al., 1998; Glick, 2005). A key feature of GR12-2 is that the bacterium produces ACC deaminase that converts ACC to ammonia and α-ketobutyrate. This conversion lowers the pool of ACC in the root environment, thereby reducing the amount of ethylene and consequently its inhibition of root growth. The bacterium takes advantage of this situation using ACC as a source of nitrogen. Thus, a balanced interplay of different factors including bacterial IAA biosynthesis rather than IAA production per se is needed to stimulate plant growth (Xie et al., 1996).

IAA in Rhizobium–legume symbiosis

Most Rhizobium species have been shown to produce IAA via different pathways (Badenochjones et al., 1983; Theunis et al., 2004), and many studies indicate that changes in auxin balance in the host plant are a prerequisite for nodule organogenesis (Mathesius et al., 1998). Auxins are involved in multiple processes including cell division, differentiation and vascular bundle formation. These three events are also necessary for nodule formation as such. It seems likely that auxins play a role in nodulation. Nevertheless, the exact role of IAA in the different stages of Rhizobium–plant symbiosis remains unclear.

A number of experiments suggest that rhizobia, in particular Rhizobium Nod factors (lipo-chitin oligosaccharides, which are produced by rhizobia upon triggering nod gene expression by plant-derived flavonoids) interfere with auxin transport. Moreover, the application of synthetic polar auxin transport (PAT) inhibitors, which interfere with the hormone balance in the root, can induce pseudonodule structures on the root (Allen et al., 1953; Hirsch et al., 1989; Wu et al., 1996). Direct measurements of auxin transport using radiolabeled auxin showed that rhizobia locally inhibit acropetal auxin transport capacity in vetch (Vicia sativa) roots within 24 h after inoculation (Boot et al., 1999). In addition, the expression of an auxin-responsive promoter (GH3) was reduced acropetally from the inoculation site, between 12 and 24 h following rhizobia inoculation or addition of Nod factors (Mathesius et al., 1998). This was followed by an apparent increase in auxin accumulation at the site of nodule initiation in the inner cortex. By contrast, in the determinate legume Lotus japonicus, no auxin transport inhibition could be measured after inoculation (Pacios-Bras et al., 2003). However, an increase of GH3 expression was still located in the nodule initials, suggesting that high auxin levels are required for nodule initiation. Moreover, it has been suggested that the expression of the AUX-1-like protein LAX in developing Medicago truncatula nodule primordia is important for a continuous flow of auxin into the forming primordium (de Billy et al., 2001). It is therefore likely that auxin transport regulation is part of the process leading to nodule initiation.

Very recently, it has been demonstrated that a cytokinin receptor (HIT1 gene in L. japonicus) is involved in the Nod factor signaling cascade in Lotus as well as in Medicago (Murray et al., 2007; Tirichine et al., 2007). As the effect of cytokinins is dependent on the auxin/cytokinin balance, these findings may give a new dimension to the role of auxin in nodulation.

Other observations suggest that microbially released IAA could play a role in rhizobia–plant symbiosis. It was demonstrated that the specific nod inducers, flavonoids, also stimulate the production of IAA by Rhizobium (Prinsen et al., 1991). Moreover, in Rhizobium sp. NGR234 this flavonoid induction is dependent on the transcriptional regulators NodD1 and NodD2 and the presence of the nod-box NB15 upstream of the y4wEFG operon required for IAA synthesis (Theunis et al., 2004). The link between Nod factors as symbiotic signaling molecules and rhizobial IAA biosynthesis points to a role for IAA in the Rhizobium–bean symbiosis. Knocking-out the flavonoid-dependent IAA biosynthesis in NGR234 did not affect nodulation significantly on Vigna and Tephrosia, although preliminary results with Lablab have shown NGR234 to be Fix+ while the IAA mutants are Fix (Theunis, 2005).

In addition, root nodules have been shown to contain more IAA than nonnodulated roots (Dullaart & Duba, 1970; Badenochjones et al., 1983; Basu & Ghosh, 1998; Theunis, 2005; Ghosh & Basu, 2006), and auxins could be important for maintaining a functional root nodule (Badenochjones et al., 1983). In nodules induced by low IAA-producing mutants of Rhizobium sp. NGR234, the IAA content is lower than in nodules induced by the wild-type strain, indicating that at least part of the IAA in nodules derives from the bacteria (Theunis, 2005). Bacteroids of plants inoculated with mutant Bradyrhizobium japonicum strains overproducing IAA contain high amounts of IAA in comparison with wild-type bacteroids (Hunter, 1989), supporting the hypothesis that increased IAA biosynthesis in nodules is of prokaryotic origin. Moreover, introduction of a second synthesis pathway for auxin synthesis in rhizobia led to larger nodules, an increase in nodule acetylene reduction ability and a delay in nodule senescence (Camerini et al., 2004). Similarly, a mutant of Br. japonicum that produces 30-fold more IAA than the wild-type strain showed higher nodulation efficiency (Kaneshiro & Kwolek, 1985).

The application of exogenous IAA can enhance nodulation on Medicago and Phaseolus vulgaris when added at very low concentrations (up to 10−8 M) to the medium, while high concentrations inhibit nodulation (Plazinski & Rolfe, 1985; van Noorden et al., 2006). Combined application of Rhizobium and Azospirillum can also increase nodulation as demonstrated in several studies (Okon & Itzigsohn, 1995; Burdman et al., 1996). Similar to the IAA effect on nodulation, the effect of Azospirillum is dependent on the concentration of the inoculum. Better root development induced by Azospirillum IAA production could explain the increased nodulation but also additional factors, such as changes in flavonoid metabolism, were suggested to be involved (Burdman et al., 1996).

IAA in phytopathogenesis, other than gall- or tumor-inducing pathogens

Besides gall- and tumor-inducing plant pathogens, other phytopathogens like various Ps. syringae species also synthesize IAA (Glickmann et al., 1998; Buell et al., 2003). Infection can result in necrotic lesions often surrounded by chlorotic halos. Here, the role of IAA in disease development is not clear. In many bacterial pathogens, the hrp-gene-encoded type III secretion system that directly translocates effector proteins into the eukaryotic host cells is key to pathogenesis and the development of disease symptoms (Jin et al., 2003; He et al., 2004). Recently, a link between the TTSS and phytohormone production in the plant pathogen Ralstonia solanacearum was established through a host responsive regulator of the TTSS activation cascade, HrpG (Valls et al., 2006). It was shown that HrpG controls, in addition to that of the TTSS, the expression of a previously undescribed TTSS-independent pathway that includes a number of other virulence determinants and genes probably involved in adaptation to life in the host and which includes IAA and ethylene biosynthesis genes. These results provide a new, integrated view of plant bacterial pathogenicity, in which a common regulator activates synchronously upon infection the TTSS, other virulence determinants and a number of adaptive functions which act cooperatively to cause disease. In Ps. syringae the presence of a functional Hrp promoter upstream of the iaaL gene involved in IAA biosynthesis further supports the role for IAA production in virulence (Fouts et al., 2002). However, the function of bacterial IAA in pathogenesis and disease development remains unclear. New intriguing insights have come from studies related to plant defense.

IAA in plant defense

Plants respond to bacterial infection using a two-branched innate immune system. The first branch, the basal defense, recognizes and responds to molecules common to many classes of microorganisms, including nonpathogens. The interaction between pathogen/microbial-associated molecular patterns (PAMPs/MAMPs) and the plant pathogen recognition receptors (PRRs) play a key role in activation of the plant basal defense response (Abramovitch et al., 2006). The second branch, the hypersensitive response (HR)-based response, responds to pathogen virulence factors, either directly or through their effects on host targets. This second, later response is mediated by plant disease resistance genes (R genes) (for recent reviews see Abramovitch et al., 2006; Chisholm et al., 2006; Jones & Dangl, 2006). Navarro et al. (2006) demonstrated a link between auxin signaling in plants and resistance to bacterial pathogens. Bacterial PAMPs downregulate auxin signaling in Arabidopsis by targeting auxin receptor transcripts, as part of a plant-induced immune response. It has been observed previously that bacterial quorum sensing (QS) molecules such as N-acylhomoserine lactones downregulate some auxin-induced genes (Mathesius et al., 2003), raising the question of whether other bacterial molecules recognized by the plant also decrease auxin signaling. The results of Navarro et al. (2006) suggest that lowering plant auxin signaling can increase resistance to bacterial pathogens. A possible mechanism is the expression of auxin-repressed plant defense genes (online supplementary material to Navarro et al., 2006). They further showed that exogenous application of auxin enhances susceptibility to the bacterial pathogen. These findings allow us to hypothesize that bacterial IAA production may contribute to circumvent the host defense system by derepressing auxin signaling. In this way, IAA biosynthesis may play an important role in bacterial resistance and colonization on the plant (Remans et al., 2006; see Fig. 2).


Figure 2.  IAA in pathogenic and beneficial microorganism–plant interactions. A model suggested for the role of bacterial IAA production in microorganism–plant interactions. Signaling taking place in the plant is indicated in gray boxes; signaling taking place in bacterial cells is indicated in white boxes. Full lines indicate demonstrated links; dashed lines indicate hypothesized links. AHL, N-acyl homoserine lactone; IAA, indole-3-acetic acid; MAMP, microbial-associated molecular pattern; PAMP, pathogen-associated molecular pattern; QS, quorum sensing; TIR, transport inhibitor response.

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Different reports supporting this hypothesis for interactions between plants and pathogenic as well as beneficial bacteria can be cited.

Firstly, it has been observed in various studies, including high-throughput analyses, that plant-colonizing bacteria upregulate auxin signaling in plants. An overview of these reports is given in Table 3. For some of the bacterial strains used in these studies, it has been described that they possess IAA biosynthesis genes. However, it has not yet been proven that bacterial IAA effectively contributes to modulation of auxin signaling as observed in the plant. Thilmony et al. (2006) reported that the upregulation of IAA signaling in Arabidopsis upon colonization of Ps. syringae DC3000 is partially dependent on the TTSS and the phytotoxin corotanine, which contributes to virulence and disease development. This may be linked to the presence of a functional Hrp promoter upstream of the iaaL gene involved in IAA production in Ps. syringae, which suggests that expression of IAA biosynthesis genes is dependent on the Hrp system (Fouts et al., 2002). However, the use of an IAA mutant strain is essential to unravel the role of bacterial IAA in modulating plant IAA signaling upon colonization.

Table 3.   Examples of modulation in plant auxin signaling upon colonization by plant-associated bacteria (pathogenic as well as PGPR)
Bacterial strain usedHost plantMethodologyIAA-related signaling induced upon bacterial colonizationReference
  1. IAA, indole-3-acetic acid; PGPR, plant-growth promoting rhizobacterium; Pst, Pseudomonas syringae pv. tomato.

Xantomonas campestris pv. campestris (pathogen)ArabidopsisMeasurement of hormone levels in plant tissue upon inoculationAccumulation of IAA in Arabidopsis leaves upon inoculationO'Donnell et al. (2003)
Pseudomonas syringae pv. tomato DC3000 (pathogen)ArabidopsisSimultaneous analysis of phytohormones, phytotoxins and volatile compounds in plantsAccumulation of IAA in Arabidopsis leaves together with accumulation of corotanine, salicylic acid, jasmonic acid and abscisic acid in Arabidopsis leaves upon inoculationSchmelz et al. (2003)
Pseudomonas syringae pv. tomato DC3000 (pathogen)ArabidopsisArabidopsis ATH1 Affymetrix Gene Chip in combination with Pst wild-type and mutant strains and E. coli wild-type and mutant strainsDifferential expression of a total of 44 auxin-related genes upon inoculation. Taken together the results suggest that Pst is impacting host auxin signaling, potentially derepressing the pathway, altering auxin movement and activating biosynthesis of the hormone.Thilmony et al. (2006)
Pseudomonas thivervalensis strain MLG45 (PGPR)ArabidopsisArabidopsis Y2001 AFGC DNA microarray in combination with MLG45 wild-type (Newman et al., 1994; Schenk et al., 2000; White et al., 2000)Upregulation of a set of auxin response-related genes, including xyloglycan endo-1,4-β-d glucanase precursor (At2g30270), a putative auxin-regulated protein (At2g33830) and heat-, auxin-, ethylene- and wounding-induced small protein (At4g02380) upon inoculationCartieaux et al. (2003)
Pseudomonas fluorescens FPT9601-T5 (PGPR)ArabidopsisArabidopsis ATH1 Affymetrix Gene Chip in combination with FPT9601-T5 wild-typeUpregulation of a set of auxin response-related genes, including xyloglycan endo-1,4-β-d glucanase precursor (At2g30270), a putative auxin-regulated protein (At2g33830) and heat-, auxin-, ethylene- and wounding-induced small protein (At4g02380) upon inoculationWang et al. (2005)
Sinorhizobium meliloti Rm1021MedicagoMedicago Affymetrix gene chip in combination with Rm1021 wild-type and mutant strainsUpregulation of auxin-responsive protein TC40969_RC_at in nodules compared with rootsBarnett et al. (2004)
Pseudomonas fluorescens WCS417rArabidopsisAffymetrix GeneChip containing probe sets for c. 8000 Arabidopsis genes (Zhu & Wang, 2000)Upregulation of two auxin-induced proteins (15017_at and 16751_at)Verhagen et al. (2004)

Secondly, it has been observed previously that auxins interfere with parts of the host defense system. Auxins and cytokinins are able to block several pathogenesis-related (PR) enzymes, including β-glucanase (Mohnen et al., 1985; Jouanneau et al., 1991) and chitinase (Shinshi et al., 1987) at the mRNA level. Furthermore, comparing gene expression profiles of Arabidopsis plants treated with IAA vs. nontreated control plants using the Affymetrix ATH1 Gene Chip revealed that some proteins of the disease resistance responsive family are downregulated in IAA-treated plants (Redman et al., 2004).

Another plant defense strategy is the HR, characterized by necrosis of plant cells in the inoculated area. In this way, the bacteria are limited to the area originally inoculated and do not spread beyond its edges. The HR is thought to function in the limitation of the growth of the microorganism and is therefore associated with disease resistance (Klement, 1982). Robinette & Matthysse (1990) reported that bacterial auxin of Ps. savastanoi is required to block the HR in tobacco leaves induced by Ps. syringae pv. phaseolicola.

Interestingly, the role of bacterial IAA in induced system resistance (ISR) elicited by some PGPR has been investigated in several studies but in none of the reported studies did it appear that IAA was involved in ISR (Oberhansli et al., 1991; Beyeler et al., 1999; Cartieaux et al., 2003; Suzuki et al., 2003). Verhagen et al. (2004) showed that ISR in Arabidopsis induced by Ps. fluorescens WCS417r is not associated with changes in the expression of genes encoding PR proteins. Taking these reports together, they show consistency for the link between auxin signaling and PR protein expression.

Thirdly, it has been shown that bacterial IAA biosynthesis contributes to colonization capacity and fitness on the host. A low IAA-producing mutant of Ps. fluorescens HP72 is reduced in colonization ability on bentgrass roots as compared with the wild-type (Suzuki et al., 2003). Similarly, inactivation of the IPyA pathway in Pa. agglomerans pv. gypsophilae caused a 14-fold reduction in the population of Pa. agglomerans pv. gypsophilae on bean plants. Inactivation of the IAM pathway did not affect the colonization ability (Manulis et al., 1998). An iaaM mutant of Ps. syringae pv. syringae retained the ability to colonize the bean phylloplane but the role of the IPyA pathway in colonization was not studied in this strain (Mazzola & White, 1994). Taken these results together, they suggest that the IPyA biosynthesis pathway rather than the IAM pathway contributes to colonization capacity.

Studies of bacterial gene expression further support the importance of bacterial IAA biosynthesis during plant colonization, demonstrating that the ipdC gene in Pa. agglomerans pv. gypsophilae is strongly induced during plant colonization (Manulis et al., 1998; Brandl et al., 2001), while the iaaM gene is expressed during later stages in the interaction with the plant (Manulis et al., 1998). Erwinia chrysanthemi 3937 in interaction with spinach leaves shows an upregulation of iaaM expression (Yang et al., 2004). Examining the influence of sugarbeet exudates on the transcriptome of Ps. aeruginosa PAO1, no specific IAA biosynthesis genes were found to be induced. However, a tryptophan permease with tryptophan being a precursor for IAA was strongly upregulated, independently from the sugarbeet variety (Mark et al., 2005).

It is logical to postulate that bacteria use IAA as part of their colonization strategy by stimulating proliferation of plant tissues and thus enhanced colonization surface and exudation nutrients for bacterial growth (Fig. 2). The link between plant defense and auxin signaling gives an extra dimension to the role of bacterial IAA in colonization ability.

Taking the reports described above together, auxin signaling seems to interfere with the basal defence (PAMP recognition) as well as with the R-mediated defence response (HR, activation of PR proteins). As proposed by Abramovitch et al. (2006), the distinctions that are made between basal and R-protein-mediated defenses might need to be revised given that the PRR–PAMP interaction shares many properties with avirulence (Avr)–R protein interactions. In addition, the basal and R-protein-mediated defense pathways might share some common signaling components or physical defense mechanisms. For example, HR-like programmed cell death has been reported in response to PAMPs, and shared mitogen-activated protein kinase (MAPK) cascades are associated with both PRR and R-gene-mediated signaling. Further research is needed to unravel the role of bacterial auxin synthesis in the different dimensions of plant defense (Abramovitch et al., 2006).

Interestingly, some similarity between auxin signaling in bacteria–plant interactions, in which IAA is produced by both partners and seems to play a role in circumvention of the host defense, can be found with signaling by bacterial QS molecules in bacteria–host interactions. Well-described QS signaling molecules such as N-acyl homoserine lactones (AHLs) exhibit structural similarities to many eukaryotic hormones and a growing number of reports have documented apparent biological effects of AHLs on eukaryotic cells. In bacteria–animal interactions, QS signals appear to be used by bacteria to prevent the host immune system from mounting an effective defense and thus from establishing a productive infection in the host (Shiner et al., 2005). The reverse communication conduit also appears to be open as mammalian hormones can interact with components of the bacterial QS machinery (reviewed by Shiner et al., 2005). The growing number of examples of interkingdom signaling molecules evokes the question regarding the role of IAA as a signaling molecule in bacteria.

IAA as a signaling molecule in bacteria

  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information

In addition to the hypothesis that bacterial IAA contributes to circumvent the host defense by derepressing the auxin signaling in the plant, IAA also can have a direct effect on bacterial survival and its resistance to plant defense (Remans et al., 2006; see Fig. 2). Evidence has been accumulating that some microorganisms, independent of their ability to produce IAA, make use of auxin as a signaling molecule steering microbial behavior.

Examples of IAA as a signaling molecule in microorganisms

Research on the regulation of the IAA synthesis in Azospirillum resulted in new insights that IAA regulates expression of genes involved in IAA synthesis by a positive feedback mechanism (Vande Broek et al., 1999; Lambrecht et al., 2000), and that a motif known as an auxin responsive element from plant studies, AuxRe, is present in the upstream region of the Azospirillum gene ipdC known to be regulated by IAA (Lambrecht et al., 1999; Vande Broek et al., 2005). Comparative analysis shows a striking similarity, in terms of the mechanism of gene regulation, with indole signaling in Escherichia coli, postulated to be a mechanism of QS signaling (Wang et al., 2001; Domka et al., 2006; Walters & Sperandio, 2006). Wang et al. demonstrated that indole activates transcription of tnaAB, gabT and astD. Activation of the tnaAB operon is predicted to induce more indole production. astD and gabT are involved in pathways that degrade amino acids to pyruvate or succinate. These results led the authors to speculate that signaling by indole may have a role in adaptation of bacterial cells to a nutrient-poor environment where amino acid catabolism is an important energy source (Wang et al., 2001). Other targets of indole-mediated signaling were found recently indicating a role for indole signaling in biofilm formation (Domka et al., 2006) and in the stable maintenance of multicopy plasmids (Chant & Summers, 2007). These findings on indole signaling and the similarity with IAA signaling in Azospirillum pose questions regarding targets of IAA signaling in Azospirillum.

The signaling role of IAA has been further demonstrated in other microbial species. In Ag. tumefaciens IAA inhibits vir gene expression by competing with the inducing phenolic compound acetosyringone for interaction with VirA (Liu & Nester, 2006). The authors postulate this vir gene inhibition by IAA as a putative negative feedback system upon increased IAA production by transformed plant cells. However, it is not known whether the amount of exuded IAA from the transformed plant tissue is within the concentration range to downregulate vir gene expression.

In Ps. syringae pv. syringae, IAA was shown to be involved in the expression of syringomycin synthesis which is required for full virulence of Ps. syringae pv. syringae strains on stone fruits (Xu & Gross, 1988a, b). IAA mutants of Ps. syringae pv. syringae were significantly reduced in syringomycin production (Mazzola & White, 1994).

Recently, the use of an iaaM deletion mutant of Erwinia chrysanthemi 3937 indicated a positive role of IAA biosynthesis on TTSS and exoenzymes through the Gac-Rsm posttranscriptional regulatory pathway. Compared with wild-type Er. chrysanthemi 3937, the expression level of an oligogalacturonate lyase, ogl, and three endo-pectate lyases, pelD, pelI and pelL, was reduced in the iaaM mutant. In addition, the transcription of TTSS genes, dspE (a putative TTSS effector) and hrpN (TTSS hairpin), was found to be diminished in the iaaM mutant of Ee. chrysanthemi 3937 (Yang et al., 2007).

Looking at the unicellular eukaryote Saccharomyces cerevisiae, it is worth mentioning that addition of IAA to the culture medium provoked invasive growth and differential gene expression (Prusty et al., 2004). Among the genes induced by IAA, a gene involved in adhesion, FLO11, was detected, suggesting that FLO11 activation by elevated concentrations of IAA that occur at plant wound sites might be crucial for feral yeast cells to infect wound sites in plants (Verstrepen & Klis, 2006). Similarly, activation of adhesins in animal pathogens occurs when the cells perceive an opportunity for infection, enabling cells to adhere to the appropriate tissue and establish a colony or biofilm of infectious cells (Verstrepen et al., 2004; Domergue et al., 2005).

In E. coli evidence that IAA might be a signal able to coordinate of bacterial behavior enhancing protection against damage by adverse conditions was recently described by Bianco et al. (2006a). They showed that IAA induces the expression of genes related to survival under stress conditions. Here, it has to be taken into account that auxin molecules can interact with cell-wall peroxidases, inducing the formation of reactive oxygen species (ROS) within the cell wall (Kawano et al., 2001). Concerning the differential gene expression in E. coli upon IAA addition, it is not clear whether these genes are induced upon IAA as a signaling molecule or upon IAA as a molecule provoking a stress condition by induction of ROS. Unfortunately, only indole and not acetic acid, neither a ROS-inducing compound, were included as a control to study IAA-altered gene expression, leaving doubt regarding whether the expression profile presented is IAA specific. A subsequent report of Bianco et al. (2006b) further supported the observation that IAA is able to induce changes in gene expression in E. coli. In their study, it was observed that genes involved in the central metabolic pathways such as the tricarboxylic acid cycle (TCA), glyoxylate shunt and amino acid biosynthesis (leucine, isoleucine, valine and proline) were upregulated by IAA, whereas the fermentative adhE gene was downregulated. Data on differential gene expression upon addition of appropriate control metabolites are missing, preventing the distinction between IAA-specific induced genes and genes altered in expression by structurally related metabolites.

For cyanobacteria it has been shown that IAA triggers differentiation of cyanobacterial hormogenia (Bunt, 1961), although direct evidence for IAA signaling in cyanobacteria has not been described. In view of the fact that the progenitors of extant cyanobacteria were ancestors of plastids, the possible evolutionary link between IAA signaling in plants and cyanobacteria is worth examining. Interestingly, IAA plays a key role in modulating the level of the bacterial alarmone guanosine 5′-diphosphate 3′-diphosphate (ppGpp) in the chloroplasts of plant cells. In bacteria ppGpp mediates the ‘stringent control’ upon stress conditions (reviewed by Braeken et al., 2006). Takahashi et al. (2004) detected ppGpp for the first time in the chloroplasts of plant cells. They further showed that plant hormones including jasmonic acid, abscisic acid and ethylene modulate levels of ppGpp in plants while IAA blocks the effect of other plant hormones on ppGpp. These data point towards research into the role of IAA and other plant hormones in modulation of ppGpp levels in bacterial cells.

Finally, it was reported by Liu & Nester (2006) that high concentrations of IAA (200 μM) inhibit growth of many plant-associated bacteria but not the growth of bacteria that occupy other ecological niches. This emphasizes the role of IAA as a signaling molecule in microorganism–plant interactions.

The findings representing IAA as a signaling molecule in bacteria shed new light on the role of IAA in microorganism–plant interactions.

IAA transport and reception in bacteria

A crucial issue and major challenge in studying IAA as a signaling molecule in bacteria is the mechanism of IAA reception and transport in bacteria. As yet, no receptor nor a membrane transport system for IAA has been described in bacteria. The search for auxin receptors and transport systems has mainly focused on plants, with recent breakthroughs including the discovery of the Arabidopsis auxin receptor TIR1 (Dharmasiri et al., 2005; Kepinski & Leyser, 2005) and mechanisms of auxin transport (for a recent review see Kramer & Bennett, 2006). Recent discoveries indicating that IAA can act also as a signaling molecule in bacteria have given attention to the question of IAA receptors and transport systems in bacteria. The capacity of some bacteria such as Pseudomonas and Bradyrhizobium to degrade IAA (Proctor, 1958; Tsubokura et al., 1961; Mino, 1970; Egebo et al., 1991; Jensen et al., 1995; Olesen & Jochimsen, 1996; Leveau & Lindow, 2005) indicates that the uptake of IAA by bacteria does occur. Transport of IAA over plant cell membranes occurs through a combination of membrane diffusion and carrier-mediated transport (reviewed by Kramer & Bennett, 2006). IAA can enter a plant cell either in its protonated form (IAAH) by membrane diffusion or in its anionic form (IAA) by the action of a proton-driven auxin influx carrier system. Once inside the cell, IAA is predominantly in anionic form, necessitating carrier-mediated transport to exit the plant cell (Delbarre et al., 1996).

Membrane diffusion of IAAH is often argued to be the predominant flux of auxin into plant cells (Bean et al., 1968; Gutknecht & Walter, 1980). Also in bacteria, the ability of protonated auxin to diffuse across the bacterial lipid membrane needs to be considered. IAA is a weak acid with a dissociation constant (pK) of 4.8 (Delbarre et al., 1996). It thus partitions between the anion IAA and the protonated IAAH according to the environmental pH. In neutral or basic conditions, IAA will dominate (99.4% ionized at pH 7), whereas in strongly acidic compartments IAAH dominates (99.8% protonated at pH 2). The rhizosphere is generally considered to be a weakly acid environment (Hinsinger et al., 2003), and therefore it is expected that a considerable part of IAA is in its protonated form in the rhizosphere. This leads to the hypothesis that IAA can enter the bacterial cell by membrane diffusion, dependent on the permeability of the bacterial membrane and the environmental pH.

Interestingly, studies on IAA degradation report IAA degradation capacity at a pH of 7.0–7.1. This indicates that IAA can enter the bacterial cell, suggesting the existence of a proton-driven auxin influx carrier (Proctor, 1958; Tsubokura et al., 1961; Mino, 1970; Egebo et al., 1991; Jensen et al., 1995; Olesen & Jochimsen, 1996; Leveau & Lindow, 2005).

For the synthetic auxin 2,4-dichlorophenoxyacetate (2,4-D) an active transport system has been described in several 2,4-D-degrading bacteria, for example Ralstonia, Bradyrhizobium and Delftia (Leveau et al., 1998; Kitagawa et al., 2002; Muller & Hoffmann, 2006). 2,4-D uptake was shown to be an energy-dependent process involving a transport protein encoded by a gene (tfdK in Ralstonia and Delftia, cadK in Bradyrhizobium) that shows similarity to genes encoding the major facilitator superfamily transporters. In Delftia acidovorans, it was further observed that the presence of the uncoupler carbonylcyanide m-chlorophenylhydrazone led to strong inhibition of 2,4-D uptake, suggesting proton symport as the likely active mechanism (Muller & Hoffmann, 2006). This shows analogy to active IAA import in plant cells, which is driven by proton influx (Li et al., 2005). Interruption of the gene tdfK encoding a 2,4-D transport protein in Ralstonia eutropha decimated 2,4-D uptake rates but did not abolish uptake completely, indicating that alternative mechanisms for 2,4-D uptake (e.g. membrane diffusion) exist (Leveau et al., 1998).

Transfer of cadRABKC genes, involved in 2,4-D degradation in Bradyrhizobium sp. strain HW13, to a nondegrader Sinorhizobium meliloti Rm1021 enabled this strain to degrade 2,4-D. Of note here is the observation that functionality of the gene cadK encoding the transport system was not necessary to turn S. meliloti Rm1021 into a 2,4-D degrader. These data suggest that the wild-type strain of S. meliloti Rm1021 possesses a mechanism for 2,4-D uptake despite its inability to degrade 2,4-D (Kitagawa et al., 2002).

The question as to what extent 2,4-D transport systems are comparable with IAA transport in bacteria remains unanswered. Structural differences between 2,4-D and IAA can limit the extrapolation of the 2,4-D transport system to IAA transport. Recently, two articles were published tackling the structure–activity relationships of auxin-like molecules (Ferro et al., 2006, 2007). Using a computational approach (Molecular Quantum Similarity Measures) and subsequent statistical analysis to identify structural similarity groups, the authors showed that IAA and 2,4-D share the same quantum spatial regions, indicating structural similarity. However, differences between IAA and 2,4-D have been observed in binding activity to plant auxin transporters/receptors (Venis & Napier, 1995; Napier et al., 2002; Kepinski & Leyser, 2005; Badescu & Napier, 2006).

Ongoing plant research might provide other relevant information on putative IAA transporters and receptors in bacteria. Advancement in understanding IAA signaling pathways in plants has been truly spectacular over the past 5 years (for recent reviews on auxin receptors see Badescu & Napier, 2006; Parry & Estelle, 2006; and on auxin transport see Fleming, 2006; Kramer & Bennett, 2006). Back-to-back papers identified the F-box protein transport inhibitor response 1 (TIR1) as a plant receptor for auxin (Dharmasiri et al., 2005; Kepinski & Leyser, 2005). TIR1 belongs to a small protein family which is part of the Arabidopsis F-box family. Currently, three other TIR1-related F-box protein/receptors (AFB1, AFB2, AFB3) have been identified as auxin receptors in Arabidopsis (Dharmasiri et al., 2005; Parry & Estelle, 2006). Exploiting the NCBI database using the blast algorithm to search for homology between the amino acid sequence of TIR1 (Dharmasiri et al., 2005) and bacterial proteins, no strong homology was found. However, a putative F-box-like protein was detected in CandidatusProtochlamydiaamoebophila UWE25 (see supplementary Table S1).

TIR1 functions as part of a molecular complex SCFTIR1 that attaches the cell's garbage tag, ubiquitin, to proteins destined to be recycled. Auxin, by glomming onto TIR1, helps the SCFTIR1 complex to ubiquitinate Aux/IAA proteins. When the Aux/IAA proteins are broken down, the genes they repress turn on. Interestingly, similarity for the functionality of the SCFTIR receptor system can be found with another indole receptor, the tryptophan receptor of bacteria. However, the TIR1 pathway has extra layers of control built in. Tryptophan binds to the bacterial Trp repressor protein to induce a conformational change that allows it to bind directly to the trp operator sequence and so control gene expression (Ramesh et al., 1994). Arguably, a switching error in such a system will be immediately amplified. The activity of TIR1 is one step removed from transcriptional regulation by the ubiquitination system, allowing small errors to be buffered (Dharmasiri et al., 2005; Parry & Estelle, 2006).

The TIR1-like signaling cannot account for all auxin responses in plants (reviewed by Badescu & Napier, 2006). Regulation through proteolysis and transcriptional activity, occurring upon TIR1-auxin signaling, takes time; it is inevitably much slower than membrane depolarization, for example. Therefore, rapid auxin responses in plants are unlikely to be TIR1-mediated and another type of auxin receptor is expected to be involved in rapid auxin-mediated responses (Badescu & Napier, 2006). Detailed auxin binding data have been reported for only one other protein, the auxin-binding protein 1 (ABP1) (Venis & Napier, 1995; Napier et al., 2002). Besides its strong ability to bind auxin, the physiological role of ABP1 remains unclear (Napier et al., 2002). The majority of ABP1 is localized in the endoplasmatic reticulum, where the pH is too high for auxin binding. However, some ABP1 is also found on the plasma membrane, and ABP1 antibody experiments have implicated this pool in auxin-mediated cell expansion. Exploiting the NCBI database using blast software, some homology was found between ABP1 and putative auxin-binding proteins in various bacteria, for example S. meliloti, Shewanella amazonensis, Ps. syringae pv. syringae, Ps. syringae pv. phaseolicola and Ps. syringae pv. tomato (Table S1). It will be interesting to unravel the role of these putative auxin-binding-like proteins in bacteria.

In addition, genetic studies in Arabidopsis have led to the identification of AUX1, pGlycoprotein (PGP, an ABC transporter) and PIN classes as IAA influx and efflux facilitators (Parry et al., 2001; Paponov et al., 2005; Geisler & Murphy, 2006; see review by Kramer and Bennett, 2006). In a broad set of bacteria, e.g. various Pseudomonas species (Ps. fluorescens, Ps. syringae and Ps. putida), Bradyrhizobium, Mesorhizobium, Sinorhizobium and Rhizobium species, proteins showing strong homology (E values between 4e-90 and 1e-58) in amino acid sequence with the plant PGP transporter were detected (Table S1). As PGP is an ABC transporter, the homology between PGP and bacterial proteins is not surprising given that ABC transporters are common transport systems in bacteria. Determination of the specificity of the bacterial ABC transporters that are homologous to the plant auxin transporter PGP is required to unravel their putative role in IAA transport in bacteria.

In addition, some degree of homology (Table S1) in amino acid sequence was found between the plant auxin transport facilitator PIN and bacterial proteins predicted as auxin efflux carriers in various species belonging to, among others, Ralstonia, Burkholderia and Mesorhizobium, which are 2,4-D degraders (Leveau et al., 1998; Kitagawa et al., 2002).

Taking these data together, it can be suggested that certain similarity in IAA reception and transport/IAA signaling between plants and bacteria may exist.

Conclusions and perspectives

  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information

Over 120 years after Darwin's description of IAA as ‘a matter which transmits its effects from one part of the plant to another,’ plant and microbial research results allow us to identify IAA as a multivalent signaling molecule and as ‘a matter which transmits its effects within plants and among plants and bacterial cells.’ Emerging views on IAA as a common language between bacteria and plants pave the way for future research on IAA signaling in microorganisms. A recent editorial in Science (Vogel, 2006) emphasized the importance of the advancement in unraveling IAA signaling pathways in plant communication. The moment to extend this knowledge to other kingdoms seems highly favorable. Current postgenomic studies already indicate a role for IAA signaling in bacteria and microorganism–plant interactions. However, dedicated functional genomic studies are needed to unravel the function and mechanism of IAA signaling in bacteria and during the different stages of microorganism–plant interactions. The increasing amount of genomic data will further broaden insight into the distribution and evolution of the capacity to participate in IAA signaling among organisms. It is clear that not only plants and bacteria will take part in the IAA conversations, but that researchers in plant science and microbiology will undoubtedly continue talking about this intriguing molecule.


  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information

S.S. is financed in part by the Fund for Scientific Research Flanders (G.0085.03) and in part by the Belgian Government (IUAP P5/03). R.R. is a recipient of a predoctoral fellowship from the ‘Vlaamse Interuniversitaire Raad (VLIR)’. We acknowledge financial support from the K.U. Leuven (CoE SymBioSys).


  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information
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Supporting Information

  1. Top of page
  2. Abstract
  3. Introduction
  4. IAA biosynthesis pathways in bacteria
  5. Genome-wide screening for key genes in IAA biosynthesis
  6. Factors that influence bacterial IAA biosynthesis
  7. Bacterial IAA in plant–microorganism interactions
  8. IAA as a signaling molecule in bacteria
  9. Conclusions and perspectives
  10. Acknowledgements
  11. References
  12. Supporting Information

Table S1. Homology to plant proteins involved in IAA reception and transport.

femsre+72_suppmat.doc49KSupporting info item

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