Genetics and functional genomics of legume nodulation
Introduction
Nodulation is a highly host-specific interaction in which, with few exceptions, specific rhizobial strains infect a limited range of plant hosts. Plants secrete (iso)flavonoids that are recognized by the compatible bacteria, resulting in the induction of nodulation genes. These nodulation genes encode enzymes that synthesize a specific lipo-chitin nodulation signal (Nod signal), which activates many of the early events in the root hair infection process [1, 2, 3, 4, 5]. During the infection process, the bacteria enter the plant via the root epidermis and induce the reprogramming of root cortical cell development and the formation of a nodule. In the most well-studied cases, infection occurs through root hairs. The first observable event in the infection process is the curling of the root hair, which likely occurs through the gradual and constant reorientation of the direction of root hair growth. The bacteria become enclosed within the root hair curl where the plant cell wall is degraded, the cell membrane is invaginated and an intracellular tubular structure (i.e. the infection thread) is initiated. It is within this infection thread that the bacteria enter the root hair cell and eventually ramify into the root cortex. Before the infection thread reaches the base of the root hair cell, the root cortical cells are induced to de-differentiate, activating their cell cycle and causing them to divide to form the nodule primordium. In addition to the cortical cells, pericycle cells are also activated and undergo some cell divisions. When the infection thread reaches the cells of the developing primordium, the bacteria are released into cells via endocytosis. Inside a plant cell, the bacteria are enclosed in vacuole-like structures (symbiosomes) in which they differentiate into bacteroids. It is within these symbiosomes that the bacteria convert N2 to NH3. The nodule is a true organ in which there is cellular specialization. For example, in addition to infected plant cells, uninfected plant cells also carry out the function of nitrogen assimilation and a well-developed symplastic transport system allows the exchange of nutrients between the nodule and peripheral vascular tissue.
Large gaps remain in our understanding of root hair infection by rhizobia owing, in part, to the considerable amount of attention focused only on the pre-infection signaling events. Even here, current understanding is largely observational with relatively little information available on molecular mechanisms (c.f. [1]). More recently, significant advances have been made through the analysis of a variety of plant mutants in which early infection is blocked.
Section snippets
Mutants in which nodulation is defective have begun to reveal the pathway of Nod signal recognition
The establishment of Lotus japonicus and Medicago truncatula as legume genetic model systems has greatly expedited discoveries concerning the nodulation process [6, 7]. Analysis of nodulation-defective plant mutants (Table 1) has resulted in the development of a rudimentary pathway for Nod signal recognition (Figure 1).
The Nod- (defective in nodule formation) mutants cannot form nodules. Perhaps the most interesting are the L. japonicus nfr1 and nfr5 mutants, formerly known as sym1 and sym5,
Hypernodulation plant mutants
The hypernodulation mutants are capable of forming an excessive number of nodules when compared with wildtype plants (Figure 3). For example, the L. japonicus sym78 mutant hypernodulation aberrant root1-1 (har1-1) is a hypernodulation mutant [35]. The HAR1 gene encodes a LRR-RLK that shares high homology with CLAVATA1, a protein that controls shoot apical meristem identity [36]. Grafting experiments between HAR1-defective and wildtype plants showed that hypernodulation is shoot controlled and
Did the Nod-factor signaling pathway evolve from a more ancient chitin signaling pathway?
The base structure of the Nod signal is a short chitin polymer (of 3–6 residues). It is therefore similar to the chitin polymers that can be hydrolytically released from the cell walls of plant pathogenic fungi. Such chitin polymers are well characterized as potent elicitors of plant defense responses in a wide variety of plants, and chitin perception appears to be evolutionarily well conserved in flowering plants. Indeed, Day et al. [44] showed that the Nod signal from Bradyrhizobium japonicum
Functional characterization of nodule biology through -omics approaches
The application of DNA microarray and transcript profiling studies to nodulation is relatively recent compared with the various profiling studies conducted on Arabidopsis. However, the large numbers of expressed sequence tags (ESTs) available for legume plants, in addition to cDNA, oligonucleotide and Affymetrix microarrays, have made large-scale transcriptomic studies on nodulation possible. Second-generation high-density arrays also contain probe features that allow the parallel expression of
Conclusions
The adoption of model legumes for genetic analysis of nodulation has led to major advances in our understanding of the initial steps in Nod signal recognition and subsequent signaling. However, much remains to be elucidated concerning downstream events and the details of cellular processes that construct the infection thread and specialized nodule structures. We are in the early stages of integrating transcript, protein and metabolite data for the study of plant–microbe interactions. Advances
References and recommended reading
Papers of particular interest, published within the annual period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
Special thanks to Xuechang Zhang (University of Missouri) for preparing Figure 2 and to Debbie Ellis (University of Tennessee) for the photographs in Figure 3. Ongoing related research in the Stacey laboratory is funded by grants from the US Department of Energy (DE-FG02-02ER15309), the National Science Foundation (NSF) (DBI-0421620), and the National Research Initiative (NRI) of the US Department of Agriculture (USDA) Cooperative State Research, Education and Extension Service
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