"Frontmatter". In: Plant Genomics and Proteomics

Rhizobium symbiosis in particular have been isolated, and these mutants
define more than 50 symbiotic loci that are indispensable for either or both
the formation and functioning of a root nodule and the formation of the
arbuscular mycorrhiza symbiosis (Staskawitz and Parniske, 2001). Specifi-
cally, the mutants available in the model legumes Lotus japonicus and 
Medicago truncatula can be divided into four classes on the basis of their phe-
notypes (Stougaard, 2001):
∑ Nonnodulating—These mutants are expected to be impaired in the
early events necessary for the establishment of the infection.
∑ Ineffective nodulating mutants—These mutants can participate in the
early events associated with the development of nodules, but the
process cannot be completed so that either nodule organogenesis or
nodule function cannot be completed.
∑ Mutants with increased or decreased nodule numbers—Supernodu-
lation, the increase in nodule numbers, could result from mutations
in genes that regulate the nodule number. A reduced number of
nodules may be caused either by mutations that regulate nodule
number, as with supernodulation mutants, or by mutations that
impair nodule formation but do not prevent it from occasionally
developing to completion. 
∑ Mutants with delayed nodulation.
Missing from the mutant types in the model legumes are the spontaneous
nodulation and “tumorlike” nodules that have been described in alfalfa
(Stougaard, 2001). 
In many cases the events occurring on the microbial side of the symbi-
otic relationships have been better characterized because of the relative ease
of working with the symbiont compared with the root system. The sequenc-
ing of the symbiotic chromosome in broad host-range Rhizobium NGR 234
has led to the characterization of the type III secretion systems that had pre-
viously been thought to be unique to pathogenic bacteria (Marie et al., 2001).
B
I O T I C
I
N T E R A C T I O N S
1 3 9

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Again, genomic approaches will have a major impact on the separation of
the different processes that determine whether or not an interaction will
progress down the path of symbiotic coexistence or pathogenic destruction. 
The processes of infection and nodule development have been well doc-
umented, and therefore the isolation of mutants involved in nodulation has
been possible. The interaction between the plant and mycorrhiza has been
more difficult to detail because the process is not as amenable to study.
However, a number of genetically defined loci that control some of the steps
in both the nodulation and mycorrhizal interactions have been identified. A
schematic view of the early symbiotic events in both of these processes is
provided by Figure 7.3. 
The seemingly complex interactions that control pathogenesis and sym-
biosis, and how the two interactions differ from one another, is amenable to
being unraveled with the genomics and proteomics tools currently available.
The development of custom microarrays with ESTs, and putative genes iden-
tified from complete genomic sequences, from the various stages of infec-
tion (both symbiotic and pathogenic) including representatives from both of
the players in the interaction will facilitate the identification of the impor-
tant genes involved in the control of the interaction. The use of yeast two-
hybrid systems to determine the interactions between plant and microbial
proteins at various stages of the process will also identify the important reac-
tions necessary for resistance, susceptibility, or symbiosis. The development
1 4 0
7. I
N T E R A C T I O N S W I T H T H E
E
X T E R N A L
E
N V I R O N M E N T
MtDMl1
MtDMl2
MtDMl3
PsSym8
PsSym19
PsSym9
PsSym30
Ca
2
+
Ca
2
+
Mycorrhiza
signal(s)?
Mycorrhizal
invasion
LjSym
30
LjSym
23
LjSym
15
LjSym
4
LjSym
3
LjSym
2
LjNin
MtNsp
Rhizobium
Nod factor(s)
LjSym1
LjSym5
PsSym10
Common pathway
Infection thread
Cell division
Nodule organogenesis
FIGURE 7.3.
Analysis of Lotus, Medicago, and pea mutants for rhizobial and myc-
orrhizal interaction defines common steps in the endosymbiotic pathway. The allo-
cation of symbiotic loci to various parts of the pathway is tentative and is based on
phenotype, rather than on genetic tests of epistasis. The order of appearance does
not therefore indicate the precise order of function. Common pathway genes
MtDMI1, MtDMI2, MtDMI3, PsSym8, PsSym19, PsSym9, and PsSym30 were ordered
according to calcium spiking. Except for Ljnin, none of the genes have been cloned.
(Reprinted from Curr. Opin. Plant Biol. 4, Stougaard, Genetics and genomics of root
symbiosis, 328–335, Copyright 2001, with permission from Elsevier.)

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of metabolomics will be important in defining the roles of signaling mole-
cules in the initiation and progression of all of these interactions. Finally, the
availability of forward and reverse genetic strategies in both the host and
the invader will permit the development of mutants to test the importance
of the genes identified as being involved in these interactions.