5.5.2 Regulation of Genes Involved
in Symbiotic Metabolism
In most rhizobia, cascading control is common to
regulate gene expression for nitrogenfixation and
symbiotic metabolism (Terpolilli et al. 2012 ).
Such cascades are not fully conserved among
rhizobial species. For example, inS. meliloti, the
FixL kinase that senses oxygen and its cognate
response regulator FixJ are required to express
nifAandfixK, for transcription of othernifgenes
andfixNOPQgenes, respectively. InB. japoni-
cum, phosphorelay from redox-sensing RegS to
RegR is required to expressnifA, since onlyfixK2
but notnifAis under the direct control of FixL/
FixJ. In addition, the alternative sigma factor
RpoN is required for transcription of NifA-
induced genes.
TheM. lotisymbiosis islands carry twonifA
genes,nifA1located adjacent tonifB(the same
genomic context as inS. meliloti) andnifA2sit-
uated away from knownnifgenes. There is also
onerpoNgene, designated asrpoN2, in addition
torpoN1(mll3196) located on the core chro-
mosome. Other genes in the common cascade,
such as fixL (mll6607), fixJ (mll6606), fixK
(mll6578),regS(mlr5307), andregR(mlr5308),
are not located on symbiosis islands but are on
the core chromosome. Mutational and expression
analysis using both MAFF303099 and R7A
indicates thatnifA2but notnifA1is essential for
symbiotic nitrogenfixation (Nukui et al. 2006 ;
Sullivan et al. 2001 , 2013 ). Only, rpoN2 is
required for nitrogen fixation (Sullivan et al.
2013 ). Further analysis indicated that FixL/FixJ
and RegS/RegR are dispensable forM. lotito
carry out symbiotic nitrogenfixation, unlike the
other rhizobial counterparts (Sullivan et al.
2013 ). These analyses led Sullivan et al. tofind a
novel LacI/GalR family regulator FixV that is
encoded adjacent tonifA2and activatesnifA2
expression, possibly in response to a host-
derived inositol metabolite. NifA2 then activates
expression of several genes includingrpoN2and
nifA1(Sullivan et al. 2013 ). Taken together, gene
regulation of symbiotic nitrogen fixation in
M. lotiis peculiar to this species.
5.5.3 Regulation of Genes Involved
in Protein SecretionThe T3SS and T4SS in M. loti strains have
acquired the capacity to be induced by host
flavonoids. These systems have specific tran-
scriptional activators, TtsI and VirA/VirG, to
express other genes for the secretion system. TtsI
binds totts-boxes and induces transcription of
otherttsorrhcgenes (Krause et al. 2002 ; Zehner
et al. 2008 ; Wassem et al. 2008 ). Likewise, VirG
activated by VirA binds tovir-boxes and induces
transcription of othervirgenes (Leroux et al.
1987 ; Winans et al. 1986 ). In MAFF303099,
there is anod-box sequence upstream ofttsIthat
is responsible for transcriptional induction upon
receiving plantflavonoid. TtsI-dependentnopX
gene expression was evidenced by experiments
with heterologousR. leguminosarumNodD and
naringenin (Okazaki et al. 2010 ). In R7A, anod-
box sequence is found upstream ofvirA.The
location of thecis-element enables induction of
virAby NodD with host-derivedflavonoid and
subsequent activation of VirG to express T4SS
machinery (Hubber et al. 2007 ).5.5.4 Regulation of Genes Involved
in Island TransferThe regulation of symbiosis island transfer has
been extensively studied inM. lotistrain R7A, the
only strain where the island has been shown to be
mobile. The symbiosis island in MAFF303099
has a transposon insertion in theoriTsite on the
island, while the NZP2037 island has been dis-
rupted by recombination. Hence, both of these
islands have likely lost mobility. ICEMlSymR7A
chromosomal excision and conjugative transfer
are stimulated by the quorum-sensing regulator
TraR in complex with N-(3-oxohexanoyl)-L-
homoserine lactone (3-oxo-C6-HSL). This quo-
rum-sensing stimulation results in the expression
of two conserved genes,msi172and msi171,
that then control downstream excision and
transfer steps. Quorum sensing and ICEMl-
SymR7A excision/transfer are inhibited in the5 Genome Sequence and Gene Functions... 53