chromosome (Kasai-Maita et al. 2013 ). It is also
known that most rhizobia do not possess this
gene to catalyze the condensation of acetyl
coenzyme A andα-ketoglutarate to form homo-
citrate (Masson-Boivin et al. 2009 ). Intriguingly,
this bacterial inability to synthesize homocitrate
can be compensated by the host’s capacity to
supply the compound, as shown using aL. japo-
nicusmutant lacking theFEN1gene encoding
homocitrate synthase (Hakoyama et al. 2009 ).
The remainingnifgenes,nifWandnifZ, may
not be essential for nitrogenase function; how-
ever, their products can have roles in the matu-
ration or stabilization of the MoFe protein (Rubio
and Ludden 2008 ). In addition to the role in
FeMo-co synthesis with NifEN, NifH is also
required for maturation of the P clusters in the
MoFe protein (Ribbe et al. 2002 ).
As described above, reducing equivalents and
free energy are needed to carry out the nitroge-
nase reaction. For electron transport to nitroge-
nase, it is postulated thatfixABC encodes an
oxidoreductase complex composed of electron
transferflavoprotein (ETF) homologues and an
ETF ubiquinone oxidoreductase homologue and
that fixX encodes a ferredoxin-like protein to
deliver electrons to nitrogenase. Nevertheless,
experimental support for this postulation is still
awaited. To generate ATP to be used by nitro-
genase, rhizobial cells need to take up energy
substrate(s) to generate membrane potential and
ATP. The C4-dicarboxylate transport protein
encoded by the conserveddctAgene is required
for the uptake of the energy substrate, C4-dicar-
boxylates such as malate that are supplied by
plant host, and its expression is regulated by the
products of the adjacentdctBDgenes. A set of
genes homologous todctA–dctBDis present on
the MAFF303099 and R7A core chromosomes
(mll7237andmlr7238– 7239 in MAFF303099),
but these genes are non-functional because of a
defect in thedctBgene (J. Weaver and C. Ronson,
unpublished data). The products of fixNOPQ
constitute an energy-transducing cytochrome
cbb 3 oxidase that has high affinity for oxygen to
meet the microaerobic conditions of the nodule
environment. Adjacent tofixNOPQ, there are
genesfixGHISthat encodes proteins essential for
maturation of the oxidase. MAFF303099 has
another set offixNOPQandfixGHISgenes on the
core chromosome (Kaneko et al. 2000 ), and both
sets are induced under free-living microaerobic
conditions as well as under symbiotic conditions
(Uchiumi et al. 2004 ).5.4.3 Genes for Island MobilizationThere are more than 20 conserved genes that are
probably involved in conjugative transfer of the
symbiosis island. These include genes encoding
proteins that constitute the transfer machinery as
well as several regulatory genes (see below).
Products ofrdfSandrlxSfunction in excision
and processing of DNA, while those oftraGand
thetrbBCDEJLFGIoperon function in mating-
pore formation (Ramsay et al. 2006 , 2009 ).5.4.4 Genes for Metabolism
of Vitamins and Other
CompoundsThere are conserved gene sets for biotin synthesis
(Sullivan et al. 2001 ), nicotinic acid mononucle-
otide (NaMN) synthesis, and thiamine biosyn-
thesis (Kaneko et al. 2000 ; Sullivan et al. 2002 ;
Kasai-Maita et al. 2013 ). Non-symbiotic meso-
rhizobia are auxotrophic for these three vitamins
(Sullivan et al. 1996 ), and these genes are absent
from the MAFF303099 core chromosome.
Therefore, symbiosis island transfer confers
vitamin independence on the recipient mesorhi-
zobia, as well as the ability to nodulate andfix
nitrogen withLotusspecies. Also conserved are 8
genes,glyA, metK, metE, ltaM, aatA, asnB, dapA,
andmaaL, encoding enzymes involved in amino
acid metabolism. Most of these genes are highly
expressed in bacteroids but are not essential for
nitrogenfixation (Sullivan et al. 2013 ).5 Genome Sequence and Gene Functions... 51