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the strings are slightly out of tune with each
other, the sound will ‘beat’ up and down in
intensity. The beat frequency is simply the
difference between the frequencies of the two
notes. Similarly, the spatial beat frequency
in these experiments is the difference
between the momenta of the electrons in
the two bands. The authors measured this
momentum difference as a function of
energy, confirming the predictions of bandtheory calculations.
The existence of two separate bands in
metallic nanotubes also has technological
implications. An obstacle to using nanotubes as electronic wires is that the conducting electrons sometimes reflect backwards,
by bouncing off a structural defect in the
tube or off a smoother variation in electrical
potential caused by charges outside the tube.
In metallic tubes, resistance to switching the
direction of motion makes electrons unlikely
to reflect off a smoothly varying potential.
This protection is not strong enough to prevent reflections from structural defects in a
nanotube, but fortunately, improved techniques for growing nanotubes have raised
the prospect of entirely defect-free tubes12.
Together, these properties suggest that
nanotubes may soon be able to conduct
electrons over many micrometres, making
them a viable, much smaller alternative to
conventional electronic wires.
■
David Goldhaber-Gordon, currently of the Harvard
Society of Fellows, will from 1 September be in the
Department of Physics and the Geballe Laboratory
for Advanced Materials, Stanford University, 476
Lomita Mall, Stanford, California 94305-4045, USA.
e-mail: [email protected]
Ilana Goldhaber-Gordon is in the Department of
Biology, Massachusetts Institute of Technology,
77 Massachusetts Avenue, Cambridge,
Massachusetts 02139, USA.
e-mail: [email protected]
1. Iijima, S. Nature 354, 56–58 (1991).
2. Andriotis, A. N., Menon, M., Srivastava, D. & Chernozatonskii,
L. Phys. Rev. Lett. 87, 066802 (2001).
3. Lemay, S. G. et al. Nature 412, 617–620 (2001).
4. Dresselhaus, M. S., Dresselhaus, G. & Eklund, P. C. Science of
Fullerenes and Carbon Nanotubes (Academic, New York, 1996).
5. Odom, T. W., Huang, J., Kim, P. & Lieber, C. M. Nature 391,
62–64 (1998).
6. Wildoer, J. W. G., Venema, L. C., Rinzler, A. G., Smalley, R. E. &
Dekker, C. Nature 391, 59–62 (1998).
7. Crommie, M. F., Lutz, C. P. & Eigler, D. M. Nature 363, 524–527
(1993).
8. Kane, C. L. & Mele, E. J. Phys. Rev. B 59, R12759–R12762
(1999).
9. Ando, T. & Nakanishi, T. J. Phys. Sci. Jap. 67, 1704–1713 (1998).
10. McEuen, P. L. et al. Phys. Rev. Lett. 83, 5098–5101 (1999).
11. Goldhaber, M., Grodzins, L. & Sunyar, A. W. Phys. Rev. 109,
1015–1017 (1958).
12. Liang, W. et al. Nature 411, 665–669 (2001).
Genome sequencing
The ABC of symbiosis
J. Allan Downie and J. Peter W. Young
The latest bacterial genome to be completely sequenced has three
separate parts and as many genes as yeast. The bacterium needs these
genes for its complex life in and around its legume plant partner.
t is a truth universally acknowledged, that
there are only two kinds of bacteria. One is
Escherichia coli and the other is not. Anything that E. coli does is a universal truth
about bacteria; anything it does not do must
I
be a specialization. This coli-centric view has
made life a little easier for generations of
students, but it has taken some knocks lately.
Not only have E. coli fans seen their favourite
bacterium beaten to the genome finishing
rRNA
repABC
rRNA
pSymA
1.35 Mbp
rRNA
nif/fix
nod
Chromosome
3.65 Mbp
repA3B3
repABC
Arg –
tRNA
pSymB
1.7 Mbp
exo
NATURE | VOL 412 | 9 AUGUST 2001 | www.nature.com
© 2001 Macmillan Magazines Ltd
line1 by several outsiders2–5, but the genome
of the laboratory workhorse, E. coli strain
K12, looks paltry even in comparison with
better-endowed E. coli strains6. As the number of completely sequenced genomes
increases week by week7, we are beginning
to see just how rich life can be in the real
bacterial world.
Freshly completed is the sequence of
Sinorhizobium meliloti 8–11. This bacterium
is a ‘rhizobium’ — it can form nodules1 on
the roots of legume plants, converting (fixing) atmospheric nitrogen to a biologically
usable form. The S. meliloti genome is
revealed in four papers by Galibert and
colleagues in Science and Proceedings of the
National Academy of Sciences 8–11. Why so
many papers? One answer is that this organism essentially has three genomes (Fig. 1).
Another is that the sequence will reveal wider
truths about bacteria.
The coli-centric view of a normal bacterial genome is that it consists of a single
circular chromosome. There may also be
one or two plasmids. These small circular
DNA molecules are present in many copies;
they carry a few genes that can be very
handy (such as those conferring antibiotic
resistance) but are generally unnecessary.
So when we find a large circular genetic
element, twice the size of some whole bacterial genomes, maintained at just one or
two copies per cell and carrying more than
1,000 genes, surely we are looking at a
chromosome? Not if it is pSymA, at 1.35
million base pairs (Mbp) the smallest of the
three elements of the S. meliloti genome9.
This is a megaplasmid, and is not essential
for growth.
Next up in size is pSymB, another
megaplasmid at 1.7 Mbp, which is essential
— for reasons that are now clear10. For
instance, it encodes the cell’s only transfer
RNA that recognizes the nucleotide triplet
CCG, and so is vital for protein synthesis.
Finally, S. meliloti’s ‘real’ chromosome
Figure 1 The three components of the
Sinorhizobium meliloti genome8–11: a
chromosome and two megaplasmids. Red, green
and blue regions have a guanosine cytidine
(G C) content of less than 60% (averaged over
10-kilobase windows). The positions of some
genes are shown, including those needed for the
synthesis of ribosomal RNA (rRNA) and for
plasmid replication (rep genes), as well as the
gene encoding the essential transfer RNA (ArgtRNA) that recognizes the nucleotide triplet
CCG. Also shown are the gene regions required
for the bacterium to form nodules on the roots
of legumes (nod genes), for the formation of
external polysaccharides (exo genes), and for
symbiotic nitrogen fixation (nif/fix genes).
597
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weighs in at 3.65 Mbp. It carries all three sets
of the genes for making ribosomal RNA, and
most of the genes needed for basic metabolism11. The genome of another rhizobium,
Mesorhizobium loti 12, is on a similar scale,
although it has a chromosome of 7.0 Mbp
and two plasmids of 0.35 Mbp and 0.2 Mbp.
Clearly we need to rethink our concept
of bacterial genome organization; it is no
longer straightforward to draw a distinction
between plasmids and chromosomes. In
their mode of replication, pSymA and pSymB
are definitely plasmids: unlike the S. meliloti
chromosome, they have the replication and
stability genes (repABC) that are common
to most rhizobial plasmids13. On the other
hand, pSymB, like the chromosome, carries
essential genes.
Perhaps the most intriguing difference
between the genetic elements of S. meliloti
is that, as Galibert and colleagues8–11 find,
pSymA has an average of 60.4% guanosine
and cytidine (GC) nucleotides, whereas
the chromosome and pSymB have significantly more (62.7% and 62.4%, respectively). This is partly explained by the
higher incidence on pSymA of mobile genetic
elements, which tend to have a low GC
content. Yet many other genes on pSymA —
including nearly all known nodulationrelated (nod) genes — also have a much lower
GC content than do typical chromosomal
genes (Fig. 1).
Differences in GC content between
accessory genes (needed for specialist functions such as nodulation) and housekeeping
(essential) genes are common in bacterial
genomes. They are usually interpreted as a
sign that the accessory DNA originally came
from a bacterium with a different genomic
make-up6,12. Although plausible in many
cases, this explanation hits a snag with rhizobia. Nearly all known nod genes — which are
unique to rhizobia — have a low GC
content, yet all rhizobial chromosomes
have a high GC content. This is true even
for Burkholderia strain STM678, the most
distantly related rhizobium yet discovered14.
If the nod genes evolved in a genome that
matched their low GC content, we haven’t
found it yet. Alternatively, is it possible that
different parts of the genome could diverge
in composition while sharing the same cell,
perhaps because of differences in mutation
or selection pressures? This is plausible,
although the idea is more widely accepted for
eukaryotes than for bacteria.
The authors8 also find that the genome
of S. meliloti is large for a bacterium, with
over 6,200 genes — as many as yeast. Yet
even these do not reflect the full repertoire of
genes potentially available to rhizobia. Fewer
than half of the 400 or so genes identified
on one of the plasmids of a closely related
Sinorhizobium strain15 are found in S.
meliloti 8, while a third of the 7,000 genes in
M. loti 12 are missing from S. meliloti 8.
598
Such large and variable genomes may be
necessary for growth and survival in the
complex environments of the soil and plant
root. Many of the genes on the S. meliloti
megaplasmids encode proteins that allow
the organism to adapt to different environments. About 14% of the genes on pSymB
appear to be involved in the production
of cell-surface polysaccharides, which are
probably important for survival and to allow
the bacterium to attach to the surface of
plant roots. Another 20% are devoted to
solute uptake. On pSymA, 14% of the genes
are likely to be involved in importing and
exporting molecules, and about 8% are related to nitrogen metabolism. These, together
with the many plasmid genes for using
diverse substrates, may enable S. meliloti to
survive in soil, ready to jump at the chance of
infecting a legume root.
Rhizobia have specific and intimate
interactions with eukaryotic cells: they
adhere to plant roots, invade root cells and
stimulate cell proliferation. Although the
nod genes appear to be unique to rhizobia,
the S. meliloti genome sequence also reveals
several possible parallels with the way pathogenic bacteria interact with animal cells. The
S. meliloti chromosome11 has counterparts
of genes that are involved in the invasion of
human red blood cells by the Oroya fever
bacterium Bartonella; in the virulence of
Shigella; in interactions between enteropathogenic E. coli and epithelial cells; and
in the lysis of blood cells by Treponema.
Studies of these and other rhizobial genes
will illuminate both bacterial pathogenesis
and the nitrogen-fixing symbiotic partnership between rhizobia and legumes.
■
J. Allan Downie is in the Department of Genetics,
John Innes Institute, Colney Lane, Norwich NR4
7UH, UK.
e-mail: [email protected]
J. Peter W. Young is in the Department of Biology,
University of York, York YO10 5YW, UK.
e-mail: [email protected]
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2.
3.
4.
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Chemistry
On the threshold of stability
Heinz D. Roth
Carbenes are short-lived compounds containing a highly reactive carbon
atom, which makes them difficult to study. A stabilized derivative may lead
to new magnetic materials.
arbon usually has four atoms or groups
bonded to it. Many reactions in organic
chemistry involve breaking one of
these covalent bonds, so chemists are naturally interested in the reactive and unstable
species of carbon that fleetingly form during
these reactions. The most common carbon
intermediates are trivalent species, which
form only three bonds. Covalent bonds form
when adjacent atoms share two electrons, so
many trivalent carbon compounds have one
unpaired electron. Intermediates containing
a divalent carbon atom that forms only two
covalent bonds, such as CH2, are even more
reactive than their trivalent cousins. Such
species, called carbenes, have two nonbonding electrons on the same carbon
atom. Despite the importance of carbenes to
organic synthesis, their short microsecond
lifetimes make them difficult to study. On
page 626 of this issue, Tomioka and colleagues1 report the successful preparation of
the first triplet carbene with a long lifetime
C
© 2001 Macmillan Magazines Ltd
— almost 20 minutes at room temperature.
A truly stable version of this particular carbene could lead to useful magnetic materials.
Studying unstable carbon intermediates
requires the reactions to be slowed down or
the measurements speeded up. Fast timeresolved spectroscopic methods make it
easier to study short-lived intermediates at
room temperatures, whereas conventional
spectroscopic methods can be used at low
temperatures because reaction rates are
slower. Alternatively, adding appropriate
groups to the reactive carbon can stabilize
the transient species. Following on from the
discovery by Gomberg in 1900 of the first
fairly stable trivalent carbon species, the
existence of trivalent compounds was confirmed by stabilizing the elusive species to
form isolated molecules, and, later, by fast
spectroscopic methods. The chemistry of
trivalent carbon is now well understood,
but the story of carbenes has taken much
longer to unfold. It wasn’t until the 1950s
NATURE | VOL 412 | 9 AUGUST 2001 | www.nature.com