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28/9 N+Vs Layoutmx news and views mophilic Archaea? The explanation is three- transfer of smaller gene fragments between Daedalus fold and lies in the intense interest in the bio- species tends to be more common, raising chemistry of these unusual organisms, in the the question of why this seems not to have Talking to animals possibility that they represent the earliest happened for T. acidophilum. forms of life, and in the biotechnological One issue can be almost settled by the Last week Daedalus presented his mobile potential of their genes and gene products. details of this new genome sequence: whether ‘Ultraphone’ for silent speech. The user Thermoplasma acidophilum has one of T. acidophilum is an ancestor of eukaryotic whispers or mouths his message silently. the smallest of the archaeal genomes to have cells. Ruepp et al. compared T. acidophilum His voiced tone is replaced by an inaudible been sequenced so far. Even so, the speed at genes with those in bacterial and eukaryotic ultrasonic tone launched into his mouth. which Ruepp et al.1 sequenced the genome databases. The results show that, if anything, His tongue and palate modulate this into was remarkable. The full sequence of over the T. acidophilum genes are more similar to inaudible ultrasonic speech. A heterodyne 1.5 million base pairs was obtained from bacterial genes than to eukaryotic ones. Key circuit downshifts it back to an audio only 7,855 sequencing reactions — an effec- ‘marker’ genes found in eukaryotes (such as signal, which is transmitted. tive yield of 199 base pairs per reaction, genes encoding subunits of the nuclear pore Daedalus now has a biological use for compared with the 66 base pairs per reaction complex) are not found in the T.acidophilum the technique. Many animals — cats, dogs, for the slightly larger genome of the hyper- genome. bats, rats and many insects — communicate thermophilic bacterium Thermotoga mari- Finally, on a different note, the comple- partly or mainly in the ultrasonic band, tima11. The keys to this efficiency were the tion of another genome sequence reminds above human hearing. Instruments can use of sequencing vectors containing very us how much we still do not know about downshift their voices into the audio band, large DNA inserts; an extended-sequencing gene function as a whole. Of the predicted as the Ultraphone does. But the Ultraphone method referred to as ‘primer walking’; and 1,509 open reading frames in the T. aci- also performs the converse operation. It a policy of stopping the sequencing of an dophilum genome, 29% are akin only to upshifts the human voice into a range much insert when the primer walking encoun- ‘hypothetical’ open reading frames in other more significant to animal ears. tered a stretch of DNA whose sequence was genomes, and 16% have no relatives else- So DREADCO animal keepers are now already known. where. This means that, as yet, we do not speaking to their charges on an adapted So, what can we learn from this genome? know what 45% of the protein-coding Ultraphone. Its intense ultrasonic beam The most startling observation is the high regions in the T. acidophilum genome do. lets them ‘speak’ loudly and clearly in this proportion of genes that seem to have been That is a lot of genes. These percentages are waveband. Its wideband microphone and acquired from other species. For example, typical for newly sequenced genomes. But heterodyne circuit downshifts the animals’ 17% of all identified ‘open reading frames’ the results serve as a reminder of the need ultrasonic responses back into the audio (the parts of genes that encode proteins) both for more advanced data-mining tech- for human recognition. The ultrasonic have relatives in the not-yet-completely niques (which would increase our ability to frequency of the ‘Animal Ultraphone’ can sequenced genome of the archaeon Sulfo- pick out similar sequences from different be adjusted to the band in which the lobus solfataricus. genomes and to identify putative functions) conversation seems to flow most freely. There may be several reasons why and for the continuation of more classical Laboratory rats are the first subjects. T. acidophilum has such an extraordinary molecular and functional research. I These bright and companionable rodents ability to acquire external genes. First, envi- Don Cowan is in the Department of Biochemistry can be tamed quite well by normal means. ronmental proximity is clearly important. and Molecular Biology, University College London, An added vocal channel should bring them Microorganisms of the genus Sulfolobus Gower Street, London WC1E 6BT, UK. even closer to human understanding. The might be the most common archaeal species e-mail: [email protected] DREADCO staff are trying to imitate their in the habitat occupied by T. acidophilum. In 1. Ruepp, A. et al. Nature 407, 508–513 (2000). language, and give them ultrasonic ‘names’ addition, a further 17% of the open-reading 2. Darland, G. et al. Science 170, 1416–1418 (1970). that they can recognize. Bats, those 3. Woese, C. R. & Fox, G. E. Proc. NY Acad. Sci. 74, 5088–5090 frames of T. acidophilum are ‘bacteria-like’. (1977). ultrasonic experts, may also respond to the So it might also have acquired some of its 4. Kawarabayasi, Y. et al. DNA Res. 6, 83–101 (1999). Ultraphone; insects are probably too dim. genes from bacteria such as Alicyclobacillus, 5. Klenk, H. P. et al. Nature 390, 364–370 (1997). But the main impact of the Animal Thiobacillus or Sulfobacillus, the habitats of 6. Smith, D. R. et al. J. Bacteriol. 179, 7135–7155 (1997). Ultraphone will be on domestic cats. These 7. Bult, C. J. et al. Science 273, 1058–1073 (1996). which overlap with that of Thermoplasma. 8. Maeder, D. L. et al. Genetics 152, 1299–1305 (1999). intelligent pets are famous for their aloof Second, the absence of a conventional, pro- 9. Kawarabayasi, Y. et al. DNA Res. 5, 55–76 (1998). independence. They notoriously refuse to tective cell wall could be particularly signifi- 10.Kawashima, T. et al. Proc. J. Acad. B 75, 213–218 (1999). learn (or at any rate to obey) even the cant: a cell wall is a major barrier to the entry 11.Nelson, K. E. et al. Nature 399, 323–329 (1999). simplest commands. To them, human 12.Pace, N. R. Science 276, 734–739 (1997). of large molecules into a cell. Finally, the T. speech is probably a low vague mumbling. acidophilum genome might not be protected But talked to in the right ultrasonic band, by a restriction/modification system, a set of even the most suspicious cat should enzymes designed to recognize and destroy Corrections become alert and responsive. It might even foreign DNA. The organism has no ‘restric- In the News & Views article “Global change: Plankton reply in tones that, downshifted to mellow tion endonuclease’ activity, although its cooled a greenhouse" by Birger Schmitz (Nature 407, audio by the Animal Ultraphone, appeal to genome might encode a DNA methyltrans- 143–144; 2000), the period of ‘superwarm’ conditions at the human ear. ferase, normally part of a restriction/modifi- the Palaeocene/Eocene boundary should have been cited Feline–human relations will be cation system, and restriction endonuclease as lasting about 60,000 (not 150,000) years. Proof correc- transformed. Bonded at last by mutually genes have little sequence similarity and can- tions made to the paper concerned (by S. Bains et al. 407, appreciated vocal expression, cats and cat- not be recognized in a gene sequence. 171–174; 2000) were not passed on to the News & Views lovers will bestow far more warmth and Interestingly, the Sulfolobus-like genes in author. company upon each other, bringing a new the T. acidophilum genome are clustered into In Jim Gillon’s "Earth systems: Feedback on Gaia" and welcome closeness to a long-standing several (at least five) discrete regions. Ruepp (Nature406, 685–686; 2000) a huge expansion of vegeta- association. And the true intelligence of et al. conclude that only a few gene-transfer tion was cited as having taken place 550 million years ago. these friends of Man may at last become events occurred, each involving movements The generally accepted date for that expansion is around apparent. David Jones of large chunks of genetic sequence. But the 400 million years ago. © 2000 Macmillan Magazines Ltd NATURE | VOL 407 | 28 SEPTEMBER 2000 | www.nature.com 467 news and views et al.1, along with Bellocchio et al.4, now show Global change that the expression of BNPI in cell lines leads to specific, ATP-dependent uptake of gluta- mate into vesicles. Does this mean that this Plankton cooled a greenhouse protein is what makes a neuron glutamater- Birger Schmitz gic? Takamori et al.1 go on to show that the expression of BNPI in a cell line that can be stimulated by the excitatory neurotransmit- cientists who can perform laboratory marine microorganisms called foraminifera ter acetylcholine results in the release of experiments are lucky — a megaloma- show that surface-water temperatures off packets of glutamate from the cells. Finally, Sniac climatologist can only dream of the coast of Antarctica rose from about 13 °C they convincingly show that neurons that putting an Earth-like planet in a giant test to 20 °C (ref. 2). Subtropical regions also normally release the neurotransmitter tube, pumping billions of tonnes of CO2 into became warmer; but the higher the latitude, GABA can be persuaded to release glutamate its atmosphere, and registering the effects on the greater was the effect3,4. The warming instead by the artificial expression of BNPI. life and climate. Fortunately, there are other coincides with some of the most dramatic So it seems that the vesicular glutamate approaches.
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