Molecular Probing of Deep Secrets Days Each

news and views

insight into the molecules that define and Lee Niswander is at the Memorial Sloan Kettering distinguish the identity of fore- and Cancer Center, Department of Molecular Biology, hindlimbs. But many questions remain. and the Howard Hughes Medical Institute, 1275 How is restricted expression of the Pitx and York Avenue, New York, New York 10021, USA. Tbx genes controlled? How do these genes e-mail: [email protected] specify the distinct bone, tendon and 1. Takeuchi, J. K. et al. Nature 398, 810–814 (1999). 100 YEARS AGO muscle structure of each limb? What role 2. Rodriguez-Esteban, C. et al. Nature 398, 814–818 (1999). 3. Logan, M. & Tabin, C. J. Science 283, 1736–1739 (1999). Mr A. Hall, of Highbury, has designed an did these genes or their ancestors play in 4. Szeto, D. P. et al. Genes Dev. 13, 484–494 (1999). almanac with the object of eliminating the development of limb types during 5. Stephens, T. D. et al. Dev. Biol. 133, 1–7 (1989). the inconvenience consequent on the evolution? The rapid identification of these 6. Saunders, J. W. J., Cairns, J. M. & Gasseling, M. T. J. Morphol. various days of the months falling on genes, their targets and their phylogenetic 101, 57–88 (1957). 7. Basson, C. T. et al. Nature Genet. 15, 30–35 (1997). different week days, owing to the relatives suggests that these gaps in our 8. Li, Q. Y. et al. Nature Genet. 15, 21–29 (1997). changing number of days in each month. understanding will be filled quickly. 9. Smith, J. Trends Genet. 15, 154–158 (1999). His scheme is to make New Year’s Day separate from the rest, calling it January Microbial ecology 0, and then divide the remaining 364 days into thirteen months of twenty-eight Molecular probing of deep secrets days each. Following this plan, therefore, Roger Summons any particular day of the month will always fall on the same day of the week, and this would, of course, be convenient echniques from molecular biology organisms also had sequences unlike any for many purposes. The extra month he and organic geochemistry have been cloned from contemporary freshwater and proposes to denote by the name Tcombined to provide a new tool for marine environments. “Christember.” The almanac sent us is microbial ecologists, as shown by ribosomal As well as being new to science, these printed on this principle, and a useful RNA surveys and carbon isotopic analysis of organisms have created an unusual sedi- item included is the table of sedimentary lipids reported by Hinrichs et ment chemistry. Analyses of the membrane corresponding dates between the al. on page 802 of this issue1. Several lines of lipid and stable carbon isotope distributions Gregorian, Julian, Jewish and evidence suggest that methane gas seeping of the samples tell us not only about their Mohammedan calendars. from unstable methane hydrates supports a history, but also about their carbon metabo- From Nature 27 April 1899. newly discovered microbial community, lism. Methane is renowned for containing which is unusual both in its genetic relation- less 13C than virtually any other biological 50 YEARS AGO ships and in its metabolism. product on Earth, and large amounts of it are During Easter 1947, an inspection was The concept of microbial diversity has produced where organic matter is buried. made of the seaweed cast up on the west been transformed by the growth in sequence Organic matter in the Eel River basin sam- mainland of Orkney. One heavy cast, 3 ft. data from ribosomal RNA (16S rRNA)2. The ples had less 13C than nearby controls, and thick at the water’s edge, was found in a cloning and sequencing of RNA from methane gas bubbling into the water column sandy bay north of the graveyard microbes living in their natural environ- had more 13C than near-surface methane northwest of Stromness … . There is little ments has revealed a genetic diversity hydrates in the same region. This is a power- chance of anything remaining intact beyond the dreams of researchers whose ful indicator that some members of the before being cast ashore as the Atlantic tools were limited to microscopy and cell microbial community were consuming part waters break on this coast. The cast culturing3,4. RNA molecular probes have of the methane from the decomposing weed on this occasion, composed mainly revealed previously unknown evolutionary hydrate. of the fronds of Laminaria Cloustoni, had lineages, as well as associations between the Confirmation came from the carbon acted as a buffer for several large shells, genetic structure of communities and their isotope contents of individual lipids present such as Pecten, which were found intact. ecophysiology5. in the samples. Archaea have a diagnostic Normally, such shells become so broken As Hinrichs and co-workers1 have membrane component, a glycerol ether up that they merely add to the shell sand shown, 16S rRNA cloned from shallow lipid known as ‘archaeol’. Some members of comprising the foreshore in this region. sediment samples above unstable methane the Methanosarcinales also have a unique From among the cast weed a bivalve, 4 hydrate deposits in the Eel River basin, off- variant of this lipid, Sn-2-hydroxyarchaeol. in. long, was picked up which when shore California, is dominated by a variety Both of these compounds were present in discovered had its two halves hinged; the of previously unknown genes from archaea, the seep samples, but absent from controls, contents were absent. It has now been which along with bacteria and eukaryotes and so depleted in 13C that they could only identified as Tellina magna, a native of comprise the three domains of life on Earth. be the products of methane-consuming the East American coast, North Carolina These were accompanied by sequences from archaea. So, we have the enigma of organ- to West Indies — and is, I am informed, known anaerobes, including sulphate- isms living on a diet of methane that have the first recorded instance of a marine reducing and Gram-positive bacteria. the same membrane lipids as organisms invertebrate from the American continent There were two main types of archaea dis- normally associated with methane produc- to be found in British waters. Subsequent covered in the seep sediments, with some tion. Hinrichs et al.1 hypothesize that cells visits to the same area have produced clones closely related to known meth- containing the 13C-depleted lipids and the only limpet shells and one small bivalve. anogens (anaerobic methane-producing newly discovered 16S rRNA genes are one There can be no doubt the cast weed bacteria) of the order Methanosarcinales. and the same. was responsible for bringing the shell Most sequences, however, were from a new Little is known about the specific meta- ashore intact. How the animal (or its and closely similar group that was distinct bolic processes of the microbes found in the ancestors) crossed the Atlantic can only from, but related to, the methanogenic Eel River basin and other methane-rich sedi- be speculation. orders Methanomicrobiales and Meth- ments. Carbon isotope and biomarker lipid From Nature 30 April 1949. anosarcinales. Besides being distinguish- patterns are quite different from those that able from known methanogens, these new characterize ‘conventional’ aerobic methane

752 © 1999 Macmillan Magazines Ltd NATURE | VOL 398 | 29 APRIL 1999 | www.nature.com news and views consumption, and which have been mea- marker lipids for sulphate-reducing bacte- work of Thiel et al.8 shows how this type of sured in mussel communities at the surface ria having even less 13C content. Moreover, knowledge can be used to project back in of methane seeps6. Given that the sediments biomarkers for archaea are among the most time. are anaerobic, and that there are sulphate- 13C-depleted yet reported. So, there is a neat Through various lines of investigation, reducing bacteria present, it is virtually cer- alignment of geochemical patterns for a anaerobic methane oxidation has been tain that methane is being oxidized at the modern seep site and a 20 million-year-old demonstrated as a viable metabolism for expense of sulphate. Independent studies counterpart. the deep biosphere and can be added to the using radiotracers, stable isotopes and These papers are exciting in the way they compendium of ways in which microbes mass-balance analyses, point to a consor- chart a new direction for biogeochemists. manipulate the distribution of chemical tium of methanogens (somehow operating Studies of biogeochemical processing in elements on a global scale. These microbes in reverse) and sulphate-reducing bacteria, contemporary environments, and particu- may eventually be cultured and their meta- which together are responsible for anaerobic larly within the deep biosphere, can now be bolic processes opened to further study. methane oxidation7. However, until now, undertaken with more certainty about the The combined organic-geochemical and specific information about their genetic rela- ecology and physiology of the microbes. The molecular-biological strategy used by Hin- tionships has been lacking. The hypothesis new molecular probes that Hinrichs and richs et al. is an important development favoured by Hinrichs et al. is that the new colleagues have developed may soon be in the study of global biogeochemical archaea are not simply methanogens operat- applied in a more quantitative manner. This cycles. ing in reverse, but a new group for which will greatly strengthen our understanding of Roger Summons is at the Australian Geological methane consumption is the predominant, lipid biomarkers and their relationships to Survey Organisation, GPO Box 378, Canberra City, or even exclusive, metabolism. If this is precursor organisms. These relationships ACT 2601, Australia. proven, it will have far-reaching con- were previously established indirectly, and e-mail: [email protected] sequences for our understanding of the sometimes haphazardly, from lipid analyses 1. Hinrichs, K., Hayes, J. M., Sylva, S. P., Brewer, P. G. & DeLong, physiology and evolution of archaea as of organisms in cultures and corresponding E. F. Nature 398, 802–805 (1999). well as their role in the carbon cycle. samples from natural environments. Be- 2. Pace, N. R. Science 276, 734–740 (1997). Research conducted independently by cause the majority of rRNA genes cloned 3. Giovannoni, S. J., Britschgi, T. B., Moyer, C. L. & Field, K. G. 8 Nature 345, 60–63 (1990). Volker Thiel and co-workers has shown from natural environments are new to sci- 4. Ward, D. M., Weller, M. R. & Bateson, M. M. Nature 345, 63–65 that distinctive limestones, the so-called ence, there is an obvious knowledge gap. As (1990). ‘calcari a Lucina’ that are widely distributed this is rectified and linked to compound- 5. Moore, L. R., Rocap, G. & Chisholm, S. W. Nature 393, 464–467 in the Apennines, carry a similar geochemi- specific isotopic analyses of characteristic (1998). cal signature for methane venting. These biomarkers, not just with carbon, but also 6. Jahnke, L. L., Summons, R. E., Dowling, L. M. & Zahiralis, K. D. Appl. Environ. Microbiol. 61, 576–582 (1995). Miocene-age carbonates, in places packed with nitrogen, hydrogen, oxygen and sul- 7. Hoehler, T. M., Alperin, M. J., Albert, D. B. & Martens, C. S. with the remains of tubeworms, are highly phur, we have a key to improved informa- Glob. Biogeochem. Cycles 8, 451–463 (1994). 13 depleted in C, with intracrystalline bio- tion about biogeochemical processing. The 8. Thiel, V. et al. Geochim. Cosmochim. Acta (in the press). Cell biology Coated-pit dynamics

Endocytosis — the process by which cell- of coated pits also seems to be coordinated surface receptors and other membrane by an underlying membrane skeleton. proteins are taken up into the cell — Coated pits appeared and disappeared at occurs mainly through coated pits. These defined, rather than random, sites on the pits are specific sites on the plasma plasma membrane. Indeed, once membrane where clathrin and the adapter fluorescence at a coated pit disappeared, it protein AP-2 associate with the cargo. The usually reappeared at the same site. This pit invaginates, then a clathrin-coated meant that coated pits did not form at all vesicle is pinched off. Despite extensive over large areas of the membrane. characterization, we do not know whether These observations are difficult to these coated pits form randomly or at reconcile with the conventional view of specific sites on the plasma membrane; how coated pits are formed. Diffusible how long they persist before detaching as labelled with GFP–clathrin appear transmembrane receptors or membrane- coated vesicles; and how quickly coated gradually, persist for several seconds, then docking sites are thought to recruit AP-2 vesicles uncoat. disappear abruptly without moving far and clathrin to form a coated pit. But the Reporting in the first issue of Nature from where they originated. That is, new data indicate that coated-pit Cell Biology (1, 1–7; 1999), Gaidarov and detached coated vesicles are stripped of formation is coupled to events at the colleagues now provide an insight into their clathrin coat in the vicinity of the pit membrane skeleton, possibly through these questions. They looked at the — they do not move through the scaffold proteins found in specific (and formation and internalization of coated cytoplasm first. Surprisingly, Gaidarov et limited) places. Future work with GFP pits in living cells, using a fusion protein of al. saw that the coated pits and vesicles do fusion proteins should resolve this green fluorescent protein (GFP) and the not move outside regions of about 0.5–0.8 discrepancy, allowing us to see how coated clathrin light-chain. Their work, which Ȗm in diameter (see picture). But pits form and work in a living cell. reveals an important relationship between latrunculin B — which inhibits actin Jennifer Lippincott-Schwartz the structural organization of clathrin- assembly — relaxes this restricted Jennifer Lippincott-Schwartz is in the Cell Biology coated pits and the membrane mobility, implying that an actin-based and Metabolism Branch, NICHD, National cytoskeleton, has implications for framework maintains the structural Institutes of Health, 18 Library Drive, Bethesda, organization of the plasma membrane. organization of clathrin-coated pits. Maryland 20892-5430, USA. The authors found that coated pits The authors found that the formation e-mail: [email protected]