the Archaea - BioScience

12 Pages·2007·2.9 MB·English

Recent Excitemenabto ut
the Archaea
The Archaeaa re valuablef or studying basic biological questions
and have novel biotechnologya pplications
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Ken F. Jarrell, Douglas P. Bayley, Jason D. Correia, and Nikhil A. Thomas loa
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Microbial life has inhabited genetic data followed that was gen- m h
this planet for approxi- The days of the erally in support of the basic classifi- ttp
3 billion myeaaterlsy lo3n.7g ebri lltihonan yepalarsn-t-s Archaea being considered catOiorni gsineta lfloyr, tht hbey DWomoeasien. Archaea s://aca
and animals. The development of consisted mainly of organisms found de
higher life forms on Earth was de- as just "odd bacteria"- in unusual or extreme environments, mic
pcoenntdiennute do n mexiicsrteonocreg anoisf mps,l anatn da tnhde adapted to living in saurec ha balse t thoe gerxotwre mine s hataulorpathiinlegs c, ownhceicnh- .oup.c
animal life absolutely requires the extreme environments trations of sodium chloride; the om
continued activity of microbial life. methanogens, which require extremely /bio
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form of mitochondria and chloro- dependent thermophiles, which are ce
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continuing role that microorganisms into one eukaryotic domain (the members of the Archaea have been stra
play in geochemical cycles, the entire Eukarya) and two prokaryotic do- greatly expanded, mainly by the iso- ct/4
biosphere is dependent on the activi- mains (the Bacteria and the Archaea) lation of organisms that extend the 9/7
ties of microorganisms. Certainly, as was based, at the time, mainly on limits of life on both the temperature /5
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sphere" (Woese 1998). parisons demonstrated that a group of up to 113 'C, and others grow in pH 70
Ever since Woese and his col- of unusual prokaryotic organisms, values that approach zero. In addi- 4 b
leagues first proposed that there are originally called the Archaebacteria tion, archaea have been discovered y g
three basic lines of evolutionary de- and later the Archaea (Woese et al. that grow under the less extreme ue
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scent (Woese and Fox 1977), an odd 1990), constitutes a clear and separate conditions favored by most bacteria. t o
collection of microorganisms called domain that is as distantly related to The harsh environments in which n 0
Bacteria as to Eukarya. The Domain many archaea flourish, often outside 5 A
Kqueene nFs.u J.caar)ri se lal (per-mofaesils:o rja arnrde lJlkas@onp oDs.t . AEurcrhyaaerach caoenottaai n(cso mtwpor iksiinngg dmoemthsa, ntoh-e tinhter irgeuaeldm s coife nbtaiscttse riniatle rgersotewdt hin, shtraavte- pril 20
Correiaa nd Nikhil A. Thomasa re gradu- gens, extreme halophiles, and some egies of coping with life at the ex- 19
ate studentsi n the Departmento f Micro- hyperthermophiles) and the Cren- tremes as well as scientists who wish
biology and Immunology,Q ueen's Uni- archaeota (originally comprising just to harness archaeal enzymes for bio-
versity, Kingston, Ontario, Canada K7L hyperthermophiles, but now thought technological applications. In addi-
3N6. Douglas P. Bayleyi s a postdoctoral to include a variety of nonthermophilic tion, many scientists have sought to
fellow in the Departmento f Microbiol- members). Despite the morphological gain a better understanding of cer-
ogy, East CarolinaU niversity,G reenville, resemblance of archaea to bacterial tain eukaryotic processes by study-
NmCet h2a7n8o5g8e.n icJa arrcrhealle ah faosr twheo rpkaesdt twono cells (e.g., lack of a nuclear mem- ing the somewhat simpler archaeal
decades.F or the past 10 years,h is lab has brane), many archaeal processes, model. Still other researchers study
beens tudyingt he uniquef lagellas tructure such as transcription, are much more archaea to learn more about the ori-
of the archaea. 1999 American Institute similar to those of eukaryotes. More- gin and evolution of life itself or to
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of BiologicalS ciences. over, a wealth of biochemical and delve into systems that appear to be
530 BioScience Vol. 49 No. 7
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Figure1 . Detectiono f microbesi n an environmentasl ampleb y polymerasec hain reaction( PCR).S amplesa re obtained (step 1) and /bio
genomicD NA is purifiedf rom the mixed culture( step 2; for conveniencew e show only threeg enomes,w hereasm illions would be sc
present).N ext, 16S rRNA-specificp rimersa re used for PCR amplificationo f the 16S rRNA gene (step 3), yieldingP CR fragments ien
of specific 16S rRNA genes (step 4). These fragmentsa re collectively ligated into a cloning vector (step 5), the plasmids are ce
tinradnivsifdourmalce odiln otnoi eEss acrhee arnicahlyiazc eodlit (os tdeept 6er),m ainndet t hraen ssefqouremnacneo tsfa rthe pe l1a6teSd r oRnNtoA s goelinde m freadgimumen( stt( estpe 7p) 8. F).i Sneaell tye,xp tl afsomr didestp auilrsi.f iedf rom /artic
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unique to the archaeal domain. The cesses in both archaea and eukary- pH (habitat of the thermoacidophilic bs
recent sequencing of the entire ge- otes-all basic research findings that archaea). As already noted, how- trac
nomes of several archaea have pro- call into question old paradigms ever, recent molecular data suggest t/4
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vided a wealth of knowledge about about the Archaea and that suggest that Archaea are much more widely /7
archaeal genes that are bacterial-like novel applications of the Archaea in distributed than previously thought. /53
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(e.g., those encoding major meta- biotechnology. /2
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bolic pathway enzymes), ones that Identification of noncultured archaea. 67
are eukaryal-like (e.g., those for tran- Archaeale cology Because of the tendency of the 04
scription factors and RNA poly- and identification Archaea to occupy extreme environ- by
merase subunits), and still others that ments, many species of archaea have gu
e
tahpopseea rr etloa tbeed atroc hfalaegael-lslap ecstifriucc tu(er.eg).., tTahtse wAorrclhdaweiad eo, ccbuupt yo nvea roifo uths e hhaablli-- ubnecdaouusbet etdhleyy cnaont nyoett bbee ecnu ltidiveantteidfi eidn st on
New molecular techniques that al- marks of these microbes has been the lab. This inability may be due to 05
low scientists to detect the presence that they are generally present in the fact that the elevated tempera- Ap
of organisms in environments with- what are usually described as "ex- ture or pressure of the original habi- ril 2
out the prior necessity of culturing treme environments." Such environ- tat cannot be suitably duplicated in, 01
9
the organism in the lab have opened ments (Table 1) include those devoid or en route to, the laboratory or that
the way for more extensive studies of of oxygen (home to anaerobic a proper growth medium has not
the distribution of the archaea. archaea); those saturated with salt been developed for some of the more
In this article, we discuss major (inhabited by halophilic archaea); fastidious organisms. In addition, some
recent discoveries reported from aqueous environments, such as deep archaea appear to be involved in sym-
studies of the Archaea. These in- sea hydrothermal vents, where the biotic relationships that have proven
clude the evidence of the widespread temperature exceeds 100 *C (in which difficult to reproduce in the lab.
distribution of Archaea, the analyses thermophilic and hyperthermophilic A number of techniques have been
of several completely sequenced archaea thrive); and even combina- used to explore the microbial con-
archaeal genomes, the discovery of tions of environmental extremes, tent of such uncultivatible microbial
some similar basic biological pro- such as high temperature and low samples. One method makes use of
July 1999 531
Table 1. Environmental extremes inhabited by archaea. lab. Studies of this type have demon-
strated that archaea are much more
Extreme feature Natural habitat Examples diverse and numerous than previ-
Temperature Deep-sea hydrothermal Pyrococcus fumarii (growth to 113 ?C) ously believed and occupy a wider
vents, hot springs, range of habitats.
volcanic areas
Archaeal habitats: From one extreme
pH Solfataric springs Picrophilus oshimae (growth to near
to another. One of the most amazing
pH 0)
scientific findings of the past 25 years
Salt Dead Sea, Great Salt Halobacterium salinarum (growth in was the discovery of "black smok-
Lake, salterns 5.2M NaCl) ers" at the bottom of oceans (Tunni-
cliffe 1992). In these areas, the ocean
Anaerobiosis Rumen, sewage Methanospirillum hungatei (redox
digestors, swamps potential of less than -330 mV) floor spews forth superheated water
whose temperatures reach 350 ?C or
Salt/pH Soda lakes Natronobacterium magadii (pH 8.5-11, more. This water is laden with min- Do
2-5.2M NaCI) erals, and when it mixes with the wn
Temperature/pH Acidic hot springs, coal Sulfolobus acidocaldarius (pH 2, 75 ?C) surrounding cold ocean water, min- load
refuse piles erals such as sulfide precipitate, cre- ed
ating the "chimney" that gives black fro
Anaerobiosis/salt Great Salt Lake Methanohalophilus mahii (anaerobic, smokers their name. Unlike the ma- m
sbeadcitmereinalt , msaaltisn e cyano- 2M NaCI) jority of the deep ocean floor, which http
ibsl aac k" dsemseorkte,"r st hteee mar ewasit hsu lrirfeo.u Mndainngy s://ac
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domain-, kingdom-, genus-, species-, using specific PCR primers. Because new species of macroscopic life have de
and even strain-specific oligonucle- of the highly conserved nature of the been found in such areas, and several mic
otide primers that are specific for rRNA molecule, so-called universal novel bacterial and archaeal species .o
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certain highly conserved genes (Pace primers have been developed that have been isolated from the areas p.c
et al. 1986). The primers can be used will amplify the SSU rRNA gene se- around the erupting smokers. The om
to generate probes for in situ hybrid- quence from all organisms. Alterna- entire ecosystem in the vicinity of the /b
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ization experiments. Such probes tively, specific primers can be used black smokers is based on chemo- sc
have been generated to the SSU rRNA that will amplify SSU rRNA se- synthesis (i.e., growth on an inor- ien
genes from a number of organisms quences from only one of the do- ganic substrate using chemical oxida- ce
b(ia.ec.t,1er6iSa arnRdN aArc hgaeneae,s ainnd t h18e Sc raRseN oAf mwhaiicnhs. iTdehael lrye sruelptrinegse nPtC aR m pirxotudruec tos,f tiinodne penenerdgeyn)t anodf iss aollmaro ste ncoemrgpyl etaenlyd /article
genes in the case of eukaryotic cells). the SSU rRNA gene sequences from photosynthesis. -ab
These genes are well suited for deter- all of the organisms present in the The upper temperature limit for stra
mdiifnfeirnegn t tohreg arneilsamtiso nbsehciapus se bthetewy eoecn- soanme pdleo m(oari na,l l ionf tthhee ocragsea noisfm tsh ef rdoom- tlhifee iisso lcaotniotnin uoofu snloyv ebl ehinygp errathiseerdm ob-y ct/49
cur in all organisms and because main-specific primers), are ligated philic archaea, often from samples /7/5
different positions within the gene into cloning vectors and transformed taken at areas surrounding the black 30
evolve at different rates, which al- into Escherichia coli cells. smokers. The current record is held /23
6
lows both large and small phyloge- Sequencing of the DNA insert in by a recently isolated archaeon, 70
netic distances to be measured (Woese individual clones supplies the data Pyrolobus fumarii, which has an 4 b
1987). necessary for comparison to known optimum temperature for growth of y g
A logical extension of the hybrid- SSU rRNA sequences. If the sequence 106 ?C but can grow at 113 ?C ue
s
ization technique is the use of the obtained from an unknown organ- (Bl6chl et al. 1997). This organism t o
polymerase chain reaction (PCR), ism matches an existing sequence, even survives autoclaving at 121 ?C n 0
which takes advantage of two prim- the conclusion would be that the for 1 hour. By contrast, no bacte- 5 A
tehres tor RthNeA S SUge rnResN Af rgoemn e otor gaamnipslmifsy oprrgeasennist min, thoer s aam pclleo.s eS eqrueelantcievse ,t haist rteiummp eirsa ytuert eks noowf n1 0t0h a?t Cc aonr ggrroeawt eart. pril 20
present in an environmental sample are dissimilar from those already (The most thermophilic bacteria are 19
without the necessity of actually known indicate novel microbes. members of the genera Thermotoga
growing the particular organism in Comparison of the sequence to ones and Aquifex, which grow optimally
the lab. To pursue this strategy, total already present in the databases can at approximately 85 ?C.)
DNA is prepared from an environ- suggest the taxonomic group to Study of the mechanisms that al-
mental sample containing a mixture which the unknown organism be- low these archaea to survive such
of organisms-for example, a sample longs and possibly even something extreme temperatures has been an
obtained from an ocean floor by a about its physiology. This informa- active area of research. For example,
submarine, as shown in Figure 1. tion may, in turn, provide research- it has led to the discovery of archaeal
Total DNA is prepared from the ers with clues about media and en- histones, which are closely related to
mixed population of organisms, and richment techniques that may allow eukaryal histones. The binding of
SSU rRNA sequences are amplified for isolation of the organism in the archaeal histones to duplex DNA can
532 BioScience Vol. 49 No. 7
elevate the meltingt emperatureo f are autotrophic and appear to eke as well as the polar seas. Nonthermo-
the DNA by 20 ?C. It has been sug- out a living by using subterranean philic crenarchaeota have also been
gested that histones might have sources of hydrogen and bicarbon- found in symbiotic association with
evolved in an ancestor of the Archaea ate. In these habitats, H2 is generated marine invertebrates, such as sea cu-
and Eukarya to overcome the diffi- through the reaction of oxygen-poor cumbers (McInerney et al. 1995) and
culties of maintaining genome integ- water with iron-bearing minerals. marine sponges (Preston et al. 1996).
rity and function in high-tempera- Interest in deep subsurface micro- These findings support the notion
ture environments-habitats in biota, both archaea and bacteria, that, although often found in ex-
whichh yperthermophilestsi ll dwell stems from observations that many treme environments, the Archaea are
today (Pereira et al. 1997). In addi- of these habitats appear to have been truly ubiquitous and may be present
tion, high cytoplasmic concentrations completely isolated from the surface in habitats previously thought to be
of unusual solutes, such as cyclic- for millions of years, leading re- too "normal." Some researchers have
2,3-diphosphoglycerathee, lpt o pre- searchers to believe that these mi- even suggested that, in light of the
vent DNA melting in some hyper- crobes may possess unusual traits newfound ubiquity of archaea and
thermophilica rchaea.F inally,t here that might be useful in biotechnol- the association of some archaea as Do
is the possibility that hyperthermo- ogy or medical applications. More- symbionts of metazoan hosts, the wn
philes employ novel enzymes with over, some scientists believe that the possibility of some disease-causing loa
unusual biochemical features to re- deep subsurface of other planets may archaea being discovered in the fu- de
d
pair DNA, because sequence analy- be similar to that of Earth and that, ture should not be ruled out (Stein fro
ses suggest that hyperthermophilic if life exists outside our planet, it and Simon 1996). m
archaea do not have the DNA repair may most logically be found in the Compared to marine environ- http
gbeancteesr itah ata nhda veeu kbaereyno tiedse nt(iGfireodg ainn dbeoedpie ss.u bTshuursf,a cset uodfy ootfh emr icprloaonregtaanry- mofe anrtsc,h waehailc hs pceocnietsa,i nt hae l aurpgpee nr ulamybeerrs s://ac
1998). isms that live deep within the earth's of soil are not generally considered ad
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Archaea also represent the pro- surface may make the search for ex- ideal habitats for archaea. Neverthe- m
karyotic record holders for optimal traterrestrial life more focused and less, molecular methods have re- ic.o
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growth at acidic pH. Until recently, ultimately more successful. vealed the presence of archaea in p
this distinction belonged to the Among the many less extreme such habitats, including the soils of .co
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archaeon Thermoplasma acido- habitats occupied by archaea are the the Amazon region (Borneman and /b
philum, which grows optimally at cold surface marine waters near Ant- Triplett 1997), Wisconsin (Bintrim ios
c
60 ?C and pH 1.8-2.0. Recently, arctica. The prokaryotic population et al. 1997), and Finland (Jurgens et ien
however, novel archaea have been of these waters was found to consist al. 1997). Analysis of the amplified ce
pishoillaicte tdh atnh aTt .a arcei dcolepahrillyu mm o(rSec ahcleidpoe-r o1f9 9u4p) .t oM 3o4r%eo vaerrc,h taheeas e( DarecLhoanega ewte arle. aSrScUh aeraR NthAat lgiveen eins three vuepapleedr latyhearts /article
et al. 1995). One isolate, Picrophilus of the crenarchaeota kingdom, which of soil fall into a cluster that diverges -a
b
ogsrhowimtha e,o f h0a.7s aan dp Hca n ogprtoimwu smig niffoir- htaaidn pornelvyi ouhsylpye rbteheenr mthoopuhgihlitc tom ceomn-- daneedp, lys ufrrpomris tihneg lcyr,e nhaarsc hitase ocltoas leinste aagfe- strac
cantly at a pH approaching zero. bers. These microbes have not been filiation to planktonic archaea. Evi- t/49
Such organisms are ideal models for cultured, and their role in nature is dently, the diversity of archaea in the /7/5
studying the bioenergetic problems unknown. However, considering soil is much higher than previously 30
that accompany growth at such low their abundance and distribution, thought, and archaea must now be /23
pH. For example, these cells must these uncultured archaea are likely considered as members of the micro- 67
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function with a huge pH gradient to to be involved in biogeochemical pro- bial communities present in these 4 b
maintain a relatively neutral intra- cesses with global-scale impacts. In- nonextreme environments. As with y g
cellular pH. Perhaps not unexpect- deed, Pace (1997) has suggested that the vast numbers of archaea found in ue
edly, the cytoplasmic membrane of this large population of low-tem- ocean waters, the key question is: st o
P. oshimae has been shown to ex- perature crenarchaeotes may be re- What processes are these uncultured n 0
hibit an extremely low permeability sponsible, in part, for a hitherto un- archaea performing in these soil en- 5 A
to Aprnoottohnesr. environmental frontier lsiuthspoetrcotepdh yo.c ean food chain based on vcuirlotinvmateen tst?h eIste s honuolnde xbter epmoosspihbillei ct o pril 2
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penetrated by the Archaea is the re- Additional low-temperature cren- archaea in the laboratory because 19
gion several kilometers below the archaeota have recently been discov- they grow in "normal" conditions in
surface of the earth (Fredrickson and ered that thrive in a variety of other nature. Such an advance would be a
Onstott 1996). Such deep subsur- nonextreme habitats, including me- boon to researchers, who would be
face habitats are not nearly as popu- sophile (temperature usually 20-45 able to conduct experiments in
lated as topsoil, but initiatives aimed ?C) and even psychrophile (tempera- archaeal systems without having to
at examining life deep within the ture usually below 15 ?C) environ- deal with the requirements of most
earth have nonetheless shown that ments. The sources of these microbes currently isolated archaea for high
these habitats are home to many include freshwater sediments (Mac- temperature, high salt, high pres-
novel organisms, including methano- Gregor et al. 1997, Schleper et al. sure, extreme pH, or anaerobic con-
genic archaea (Kotelnikova and 1997) and subsurface ocean waters ditions (Bernander 1998).
Pederson 1997). These methanogens (DeLong 1992, Fuhrman et al. 1993), Reexamination of even traditional
July 1999 533
Table 2. Genome sizes of selected members of the bacterial and archaeal domains. the products they encode will even-
tually be the benchmark for defining
Organism Domain Genomes ize (Mb) these prokaryotes at the domain level.
Escherichiac oli (commong ut bacterium) Bacteria 4.60 But, even now, "if you compare major
Neisseriag onorrhoeae( gonorrheac ausativea gent) Bacteria 2.20 mechanisms of the cellular informa-
Pseudomonas aeruginosa (opportunistic pathogen) Bacteria 5.90 tion network, you cannot mistake an
Mycoplasma pneumoniae (mycoplasmal Bacteria 0.81 archaeon with a bacterium or a eu-
pneumoniac ausativea gent)
karyote" (Forterre 1997).
Aquifex aeolicus (hyperthermophile) Bacteria 1.50
Methanococcus jannaschii (hyperthermophilic Archaea 1.66
methanep roducer) Genome structure. The archaeal ge-
Methanobacterium thermoautotrophicum Archaea 1.75 nome sequences that are currently
(thermophilicm ethanep roducer) available have a mosaic nature
Asurlcfhaateeo rgeldoubuces rf)u lgidus (hyperthermophilic Archaea 2.18 (Ouzounis and Kyrpides 1996) that
combines features of both bacterial
Pyrococcus horikoshii (hyperthermophile) Archaea 1.80 D
Halobacterium salinarum (extreme halophile) Archaea 4.0 and eukaryotic genomes. The orga- o
w
Sulfolobus solfataricus (thermoacidophile) Archaea 3.05 nization of a typical archaeal ge- n
nome and its expression appear to loa
d
resemble those in the Bacteria, as ed
archael sites with new molecular tech- organism isolated from the rusticles does the fact that archaeal genomes fro
niques has yielded unexpected re- is a novel archaeon that is distantly consist of a single circular chromo- m h
sults. Large numbers of novel ther- related to Halovibrio variabilis, some (Keeling et al. 1994). Exami- ttp
mdeotpechtielidc ianr hchota esaplr isnpgesc ie(Ss tehtatvere ebte aenl. wthhei cGh rewaat s Soarlti gLinaaklely (Bisroolwatne d1 9f9ro8m). Anartcihoane ao af nsde ltehcet eBda cmteermia breervse aolsf ththaet s://ac
a
1993, Barns et al. 1994), suggesting The role of this organism in the ac- the size of their genomes is broadly de
that the number and diversity of tivity of the rusticles devouring the comparable (Table 2). Archaeal genes mic
archaea present in extreme habitats Titanic is as yet unknown. tend to be organized in cotranscribed .o
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may be much higher than previously units, producing polycistronic p.c
believed. Among the archaeal 16S Archaeal genomics mRNAs-a type of gene organiza- om
rRNA sequences newly isolated and tion that is present in bacteria but /b
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sequenced, most bear no close simi- The recent publication of complete not eukaryotes. Interestingly, archaea sc
larity to those from any cultured genome sequences of several archaeal can have, within the same operon, ien
archaea. Development of techniques species (Methanococcus jannaschii, some genes homologous to genes ce
tforo mgr oaw grpeuartee r cvualtruierteys ooff haarbchitaaetas fBuulglti duets , Kall. en1k9 e9t6 a; l. A19r9c7h;a Meoegtlhobanuos - hfooumnodl ogino ubs acttoer igae naensd foouthnedr inge neues- /article
should allow for the identification of bacterium thermoautotrophicum, karyotes. It is not known whether -ab
a host of unusual physiologies, add- Smith et al. 1997; and Pyrococcus operons are indicative of the genome stra
iinngg souf btshteasnet ioarllgya ntois mous.r understand- hhaosr ikinotsrhoidi,u Kceadw vaarastb aaymaosiu entt sa l.o 1f 9n9e8w) tshtrouucgthu rteh eo fs iam upnliicvietyrs aanl da nacdevsatnorta, gaels- ct/49
New habitats for archaea are con- data about the unique characteris- of such gene organization have /7/5
tinually being discovered. One of the tics of these prokaryotes. Previously, proven successful for prokaryotes. 30
more interesting is the RMS Titanic. archaeal genomes were identified as An interesting aspect of several /23
6
Since striking an iceberg and sinking having similarities to both prokary- archaeal genomes is the presence of 70
in the North Atlantic almost 90 years otes and eukaryotes, and the Archaea inteins (i.e., protein sequences that 4 b
ago, the Titanic has been devoured by were thus defined in such terms. are embedded in frame within a pre- y g
a complex community of microbes, Howeve'r, with many of the open cursor protein sequence and that are ue
s
which are extracting the iron from reading frames (ORFs) from archaeal subsequently removed by self-splic- t o
the steel of the superstructure of the genomes having no significant matches ing; Perler et al. 1994). Interestingly, n 0
great ship, a process that is likely to to ones in universal gene databases, 18 inteins were found in coding se- 5 A
rdeescualdt eisn. Tithse cmolilcarposbei ailn c othmem cuonmitiinegs tnhael lytr bueei nngo vreevlteya loefd .t hOer idgoinmaalliyn, 5is6 %fi- wqueerne ceids eninti fMied. jainn nAas. chfuiil,g idbuust. nTonhee pril 20
form huge "rusti cicles," or "rusticles," of the 1738 ORFs in the genome of best-studied examples of inteins are 19
some of them meters in length, that M. jannaschii lacked a counterpart those associated with the DNA poly-
hang from the ship (Wells and Mann in the public databases (Bult et al. merases from M. jannaschii, Thermo-
1997). The total mass of the rusticles, 1996). Continued evaluation has re- coccus litoralis, and Pyrococcus sp.
which are composed of 20-35 % iron duced this number considerably, but The excised inteins usually have se-
extracted from the ship's steel, has it is still evident that the Archaea, quence similarity to so-called hom-
been estimated at 600 tons. Although like the Bacteria and the Eukarya, ing endonucleases, and endonuclease
iron bacteria are of primary impor- will be characterized by a significant activity has been demonstrated for
tance in extracting the iron that forms proportion of its genome being com- the inteins of the DNA polymerases
the rusticle, the rusticles are com- posed of genes that are unique. As from T. litoralis and Pyrococcus sp.
posed of a community of perhaps more archaeal genomes are charac- Genomic analysis has identified dif-
dozens of microbial species. One terized, archaeal-specific genes and ferent intein sequences in different
534 BioScience Vol. 49 No. 7
archaeal species, suggesting that of DNA polymerases that shows no capable of unique biological pro-
intein sequences have diversified. The sequence homology to any previously cesses. Indeed, the Archaea inhabit
significance of these self-splicing se- described DNA polymerases has re- harsh environments that most likely
quences in vivo is unclear, although cently been discovered in Archaea demand altered or unique metabolic
a strong presumption is that they (Ishino et al. 1998). At least two activity.
provide an additional level of con- separate gene products appear to be Several groups of proteins, such
trol for gene activity (i.e., beyond required to form the catalytic center as chaperones and DNA repair pro-
transcription and translation). Study of this new DNA polymerase. teins, are seemingly underrepresented
of the complete archaeal genome se- Comparative genomics allows for in the genome of M. jannaschii as
quences has also revealed the pres- universal proteins (i.e., common to compared to members of the other
ence of a limited number of introns all domains of life) to be compared two domains (Koonin et al. 1997).
(sequences spliced out of mRNA be- and analyzed, aiding in the identifi- The absence of the chaperones DnaK
fore translation) in some archaeal cation of metabolic processes shared (HSP70) and DnaJ (HSP90) is par-
genomes. For example, in Sulfolobus by all extant life forms. Ouzounis ticularly unusual because these pro-
solfataricus, introns have been found and Kyrpides (1996) have compiled teins are among the most conserved Do
in six tRNA genes (Sensen et al. a set of universal metabolic enzyme in nature and appear to be required wn
1998). The enzyme involved in and protein families. These proteins by all living cells. Even more surpris- loa
d
archaeal intron splicing is a homo- are generally responsible for essen- ing is the fact that a DnaK homo- ed
logue of two subunits of the eukary- tial metabolic processes, such as the logue has been found in other fro
otic endoribonuclease that is involved biosynthesis of ATP, amino acids, archaea, including methanogens. Pre- m
in intron removal in eukaryotes and nucleosides. In addition, infor- sumably, the functions of the miss- http
(Lykke-Andersen et al. 1997). mnoamtieosn ifnrdoimca tceosm pthleatte parroctheiane alt rgaef-- ibnege nc harepaesrsoingnese do f tMo . joatnhnera,s cphoiis shibavlye s://ac
a
Functional genomics. At present, ficking and secretion are functionally archaeal-specific, proteins. de
little is known about the replication conserved in all three domains of life At present, many additional mic
of archaeal genomes-that is, (Bult et al. 1996). Signal peptides, archaeal genomes are being se- .o
u
whether they have a single origin of membrane targeting and transloca- quenced, and new questions will un- p.c
replication or multiple origins. Even tion systems, and signal peptidases doubtedly arise from the findings. om
analysis of complete genome se- are all present in archaeal species, Previously, rRNA sequences and con- /b
quences of several archaea has failed although protein trafficking in served protein families served to iden- ios
c
to identify the origin(s) of replica- archaea is poorly understood. In most tify universal and unique features of ien
tion. It is not even known if replica- cases, archaeal proteins involved in extant life; however, comparative ce
tuinonid ioref ctthioen aarl chaeoarl cbhirdoimreocstoiomnea l is tghaen ict rainosnpso rmt oorfe sculogsaerlsy arneds eminbolre- gtoe nsotmudicysi nhga sc aodmdpelde xa nseywst eampps.r oTachhe /article
(Bernander 1998). It appears that those of bacteria than eukaryotes. complete data sets provided by ge- -ab
most of the proteins involved in the With complete genomes available, nome sequences will allow scientists stra
rsoepmliec, atiinocnl uodfi ntgh e DaNrcAh aepaoll ycmhreoramsoe,- ibti obcehceommiceas l ppaotshsiwbaley s toof proeocorlnys tsrtuucdt- tuon tetesstat blnee win hthyep optahsets. es that were ct/49
DNA helicase, and DNA ligase, are ied organisms, such as archaea, on /7/5
Eeuakralyr ysatlu-ldikiees o(fB eDrnNaAn derre pli1c9a9ti8o)n. tqhuee nbcaes ics onosf erthvea tihoing h odf etghreeier omf etsae-- Archaealc ell biology 30/23
6
demonstrated that halophilic archaea bolic enzymes to those of bacteria. Although the division of life into 70
are sensitive to specific inhibitors of In particular, many metabolic path- three domains was originally based 4 b
eukaryotic DNA polymerases (Brown way enzymes of various well-studied mainly on RNA sequence data, the y g
and Doolittle 1997). Archaeal DNA bacteria are conserved in the genome archaea clearly possess numerous ue
s
polymerase sequence data have re- of M. jannaschii. For example, the biochemical, structural, and genetic t o
vealed extensive homology to the pathways for the biosynthesis of traits that make this group of organ- n 0
eukaryote family B DNA polymerase. nucleotides and most amino acids isms distinct from members of the 5 A
mMeurlatispelse hdaivstei nbcete fna mcloilnye Bd DfrNoAm pbooltyh- jtahnant asacrhei i cliakne lby e ptroe diocctceudr baisne d Mon. oexthaemr pltew, om adnoym yaeianrss a(gToa ibt lwe a3s )f.o uFnodr pril 20
S. solfataricus and Pyrodictium oc- this sequence conservation (Koonin that archaea have ether-linked lipids 19
cultum. However, in M. jannaschii, et al. 1997). As more genome se- and that their walls lack murein,
a single family B DNA polymerase quences become available, archaeal unlike bacterial cell walls (Kandler
homologue has been identified, mak- biochemical pathways will be fur- and Konig 1985, Langworthy 1985).
ing this protein the likely candidate ther elucidated. However, other traits, such as their
for a solitary replicative enzyme In contrast to using comparative eukaryal-like transcription mecha-
(Edgell and Doolittle 1997). The genomics to identify shared genes, nism and histones, and their unique
absence of additional DNA poly- novel genes (i.e., those solely found flagella, have provided more recent
merases in archaeal species was puz- in the Archaea) can also be found by surprises.
zling because multiple DNA poly- this approach. These novel genes,
merases are present in bacteria and which represent an uncharacterized Gene expression. The transcription
eukaryotes. However, a novel family data set, may encode for proteins of DNA into RNA is performed by
July 1999 535
Table 3. Summary of selected archaeal features and their similarity to bacterial and they are functionally homologous.
eukaryal features. Interestingly, multiple TBPs and
TFIIBs have been discovered in halo-
Archaeal feature Bacteria-like Eukarya-like Archaea-specific philic archaea. Reeve et al. (1997)
Lack of nuclearm embrane + have suggested that the existence of
Ether-linkedli pids + multiple forms of these transcription
Singlec ircularc hromosome + factors may be analogous to the use
Replicationp roteins +
Histones + of multiple sigma factors by bacteria
Fibrillarin to regulate the expression of certain
Transcription genes. Study of the archaeal system
RNA polymerase + should help to define the precise roles
Promoter +
of these factors in archaea. Such stud-
TATAb indingp rotein +
TFIIB + ies should also shed light on the roles
Translation of these factors in the more complex
Ribosomal proteins + + + eukaryotic system, just as study of Do
TPoralyncsilsattrioonnfi cam cteosrssa ges + + tahne abricohcaheeaml icchaal pfuernocntieo nh eolfp ietds hroemveoa-l wnlo
Shine-Delgarnos equences + ad
Flagellac omposition + logue in eukaryotes (Forterre 1997). ed
Aabboilviety 1t 0o0 g ?rCow at temperatures + nucAleltahro umgehm brthane e, Atrhceh daeefai ninlagc kfe aa- from
ture of the Eukarya, they do contain http
RNA polymerase. Eukarya have three only two soluble factors (TATA bind- hhiosmtoonleosg yt hwati tshh atrhee pnruimclaeoryso smeqeu ecnocree s://ac
different RNA polymerases, whereas ing protein [TBP] and transcription histones of eukaryotes. Archaeal his- ad
e
bacteria have a single RNA poly- factor B [TFB], which is related to tone-DNA complexes protect approxi- m
merase enzyme that is responsible the eukaryal transcription factor mately 60 base pairs of DNA from ic.o
u
for transcribing all mRNAs (although TFIIB; Bell and Jackson 1998). Ho- nuclease digestion and resemble the p
the specificity of this enzyme for mologues of the eukaryotic transcrip- structure formed by the (H3 + H4)2 .com
different promoters can be altered tion factors TBP and TFIIB have been histone tetramer at the center of the /b
by changing one of the component identified in several archaea (Langer eukaryal nucleosome. Like eukaryal ios
c
subunits, the sigma factor). Like bac- et al. 1995, Reeve et al. 1997). The nucleosomes, archaeal nucleosome- ie
n
teria, archaea possess a single RNA archaeal promoter is similar in se- related structures that are formed in ce
ppoollyymmeerraassee , rbeuset mthbele sa rtchhoaseea l oRf NeuA- equukeanrcyea la ndT AreTlaAti veb opxo-sciotinotna intion gt he v(ii.ter.o, tahsesyem rebcleo ganti zper enfeurcrleedo sloomcaet iopnos- /article
karyotes in multi-subunit complex- RNA polymerase II promoter. The sitioning signals; Reeve et al. 1997, -a
b
titeyr iaanl dp aserqaduiegnmce ohf omologys. uTbuhne ibtsa ci-s TseAqTueAn cbeo x( tihse a ccoonnsseenrsvuesd nisu calcetoutaidlley Parecrheiareaa la nhdi sRtoeneevse w19r9a8p) . DHNoAw evine r,a strac
not seen with the aa(cid:127)2r3c1h3a'eoa l enzyme. TATA[A/T]A) located approxi- right-handed superhelix in vitro, t/49
Eight to 13 subunits have been iden- mately 20-30 bases upstream of the rather than a left-handed superhelix /7/5
tified in various archaeal RNA poly- mRNA startpoint and is common to as in the eukaryal nucleosome. The 30
merases; these subunits have more almost all eukaryotic promoters. It handedness of the archaeal DNA /23
sequence similarity to eukaryal com- is critical for steps needed for tran- superhelix in vivo is unknown. The 67
0
ponents than to bacterial ones. For scription initiation, such as RNA presence of histones in archaea may 4 b
example, the RNA polymerase of polymerase binding to the promoter. explain the presence of eukaryotic- y g
Sulfolobus acidocaldarius consists of In the Archaea, the TATA box of the like transcription factors, which may ue
13 different single-copy subunits, 9 eukaryotic promoter is replaced by a be needed to allow access of RNA st o
of which are homologous to sub- "box A" sequence (TTTA[A/T]A) lo- polymerase to "buried" promoters. n 0
units of the eukaryotic RNA poly- cated approximately 27 bp upstream Of the information processing sys- 5 A
mRNerAa sep.o lTymhee rtahsree es ulbaurgneitsst sahracrhea esae-l froAmr cthhaee tarla hnoscmroiplotigoune ss toafr tt hseit me. ini- tmemosst, utnriavnesrlsaatli,o nw itshe ecmesr tation bheo mtho-e pril 2
0
quence homology with the largest mal eukaryal transcription initiation logues common to all three domains. 19
subunits of the eukaryotic RNA poly- system may be responsible, and all However, clear and important dif-
merase (Keeling and Doolittle 1995). that is needed, for transcription ini- ferences still separate the domains.
The picture of archaeal transcrip- tiation in archaea. Schematic dia- For example, bacteria use a Shine-
tion that is coming into focus resembles grams reflecting the relative com- Delgarno sequence located just up-
that of the Eukarya, especially in terms plexity of the transcription complex stream of the translation start site to
of promoter recognition and the ac- at a promoter are shown for the identify the initiation codon. This
tual initiation of transcription, al- Bacteria, Archaea, and Eukarya in short sequence of nucleotides is
beit on a simpler scale (Keeling and Figure 2. Remarkably, substituting complementary to a sequence in the
Doolittle 1995). The main difference yeast or human TBPs for the archaeal end of the 16S ribosomal RNA and
lies in the initiation of transcription, TBP in an archaeal in vitro transcrip- helps position the ribosome for the
which in archaea appears to require tional system has demonstrated that start of translation. Eukaryotes, by
536 BioScience Vol. 49 No. 7
contrast, use a scanning mechanism gella are coupled to a chemotaxis bacteria binds to the flagellar switch
to locate the initiator codon. In system, which allows the cells to to change the rotation of the bacte-
archaea, a mixture of the bacterial sense their environment and move rial flagellum, is found in several
and eukaryal approaches is used. The toward a favorable environment or motile archaea; however, no homo-
mRNAs of archaea, like those of away from an unfavorable environ- logue of the switch protein itself has
bacteria, are not capped at their 5' ment. Bacterial flagella consist of been found in archaea. Archaea and
ends, but not all archaeal genes have three distinct parts: a basal body Bacteria seem to have developed com-
obvious Shine-Delgarno sequences; constructed of a series of rings and a pletely different ways of assembling
moreover, archaea possess several rod that is embedded in the cell enve- a flagellum, although the chemotaxis
eukaryal-like translation initiation lope; a filament composed of thou- system that interacts with the flagel-
factors (Brown and Doolittle 1997). sands of subunits of the major fla- lum is clearly conserved in both do-
Of 11 putative initiation factor pro- gella protein, flagellin; and a hook mains (Faguy and Jarrell 1999).
teins identified in the M. jannaschii that acts as a flexible coupling of the
genome, 10 are homologous to basal body to the filament. Cytoskeletal structure. It has been
eukaryal initiation factors. In regard Most major subgroupings of suggested for many years that Do
to the archaeal ribosome, the rRNA archaea, including thermophiles, hy- Sulfolobus, Thermoplasma, and wn
components are of the bacterial size perthermophiles, extreme halophiles, other archaea that lack a rigid cell loa
d
(23S, 16S, and 5S), whereas the pro- and thermoacidophiles, have flagella wall but maintain an irregular shape ed
tein components are an amalgam of that superficially resemble bacterial must have an internal cytoskeleton. fro
bacterial homologues, eukaryal ho- flagella. However, we have been However, most previous work looked m
h
mologues, and archaeal-specific pro- studying archaeal flagella for several unsuccessfully for archaeal homo- ttp
tineign sg. enAerrcahllaye alf olplorwe-sr RtNhAe bparcotceersisa-l yoethaerrs s,a tnhda t hflaavgee llpar ocpomospedos, itiaosn haanvde plorgouteeisn s ofs ucehu kaasr yaocttiicn , cmyytoosskine,l etaonnd s://ac
a
model. However, protein homo- assembly in archaea are likely to be tubulin. It now appears that a cyto- de
logues of eukaryal fibrillarin have distinct from those of bacterial fla- skeleton does exist but that it is com- mic
been identified in Methanococcus gella (Jarrell et al. 1996). Three key posed of chaperonins. Chaperonins, .o
u
vannielii and other archaea. In the pieces of evidence lead to this hy- which are found in all three domains p.c
Eukarya, small nucleolar RNAs pothesis. First, archaeal flagellins are of life, are high molecular mass com- om
(snoRNAs) bind to fibrillarin and made with leader peptides that are plexes that are identified by a typical /b
direct rRNA processing and methyl- cleaved before the flagellins are in- "double-ring" appearance in elec- ios
c
ation (Dennis 1997). At least some corporated into the flagella filament, tron micrographs and by sequence ien
archaea thus appear to possess the whereas bacterial flagellins are never similarity in their constituent pro- ce
rbRegNinAn ipnrgosc eossfi nag esuykstaermya. l-like pre- mmaadney waritchh aleeaald efrla gpeelplitnids esa. reS egcloyncod-, tceoinnsst.i tuInen btsa ctearriae a6n0d kaDrc hpareoat,e itnhse /article
Comparative studies of similar sylated; in the archaeal species known to be heat-shock proteins. -ab
processes in different organisms of- Halobacterium salinarum, this modi- Consequently, their role has been stra
ttehne ofvoestrearl l ap rboectetsesr tuhnadne trhsatat nodbitnagin eodf pfilcaastmioinc mocecmubrsr aonuet, said leo caotfi otnh et hcaytt oi-s ldeecfuinlaerd fcohra pae rdoencea.d e Uansd oenr e noofr mmaol- ct/49
solely by examination of a single difficult to reconcile with the bacte- conditions, they bind to newly syn- /7/5
organism. In their transcription and rial mode of flagella assembly, in thesized proteins and aid in proper 30
translation systems, the Archaea of- which the flagellins pass through the folding of the protein, whereas un- /23
6
fer an unusual mix of mainly rudi- hollow filament and emerge for in- der heat-shock conditions they bind 70
mentary eukaryotic features with corporation at the distal tip. to damaged proteins to prevent them 4 b
some bacterial character. Besides its Finally, there is no sequence from aggregating and, in some cases, y g
intrinsic intellectual appeal, study of similarity between archaeal flagellins to restore, with the aid of ATP hy- ue
s
the rudimentary archaeal transcrip- and bacterial flagellins. Analysis of drolysis, proper function when con- t o
tion and translation systems provides the complete genomes of M. jannaschii, ditions again became favorable. n 0
a simpler model with which to an- A. fulgidus, and P. horikoshii, all flag- Purified chaperonins from the 5 A
stiwoenrs ssotimll er eomf atihnein mg aanbyo ubta sthice qmuoerse- uelnlaiqteude starrucchtauerae, thdart ivise thhe oamrceh atehael ainr cthhaee opnr eSseunlfcoel oobfu sm afogrnmes ifuimlam ieonntss, pril 20
complex eukaryal systems. flagellum. No genes in the complete nucleotides, and "buffers" made 19
genomes of any of these archaea are from cell extracts at physiological
Flagella and chemotaxis. A signifi- homologous to any bacterial genes temperatures (Trent et al. 1997).
cant fraction of the archaeal genome encoding flagella structural proteins- From their estimate of the number of
has no counterpart in either bacte- there are no homologues of genes for chaperonins per cell (approximately
rial or eukaryal genomes. One unique flagellins, hook proteins, rod proteins, 4600), Trent et al. (1997) hypoth-
aspect of archaea that is highlighted ring proteins, or switch proteins-even esized that the chaperonins may form
by the complete genome sequence is though both A. fulgidus and P. a filament network in the cells-that
flagellation. Flagella are the usual horikoshii have homologues of nu- is, a cytoskeleton. An extensive net-
organelles for motility in prokary- merous bacterial chemotaxis genes, work of filaments could traverse the
otes. They act to propel the bacterial many of which control flagellar ac- cell 100 times if all chaperonins were
cell by rotating like a propeller. Fla- tivity. For example, CheY, which in assembled into filaments.
July 1999 537
Unusual archaeal virus. Prokaryotic replaced by enzymes from hyper- amylase from moderately thermo-
viruses, or phages, have been studied thermophilic archaea, including Pwo philic bacterial species is used to
intensely for decades, and viruses have (from Pyrococcus woesei), Pfu (from convert cornstarch to high-fructose
been found to infect virtually all major Pyrococcus furiosus), Tli (from T. corn syrup. The last step is an isomer-
groups of bacteria. Viruses vary enor- litoralis), and others sold under ization of glucose to fructose using
mously in size and shape, from fila- tradenames such as VentTM (from T. glucose isomerase, but the yield of
mentous to tailed. In all cases, how- litoralis) and DeepVentTM(f rom Pyro- fructose at 60 'C is poor, and the
ever, the nucleic acid of prokaryotic coccus sp.). An advantage of the syrup must be further enriched with
viruses had been identified as either archaeal enzymes is that, unlike Taq, fructose. Raising the temperature at
DNA or RNA, but never both. Re- they have proofreading abilities that which this step is carried out to 95
cently, however, Witte et al. (1997) result in a much lower error rate in the 'C, which would be possible with a
isolated a phage that morphologi- PCR product. In addition, these en- hyperthermophilic enzyme equiva-
cally resembles bacteriophage T4 of zymes give rise to blunt-end PCR lent, would favor fructose produc-
E. coli but infects the haloalkaliphilic products that can be easily inserted in tion and avoid the enrichment step
archaeon Natronobacterium magadii. many cloning vectors. Taq products, (Adams and Kelly 1995). A third Do
Examination of this phage demon- by contrast, often have a 3' overhang, example is the use of a-amylase in wn
strated, for the first time, the pres- necessitating further processing to starch processing. The a-amylase loa
d
ence of both RNA and DNA in a make the end blunt or the use of from P. furiosus is almost twice as e
d
mature virion. The DNA is present special vectors with a complemen- active at 98 'C than the currently fro
as a 55 kb double-stranded linear frag- tary overhang for efficient cloning. used commercial enzyme from Bacil- m
ment, but there are also several small A few restriction enzymes of lus licheniformis (Zeikus et al. 1998). http
RsizNeA r aspnegcei.e Ts ihne t hroel 8e 0o-7f 0t0h-en uRcNleAo tisdpee - karectehda eaals owriegliln, asurec hn oaws bTehinaIg fmroamr- Ipno teandtdiaitli,o n etnoz ytmheeisr bfirootmec hnhoylpoegry- s://ac
cies is not yet clear, although Witte et Thermoplasma acidophilum. An- thermophilic archaea have been stud- ad
e
al. (1997) suggest that they could be other archaeal enzyme marketed ied for clues to understand the elu- m
ic
involved in DNA packaging. commercially is PI-PspI. This enzyme sive basis of protein stability at high .o
u
is an intein-encoded endonuclease temperatures. p
.c
Biotechnology that has a specificity of 8-10 bases. Some biotech companies have om
Additional archaeal enzymes may taken a different approach to ex- /b
The majority of archaea that have soon be ready for use in other appli- tremophile enzymes by directly iso- ios
c
been identified thus far are ex- cations. For instance, a thermostable lating the DNA that encodes for use- ie
n
tremophiles; that is, they grow at ligase for the ligase chain reaction ful extremophilic enzymes without ce
ehxigtrhe msaeslt ,o fc otenmdipteiornastu rue nodre pr Hw ohric ihn v(aonlv easm tphlief iclaigtaiotnio n moeft hotwd o thseatts inof- athcetumaslelylv esi.s oDlaitvienrgs a Cthoer poorragtainoins mrse - /article
enzymes of typical bacteria are poorly adjacent oligonucleotides) would be cently signed an agreement with -a
b
active or totally inactive. Since the of obvious benefit because the liga- Yellowstone National Park, as well stra
early discovery of hyperthermo- tion must be carried out near the as with several countries, to obtain c
philes, scientists have envisioned the melting temperature of the DNA, biological samples likely to be rich in t/49
use of archaeal enzymes as a boon to and the enzyme must be stable dur- extremophiles. In a procedure termed /7/5
many industrial processes; for ex- ing the dissociation step that follows "bioprospecting," the company 30
ample, thermostable bacterial en- (which is carried out at 92 *C). Cur- clones the total DNA from these /23
6
zymes could be replaced by the much rently, a ligase from T. aquaticus is samples into expression vectors and 7
0
more stable equivalent enzyme iso- used, but a more stable equivalent then tests the clones for a wide vari- 4 b
lated from a hyperthermophilic should be available from any of a ety of enzymatic activities. For ex- y g
archaeon. Although such replace- number of hyperthermophilic archaea. ample, examination of the resulting ue
ments have been slow to occur (the In addition to these "niche" in- clones has yielded sequences that st o
sheer amounts of enzyme required dustry applications, other industries encode proteins with lipolytic and n 0
for some industrial applications are that require bulk amounts of en- proteolytic activity at high tempera- 5 A
jaurscth aneaolt enyzeytm epsr)a, ctthicea fl utufroer fomr othste zinydmuesst riaerse f ocrle caormlyp apnrioefsi tapblalen nitnagrg teot teurrael .d Dififveerresnat Ckoitrsp .o nf o"wC lmonaerzkyemts esse.v"- pril 2
0
use of extremophile enzymes (includ- market archaeal enzymes. In these Because the actual organisms that 19
ing those from many archaea) is still industries, enzyme use is estimated yield the clones are not isolated, the
bright, with several processes in the in the billions of dollars worldwide. origin of the DNA is generally not
development stages. Such industries include the food in- known. However, given the nature
dustry, in which hydrolases from of the habitats being examined (e.g.,
Commercial archaeal enzymes. One hyperthermophiles could process hot springs in Yellowstone Park), it
outstanding example of an archaeon food (e.g., hydrolyze fats) at tem- seems likely that at least some if not
enzyme replacing its bacterial coun- peratures well above those that can a majority of the "Clonezymes" may
terpart has been in PCR. In many lead to bacterial contamination prob- originate from archaea.
PCR applications, Taq DNA poly- lems. Another example is glucose
merase (from the thermophilic bac- isomerase, which is used in the manu- Archaeal liposomes and vaccine de-
terium Thermus aquaticus) has been facture of corn syrup. Currently, livery systems. Study of the Archaea
538 BioScience Vol. 49 No. 7
may have far-reaching implications Figure 2. The tran-
for the cosmetic and pharmaceutical scription complex at
industries. Archaea have unusual a promoter in Bacte- RNA pol
ether-linked lipids that could replace ria, Archaea, and
conventional ester-linked lipids in Eukarya.I n Bacteria, Bacteria
liposomes. Archaeal lipids are iso- the sigma factor sub- TTACA-35 TA-1T AAT
unit of the RNA poly-
prenoids linked to glycerol through merase is responsible -35 -10 +1
ether bonds. The ether linkage in for recognizing the
these lipids is a diagnostic feature of conserved -10 and
archaea because both bacterial and -35 regionso f thep ro-
eukaryal lipids have ester links. The moter. In Archaea,
ether link is more resistant to oxida- transcriptionr equires RNA pol
tion and high temperature than the two solublee ukaryal- TBP
ester link, making the archaeal lipid like factors (TBPa nd Archaea
membranes better suited to the ex- TFB), and the RNA D
treme environments that are often polymeraser esembles -30 +1 ow
that of Eukaryai n its n
home to the various archaeal mem- multisubunit com- loa
bers (van de Vossenberg et al. 1998). plexity. The eukaryal de
Tsohme epsr foodru vctaicocni noe f amndor de rsutga bdleel ilviperoy- tinravnoslvcersip htoiomncoo lmogpuleexs d from
abreein agm sotnugd itehde (pSopsrsiobtlte eat papll.i c1a9ti9o7n)s. oscf rtihpeti oanrc fhaacetoarl tsr, aans- RNA pol https
Archaeosomes (liposomes made with well as several other ://a
archaeal lipids) are more stable than components in addi- Eukarya cad
conventional liposomes to tempera- tion to the complex TATA30 +1 em
ture, to exposure to phopholipase RNA polymerase. -30 +1 ic.o
A2, to incubation with serum, and, up
to some extent, to exposure to bile cluding gvpA and gvpC, which en- for the other prokaryotic group, the .co
m
salts (Sprott et al. 1996). This en- code major structural proteins Bacteria. The days of the Archaea /b
hanced stability may lead to the use (Pfeifer et al. 1997). When mice were being considered as just "odd bacte- ios
of archaeosomes as an effective oral injected with gas vesicles cross-linked ria" adapted to living in extreme cie
vaccine delivery system. to a trinitrophenyl group, they environments are long past. In the nc
e
In addition, archaeosomes may be mounted a long-term, high-level im- past few years, information on the /a
more readily taken up by phagocytic mune response (DasSarma 1999). isolation, characterization, descrip- rtic
le
cells than conventional liposomes. When a peptide-encoding sequence tion, and applications of archaea has -a
In mice, a much higher humoral im- was genetically engineered into the mushroomed. For example, mainly bs
mune response occurs to protein GvpC protein and injected, it too as a result of the extremophile initia- trac
antigens encapsulated in archaeo- was presented effectively to the tive supported by the European t/4
9
somes than in conventional lipo- mouse immune system. An exciting Union, major advances in the growth, /7
somes, even comparable to Freund's possibility is that it may be possible study, and biotechnological applica- /53
0
adjuvant. A related discovery is the to incorporate HIV epitopes into the tions of hyperthermophilic archaea /2
3
demonstration that S layers (i.e., pro- GvpC protein to enable large-scale have been achieved (Aguilar et al. 67
tein or glycoprotein layers that often production of a safe, effective, and 1998). These advances include the 04
form the sole wall component exter- stable HIV vaccine. growth of hyperthermophiles to high by
nal to the cytoplasmic membrane in densities in dialysis membrane gu
e
saormchease a)w ciathn repchroyssptahlolilziep idosn to liapnod- Fonu ttuhree Ar erscehaarecah baniodr etahcet ordse vealnodp mgaens-tl ifto f baio rceeallc-tforrese st on
archaeal lipids to create something transcription system for hyper- 05
similar to an archaeal envelope Study of the Archaea for the past two thermophiles (at 90 *C). Further- Ap
(Sleytr and Sara 1997). The recrys- decades has led to a number of fun- more, emerging technologies con- ril 2
tallized S-layer proteins can then be damental discoveries that have tinue to allow scientists to search 01
9
cross-linked and used for the cova- stretched the boundaries that are previously inaccessible habitats, re-
lent attachment of other molecules. thought to limit life and have pro- vealing archaeal (and bacterial) di-
In this way they can be used as vac- vided scientists with valuable tools versity in such places as the Mariana
cine carriers, for example. for studying early evolution as well Trench sediment at a depth of 11,000
Another interesting application of as organisms with rich potential for meters (Deming 1998).
the Archaea is the use of gas vesicles biotechnological applications. Work- These and other advances bode
as antigen display vehicles. Certain ers in the field are accustomed to well for the increased role that
extreme halophiles use gas vesicles reading papers on the Archaea that hyperthermophilic and other archaea
as flotation devices. The structure time and again describe various as- will undoubtedly play in the future
and assembly of the gas vesicles is pects of archaea as novel, unique, of biotechnology. Other goals that
complex, involving 13-14 genes, in- and unlike that previously described should be accessible in the near fu-
July 1999 539