why archaea are important

18 Pages·2011·0.64 MB·English

Microbiology(2011),157,919–936 DOI10.1099/mic.0.047837-0
Major players on the microbial stage: why archaea
Review
are important
Ken F. Jarrell,1 Alison D. Walters,2 Chitvan Bochiwal,2 Juliet M. Borgia,2
Thomas Dickinson3 and James P. J. Chong2
Correspondence 1DepartmentofMicrobiologyandImmunology,Queen’sUniversity,Kingston,ONK7L3N6,Canada
KenF.Jarrell
2Department ofBiology, University of York,Wentworth Way, Heslington, YorkYO105DD, UK
[email protected]
JamesP.J.Chong 3Sheffield Hallam University, CityCampus, Howard Street, Sheffield S1 1WB,UK
[email protected]
Asmicrobiologyundergoesarenaissance,fuelledinpartbydevelopmentsinnewsequencing
technologies,themassivediversityandabundanceofmicrobesbecomesyetmoreobvious.The
Archaeahavetraditionallybeenperceivedasaminorgroupoforganismsforcedtoevolveinto
environmentalnichesnotoccupiedbytheirmore‘successful’and‘vigorous’counterparts,the
bacteria.Hereweoutlinesomeoftheevidencegatheredbyanincreasinglylargeandproductive
groupofscientiststhatdemonstratesnotonlythattheArchaeacontributesignificantlytoglobal
nutrientcycling,butalsothattheycompetesuccessfullyin‘mainstream’environments.Recentdata
suggestthattheArchaeaprovidethemajorroutesforammoniaoxidationintheenvironment.
Archaeaalsohavehugeeconomicpotentialthattodatehasonlybeenfullyrealizedintheproduction
ofthermostablepolymerases.Archaeahavefurnisheduswithkeyparadigmsforunderstanding
fundamentallyconservedprocessesacrossalldomainsoflife.Inaddition,theyhaveprovided
numerousexemplarsofnovelbiologicalmechanismsthatprovideuswithamuchbroaderviewof
theformsthatlifecantakeandthewayinwhichmicro-organismscaninteractwithotherspecies.
Thatthisinformationhasbeengarneredinarelativelyshortperiodoftime,andappearstorepresent
onlyasmallproportionofwhattheArchaeahavetooffer,shouldprovidefurtherincentivesto
microbiologiststoinvestigatetheunderlyingbiologyofthisfascinatingdomain.
Introduction extremophilicodditiestoorganismsofuniversalimportance
and have been used to elucidate fundamental biological
When Carl Woese first proposed that the tree of life
questions.Studiesofarchaeahaveproventobeenormously
encompassed three distinct lineages, including a new
fruitful: unique traits found nowhere else in nature have
prokaryotic one initially designated Archaebacteria (later
been revealed in archaea, and there are many instances of
Archaea), it would have been hard to imagine the broad
archaeal processes that combine a mosaic of bacterial and
spectrum of novel findings that study of these remarkable
eukaryalfeatureswithuniquearchaealonestocreateathird
organisms would bring to light. Indeed, in their ground-
functioning mechanism. Archaea are useful model systems
breakingpaper,inwhichWoese&Fox(1977)proposedthe
forprocessesinbotheukaryaandbacteria,andtheirmajor
third Kingdom [later Domain (Woese et al., 1990)] of
roles in various ecosystems, not just extremophilic ones,
Archaebacteria, they were represented solely by the metha-
continuetobeuncovered.Theyhaveusefulbiotechnology/
nogens.Thesewerequicklysupplementedbytheadditionof
commercialapplications,andmayyetprovetoaffecthuman
extreme halophiles and thermoacidophiles (Magrum et al.,
health in significant ways. There is continued study and
1978; Woese et al., 1978), but at that time one of the
debateabouttheirroleinevolutionand,duetotheirability
characteristics of archaebacteria was ‘their occurrence only
tothriveatthelimitsoflifeonEarth,thepossiblepresence
inunusualhabitats’.Bythe1980s,manynewhyperthermo-
of organisms that resemble the archaea in extraterrestrial
philicorganismsthatgrewoptimallyabove80 uC,andoften
environments.Inthisreview,wehighlightsomeofthemany
optimallyabove100 uC,hadbeenisolatedandshownalsoto
keyfindingsinarchaealresearch.
bearchaea(Tuetal.,1982;Zilligetal.,1981).Laterstudies
showed by molecular rather than culture methods that
Archaea and evolution
archaea are cosmopolitan, and in certain habitats, such as
The third Domain, Archaea
the oceans, are significant contributors to the biomass
(DeLong & Pace, 2001; Olsen et al., 1986; Robertson et al., In 1977, Woese and Fox proposed the Archaea as a third
2005). Over the years, archaea have gone from microbial domain of life based on small subunit rRNA (ssrRNA)
047837G2011SGM PrintedinGreatBritain 919
K.F.Jarrellandothers
sequence cataloguing. This represented a profound para- Archaea and eukarya
digm shift from the dichotomy of eukaryotic and
Although a close evolutionary relationship between
prokaryotic life forms that had previously existed. Not
eukarya and archaea is widely accepted, the origin of the
only does archaeal ssrRNA differ in primary sequence
Domain Eukarya is one of the most controversial areas of
from that of the other two domains (Bacteria and
evolutionary biology (Embley & Martin, 2006). Variations
Eukarya) but also each domain was shown to have
of two broad theories on the origin of eukaryotic cells
specific ‘signatures’ in this conserved molecule, both in
involvingtheArchaeahavebeenpresented.Thefirstposits
primary sequence and in the secondary or tertiary
that the Archaea and Eukarya shared an ancient common
structure (Roberts et al., 2008; Winker & Woese, 1991;
ancestor to the exclusion of the bacteria, while the second
Woese et al., 1990). Correlations between ssrRNA
is based upon the fusion of an archaeon with a bacterium
signatures and ribosomal protein signatures were found,
(Forterre, 2010; Gribaldo et al., 2010). Many theories
indicating that the RNA component and the domain-
propose an archaeal origin of the eukaryotic nucleus in a
specific and universal ribosomal proteins evolved in
fusion event with a bacterium, with the archaeal endo-
tandem (Roberts et al., 2008). 16S rRNA sequences were
symbiont later developing into a nucleus, although the
usedtodesigndomain-specificoligonucleotidesforuseas
archaeal and bacterial partners in the event have varied
probes (Burggraf et al., 1994; Embley et al., 1992) and
(Forterre, 2010). Most recently, the archaeal partner has
PCR primers (Hugenholtz et al., 1998) that have been
been suggested to be a member of the Thaumarchaeota,
used to determine the presence of archaea in environ-
since these organisms possess a number of eukaryotic
ments even when the organisms themselves remained
featuresnotfoundinotherarchaealphyla(Forterre,2010).
unculturable.
However, other models suggest that the nucleus is not
In addition to ssrRNA signatures, evidence for an archaeal derived from bacteria or archaea (Pace, 2006).
‘genomic signature’ has been presented. The archaeal
Horizontal gene transfer (HGT) is also cited as a major
genomic signature presented by Graham et al. (2000) is a
mechanism to explain how life on Earth evolved from one
set of over 350 genes found in archaea but lacking
universal common ancestor. Evidence exists for HGT
homologuesineitherbacteriaoreukaryotes.Thisrelatively
among members of the same domain and across domains
high number of archaeal-specific genes (most of which
(Boto, 2010), but its importance in the evolution of more
have no known function as yet) represents about 15% of
complex organisms is disputed (Koonin & Wolf, 2009).
archaeal genomes and supports the belief that the archaea
Significant HGT appears to have occurred between
are an ancient lineage of major evolutionary importance
archaeal and bacterial hyperthermophiles, as a much
(Graham et al., 2000). While this archaeal genome
higher percentage of genes from the bacterial hyperther-
signature was based almost entirely on euryarchaeota
mophiles Thermotoga and Aquifex appear to be archaea-
sequencedata,thesubsequentavailabilityofmorearchaeal
derived than those of mesophilic bacteria (Aravind et al.,
genome sequences has led to the identification of
1998;Nelsonetal.,1999).Awell-studied example ofHGT
numerous signature insertion/deletions (indels) and sig-
is reverse gyrase, which is found in all hyperthermophiles,
nature proteins in Crenarchaeota and the proposed new
suggestingacriticalroleforthisenzymeinorganismswith
Phylum Thaumarchaeota [previously classified as low-
high temperature growth optima (Brochier-Armanet &
temperature marine crenarchaeotes (Gupta & Shami,
Forterre, 2006). It has been argued that reverse gyrase was
2011)]. The development of large numbers of signature
likely transferred via one or two ancient HGT events from
patterns for archaeal phyla should greatly assist future
archaea to bacteria (Brochier-Armanet & Forterre, 2006).
classification, with the large number of Thaumarchaeota
More recent analyses support the notion that HGT from
signatureslendingsupporttotheirclassification asanovel
bacteria to archaea has actually occurred more often than
phylum.
transfer from archaea to bacteria (Kanhere & Vingron,
The extremophilic properties of many archaea have made 2009).
themafavouritestartingpointfortheoriesconcerninghow
life may have evolved in the hostile conditions of early
Archaea and extraterrestrial life
Earth.Stetter(2006)hassuggestedthatonlyhyperthermo-
philes, which were likely anaerobic chemolithoautotrophs As many archaea have been found at the limits to life on
(Berg et al., 2010), could have inhabited the early hot this planet, they have often been proposed to resemble
anaerobic Earth, and that they may have been present as what life may be like if found outside our planet. The
early as 3.9 Gyr ago. This would be consistent with the nature of Earth-like organisms that could exist on other
abilities of many extant archaea to thrive in extreme planetshasvaried,withmethanogensoftenmentioneddue
thermal environments, such as hydrothermal vents to their adaptation to anaerobic niches with little or no
(Auguet et al., 2010). This notion is also supported by organic carbon (Moissl-Eichinger, 2011), and especially
the location of hyperthermophiles as short, deep branches with respect to the possible biogenic formation of the
near the root of the tree of life, although other views methane detected on Mars (Formisano et al., 2004;
suggest that the Archaea evolved relatively recently Mumma et al., 2009; Sanderson, 2010). Some experiments
(Cavalier-Smith, 2006). suggest that terrestrial methanogens could survive under
920 Microbiology157
Whyarchaeaareimportant
Mars-like conditions (Chastain & Kral, 2010; Kendrick & layer of murein (as in Gram-positives) or murein plus an
Kral, 2006). It has recently been suggested that methane- outer membrane (as in Gram-negatives). The S-layers of
oxidizing archaea (anaerobic methane-oxidizing archaea; archaeahaveahistoricplaceinglycobiology,astheS-layer
ANME)maybeabletousethemethaneonMars,whatever of Halobacterium salinarum (cell surface glycoprotein;
its source, as a carbon and energy source, since these CSG) was the first prokaryotic protein to be shown to be
organisms have been detected in hypersaline permafrost glycosylated (Mescher & Strominger, 1976). Until that
methaneseepsonEarth(Niederbergeretal.,2010).Landis time, this post-translational modification was thought to
(2001) has argued that extreme halophiles may be present be restricted to eukaryotic cells.
on Mars and surviving trapped in salt crystals, where it is
known that they may persist, essentially indefinitely, on
Unusual appendages
Earth (McGenity et al., 2000).
Archaea, like bacteria, may have a variety of appendages
extending from the cell surface. Several appear to be
Unique structural features of archaea
unique to archaea (Fig. 1), while others, such as flagella
Cell envelopes and pili, appear superficially like organelles in bacteria
The Archaea have long been known to contain unusual buthavearchaea-uniquefeatures(Ellenetal.,2010;Nget
cell wall structures and components. Indeed, one of the al., 2008). Among these features are the grappling hook
first major distinguishing features of archaea used to appendages called hami (Fig. 1a, b), found in large
separate them from bacteria was the lack of murein in abundanceonthesurfaceofaeuryarchaeondiscoveredin
their cell envelopes (Woese et al., 1978). The cell walls of marshes in Germany (Moissl et al., 2005). A second are
the various groups of archaea are chemically and the hollow tubes, called cannulae, which connect cells of
structurally diverse. Murein is found almost ubiquitously the hyperthermophile Pyrodictium abyssi (Fig. 1c)
in bacterial cell walls but never in archaea, although some (Nickell et al., 2003). Among the appendages found in
methanogenic archaea do contain a related, but archaeal- archaea that resemble bacterial counterparts, the best
specific polymer, called pseudomurein (Kandler & Ko¨nig, studied are archaeal flagella (Jarrell & McBride, 2008;
1978; Ko¨nig et al., 1989). A very common wall type in Thomas et al., 2001). These differ fundamentally from
archaea isonenever foundinthebacterialdomain, where their bacterial namesakes, with genetic and structural
the sole wall component lying outside the cytoplasmic evidence suggesting that archaeal flagella are related to
membrane is a two-dimensional array of protein or bacterial type IV pili, organelles that mediate the surface
glycoprotein termed the S-layer (Sleytr & Beveridge, motility called twitching (Ng et al., 2006). Recent work
1999). Many bacteria have S-layers as their external on type IV-like pili of archaea has shown that the
envelope component, but bacterial S-layers are always structureisunlikethatofanybacterialpilusyetdescribed
separated from the cytoplasmic membrane by at least a (Wang et al., 2008).
Fig.1.Unusualappendagesofselectedarchaea.(a)UltrastructureofhamifromtheSM1euryarchaeon;negativestaining.Bar,
100nm.Electronmicrographsofgrapplinghooks,locatedatthedistalendsofthehami.Arrowheadsindicatelocationofthe
barbs.ReprintedfromMoissletal.(2005)withpermission.(b)ElectronmicrographofhighlevelstructuredSM1hami.Thehami
showprickles(blackarrowheads)andgrapplinghooks(whitearrowheads).ReprintedfromMoissletal.(2005)withpermission.
(c)ScanningelectronmicrographofpartofanetworkofPyrodictiumcellsandcannulae,withtubulesinaregulararray.Bar,
1mm.ReprintedfromRiegeretal.(1995)withpermission.
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K.F.Jarrellandothers
Archaeal ether-linked lipids include: Methanospirillum hungatei, covered with a pro-
teinaceoussheathcomposedofindividualhoops,andwith
Anotherfundamentaltraitidentifiedearlyinthestudyofthe
complex multilayered spacer and end plugs separating
Domain Archaea was the presence of ether-linked lipids in
individual cells within chains (Fig. 2a) (Beveridge et al.,
the cytoplasmic membrane (Woese, 2004; Zillig, 1991).
Phospholipids in the other two domains consist of linear 1985, 1991); the rectangular, ultrathin (as thin as 0.1 mm
thickness)Haloquadratumwalsbyi(Fig.2b),whichappears
fatty acids ester-linked to a glycerol backbone. Archaeal
cytoplasmicmembranesaretypicallycomposedofdiphyta- to divide at right angles, producing the appearance of
nylglycerol diethers (containing phytanyl chains consisting sheetsofpostagestamps(Burnsetal.,2007;Walsby,2005);
of20carbons)whichformalipidbilayer,althoughinsome and Thermoproteus tenax, one of the first hyperthermo-
cases, such as those of some thermoacidophiles, the philesisolated,whichhastheunusualmorphologyoflong,
membranes can consist of diphytanyldiglycerol tetraethers thin, aseptate rods which have true branching and often
(phytanylchainsof40carbons)whichspanthecytoplasmic end in spherical bodies to give a golf club appearance
membraneinaverystablelipidmonolayer(Matsumietal., (Zillig et al., 1981). However, the most unusual archaeon
2011).Mixturesofthetwotypescanbefoundinindividual may well be the hyperthermophilic Ignicoccus hospitalis. It
species,andothervariations,suchascyclopentane-contain- possesses the smallest genome of any known free-living
ing lipids, are also found. Besides these fundamental organism,atonly 1.3 Mb(Podaretal.,2008).Inaddition,
structuraldifferences,thestereochemistryofarchaeallipids it is the only cultivated archaeon known to have two
is different from those of both bacteria and eukarya. In membranes, and has an enormous intermembrane space,
archaea, 2,3-sn-glycerol backbones are used, while in the with a volume larger than that of the cytoplasm, filled
othertwodomains,1,2-sn-glycerolbackbonesareemployed with unusual vesicles (Fig. 2c) (Junglas et al., 2008).
(Matsumi et al., 2011). The ether linkage is much more Furthermore, unlike any other known archaeon or bac-
resistantthantheesterlinkagetohydrolysisuponexposure terium, the ATP synthase is localized in the outer
to the extremes of pH and temperature found in many membrane, indicating that the outer membrane is
archaealhabitats(vandeVossenbergetal.,1998),anditwas energized andthat ATPisformedintheperiplasmicspace
originally thought that the unique archaeal lipids were a (Ku¨per et al., 2010), all of which cause us to rethink basic
specific adaptation to extreme environments, before it was tenets about energy generation. I. hospitalis is also one of
realized that these lipids are a defining trait of the entire the components of the only known interaction between
archaealdomain,regardlessoftheirenvironmentalniche. twoarchaealspecies(Huberetal.,2002).Itformsaspecial
interaction with the very small Nanoarchaeum equitans
(about 1%ofthevolumeofEscherichia coli), whichseems
Unusual cell structure
unlikesymbiosis,commensalismorparasitism(Jahnetal.,
The Domain Archaea contains many isolates with extre- 2008). The connection between the two organisms can be
melyunusualstructuralfeatures(Fig.2).Ashortlistwould via unusual structures, including fine fibres at the site of
Fig. 2. Unusual structural features of selected archaea. (a) Thin section of Methanospirillum hungatei showing the unusual
multilayered spacer plugs (large arrowheads). S, sheath; W, cell wall; M, plasma membrane; small arrowheads point out
amorphousmaterialbetweenwallandplugandwithinthecellspacer.Bar,100nm.ReproducedfromSoutham&Beveridge
(1992)withpermission.(b)Phase-contrastlightmicrographsofthesquarearchaeonfromtheSinai.Divisionlinesarevisiblein
somecells(arrows).Bar,10mm.ReproducedfromWalsby(2005)withpermission.(c)UltrathinsectionofI.hospitalisstrain
KIN4/IT showing the large periplasm containing vesicles. Cy, cytoplasm; P, periplasm; V, vesicle; OM, outer membrane; bar,
1mm.ReproducedfromPaperetal.(2007)withpermission.
922 Microbiology157
Whyarchaeaareimportant
contact, or apparently by direct contact of the surfaces of change,independentofthehostcellandexogenousenergy
thetwoorganisms(Burghardtetal.,2009).N.equitansalso sources or cofactors, by forming tails at each end (Ha¨ring
has an extremely small genome of only 490 kb, encoding et al., 2005). Another virus of Acidianus with an
552 genes, the smallest of any exosymbiont (Waters et al., exceptional morphology, AFV1, is a flexible filament with
2003). Other nanosized (,500 nm diameter), uncultured claw-like ends that attach to pili on the surface of target
archaea have been identified, called ARMAN (archaeal cells (Bettstetter et al., 2003).
Richmond Mine acidiphilic nano-organisms), that have
estimated volumes near the theoretical lower limit for life
(0.009–0.04 mm3). ARMAN contain a unique intracellular Unique biochemical features of archaea
tubular structure of unknown composition and function Biochemistry of methanogenesis
that can extend to 200 nm in length (Baker et al., 2010;
Methanogenicarchaeaarestrictanaerobes,usuallyexisting
Comolli et al., 2009).
in complex communities of microbial consortia, vital for
the degradation of complex organic compounds and thus
Novel archaeal virus families forcarboncycling.Methanogensmaketheirlivingthrough
the complex and archaea-unique process of methanogen-
Many viruses that infect various archaeal species also have
esis, which involves a number of unusual cofactors and a
unique structural characteristics. Examination of high-
uniquebiochemicalpathway(DiMarcoetal.,1990;Thauer
temperature biomes, and more recently mesophilic, highly
etal.,2008;Weiss&Thauer,1993).TheconversionofCO
halophilic environments, has led to the identification of a 2
to CH occurs in a well-known step-wise process of
largevarietyofarchaealvirusesthat,bothinultrastructure 4
successive two-electron reductions, with the C group
andinthegeneticmakeupoftheirgenomes,areunlikeany 1
observed in either of the two other domains (Fig. 3) bound to a carrier at each step (Weiss & Thauer, 1993).
(Comeau et al., 2008; Prangishvili et al., 2006a). Genome Threedifferentcarriersareinvolved:methanofuran(MFR),
analysis has revealed that up to 90% of the genes of some tetrahydromethanopterin (H4MPT) and co-enzyme M
of these viruses lack homologues. Indeed, it has been (CoM-SH), with CoM-SH unique to methanogens and
suggested that all three domains of life may have a set of the others found in a limited number of other organisms.
unique dsDNA viruses (Prangishvili et al., 2006b). In Methanogenesis begins with the reduction of CO2 and its
archaeal viruses, many unusual morphotypes have been attachment to MFR, producing formyl-MFR, followed by
reported, including bottle-shaped (ampulla), fusiform, the transfer of the formyl group to H4MPT. A further two
droplet, linear and spherical forms, leading to the reduction steps of formyl-H4MPT generate methylene-
classification of many of these viruses as novel virus H MPT and finally methyl-H MPT. The methyl group is
4 4
families (http://www.ictvonline.org/virusTaxonomy.asp? thentransferredtoCoM-SH,producingmethyl-S-CoM.In
version=2009). One of the more unusual of the archaeal the final stage of methanogenesis, methyl-S-CoM is
viruses is the two-tailed virus (ATV), which is a lytic virus reduced to CH by methyl CoM reductase, an enzyme
4
active on the thermoacidophile Acidianus [75 uC, pH 3 containing the coenzyme F , another factor unique to
430
(Ha¨ringetal.,2005)].ATVisreleasedasataillessfusiform methanogens, as a prosthetic group. The other product of
virus, but then the virus undergoes a morphological the methyl-CoM reductase reaction is a heterodisulfide of
Fig.3.Unusualstructuralfeaturesofselectedarchaealviruses.(a)ElectronmicrographofparticlesofAFV1withtailstructures
intheirnativeconformation,negativelystainedwith3%uranylacetate.Bars,100nm.ReprintedfromBettstetteretal.(2003)
withpermission.(b)ElectronmicrographofAcidianusbottle-shapedvirus(ABV)particlesattachedtoeachotherwiththeirthin
filaments at the broad end. Bar, 100nm. Reprinted from Ha¨ring et al. (2005) with permission. (c) Electron micrograph of
negativelystained(2%uranylacetate)two-tailedvirions.Bar,200nm.ReprintedfromPrangishvilietal.(2006)withpermission.
http://mic.sgmjournals.org 923
K.F.Jarrellandothers
CoM and another unique factor, coenzyme B. The operation of both the semiphosphorylative and nonpho-
heterodisulfide is the substrate for heterodisulfide reduc- sphorylative pathways, as recently suggested for Sulfolobus
tase, which regenerates CoM and coenzyme B. While the andThermoproteus(Reheretal.,2010;Zapartyetal.,2008).
methanogenesis pathway is well described, the steps that Inthesemiphosphorylativeversion,theunusualstepisthe
actuallyleadtonetenergygenerationarestillthesubjectof conversion of 2-keto-3-deoxygluconate (KDG) to 2-keto-
investigation. However, there is now evidence which 3-deoxy-6-phosphogluconate(KDPG)viaphosphorylation
suggests that in hydrogenotrophic methanogens the by KDG kinase before its further conversion to pyruvate
heterodisulfidereductasestep,anexergonicreactionwhich and glyceraldehyde 3-phosphate by KDPG aldolase
appears to drive the initial endogonic step in the pathway, (Verhees et al., 2003). In the nonphosphorylative ED
may occur through a flavin-based electron bifurcation, as variation, a key enzyme is a novel KDG-specific aldolase
suggested by Thauer et al. (2008), likely at the FAD- which cleaves KDG to form pyruvate and glyceraldehydes
containingsubunitintheheterodisulfidereductase(Kaster (Reher et al., 2010). No phosphorylated hexose derivatives
et al., 2011). These two steps have recently been physically are generated, and it is only later in the pathway that
linked in a protein complex isolated from Methanococcus phosphorylation of glycerate occurs by a specific kinase to
maripaludis (Costa et al., 2010) and Methanothermobacter generate 2-phosphoglycerate. No net ATP synthesis occurs
marburgensis (Kaster et al., 2011). via this route.
These studies on archaeal central metabolism and the
Glycolytic pathways enzymes involved show the metabolic diversity of the
Archaea,whichisconsideredgreaterthanthatofeitherthe
Investigations using a variety of enzymic studies, genome
Bacteria or theEukarya(Siebers&Scho¨nheit,2005), while
sequence analysis, 13C-NMR, crystal structures and micro-
atthesametimecontributingtoamoregeneralknowledge
arrays conducted mainly on hyperthermophilic archaea
about novel enzyme families and their mechanism of
and extreme halophiles have shown that archaea use novel
action.
variations of the Embden–Meyerhof (EM) and Entner–
Doudoroff (ED) pathways, prevalent in bacteria and
eukarya, for glycolysis (Siebers & Scho¨nheit, 2005; Other unique features of archaea
Verhees et al., 2003). Unexpectedly, while most of the
Archaea are also characterized by many other unique
intermediatesoftheEMpathwayinarchaeaarethesameas
features (Table 1), including the composition of their
in the classic version of the pathway found in the other
DNA-dependent RNA polymerase (Werner, 2007), ribo-
domains, the archaea generate these intermediates with a
some structure and composition (Lecompte et al., 2002),
series of unusual enzymes involved in various phosphor-
unusual resistance to antibiotics (Bock & Kandler, 1985)
ylation and isomerization steps as well as the oxidation of
(itself a reflection of unusual walls, membranes and
glyceraldehyde 3-phosphate, the latter catalysed by glycer-
ribosomes) and a variety of modifications to tRNAs
aldehyde-3-phosphate ferredoxin oxidoreductase or a
(Edmonds et al., 1991; Gupta & Woese, 1980). There are
nonphosphorylating glyceraldehyde-3-phosphate dehydro-
novel twists on lipoylation (Posner et al., 2009), histones
genase (Reher et al., 2007; Siebers & Scho¨nheit, 2005;
which lack the N- and C-terminal extensions found in
Verhees et al., 2003). For example, while the classic EM
eukaryotic histones that are sites for post-translational
pathway contains 10 enzymes, only four have orthologues
modificationsimportantforregulation(Sandman&Reeve,
inPyrococcusfuriosus,withtheremainingstepscatalysedby
2005), and an N-linked glycosylation system which, in
novel enzymes, including a unique glucokinase and
archaea, is an amalgam of the processes observed in the
phosphofructokinase enzymes that are ADP-dependent
other two domains (Jarrell et al., 2010). Ferroplasma
rather than ATP-dependent (Sakuraba et al., 2004). The
acidiphilum is unique in possessing the vast majority of its
conversion of acetyl-CoA to acetate in anaerobic ferment-
proteins (86% of the investigated total) in the form of
ative hyperthermophiles is the major energy-conserving
iron-metalloproteins, including many that have not been
reaction for these organisms, and this reaction is catalysed
described as metalloproteins in other organisms (Ferrer
by an unusual enzyme, ADP-forming acetyl-CoA synthe-
et al., 2007).
tase, also found in some halophiles (Siebers & Scho¨nheit,
2005). In contrast, bacteria use a combination of
phosphotransacetylase and acetate kinase to do the same Archaea as model organisms
conversion. The 21st and 22nd amino acids
Archaeal modifications have also been recognized in the Selenocysteine (Sec) and pyrrolysine (Pyr) are known as
ED pathways of extreme halophiles and certain thermo- the21stand22ndaminoacids,andhavebeenshowntobe
acidophiles. Three different versions have been reported co-translationally inserted into proteins by virtue of
with variations mainly in the early steps of the pathways: specialized tRNA complexes that recognize the UGA and
semiphosphorylative, found in extreme halophiles; non- UAG stop codons, respectively. Among archaea, a
phosphorylative,foundincertainthermoacidophiles;anda restricted number of genera of methanogens are the only
branched ED pathway in which there is simultaneous known members to incorporate Sec and Pyr residues into
924 Microbiology157
Whyarchaeaareimportant
Table1.Selected unique features ofarchaea anticodon stem. Novel features associated with the
incorporation of Sec into proteins (e.g. motifs in the
Feature Reference mRNA secondary structure and a specific elongation
factor) appear not to used for the incorporation of Pyr
Ether-linkedlipids Matsumietal.(2011)
(Rother & Krzycki, 2010).
Uniquecellenvelopes Kandler&Ko¨nig(1998)
Novelsurfaceappendages Ngetal.(2008)
Newvirusfamilies Comeauetal.(2008) Transcription
ssrRNAsignatures Winker&Woese(1991)
The core transcriptional apparatus in archaea is homolog-
tRNAmodifications Gupta&Woese(1980)
oustothatofeukaryotes(Hausneretal.,1996),withRNA
Ribosomestructure Harauz&Musse(2001)
Ribosomecomposition Lecompteetal.(2002) polymerase (RNAP) in archaea showing high similarity to
Antibioticsensitivitypattern Bock&Kandler(1985) eukaryotic RNAP II (Werner, 2007). Although the first
RNApolymerasecomposition Werner(2007) structureofRNAPIIwaselucidatedinyeast(Crameretal.,
Growthabove100uC Stetter(2006) 2001), functional studies of the whole complex are highly
Methanogenesisandunique Thaueretal.(2008) challenging in eukaryotic systems. The stability of recom-
coenzymes binant RNAP subunits from the hyperthermophilic
Sulfur-oxidizingpathways Rohwerder&Sand(2007) archaeon Methanocaldococcus jannaschii allowed the first
Hyperthermophilicnitrogenfixation Mehta&Baross(2006) in vitro reconstitution of an active eukaryotic-type RNAP
Ammoniaoxidationmechanism Walkeretal.(2010) (Werner & Weinzierl, 2002). Successful reconstitution of
Lipoylation Posneretal.(2009) the 13 subunits of RNAP from M. jannaschii (Werner &
Modifiedsugar-degradingpathways Verheesetal.(2003)
Weinzierl,2002)andlaterP.furiosus(Najietal.,2007)has
allowed functional analysis of individual subunits and
residues within the complex (Naji et al., 2008; Nottebaum
proteins, almost exclusively into enzymes involved in
et al., 2008). Interestingly, most of the transcriptional
methanogenesis (Rother & Krzycki, 2010). Sec is present
regulators in archaea are homologous to bacterial proteins
in proteinsfrom all three domainsoflife, andwhile it was
(Bell & Jackson, 2001), raising some intriguing questions
first observed in bacterial formate dehydrogenase, studies
overhowthecoreandregulatoryelementsoftranscription
in archaea were crucial in elucidating the route of Sec
interact in archaea.
formation in eukarya (Su et al., 2009). Of all the amino
acids,Secisuniqueinnothavingitsownaminoacyl-tRNA
synthetase. In bacteria, selenocysteine synthase (SelA) DNA replication
catalyses the direct conversion of Ser-tRNASec to Sec-
DNA replication is another process in which archaea have
tRNASec. However, in archaea and eukarya, Sec synthesis
proven to be useful, simplified models for eukaryotic
proceeds through an intermediate, selenophosphate (Sep)-
processes.TheDNAbinding,ATPaseandhelicaseactivities
tRNASec, generated through the activity of two enzymes,
of the predicted replicative helicase in eukaryotes and
phosphoseryl-tRNASec kinase (PSTK) and Sep-tRNA:Sec-
archaea,MCM(minichromosomemaintenance),werefirst
tRNAsynthetase(SepSecS),andnoSelAhomologueshave
demonstrated using recombinant protein from
been detected. When archaeal versions of these two
Methanothermobacter thermautotrophicus (Chong et al.,
enzymes were expressed in a selA mutant of E. coli, active
2000; Kelman et al., 1999). Subsequently, detailed bio-
selenoprotein formate dehydrogenasewasproduced,prov-
chemical analysis of archaeal MCMs hasprovided signific-
ing the involvement of these proteins in the two-step
ant insight into the mechanism of action of this key
synthesis of Sec. A repeat of this experiment with the
replicationprotein(Barryetal.,2007;Jenkinson&Chong,
eukaryotic SepSecS yielded the same result, indicating a
2006; Kasiviswanathan et al., 2004). The first high-
shared pathway for Sec formation in archaea and eukarya
resolution structure of the N-terminal domain of an
(Su et al., 2009; Yuan et al., 2006).
MCM protein came from Methanothermobacter thermau-
Pyr has only been identified in the proteins of some totrophicus (Fletcher et al., 2003), and more recently the
Methanosarcinales and an extremely limited number of structure has been solved for the near full-length protein
bacteria, such as the Gram-positive bacterium from Sulfolobus solfataricus (Brewster et al., 2008) and
Desulfitobacterium hafniense (Rother & Krzycki, 2010; Methanopyrus kandleri (Bae et al., 2009). The origin
Srinivasan et al., 2002). In archaea, this residue is found bindingproteininarchaeaalsoshowssignificanthomology
almostexclusively inenzymes involvedinmethanogenesis, to the origin recognition complex (ORC) proteins in
e.g. methylamine methyltransferases in Methanosarcina eukaryotes. The elucidation of the structure of archaeal
barkeri. A small gene cluster (pylTSBCD) is sufficient for ORC bound to a DNA replication origin sequence
the biosynthesis (pylBCD) and incorporation of Pyr showed that the interaction between ORC and DNA
(pylST).DistinctfromthesituationwithSec,Pyrisligated introduces a significant bending and unwinding of the
directly onto a specific tRNA by PylS, pyrrolysyl tRNA DNA, and provided insight into the mechanistic details
synthetase. The adjoining gene, pylT, encodes the specia- of the initiation of DNA replication (Dueber et al.,
lized tRNAPyl with unique elements, such as an elongated 2007; Gaudier et al., 2007). As with transcription, DNA
http://mic.sgmjournals.org 925
K.F.Jarrellandothers
replication seems to consist of an interesting mix of of other critical eukaryotic enzymes involved in ubiquiti-
eukaryotic and bacterial features. The identification of a nation are missing. Thesedata point toanarchaealsystem
single origin of replication in Pyrococcus abyssi indicated that is more like the eukaryotic Ub system than the
that archaeal DNA replication occurs in a bacterial-like bacterial Pup system (Darwin & Hofmann, 2010).
manner,usingeukaryotic-likemachinery(Myllykallioetal.,
2000). However, multiple functioning origins have subse-
ESCRT proteins
quentlybeenidentifiedinSulfolobusandhalophilicspecies,
proving that some archaea utilize multiple replication Homologues of the eukaryotic ESCRT proteins Vps4 and
origins,asineukaryotes(Cokeretal.,2009;Lundgrenetal., ESCRT-III were recently identified in some crenarchaea
2004; Norais et al., 2007; Robinson et al., 2004). (Obita et al., 2007). In eukaryotes, the ESCRT system is
required to couple cargo sorting to vesicle formation
(Williams & Urbe´, 2007). Studies in Sulfolobus acidocal-
Proteasome darius have established that archaeal ESCRT homologues
Proteolysis is another process in which the proteins areinvolvedincelldivision(Linda˚setal.,2008;Samsonet
involved are similar in archaea and eukaryotes (for a al., 2008). The structural basis of the interaction between
review, see Maupin-Furlow et al., 2006). The first crystal Vsp4 and ESCRT-III proteins is the same in archaea and
structureofthe 20S proteasome was from Thermoplasma eukaryotes, indicating that this partnership predates the
acidophilum, and revealed that the proteasome is a divergenceofthearchaealandeukaryoticlineages(Obitaet
barrel-shaped particle made from a stack of four al., 2007). The common ancestry of the archaeal and
heptameric rings (Lo¨we et al., 1995). Subsequent studies eukaryotic ESCRT proteins means that the proteins are
of archaeal proteasomes and regulatory particles have likelytofunctionbysimilarmechanisms,albeitindifferent
provided details of the mechanism of substrate entry cellular processes.
(Rabl et al., 2008; Religa et al., 2010) and the interaction
between the substrate and the proteasome antechamber
CRISPR
(Ruschak et al., 2010). Studies of the archaeal protea-
some regulatory particle, PAN, which is a hexameric The recently discovered CRISPR (clustered, regularly
ATPase ring complex, have provided useful mechanistic interspaced short palindromic repeats) system in bacteria
insight into the regulation of eukaryotic proteolysis. and archaea is a small RNA-based defence mechanism
Structural and functional studies of PAN from M. against phages and plasmids (for a review, see Karginov &
jannaschii have identified key residues and domains Hannon,2010).CRISPRsequencesarefoundinmorethan
involvedinsubstrateunfoldingandtranslocation(Zhang 90% of archaeal genomes (Grissa et al., 2007), and several
archaeal species have been used as models for elucidating
et al., 2009a, b). The structure of PAN bound to the 20S
the mechanism by which the CRISPR system functions.
proteasome in T. acidophilum was recently solved (Yu
The single unit transcription of CRISPR repeats and
et al., 2010), and provides further details of how the
spacers before processing into small RNAs was first
regulatory particle and the core proteasome interact in
demonstrated in Archaeoglobus fulgidus (Tang et al.,
archaea and eukaryotes.
2002). Recent work has shown that as in the eukaryotic
Afeature of eukaryoticcells critical for protein turnover is RNAi system, in P. furiosus the CRISPR/Cas system uses
the ubiquitination system, whereby ubiquitin (Ub) is guide RNAs to specifically target foreign RNA for
covalently bound to proteins, targeting them for degrada- destruction (Hale et al., 2009; van der Oost & Brouns,
tion at the proteasome. Recently, pupylation, which 2009).
involves the covalent attachment of pup proteins [prokar-
yotic ubiquitin-like protein (Pup)], was shown to be a
functionally equivalent but not homologous system in Functional genomics
bacteria(Burns&Darwin,2010).Inarchaea,ubiquitin-like Archaea have been used as models for studying specific
proteins have also been reported, and recently covalent cellular processes in eukaryotes and bacteria. As the age of
attachment of SAMP (small archaeal modifier protein, functional genomics has arisen, the utility of archaea in
SAMPylation) to proteins of Haloferax volcanii was structural genomics and systems biology projects has
observed (Humbard et al., 2010). Such proteins accu- become increasingly clear (Albers et al., 2009; Bonneau
mulate in proteasome-deficient mutants, although there is etal.,2007;Facciottietal.,2007).Thestabilityofrecombi-
nodirectevidenceyettoshowthatSAMPsareinvolvedin nant proteins from thermophilic archaea has been
targeting proteins to the proteasome like their eukaryotic exploited for some time, with many key crystal structures
and bacterial counterparts, Ub and Pup, respectively being elucidated using archaeal homologues of universal
(Darwin & Hofmann, 2010). SAMPs conjugate to pro- proteins. For example, the first bacteriorhodopsin
teins via Gly (as in Ub) and not Glu (as in Pup). It (Henderson&Unwin,1977)andhigh-resolutionribosome
appears that archaea also have a eukaryotic E1 homo- (Banetal.,2000)structureswereelucidatedusingarchaeal
logue (Ub-activating enzyme) that could be involved in homologues.Amorerecentsuccessstorywasthediscovery
SAMPylation (Ranjan et al., 2011), although homologues ofanewmotifintheoligosaccharyltransferase(homologue
926 Microbiology157
Whyarchaeaareimportant
of the STT3 catalytic subunit of the eukaryotic oligosac- Expanded ecological significance of archaea
charyltransferase complex) of P. furiosus near the known
Originally, archaea were considered to be organisms
catalytic domain (Igura et al., 2008). Subsequent mutation
relegated to life in extreme environments, such as salt
of the so-called DK motif in yeast STT3 revealed its
brines, hot water springs, hydrothermal vents, extremely
essential role in catalysis. The relative ease of carrying out
acidic niches and anoxic environments, where they
structural studies in thermophilic and hyperthermophilic
contributed significantly to the ecology (Bini, 2010;
archaea has led to their use in major structural genomics
Chaban et al., 2006; Gittel et al., 2009; Liu & Whitman,
projects, in which vast numbers of proteins are purified
2008; Macalady et al., 2007). However, with the advent of
andcrystallizedusinghigh-throughputsystems.Oneofthe
culture-independent analysis techniques it has become
pioneering organisms in the field of functional genomics
increasingly evident that archaea are much more wide-
was Methanothermobacter thermautotrophicus, followed by
spread. Sequencing results imply that they are also more
hyperthermophiles such as Pyrococcus species and M.
metabolically diverse than initially thought (Fig. 4). As
jannaschii, with a large number of crystal structures of
such they represent a sizeable proportion of the microbial
their proteins being solved and deposited in databases
population in a wide variety of ‘non extreme’ environ-
(Christendatetal.,2000;Jenney&Adams,2008).Notonly
ments, such as soil, oceans and lakes (DeLong & Pace,
are the structures that emerge from these projects
2001; Schleper et al., 2005). However, the relative
informative, but the small archaeal genomes are useful
abundance of archaea varies greatly in different habitats,
fordevelopingefficienttechnologies thatcanbeappliedto
being particularly important in marine ecosystems, where
structural genomics projects using higher organisms.
archaea reach an abundance of 5–30% of the total
Additional insights into eukaryotic type II chaperonins planktonic cell population (DeLong et al., 1999; Schleper
(Ditzel et al., 1998; Zhang et al., 2010a), novel DNA et al., 2005). In a recent study using a global analytical
binding (Bell et al., 2002; Luo et al., 2007; Wardleworth approach to reveal the diversity and abundance of archaea
etal.,2002)andDNArepairmechanisms(Kvaratskhelia& in various habitats, it was observed that despite their high
White,2000;Rudolfetal.,2006),andproteintranslocation abundance, the diversity of archaea in oceans and soils is
(Mandon et al., 2009; Ng et al., 2007; Pohlschro¨der et al., far lower than that in hydrothermal vents and freshwater
2005;Ring&Eichler,2004;VandenBergetal.,2004)have ecosystems. Also, salinity rather than temperature was
also been provided using model archaeal systems. found to be responsible for this variable distribution
Fig. 4. Illustration of the role of archaea in the global biogeochemical cycles. The element cycle pathways and the archaea
involvedinthesepathwaysindicatethecontributionofthisdomaintotheglobalcycles.Asterisksindicatethepathwaysinwhich
archaeaplayamajorrole.
http://mic.sgmjournals.org 927
K.F.Jarrellandothers
(Auguet et al., 2010). The large numbers of archaea in all uniquely capable of growth at the extremely low ammonia
ecosystems indicate that they act to a much greater extent levels foundin ocean waters (Walker et al., 2010). Positive
than previously believed as major players in various correlations of archaeal cell counts and amo genes with
biogeochemical cycles. Below we summarize a select few nitrite maxima in the oceans were initially suggestive that
of these contributions. most ammonia oxidation in this environment is archaeal-
derived (Wuchter et al., 2006). Furthermore, the presence
of AOA in extreme environments and various mesophilic
Novel important roles for archaea in
biomes suggests that AOA are adapted to growth condi-
biogeochemical cycles
tionsthatdifferfromthoseofammonia-oxidizingbacteria,
Nitrogen: ammonia oxidation and nitrogen fixation
indicating niche separation (Schleper, 2010). AOA have
Ourunderstandingofthenitrogencyclehasbeenrevisedin beenfoundtobethedominantammoniaoxidizersinmost
the past few years by the discovery of ammonia oxidation surface soils. As soil depth increases, the number of AOA
carried out by archaea. Until this discovery, ammonia remains constant, whereas the number of ammonia-
oxidation, the first nitrification step of the nitrogen cycle, oxidizing bacteria decreases dramatically (Schleper &
wasthoughttobecarriedoutonlybybacterialautotrophs. Nicol, 2010). The archaeal community seems to be
Ammonia-oxidizing archaea (AOA) are members of the dominant in soils with low nitrogen and low nitrification
proposed novel Phylum Thaumarchaea, and are now rates (Schleper, 2010; Tourna et al., 2008). According to
recognized as a ubiquitous component of marine plankton Valentine (2007), the dominance of archaeal communities
(Gribaldo et al., 2010), as well as being found in almost all under limiting nutrition conditions can be attributed to
environments. AOA typically greatly outnumber bacterial theiradaptationtochronicenergystress,andthismightbe
ammonia oxidizers in many common environments, and a primary factor in differentiating bacterial and archaeal
are among the most abundant micro-organisms on Earth ecology.
(Schleper & Nicol, 2010). However, as they are difficult to
Archaea are known to be involved in other parts of the
cultivate,someaspectsoftheirphysiologyandcontribution
nitrogen cycle. The discovery of nitrogen fixation in
to biogeochemical pathways are still speculative. Meta-
methanogens extended the distribution of this important
genomic studies of both seawater (Venter et al., 2004) and
activitytothearchaealdomain,andmorerecentlyarchaeal
soilhaverevealedthepresenceofputativeammoniamono-
nitrogen fixation has been documented at hyperthermo-
oxygenase genes (amoA) in uncultivated archaea, strongly
philic temperatures (Mehta & Baross, 2006). Unusual
suggesting that members of this domain possess the ability
regulatory mechanisms have been reported for archaeal
to oxidize ammonia (Francis et al., 2007). Analysis of the
growth in pure culture of the first marine archaea to be nitrogen fixation (Leigh & Dodsworth, 2007).
culturedconfirmedchemolithoautrophicgrowthemploying
aerobic oxidation of ammonia to nitrite (Ko¨nneke et al.,
Carbon: methanogenesis and anaerobic methane
2005;Walkeretal.,2010).Whilemorecontroversial,recent
oxidation (reverse methanogenesis)
evidence suggests that soil AOA are chemolithoautotrophs
Methanogens have long been known to play an essential
aswell(Zhangetal.,2010b).
roleinthedecompositionofcomplexorganicmaterialina
Analysis of sequenced genomes indicates that AOA may variety of anaerobic habitats, such as peat bogs, digestors,
employ a unique biochemistry. Thaumarchaea contain the ricepaddies,landfillsitesandruminants(Liu&Whitman,
putative ammonia mono-oxygenase genes amoA, amoB 2008; Thauer et al., 2008). Three major pathways of
and amoC, but lack the homologues used by bacteria to methanogenesis have been elucidated, with methane
carry out the second step in the nitrification process, i.e.
derived from the reduction of CO with hydrogen or
2
the components required for electron flow between
formate, from the methyl group of acetate or from
hydroxylamine and ubiquinone (Prosser & Nicol, 2008;
methanol and methylamines. Aceticlastic-derived methane
Walker et al., 2010). Unexpectedly, it appears that
constitutesapproximatelytwo-thirdsofthetotalproduced
Nitrosopumilus maritimus utilizes a copper-based system
annuallyinthebiosphere,withmostoftheremainingone-
ofelectrontransportratherthanthetypicaliron-basedone
thirdoriginatingfromthereductionofCO withhydrogen
2
prevalentinbacteria(Walkeretal.,2010).Genomeanalysis
or formate (Ferry, 2010). The other pathway, using
has also indicated that AOA, although chemolithoauto-
methanol and methylamines as primary substrates, con-
trophslikeammonia-oxidizingbacteria,likelyfixCO ina
2 tributes comparatively minor amounts to the total
different way from bacterial ammonia oxidizers, in which
methane production and is limited to a small subset of
RuBisCo is the key enzyme. Nitrosopumilus maritimus
methanogens, such as the Methanosarcinales. After
probablyemploysamechanismsimilarbutnotidenticalto
degradationoforganicsubstratesbyavarietyofhydrolytic
the 3-hydroxypropionate/4-hydroxybutyrate pathway of
and fermentative bacteria, molecules generated by aceto-
the hyperthermophile Metallosphaera sedula for auto-
genic and syntrophic bacteria are used by methanogens in
trophic carbon assimilation (Walker et al., 2010).
the terminal step of degradation. As noted above,
AOA appear to be well adapted to oligotrophic environ- methanogenicarchaeaareuniqueintheirabilitytoconvert
ments with low oxygen, and Nitrosopumilus maritimus is a limited number of simple carbon compounds to
928 Microbiology157