mc2509.
qxd 11/09/1999 2:41 PM Page 542
542
Archaeal genomics
Terry Gaasterland
Four euryarchaeal genomes have been completely sequenced
and are publicly available: Methanococcus jannaschii,
Methanobacterium thermoautotrophicum, Pyrococcus
horikoshii and Archaeoglobus fulgidus. Four more genome
sequences, two crenarchaeal and two pyrococci, will soon be
released. In addition, seven more archaeal genome sequencing
projects are under way, including two halophiles, two
Thermoplasma, and a methanogen. These projects cover all
branches of the archaeal domain and will lead to new insights
into archaeal metabolism, DNA processing, and evolutionary
relationships with the Bacteria and Eukarya.
Addresses
Laboratory of Computational Genomics, 1230 York Avenue, The
Rockefeller University, New York, New York 10021, USA;
e-mail: gaasterl@genomes.rockefeller.edu
Current Opinion in Microbiology 1999, 2:542–547
1369-5274/99/$ — see front matter © 1999 Elsevier Science Ltd.
All rights reserved.
Abbreviations
Mb million basepairs
ORF open reading frame
rRNA ribosomal RNA
Introduction
Since the 1977 discovery of the Archaea [1], their existence
has challenged biologists to rethink the phylogenetic rela-
tionships between organisms. The placement of the
Archaea as a third domain of life, which shattered the tra-
ditional view of the prokaryote/eukaryote dichotomy, was
initially argued on the basis of the careful analysis of small-
subunit ribosomal RNA (rRNA). Besides the RNA
evidence, organisms from the newly discovered phyloge-
netic domain exhibited compelling characteristics that set
them apart from Eubacteria (e.g. methanogenesis, cell
membranes with ether-bonds, and cell walls without pep-
tidoglycan). At the same time, a large proportion of their
metabolism seems to be shared to a large degree with bac-
terial organisms, yet their transcription and translation
apparatus as well as DNA metabolism are shared more
closely with eukaryotic organisms.
In 1993, the Department of Energy (DOE) funded the
sequencing of three complete archaeal genomes:
Methanococcus jannaschii, as a collaboration between The
Institute for Genome Research (TIGR) and the University
of Illinois at Urbana-Champaign [2]; Methanobacterium ther-
moautotrophicum, as a collaboration between Genome
Therapeutics and Ohio State University [3]; and Pyrococcus
furiousus, at the University of Utah and the University of
Maryland [4]. The first two archaeal genome sequences
were released in 1996 and 1997, respectively, and were
soon complemented by the release of genome sequences
of Archaeoglobus fulgidus by TIGR [5] and Pyrococcus
horikoshii by University of Tokyo, NITE and NIBHT in
Japan [6••,7]. At the time of writing, eight archaeal
genomes are completely or nearly completely sequenced,
and sequencing of seven more genomes are underway.
Sequencing these archaeal genomes has led to insights into
the mosaic nature of relationships between prokaryotic
proteins, particularly among metabolic, transport, and
DNA processing proteins. These insights in turn have led
to a deeper molecular understanding of differences and
similarities between organisms in the major archaeal phe-
notypes. The genome sequencing projects are being
followed up by proteome projects that involve whole
genome two dimensional gel electrophoresis, mass spec-
trometry, and high-throughput protein structure
determination.
The Archaea
Four phenotypes characterize the Archaea broadly and dis-
tinguish them from Bacteria. Archaeal organisms include
methanogens, sulfur-reducing thermophiles, sulfur-
dependent thermophiles, and halophiles. Genomes from
all three categories are being sequenced or have already
been released. The methanogens (M. jannaschii and
M. thermoautotrophicum) are strict anaerobes and use varia-
tions of methanogenesis to convert CO 2, methyl
compounds, or acetate to methane. Methanogenesis serves
as a form of anaerobic respiration. In the sulfur-reducing
thermophiles (Archaeoglobus fulgidus), oxidized sulfur
species act as electron acceptors for anaerobic respiration.
Sulfur-dependent Archaea (Sulfolobus solfataricus) can grow
autotrophically using elemental sulfur as an energy source.
The halophiles (Halobacterium salinarum) require a high-
salt environment. In all Archaea, membranes are made
from ether-linked lipids bonded to glycerol, and thus differ
substantially from bacterial membranes. Like the eukary-
otes, archaeal cell walls contain no peptidoglycan, again
setting them apart from bacteria. The Thermoplasma differ
somewhat from the other Archaea: they have no cell wall,
and their cell membranes contain tetraether lipids with
mannose and glucose subunits.
Phylogenetic analysis of small-subunit rRNA sequences
distinguishes two distinct archaeal sub-domains: the
Euryarchaeotes and the Crenarchaeotes [1]. The eur-
yarchaeotes include methanogens, halophiles, and
sulfur-reducing thermophiles. Although methanogenesis is
uniform in two of the three major methanogenic eur-
yarchaeal lineages, variations occur within the
Methanomicrobiales lineage [8]. The latest branching
methanogenic euryarchaeal lineage, Methanomicrobiales,
gave rise to the extreme halophiles and sulfate-reducing
Archaea. The crenarchaeotes share a 16S rRNA signature
mc2509.qxd 11/09/1999 2:41 PM Page 543

Archaeal genomics Gaasterland 543

Figure 1

Phylogenetic distribution of ORFs across

nine genomes. An ORF is labeled as BAE, 100%

Percent of genomic open reading

BA, BE, A, AE, B or orphan as follows: the
label contains a B, A, or E if its translated 80%
protein matches a translated ORF from any Orphan
other genome in the Bacteria, Archaea or A
Eukaryotes, respectively. The label for an 60% B

frames
ORF contains the phylogenetic domain of its BA
own genome if its translation matches at 40% AE
least one ORF in any other genome. ORFs BE
that have matches in no other genome, BAE
within this group of nine genomes, are 20%
‘orphans’. Most ORFs in the two reduced
Mycoplasma genomes match ORFs in other 0%
genomes. The proportions of B (bacterial

us
.
ae

us

t
i
m
li

rm

as
hi
ia
co

liu

ric
nz

cc
only) and A (archaeal only) ORFs are

sc
on

he

Ye
ita

ta
E.

co

na

.t
um
lu

lfa
influenced by the proximity of another

en

an

M
nf

ch
ne

so
.g
.i

.j
genome — for example, E. coli and

ne
.p
H

M
M

H. influenzae are closer to each other than
any other pair of genomes, as are the two
Mycoplasma. Of particular interest is the
distribution of BAE (phylogenetically
universal), BA (bacterial–archaeal),
AE (archaeal–eukaryotic), and
BE (bacterial–eukaryotic) ORFs: the
S.
Sy
M
Genomes
Current Opinion in Microbiology
complement of AE ORFs is much smaller in ORFs. Before the sequencing of complete
Archaea than the BA or BAE complement. genomes, the AE proportion was expected
Similarly, in yeast, the complement of BE and to be much larger.
BAE ORFs is much smaller than the AE

that places them at a deeper branch point than the eur-
yarchaeotes within the archaeal domain. Crenarchaeotes
are in many instances sulfur-dependent thermophiles, and
have initially been regarded as more homogeneous than
the euryarchaotes [9]. However, isolation of small-subunit
rRNA from the open environment and the discovery
of Crenarchaeum symbiosum has led to the characterization
of deeply divergent lineages of low-temperature
Crenarchaeota [10,11].
Comparative genomics
The archaeal challenge to phylogeny has continued with
each new release of a completely sequenced archaeal
genome. Like the bacterial genomes, the archaeal genomes
contain a significant proportion (25–68%, depending on
comparison methods) of putative coding regions with no
similarity to any sequence in any other organism. A signifi-
cant proportion of putative coding regions have matches
only among other archaeal genomes (10–15%); a large num-
ber of the corresponding protein sequence families have no
known function [12•]. Of the coding regions shared exclu-
sively between Archaea and the eukaryotes yeast or
Caenorhabditis elegans (25–30% of archeael coding regions), a
large proportion (30% of the archaeal-eukolyotic coding
regions, ‘AE’ genes) encode proteins involved in transcrip-
tion, translation, and DNA metabolism [3,13••]. This is
consistent with pre-genome observations. However, the
other 70% of the AE coding regions encode proteins from
all protein functional categories, and a substantial number
are of unknown function. Also striking is the small size of
the complement of coding regions shared among archaeal
and bacterial genomes to the exclusion of the eukaryotes
(genes characteristic of prokaryotes, or ‘BA’ genes) and the
small size of the complement of phylogenetically universal
genes (genes with a counterpart in each of the three phylo-
genetic domains, or ‘BAE’ genes). As evident in the public
annotations of the organisms, the ORFs of known function
in the subset of archaeal coding regions shared exclusively
with bacterial organisms (‘BA’ ORFs) primarily encode
pathways of bacterial metabolism [2,3,5,14•,15•]. The sub-
set of genes shared among all three domains (‘BAE’) fails to
comprise a coherent subset of metabolism; nor do they
encode consistently complete metabolic pathways [13••].
Figure 1 shows the phylogenetic distribution of ORFs in
nine genomes [12•].
The existence of large numbers of archaeal genes shared
exclusively with eukaryotes and larger numbers of genes
shared with bacteria is difficult to interpret. One view is
that the archaeal genomes are a mosaic, reflecting a com-
bination of eukaryotic and bacterial features together with
new features unique to the Archaea [16]. Another inter-
pretation, consistent with the small-subunit rRNA tree,
suggests that the Archaea were involved in the formation
of the eukaryotes, as were bacterial organisms [1,17,18•]. A
complementary view suggests that substantial transfers of
genes among prokaryotes occured prior to the formation of
the eukaryotic cell [19•]. The debate has led to proposals
that classification methods return in part to morphological
features such as properties of the cell wall, argued com-
pellingly by Gupta [20].
The completion of the genome sequence from two deep-
branching thermophilic Bacteria, Aquifex aeolicus and
Thermatoga maritima, provided data to explore the degree
to which these bacterial organisms exhibit evidence of
mc2509.qxd 11/09/1999 2:41 PM Page 544
544 Genomics
lateral transfer between Archaea and Bacteria [21••]. For
example, 108 Thermatoga genes have orthologues exclu-
sively in Aquifex and Archaea, 81 of which occur in 15
clusters in the genome [22••]. This number is much high-
er for Aquifex and Thermatoga than for the other bacterial
genomes; these thermophilic genomes encode more pro-
teins that are close to Archaea than do the other bacterial
genomes. Their close proximity in the genome indicates
that they may be present by virtue of lateral transfer.
The complete genomes also provide data to infer proper-
ties of proteins that must have been present in a common
ancestor, as well as properties that may pinpoint the basis
of divergence. For example, the structure of the EgsA
(enantiomeric glycerophosphate synthetase) protein from
M. thermoautotrophicum and the functionally related protein
NAD(P)-linked sn-glycerol-3-phosphate dehydrogenase
(G-3-P) from Escherichia coli have no sequence similarity,
yet share a structure and have analogous functions [18•].
Since both proteins participate in membrane formation in
their respective organisms, one may hypothesize that
Archaea and Bacteria may have differentiated because of
changes in membrane composition.
The genomes
The complete and nearly-complete sequencing of archaeal
genomes will provide data to examine the dichotomy
between ‘eukaryotic Archaea’ and ‘bacterial Archaea’ in
much more detail than can currently be done. So far, the
four released archaeal genomes have all been euryarchaeal
organisms. Two Crenarchaotes genome sequences are
complete or nearly complete: Sulfolobus solfataricus (3.1
million basepairs [Mb]), which was initiated in Canada and
is being completed through a Canadian and European con-
sortium, and Pyrobaculum aerophilum (2.2 Mb), which is
being sequenced at Caltech with UCLA. At the time of
writing, 80% of the S. solfatoricus genome sequence is pub-
licly available (http://niji.imb.nrc.ca/sulfolobus), and the
Pyrobaculum genome sequence is complete but not yet
released. In addition to the completely sequenced
Euryarchaeote P. horikoshii genome [6••,7], two very closely
related pyrococci are also nearly completely sequenced:
Pyrococcus abyssii (1.8 Mb), by a French genome project,
and P. furiosus (2.1 Mb), mentioned earlier as one of the
original DOE projects.
In addition to these eight archaeal genomes, another seven
archaeal genome sequencing projects are underway. These
include Aeropyrum pernix K1 (1.7 Mb) at the Biotechnology
Center in Japan; Crenarchaeum symbiosum (2–3 Mb) at
Diversa Corporation; Halobacterium sp. NRC-1 (2.5 Mb) at
the University of Washington and the University of
Massachusetts; Halobacterium salinarum (4 Mb) and
Thermoplasma acidophilum (1.7 Mb) at the Max-Planck-
Institute for Biochemistry; Methanosarcina mazei (2.8 Mb)
at the Goettingen Genomics Laboratory; and
Thermoplasma volcanium GSS1, a collaborative effort
between seven research institutions and funded by the
Japanese Agency of Industrial Science and Technology.
Together, these 15 archaeal genomes cover all known
major branches of the domain Archaea (see
http://genomes.rockefeller.edu/genomelist for links to
each project).
Notable differences among Archaea
The completion of sequencing the sulfur-metabolizing
A. fulgidus 2.2 Mb genome provided genomic data from the
first non-methanogenic Archaea. Prediction of transmem-
brane domains in A. fuldigus and a follow-up annotation of
M. jannaschii (1.7 Mb) [5,23] indicated that the two organ-
isms have substantial differences in their regulatory,
transport, and sensory functions. For example, of 61
Archaeoglobus ORFs annotated as transport and binding
proteins, 30 transport branched-chain amino acids, 10 are
ABC transporters, six are proline permeases, and four
are spermidine/putrescine transporters. Of the 68 trans-
port-and-binding Methanococcus ORFs, seven transport
branched-chain amino acids, 27 are ABC transporters; and
24 transport cations. The profile of transporters helps to
characterize precisely the differences between a sulfur
reducer (Archeoglobus) and a methanogen.
The 1.8 Mb M. thermoautotrophicum genome revealed that
gene order of orthologous genes is not preserved with
respect to M. jannaschii. Even so, 19% of the ORFs from
M. thermoautotrophicum have counterparts in M. jannaschii
with 50% or more sequence identity. Proteins of unknown
function in this large complement of highly similar pro-
teins are likely to be related to methanogenesis.
Comparison of P. horikoshii to available sequence from
P. furiosus shows considerable gene rearrangement and
divergence in gene content [6••]; even so, orthologous
genes are about 70% identical.
Certain genes encoding tRNA molecules and tRNA syn-
thetases are substantially different or missing entirely in
Archaea. Specifically, lysyl-, asparginyl-, cysteinyl- and
glutaminyl-tRNA synthetases were absent in several ini-
tial Archaeal genome annotations [24]. The selenocys-
teinyl-tRNA gene could not be identified in
M. thermoautotrophicum [3]. Cysteinyl- and lysyl-tRNA
synthetases unique to Archaea have since been identified
[25,26]. A surprise was the observation that lysyl-tRNA
synthetase from Borrellia burgdorferi, the bacterium caus-
ing Lyme disease, is of the archaeal class I-type tRNA
synthetase, a unique phenomenon so far among the
Bacteria [27]. The new lysyl-tRNA synthetase was com-
pletely different from other known lysyl-tRNA syn-
thetases, indicating that other ‘missing’ functions that are
highly conserved in the Bacteria and eukaryotes may have
a different molecular origin in Archaea. The discovery of
the archaeal type of lysyl-tRNA synthetase in B. burgdor-
feri, a bacterial organism, indicates the possibility of later-
al transfer. Since the protein is dissimilar from its
functional counterparts in other bacterial organisms, it
becomes a candidate for anti-spirochete therapeutics. The
mc2509.qxd 11/09/1999 2:41 PM Page 545
archaeal form of lysyl tRNA-synthetase in B. burgdoreri
opens the possibility that alternative forms of this and the
other ‘missing’ archaeal tRNA synthetases may also have
undergone lateral transfer from archaeal to bacterial organ-
isms. Alternatively, both forms may have been present in
a common ancestor and may be more ubiquitous than pre-
viously thought or more frequently lost.
Novel operons
A striking feature of the archaeal genomes has been their
novel organization of closely located genes. For example,
the S. solfataricus genome contains a cluster of nine histi-
dine biosynthesis genes that occur in a different order from
previously known his operons [28,29]. Both Sulfolobus and
Pyrobaculum contain novel pairs of closely located neigh-
boring ORFs that encode members of the same metabolic
pathway [15•,30]. P. furiosus contains a number of new
putative operons compared with P. horikoshii, including
gene clusters for maltose and trehalose transport; phos-
phate uptake; the urea and TCA cycle; as well as
tryptophan, aromatic amino acid, arginine, isoleucine, and
valine metabolism.
The archaeal proteome: structural genomics
Since thermophilic archaeal proteins are stable at high
temperatures, they are easier to isolate than mesophilic
proteins after over-expression in E. coli. This fact has led
several structural genomics pilot projects to adopt archaeal
genomes as the source organism. The goal of structural
functional genomics is to acheive high-throughput struc-
ture determination of proteins across entire genomes. A
pilot project at UC Berkeley and Lawrence Livermore
National Laboratory seeks to solve structures in M. jan-
naschii [31•,32,33••,34,35]. This project has produced high-
confidence folds for 33 sequences of unknown function in
M. genitalium, M. jannaschii, and Haemophilus influenzae
[31•]. They have also solved the structure for a small heat-
shock protein from M. jannaschii, which will help us to
understand how small heat-shock proteins protect
substrates from denaturation [33••]. A structural genomics
project at UCLA and Los Alamos National Laboratory has
grown out of the P. aerophilum genome sequencing project,
and recently solved the structure of the translation initia-
tion factor 5a [36]. A project in Toronto is focusing on
M. thermoautotrophicum, and a project at Argonne National
Laboratory [37], although focused on the discovery of new
protein folds, uses thermophiles as the sequence source
whenever possible.
A key to the success of structural functional genomics will
be the ability to generate high-quality predicted protein
structures based on alignments with sequences of known
structures. Several groups have initiated databases of pre-
dicted structures, including [38 •] which includes
predictions for M. jannaschii. So far, genome-wide surveys
of secondary structure and integral membrane domains
give consistent distributions across all organisms [39••,40•]
but differ substantially from distributions among
Archaeal genomics Gaasterland 545
published protein structures, implying biased selection
among current solved structures.
The archaeal proteome: two-dimensional gel
isolation of proteins
As a follow-up to the sequencing of complete archaeal
genomes, the US Department of Energy has established
the Archaeal Proteomics Project as a collaboration between
Argonne National Laboratory, the University of Georgia,
and the University of Illinois. This project will use two-
dimensional gel electrophoresis and matrix-assisted laser
desorption ionization mass spectrometry to purify and char-
acterize proteins expressed in Archaea under varying
conditions, with a focus on conditions that will reveal path-
ways related to environmental bioremediation [41]. The
project uses subcellular fractionation to compartmentalize
archaeal proteins. In addition to identifying components of
potential new pathways, this work will help to confirm actu-
al coding regions that are unique to archaeal organisms.
DNA conformation, control, and repair
Having the full sequence of a genome enables studies that
relate biochemical or structural properties to patterns or
positions genome wide. One example of such a study
involves the discernment of DNA sequence patterns asso-
ciated with archaeal nucleosome positioning [42•], which
revealed that histone assemblies preferentially center on
(CTG)6 and (CTG)8 repeats. This discovery builds on
earlier work [43] that characterized archaeal histones as
tetramers that bind to approximately 60 basepairs.
Archaeal nucleosome structure appears homologous to that
of eukaryal nucleosomes, yet remain stable and functional
at high temperatures [44,45••,46]. Computational compar-
ison of 16 prokaryotic genomes has led to the observation
that hairpin formation occurs much less frequently in four
archaeal and eight bacterial genomes, supporting the theo-
ry that the Archaea use hairpins to control transcription
termination differently from E. coli, H. influenzae,
Bacillus subtilis and Chlamydia trachomatis [47•]. The
Archaea exhibit less dinucleotide bias on coding strands
than do bacterial organisms [48], indicating possible differ-
ences in DNA repair mechanisms and ambiguating the
computational detection of origin of replication.
Conclusions
Each gene in an organism has its own phylogenetic back-
ground. The complete genome sequences are giving us
evidence for collective events as well as individual trans-
fers and cross-overs. For example, the complement of
proteins shared most closely between the thermophilic
Bacteria and the Archaea are arranged in large clusters
within the bacterial genomes. In contrast, the class I-type
lysyl-tRNA synthetase that occurs in several Archaea and
in B. burgdorferi participates in pathways that are otherwise
usual for the respective organisms. Key events, such as the
differentiation of membrane composition proteins, may
mark the differentiation between Bacteria and Archaea.
The 15 complete archaeal genomes will lead to a much
mc2509.qxd 11/09/1999 2:41 PM Page 546
546 Genomics
deeper understanding of the phylogenetic domain Archaea
and the evolution of life on Earth.
Acknowledgements
Many thanks to Christoph W Sensen for his comments, corrections, and
improvements to this paper.
References and recommended reading
Papers of particular interest, published within the annual period of review,
have been highlighted as:
• of special interest
•• of outstanding interest
1. Woese C: The Archaea: their history and significance. In The
Biochemistry of Archaea (Archaeabacteria). Edited by Kates M. New
York: Elsevier Science Publishers; 1993:v-xxxix.
2. Bult C, White O, Olsen G, Zhou L, Fleischmann R, Sutton G, Blake J,
FitzGerald L, Clayton R, Gocayne J, Kerlavage A et al.: Complete
genome sequence of the methanogenic archaeon,
Methanococcus jannaschii. Science 1996, 273:1058-1073.
3. Smith D, Doucette-Stamm L, Deloughery C, Lee H, Dubois J,
Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K et al.:
Complete genome sequence of Methanobacterium
thermoautotrophicum deltaH: functional analysis and comparative
genomics. J Bacteriology 1997, 179:7135-7155.
4. Weiss R, Dunn D, Stump M, Yeh R, Cherry J, Robb F: The genome
sequence of a hyperthermophilic archaeon: Pyrococcus furiosus.
In Microbial Genome Project Section, DOE Human Genome
Program Contractor-Grantee Workshop VII: 1999, Jan, 12—16,
Oakland, CA. Washington, DC: Department of Energy; 1999:157.
5. Klenk H, Clayton R, Tomb J, White O, Nelson K, Ketchum K, Dodson
R, Gwinn M, Hickey E, Peterson J et al.: The complete genome
sequence of the hyperthermophilic, sulphate-reducing archaeon
Archaeoglobus fulgidus. Nature 1997, 360:364-370.
6. Kawarabayasi Y, Sawada M, Horikawa H, Haikawa Y, Hino Y,
•• Yamamoto S, Sekine M, Baba S, Kosugi H, Hosoyama A et al.:
Complete sequence and gene organization of the genome of a
hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3.
DNA Research 1998, 5:55-76.
The complete genome of the hyperthermophilic archae Pyrococcus
horikoshii, presented in this paper, has many duplicated open reading
frames (ORFs). 22% of encoded ORFs have no similiarity to sequences any
other organism.
7. Gonzalez J, Masuchi Y, Robb F, Ammerman J, Maeder D,
Yanagibayashi M, Tamaoka J, Kato C: Pyrococcus horikoshii sp. nov.,
a hyperthermophilic archaeon isolated from a hydrothermal vent
at the okinawa trough. Extremophiles 1998, 2:123-130.
8. Danson M: Central metabolism of the Archaea. In The Biochemistry
of Archaea (Archaeabacteria). Edited by Kates M. New York: Elsevier
Science Publishers; 1993:1-24.
9. Woese C, Kandler O, Wheelis M: Towards a natural system of
organisms: proposal for the domains archaea, bacteria, and
eucarya. Proc Natl Acad Sci USA 1990, 87:4576-4579.
10. DeLong E: Archaea in coastal marine environments. Proc Natl
Acad Sci USA 1992, 89:5685-5689.
11. Fuhrman J, McCallum K, Davis A: Novel major archaebacterial
group from marine plankton. Nature 1992, 356:148-149.
12. Gaasterland T, Ragan M: Constructing multigenome views of
• whole microbial genomes. J Microb Comp Genomics 1998,
3:177-192.
This paper presents a methodology for comparing complements of proteins
encoded in whole microbial genomes. The approach enables queries that
seek correlations between conservation of genomic distribution and conser-
vation of functional category.
13. Gaasterland T, Ragan M: Phyletic and functional patterns of ORF
•• distribution among prokaryotes. J Microb Comp Genomics 1998,
3:199-217.
The methodology introduced in [8] is applied to the analysis of whole
genomes from prokaryotic organisms, with yeast as an outlier organism. The
analysis reveals that proteins that occur only in Bacteria or only in Archaea
are not restricted to any functional category. Surprisingly, the complement of
proteins shared exclusively among both Bacteria and Archaea (prokaryotes)
is very small compared to the complements restricted to Bacteria and
Archaea, or shared among prokaryotes and yeast.
14. Ragan M, Gaasterland T: A prokaryotic view of the yeast genome.
• J Microb Comp Genomics 1998, 3:219-235.
Using the methodology introduced in [12•], the authors analyze the comple-
ment of proteins from the yeast that have counterparts in prokaryotic organ-
isms cover most of central metabolism, yet the non-prokaryotic proportion of
yeast is relatively large. The complement of proteins shared exclusively
among Archaea and yeast is overabundant in proteins involved in transcrip-
tion, transplantation and DNA processing. However, these categories cover
only 25 of those proteins. The paper analyzes distribution of bacterial coun-
terparts to yeast mitochondrial biogenesis nuclear proteins nad yeast mito-
chondrial proteins, and finds that matches to bacterial organisms are broadly
distributed and inclusive.
15. Sensen C, Charlebois R, Chow C, Clausen I, Curtis B, Doolittle W,
• Duguet M, Erauso G, Gaasterland T, Garrett R et al.: Completing the
sequence of the Sulfolobus solfataricus P2 genome. Extremophiles
1998, 2:305-312.
This paper lays out the underlying strategy to accomplishing a distributed
genome sequencing project and annotating the genome. An analysis of pro-
tein function, repeat structure, and insertion elements is given for the largest
archaeal genome undergoing sequencing.
16. Koonin E, Mushegian A, Galperin M, Walker D: Comparison of
archaeal and bacterial genomes: computer analysis of protein
sequences predicts novel functions and suggests a chimeric
origin for the archaea. Mol Microbiol 1997, 25:617-637.
17. Feng D, Cho G, Doolittle R: Determining divergence times with a
protein clock: update and reevaluation. Proc Natl Acad Sci USA
1997, 94:13028-13033.
18. Koga Y, Kyuragi T, Nishihara M, Sone N: Did archaeal and bacterial
• cells arise independently from noncellular precursors? A
hypothesis stating that the advent of membrane phospholipid
with enantiomeric glycerophosphate backbones caused the
separation of the two lines of descent. J Mol Evol 1998, 46:54-63.
The authors relate the structure of the EgsA (enantiomeric glycerophosphate
synthase) protein from M. thermoautotrophicum to the functionally related
protein NAD(P)-linked sn-glycerol-3-phosphate (G-3-P) dehydrogenase
from E. coli. The complete lack of sequence similarity indicates that the
stereostructure of cell membrane phospholipids has been since the last
common ancestor. This leads to a hypothesis that Archaea and Bacteria dif-
ferentiated by membrane composition: G-1-P in Archaea and G-3-P in
Bacteria.
19. Rivera M, Jain R, Moore J, Lake J: Genomic evidence for two
• functionally distinct gene classes. Proc Natl Acad Sci USA 1998,
95:6239-6244.
The complements of proteins from whole genomes in each phylogenetic
domain are analyzed to search for distinct classes of proteins. The authors
demonstrate that prokaryotic genes diverge into two groups: information
processing genes and non-informational metabolic genes.
20. Gupta R: What are archaebacteria: life’s third domain or
monoderm prokaryotes related to Gram-positive bacteria? A new
proposal for the classification of prokaryotic organisms. Mol
Microbiol 1998, 29:695-707.
21. Deckert G, Warren P, Gaasterland T, Young W, Lenox A, Graham D,
•• Overbeek R, Snead M, Keller M, Aujay M et al.: The complete
genome of the hyperthermophilic bacterium Aquifex aeolicus.
Nature 1998, 392:353-358.
The functional annotation of the first complete genome of a hyperther-
mophilic bacterium is presented. The early-branching bacterium Aquifex
aeolicus shares more genes exclusively with archaeal organisms than other
bacterial organisms. Even so, the metabolic and structural genes remain
broadly bacterial.
22. Nelson K, Clayton R, Gill S, Gwinn M, Daniel R, Haft H, Hickey E,
•• Peterson J, Nelson W, Ketchum K et al.: Evidence for lateral gene
transfer between archaea and bacteria from genome sequence of
Thermotoga maritima. Nat Genet 1999, 399:323-329.
This paper reports on the complete genome of the early-branching ther-
mophile Thermotoga maritima. A large complement of genes involved in
degradation of sugars and plant polysaccharides are shared exclusively with
the thermophilic bacterium Aquifex aeolicus and Archaea. This genome has
a larger percentage of genes shared exclusively with Archaea than does
Aquifex aeolicus.
23. Kyrpides N, Olsen G, Klenk H, White O, Woese C: Methanococcus
jannaschii genome: revisited. J Microb Comp Genomics 1996,
1:329-338.
24. Kim H, Vothknecht U, Hedderich R, Celic I, Soll D: Sequence
divergence of seryl-trna synthetases in archaea. J Bacteriol 1998,
180:6446-6449.
mc2509.qxd 11/09/1999 2:41 PM Page 547
25. Brown J, Robb F, Weiss R, Doolittle W: Evidence for the early
divergence of tryptophanyl- and tyrosyl-trna synthetases. J Mol
Evol 1997, 45:9-16.
26. Ibba M, Morgan S, Curnow A, Pridmore D, Vothknecht U, Gardner W,
Lin W, Woese C, Soll D: A euryarchaeal lysyl-trna synthetase:
resemblance to class I synthetases. Science 1997, 278:1119-
1122.
27. Ibba M, Bono J, Rosa P, Soll D: Archaeal-type lysyl-trna synthetase
in the lyme disease spirochete Borrelia burgdorferi. Proc Natl
Acad Sci USA 1997, 94:14383-14388.
28. Charlebois R, Sensen C, Doolittle W, Brown J: Evolutionary analysis
of the hisCGABdFDEHI gene cluster from the archaeon
Sulfolobus solfataricus P2. J Bacteriol 1997, 179:4429-4432.
29. Fani R, Mori E, Tamburini E, Lazcano A: Evolution of the structure
and chromosomal distribution of histidine biosynthetic genes.
Orig Life Evol Biosph 1998, 28:555-570.
30. Fitz-Gibbon S, Choi A, Miller J, Stetter K, Simon M, Swanson R, Kim
U: A fosmid-based genomic map and identification of 474 genes
of the hyperthermophilic archaeon Pyrobaculum aerophilum.
Extremophiles 1997, 1:36-51.
31. Dubchak I, Muchnik I, Kim S: Assignment of folds for proteins of
• unknown function in three microbial genomes. J Microb
Comp Genomics 1998, 3:171-175.
The authors use a neural-network based approach to predict protein struc-
tures for protein sequences of unknown function encoded in M. genitalium,
M. jannaschii, and H. influenzae. The method was able to produce high-con-
fidence folds for 33 sequences of unknown function.
32. Kim K, Hung L, Yokota H, Kim R, Kim S: Crystal structures of
eukaryotic translation initiation factor 5a from Methanococcus
jannaschii at 1.8 Å resolution. Proc Natl Acad Sci USA 1998,
95:10419-10424.
33. Kim K, Kim R, Kim S: Crystal structure of a small heat-shock
•• protein. Nature 1998, 394:595-599.
A new structure for a small heat-shock protein (sHSP) from M. jannaschii
has been solved as a part of a high-throughput structural genomics proto-
type project. This sHSP structure helps to understand how small heat-shock
proteins protect substrates from denaturation.
34. Kim K, Yokota H, Kim R, Kim S: Cloning, expression, and
crystallization of a hyperthermophilic protein that is homologous
to the eukaryotic translation initiation factor, eIF5A. Protein
Science 1997, 6:2268-2270.
35. Zarembinski T, Hung L, Mueller-Dieckmann H, Kim K, Yokota H, Kim R,
Kim S: Structure-based assignment of the biochemical function of
a hypothetical protein: a test case of structural genomics. Proc
Natl Acad Sci USA 1998, 95:15189-15193.
36. Peat T, Newman J, Waldo G, Berendzen J, Terwilliger T: Structure of
translation initiation factor 5a from Pyrobaculum aerophilum at
1.75 Å resolution. Structure 1998, 6:1207-1214.
37. Gaasterland T: Structural genomics: bioinformatics in the driver’s
seat. Nat Biotech 1998, 16:625-627.
38. Sáchez R, Šali A: Large-scale protein structure modeling of the
• Saccharomyces cerevisiae genome. Proc Natl Acad Sci USA 1998,
95:13597-13602.
The authors have carried out a genome-wide prediction of structures for pro-
teins encoded in the yeast genome. They were able to build homology mod-
els for the 3D structure for domains in 1071 proteins in yeast. Only 40 of
Archaeal genomics Gaasterland 547
these yeast proteins had experimentally determined structures. A database
system makes the results available on the World Wide Web at
http://guitar.rockefeller.edu/modbase.
39. Wallin E, von Heijne G: Genome-wide analysis of integral
•• membrane proteins from eubacterial, archaean, and eukaryotic
organisms. Protein Science 1998, 7:1029-1038.
This paper presents a statistical analysis of integral membrane proteins
encoded in the complete genomes of organisms from all phylogenetic
domains. One-fifth to one-third of encoded proteins are predicted to be
membrane proteins, and most are predicted to have more positively charged
residues in the cytoplasmic segments than in the external segments.
40. Gerstein M: Patterns of protein-fold usage in eight microbial
• genomes: a comprehensive structural census. Proteins 1998,
33:518-534.
This paper reports on the distribution of known folds across proteins from
complete genomes. The approach counted protein sequences with suffi-
cient sequence similarity to sequences with known structure to indicate
conservation of structure. The resulting fold distribution is distinct from that
in the protein databank (PDB) of protein molecule structures.
41. Giometti C, Tollaksen S, Liang X, Adams M, Holden J, Menon A, Schut
G, Reich C, Olsen G: Archaeal proteomics. In Microbial Genome
Project Section, DOE Human Genome Program Contractor-Grantee
Workshop VII: 1999 Jan 12—16, Oakland, CA. Washington, DC:
Department of Energy; 1999:150.
42. Sandman K, Reeve J: Archaeal nucleosome positioning by CTG
• repeats. J Bacteriology 1999, 181:1035-1038.
The authors demonstrate that archaeal histones assemble on genomic DNA
preferentially in (CTG)6 and (CTG)8 repeats. Archaeal histones also recog-
nize eukoryotic nucleosome positioning signals.
43. Pereira S, Reeve J: Histones and nucleosomes in Archaea and
Eukarya: a comparative analysis. Extremophiles 1998, 2:141-148.
44. Bell S, Jaxel C, Nadal M, Kosa P, Jackson S: Temperature, template
topology, and factor requirements of archaeal transcription. Proc
Natl Acad Sci USA 1998, 95:15218-15222.
45. Li W, Grayling R, Sandman K, Edmondson S, Shriver J, Reeve J:
•• Thermodynamic stability of archaeal histones. Biochemistry 1998,
37:10563-10572.
A comprehensive analysis of the effect of temperature, salt and pH on the
stability of archaeal histones yields insights into the relationships between
stability and structural features. Unfolding is found to be 90 reversible with
recovery of function. The paper discusses how structural features may lead
to differences in stability.
46. Pereira S, Grayling R, Lurz R, Reeve J: Archaeal nucleosomes. Proc
Natl Acad Sci USA 1997, 94:12633-12637.
47. Washio T, Sasayama J, Tomita M: Analysis of complete genomes
• suggests that many prokaryotes do not rely on hairpin formation
in transcription termination. Nucleic Acids Research 1998,
26:5456-5463.
The authors compute free energies of mRNA hairpin structures near stop
codons across complete annotated bacterial and archaeal genomes. Four of
16 bacterial genomes show a significant increase in strong hairpins at 30 bp
downstream from stop condons. The other bacterial genomes and the
archaeal genomes show no indication of hairpins corresponding to down-
stream regions of stop codons. This indicates that hairpin formation at tran-
scription termination sites may be restricted to a subset of organisms.
48. Mrazek J, Karlin S: Strand compositional asymmetry in bacterial
and large viral genomes. Proc Natl Acad Sci USA 1998,
95:3720-3725.