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time a case in which different transport mechanisms

are genetically linked to a conserved carbohydrate

metabolic cluster. Even transporters of the unusual

class of binding protein-dependent secondary transpor-

ters were found linked to this cluster. It was suggested

that the different classes of transporters have evolved

from secondary transporters by association with bind-

ing proteins, ATPases and phosphorylating enzymes,

thereby gaining higher substrate affinities and trans-

location power [12]. It is possible that in this cluster

we can see the subtlety by which evolution can take

place at the genome level.

AcknowledgementsWe thank Wil Konings for helpful discussion. T.H.P. was supported by

the Netherlands Organization for Scientific Research (NWO) grant no.

805–19–046 P.

References

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kinase for L-xylulose opens a new pathway for the utilization of 

L-lyxose by Escherichia coli. J. Biol. Chem. 269, 29665–29669

2 Badıa, J. et al. (1998) A rare 920-kilobase chromosomal inversion

mediated by IS1 transposition causes constitutive expression of the

 yiaK–S operon for carbohydrate utilization in Escherichia coli. J. Biol.

Chem. 273, 8376–8381

3 Ibanez, E. et al. (2000) Regulation of expression of the yiaKLM-

 NOPQRS operon for carbohydrate utilization in Escherichia coli:

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4 Ibanez, E. et al. (2000) Role of the yiaR and yiaS genes of Escherichia

coli in metabolism of endogenously formed L-xylulose. J. Bacteriol.

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distributed in bacteria? Microbiology 143, 2519–2520

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 yjf-sga and yia-sgb operons. J. Bacteriol. 184, 302–3068 Yasueda, H. et al. (1999) Bacillus subtillis yckG and yckF encode two

keyenzymes of theribulosemonophosphate pathway used by methylo-

trophs, and yckH  is required for their expression. J. Bacteriol. 181,

7154–7160

9 Zhang, Z. et al. (2003) The ascorbate transporter of  Escherichia coli.

 J. Bacteriol. 185, 2243–2250

10 Postma, P.W. et al. (1996) Phosphoenolpyruvate:carbohydrate phos-

photransferase systems. In Escherichia coli and Salmonella: Cellular

and Molecular Biology (Neidhardt, F.C. et al., eds), pp. 1149–1174,

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proteins: binding protein-dependent secondary transporters. Mol.

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12 Driessen, A.J.M. et al. (2000) Diversity of transport mechanisms:

common structural principles. Trends Biochem. Sci. 25, 397–401

13 Rabus, R. et al. (1999) TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active trans-

porters. Microbiology 145, 3431–3445

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periplasmic (TRAP) transporters of bacteria and archaea. FEMS

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15 Poolman, B. and Konings, W.N. (1993) Secondary solute transport in

bacteria. Biochim. Biophys. Acta 1183, 5–39

16 Higgins, C.F. (2001) ABC transporters: physiology, structure and

mechanism - an overview. Res. Microbiol. 152, 205–210

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0966-842X/$ - see front matter q 2003 Elsevier Ltd. All rights reserved.doi:10.1016/j.tim.2003.11.001

| Microbial Genomics

All things great and small

Claire M. Fraser

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

The report in 2002 of a novel archaeal species, the first

representative of an unknown phylum, reminded us of 

the tremendous microbial diversity that remains to be

discovered on this planet [1]. Nanoarchaeum equitans (the

tiny archaea that rides the fire ball) is a small spherical cell

that grows attached to the surface of its archaeal host,

 Igniococcus spp. These organisms were isolated from a hot

submarine vent in the Kolbeinsey ridge, north of Iceland,

and can be grown in the laboratory in anaerobic cultures at

90 8C in the presence of S, H2 and CO2. It was by micro-

scopic examination of the Igniococcus cells that their

‘rider’, N. equitans, was discovered and by which it was

subsequently demonstrated that N. equitans is an obligate

symbiont of  Igniococcusspp. that cannot be grown alone in

culture. Equally surprising was that ‘universal’ primersdesigned to amplify ssRNA genes from bacterial and

archaeal species failed to yield a product from N. equitans

by the polymerase chain reaction (PCR). Subsequent

comparison of the ssRNA gene sequence from N. equitans

with those of other archeal species identified it as the first

member of a novel phylum, the Nanoarchaeota, which

represents the most deeply branching archaeal lineage

to date. Estimation of genome size by pulse field gel

electrophoresis suggested that N. equitans represents a

minimal organism with a genome of ,500 kb.

The much anticipated genomic sequence of  N. equitans

was published recently [2]. Its genome size of 490 885 bp

makes this the smallest prokaryotic genome deciphered to

date. Despite its small genome size, this archaeon has one

of the highest gene densities reported to date, with ,95%

of the genome representing predicted coding sequencesand stable RNAs. Most of the genes involved in infor-

mation processing (DNA replication, transcription and

translation) show most similarity to their counterparts inCorresponding author: Claire M. Fraser (cmfraser@tigr.org).

Update TRENDS in Microbiology  Vol.12 No.1 January 2004 7

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the Euryarchaeota. In contrast to the genomes described

for other minimal microbial species that appear to be

undergoing reductive evolution, N. equitans contains few

pseudogenes. It is not at all surprising, given its small

genome size, that N. equitans lacks essentially all known

metabolic pathways and contains only a minimal number

of putative transporters. It does, however, contain several

proteases and peptidases that might allow it to degrade

proteins that are derived from either its environment or

host. Perhaps more surprising is what is present in this

small genome. N. equitans contains an impressive reper-

toire of DNA repair enzymes, a feature not usually seen in

other minimal genomes. It is probable that this full set of 

DNA repair genes is necessary to repair the DNA damage

that occurs at its high growth temperature, although it is

tempting to speculate that there might be other reasons for

this capability.

  Another unusual feature of the N. equitans genomeis the presence of a large number of split noncontig-

uous genes that are fused in other archaeal genomes.

The splits, for the most part, occur between functional

domains in the translated proteins. It has been

postulated that multidomain proteins have evolved

from the fusion of less complex domains [3]. The

finding of several split genes, together with the

placement of  N. equitans in the most deeply branching

archaeal lineage is consistent with its early divergence

in the evolution of the Archaea. Whether other

members of the phylum Nanoarchaeota exist, waiting

to be discovered, remains to be determined. If they can

be found, it is probable that additional genomesequence data from these smallest of microbes would

reveal much about the evolution of microbial life.

  At the other end of the microbial spectrum is the

marine planctomycete, Pirellula spp. strain 1, which

has the largest circular genome of 7.145 Mbp that has

been sequenced to date [4]. The only larger genomes to

be found are those from Streptomyces coelicolour [5]

and Streptomyces avermitilis [6], but these are linear

chromsomes. Pirellula spp. are ubiquitously distributed

in terrestrial and marine environments, and are

important because of the roles that they play in global

carbon and nitrogen cycles. They are members of the

Planctomycetes, which might represent the deepest

branching bacterial lineage [7]. However, this phyloge-

netic placement is still somewhat controversial. Planc-

tomycetes share several unusual features including a

budding mode of reproduction similar to that observed

for Caulobacter crescentus, a cell wall that lacks

peptidoglycan, and a membrane surrounding the

chromosome. Therefore, there is much to be learned

about this relatively unknown bacterial group.

Given the paucity of molecular studies on Planctomy-

cetes, it was not unexpected to find that more than half of 

the predicted coding sequences do not display a significant

similarity to sequences in the available databases. What

was surprising was that less than 25% of the predicted

coding sequences in the Pirellula spp. genome repre-sent gene paralogs, because in many larger prokaryotic

genomes ,30– 50% of the predicted coding sequences

appear to have arisen through gene duplication events. It

was notable that almost 20% of the potential proteins for

which a signficant BLAST hit was obtained were most

similar to proteins in the Archaea or Eukaryotes, and the

remaining 80% that were most similar to bacterial

proteins were widely distributed across the phylogenetic

tree. Phylogenetic analysis of a limited set of genes

suggested a distant relationship to Chlamydia species,

which is consistent with the fact that both lack a

peptidoglycan cell wall.

Genome analysis has revealed several contradictions

for an environmental organism with a genome size of 

7.145 Mbp. Fewer transporters and predicted regulat-

ory genes were identified than might be expected,

given that the number of genes in these functional

categories tends to correlate with genome size. The

presence of a large number of predicted codingsequences for nitrate transport and nitrate or nitrite

reduction are an exception, and this observation is

consistent with the fact that Pirellula must survive in

a nitrogen-limited marine environment. Another fea-

ture that sets Pirellula apart from other microbes is

the large number of sulfatases encoded in the genome

– at least two orders of magnitude greater than seen in

any other completely sequenced microbial genome to

date. Because inorganic sulfur is not limited in marine

environments, this raises questions regarding the roles

that the large numbers of sulfatases play in the biology

of  Pirellula. It has been suggested that these might be

important in the degradation of sulfated glycopolymersthat are found in abundance in marine snow and to

which Pirellula can attach using a polar stalk.

It will be of great interest to compare the genome of 

 Pirellula spp. to that of  Gemmata obscuriglobus, a

freshwater Planctomycete, for which genome sequen-

cing is underway. As the analysis of the smallest and

largest circular bacterial chromosomes have recently

revealed, there are still many fascinating discoveries

that remain to be made regarding environmental

microbes.

References1 Huber, H. et al. (2002) Nature 417, 63–67

2 Waters, E. etal. (2003) The genome of  Nanoarchaeum equitans: Insights

into early archaeal evolution and derived parasitism. Proc. Natl. Acad.

 Sci. U. S. A. 100, 12984– 12988

3 Gilbert, W.F. (1987) The exon theory of genes. Cold Spring Harb. Symp.

Quant. Biol. 52, 901–905

4 Glockner, F.O. et al. (2003) Complete genome sequence of the marine

planctomycete Pirellula sp. strain 1. Proc. Natl. Acad. Sci.U. S. A. 100,

8298–8303

5 Bentley, S.D. et al. (2002) Complete genome sequence of the model

actinomycete Streptomyces coelicolor A3(2). Nature 417, 141–147

6 Omura, S. et al. (2001) Genome sequence of an industrial microorgan-

ism Streptomyces avermitilis: deducing the ability of producing

secondary metabolites. Proc. Natl. Acad. Sci. U. S. A. 98, 12215–12220

7 Brochier, C. and Philippe, H. (2002) A non-hyperthermophilic ancestor

for Bacteria. Nature 417, 244

0966-842X/$ - see front matter q 2003 Elsevier Ltd. All rights reserved.doi:10.1016/j.tim.2003.11.009

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