Genomics against flatulence

In the past several months, eukaryotic genome sequencing has brought us the complete genome of the tiny green alga Ostreococcus ‘lucimarinus’ (Palenik et al., 2007) and a draft genome of the mosquito Aedes aegypti (Nene et al., 2007). Given that the genome sequence of another Ostreococcus species, Ostreococcus tauri, has been sequenced less than a year ago (Derelle et al., 2006), the availability of the O. lucimarinus genome opens a possibility to study the evolution of this unicellular planktonic organism and its adaptation to the life in the surface layer of the sea. There has been also exciting news from archaeal and bacterial genome sequencing. The list of recently sequenced genomes (Table 1) includes bacteria that inhabit a variety of ecological niches and degrade numerous environmental contaminants, as well as two γ-proteobacteria with near-minimal gene sets.

Table 1.

Recently completed microbial genomes (April–June 2007).

Species name	Taxonomy	GenBank accession	Genome size (bp)	Proteins (total)	Sequencing centrea	Reference
New organisms
Ostreococcus lucimarinus	Eukaryota, Viridiplantae	CP000581–CP000601	13 200 000 (Total)	7651	JGI	Palenik et al. (2007)
Methanobrevibacter smithii	Euryarchaeota	CP000678	1 853 160	1795	Washington U.	Samuel et al. (2007)
Metallosphaera sedula	Crenarchaeota	CP000682	2 191 517	2256	JGI	Unpublished
Pyrobaculum arsenaticum	Crenarchaeota	CP000660	2 121 076	2298	JGI	Unpublished
Clavibacter michiganensis	Actinobacteria	AM711867AM711866AM711865	3 297 891 69 989 27 357	3029	University of Bielefeld, Germany
Mycobacterium gilvum	Actinobacteria	CP000656–CP000659	5 982 829 (Total)	5579	JGI	Unpublished
Salinispora tropica	Actinobacteria	CP000667	5 183 331	4536	JGI	Udwary et al. (2007)
Flavobacterium johnsoniae	Bacteroidetes	CP000685	6 096 872	5017	JGI	Unpublished
Prosthecochloris vibrioformis	Chlorobi	CP000607	1 966 858	1753	JGI	Unpublished
Dehalococcoides sp. BAV1	Chloroflexi	CP000688	1 341 892	1371	JGI	Unpublished
Roseiflexus sp. RS-1	Chloroflexi	CP000686	5 801 598	4517	JGI	Unpublished
Synechococcus sp. RCC307	Cyanobacteria	CT978603	2 224 914	2535	Genoscope	Unpublished
Synechococcus sp. WH 7803	Cyanobacteria	CT971583	2 366 980	2533	Genoscope	Unpublished
Caldicellulosiruptor saccharolyticus	Firmicutes	CP000679	2 970 275	2679	JGI	Unpublished
Clostridium botulinum	Firmicutes	AM412317AM412318	3 886 916 16 344	3592	Sanger Institute	Sebaihia et al. (2007)
Lactobacillus reuteri	Firmicutes	CP000705	1 999 618	1900	JGI	Unpublished
Mycoplasma agalactiae	Firmicutes	CU179680	877 438	742	Genoscope	Sirand-Pugnet et al. (2007)
Pelotomaculum thermopropionicum	Firmicutes	AP009389	3 025 375	2920	Marine Biotech. Institute	Kosaka et al. (2006)
Streptococcus suis 05ZYH33	Firmicutes	CP000407	2 096 309	2186	BIG – Beijing	Chen et al. (2007)
Streptococcus suis 98HAH33	Firmicutes	CP000408	2 095 698	2189	BIG – Beijing	Chen et al. (2007)
Acidiphilium cryptum	α-Proteobacteria	CP000689–CP000697	3 963 080 (Total)	3559	JGI	Unpublished
Bradyrhizobium sp. BTAi1	α-Proteobacteria	CP000494CP000495	8 264 687 228 826	7622	JGI	Giraud et al. (2007)
Bradyrhizobium sp. ORS278	α-Proteobacteria	CU234118	7 456 587	6717	Genoscope	Giraud et al. (2007)
Brucella ovis	α-Proteobacteria	CP000708CP000709	2 111 370 1 164 220	2892	TIGR	Unpublished
Orientia tsutsugamushi	α-Proteobacteria	AM494475	2 127 051	1182	Seoul National University, Korea	Cho et al. (2007)
Sphingomonas wittichii	α-Proteobacteria	CP000699CP000700CP000701	5 382 261 310 228 222 757	5345	JGI	Unpublished
Polynucleobacter sp. QLW-P1DMWA-1	β-Proteobacteria	CP000655	2 159 490	2077	JGI	Unpublished
Aeromonas salmonicida	γ-Proteobacteria	CP000644CP000645CP000646	4 702 402 166 749 155 098	4413	NRC – Halifax	Unpublished
Candidatus Vesicomyosocius okutanii	γ-Proteobacteria	AP009247	1 022 154	937	JAMSTEC	Kuwahara et al. (2007)
Dichelobacter nodosus	γ-Proteobacteria	CP000513	1 389 350	1280	TIGR	Myers et al. (2007)
Enterobacter sp. 638	γ-Proteobacteria	CP000653CP000654	4 518 712 157 749	4240	JGI	Unpublished
Pseudomonas mendocina	γ-Proteobacteria	CP000680	5 072 807	4594	JGI	Unpublished
Pseudomonas stutzeri	γ-Proteobacteria	CP000304	4 567 418	4128	BRI – Beijing	Unpublished
Psychrobacter sp. PRwf-1	γ-Proteobacteria	CP000713CP000714CP000715	2 978 976 13 956 2 117	2385	JGI	Unpublished
Shewanella putrefaciens	γ-Proteobacteria	CP000681	4 659 220	3972	JGI	Unpublished
Geobacter uraniumreducens	δ-Proteobacteria	CP000698	5 136 364	4357	JGI	Unpublished
Thermotoga petrophila	Thermotogae	CP000702	1 823 511	1785	JGI	Unpublished
New strains
Mycobacterium tuberculosis H37Ra	Actinobacteria	CP000611	4 419 977	4034	Fudan University, Shanghai, China	Unpublished
Staphylococcus aureus spp. aureusJH9	Firmicutes	CP000703CP000704	2 906 700 30 429	2726	JGI	Unpublished
Rhodobacter sphaeroides ATCC 17025	α-Proteobacteria	CP000661–CP000666	4 557 127 (Total)	4333	JGI	Unpublished
Legionella pneumophila str. Corby	γ-Proteobacteria	CP000675	3 576 470	3206	Fritz Lipmann Institute, Jena, Germany	Unpublished
Pseudomonas putida F1	γ-Proteobacteria	CP000712	5 959 964	5252	JGI	Unpublished
Vibrio choleraeO395	γ-Proteobacteria	CP000627CP000626	3 024 069 1 108 250	3875	TIGR	Unpublished
Yersinia pestis Pestoides F	γ-Proteobacteria	CP000668CP000670CP000669	4 517 345 137 010 71 507	4069	JGI	Unpublished

^aSequencing centre names are abbreviated as follows: JGI, US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; Washington U., Washington University School of Medicine, St. Louis, MO, USA; Genoscope, Centre National de Séquençage, Evry cedex, France; Sanger Institute, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK; Marine Biotech. Institute, Marine Biotechnology Institute, Heita, Kamaishi, Iwate, Japan; BIG – Beijing, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; TIGR, The Institute of Genomic Research (since October 2006 – J. Craig Venter Institute), Rockville, MD, USA; NRC-Halifax, NRC Institute for Marine Biosciences, Halifax, Nova Scotia, Canada; JAMSTEC, Japan Agency for Maine-Earth Science and Technology, Natsushima-cho, Yokosuka, Japan; BRI – Beijing, The Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, HaiDian, Beijing, China.

Archaea (archaebacteria) are generally viewed as free-living organisms capable of surviving at extremely high temperatures, salt concentrations and extreme pH values. The discoveries, primarily in the past several years, of various mesophilic archaea have done little to shatter the perception of archaea as exotic organisms with little relevance to everyday human life. Indeed, there are no known human pathogens among the Archaea. Nevertheless, archaea play a key role in human gut, accounting for one of its activities that usually goes unmentioned, namely, production of gas. Some of this gas, consisting largely of methane and hydrogen, makes it all the way back the gastrointestinal tract and shows up in human breath. Most of the gas, however, is released from the large intestine the natural way, by some estimates, up to 0.5 l day⁻¹ (see McKay et al., 1985; Suarez et al., 1997). Although the excreted gas has a complex and variable chemical composition, its methane component is produced by methanogenic bacteria, which, as we now know, are actually not bacteria but archaea. Isolation of methanogens from human feces was first reported almost 40 years ago (Nottingham and Hungate, 1968). The isolated organism was similar to the ruminal methanogen Methanobacterium ruminantium, described by Paul H. Smith and Robert E. Hungate (1958) several years earlier. The culture counts, estimated from serial dilutions, were in the range of 2 × 10⁷ to 2 × 10⁹ organisms g⁻¹. In the spirit of the time, the validity of the latter figure is discussed in the article (which is freely available on line at the Journal of Bacteriology website http://jb.asm.org/cgi/reprint/96/6/2178 or through PubMed Central) with the following details:

The sample showing 2 × 10⁹ methanogenic bacteria per gram was obtained from a patient in the Veterans Administration Hospital, Madison, Wis., by E. M. Lapinski. Unusually large quantities of methane had been detected in the expired gas of this patient. A fecal sample was sent airmail to Davis, California, sealed with no access of oxygen. Presumably, the lower than body temperature in transit prevented growth, and the value found is an approximation of the viable bacteria in the sample.

In a subsequent revision of metanogen taxonomy, M. ruminantium was transferred to the genus Methanobrevibacter with one of its species named Methanobrevibacter smithii, after Paul H. Smith (Balch et al., 1979). Methanobrevibacter smithii has been detected in human feces, human dental plaque and human vaginal samples, as well as in anaerobic environments such as activated sludge (Miller et al., 1982; Belay et al., 1988; 1990). The metabolic role of M. smithii and its interactions with bacterial gut flora have been subject of intensive studies (Samuel and Gordon, 2006), which recently culminated in determining the complete genome sequence of this organism. In the spirit of the current times, the description of M. smithii genome (Samuel et al., 2007) offers a detailed analysis of its intermediary metabolism but avoids mentioning the most conspicuous contribution of this organism to the human well-being. Still, the authors introduce the notion of ‘antiarchaeal’ drugs that could be used to control the population of M. smithii in the lower intestine. Taking into account the contribution of methanogenic archaea to the global warming (see our previous column, Galperin, 2007), a search for antimethanogen compounds could be quite an important undertaking. Accordingly, studies of methanogenesis and archaeal metabolism in general, which until recently appeared to be of purely academic interest, are suddenly finding unexpected applications in drug design.

Two other recently sequenced archaeal genomes belong to Crenarchaea. Metallosphaera sedula strain DSM 5348 is an aerobic thermoacidophile related to Sulfolobus spp. that was first isolated from a thermal pond in the Pisciarelli Solfatara in Italy (Huber et al., 1989). It can grow at temperatures ranging from 50 to 79°C with optimal growth at 74°C and pH 2. Metallosphaera sedula is capable of oxidizing sulfidic ores, such as pyrite, making it an attractive organism for use in bioleaching of metals. Several of its respiratory complexes have been characterized (Kappler et al., 2005); the genome sequence should allow identification of the rest of them.

Just 2 months after completing the sequence of Pyrobaculum calidifontis (GenBank accession number CP000561), JGI scientists have released the genome of Pyrobaculum arsenaticum, the fourth member of that genus with a completely sequenced genome. Pyrobaculum arsenaticum is a strictly anaerobic, hyperthermophilic archaeon, isolated from a hot spring in Italy. It could grow chemoautotrophically with CO₂ as carbon source, H₂ as electron donor and arsenate, thiosulfate or elemental sulfur as electron acceptors (Huber et al., 2000). It could also grow organotrophically, using sulfur, selenate or arsenate as electron acceptors. H₂S was formed from sulfur or thiosulfate, arsenite from arsenate, whereas reduction of selenate produced elemental selenium. The variety of electron acceptors used by different Pyrobaculum spp. as well as their different tolerance towards oxygen make comparative analysis of these genomes a very interesting task.

Among all the members of the phylum Actinobacteria with completely sequenced genomes, Clavibacter michiganensis is only the second phytopathogen. The sequenced strain C. michiganensis spp. michiganensis is a pathogen of tomato that causes bacterial wilt and canker. This species includes four other subspecies. One of them, C. michiganensis spp. sepedonicus, is responsible for ring rot of potato; its genome is being sequenced at the Sanger Institute. Three other subspecies of C. michiganensis infect, respectively, maize, wheat and alfalfa (Jahr et al., 1999; Gartemann et al., 2003).

Mycobacterium gilvum (previously referred to as Mycobacterium flavescens strain PYR-GCK) has been isolated in the sediment from the Grand Calumet River in Indiana as a strain capable of using pyrene as a sole source of carbon and energy. This strain was also capable of metabolizing such polycyclic aromatic hydrocarbons (PAHs) as phenanthrene and fluoranthene, but not naphthalene, chrysene, anthracene, fluorene, or benzo[a]pyrene (Dean-Ross and Cerniglia, 1996). The first step of pyrene degradation is catalysed by the same two-subunit aromatic ring-hydroxylating dioxygenase NidAB as the one found in Mycobacterium vanbaalenii and other PAH-degrading mycobacteria (Brezna et al., 2003). Thus, M. gilvum probably differs from them in the downstream steps of PAH degradation, which now could be deduced through genome comparisons.

Salinispora tropica strain CNB-440 is a marine actinomycete, the first sequenced representative of the unique genus within the phylum Actinobacteria that is widespread in tropical and subtropical marine sediments (Jensen and Mafnas, 2006). Its cultivation has been achieved by including seawater into the growth medium (Mincer et al., 2002), which is why Salinispora spp. are now considered obligate marine bacteria. Accordingly, comparing the genome of S. tropica to other actinobacterial genomes offers a chance to examine how members of this genus have adapted to the marine life. JGI scientists are currently sequencing the genome of Salinispora arenicola, the second cultured representative of this genus (Maldonado et al., 2005). In addition to its ecological significance, S. tropica is remarkable as a producent of the various halogenated macrolides, including the anticancer agent salinosporamide A, a potent inhibitor of the 20S proteasome (Williams et al., 2005). A detailed analysis of S. tropica genome is expected to clarify the macrolide biosynthesis pathway(s) and allow genetic manipulation leading to an in improved production of salinosporamide A and other secondary metabolites (Udwary et al., 2007).

Flavobacterium johnsoniae (formerly Cytophaga johnsonae), first described by Roger Stanier (1947), is an aerobic bacterium that is commonly found in soil and freshwater. It is a member of the phylum Bacteroidetes, also known as the Cytophaga-Flavobacterium-Bacteroides group. Flavobacterium johnsoniae has attracted significant attention in the recent past, both as an effective chitin degrader and as a model organism for studying gliding motility (McBride, 2001; 2004). Remarkably, these two activities seem to be linked, as defects in gliding motility also affect chitin utilization (Braun et al., 2005). The reason for that is degradation of chitin and other insoluble biopolymers by F. johnsoniae apparently requires direct contact of cell with the substrate. This resembles cellulose digestion by the closely related Cytophaga hutchinsonii, whose genome has been sequenced at the JGI a year ago (Xie et al., 2007).

Prosthecochloris vibrioformis (a synonym of Chlorobium phaeovibrioides, Imhoff, 2003) is a green sulfur phototrophic bacterium, a member of the phylum Chlorobi, which already has four members with sequenced genomes. Like other Chlorobi, P. vibrioformis gains energy by anoxygenic photosynthesis using thiosulfate as an electron acceptor and reducing it to elemental sulfur, which accumulates as extracellular globules. The cells of P. vibrioformis have brownish colour owing to the large amounts of bacteriochlorophyll e and carotenoids in their chlorosomes.

Roseiflexus sp. strain RS-1, also an anoxygenic photosynthetic bacterium, is the first phototrophic representative of the phylum Chloroflexi to have a completely sequenced genome. The 5.2-Mb genome of another phototrophic member of the Chloroflexi, Chloroflexus aurantiacus strain J-10-fl has been available in GenBank for the past 5 years (accession no. AAAH00000000) but still remains at the stage of 77 contigs. Three more representatives of this phylum are members of the genus Dehalococcoides which have lost the photosynthetic genes in the process of genome contraction during their adaptation to reductive dehalogenation (see below). In contrast to P. vibrioformis, Roseiflexus sp. does not contain chlorosomes and its major photosynthetic pigment is bacteriochlorophyll a. Comparative analysis of the genomes of members of Chlorobi and Chloroflexi could provide valuable information about mechanisms of anoxygenic photosynthesis.

Dehalococcoides sp. strain BAV1 is also a member of Chloroflexi, the third representative of the genus Dehalococcoides to have a completely sequenced genome. All three Dehalococcoides spp. are capable of metabolizing chlorinated hydrocarbons, including tetrachloroethene (PCE) and trichloroethene (TCE), which are commonly used as solvents and are major contaminants of soil and groundwater. Although Dehalococcoides ethenogenes strain 195 was originally reported to be capable of metabolizing PCE and TCE all the way to ethene, its cultures were found to accumulate 1,1-dichloroethene and vinyl chloride, which is a known human carcinogen (Maymo-Gatell et al., 1997; 2001). Dehalococcoides sp. CBDB1 can dechlorinate a variety of chlorobenzens but is also incapable of using dichloroethene or vinyl chloride (Kube et al., 2005). In contrast, the newly sequenced Dehalococcoides sp. strain BAV1 could grow using vinyl chloride and all dichloroethene isomers as electron acceptors. In addition, it could cometabolize PCE and TCE. Thus, strain BAV1 can be used for complete detoxification of PCE and TCE, that is, degradation of these compounds to environmentally benign ethene and inorganic chloride (He et al., 2003a,b). Comparative analysis of all three strains could provide clues to the mechanisms of reductive dehalogenation and the substrate specificities of the corresponding enzymes.

Clostridium botulinum is a well-known agent of food poisoning. Its spores are resistant to heat and survive exposure to air. In anaerobic conditions, which often exist in poorly prepared canned foods, C. botulinum spores germinate into vegetative cells. Growing vegetative cells secrete a variety of proteases and one or more toxic neuropeptides, known collectively as the botulinum toxin. Consumption of food contaminated with nanogram quantities of the botulinum toxin can be fatal for humans, as the toxin causes paralysis of chest muscles, which leads to asphyxiation. In addition, C. botulinum occasionally infects open wounds. The genome description (Sebaihia et al., 2007) includes a detailed comparison of five Clostridium spp., particularly with respect to the structure of the cell surface, extracellular enzymes and the regulation of toxin production. One cannot help noting that this deadly toxin has become a popular tool in cosmetology and has been suggested for a number of other applications, such as treatment of chronic migraines.

Two other members of the order Clostridiales in the current list (Table 1) are finding more traditional uses in biotechnology. Caldicellulosiruptor saccharolyticus is an anaerobic thermophilic bacterium that was isolated from a thermal spring in New Zealand (Sissons et al., 1987). Both the genus name, meaning literally ‘hot cellulose disruptor’, and the species name, which means ‘lysing sugar’, reflect the ability of the organism to metabolize a variety of mono- and polysaccharides, such as arabinose, amorphous cellulose, fructose, galactose, glucose, glycogen, lactose, laminarin, lichenin, mannose, maltose, pullulan, pectin, rhamnose, starch, sucrose, xylan and xylose (Rainey et al., 1994). Based on its inability to form spores, C. saccharolyticus was first assigned to a separate lineage within the Bacillus/Clostridium subphylum of the Gram-positive bacteria (the current Firmicutes), but later recognized as a member of the order Clostridiales. The ability of C. saccharolyticus to grow at 70°C, hydrolysing both α- and β-glucans, including cellulose and pectin, makes it an attractive candidate for conversion of plant biomass into biofuel. Comparison of the genomic sequence of C. saccharolyticus with those of related organisms could provide an insight in the mechanisms and regulation of cellulose degradation.

Pelotomaculum thermopropionicum, also a member of Clostridiales, is a thermophilic propionate-oxidizing anaerobic bacterium, isolated in 2000 from anaerobic sludge blanket reactor in Niigata, Japan. It grows best in a syntrophic association with methanogenic archaea, metabolizing propionate, ethanol, lactate, butanol, pentanol, 1,3-propanediol, propanol and ethylene glycol (Imachi et al., 2002). Even before the completion of the genome sequencing, Kosaka and colleagues (2006) analysed the propionate fermentation pathway of P. thermopropionicum and compared it with the corresponding pathway of the actinobacterium Propionibacterium acnes.

Acidiphilium cryptum strain JF-5 has been isolated from an acidic coal mine lake situated in the Lusatian mining area in east central Germany. It is a facultatively anaerobic, extremely acidophilic heterotrophic α-proteobacterium that can reduce soluble and solid-phase Fe(III) using glucose as the electron donor (Küsel et al., 1999). It is also capable of reducing Cr(VI), which makes it an interesting model organism for studying metal reduction at extremely low pH values.

Sphingomonas wittichii (formerly Sphingomonas sp. strain RW1) is an aerobic α-proteobacterium that was isolated in the course of screening for dibenzo-p-dioxin-utilizing bacteria from the water samples collected from the River Elbe downstream of the city of Hamburg, Germany (Wittich et al., 1992). This organism could grow using both the biaryl ethers dibenzo-p-dioxin and dibenzofuran as the sole sources of carbon and energy. Polychlorinated dibenzo-p-dioxins and dibenzofurans are widespread contaminants of the environment that can be formed as by-products during the manufacture of pesticides, incineration of halogen-containing chemicals and of industrial and domestic waste, and bleaching of paper pulp (Wittich et al., 1992). The rare ability of S. wittichii to completely degrade these toxic compounds makes it an organism of choice for bioremediation of contaminated soil (Halden et al., 1999). While dioxin dioxygenase of S. wittichii has been characterized and the likely pathway of its degradation delineated several years ago (Armengaud et al., 1998; 1999), the genome sequence should lead to a much better understanding of the cellular adaptations to dioxin degradation.

Among the recently sequenced γ-proteobacterial genomes, two are remarkable because of their unusually small size. One of them, Candidatus Vesicomyosocius okutanii is an intracellular symbiont, inhabiting gill epithelial cells of the deep-sea clam Calyptogena okutaniis, which lives in the vicinity of hydrothermal vents (Kuwahara et al., 2007). In contrast to insect symbionts, some of which have very small genomes, Cand. V. okutanii is an autotroph, more specifically a thioautotroph. Its genome is also quite small, only 1 Mb in size, and codes for mere 937 proteins. Still, their products are sufficient to support thioautotrophic metabolism, as they include enzymes catalysing synthesis of almost all amino acids and various cofactors, RubisCO for CO₂ fixation, as well as enzymes of glycolysis, pentose phosphate cycle, and partial TCA cycle. Sulfide is used as electron donor and converted to sulfate, while oxygen and nitrate serve as terminal electron acceptors. However, several supposedly essential genes are missing, e.g. cell division genes ftsA, ftsL, ftsN, ftsX and ftsZ and lipoprotein localization genes lolA, lolB and lolC (Kuwahara et al., 2007). The absence of cell division genes may be linked to the fact that each host cell carries only a single cell of Cand. V. okutanii, which is vertically transferred through clam oocytes.

If Cand. V. okutanii has the smallest autotrophic genome sequenced to date, the sheep pathogen Dichelobacter nodosus has the smallest genome of any anaerobe. The genome of D. nodosus, the causative agent of ovine foot rot, is less than 1.4 Mb in size and codes for less than 1300 proteins (Myers et al., 2007). However, these genes are apparently all significant, as there are few paralogues and very few pseudogenes. Given that D. nodosus belongs to an early branching group of γ-Proteobacteria, the authors suggest that its evolutionary history differed from that of most other organisms with very small genomes, which are either obligate intracellular pathogens or symbionts. Thus, massive gene loss through pseudogenization probably played only a minor role in extensive genome reduction, if any, in the evolution of D. nodosus.

Of the three recently sequenced pseudomonad genomes (Table 1), Pseudomonas putida F1 is by far the best-studied one. This obligately aerobic bacterium was originally isolated from a polluted creek in Urbana, Illinois, by enrichment with ethylbenzene as the sole source of carbon and energy (Gibson et al., 1968). This strain can also grow on benzene, toluene and p-cymene, which are common contaminants of groundwater, leaking from underground gasoline storage tanks. When provided with a carbon source for growth, P. putida F1 can oxidize a variety of aromatic and aliphatic compounds that do not support its growth. This list includes nitrotoluenes, chlorobenzenes, chlorophenols and trichloroethylene. The mechanism of toluene degradation by P. putida F1 toluene dioxygenase and its regulation have been studied in much detail (Zylstra et al., 1988; Lau et al., 1997). Remarkably, P. putida F1 senses benzene, ethylbenzene and trichloroethylene, perceiving them as chemoattractants (Parales et al., 2000). Both strains of P. putida, F1 and KT2240, whose genome was sequenced 5 years ago (Nelson et al., 2002; Dos Santos et al., 2004), have great potential for use in bioremediation.

The Shewanella genome sequencing project has released yet another complete genome, this time of the facultative anaerobe Shewanella putrefaciens. While some strains of S. putrefaciens have been isolated from clinical samples and appear to be opportunistic human pathogens (Holt et al., 2005), the sequenced strain is interesting primarily because of its capability to effectively reduce polyvalent metals and radionuclides including solid phase oxides of Fe, Mn, Cr, U(VI) and Tc (VII), using lactate as the electron donor.

The δ-proteobacterium Geobacter uraniumreducens is also a powerful reducer of metals. The sequenced strain G. uraniumreducens Rf4 has been isolated from a contaminated aquifer at the former uranium ore processing facility in Rifle, Colorado (Anderson et al., 2003). Injection of acetate (1–3 mM) into the groundwater led to an enrichment of the groundwater with G. uraniumreducens, which coincided with a decrease in U(VI) levels. Comparison of G. uraniumreducens genome sequence with that of Geobacter metallireducens and other metal-reducing bacteria should help in finding the best strains for bioremediation of uranium and other radionuclides.

Eight years after the publication of the genome sequence of an obligately anaerobic hyperthermophilic bacterium Thermotoga maritima (Nelson et al., 1999), the genome of a second member of the phylum Thermotogae has been released. While also an obligate anaerobe similar to T. maritima in its sugar utilization profile, Thermotoga petrophila strain RKU-1 has been isolated from a deep subterranean oil reservoir in Niigata, Japan, and could grow at a much wider range of temperatures, from 48 to 88°C, with an optimum at 80°C (Takahata et al., 2001). These features make T. petrophila an attractive source of thermostable enzymes, as well as a convenient model organism to study the mechanisms of thermotolerance in bacteria.

The list of the recently sequenced genomes also includes several important bacterial pathogens. The genome of Orientia (formerly Rickettsia) tsutsugamushi, the causative agent of scrub typhus, is remarkable primarily for the abundance of repeat elements, including numerous tra genes, transposases, phage integrases, reverse transcriptases and potential host–cell interaction proteins (Cho et al., 2007). Genome sequencing of two strains of Streptococcus suis serotype 2, which caused an outbreak of streptococcal toxic shock syndrome in China, revealed a shared pathogenicity island that appeared responsible for the high-virulence phenotype (Chen et al., 2007). In an article with an unusually impressive title, genome analysis of the ruminant pathogen Mycoplasma agalactiae and closely related mycoplasmas revealed traces of horizontal gene transfer, suggesting that it could have played a role in the mycoplasmal evolution (Sirand-Pugnet et al., 2007). The fifth complete genome of a Brucella spp. comes from the sheep pathogen Brucella ovis, which causes ovine contagious epididymitis in rams and premature abortion in pregnant ewes. It should be noted that in 1988, the ICSB Subcommittee on the Taxonomy of Brucella concluded that the Brucella is a monospecific genus with a single species Brucella melitensis. Indeed, all Brucella spp. have genomes consisting of two chromosomes with similar sizes, similar G + C content of 57.2% and encoding many proteins that are 99–100% identical. Thus, B. ovis is currently considered an accepted synonym for Brucella melitensis biovar Ovis.

The genome of Aeromonas salmonicida spp. salmonicida strain A449 was sequenced in an effort to find new ways to control this widespread fish pathogen. The draft version of the genome has already been used to construct A. salmonicida DNA microarray and identify potential virulence genes and candidates for vaccine development (Nash et al., 2006).

Last but not least, a recent article has uncovered the function of one of widespread ‘conserved hypothetical’ genes. This gene, which has been designated yebR in Escherichia coli, ytsP in Bacillus subtilis and YKL069w in Saccharomyces cerevisiae, has been shown to encode an enzyme that reduces free methionine sulfoxide (Lin et al., 2007). Two previously identified methionine sulfoxide reductases act predominantly on oxidized methionine residues in protein and cannot protect the cellular pool of free amino acid from oxidation. This work is yet another proof that ‘house-cleaning’ is a major cellular function that might employ a fair number of the uncharacterized ‘hypothetical’ proteins (see Galperin et al., 2006 for a review).