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Environ Microbiol. Author manuscript; available in PMC Oct 29, 2008.
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PMCID: PMC2575129
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The Complete Genome Sequence of Moorella thermoacetica (f. Clostridium thermoaceticum)

Summary

This paper describes the genome sequence of M. thermoacetica (f. Clostridium thermoaceticum), which is the model acetogenic bacterium that has been widely used for elucidating the Wood-Ljungdahl pathway of CO and CO2 fixation. This pathway, which is also known as the reductive acetyl-CoA pathway, allows acetogenic (often called homoacetogenic) bacteria to convert glucose stoichiometrically into three mol of acetate and to grow autotrophically using H2 and CO as electron donors and CO2 as an electron acceptor. Methanogenic archaea use this pathway in reverse to grow by converting acetate into methane and CO2. Acetogenic bacteria also couple the Wood-Ljungdahl pathway to a variety of other pathways to allow the metabolism of a wide variety of carbon sources and electron donors (sugars, carboxylic acids, alcohols, and aromatic compounds) and electron acceptors (CO2, nitrate, nitrite, thiosulfate, dimethylsulfoxide, and aromatic carboxyl groups). The genome consists of a single circular 2628784 bp chromosome encoding 2615 open reading frames, which includes 2523 predicted protein-encoding genes. Of these, 1834 genes (70.13%) have been assigned tentative functions, 665 (25.43%) matched genes of unknown function, and the remaining 24 (0.92%) had no database match. Two thousand three hundred eighty-four (91.17%) of the ORFs in the M. thermoacetica genome can be grouped in ortholog clusters. This first genome sequence of an acetogenic bacterium provides important information related to how acetogens engage their extreme metabolic diversity by switching among different carbon substrates and electron donors/acceptors and how they conserve energy by anaerobic respiration. Our genome analysis indicates that the key genetic trait for homoacetogenesis is the core acs gene cluster of the Wood-Ljungdahl pathway.

Introduction

Here we report the first complete genome sequence of an acetogenic bacterium. Acetogens are obligately anaerobic bacteria that use a mechanism of anaerobic CO and CO2 fixation, called the reductive acetyl-CoA or the Wood-Ljungdahl pathway as their main mechanism for energy conservation and for synthesis of acetyl-CoA and cell carbon from CO2 (Drake et al., 1994). Other terms to describe an organism using this type of metabolism are “homoacetogen” and “CO2-reducing acetogen”. We determined the genome sequence of Moorella thermoacetica, originally named Clostridium thermoaceticum, which has been the model acetogen since its isolation in 1942 (Fontaine et al., 1942) for elucidating the Wood-Ljungdahl pathway. As discussed below, this pathway is found in a broad range of phylogenetic classes, and is used in both the oxidative and reductive directions. Besides being used for energy production and autotrophic carbon assimilation in acetogens (Ljungdahl, 1994; Ragsdale, 1997; Drake et al., 2002), the Wood-Ljungdahl pathway is used for acetate catabolism by sulfate reducing bacteria (Schauder et al., 1988; Spormann and Thauer, 1988) and aceticlastic methanogens (Ferry, 1999) and for CO2 fixation by hydrogenotrophic methanogens (Stupperich et al., 1983; Ladapo and Whitman, 1990).

As early as 1932, organisms were discovered that could convert H2 and CO2 into acetic acid (Fischer et al., 1932). In 1936, Wieringa reported the first acetogenic bacterium, Clostridium aceticum (Wieringa, 1936, 1940), which was reisolated in 1981 (Braun et al., 1981). M. thermoacetica (Collins et al., 1994), a clostridium in the Thermoanaerobacteriaceae family, attracted wide interest when it was isolated because of its unusual ability to convert glucose almost stoichiometrically to three moles of acetic acid (Fontaine et al., 1942). It took many years to uncover the biochemical reactions responsible for this homoacetogenic pathway. The novelty of this pathway was recognized with the discovery that growth of M. thermoacetica on glucose involves incorporation of two molecules of CO2 directly into acetic acid (Barker and Kamen, 1945; Wood, 1952). The isolation of Acetobacterium woodii in 1977 and the description of methods to isolate organisms that can grow on H2 and CO2 (Balch et al., 1977) led to the isolation of many acetogens that can grow autotrophically, and in 1983 M. thermoacetica was shown to grow on H2/CO2 (Kerby and Zeikus, 1983). The identification of a hydrogenase in 1982 provided a biochemical basis for autotrophic growth of acetogens on hydrogen (Drake, 1982). Subsequently, acetogens have been shown to use a wide variety of carbon sources and electron donors and acceptors. M. thermoacetica is a versatile heterotroph, growing on sugars, two-carbon compounds (glyoxylate, glycolate, and oxalate), lactate, pyruvate, short-chain fatty acids, and methoxylated aromatic compounds. Besides CO2, electron acceptors include nitrate, nitrite, thiosulfate, and dimethylsulfoxide.

Acetogenic bacteria play an important role in the global carbon cycle, producing over 1012 kg (10 billion US tons) of acetic acid on a huge scale annually (Wood and Ljungdahl, 1991; Drake et al., 1994), which dwarfs the total output of acetate (an important chemical feedstock) by the world’s chemical industry (~1010 kg/yr). While most acetogens like M. thermoacetica are in the phylum Firmicutes, acetogens include Spirochaetes (Leadbetter et al., 1999; Salmassi and Leadbetter, 2003), δ-proteobacteria like Desulfotignum phosphitoxidans (Schink et al., 2002), and Acidobacteria like Holophaga foetida(Liesack et al., 1994). Important in the biology of the soil, lakes, and oceans, acetogens have been isolated from diverse environments, including the GI tract of animals and termites (Breznak, 1994; Mackie and Bryant, 1994), rice paddy soils (Rosencrantz et al., 1999), hypersaline waters (Ollivier et al., 1994), surface soils (Peters and Conrad, 1995; Kusel et al., 1999), and deep subsurface sediments (Liu and Suflita, 1993). Like methanogens, acetogens act as a H2 sink, depleting H2 that is generated in anaerobic environments during the natural biodegradation of organic compounds. Since the build-up of H2 inhibits biodegradation by creating an unfavorable thermodynamic equilibrium, acetogens enhance biodegradative capacity by coupling the oxidation of hydrogen gas to the reduction of CO2 to acetate. Acetogens also have been found in a methanogenic mixed population from an army ammunition manufacturing plant waste water treatment facility (Adrian and Arnett, 2004) and a dechlorinating community that has been enriched for bioremediation (Macbeth et al., 2004).

For organisms that house acetogens in their digestive systems, like humans, termites, and ruminants (Greening and Leedle, 1989; Tholen and Brune, 1999; Chassard and Bernalier-Donadille, 2006), the acetate generated by microbial metabolism is a beneficial nutrient for the host and for other microbes within the community. In these ecosystems, acetogens can compete directly with hydrogenotrophic methanogenic archaea, or interact syntrophically with acetotrophic methanogens that use H2 and CO2 to produce methane (Chassard and Bernalier-Donadille, 2006). Organisms containing the acs gene cluster are also enriched in the marine and terrestrial vertebrate and invertebrate gut biomes (Gill et al., 2006; Warnecke et al., 2007). In the termite gut, acetogens are the dominant hydrogen sinks (Pester and Brune, 2007), and it has been proposed that acetate is the major energy source for the termite (Odelson and Breznak, 1983). However, methanogens are the dominant hydrogenotrophs in many environments since methanogens have a lower threshold for H2 than acetogens (Le Van et al., 1998) and since the energy yield from the conversion of CO2 and H2 to methane is greater than that for conversion to acetate (Schink, 1997). Under such conditions, acetogens must often resort to other metabolic pathways for growth and, thus, have a highly diverse metabolic menu that comprises the biodegradation products of most natural polymers like cellulose and lignin, including sugars, alcohols, organic acids and aldehydes, aromatic compounds, and inorganic gases like CO, H2, and CO2. They also can use a variety of electron acceptors, e.g., CO2, nitrate, dimethylsulfoxide, fumarate, and protons. The M. thermoacetica genome sequence described here provides important information related to how acetogens engage this extreme metabolic diversity and how they switch with such facility among different carbon substrates and electron donors and acceptors.

Results

General genome features

The major features of the M. thermoacetica genome are listed in Table 1 and shown in Supplementary Figure S1. The genome consists of a single circular 2,628,784 bp chromosome that has a GC content of 56 % (Supplementary Figure S1). Base pair one of the chromosome was assigned within the putative origin of replication. The genome contains 51 tRNAs, 3 rRNAs (5S, 16S, and 23S), and 38 other RNAs predicted by the Rfam. Analysis of 16S rRNA sequences confirmed that M. thermoacetica belongs to the phylum Clostridia (Figure 1) and to the class Thermoanaerobacteriaceae. Figure 1 also highlights the known homoacetogenic microbes, revealing the wide distribution of phylogenetic classes in which this trait appears, clearly indicating that acetogenesis is a metabolic, not a phylogenetic trait. Besides the bacteria shown in Fig. 1, which are related to M. thermoacetica, the Wood-Ljungdahl pathway is also found in archaea. On the other hand, homoacetogenesis is a rare occurrence within a particular phylum. For example, two relatives of M. thermoacetica in the Thermoanaerobacteriaceae family whose genomes have been sequenced, Thermoanaerobacter tengcongensis (Bao et al., 2002), and Thermoanaerobacter ethanolicus, (draft sequence available at JGI), can also grow anaerobically on several mono- and disaccharides, and starch (Wiegel and Ljungdahl, 1981); however, among these three strains, only M. thermoacetica is homoacetogenic, and only M. thermoacetica has acetyl coenzyme A synthase (ACS), a key enzyme in the Wood-Ljungdahl pathway. Fermentation of glucose by T. tengcongensis or T. ethanolicus yields ethanol and/or acetate, 1.5–2 moles of CO2, and small amounts of H2. Thus, the genomic results clearly indicate that the trait of acetogenesis was distributed by horizontal transfer of the core genes of the Wood-Ljungdahl pathway.

Figure 1
16S rRNA-based phylogenetic tree of acetogens and their close neighbors
Table 1
General features of the M. thermoacetica genome.

The M. thermoacetica genome contains 2523 predicted protein-encoding genes, of which 1834 (70.13%) have been assigned tentative functions. Six hundred sixty-five predicted proteins (25.43%) matched proteins of unknown function, and the remaining 24 (0.92%) had no database match. A total of 429 paralogous protein families were identified in M. thermoacetica strain ATCC 39073, containing 1307 predicted proteins (49.98% of the total). Two thousand three hundred eighty-four (91.17%) of the ORFs in the M. thermoacetica genome can be grouped in ortholog clusters. Fifty-eight pseudogenes were identified in the M. thermoacetica genome by the IMG annotation. A complete list of pseudogenes and gene remnants is provided in Supplementary Table S1. Analysis of these genes in M. thermoacetica indicates that 41 out of 58 are redundant genes, with paralogs in the M. thermoacetica genome. The seventeen that do not have paralogs encode either putative or hypothetical proteins. These results suggest that elimination of the functions of these redundant genes may be tenuously ascribed to selective pressures.

The Wood-Ljungdahl pathway genes

Figure 2 shows the genes encoding the key enzymes in the Wood-Ljungdahl pathway of CO2 fixation in which two molecules of CO2 are reduced to a methyl and a carbonyl group, and are joined with coenzyme A (CoA) to make acetyl-CoA. Acetyl-CoA is then incorporated into cell carbon or converted to acetyl phosphate, whose phosphoryl group is transferred to ADP to generate ATP and acetate, the main growth product of acetogenic bacteria (for reviews see (Ljungdahl, 1986; Drake and Daniel, 1997; Ragsdale, 1997)). This pathway has been described to consist of an Eastern (blue coloring scheme) and a Western (red) branch (Figure 2) (Ragsdale, 1997).

Figure 2
The Wood-Ljungdahl pathway of CO2 fixation

Genes encoding the Eastern branch of the Wood-Ljungdahl pathway

The genes encoding enzymes in the Eastern branch of the pathway that are involved in the conversion of CO2 to methyl-H4folate (Fig. 2) are common to most organisms, though they are expressed at much higher levels in acetogens. As shown in Figure 3, many of the genes encoding functions of the Eastern branch of the pathway are dispersed on the genome at locations distant from the core genes of the Wood-Ljungdahl pathway, which are involved in converting methyl-H4folate, CoA, and CO2 to acetyl-CoA. The functional assignments of all these genes (except phosphotransacetylase, below) are backed by biochemical evidence based on protein sequence analysis of well-characterized enzymes.

Figure 3
Arrangement of Wood-Ljungdahl pathway genes in the acs gene cluster and in the chromosome

Conversion of CO2 to formate is catalyzed by the well characterized selenocysteine-containing formate dehydrogenase (Li et al., 1966; Andreesen and Ljungdahl, 1973; Yamamoto et al., 1983). Moth_2312 and Moth_2313, which are actually one gene, match the sequence deposited by Li, Ljungdahl, and Gollin in GenBank (gi 1658401) as the formate dehydrogenase a subunit. The two ORFs were separated in the original genome annotation because they contain the codon for selenocysteine, a stop codon in most contexts. Moth_2314 matches the sequence of the β subunit. In acetogens, formate dehydrogenase catalyzes an especially interesting reaction since the reduction of CO2 to formate (Eo = −420) is coupled to the oxidation of NADPH to NADP+ (Eo = −340 mV). The M. thermoacetica formate dehydrogenase was the first enzyme shown to contain tungsten (Ljungdahl and Andreesen, 1975). Another selenocysteine-containing formate dehydrogenase (Moth_2193), which appears to be part of a formate hydrogen lyase system (Moth_2184-2193), is described below.

The genes encoding 10-formyl-H4folate synthetase (Moth_0109), and the bifunctional 5,10-methenyl-H4folate cyclohydrolase/5,10-methylene-H4folate dehydrogenase (Moth_1516) are dispersed on the genome and distant from the acs gene cluster by at least 300 genes (Fig 3). In the reaction catalyzed by 10-formyl-H4folate synthetase, formate undergoes an ATP-dependent condensation with H4folate, forming 10-formyl-H4folate. This enzyme has been purified, characterized, and sequenced from a number of sources including M. thermoacetica (Himes and Wilder, 1968; O’Brien et al., 1975; McGuire and Rabinowitz, 1978; Lovell et al., 1988; Lovell et al., 1990). In higher organisms, this enzyme exists as one of the activities of a trifunctional C1-H4folate synthase (also containing cyclohydrolase and dehydrogenase) (Staben and Rabinowitz, 1986; Shannon and Rabinowitz, 1988), whereas the bacterial formyl-H4folate synthetases are monofunctional and share similar properties (Lovell et al., 1990). While the cyclohydrolase and dehydrogenase are part of a bifunctional protein in M. thermoacetica, they are monofunctional proteins in other acetogens, e.g., Clostridium formicoaceticum and Acetobacterium woodii (Moore et al., 1974; Clark and Ljungdahl, 1982; Ragsdale and Ljungdahl, 1984).

The enzyme that catalyzes the last step in the eastern branch is encoded by the 5,10-methylene-H4folate reductase gene (Moth_1191). In M. thermoacetica, this is an oxygen-sensitive enzyme containing an iron–sulfur cluster, zinc, and FAD, which utilizes reduced ferredoxin as an electron donor (Clark and Ljungdahl, 1984; Park et al., 1991). Thauer et al. (Thauer et al., 1977) suggested that the 5,10-methylene-H4folate reductase may link to an electron transport chain that begins with an electron donor (e.g., hydrogenase, CODH, or NADH dehydrogenase) through membrane-bound electron carriers, finally to methylene-H4folate. In this scenario, electron transport could result in the generation of a transmembrane proton potential coupled to ATP synthesis. In A. woodii, one of the steps involving methylene-H4folate reductase, the methyltransferase or the CFeSP (see Figure 2) was shown to generate a sodium motive force across the membrane (Heise et al., 1989). However, since the reductase appears to be located in the cytoplasm in M. thermoacetica (Clark and Ljungdahl, 1984) and in other organisms, it appeared that this is not the energy-conserving step in the Wood-Ljungdahl pathway (Muller, 2003). On the other hand, the location of the 5,10-methylene-H4folate reductase gene very near genes encoding a hydrogenase (Moth_1193) and heterodisulfide reductase (Moth_1194-1196), which are directly downstream from the acs gene cluster (Moth_1197-1204), suggests a possible mechanism of energy conservation involving the reductase. Thus, perhaps methylene-H4folate reductase links to the membrane-associated hydrogenase and/or heterodisulfide reductase to generate the proton motive force.

Genes encoding the Western branch of the Wood-Ljungdahl pathway

The core genes of the Western branch of the Wood-Ljungdahl pathway were first identified in M. thermoacetica by a reverse genetics approach to be located in the acs gene cluster (Figure 3b), which contains genes encoding carbon monoxide dehydrogenase (CODH), acetyl-CoA synthase (ACS), methyltransferase (MeTr), and both subunits of the corrinoid iron-sulfur protein (CFeSP) (Roberts et al., 1989). The acs gene cluster also includes a gene encoding an iron-sulfur protein of unknown function (orf7), and two genes, cooC and acsF, that encode proteins with sequences that are 44 and 27 percent identical to that of Rhodospirillum rubrum cooC, which is required for nickel insertion into carbon monoxide dehydrogenase (Jeon et al., 2001). Thus, the ubiquitous genes in the Eastern branch of the Wood-Ljungdahl pathway are scattered around the genome, while what can be considered to be the “core set of Wood-Ljungdahl genes” in the Western part of the pathway are co-localized. The genome sequence reveals an additional carbon monoxide dehydrogenase (Moth_1972), which is similar to an uncharacterized carbon monoxide dehydrogenase from Clostridium cellulolyticum and to CODH IV from Carboxydothermus hydrogenoformans (Wu et al., 2005), and is unlinked to the acs gene cluster.

Phosphotransacetylase has been characterized from M. thermoacetica (Drake et al., 1981), but the gene sequence has not been reported. M. thermoacetica lacks any gene that is homologous to the phosphotransacetylase genes whose products are used for phosphorylation of acetate from acetyl-CoA in related organisms, like Clostridium acetobutyricum (Boynton et al., 1996). However, Moth_1181 and Moth_0864 are homologous to the recently characterized pduL, which is used for 1,2-propanediol degradation by Salmonella enterica (Liu et al., 2007). Therefore, Moth_1181 and Moth_0864 are likely to encode phosphotransacetylases in M. thermoacetica. The acetate kinase (Moth_0940) gene is distant from and, thus, is not linked to Moth_1181, Moth_0864, or the acs gene cluster; however, Moth_1181 is located only 16 genes downstream of the methyltransferase in the Wood-Ljungdahl pathway (or ten genes further downstream from that of the gene encoding methylene-H4folate reductase).

Comparison of Wood-Ljungdahl pathway gene clusters

Acetyl-CoA synthase (COG1614, acsB) is found in five Clostridia, three Deltaproteobacteria, and three Dehalococcoidetes species among the completely sequenced bacteria, and in the almost complete genome sequence of the uncultured bacterium Kuenenia stuttgartiensis (Strous et al., 2006), and seems to be a marker for the presence of the Wood-Ljungdahl pathway in bacteria. COG1614 is also found in archaea and corresponds to the ~53 kDa beta subunit that harbors the active site dinickel-iron-sulfur cluster of acetyl-CoA decarbonylase synthase in methanogens and archaeoglobus (Pfam 03598, cdhC) (Maupin-Furlow and Ferry, 1996; Gencic and Grahame, 2003). From these genomes with acetyl-CoA synthase genes, only Dehalococcoides ethenogenes (Seshadri et al., 2005), and Dehalococcoides sp. BAV1 and CBDB1 do not have the complete Wood-Ljungdahl pathway. Though these genomes encode many enzymes that are part of the pathway, they lack homologs of known methylene-tetrahydrofolate reductase, methyltransferase (acsE), CO dehydrogenase (acsA), phosphotransacetylase (pta or pduL), and acetate kinase sequences. We have been unable to locate any gene in the Dehalococcoides genome that is homologous to any of the CODH (acsA) genes from M. thermoacetica or C. hydrogenoformans. Given the small genome size and metabolic specialization of D. ethenogenes, one can speculate that the complete pathway was present in an ancestor, and has partly been lost as the organism’s metabolism became limited to its current capabilities. Alkaliphilus metalliredigenes (Ye et al., 2004), Carboxydothermus hydrogenoformans (Wu et al., 2005), two Clostridium difficile strains, two Desulfitobacterium hafniense strains (Nonaka et al., 2006), Syntrophobacter fumaroxidans (Harmsen et al., 1998), Deltaproteobacterium MLMS-1, K. stuttgartiensis (Strous et al., 2006), and Candidatus Desulfococcus oleovorans Hxd3, formerly Deltaproteobacterium Hxd3 (So et al., 2003), appear to have complete Wood-Ljungdahl pathways, although none of these organisms produces acetate as their main growth product.

Since acetogenesis is a physiological trait that is not phylogenetically conserved (see Figure 1), we reasoned that co-occurrence of acetyl-CoA synthase with a set of genes only in genomes of acetogenic bacteria could provide clues about which genes are required to confer the ability to grow as an acetogen. Thus, the M. thermoacetica genome was compared to those of all Firmicute, Chlorflexi, and Deltaproteobacterial sequences available at IMG, using a Blast analysis of each M. thermoacetica genes against these other genomes, to find M. thermoacetica genes with homologs in the other bacterial genomes that also have acetyl-CoA synthase, but without homologs in any of the sequences without acetyl-CoA synthase. The only genes that show this pattern of co-occurrence and co-omission are ACS and both subunits of the corrinoid iron-sulfur protein (CFeSP). The CFeSP must have a highly conserved function as part of the Wood-Ljungdahl pathway, since homologs of the CFeSP genes are not found in any genome that does not also have acetyl-CoA synthase and other Wood-Ljungdahl pathway genes.

The Wood-Ljungdahl pathway gene clusters in these twelve bacteria can be divided into five groups within which the order of genes is absolutely conserved (Figure 4). These groupings mostly follow the currently accepted taxonomy found at NCBI. The M. thermoacetica, C. hydrogenoformans, D. hafniense, and K. stuttgartensis (group A) genes are arranged in the same way, and, like M. thermoacetica, C. hydrogenoformans has genes encoding heterodisulfide reductase directly following acsE. The K. stuttgartiensis gene cluster is identical in arrangement to the D. hafniense gene cluster, except for the insertion of a gene with sequence similar to clp protease sequences and one small gene of unknown function after acsB. The S. fumaroxidans and Candidatus Desulfococcus oleovorans (group B) gene clusters are alike, and minimal, with only the acsABCDE genes. C. D. oleovorans has four proteins in the same COG (3640) as the M. thermoacetica accessory proteins, and S. fumaroxidans has two proteins from this COG, but none of the genes encoding these putative accessory proteins are near the acs gene cluster in either species. A. metalliredigenes and C. difficile (group C) have much larger Wood-Ljungdahl pathway gene clusters, which, besides the genes present in the M. thermoacetica acs gene cluster, include genes encoding formyl-tetrahydrofolate synthetase (fts), the bifunctional formyl-tetrahydrofolate cyclohydrolase/methylene-tetrahydrofolate dehydrogenase (folD), and methylene-tetrahydrofolate reductase, which function in the eastern branch of the pathway (Figure 2). The three Dehalococcoides species (group D) have gene clusters that include acsBCD, fts, and folD; however, they surprisingly lack acsA. The deltaproteobacterium MLMS-1 gene cluster (group E) is similar to the Dehalococcoides Wood-Ljungdahl gene clusters, but includes acsA, genes which belong in COG0493 and COG3383 (see the anaerobic respiration and electron acceptors discussions), one heterodisulfide reductase subunit A gene, and two genes encoding homologs of the archaeal hydrogenase delta subunit that is found in the HDR gene clusters in M. thermoacetica. Based on this analysis, it appears that the core genes of the Wood-Ljungdahl pathway are located in the acs gene cluster, which includes acsA-acsE, and acquisition of this gene cluster might be sufficient for gaining the ability to grow as an acetogen.

Figure 4
Wood-Ljungdahl pathway gene clusters described in the text

Genes involved in anaerobic respiration

In the Wood-Ljungdahl pathway, one ATP is consumed in the formation of formyl-tetrahydrofolate from tetrahydrofolate and formate in the formyl-tetrahydrofolate synthase reaction (Sun et al., 1969), and one is generated by phosphoryl transfer to ADP in the acetate kinase reaction (Figure 2) (Schaupp and Ljungdahl, 1974). Therefore, there is no net gain of ATP by substrate level phosphorylation during autotrophic growth. Thus, it is clear that ATP is generated by anaerobic respiration. During growth using the Wood-Ljungdahl pathway, energy should be conserved by transfer of electrons along a membrane-bound electron transfer chain, coincident with generation of a transmembrane proton gradient (Figure 5). M. thermoacetica has an F1F0ATP synthase, which could use this proton gradient to drive ATP synthesis (Das and Ljungdahl, 1997). The genes encoding the eight subunits of the ATP synthase are Moth_2377-84. M. thermoacetica has integral membrane-bound electron carriers including b cytochromes (see Table 2) and a menaquinone (Gottwald et al., 1975; Hugenholtz et al., 1987; Das et al., 1989) that could be part of this system. There is evidence in the M. thermoacetica genome for genes that encode systems that could be associated with energy generation by transmembrane proton gradient formation (Table S2), including NADH dehydrogenase, hydrogenase or formate hydrogen lyase, and heterodisulfide reductase.

Figure 5
Possible energy conserving pathways
Table 2
Cytochromes present in the M. thermoacetica genome.

There is considerable homology of both subunit compositions and sequences among NADH dehydrogenases and some energy conserving NiFe hydrogenases (Deppenmeier, 2004; Hedderich, 2004). Examples of the former are mitochondrial complex I and E. coli NADH dehydrogenase I. The latter include E. coli hydrogenases 3 and 4, which are parts of formate hydrogen lyase complexes (Andrews et al., 1997), the CO-inducible hydrogenase from Rhodospirillum rubrum (Fox et al., 1996), a CO dehydrogenase-associated hydrogenase from Carboxydothermus hydrogenoformans (Soboh et al., 2002), and the Ech hydrogenase of Methanosarcina barkeri (Meuer et al., 1999). Two sets of M. thermoacetica genes, Moth_0977-87 and Moth_2184-92, encode proteins homologous to these complexes. A BLAST search of C. hydrogenoformans, E. coli, M. barkeri, and R. rubrum genomes with genes from Moth_0977-87 (Table 3) shows that these genes are most closely related to NADH dehydrogenase I in bacteria, and to the F420-dependent hydrogenase of M. barkeri. In some bacteria, as shown in Table 3 for R. rubrum and E. coli, the NADH dehydrogenase operon contains genes encoding subunits E, F, and G of the NADH dehydrogenase complex. In M. thermoacetica, homologs to these subunits are encoded separately, on two different gene clusters, Moth_1717-9 and Moth_1886-8. Moth_1717 and Moth_1888 align only with the first 240 and 280 amino acids of nuoG sequences from E. coli and Thermus thermophilus. In T. thermophilus, this N-terminal portion of the protein has the residues that ligate the three iron-sulfur clusters that are involved in electron transfer through the NADH dehydrogenase complex (Sazanov and Hinchliffe, 2006).

Table 3
Comparison of Moth_0977-87 with genes encoding C. hydrogenoformans, R. rubrum, and E. coli NADH dehydrogenase I and M. barkeri F-420 dependent hydrogenase.

Proteins encoded by Moth_2184-92 (Table 4) are most closely related to E. coli hydrogenases 4 and 3 among experimentally characterized proteins. In C. hydrogenoformans, Moth_2184-88 and Moth_2190-92 are most closely related to CO-associated hydrogenase, although there is lower sequence homology between these M. thermoacetica genes and CO-associated hydrogenase than between Moth_2184-92 and E. coli hydrogenases 3 and 4. Moth_2184-90 are more similar to subunits of hydrogenase 4 than subunits of hydrogenase 3, and Moth_2187-89 encode homologs of E. coli hydrogenase 4 genes hyfDEF, which do not have homologs in hydrogenase 3. Hydrogenase 3 does not generate a proton gradient, and probably is used by E. coli to metabolize formate produced during fermentative growth. From their analysis of the hyf gene cluster, Andrews et al. concluded that hydrogenase 4 is likely to have proton-translocating ability (although this has not been verified experimentally), because, like the NADH dehydrogenase I complex and the R. rubrum CO-inducible hydrogenase, and unlike hydrogenase 3 from E. coli, hyfBEF are homologous to ND2, ND4, and ND5 components of the quinone-reducing and proton translocating machinery in NADH dehydrogenase I (Andrews et al., 1997). M. thermoacetica genes Moth_2176-83, which are immediately downstream from this second gene cluster, are homologs of the hypA-F, hycI, and hycH genes of E. coli, which make up an operon that is required for maturation of the Ni-Fe hydrogenase 3 (Lutz et al., 1991; Blokesch et al., 2004). Immediately upstream of the hydrogenase gene cluster is a gene encoding a selenocysteine-containing formate dehydrogenase (Moth_2193) that is separate from the formate dehydrogenase that feeds formate into the Wood-Ljungdahl pathway. It is likely that Moth_2184-93 encodes a formate hydrogenlyase system, which by homology to hydrogenase 4, could generate a proton gradient in the presence of formate.

Table 4
Comparison of Moth_2184-92 with hydrogenases from C. hydrogenoformans and E. coli.

In methanogenic archaea, hydrogenases distinct from the Ech hydrogenase discussed above are also involved in energy generation as parts of membrane-bound electron transport systems, along with heterodisulfide reductase. In these systems, electrons are transferred from hydrogen to the disulfide formed between coenzyme M and coenzyme B during the last step in methanogenesis. Both two-subunit heme b-containing and three-subunit (non-heme) heterodisulfide reductases have been characterized (Setzke et al., 1994; Deppenmeier, 2004). Although it is not an archaeon, M. thermoacetica has three heterodisulfide reductase gene clusters that are homologous to the three-subunit heterodisulfide reductase from Methanothermobacter marburgensis (Table 5), one of which (Moth_1196) is directly after the CODH/ACS gene cluster. Moth_0441 (a heterodisulfide reductase A subunit) includes about 200 amino acids (from 400–600) that do not align with HdrA domains from Methanosarcina or most bacterial hits. These amino acids align with lower E-values with sequences from Syntrophobacter fumaroxidans, Methanosarcina mazei, an uncultured archaeon, Desulfotomaculum reducens, two Geobacter species, and Candidatus Desulfococcus oleovorans. Moth_1194 aligns with HdrA, except between amino acids 150 and 550. This region aligns with COG0493, which is made of the NADPH-dependent glutamate synthase beta chain, and related oxidoreductases. Moth_0811 and Moth_0812 make up one selenocysteine-containing gene, which aligns with other HdrA sequences along its full length.

Table 5
Heterodisulfide reductase gene clusters in the M. thermoacetica genome.

Genes involved in autotrophic growth

One-carbon compounds that M. thermoacetica can use for growth include H2/CO2, CO, formate, methanol, and methyl groups from many methoxylated aromatic compounds. The enzymes that catalyze transfer of the methyl group of methoxylated aromatic compounds to tetrahydrofolate are encoded by mtvABC (Moth_0385-7 and Moth_1316-8), and have been purified and identified biochemically by enzymatic function and protein sequence analysis (Naidu and Ragsdale, 2001). This pathway is shown in Figure 6, along with that of a methanol methyltransferase system (MtaABC, encoded by (Moth_1208-9 and Moth_2346) was recently characterized from M. thermoacetica (Das et al., 2007). M. thermoacetica has two nearly identical mtvA genes, each of which is next to a gene that we assign as mtvB, and a predicted cobalamin-binding mtvC gene. The putative mtvB genes are eighty percent identical to each other, and the mtvC genes differ by one amino acid. Both mtvA and mtvC genes are similar to cobalamin-dependent methionine synthase (5-methyltetrahydrofolate:homocysteine S-methyltransferase, encoded by metH in E. coli).

Figure 6
Methyl groups from methanol and vanillate linked to the Wood-Ljungdahl pathway

The two mtvB genes are most similar to uroporphyrinogen decarboxylase sequences, among experimentally characterized proteins, although the function of MtvB is clearly associated with methyl transfer. In addition to these mtv genes, M. thermoacetica encodes several homologs of MtvA, MtvB and MtvC (Table 6). It is possible that some of these homologs are used for growth on methyl donors other than vanillate and methanol. Many homologs of the M. thermoacetica MtvA and C proteins are also found in Desulfitobacterium hafniense, which can also demethylate methoxylated aromatic compounds (Neumann et al., 2004). These are arranged in clusters with A and C genes and sequences aligning either with M. thermoacetica MtvB or sequences of similar function from Acetobacterium dehalogenans. One of the M. thermoacetica MtvB homologs (Moth_1314) is fused to a domain that has not been functionally identified, and does not align with any COG identified at NCBI. Sequences that align with this whole fusion are found in D. hafniense, Archaeoglobus fulgidus and Alkaliphilus metalliredigenes.

Table 6
MtvA, MtvB, and MtvC homologs in the M. thermoacetica genome.

Genes involved in heterotrophic growth

M. thermoacetica can grow heterotrophically on fructose, glucose, xylose, ethanol, n-propanol, n-butanol (Beaty and Ljungdahl, 1991), oxalate and glyoxylate (Daniel and Drake, 1993), glycolate (Seifritz et al., 1999), pyruvate (Barker and Kamen, 1945), and lactate (Gößner et al., 1999). M. thermoacetica encodes a complete Embden-Meyerhof-Parnas pathway and all enzymes that are part of the oxidative branch of the pentose phosphate pathway (Supplementary Figure S2). Glucose and xylose are converted stoichiometrically to acetate by M. thermoacetica (Fontaine et al., 1942; Barker and Kamen, 1945). It seems likely that fructose is metabolized by the same pathway as glucose (Supplementary Figure S3), since growth yields of the two substrates are very similar (Andreesen et al., 1973).

Ethanol, propanol, and butanol are oxidized to acetate, propionate, and butyrate by M. thermoacetica (Beaty and Ljungdahl, 1991). Eight genes from four COGs containing alcohol dehydrogenases are present in the genome (Supplementary Table S3). Proteins encoded by three genes from COG2414, tungsten-containing aldehyde:ferredoxin oxidoreductases, might catalyze the second step in growth on these alcohols.

The pathways for growth of M. thermoacetica on the two-carbon substrates oxalate, glyoxylate, and glycolate are not known. The stoichiometries of acetate production suggest that they are oxidized by two, four, and six electrons, respectively (Seifritz et al., 1999). Given differences in growth on these three substrates, it seems likely that M. thermoacetica uses different pathways for their oxidation. Only partial pathways known to be involved in glycolate metabolism in other organisms are present in M. thermoacetica. In E. coli, the glycolate metabolism genes in E. coli are located in an operon, which includes glcA (encodes a glycolate permease), glcB (encodes malate synthase), glcG (function is unknown), glcF, E, and D (encode the three subunits of glycolate oxidase), and glcC (encodes a transcriptional activator) (Pellicer et al., 1996), and the first enzymatic step is oxidation of glycolate to glyoxylate via an FMN-dependent oxidase (GlcDEF). The M. thermoacetica genes are arranged in two clusters, one containing glcDEF homologs (Moth_0037-39), and the other containing homologs to glcACF, an unknown protein, another glcF, and a sequence that aligns with glcD and E (Moth_2303-8). The glycolate permease gene (glcA) in E. coli and the proposed M. thermoacetica glcA are very similar to L-lactate permeases (Núñez et al., 2001). No homolog of malate synthase was found in M. thermoacetica, but M. thermoacetica does have a gene, Moth_1954, with 51 percent sequence identity to a possible glyoxylate reductase that has been purified from Thermococcus litoralis (Ohshima et al., 2001). This enzyme catalyzes formation of malate from glyoxylate and acetyl-CoA and is homologous to D-lactate dehydrogenase.

M. thermoacetica is able to grow on lactate and pyruvate. Lactate is probably converted to pyruvate by Moth_1826, which is similar to both Clostridium acetobutylicum and Thermotoga maritima L-lactate dehydrogenases. Pyruvate is metabolized using pyruvate:ferredoxin oxidoreductase (PFOR), which catalyzes the oxidative cleavage of pyruvate and attachment of the two carbon fragment to CoA, forming acetyl-CoA, CO2, and reduced ferredoxin (Supplementary Figure S4). PFOR is also essential in sugar metabolism, since it couples the Embden-Meyerhoff-Parnas pathway to the Wood-Ljungdahl pathway. In sugar metabolism, 4 additional electrons are available from the glyceraldehyde-phosphate dehydrogenase reaction, so 1 mol of glucose, i.e., 2 mol of pyruvate are required to supply the 8 electrons for reducing 2 mol of CO2 to acetate. The PFOR that has been purified from M. thermoacetica is a homodimer, with a subunit mass of 120 kDa (Furdui and Ragsdale, 2002). The gene encoding this enzyme, Moth_0064, is a fusion of three COGs, COG0674, COG1014, COG1013, which are annotated as alpha, gamma, and beta subunits. Five other sets of genes belonging to the same COGs as PFOR (Supplementary Table S4) could encode authentic pyruvate:ferredoxin oxidoreductases, but they could also encode other proteins in the oxoglutamate oxidoreductase family, like 2-ketoisovalerate oxidoreductase, indolepyruvate oxidoreductase, and 2-ketoglutarate oxidoreductase. Many of the residues that are known to be important in the well-characterized PFOR from Desulfovibrio africanus are conserved in the PFOR-like gene clusters of M. thermoacetica. These include residues that bind iron-sulfur clusters, thiamine pyrophosphte, and pyruvate. Conservation of these residues suggests that these M. thermoacetica gene clusters likely encode enzymes that perform similar functions to PFOR. Variation in the residue that forms a hydrophobic interaction with the methyl group of pyruvate in the D. africanus enzyme could be due to different substrate specificity of the protein products of these different gene clusters. For example, the replacement of this residue with a glycine residue could accommodate a substrate larger than pyruvate.

Genes involved in utilization of electron acceptors other than CO2

M. thermoacetica can use electron acceptors other than CO2 during heterotrophic growth. When nitrate and CO2 are both supplied, nitrate is used preferentially (Seifritz et al., 1993). In medium containing a carbon source for heterotrophic growth, addition of nitrate stimulates growth, and reducing equivalents from H2 and one-carbon substrates are used to make ammonium, while acetate production is decreased. Work by Fröstl et al. and Arendsen et al. (Fröstl et al., 1996; Arendsen et al., 1999) suggest that carbon incorporation through the Wood-Ljungdahl pathway is repressed by nitrate. Nitrite (Seifritz et al., 2003), dimethylsulfoxide and thiosulfate (Beaty and Ljungdahl, 1991) are also electron sinks for M. thermoacetica. Some of these electron acceptors could be reduced by oxidoreductases similar to DMSO and TMAO reductases found in Escherichia coli and many other organisms. These proteins use molybdopterin cofactors, are often membrane associated, and in some cases are transported to the periplasm by twin-arginine transport (TAT) systems.

M. thermoacetica genes similar to the E. coli DMSO and TMAO reductases have been identified. The E. coli DMSO reductase has three subunits. DmsA is the molybdopterin-containing catalytic subunit (COG0243), DmsB is an iron-sulfur electron transfer subunit (COG0437), and DmsC is a membrane anchor subunit (COG3302). TMAO reductase has a cytochrome subunit instead of DmsC and B-like subunits. M. thermoacetica has eight genes belonging to COGs 0243 and 3383, which are made up of molybdopterin-containing proteins, shown in Table 7. Five of these genes are adjacent to COG0437 proteins. One homolog of the E. coli DmsC subunit is also present in M. thermoacetica. No oxidoreductase subunit homologous to the pentaheme cytochrome c family TorC subunit of the TMAO reductase in E. coli (gi 2506330, COG3005) (Gon et al., 2001) was found in M. thermoacetica. This subunit connects TMAO reductase in E. coli with respiration via the quinone pool. Thus, in M. thermoacetica, it is likely that one of the electron transfer proteins discussed above in the Anaerobic Respiration section couples TMAO and DMSO-derived electrons to the quinone pool.

Table 7
Gene clusters containing predicted molybdopterin subunits in COGs 0243 and 3383.

Analysis of the N-terminal sequences of the molybdopterin oxidoreductases shows that three of the genes include likely TAT signal sequences. M. thermoacetica encodes TatA and TatC proteins (Moth_1278 and Moth_1279), but does not have a tatB gene. This is also true of Bacillus subtilis, which uses a system composed of A and C subunits (Jongbloed et al., 2004). Two genes similar to torD, flanking a gene cluster that encodes three molybdopterin-containing oxidoreductases, two of which have TAT sequences, might be chaperones for the twin-arginine transport system (Hatzixanthis et al., 2005; Genest et al., 2006).

In addition to the molybdopterin oxidoreductases, M. thermoacetica has additional genes that could be involved in growth on electron acceptors other than CO2, e.g., sulfite and nitrate (Supplementary Table 5). One gene cluster has three genes that have about 80 percent sequence identity with the dissimilatory sulfite reductase (dsrAB) and the gene dsrD, of unknown function, from Desulfotomaculum thermocisternum (Larsen et al., 1999). Directly upstream from these genes are a gene similar to the membrane component of E. coli nitrate reductase, narI, a gene similar to nrfD which is a transmembrane component of E. coli nitrite reductase, two predicted iron-sulfur containing proteins, and a cytochrome c. The dissimilatory sulfite reductase does not have any likely transmembrane regions, but the additional genes might serve to connect the reductase to a membrane-bound respiratory pathway. One other possible sulfite reductase gene cluster, Moth_1629-32, has dsrAB genes, and two genes similar to dsrC from Archaeoglobus fulgidus, whose function is not fully resolved. The genes in this cluster have only about 30 percent sequence identity to the most closely related genes in GenBank. The four genes in this second cluster have no predicted transmembrane domains.

Expanded gene groups in M. thermoacetica based on comparative COG analysis

The M. thermoacetica genome was compared with those of T. ethanolicus and T. tengcongensis to obtain insights into M. thermoacetica’s wide metabolic range. We analyzed the placement of M. thermoacetica, T. ethanolicus, and T. tengcongensis genes in COGs to identify functions with increased representation in M. thermoacetica. Supplementary Table S6 shows some of the COGs with increased representation along with the number of genes belonging to each COG. The largest expansions in M. thermoacetica, relative to the other Thermoanaerobacteriaceae genome sequences, are in COGs that could encode proteins involved in electron transfer to or from growth substrates, including molybdopterin oxidoreductases in the dimethylsulfoxide reductase family detailed above, and in the xanthine dehydrogenase family (Kisker et al., 1999), with subunits in COGs 1529, 1319, and 2080. The xanthine dehydrogenase subunits might be part of a pathway of purine degradation including amidohydrolase genes (COG0402), which are adjacent to two of the xanthine dehydrogenase genes. The COGs containing heterodisulfide reductase and sulfite reductase discussed above are absent from T. ethanolicus and T. tengcongensis, except for one subunit A homolog in T. ethanolicus. M. thermoacetica has thirteen genes representing two COGs of proteins that are likely to contain iron-sulfur clusters, and that seem to have diverse functions in the M. thermoacetica genome. COG0247 is part of the possible glycolate oxidase proposed above as the homolog of E. coli glcF. COG0247 sequences are also adjacent to a heterodisulfide reductase A gene (Moth_1453) that is unlinked to any other heterodisulfide reductase subunits, and to one of the sulfite reductase gene clusters. A gene encoding a COG0437 protein is part of the same sulfite reductase gene cluster, and other COG0437 proteins are predicted to be encoded by genes adjacent to many of the molybdopterin oxidoreductase genes, and is found in two gene clusters with aldehyde-ferredoxin oxidoreductases (COG2414).

M. thermoacetica has four genes in COG1251, which contains NAD(P)H dependent nitrite reductase subunits similar to E. coli’s cytoplasmic nirB. However, M. thermoacetica lacks the gene encoding the other subunit of the enzyme found in E. coli, nirD (COG2146). One COG1251 gene is within an apparent glutamate synthase operon (Moth_1289-94), while another is adjacent to a gene cluster containing COG0437, an aldehyde-ferredoxin oxidoreductase, and a gene similar to E. coli’s MoaD, which is involved in molybdopterin biosynthesis (Moth_0721-24). The third COG1251 gene is in a gene cluster with COG0243 and the lone heterodisulfide reductase A gene (Moth_1452-54), while the fourth is next to a hypothetical protein sequence of unknown function.

Another large expansion is in COGs related to methyl transfer reactions. Included in these COGs are the methyltransferase of the Wood-Ljungdahl pathway (Figure 2) and other genes that could feed methyl groups into this pathway, including mtvA and mtvC homologs, and COG0407 which includes mtvB (Table 6). Four COG0407 genes are positioned close to mtvA and mtvC homologs, and four are adjacent to two putative sugar phosphate permeases that are members of family 1 of the major facilitator superfamily, in COG2271, which is also expanded in M. thermoacetica.

Another expanded COG group contains components of ABC-type nitrate/sulfonate/bicarbonate transport systems. These are represented by four gene clusters, each containing an ATPase, a permease component, and a periplasmic component. Each of the Thermoanaerobacter species encodes one complete transporter from these three COGs.

Genes involved in cofactor synthesis

The only vitamin required for M. thermoacetica’s growth is nicotinic acid, a precursor of NAD and NADP (Lundie and Drake, 1984). M. thermoacetica appears to have genes encoding the phosphoribosyl transferase (Moth_1836), adenylyltransferase (Moth_0564), and glutamine dependent NAD synthetase (Moth_0553) needed for conversion of nicotinic acid to NAD (Moth_1836, Moth_0564, and Moth_0553).

Since only one vitamin is required for growth, genes encoding pathways for synthesis of all other cofactors should be present in the genome. Two metabolic routes for the synthesis of tetrahydrofolate are the de novo synthesis pathway (Supplementary Figure S5), and a salvage pathway. In E. coli, the de novo synthesis pathway requires the activities of the proteins encoded by the genes folE, folB, folK, folP, folC and folA to produce the final product, 6-(S)-tetrahydrofolate. M. thermoacetica has no folA gene, but the isoenzyme encoded by ydgB (folM) is present in three copies. The activities of two other enzymes from this pathway have been measured in E. coli, but the genes that encode the proteins are not yet known, so no comparison is possible with the M. thermoacetica genome. The functions of the tetrahydrofolate salvage pathway in M. thermoacetica, which regenerates tetrahydrofolate from 5- or 10-formyl-tetrahydrofolate could be accomplished by methylene-tetrahydrofolate dehydrogenase/methenyl-tetrahydrofolate cyclohydrolase of the Wood-Ljungdahl pathway (Moth_1516) and Moth_2045, a phosphoribosylglycinamide formyl-transferase.

M. thermoacetica has a complete pathway of cobalamin biosynthesis. Cobalamin is a central cofactor in the autotrophic metabolism of M. thermoacetica, linking the methyl and carbonyl branches of the Wood-Ljungdahl pathway, with the methylated corrinoid iron-sulfur protein serving as a substrate of the acetyl-CoA synthase reaction. M. thermoacetica contains over twenty different types of cobalamin or precursors that total 300 – 700 nmol per gram of cells (Ljungdahl et al., 1966). The levels of corrinoids and their structural diversity in anaerobic bacteria have been reviewed (Stupperich et al., 1990). Both the anaerobic branch of corrin ring synthesis and the common branch of the adenosyl-cobalamin pathway are intact. Although several genes in the aerobic pathway of corrin ring synthesis are also present in the M. thermoacetica genome, these genes are not specific to the aerobic route, and genes that are unique to the aerobic pathway are absent in M. thermoacetica. Almost all of the cobalamin biosynthesis genes are located within a single gene cluster (Moth_1087-1104) in the M. thermoacetica genome. ABC transporters, which are encoded by cbiM, N, Q, and O, mediate high affinity transport of cobalt ions for B12 synthesis. Three gene clusters (Moth_1219 to Moth_1222, Moth_1861 to Moth_1863 and Moth_2427 to Moth_2429) have combinations of cbiM, N, Q and O genes.

As expected from the numbers of DMSO reductase and xanthine oxidase family proteins encoded in the M. thermoacetica genome, this organism has genes that could be used to synthesize molybdenum cofactors (Supplementary Figure 6). Most of these were found based on their homology to E. coli and Arabidopsis thaliana genes (Schwartz, 2005). M. thermoacetica has homologs of all E. coli molybdenum cofactor synthesis genes except for moaE, which encodes the large subunit of molybdopterin synthase. Some M. thermoacetica homologs of mogA, moaC, moaA, and moeA are found in one cluster of genes (Moth_2132 to Moth_2137), along with a gene belonging to pfam03473, which is a family of predicted sulfur-carrying proteins which are sometimes associated with molybdenum cofactor sulfurase domains, as in molybdopterin synthase. Another gene cluster (Moth_1819 to Moth_1824) has a gene homologous to mobB from E. coli, the function of which is not known, another moeA homolog, a gene that matches the c-terminal half of mobA, and three subunits of a possible ABC-type molybdate transporter, homologous to modABC from E. coli.

Transporter Genes

Two hundred ten transport genes, constituting approximately one hundred thirty transport systems, were identified in the M. thermoacetica genome (Supplementary Table 7). These include six alpha-helical membrane channels for the transport of anions, cations and small solutes. The genome encodes sixty-one secondary permeases, which transport a variety of substrates that include amino acids, sugars, anions, cations, nucleotides, and toxic drugs. Sixteen belong to the Major Facilitator Superfamily (MFS), two are RND-type transporters, six are DMT-type drug and metabolite transporters, and three belong to the MOP superfamily. One hundred three proteins encoded in the genome constitute approximately thirty-five ABC-type transport systems, which are predicted to transport anions, cations, peptides, amino acids, vitamins, heavy metal ions, and toxic drugs. The genome also encodes four polypeptides that form a single fructose-type sugar-transporting phosphotransferase system. Three cation-transporting P-type ATPases were also recognized in the genome. Approximately nineteen putative transporters with unknown substrates were also identified in the genome.

Motility Genes

M. thermoacetica is not motile, although stains show peritrichous flagella (Fontaine et al., 1942). Thirty-five M. thermoacetica genes encode proteins forming entire components and substructure of flagella, such as motor, switch complex, basal body, and filament (Supplementary Figure S7). These proteins fall into at least six groups: hook-associated proteins (FlgK and FlgL), basal and hook proteins (FlgE), capping proteins (FliD), biosynthesis secretory proteins (FlhA, FlhB, FliF, FliH and FliI), flagella formation proteins, motor proteins (FliG and FliM) and basal proteins (FlgC and FlgB). However, genes encoding the accessory flagellar assembly proteins, FlgA, FlhC, FlhD, and FliT, could not be identified in the M. thermoacetica genome. The organization of the genes for the general component of the flagellar proteins export apparatus appears to be similar to that found in Bacillus subtilis (Macnab, 2004). A similar gene cluster exists in Thermoanaerobacter tengcongensis, which also does not have functional flagella in cultures, but seems to have many of the genes for flagellar assembly and chemotaxis (Xue et al., 2001; Bao et al., 2002). From the genome annotation, M. thermoacetica also has an elaborate cascade of chemotaxis genes, including 6 chemoreceptors, together with a complete set of flagellar genes, most located within three large clusters of about 70 genes (Moth_0740-7, Moth_0764-91, Moth_0797-Moth_0805). The only exception is CheZ, which is not found in the Moorella or Thermoanaerobacter tengcongensis genomes. CheZ, a protein known to accelerate dephosphorylation of the response regulator CheY, has only been found in a few non-thermophilic gram negative bacteria, such as E. coli (Blattner et al., 1997), P. aeruginosa (Stover et al., 2000), and V. cholerae (Heidelberg et al., 2000), and it is not essential for flagellar motility and its chemotaxis (Scharf et al., 1998). The presence of genes involved in flagellar structure and movement in both non-motile M. thermoacetica and T. tengcongensis suggests either that they might be inactive or activated only under certain environmental conditions or that they have lost function only recently before divergence of these two species. In the proteomics study, two key gene products of the flagella formation, motor proteins (FliG and FliM) and basal proteins (FlgC and FlgB) were not detected, supporting the suspicion that incomplete gene expression may cause the absence of flagella in the cultured cells (Wang et al., 2004).(Wang et al., 2004)

Discussion

This paper describes the first genomic sequence of an acetogen. The genomic results clearly indicate that the trait of acetogenesis is a phylogenetic, not a metabolic trait. To identify a set of genes that are responsible for the acetogenic lifestyle, the M. thermoacetica genome was compared to those of all Firmicute, Chlorflexi, and Deltaproteobacterial sequences available at IMG. Surprisingly, the only M. thermoacetica genes with homologs in the other bacterial genomes that also have acetyl-CoA synthase, but lack homologs in any of the genome sequences without acetyl-CoA synthase, are acetyl-CoA synthase itself and the two subunits of the corrinoid iron-sulfur protein (CFeSP). While the genes encoding the H4folate-dependent enzymes in the Eastern part of the pathway are scattered around the genome, the “core set of Wood-Ljungdahl genes” (acsA-acsE) in the Western part of the pathway are co-localized. Being required for general C-1 metabolism in all organisms, the Eastern branch genes are ubiquitous; thus, we suggest that acquisition of the acs gene cluster by horizontal transfer might be sufficient for gaining the ability to utilize the Wood-Ljungdahl pathway. For some organisms, this would confer the ability to grow as a homoacetogen; for others (sulfate reducers and aceticlastic methanogens), the ability to oxidize acetate. Acquisition of the core Wood-Ljungdahl genes would allow a wide variety of organisms, including archaea and a broad range of bacterial phyla (Firmicute, Chlorflexi, and Deltaproteobacteria), to fix CO and CO2 by the reductive acetyl-CoA pathway. The simple strategy of the Wood-Ljungdahl pathway of successively joining two one-carbon compounds to make a two-carbon compound has been envisioned to be the earliest form of metabolism (Martin and Russell, 2007).

The genomic analysis also revealed a second CODH (Moth_1972), which has not been characterized biochemically. Other genomes contain multiple CODHs, like C. hydrogenoformans, which contains five CODHs (Wu et al., 2005). The only genes that could be identified to encode a phosphotransacetylase in M. thermoacetica (Moth_1181 and Moth_0864), are homologous to the recently characterized novel enzyme from Salmonella enterica called pduL (Liu et al., 2007); thus, it is important to test this function by performing biochemical assays on these putative phosphotransacetylases.

Perhaps not surprisingly, given the metabolic diversity of acetogenic microbes, the largest COG expansions in M. thermoacetica, relative to the other Thermoanaerobacteriaceae genome sequences, involve electron transfer proteins. How electron donors and acceptors interact with respiratory pathways in M. thermoacetica also remains an open question. Although the enzymes in the Wood-Ljungdahl pathway have been characterized, it has been unclear how acetogens gain energy, since there is no net ATP synthesis by substrate-level phosphorylation. Homologs of NADH dehydrogenase I (Table 3) and archaeal heterodisulfide reductase (Table 5) are present in the genome. Other genes identified that may play important roles in electron transfer linked proton translocation are Moth_2184-90, with significant homology to the genes encoding the subunits of E. coli’s hydrogenase 4 (Table 4), which has been proposed to have proton translocating ability (Andrews et al., 1997). These various sets of genes could encode partial or complete membrane-bound complexes that would function in anaerobic respiration by generating a transmembrane proton gradient for use by the F1F0ATP synthase (Moth_2377-84). Localization of genes encoding homologs of heterodisulfide reductase (Moth_1194-Moth_1196), a hydrogenase (Moth_1193), and 5,10-methylene-H4folate reductase (Moth_1191) near the acs gene cluster are consistent with a suggestion that the reductase and a hydrogenase might link to CODH to generate a proton motive force, driving anaerobic respiration in acetogens (Thauer et al., 1977).

M. thermoacetica contains eight genes encoding molybdopterin-containing proteins, that are likely to encode the reductases that allow growth on nitrate (Fröstl et al., 1996), dimethylsulfoxide, and thiosulfate (Beaty and Ljungdahl, 1991), as well as reductases for other electron acceptors not yet identified (Table 7). These molybdopterin-dependent proteins would then link to the membrane-bound respiratory systems described in the previous paragraph. The genomic information described here should help identify the specific membrane-associated proteins that are recruited to allow growth on these various electron acceptors. It is likely that these electron transfer components are differentially expressed growth condition, and the large number of them might be part of M. thermoacetica’s strategy for fine-tuning its growth to specific environmental conditions. The presence of so many different sets of genes that are likely to encode proteins involved in energy generation by electron and proton transport (for example, the presence of three heterodisulfide reductase gene clusters) could be part of this strategy. That cytochrome b, which is found in membranes of M. thermoacetica cells grown using the Wood-Ljungdahl pathway, is down-regulated in cells grown on nitrate (Arendsen et al., 1999) indicates that the respiratory pathway used in connection with the Wood-Ljungdahl pathway is different than the one used during growth on nitrate, at least in some components.

Other expanded gene groups that were identified in M. thermoacetica include methyltransferases, which are required for growth on various methyl group donors (methanol, methoxylated aromatics), and ABC-type nitrate/sulfonate/bicarbonate transport systems, which also perhaps reflect the ability of acetogens to grow on a wide variety of substrates. Methyltransferase genes that link to the Wood-Ljungdahl pathway (besides acsCDE) include mtaABC (Moth_1208-Moth_1209) encoding the methanol:methyl-H4folate methyltransferase system, mtvABC (Moth_1316-1318 and Moth_385- Moth_387), which transfers the methyl group of methoxylated aromatic compounds to H4folate, and several other methyltransferase genes whose specific biochemical function have not been assigned.

We were unable to predict the pathways by which M. thermoacetica metabolizes the two-carbon organic acids oxalate, glyoxylate, and glycolate (Seifritz et al., 1999). The most reduced compound among these is glycolate, which is oxidized to glyoxylate in E. coli (Pellicer et al., 1996) by an FMN- and H2O2-dependent glycolate oxidase, which is encoded by the glcDEF genes that are homologous to genes located in two gene clusters in M. thermoacetica. However, it seems unlikely that the anaerobe M. thermoacetica uses an oxidase mechanism. Homologs of malate synthase (GlcB), which catalyzes formation of malate from glyoxylate and acetyl-CoA, or glyoxylate carboligase (converts two mol of glyoxylate to form tartronate semialdehyde), were not found in M. thermoacetica, which is consistent with the lack of enzymatic activities for these proteins in extracts of cells grown on glyoxylate (Seifritz et al., 2002). Perhaps malate is formed from glyoxylate and acetyl-CoA by a glyoxylate reductase homolog (Moth_1954). Homologs of proteins in the pathway of oxalate metabolism in Oxalobacter formigenes, which begins with oxalyl-CoA formation, were also missing from the M. thermoacetica genome. A hint for the oxalate metabolic pathway is that a 33 kDa protein is induced when M. thermoacetica is grown on oxalate (Daniel and Drake, 1993); however, no sequence information for this protein has yet been described. Postgenomic studies will likely uncover how acetogens use the glc gene cluster and/or other genes to metabolize oxalate, glyoxylate, and glycolate under anaerobic conditions. Identifying the mechanism of growth on oxalate should be particularly interesting, because during oxalate-dependent growth, M. thermoacetica uses CO2 preferentially over nitrate as a terminal electron acceptor. Oxalate is the only substrate for M. thermoacetica for which this preference has been found.

Knowing the complete genome sequence of M. thermoacetica will be a valuable tool to help understand the growth of this organism and the acetogenic lifestyle. The genome sequence enables protein expression studies and microarrays, which should address important questions arising from annotation of this genome sequence. For example, growth of M. thermoacetica on oxalate and glyoxylate, followed by 2D electrophoresis analysis of proteins could uncover shifts in protein expression that would uncover what pathways are used. Protein and gene expression studies, on cells grown on different electron acceptors, could help identify the pathways of anaerobic respiration in M. thermoacetica. Such experiments will uncover how electrons are passed from electron donor to electron acceptor during growth, and how M. thermoacetica switches among different donors and acceptors, depending on what substrates are available in its environment. Similar studies may reveal how M. thermoacetica grows in different environments and in different ecological settings; for example, how its metabolism and gene expression patterns change when an acetogen is part of a microbial community or in coculture with a methanogen or sulfate reducer that can act as a H2 sink. In turn, proteomic and microarray studies should help us improve the annotation of the genome, by allowing us to identify specific biochemical functions and metabolic roles for genes of unknown or partially known function.

Experimental Procedures

DNA extraction and purification

M. thermoacetica cells were grown at 55 °C in the presence of 100 mM glucose (18 g/liter) under 100% CO2 in the medium described by Ljungdahl and Andreesen (Ljungdahl and Andreesen, 1978), containing yeast extract and tryptone. Another sample of DNA was prepared from cells grown at 58 °C on 200 mM methanol under 100 % CO2 in Drake’s medium (Seifritz et al., 1993). The DNA was then isolated according to the procedure of Marmur (Marmur, 1961) and stored frozen at −20 °C in 10 mM Tris/HCl, pH 8.0 and 1 mM EDTA at a concentration of 438 μg/ml.

Genome sequencing

The genome of M. thermoacetica was sequenced at the Joint Genome Institute (JGI) using a combination of 3 kb, 6 kb, 7kb, and 37kb (fosmid) DNA libraries. All general aspects of library construction and sequencing performed at the JGI can be found at http://www.jgi.doe.gov/. Draft assemblies were based on 41897 total reads. All four libraries provided 18x coverage of the genome. The Phred/Phrap/Consed software package (www.phrap.com) was used for sequence assembly and quality assessment (Han and Chain, 2006). After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher (Abraham et al., 2006) or transposon bombing of bridging clones (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, custom primer walk, and PCR amplification (Roche Applied Science, Indianapolis, IN). A total of 3345 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. The completed genome sequence of M. thermoacetica contains 45242 reads, achieving an average of 8-fold sequence coverage per base with an error rate less than 1 in 100,000

Annotation

Automated gene modeling was completed by combining results from Critica, Generation, and Glimmer modeling packages, and comparing the translations to GenBank’s nonredundant database using the basic local alignment search tool for proteins (BLASTP). Predicted coding sequences were subjected to manual analysis using JGI’s gene models quality assessment pipeline. The predicted functions were further analyzed by using the Integrated Microbial Genomes (IMG) annotation pipeline (http://img.jgi.doe.gov) (Markowitz et al., 2006).

Comparative analysis

Comparative analysis of M. thermoacetica ATCC 39073, Thermoanaerobacter tengcongensis MB4, and Thermoanaerobacter ethanolicus 39E was performed by using a set of tools available at IMG. Unique and orthologous M. thermoacetica genes were identified by using BLASTp (cutoff scores of E < 10−2 and 20% identity and reciprocal hits with cutoffs of E < 10−5 and 30%, respectively). The transporter database (TCDB; http:/www.tcdb.org) (Saier et al., 2006) was used to identify all the transporters in the genome of M. thermoacetica. Twin arginine transport signal sequences were predicted by the TatP server at http://www.cbs.dtu.dk/services/TatP/ (Bendtsen et al., 2005). Metabolic pathways were constructed with reference to MetaCyc (Caspi et al., 2006) and PubMed. Identification numbers given in the text for individual genes are IMG locus tag numbers, which can be used to search for genes at the Integrated Microbial Genomes website.

Phylogenetic trees

The phylogenetic tree was made using pre-aligned 16S rRNA sequences derived from the Ribosomal Database site (http://rdp.cme.msu.edu/index.jsp) (Cole et al., 2007). Manual alignment adjustments were made as needed with the assistance of the BioEdit multiple alignment tool of Hall (http://www.mbio.ncsu.edu/BioEdit/bioedit.html). The refined multiple alignment was used as input for generation of a phylogenetic tree using the program package version 3.1 (Kumar et al., 2004). The Neighbor Joining (Saitou and Nei, 1987), Minimum Evolution (Nei et al., 1998; Takahashi and Nei, 2000), UPGMA (Nei and Kumar, 2000), and Maximum Parsimony (Fitch, 1971) methods with the default settings were employed to obtain phylogenetic trees. Both the distance- and character-based trees yielded similar clusters and arrangements of taxa.

Nucleotide sequence accession number

The sequence data described here have been deposited in GenBank under accession number CP000232.

Supplementary Material

Supp 1

Acknowledgments

We are grateful to the DOE Joint Genome Institute for selecting M. thermoacetica for sequencing and to many people at JGI who were involved in the sequencing effort. The work was supported by a grant from NIH (GM39451, SWR). We thank Thomas Morton for extracting one of the DNA samples used in these studies.

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