The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth Michael J. McInerney*, Lars Rohlin†, Housna Mouttaki*, UnMi Kim†, Rebecca S. Krupp†, Luis Rios-Hernandez*, Jessica Sieber*, Christopher G. Struchtemeyer*, Anamitra Bhattacharyya‡, John W. Campbell‡, and Robert P. Gunsalus†§ *Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019; ‡Integrated Genomics, 2201 West Campbell Park Drive, Chicago, IL 60612; and †Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095 Edited by Ralph S. Wolfe, University of Illinois at Urbana–Champaign, Urbana, IL, and approved March 12, 2007 (received for review November 27, 2006) Biochemically, the syntrophic bacteria constitute the missing link in Table 1. Reactions involved in syntrophic metabolism our understanding of anaerobic flow of carbon in the biosphere. ⌬G°Ј*, ⌬GЈ†, The completed genome sequence of Syntrophus aciditrophicus SB, Reactions kJ/mol kJ/mol a model fatty acid- and aromatic acid-degrading syntrophic bac- terium, provides a glimpse of the composition and architecture of Methanogenic H2 consumption ϩ Ϫ ϩ ϩ 3 ϩ Ϫ Ϫ the electron transfer and energy-transducing systems needed to 4H2 HCO3 H CH4 3H2O 135.6 15.8 exist on marginal energy economies of a syntrophic lifestyle. The Syntrophic metabolism Ϫ ϩ 3 Ϫ ϩ Ϫ ϩ ϩ Ϫ genome contains 3,179,300 base pairs and 3,169 genes where 1,618 Propionate 3H2O Ace HCO3 76.1 16.9 ϩ ϩ genes were assigned putative functions. Metabolic reconstruction H 3H2 Ϫ ϩ 3 Ϫ ϩ ϩ ϩ ϩ Ϫ of the gene inventory revealed that most biosynthetic pathways of Butyrate 2H2O 2 Ace H 2H2 48.6 39.2 Ϫ ϩ 3 Ϫ ϩ Ϫ ϩ ϩ Ϫ a typical Gram-negative microbe were present. A distinctive fea- Benzoate 7H2O 3 Ace HCO3 70.1 68.5 ϩ ϩ ture of syntrophic metabolism is the need for reverse electron 3H 3H2 transport; the presence of a unique Rnf-type ion-translocating *Calculated from the data in Thauer et al. (46) with the free energy of electron transfer complex, menaquinone, and membrane-bound formation for benzoate given in ref. 47. Fe-S proteins with associated heterodisulfide reductase domains †Calculated on the basis of the following conditions observed in methano- suggests mechanisms to accomplish this task. Previously unde- genic ecosystems: partial pressures of H2 of 1 Pa and of CH4 of 50 kPa, 50 mM scribed approaches to degrade fatty and aromatic acids, including bicarbonate, and the concentrations of the substrates and acetate (AceϪ)at multiple AMP-forming CoA ligases and acyl-CoA synthetases seem 0.1 mM each. to be present as ways to form and dissipate ion gradients by using a sodium-based energy strategy. Thus, S. aciditrophicus, although nutritionally self-sufficient, seems to be a syntrophic specialist with interaction between microbial species is termed syntrophy. The limited fermentative and respiratory metabolism. Genomic analy- ubiquity of syntrophic metabolism in many anoxic environments sis confirms the S. aciditrophicus metabolic and regulatory com- emphasizes that metabolic cooperation among microbial species mitment to a nonconventional mode of life compared with our is required for complete destruction of organic matter where the prevailing understanding of microbiology. catalytic unit is a microbial consortium composed of two or more microbial species. Many syntrophic associations are highly or- anaerobic food chains ͉ syntrophic metabolism ͉ ganized, multicellular structures where the partners are in close fatty acid and benzoate utilization physical proximity to each other (6, 10, 11). However, little is known about the molecular mechanisms involved in the forma- tion and maintenance of these catalytic units. Even under yntrophus aciditrophicus is a rod-shaped, Gram-negative bac- optimal growth conditions, free energy changes are close to Sterium that degrades fatty acids, benzoate, cyclohexane equilibrium (12–14) and the available free energy must be shared carboxylate, cyclohex-1-ene carboxylate, and crotonate in cocul- by the different organisms (4). Truly, syntrophy represents an ture with hydrogen/formate-using methanogens or sulfate re- extreme existence, that of a marginal energy economy. ducers (1, 2). Phylogenetically, S. aciditrophicus is a member of A distinctive feature of syntrophic metabolism is the need for the delta subdivision of the Proteobacteria along with sulfate reverse electron transfer because critical oxidation-reduction reducers and Geobacter species. It is representative of a broad reactions result in a negative ⌬EЈ, i.e., a thermodynamically class of syntrophic bacteria that have an essential role in the unfavorable direction. The production of hydrogen (EЈ of Ϫ261 anaerobic recycling of organic matter to methane and carbon mV at 1 Pa H2) or formate (EЈ of Ϫ258 mV at 1 ␮M formate) dioxide, along with the fermentative and methanogenic organ- (4) from electrons generated in the oxidation of acyl-CoA isms. Whereas the carbon and energy yielding pathways of the latter two microbial groups are well understood, extremely little is known about the metabolism of syntrophs because so few Author contributions: M.J.M., A.B., J.W.C., and R.P.G. designed research; M.J.M., L.R., H.M., strains are available in pure culture. They reproduce slowly A.B., J.W.C., and R.P.G. performed research; M.J.M., L.R., L.R.-H., C.G.S., A.B., and J.W.C. (generation times of 24–50 h), with low yield, and require contributed new reagents/analytic tools; M.J.M., L.R., H.M., U.K., R.S.K., L.R.-H., J.S., C.G.S., symbiotic partners to survive and express their syntrophic life- A.B., J.W.C., and R.P.G. analyzed data; and M.J.M., L.R., J.W.C., and R.P.G. wrote the paper. style. Biochemically, they constitute the missing link in our Conflict of interest statement: J.W.C. and A.B. were employed by Integrated Genomics, Inc., which performed DNA sequencing and gene-calling analysis under contract to the Univer- understanding of anaerobic flow of carbon in the biosphere. sity of California at Los Angeles. They may be viewed as having commercial interests in the A wide range of organic compounds including alcohols, fatty product as a representation of their company’s performance. acids, aromatic acids, organic acids such as lactate and glycolate, This article is a PNAS Direct Submission. many amino acids, sugars, and hydrocarbons including methane Data deposition: The sequence reported in this paper has been deposited in the GenBank are degraded syntrophically under anaerobic conditions (3–9). database (accession no. CP000252). The degradation of these compounds is thermodynamically §To whom correspondence should be addressed. E-mail: [email protected]. unfavorable unless hydrogen and/or formate are maintained at This article contains supporting information online at www.pnas.org/cgi/content/full/ low levels by hydrogen/formate-consuming microorganisms such 0610456104/DC1. as the methanogens (Table 1). This thermodynamically based © 2007 by The National Academy of Sciences of the USA 7600–7605 ͉ PNAS ͉ May 1, 2007 ͉ vol. 104 ͉ no. 18 www.pnas.org͞cgi͞doi͞10.1073͞pnas.0610456104 Downloaded by guest on September 30, 2021 Table 2. General features of the S. aciditrophicus genome*† to individual microbial genomes, best reciprocal BLAST hits ␦ Category Amount revealed closest associations to the -proteobacteria: Geobacter metallireducens (1,118 reciprocal gene hits), Pelobacter carbin- DNA contigs 1 olicus (1,131), and Geobacter sulfurreducens (1,099) (SI Fig. 4). DNA sequenced 3,179,300 bp Approximately 1,100 genes are similar and are well conserved Coding sequence 2,812,658 bp across the 25 Gram-negative species shown. The remaining genes G ϩ C content 51.46% (Ϸ2,000) represent a recently discovered complement within the Transfer RNAs 48 S. aciditrophicus genome. Ribosomal RNA operons 1 In another comparison, the best BLAST hit to any microbial Pseudogenes 0 gene was determined (SI Fig. 5) and showed only 374, 250, and ORFs‡, total 3,169 (100%) 224 closest hits to the genomes of G. metallireducens, G. sul- ORFs with assigned function 1,618 (51%) furreducens, and Pelobacter carbinolicus, respectively. Notably ORFs without assigned function 1,551 (49%) three archaeal genomes, Methanosarcina mazei, Methanospiril- ORFs without function, no database match 421 (13.3%) lum hungatei, and Methanosarcina acetivorans gave 14–31 best ORFs in chromosomal clusters 1,493 (47.1) BLAST hits each, suggesting the possibility of lateral gene ORFs in paralog clusters 786 (24.8%) transfer events from these potential syntrophic partners. A ORFs with Pfam matches 1,852 (58.4%) significant fraction of these genes have energy/Co-A related ORFs with COG matches 1,986 (62.8%) functions or are transposases. *According to ERGO database (www.integratedgenomics.com). †The protein similarity cutoff score used was 1.0eϪ05. Central Metabolism. The 1,618 functionally assigned S. aciditro- ‡ORFs, open-reading frames, coding regions phicus genes were organized into pathways, revealing that most biosynthetic pathways considered essential for viability of a typical Gram-negative organism seem to be present (e.g., bio- intermediates to their respective enoyl-CoA intermediates [EЈ synthesis of amino acids, purines, pyrimidines, and many cofac- of Ϫ10 mV; (15)] represents a considerable energy barrier (i.e., tors). The undetected steps in amino acid formation include ⌬EЈϳϪ250 mV). Thus, the membrane components involved in genes encoding homoserine kinase (threonine biosynthesis), the generation and use of ion gradients are predicted to be key threonine deaminase (conversion of threonine to isoleucine), features of syntrophic metabolism. 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltrans- The genome sequence of S. aciditrophicus provides the first ferase or acetyldiaminopimelate aminotransferase (lysine bio- glimpse of the genetic program directing energy conservation synthesis), phosphoribosyl-ATP diphosphatase, and histidinol and reverse electron transport, which are essential features of the phosphatase (histidine biosynthesis).