Genome sequence of Picrophilus torridus and its implications for life around pH 0 O. Fu¨ tterer*, A. Angelov*, H. Liesegang*, G. Gottschalk*, C. Schleper†, B. Schepers‡, C. Dock‡, G. Antranikian‡, and W. Liebl*§ *Institut of Microbiology and Genetics, University of Goettingen, Grisebachstrasse 8, D-37075 Goettingen, Germany; †Institut of Microbiology and Genetics, Technical University Darmstadt, Schnittspahnstrasse 10, 64287 D-Darmstadt, Germany; and ‡Technical Microbiology, Technical University Hamburg–Harburg, Kasernenstrasse 12, 21073 D-Hamburg, Germany Edited by Dieter So¨ll, Yale University, New Haven, CT, and approved April 20, 2004 (received for review February 26, 2004) The euryarchaea Picrophilus torridus and Picrophilus oshimae are (4–6). After analysis of a number of archaeal and bacterial ge- able to grow around pH 0 at up to 65°C, thus they represent the nomes, it has been argued that microorganisms that live together most thermoacidophilic organisms known. Several features that swap genes at a higher frequency (7, 8). With the genome sequence may contribute to the thermoacidophilic survival strategy of P. of P. torridus, five complete genomes of thermoacidophilic organ- torridus were deduced from analysis of its 1.55-megabase genome. isms are available, which allows a more complex investigation of the P. torridus has the smallest genome among nonparasitic aerobic evolution of organisms sharing the extreme growth conditions of a microorganisms growing on organic substrates and simulta- unique niche in the light of horizontal gene transfer. neously the highest coding density among thermoacidophiles. An exceptionally high ratio of secondary over ATP-consuming primary Methods transport systems demonstrates that the high proton concentra- Sequencing Strategy. Genomic DNA of P. torridus strain DSM 9790 tion in the surrounding medium is extensively used for transport was extracted and sheared randomly. A shotgun library was con- processes. Certain genes that may be particularly supportive for structed by using fractions with sizes ranging from 2 to 3 kb. All the extreme lifestyle of P. torridus appear to have been internal- generated sequences were assembled into contigs with the PHRAP ized into the genome of the Picrophilus lineage by horizontal gene assembling tool (9) and have been edited with GAP4 of the STADEN transfer from crenarchaea and bacteria. Finally, it is noteworthy software package (10). A total of 25,694 sequences were aligned MICROBIOLOGY that the thermoacidophiles from phylogenetically distant branches leading to a database with a 9.4-fold coverage and a statistical error of the Archaea apparently share an unexpectedly large pool of rate of below 1 in 2,000,000 bp. Gap closure was accomplished by genes. primer walking on plasmids originating from the plasmid library and from PCRs with chromosomal DNA as template. Gene and gene order comparison with already sequenced genomes served icrophilus torridus is a thermoacidophilic euryarchaeon thriving as verification for the assembly of the contigs to the closed optimally at 60°C and pH 0.7. Strains of this species were first P chromosome. isolated from a dry solfataric field in northern Japan. In addition to being moderately thermophilic, the Picrophilaceae are the most ORF Prediction and Annotation. ORFs likely to encode proteins were acidophilic organisms known and are also able to grow at negative predicted by the YACOP software package (11) (www.g2l.bio.uni- pH values. It was reported for P. torridus that even adaptation to goettingen.de͞software), based on the algorithms CRITICA (12), conditions such as those in 1.2 M sulfuric acid is possible (1). ORPHEUS (13), and GLIMMER (14). Automatic and manual anno- Another unusual trait of Picrophilus is a very low intracellular pH tation was accomplished with the ERGO annotation tool (Integrated of 4.6, in contrast to other thermoacidophilic organisms that Genomics), which was refined by searches against PFAM, PROSITE, maintain internal pH values close to neutral (2, 3). The high PRODOM, and COGS databases, in addition to the BLASTP (15) versus specialization of Picrophilus strains for growth in extremely acidic SWISSPROT, NR, and TCDB databases. Putative signal peptides were habitats is evident from their inability to grow at pH values above predicted by using the SIGNALP program (16). 4.0, and makes them model organisms to study thermoacidophilic adaptation. Points of major interest include questions about prop- Homology Prediction and Horizontal Gene Transfer. For gene com- erties and mechanisms that ensure viability under these conditions. parison, homology was specified as 30% amino acid sequence Specific adaptation mechanisms can be expected at the levels of (i) identity. Ortho- and paralogous sequences were counted only once. structure and function of biomolecules and (sub-)cellular struc- The threshold for specifying genes into the categories archaeal, tures, (ii) physiology and metabolic features, and (iii) regulation of bacterial, eukaryotic, or thermoacidophilic was set at a BLAST gene expression. For example, P. torridus cells need a specifically e-value of 1e-05 at the amino acid sequence level. adapted membrane. Indeed, the membrane of P. torridus displays a very low proton permeability, is highly acid stable, and loses its Results integrity when incubated at pH 7 (2). Furthermore, an acid-stable General Features of the P. torridus Genome. The genome of P. cell envelope and acid-resistant extracellular enzymes for the torridus consists of a 1,545,900-bp large single circular chromosome degradation of polymeric or oligomeric carbon sources are re- and contains 1,535 ORFs (Table 1). A total of 92% of the sequence quired. Finally, the organism needs to generate metabolic energy in is coding, which represents the highest coding density in the substantial amounts to maintain the intracellular pH at an accept- genomes of the thermoacidophile group (89%, 87%, 85%, and 85% able value. for Thermoplasma acidophilum, Thermoplasma volcanii, Sulfolobus The phylogenetic position of P. torridus lies within the order of Thermoplasmales, which comprises the thermoacidophilic group of the euryarchaeal branch of the domain Archaea, consisting of the This paper was submitted directly (Track II) to the PNAS office. Thermoplasmaceae, Ferroplasmaceae, and Picrophilaceae (Fig. 1). A Abbreviation: ABC, ATP-binding cassette. second group of thermoacidophiles can be found inside the cren- Data deposition: The sequence reported in this paper has been deposited in the GenBank archaeal branch, the Sulfolobaceae. With only a few exceptions, database (accession no. AE017261). members of both groups are aerobic or microaerophilic, hetero- §To whom correspondence should be addressed. E-mail: [email protected]. trophic organisms that are often found to share the same habitat © 2004 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0401356101 PNAS ͉ June 15, 2004 ͉ vol. 101 ͉ no. 24 ͉ 9091–9096 Downloaded by guest on October 1, 2021 Fig. 1. 16S rRNA phylogenetic tree. Highlighted are the two thermoacidophilic groups of the archaea. Sequences were aligned with the CLUSTALW algorithm. The tree was build by neighbor joining by using the Kimura 2-parameter for distance calculation. solfataricus, and Sulfolobus tokodaii, respectively). For 74% of all Pyrococcus furiosus, meaning that in this case ecological closeness ORFs found in the genome, it was possible to assign a function. Of overrides phylogenetic relatedness. The statement that P. torridus the 397 hypothetical ORFs, 79 are unique to P. torridus, whereas shares nearly the same number of homologs with T. acidophilum 318 showed similarities to hypothetical ORFs of other organisms. and S. solfataricus but significantly fewer homologs with Pyrococcus Interestingly, 174 of the latter ORFs have orthologs only in the furiosus remains true even when lowering the threshold for homol- genomes of other thermoacidophilic organisms, indicating that the ogy prediction from 30% to 25% identity. thermoacidic environment forms an old and genetically distinct The genome sequence data indicate that, in contrast to a previous niche of life (see supporting information, which is published on the report (4), the DNA-dependent RNA polymerase (RNAP) of P. PNAS web site). This is supported by whole genome comparison of the amino acid sequences of the complete genomes of three prominent members of the thermoacidophilic group, P. torridus, T. acidophilum, and the crenarchaeon S. solfataricus, for homology (Fig. 2). P. torridus and T. acidophilum display significant homology in 66% of all genes, and these two euryarchaea share 58% and 62% genes, respectively, with the crenarchaeon S. solfataricus, but only Ϸ35% with the phylogenetically more closely related euryarchaeon Table 1. General features of the P. torridus genome sequence General features Number Size, bp 1,545,900 Coding region, % 91.7 G ϩ C content, % 36 Total number of ORFs 1,535 ORFs with assigned function 983 ORFs without function 553 ORFs without function or similarity 73 ORFs without function, with similarity 480 ORFs with putative signal peptides 121 ORFs involved in transport 170 Stable RNAs rRNAs 1 5S; 1 16S; 1 23S tRNAs 47 Fig. 2. Occurrence of homologous ORFs in P. torridus, T. acidophilum, and S. solfataricus. The size of the circles is proportional to the size of the genomes. 9092 ͉ www.pnas.org͞cgi͞doi͞10.1073͞pnas.0401356101 Fu¨ tterer et al. Downloaded by guest on October 1, 2021 torridus is identical