incubated with 20 ml Sepharose-immobilized monoclonal anti-HA antibodies (Covance). Beads were washed with buffer T without BSA before elution. DSP-induced crosslinks in eluted proteins were thiol-cleaved before separation by 8-16% SDS-PAGE and detection by Sypro Ruby (Bio-Rad). Quinone analysesLipid extractions and quinone detection were performed as described 19 . Hydrogenosomes (5.5 mg protein) were extracted and resuspended in 150 ml 9:1 methanol/ethanol, of which 50 ml was injected onto an HPLC system linked to an ECD. Sequence analysesAccession numbers for sequences used to reconstruct NuoF and NuoE phylogenies are listed in Supplementary Tables 2 and 3. NuoF sequences were aligned with CLUSTALX. NuoE sequences were aligned with Wisconsin Package Version 10.2 programs (Genetics Computer Group). A profile hidden Markov model (HMM) was built from Escherichia coli, Neurospora crassa, Bos taurus, Paracoccus denitrificans and Thermus thermophilus sequences with HMMBUILD. Additional sequences were aligned to the profile with HMMALIGN. Both alignments were edited to remove C-and N-terminal extensions. Analyses of NuoF and NuoE evolution were performed with MRBAYES 30 with the JTT amino-acid substitution model and with two Markov chains Monte Carlo. Chains were run for 100,000 generations, with sampling every 50 generations. The first 5,000 generations were discarded as burn-in. Consensus trees satisfying the more than 50 majority rule were drawn with Treeview, and probabilities of branch partitions were calculated.

The genome of Streptococcus sanguinis is a circular DNA molecule consisting of 2,388,435 bp and is 177 to 590 kb larger than the other 21 streptococcal genomes that have been sequenced. The G؉C content of the S. sanguinis genome is 43.4%, which is considerably higher than the G؉C contents of other streptococci. The genome encodes 2,274 predicted proteins, 61 tRNAs, and four rRNA operons. A 70-kb region encoding pathways for vitamin B 12 biosynthesis and degradation of ethanolamine and propanediol was apparently acquired by horizontal gene transfer. The gene complement suggests new hypotheses for the pathogenesis and virulence of S. sanguinis and differs from the gene complements of other pathogenic and nonpathogenic streptococci. In particular, S. sanguinis possesses a remarkable abundance of putative surface proteins, which may permit it to be a primary colonizer of the oral cavity and agent of streptococcal endocarditis and infection in neutropenic patients.

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