DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: Evidence for a new type of sulfur-reducing enzyme complex

DNA microarrays were constructed by using 271 open reading frame (ORFs) fro m the genome of the archaeon Pyrococcus furiosus. They were used to investi gate the effects of elemental sulfur (S degrees) on the levels of gene expr ession in cells grown at 95 degreesC with maltose as the carbon source. The ORFs included those that are proposed to encode proteins mainly involved i n the pathways of sugar and peptide catabolism, in the metabolism of metals , and in the biosynthesis of various cofactors, amino acids, and nucleotide s. The expression of 21 ORFs decreased by more than fivefold when cells wer e grown with S degrees and, of these, 18 encode subunits associated with th ree different hydrogenase systems. The remaining three ORFs encode homologs of ornithine carbamoyltransferase and HypF, both of which appear to be inv olved in hydrogenase biosynthesis, as well as a conserved hypothetical prot ein. The expression of two previously uncharacterized ORFs increased by mor e than 25-fold when cells were grown with S degrees. Their products, termed SipA and SipB (for sulfur-induced proteins), are proposed to be part of a novel S'-reducing, membrane-associated, iron-sulfur cluster-containing comp lex. Two other previously uncharacterized ORFs encoding a putative flavopro tein and a second FeS protein were upregulated more than sixfold in S degre es -grown cells, and these are also thought be involved in S degrees reduct ion. Four ORFs that encode homologs of proteins involved in amino acid meta bolism were similarly upregulated in S degrees -grown cells, a finding cons istent with the fact that growth on peptides is a S'-dependent process. An ORF encoding a homolog of the eukaryotic rRNA processing protein, fibrillar in, was also upregulated sixfold in the presence of S degrees, although the reason for this is as yet unknown. Of the 20 S degrees -independent ORFs t hat are the most highly expressed (at more than 20 times the detection limi t), 12 of them represent enzymes purified from P. furiosus, but none of the products of the 34 S degrees -independent ORFs that are not expressed abov e the detection limit have been characterized. These results represent the first derived from the application of DNA microarrays to either an archaeon or a hyperthermophile.