Sponges (Porifera) are the phylogenetically oldest metazoan organisms. From one member of the siliceous sponges, Geodia cydonium, the cDNA encoding a putative SOS protein, the AidB-like protein of the Ada system from bacteria, was isolated and characterized. The cDNA, GCaidB, comprises an open reading frame of 446 amino acid (aa) residues encoding a polypeptide with a calculated Mr of 49,335. This molecule shows high similarity to the bacterial AidB proteins from Mycobacterium tuberculosis and Escherichia coli and somewhat lower similarities to acyl-CoA dehydrogenases (ADHs) and acyl-CoA oxidases (AOXs). Northern blot analysis confirmed the presence of the complete transcript. The deduced sponge aa sequence, GC_aidB, possesses the two characteristic acyl-CoA dehydrogenase signatures 1 and 2. Incubation of the sponge with N-methyl-N'-nitro-N-nitrosoguanidine causes a strong increase in the 2.1-kb large transcript of GCaidB; maximal expression is seen after 24 h of incubation with this DNA methylating agent. ADHs and AOXs can be grouped, depending on the position of the catalytically important Glu residue, into the Glu-Gly (Glu adjacent to Gly) class and the Glu-Arg (Glu adjacent to Arg) class. The phylogenetically oldest metazoan AidB-like molecule, GC_aidB of G. cydonium, belongs to the Glu-Gly class of ADHs. Phylogenetic analyses of the Glu-Gly class enzymes, with the described AidB-like protein from G. cydonium and the bacterial AidB polypeptides, together with metazoan ADHs and AOXs, revealed that the AidB(-like) proteins diverged first from a common ancestor, while the eukaryotic AOX and ADA polypeptides as well as the GHDs appeared later. According to the analyses, the very long-chain ADHs are older than the medium-chain, short-chain, and branched-chain ADHs. Inclusion of the phylogenetical oldest member of the Glu-Arg class of enzymes, the bacterial ADH-CaiA sequence in these analyses, revealed that this class of enzymes appeared later in evolution and arose from the Glu-Gly class perhaps after gene duplication.