This work assesses relationships for 30 complete prokaryotic genomes between the presence of the ShineDalgarno (SD) sequence and other gene features, including expression levels, type of start codon, and distance between successive genes. A significant positive correlation of the presence of an SD sequence and the predicted expression level of a gene based on codon usage biases was ascertained, such that predicted highly expressed genes are more likely to possess a strong SD sequence than average genes. Genes with AUG start codons are more likely than genes with other start codons, GUG or UUG, to possess an SD sequence. Genes in close proximity to upstream genes on the same coding strand in most genomes are significantly higher in SD presence. In light of these results, we discuss the role of the SD sequence in translation initiation and its relationship with predicted gene expression levels and with operon structure in both bacterial and archaeal genomes.

Based primarily on 16S rRNA sequence comparisons, life has been broadly divided into the three domains of Bacteria, Archaea, and Eukarya. Archaea is further classified into Crenarchaea and Euryarchaea. Archaea generally thrive in extreme environments as assessed by temperature, pH, and salinity. For many prokaryotic organisms, ribosomal proteins (RP), transcription͞translation factors, and chaperone genes tend to be highly expressed. A gene is predicted highly expressed (PHX) if its codon usage is rather similar to the average codon usage of at least one of the RP, transcription͞ translation factors, and chaperone gene classes and deviates strongly from the average gene of the genome. The thermosome (Ths) chaperonin family represents the most salient PHX genes among Archaea. The chaperones Trigger factor and HSP70 have overlapping functions in the folding process, but both of these proteins are lacking in most archaea where they may be substituted by the chaperone prefoldin. Other distinctive PHX proteins of Archaea, absent from Bacteria, include the proliferating cell nuclear antigen PCNA, a replication auxiliary factor responsible for tethering the catalytic unit of DNA polymerase to DNA during highspeed replication, and the acidic RP P0, which helps to initiate mRNA translation at the ribosome. Other PHX genes feature Cell division control protein 48 (Cdc48), whereas the bacterial septation proteins FtsZ and minD are lacking in Crenarchaea. RadA is a major DNA repair and recombination protein of Archaea. Archaeal genomes feature a strong Shine-Dalgarno ribosome-binding motif more pronounced in Euryarchaea compared with Crenarchaea.acidic ribosomal proteins ͉ Archaea ͉ highly expressed proteins ͉ thermosome T he identity of the three domains of life (1) and their relationships are controversial (2-11). Archaea form a heterogeneous clade composed of a mosaic of bacterial, eukaryotic, and unique features. Archaea and Eukarya share many homologous genes involved in information processing (replication, transcription, and translation), whereas Archaea and Bacteria share many morphological structures and metabolic proteins (10, 12). Of 19 archaeal genomes completely sequenced (Table 1, mid-2004), 4 are from Crenarchaea and 14 are from Euryarchaea. Nanoarchaeum equitans, a parasitic archaeon that lives in coculture with the archaeon Ignicoccus, has been tentatively assigned to the separate group of Nanoarchaea. Most sequenced archaea, to date, are thermophilic, generally prefer extreme environments, and are found in most ecosystems. The four sequenced crenarchaea are all hyperthermophiles (optimal growth temperature, Ն75°C), although mesophilic crenarchaea have been putatively found in pelagic waters (3, 13). Among the Euryarchaea, six are methanogens, including three mesophiles, Methanosarcina acetivorans, Methanosarcina mazei, and Methanococcus maripaludis. Halobacterium NRC-1 is also mesophilic, thriving in high salt concentrations. Most sequenced archaea, excluding methanogens (lifestyle strictly anaerobic, meta...