b Despite major progresses in genetic studies of hyperthermophilic archaea, recombinant protein production in these organisms always suffers from low yields and a robust expression system is still in great demand. Here we report a versatile vector that confers high levels of protein expression in Sulfolobus islandicus, a hyperthermophilic crenarchaeon. Two expression vectors, pSeSD and pEXA, harboring 11 unique restriction sites were constructed. They contain coding sequences of two hexahistidine (6؋His) peptide tags and those coding for two protease sites, the latter of which make it possible to remove the peptide tags from expressed recombinant proteins. While pEXA employed an araS promoter for protein expression, pSeSD utilized P araS-SD , an araS derivative promoter carrying an engineered ribosome-binding site (RBS; a Shine-Dalgarno [SD] sequence). We found that P araS-SD directed high levels of target gene expression. More strikingly, N-terminal amino acid sequencing of recombinant proteins unraveled that the protein synthesized from pEXA-N-lacS lacked the designed 6؋His tag and that translation initiation did not start at the ATG codon of the fusion gene. Instead, it started at multiple sites downstream of the 6؋His codons. Intriguingly, inserting an RBS site upstream of the ATG codon regained the expression of the 6؋His tag, as shown with pSeSD-N-lacS. These results have yielded novel insight into the archaeal translation mechanism. The crenarchaeon Sulfolobus can utilize N-terminal coding sequences of proteins to specify translation initiation in the absence of an RBS site. C urrently, studying functions of thermophilic archaeal proteins, such as the enzymes involved in DNA replication, gene transcription, and protein translation (10), as well as clustered regularly interspaced palindromic repeat (CRISPR)-associated (Cas) proteins (11, 32), relies almost exclusively on production of recombinant protein from a mesophilic bacterial host such as Escherichia coli and characterization of purified enzymes. However, there is a major drawback in this approach: many thermophilic proteins are insoluble in mesophilic bacterial cells, forming inclusion bodies. Apparently, producing recombinant thermophilic proteins in a homologous host should resolve the problem of protein solubility.For the past few decades, consistent efforts have been devoted to developing protein expression systems for hyperthermophilic organisms and to establishing genetic tools for studying functions of archaeal genes. As a result, methodologies for gene inactivation and genetic complementation have been established for several model archaeal organisms (reviewed in reference 15), including three hyperthermophilic archaea, the euryarchaea Thermococcus kodakarensis (22) and Pyrococcus furiosus (30), and the crenarchaeon Sulfolobus. While both T. kodakarensis and P. furiosus require an anaerobic condition for growth, Sulfolobus species grow aerobically, which is advantageous for laboratory manipulation. Currently, three Sulfolobus species have be...