Poorly-conserved ORFs in the genome of the archaeon Halobacterium sp. NRC-1 correspond to expressed proteins

Motivation: A large fraction of Open Reading Frames (ORFs) identified as “hypothetical” proteins correspond to either “conserved hypothetical” proteins, representing sequences homologous to ORFs of unknown function from other organisms or to hypothetical proteins lacking any significant sequence similarity to other ORFs in the databases. Elucidating the functions and 3D structures of such orphan ORFs, termed ORFans or PCOs (poorly conserved ORFs), is essential for understanding biodiversity. However, it has been claimed that many ORFans may not encode for expressed proteins. Results: A genome-wide experimental study of “paralogous PCOs” in the halophilic archaea Halobacterium sp. NRC-1 was conducted. Paralogous PCOs are ORFs with at least one homolog in the same organism, but with no clear homologs in other organisms. The results reveal that mRNA is synthesized for a majority of the Halobacterium sp. NRC-1 paralogous PCO families, including those composed of relatively short proteins, strongly suggesting that these Halobacterium sp. NRC-1 paralogous PCOs correspond to true, expressed proteins. Hence, further computational and experimental studies aimed at characterizing PCOs in this and other organisms are merited. Such efforts could shed light on PCOs’ functions and origins, thereby serving to elucidate the vast diversity observed in the genetic material. Contact: J. Eichler, e-mail: [email protected]; D. Fischer, e-mail: [email protected]; B. Shaanan, e-mail: [email protected]