Small proteins in Archaea

Up to now research on proteins focused on proteins larger than 70 amino acids. But recent data clearly show that proteins smaller than 70 amino acids are synthesised in the cell and fulfil important cellular functions in bacteria and eukaryotes. However, very little is known about these small proteins in archaea.
Therefore we want to study the function of small proteins (10-70 amino acids) in Haloarchaea. We want to identify the small proteome of the halophilic archaeon Haloferax volcanii as well as investigate selected small stress related proteins.
So far we could identify 34 expressed small proteins in H. volcanii and we selected four proteins for in depth studies. We will generate deletion strains for the respective proteins and investigate those thoroughly for phenotypes.

Work in this project is done in the frame of the DFG priority programme SPP 2002 "Small Proteins in Prokaryotes, an Unexplored World".

Small Proteins can be encoded in 5´ or 3´ UTR regions, in alternative frames of an existing ORF or in a noncoding RNA. Different examples for this are shown. A. Example for a conventional mRNA containing an open reading frame with additional 5´ and 3´ UTR sequences. B. An ORF for a small protein (shown in red) can be located in the 5´ UTR of an mRNA or in the 3´ UTR of an mRNA (C.). D. An alternative frame (altORF) overlapping with an existing ORF can likewise encode a small protein. E. A noncoding RNA can have a dual function: it can act as regulatory RNA but it can additionally function as an mRNA coding for a small protein. — Small Proteins can be encoded in 5´ or 3´ UTR regions, in alternative frames of an existing ORF or in a noncoding RNA. A. Example for a conventional mRNA containing an open reading frame with additional 5´ and 3´ UTR sequences. B. An ORF for a small protein (shown in red) can be located in the 5´ UTR of an mRNA or in the 3´ UTR of an mRNA (C.). D. An alternative frame (altORF) overlapping with an existing ORF can likewise encode a small protein. E. A noncoding RNA can have a dual function: it can act as regulatory RNA but it can additionally function as an mRNA coding for a small protein.