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Abstract
Zinc finger domains are highly structured and can mediate interactions to DNA, RNA, proteins, lipids, and small molecules. Accordingly, zinc finger proteins are very versatile and involved in many biological functions. Eukaryotes contain a wealth of zinc finger proteins, but zinc finger proteins have also been found in archaea and bacteria. Large zinc finger proteins have been well studied, however, in stark contrast, single domain zinc finger µ-proteins of less than 70 amino acids have not been studied at all, with one single exception. Therefore, 16 zinc finger µ-proteins of the haloarchaeon Haloferax volcanii were chosen and in frame deletion mutants of the cognate genes were generated. The phenotypes of mutants and wild-type were compared under eight different conditions, which were chosen to represent various pathways and involve many genes. None of the mutants differed from the wild-type under optimal or near-optimal conditions. However, 12 of the 16 mutants exhibited a phenotypic difference under at least one of the four following conditions: Growth in synthetic medium with glycerol, growth in the presence of bile acids, biofilm formation, and swarming. In total, 16 loss of function and 11 gain of function phenotypes were observed. Five mutants indicated counter-regulation of a sessile versus a motile life style in H. volcanii. In conclusion, the generation and analysis of a set of deletion mutants demonstrated the high importance of zinc finger µ-proteins for various biological functions, and it will be the basis for future mechanistic insight.
Highlights
For a long time, very small proteins (μ-proteins) have been nearly totally neglected
The annotated proteins of H. volcanii were retrieved from the Halolex genome database and sorted according to their predicted size
This accounts for about 13% of all annotated proteins of H. volcanii, and small proteins represent a considerable fraction of the H
Summary
Very small proteins (μ-proteins) have been nearly totally neglected. Genome annotations typically used a lower limit of 100 codons to include an open reading frame (ORF) as a predicted protein-coding gene. The annotation of a vast number of false-positive genes was prevented, on the other hand, real genes for μ-proteins were not included and they escaped attention. During the last years the awareness has emerged that many μ-proteins do exist in prokaryotes, as well as in eukaryotes, and that they have important biological functions. Several recent reviews summarize the current knowledge about μ-proteins in prokaryotes [1,2,3] and in eukaryotes [4,5,6]. Two databases for μ-proteins have been established during the last two years [7,8]
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