Deniz Üresin (Frankfurt a. M. / DE), Andreas Borst (Frankfurt a. M. / DE), Dennis Pyper (Frankfurt a. M. / DE), Lydia Hadjeras (Würzburg / DE), Rick Gelhausen (Freiburg i. Br. / DE), Rolf Backofen (Freiburg i. Br. / DE), Cynthia M. Sharma (Würzburg / DE), Harald Schwalbe (Frankfurt a. M. / DE), Jörg Soppa (Frankfurt a. M. / DE)
Zinc finger proteins are known to fulfil many different roles in eukaryotes, e.g. as transcription factors, ribosomal proteins, regulators of membrane proteins, or molecular scaffolds. In archaea, they are severely understudied. In addition, most well-studied eukaryotic zinc finger proteins are large proteins containing several small zinc finger domains. In contrast, in archaea the majority of putative zinc finger proteins are very small and await experimental characterization.
Haloferax volcanii is a halophilic archaeon that can easily be cultivated, making it a frequently used model organism. Its genome encodes 282 small proteins (less than 70 amino acids), most of them having no annotated function yet. 43 of those proteins contain at least two CPXCG-like motifs, making them putative one-domain zinc finger proteins of unknown function.
For the analysis of these zinc finger µ-proteins more than 30 single gene in frame deletion mutants have been generated until now. They were compared to the wildtype concerning e.g. growth behaviour in different media, swarming, and biofilm formation. Most of the mutants showed a strong phenotype under at least one of the conditions tested, proving that the zinc finger -proteins fulfil various important functions in haloarchaea1. Co-affinity purifications have been initiated to screen for protein interaction partners. A biochemical zinc assay was performed to investigate which of the putative zinc fingers actually bind zinc ions.
The proteins HVO_0758 and HVO_2753 have been studied in detail2,3. RNA-Seq analyses (coll. with C. Sharma, Würzburg) revealed that movement/chemotaxis genes are downregulated in the deletion mutants, in excellent agreement with their inability to swarm. Determination of the NMR solution structures (coll. with H. Schwalbe, Frankfurt) revealed distinct structural differences between the two proteins.
Taken together, we could show that haloarchaeal zinc finger µ-proteins are important for various biological functions, e.g. glycerol metabolism, biofilm formation and swarming.
1Nagel et al. (2019) Genes 10:361
2Zahn et al. (2020) FEBS J. 288:2042
3Üresin et al. (2023) Front Microbiol. 14:1280972