Identification of New Members of Hydrophobin Family Using Primary Structure Analysis

Hydrophobins are fungal proteins that can turn into amphipathic membranes at hydrophilic/hydrophobic interfaces by self-assembly. The assemblages by Class I hydrophobins are extremely stable and possess the remarkable ability to change the polarity of the surface. One of its most important industrial applications is its usage as paint. Without detailed knowledge of the 3D structure and self-assembly principles of hydrophobins, it is difficult to make significant progress in furthering its research. In order to provide useful information to hydrophobin researchers, we analyzed primary structure of hydrophobins to gain more insight about these proteins. In this paper, we presented an in-depth primary sequence analysis using batch BLAST search of the database, sequence filtering by programming and motif finding by MEME. We used batch BLAST to find similar sequences in the NCBI nr database. Then we used MEME to find out motifs. Based on the newly found motifs and the well-known C-CC-C-C-CC-C pattern we used MAST to search the entire nr database. At the end, domain search and phylogenetic analysis were conducted to confirm the result. After searching the nr database with the new PSSM-format motifs identified by MEME, many sequences from various species were found by MAST. Filtering process by pattern, domain and length left 9 qualified candidates. All of them possess the common pattern and hydrophobin domain. From the multiple sequence alignment result, we can see that some of them are grouped very close to other known hydrophobins, which means their phylogenetic relationship is very close and it is highly plausible that they are indeed hydrophobin proteins. Key words: Hydrophobin,

[1]  D. Higgins,et al.  Finding flexible patterns in unaligned protein sequences , 1995, Protein science : a publication of the Protein Society.

[2]  J. Mackay,et al.  The hydrophobin EAS is largely unstructured in solution and functions by forming amyloid-like structures. , 2001, Structure.

[3]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.

[4]  Han A. B. Wösten,et al.  Insoluble hydrophobin complexes in the walls of Schizophyllum commune and other filamentous fungi , 1993, Archives of Microbiology.

[5]  J. Wessels.  DEVELOPMENTAL REGULATION OF FUNGAL CELL-WALL FORMATION , 1994 .

[6]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[7]  J. Wessels,et al.  Hydrophobins: proteins that change the nature of the fungal surface. , 1997, Advances in microbial physiology.

[8]  Frank H. J. Schuren,et al.  Targeted mutation of the SC3 hydrophobin gene of Schizophyllum commune affects formation of aerial hyphae , 1996 .

[9]  M. Nei,et al.  The neighbor-joining method , 1987 .

[10]  Michael Gribskov,et al.  Combining evidence using p-values: application to sequence homology searches , 1998, Bioinform..

[11]  Ronen Zangi,et al.  Molecular dynamics study of the folding of hydrophobin SC3 at a hydrophilic/hydrophobic interface. , 2002, Biophysical journal.

[12]  Peer Bork,et al.  SMART, a simple modular architecture research tool , 1998 .