The basic structure of filamentous phage and its use in the display of combinatorial peptide libraries

Combinatorial peptide libraries have been playing a major role in the search for new drugs, ligands, enzyme substrates, and other specifically interacting molecules. The principal features of these libraries require a versatile repertoire, an easily identifiable tag for each of the library members, a simple method of synthesis, and a compability with the biochemical milieu. Two types of combinatorial libraries are in use: synthetic libraries and biological (mainly phage display) ones. An advantage of the biological libraries is due to the ability of each of the library members to replicate itself and to the fact that they carry their own coding sequences. The uniqueness of filamentous phage is that of its five virion proteins, three can tolerate the insertion of foreign peptides, each in a distinctive manner. The major coat protein, pVIII, is capable of displaying hundreds of peptide copies over the phage virion, pIII can display either one or five copies, and pVI, as opposed to the first two, displays its peptides such that the carboxy terminus is oriented outward. A major drawback of filamentous phage is its size. The length of an intact phage particle is 930 nm and it contains an ssDNA of 6400 bp. 2800 copies of the major coat protein form a “fish scale” cover over most of the virion DNA, whereas five copies of pIII, which has been the major protein used for library display, and five copies of pVI are located at one end of the filamentous virion. There is no doubt that in order to improve the quality of filamentous phage libraries, the size of phage should be drastically reduced. Comprehensive research on the phage life cycle and its structure will lead us to the construction of miniature phage and to other methods that will enable an in vivo expanding of the library repertoire as well as to binding-induced specific clone-proliferation.     

The extreme N-terminal domain of a hordeivirus TGB1 movement protein mediates its localization to the nucleolus and interaction with fibrillarin

The hordeiviral movement protein encoded by the first gene of the triple gene block (TGBp1) of Poa semilatent virus (PSLV), interacts with viral genomic RNAs to form RNP particles which are considered to be a form of viral genome capable of cell-to-cell and long-distance transport in infected plants. The PSLV TGBp1 contains a C-terminal NTPase/helicase domain (HELD) and an N-terminal extension region consisting of two structurally and functionally distinct domains: an extreme N-terminal domain (NTD) and an internal domain (ID). This study demonstrates that transient expression of TGBp1 fused to GFP in Nicotiana benthamiana leaves results in faint but obvious fluorescence in the nucleolus in addition to cytosolic distribution. Mutagenesis of the basic amino acids inside the NTD clusters A ¹¹⁶KSKRKKKNKK¹²⁵ and B ¹⁷⁵KKATKKESKKQTK¹⁸⁷ reveals that these clusters are indispensable for nuclear and nucleolar targeting of PSLV TGBp1 and may contain nuclear and nucleolar localization signals or their elements. The PSLV TGBp1 is able to bind to fibrillarin, the major nucleolar protein (AtFib2 from Arabidopsis thaliana) in vitro. This protein–protein interaction occurs between the glycine-arginine-rich (GAR) domain of fibrillarin and the first 82 amino acid residues of TGBp1. The interaction of TGBp1 with fibrillarin is also visualized in vivo by bimolecular fluorescence complementation (BiFC) during co-expression of TGBp1 or its deletion mutants, and fibrillarin as fusions to different halves of YFP in N. benthamiana plants. The sites responsible for nuclear/nucleolar localization and fibrillarin binding, have been located within the intrinsically disordered TGBp1 NTD. These data could suggest that specific functions of hordeivirus TGBp1 may depend on its interaction with nucleolar components.     

Interaction of the Bordetella pertussis filamentous hemagglutinin with heparin

Heparin, a glycosaminoglycan synthesized in connective tissue-mast cells, appeared to inhibit the hemagglutination of rabbit erythrocytes induced by the filamentous hemagglutinin (FHA), a major adhesin of Bordetella pertussis. This inhibition suggested an interaction of heparin with the FHA region responsible for the hemagglutination activity. FHA-heparin interactions may play a role in bacterial attachment and persistence in the lungs during human pertussis. To confirm a direct FHA-heparin interaction, heparin was used as ligand in an affinity chromatography procedure. This technique allowed to purify FHA directly from the bacterial culture medium in a single-step using heparin-Sepharose CL-6B or Zetaffinity heparin 60 disks. The purified FHA was highly immunoreactive with anti-FHA monoclonal antibodies and showed no signs of degradation after 15 successive cycles of freezing-thawing. The described purification method is simple, and suitable for the rapid preparation of FHA.     

Fish assemblage structure in relation to macrophytes and filamentous epiphytes in shallow non-tidal rocky- and soft-bottom habitats

Synopsis The fish assemblage in nineteen shallow water (0–3 m) areas on the Swedish west coast, including an estuarine zone, was assessed during spring and autumn 1989 and autumn 1990, using semi-quantitative survey nets. Samples of macrovegetation were collected concurrently for estimates of species composition and biomass. Nine stations had rocky-bottom substrata and ten had soft-bottom substrata all characterized by high coverage of macrovegetation and variously overgrown with epiphytic filamentous algae. Fish assemblage structures were compared and related to vegetation biomass, substrata and estuarine influences. At rocky-bottom stations total fish biomass was positively correlated with total vegetation biomass and negatively correlated with the proportion of filamentous algae during autumn samplings. In soft-bottom habitats variation in vegetation was small between stations, and no correlation existed between vegetation biomass and fish biomass. However, the number of fish species in soft-bottom habitats decreased significantly with increasing dominance of filamentous algae. The component species of the fish assemblage varied in their relation to the vegetation biomass and structure suggesting differences in degree of association with vegetation at the species level. Multivariate analysis based on fish species composition and on vegetation assemblages at the individual stations, yielded two major groups in accordance with division of the substrate into rocky- and soft-bottom habitats. Vegetation biomass superimposed on the fish assemblage ordination indicated a relationship between vegetation biomass and fish assemblage structure. Location of stations, in relation to the estuary was reflected in subgroups formed in the fish assemblage based cluster and ordination, suggesting a substantial estuarine influence on the fish assemblages. Thus, substrate type, vegetation biomass and structure, and estuarine influence are all potential structuring factors for the fish assemblages. In our study, vegetation structure seems to be of major importance and changes such as increased dominance of filamentous algae, like that observed in coastal areas in Sweden, might cause significant changes in fish assemblage structure.