The putative single-stranded DNA-binding protein of the filamentous bacteriophage, Ifl. Amino acid sequence of the protein and structure of the gene

Structure and assembly of filamentous bacteriophages

Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of "minor" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.

A novel rolling-circle-replicating plasmid from Pseudomonas putida P8: molecular characterization and use as vector

In Pseudomonas putida P8, three cryptic circular plasmids were detected, i.e. pPP8-1 (2.5 kbp), pPP8-2 (42 kbp) and pPP8-3 (approximately 100 kbp). Cloning and complete sequencing of pPP8-1 revealed a 2534 bp element harbouring four open reading frames (ORFs A, B, C and D). No function could be attributed to the latter three ORFs, whereas the predicted ORF A gene product is homologous to replication proteins known from small multicopy plasmids of Gram-positive bacteria and single-stranded (ss) phages, genetic elements replicating via a rolling circle (RC) mechanism involving characteristic ssDNA intermediates. Consistently, a double-strand origin of replication, highly conserved in rolling-circle-replicating (RCR) elements, was identified in pPP8-1, along with a putative single-strand origin. Beyond this, ss replication intermediates were confirmed by Southern analysis and mungbean-nuclease digestion. This being the first element of this type known in pseudomonads, a kanamycin-resistance gene was ligated into pPP8-1 and the resulting vector was successfully used for the transformation of both Escherichia coli and P. putida.

Filamentous phage structure, infection and assembly

The structural model of filamentous phage derived by X-ray fibre diffraction is supported by spectroscopic and genetic experiments. The structure of the receptor-binding domain at the end of the phage and the structure of the phage-coded intracellular DNA-binding protein have been determined at high resolution. The recent dissection of the virus life cycle by genetic and biochemical analyses, combined with structural information, suggests models for virus infection and assembly.

Upstream stimulators for recoding

Recent progress in elucidation of 5' stimulatory elements for translational recoding is reviewed. A 5' Shine-Dalgarno sequence increases both +1 and -1 frameshift efficiency in several genes; examples cited include the E. coli prfB gene encoding release factor 2 and the dnaX gene encoding the gamma and tau subunits of DNA polymerase III holoenzyme. The spacing between the Shine-Dalgarno sequence and the shift site is critical in both the +1 and -1 frameshift cassettes; however, the optimal spacing is quite different in the two cases. A frameshift in a mammalian chromosomal gene, ornithine decarboxylase antizyme, has recently been reported; 5' sequences have been shown to be vital for this frameshift event. Escherichia coli bacteriophage T4 gene 60 encodes a subunit of its type II DNA topoisomerase. The mature gene 60 mRNA contains an internal 50 nucleotide region that appears to be bypassed during translation. A 16 amino acid domain of the nascent peptide is necessary for this bypass to occur.

C2, and unusual filamentous bacterial virus: protein sequence and conformation, DNA size and conformation, and nucleotide/subunit ratio

Inovirus C2 is 1295 nm long and 6.8 nm in diameter, and its mass is 24 million Da. Its genome is a topologically circular, single-stranded DNA molecule of 8100 nucleotides. The DNA is packed in the virion as two antiparallel strands, with a rise per nucleotide in each strand of 3.2 A; it can be assigned spectroscopic properties like those of base-stacked, right-handed, double-stranded DNA. The stoichiometric ratio (n/s) of nucleotides to subunits of the major coat protein is close to 2. The protein subunit contains 52 amino acids, and the DNA sequence of its gene does not encode a signal peptide. The protein conformation in the virion is helical, mostly alpha-helix with perhaps some 3(10)-helix. The amino acid sequence of the DNA interaction domain of the subunit is unique among Inovirus species. On the basis of its coat protein sequence and available theories of helical symmetry in such structures, C2 appears to be either an unusual member of filamentous virus symmetry class II or the defining member of a new symmetry class.

rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift

Base pairing between the 3' end of 16S rRNA and mRNA is shown to be important for the programmed -1 frameshifting utilized in decoding the Escherichia coli dnaX gene. This pairing is the same as the Shine-Dalgarno pairing used by prokaryotic ribosomes in selection of translation initiators, but for frameshifting the interaction occurs within elongating ribosomes. For dnaX -1 frameshifting, the 3' base of the Shine-Dalgarno sequence is 10 nucleotides 5' of the shift site. Previously, Shine-Dalgarno rRNA-mRNA pairing was shown to stimulate the +1 frameshifting necessary for decoding the release factor 2 gene. However, in the release factor 2 gene, the Shine-Dalgarno sequence is located 3 nucleotides 5' of the shift site. When the Shine-Dalgarno sequence is moved to the same position relative to the dnaX shift site, it is inhibitory rather than stimulatory. Shine-Dalgarno interactions by elongating ribosomes are likely to be used in stimulating -1 frameshifting in the decoding of a variety of genes.