Heat cleavage of bacteriophage T4 gene 23 product produces two peptides previously identified as head proteins

Influence of Protein Hydrolysis on the Freeze-thaw Stability of Emulsions Prepared with Soy Protein - Dextran Conjugates

Protein hydrolysis on the freeze-thaw stability of emulsions prepared with soy protein - dextran conjugates were investigated. Soy protein isolate-dextran (SPI-D) and soy protein hydrolysates-dextran (SPH-D) conjugates with different degree of hydrolysis (DH) were formed by Maillard reaction. The formation of protein-polysaccharide conjugates between SPI/SPH and dextran molecules was confirmed by SDS-PAGE; this finding was consistent with the degree of glycation and the browning index. The freeze-thaw emulsion stability was investigated. The results confirmed that the SPH3-D (DH at 3%) emulsion with 3% DH of SPI exhibited the lowest creaming index after experiencing 1, 2, and 3 freeze-thaw cycles , with results of 7.69%, 20.74% and 31.30%, respectively. The SPH3-D emulsion had a significantly lower average particle size, which was reduced by 48.28% compared to the SPI-D emulsion. Meanwhile, the SPH3-D solution had low interfacial tension. The confocal laser scanning microscopy analysis indicated that the SPH3-D emulsions were strongly stable against the freeze-thaw treatment and could be used as effective emulsifiers in frozen foods.

Genome sequence of the lytic bacteriophage P1201 from Corynebacterium glutamicum NCHU 87078: evolutionary relationships to phages from Corynebacterineae

P1201 is a lytic corynephage of Corynebacterium glutamicum NCHU 87078. Its genome consists of a linear double-stranded DNA molecule of 70,579 base pairs, with 3'-protruding cohesive ends of ten nucleotides. We have identified 69 putative open reading frames, including three apparent genes (thymidylate synthase, terminase, and RNR alpha subunit genes) that are interrupted by an intein. Protein-splicing activities of these inteins were demonstrated in Escherichia coli. Three structural proteins including major capsid and major tail proteins were separated by SDS-PAGE and identified by both LC-MS-MS and N-terminal sequence analyses. Bioinformatics analysis indicated that only about 8.7% of its putative gene products shared substantial protein sequence similarity with the lytic corynephage BFK20 from Brevibacterium flavum, the only corynephage whose genome had been sequenced to date, revealing that the P1201 genome is distinct from BFK20. The mosaic-like genome of P1201 indicates extensive horizontal gene transfer among P1201, Gordonia terrae phage GTE5, mycobacteriophages, and several regions of Corynebacterium spp. genomes.

Whole genome sequencing of a novel temperate bacteriophage ofP. aeruginosa: evidence of tRNA gene mediating integration of the phage genome into the host bacterial chromosome

Whole genome sequencing of a novel Pseudomonas aeruginosa temperate bacteriophage PaP3 has been completed. The genome contains 45 503 bp with GC content of 52.1%, without more than 100 bp sequence hitting homologue in all sequenced phage genomes. A total of 256 open reading frames (ORFs) are found in the genome, and 71 ORFs are predicated as coding sequence (CDS). All 71 CDS are divided into the two opposite direction groups, and both groups meet at the bidirectional terminator site locating the near middle of the genome. The genome is dsDNA with 5'-protruded cohesive ends and cohesive sequence is 'GCCGGCCCCTTTCCGCGTTA' (20 mer). There are four tRNA genes (tRNA(Asn), tRNA(Asp), tRNA(Tyr) and tRNA(Pro)) clustering at the 5'-terminal of the genome. Analysis of integration site of PaP3 in the host bacterial genome confirmed that the core sequence of (GGTCGTAGGTTCGAATCCTAC-21mer) locates at tRNA(Pro) gene within the attP region and at tRNA(Lys) gene in the attB region. The results indicated that 3'-end of tRNA(Pro) gene of the PaP3 genome is involved in the integration reaction and 5'-end of tRNA(Lys) gene of host bacteria genome is hot spot of the integration.

Bacteriophage T4 genome

Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.

Structural basis for oligosaccharide recognition by Pyrococcus furiosus maltodextrin-binding protein

A maltodextrin-binding protein from Pyrococcus furiosus (PfuMBP) has been overproduced in Escherichia coli, purified, and crystallized. The crystal structure of the protein bound to an oligosaccharide ligand was determined to 1.85 A resolution. The fold of PfuMBP is very similar to that of the orthologous MBP from E. coli (EcoMBP), despite the moderate level of sequence identity between the two proteins (27 % identity, 46 % similarity). PfuMBP is extremely resistant to heat and chemical denaturation, which may be attributed to a number of factors, such as a tightly packed hydrophobic core, clusters of isoleucine residues, salt-bridges, and the presence of proline residues in key positions. Surprisingly, an attempt to crystallize the complex of PfuMBP with maltose resulted in a structure that contained maltotriose in the ligand-binding site. The structure of the complex suggests that there is a considerable energy gain upon binding of maltotriose in comparison to maltose. Moreover, isothermal titration calorimetry experiments demonstrated that the binding of maltotriose to the protein is exothermic and tight, whereas no thermal effect was observed upon addition of maltose at three temperatures. Therefore, PfuMBP evidently is designed to bind oligosaccharides composed of three or more glucopyranose units.

Identification of bacteriophage T4 virion proteins by transverse pore-gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis and dual amino acid labeling

We have developed a horizontal N,N'-methylenebisacrylamide (Bis) acrylamide gradient sodium dodecyl sulfate (SDS) gel system that permits the evaluation of the purity of individual protein bands in complex mixtures. A Bis gradient gel is poured vertically and, after polymerization, reoriented horizontally. A single large sample spanning the top of the gel is then run down at right angles to the gradient. The relative mobility of a few proteins varies considerably from the rest, causing them to merge with and cross other bands as the Bis concentration changes. Band splitting revealed that several bands previously thought to represent a single species are actually comprised of comigrating proteins. Once the Bis/monomer concentration offering the best separation was identified, we sought a simple method for identifying the genetic origin of bands, since many proteins now migrated in new positions on the gel. We reasoned that if infected cells were simultaneously labeled with [35S]methionine and [3H]leucine and the purified virion proteins analyzed to determine their 35S/3H ratio, we could identify most proteins by comparing this ratio with one calculated from the T4 DNA sequence. Our expectations were realized, and we here report the separation and identification of all T4 virion proteins. Finally, we comment on the incorporation of various changes to the original Laemmli SDS-polyacrylamide gel formulations that have been reported in the literature.

Cloning and nucleotide sequence of the major capsid protein from Lactococcus lactis ssp. cremoris bacteriophage F4-1

The gene (mcp) coding for the major capsid protein (MCP) of the Lactococcus lactis ssp. cremoris bacteriophage F4-1 has been cloned and its nucleotide sequence determined. The mcp gene was localized, by Western blotting with rabbit antiserum against intact bacteriophage, within a 3.3-kb HindIII-Spe I fragment and the sequence of the entire region determined. The 35-kDa MCP is coded for by a 905-bp open reading frame preceded by a putative ribosome-binding site. Deletion analysis and N-terminal sequencing of the MCP confirmed the identification of the gene coding for this bacteriophage MCP.

Role of the major capsid protein of phage T4 in DNA packaging from structure-function and site-directed mutagenesis studies

Heat cleavage of asp-pro peptide bonds was used to probe the primary structures of the Phage T4 major capsid protein precursor, gp23, its mature capsid form gp23*, and a DNA-dependent ATPase, called capsizyme. This analysis suggests that capsizyme is a gp23** resulting from the N-terminal processing found in gp23* as well as shortening at the C-terminus. Photoaffinity labeling with Azido-ATP and BrU-DNA, followed by heat cleavage, suggests binding sites for these compounds toward the C-terminus of gp23**, suggesting localization of functions within the gp23 primary sequence. Site-directed mutagenesis experiments were targeted therefore to the C-terminal end of g23 as well as to its processing sites. N-terminal processing site modification supports the consensus gp21 proteinase cleavage rule, whereas mutagenesis at the C-terminus suggests that the C-terminal alteration is unlikely to result from a gp21-morphogenesis proteinase cleavage. Amino acid replacements in gp23 at newly introduced amber sites reveal a new g23 mutant phenotype, defective partially DNA-filled heads, in support of the hypothesis that gp23 and its products function directly in the DNA packaging mechanism.

Analysis of near-neighbor contacts in bacteriophage T4 wedges and hubless baseplates by using a cleavable chemical cross-linker

Although bacteriophage T4 baseplate morphogenesis has been analyzed in some detail, there is little information available on the spatial arrangement and associations of its 150 subunits. We have therefore carried out the first analysis of its near-neighbor interactions by using the cleavable chemical cross-linker ethylene glycolbis(succinimidylsuccinate). In this report, we describe the cross-linked complexes that have been identified in the one-sixth arms or wedges and also in baseplatelike structures called rings consisting of six wedges but lacking the central hub, both of which are purified from T4 gene 5- -infected cells. Thirty different complexes were identified, of which about half contain multimers of a single species and half contain two different species. In general, the complexes reflect and support the assembly pathway derived by Kikuchi and King (Y. Kikuchi and J. King, J. Mol. Biol. 99:695-716, 1975) but broaden its scope to include such complexes as gp25-gp53, gp25-gp48, and gp48-gp53, which locate the gp48 binding site over the inner edge of the ring but outside the central hub. The data also supports the view that wedges are assembled from the outer edge inward toward the central hub. Wedge-wedge contact in rings was mediated primarily by gp12 and gp9, the absence of which dramatically destabilized the ring----wedge equilibrium in favor of wedges. Although no heterologous complexes containing gp9 were identified, gp12 contacts unique to rings were observed with both gp10 and gp11.