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- Ahlgren-Berg, Alexandra, et al.
(author)
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A comparison of the DNA binding and bending capacities and the oligomeric states of the immunity repressors of heteroimmune coliphages P2 and W Phi
- 2007
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 35:10, s. 3167-3180
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Journal article (peer-reviewed)abstract
- Bacteriophages P2 and W Phi are heteroimmune members of the P2-like family of temperate Escherichia coli phages. Temperate phages can grow lytically or form lysogeny after infection. A transcriptional switch that contains two convergent promoters, Pe and Pc, and two repressors regulate what life mode to enter. The immunity repressor C is the first gene of the lysogenic operon, and it blocks the early Pe promoter. In this work, some characteristics of the C proteins of P2 and W Phi are compared. An in vivo genetic analysis shows that W Phi C, like P2C, has a strong dimerization activity in the absence of its DNA target. Both C proteins recognize two directly repeated sequences, termed half-sites and a strong bending is induced in the respective DNA target upon binding. P2C is unable to bind to one half-site as opposed to W Phi, but both half-sites are required for repression of W Phi Pe. A reduction from three to two helical turns between the centers of the half-sites in W Phi has no significant effect on the capacity to repress Pe. However, the protein-DNA complexes formed differ, as determined by electrophoretic mobility shift experiments. A difference in spontaneous phage production is observed in isogenic lysogens.
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- Alam, Md. Minhaj, et al.
(author)
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Surface pore initiated fatigue failure in laser clad components
- 2013
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In: Journal of laser applications. - : Laser Institute of America. - 1042-346X .- 1938-1387. ; 25:3
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Journal article (peer-reviewed)abstract
- A laser clad and machined cylindrical structural steel rod was fatigue tested under four-point bending load. The resulting fracture could be tracked back to a spherical surface pore in the Co-based coating. Due to an oxide inclusion, the pore was not identified by dye penetrant inspection. Two circular buckling strain patterns that were detected beside the pore at the surfaces after fracture confirm local plastic deformation prior to crack initiation. In order to calculate the stress field around the surface pore, linear elastic finite element analysis was carried out. For four-point bending load, a surface pore generally exceeds the maximum stress of a smooth rod as long as the pore is located within an azimuthal angle of ±55°, which was the case for the presented as well as for another pore initiated sample.
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- Henriksson Peltola, Petri, 1965-
(author)
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Molecular Studies of Three Coliphage Repressor Proteins P2 C, P2 Hy dis C and Wphi C : Kinetics, Oligomeric States and Structural Studies
- 2007
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Doctoral thesis (other academic/artistic)abstract
- P2, P2 Hy dis and WΦ are heteroimmune and closely related E. coli phages that can either grow lytically or form lysogeny after infection. The developmental switch region that contains two divergent promoters, the early Pe and the lysogenic Pc promoter, and two repressors, controls the life mode of the phage. The first gene product from the lysogenic operon is the immunity C repressor protein which recognizes an operator consisting of two direct repeats (denoted half sites) flanking the -35 and -10 regions of Pe. Though the identity of the structural genes is > 96%, the immunity C repressors only show the between 43-63% identity. P2 C, P2 Hy dis C and WΦ C bind to different operators that vary in sequence, length, center-to-center spacing and location relative to the Pe promoter. The C repressors have different affinities to their operators and show different binding patterns. The binding capacity of the C proteins is not affected by point mutations of one or both half sites, which was unexpected since in vivo the proteins are unable to repress the operator where both half sites contain a point mutation. Deletions in the spacing between the half sites change the band pattern, but the repression capacity of WΦ C was unaffected. Only WΦ C is able to bind to just one half site. P2 C, P2 Hy dis C and WΦ C have the best affinity to their wild type operator, which was expected. Dissociation events of P2 and P2 Hy dis C were bi- and triphasic. Consequently, the kinetics and the nature of complexes formed show clearly that these three closely related bacteriophages have evolved in different directions. The N-terminal part of the C protein contains four α-helices, and the secondary structure predictions show two possible DNA-binding helices. According to the alanine scanning helix 3 might be the DNA-recognition helix since the mutations in this helix removed the repression capacity of the C protein in vivo.
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- Koistinen, Ville Mikael, et al.
(author)
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Side-stream products of malting: a neglected source of phytochemicals
- 2020
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In: npj Science of Food. - : Springer Science and Business Media LLC. - 2396-8370. ; 4:1
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Journal article (peer-reviewed)abstract
- Whole grain consumption reduces the risk of several chronic diseases. A major contributor to the effect is the synergistic and additive effect of phytochemicals. Malting is an important technological method to process whole grains; the main product, malted grain, is used mainly for brewing, but the process also yields high amounts of side-stream products, such as rootlet. In this study, we comprehensively determined the phytochemical profile of barley, oats, rye, and wheat in different stages of malting and the subsequent extraction phases to assess the potential of malted products and side-streams as a dietary source of bioactive compounds. Utilizing semi-quantitative LC–MS metabolomics, we annotated 285 phytochemicals from the samples, belonging to more than 13 chemical classes. Malting significantly altered the levels of the compounds, many of which were highly increased in the rootlet. Whole grain cereals and the malting products were found to be a diverse and rich source of phytochemicals, highlighting the value of these whole foods as a staple. The characterization of phytochemicals from the 24 different sample types revealed previously unknown existence of some of the compound classes in certain species. The rootlet deserves more attention in human nutrition, rather than its current use mainly as feed, to benefit from its high content of bioactive components.
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- Massad, Tariq, et al.
(author)
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Crystal structure of the P2 C-repressor : a binder of nonpalindromic direct DNA repeats
- 2010
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 38:21, s. 7778-7790
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Journal article (peer-reviewed)abstract
- As opposed to the vast majority of prokaryoticrepressors, the immunity repressor of temperateEscherichia coli phage P2 (C) recognizes nonpalindromicdirect repeats of DNA rather thaninverted repeats. We have determined the crystalstructure of P2 C at 1.8A ° . This constitutes the firststructure solved from the family of C proteins fromP2-like bacteriophages. The structure reveals thatthe P2 C protein forms a symmetric dimer orientedto bind the major groove of two consecutive turns ofthe DNA. Surprisingly, P2 C has great similarities tobinders of palindromic sequences. Nevertheless, thetwo identical DNA-binding helixes of the symmetricP2 C dimer have to bind different DNA sequences.Helix 3 is identified as the DNA-recognition motif inP2 C by alanine scanning and the importance for theindividual residues in DNA recognition is defined.A truncation mutant shows that the disorderedC-terminus is dispensable for repressor function.The short distance between the DNA-bindinghelices together with a possible interaction betweentwo P2 C dimers are proposed to be responsible forextensive bending of the DNA. The structure providesinsight into the mechanisms behind the mutants ofP2 C causing dimer disruption, temperature sensitivityand insensitivity to the P4 antirepressor.
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