Evolutionary history of bacteriophages with double-stranded DNA genomes

Background

Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses and recombinational exchanges of genes are so pervasive in phages that the plausibility of phylogenetic inference in phage kingdom has been questioned.

Results

We compiled the profiles of presence and absence of 803 orthologous genes in 158 completely sequenced phages with double-stranded DNA genomes and used these gene content vectors to infer the evolutionary history of phages. There were 18 well-supported clades, mostly corresponding to accepted genera, but in some cases appearing to define new taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence alignments of phage proteins were exploited to infer 294 specific acts of intergenome gene transfer.

Conclusion

A notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics.

Open peer review

This article was reviewed by Eugene Koonin, Nicholas Galtier and Martijn Huynen.     

Structural and functional properties of αβ-heterodimers of tropomyosin with myopathic mutations Q147P and K49del in the β-chain

Tropomyosin (Tpm) is an α-helical coiled-coil actin-binding protein that plays a key role in the Ca²⁺-regulated contraction of striated muscles. Two Tpm isoforms, α (Tpm 1.1) and β (Tpm 2.2), are expressed in fast skeletal muscles. These Tpm isoforms can form either αα and ββ homodimers, or αβ heterodimers. However, only αα-Tpm and αβ-Tpm dimers are usually present in most of fast skeletal muscles, because ββ-homodimers are relatively unstable and cannot exist under physiologic conditions. Nevertheless, the most of previous studies of myopathy-causing mutations in the Tpm β-chains were performed on the ββ-homodimers. In the present work, we applied different methods to investigate the effects of two myopathic mutations in the β-chain, Q147P and K49del (i.e. deletion of Lys49), on structural and functional properties of Tpm αβ-heterodimers and to compare them with the properties of ββ-homodimers carrying these mutations in both β-chains. The results show that the properties of αβ-Tpm heterodimers with these mutations in the β-chain differ significantly from the properties of ββ-homodimers with the same substitutions in both β-chains. This indicates that the αβ-heterodimer is a more appropriate model for studying the effects of myopathic mutations in the β-chain of Tpm than the ββ-homodimer which virtually does not exist in human skeletal muscles.     

Chlorophyll fluorescence induction and relaxation system for the continuous monitoring of photosynthetic capacity in photobioreactors

The development of high‐performance photobioreactors equipped with automatic systems for non‐invasive real‐time monitoring of cultivation conditions and photosynthetic parameters is a challenge in algae biotechnology. Therefore, we developed a chlorophyll (Chl) fluorescence measuring system for the online recording of the light‐induced fluorescence rise and the dark relaxation of the flash‐induced fluorescence yield (Qa^? ? re‐oxidation kinetics) in photobioreactors. This system provides automatic measurements in a broad range of Chl concentrations at high frequency of gas‐tight sampling, and advanced data analysis. The performance of this new technique was tested on the green microalgae Chlamydomonas reinhardtii subjected to a sulfur deficiency stress and to long‐term dark anaerobic conditions. More than thousand fluorescence kinetic curves were recorded and analyzed during aerobic and anaerobic stages of incubation. Lifetime and amplitude values of kinetic components were determined, and their dynamics plotted on heatmaps. Out of these data, stress‐sensitive kinetic parameters were specified. This implemented apparatus can therefore be useful for the continuous real‐time monitoring of algal photosynthesis in photobioreactors.     

Deficiency of mouse mast cell protease 4 mitigates cardiac dysfunctions in mice after myocardium infarction

Mouse mast cell protease-4 (mMCP4) is a chymase that has been implicated in cardiovascular diseases, including myocardial infarction (MI). This study tested a direct role of mMCP4 in mouse post-MI cardiac dysfunction and myocardial remodeling. Immunoblot and immunofluorescent double staining demonstrated mMCP4 expression in cardiomyocytes from the infarct zone from mouse heart at 28 day post-MI. At this time point, mMCP4-deficient Mcpt4^?/? mice showed no difference in survival from wild-type (WT) control mice, yet demonstrated smaller infarct size, improved cardiac functions, reduced macrophage content but increased T-cell accumulation in the infarct region compared with those of WT littermates. mMCP4-deficiency also reduced cardiomyocyte apoptosis and expression of TGF-β1, p-Smad2, and p-Smad3 in the infarct region, but did not affect collagen deposition or α-smooth muscle actin expression in the same area. Gelatin gel zymography and immunoblot analysis revealed reduced activities of matrix metalloproteinases and expression of cysteinyl cathepsins in the myocardium, macrophages, and T cells from Mcpt4^?/? mice. Immunoblot analysis also found reduced p-Smad2 and p-Smad3 in the myocardium from Mcpt4^?/? mice, yet fibroblasts from Mcpt4^?/? mice showed comparable levels of p-Smad2 and p-Smad3 to those of WT fibroblasts. Flow cytometry, immunoblot analysis, and immunofluorescent staining demonstrated that mMCP4-deficiency reduced the expression of proapoptotic cathepsins in cardiomyocytes and protected cardiomyocytes from H₂O₂-induced apoptosis. This study established a role of mMCP4 in mouse post-MI dysfunction by regulating myocardial protease expression and cardiomyocyte death without significant impact on myocardial fibrosis or survival post-MI in mice.     

Elevated α-Linolenic Acid Content in Extra-plastidial Membranes of Tomato Accelerates Wound-Induced Jasmonate Generation and Improves Tolerance to the Herbivorous Insects Heliothis peltigera and Spodoptera littoralis

Journal of Plant Growth Regulation - In tomato, desaturation of linoleic acid (18:2) to α-linolenic acid (18:3) is mediated in the plastidial membranes by the ω-3 fatty acid desaturases 7...     

The effect of the antibiotic AL-87 on the amino acid yield from Staphylococcus aureus 209P cells]

Antibiotic AL-87 has been studied for its effect on the composition of intracellular free amino acids and of amino acids in culture fluid of Staphylococcus aureus 209 P. It is established that the content of amino acids in the culture fluid of S. aureus 209 P is doubled due to antibiotics, while the content of intracellular free amino acids considerably decreases. Spectrum of free amino acids of S. aureus 209 P is presented by 17 basic amino acids. When there is a sub-bacteriostatic concentration of the antibiotic in the medium all free amino acids tend to leave the cells, the content of aspartic acid, serine, threonine and leucine in the medium being increased. Data obtained when studying the effect of antibiotic AL-87 on the composition of free amino acids of Staphylococcus agree well with the previously obtained results from the study of the fatty acid composition of cells. In the light of these data it may be supposed that an increase of the membrane permeability and as a result of it an outlet of amino acids into the medium is one of constituents of the mechanism of antibiotic AL-87 action on Staphylococcus cells.     

Effects of Suramin on PMN Interactions with Different Surfaces

Human polymorphonuclear leukocytes (PMN) were found to tightly adhere on endothelial (lines EAhy926 and ECV304) and collagen surfaces under the influence of the chemotherapeutic drug suramin. This was observed by scanning electron microscopy and quantitated by myeloperoxidase assays. Suramin also inhibited Ca²⁺ ionophore A23187-stimulated leukotriene (LT) synthesis in PMN interaction with endothelial cells or with collagen surface. Suramin decreased the release of radiolabeled arachidonic acid (AA) and 5-lip-oxygenase (5-LO) metabolites by prelabeled PMN stimulated with A23187. Using agents releasing the suramin-stimulated adhesion namely jasplakonolide and dextran sulfate, we observed a reversal of the suramin effect on leukotriene synthesis. Jasplakonolide released the adhesion of PMN on endothelial and collagen-coated surfaces and restored 5-LO activity. Dextran-sulfate released adhesion on collagen-coated surfaces and abolished suramin inhibition. Arachidonate could also overcome adhesion and inhibition of 5-LO. We conclude that suramin-induced tight attachment of PMN on to solid surfaces lead to decreased leukotriene synthesis during subsequent A23187 stimulation in the absence of exogenous substrates.     

The use of batumin-containing disks for the rapid identification of staphylococci

The study of 467 microbial strains obtained from collections and from clinical sources revealed that microorganisms of the genus Staphylococcus were highly sensitive to batumin, a new antibiotic obtained from bacteria of the genus Pseudomonas. 378 strains of 15 Staphylococcus species proved to be highly sensitive to the diagnostic preparation "Diastaph", developed on the basis of batumin (antibiotic-impregnated discs); After 18-hour incubation the diameter of the growth inhibition zones on agar-containing culture media was 18-38 mm. Strains belonging to the genera Micrococcus, Dermacoccus, Kocuria and Kytococcus, as well as the tested representatives of other taxa (Planococcus, Streptococcus, Corynebacterium, Acinetobacter, Pseudomonas, Neisseria, the representatives of all tested genera of the family Enterobacteriaceae, fungi of the genus Candida) were insensitive to the diagnosticum. "Diastaph" permits not only the rapid identification of staphylococci pure cultures, but also the determination of their presence in association with other microbial species directly in pathological material, which makes it possible to recommend this diagnostic preparation for use in medical, veterinary and sanitary microbiology.