Packaging of genomes in bacteriophages: a comparison of ssRNA bacteriophages and dsDNA bacteriophages.

In complex DNA bacteriophages like lambda, T4, T7, P22, P2, the DNA is packaged into a preformed precursor particle which sometimes has a smaller size and often a shape different from that of the phage head. This packaging mechanism is different from the one suggested for the RNA phages, according to which RNA nucleates the shell formation. The different mechanisms could be understood by comparing the genomes to be packaged: single stranded fII RNA has a very compact structure with high helix content. It might easily form quasispherical structures in solution (as seen in the electron microscope by Thach & Thach (1973)) around which the capsid could assemble. Double stranded phage DNA, on the other hand, is a rigid molecule which occupies a large volume in solution and has to be concentrated 15-fold during packaging into the preformed capsid, and the change in the capsid structure observed hereby might provide the necessary DNA condensation energy.     

HIV-Derived ssRNA Binds to TLR8 to Induce Inflammation-Driven Macrophage Foam Cell Formation

Even though combined anti-retroviral therapy (cART) dramatically improves patient survival, they remain at a higher risk of being afflicted with non-infectious complications such as cardiovascular disease (CVD). This increased risk is linked to persistent inflammation and chronic immune activation. In this study, we assessed whether this complication is related to HIV-derived ssRNAs inducing in macrophages increases in TNFα release through TLR8 activation leading to foam cell formation. HIV ssRNAs induced foam cell formation in monocyte-derived macrophages (MDMs) in a dose-dependent manner. This response was reduced when either endocytosis or endosomal acidification was inhibited by dynasore or chloroquine, respectively. Using a flow cytometry FRET assay, we demonstrated that ssRNAs bind to TLR8 in HEK cells. In MDMs, ssRNAs triggered a TLR8-mediated inflammatory response that ultimately lead to foam cell formation. Targeted silencing of the TLR8 and MYD88 genes reduced foam cell formation. Furthermore, foam cell formation induced by these ssRNAs was blocked by an anti-TNFα neutralizing antibody. Taken together in MDMs, HIV ssRNAs are internalized; bind TLR8 in the endosome followed by endosomal acidification. TLR8 signaling then triggers TNFα release and ultimately leads to foam cell formation. As this response was inhibited by a blocking anti-TNFα antibody, drug targeting HIV ssRNA-driven TLR8 activation may serve as a potential therapeutic target to reduce chronic immune activation and inflammation leading to CVD in HIV+ patients.     

The Formation of the Theory of Homology in Biological Sciences

Homology is among the most important comparative concepts in biology. Today, the evolutionary reinterpretation of homology is usually conceived of as the most important event in the development of the concept. This paradigmatic turning point, however important for the historical explanation of life, is not of crucial importance for the development of the concept of homology itself. In the broadest sense, homology can be understood as sameness in reference to the universal guarantor so that in this sense the different concepts of homology show a certain kind of "metahomology". This holds in the old morphological conception, as well as in the evolutionary usage of homology. Depending on what is (or was) taken as a guarantor, different types of homology may be distinguished (as idealistic, historical, developmental etc.). This study represents a historical overview of the development of the homology concept followed by some clues on how to navigate the pluralistic terminology of modern approaches to homology.     

Complex Formation of Starch with Organic Substances

Cell free extracts of Hansenula miso IFO 0146 contained an enzyme which catalyzed acyloin condensation of acetaldehyde and α-ketoglutarate to form 5～hydroxy-4-ketohexanoic acid (HKH). The enzyme was specific for acetaldehyde and α-ketoglutarate. Condensation could not be demonstrated between α-ketoglutarate and other aldehydes tested (formaldehyde, propionaldehyde or butyraldehyde). No reaction occurred when boiled enzyme was used. The apparent Km values (at pH 7.5) for acetaldehyde and α-ketoglutarate are 24.4 mM and 3.2 mM, respectively. TPP and Mg²⁺ were not required for the reaction. The optimum pH of the reaction was 7.5～8.5. The reaction was inhibited by EDTA, PCMB and PMS. The enzyme forming HKH was different from that forming acetoin because the latter required TPP and was repressed when cells were grown in lactate medium while the former did not require TPP and was formed independently of its substrate. The product of this condensing reaction was isolated and identified as HKH from its chemical properties.     

An RNA-Binding Complex Involved in Ribosome Biogenesis Contains a Protein with Homology to tRNA CCA-Adding Enzyme

A multitude of proteins and small nucleolar RNAs transiently associate with eukaryotic ribosomal RNAs to direct their modification and processing and the assembly of ribosomal proteins. Utp22 and Rrp7, two interacting proteins with no recognizable domain, are components of the 90S preribosome or the small subunit processome that conducts early processing of 18S rRNA. Here, we determine the cocrystal structure of Utp22 and Rrp7 complex at 1.97 Å resolution and the NMR structure of a C-terminal fragment of Rrp7, which is not visible in the crystal structure. The structure reveals that Utp22 surprisingly resembles a dimeric class I tRNA CCA-adding enzyme yet with degenerate active sites, raising an interesting evolutionary connection between tRNA and rRNA processing machineries. Rrp7 binds extensively to Utp22 using a deviant RNA recognition motif and an extended linker. Functional sites on the two proteins were identified by structure-based mutagenesis in yeast. We show that Rrp7 contains a flexible RNA-binding C-terminal tail that is essential for association with preribosomes. RNA–protein crosslinking shows that Rrp7 binds at the central domain of 18S rRNA and shares a neighborhood with two processing H/ACA snoRNAs snR30 and snR10. Depletion of snR30 prevents the stable assembly of Rrp7 into preribosomes. Our results provide insight into the evolutionary origin and functional context of Utp22 and Rrp7.     

Homology Model of the CDK1/cyclin B Complex

Abstract

We describe a refined homology model of a CDK1/cyclin B complex that was previously used for the structure-based optimization of the Paullone class of inhibitors. The preliminary model was formed from the homologous regions of the deposited CDK2/cyclin A crystal structure. Further refinement of the CDK1/cyclin B complex was accomplished using molecular mechanics and hydropathic analysis with a protocol of constraints and local geometry searches. For the most part, our CKD1/cyclin B homology model is very similar to the high resolution CDK2/cyclin A crystal structure regarding secondary and tertiary features. However, minor discrepancies between the two kinase structures suggest the possibility that ligand design may be specifically tuned for either CDK1 or CDK2. Our examination of the CDK1/cyclin B model includes a comparison with the CDK2/cyclin A crystal structure in the PSTAIRE interface region, connecting portions to the ATP binding domain, as well as the ATP binding site itself.     

Polynucleotide phosphorylase binds to ssRNA with same affinity as to ssDNA

Polynucleotide phosphorylase (PNPase, polyribonucleotide nucleotidyltransferase, EC 2.7.7.8) is a multifunctional protein, with a 3'-5' processive exoribonuclease, a Pi exchange, an RNA polymerase and an autoregulatory activity. The interaction between this enzyme and the mRNA target is crucial for its activities. In the present study, we characterized the interaction of PNPase with its mRNA regulatory region and ssRNA, as well as with ssDNA and dsDNA by determining K(d). Our results indicate that PNPase has high affinity for its mRNA, ssRNA and for ssDNA (K(d) approximately 10-20 nM). However, this enzyme exhibits a lower affinity for dsDNA (K(d) approximately 200-1400 nM). Possible implications of these results on the molecular mechanisms by which PNPase is regulated and degrades mRNA are discussed.     

结合RT-PCR体外扩增检测HCV ssRNA的研究

本研究旨在以HCV为平台,在简化RT-PCR基础上,结合体外转录,建立一种特异、高效、简便的检测血清中HCV RNA的体外转录合成系统.本法扩增终产物为特定极性的ssRNA,其特异性经凝胶电泳和斑点杂交确定;RNA定量分析结果显示本法核酸扩增效率高于巢式PCR近20倍.     

On Homology between the Neural Complex of Tunicates and the Hypophysis of Vertebrates

The organs of the tunicate neural complex and parts of the vertebrate hypophysis were compared on the basis of morphological, physiological, embryological, and endocrinological debatable data. The hypothesis of the homology between the tunicate neural gland and ciliary organ (together with the dorsal tube) and the vertebrate neurohypophysis and adenohypophysis, respectively, is substantiated. In contrast to the hypophysis, the neural complex is a multifunctional structure. The presence of hormonelike substances (typical of the adenohypophysis) in the neural gland testifies to the independent evolution of the neural complex and hypophysis, both of them originating from some “protohypophysis” of hypothetical protovertebrates.     

Homology in Development and the Development of the Homology Concept

Homology is a central concept for Developmental Evolution. HereI argue that homology should be explained within the referenceprocesses of development and evolution; development becauseit is the proximate cause of morphological characters and evolutionbecause it deals with organic transformations and stability.This was already recognized by Hans Spemann in 1915. In a seminalessay "A history and critique of the homology concept" Spemannanalyzed the history and present problems of the homology concept.Here I will continue Spemann's project and analyze some of the20th century contributions to homology. I will end with a fewreflections about the connections between developmental processesand homology and conclude that developmental processes are inherentin (i) the assessment of homology, (ii) the explanation of homology,(iii) the origin of evolutionary innovations (incipient homologues),and (iv) can be considered homologous themselves.     

Formation of an Inclusion Complex of Anthocyanin with Cyclodextrin

A new gallotannin named kurigalin was isolated from the bark of chestnut tree. The chemical structure of kurigalin was established as 2,5,6-tri-O-galloyl-α,β-d-hamamelose (I) on the basis of enzymatic hydrolyses and spectral analyses.     

dsDNA and protein co-delivery in triticale microspores

The efficiency of cell-penetrating peptide (CPP)-mediated dsDNA transfection in triticale microspores was investigated through transient and stable integration of the β-glucoronidase (GUS) reporter gene and expression assays in microspore-derived embryos and plantlets. The RecA protein, usually associated with prokaryote homologous recombination, was also tested for its capacity to protect the linear transgene from degradation. Transfections mediated by the CPP nanocarriers Tat2 and Pep1 reduced the number of regenerated embryos from 158 in the control to 122 and 100, respectively. The co-delivery of CPP-dsDNA with RecA protein also resulted in fewer embryos, 87 and 104 for Tat2 and Pep1, respectively. Delivery of dsDNA with Tat2 or Pep1, without RecA, resulted in the highest frequencies of GUS activity in regenerated embryos, at 26%. Co-delivery with RecA decreased the percentage of GUS-positive embryos to 16%. Interestingly, co-delivered RecA-dsDNA reduced the loss of integrity of inserted genetic construct, as observed by polymerase chain reaction (PCR) amplification of the 5′ and 3′ ends. GUS activity was also detected in mature haploid and diploid plants. Of all treatments, 31 T₀ plants tested positive for the GUS gene by quantitative PCR, although 50% were derived from the single treatment dsDNA-Tat2. The estimated copy number of the GUS transgene varied between four and eight. This study provides the foundations for CPP-mediated co-delivery of dsDNA and protein RecA in haploid microspore nuclei for functional genomic studies in crop species.     

M-Cadherin-Mediated Cell Adhesion and Complex Formation with the Catenins in Myogenic Mouse Cells

M-cadherin is a member of the multigene family of calcium-dependent intercellular adhesion molecules, the cadherins, which are involved in morphogenetic processes. Amino acid comparisons between M-cadherin and E-, N-, and P-cadherin suggested that M-cadherin diverged phylogenetically very early from these classical cadherins. It has been shown that M-cadherin is expressed in prenatal and adult skeletal muscle. In the cerebellum, M-cadherin is present in an adherens-type junction which differs in its molecular composition from the E-cadherin-mediated adherens-type junctions. These and other findings raised the question of whether M-cadherin and the classical cadherins share basic biochemical properties, notably the calcium-dependent resistance to proteolysis, mediation of calcium-dependent intercellular adhesion, and the capability to form M-cadherin complexes with the catenins. Here we show that M-cadherin is resistant to trypsin digestion in the presence of calcium ions but at lower trypsin concentrations than E-cadherin. When ectopically expressed in LMTK⁻cells, M-cadherin mediated calcium-dependent cell aggregation. Finally, M-cadherin was capable of forming two distinct cytoplasmic complexes in myogenic cells, either with α-catenin/β-catenin or with α-catenin/plakoglobin, as E- and N-cadherin, for example, have previously been shown to form. The relative amount of these complexes changed during differentiation from C2C12 myoblasts to myotubes, although the molecular composition of each complex was unaffected during differentiation. These results demonstrate that M-cadherin shares important features with the classical cadherins despite its phylogenetic divergence.     

Synonymous Mutations Reduce Genome Compactness in Icosahedral ssRNA Viruses

Recent studies have shown that single-stranded (ss) viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison, it has been suggested that wild-type viral RNA may have evolved to be atypically compact so as to aid its encapsidation and assist the viral assembly process. To further explore the compactness selection hypothesis, we systematically compare the predicted sizes of >100 wild-type viral sequences with those of their mutants, which are evolved in silico and subject to a number of known evolutionary constraints. In particular, we enforce mutation synonynimity, preserve the codon-bias, and leave untranslated regions intact. It is found that progressive accumulation of these restricted mutations still suffices to completely erase the characteristic compactness imprint of the viral RNA genomes, making them in this respect physically indistinguishable from randomly shuffled RNAs. This shows that maintaining the physical compactness of the genome is indeed a primary factor among ssRNA viruses’ evolutionary constraints, contributing also to the evidence that synonymous mutations in viral ssRNA genomes are not strictly neutral.     

New dsDNA binding unnatural oligopeptides with pyrimidine selectivity

Solid phase peptide library screening followed by extension of a lead recognition element for binding to a dsDNA sequence (NF binding site of IL6) using solution phase screening, delivered a new DNA binding peptide, Ac-Arg-Ual-Sar-Chi-Chi-Tal-Arg-CONH2. In the present research, the contribution of the different amino acid side chains to the binding strength of the peptide to dsDNA was investigated using an ethidium bromide displacement test. Based on these results, the lead structure was optimized by deconvolution. Eight new unnatural amino acids were evaluated at two positions of the heptapeptide replacing the Ual-Sar fragment. The strongest dsDNA binding was observed using ([(3-chlorophenyl)methyl]amino)acetic acid (Cbg) and beta-cyclohexyl-l-alanine (Cha) respectively, at those two positions. A 10-fold increase in affinity compared to the Ual-Sar sequence was obtained. Further enhancement of dsDNA binding was obtained with hybrid molecules linking the newly developed peptide fragment to an acridine derivative with a flexible spacer. This resulted in ligands with affinities in the microM range for the dsDNA target (K(d) of 2.1 x 10(-6) M). DNase I footprinting with the newly developed oligopeptide motifs showed the presence of a pronounced pyrimidine specificity, while conjugation to an intercalator seems to redirect the interaction to mixed sequences. This way, new unnatural oligopeptide motifs and hybrid molecules have been developed endowed with different sequence selectivities. The results demonstrate that the unnatural peptide library approach combined with subsequent modification of selected amino acid positions, is very suited for the discovery of novel sequence-specific dsDNA binding ligands.     

渗漏型UGA终止密码在植物病毒相关基因组中的作用

弱毒疫苗ToMV-K的复制酶基因在2670-2672核苷酸处发生UGA突变,研究表明该突变是导致病毒弱化的主要原因。通过ToMV-K复制酶的突变区与其它具有UGA渗漏终止密码的植物ssRNA病毒基因组通读结构区的分析和比较,发现ToMV-K和其它植物病毒的UGA渗漏与通读相关基因的共同特征：CGG基元,通读区的α-螺旋结构和一些疏水氨基酸残基使UGA的通读成为可能。这些渗漏与通读的特征可能才是ToMV\|K致弱的根本原因。可以根据这一模式,探讨对其它植物ssRNA的病毒如PVX、PVY、CMV等的基因组改造和致弱研究。