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Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes  [PDF]
Ariel Afek?,Hila Cohen?,Shiran Barber-Zucker?,Raluca Gordan?,David B. Lukatsky
PLOS Computational Biology , 2015, DOI: 10.1371/journal.pcbi.1004429
Abstract: Recent genome-wide experiments in different eukaryotic genomes provide an unprecedented view of transcription factor (TF) binding locations and of nucleosome occupancy. These experiments revealed that a large fraction of TF binding events occur in regions where only a small number of specific TF binding sites (TFBSs) have been detected. Furthermore, in vitro protein-DNA binding measurements performed for hundreds of TFs indicate that TFs are bound with wide range of affinities to different DNA sequences that lack known consensus motifs. These observations have thus challenged the classical picture of specific protein-DNA binding and strongly suggest the existence of additional recognition mechanisms that affect protein-DNA binding preferences. We have previously demonstrated that repetitive DNA sequence elements characterized by certain symmetries statistically affect protein-DNA binding preferences. We call this binding mechanism nonconsensus protein-DNA binding in order to emphasize the point that specific consensus TFBSs do not contribute to this effect. In this paper, using the simple statistical mechanics model developed previously, we calculate the nonconsensus protein-DNA binding free energy for the entire C. elegans and D. melanogaster genomes. Using the available chromatin immunoprecipitation followed by sequencing (ChIP-seq) results on TF-DNA binding preferences for ~100 TFs, we show that DNA sequences characterized by low predicted free energy of nonconsensus binding have statistically higher experimental TF occupancy and lower nucleosome occupancy than sequences characterized by high free energy of nonconsensus binding. This is in agreement with our previous analysis performed for the yeast genome. We suggest therefore that nonconsensus protein-DNA binding assists the formation of nucleosome-free regions, as TFs outcompete nucleosomes at genomic locations with enhanced nonconsensus binding. In addition, here we perform a new, large-scale analysis using in vitro TF-DNA preferences obtained from the universal protein binding microarrays (PBM) for ~90 eukaryotic TFs belonging to 22 different DNA-binding domain types. As a result of this new analysis, we conclude that nonconsensus protein-DNA binding is a widespread phenomenon that significantly affects protein-DNA binding preferences and need not require the presence of consensus (specific) TFBSs in order to achieve genome-wide TF-DNA binding specificity.
Bone Formation in a Scaffold Composed of Cylindrical Hydroxyapatite and Tryptophan- or Lysine-Coated Sponge in Vivo  [PDF]
Masataka Yoshikawa, Hideyuki Kakigi, Hiroshi Maeda, Ikuo Nishikawa, Hideaki Ikenaga, Takeshi Inamoto, Norimasa Tsuji
Journal of Biomedical Science and Engineering (JBiSE) , 2015, DOI: 10.4236/jbise.2015.86037
Abstract: Because of the three-dimensional structure of bone or hard tissue such as a tooth, a scaffold is necessary for its regeneration by cellular engineering. Commonly, for in vivo examination, hydroxyapatite (HA) has been used as such a scaffold. Cylindrical HA with a hollow center, which included a columnar formalin-treated polyvinyl alcohol sponge, was used in this examination as a scaffold. The sponge had been coated with L-tryptophan or L-lysine before insertion into the hollow center of the HA. Rat bone marrow cells (rBMCs) derived from the femur were seeded in the sponge before insertion into the hollow center of HA. The number of rBMCs seeded in each sponge was 1.5 × 106. These scaffolds were implanted subcutaneously into the backs of Fischer 344 rats for 6 weeks. In the amino-acid-coated sponge in HA, osteogenesis was found histologically. An osteocalcin level of approximately 10 ug was measured in the scaffolds with L-tryptophan-coated formalized poly-vinyl alcohol sponge containing rBMCs, 4 ug on average in the scaffolds with L-lysine-coated sponge containing the cells and about 2 ug in each scaffold with uncoated sponge containing the cells. The structure of the scaffolds used in this study was thought to be suitable for osteogenesis by rBMCs. It was concluded that tryptophan, as a factor for bone formation by stem cells, functioned by promoting cell adhesion and the differentiation of stem cells into osteoblasts.
Decrease in Lysine and Tryptophan Content in S2 Inbred Lines from a Quality Protein Maize (QPM) Variety in a Breeding Program  [PDF]
Kabwe Nkongolo, Kankolongo Mbuya
American Journal of Plant Sciences (AJPS) , 2015, DOI: 10.4236/ajps.2015.61021
Abstract: Several countries in Africa, Latin America along with China have incorporated QPM in their Agricultural development plan. A new quality protein maize variety (QPM) was developed by breeders and farmers using the participatory breeding approach in the DR-Congo. It is adapted to all the maize growing regions in the country. Inbred lines from this new variety were produced for further development of maize synthetic populations. The main objective of the present study is to determine the level of amino acid changes in early generations of inbred lines. The results of the study revealed a significant decrease of 33% and 38% of tryptophan in S1 and S2 inbred lines compared to the original parental MUDISHI 3 population, respectively. There was a decrease of 15% of lysine in S2 inbred lines compared to the parental MUDISHI 3. Actually, S2 inbred lines of MUDISHI 3 contain similar level of lysine compared to the genetically improved normal maize (Salongo 2) that is currently released. The development of composite lines is recommended over synthetic populations to maintain the high levels of lysine and tryptophan along with other desirable agronomic characteristics since they involve the intercrossing of open pollinated varieties.

Tang Xianghui,

动物学研究 , 1988,
Abstract: The tryptophan, arginine and lysinc residues of cecropin D were modified by N-bromosuccinimide (NBS), 1, 2 -cyclohexanedione ( CHD ) and maleic anhydride (MLH) respectively. It was found that the tryptophan residue bore little relationship to the antibacterial activity of the peptide against Escherichia coli D31, but that the arginine and lysine residues were important to the antibacterial activity. The modification of the arginine or lysine residue of cecropin D resulted in a total loss of its antibacterial activity against E. coli D31. When the arginine and lysine residues were each regenerated from the modified structures the antibacterial aciivity of cecropin D was recovered. These results suggest that the antibacterial activity of cecropin D is related to the charge in the molecule. Ouchterlony double immunodiffusion showed that the antigenic determinant of cecropin D is closely connected with the arginine residues in the peptide.
C-terminal motif prediction in eukaryotic proteomes using comparative genomics and statistical over-representation across protein families
Ryan S Austin, Nicholas J Provart, Sean R Cutler
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-191
Abstract: We examined the statistical over-representation of position-specific C-terminal tripeptides in 7 eukaryotic proteomes. Sequence randomization models and simple-sequence masking were applied to the successful reduction of background noise. Similarly, as C-terminal homology among members of large protein families may artificially inflate tripeptide counts in an irrelevant and obfuscating manner, gene-family clustering was performed prior to the analysis in order to assess tripeptide over-representation across protein families as opposed to across all proteins. Finally, comparative genomics was used to identify tripeptides significantly occurring in multiple species. This approach has been able to predict, to our knowledge, all C-terminally anchored targeting motifs present in the literature. These include the PTS1 peroxisomal targeting signal (SKL*), the ER-retention signal (K/HDEL*), the ER-retrieval signal for membrane bound proteins (KKxx*), the prenylation signal (CC*) and the CaaX box prenylation motif. In addition to a high statistical over-representation of these known motifs, a collection of significant tripeptides with a high propensity for biological function exists between species, among kingdoms and across eukaryotes. Motifs of note include a serine-acidic peptide (DSD*) as well as several lysine enriched motifs found in nearly all eukaryotic genomes examined.We have successfully generated a high confidence representation of eukaryotic motifs anchored at the C-terminus. A high incidence of true-positives in our results suggests that several previously unidentified tripeptide patterns are strong candidates for representing novel peptide motifs of a widely employed nature in the C-terminal biology of eukaryotes. Our application of comparative genomics, statistical over-representation and the adjustment for protein family homology has generated several hypotheses concerning the C-terminal topology as it pertains to sorting and potential protein interaction si
A tryptophan-rich peptide acts as a transcription activation domain
Chen-Huan Lin, Grace Lin, Chia-Pei Chang, Chien-Chia Wang
BMC Molecular Biology , 2010, DOI: 10.1186/1471-2199-11-85
Abstract: We report herein that the N-terminal domain of yeast valyl-tRNA synthetase can function as an AD when fused to a DNA-binding protein, LexA, and turn on reporter genes with distinct LexA-responsive promoters. The transcriptional activity was mainly attributed to a five-residue peptide, WYDWW, near the C-terminus of the N domain. Remarkably, the pentapeptide per se retained much of the transcriptional activity. Mutations which substituted tryptophan residues for both of the non-tryptophan residues in the pentapeptide (resulting in W5) significantly enhanced its activity (~1.8-fold), while mutations which substituted aromatic residues with alanine residues severely impaired its activity. Accordingly, a much more active peptide, pentatryptophan (W7), was produced, which elicited ~3-fold higher activity than that of the native pentapeptide and the N domain. Further study indicated that W7 mediates transcription activation through interacting with the general transcription factor, TFIIB.Since W7 shares no sequence homology or features with any known transcription activators, it may represent a novel class of AD.Eukaryotic transcriptional activators that stimulate transcription initiation of a particular set of target genes usually consist of a sequence-specific DNA-binding domain (DBD) and a transcription activation domain (AD). The DBD targets these activators to a specific location in the promoter region of a gene, and the AD mediates transcription initiation by recruiting gene-specific factors, chromatin-remodeling factors, mediator complexes, and general transcription factors [1,2]. DBDs are classified into several distinct patterns or motifs according to their sequences and structural similarities. In contrast, ADs do not share significant sequence homologies, and therefore no specific motif has been defined. Despite this, several classes of ADs with distinctive sequence features were identified, including acidic activators [3], glutamine-rich activators [4], and pro
The Interaction Between Dietary Valine and Tryptophan Content and Their Effect on the Performance of Piglets  [PDF]
Sam Millet
Animals , 2012, DOI: 10.3390/ani2010076
Abstract: Four experimental diets for newly weaned pigs were formulated: (1) low valine and low tryptophan; (2) low valine and high tryptophan; (3) high valine and low tryptophan and (4) high valine and high tryptophan. Dietary standardized ileal digestible (SID) lysine content was 1.06 g/kg. The SID valine to SID lysine ratio was 0.58 and 0.67 for the low and high valine diets, respectively, and SID tryptophan to SID lysine ratios were 0.19 and 0.22 for the low and high tryptophan diets, respectively. In total, 64 pens of 6 pigs (3 barrows and 3 gilts) were divided over the four experimental treatments. No interaction between dietary supply of valine and tryptophan was observed ( P > 0.1 for all parameters). Increasing the dietary valine content increased the daily feed intake, daily gain and gain:feed ( P < 0.001 for all three parameters). Increasing the dietary tryptophan content improved gain:feed during the first 2 weeks ( P < 0.05) and overall ( P < 0.05). Valine supply had a greater effect on performance results than tryptophan supply. It may thus be beneficial to provide a diet with an optimal dietary concentration of valine even if other amino acids are at suboptimal dietary levels.
Digestible tryptophan levels for 30 to 60 kg pigs
Apol?nio, Lourdes Rom?o;Donzele, Juarez Lopes;Oliveira, Rita Flávia Miranda de;Saraiva, Alysson;Silva, Francisco Carlos de Oliveira;Ferreira, Aloízio Soares;Kill, Jo?o Luís;Haese, Douglas;
Revista Brasileira de Zootecnia , 2011, DOI: 10.1590/S1516-35982011001100015
Abstract: the objective of this study was to evaluate the effects of increasing dietary digestible tryptophan levels on performance and carcass traits of growing pigs. fifty crossbred castrated male pigs, with average initial and final body weight of 29.0 ± 1.20 kg and 60.4 ± 1.95 kg were allotted in a completely randomized block design, with five treatments (0.125, 0.133, 0.141, 0.149, and 0.157% of digestible tryptophan, corresponding to digestible tryptophan:lysine relations of 15.0, 16.0, 17.0, 18.0, and 19.0%, respectively) and five replicates, with two pigs per experimental unit, which was represented by the pen. experimental diets and water were supplied ad libitum throughout the experimental period. averages of minimum and maximum temperatures inside the facility were of 24.3 ± 0.87 oc and 28.0 ± 1.82 oc, respectively. feed intake and body weight gain increased linearly with increasing dietary tryptophan levels. however, there was no effect of digestible tryptophan on feed conversion or protein deposition of pigs. the highest tryptophan level evaluated (0,157%), corresponding to a digestible tryptophan:lysine relation of 19.0%, provided the greatest weight gain of 30 to 60 kg castrated male pigs.
Optimal Time-Series Motifs  [PDF]
Josif Grabocka,Nicolas Schilling,Lars Schmidt-Thieme
Computer Science , 2015,
Abstract: Motifs are the most repetitive/frequent patterns of a time-series. The discovery of motifs is crucial for practitioners in order to understand and interpret the phenomena occurring in sequential data. Currently, motifs are searched among series sub-sequences, aiming at selecting the most frequently occurring ones. Search-based methods, which try out series sub-sequence as motif candidates, are currently believed to be the best methods in finding the most frequent patterns. However, this paper proposes an entirely new perspective in finding motifs. We demonstrate that searching is non-optimal since the domain of motifs is restricted, and instead we propose a principled optimization approach able to find optimal motifs. We treat the occurrence frequency as a function and time-series motifs as its parameters, therefore we \textit{learn} the optimal motifs that maximize the frequency function. In contrast to searching, our method is able to discover the most repetitive patterns (hence optimal), even in cases where they do not explicitly occur as sub-sequences. Experiments on several real-life time-series datasets show that the motifs found by our method are highly more frequent than the ones found through searching, for exactly the same distance threshold.
Of Bits and Bugs — On the Use of Bioinformatics and a Bacterial Crystal Structure to Solve a Eukaryotic Repeat-Protein Structure  [PDF]
Almut Graebsch,Stéphane Roche,Dirk Kostrewa,Johannes S?ding,Dierk Niessing
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013402
Abstract: Pur-α is a nucleic acid-binding protein involved in cell cycle control, transcription, and neuronal function. Initially no prediction of the three-dimensional structure of Pur-α was possible. However, recently we solved the X-ray structure of Pur-α from the fruitfly Drosophila melanogaster and showed that it contains a so-called PUR domain. Here we explain how we exploited bioinformatics tools in combination with X-ray structure determination of a bacterial homolog to obtain diffracting crystals and the high-resolution structure of Drosophila Pur-α. First, we used sensitive methods for remote-homology detection to find three repetitive regions in Pur-α. We realized that our lack of understanding how these repeats interact to form a globular domain was a major problem for crystallization and structure determination. With our information on the repeat motifs we then identified a distant bacterial homolog that contains only one repeat. We determined the bacterial crystal structure and found that two of the repeats interact to form a globular domain. Based on this bacterial structure, we calculated a computational model of the eukaryotic protein. The model allowed us to design a crystallizable fragment and to determine the structure of Drosophila Pur-α. Key for success was the fact that single repeats of the bacterial protein self-assembled into a globular domain, instructing us on the number and boundaries of repeats to be included for crystallization trials with the eukaryotic protein. This study demonstrates that the simpler structural domain arrangement of a distant prokaryotic protein can guide the design of eukaryotic crystallization constructs. Since many eukaryotic proteins contain multiple repeats or repeating domains, this approach might be instructive for structural studies of a range of proteins.
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