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Genetic Paralog Analysis and Simulations  [PDF]
Stanislaw Cebrat,Jan P. Radomski,Dietrich Stauffer
Quantitative Biology , 2003,
Abstract: Using Monte Carlo methods, we simulated the effects of bias in generation and elimination of paralogs on the size distribution of paralog groups. It was found that the function describing the decay of the number of paralog groups with their size depends on the ratio between the probability of duplications of genes and their deletions, which corresponds to different selection pressures on the genome size. Slightly different slopes of curves describing the decay of the number of paralog groups with their size were also observed when the threshold of homology between paralogous sequences was changed.
SRA-Domain Proteins Required for DRM2-Mediated De Novo DNA Methylation  [PDF]
Lianna M. Johnson,Julie A. Law,Anuj Khattar,Ian R. Henderson,Steven E. Jacobsen
PLOS Genetics , 2008, DOI: 10.1371/journal.pgen.1000280
Abstract: De novo DNA methylation and the maintenance of DNA methylation in asymmetrical sequence contexts is catalyzed by homologous proteins in plants (DRM2) and animals (DNMT3a/b). In plants, targeting of DRM2 depends on small interfering RNAs (siRNAs), although the molecular details are still unclear. Here, we show that two SRA-domain proteins (SUVH9 and SUVH2) are also essential for DRM2-mediated de novo and maintenance DNA methylation in Arabidopsis thaliana. At some loci, SUVH9 and SUVH2 act redundantly, while at other loci only SUVH2 is required, and this locus specificity correlates with the differing DNA-binding affinity of the SRA domains within SUVH9 and SUVH2. Specifically, SUVH9 preferentially binds methylated asymmetric sites, while SUVH2 preferentially binds methylated CG sites. The suvh9 and suvh2 mutations do not eliminate siRNAs, suggesting a role for SUVH9 and SUVH2 late in the RNA-directed DNA methylation pathway. With these new results, it is clear that SRA-domain proteins are involved in each of the three pathways leading to DNA methylation in Arabidopsis.
A Method to Identify p62's UBA Domain Interacting Proteins
Pridgeon Julia W.,Geetha Thangiah,Wooten Marie W.
Biological Procedures Online , 2003, DOI: 10.1251/bpo66
Abstract: The UBA domain is a conserved sequence motif among polyubiquitin binding proteins. For the first time, we demonstrate a systematic, high throughput approach to identification of UBA domain-interacting proteins from a proteome-wide perspective. Using the rabbit reticulocyte lysate in vitro expression cloning system, we have successfully identified eleven proteins that interact with p62’s UBA domain, and the majority of the eleven proteins are associated with neurodegenerative disorders, such as Alzheimer’s disease. Therefore, p62 may play a novel regulatory role through its UBA domain. Our approach provides an easy route to the characterization of UBA domain interacting proteins and its application will unfold the important roles that the UBA domain plays.
Heterogeneous Conservation of Dlx Paralog Co-Expression in Jawed Vertebrates  [PDF]
Mélanie Debiais-Thibaud, Cushla J. Metcalfe, Jacob Pollack, Isabelle Germon, Marc Ekker, Michael Depew, Patrick Laurenti, Véronique Borday-Birraux, Didier Casane
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0068182
Abstract: Background The Dlx gene family encodes transcription factors involved in the development of a wide variety of morphological innovations that first evolved at the origins of vertebrates or of the jawed vertebrates. This gene family expanded with the two rounds of genome duplications that occurred before jawed vertebrates diversified. It includes at least three bigene pairs sharing conserved regulatory sequences in tetrapods and teleost fish, but has been only partially characterized in chondrichthyans, the third major group of jawed vertebrates. Here we take advantage of developmental and molecular tools applied to the shark Scyliorhinus canicula to fill in the gap and provide an overview of the evolution of the Dlx family in the jawed vertebrates. These results are analyzed in the theoretical framework of the DDC (Duplication-Degeneration-Complementatio?n)model. Results The genomic organisation of the catshark Dlx genes is similar to that previously described for tetrapods. Conserved non-coding elements identified in bony fish were also identified in catshark Dlx clusters and showed regulatory activity in transgenic zebrafish. Gene expression patterns in the catshark showed that there are some expression sites with high conservation of the expressed paralog(s) and other expression sites with events of paralog sub-functionalization during jawed vertebrate diversification, resulting in a wide variety of evolutionary scenarios within this gene family. Conclusion Dlx gene expression patterns in the catshark show that there has been little neo-functionalization in Dlx genes over gnathostome evolution. In most cases, one tandem duplication and two rounds of vertebrate genome duplication have led to at least six Dlx coding sequences with redundant expression patterns followed by some instances of paralog sub-functionalization. Regulatory constraints such as shared enhancers, and functional constraints including gene pleiotropy, may have contributed to the evolutionary inertia leading to high redundancy between gene expression patterns.
Using Isothermal Kinetic Results to Estimate the Kinetic Triplet of Catalytically Cracking of HDPE  [PDF]
Mohammad Reza Shishesaz,Mohammad Hossein Madahi
American Journal of Oil and Chemical Technologies , 2013, DOI: 10.14266
Abstract: The Arrhenius parameters and the reaction model of catalytically cracking of high-density polyethylene (HDPE) have been estimated from isothermal kinetic results. We introduced a new catalyst that is able to convert waste plastics to fuel oil and introduced new method to record mass decrease with time under pure static condition. A best fit of the theoretical reduced-time plot (RTP) to an experimental one led to the conclusion that ‘contracting cylinder’ model would represent the HDPE catalytically cracking.
Kinetics of catalytically activated duplication in aggregation growth

Wang Hai-Feng,Lin Zhen-Quan,Gao Yan,Xu Chao,

中国物理 B , 2009,
Abstract: We propose a catalytically activated duplication model to mimic the coagulation and duplication of the DNA polymer system under the catalysis of the primer RNA. In the model, two aggregates of the same species can coagulate themselves and a DNA aggregate of any size can yield a new monomer or double itself with the help of RNA aggregates. By employing the mean-field rate equation approach we analytically investigate the evolution behaviour of the system. For the system with catalysis-driven monomer duplications, the aggregate size distribution of DNA polymers ak(t) always follows a power law in size in the long-time limit, and it decreases with time or approaches a time-independent steady-state form in the case of the duplication rate independent of the size of the mother aggregates, while it increases with time increasing in the case of the duplication rate proportional to the size of the mother aggregates. For the system with complete catalysis-driven duplications, the aggregate size distribution ak(t) approaches a generalized or modified scaling form.
Pulling and Pushing a Cargo With a Catalytically Active Carrier  [PDF]
M. N. Popescu,M. Tasinkevych,S. Dietrich
Physics , 2011, DOI: 10.1209/0295-5075/95/28004
Abstract: Catalytically active particles suspended in a liquid can move due to self-phoresis by generating solute gradients via chemical reactions of the solvent occurring at parts of their surface. Such particles can be used as carriers at the micro-scale. As a simple model for a carrier-cargo system we consider a catalytically active particle connected by a thin rigid rod to a catalytically inert cargo particle. We show that the velocity of the composite strongly depends on the relative orientation of the carrier-cargo link. Accordingly, there is an optimal configuration for the linkage. The subtlety of such carriers is underscored by the observation that a spherical particle completely covered by catalyst, which is motionless when isolated, acts as a carrier once attached to a cargo.
Characterization of Ubiquitin-Activating Enzyme Uba1 in the Nucleus by Its Mammalian Temperature-Sensitive Mutant  [PDF]
Kimihiko Sugaya, Yoshie Ishihara, Sonoe Inoue, Hideo Tsuji
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0096666
Abstract: Temperature-sensitive (ts) CHO-K1 mutant tsTM3 exhibits chromosomal instability and cell-cycle arrest in the S to G2 phases with decreased DNA synthesis at the nonpermissive temperature, 39°C. Previously, complementation tests with other mutants showed that tsTM3 harbors a genetic defect in the ubiquitin-activating enzyme Uba1. Sequence comparison of the Uba1 gene between wild-type and mutant cells in this study revealed that the mutant phenotype is caused by a G-to-A transition that yields a Met-to-Ile substitution at position 256 in hamster Uba1. The ts defects in tsTM3 were complemented by expression of the wild-type Uba1 tagged with green fluorescent protein. Expression of the Uba1 primarily in the nucleus appeared to rescue tsTM3 cells. Incubation at 39°C resulted in a decrease of nuclear Uba1 in tsTM3 cells, suggesting that loss of Uba1 in the nucleus may lead to the ts defects. Analyses with the fluorescent ubiquitination-based cell cycle indicator revealed that loss of function of Uba1 leads to failure of the ubiquitin system in the nucleus. Incubation at 39°C caused an increase in endogenous geminin in tsTM3 cells. A ts mutation of Uba1 found in tsTM3 cells appears to be a novel mutation reflecting the important roles of Uba1 in nucleus.
Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction
Yavor Hadzhiev, Michael Lang, Raymond Ertzer, Axel Meyer, Uwe Str?hle, Ferenc Müller
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-6-r106
Abstract: We demonstrate that the sonic hedgehog a (shha) paralogs sonic hedgehog b (tiggy winkle hedgehog; shhb) genes of fishes have a modified ar-C enhancer, which specifies a diverged function at the embryonic midline. We have identified several conserved motifs that are indicative of putative transcription factor binding sites by local alignment of ar-C enhancers of numerous vertebrate sequences. To trace the evolutionary changes among paralog enhancers, phylogenomic reconstruction was carried out and lineage-specific motif changes were identified. The relation between motif composition and observed developmental differences was evaluated through transgenic functional analyses. Altering and exchanging motifs between paralog enhancers resulted in reversal of enhancer specificity in the floor plate and notochord. A model reconstructing enhancer divergence during vertebrate evolution was developed.Our model suggests that the identified motifs of the ar-C enhancer function as binary switches that are responsible for specific activity between midline tissues, and that these motifs are adjusted during functional diversification of paralogs. The unraveled motif changes can also account for the complex interpretation of activator and repressor input signals within a single enhancer.Phylogenetic footprinting can predict conserved cis-regulatory modules (CRMs) of genes that span over a number of transcription factor binding sites. However, divergence in sequence and function of CRMs over large evolutionary distances may hinder the utility of phylogenetic footprinting methodology [1-5]. Therefore, it is paramount also to investigate functionally the molecular mechanisms that underlie the function and divergence of CRMs. A vexing problem in elucidating the evolution of CRMs is that only a relatively small number of enhancers and other CRMs have thus far been characterized in sufficient detail to allow development of more general rules about their conserved structures and evolutionar
Structural Analysis of the UBA Domain of X-linked Inhibitor of Apoptosis Protein Reveals Different Surfaces for Ubiquitin-Binding and Self-Association  [PDF]
Man Kit Tse, Sin Kam Hui, Yinhua Yang, Si-Tao Yin, Hong-Yu Hu, Bing Zou, Benjamin Chun Yu Wong, Kong Hung Sze
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028511
Abstract: Background Inhibitor of apoptosis proteins (IAPs) belong to a pivotal antiapoptotic protein family that plays a crucial role in tumorigenesis, cancer progression, chemoresistance and poor patient-survival. X-linked inhibitor of apoptosis protein (XIAP) is a prominent member of IAPs attracting intense research because it has been demonstrated to be a physiological inhibitor of caspases and apoptosis. Recently, an evolutionarily conserved ubiquitin-associated (UBA) domain was identified in XIAP and a number of RING domain-bearing IAPs. This has placed the IAPs in the group of ubiquitin binding proteins. Here, we explore the three-dimensional structure of the XIAP UBA domain (XIAP-UBA) and how it interacts with mono-ubiquitin and diubiquitin conjugates. Principal Findings The solution structure of the XIAP-UBA domain was determined by NMR spectroscopy. XIAP-UBA adopts a typical UBA domain fold of three tightly packed α-helices but with an additional N-terminal 310 helix. The XIAP-UBA binds mono-ubiquitin as well as Lys48-linked and linear-linked diubiquitins at low-micromolar affinities. NMR analysis of the XIAP-UBA–ubiquitin interaction reveals that it involves the classical hydrophobic patches surrounding Ile44 of ubiquitin and the conserved MGF/LV motif surfaces on XIAP-UBA. Furthermore, dimerization of XIAP-UBA was observed. Mapping of the self-association surface of XIAP-UBA reveals that the dimerization interface is formed by residues in the N-terminal 310 helix, helix α1 and helix α2, separate from the ubiquitin-binding surface. Conclusion Our results provide the first structural information of XIAP-UBA and map its interaction with mono-ubiquitin, Lys48-linked and linear-linked diubiquitins. The notion that XIAP-UBA uses different surfaces for ubiquitin-binding and self-association provides a plausible model to explain the reported selectivity of XIAP in binding polyubiquitin chains with different linkages.
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