Executionary pathway for apoptosis：lessons from mutant mice

Apoptosis or programmed cell death(PCD) is an evolutionarily conserved cellular process that is essential for normal development and homeostasis of multicellular organisms.Defects in the apoptosis signaling result in many diseases including autoimmune diseases and cancer.The apoptosis signaling pathway was first described genetically in the nematode Caenorhabditis elegans which serves as a framework for the more complex apoptotic pathways that exist in mammals.In this review,we will discuss the apoptotic pathways that are emerging in mammals as elucidated by studies of gene-targeted mutant mice.     

Hemicentins： What have we learned from worms？

Hemicentins are conserved extracellular matrix proteins discovered in Caenorhabditis elegans, with orthologs in all vertebrate species including human and mouse. Hemicentins share a single, highly conserved amino-terminal von Willebrand A domain, followed by a long （〉40） stretch of immunoglobulin repeats, multiple tandem epidermal growth factors and a fibulin-like carboxy-terminal module. C. elegans has a single hemicentin gene that has pleiotropic functions in transient cell contacts that are required for cell migration and basement membrane invasion and in stable contacts at hemidesmosome-mediated cell junctions and elastic fiber-like structures. Here, we summarize what is known about the function ofhemicentin in C. elegans and discuss implications for hemicentin function in other species.     

Structure,expression,and developmental function of early divergent forms of metalloproteinases in Hydra

Metalloproteinases have a critical role in a broad spectrum of cellular processesranging from the break-down of extracellular matrix to the processing of signaltransduction-related proteins.These hydrolytic functions underlie a variety of mechanisms related to developmental processes as well as disease states.Structural analysis of metalloproteinases from both invertebrate and vertebrate species indicates that these enzymes are highly conserved and arose early during metazoan evolution.In this regard,studies from vari-ous laboratories have reported that a number of classes of metalloproteinases are found in hydra,a member of Cnidaria,the second oldest of existing animal phyla.These studies demonstrate that the hydra genome contains at least three classes of metalloproteinases to include members of the 1)astacin class,2)matrix met-alloproteinase class,and 3)neprilysin class.Functional studies indicate that these metalloproteinases play diverse and important roles in hydra morphogenesis and cell differentiation as well as specialized functions in adult polyps.This article will review the structure,expression,and function of these metalloproteinases in hydra.     

Structure, expression, and developmental function of early divergent forms of metalloproteinases in Hydra

Metalloproteinases have a critical role in a broad spectrum of cellular processes ranging from the breakdown of extracellular matrix to the processing of signal transduction-related proteins. These hydrolytic functions underlie a variety of mechanisms related to developmental processes as well as disease states. Structural analysis of metalloproteinases from both invertebrate and vertebrate species indicates that these enzymes are highly conserved and arose early during metazoan evolution. In this regard, studies from various laboratories have reported that a number of classes of metalloproteinases are found in hydra, a member of Cnidaria, the second oldest of existing animal phyla. These studies demonstrate that the hydra genome contains at least three classes of metalloproteinases to include members of the 1) astacin class, 2) matrix met-alloproteinase class, and 3) neprilysin class. Functional studies indicate that these metalloproteinases play diverse and important roles in hydra morphogenesis and ce     

The Synaptonemal Complex of Basal Metazoan Hydra:More Similarities to Vertebrate than Invertebrate Meiosis Model Organisms

The synaptonemal complex （SC） is an evolutionarily well-conserved structure that mediates chromosome synapsis during prophase of the first meiotic division. Although its structure is conserved, the characterized protein components in the current metazoan meiosis model systems （Drosophila melanogaster, Caenorhabditis elegans, and Mus musculus） show no sequence homology, challenging the question of a single evolutionary origin of the SC. However, our recent studies revealed the monophyletic origin of the mammalian SC protein components. Many of them being ancient in Metazoa and already present in the cnidarian Hydra. Remarkably, a comparison between different model systems disclosed a great similarity between the SC components of Hydra and mammals while the proteins of the ecdysozoan systems （D. rnelanogaster and C. elegans） differ significantly. In this review, we introduce the basal-branching metazoan species Hydra as a potential novel invertebrate model system for meiosis research and particularly for the investigation of SC evolution, function and assembly. Also, available methods for SC research in Hydra are summarized.     

Genetic regulation of programmed cell death in Drosophila

Programmed cell death plays an important role in maintaining homeostasis during animal development,and has been conserved in animals as different as nematoes and humans. Recent studies of Drosophila have provided valuadle information toward our understanding of genetic regulation of death.Different signals trigger the novel death regulators rpr,hid,and grim,that utilize the evolutionarily conserved iap and ark genes to modulate caspase function.Subsequent removal of dying cells also appears to be accomplished by conserved mechanisms.The similarity between Drosophila and human in cell death signaling pathways illustrate the promise of fruit flies as a model system to elucidatek the mechanisms underlying regulation of programmed cell death.     

LATERAL ROOTLESS2, a Cyclophilin Protein, Regulates Lateral Root Initiation and Auxin Signaling Pathway in Rice

Dear Editor, Cyclophilins （CYP） are a class of highly conserved pepti- dyl-prolyl cis-trans isomerases （PPlases） that play important roles in various biological processes in eukaryotes （reviewed in Romano et al. （2004））. In higher plants, a conserved sin- gle domain cyclophilin has been identified as a novel com- ponent of the auxin signaling pathway by analyzing the tomato diageotropica （dgt） mutant （Ivanchenko et al., 2006; Oh et al., 2006）. The dgt mutant displays a lateral-rootless and auxin-resistant phenotype （Ivanchenko et aL, 2006）. Further studies revealed that mutations in the DGT-like genes of Physcomitrella patens also exhibited an auxin-resistant phenotype, suggesting a conserved role of DGT-like proteins in auxin signaling. Moreover,     

A paradox: rapid evolution rates of germline-limited sequences are associated with conserved patterns of rearrangements in cryptic species of Chilodonella uncinata(Protista,Ciliophora)

Some of the most extreme genome wide rearrangements are found in ciliates, which are unique in possessing both germline micronucleus and somatic macronucleus in every cell/organism. A series of DNA rearrangement events, including DNA elimination, chromosomal fragmentation, gene unscrambling and alternative processing, happen during macronuclear development. To assess the molecular evolution of macronuclear and germline-limited sequences in different cryptic species of Chilodonella uncinata, we characterized the actin, α-tubulin and β-tubulin genes in the micronucleus and macronucleus genomes of USA-SC2 strain and compared them with other strains(i.e. cryptic species). Three main results are:(i) rearrangement patterns between germline and soma are conserved for each gene among the cryptic species of C. uncinata;(ii) in contrast, the germlinelimited regions are highly divergent in sequence and length among the cryptic species;(iii) pointer shifting is frequent among the cryptic species. We speculate that pointer sequences may serve as the buffer between the conserved macronuclear destined sequences and rapidly-evolving internal eliminated sequences. The data combined with previous studies demonstrate the plasticity of gene rearrangement among different groups of ciliates and add to the growing data for the role of genome rearrangements in species differentiation.     

In silico Analysis of Sequential,Structural and Functional Diversity of Wheat Cystatins and Its Implication in Plant Defense

Phytocystatins constitute a multigene family that regulates the activity of endogenous and/or exogenous cysteine proteinases.Cereal crops like wheat are continuously threatened by a multitude of pathogens,therefore cystatins offer to play a pivotal role in deciding the plant response.In order to study the need of having diverse specificities and activities of various cystatins,we conducted comparative analysis of six wheat cystatins(WCs) with twelve rice,seven barley,one sorghum and ten corn cystatin sequences employing different bioinformatics tools.The obtained results identified highly conserved signature sequences in all the cystatins considered.Several other motifs were also identified,based on which the sequences could be categorized into groups in congruence with the phylogenetic clustering.Homology modeling of WCs revealed 3D structural topology so well shared by other cystatins.Protein-protein interaction of WCs with papain supported the notion that functional diversity is a consequence of existing differences in amino acid residues in highly conserved as well as relatively less conserved motifs.Thus there is a significant conservation at the sequential and structural levels;however,concomitant variations maintain the functional diversity in this protein family,which constantly modulates itself to reciprocate the diversity while counteracting the cysteine proteinases.     

Construction and characterization of an HCV-derived multi-epitope peptide antigen containing B-cell HVR1 mimotopes and T-cell conserved epitopes

Hepatitis C(HCV) genome is highly variable,particularly in the hypervariable region 1 (HVR1) of its E2 envelope gene.The variability of HCV genome has been a major obstacle for de-veloping HCV vaccines.Due to B-cell HVR1 mimotopes mimicking the antigenicity of natural HVR1 epitopes and some T-cell epitopes from the consensus sequence of HCV genes conserving among the different HCV genotypes,we synthesized an minigene of HCV-derived multi-epitope peptide an-tigen(CMEP) ,which contains 9 B-cell HVR1 mimotopes in E2,2 conserved CTL epitopes in C,1 conserved CTL epitope in NS3 and 1 conserved Th epitope in NS3.This minigene was cloned into a GST expression vector to generate a fusion protein GST-CMEP.The immunogenic properties of CEMP were characterized by HCV infected patients' sera,and found that the reactivity frequency reached 75%.The cross reactivity of anti-CEMP antibody with different natural HVR1 variants was up to 90%.Meanwhile,we constructed an HCV DNA vaccine candidate,plasmid pVAX1.0-st-CMEP carrying the recombinant gene(st) of a secretion signal peptide and PADRE universal Th cell epitope sequence in front of the CMEP minigene.Immunization of rabbits with pVAX1.0-st-CMEP resulted in the production of antibody,which was of the same cross reactivity as the fusion protein GST-CMEP.Our findings indicate that the HCV-derived multi-epitope peptide antigen in some degree possessed the characteristics of neutralizing HCV epitopes,and would be of the value as a candidate for the development of HCV vaccines.     

Functional and structural analysis of two fibrinogen-activating enzymes isolated from the venoms of Crotalus durissus terrificus and Crotalus durissus collilineatus

Fibrinogen-activating enzymes, widely distributed in Crotalidae and Viperidae venoms, are single-chain glycosylated serine proteases that display high macromolecular selectivity and are often referred to as thrombin-like enzymes （TLEs）. TLEs serve as structural models to extend our understanding of the structure-function relationships of blood coagulation factors, have been clinically used for the treatment of thrombotic diseases, and are used as tools in clinical assays. The combination of gel filtration and ion-exchange chromatography proved to be successful in obtaining milligram quantities of pure samples of TLEs from the venoms of Crotalus durissus terrificus （white venom） and Crotalus durissus collilineatus （yellow venom）. Functional characterization indicates that both enzymes preferentially degrade the Bβ chain of bovine fibrinogen and possess edema-inducing and coagulant activities. However, the TLE from C. d. collilineatus venom shows twofold higher coagulant activity with a minimum coagulant dose （MCD） of 0.6 μg/μl, whereas the enzyme isolated from C. d. terrificus indicated an MCD of 1.5 μg/μl. Molecular modeling of gyroxin and structural comparisons with other highly conserved snake venom serine proteases, underlines the key role played by the surface charge distribution and the double insertion in the 174surface loop in macromolecular substrate recognition by TLEs.     

Modulation of the MAP kinase signaling cascade by Raf kinase inhibitory protein

Proteins like Rafkinase inhibitory protein (RKIP) that serve as modulators of signaling pathways, either by promoting or inhibiting the formation of productive signaling complexes through protein-protein interactions, have been demonstrated to play an increasingly important role in a number of cell types and organisms. These proteins have been implicated in development as well as the progression of cancer. RKIP is a particularly interesting regulator, as it is a highly conserved, ubiquitously expressed protein that has been shown to play a role in growth and differentiation in a number of organisms and can regulate multiple signaling pathways. RKIP is also the first MAP kinase signaling modulator to be identified as playing a role in cancer metastasis, and identification of the mechanism by which it regulates Raf-1 activation provides new targets for theraoeutic intervention.     

The mechanism and function of active DNA demethylation in plants

DNA methylation is a conserved and important epigenetic mark in both mammals and plants.DNA methylation can be dynamically established,maintained,and removed through different pathways.In plants,active DNA demethylation is initiated by the RELEASE OF SILENCING 1(ROS1)family of bifunctional DNA glycosylases/lyases.Accumulating evidence suggests that DNA demethylation is important in many processes in plants.In this review,we summarize recent studies on the enzymes and regulatory factors that have been identified in the DNA demethylation pathway.We also review the functions of active DNA demethylation in plant development as well as biotic and abiotic stress responses.Finally,we highlight those aspects of DNA demethylation that require additional research.     

SynV and SynX: A story more than DNA synthesis

正Genomes have been studied by biologists for decades with a goal to decipher the origin,evolution,and nature of life on earth.These studies often rely on genetic manipulations such as deletions and insertions(a top-down approach),but recent advances in DNA synthesis provide a new option—whole genome synthesis(a bottom-up approach).While several bacterial and viral genomes have been successfully     

Evolutionary conservation and DNA binding properties of the Ssh7 proteins from Sulfolobus shibatae

The thermoacidophilic archaeon Sulfolobus shibatae synthesizes a large amount of the 7-ku DMA binding proteins known as Ssh7. Our hybridization experiments showed that two Ssh7-encoding genes existed in the genome of S. shibatae. These two genes, designated ssh7a and ssh7b, have been cloned, sequenced and expressed in Escherichia coli. The two Ssh7 proteins differ only at three amino acid positions. In addition, the cis-regulatory sequences of the ssh7a and ssh7b genes are highly conserved. These results suggest the presence of a selective pressure to maintain not only the sequence but also the expression of the two genes. We have also found that there are two genes encoding the 7-ku protein in Sulfolobus solfataricus. Based on this and other studies, we suggest that the gene encoding the 7-ku protein underwent duplication before the separation of Sulfolobus species. Binding of native Ssh7 and recombinant (r)Ssh7 to short duplex DNA fragments was analyzed by electrophoretic mobility shift assays. Both n