Interactions between HMG proteins and the core sequence of DNaseI hypersensitive site 2 in the locus control region (LCR) of the human β-Mike globin gene cluster

HMG proteins are abundant chromosomal non-histone proteins. It has been suggested that the HMG proteins may play an important role in the structure and function of chromatin. In the present study, the binding of HMG proteins (HMG1/2 and HMG14/17) to the core DNA sequence of DNasel hypersensitive site 2 (HS2core DNA sequence, -10681-10970 bp) in the locus control region (LCR) of the human β-like globin gene cluster has been examined by using both the in vitro nucleosome reconstitution and the gel mobility shift assays. Here we show that HMG1/2 can bind to the naked HS2core DNA sequence, however, HMG 14/17 cannot. Using the in vitro nucleosome reconstitution we demonstrate that HMG14/17 can bind to the HS2core DNA sequence which is assembled into nucleosomes with the core histone octamer transferred from chicken erythrocytes. In contrast, HMG 1/2 cannot bind to the nucleosomes reconstituted in vitro with the HS2core DNA sequence. These results indicate that the binding patterns between HMG proteins and t     

Genes encoding a group of related small secreted proteins from the gut of Hessian fly larvae [Mayetiola destructor （Say）]

A group of related genes has been isolated and characterized from the gut of Hessian fly larvae [Mayetiola destructor （Say）]. Members in this group appear to encode proteins with secretary signal peptides at the N-terminals. The mature putative proteins are small, acidic proteins with calculated molecular masses of 14.5 to 15.3 kDa, and isoelectric points from 4.56 to 4.88. Northern blot analysis revealed that these genes are expressed predominantly in the gut of Hessian fly larvae and pupae. Two related genes, GIOK1 and GIOK2, were isolated as tandem repeats. Both genes contain three exons and two introns. The intron/exon boundaries were conserved in terms of amino acid encoding, suggesting that they arose by gene duplication. The fact that the frequency of this group of clones in a gut cDNA library higher than that of total cDNA clones encoding digestive enzymes suggested that this group of proteins may perform an important function in the gut physiology of this insect. However, the exact functions of these proteins are as yet known since no sequence similarity could be identified between these proteins and any known sequences in public databases using standard methods.     

Physicochemical bases for protein folding,dynamics, and protein-ligand binding

Proteins are essential parts of living organisms and participate in virtually every process within cells.As the genomic sequences for increasing number of organisms are completed,research into how proteins can perform such a variety of functions has become much more intensive because the value of the genomic sequences relies on the accuracy of understanding the encoded gene products.Although the static three-dimensional structures of many proteins are known,the functions of proteins are ultimately governed by their dynamic characteristics,including the folding process,conformational fluctuations,molecular motions,and protein-ligand interactions.In this review,the physicochemical principles underlying these dynamic processes are discussed in depth based on the free energy landscape(FEL)theory.Questions of why and how proteins fold into their native conformational states,why proteins are inherently dynamic,and how their dynamic personalities govern protein functions are answered.This paper will contribute to the understanding of structure-function relationship of proteins in the post-genome era of life science research.     

Regulation of Actin Dynamics in Pollen Tubes： Control of Actin Polymer Level

Actin cytoskeleton undergoes rapid reorganization in response to internal and external cues. How the dynamics of actin cytoskeleton are regulated, and how its dynamics relate to its function are fundamental questions in plant cell biology. The pollen tube is a well characterized actin-based cell morphogenesis in plants. One of the striking features of actin cytoskeleton characterized in the pollen tube is its surprisingly low level of actin polymer. This special phenomenon might relate to the function of actin cytoskeleton in pollen tubes. Understanding the molecular mechanism underlying this special phenomenon requires careful analysis of actin-binding proteins that modulate actin dynamics directly. Recent biochemical and biophysical analyses of several highly conserved plant actin-binding proteins reveal unusual and unexpected properties, which emphasizes the importance of carefully analyzing their action mechanism and cellular activity. In this review, we highlight an actin monomer sequestering protein, a barbed end capping protein and an F-actin severing and dynamizing protein in plant. We propose that these proteins function in harmony to regulate actin dynamics and maintain the low level of actin polymer in pollen tubes.     

Pathogenesis and Associated Diseases of Kaposi's Sarcoma-associated Herpesvirus

Kaposi's sarcoma-associated herpesvirus(KSHV)is the primary etiological agent of Kaposi's sarcoma,primary effusion lymphoma and muticentric Castleman's disease.In common with the other herpesviruses,KSHV exhibits both latent and lytic life cycles,both of which are characterized by distinct gene expression profiles and programs.KSHV encodes proteins which play essential roles in the inhibition of host adaptive and innate immunity,the inhibition of apoptosis,and the regulation of the cell cycle.KSHV also encodes several proteins which have transforming and intrcellular signalling activity.     

Pathogenesis and Associated Diseases of Kaposi＇s Sarcoma-associated Herpesvirus

Kaposi＇s sarcoma-associated herpesvirus （KSHV） is the primary,etiological agent of Kaposi＇s sarcoma, primary effusion lymphoma and muticentric Castleman＇s disease. In common with the other herpesviruses, KSHV exhibits both latent and lyric life cycles, both of which are characterized by distinct gene expression profiles and programs. KSHV encodes proteins which play essential roles in the inhibition of host adaptive and innate immunity, the inhibition of apoptosis, and the regulation of the cell cycle. KSHV also encodes several proteins which have transforming and intrcellular signalling activity.     

The characteristics of the spindle fiber attachments（SFAs） enriched fraction from mouse nuclei

The characteristics of the particulate mouse centromere enriched fraction from isolated nuclei obtained in our laboratory were investigated by indirect immunofluorescence,test of the activity of microtubule organizing center(MTOC),SDS-PAGE,and fluorescence in situ hybridization.Most of the particles of the fraction are complexes of DNA and kinetochore proteins and show MTOC activity.The DNA isolated from the fraction can hybridize with DNA in the regions of the primary constrictions of all chromosomes of ascions of the primary constrictions of all chromosomes of ascites cells.The kinetochore proteins isolated from the fraction are mainly those with molecular weight of 55 KD and 59 KD.Results suggested that the fraction obtained is a centromere enriched nuclear fraction as indicated in our previous report.     

TRIM-9 functions in the UNC-6/UNC-40 pathway to regulate ventral guidance

TRIpartite Motif(TRIM) family proteins are ring finger domain-containing,multi-domain proteins implicated in many biological processes. Members of the TRIM-9/C-I subfamily of TRIM proteins,including TRIM-9,MIDI and MID2,have neuronal functions and are associated with neurological diseases.To explore whether the functions of C-I TRIM proteins are conserved in invertebrates,we analyzed Caenorhabditis elegans and Drosophila trim-9 mutants.C.elegans trim-9 mutants exhibit defects in the ventral guidance of h...     

Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins

Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylo-genetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ?81 aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ?10 exons of small size [?176 nucleotides (nt)]. Streptophyta have on average only ?5.7 exons of medium size (?230 nt). Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400 nt). Among sub-cellular compartments, membrane proteins are the largest (?520 aa), whereas the smallest proteins correspond to the gene ontology group of ribosome (?240 aa). Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ?34%more but ?20%smal-ler proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.     

Preliminary investigation of sequence-independent DNA binding proteins in rat skeletal muscle sarcoplasmic reticulum and their function

To observe the binding of plasmid DNA to non-nuclear DNA binding proteins in sar-coplasmic reticulum (SR) and the effects of this binding on SR function, sarcoplasmic reticulum proteins in rat skeletal muscle were isolated by differential centrifuge and sucrose density-gradient centrifuge. The results showed that there are two sequence-independent DNA binding proteins in SR proteins, the molecular weights of which are 83 and 58 ku, respectively. Ca2 uptake and release of SR were remarkably promoted by the binding of plasmid DNA to DNA binding proteins in SR, the mechanism is probably through increasing of Ca2 -ATPase activity in SR and changing of character of Ca2 release channel ryanodine receptors induced by the binding. These results suggest that there exist DNA binding proteins in SR and its binding to DNA may affect Ca2 transport of SR.     

Adaptive Evolution of cry Genes in Bacillus thuringiensis： Implications for Their Specificity Determination

The cry gene family, produced during the late exponential phase of growth in Bacillus thuringiensis, is a large, still-growing family of homologous genes, in which each gene encodes a protein with strong specific activity against only one or a few insect species. Extensive studies are mostly focusing on the structural and functional relationships of Cry proteins, and have revealed several residues or domains that are important for the target recognition and receptor attachment. In this study, we have employed a maximum likelihood method to detect evidence of adaptive evolution in Cry proteins, and have identified 24 positively selected residues, which are all located in Domain Ⅱ or Ⅲ. Combined with known data from mutagenesis studies, the majority of these residues, at the molecular level, contribute much to the insect specificity determination. We postulate that the potential pressures driving the diversification of Cry proteins may be in an attempt to adapt for the ＂arm race＂ between δ-endotoxins and the targeted insects, or to enlarge their target spectra, hence result in the functional divergence. The sites identified to be under positive selection would provide targets for further structural and functional analyses on Cry proteins.     

Selective degradation of the IκB kinase （IKK） by autophagy

Proteasome-mediated degradation and autophagy are the two major pathways mediating the turnover of cellular proteins. The proteasomal pathway is known to be a highly specific and regulated process mediating the degradation of short-lived proteins such as many important factors involved in cellular signaling. In contrast, it is generally thought that autophagy is rather nonselective as it is responsible for the bulk degradation of long-lived proteins and organelles. Challenging this general view, in this issue of Cell Research, Qing et al. report that selective degradation of the IκB kinase （IKK） triggered by the loss of Hsp90 function is mediated by autophagy [1].     

Vacuole import and degradation pathway: Insights into a specialized autophagy pathway

Glucose deprivation induces the synthesis of pivotagluconeogenic enzymes such as fructose-1,6-bisphos-phatase, malate dehydrogenase, phosphoenolpyruvatecarboxykinase and isocitrate lyase in Saccharomycescerevisiae. However, following glucose replenishment,these gluconeogenic enzymes are inactivated and de-graded. Studies have characterized the mechanismsby which these enzymes are inactivated in response toglucose. The site of degradation of these proteins hasalso been ascertained to be dependent on the dura-tion of starvation. Glucose replenishment of short-termstarved cells results in these proteins being degradedin the proteasome. In contrast, addition of glucose tocells starved for a prolonged period results in theseproteins being degraded in the vacuole. In the vacuoledependent pathway, these proteins are sequestered inspecialized vesicles termed vacuole import and degra-dation (Vid). These vesicles converge with the endo-cytic pathway and deliver their cargo to the vacuolefor degradation. Recent studies have identified thatinternalization, as mediated by actin polymerization, isessential for delivery of cargo proteins to the vacuolefor degradation. In addition, components of the targetof rapamycin complex 1 interact with cargo proteins during glucose starvation. Furthermore, Tor1p dissoci-ates from cargo proteins following glucose replenish-ment. Future studies will be needed to elaborate on the importance of internalization at the plasma membrane and the subsequent import of cargo proteins into Vid vesicles in the vacuole dependent degradation pathway.     

植物防御系统中抗病相关基因的研究进展

本文论述了植物防御系统中抗病相关基因（resistance gene,R基因）的研究进展。列表总结了迄今已克隆的R基因,并将其归为四种不同的类型。综述了不同基因表达产物-R蛋白在细胞中的定位及其相应的功能。此外,还对R基因编码区的多态性、R基因在染色体上排列方式以及R基因的进化与起源等问题进行了讨论。 Abstract:This review comments on recent advances in research of disease resistance genes(R Genes) in defence system of plants.The R genes cloned up to date are summarized and classified roughly into four classes listed in the Table 1.The location and the founction of the R proteins,i.e.,the expressed products of different R genes in the cells are reviewed.In addition,the polymophism of coding region of R genes,the different fashions of R gene arrangement on the chromosomes,and the evolution and origin of R genes are discussed.     

Quantitative analysis of secretome from adipocytes regulated by insulin

Adipocyte is not only a central player involved in storage and release of energy, but also in regulation of energy metabolism in other organs via secretion of peptides and proteins. During the pathogenesis of insulin resistance and type 2 diabetes, adipocytes are subjected to the increased levels of insulin, which may have a major impact on the secretion of adipokines. We have undertaken cleavable isotope-coded affinity tag （cICAT） and label-free quantitation approaches to identify and quantify secretory factors that are differentially secreted by 3T3-L1 adipocytes with or without insulin treatment. Combination of cICAT and label-free results, there are 317 proteins predicted or annotated as secretory proteins. Among these secretory proteins, 179 proteins and 53 proteins were significantly upregulated and down-regulated, respectively. A total of 77 reported adipokines were quantified in our study, such as adiponectin, cathepsin D, cystatin C, resistin, and transferrin. Western blot analysis of these adipokines confirmed the quantitative results from mass spectrometry, and revealed individualized secreting patterns of these proteins by increasing insulin dose. In addition, 240 proteins were newly identified and quantified as secreted proteins from 3T3-L1 adipocytes in our study, most of which were up-regulated upon insulin treatment. Further comprehensive bioinformatics analysis revealed that the secretory proteins in extracellular matrix-receptor interaction pathway and glycan structure degradation pathway were significantly upregulated by insulin stimulation.     

Chaperone function and mechanism of small heat-shock proteins

Small heat-shock proteins （sHSPs） are ubiquitous ATP-independent molecular chaperones that play crucial roles in protein quality control in cells. They are able to prevent the aggregation and/or inactivation of various non-native sub- strate proteins and assist the refolding of these substrates independently or under the help of other ATP-dependent chaperones. Substrate recognition and binding by sHSPs are essential for their chaperone functions. This review focuses on what natural substrate proteins an sHSP pro- tects and how it binds the substrates in cells under fluctuat- ing conditions. It appears that sHSPs of prokaryotes, although being able to bind a wide range of cellular pro- teins, preferentially protect certain classes of functional proteins, such as translation-related proteins and metabolic enzymes, which may well explain why they could increase the resistance of host cells against various stresses. Mechanistically, the sHSPs of prokaryotes appear to possess numerous multi-type substrate-binding residues and are able to hierarchically activate these residues in a temperature-dependent manner, and thus act as tempera- ture-regulated chaperones. The mechanism of hierarchical activation of substrate-binding residues is also discussed regarding its implication for eukaryotic sHSPs.     

The Chloroplast Outer Envelope Membrane： The Edge of Liaht and Excitement

The chloroplast is surrounded by a double-membrane envelope at which proteins, ions, and numerous metabolites including nucleotides, amino acids, fatty acids, and carbohydrates are exchanged between the two aqueous phases, the cytoplasm and the chloroplast stroma. The chloroplast envelope is also the location where the biosynthesis and accumulation of various lipids take place. By contrast to the inner membrane, which contains a number of specific transporters and acts as the permeability barrier, the chloroplast outer membrane has often been considered a passive compartment derived from the phagosomal membrane. However, the presence of galactoglycerolipids and β-barrel membrane proteins support the common origin of the outer membranes of the chloroplast envelope and extant cyanobacteria. Furthermore, recent progress in the field underlines that the chloroplast outer envelope plays important roles not only for translocation of various molecules, but also for regulation of metabolic activities and signaling processes. The chloroplast outer envelope membrane offers various interesting and challenging questions that are relevant to the understanding of organelle biogenesis, plant growth and development, and also membrane biology in general.