Regulatory variance of aspartate transcarbamoylase among strains ofYersinia enterocolitica andYersinia enterocolitica-like organisms

Aspartate transcarbamoylase (ATCase) has been isolated and characterized from 20 different strains ofYersinia enterocolitica andY. enterocolitica-like organisms. A variety of regulatory properties have emerged for the ATCases from the different strains. These regulatory properties may be used as a taxonomic tool to divideY. enterocolitica andY. enterocolitica-like organisms into separate groups. Results are in accord with the recent assignment ofY. enterocolitica andY. enterocolitica-like organisms to four DNA-relatedness groups and four correspondingYersinia species.     

Molecular mechanisms of the decision between life and death: regulation of apoptosis by apoptosis signal-regulating kinase 1.

Coordination and balance between cell survival and apoptosis is crucial for normal development and homeostasis of multicellular organisms. Defects in control of this balance may contribute to a variety of diseases including cancer, autoimmune and neurodegenerative conditions. Although a large number of pro- and anti-apoptotic factors acting for or against the final death event have been and are being discovered at an extraordinary pace with the recent progress in this area, the molecular mechanisms determining whether a cell lives or dies are not fully understood. Phosphorylation and dephosphorylation of intracellular effector molecules are the most common and important regulatory mechanisms in signal transduction and control a variety of cellular events from cell growth to apoptosis. Apoptosis signal-regulating kinase 1 (ASK1) is a member of the mitogen-activated protein (MAP) kinase kinase kinase family, which activates both the SEK1-JNK and MKK3/6-p38 MAP kinase pathways and constitutes a pivotal signaling pathway in cytokine- and stress-induced apoptosis. This review provides recent findings on the molecular mechanisms which determine cell fate such as survival, proliferation, differentiation or apoptosis, with special focus on the regulatory mechanisms of ASK1-mediated apoptosis.     

Reproductive aging: insights from model organisms

Aging was once thought to be the result of a general deterioration of tissues as opposed to their being under regulatory control. However, investigations in a number of model organisms have illustrated that aspects of aging are controlled by genetic mechanisms and are potentially manipulable, suggesting the possibility of treatment for age-related disorders. Reproductive decline is one aspect of aging. In model organisms and humans of both sexes, increasing age is associated with both a decline in the number of progeny and an increased incidence of defects. The cellular mechanisms of reproductive aging are not well understood, although a number of factors, both intrinsic and extrinsic to an organism's germline, may contribute to aging phenotypes. Recent work in a variety of organisms suggests that nuclear organization and nuclear envelope proteins may play a role in these processes.     

Algebraic connectivity may explain the evolution of gene regulatory networks

Gene expression is a result of the interplay between the structure, type, kinetics, and specificity of gene regulatory interactions, whose diversity gives rise to the variety of life forms. As the dynamic behavior of gene regulatory networks depends on their structure, here we attempt to determine structural reasons which, despite the similarities in global network properties, may explain the large differences in organismal complexity. We demonstrate that the algebraic connectivity, the smallest non-trivial eigenvalue of the Laplacian, of the directed gene regulatory networks decreases with the increase of organismal complexity, and may therefore explain the difference between the variety of analyzed regulatory networks. In addition, our results point out that, for the species considered in this study, evolution favours decreasing concentration of strategically positioned feed forward loops, so that the network as a whole can increase the specificity towards changing environments. Moreover, contrary to the existing results, we show that the average degree, the length of the longest cascade, and the average cascade length of gene regulatory networks cannot recover the evolutionary relationships between organisms. Whereas the dynamical properties of special subnetworks are relatively well understood, there is still limited knowledge about the evolutionary reasons for the already identified design principles pertaining to these special subnetworks, underlying the global quantitative features of gene regulatory networks of different organisms. The behavior of the algebraic connectivity, which we show valid on gene regulatory networks extracted from curated databases, can serve as an additional evolutionary principle of organism-specific regulatory networks.     

Molecular biology of bacterial bioluminescence.

The cloning and expression of the lux genes from different luminescent bacteria including marine and terrestrial species have led to significant advances in our knowledge of the molecular biology of bacterial bioluminescence. All lux operons have a common gene organization of luxCDAB(F)E, with luxAB coding for luciferase and luxCDE coding for the fatty acid reductase complex responsible for synthesizing fatty aldehydes for the luminescence reaction, whereas significant differences exist in their sequences and properties as well as in the presence of other lux genes (I, R, F, G, and H). Recognition of the regulatory genes as well as diffusible metabolites that control the growth-dependent induction of luminescence (autoinducers) in some species has advanced our understanding of this unique regulatory mechanism in which the autoinducers appear to serve as sensors of the chemical or nutritional environment. The lux genes have now been transferred into a variety of different organisms to generate new luminescent species. Naturally dark bacteria containing the luxCDABE and luxAB genes, respectively, are luminescent or emit light on addition of aldehyde. Fusion of the luxAB genes has also allowed the expression of luciferase under a single promoter in eukaryotic systems. The ability to express the lux genes in a variety of prokaryotic and eukaryotic organisms and the ease and sensitivity of the luminescence assay demonstrate the considerable potential of the widespread application of the lux genes as reporters of gene expression and metabolic function.     

Cell cycle control of spindle elongation

Different organisms employ a variety of strategies to segregate their chromosomes during mitosis. Despite these differences, however, the basic regulatory principles that govern this intricate process are evolutionarily conserved. Above all, rapid dephosphorylation of mitotic phosphoproteins upon the metaphase-to-anaphase transition has proven to be essential for proper function of the mitotic spindle and accurate chromosome segregation in all eukaryotes. Recently, a central midzone component, the microtubule crosslinker Ase1/PRC1 (anaphase spindle elongation 1/protein regulating cytokinesis 1), was uncovered as a universal target of such control mechanism. Depending on its phosphorylation status, Ase1 either restrains spindle elongation in metaphase or promotes it after anaphase onset via recruitment of kinesin motor proteins to the midzone. Here we discuss the potential role of Ase1/PRC1 as a central regulatory platform that interconnects distinct functions of the midzone such as spindle stability, spindle elongation and cytokinesis. Additionally, we provide a comparative overview of the chromosome segregation strategies used by the main model organisms.     

Positive feedback in cellular control systems

Feedback loops have been identified in a variety of regulatory systems and organisms. While feedback loops of the same type (negative or positive) tend to have properties in common, they can play distinctively diverse roles in different regulatory systems, where they can affect virulence in a pathogenic bacterium, maturation patterns of vertebrate oocytes and transitions through cell cycle phases in eukaryotic cells. This review focuses on the properties and functions of positive feedback in biological systems, including bistability, hysteresis and activation surges.     

硫氧还蛋白-1(Trx1)氧化还原状态的检测

硫氧还蛋白-1(thioredoxin-1,Trx1)是一种广泛存在于生物体内的氧化还原调节蛋白,其氧化还原状态的变化是细胞内发挥氧化还原调控作用的重要过程.本文建立了Trx1氧化还原状态的检测方法—氧化还原蛋白免疫印迹法(redox Western blot),即通过碘乙酸(IAA)标记Trx1,根据蛋白所带负电荷的不同,达到分离蛋白氧化与还原状态的目的,并根据能斯特方程计算出相应的氧化还原电势.本方法是在蛋白免疫印迹(Western blot)的基础上建立的,具有低成本、易操作的特点.实验中分别采用H2O2和DTT处理样本,利用此方法检测了细胞裂解液中、细胞内及过表达Trx1氧化还原电势的变化;并检测了HEK293细胞不同生长时期Trx1的氧化还原状态.     

Wide distribution of homologs of Escherichia coli Kdp K+-ATPase among gram-negative bacteria.

We used Southern blotting to screen a variety of bacterial genes for homology to the kdp genes of Escherichia coli, genes that encode an ATP-driven K+ transport system. We found that most enterobacteria have sequences homologous to those of the three kdp structural genes and the kdpD regulatory gene. A number of distantly related species, including some cyanobacteria, have sequences homologous to those of the structural genes but not the regulatory gene. In all cases only a single region of homology was found. These results suggest that ATP-driven transport systems similar to the Kdp system in structure and regulation are found in many enteric organisms. In other gram-negative organisms, the ATPase is more divergent, retaining good homology at the DNA level only to the highly conserved phosphorylated subunit of the ATPase.     

Adaptive Dynamics of Regulatory Networks: Size Matters

To accomplish adaptability, all living organisms are constructed of regulatory networks on different levels which are capable to differentially respond to a variety of environmental inputs. Structure of regulatory networks determines their phenotypical plasticity, that is, the degree of detail and appropriateness of regulatory replies to environmental or developmental challenges. This regulatory network structure is encoded within the genotype. Our conceptual simulation study investigates how network structure constrains the evolution of networks and their adaptive abilities. The focus is on the structural parameter network size. We show that small regulatory networks adapt fast, but not as good as larger networks in the longer perspective. Selection leads to an optimal network size dependent on heterogeneity of the environment and time pressure of adaptation. Optimal mutation rates are higher for smaller networks. We put special emphasis on discussing our simulation results on the background of functional observations from experimental and evolutionary biology.     

The OSBP-related proteins: a novel protein family involved in vesicle transport,cellular lipid metabolism,and cell signalling

Proteins/genes showing high sequence homology to the mammalian oxysterol binding protein (OSBP) have been identified in a variety of eukaryotic organisms from yeast to man. The unifying feature of the gene products denoted as OSBP-related proteins (ORPs) is the presence of an OSBP-type ligand binding (LB) domain. The LB domains of OSBP and its closest homologue bind oxysterols, while data on certain other family members suggest interaction with phospholipids. Many ORPs also have a pleckstrin homology (PH) domain in the amino-terminal region. The PH domains of the family members studied in detail are known to interact with membrane phosphoinositides and play an important role in the intracellular targeting of the proteins. It is plausible that the ORPs constitute a regulatory apparatus that senses the status of specific lipid ligands in membranes, using the PH and/or LB domains, and mediates information to yet poorly known downstream machineries. Functional studies carried out on the ORP proteins in different organisms indicate roles of the gene family in diverse cellular processes including control of lipid metabolism, regulation of vesicle transport, and cell signalling events.     

The OSBP-related proteins: a novel protein family involved in vesicle transport,cellular lipid metabolism,and cell signalling

Proteins/genes showing high sequence homology to the mammalian oxysterol binding protein (OSBP) have been identified in a variety of eukaryotic organisms from yeast to man. The unifying feature of the gene products denoted as OSBP-related proteins (ORPs) is the presence of an OSBP-type ligand binding (LB) domain. The LB domains of OSBP and its closest homologue bind oxysterols, while data on certain other family members suggest interaction with phospholipids. Many ORPs also have a pleckstrin homology (PH) domain in the amino-terminal region. The PH domains of the family members studied in detail are known to interact with membrane phosphoinositides and play an important role in the intracellular targeting of the proteins. It is plausible that the ORPs constitute a regulatory apparatus that senses the status of specific lipid ligands in membranes, using the PH and/or LB domains, and mediates information to yet poorly known downstream machineries. Functional studies carried out on the ORP proteins in different organisms indicate roles of the gene family in diverse cellular processes including control of lipid metabolism, regulation of vesicle transport, and cell signalling events.     

Isolation, characterization and manipulation of cellulase genes

The complete hydrolysis of cellulose requires a number of different enzymes including endoglucanase, exoglucanase and beta-glucosidase. These enzymes function in concert as part of a 'cellulase'complex called a cellulosome. In order (i) to develop a better understanding of the biochemical nature of the cellulase complex as well as the genetic regulation of its integral components and (ii) to utilize cellulases either as purified enzymes or as part of an engineered organism for a variety of purposes, researchers have, as a first step, used recombinant DNA technology to isolate the genes for these enzymes from a variety of organisms. This review provides some perspective on the current status of the isolation, characterization and manipulation of cellulase genes and specifically discusses (i) strategies for the isolation of endoglucanase, exoglucanase and beta-glucosidase genes; (ii) DNA sequence characterization of the cellulase genes and their accompanying regulatory elements; (iii) the expression of cellulase genes in heterologous host organisms and (iv) some of the proposed uses for isolated cellulase genes.