General Control Mechanism Research Articles

The one‐component system ArnR: a membrane‐bound activator of the crenarchaeal archaellum

Linking the motility apparatus to signal transduction systems enables microbes to precisely control their swimming behaviour according to environmental conditions. Bacteria have therefore evolved a complex chemotaxis machinery, which has presumably spread through lateral gene transfer into the euryarchaeal subkingdom. By contrast Crenarchaeota encode no chemotaxis-like proteins but are nevertheless able to connect external stimuli to archaellar derived motility. This raises fundamental questions about the underlying regulatory mechanisms. Recently, we reported that the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius becomes motile upon nutrient starvation by promoting transcription of flaB encoding the filament forming subunits. Here we describe two transcriptional activators as paralogous one-component-systems Saci_1180 and Saci_1171 (ArnR and ArnR1). Deletions of arnR and arnR1 resulted in diminished flaB expression and accordingly the deletion mutants revealed impaired swimming motility. We further identified two inverted repeat sequences located upstream of the flaB core promoter of S. acidocaldarius. These cis-regulatory elements were shown to be critical for ArnR and ArnR1 mediated flaB gene expression in vivo. Finally, bioinformatic analysis revealed ArnR to be conserved not only in Sulfolobales but also in the crenarchaeal order of Desulfurococcales and thus might represent a more general control mechanism of archaeal motility.

Pax6 Interactions with Chromatin and Identification of Its Novel Direct Target Genes in Lens and Forebrain

Pax6 encodes a specific DNA-binding transcription factor that regulates the development of multiple organs, including the eye, brain and pancreas. Previous studies have shown that Pax6 regulates the entire process of ocular lens development. In the developing forebrain, Pax6 is expressed in ventricular zone precursor cells and in specific populations of neurons; absence of Pax6 results in disrupted cell proliferation and cell fate specification in telencephalon. In the pancreas, Pax6 is essential for the differentiation of α-, β- and δ-islet cells. To elucidate molecular roles of Pax6, chromatin immunoprecipitation experiments combined with high-density oligonucleotide array hybridizations (ChIP-chip) were performed using three distinct sources of chromatin (lens, forebrain and β-cells). ChIP-chip studies, performed as biological triplicates, identified a total of 5,260 promoters occupied by Pax6. 1,001 (133) of these promoter regions were shared between at least two (three) distinct chromatin sources, respectively. In lens chromatin, 2,335 promoters were bound by Pax6. RNA expression profiling from Pax6+/− lenses combined with in vivo Pax6-binding data yielded 76 putative Pax6-direct targets, including the Gaa, Isl1, Kif1b, Mtmr2, Pcsk1n, and Snca genes. RNA and ChIP data were validated for all these genes. In lens cells, reporter assays established Kib1b and Snca as Pax6 activated and repressed genes, respectively. In situ hybridization revealed reduced expression of these genes in E14 cerebral cortex. Moreover, we examined differentially expressed transcripts between E9.5 wild type and Pax6−/− lens placodes that suggested Efnb2, Fat4, Has2, Nav1, and Trpm3 as novel Pax6-direct targets. Collectively, the present studies, through the identification of Pax6-direct target genes, provide novel insights into the molecular mechanisms of Pax6 gene control during mouse embryonic development. In addition, the present data demonstrate that Pax6 interacts preferentially with promoter regions in a tissue-specific fashion. Nevertheless, nearly 20% of the regions identified are accessible to Pax6 in multiple tissues.

Modeling Synchronous Muscle Function in Insect Flight: a Bio-Inspired Approach to Force Control in Flapping-Wing MAVs

Micro-aerial vehicles (MAV) and their promising applications--such as undetected surveillance or exploration of environments with little space for land-based maneuvers--are a well-known topic in the field of aerial robotics. Inspired by high maneuverability and agile flight of insects, over the past two decades a significant amount of effort has been dedicated to research on flapping-wing MAVs, most of which aim to address unique challenges in morphological construction, force production, and control strategy. Although remarkable solutions have been found for sufficient lift generation, effective methods for motion control still remain an open problem. The focus of this paper is to investigate general flight control mechanisms that are potentially used by real insects, thereby providing inspirations for flapping-wing MAV control. Through modeling the insect flight muscles, we show that stiffness and set point of the wing's joint can be respectively tuned to regulate the wing's lift and thrust forces. Therefore, employing a suitable controller with variable impedance actuators at each wing joint is a prospective approach to agile flight control of insect-inspired MAVs. The results of simulated flight experiments with one such controller are provided and support our claim.

Association between gene polymorphisms of propanoate metabolism pathway and meat quality as well as carcass traits in pigs

In order to gain more extensive insight into detailed genetic control mechanisms of porcine meat quality and mine novel candidate genes, this study focused on the relationship between the genes of propanpate metabolism pathway and porcine meat quality as well as carcass traits based on the candidate gene set approach. Thirty-seven DLY pigs were tested in this study. A total of 36 SNPs within 7 candidate genes of propanoate metabolism pathway were genotyped and association analysis was conducted via Least Squares method, Multivariate multiple regression model, and a model-based multifactor dimensionality reduction method (MB-MDR). As a result, four SNPs in genes PCCB, MUT, MCEE, and ACSS1 were significantly associated with DLY pig meat quality or carcass traits (P<0.05). Results of MB-MDR analysis demonstrated that the interactions between multiple SNPs were significantly associated with the backfat thickness, water content, and fat content (P<0.05). ACSS2 was significantly associated with fat content; MCEE and MUT significantly influenced backfat thickness; and PCCB was related to fat weight. Moreover, the interactions between the genes in the propanoate metabolism pathway had remarkable influence in porcine meat quality and carcass traits.

Dynamic Compression of Chondrocyte-Agarose Constructs Reveals New Candidate Mechanosensitive Genes

Articular cartilage is physiologically exposed to repeated loads. The mechanical properties of cartilage are due to its extracellular matrix, and homeostasis is maintained by the sole cell type found in cartilage, the chondrocyte. Although mechanical forces clearly control the functions of articular chondrocytes, the biochemical pathways that mediate cellular responses to mechanical stress have not been fully characterised. The aim of our study was to examine early molecular events triggered by dynamic compression in chondrocytes. We used an experimental system consisting of primary mouse chondrocytes embedded within an agarose hydrogel; embedded cells were pre-cultured for one week and subjected to short-term compression experiments. Using Western blots, we demonstrated that chondrocytes maintain a differentiated phenotype in this model system and reproduce typical chondrocyte-cartilage matrix interactions. We investigated the impact of dynamic compression on the phosphorylation state of signalling molecules and genome-wide gene expression. After 15 min of dynamic compression, we observed transient activation of ERK1/2 and p38 (members of the mitogen-activated protein kinase (MAPK) pathways) and Smad2/3 (members of the canonical transforming growth factor (TGF)-β pathways). A microarray analysis performed on chondrocytes compressed for 30 min revealed that only 20 transcripts were modulated more than 2-fold. A less conservative list of 325 modulated genes included genes related to the MAPK and TGF-β pathways and/or known to be mechanosensitive in other biological contexts. Of these candidate mechanosensitive genes, 85% were down-regulated. Down-regulation may therefore represent a general control mechanism for a rapid response to dynamic compression. Furthermore, modulation of transcripts corresponding to different aspects of cellular physiology was observed, such as non-coding RNAs or primary cilium. This study provides new insight into how chondrocytes respond to mechanical forces.

Dynamic regulation of growing domains for elongating and branching morphogenesis in plants

With their continuous growth, understanding how plant shapes form is fundamentally linked to understanding how growth rates are controlled across different regions of the plant. Much of a plant's architecture is generated in shoots and roots, where fast growth in tips contrasts with slow growth in supporting stalks. Shapes can be determined by where the boundaries between fast- and slow-growing regions are positioned, determining whether tips elongate, branch, or cease to grow. Across plants, there is a diversity in the cell wall chemistry through which growth operates. However, prototypical morphologies, such as tip growth and branching, suggest there are common dynamic constraints in localizing chemical growth catalysts. We have used Turing-type reaction-diffusion mechanisms to model this spatial localization and the resulting growth trajectories, characterizing the chemistry-growth feedback necessary for maintaining tip growth and for inducing branching. The mechanism defining the boundaries between fast- and slow-growing regions not only affects tip shape, it must be able to form new boundaries when the pattern-forming dynamics break symmetry, for instance in the branching of a tip. In previous work, we used an arbitrary concentration threshold to switch between two dynamic regimes of the growth catalyst in order to define growth boundaries. Here, we present a chemical dynamic basis for this threshold, in which feedback between two pattern-forming mechanisms controls the extent of the regions in which fast growth occurs. This provides a general self-contained mechanism for growth control in plant morphogenesis (not relying on external cues) which can account for both simple tip extension and symmetry-breaking branching phenomena.

Interaction between microRNAs and actin-associated protein Arpc5 regulates translational suppression during male germ cell differentiation

Decoupling of transcription and translation during postmeiotic germ cell differentiation is critical for successful spermatogenesis. Here we establish that the interaction between microRNAs and actin-associated protein Arpc5 sets the stage for an elaborate translational control mechanism by facilitating the sequestration of germ cell mRNAs into translationally inert ribonucleoprotein particles until they are later translated. Our studies reveal that loss of microRNA-dependent regulation of Arpc5, which controls the distribution of germ cell mRNAs between translationally active and inactive pools, results in abnormal round spermatid differentiation and impaired fertility. Interestingly, Arpc5 functions as a broadly acting translational suppressor, as it inhibits translation initiation by blocking 80S formation and facilitates the transport of mRNAs to chromatoid/P bodies. These findings identify a unique role for actin-associated proteins in translational regulation, and suggest that mRNA-specific and general translational control mechanisms work in tandem to regulate critical germ cell differentiation events and diverse somatic cell functions.

Maternally-preset program of apoptosis and caspases involved in execution of the apoptosis at midblastula transition (MBT) but not before in &amp;lt;i&amp;gt;Xenopus laevis&amp;lt;/i&amp;gt; embryogenesis

To study gene control mechanisms in Xenopus embryos, we analyzed polyamines, cloned SAMDC (S-adenosylmethionine decarboxylase), a key enzyme of polyamine metabolism, and microinjected its mRNA into Xenopus fertilized eggs. The microinjection induced a large increase in SAMDC activity, exhaustion of the substrate SAM (S-adenosylmethionine), and execution of apoptosis at the stage called midblastula transition (MBT). By tracing GFP (green fluorescence protein)-marked apoptotic cells, we reached a conclusion that the apoptosis provides pre-blastula embryos with a fail-safe mechanism of early development. We analyzed caspase mRNAs and found that caspase-9 and -3 mRNAs are maternal mRNA and activation of caspase-9 is one of the key steps for the execution of the apoptosis. We also found that over- expression of caspase-8, and in addition p53, a tumor suppressor protein, also induces apoptosis at MBT, just like the overexpression of SAMDC and caspase-9 does. The apoptosis induced by p53 was suppressed by Xdm-2, a negative regulator of p53, and by a peptide inhibitor and a dominant-negative type mutant of caspase-9, but not by those of caspase-8. By contrast, apoptosis induced by SAMDC was suppressed by peptide inhibitors and dominant-negative mutants of both caspase-9 and caspase-8, but not by Xdm-2. Unlike caspase-9 mRNA, caspase-8 mRNA was not a maternal mRNA, but newly expressed during cleavage stage (pre-MBT stage) only in embryos overexpressed with SAMDC. In SAMDC-induced apoptotic embryos activities to process procaspase-8 and procaspase-9 appeared, whereas in p53-induced apoptotic embryos only activity to process procaspase-9 appeared. Thus, Xenopus embryos have at least two pathways to execute the maternal program of apoptosis: One induced by SAMDC overexpression through activation of caspase-9 and do novo expression of caspase-8 gene, and the other induced by p53 overexpression through activation of caspase-9 but not caspase-8. In Xenopus embryos, it has long been believed that zygotic genes are silent until MBT, but results obtained with caspase-8 may provide a novel example of gene expression before MBT.

Human gene control by vital oncogenes: revisiting a theoretical model and its implications for targeted cancer therapy.

An important assumption of our current understanding of the mechanisms of carcinogenesis has been the belief that clarification of the cancer process would inevitably reveal some of the crucial mechanisms of normal human gene regulation. Since the momentous work of Bishop and Varmus, both the molecular and the biochemical processes underlying the events in the development of cancer have become increasingly clear. The identification of cellular signaling pathways and the role of protein kinases in the events leading to gene activation have been critical to our understanding not only of normal cellular gene control mechanisms, but also have clarified some of the important molecular and biochemical events occurring within a cancer cell. We now know that oncogenes are dysfunctional proto-oncogenes and that dysfunctional tumor suppressor genes contribute to the cancer process. Furthermore, Weinstein and others have hypothesized the phenomenon of oncogene addiction as a distinct characteristic of the malignant cell. It can be assumed that cancer cells, indeed, become dependent on such vital oncogenes. The products of these vital oncogenes, such as c-myc, may well be the Achilles heel by which targeted molecular therapy may lead to truly personalized cancer therapy. The remaining problem is the need to introduce relevant molecular diagnostic tests such as genome microarray analysis and proteomic methods, especially protein kinase identification arrays, for each individual patient. Genome wide association studies on cancers with gene analysis of single nucleotide and other mutations in functional proto-oncogenes will, hopefully, identify dysfunctional proto-oncogenes and allow the development of more specific targeted drugs directed against the protein products of these vital oncogenes. In 1984 Willis proposed a molecular and biochemical model for eukaryotic gene regulation suggesting how proto-oncogenes might function within the normal cell. That model predicted the existence of vital oncogenes and can now be used to hypothesize the biochemical and molecular mechanisms that drive the processes leading to disruption of the gene regulatory machinery, resulting in the transformation of normal cells into cancer.

How Frontoparietal Brain Regions Mediate Imitative and Complementary Actions: An fMRI Study

The ‘mirror neuron system’ (MNS), located within inferior parietal lobe (IPL) and inferior frontal gyrus (IFG), creates an internal motor representation of the actions we see and has been implicated in imitation. Recently, the MNS has been implicated in non-identical responses: when the actions we must execute do not match those that we observe. However, in such conflicting situations non action-specific cognitive control networks also located in frontoparietal regions may be involved. In the present functional magnetic resonance imaging (fMRI) study participants made both similar and dissimilar actions within two action contexts: imitative and complementary. We aimed to determine whether activity within IPL/IFG depends on (i) responding under an imitative versus complementary context (ii) responding with similar versus dissimilar responses, and (iii) observing hand actions versus symbolic arrow cue stimuli. Activity within rIPL/rIFG regions was largest during observation of hand actions compared with arrow cues. Specifically, rIPL/rIFG were recruited only during the imitative context, when participants responded with similar actions. When responding to symbolic arrow cues, rIPL/rIFG activity increased during dissimilar responses, reflecting increased demands placed on general cognitive control mechanisms. These results suggest a specific role of rIPL/rIFG during imitation of hand actions, and also a general role of frontoparietal areas in mediating dissimilar responses to both hand actions and symbolic stimuli. We discuss our findings in relation to recent work that has examined the role of frontoparietal brain structures in joint-actions and inter-actor cooperation. We conclude that the specific brain regions identified here to show increased activation during action observation conditions are likely to form part of a mechanism specifically involved in matching observed actions directly with internal motor plans. Conversely, observation of arrow cues recruited part of a wider cognitive control network involved in the rapid remapping of stimulus-response associations.

Concurrent Redundancy Problem and Control Methods

数据竞争问题是并发程序开发与测试难题,发现数据竞争可能导致计算重复,重复会导致系统性能下降.从实例出发定义了并发计算重复问题(concurrent computation redundancy problem,简称CCRP),给出了相关性能指标和判断方法,设计了通用并发重复控制机制.并发程序一般都可以基于生产者-消费者模型进行CCRP 分析.以带数据源的生产者-消费者为例详细分析了CCRP,给出了单条件、条件交叉两种重复控制算法,算法具有不同的适用范围,都可以作为固定模式来解决CCRP,基于Petri 网作了相关性质的证明与仿真.并发程序实验结果说明了并发重复控制的必要性和有效性,比较了两种算法的差异.该研究对于数据竞争检测、并发程序设计具有参考价值.关键词: 并发控制;Petri 网;数据竞争;并发计算重复;并发重复控制

Mechanism for gene control by a natural allosteric group I ribozyme

An allosteric ribozyme consisting of a metabolite-sensing riboswitch and a group I self-splicing ribozyme was recently found in the pathogenic bacterium Clostridium difficile. The riboswitch senses the bacterial second messenger c-di-GMP, thereby controlling 5'-splice site choice by the downstream ribozyme. The proximity of this allosteric ribozyme to the open reading frame (ORF) for CD3246 suggests that coenzyme-mediated regulation of splicing controls expression of this putative virulence gene. In the presence of c-di-GMP, the allosteric ribozyme in the CD3246 precursor transcript generates a spliced transcript that retains the riboswitch aptamer. In the absence of c-di-GMP, the ribozyme mediates an alternative GTP attack that results in a truncated transcript (alternative GTP-attack product). Using reporter assays in Escherichia coli, we investigated the difference in gene expression between the spliced product and the alternative GTP-attack product. We provide evidence that CD3246 gene expression is activated if allosteric ribozyme splicing creates a ribosome binding site (RBS) for translation from a UUG start codon. In addition, biochemical and genetic analyses reveal that the riboswitch may further control CD3246 expression by revealing or occluding this newly formed RBS. Therefore, this architecture provides the riboswitch with a mechanism for extended regulation after splicing has occurred or as a backup mechanism for suppression of translation in the event of misregulated splicing.

A General control mechanism of energy flow in the excited state of polyenic biochromophores

Quantum dynamics in photobiology is a highly controversial subject of modern research. In particular, the role of low-frequency vibrational coherence of biochromophores has been intensely discussed. Coherent control of polyenic chromophores, like carotenoids and retinoids, has been showing that the manipulation of such low frequency coherences may play a crucial role in the evolution of excited population and therefore in the efficiency of photosynthesis. However, no precise control mechanism has been derived. In order to clarify this open question, we combined quantum dynamical modelling with a sensitive experimental technique, namely Pump-Degenerate Four Wave Mixing (Pump-DFWM). In this work we investigate in detail the internal conversion channel of beta-carotene, an important polyenic chromophore, under multipulse excitation and focus on the role of the non-adiabatic coupling between excited-state potentials and the internal energy loss. Our control mechanism is based on the interference between wavepackets in the excited state, which leads to a transient evolution of the vibrational population dependent on the relative phase between excitation sub-pulses. Such a transient evolution can affect the branching ratio between competing channels in the excited state. Therefore, our results are able to rationalize pulse shapes found in a whole class of coherent control experiments involving polyenic biochromophores, like in light harvesting complexes and in bacteriorhodopsin.

Transcriptional control mechanisms of genes of lipid and fatty acid metabolism in the Atlantic salmon ( Salmo salar L.) established cell line, SHK-1

The regulatory control mechanisms of lipid and fatty acid metabolism were investigated in Atlantic salmon. We identified sterol regulatory element binding protein (SREBP) genes in salmon and characterised their response, and the response of potential target and other regulatory genes including liver X receptor (LXR), to cholesterol and long-chain polyunsaturated fatty acids (LC-PUFA) in the salmon established cell line, SHK-1. Two cDNAs for SREBPs homologous to mammalian SREBP-1 and SREBP-2 were characterised. We identified three groups of genes whose expression responded differently to the treatments. One group of genes, including cholesterol biosynthetic genes, showed increased expression in response to lipid depletion but supplementary cholesterol or LC-PUFA had no further effect. The expression of a second group of genes belonging to fatty acid biosynthetic pathways, included fatty acid synthase, Δ6 and Δ5 fatty acyl desaturases, also increased after lipid depletion but this was negated by cholesterol or by LC-PUFA supplementation. The expression of a third group of genes including acyl-CoA oxidase, HMG-CoA reductase and Elovl5 elongase was increased by cholesterol treatment but was not affected by lipid depletion or by LC-PUFA. This same pattern of expression was also shown by liver X receptor (LXR), indicating that acyl-CoA oxidase, HMG-CoA reductase and Elovl5 are possible direct targets of LXR. This suggests that salmon Elovl5 may be regulated differently from mammalian Elovl5, which is an indirect target of LXR, responding to LXR-dependent increases in SREBP-1.

Target sequences for microRNAs within the Tff gene cluster

Despite the increasing interest focusing on control of gene activity by microRNAs this abundant class of thousands of regulatory transcripts still requires elucidation of open questions concerning selection of targets and mechanisms of complementarity, multiplicity and cooperativity of microRNAs, to name some immediate issues. In silico microRNA target prediction is often the first line of approaching the complex system and helping in setting search priorities for experimental validation of such mechanisms of gene control. We now used a well studied gene cluster coding for the trefoil peptide family (Tff1, Tff2, Tff3) with all its sequence data and information on factors driving gene expression and a combined computer-based set of target prediction programs to collect microRNAs involved in Tff gene regulation. The sequence preference of specific microRNAs was mapped and their multiplicity and cooperativity were denoted to establish an interactive regulatory profile. This computational venue will subsequently allow enhanced and specific in vitro confirmation of the regulatory networks in cellular systems and possibly later on in transgenic animal models.

The Role of the Left Head of Caudate in Suppressing Irrelevant Words

Suppressing irrelevant words is essential to successful speech production and is expected to involve general control mechanisms that reduce interference from task-unrelated processing. To investigate the neural mechanisms that suppress visual word interference, we used fMRI and a Stroop task, using a block design with an event-related analysis. Participants indicated with a finger press whether a visual stimulus was colored pink or blue. The stimulus was either the written word "BLUE," the written word "PINK," or a string of four Xs, with word interference introduced when the meaning of the word and its color were "incongruent" (e.g., BLUE in pink hue) relative to congruent (e.g., BLUE in blue) or neutral (e.g., XXXX in pink). The participants also made color decisions in the presence of spatial interference rather than word interference (i.e., the Simon task). By blocking incongruent, congruent, and neutral trials, we identified activation related to the mechanisms that suppress interference as that which was greater at the end relative to the start of incongruency. This highlighted the role of the left head of caudate in the control of word interference but not spatial interference. The response in the left head of caudate contrasted to bilateral inferior frontal activation that was greater at the start than at the end of incongruency, and to the dorsal anterior cingulate gyrus which responded to a change in the motor response. Our study therefore provides novel insights into the role of the left head of caudate in the mechanisms that suppress word interference.

Lightweight Encryption of Hierarchical Access Control Mechanism Key Using Tribes of Farey Fractions and its Analysis

In this paper we propose a mechanism to develop a lightweight encryption technique. We encrypt hierarchical single key-lock access control mechanism key by encoding key (key number). Key number is derived using Chinese reminder theorem and tribes of Gaussian or rational Farey fractions are used to encode the key number. The advantages of the proposed mechanism are i) no decoding overhead as access rights are derived without decoding the encoded the key number, ii) no need to derive the key number for already existing files. Hence this method secures access control system by encoding the key number and acts as a thin layer of security; however the performance of retrieval system remains unchanged. General Terms Access control mechanism, Cryptography, Network Security.

A nuclear targeting system in Plasmodium falciparum

BackgroundThe distinct differences in gene control mechanisms acting in the nucleus between Plasmodium falciparum and the human host could lead to new potential drug targets for anti-malarial development. New molecular toolkits are required for dissecting molecular machineries in the P. falciparum nucleus. One valuable tool commonly used in model organisms is protein targeting to specific sub-cellular locations. Targeting proteins to specified locations allows labeling of organelles for microscopy, or testing of how the protein of interest modulates organelle function. In recent years, this approach has been developed for various malaria organelles, such as the mitochondrion and the apicoplast. A tool for targeting a protein of choice to the P. falciparum nucleus using an exogenous nuclear localization sequence is reported here.MethodsTo develop a nuclear targeting system, a putative nuclear localization sequence was fused with green fluorescent protein (GFP). The nuclear localization sequence from the yeast transcription factor Gal4 was chosen because of its well-defined nuclear localization signal. A series of truncated Gal4 constructs was also created to narrow down the nuclear localization sequence necessary for P. falciparum nuclear import. Transfected parasites were analysed by fluorescent and laser-scanning confocal microscopy.ResultsThe nuclear localization sequence of Gal4 is functional in P. falciparum. It effectively transported GFP into the nucleus, and the first 74 amino acid residues were sufficient for nuclear localization.ConclusionsThe Gal4 fusion technique enables specific transport of a protein of choice into the P. falciparum nucleus, and thus provides a tool for labeling nuclei without using DNA-staining dyes. The finding also indicates similarities between the nuclear transport mechanisms of yeast and P. falciparum. Since the nuclear transport system has been thoroughly studied in yeast, this could give clues to research on the same mechanism in P. falciparum.

Allosteric Mechanism of Pyruvate Kinase from Leishmania mexicana Uses a Rock and Lock Model

Allosteric regulation provides a rate management system for enzymes involved in many cellular processes. Ligand-controlled regulation is easily recognizable, but the underlying molecular mechanisms have remained elusive. We have obtained the first complete series of allosteric structures, in all possible ligated states, for the tetrameric enzyme, pyruvate kinase, from Leishmania mexicana. The transition between inactive T-state and active R-state is accompanied by a simple symmetrical 6 degrees rigid body rocking motion of the A- and C-domain cores in each of the four subunits. However, formation of the R-state in this way is only part of the mechanism; eight essential salt bridge locks that form across the C-C interface provide tetramer rigidity with a coupled 7-fold increase in rate. The results presented here illustrate how conformational changes coupled with effector binding correlate with loss of flexibility and increase in thermal stability providing a general mechanism for allosteric control.

Numbers on the edges: A simplified and scalable method for quantifying the Gene Regulation Function

The gene regulation function (GRF) provides an operational description of a promoter behavior as a function of the concentration of one of its transcriptional regulators. Behind this apparently trivial definition lies a central concept in biological control: the GRF provides the input/output relationship of each edge in a transcriptional network, independently from the molecular interactions involved. Here we discuss how existing methods allow direct measurement of the GRF, and how several trade-offs between scalability and accuracy have hindered its application to relatively large networks. We discuss the theoretical and technical requirements for obtaining the GRF. Based on these requirements, we introduce a simplified and easily scalable method that is able to capture the significant parameters of the GRF. The GRF is able to predict the behavior of a simple genetic circuit, illustrating how addressing the quantitative nature of gene regulation substantially increases our comprehension on the mechanisms of gene control.