Analysis of Urs(g)-Mediated Glucose Repression of the Gal1 Promoter of Saccharomyces Cerevisiae

Repression of GAL1 expression during growth on glucose is mediated in part by cis-acting promoter elements designated URSG. We show that oligonucleotides containing sequences from two regions of URSG confer glucose repression upon a heterologous promoter. Repression caused by URSG is dependent on trans-acting factors of the glucose repression pathway and is independent of orientation or location within a promoter, suggesting that URSG contains binding sites for a glucose-activated repressor protein(s). Genetic analysis identified three apparently novel genes (URR1, URR3 and URR4) that are specifically required for URSG-mediated repression and may encode such repressor proteins. Mutations in the URR genes suppress the defect in URSG derepression caused by a snf1 mutation.     

LysM结构域及其与植物-真菌相互作用的关系

在长期的进化过程中,植物与真菌之间形成了复杂而又紧密的联系,其中最主要的就是侵染与防御的关系。植物的抗病性由于涉及农作物、林木的生长与产量,逐渐成为研究热点。在植物免疫系统中,对病原真菌的识别是一个重要环节。目前认为在这一过程中,LysM结构域起到了极为关键的作用。植物细胞膜上有含LysM结构域的识别受体,该受体可以结合真菌细胞壁上的几丁质,并将信号传递到胞内,从而启动免疫反应。在真菌中,同样具有含LysM结构域的基因,主要是一类效应因子。它们可能参与真菌在侵染过程中的"伪装",以逃避植物的识别。该文以LysM结构域在植物-真菌相互作用中扮演的角色为着眼点,讨论有关研究的意义与趋势,并对如何利用LysM结构域的相关研究进行有效的抗病育种提出了新的设想。     

Roles of the Catalytic Domain and Two Cellulose Binding Domains of Thermomonospora fusca E4 in Cellulose Hydrolysis

Thermomonospora fusca E4 is an unusual 90.4-kDa endocellulase comprised of a catalytic domain (CD), an internal family IIIc cellulose binding domain (CBD), a fibronectinlike domain, and a family II CBD. Constructs containing the CD alone (E4-51), the CD plus the family IIIc CBD (E4-68), and the CD plus the fibronectinlike domain plus the family II CBD (E4-74) were made by using recombinant DNA techniques. The activities of each purified protein on bacterial microcrystalline cellulose (BMCC), filter paper, swollen cellulose, and carboxymethyl cellulose were measured. Only the whole enzyme, E4-90, could reach the target digestion of 4.5% on filter paper. Removal of the internal family IIIc CBD (E4-51 and E4-74) decreased activity markedly on every substrate. E4-74 did bind to BMCC but had almost no hydrolytic activity, while E4-68 retained 32% of the activity on BMCC even though it did not bind. A low-activity mutant of one of the catalytic bases, E4-68 (Asp55Cys), did bind to BMCC, although E4-51 (Asp55Cys) did not. The ratios of soluble to insoluble reducing sugar produced after filter paper hydrolysis by E4-90, E4-68, E4-74, and E4-51 were 6.9, 3.5, 1.3, and 0.6, respectively, indicating that the family IIIc CBD is important for E4 processivity.     

Mutations in DNA Binding and Transactivation Domains Affect the Dynamics of Parvovirus NS1 Protein

The multifunctional replication protein of autonomous parvoviruses, NS1, is vital for viral genome replication and for the control of viral protein production. Two DNA-interacting domains of NS1, the N-terminal and helicase domains, are necessary for these functions. In addition, the N and C termini of NS1 are required for activation of viral promoter P38. By comparison with the structural and biochemical data from other parvoviruses, we identified potential DNA-interacting amino acid residues from canine parvovirus NS1. The role of the identified amino acids in NS1 binding dynamics was studied by mutagenesis, fluorescence recovery after photobleaching, and computer simulations. Mutations in the predicted DNA-interacting amino acids of the N-terminal and helicase domains increased the intranuclear binding dynamics of NS1 dramatically. A substantial increase in binding dynamics was also observed for NS1 mutants that targeted the metal ion coordination site in the N terminus. Interestingly, contrary to other mutants, deletion of the C terminus resulted in slower binding dynamics of NS1. P38 transactivation was severely reduced in both N-terminal DNA recognition and in C-terminal deletion mutants. These data suggest that the intranuclear dynamics of NS1 are largely characterized by its sequence-specific and -nonspecific binding to double-stranded DNA. Moreover, binding of NS1 is equally dependent on the N-terminal domain and conserved β-loop of the helicase domain.     

Drosophila CK2 regulates eye morphogenesis via phosphorylation of E(spl)M8

The Notch effector E(spl)M8 is phosphorylated at Ser159 by CK2, a highly conserved Ser/Thr protein kinase. We have used the Gal4-UAS system to assess the role of M8 phosphorylation during bristle and eye morphogenesis by employing a non-phosphorylatable variant (M8SA) or one predicted to mimic the 'constitutively' phosphorylated protein (M8SD). We find that phosphorylation of M8 does not appear to be critical during bristle morphogenesis. In contrast, only M8SD elicits a severe 'reduced eye' phenotype when it is expressed in the morphogenetic furrow of the eye disc. M8SD elicits neural hypoplasia in eye discs, elicits loss of phase-shifted Atonal-positive cells, i.e. the 'founding' R8 photoreceptors, and consequently leads to apoptosis. The ommatidial phenotype of M8SD is similar to that in Nspl/Y; E(spl)D/+ flies. E(spl)D, an allele of m8, encodes a truncated protein known as M8*, which, unlike wild type M8, displays exacerbated antagonism of Atonal via direct protein-protein interactions. In line with this, we find that the M8SD-Atonal interaction appears indistinguishable from that of M8*-Atonal, whereas interaction of M8 or M8SA appears marginal, at best. These results raise the possibility that phosphorylation of M8 (at Ser159) might be required for its ability to mediate 'lateral inhibition' within proneural clusters in the developing retina. This is the first identification of a dominant allele encoding a phosphorylation-site variant of an E(spl) protein. Our studies uncover a novel functional domain that is conserved amongst a subset of E(spl)/Hes repressors in Drosophila and mammals, and suggests a potential role for CK2 during retinal patterning.     

Essential Roles for Mycobacterium tuberculosis Rel beyond the Production of (p)ppGpp

In Mycobacterium tuberculosis, the stringent response to amino acid starvation is mediated by the M. tuberculosis Rel (Rel_Mtb) enzyme, which transfers a pyrophosphate from ATP to GDP or GTP to synthesize ppGpp and pppGpp, respectively. (p)ppGpp then influences numerous metabolic processes. Rel_Mtb also encodes a second, distinct catalytic domain that hydrolyzes (p)ppGpp into pyrophosphate and GDP or GTP. Rel_Mtb is required for chronic M. tuberculosis infection in mice; however, it is unknown which catalytic activity of Rel_Mtb mediates pathogenesis and whether (p)ppGpp itself is necessary. In order to individually investigate the roles of (p)ppGpp synthesis and hydrolysis during M. tuberculosis pathogenesis, we generated Rel_Mtb point mutants that were either synthetase dead (Rel_Mtb^H344Y) or hydrolase dead (Rel_Mtb^H80A). M. tuberculosis strains expressing the synthetase-dead Rel_Mtb^H344Y mutant did not persist in mice, demonstrating that the Rel_Mtb (p)ppGpp synthetase activity is required for maintaining bacterial titers during chronic infection. Deletion of a second predicted (p)ppGpp synthetase had no effect on pathogenesis, demonstrating that Rel_Mtb was the major contributor to (p)ppGpp production during infection. Interestingly, expression of an allele encoding the hydrolase-dead Rel_Mtb mutant, Rel_Mtb^H80A, that is incapable of hydrolyzing (p)ppGpp but still able to synthesize (p)ppGpp decreased the growth rate of M. tuberculosis and changed the colony morphology of the bacteria. In addition, Rel_Mtb^H80A expression during acute or chronic M. tuberculosis infection in mice was lethal to the infecting bacteria. These findings highlight a distinct role for Rel_Mtb-mediated (p)ppGpp hydrolysis that is essential for M. tuberculosis pathogenesis.     

On the mechanism underlying the divergent retinal and bristle defects of M8* (E(spl)D) in Drosophila

Our results, using endogenous mutants and Gal4‐UAS driven transgenes, implicate multisite phosphorylation in repression by E(spl)M8. We propose that these phosphorylations occur in the morphogenetic furrow (MF) to reverse an auto‐inhibited state of M8, enabling repression of Atonal during R8 specification. Our studies address the paradoxical behavior of M8*, the truncated protein encoded by E(spl)D. We suggest that differences in N signaling in the bristle versus the eye underlie the antimorphic activity of M8* in N⁺ (ectopic bristles) and hypermorphic activity in N^spl (reduced eye). Ectopic M8* impairs eye development (in N^spl) only during establishment of the atonal feedback loop (anterior to the MF), but is ineffective after this time point. In contrast, a CK2 phosphomimetic M8 lacking Groucho (Gro) binding, M8SDΔGro, acts antimorphic in N⁺ and suppresses the eye/R8 and bristle defects of N^spl, as does reduced dosage of E(spl) or CK2. Multisite phosphorylation could serve as a checkpoint to enable a precise onset of repression, and this is bypassed in M8*. Additional implications are discussed. genesis 47:456–468, 2009. © 2009 Wiley‐Liss, Inc.     

The two Tribolium E(spl) genes show evolutionarily conserved expression and function during embryonic neurogenesis

Tribolium castaneum is a well-characterised model insect, whose short germ-band mode of embryonic development is characteristic of many insect species and differs from the exhaustively studied Drosophila. Mechanisms of early neurogenesis, however, show significant conservation with Drosophila, as a characteristic pattern of neuroblasts arises from neuroectoderm proneural clusters in response to the bHLH activator Ash, a homologue of Achaete–Scute. Here we study the expression and function of two other bHLH proteins, the bHLH-O repressors E(spl)1 and E(spl)3. Their Drosophila homologues are expressed in response to Notch signalling and antagonize the activity of Achaete–Scute proteins, thus restricting the number of nascent neuroblasts. E(spl)1 and 3 are the only E(spl) homologues in Tribolium and both show expression in the cephalic and ventral neuroectoderm during embryonic neurogenesis, as well as a dynamic pattern of expression in other tissues. Their expression starts early, soon after Ash expression and is dependent on both Ash and Notch activities. They act redundantly, since a double E(spl) knockdown (but not single knockdowns) results in neurogenesis defects similar to those caused by Notch loss-of-function. A number of other activities have been evolutionarily conserved, most notably their ability to interact with proneural proteins Scute and Daughterless.     

Global Profiling of Huntingtin-associated protein E (HYPE)-Mediated AMPylation through a Chemical Proteomic Approach

AMPylation of mammalian small GTPases by bacterial virulence factors can be a key step in bacterial infection of host cells, and constitutes a potential drug target. This posttranslational modification also exists in eukaryotes, and AMP transferase activity was recently assigned to HYPE Filamentation induced by cyclic AMP domain containing protein (FICD) protein, which is conserved from Caenorhabditis elegans to humans. In contrast to bacterial AMP transferases, only a small number of HYPE substrates have been identified by immunoprecipitation and mass spectrometry approaches, and the full range of targets is yet to be determined in mammalian cells. We describe here the first example of global chemoproteomic screening and substrate validation for HYPE-mediated AMPylation in mammalian cell lysate. Through quantitative mass-spectrometry-based proteomics coupled with novel chemoproteomic tools providing MS/MS evidence of AMP modification, we identified a total of 25 AMPylated proteins, including the previously validated substrate endoplasmic reticulum (ER) chaperone BiP (HSPA5), and also novel substrates involved in pathways of gene expression, ATP biosynthesis, and maintenance of the cytoskeleton. This dataset represents the largest library of AMPylated human proteins reported to date and a foundation for substrate-specific investigations that can ultimately decipher the complex biological networks involved in eukaryotic AMPylation.Covalent posttranslational modification (PTM) of hydroxyl-containing amino acids in proteins by adenosine monophosphate (AMP), called AMPylation or adenylylation, was first discovered almost a half century ago as a mechanism controlling the activity of bacterial glutamine synthetase (1). This unusual PTM was unknown in eukaryotes until it was identified in 2009 in the context of bacterial infection, when Yarbrough et al. reported AMPylation of host small GTPases by bacterial virulence factor Vibrio outer protein S (VopS) from Vibrio parahemeolyticus. In this context, AMPylation precludes interactions with downstream binding partners and causes actin cytoskeleton collapse leading to cell death (2). Since then, the field of AMPylation has grown substantially, with reports describing AMPylation activity of other bacterial effectors, like Immunoglobulin binding protein A (IbpA) in Histophilus somni (3) and Defects in Rab1 recruitment protein A (DrrA) in Legionella pneumophila (4). These new bacterial AMPylators share a common substrate class (small GTPases); however, they differed in the identity of their catalytic residues and architecture of their active sites. Accordingly, bacterial AMP transferases have been classified as either filamentation induced by cyclic AMP (FIC) or adenylyl transferase (AT)¹ domain containing enzymes, with catalytic His or Asp residues, respectively.Although adenylylation has been most extensively described in the context of bacterial infection, there is a growing interest in elucidating the scope of this PTM in a native eukaryotic context. Among the ca. 3000 FIC proteins identified so far by sequence alignment, only a single enzyme has been identified in eukaryotes: Huntingtin-associated protein E (HYPE), also known as FICD. HYPE is conserved from C. elegans to humans, and mRNA expression data suggest that it is present at low levels in all human tissues (3). Apart from the catalytic FIC domain, the protein consists of one transmembrane helix and two tetratricopeptide repeat motifs that point to localization at a membrane and amenability toward protein–protein interactions, respectively. We recently added to this picture by solving the first crystal structure of Homo sapiens HYPE (5), illustrating that the only human FIC is substantially different from its bacterial cousins (6, 7). HYPE was shown to form stable asymmetric dimers supported by the extended network of contacts exclusive to the FIC domains, while the tetratricopeptide repeat motifs have a more flexible arrangement and appear to be exposed for protein–protein interactions in the vicinity of the membrane. In addition, we confirmed the similarity of the active site architecture to other FIC proteins for which a crystal structure is available, with the catalytic loop comprising the invariant catalytic His³⁶³ (8), and further substantiated the role of a critical residue Glu²³⁴ in an inhibitory helix (9) that may be responsible for regulating HYPE enzymatic activity.Various catalytic activities have been demonstrated for FIC proteins, including nucleotide (AMP, GMP, and UMP) transfer as well as phosphorylation and phosphocholination (10–13). We and others (3, 5, 14, 15) have demonstrated that HYPE can function in protein AMPylation, although the activity of the wild-type (WT) enzyme is very weak, consistent with active site obstruction by Glu²³⁴. It is hypothesized that this intramolecular inhibition can be relieved by specific but as yet unknown protein–protein interactions or by the removal of the conserved Glu. Indeed, the E234G mutation substantially boosts HYPE''s activity as demonstrated by the elevated auto-AMPylation of HYPE itself (5, 9) and a few of its recently reported substrates, including the ER chaperone BiP in vivo (14, 15) and several histone proteins in vitro (16, 17). HYPE activity was initially implicated in visual neurotransmission in flies (18) and later in regulation of the unfolded protein response (UPR) in transfected cells, although there is limited consensus over the mechanism (14, 15). Most recently, it has been proposed that HYPE activity might have a role in regulation of gene expression; however, the mechanistic details remain to be elucidated (17).AMPylation profiling is not a trivial task (19), and several strategies have emerged over the past few years ranging from labeling with radioactive ATP (2, 3) and immunoprecipitation with AMPylation-specific antibodies (20, 21) to mass spectrometry (MS) approaches focused on AMP fragmentation (22, 23). Although these methods contributed significantly to developments in the field, they also suffer from certain drawbacks, including low sensitivity, high background, limited quantitative power, and limited amenability to high-throughput (HT) substrate identification. In contrast, chemoproteomic strategies involving application of substrate analogues (substrate probes) equipped with small and inert chemical handles in combination with sensitive detection by MS can facilitate rapid visualization and/or robust enrichment of modified proteins and can provide superior performance in HT profiling of numerous challenging PTMs (24). AMPylation-specific substrate probes have been developed, and their robust performance was evaluated in vitro, albeit to date only in the context of bacterial effector-mediated AMPylation (25–27). We previously showed that a bioorthogonal substrate probe (26) is well tolerated in the active site of human HYPE and, moreover, that it has potential for chemoproteomic profiling of HYPE substrates in vitro when combined with ligation through copper-catalyzed azide alkyne cycloaddition (CuAAC) to a dedicated capture reagent decorated with a biotin affinity handle and carboxytetramethylrhodamine (TAMRA) fluorophore (5).Herein, we present the first global AMPylation profile in a native eukaryotic context utilizing a bioorthogonal ATP analogue and chemoproteomic methodology. We first demonstrate efficient enrichment and fast visualization of potential HYPE substrates in cell lysates by in-gel fluorescence, followed by robust identification via shotgun proteomics on a QExactive mass spectrometer. Furthermore, we extensively validate candidate substrates via HYPE titration and ATP competition experiments with a quantitative MS-based readout, as well as Western blotting and direct MS/MS evidence for AMP modification. Finally, we analyze HYPE interaction partners in vivo, providing a link between our discoveries in lysates and a physiologically relevant context, delivering the first experimentally validated library of HYPE substrate proteins.     

P53参与抑制PC-1基因转录的结构域分析

目的:分析P53分子参与抑制PC-1基因转录的结构域。方法:构建P53分子突变体;将前列腺癌LNCaP细胞瞬时转染野生型或突变型p53及含PC-1启动子的荧光素酶表达载体p4939,分析PC-1启动子的转录活性。结果:P53分子N端转录激活域及富含脯氨酸功能域突变体没有减弱对PC-1启动子的转录抑制作用,而特异性DNA结合域上175、273位突变体和C端339～346位氨基酸的缺失突变体都减弱了对PC-1启动子转录的抑制作用;另外P53分子第175和273位突变体在前列腺癌细胞中对野生型P53的转录抑制功能表现出显性负效应。结论:P53分子特异性DNA结合域和C端结构域参与对PC-1基因启动子的转录抑制,而P53突变体的显性负效应可能是PC-1在前列腺癌进展中表达失调的因素之一。     

The Insulin-Like Growth Factor (IGF) Receptor Type 1 (IGF1R) as an Essential Component of the Signalling Network Regulating Neurogenesis

The insulin-like growth factor receptor type 1 (IGF1R) signalling pathway is activated in the mammalian nervous system from early developmental stages. Its major effect on developing neural cells is to promote their growth and survival. This pathway can integrate its action with signalling pathways of growth and morphogenetic factors that induce cell fate specification and selective expansion of specified neural cell subsets. This suggests that during developmental and adult neurogenesis cellular responses to many signalling factors, including ligands of Notch, sonic hedgehog, fibroblast growth factor family members, ligands of the epidermal growth factor receptor, bone morphogenetic proteins and Wingless and Int-1, may be modified by co-activation of the IGF1R. Modulation of cell migration is another possible role that IGF1R activation may play in neurogenesis. Here, I briefly overview neurogenesis and discuss a role for IGF1R-mediated signalling in the developing and mature nervous system with emphasis on crosstalk between the signalling pathways of the IGF1R and other factors regulating neural cell development and migration. Studies on neural as well as on non-neural cells are highlighted because it may be interesting to test in neurogenic paradigms some of the models based on the information obtained in studies on non-neural cell types.     

水稻斑点叶突变体spl101和spl102的筛选及候选基因鉴定

斑点叶突变体是指植物在正常生长条件下叶片或叶鞘上自发形成、且与病原菌侵染产生的病斑类似的一类突变体,筛选并研究斑点叶突变体对揭示植物抗病反应机理具有重要意义。为了进一步研究斑点叶的形成机制,本文通过EMS诱变品种宽叶粳(KYJ),筛选得到两个斑点叶突变体spl101和spl102。这两个突变体在生长发育晚期(抽穗期以后)形成严重的类病斑。遗传分析表明,spl101和spl102均受隐性单基因控制。利用Mutmap方法对候选基因进行克隆,结果显示,spl101和spl102的候选基因均为OsEDR1,该基因与类病斑发生有关。在spl101中,OsEDR1基因突变发生在第6外显子和第6内含子的交接处,该突变导致第6内含子的错误识别,最终造成移码突变。在spl102中,OsEDR1基因突变发生在第10外显子上,导致一个苯丙氨酸(F)变成半胖氨酸(C)。因此,本研究鉴定了两个新的OsEDR1等位突变,对OsEDR1抗病反应机理的进一步研究及丰富水稻种质资源具有积极意义。同时验证了利用Mutmap方法克隆水稻突变基因的有效性。