The stem cell leukaemia (SCL) gene: a critical regulator of haemopoietic and vascular development.
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Animals↗
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Functional evaluation of serine/threonine residues in the P-Loop of Rhodobacter sphaeroides phosphoribulokinase.
The N-terminal region of phosphoribulokinase (PRK) has been proposed to contain a "P-loop" or "Walker A" motif. In Rhodobacter sphaeroides PRK, four alcohol side chains, contributed by S14, T18, S19, and T20, map within the P loop and represent potential Mg-ATP ligands. Each of these has been individually replaced with an alanine and the impact of these substitutions on enzyme-ATP interactions and overall catalytic efficiency evaluated. Each mutant PRK retains the ability to tightly bind the positive effector, NADH (0.7-0.9 per site), and exhibits allosteric activation, suggesting that the proteins retain a high degree of structural integrity. Similarly, each mutant PRK retains the ability to stoichiometrically (0.7-1.2 per site) bind the alternative substrate trinitrophenyl-ATP. Despite the large size of the PRK oligomer (8 x 32 kDa), (31)P NMR can be used to detect stoichiometrically bound Mg-ATP substrate, which produces markedly broadened peaks in comparison with signals from unbound Mg-ATP. Elimination of alcohol substituents in mutants T18A, S19A, or T20A produces enzymes which retain the ability to form stable PRKMg-ATP complexes. Each mutant complex is characterized by (31)P resonances for alpha- and gamma-phosphoryls of bound Mg-ATP which are narrower than measured for wild-type PRKMg-ATP; signals for the beta-phosphoryl are poorly detectable for mutant PRKMg-ATP complexes. Kinetic characterization indicates that these mutants differ markedly with respect to catalytic activity. T20A exhibits V(m) comparable to wild-type PRK, while V(m) is diminished by 8-fold for T18A and by 40-fold for S14A. In contrast to these modest effects, S19A exhibits decreases in V(m) and V(m)/K(Ru5P) of 500-fold and >15000-fold, respectively. S19A and T18A exhibit only modest (6-7-fold) increases in S(1/2) for ATP but larger (30-45-fold) increases in K(m) for Ru5P. K(I) values for the competitive inhibitor, 6-phosphogluconate, do not significantly change upon mutation of T18 or S19, suggesting that these residues are not crucial to Ru5P binding. A role for the alcohol group of S19, the eighth residue in P-loop motif, as a ligand to the Mg-ATP substrate seems compatible with the characterization data; adjacent alcohols do not efficiently function as surrogates. Such a proposed function for S19 is compatible with its proximity to E131, the acidic residue in a putative Walker B motif and probable second Mg-ATP ligand in PRK's active site.
Adenosine Triphosphate↗
Probing the mechanism of ATP hydrolysis and substrate translocation in the AAA protease FtsH by modelling and mutagenesis.
We have built a homology model of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli based on the crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein. The resulting model of the hexameric ring of the ATP-bound form of the AAA ATPase suggests a plausible mechanism of ATP binding and hydrolysis, in which invariant residues of Walker motifs A and B and the second region of homology, characteristic of the AAA ATPases, play key roles. The importance of these invariant residues was confirmed by site-directed mutagenesis. Further modelling suggested a mechanism by which ATP hydrolysis alters the conformation of the loop forming the central hole of the hexameric ring. It is proposed that unfolded polypeptides are translocated through the central hole into the protease chamber upon cycles of ATP hydrolysis. Degradation of polypeptides by FtsH is tightly coupled to ATP hydrolysis, whereas ATP binding alone is sufficient to support the degradation of short peptides. Furthermore, comparative structural analysis of FtsH and a related ATPase, HslU, reveals interesting similarities and differences in mechanism.
ATP-Dependent Proteases↗
Structural requirements for the binding of tRNA Lys3 to reverse transcriptase of the human immunodeficiency virus type 1.
Reverse transcription of the human immunodeficiency virus type 1 (HIV-1) RNA genome is primed by the cellular tRNA Lys3 molecule. Packaging of this tRNA primer during virion assembly is thought to be mediated by specific interactions with the reverse transcriptase (RT) protein. Portions of the tRNA molecule that are required for interaction with the RT protein remain poorly defined. We have used an RNA gel mobility shift assay to measure the in vitro binding of purified RT to mutant forms of tRNA Lys3. The anticodon loop could be mutated without eliminating RT recognition. However, mutations in the T psi C stem were found to partially interfere with RT binding, and D arm mutants were completely inactive in RT binding. Interestingly, binding of the RT protein to tRNA Lys3 facilitates the subsequent annealing of template strand to the 3'-terminus of the tRNA molecule. Consistent with this finding, we demonstrate that mutant HIV-1 virions lacking the RT protein do contain a viral RNA genome without an associated tRNA Lys3 primer. We also found that a preformed primer tRNA-template complex is efficiently recognized by RT protein in vitro. Extension of the template molecule over the T psi C loop did result in complete inhibition of RT binding, suggesting the presence of additional recognition elements in the T psi C loop. These results, combined with a comparative sequence analysis of tRNA species present in HIV-1 virions and RNA motifs selected in vitro for high affinity RT binding, suggest that RT recognizes the central domain of the tRNA tertiary structure, which is formed by interaction of the D and T psi C loops.
Base Sequence↗
SCOR: Structural Classification of RNA, version 2.0.
SCOR, the Structural Classification of RNA (http://scor.lbl.gov), is a database designed to provide a comprehensive perspective and understanding of RNA motif three-dimensional structure, function, tertiary interactions and their relationships. SCOR 2.0 represents a major expansion and introduces a new classification organization. The new version represents the classification as a Directed Acyclic Graph (DAG), which allows a classification node to have multiple parents, in contrast to the strictly hierarchical classification used in SCOR 1.2. SCOR 2.0 supports three types of query terms in the updated search engine: PDB or NDB identifier, nucleotide sequence and keyword. We also provide parseable XML files for all information. This new release contains 511 RNA entries from the PDB as of 15 May 2003. A total of 5880 secondary structural elements are classified: 2104 hairpin loops and 3776 internal loops. RNA motifs reported in the literature, such as 'Kink turn' and 'GNRA loops', are now incorporated into the structural classification along with definitions and descriptions.
Animals↗
The molecular biology of pediatric lymphomas.
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Cell Lineage↗
Development of the Drosophila olfactory sense organs utilizes cell-cell interactions as well as lineage.
We have examined the mechanisms underlying the development of the olfactory sense organs on the third segment of the antenna of Drosophila. Our studies suggest that a novel developmental strategy is employed. Specification of the founder or precursor cell is not governed by the genes of the achaete-scute complex. Another basic helix-loop-helix encoding gene, atonal, is essential for determination of only a subset of the sensilla types--the sensilla coeloconica. Therefore, we predict the existence of additional proneural genes for the selection of sensilla trichoidea and sensilla basiconica. The choice of a founder cell from the presumed proneural domain is regulated by Notch activity. Soon after delamination of the founder cell, two to three additional neighboring cells also take on a sensory fate and these cells together form a presensillum cluster. The selection of neighbors does not occur when endocytosis is blocked using a temperature sensitive allele of shibire, thus suggesting that cell-cell communication is required for this step. The cells of the cluster divide once before terminal differentiation which is influenced by Notch activity. The final cell number within each sensillum is controlled by programmed cell death.
Animals↗
A proline-rich region of the third intracellular loop imparts phenotypic beta 1-versus beta 2-adrenergic receptor coupling and sequestration.
beta-Adrenergic receptor (beta AR) subtypes differ not only by characteristic ligand affinities but also in the manner and extent to which they mediate agonist-promoted events such as activation of adenylyl cyclase and receptor sequestration. We utilized mutagenesis and recombinant expression in Chinese hamster fibroblasts to examine the effect of an unusual proline-rich 24-amino acid sequence (PARPPSPSPSPVPAPAPPPGPPRP) present in the third intracellular loop of the beta 1AR, but not in the beta 2AR, on the aforementioned receptor-mediated events. Cells expressing the wild-type beta 2AR stimulated adenylyl cyclase in response to the agonist isoproterenol with an EC50 approximately 5-fold lower than that observed with the beta 1AR (0.53 +/- 0.14 versus 2.47 +/- 0.52 nM, p < 0.01). Deletion of the proline-rich sequence from the beta 1AR resulted in an improvement in isoproterenol-stimulated adenylyl cyclase to an EC50 value intermediate to that observed in the wild-type receptors (1.14 +/- 0.08 nM, p < 0.05 versus wild-type beta 1AR). In contrast, insertion of this sequence into the beta 2AR impaired its ability to mediate this process. Similar results were observed for receptor sequestration. Wild-type beta 1-and beta 2AR underwent maximal agonist-promoted sequestration of 25.9 +/- 4.0 and 60.0 +/- 3.3%, respectively. Deletion of the proline-rich region from the beta 1AR improved maximal sequestration to 43.0 +/- 2.7% (p < 0.01 versus wild-type beta 1AR), while insertion of the sequence into the beta 2AR impaired sequestration to 33.9 +/- 2.7% (p < 0.001 versus wild-type beta 2AR). We conclude that the distinct phenotypic patterns observed for these two agonist-promoted events in the beta 1AR and beta 2AR subtypes are partially due to the conformational effects of this proline-rich third intracellular loop sequence. Such regions, which are also found in some other G-protein-coupled receptors, may represent a general motif responsible for attenuating certain agonist-promoted receptor events.
Adenylyl Cyclases↗
Kinetics of E2A basic helix-loop-helix-protein expression during myelopoiesis and primary B cell differentiation.
The DNA-binding factors encoded by the E2A gene, which include the basic helix-loop-helix proteins E12 and E47, are thought to regulate Ig gene expression. In the rat these factors are products of the Pan locus and are referred to as Pan-2 and Pan-1, respectively. To determine when during B cell differentiation Pan (E2A) DNA-binding proteins are first expressed, cells from a newly developed rat long term lymphoid bone marrow culture system were analyzed molecularly and phenotypically using a newly defined anti-Pan mAb. The data indicate that Pan-expressing cells appear in B cell progenitors before the appearance of the CD45R B lineage-associated Ag or microH chain protein. The results also indicate that Pan proteins are present in cells that had undergone D-JH rearrangements. Finally, although Pan (E2A) proteins are present in myeloid precursors, expression is extinguished as differentiation into mature myeloid cells occurs.
Animals↗
Discrimination of subtype B and non-subtype B strains of human immunodeficiency virus type 1 by serotyping: correlation with genotyping.
The ability of a peptide-based serotyping assay to differentiate human immunodeficiency virus (HIV) type 1 (HIV-1) subtype B infections from non-subtype B infections was investigated with 166 anti-HIV-1- and HIV RNA-positive (by PCR) serum or plasma specimens. The specimens were divided genetically into those infected with subtype B and non-subtype B by application of a screening heteroduplex mobility assay (HMA) that used plasmids for subtypes A and B alone. Specimens that were not clearly infected with HIV-1 subtype B by HMA or for which the two methods had discordant results in distinguishing those infected with subtype B from those infected with non-subtype B were then investigated with a full HMA plasmid panel and, for selected specimens, env sequencing. For the 141 genotyped and serotypically reactive specimens, the correlation between genotyping and serotyping (all subtypes) was 69%. Of the 67 specimens that reacted monotypically as serotype B, 64 were shown to be infected with genotype B (positive predictive value, 96%). Of the 82 specimens that contained genotype B nucleic acid, 64 reacted monotypically as serotype B (sensitivity, 78%), and 4 specimens reacted with a single non-subtype B peptide; the viruses in 14 specimens could not be assigned a serotype. Initial screening results had indicated that 12 samples had results discordant between restricted HMA and serotyping. The V3 loop amino acids of the infecting HIV strains from the seven specimens with discordant serology results were analyzed. For five specimens discordance occurred when the amino acid sequence of the infecting virus closely resembled those of more than one consensus peptide antigen or when the observed V3 crown motif of the strain was atypical for the genetic subtype present. For the other two specimens no explanation for the discordance was identified. Five specimens gave unclear or discordant results in the initial HMA screen, but the results were resolved when the full plasmid panel was used. Serotyping, although of limited sensitivity, distinguishes between subtype B and non-subtype B infections with a high degree of specificity. However, it poorly differentiates the major non-subtype B subtypes, particularly subtypes A and C. When HIV-1 subtype B predominates, serological typing and/or subtype-restricted HMA screening usefully distinguishes between subtype B and non-subtype B infections.
Amino Acid Sequence↗
Two non-contiguous regions contribute to nidogen binding to a single EGF-like motif of the laminin gamma 1 chain.
High affinity binding of nidogen to laminin is mediated by an EGF-like repeat gamma 1III4 of the mouse laminin gamma 1 chain and has now been restricted to two short noncontiguous regions of its 56 residue sequence by use of synthetic peptides and recombinant mutants. Disulfide loop a,b of the repeat and a modified loop a,c could completely inhibit binding, with a 5000-fold or 300-fold reduced affinity respectively. Synthetic loops c and d lacked inhibitory activity. Some binding contribution of Tyr819 in loop c was, however, shown by mutation and side chain modification. Together with studies of loop chimeras, this indicated a distinct cooperativity between the two binding sites. The major binding site of loop a was localized to the heptapeptide NIDPNAV (position 798-804). A change of Asp800 to Asn or Ala803 to Val caused a strong reduction in binding activity, while only small effects were observed for the changes Pro801 to Gln and Ile799 to Val. The latter replacement corresponds to the single substitution found in the same region of the Drosophila laminin gamma 1 chain. However, the changes Asn802 to Ser or Val804 to Ser, both known to exist in the laminin gamma 2 chain, were deleterious mutations. This demonstrated conservation of binding structures in laminins of distantly related species, but not between homologous chains of laminin isoforms.
Amino Acid Sequence↗
The E2A and tal-1 helix-loop-helix proteins associate in vivo and are modulated by Id proteins during interleukin 6-induced myeloid differentiation.
The immunoglobulin enhancer-binding proteins, E12 and E47, encoded by the E2A gene belong to the basic helix-loop-helix (bHLH) family of regulatory proteins and act as transcriptional activators. In addition to their critical role in B-lymphocyte development, the E12 and E47 proteins have been implicated in the induction of myogenesis as heterodimeric partners of myogenic bHLH proteins, MyoD and myogenin. Here we demonstrate that the E2A proteins form heterodimers with the bHLH oncoprotein tal-1 in myeloid and erythroid cells and that these heterodimers specifically bind to the CANNTG DNA motif. Heterodimerization with tal-1 represses transactivation by E47 and could function to prevent the expression of immunoglobulin genes in cells other than B lymphocytes. DNA binding by E2A-tal-1 heterodimers in the M1 mouse myeloid cell line is abrogated upon terminal macrophage differentiation induced by the cytokine interleukin 6. The loss of E2A-tal-1 DNA binding is correlated with elevated expression of mRNA encoding the dominant negative HLH proteins, Id1 and particularly Id2. Moreover, recombinant Id proteins inhibit the E2A-tal-1-specific DNA binding activity from undifferentiated M1 cells. These results suggest that E2A-tal-1 heterodimers may play a role in preventing terminal differentiation in the myeloid lineage and provide a possible explanation for oncogenic transformation induced by ectopic tal-1 expression in acute T-cell lymphoblastic leukemias.
Animals↗
Furin-induced cleavage and activation of Shiga toxin.
Shiga toxin has a single A subunit non-covalently associated with a pentamer of B subunits. The toxin has a trypsin-sensitive region near the COOH-terminal end of the A-chain, and upon cleavage, two disulfide bonded fragments, A1 and A2, are generated. These fragments are also formed upon incubation with cells. The disulfide loop contains the sequence (Arg-X-X-Arg), which is a consensus motif for cleavage by the membrane-anchored protease furin. We found that a soluble form of furin cleaves intact A-chain producing A1 and A2 fragments, and furin also seems to be responsible for rapid cellular cleavage of Shiga toxin. LoVo cells, which normally do not produce functional furin, cleave intact A-chain very efficiently when transfected with furin (LoVo/fur), whereas a control cell (LoVo/neo) cleaves the toxin very slowly. To investigate the role of this cleavage for intoxication of cells, we studied the ability of unnicked and furin-nicked toxin to inhibit protein synthesis in LoVo/fur and LoVo/neo cells. LoVo/fur cells were intoxicated equally well with unnicked and nicked toxin, whereas in LoVo/neo cells nicked toxin was about 20 times more active than unnicked toxin. The results suggest that cleavage of Shiga toxin is important for intoxication of cells, and they indicate that furin can cleave and thereby activate Shiga toxin in cells.
Amino Acid Sequence↗
A zinc-binding domain is required for targeting the maternal nuclear protein PwA33 to lampbrush chromosome loops.
In oocytes of the newt Pleurodeles waltl, the maternal nuclear protein PwA33 occurs on the lampbrush chromosomes and in some nucleoplasmic particles of the germinal vesicle. PwA33 is a modular protein and we used site-directed mutagenesis to alter the sequences encoding two metal-binding regions, the C3HC4 (or RING finger) and B-box motifs. Several mutant clones were generated and their synthetic transcripts were injected into Pleurodeles oocytes for in vivo analysis. In the oocyte, all translation products localized in the germinal vesicle. Proteins encoded by RING finger mutant clones were distributed in a pattern identical to that of the wild type protein, but when His266 of the B-box was mutated, PwA33 failed to localize in the lampbrush chromosomes and the nucleoplasmic particles. Using an in vitro colorimetric assay, we demonstrated that PwA33 is a zinc-binding protein and that mutations in the RING finger and B-Box altered its metal-binding properties. The RING finger motif bound two Zn2+ ions and the binding ratios of several mutants were consistent with the tertiary structure recently proposed for this motif. The B-box coordinated one Zn2+ and this binding was inhibited by the His266 mutation. The failure of the His266 mutation to bind zinc and to localize properly within the germinal vesicle suggests that an intact B-box is required for normal functioning of the PwA33 protein in the oocyte.
Amino Acid Sequence↗
A HANDful of questions: the molecular biology of the heart and neural crest derivatives (HAND)-subclass of basic helix-loop-helix transcription factors.
The HAND subclass of basic Helix-loop-helix factors is comprised of two members HAND1 and HAND2. HAND genes are present within the genomes of organisms ranging from flies to man. Experiments employing chick embryology, tissue culture, and gene targeting in mice show that HAND function is critical for the specification and/or differentiation of extraembryonic structures that include the yolk sac, placenta, and the cells of the trophoblast lineages. HAND factors also play key roles in cardiac, gut, sympathetic neuronal development and in the proper development of tissues populated by HAND-expressing neural crest cells, including regions of the developing vasculature, the limbs, the jaw, and teeth. Surprisingly, nearly 10 years after their initial identification and characterization, little is understood about the nature of the downstream target genes which HAND1 and HAND2 regulate, whether the nature of their transcriptional regulation is positive or negative, or if they modulate genetic programs common to these diverse tissue types or if they drive unique subsets of genes that contribute to tissue identity. At the core of these questions is by which mechanisms do HAND factors modulate biological activity? Do they behave like classical class B bHLH factors or is their function more complex requiring a rethinking of the dogma? What follows is a review of what is currently known about HAND factors and a reflection on why elucidating their role in the biological programs within which they participate has been so difficult.
Amino Acid Sequence↗
E-proteins directly regulate expression of activation-induced deaminase in mature B cells.
Activated mature B cells in which the DNA-binding activity of E-proteins has been disrupted fail to undergo class switch recombination. Here we show that activated B cells overexpressing the antagonist helix-loop-helix protein Id3 do not induce expression of the murine Aicda gene encoding activation-induced deaminase (AID). A highly conserved intronic regulatory element in Aicda binds E-proteins both in vitro and in vivo. The transcriptional activity of this element is regulated by E-proteins. We show that the enforced expression of AID in cells overexpressing Id3 partially restores class switch recombination. Taken together, our observations link helix-loop-helix activity and Aicda gene expression in a common pathway, in which E-protein activity is required for the efficient induction of Aicda transcription.
Animals↗
Id1 regulation of cellular senescence through transcriptional repression of p16/Ink4a.
The Id family of helix-loop-helix (HLH) transcriptional regulatory proteins does not possess a basic DNA-binding domain and functions as a negative regulator of basic HLH transcription factors. Id proteins coordinate cell growth and differentiation pathways within mammalian cells and have been shown to regulate G(1)-S cell-cycle transitions. Although much recent data has implicated Id1 in playing a critical role in modulating cellular senescence, no direct genetic evidence has been reported to substantiate such work. Here we show that Id1-null primary mouse embryo fibroblasts undergo premature senescence despite normal growth profiles at early passage. These cells possess increased expression of the tumor-suppressor protein p16/Ink4a but not p19/ARF, and have decreased cyclin-dependent kinase (cdk) 2 and cdk4 kinase activity. We also show that Id1 is able to directly inhibit p16/Ink4a but not p19/ARF promoter activity via its HLH domain, and that Id1 inhibits transcriptional activation at E-boxes within the p16/Ink4a promoter. Our data provide, to our knowledge, the first genetic evidence for a role for Id1 as an inhibitor of cellular senescence and suggest that Id1 functions to delay cellular senescence through repression of p16/Ink4a. Because epigenetic and genetic abrogation of p16/Ink4a function has been implicated in the evolution of several human malignancies, we propose that transcriptional regulation of p16/Ink4a may also provide a mechanism for the dysregulation of normal cellular growth controls during the evolution of human malignancies.
Animals↗
Herpes simplex virus 1 alpha regulatory protein ICP0 functionally interacts with cellular transcription factor BMAL1.
The infected cell protein no. 0 (ICP0) of herpes simplex virus 1 (HSV-1) is a promiscuous transactivator shown to enhance the expression of gene introduced into cells by infection or transfection. At the molecular level, ICP0 is a 775-aa ring finger protein localized initially in the nucleus and late in infection in the cytoplasm and mediates the degradation of several proteins and stabilization of others. None of the known functions at the molecular level account for the apparent activity of ICP0 as a transactivator. Here we report that ICP0 functionally interacts with cellular transcription factor BMAL1, a member of the basic helix-loop-helix PER-ARNT-SIM (PAS) super family of transcriptional regulators. Specifically, sequences mapped to the exon II of ICP0 interacted with BMAL1 in the yeast two-hybrid system and in reciprocal pull-down experiments in vitro. Moreover, the enhancement of transcription of a luciferase reporter construct whose promoter contained multiple BMAL1-binding sites by ICP0 and BMAL1 was significantly greater than that observed by ICP0 or BMAL1 alone. Although the level of BMAL1 present in nuclei of infected cells remained unchanged between 3 and 8 h after infection, the level of cytoplasmic BMAL1 was reduced at 8 h after infection. The reduction of cytoplasmic BMAL1 was significantly greater in cells infected with the ICP0-null mutant than in the wild-type virus-infected cells, suggesting that ICP0 mediates partial stabilization of the protein. These results indicate that ICP0 interacts physically and functionally with at least one cellular transcription-regulatory factor.
ARNTL Transcription Factors↗