Massimo Malcovati

[27] AMP- and fructose 1,6-bisphosphate-activated pyruvate kinases from Escherichia coli

Publisher Summary This chapter presents an assay method, purification, and properties of AMP- and fructose 1,6-bisphosphate-activated pyruvate kinases from Escherichia coli . Two noninterconvertible forms of pyruvate kinase are detected in Escherichia coli. Both show positive cooperative effects with respect to the substrate phosphoenolpyruvate; one of them is activated by fructose 1,6-bisphosphate and inhibited by ATP and succinyl-CoA, whereas the second is activated by AMP and by several intermediates of the hexose phosphate pathway. The approaches successfully used for the continuous assay of E. coli pyruvate kinase include both direct and coupled methods. The chapter discusses the lactate dehydrogenase coupled assay, because it is the most widely used and requires minimal amount of enzyme. The different physical and kinetic properties of the two forms of pyruvate kinase from E. coli allow differential assay in crude extracts containing both. The purification steps involved include preparation of the crude extract and diethylaminoethyl (DEAE)-cellulose chromatography. Further purification of type 1 pyruvate kinase is done following heat treatment, affinity chromatography on phosphocellulose, Sephacryl S-200 chromatography, and DEAE-Sephadex chromatography. Further purification of type II pyruvate kinase involves affinity chromatography on phosphocellulose and DEAE-Sephadex chromatography.

Evidence Against a Major Role for Integrins in Calcium-Dependent Intercellular Adhesion of Epidermal Keratinocytes

It is well established that integrins mediate keratinocyte adhesion to extracellular matrix proteins, but, in addition, there is some evidence that they mediate intercellular adhesion. We have investigated the role of integrins in keratinocyte-keratinocyte adhesion by adding anti-integrin antibodies to cells in three assays that differ according to the calcium ion concentration of the medium, the presence or absence of an adhesive substrate (glass or tissue culture plastic) and the timing of antibody addition. As previously reported by Larjava et al., (J. Cell Biol. 110:803-815), a monoclonal antibody to the beta 1 subunit perturbed cell-cell adhesion when added to adherent monolayers in low calcium medium (0.1 mM calcium ions), but did not prevent cell-cell adhesion or stratification induced by raising the level of calcium ions to 1.8mM (the concentration in standard medium). Monoclonal antibodies to both the alpha 3 and beta 1 subunits inhibited the attachment, spreading and motility of keratinocytes in low or standard calcium medium when added at the time of plating; however, they had only a modest effect on the accumulation of cells in adherent clusters. Aggregation of keratinocytes in suspension required a calcium ion concentration of greater than 0.1mM and was not inhibited by any of a large panel of anti-integrin antibodies, including three new antibodies that recognise alpha 2 beta 1. We conclude that any inhibitory effects of individual anti-integrin antibodies on cell-cell adhesion are abrogated by a calcium ion concentration above 0.1mM and that in low calcium medium at least some of the inhibition of cell-cell adhesion is a consequence of the inhibition of cell-substrate adhesion and motility.

Crystal structure of apo-avidin from hen egg-white

The three-dimensional structure of hen egg-white apo-avidin, crystallized in a tetragonal crystal form, has been refined to a crystallographic R-factor of 0.164 (for the 6390 observed reflections in the 10.0 to 2.8 A resolution range). As in the case of holo-avidin, from which starting atomic co-ordinates were derived, the functional tetramer shows 2-pseudo 22 molecular symmetry. Each promoter is organized in an eight-stranded antiparallel orthogonal beta-barrel, with extended loop regions, which define the biotin binding pocket in the protomer core. In the absence of biotin the binding site is only partly occupied by water molecules. The structure of the binding site residues, as observed in apo-avidin, is highly complementary to that of the incoming biotin molecule, accounting for prompt and specific recognition. A crystal lattice contact may play a role in stabilizing the conformation of one protein loop, part of the biotin-binding pocket.

Culture techniques for human keratinocytes

The two main approaches developed for in vitro culture of human keratinocytes are reviewed and discussed. The older technique is based on the use of a serum-containing medium and of a feeder-layer of lethally irradiated mouse fibroblasts; the second relies upon serum-free media, in the absence of a feeder-layer. While the former technique is most widely used for the preparation of epithelial sheets for grafting, the latter is best suited for studies on the biological properties of keratinocytes.

Congenital afibrinogenemia: first identification of splicing mutations in the fibrinogen Bbeta-chain gene causing activation of cryptic splice sites.

Congenital afibrinogenemia is a rare inherited coagulopathy, characterized by very low or unmeasurable plasma levels of immunoreactive fibrinogen. So far, 25 mutations have been identified in afibrinogenemia, 17 in the Aalpha, 6 in the gamma, and only 2 in the Bbeta fibrinogen-chain genes. Here, 2 afibrinogenemic probands, showing undetectable levels of functional fibrinogen, were screened for causative mutations at the genomic level. Sequence analysis of the 3 fibrinogen genes disclosed 2 novel homozygous mutations in introns 6 and 7 of the Bbeta-chain gene (IVS6 + 13C > T and IVS7 + 1G > T), representing the first Bbeta-chain gene splicing mutations described in afibrinogenemia. The IVS6 + 13C > T mutation predicts the creation of a donor splice site in intron 6, whereas the IVS7 + 1G > T mutation causes the disappearance of the invariant GT dinucleotide of intron 7 donor splice site. To analyze the effect of these mutations, expression plasmids containing Bbeta-chain minigene constructs, either wild-type or mutant, were transfected in HeLa cells. Assessed by semiquantitative analysis of reverse transcriptase-polymerase chain reaction products, the IVS7 + 1G > T mutation resulted in multiple aberrant splicings, while the IVS6 + 13C > T mutation resulted in activation of a new splice site 11 nucleotides downstream of the physiologic one. Both mutations are predicted to determine protein truncations, supporting the importance of the C-terminal domain of the Bbeta chain for fibrinogen assembly and secretion.

Congenital afibrinogenemia: intracellular retention of fibrinogen due to a novel W437G mutation in the fibrinogen Bβ-chain gene

Congenital afibrinogenemia is a rare autosomal recessive coagulation disorder characterised by hemorrhagic manifestations of variable entity and by severe plasma fibrinogen deficiency. Among the 31 afibrinogenemia-causing mutations so far reported, only 2 are missense mutations and both are located in the fibrinogen Bbeta-chain gene. Direct sequencing of the fibrinogen gene cluster in two afibrinogenemic Iranian siblings revealed a novel homozygous T>G transversion in exon 8 (nucleotide position 8025) of the fibrinogen Bbeta-chain gene. The resulting W437G missense mutation involves a highly conserved amino acid residue, located in the C-terminal globular D domain. The role of the W437G amino acid substitution on fibrinogen synthesis, folding, and secretion was assessed by in vitro expression experiments in COS-1 cells, followed by qualitative and quantitative analyses of intracellular and secreted mutant fibrinogen. Results of both pulse-chase experiments and enzyme-linked immunosorbent assays demonstrated intracellular retention of the mutant W437G fibrinogen and marked reduction of its secretion. These data, besides elucidating the pathogenetic role of the W437G mutation in afibrinogenemia, underline the importance of the Bbeta-chain D domain in fibrinogen folding and secretion.

A novel two base pair deletion in the factor V gene associated with severe factor V deficiency

We studied a family in which the proband, a 13‐year‐old boy, had unmeasurable plasma levels of coagulation factor V antigen and activity. Clinical symptoms were severe, with several episodes of haemorrhages in the mucosal tracts (gastrointestinal, nose and urinary) and recurrent haemarthroses that caused permanent arthropathy. Sequence analysis of the factor V gene demonstrated the presence of a novel 2 base pair (bp) homozygous deletion in exon 13 at positions 2833–2834. This mutation, present in the heterozygous state in the asymptomatic mother and absent in the healthy brother, introduced a frameshift and a premature stop at codon 900. This would predict the synthesis of a truncated factor V molecule, lacking part of the B domain and the complete light chain. Because of the existence of a surveillance mechanism that selectively recognizes and degrades mRNA molecules carrying premature termination codons, we analysed the relative abundance of mutant vs. wild‐type mRNA molecules in the platelets of the heterozygous probands mother. The mutant mRNA was significantly reduced in amount (mutant/wild‐type ratio 0·35). This is the first reported mutation in the factor V gene causing severe factor V deficiency, the effect of which was quantitatively analysed at mRNA level.

Congenital afibrinogenaemia caused by uniparental isodisomy of chromosome 4 containing a novel 15-kb deletion involving fibrinogen Aα-chain gene

Among rare inherited deficiencies of coagulation factors, congenital afibrinogenaemia is characterised by the lack of fibrinogen in plasma. In the last few years, several genetic defects underlying afibrinogenaemia (mostly point mutations) have been described in the fibrinogen gene cluster. In this study, the molecular basis responsible for afibrinogenaemia in a Thai proband was defined. Point mutation screening was accomplished by directly sequencing the three fibrinogen genes. The impossibility to amplify fibrinogen Aα-chain gene (FGA) exons 5 and 6 suggested the presence of a homozygous deletion. A specific long-range PCR assay enabled the identification of a novel 15-kb deletion, representing the largest afibrinogenaemia-causing deletion described so far. Direct sequencing of the deletion junction allowed mapping of the breakpoints in FGA intron 4 and in the intergenic region between Aα- and Bβ-chain genes. Since the mutation was inherited only from the mother and nonpaternity was ruled out, a maternal uniparental disomy (UPD) was hypothesised. UPD test, carried out with markers covering the whole chromosome 4, revealed that maternal isodisomy was responsible for homozygosity of the 15-kb deletion in the proband. The apparently normal phenotype of the proband, except for afibrinogenaemia, suggests that UPD for chromosome 4 is clinically silent. This represents the first case of a documented complete isodisomy of chromosome 4 causing the phenotypic expression of a recessive disorder. In silico analyses of the regions surrounding the breakpoints suggested that the 15-kb deletion might have originated from an inappropriate repair of a double-strand break by the nonhomologous end joining mechanism.

Characterization of the genomic structure of the human neuronal nicotinic acetylcholine receptor CHRNA5/A3/B4 gene cluster and identification of novel intragenic polymorphisms

AbstractGenes coding for the α5, α3, and β4 subunits (CHRNA5, CHRNA3, and CHRNB4) of the neuronal nicotinic acetylcholine receptors (nAChRs) are clustered on chromosome 15q24. Linkage of this chromosomal region to autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), an idiopathic partial epilepsy, was reported in one family. Moreover, mutations in other neuronal nAChR subunit genes coding for the α4 (CHRNA4) and the β2 (CHRNB2) subunits were associated with ADNFLE. Apart from the exon-intron structure of CHRNA3, the genomic organization of this gene cluster was unknown, making comprehensive mutational analyses impossible. The genomic structure of CHRNA5 and CHRNB4 is here reported. Moreover, two hitherto unknown introns were identified within the 3′ untranslated region of CHRNA3, causing a partial tail-to-tail overlap with CHRNA5. Four novel intragenic polymorphisms were identified and characterized in the cluster.

Exclusion of linkage of nine neuronal nicotinic acetylcholine receptor subunit genes expressed in brain in autosomal dominant nocturnal frontal lobe epilepsy in four unrelated families

Abstract Members of the ligand-gated neuronal nicotinic acetylcholine receptor (nAChR) gene family (CHRNA4 and CHRNB2, coding for the α4 and β2 subunits, respectively) are involved in autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE). However, ADNFLE is genetically heterogeneous and mutations in CHRNA4 and CHRNB2 account for only a minority of ADNFLE cases. Additional nAChR subunits expressed in the brain are candidates for this epilepsy. The involvement of all genes coding for brain-expressed nAChR subunits, with known chromosome localization (CHRNB2, 1q21; CHRNA2, 8p21; CHRNA6, CHRNB3, 8p11.2; CHRNA7, 15q14; CHRNA5/A3/B4, 15q24 and CHRNA4, 20q13.2) was investigated in four unrelated ADNFLE Italian families for at least three generations. Families were selected on the basis of anamnestic and videopolysomnographic analyses. Individuals were typed for polymorphic markers located in the above mentioned chromosome regions. Linkage and mutation analyses were performed. In none of the families was linkage between ADNFLE and the analysed chromosome regions detected. These findings support the hypothesis that genes different from those coding for α2-7 and β2-4 neuronal nAChR subunits could be responsible for ADNFLE.