Biomedical subjects

N Mathias

Publications and source records attributed to N Mathias.

14 recordsLinked to original sources

PubMed2001

Small worlds: how and why.

We investigate small-world networks from the point of view of their origin. While the characteristics of small-world networks are now fairly well understood, there is as yet no work on what drives the emergence of such a network architecture. In situations such as neural or transportation networks, where a physical distance between the nodes of the network exists, we study whether the small-world topology arises as a consequence of a tradeoff between maximal connectivity and minimal wiring. Using simulated annealing, we study the properties of a randomly rewired network as the relative tradeoff between wiring and connectivity is varied. When the network seeks to minimize wiring, a regular graph results. At the other extreme, when connectivity is maximized, a "random" network is obtained. In the intermediate regime, a small-world network is formed. However, unlike the model of Watts and Strogatz [Nature 393, 440 (1998)], we find an alternate route to small-world behavior through the formation of hubs, small clusters where one vertex is connected to a large number of neighbors.

Algorithms↗

PubMed2000

The abundance of Met30p limits SCF(Met30p) complex activity and is regulated by methionine availability.

Ubiquitin-mediated degradation plays a crucial role in many fundamental biological pathways, including the mediation of cellular responses to changes in environmental conditions. A family of ubiquitin ligase complexes, called SCF complexes, found throughout eukaryotes, is involved in a variety of biological pathways. In Saccharomyces cerevisiae, an SCF complex contains a common set of components, namely, Cdc53p, Skp1p, and Hrt1p. Substrate specificity is defined by a variable component called an F-box protein. The F- box is a approximately 40-amino-acid motif that allows the F-box protein to bind Skp1p. Each SCF complex recognizes different substrates according to which F-box protein is associated with the complex. In yeasts, three SCF complexes have been demonstrated to associate with the ubiquitin-conjugating enzyme Cdc34p and have ubiquitin ligase activity. F-box proteins are not abundant and are unstable. As part of the SCF(Met30p) complex, the F-box protein Met30p represses methionine biosynthetic gene expression when availability of L-methionine is high. Here we demonstrate that in vivo SCF(Met30p) complex activity can be regulated by the abundance of Met30p. Furthermore, we provide evidence that Met30p abundance is regulated by the availability of L-methionine. We propose that the cellular responses mediated by an SCF complex are directly regulated by environmental conditions through the control of F-box protein stability.

Amino Acid Sequence↗

PubMed1999

The abundance of cell cycle regulatory protein Cdc4p is controlled by interactions between its F box and Skp1p.

Posttranslational modification of a protein by ubiquitin usually results in rapid degradation of the ubiquitinated protein by the proteasome. The transfer of ubiquitin to substrate is a multistep process. Cdc4p is a component of a ubiquitin ligase that tethers the ubiquitin-conjugating enzyme Cdc34p to its substrates. Among the domains of Cdc4p that are crucial for function are the F-box, which links Cdc4p to Cdc53p through Skp1p, and the WD-40 repeats, which are required for binding the substrate for Cdc34p. In addition to Cdc4p, other F-box proteins, including Grr1p and Met30p, may similarly act together with Cdc53p and Skp1p to function as ubiquitin ligase complexes. Because the relative abundance of these complexes, known collectively as SCFs, is important for cell viability, we have sought evidence of mechanisms that modulate F-box protein regulation. Here we demonstrate that the abundance of Cdc4p is subject to control by a peptide segment that we term the R-motif (for "reduced abundance"). Furthermore, we show that binding of Skp1p to the F-box of Cdc4p inhibits R-motif-dependent degradation of Cdc4p. These results suggest a general model for control of SCF activities.

Binding Sites↗

PubMed1998

Modification of yeast Cdc53p by the ubiquitin-related protein rub1p affects function of the SCFCdc4 complex.

The RUB1/NEDD-8 family of ubiquitin-related genes is widely represented among eukaryotes. Here we report that Cdc53p in Saccharomyces cerevisiae, a member of the Cullin family of proteins, is stably modified by the covalent attachment of a single Rub1p molecule. Two genes have been identified that are required for Rub1p conjugation to Cdc53p. The first gene, designated ENR2, encodes a protein with sequence similarity to the amino-terminal half of the ubiquitin-activating enzyme. By analogy with Aos1p, we infer that Enr2p functions in a bipartite Rub1p-activating enzyme. The second gene is SKP1, shown previously to be required for some ubiquitin-conjugation events. A deletion allele of ENR2 is lethal with temperature-sensitive alleles of cdc34 and enhances the phenotypes of cdc4, cdc53, and skp1, strongly implying that Rub1p conjugation to Cdc53p is required for optimal assembly or function of the E3 complex SCFCdc4. Consistent with this model, both enr2delta and an allele of Cdc53p that is not Rub1p modified, render cells sensitive to alterations in the levels of Cdc4p, Cdc34p, and Cdc53p.

Amino Acid Sequence↗

PubMed1998

An essential domain within Cdc34p is required for binding to a complex containing Cdc4p and Cdc53p in Saccharomyces cerevisiae.

The CDC34 gene of the yeast Saccharomyces cerevisiae encodes a ubiquitin-conjugating protein that transfers ubiquitin onto substrates to signal rapid degradation via the proteasome. Cdc34p has been implicated in signaling the destruction of a variety of substrates including the cyclin-dependent kinase inhibitor, Sic1p, which must be degraded for cells to enter S-phase. Mutants lacking CDC34 activity fail to degrade Sic1p and fail to enter S-phase, a phenotype that is also shared with cells lacking CDC4 and CDC53 activity. Here we demonstrate that Cdc4p, Cdc34p, and Cdc53p interact in vivo. We have mapped a Cdc4p/Cdc53p-binding region on Cdc34p; this region is essential for S-phase entry and thus the association of these three proteins is required for Sic1p degradation. All three proteins migrate in gel filtration to sizes that greatly exceed their actual size suggesting that they form stable associations with other proteins and we observe Cdc4p, Cdc34p, and Cdc53p fractionating into overlapping families of high molecular weight complexes. Finally, we demonstrate that Cdc4p, Cdc34p, and Cdc53p are stable throughout the cell cycle and that Cdc34p permanently resides as part of a complex throughout the cell cycle. This suggests that all Cdc34p substrates are ubiquitinated by a similar high molecular weight complex.

Anaphase-Promoting Complex-Cyclosome↗

PubMed1996

Cdc53 targets phosphorylated G1 cyclins for degradation by the ubiquitin proteolytic pathway.

In budding yeast, cell division is initiated in late G1 phase once the Cdc28 cyclin-dependent kinase is activated by the G1 cyclins Cln1, Cln2, and Cln3. The extreme instability of the Cln proteins couples environmental signals, which regulate Cln synthesis, to cell division. We isolated Cdc53 as a Cln2-associated protein and show that Cdc53 is required for Cln2 instability and ubiquitination in vivo. The Cln2-Cdc53 interaction, Cln2 ubiquitination, and Cln2 instability all depend on phosphorylation of Cln2. Cdc53 also binds the E2 ubiquitin-conjugating enzyme, Cdc34. These findings suggest that Cdc53 is a component of a ubiquitin-protein ligase complex that targets phosphorylated G1 cyclins for degradation by the ubiquitin-proteasome pathway.

Amino Acid Sequence↗

PubMed1996

Ubiquitin-dependent proteolysis and cell cycle control in yeast.

Genetic and biochemical data indicate that ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression. In general, mutations in some genes that encode proteins involved in the ubiquitin pathway cause cell cycle defects and affect the turnover of cell cycle regulatory proteins. Furthermore, some cell cycle regulatory proteins are short-lived, ubiquitinated, and degraded by the ubiquitin pathway. This review will examine how the ubiquitin pathway plays a role in regulating progression from the G1 to the S phase of the cell cycle, as well as the G2 to M phase transition.

Anaphase-Promoting Complex-Cyclosome↗

PubMed1996

Cdc53p acts in concert with Cdc4p and Cdc34p to control the G1-to-S-phase transition and identifies a conserved family of proteins.

Regulation of cell cycle progression occurs in part through the targeted degradation of both activating and inhibitory subunits of the cyclin-dependent kinases. During G1, CDC4, encoding a WD-40 repeat protein, and CDC34, encoding a ubiquitin-conjugating enzyme, are involved in the destruction of these regulators. Here we describe evidence indicating that CDC53 also is involved in this process. Mutations in CDC53 cause a phenotype indistinguishable from those of cdc4 and cdc34 mutations, numerous genetic interactions are seen between these genes, and the encoded proteins are found physically associated in vivo. Cdc53p defines a large family of proteins found in yeasts, nematodes, and humans whose molecular functions are uncharacterized. These results suggest a role for this family of proteins in regulating cell cycle proliferation through protein degradation.

Amino Acid Sequence↗

PubMed1995

Intragenic suppression among CDC34 (UBC3) mutations defines a class of ubiquitin-conjugating catalytic domains.

Ubiquitin-conjugating (E2) enzymes contain several regions within their catalytic domains that are highly conserved. However, within some of these conserved regions are several residues that may be used to define different classes of catalytic domains for the E2 enzymes. One class can be defined by the Ubc1 protein, which contains K-65, D-90, and D-120, while the corresponding positions within the Cdc34 (Ubc3) protein, which defines a second class of enzymes, contain S-73, S-97, and S-139, respectively. The presence of these differences within otherwise highly conserved regions of this family suggests that these residues may be critical for the specificity of Cdc34 function or regulation. Therefore, we have constructed a series of cdc34 alleles encoding mutant proteins in which these serine residues have been changed to other amino acid residues, including alanine and aspartic acid. In vivo complementation studies showed that S-97, which lies near the active site C-95, is essential for Cdc34 function. The addition of a second mutation in CDC34, which now encoded both the S97D and S73K changes, restored partial function to the Cdc34 enzyme. Moreover, the deletion of residues 103 to 114 within Cdc34, which are not present in the Ubc1-like E2s, allowed the S73K/S97D mutant to function as efficiently as wild-type Cdc34 protein. Finally, the cloning and sequencing of the temperature-sensitive alleles of CDC34 indicated that A-62 is also unique to the Cdc34 class of E2 enzymes and that mutations at this position can be detrimental to Cdc34 function. Our results suggest that several key residues within conserved regions of the E2 enzyme family genetically interact with each other and define a class of E2 catalytic domains.

Amino Acid Sequence↗

PubMed1994

Highly informative compound haplotypes for the human Y chromosome.

A collection of polymorphic DNA sequences has been used to analyse the variability of a panel of 91 Y chromosomes. Some sequences (DYZ1 and DYZ2) were highly polymorphic and allowed all of the chromosomes to be distinguished. Other sequences were less polymorphic and were used to construct a haplotype for each chromosome and to assign chromosomes to groups. The best understood of these loci could be used to construct a tree showing the evolutionary relationships between the groups of Y chromosomes. In general, Y chromosomes from different ethnic backgrounds belong to different groups.

Base Sequence↗

PubMed1993

[Physical urticaria and angioedema in children].

Urticaria and physical angioedema frequency is hard to evaluate in children. In this series, we keep 53/1000. Physical urticaria is found in 36% of the cases and concerns cholinergic urticaria, urticaria to cold, idiopathic dermographism and mastocytosis, and delayed urticaria to pressure. The authors insist on the interest of the etiologic research in these forms of infantile urticaria.

Angioedema↗

PubMed1991

Improved methods for the detection of beta-galactosidase activity in colonies of Escherichia coli using a new chromogenic substrate: VBzTM-gal (2-(2-(4-(beta-D-galactopyranosyloxy)-3-methoxyphenyl)-vinyl)-3- methylbenzothiazolium toluene-4-sulphonate).

The use of a new substrate 2-(2-(4-(beta-D-galactopyranosyloxy)-3- methoxyphenyl)-vinyl)-3-methylbenzothiazolium toluene-4-sulphonate (VB-zTM-gal) is described for the detection of beta-galactosidase activity in colonies of wild type and mutant strains of Escherichia coli. On enzymic hydrolysis this substrate, which is soluble in water, released a chromophore which is red at pH 7 and bound to cellulose and nitrocellulose. The best procedure for the detection of activity was to grow colonies on standard nitrocellulose membranes (pore size 0.45 microns) laid onto an agar plate and to float the membranes over a solution of the substrate. Coloured colonies developed within 3 min, which were stable at 4 degrees C for several days, and this identified the expression of beta-galactosidase activity. This was found to be more specific than methods using triphenyltetrazolium or Eosin Methylene Blue media, and more economical than methods using X-gal (5-bromo-4-chloro-3-indolyl beta-D-galactopyranoside). VBzTM-gal should have applications in gene cloning technology and in the detection of coliform organisms in polluted water.

Chromogenic Compounds↗

PubMed1987

[Chronic urticaria--an inventory proposed by the Urticaria Study and Research Group].

The Urticaria Study and Research Group (Groupe d'Etudes et de Researches de l'Urticaria, G.E.R.U.) was formed in the Dermatology Department of the Hôpital Michel Levy in 1983 and now it continues to operate in the new Dermatology Department of the C.H.U. Timone Adultes. This has been possible because in four years 400 cases of urticaria have been seen and computerized information on these will appear in the next issue. As a result of this experience, we have been able to lay out a prospective study and develop a rigorous methodology.

Chronic Disease↗

PubMed1980

Dose-response relation of CSF sodium and renal sodium excretion, and its absence in homozygous Brattleboro rats.

Constant intraventricular infusion (3.3--6.6 microliters/min) of artificial cerebrospinal fluid with sodium concentrations of 100, 150, 200, 250, 300, and 350 mM produced a linear dose-related change in renal sodium excretion in conscious, unrestrained Sprague-Dawley rats. The periventricular receptors stimulated were able to evoke substantial changes in body sodium balance; the 350 mM Na CSF produced an estimated 14% deficit in the content of Na in the extracellular fluid over a 5-hour infusion period. This is the first demonstration of such a dose-response relation over a wide range of CSF Na concentration (above and below normal) in conscious animals. Both the dose-response relation, and the magnitude of the effects, suggests an important physiologic role for this control mechanism. The natriuresis in response to 300 mM sodium infusion was identical in Long-Evans Brattleboro rats heterozygous for diabetes insipidus (DI), and in Sprague-Dawley rats, but was completely absent in homozygous animals. Although the experimental methods (conscious unrestrained rats) precluded simultaneous evaluation of efferent pathways other than antidiuretic hormone (ADH), the evidence from the DI rats suggests that ADH may be the efferent pathway for the response.

Animals↗