Measure representation and multifractal analysis of complete genomes

This paper introduces the notion of measure representation of DNA sequences. Spectral analysis and multifractal analysis are then performed on the measure representations of a large number of complete genomes. The main aim of this paper is to discuss the multifractal property of the measure representation and the classification of bacteria. From the measure representations and the values of the $D_{q}$ spectra and related $C_{q}$ curves, it is concluded that these complete genomes are not random sequences. In fact, spectral analyses performed indicate that these measure representations considered as time series, exhibit strong long-range correlation. For substrings with length K=8, the $D_{q}$ spectra of all organisms studied are multifractal-like and sufficiently smooth for the $C_{q}$ curves to be meaningful. The $C_{q}$ curves of all bacteria resemble a classical phase transition at a critical point. But the 'analogous' phase transitions of chromosomes of non-bacteria organisms are different. Apart from Chromosome 1 of {\it C. elegans}, they exhibit the shape of double-peaked specific heat function.Comment: 12 pages with 9 figures and 1 tabl

Mutation of a tyrosine in the H3-H4 ectodomain of Na,K-ATPase alpha subunit confers ouabain resistance.

In a highly ouabain-resistant clone from the Madin-Darby canine kidney cell line (Ki > 4 mM), we have previously identified mutations (C113 to Y or C113 to F) in the first transmembrane helix (H1) of the Na,K-ATPase alpha subunit that increase the Ki of a ouabain-sensitive Na,K pump by 1000-fold. Here we report another mutation (Y317 to C) located in the extracellular segment that joins the third and fourth transmembrane domains (H3-H4 ectodomain) of the alpha subunit that also changes ouabain sensitivity of the Na pump. When this mutation (Y317C) was introduced into the Na,K-ATPase alpha 1 subunit of Xenopus laevis, the ouabain inhibition constant increased by a factor of 5, from 130 (wild type) to 800 nM (mutant). However, the expression of double mutants (C113Y + Y317C) in Xenopus oocytes resulted in highly ouabain-resistant Na,K pumps (Ki approximately 7 mM), reproducing the phenotype of the original Madin-Darby canine kidney cell line. When a more conservative change (Y317F) was introduced into the Na,K-ATPase alpha 1 subunit of X. laevis, the ouabain koff increased and expression of double mutants (C113Y + Y317F) resulted in an intermediate ouabain-resistant Na,K pump (Ki approximately 500 microM). We propose that, in addition to the previously identified H1-H2 ectodomain of Na,K-ATPase alpha subunit, the H3-H4 ectodomain also participates in the structure and/or the function of the ouabain binding site. In this respect, the Y317 plays a critical role since the most conservative change Y313 to F is sufficient to significantly affect ouabain binding

Primary sequence and functional expression of a novel ouabain-resistant Na,K-ATPase. The beta subunit modulates potassium activation of the Na,K-pump.

In order to understand the molecular mechanism of ouabain resistance in the toad Bufo marinus, Na,K-ATPase alpha and beta subunits have been cloned and their functional properties tested in the Xenopus laevis oocyte expression system. According to sequence comparison between species, alpha 1, beta 1, and beta 3 isoforms were identified in a clonal toad urinary bladder cell line (TBM 18-23). The sequence of the alpha 1 isoform is characterized by two positively charged amino acids (Arg, Lys) at the N-terminal border of the H1-H2 extracellular loop and no charged amino acid at the C terminus, a pattern distinct from the ouabain-resistant rat alpha 1 isoform. The coexpression of alpha 1 beta 1 or alpha 1 beta 3 TBM subunits in the Xenopus oocyte resulted in the expression of identical maximum Na,K-pump currents with identical inhibition constant for ouabain (Ki) (alpha 1 beta 1: 53 +/- 3 microM; n = 7 vs. alpha 1 beta 3: 57 +/- 3.0 microM; n = 8) but distinct potassium half activation constant (K1/2) (alpha 1 beta 1: 0.87 +/- 0.08 mM, n = 16; alpha 1 beta 3: 1.29 +/- 0.07 mM, n = 17; p less than 0.005). We conclude that (i) the TBM alpha 1 isoform is necessary and sufficient to confer the ouabain resistant phenotype; (ii) the beta 3 or beta 1 subunit can associate with the alpha 1 equally well without affecting the ouabain-resistant phenotype; (iii) some specific sequence of the beta subunit can modulate the activation of the Na,K-pump by extracellular potassium ions

Sodium transport systems in human chondrocytes II. Expression of ENaC, Na+ K+ 2CI- cotransporter and Na+ H+ exchangers in healthy

In this article, the second of two, we continue our studies of sodium-dependent transport systems in human cartilage from healthy individuals and with osteoarthritis (OA) and rheumatoid arthritis (RA). We demonstrate the presence of the epithelia1 sodium channel (ENaC), previously undescribed in chondrocytes. This system is composed of three subunits, a, 13 and y. We have shown that the human chondrocytes express at least the a and the l3 subunit of ENaC. The expression of these subunits is altered in arthritic chondrocytes. In RA samples the quantity of a and B is significantly higher than in control samples. On the other hand, ENaC a and B subunits are absent in the chondrocytes of OA cartilage. Human chondrocytes also possess three isoforms of the Na+/H+ exchanger (NHE), NHE1, NHE2 and NHE3. The NHE system is composed of a single protein and is believed to participate in intracellular pH regulation. Furthermore, our studies indicate that at least one isoform of the electroneutral Naf/K+/2C1- cotransporter (NKCC) is present in human chondrocytes. There are no obvious variations in the relative expression of NHE isoforms or NKCC between healthy and arthritic cartilage. Our data suggests that chondrocytes from arthritic cartilage may adapt to changes in their environmental sodium concentration through variations in ENaC protein levels. ENaC is also likely to serve as a major sodium entry mechanism, a process that, along with cytoskeletal proteins, may be part of mechanotransduction in cartilage