Towards a resolution on the inherent methodological weakness of the "effective number of codons used by a gene"

Recently Anders Fuglsang provided a modified way for calculating N(c) when biased discrepancy is present in a gene [Biochem. Biophys. Res. Commun. 317 (2004) 957]. Instead of taking the average codon homozygosity for each synonymous family type (as proposed by Wright) [Gene 87 (1990) 23] Fuglsang considered codon homozygosity of each amino acid individually. Marsashi and Najafabadi [Biochem. Biophys. Res. Commun. 324 (2004) 1] in their recent article demonstrated that the readjustment for overestimation at the level of individual amino acids results in loss of considerable amount of information. Immediately after the publication of Marsashi and Najafabadi, Fuglsang proposed that codon homozygosities can be calculated based on the classical population genetics [Biochem. Biophys. Res. Commun. 327 (2005) 1]. Though Fuglsang's approach is a novel one, it fails when any of the amino acids are absent in a gene. However, the inherent cause of overestimation at the level of individual amino acids is still obscured in the literature. Here in this communication we have presented a general condition where effective number of codons is overestimated using Wright's formula and also we propose a new way to calculate N(c), which is independent of amino acid composition.     

Correlations between genomic GC levels and optimal growth temperatures: some comments

Regarding the existence of any specific correlation between optimal growth temperature and genomic GC levels, Musto et al. [FEBS Lett. 573 (2004) 73] have recently performed analysis on 20 prokaryotic families and showed that in most of the families there exists a positive correlation between these two parameters. On the basis of these results they claimed that optimal growth temperature is one of the factors that influence genomic GC composition in prokaryotes. In a subsequent article, Marashi and Ghalanbor [Biochem. Biophys. Res. Commun. 325 (2004) 381] have demonstrated that the correlation values change substantially when very few points in some of the families were excluded from the data set of Musto et al. [FEBS Lett. 573 (2004) 73]. But Marashi and Ghalanbor have not provided any reason behind this. The points excluded by Marashi and Ghalanbor are actually the outliers in the data set, which strongly affect the correlation coefficients. But the presence of outliers in large data set hardly had any effect on the correlation values. Marashi and Ghalanbor have excluded points from only those families that have small sample sizes and observed a substantial change in correlation coefficient values. Therefore, we argue that any conclusion drawn for a small sample size having outliers is always questionable. Although Musto's approach is a novel one, but to make any generalization one needs to be careful about the flawlessness in the data set.     

Oligomeric Aip2p/Dld2p modifies the protein conformation of both properly folded and misfolded substrates in vitro

Oligomeric actin-interacting protein 2 (Aip2p) [Nat. Struct. Biol. 2 (1995) 28]/D-lactate dehydrogenase protein 2 (Dld2p) [Yeast 15 (1999) 1377, Biochem. Biophys. Res. Commun. 295 (2002) 910] exhibits the unique grapple-like structure with an ATP-dependent opening [Biochem. Biophys. Res. Commun. 320 (2004) 1271], which is required for the F-actin conformation modifying activity in vitro and in vivo [Biochem. Biophys. Res. Commun. 319 (2004) 78]. To further investigate the molecular nature of oligomeric Aip2p/Dld2p, the substrate specificity of its binding and protein conformation modifying activity was examined. In the presence of 1mM ATP or AMP-PNP, oligomeric Aip2p/Dld2p bound to all substrates so far examined, and modified the conformation of actin, DNase I, the mature form of invertase, prepro-alpha-factor, pro-alpha-factor, and mitochondrial superoxide dismutase, as determined by the trypsin susceptibility assay. Of note, the activity could modify even the conformation of pathogenic highly aggregated polypeptides, such as recombinant prion protein in beta-sheet form, alpha-synuclein, and amyloid beta (1-42) in the presence of ATP. The in vivo protein conformation modifying activity, however, depends on the growth stage; the most significant substrate modification activity was observed in yeast cells at the log phase, suggesting the presence of a cofactor/s in yeast cells, where F-actin is supposed to be a major target in vivo. These data further support our previous notion that the oligomeric Aip2p/Dld2p may belong to an unusual class of molecular chaperones [Biochem. Biophys. Res. Commun. 320 (2004) 1271], which can target both properly folded and misfolded proteins in an ATP-dependent manner in vitro.     

The source of oxygen in the reaction catalysed by collagen lysyl hydroxylase.

The synthetic peptides (Pro-Pro-Gly)5 and (Ile-Lys-Gly)5-Phe were hydroxylated with collagen prolyl hydroxylase and lysyl hydroxylase in an 18O2 atmosphere. The oxygen atoms in the hydroxy groups of hydroxyproline and hydroxylysine were 87% and 6.5% respectively derived from the atmospheric 18O2. The results are consistent with those reported previously for proline hydroxylation in vivo [Fujimoto & Tamiya (1962) Biochem. J. 84, 333-335; Prockop, Kaplan & Udenfriend (1962) Biochem. Biophys. Res. Commun. 9, 192-196; Fujimoto & Tamiya (1963) Biochem. Biophys. Res. Commun. 10, 498-501; Prockop, Kaplan & Udenfriend (1963) Arch. Biochem. Biophys. 101, 499-503] and in vitro [Cardinale, Rhoads & Udenfriend (1971) Biochem. Biophys. Res. Commun. 43, 537-543] and for lysine hydroxylation in vivo [Fujimoto & Tamiya (1963) Biochem. Biophys. Res. Commun. 10, 498-501]. In view of the similarities of these two oxygenase-type hydroxylation reactions the participation of intermediates is proposed, the oxygen atoms of which are exchangeable with those of water. The atmospheric oxygen atoms incorporated into the intermediate must be equilibrated with water oxygen atoms in the slower lysyl hydroxylase reaction.     

Correspondence regarding October 31, 2003, Breakthroughs and Views by K. Brown and P.L. Carmichael

A. Fuglsang [Biochem. Biophys. Res. Commun. 317 (2004) 957-964] suggested that effective number of codons for individual amino acids (Nc-values) should be re-adjusted to the number of synonymous codons of those amino acids, in order to prevent the overestimation of the effective number of codons. Here, it is shown that re-adjustment at the level of individual amino acids results in loss of considerable amounts of information. Furthermore, we have shown that theoretical Nc-values are functions of GC3s (and GC1s); as a result, when an amino acid Nc-value exceeds the related theoretical Nc-value, the implication of re-adjustment depends on the GC composition of the gene.     

Hsp56 mRNA in Paracentrotus lividus embryos binds to a mitochondrial protein

We previously demonstrated that Paracentrotus lividus Hsp56 mitochondrial chaperonin is constitutively expressed during development, that it has a specific territorial distribution, both in normal and heat-shocked embryos, and that its amount increases after heat shock [Roccheri MC, Patti M, Agnello M, Gianguzza F, Carra E, Rinaldi AM. Localization of mitochondrial Hsp56 chaperonin during sea urchin development. Biochem Biophys Res Commun 2001;287:1093-98] and cadmium treatment [Roccheri MC, Agnello M, Boneventura R, Matranga V. Cadmium induces the expression of specific stress proteins in sea urchin embryos. Biochem Biophys Res Commun 2004;321:80-7]. In this study, we looked at Hsp56 mRNA during normal development and under stress conditions. The messenger is almost constantly expressed at all stages of development and its amount is steadily increased in stressed embryos. Moreover, we found, using T1 RNase protection assay, that the most proximal region of the 3'-UTR of the Hsp56 mRNA binds a 40 kDa protein: this factor is more abundant in the mitochondrial extract and, more specifically, in the outer membrane of the organelle.     

Mechanism for action of electromagnetic fields on cells

A biophysical model for the action of oscillating electric fields on cells, presented by us before [Biochem. Biophys. Res. Commun. 272(3) (2000) 634-640], is extended now to include oscillating magnetic fields as well, extended to include the most active biological conditions, and also to explain why pulsed electromagnetic fields can be more active biologically than continuous ones. According to the present theory, the low frequency fields are the most bioactive ones. The basic mechanism is the forced-vibration of all the free ions on the surface of a cell's plasma membrane, caused by an external oscillating field. We have shown that this coherent vibration of electric charge is able to irregularly gate electrosensitive channels on the plasma membrane and thus cause disruption of the cell's electrochemical balance and function [Biochem. Biophys. Res. Commun. 272(3) (2000) 634-640]. It seems that this simple idea can be easily extended now and looks very likely to be able to give a realistic basis for the explanation of a wide range of electromagnetic field bioeffects.     

Effect of pyridoxal phosphate on the formation of cytochrome c1-c and cytochrome c-cytochrome oxidase complexes.

The cytochrome c-cytochrome oxidase complex is formed when c reacts with cytochrome oxidase (Kuboyama et al. (1962) Biochem. Biophys. Res. Commun. 9, 534) and the cytochrome c1-cytochrome c complex is formed when c reacts with cytochrome c1 in the presence of the hinge protein (Kim, C.H. and King, T.E. (1981) Biochem. Biophys. Res. Commun. 101, 607). Both complexes are considered to be possible intermediates in electron transfer reaction between these cytochromes. Triply substituted modified cytochrome c by pyridoxal phosphate at lysine residues (Lys-79, 86 and one to be identified) abolishes both complex formations and electron transfer activity with succinate cytochrome c reductase or cytochrome oxidase.     

Distribution of neuromedin U receptor subtype 2 mRNA in the rat brain

Neuromedin U (NMU) is a family of peptides found in the gut and the central nervous system [Neuroscience 25 (1988) 797; Biochem. Biophys. Res. Commun. 130 (1985) 1078]. While several peripheral activities such as uterus stimulating and hypertensive effects have been described for NMU [Biochem. Biophys. Res. Commun. 130 (1985) 1078], its role in the CNS remains poorly understood. Recently, we reported the identification of two receptors for NMU (NMU1R and NMU2R), and demonstrated that NMU may play a role in regulating feeding behavior. The central effect of NMU is likely mediated primarily via NMU2R, since NMU1R is detectable only in the periphery, but not in the brain [Nature 406 (2000) 70]. In this report, we describe detailed mapping of NMU2R mRNA expression in the rat brain by in situ hybridization. The most intense signals were observed in the ependymal cell layer along the wall of the third ventricle in the hypothalamus, CA1 region of the hippocampus, indusium griseum and septohippocampal nucleus. Moderate expression was detected in the hypothalamic paraventricular nucleus, dorsal raphe nucleus as well as a number of other brain structures. The presence of NMU2R in the hypothalamus is consistent with its role in energy balance. Significant levels of expression of NMU2R elsewhere in the brain may suggest additional physiological functions for this neuropeptide.     

A new subunit of horse liver alcohol dehydrogenase and subunit composition of the polymorphic form.

The most cathodal (on starch-gel electrophoresis), steroid-active band of horse liver alcohol dehydrogenase, whose catalytic properties were shown to be dependent on the livers used as a starting material [Pietruszko (1974) Biochem. Biophys. Res. Commun. 60, 687-694], has been prepared from A-type and S-type horse livers by identical methods. Results presented here show that different isoenzymes are present in these preparations.     

Isolation and sequence determination of peptide components of atrial natriuretic factor

The independent isolation and sequence determination in our laboratories of three closely related Atrial Natriuretic Factor peptides from rat atria confirm the sequences of ANF peptides reported by Seidah et al and synthesized by Nutt et al [Proc. Natl. Acad. Sci., (1984) in press] and contain the sequences reported by Flynn et al [Biochem. Biophys. Res. Commun. (1983) 117: 859-865] and by Currie et al [Science (1984) 223: 67-69]. In addition, we provide proof for a C-terminal tyrosine rather than tyrosine amide in our isolated peptides.     

Activation of the binding of C1q to immune complexes by zinc

ZnSO4 promotes the binding of C1q to immune complexes over the same concentration range (10(-5)-10(-4) M) that it inhibits binding of C1 to cell-bound immunoglobulin [Biochem. Biophys. Res. Commun. (1981) 103, 856-862]. At higher concentrations (10(-3)-2 X 10(-2) M) ZnSO4 inhibited the binding of C1q to immune complexes, [Ki = (6 +/- 2) X 10(-3) M]. This inhibition could be correlated with a ZnSO4-induced change in the tryptophan fluorescence of C1q [delta F 25%, Kd = (9.9 +/- 1.0) X 10(-3) M].     

Glucose regulation of beta-defensin-1 mRNA in human renal cells

We previously showed that beta-defensin-1 (BD-1), an anti-microbial peptide, is up-regulated during progressive hyperglycemia in the kidneys of the GK rat [R.A. Page, C.A. Morris, J.D. Williams, C.J. von Ruhland, A.N. Malik, Isolation of diabetes-associated kidney genes using differential display, Biochem. Biophys. Res. Commun. 232 (1997) 49-53, R.A. Page, A.N. Malik, Elevated levels of beta-defensin-1 mRNA in diabetic kidneys of GK rats, Biochem. Biophys. Res. Commun. 310 (2003) 513-521]. In this paper, we show that human beta-defensin-1 (hBD-1) mRNA is directly up-regulated by glucose in cultured human renal cells. hBD-1 mRNA levels increased by approximately 7-fold and approximately 4-fold in human embryonic kidney (HEK) cells and human mesangial cells (HMC) grown in 25mM glucose for four days, as determined by quantitative real-time PCR. Immunofluorescence showed that the hBD1 protein is located in the cytoplasm of HEK cells and transfected HMCs. The highest levels of hBD-1 mRNA were found in the kidney compared with 21 other human tissues. The increased expression of hBD-1 mRNA in cultured HMCs in high glucose suggests a role for hBD-1 in the molecular pathways induced during hyperglycemia.     

Inactivation of mitochondrial respiratory chain complex I leads mitochondrial nitric oxide synthase to become pro-oxidative

We recently demonstrated that mitochondrial nitric oxide synthase (mtNOS) functionally couples with mitochondrial respiratory chain complex I to produce nitric oxide [M.S. Parihar, R.R. Nazarewicz, E. Kincaid, U. Bringold, P. Ghafourifar, Association of mitochondrial nitric oxide synthase activity with respiratory chain complex I, Biochem. Biophys. Res. Commun. 366 (2008) 23-28] [1]. The present report shows that inactivation of complex I leads mtNOS to become pro-oxidative. Our findings suggest a crucial role for mtNOS in oxidative stress caused by mitochondrial complex I inactivation.     

Nomenclature of lipoxins and related compounds derived from arachidonic acid and eicosapentaenoic acid

Oxygenated derivates of arachidonic acid and eicosapentaenoic acid which contain conjugated tetraene structures and are non-cyclized C20 carboxylic acids were first isolated and characterized from human and porcine leukocytes (Serhan, C.N. et al, 1984, Biochem. Biophys. Res. Commun. 118, 943-949; Wong, P.Y.-K., et al, 1985, Biochem. Biophys. Res. Commun. 126, 765-775). The trivial names lipoxins and lipoxenes have been introduced for compounds belonging to each of these series. Here, we propose that tetraene-containing compounds derived from arachidonic acid be denoted as lipoxins (LX) of the four series (i.e. lipoxin A4 or LXA4 and lipoxin B4 or LXB4) and those derived from eicosapentaenoic be termed lipoxins of the five series (i.e. lipoxin A5 or LXA5 and lipoxin B5 or LXB5).     

Oligomeric Aip2p/Dld2p forms a novel grapple-like structure and has an ATP-dependent F-actin conformation modifying activity in vitro

In order to investigate the molecular mechanism of the F-actin conformation modifying activity [Biochem. Biophys. Res. Commun. 319 (2004) 78] of actin-interacting protein 2 (Aip2p) [Nat. Struct. Biol. 2 (1995) 28]/D-lactate dehydrogenase protein 2 (Dld2p) [Yeast 15 (1999) 1377; Biochem. Biophys. Res. Commun. 295 (2002) 910], the ultrastructure and the regulatory mechanism of the activity were further examined. Interestingly, a novel oligomeric grapple-like structure of 10-12 subunits with an ATP-dependent opening was observed. ATP regulates the opening and closing of the "gate" that forms the opening within oligomeric Aip2p/Dld2p, where binding to the substrate occurs while in the open form. In the presence of ATP (open state of oligomeric Aip2p/Dld2p), oligomeric Aip2p/Dld2p bound the F-actin fiber within the opening, whereas in the absence of ATP (closed state of oligomeric Aip2p/Dld2p), no binding was observed. Simultaneously, the oligomeric Aip2p/Dld2p increased the trypsin susceptibility of F-actin in an ATP-dependent manner. Use of the non-hydrolyzable ATP analogue AMP-PNP yielded similar results to those observed with ATP, suggesting that ATP binding rather than ATP hydrolysis is required for the protein conformation modifying reaction of oligomeric Aip2p/Dld2p. Endogenous Aip2p/Dld2p purified from Saccharomyces cerevisiae also exhibited such protein conformation modifying activity, but monomeric Aip2p/Dld2p with a C-terminal coiled-coil region-truncation failed to exhibit the activity. These data suggest that the oligomerization of Aip2p/Dld2p, which exhibits the unique grapple-like structure with an ATP-dependent opening, is required for the F-actin conformation modifying activity.     

Platelet-derived growth factor stimulates the phosphorylation of ribosomal protein S6

The human platelet derived-growth factor (PDGF) is both a potent mitogen and a strong chemoattractant protein for cells involved in inflammation and repair. In seeking mechanisms by which PDGF might initiate specific activities in target cells, it was found that highly purified PDGF stimulates the phosphorylation of an Mr approximately 33000 protein in confluent Swiss mouse 3T3 cells [Biochem. Biophys. Res. Commun. (1981) 103, 355-361]. The Mr approximately 33000 protein has now been recovered in polysomes by differential centrifugation and identified as ribosomal protein S6 by two-dimensional polyacrylamide gel electrophoresis.     

Cellular transport of lysosomal enzymes: an alternative hypothesis.

Hickman & Neufeld [(1972) Biochem, Biophys. Res. Commun. 49, 992-999] have proposed that lysosomal enzymes reach the lysosomes by means of exocytosis and subsequent pinocytic reincorporation. The results leading to this conclusion are re-assessed and an alternative explanation is advanced that relates to the necessity for membrane recycling in endocytic cells.     

Identification of essential lysyl and cysteinyl residues in spinach ribulosebisphosphate carboxylase/oxygenase modified by the affinity label N-bromoacetylethanolamine phosphate

We reported earlier (Schloss, J. V., and Hartman, F. C. (1977) Biochem. Biophys. Res. Commun. 77, 230-236) that N-bromoacetylethanolamine phosphate is an affinity label for spinach ribulosebisphosphate carboxylase/oxygenase. We now show inactivation to be correlated directly with the alkylation either of a single lysyl residue (in the presence of Mg2+) or of 2 different cysteinyl residues (in the absence of Mg2+), consistent with the likelihood that these residues are located in the active site region. This proposition is further supported by the demonstration that the residues are protected from alkylation by substrate, a competitive inhibitor, or the transition state analog 2-carboxyribitol bisphosphate. Tryptic peptides that contain the modified residues have been isolated and sequenced. One of the 2 cysteinyl residues that are subject to alkylation is only 3 residues distant in sequence from the lysyl residue modified by bromoacetylethanolamine phosphate. This lysyl residue is identical with 1 of the 2 lysyl residues alkylated by the previously described affinity label, 3-bromo-1,4-dihydroxy-2-butanone 1,4-bisphosphate (Stringer, C. D., and Hartman, F. C. (1978) Biochem. Biophys, Res. Commun. 80, 1043-1048).     

Type A allatostatins from Drosophila melanogaster and Diplotera puncata activate two Drosophila allatostatin receptors, DAR-1 and DAR-2, expressed in CHO cells

The type-A allatostatins A (AST-A) are a group of insect peptides with a common C-terminal motif Y/FXFGL-NH(2). The existence of at least four putative type A Drosophila melanogaster ASTs (called type A drostatins or DST-As) has been predicted from the sequence of a recently cloned DST-A preprohormone [C. Lenz et al. (2000) Biochem. Biophys. Res. Commun. 273, 126-1131]. SRPYSFGL-NH(2), (DST-3A), the only DST isolated from Drosophila so far, activated the first cloned DST-A GPCR (DAR-1) [N. Birgül et al. (1999) EMBO J. 18, 5892-5900]. A newly cloned orphan Dm GPCR, which shares 47% overall and 60% transmembrane region sequence identity with DAR-1, was classified as a second putative Dm DST-A receptor (DAR-2) [C. Lenz et al. (2000) Biochem. Biophys. Res. Commun. 273, 571-577]. Although activation of DAR-2 by DSTs has been postulated, no experimental evidence for that has been presented to date. In this study, we expressed both DAR-1 and DAR-2 in CHO cells and used a GTPgammaS and a Ca(2+) mobilization assay for pharmacological evaluation of the receptors. Synthetically prepared DST-As, as well as selected Diplotera punctata (cockroach) ASTs, activated DAR-1 and DAR-2 in both functional assays indicating ligand redundancy and cross species activity. Cell pretreatment with pertussis toxin led to some differences in the nature and magnitude of signaling pathways at the DAR-1 and DAR-2 receptors, suggesting possible differential coupling to cellular effector system(s) and distinct biological functions of each receptor in vivo.