Evolution of eutherian cytochrome c oxidase subunit II: heterogeneous rates of protein evolution and altered interaction with cytochrome c

Cytochrome c oxidase subunit II (COII), encoded by the mitochondrial genome, exhibits one of the most heterogeneous rates of amino acid replacement among placental mammals. Moreover, it has been demonstrated that cytochrome c oxidase has undergone a structural change in higher primates which has altered its physical interaction with cytochrome c. We collected a large data set of COII sequences from several orders of mammals with emphasis on primates, rodents, and artiodactyls. Using phylogenetic hypotheses based on data independent of the COII gene, we demonstrated that an increased number of amino acid replacements are concentrated among higher primates. Incorporating approximate divergence dates derived from the fossil record, we find that most of the change occurred independently along the New World monkey lineage and in a rapid burst before apes and Old World monkeys diverged. There is some evidence that Old World monkeys have undergone a faster rate of nonsynonymous substitution than have apes. Rates of substitution at four-fold degenerate sites in primates are relatively homogeneous, indicating that the rate heterogeneity is restricted to nondegenerate sites. Excluding the rate acceleration mentioned above, primates, rodents, and artiodactyls have remarkably similar nonsynonymous replacement rates. A different pattern is observed for transversions at four-fold degenerate sites, for which rodents exhibit a higher rate of replacement than do primates and artiodactyls. Finally, we hypothesize specific amino acid replacements which may account for much of the structural difference in cytochrome c oxidase between higher primates and other mammals.      

Molecular evolution of cytochrome c oxidase: rate variation among subunit VIa isoforms

Cytochrome c oxidase (COX) consists of 13 subunits, 3 encoded in the mitochondrial genome and 10 in the nucleus. Little is known of the role of the nuclear-encoded subunits, some of which exhibit tissue-specific isoforms. Subunit VIa is unique in having tissue-specific isoforms in all mammalian species examined. We examined relative evolutionary rates for the COX6A heart (H) and liver (L) isoform genes along the length of the molecule, specifically in relation to the tissue-specific function(s) of the two isoforms. Nonsynonymous (amino acid replacement) substitutions in the COX6AH gene occurred more frequently than in the ubiquitously expressed COX6AL gene. Maximum-parsimony analysis and sequence divergences from reconstructed ancestral sequences revealed that after the ancestral COX6A gene duplicated to yield the genes for the H and L isoforms, the sequences encoding the mitochondrial matrix region of the COX VIa protein experienced an elevated rate of nonsynonymous substitutions relative to synonymous substitutions. This is expected for relaxed selective constraints after gene duplication followed by purifying selection to preserve the replacements with tissue-specific functions.      

Helicobacter pylori strains vary cell shape and flagellum number to maintain robust motility in viscous environments

The helical shape of the human stomach pathogen Helicobacter pylori has been suggested to provide mechanical advantage for penetrating the viscous stomach mucus layer. Using single‐cell tracking and quantitative morphology analysis, we document marked variation in cell body helical parameters and flagellum number among H. pylori strains leading to distinct and broad speed distributions in broth and viscous gastric mucin media. These distributions reflect both temporal variation in swimming speed and morphologic variation within the population. Isogenic mutants with straight‐rod morphology showed 7–21% reduction in speed and a lower fraction of motile bacteria. Mutational perturbation of flagellum number revealed a 19% increase in speed with 4 versus 3 median flagellum number. Resistive force theory modeling incorporating variation of both cell shape and flagellum number predicts qualitative speed differences of 10–30% among strains. However, quantitative comparisons suggest resistive force theory underestimates the influence of cell body shape on speed for helical shaped bacteria.     

Activation and expansion of cytotoxic T lymphocytes from tumor-draining lymph nodes

Summary Large numbers of cytotoxic T lymphocytes (CTL) could be generated from tumor-draining lymph nodes (DLN) from mice bearing PHS-5 tumor by culturing at low density with autologous tumor cell stimulators and 20 U/ml recombinant interleukin-2 (IL-2). Outgrowth of metastatic tumor cells in culture was prevented by use of this hypoxanthine/aminopterin/thymidine-sensitive mutant of P815, PHS-5. After 9 days in culture, lymphoid cells demonstrated specific cytotoxicity against autologous tumor target cells. Lymph node cells could be expanded continuously in culture with repeated tumor stimulation with up to 7500-fold increase in cell number by 6 weeks; although CTL could be activated from tumor-bearing host spleen cells in short-term culture, they showed no significant growth in long-term cultures. Phenotypically, DLN cells were a mixture of CD8⁺ and CD4⁺ cells immediately after harvest but after 2 weeks in culture they were predominantly CD8⁺ CD4^–. CTL could be generated from tumor-bearing mice 10–14 days after i.d. tumor inoculation into the abdominal wall, but the immune response declined both in spleen and DLN by 21 days. Much greater CTL activity could be generated from axillary DLN that contained metastases than from non-draining popliteal nodes that were free of metastatic tumor cells. Some CTL activity could be generated from DLN with the addition of IL-2 alone but was further increased by the addition of more tumor cells as stimulators. When adoptively transferred to a host with 3-day P815 liver metastases, lymphocytes from DLN activated in vitro were able to reduce or eliminate metastases with very little or no IL-2 administered concomitantly. As few as 10⁶ cells were therapeutically effective, and in vivo efficacy was tumor-specific, since L5178Y liver metastases were not affected.This work was supported in part by grants CA42443, CA48075 and T32-CA09210 from the National Cancer Institute, Department of Health and Human ServicesRecipient of the Canadian Cancer Society McEachern Fellowship.     

The DNA sequence of argI from Escherichia coli K12.

The argI gene from E. coli K12 has been sequenced. It contains an open reading frame of 1002 bases which encodes a polypeptide of 334 amino acids. Three such polypeptides are required to form the functional catalytic trimer (c3) of ornithine transcarbamoylase (OTCase-1, EC 2.1.3.3). The molecular mass of the mature trimer deduced from the amino acid sequence is 114,465 daltons. An altered form of argI was produced when a 1.6 kilobase DdeI fragment was subcloned into the HincII site of plasmid pUC8 extending the open reading frame an additional 20 nucleotides. It has been previously reported that the amino-terminal region of the respective polypeptides of argI, argF, and pyrB of E. coli possessed significant homology. In contrast, the homologous promoter/operator regions of argI and argF did not appear to share any homologies with pyrB. However, a closer scrutiny of the nucleotide sequence immediately preceding the pyrBI attenuator revealed a remarkable similarity to the argI and argF control region.     

Isolation of bovine aortic endothelial cell plasma membranes: identification of membrane-associated cytoskeletal proteins

The plasma membrane of bovine aortic endothelium was isolated, characterized, and found to contain at least four membrane-associated cytoskeletal proteins. Exposure of the plasma membranes to salt media (up to 1M KCl) resulted in the release of 30% of the total plasma membrane-associated proteins and extraction with 1% Triton X-100, 60%. At least four heavily glycosylated bands (185-, 165-, 150-, and 130,000 mol-wt) were evident. The Triton-insoluble pellet fraction contained several major polypeptides (30-, 43-, 58-, and 240,000 mol-wt), two of which were identified by immunoblotting as cytoplasmic actin (43,000 mol-st) and vimentin (58,000 mol-wt). Strikingly, vimentin and a 240,000 mol-wt polypeptide were routinely present in approximately a mole ratio of 4:1 in more than 60% of the plasma membrane preparations. We also report the presence of a 2.1-like and a 4.1-like protein associated with plasma membranes. The 2.1-like protein demonstrated similar solubilities and apparent molecular weight (210,000) as erythroid protein 2.1. Likewise, the endothelial 4.1-like protein exhibited similar solubilities and apparent molecular weight as erythroid protein 4.1. Immunofluorescence staining of fixed and permeabilized cultures with anti-2.1 antibodies showed a fibrillar pattern. In contrast, cells stained with anti-protein 4.1 were brightly fluorescent, bearing both a diffuse and punctate pattern. This paper presents several novel observations pertaining to the composition of bovine aortic endothelial cell plasma membranes, namely: the presence of two erythroid-like cytoskeletal polypeptides; the presence of vimentin and a 240,000 mol-wt polypeptide in a 4:1 mole ratio in more than 60% of the plasma membrane preparations and the co-elution in a 4:1 mol ratio with a protein perturbant; and the inability to release actin from the plasma membrane preparations, suggesting the association of actin with other molecules in the plasma membrane preparation.     

Anomalies in mineralization of low concentrations of organic compounds in lake water and sewage

The rates of mineralization of nitrilotriacetic acid (NTA), 2,4-dichlorophenoxyacetic acid (2,4-D), p-nitrophenol, aniline, and isopropyl N-phenylcarbamate (IPC) at one or more concentrations ranging from 100 pg/ml to 1.0 microgram/ml were proportional to chemical concentrations in samples of three lakes. The rates at 100 pg of NTA, 2,4-D, p-nitrophenol, and aniline per ml in samples of one or more lakes were less than predicted, assuming the rates were linearly related to the concentration. Neither NTA nor 2,4-dichlorophenol at 2.0 ng/ml was mineralized in some lake waters, but higher levels of the two chemicals were converted to CO2 in samples of the same waters. In samples from two lakes, little or no mineralization of IPC or 2,4-D occurred at 1.0 microgram/ml, but 10 ng/ml or lower levels of the herbicides were mineralized. The mineralization in sewage of 1.0 microgram of NTA per ml was biphasic; about 20% of the substrate was mineralized in 20 h, and mineralization was only reinitiated after a period of 130 h. The biphasic transformation was not a result of the accumulation of organic products, and it was still evident if protozoan activity was inhibited. NTA also underwent a biphasic mineralization in lake waters, and the biphasic pattern was not altered by additions of growth factors and inorganic nutrients. From 40 to 60% of the carbon of aniline added to lake water at levels of 100 pg/ml to 1.0 microgram/ml was mineralized, but more than 90% of the carbon of NTA, 2,4-D, or p-nitrophenol added to lake water at 10 ng/ml or 1.0 microgram/ml was mineralized.(ABSTRACT TRUNCATED AT 250 WORDS)     

Harderian gland porphyrin, lysosomal and type II 5'-deiodinase rhythms in Sprague-Dawley and Fischer-344 rats kept under chronic long- or short-photoperiod conditions.

1. Harderian gland porphyrin concentrations were 1.5-fold higher in Fischer-344 male rats than in Sprague-Dawley male rats and there were no differences due to exposure to LD 14:10 (LP) or LD 10:14 (SP) lighting conditions for 8 weeks in either strain. 2. 24-hr periodic regression analyses of porphyrin concentration detected a significant rhythm in both lighting conditions in both strains, with no differences in acrophase due to lighting conditions. 3. In both strains, porphyrin levels were highest in the late phase-early dark period and fell during the early part of the dark period. 4. Acid phosphatase activity did not vary with time (circadian rhythm), strain or photoperiodic lighting condition. 5. Circadian rhythms in beta-glucuronidase, alpha-mannosidase and hexosaminidase activity were present in some instances, but, probably due to the low amplitude to these rhythms, a consistent effect of strain or housing condition was not found. When 24-hr rhythms were observed in either strain, the acrophase occurred during the afternoon-early evening daylight period. 6. A significant effect of strain on mean values of type II 5'-deiodinase activity was noted in Fischer-344 rats. 7. Significant rhythms in type II 5'-deiodinase activity were found in both strains exposed to LD 10:14.     

Derepression of nitrogenase by addition of malate to cultures of Rhodospirillum rubrum grown with glutamate as the carbon and nitrogen source.

Rhodospirillum rubrum grown in continuous culture with glutamate as the sole fixed C and N source produced no nitrogenase, and the cultures were characterized by high extracellular ammonium concentrations. Addition of organic acids derepressed nitrogenase. Glutamate dehydrogenase, glutamine synthetase, glutamate synthase, malate dehydrogenase, nitrogenase, and ammonium were assayed before and after malate addition.     

Influence of collagen gel substratum on response to low-density lipoprotein by cultured human skin fibroblasts

The effect of low-density lipoprotein (LDL) on accumulation of glycosaminoglycans (GAG) was compared in cultures of human skin fibroblasts on a conventional plastic substratum and in a native type I collagen gel. The 24-h incorporation of [3H]glucosamine and Na2(35)SO4 into GAG secreted into the medium or associated with the substratum and cell surface (SCA) was measured in cells at subconfluent densities. When cells were grown on plastic, 13-25% of the labeled GAG was in the SCA pool. Cells cultured within a collagen gel matrix incorporated three times more [3H]glucosamine and up to five times more [35S]sulfate into this pool. The addition of LDL (300 micrograms protein/mL) to the medium increased the level of total GAG incorporation of [3H]glucosamine by 40-50% and of [35S]sulfate by 15-20% on both substrata. For cells on plastic the relative increase in the medium and SCA pool was similar, whereas for cells in collagen gel the response to LDL was twice as great in the SCA pool as in the medium. The distribution of GAG types was unaffected by LDL; hyaluronic acid remained the principal GAG in the media pools of both substrata, heparan sulfate remained the main SCA GAG in cultures on plastic, and dermatan sulfate remained the dominant GAG in the SCA pool of collagen gel cultures. LDL degradation was measured at intervals up to 48 h after the addition of 125I-labeled LDL. The rate of accumulation of degraded LDL products was lower in collagen gel cultures, but the final levels achieved were the same in the two substrata. Concentrations of total cell cholesterol were similar, although the increases in free cholesterol induced by LDL were 26% greater in cells within collagen gel than in those on plastic. We conclude that fibroblasts grown within a collagen gel, as compared with those on a plastic substratum, (i) accumulate more GAG that remain attached to the substratum and cell surface; (ii) respond to LDL with a similar degree of increase in GAG accumulation, but more of the increase is found in the substratum and cell surface compartment; and (iii) accumulate more intracellular free cholesterol in response to LDL.