DNA Synthesis in Chloroplasts: III. THE DNA GYRASE INHIBITORS NALIDIXIC ACID AND NOVOBIOCIN INHIBIT BOTH THYMIDINE INCORPORATION INTO DNA AND PHOTOSYNTHETIC OXYGEN EVOLUTION BY ISOLATED CHLOROPLASTS

The influence of two DNA gyrase inhibitors, nalidixic acid andnovobiocin, on DNA synthesis in isolated pea chloroplasts wasexamined. Novobiocin at 1–5 mol m^–3 markedly lowered[³H]thymidine incorporation into DNA (30–95% inhibition);while less effective, nalidixic acid at similar concentrationsalso diminished incorporation (25–35% inhibition). Theinhibition of chloroplast DNA (ctDNA) biosynthesis by nalidixicacid and novobiocin was confirmed by autoradiography and densitometry.These data are consistent with the view that chloroplasts containa DNA gyrase-like enzyme which is necessary for DNA replication.Despite this, interpretation of the results is not straightforward,as both nalidixic acid and novobiocin also inhibited photosyntheticactivity. Each substance (at millimolar levels) reduced ferricyanide-dependentO₂ evolution in isolated chloroplasts. However, at lower concentrations(0.05–0.3 mol m^–3) they slightly enhanced photosyntheticelectron flow; thus, these compounds may act as uncouplers ofphotophosphorylation as well as inhibitors of electron transport.Nalidixic acid and novobiocin at relatively low (0.1 mol m^–3)concentrations also strongly reduced CO₂-dependent O₂ evolution(an index of CO₂ photo-assimilation) in isolated plastids. Thus,caution must be exercised in assessing results from studiesin which nalidixic acid and novobiocin are used with whole plants,cells, protoplasts or isolated chloroplasts. Key words: Chloroplast, DNA replication, novobiocin, nalidixic acid, DNA gyrase     

Glycoprotein Biosynthesis in Chlamydomonas: I. IN VITRO INCORPORATION OF GALACTOSE FROM UDP-[C]GALACTOSE INTO MEMBRANE-BOUND PROTEIN

A crude membrane fraction from Chlamydomonas reinhardii was found to catalyze d-galactose transfer from UDP-galactose to endogenous proteins. Highest incorporation rates were achieved by incubation at 25 degrees C and pH 7.5 in the presence of 10 millimolar Fe(2+). Hydrolytic studies on the labeled polymer revealed that radioactivity was attached to protein via an alkali-stable and acid-labile linkage. Identification of galactose as the only labeled sugar in the acid hydrolysate and results of a tentative estimation of the molecular weight of the charged alkaline degradation product indicate that monomeric galactose units are transferred to form an O-glycosidic bond with peptidyl hydroxyproline. No indications were found for a similar linkage to serine which, in contrast to the hydroxyproline-O-glycoside linkage, is acid-stable but is cleaved by beta-elimination. Chromatography of the sodium dodecyl sulfate-solubilized polymer on Sepharose-6B demonstrated that galactosyl residues are mainly associated with proteins which are of considerably higher molecular weight than are the majority of sodium dodecyl sulfate-denatured membrane proteins in this fraction.     

RADIOAUTOGRAPHIC STUDY OF IN VIVO AND IN VITRO INCORPORATION OF FUCOSE-3H INTO THYROGLOBULIN BY RAT THYROID FOLLICULAR CELLS

The incorporation of fucose-³H in rat thyroid follicles was studied by radioautography in the light and electron microscopes to determine the site of fucose incorporation into the carbohydrate side chains of thyroglobulin, and to follow the migration of thyroglobulin once it had been labeled with fucose-³H. Radioautographs were examined quantitatively in vivo at several times after injection of fucose-³H into rats, and in vitro following pulse-labeling of thyroid lobes in medium containing fucose-³H. At 3–5 min following fucose-³H administration in vivo, 85% of the silver grains were localized over the Golgi apparatus of thyroid follicular cells. By 20 min, silver grains appeared over apical vesicles, and by 1 hr over the colloid. At 4 hr, nearly all of the silver grains had migrated out of the cells into the colloid. Analysis of the changes in concentration of label with time showed that radioactivity over the Golgi apparatus increased for about 20 min and then decreased, while that over apical vesicles increased to reach a maximum at 35 min. Later, the concentration of label over the apical vesicles decreased, while that over the colloid increased. Similar results were obtained in vitro. It is concluded that fucose, which is located at the end of some of the carbohydrate side chains, is incorporated into thyroglobulin within the Golgi apparatus of thyroid follicular cells, thereby indicating that some of these side chains are completed there. Furthermore, the kinetic analysis demonstrates that apical vesicles are the secretion granules which transport thyroglobulin from the Golgi apparatus to the apex of the cell and release it into the colloid.     

Metabolism of Vertebrate Amino Sugars with N-Glycolyl Groups: INCORPORATION OF N-GLYCOLYLHEXOSAMINES INTO MAMMALIAN GLYCANS BY FEEDING N-GLYCOLYLGALACTOSAMINE

The outermost positions of mammalian cell-surface glycans are predominantly occupied by the sialic acids N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc). To date, hydroxylation of CMP-Neu5Ac resulting in the conversion into CMP-Neu5Gc is the only known enzymatic reaction in mammals to synthesize a monosaccharide carrying an N-glycolyl group. In our accompanying paper (Bergfeld, A. K., Pearce, O. M., Diaz, S. L., Pham, T., and Varki, A. (2012) J. Biol. Chem. 287, jbc.M112.363549), we report a metabolic pathway for degradation of Neu5Gc, demonstrating that N-acetylhexosamine pathways are tolerant toward the N-glycolyl substituent of Neu5Gc breakdown products. In this study, we show that exogenously added N-glycolylgalactosamine (GalNGc) serves as a precursor for Neu5Gc de novo biosynthesis, potentially involving seven distinct mammalian enzymes. Following the GalNAc salvage pathway, UDP-GalNGc is epimerized to UDP-GlcNGc, which might compete with the endogenous UDP-GlcNAc for the sialic acid biosynthetic pathway. Using UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase-deficient cells, we confirm that conversion of GalNGc into Neu5Gc depends on this key enzyme of sialic acid biosynthesis. Furthermore, we demonstrate by mass spectrometry that the metabolic intermediates UDP-GalNGc and UDP-GlcNGc serve as substrates for assembly of most major classes of cellular glycans. We show for the first time incorporation of GalNGc and GlcNGc into chondroitin/dermatan sulfates and heparan sulfates, respectively. As demonstrated by structural analysis, N-glycolylated hexosamines were found in cellular gangliosides and incorporated into Chinese hamster ovary cell O-glycans. Remarkably, GalNAc derivatives altered the overall O-glycosylation pattern as indicated by the occurrence of novel O-glycan structures. This study demonstrates that mammalian N-acetylhexosamine pathways and glycan assembly are surprisingly tolerant toward the N-glycolyl substituent.     

LIFE-CYCLE COMPONENTS OF SELECTION IN ERIGERON ANNUUS: II. GENETIC VARIATION

Genetic variation for seedling and adult fitness components was measured under natural conditions to determine the relative importance of the seedling stage for lifetime fitness in Erigeron annuus. Variation in lifetime reproductive success can result from both the persistent effects of genetic variation expressed among seedlings and from variation in adult fitness components. Analysis of covariance was used to separate the stage specific from the cumulative effects of genetic variance expressed earlier in the life cycle. E. annuus produces seeds through apomixis, which allowed measurement of the fitness of replicate genotypes from germination through the entire life cycle. There were significant differences among genotypes for date of emergence, seedling size, survivorship and fecundity, but heritabilities were low, indicating slow response to selection. For all characters, environmental components of variance were one to two orders of magnitude larger than genetic variance components, resulting in broad sense heritabilities less than 0.1. For seedling size and fecundity, all of the genetic variance was in the form of genotype-environment interactions, often with large negative genetic correlations across environments. In contrast, genotypes differed in mean survivorship through one year, but there were no genotype-environment interactions for viability. Genetic differences in viability were primarily expressed as differences in overwinter survivorship. Genotype × environment interactions among sites and blocks were generated early in the life cycle while the genotype × environment interactions in response to competitive environment (open, annual cover, perennial cover) first appeared in adult fecundity. Genetic variation in lifetime fitness was not significant, despite a fourfold difference in mean fitness among genotypes.     

PLASTID FUNCTION IN PLANT TISSUE CULTURES. I. PORPHYRIN SYNTHESIS BY DARK-GROWN HAPLOID AND DIPLOID ALBINO CULTURES

Tissue cultures lacking chlorophyll formed porphyrins when fed δ-aminolevulinic acid, a precursor of tetrapyrroles. When grown in the dark tissues from Ginkgo biloba L., Taxus, and Rosa formed protoporphyrin and several unidentified compounds. When grown in the light cultures did not form these pigments. The protoporphyrin was detected in the tissues after 3–6 hours incubation with δ-aminolevulinic acid; it was localized in the plastids by ultraviolet light microscopy and was identified by extraction procedures, chromatography, and absorption spectroscopy. No magnesium protoporphyrins were found, suggesting that chlorophyll synthesis was blocked at this point. Both male and female haploid albino tissues from Ginkgo formed protoporphyrin. The female albino tissue was derived from a chlorophyll-containing tissue culture from the female gametophyte by serially subculturing the green tissue in the dark. Upon exposing the female albino tissue to light, no greening occurred. The treatments used thus far have not caused chloroplasts to develop in the haploid albino tissues, even though the tissues contain many amyloplasts. Concurrent with the loss of chloroplasts, the female tissue loses all capacity to differentiate specialized cells, such as tracheids, resin cells, and chlorenchyma.     

POLYPHYLETIC ORIGINS OF ASEXUALITY IN DAPHNIA PULEX. II. MITOCHONDRIAL-DNA VARIATION

Allozyme studies of the cladoceran Daphnia pulex have shown that most populations reproduce by obligate parthenogenesis, although some cyclically parthenogenetic populations remain throughout the southern portion of its range. Clonal diversity within the obligate parthenogens is extremely high and has been attributed to the polyphyletic origin of asexuality. Specifically, it has been proposed that the clonal diversity in the obligate parthenogens was generated via the spread of a sex-limited meiosis suppressor through populations of a cyclically parthenogenetic ancestor. In this study, analysis of polymorphism of restriction-endonuclease sites in the mitochondrial genome, in conjunction with allozyme analysis, was used to determine whether obligate parthenogenesis has a monophyletic or polyphyletic origin in D. pulex. An allozyme survey of 77 populations from Ontario and Michigan was first conducted to determine breeding systems and levels of clonal diversity (Hebert et al., 1989). Mitochondrial-DNA variation was then surveyed in one isolate of each clone from each population reproducing by obligate parthenogenesis and in 2–4 isolates from each population reproducing by cyclic parthenogenesis. Seventeen restriction enzymes were used in this analysis. Thirty-five mitochondrial genotypes were found among the 36 obligate clones (as identified by allozyme analysis), while 17 mitochondrial genotypes were identified among 40 cyclic isolates from 14 populations. Five mitochondrial genotypes were found in both groups. Parsimony and phenetic-clustering methods were used to construct trees showing the genetic relationship among mitochondrial genotypes. The results clearly show that obligate parthenogenesis had a polyphyletic origin in this species. The close relationship between cyclic and obligate parthenogens in the Great Lakes region suggests that many obligate clones have recently been derived from cyclic populations and that the generation of clones is still occurring in this area. Patterns of clonal diversity based on the joint consideration of allozyme and mitochondrial-DNA data are discussed.     

SEX RATIO VARIATION IN A PARASITIC WASP II. DIALLEL CROSS

Sex ratio has been studied from many theoretical and empirical perspectives, but a general assumption in sex ratio research is that changes in sex ratio occur because of selection on sex ratio itself. I carried out a quantitative genetic experiment—a diallel cross among three strains—on a parasitic wasp, Muscidifurax raptor (Hymenoptera: Pteromalidae), to measure genetic variation for sex ratio. I also tested whether sex ratio may change as a consequence of selection on other life-history traits by estimating genetic covariances between sex ratio, fecundity, longevity, and development time. Most of the variation among strains could be accounted for by a maternal effect, likely caused by a microsporidian parasite that was transmitted through the West Germany (WG) strain. Genetic variation was small by comparison, but almost all traits were affected by dominance. The only significant additive genetic effect was for fecundity early in life. Upon crossing, all traits displayed heterosis: more female-biased sex ratio, greater fecundity, longer life, and faster development time. All life-history traits were correlated phenotypically, but the correlations were mainly the result of decreased performance in crosses with the WG strain that carried the microsporidian parasite. Dominance genetic correlations were also found between sex ratio, fecundity, and longevity. How the correlation between sex ratio and other life-history traits would affect sex ratio evolution depends upon the frequencies of sex-ratio genotypes within a population as well as the signs of the correlations, because sex ratio is under frequency-dependent selection whereas other traits are generally under directional selection. Although the results from crosses among laboratory populations should be approached with caution, the inbreeding depression (the difference between inbred and outcrossed progeny) found in M. raptor implies that the evolution of a female-biased sex ratio could be affected by selection for inbreeding avoidance.     

ALTERATIONS IN 3H-THYMIDINE INCORPORATION INTO DNA INDUCED BY METHYL CCNU [1-(2-CHLOROETHYL)-3-(4-METHYL CYCLOHEXYL)-1-NITROSOUREA] IN NORMAL AND TUMOROUS TISSUES IN VIVO

Methyl CCNU produces a suppression of tritiated thymidine (³H-TdR) incorporation into DNA in vivo in normal bone marrow and gastrointestinal tissues which is different in magnitude and duration from that seen in L1210 ascites tumor in the same animals. This suppression and recovery pattern is not seen in animals bearing L1210 ascites tumor resistant to MeCCNU. Where a different pattern of recovery is seen between normal host target tissues and tumor, the pattern can be exploited to increase the cure rate of animals bearing advanced L1210 ascites tumor with properly spaced second doses of MeCCNU. Additional information on the potential toxicity of second doses of MeCCNU can be predicted from knowledge of the time of recovery of DNA synthesis in the normal host target tissues.     

Coagulation Factor XIIIa Substrates in Human Plasma: IDENTIFICATION AND INCORPORATION INTO THE CLOT

Coagulation factor XIII (FXIII) is a transglutaminase with a well defined role in the final stages of blood coagulation. Active FXIII (FXIIIa) catalyzes the formation of ϵ-(γ-glutamyl)lysine isopeptide bonds between specific Gln and Lys residues. The primary physiological outcome of this catalytic activity is stabilization of the fibrin clot during coagulation. The stabilization is achieved through the introduction of cross-links between fibrin monomers and through cross-linking of proteins with anti-fibrinolytic activity to fibrin. FXIIIa additionally cross-links several proteins with other functionalities to the clot. Cross-linking of proteins to the clot is generally believed to modify clot characteristics such as proteolytic susceptibility and hereby affect the outcome of tissue damage. In the present study, we use a proteomic approach in combination with transglutaminase-specific labeling to identify FXIIIa plasma protein substrates and their reactive residues. The results revealed a total of 147 FXIIIa substrates, of which 132 have not previously been described. We confirm that 48 of the FXIIIa substrates were indeed incorporated into the insoluble fibrin clot during the coagulation of plasma. The identified substrates are involved in, among other activities, complement activation, coagulation, inflammatory and immune responses, and extracellular matrix organization.     

RNA Synthesis in Phaseolus Chloroplasts: II. RIBONUCLEIC ACID SYNTHESIS IN CHLOROPLASTS FROM DEVELOPING AND SENESCING LEAVES

The rate of RNA synthesis in chloroplasts from the primary leavesof Phaseolus vulgaris L. cv. Canadian Wonder was measured invitro as plant age increased. The rate per leaf began to fallbefore the leaf was 70% expanded. At full expansion, activityhad fallen by 70%. Chloroplast RNA synthesis per unit chlorophyllwas falling before the leaf was 25% expanded. When all parts of the plant above the mature primary leaveswere removed (detopping) chloroplast RNA synthesis in theseleaves rose within 36 h. The rate increased to a maximum 3–4d after detopping, when it was 5–10 times control values;thereafter it fell again. The chlorophyll content began to increaseabout 4 d after detopping, eventually rising by 100%. Detoppingcaused a 3-fold increase in the Triton X-100-soluble DNA contentof chloroplast preparations, measured after 3.5 d. At that timethe rate of RNA synthesis per unit Triton-soluble DNA was thesame in chloroplasts from the primary leaves of intact and detoppedplants. Detopping also resulted in an increase in the depthof the leaf palisade layer. The effects of detopping on chloroplasts were prevented by darknessand reduced by shading. Increased chloroplast RNA polymerase activity was also inducedin the primary leaves by placing a polythene bag over intactplants, enclosing everything above these leaves. Removal ofthe roots from detopped plants prevented the rise in the rateof chloroplast RNA synthesis.     

DEVELOPMENTAL ANATOMY OF LIGHT-INDUCED ROOT NODULATION BY ZAMIA PUMILA L. SEEDLINGS IN STERILE CULTURE

The developmental anatomy of Zamia pumila L. root apices was studied during light-induced nodulation. Dark-grown roots had an apical organization identical to that of other cycads and similar to that of other gymnosperms. A distinct protoderm was not observed in these roots, which had a large open meristem and a root cap with a well-defined columella. During nodulation, the meristem became reduced in size, and its constituent cells became vacuolate until all but a few resembled ground tissue. The root cap senesced during nodulation, and a recognizable root cap was absent from mature nodules. A file of densely cytoplasmic cells with centrally positioned nuclei developed in the nodule cortex. This layer was continuous across the nodule apex, and was identical to the presumptive algal-zone described previously by other authors. Light-induced nodules branched dichotomously and were identical to algal-free nodules described by other authors. In dichotomously branched nodules, each lobe was covered by a parenchymatous mantle analogous to a root cap. A unicellular layer similar to the presumptive algal zone spanned the gap between opposite nodule lobes, and extended beneath each lobe before terminating in the cortex. Typical meristematic regions were not observed in these nodules. Based on cell sizes and patterns, a meristematic zone was thought to exist between the mantle and the inner cortex.     

LIMITATIONS IN THE USE OF [3H]THYMIDINE INCORPORATION INTO DNA AS AN INDICATOR OF EPIDERMAL KERATINOCYTE PROLIFERATION IN VITRO

The validity of using the incorporation of [³H]thymidine into DNA as an indicator of epidermal keratinocyte proliferation in vitro has been investigated. Other parameters of cell proliferation, direct count of cell number and measurement of DNA content, consistently fail to correlate with changes in [³H]thymidine incorporation into DNA in primary and first passage cultures of rabbit and human epidermal keratinocytes. Maximum incorporation of [³H]thymidine precedes the active growth period by three days. Incorporation declines markedly during the proliferative period. Thymidine kinase activity decreases during the proliferative growth phase. Incorporation of another pyrimidine nucleotide precursor, [¹⁴C]aspartic acid, suggests that in epidermal keratinocytes in vitro the extent of utilization of the salvage and the de novo pathways may be inversely related. In such cases [³H]thymidine incorporation into TCA precipitable material fails to reflect accurately cell proliferation.