The Nutrition of Parauronema acutum*

SYNOPSIS. A symbiote-free strain of Parauronema acutum, 110–3, a small marine hymenostome ciliate has been cultured in a synthetic medium consisting of amino acids, purine derivatives, vitamins, lipids and artificial sea water. Populations of ～ 1.3 × 10⁶ per ml were obtained in 5 to 6 days at 27 C in the dark in medium prepared in sea water, density = 1.015 g/cc at a surface to volume ratio of 5 cm²/ml. The pH optimum was 7.2. The following amino acids were determined to be essential for the growth of this strain: arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine (or glycine), threonine, tryptophan and valine: guanine, guanosine or guanylic acid, but not adenine, adenosine, adenylic acid, hypoxanthine, inosine, inosinic acid, xanthine, xanthosine, or xanthylic acid, satisfied the need for a purine for growth of this organism. Pyrimidines were not required for growth. Of the vitamins tested, folic acid, nicotinamide, d-pantothenic acid, pyridoxal HCl, riboflavin, thiamine HCl and thioctic acid were essential for growth; biotin was not. Growth in the absence of lipids was transplantable, but amounted to ～ 3% that obtained in medium containing a mixture of asolectin, animal cephalin and Tween 80. Asolectin alone at high concentrations was almost as effective as the lipid mixture in supporting growth. Purified phospholipids such as phosphatidyl serine, phosphatidyl choline and phosphatidyl inositol were less effective on an individual basis. In minimal medium containing only the “essential” amino acids, growth was less than 5% that obtained in the complete medium, but could be restored to maximal by the addition of either glutamic acid or aspartic acid. A number of substances, including sugars, amino acids and Krebs cycle intermediates, partially restored growth under these conditions. Only glycogen, starch and glucose-1-phosphate, tested individually, were as effective as glutamic acid or aspartic acid in restoring growth to optimal levels.     

Glycogen in the Marine Protozoon Parauronema acutum*

SYNOPSIS. The carbohydrate which accumulates in the cytoplasm of the marine protozoon, Parauronema acutum, during normal growth was isolated, purified and characterized chemically. The highly purified material yielded only glucose residues following hydrolysis in 0.6 N HCl for 3 h at 100 C; measurement of total carbohydrate by the phenol-sulfuric acid method and by treatment with amylo-glucosidase and glucose oxidase gave similar values. Aqueous solutions of the purified material reacted with iodine to form a complex which exhibited an absorption peak at 456 nm with a shift to 484 nm in the presence of 50% saturated (NH₄)₂SO₄. Digestion with α-amylase, β-amylase, and isoamylase yielded 71%, 45% and 8.3% hydrolysis, respectively. Treatment sequentially with both isoamylase and β-amylase gave complete hydrolysis of the polymer. The average chain length (CL) determined by the isoamylase procedure was 12. These observations are consistent with the view that the carbohydrate isolated from the protozoan is a polymer consisting of α-D-glucose residues arranged in chains containing α-(1→4) linkages with branch points containing α-(1→6) linkages occurring once on the average of ～ 12 glucose residues and, as such, is indistinguishable from glycogen isolated from mammalian sources.     

Purine-Excretory Nature of Refractile Bodies in the Marine Ciliate Parauronema acutum*

SYNOPSIS. A method was developed for the isolation and purification of crystalline, highly refractile bodies found in the cytoplasm of a symbiote-free strain of the marine hymenostome ciliate, Parauronema acutum, strain 110–3. Chemical analysis of the purified refractile bodies revealed an abundance of the purines, hypoxanthine and guanine. It was evident from studies involving the use of ¹⁴C-labeled precursors that both hypoxanthine and guanine are derived from higher purine derivatives. We postulate that these bodies are excretory in function and that guanine and hypoxanthine are major endproducts of purine metabolism of P. acutum.     

DNA base composition and genome size of the prokaryotic symbiont in Riftia pachyptila (Pogonophora)

Abstract It has been proposed that Riftia pachyptila , a pogonophoran tube worm abundant at hydrothermal deep sea vents, metabolizes solely via a chemoautotrophic symbiosiols. The symbionts resemble sulfur oxidizing bacteria and form the specific 'trophosome' tissue. Samples of DNA purified from trophosome and vestimentum (muscle) tissues of R. pachyptila were comparatively characterized by thermal denaturation studies, and by analysis of renaturation kinetics. The results show that the great majority of trophosome DNA is homogeneous and prokaryotic with a base ratio of approx. 58 mol% G + C. Its genome size (genetic complexity) is typical of free-living bacteria. Approx. 5% of trophosome DNA appears to be invertebrate DNA equivalent to that found in the vestimentum tissue which lacks symbionts.     

Activation of Polynuclear Aromatic Hydrocarbons to Mutagens by the Marine Ciliate Parauronema acutum

The marine ciliate Parauronema acutum converted 2-aminofluorene and 2-acetylaminofluorene to compounds with mutagenic activity in the Ames Salmonella test. The ciliate, however, did not activate benzo (α)pyrene or benzanthracene or destroy the mutagenic properties of nitrosoguanidine. Homogenates, when substituted for the liver S-9 fraction in the Salmonella/microsome test, activated 2-aminofluorene and 2-acetylaminofluorene to mutagens. Benzo(α)pyrene and benzanthracene were not activated, nor was nitrosoguanidine inactivated. Phenobarbitol did not induce or increase the amount of activating activity. The activation showed no requirement for the reduced nicotinamide adenine dinucleotide phosphate-regenerating system required by liver P-450 cytochromes. Upon differential sedimentation of a cell homogenate, the majority of the activity sedimented with a small-particle fraction with sedimentation properties like those of microsomes from higher eucaryotes. Benzo(α)pyrene, although not metabolized, was accumulated by cultures of P. acutum at a linear rate and was not appreciably released (10%) after removal of benzo(α)pyrene from the incubation medium. Hence, this ciliate could convert certain polynuclear aromatic hydrocarbons to mutagens and accumulate others.     

Neutral lipids, their fatty acids, and the sterols of the marine ciliated protozoon, Parauronema acutum

The neutral lipids and their fatty acids and the sterol fractions of the marine ciliated protozoon, Parauronema acutum, were characterized. The neutral lipids consisted of triglycerides (30%), sterols (29%), free fatty acids (24%), steryl esters (9%), and diglycerides (8%) and small amounts of fatty alcohols. The fatty acid profiles of these lipids were very similar although quantitative differences were detected. Saturated fatty acids, primarily 14:0, 16:0, and 18:0 constituted 20-30% of the total. Unsaturated fatty acids containing one to three double bonds, primarily 18:1(9), 18:2 (9,12), 18:3 (9, 12, 15) and 20:3 (11, 14, 17), constituted 35-50% of the total. Highly unsaturated fatty acids, 18:4 (6, 9, 12, 15), 20:5 (5, 8, 11, 14, 17) and 22:6 (4, 7, 10, 16, 19), constituted 16-25% of the total. The fatty alcohols consisted of 14:0 (2%), 16:0 (66%), 18:0 (3%), 20:0 (8%), and 22:0 (21%). The sterols of Parauronema acutum consisted of cholesterol (53%), campesterol (32%), desmosterol (7%), and beta-sitosterol (8%).     

The process of genome shrinkage in the obligate symbiont Buchnera aphidicola

Background  

Very small genomes have evolved repeatedly in eubacterial lineages that have adopted obligate associations with eukaryotic hosts. Complete genome sequences have revealed that small genomes retain very different gene sets, raising the question of how final genome content is determined. To examine the process of genome reduction, the tiny genome of the endosymbiont Buchnera aphidicola was compared to the larger ancestral genome, reconstructed on the basis of the phylogenetic distribution of gene orthologs among fully sequenced relatives of Escherichia coli and Buchnera.     

Evolution of genome size and DNA base composition in reptiles

The evolution of genome size and base composition of DNA from various reptiles has been studied. DNA amount was measured cytophotometrically and GC concentration estimated by thermal denaturation. The Reptilia appear to be a fairly homogeneous group with respect to DNA quantity, although chelonians stand out because of their higher inter- and intrafamilial variability and DNA content. Quantitative DNA variations do not show a single evolutionary trend, but rather seem to have followed different patterns within each group.The differences in genome size between related species seem to be mainly the result of duplication or loss of DNA sequences characterized by a similar mean denaturation temperature. This agrees with observations of other authors that quantitative variations in reptiles are mainly due to differences in the amount of repetitive DNA.Several hypotheses on the significance of quantitative DNA variations in reptiles are discussed.     

Changes in the Fatty Acid Composition of the Marine Ciliated Protozoan Parauronema acutum with Increasing Culture Age and Adaptation to Changing Sodium Chloride Concentrations

Changes in the fatty acid composition of the membrane lipids of the marine ciliate. Parauronema acutum were studied in ciliates harvested from early logarithmic, decelerating logarithmic and stationary phase culture. The relative amounts of 18:1 (9) and 18:2 (9, 12) decreases in both the phospholipid and the neutral sphingolipid fractions with increasing culture age. The content of 18:4 (6, 9, 12, 15), 20:5 (5, 8, 11, 14, 17) and 22:6 (4, 7, 10, 13, 16, 19) in these same lipids increases with culture age. While P. acutum was isolated as a marine ciliate and is usually grown in a medium containing 2.8% NaCl concentration, it actually grows well over NaCl concentration of 1% to 3% and will grow suboptimally without added NaCl. NaCl concentrations above 3% are inhibitory, although suboptimal growth occurs at 5% NaCl concentration. Lipids obtained from ciliates grown at either 1.5% or 2.8% NaCl have essentially identical FAME profiles. Lipids obtained from ciliates grown at either higher or lower concentrations of NaCl show marked changes in FAME profile. In both cases 18:2 (9, 12) content greatly increases while the content of 18 and 20 carbon highly unsaturated fatly acids, particularly 22:6 (4, 7, 10, 13, 16, 19), decreases.     

Plant DNA flow cytometry and estimation of nuclear genome size

BACKGROUND: DNA flow cytometry describes the use of flow cytometry for estimation of DNA quantity in cell nuclei. The method involves preparation of aqueous suspensions of intact nuclei whose DNA is stained using a DNA fluorochrome. The nuclei are classified according to their relative fluorescence intensity or DNA content. Because the sample preparation and analysis is convenient and rapid, DNA flow cytometry has become a popular method for ploidy screening, detection of mixoploidy and aneuploidy, cell cycle analysis, assessment of the degree of polysomaty, determination of reproductive pathway, and estimation of absolute DNA amount or genome size. While the former applications are relatively straightforward, estimation of absolute DNA amount requires special attention to possible errors in sample preparation and analysis. SCOPE: The article reviews current procedures for estimation of absolute DNA amounts in plants using flow cytometry, with special emphasis on preparation of nuclei suspensions, stoichiometric DNA staining and the use of DNA reference standards. In addition, methodological pitfalls encountered in estimation of intraspecific variation in genome size are discussed as well as problems linked to the use of DNA flow cytometry for fieldwork. CONCLUSIONS: Reliable estimation of absolute DNA amounts in plants using flow cytometry is not a trivial task. Although several well-proven protocols are available and some factors controlling the precision and reproducibility have been identified, several problems persist: (1) the need for fresh tissues complicates the transfer of samples from field to the laboratory and/or their storage; (2) the role of cytosolic compounds interfering with quantitative DNA staining is not well understood; and (3) the use of a set of internationally agreed DNA reference standards still remains an unrealized goal.     

Cell size does not always correspond to genome size: phylogenetic analysis in geckos questions optimal DNA theories of genome size evolution

At higher taxonomic levels, a significant correlation between genome size (GS) and erythrocyte size (ES) has been reported for many taxa. Under optimal DNA theories, several mechanisms presuming a causative link between GS and ES have been proposed to explain this seemingly general pattern. The correlation between GS and ES has been rarely tested among closely related organisms within an explicit phylogenetic framework. Eyelid geckos (family Eublepharidae) serve as a proper group to conduct such an analysis. We used flow cytometry to measure GS in 15 forms of eublepharids and conducted a phylogenetic reconstruction of GS and ES to test the successiveness of evolutionary shifts in these traits. Most parsimoniously, there were two independent increases and two decreases in GS during the evolution of eublepharids. Nevertheless, changes in GS and ES were not phylogenetically associated in a manner predicted by optimal DNA theories. Our results question the generality of causative bonds between DNA content and cell size and demonstrate that cell size cannot always serve as a proxy of GS. We suggest there is no need to expect a direct causative link between GS and ES to explain the correlation between GS and cell size at higher taxonomic levels. Such a correlation can be explained by simple mechanistic constraints and a combination of the population-genetic model of genome complexity with cell-size-metabolic rate relationship.     

Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size

Genome duplication in free-living cellular organisms is performed by DNA replicases that always include a DNA polymerase, a DNA sliding clamp and a clamp loader. What are the evolutionary solutions for DNA replicases associated with smaller genomes? Are there some general principles? To address these questions we analyzed DNA replicases of double-stranded (ds) DNA viruses. In the process we discovered highly divergent B-family DNA polymerases in phiKZ-like phages and remote sliding clamp homologs in Ascoviridae family and Ma-LMM01 phage. The analysis revealed a clear dependency between DNA replicase components and the viral genome size. As the genome size increases, viruses universally encode their own DNA polymerases and frequently have homologs of DNA sliding clamps, which sometimes are accompanied by clamp loader subunits. This pattern is highly non-random. The absence of sliding clamps in large viral genomes usually coincides with the presence of atypical polymerases. Meanwhile, sliding clamp homologs, not accompanied by clamp loaders, have an elevated positive electrostatic potential, characteristic of non-ring viral processivity factors that bind the DNA directly. Unexpectedly, we found that similar electrostatic properties are shared by the eukaryotic 9-1-1 clamp subunits, Hus1 and, to a lesser extent, Rad9, also suggesting the possibility of direct DNA binding.     

Extrachromosomal DNA of the symbiont Sodalis glossinidius

The extrachromosomal DNA of Sodalis glossinidius from two tsetse fly species was sequenced and contained four circular elements: three plasmids, pSG1 (82 kb), pSG2 (27 kb), and pSG4 (11 kb), and a bacteriophage-like pSG3 (19 kb) element. The information suggests S. glossinidius is evolving towards an obligate association with tsetse flies.     

The genome of Oscheius tipulae: determination of size, complexity, and structure by DNA reassociation using fluorescent dye.

This work describes the physicochemical characterization of the genome and telomere structure from the nematode Oscheius tipulae CEW1. Oscheius tipulae is a free-living nematode belonging to the family Rhabditidae and has been used as a model system for comparative genetic studies. A new protocol that combines fluorescent detection of double-stranded DNA and S1 nuclease was used to determine the genome size of O. tipulae as 100.8 Mb (approximately 0.1 pg DNA/haploid nucleus). The genome of this nematode is made up of 83.4% unique copy sequences, 9.4% intermediate repetitive sequences, and 7.2% highly repetitive sequences, suggesting that its structure is similar to those of other nematodes of the genus Caenorhabditis. We also showed that O. tipulae has the same telomere repeats already found in Caenorhabditis elegans at the ends and in internal regions of the chromosomes. Using a cassette-ligation-mediated PCR protocol we were able to obtain 5 different putative subtelomeric sequences of O. tipulae, which show no similarity to C. elegans or C. briggsae subtelomeric regions. DAPI staining of hermaphrodite gonad cells show that, as detected in C. elegans and other rhabditids, O. tipulae have a haploid complement of 6 chromosomes.     

The problem of the eukaryotic genome size

The current state of knowledge concerning the unsolved problem of the huge interspecific eukaryotic genome size variations not correlating with the species phenotypic complexity (C-value enigma also known as C-value paradox) is reviewed. Characteristic features of eukaryotic genome structure and molecular mechanisms that are the basis of genome size changes are examined in connection with the C-value enigma. It is emphasized that endogenous mutagens, including reactive oxygen species, create a constant nuclear environment where any genome evolves. An original quantitative model and general conception are proposed to explain the C-value enigma. In accordance with the theory, the noncoding sequences of the eukaryotic genome provide genes with global and differential protection against chemical mutagens and (in addition to the anti-mutagenesis and DNA repair systems) form a new, third system that protects eukaryotic genetic information. The joint action of these systems controls the spontaneous mutation rate in coding sequences of the eukaryotic genome. It is hypothesized that the genome size is inversely proportional to functional efficiency of the anti-mutagenesis and/or DNA repair systems in a particular biological species. In this connection, a model of eukaryotic genome evolution is proposed.