Characterization of a novel eukaryal nick-sealing RNA ligase from Naegleria gruberi

The proteome of the amoebo-flagellate protozoan Naegleria gruberi is rich in candidate RNA repair enzymes, including 15 putative RNA ligases, one of which, NgrRnl, is a eukaryal homolog of Deinococcus radiodurans RNA ligase, DraRnl. Here we report that purified recombinant NgrRnl seals nicked 3′-OH/5′-PO₄ duplexes in which the 3′-OH strand is RNA. It does so via the “classic” ligase pathway, entailing reaction with ATP to form a covalent NgrRnl–AMP intermediate, transfer of AMP to the nick 5′-PO₄, and attack of the RNA 3′-OH on the adenylylated nick to form a 3′–5′ phosphodiester. Unlike members of the four known families of ATP-dependent RNA ligases, NgrRnl lacks a carboxy-terminal appendage to its nucleotidyltransferase domain. Instead, it contains a defining amino-terminal domain that we show is important for 3′-OH/5′-PO₄ nick-sealing and ligase adenylylation, but dispensable for phosphodiester synthesis at a preadenylylated nick. We propose that NgrRnl, DraRnl, and their homologs from diverse bacteria, viruses, and unicellular eukarya comprise a new “Rnl5 family” of nick-sealing ligases with a signature domain organization.     

Large genetic heterogeneity within amoebas of the species Naegleria gruberi and evolutionary affinities to the other species of the genus

The allozyme survey was extended to 7 strains of Naegleria gruberi and N. jadini in order to further characterize the genetic structure of these free-living amoebas. As formerly known for several characters the electrophoretic evidence reveals considerable heterogeneity at the genetic level among N. gruberi strains. Moreover, 2 distinct gene pools, that might likely represent natural taxa, are clearly identified. The single strain of N. jadini appears evolutionarily related to 1 group of N. gruberi which is also related to N. a. australiensis.     

Chloroplast DNA microsatellite analysis supports a polyphyletic origin for barley

Five barley chloroplast DNA microsatellites (cpSSRs) were used to study genetic relationships among a set of 186 barley accessions—34 Hordeum vulgare ssp. spontaneum (HS accessions) from Morocco, Ethiopia, Cyprus, Crete, Libya, Iraq, Iran, Turkey, Afghanistan and Israel, 122 H. vulgare ssp. vulgare landraces (HV landraces) from Spain, Bolivia (old Spanish introductions), Morocco, Libya and Ethiopia and 20 modern European spring barleys (HV cultivars). All loci were polymorphic in the material studied, with the number of alleles per locus ranging from two to three. Fifteen multi-locus haplotypes were observed, 11 in HS accessions and seven in HV landraces and cultivars. Of the seven haplotypes found in the HV lines, three were shared with the HS accessions, and four were unique. Cluster analysis revealed two main groups, one consisting of HS accessions from Ethiopia and the HV landraces from Spain, Bolivia (old Spanish), Morocco and Ethiopia, whereas the other larger group contained all of the other accessions studied. Based on these grouping and the existence of haplotypes found in the HV landraces and cultivars but not in the HS wild barley, a polyphyletic origin is proposed for barley, with further centres of origin in Ethiopia and the Western Mediterranean.     

Preparation and Properties of Mitochondria from Naegleria gruberi*

Whole cell respiration rates were measured polarographically for Naegleria gruberi during growth in agitated cultures. Log growth phase amebae consumed 80 ng atoms O/min/mg cell protein. At stationary phase, respiration rate decreased 4–fold. Intact mitochondria were isolated from N. gruberi and their oxidative and phosphorylative capacities were studied polarographically. As with the mammalian system, the mitochondria oxidized succinate and NAD-linked substrates, but unlike rat liver mitochondria, those from the protozoan rapidly oxidized citrate and NADH. The rates of substrate oxidation were ADP-dependent, with ADP:O ratios equalling ? 2.8 for NAD-linked substrates and ? 2.2 for succinate. The respiratory control ratios. 2 to 4 for 11 substrates, were dependent on Pi, Mg²⁺, and serum albumin. Potassium cyanide, azide, malonale, and rotenone inhibited electron transport the same way as that of the mammalian system: however, amytal inhibited both glutamate and succinate respiration. Pentachlorophenol, DNP, and bilirubin uncoupled oxidation from phosphorylation. Difference spectra of oxidized and dithionite-reduced mitochondria had distinct absorption bands of flavins and of c-, b-, and α-type cytochromes.     

Molecular phylogeny of cuckoos supports a polyphyletic origin of brood parasitism

We constructed a molecular phylogeny of 15 species of cuckoos using mitochondrial DNA sequences spanning 553 nucleotide bases of the cytochrome b gene and 298 nucleotide bases of the ND2 gene. A parallel analysis for the cytochrome b gene including published sequences in the Genbank database was performed. Phylogenetic analyses of the sequences were done using parsimony, a sequence distance method (Fitch-Margoliash), and a character-state method which uses probabilities (maximum likelihood). Phenograms support the monophyly of three major clades: Cuculinae, Phaenicophaeinae and Neomorphinae-Crotophaginae. Clamator, a strictly parasitic genus traditionally included within the Cuculinae, groups together with Coccyzus (a nonobligate parasite) and some nesting cuckoos. Tapera and Dromococcyx, the parasitic cuckoos from the New World, appear as sister genera, close to New World cuckoos: Neomorphinae and Crotophaginae. Based on the results, and being conscious that a more strict resolution of the relationships among the three major clades is required, we postulate that brood parasitism has a polyphyletic origin in the Cuculiformes, with parasite species being found within the three defined clades. Evidence suggests that species within each clade share a common parasitic ancestor, but some show partial or total loss of brood parasitic behaviour.     

Small-subunit ribosomal RNA gene sequences of Phaeodarea challenge the monophyly of Haeckel's Radiolaria

In his grand monograph of Radiolaria, Ernst Haeckel originally included Phaeodarea together with Acantharea and Polycystinea, all three taxa characterized by the presence of a central capsule and the possession of axopodia. Cytological and ultrastructural studies, however, questioned the monophyly of Radiolaria, suggesting an independent evolutionary origin of the three taxa, and the first molecular data on Acantharea and Polycystinea brought controversial results. To test further the monophyly of Radiolaria, we sequenced the complete small subunit ribosomal RNA gene of three phaeodarians and three polycystines. Our analyses reveal that phaeodarians clearly branch among the recently described phylum Cercozoa, separately from Acantharea and Polycystinea. This result enhances the morphological variability within the phylum Cercozoa, which already contains very heterogeneous groups of protists. Our study also confirms the common origin of Acantharea and Polycystinea, which form a sister-group to the Cercozoa, and allows a phylogenetic reinterpretation of the morphological features of the three radiolarian groups.     

Superprecipitation of an actomyosin-like complex isolated from Naegleria gruberi amoebae

A protein complex similar to muscle actomyosin and plasmodial myosin B has been isolated from Naegleria gruberi amoebae. This extract, which comprises approximately 0.7% of the total cell protein, has the solubility properties of actomyosin, displays Ca²⁺-activated, Mg²⁺-inhibited ATPase activity, forms microfilaments, and undergoes a strong superprecipitation reaction. Superprecipitation is initiated by ATP and is preceded by a very brief clearing phase. Although added Mg²⁺ is not essential for superprecipitation of the extract, the reaction proceeds maximally when 7 mM Mg²⁺ is provided. This extract does not appear to have a Ca²⁺ requirement, and superprecipitation is in fact inhibited by added Ca²⁺ ion at all concentrations greater than 0.1 mM. Both ATPase activity and superprecipitation of the actomyosin-like complex are inhibited by the sulfhydryl inhibitor salyrgan.     

Transformation in Naegleria gruberi: patterns of RNA synthesis examined by polyacrylamide gel electrophoresis

Naegleria gruberi were grown on bacteria and methods were devised to free the cellular RNA from bacterial RNA contamination. Use of actinomycin D and cycloheximide showed that the transformation of Naegleria from amoeba to flagellate required RNA synthesis for 30 min and protein synthesis for 40 min after the initial stimulus of distilled water. Comparison of the patterns of RNA synthesized during transformation with those during growth indicated a considerable amount of new RNA produced during the phenotypic change. Most marked was the increase in RNA co-migrating on polyacrylamide gels with the small ribosomal sub-unit RNA, together with RNAs between the latter and transfer RNA. These results were compared with other published results using axenically-grown cells cells and sucrose density gradient centrifugation. Cells placed in 80 mM NaCl instead of distilled water fail to transform but the pattern of newly-synthesized RNAs was not significantly different from that seen in transforming cells. This suggested that high salt concentrations inhibit transformation by inhibiting synthesis and/or assembly of certain proteins rather than RNA synthesis. Eluted material from various regions of polyacrylamide gels containing RNA extracted from transforming cells was used in a cell-free system. Incorporation of 3H-glutamic acid but not 3H-tryptophan was stimulated by material extracted from the 18S regions of the gels.     

Intranuclear Virus-like Bodies in the Amoeboflagellate Naegleria gruberi*

SYNOPSIS. Intranuclear virus-like bodies were seen in cultures of the EG strain of Naegleria gruberi from soil. Introduction of these virus-like particles into cultures seemed to coincide with use of chicken embryo extract as a supplement in culture media used to maintain axenic amoebae in the laboratory; the appearance of the virus-like units is triggered by transfer of axenic lines of N. gruberi EG into monobacterial culture medium. The particles, ～ 100 nm in diameter, are mainly restricted to the nucleus of the cell. Passage of particles from the nucleoplasm into the cytoplasm is suggested by theit association with tubular projections from the nuclear membrane, and particles have been seen in the cytoplasm of the amoebae. The virus-like bodies resemble reovirus.     

Comparison of Naegleria fowleri and Naegleria gruberi Cultivated in the Same Nutrient Medium1

The human pathogenic amoeboflagellate Naegleria fowleri and the nonpathogenic species N. gruberi can be cultivated axenically but usually in different media. Naegleria fowleri 6088 has been adapted to grow in Balamuth H-4 medium, usually used to propagate N. gruberi nB81. and nB81 has been adapted to grow in supplemented Nelson's medium, usually used to propagate N. fowleri. N. gruberi nB81. grown in either medium, enflagellated 135 to 150 min after subculture to non-nutrient amoeba saline, whereas 6088 required 225 min. Naegleria gruberi nB81 grown in either medium was agglutinated by 100 ug concanavalin A/ml, whereas N. fowleri 6088 was not. Naegleria fowleri and N. gruberi grown in Nelson's medium became rounded to a greater extent upon chilling at 5° C and remained rounded longer than Naegleria grown in Balamuth medium. The specificity of the surface antigens was an inherent characteristic of each species and not dependent upon the propagating medium. but Naegleria grown in Nelson's medium was agglutinated more reproducibly and more effectively by antiserum. N. gruberi was somewhat more resistant to acriflavine, actinomycin D, cycloheximide, or tetracycline than N. fowleri, regardless of the culture medium. Naegleria fowleri 6088 grown in Nelson's medium, however, was more resistant to actinomycin D, daunomycin. mithramycin. sulfamethoxazole, or tyrocidine than 6088 grown in Balamuth medium. There are limitations on the validity of comparisons of N. fowleri and N. gruberi based upon cultures grown in different media.     

Acriflavin Inhibition of Morphogenesis in Naegleria gruberi*

SYNOPSIS. When amoeboid organisms of Naegleria gruberi are treated with acriflavin at concentrations under 70 μg/ml, they still can form flagellates. Acriflavin between 70 μg/ml and 110 μg/ml increasingly inhibits morphogenesis. The effect of acriflavin is specific for the morphogenetic system since amoeboid organisms treated with acriflavin between 110 and 200 μg/ml are not otherwise inhibited and behave like the controls.     

Ribonucleoprotein-Containing Vesicles in Cysts of Naegleria gruberi*

SYNOPSIS. Ultraviolet microscopy and electron microscope autoradiography were used to study ribonucleoprotein in cysts of Naegleria gruberi. The absorption maximum for cysts is at 265 nm with little detectable absorption occurring at 295 nm. Pre-cystic trophozoites absorb less strongly than the cysts at 265 mm. Acridine orange staining indicated concentrations of ribose nucleic acid or ribonucleoprotein in the cytoplasm of young cysts. The dye stained discrete vesicles in the cytoplasm. Tritiated uridine and tritiated proline were used to follow changes in RN-protein at encystment. Label was incorporated into vesicles filled with ribosome-like particles. These are presumably the sites of acridine orange staining. Relatively little label was associated with the cyst cytoplasmic matrix; most of the silver grains lay over the nucleus and cytoplasmic organelles. The vesicles are believed to represent autophagosomal-type vacuoles with the contents derived from breakdown of organelles such as mitochondria. The path of label into the vesicles is via lysis of labeled cytoplasmic organelles. The RN-protein vesicles of Naegleria gruberi cysts are compared to the chromatoid bodies of Entamoeba invadens. It is concluded that, tho differences in detail are present, the role of the structures in the cysts is probably the same. They are a ready source of amino acids and ribosomes in a dedifferentiated or pool state to be used for synthetic reactions that accompany resumption of trophic existence.     

Electrophoretic Karyotype and Linkage Groups of the Amoeboflagellate Naegleria gruberi

ABSTRACT. We have constructed a molecular karyotype for two strains of Naegleria gruberi using pulsed field gel electrophoresis. Each strain has about 23 chromosomes, considerably more than any previous estimate. These chromosomes range in size from 400 kilobasepairs to over 2,000 kilobasepairs. In Naegleria , construction of the DNA karyotype depends on assessment of the anomalous electrophoretic mobility of the circular ribosomal RNA genes. We have determined the chromosomal locations of an identified unique gene (flagellar calmodulin) and four identified multigene families (α- and β-tubulin, actin, ubiquitin), as well as three differentially expressed genes of unknown functions. The ca. 12 actin genes are dispersed over at least seven chromosomes, whereas the majority of the more than eight α-tubulin genes are confined to a single chromosome. The ubiquitin genes are found on five chromosomes in one strain and seven in the other and the β-tubulin genes are on three or four. Our observations provide a foundation for molecular genetic studies in this organism.     

Synthesis and assembly of the cytoskeleton of Naegleria gruberi flagellates

When Naegleria gruberi flagellates were extracted with nonionic detergent and stained by the indirect immunofluorescence method with AA-4.3 (a monoclonal antibody against Naegleria beta-tubulin), flagella and a network of cytoskeletal microtubules (CSMT) were seen. When Naegleria amebae were examined in the same way, no cytoplasmic tubulin-containing structures were seen. Formation of the flagellate cytoskeleton was followed during the differentiation of amebae into flagellates by staining cells with AA-4.3. The first tubulin containing structures were a few cytoplasmic microtubules that formed at the time amebae rounded up into spherical cells. The formation of these microtubules was followed by the appearance of basal bodies and flagella and then by the formation of the CSMT. The CSMT formed before the cells assumed the flagellate shape. In flagellate shaped cells the CSMT radiate from the base of the flagella and follow a curving path the full length of the cell. Protein synthetic requirements for the formation of CSMT were examined by transferring cells to cycloheximide at various times after initiation. One-half the population completed the protein synthesis essential for formation of CSMT 61 min after initiation of the differentiation. This is 10 min after the time when protein synthesis for formation of flagella is completed and 10-15 min before the time when the protein synthesis necessary for formation of the flagellate shape is completed.