Restriction map, partial cloning and localization of 9S and 12S kinetoplast RNA genes on the maxicircle component of the kinetoplast DNA of Leishmania tarentolae.

We have constructed a restriction map of the maxicircle component of the kinetoplast DNA of Leishmania tarentolae for the enzymes EcoRI, Bam HI, HaeIII, HpaII, SalI, BglII and HindIII. The 9 and 12S kinetoplast RNAs were localized on this map. Two fragments of this maxicircle molecule were cloned in the bacterial plasmid, pBR322, including a 4.4 . 10(6) dalton EcoRI/BamHI fragment which contains the 9 and 12S RNA genes.     

Primary and secondary structure of rat 28 S ribosomal RNA.

The primary structure of rat (Rattus norvegicus) 28 S rRNA is determined inferred from the sequence of cloned rDNA fragments. The rat 28 S rRNA contains 4802 nucleotides and has an estimated relative molecular mass (Mr, Na-salt) of 1.66 X 10(6). Several regions of high sequence homology with S. cerevisiae 25 S rRNA are present. These regions can be folded in characteristic base-paired structures homologous to those proposed for Saccharomyces and E. coli. The excess of about 1400 nucleotides in the rat 28 S rRNA (as compared to Saccharomyces 25 S rRNA) is accounted for mainly by the presence of eight distinct G+C-rich segments of different length inserted within the regions of high sequence homology. The G+C content of the four insertions, containing more than 200 nucleotides, is in the range of 78 to 85 percent. All G+C-rich segments appear to form strongly base-paired structures. The two largest G+C-rich segments (about 760 and 560 nucleotides, respectively) are located near the 5'-end and in the middle of the 28 S rRNA molecule. These two segments can be folded into long base-paired structures, corresponding to the ones observed previously by electron microscopy of partly denatured 28 S rRNA molecules.     

Maxicircle (mitochondrial) genome sequence (partial) of Leishmania major: gene content, arrangement and composition compared with Leishmania tarentolae

We report 8420 bp of DNA sequence data from the maxicircle (mitochondrial) genome of Leishmania major (MHOM/SU/73/5ASKH), a much larger portion of this genome than has been reported previously from any Leishmania species infecting humans. This region contains 10 partial and complete genes: 5 protein-encoding genes (COII, COIII, ND1, ND7 and Cyt b); two ribosomal RNA subunits (12S and 9S) and three unidentified open reading frames (MURF1, MURF4 (ATPase6) and MURF5), as in the lizard-infecting species L. tarentolae. The genes from L. major exhibit 85-87% identity with those of L. tarentolae at the nucleotide level and 71-94% identity at the amino acid level. Most differences between sequences from the two species are transversions. The gene order and arrangement within the maxicircle of L. major are similar to those in L. tarentolae, but base composition and codon usage differ between the species. Codons assigned for initiation for protein-coding genes available for comparison are similar in five genes in the two species. Pre-editing was identified in some of the protein-coding genes. Short intergenic non-coding regions are also present in L. major as they are in L. tarentolae. Intergenic regions between 9S rRNA and MURF5, MURF1 and ND1 genes are G+C rich and considered to be extensive RNA editing regions. The RNA editing process is likely to be conserved in similar pattern in L. major as in L. tarentolae.     

The nucleotide sequence and predicted secondary structure of small subunit (18S) ribosomal RNA from Spirometra erinaceieuropaei

The nucleotide (nt) sequence of a small subunit (18S) ribosomal RNA gene from the plerocercoid of Spirometra erinaceieuropaei (SEP) was determined. The gene with 2182 bp in length is larger than that of most eukaryotes. Extra nt sequences occur in regions known to be variable (V4 and V7). The predicted secondary structure of the nt positions 679–933 (V4) revealed different helices from that of other eukaryotes. The region between nt positions 1540 and 1749 (V7) was different from that of other eukaryotes, but the secondary structure prediction by computer analysis demonstrated that this part of 18S rRNA sequence from S. erinaceieuropaei may form a single extended helix. Nt that were aligned with those of nine other parasites were used to estimate phylogenetic relationships. The data presented here clearly indicate that S. erinaceieuropaei is closely related to Echinococcus granulosus.     

Xenopus laevis 18S ribosomal RNA: experimental determination of secondary structural elements, and locations of methyl groups in the secondary structure model.

18S ribosomal RNA from X. laevis was subjected to partial digestion with ribonucleases A or T1 under a variety of conditions, and base-paired fragments were isolated. Sequence analysis of the fragments enabled five base-paired secondary structural elements of the 18S RNA to be established. Four of these elements (covering bases 221-256, 713-757, 1494-1555 and 1669-1779) confirm our previous secondary structure predictions, whereas the fifth (comprising bases 1103-1125) represents a phylogenetically conserved "switch" structure, which can also form in prokaryotic 16S RNA. The results are incorporated into a refined model of the 18S RNA secondary structure, which also includes the locations of the many methyl groups in X. laevis 18S RNA. In general the methyl groups occur in non-helical regions, at hairpin loop ends, or at helix boundaries and imperfections. One large cluster of 2'-O-methyl groups occurs in a region of complicated secondary structure in the 5'-one third of the molecule.     

Primary structure of rabbit 18S ribosomal RNA determined by direct RNA sequence analysis

The primary structure of rabbit 18S ribosomal RNA was determined by nucleotide sequence analysis of the RNA directly. The rabbit rRNA was specifically cleaved with T1 ribonuclease, as well as with E. coli RNase H using a Pst 1 DNA linker to generate a specific set of overlapping fragments spanning the entire length of the molecule. Both intact and fragmented 18S rRNA were end-labeled with [32P], base-specifically cleaved enzymatically and chemically and nucleotide sequences determined from long polyacrylamide sequencing gels run in formamide. This approach permitted the detection of both cistron heterogeneities and modified bases. Specific nucleotide sequences within E. coli 16S rRNA previously implicated in polyribosome function, tRNA binding, and subunit association are also conserved within the rabbit 18S rRNA. This conservation suggests the likelihood that these regions have similar functions within the eukaryotic 40S subunit.     

Nucleotide sequence, secondary structure and evolution of the 5S ribosomal RNA from five bacterial species

The nucleotide sequences of the 5S ribosomal RNAs of the bacteria Agrobacterium tumefaciens, Alcaligenes faecalis, Pseudomonas cepacia, Aquaspirillum serpens and Acinetobacter calcoaceticus have been determined. The sequences fit in a generally accepted model for 5S RNA secondary structure. However, a closer comparative examination of these and other bacterial 5S RNA primary structures reveals the potential of additional base pairing and of multiple equilibria between a set of slightly different alternative secondary structures in one area of the molecule. The phylogenetic position of the examined bacteria is derived from a 5S RNA sequence alignment by a clustering method and compared with the position derived on the basis of 16S ribosomal RNA oligonucleotide catalogs.     

The 3''-terminal sequence of mitochondrial 13S ribosomal RNA.

We have examined the 3'-terminal sequence of the "small" structural ribosomal RNA ("13S") of hamster cell mitochondria, using a procedure involving [3H]isoniazide labeling of samples subjected to sequential periodate oxidation and beta-elimination. The terminus was found to be PyUAUUAOH, which is similar, but not identical, to the corresponding terminus of eukaryotic cytoplasmic 18S rRNA.     

Primary sequence of the 16S ribosomal RNA of Escherichia coli.

Recent progress in the nucleotide sequence analysis of the 16S ribosomal RNA from E. coli is described. The sequence which has been partially or completely determined so far encompasses 1520 nucleotides, i.e. about 95% of the molecule. Possible features of the secondary structure are suggested on the basis of the nucleotide sequence and data on sequence heterogeneities, repetitions and the location of modified nucleotides are presented. In the accompanying paper, the use of the nucleotide sequence data in studies of the ribosomal protein binding sites is described.     

Leishmania: genus identification based on a specific sequence of the 18S ribosomal RNA sequence

The analysis of PvuII restriction patterns of Leishmania spp. and Trypanosoma spp. genomic DNA showed genus distinctive profiles. A specific PvuII site was detected in the 5' domain of 18S ribosomal DNA of Leishmania. A 20-mer oligonucleotide encompassing this PvuII region was synthesized. This sequence, when utilized as probe, on short exposures of dot tests, detected 10(3) whole promastigotes of all Leishmania species analyzed but did not hybridize with T. cruzi or human nucleic acids. Two other oligonucleotides were synthesized to be used as primers for amplification through polymerase chain reaction of the 18S ribosomal DNA region containing the PvuII site. The probes described may be useful for the detection of Leishmania spp. under clinical and epidemiological trials.     

Primary and secondary structure of the 18 S ribosomal RNA of the insect species Tenebrio molitor

The sequence of the 18 S rRNA of Tenebrio molitor is reported. A detailed secondary structure model for eukaryotic small subunit rRNAs is proposed. The model comprises 48 universal helices that eukaryotic and prokaryotic small subunit rRNAs have in common, plus a number of helices in areas of variable secondary structure. For the central area of the model, an alternative structure is possible, applicable only to eukaryotic small subunit rRNAs. Possibly, small subunit rRNA switched to this alternative conformation after the eukaryotic branch had been established in evolution. Another possibility is that the two conformers represent a dynamic structural switch functioning during the translational activity of the eukaryotic ribosome.     

Characterization of mitochondrial ribosomal RNA genes in gadiformes: sequence variations,secondary structural features,and phylogenetic implications

Secondary structure features of mitochondrial ribosomal RNAs (mt-rRNAs) of bony fishes were investigated by a DNA sequence alignment approach. The small subunit (SSU) and large subunit (LSU) mt-rRNA genes were found to contain several additional variable regions compared to their mammalian counterparts. Fish mt-LSU rRNA genes were found to be longer than the mammalians due to increased length of some of the variable regions. The 5' and 3' ends of Atlantic cod mt-rRNAs were precisely mapped. The 3' ends of mt-SSU rRNAs were found to be homogenous and mono-adenylated, whereas that of the mt-LSU rRNAs were heterogenous and oligo-adenylated. The 5' ends of mt-SSU rRNAs appeared to be heterogenous, corresponding to the presumed first and second positions of the gene. Sequences of the central domain and the D-domain of the mt-SSU and mt-LSU rRNA genes, respectively, were determined and characterized for 11 gadiform species (representing the families Gadidae, Lotidae, Ranicipitidae, Merlucciidae, Phycidae, and Macrouridae) and one Lophiidae species. Detailed secondary structure models of the RNA regions are presented for the Atlantic cod (Gadus morhua) and Roundnose grenadier (Coryphaeonides rupestris). Saturation plots revealed that DNA nucleotide positions corresponding to unpaired RNA regions become saturated with transitions at sequence divergence levels about 0.15. Phylogenetic analyses revealed some aspects of gadiform relationships. Gadidae was identified as the most derived of the gadiform families. Lotidae was found to be the family closest related to Gadidae, and Ranicipitidae was also recognized as a derived gadiform taxon.     

The sequence of the 5.8 S ribosomal RNA of the crustacean Artemia salina. With a proposal for a general secondary structure model for 5.8 S ribosomal RNA.

We report the primary structure of 5.8 S rRNA from the crustacean Artemia salina. The preparation shows length heterogeneity at the 5'-terminus, but consists of uninterrupted RNA chains, in contrast to some insect 5.8 S rRNAs, which consist of two chains of unequal length separated in the gene by a short spacer. The sequence was aligned with those of 11 other 5.8 S rRNAs and a general secondary structure model derived. It has four helical regions in common with the model of Nazar et al. (J. Biol. Chem. 250, 8591-8597 (1975)), but for a fifth helix a different base pairing scheme was found preferable, and the terminal sequences are presumed to bind to 28 S rRNA instead of binding to each other. In the case of yeast, where both the 5.8 S and 26 S rRNA sequences are known, the existence of five helices in 5.8 S rRNA is shown to be compatible with a 5.8 S - 26 S rRNA interaction model.     

Molecular systematics of North American phoxinin genera (Actinopterygii: Cyprinidae) inferred from mitochondrial 12S and 16S ribosomal RNA sequences

The cyprinid fish fauna of North America is relatively large, with approximately 300 species, and all but one of these are considered phoxinins. The phylogenetic relationships of the North American phoxinins continue to pose difficulties for systematists. Results of morphological analyses are not consistent owing to differences interpreting and coding characters. Herein, we present phylogenetic analyses of mitochondrial 12S and 16S ribosomal RNA sequence data for representatives of nearly all genera of North American phoxinins. The data were analysed using parsimony, weighted parsimony, maximum likelihood and bayesian analyses. Results from weighted parsimony, likelihood and the bayesian analysis are largely consistent as they all account for differing substitution rates between transitions and transversions. Several major clades within the fauna can be recognized and are strongly supported by all analyses. These include the western clade, creek chub–plagopterin clade and the open posterior myodome clade. The shiner clade is nested in the open posterior myodome clade and is the most species-rich clade of North American phoxinins. Relationships within this clade were not well resolved by our analyses. This may reflect the inability of the mitochondrial RNA genes to resolve recent speciation events or taxon sampling within the shiner clade.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 63–80.     

Molecular phylogeny of elopomorph fishes inferred from mitochondrial 12S ribosomal RNA sequences

Wang, C. H., Kuo, C. H., Mok, H. K. & Lee, S. C. (2003). Molecular phylogeny of elopomorph fishes inferred from mitochondrial 12S ribosomal RNA sequences. — Zoologica Scripta , 32 , 231–241.
Fishes of the superorder Elopomorpha include tenpounders ( Elops ), tarpon ( Megalops ), bonefishes ( Albula ), spiny eels ( Notacanthus ), apodes, and gulper eels; despite highly diversified morphological features, all undergo a leptocephalus larval stage and are thus treated (although with some dissenting views) as monophyletic. Following analysis of 12S rRNA sequences we present results that confirm a monophyletic Elopomorpha clearly separated from Clupeomorpha. Elops and Megalops share a common ancestor and are clustered in a subclade at the bottom of Elopomorpha. Albula and Notacanthus share a common ancestor forming the sister group to Anguilliformes. Saccopharyngiformes is not a sister group of Anguilliformes, as the single species sequenced here is nested deeply within the latter. Neither the suborder Congroidei nor the superfamily Congroidea within Anguilliformes are monophyletic.