Characterization of two types of rRNA gene repeat units from the crustacean Artemia

Actin gene structure in two Artemia species, A. franciscana and A. parthenogenetica

Genomic clones coding for actin have been isolated from two species of the crustacean Artemia, A. parthenogenetica and A. franciscana. The Act211 isoform gene was isolated from A. parthenogenetica, and the two other isoform genes, Act302 and Act403, were isolated from A. franciscana. The comparison of the nucleotide sequence of genomic and cDNA clones showed an interspecific divergence of 4% in translated and 6.1% in untranslated regions. However, the establishment of the partial structure of the Act211 gene in A. franciscana and of the Act302 gene in A. parthenogenetica suggests their similarity in the two species. The Act211 gene is divided into four exons, the Act302 gene into six exons, and the Act403 gene into seven exons. The three genes have introns in the 5' untranslated region and between codons 41 and 42. The Act211 and 403 genes have one common intron in codon 168. The Act302 and 403 genes have common introns between codons 121-122, 246-247, and within codon 301. While introns in the 5' untranslated region and between codons 41-42 and 121-122 are present in many organisms, the introns in positions 168 and 246-247 had only been found previously in actin genes from the nematode Onchocerca volvulus and the green alga Volvox carterii, respectively. The intron in position 301 had not been reported before. The transcription initiation sites of these three genes as well as the nucleotide sequences of the promoter regions have been also determined.

Cloning of a cDNA encoding an Artemia franciscana Na/K ATPase alpha-subunit

Clones of cDNA that code for an isoform of the Artemia franciscana Na/K ATPase alpha subunit (NaKA alpha) have been isolated. The sequence of the longest of these clones (pArATNa136) is 3595 nucleotides; it codes for a 1004-amino acid protein whose sequence is identical to that of two previously sequenced Artemia NaKA alpha peptides. The encoded protein is over 73% identical to Drosophila melanogaster and vertebrate NaKA alpha s, and 73.8% identical to another Artemia NaKA alpha isoform previously described (named alpha 2850 in this article). The two Artemia cDNA clones code for mRNAs of different size; the clone pArATNa136 codes for a 4.5-kb mRNA while the alpha 2850 clone codes for a 3.6-kb mRNA. The degree of homology and the different size of the mRNAs encoded by both cDNAs suggest that they code for two different isoforms of the protein.

Complementary DNA cloning of a protein highly homologous to mammalian sarcoplasmic reticulum Ca-ATPase from the crustacean Artemia

Complementary DNA clones coding for an Artemia ATPase have been isolated using an oligonucleotide probe for a region highly conserved between P-type ATPases. The nucleotide sequence of three overlapping clones, 3309 base-pairs, has been established. This sequence includes 78 nucleotides of 5' untranslated sequence, an open reading frame of 3009 nucleotides and 222 nucleotides of 3' untranslated sequences. The amino acid sequence predicted for the coding region is 71% similar to that of slow and fast twitch rabbit muscle sarcoplasmic reticulum Ca-ATPases. The homology is specially high in some regions of the protein that include the previously described regions that are similar between all known P-type ATPases, as well as transmembrane domains and intra- and extracellular domains adjacent to the membrane that are not conserved in P-type ATPases but have been proposed to be involved in calcium binding and transport in rabbit sarcoplasmic reticulum Ca-ATPases. Probes of this likely sarcoplasmic reticulum Ca-ATPase hybridize to two mRNAs of 5200 and 4500 bases. Although both mRNAs are already present in cryptobiotic embryos, the levels of the 5200 base mRNA decrease after development is reassumed, being undetectable after hatching of the nauplii. The levels of the 4500 base mRNA increase during development; maximal levels are reached by ten hours and are maintained at later stages of development.

The 5S rRNA-histone repeat in the crustacean Artemia: structure, polymorphism and variation of the 5S rRNA segment in different populations

5S rRNA genes are linked to the histone genes in the 13 populations of the crustacean Artemia that we have studied. In all cases, two types of repeat units are found. Southern blot analysis of all populations shows that they can be grouped into three classes: a) American bisexuals; b) Eurasian bisexuals, and c) parthenogenetic organisms (all from Eurasia). Restriction analysis of a bisexual population from San Francisco Bay shows that the two repeat units are of 9.0 and 8.5 kb (with minor heterogeneities of restriction sites). In parthenogenetic organisms, the two repeat units are of approximately 12 kb. Sequencing data from the region of the 5S rRNA from the San Francisco Bay population, shows that in both types of units, the single 5S rRNA gene (315 bp in length), is located 430 bp downstream the 3' regulatory sequences of the H2A gene, the last gene in the histone cluster. We have isolated three clones that contain 5S rRNA sequences. Two of them (one from an American bisexual and the other from a parthenogenetic population) contain histone and 5S rRNA genes, both with the same transcriptional polarity. The third clone, lacking histone genes, is likely to be an orphon derived from the parthenogenetic population.

Characterization of the ribosomal DNA from Trichinella spiralis

Ribosomal DNA (rDNA) from three isolates of Trichinella was cloned into phage and sublcloned into the plasmid pBR322. The basic repeat unit of rDNA was variable in size, with the mapped clones ranging from 10-12 kb. There were differences in restriction sites within the genic region among the three isolates which were due to variations in the internal transcribed region (ITS) and the intergenic spacer (IGS). Three RsaI sites were mapped to the IGS repeat unit of the isolate AF1, and one RsaI site was mapped to the IGS repeat unit of Trichinella spiralis pseudospiralis (isolate Tp). The number of repetitive units in the IGS region varied markedly within and between the isolates. It was estimated that the basic repeat unit for the rDNA of isolate P1 was 10.6-28 kb, for AF1 10.7-37 kb, and for Tp it was 11-14.9 kb. There appeared to be a greater frequency of some sizes of the basic repeat unit in each of the populations, based on the relative intensity with which certain bands hybridize to the probe.

Isolation of cDNA clones coding for mitochondrial 16S ribosomal RNA from the crustacean Artemia

cDNA clones coding for Artemia mitochondrial 16S ribosomal RNA (rRNA) have been isolated. The clones cover from nucleotide 650 of the RNA molecule to its 3' end. The comparison of Artemia sequence with both vertebrate and invertebrate mitochondrial 16S rRNA sequences has shown the existence of regions of high similarity between them. A model for the secondary structure of the 3' half of Artemia mitochondrial 16S rRNA is proposed. The size of the rRNA molecule has been estimated at 1.35 kb. Despite the similarity of the Artemia gene to insect rRNA in size, sequence and secondary structure, the G + C content of the Artemia gene (42%) is closer to that of mammals than to the insect genes. The number of mitochondria in Artemia has been estimated at 1500 per diploid genome in the cyst and 4000 in the nauplius. In contrast, the amount of mt 16S rRNA is constant at all stages of Artemia development.

Identification of the transcriptional initiation site of ribosomal RNA genes in the crustacean Artemia

The proximal part of the Intergenic Spacer, as well as most of the External Transcribed Spacer of the ribosomal RNA type I genes from the crustacean Artemia have been sequenced. We have identified in the Intergenic Spacer five repeats of around 600 bp in length and, possibly, two imperfect or truncated repeats, derived from the principal ones. These sequences are separated by 485 bp from the 17S rRNA coding sequence. We have also identified the start point of transcription by S1 nuclease analysis. This start point is found 248 bp inside the first repeat. The sequence around the start point shows homology with that described for other members of the same phylum, mostly insects. The most conserved regions are from -1 to +25, and the G residue at position -16. At least the three 600-bp repeats upstream from that containing the promoter also contain the start point sequence, and could therefore act as initiation sites for snPIRNA and/or as enhancer sequences for ribosomal RNA gene transcription.

In vivo transcription from multiple spacer rRNA gene promoters during early development and evolution of the intergenic spacer in the brine shrimp Artemia

The control of ribosomal RNA (rRNA) gene expression during development can be productively studied by examination of the relationship between promoter structure and function as well as the processing of primary transcripts. Toward this end total cell RNA was extracted from embryos at various stages and probed with cloned rRNA genes using the "dot blot" method. This exercise showed that rRNA gene expression is a stage-specific process and is thus under developmental control. S1 nuclease protection experiments localized fourteen different upstream DNA sites encoding 5'-termini of pre-rRNAs during this synthetic phase of development. There is no indication of any spacer fail-safe terminator function. The S1 approach contributed to the sequencing of several of the sites. Comparative sequence alignments reveal short conserved regions in DNAs corresponding to these sites, which are shown to fall into two structural classes. Sites 3, 4, 6 and 9 are proposed to function in transcription initiation and are found to have the consensus sequence 5'...T-A-T-A-T-Pu-Pu-Pu-G-Pu-Pu-G-T-C-A 3'. Sites 1, 2, 5 and 8 which are proposed to function in 5'-processing have the consensus sequence; 5'...Pu-G-T-Pu-T-T-G 3'. These short sequence conserved regions are hypothesized to serve as recognition signals for proteins within the rDNA transcription initiation complex and for 5'-processing enzymes, respectively. Sequencing of the intergenic spacer region from which a model for spacer evolution is derived shows that tandem ca 600 bp subrepeats explain much of the multiplicity observed within control sites.