A repetitive DNA sequence in the salmonid fishes similar to a retroviral long terminal repeat

Sperm nuclear basic proteins of two closely related species of Scorpaeniform fish (Sebastes maliger, Sebastolobus sp.) with different sexual reproduction and the evolution of fish protamines

In this paper, we present a review of sperm nuclear basic proteins (SNBPs) in teleost fish. The distribution of the three basic groups of SNBPs [histone (H)-type, protamine-like (PL)-type and protamine (P)-type], their evolution and possible relation to the mode of fertilization are described. In this regard, we have characterized the SNBPs from two closely related species of Scorpaeniform fish: internally fertilizing Sebastes maliger and externally fertilizing Sebastolobus sp., both in the family Scorpaenidae. Despite the different reproductive behavior of these two closely related rockfish species, in both instances the SNBP consists of protamines. However, there is a significant increase in the arginine content of the protamine in the internally fertilizing rockfish. The relevance of this observation is discussed within the context of the P-type SNBP in teleosts. The rapid evolution of teleost protamines, including those in rockfish, has also allowed us to obtain a molecular phylogeny for this group of bony fish that is almost indistinguishable from that currently available from the use of conventional anatomical/paleontological markers.

Physical distribution of SINE elements in the chromosomes of Atlantic salmon and rainbow trout

SINE sequences are interspersed throughout virtually all eukaryotic genomes. In the family Salmonidae three families of SINEs have been identified. In this work we have attempted to characterize and locate by means of fluorescent in situ hybridization (FISH) one of these families (HpaI) in the genome of Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Our results show that these SINEs are interspersed throughout all the chromosome pairs except for the heterochromatin-positive areas, generating a banding pattern that could be useful for chromosome identification in both species.

Gypsy/Ty3-class retrotransposons integrated in the DNA of herring, tunicate, and echinoderms

Eight new examples of retrotransposons of the Gypsy/Ty3 class have been identified in marine species. A 525-nt pol gene-coding region was amplified using degenerate primers from highly conserved regions and has extended the range of recognition of Gypsy/Ty3 far beyond those previously known. The following matrix shows the percentage AA divergence of the translations of this segment of the pol gene coding region. [table: see text] The underlines separate three groups of retrotransposons that can be recognized on the basis of this amino acid sequence. The new upper group shows surprising amino acid sequence similarity among members from the DNA of herring, sea urchin, starfish, and a tunicate. For example, the herring element differs by only 41% from the Ciona element and 46% from the sea urchin element. The group between the lines includes members close to previously known elements (marked by asterisks) and has so far been found only in sea urchins. The two upper groups differ from each other by 55-60% and yet members of both groups (e.g., Spr1 and Spr2) are integrated into the DNA of one species--S. purpuratus. Below the lower underline is listed the only known representative of a very distant group, which occurs in starfish DNA. In spite of large divergence, amino acid sequence comparisons indicate that all of the elements shown in the array are members of the LTR-containing class of retrotransposons that includes Gypsy of Drosophila and Ty3 of yeast. Of all known mobile elements this class shows the closest sequence similarity to retroviruses and has the same arrangement of genes as simpler retroviruses.

Preliminary analysis of the polypeptides of the salmon leukemia virus (SLV) and evidence for development of a bimodal viremia following SLV infection

A retrovirus, known as salmon leukemia virus (SLV), was purified from farm-reared chinook salmon (Oncorhynchus tshawytscha) with plasmacytoid leukemia (PL). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of purified SLV revealed the presence of 9 virus-associated polypeptides with molecular weights from 82 kDa to 15 kDa. Endoglycosidase digestion and alcian blue staining of viral polypeptides separated by SDS-PAGE, and immunoprecipitation experiments using hyperimmune antisera suggest that the non-glycosylated 27 kDa polypeptide may represent a capsid-associated protein and the 82 kDa glycoprotein may represent an envelope-associated protein, which appears to be composed of a 67 kDa protein moiety. Fish injected with PL-positive tissue homgenate developed a bimodal viremia, as indicated by the presence of cell-free, virus-associated reverse transcriptase activity and SLV in serum of fish from 1 to 3 wk post-injection and again from 7 wk on through the rest of the study. If horizontal transmission of SLV and PL occurs in infected chinook salmon, it is most likely to occur after the second viremic period begins.

On the evolution of protamines in bony fish: alternatives to the "retroviral horizontal transmission" hypothesis

Fish protamines are highly specialized molecules which are responsible for chromatin condensation during the last stages of spermatogenesis (spermiogenesis). However, not all fish contain protamines in their sperm nuclei; rather, there seems to be a random distribution of protamines within this group. The origin of this sporadic presence of protamines in the sperm and its significance have not yet been precisely determined. In this paper we have conducted an exhaustive survey of the literature available on the different types of nuclear protein composition of the sperm of teleost fish in order to try to correlate these data with what is presently known about the taxonomy of this group. The results of this analysis have allowed us to make the following observations. The divergence between protamines and histones has occurred several times during the evolution of the bony fish. However, the relative frequency of this divergence is almost negligible during the differentiation of genera and species (intrafamily variation) and is very small during the differentiation of families (interfamily variation). Nevertheless, the divergence is very noticeable among the different orders. It is therefore possible to conclude from all this that the sporadic distribution of protamines in bony fish is not a random event as initially believed. Furthermore, such a heterogeneous distribution of protamines cannot be easily accounted for by a mechanism of horizontal retroviral transmission through repeated and independent acquisition of a protamine gene as has been recently proposed (Jankowski, Stater, Dixon (1986) J Mol Evol 23:1-10). Rather, it could possibly be explained by a repeated and independent loss of the expression of the protamine gene (or loss of the gene itself) which mainly occurred during the diversification of the orders of this group.

A repetitive element in the genome of Atlantic salmon, Salmo salar

When Atlantic salmon (Salmo salar) genomic DNA is digested with the restriction endonuclease BglI and the fragments separated by agarose-gel electrophoresis, bands corresponding to approximately 430 and 923 bp are visualized after EtdBr staining. The 923-bp band was excised from a preparative gel and used to screen a salmon genomic library for recombinant phage (re-phage) containing the repeat. The BglI repeat element is tandemly arrayed, and an array from one re-phage has been sequenced. The BglI repeats comprise 2.3% of the S. salar genome and have been found in the vicinity of rDNA genes (encoding ribosomal RNA). Southern blot hybridization detects a homologue of the Atlantic salmon BglI repeat in the brown trout (Salmo trutta) genome, but not in other salmonids. However, a DNA fragment with sequence homology to part of the BglI repeat has recently been isolated from Arctic charr (Salvelinus alpinus; S.E. Hartley and W.S.D., unpublished data). In addition, the BglI repeat detects RFLPs in Atlantic salmon.

Identification of two families of satellite-like repetitive DNA sequences from the zebrafish (Brachydanio rerio)

To further our understanding of the structure and organization of the zebrafish genome, we have undertaken the analysis of highly and middle-repetitive DNA sequences. We have cloned and sequenced two families of tandemly repeated DNA fragments. The monomer units of the Type I satellite-like sequence are 186 bp long, A+T-rich (65%), and exhibit a high degree of sequence conservation. The Type I satellite-like sequence constitutes 8% of the zebrafish genome, or approximately 8 x 10(5) copies per haploid genome. Southern analysis of genomic DNA, digested with several restriction endonucleases, shows a ladder of hybridizing bands, consistent with a tandem array, and suggests longer range periodic variations in the sequence of the tandem repeats. The Type II satellite has a monomer length of 165 bp, is also A+T-rich (68%), and constitutes 0.2% of the zebrafish genome (22,000 copies per haploid genome). Southern analysis reveals a complex pattern rather than a ladder of regularly spaced hybridizing bands.

Isolation of a putative retrovirus pol gene fragment from trout

1. A 220 bp DNA fragment was obtained from three different species of salmonids during PCR analysis using a primer sequence based on human beta-2 microglobulin. All of the 220 bp fragments showed strong homology to each other. 2. Several of the DNA sequences also contained protein reading frames. Searching DNA and protein databases revealed significant homology to a segment of the pol gene (reverse transcriptase) from various retroviruses. Phylogenetic analysis at both the DNA and the protein levels showed clustering of the fish sequences and the closest viral sequence was the Moloney murine leukaemia virus (MoMuLV). Southern analysis indicated that there are several copies of the gene dispersed throughout the salmonid genome. 3. Preliminary results suggest that these sequences may be unique to the family Salmonidae. This would suggest that this retrovirus was incorporated in the DNA of an ancestral salmonid prior to the evolution and divergence of this family of fish.

Vertebrate protamine gene evolution I. Sequence alignments and gene structure

The availability of the amino acid sequence for nine different mammalian P1 family protamines and the revised amino acid sequence of the chicken protamine galline (Oliva and Dixon 1989) reveals a much close relationship between mammalian and avian protamines than was previously thought (Nakano et al. 1976). Dot matrix analysis of all protamine genes for which genomic DNA or cDNA sequence is available reveals both marked sequence similarities in the mammalian protamine gene family and internal repeated sequences in the chicken protamine gene. The detailed alignments of the cis-acting regulatory DNA sequences shows several consensus sequence patterns, particularly the conservation of a cAMP response element (CRE) in all the protamine genes and of the regions flanking the TATA box, CAP site, N-terminal coding region, and polyadenylation signal. In addition we have found a high frequency of the CA dinucleotide immediately adjacent to the CRE element of both the protamine genes and the testis transition proteins, a feature not present in other genes, which suggests the existence of an extended CRE motif involved in the coordinate expression of protamine and transition protein genes during spermatogenesis. Overall these findings suggest the existence of an avian-mammalian P1 protamine gene line and are discussed in the context of different hypotheses for protamine gene evolution and regulation.

Characterization of elastin protein and mRNA from salmonid fish (Oncorhynchus kisutch)

1. Elastin was isolated from the bulbus arteriosus of a salmonid fish. Monoclonal and polyclonal antibodies, elicited against a CNBr digest of this protein, immunoprecipitated a polypeptide of Mr 43,000 from fish cell culture medium. 2. Cell-free translation of salmon poly A+ RNA produced a protein of approximately 43 kD that was immunoprecipitated with anti-elastin antibodies. The corresponding mRNA had an approximate Mr of 2 kb. 3. Despite similarities in amino acid composition, the differences in Mr between mammalian and salmon mRNA and protein suggest a divergence of fish and higher vertebrate elastins from an earlier ancestral gene.

A new family of repetitive, retroposon-like sequences in the genome of the rainbow trout

We have identified a new family of interspersed, moderately repetitive DNA elements, termed the RSg-1 family, in the genome of the rainbow trout. Two of the elements examined here are situated upstream of sequences which code for trout nuclear proteins; a protamine gene (p101) and the clustered histone H4 gene. Sequence comparison of various RSg-1 elements indicated a high degree of nucleotide sequence homology between different members of the family. These repetitive elements exhibit well defined 3' ends which contain poly(A) segments preceded by the consensus polyadenylation signal AATAAA. Sequences flanking the 3' end of the poly(A) tract also conform to a consensus sequence. A similar sequence is also found flanking the 5' terminus of the element in the protamine clone p101, and thus may represent a target-site duplication generated upon insertion of the element into the genome. These characteristics, together with the heterogeneous nature of the 5' ends of the elements, are reminiscent of processed pseudogenes and retroposons such as the mammalian L1 family of interspersed repetitive elements.

Sequence similarities of the protamine genes: implications for regulation and evolution

With the recent availability of the primary structural data for the trout, bovine, and mouse protamine genes, a detailed comparison of their structures has been made. This has revealed extensive conservation of potentially biologically significant regions. An inverse correlation is apparent between gene copy number and the number of sequence-distinct protamines synthesized with the number of CP-box-like (CCYPCCC) putative transcription modulating sequences situated 5' to these genes. A common nucleotide sequence 5' to the CP-box-like putative transcription modulating sequence(s) at the end of a common region has been identified. It is postulated that this is the testis-specific protamine P1 transcription regulator sequence. Evidence based on sequence similarity is also provided for the existence of a primordial protamine gene and a scheme for the evolution of vertebrate protamine genes is proposed.

Characterization of a protamine gene from the chum salmon (Oncorhynchus keta)

We have cloned and sequenced a protamine gene from the chum salmon (Oncorhynchus keta). This gene sequence is highly homologous to one found in the rainbow trout (Salmo gairdneri), including the conservation of two structurally different repetitive elements. One of these repeats resembles a nonviral retroposon and the second is similar to a retroviral-like transposable element. The degree of sequence divergence between the O. keta and S. gairdneri genes is much less within the transcription unit than in the repetitive elements or the remainder of the flanking DNA, suggesting that since the coding and the untranslated regions are highly conserved, both contribute significantly to the structure and stability of protamine mRNA (or its cognate messenger ribonucleoprotein) and this may be important for the translational control of protamine synthesis.