Transcriptionally active and inactive gene repeats within the D. melanogaster 5S RNA gene cluster

Systematic analysis and evolution of 5S ribosomal DNA in metazoans

Several studies on 5S ribosomal DNA (5S rDNA) have been focused on a subset of the following features in mostly one organism: number of copies, pseudogenes, secondary structure, promoter and terminator characteristics, genomic arrangements, types of non-transcribed spacers and evolution. In this work, we systematically analyzed 5S rDNA sequence diversity in available metazoan genomes, and showed organism-specific and evolutionary-conserved features. Putatively functional sequences (12,766) from 97 organisms allowed us to identify general features of this multigene family in animals. Interestingly, we show that each mammal species has a highly conserved (housekeeping) 5S rRNA type and many variable ones. The genomic organization of 5S rDNA is still under debate. Here, we report the occurrence of several paralog 5S rRNA sequences in 58 of the examined species, and a flexible genome organization of 5S rDNA in animals. We found heterogeneous 5S rDNA clusters in several species, supporting the hypothesis of an exchange of 5S rDNA from one locus to another. A rather high degree of variation of upstream, internal and downstream putative regulatory regions appears to characterize metazoan 5S rDNA. We systematically studied the internal promoters and described three different types of termination signals, as well as variable distances between the coding region and the typical termination signal. Finally, we present a statistical method for detection of linkage among noncoding RNA (ncRNA) gene families. This method showed no evolutionary-conserved linkage among 5S rDNAs and any other ncRNA genes within Metazoa, even though we found 5S rDNA to be linked to various ncRNAs in several clades.

The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae)

The linkage between 5S ribosomal DNA and other multigene families has been detected in many eukaryote lineages, but whether it provides any selective advantage remains unclear. In this work, we report the occurrence of linked units of 5S ribosomal DNA (5S rDNA) and U1 small nuclear DNA (U1 snDNA) in 10 razor shell species (Mollusca: Bivalvia: Pharidae) from four different genera. We obtained several clones containing partial or complete repeats of both multigene families in which both types of genes displayed the same orientation. We provide a comprehensive collection of razor shell 5S rDNA clones, both with linked and nonlinked organisation, and the first bivalve U1 snDNA sequences. We predicted the secondary structures and characterised the upstream and downstream conserved elements, including a region at -25 nucleotides from both 5S rDNA and U1 snDNA transcription start sites. The analysis of 5S rDNA showed that some nontranscribed spacers (NTSs) are more closely related to NTSs from other species (and genera) than to NTSs from the species they were retrieved from, suggesting birth-and-death evolution and ancestral polymorphism. Nucleotide conservation within the functional regions suggests the involvement of purifying selection, unequal crossing-overs and gene conversions. Taking into account this and other studies, we discuss the possible mechanisms by which both multigene families could have become linked in the Pharidae lineage. The reason why 5S rDNA is often found linked to other multigene families seems to be the result of stochastic processes within genomes in which its high copy number is determinant.

Evolutionary dynamics of the 5S rDNA gene family in the mussel Mytilus: mixed effects of birth-and-death and concerted evolution

In higher eukaryotes, the gene family encoding the 5S ribosomal RNA (5S rRNA) has been used (together with histones) to showcase the archetypal example of a gene family subject to concerted evolution. However, recent studies have revealed conspicuous features challenging the predictions of this model, including heterogeneity of repeat units, the presence of functional 5S gene variants as well as the existence of 5S rDNA divergent pseudogenes lacking traces of homogenization. In the present work, we have broadened the scope in the evolutionary study of ribosomal gene families by studying the 5S rRNA family in mussels, a model organism which stands out among other animals due to the heterogeneity it displays regarding sequence and organization. To this end, 48 previously unknown 5S rDNA units (coding and spacer regions) were sequenced in five mussel species, leading to the characterization of two new types of units (referred to here as small-beta 5S rDNA and gamma-5S rDNA) coexisting in the genome with alpha and beta rDNA units. The intense genetic dynamics of this family is further supported by the first description of an association between gamma-5S rDNA units and tRNA genes. Molecular evolutionary and phylogenetic analyses revealed an extensive lack of homology among spacer sequences belonging to different rDNA types, suggesting the presence of independent evolutionary pathways leading to their differentiation. Overall, our results suggest that the long-term evolution of the 5S rRNA gene family in mussels is most likely mediated by a mixed mechanism involving the generation of genetic diversity through birth-and-death, followed by a process of local homogenization resulting from concerted evolution in order to maintain the genetic identities of the different 5S units, probably after their transposition to independent chromosomal locations.

Cerastodermaglaucum5S ribosomal DNA: characterization of the repeat unit, divergence with respect toCerastoderma edule, and PCR–RFLPs for the identification of both cockles

The 5S rDNA repeat unit of the cockle Cerastoderma glaucum from the Mediterranean and Baltic coasts was PCR amplified and sequenced. The length of the units was 539–568 bp, of which 120 bp were assigned to the 5S rRNA gene and 419–448 bp to the spacer region, and the G/C content was 46%–49%, 54%, and 44%–47%, respectively. Two types of units (A and B), differing in the spacer, were distinguished based on the percentage of differences and clustering in phylogenetic trees. A PCR assay with specific primers for each unit type indicated that the occurrence of both units is not restricted to the sequenced individuals. The 5S rDNA units of C. glaucum were compared with new and previously reported sequences of Cerastoderma edule. The degree of variation observed in C. edule was lower than that in C. glaucum and evidence for the existence of units A and B in C. edule was not found. The two cockles have the same coding region but displayed numerous fixed differences in the spacer region and group separately in the phylogenetic trees. Digestion of the 5S rDNA PCR product with the restriction enzymes HaeIII and EcoRV revealed two RFLPs useful for cockle identification.Key words: Cerastoderma, cockle identification, 5S ribosomal DNA, nontranscribed spacer variation, PCR-RFLP.

The 5S rDNA of mussels Mytilus galloprovincialis and M. edulis: sequence variation and chromosomal location

The 5S ribosomal DNA of the mussels Mytilus galloprovincialis and M. edulis was amplified by PCR using contiguous primers. The most general 5S rDNA amplification pattern consisted of several products in both mussels. Two main PCR products of about 250 bp and 760 bp were cloned and sequenced, revealing two classes of 5S rDNA units. These were characterized as containing an identical coding region of 119 bp but with highly divergent spacers. Clones of each unit type exhibited minimal differences except those of the large unit of M. edulis. The sequences analysed of the two mussels possess the same coding region and only six fixed base changes on the spacers. FISH, carried out with specific probes, consistently showed hybridization signals on the largest metacentric pair (two differentiated sites) and with variable frequency on two other metacentric pairs (one site on each pair). Differences in the 5S rDNA distribution between both mussels were not found. In M. edulis, chromosomes carrying 18S-28S rDNA were also identified by FISH. These correspond to two submetacentric-subtelocentric pairs, as was previously reported in M. galloprovincialis, demonstrating that the two rDNA multigene families are located on different chromosome pairs in these mussels.

A TRF1:BRF complex directs Drosophila RNA polymerase III transcription

It has been generally accepted that the TATA binding protein (TBP) is a universal mediator of transcription by RNA polymerase I, II, and III. Here we report that the TBP-related factor TRF1 rather than TBP is responsible for RNA polymerase III transcription in Drosophila. Immunoprecipitation and in vitro transcription assays using immunodepleted extracts supplemented with recombinant proteins reveals that a TRF1:BRF complex is required to reconstitute transcription of tRNA, 5S and U6 RNA genes. In vivo, the majority of TRF1 is complexed with BRF and these two proteins colocalize at many polytene chromosome sites containing RNA pol III genes. These data suggest that in Drosophila, TRF1 rather than TBP forms a complex with BRF that plays a major role in RNA pol III transcription.

Purification and characterization of transcription factor IIIA from higher plants

Transcription factor IIIA (TF IIIA) binds and specifically activates transcription of eukaryotic 5S rRNA genes. It also forms a 7S ribonucleoprotein complex with mature 5S rRNA. Here, we describe the purification and properties of pTF IIIA from higher plants. The purified protein from tulip (Tulipa whittalii) has a molecular mass of about 40 kDa and also binds 5S rRNA and 5S rRNA genes. pTF IIIA also facilitates the transcription of a 5S rRNA gene in a HeLa cell extract.

Structural evolution of the Drosophila 5S ribosomal genes

We compare the 5S gene structure from nine Drosophila species. New sequence data (5S genes of D. melanogaster, D. mauritiana, D. sechellia, D. yakuba, D. erecta, D. orena, and D. takahashii) and already-published data (5S genes of D. melanogaster, D. simulans, and D. teissieri) are used in these comparisons. We show that four regions within the Drosophila 5S genes display distinct rates of evolution: the coding region (120 bp), the 5'-flanking region (54-55 bp), the 3'-flanking region (21-22 bp), and the internal spacer (149-206 bp). Intra- and interspecific heterogeneity is due mainly to insertions and deletions of 6-17-bp oligomers. These small rearrangements could be generated by fork slippages during replication and could produce rapid sequence divergence in a limited number of steps.

A possible role for the 60-kD Ro autoantigen in a discard pathway for defective 5S rRNA precursors

The Ro autoantigen is a 60-kD protein that is usually found in small cytoplasmic RNA-protein complexes known as Ro RNPs. Although the Ro RNPs are abundant and conserved components of a variety of vertebrate and invertebrate cells, their function is unknown. We have discovered that the Ro protein is also found complexed with certain variant 5S rRNAs in Xenopus oocytes. These RNAs contain one or more point mutations compared with the major oocyte 5S rRNA sequence as well as additional nucleotides at the 3' end. We demonstrate that the Ro protein binds specifically mutant 5S rRNAs containing 3' terminal extensions. These mutant RNAs are processed inefficiently to mature 5S rRNA and most eventually are degraded. The observation that the Ro autoantigen specifically associates with defective 5S rRNA precursors suggests that this protein may function as part of a novel quality control or discard pathway for 5S rRNA production.

Characterization of 5S rRNA genes from mouse

In order to characterize the transcriptional regulation of the 5S rRNA genes we have isolated a bona fide gene and a pseudogene from mouse cells. These 5S rRNA genes contain a 12-bp sequence designated as the D-box, located in position -33 to -22 bp, and two Sp1-binding sites in the 5'-flanking region. The D-box is conserved in human and hamster 5S rRNA genes although in slightly different upstream positions. The bona fide mouse 5S rRNA gene was transcribed in a HeLa S-100 extract. The transcriptional activity of this gene was only 50% of that of the human gene, indicating the involvement of species-specific transcription factors and/or polymerases. The pseudogene which contains the D-box, but with position +25 to +35 bp deleted, showed no transcriptional activity. Deletion of the D-box in the 5'-flanking sequence abolished transcriptional activity, indicating that this conserved sequence is of importance for gene expression.

Characterization of human 5S rRNA genes

The human 5S rRNA genes are found in clusters of tandem repeated units. We have cloned and partially characterized six restriction fragments from two clusters of 2.3 kb and 1.6 kb repeats, respectively. Four fragments from the cluster of 2.3 kb repeats contain a 5S rRNA gene and one fragment contains a gene variant with an additional nucleotide in the internal control region. A fragment from the 1.6 kb cluster contains a gene and is highly homologous to the 2.3 kb repeats, except for a large deletion in the 3'-flanking region starting 12 bp downstream of the gene. The number of genes and closely related gene variants is found to be 300-400 per haploid human genome. 100-150 of these are found in 2.3 kb repeats and 5-10 are found in 1.6 kb repeats. The total number of 5S rRNA sequences, including pseudogenes, is 1700-2000 per haploid genome. The genes and the gene variant are transcribed equally efficient in a HeLa cell extract. If 5'-flanking sequences, including a GC-motif in the -40 region, are removed from the genes, transcription is reduced with a factor 10 or more, suggesting that sequences upstream of the coding region are important for the level of transcription.

Structure and organization of ribosomal DNA

Three trends are seen in the organization of ribosomal DNA genes during evolution: 1) gradual separation and separability of the regulation of transcription of 5S and larger subunit rRNAs; 2) retention of a transcription unit containing both large and small rRNAs; and 3) clustering of genes for both 5S and 18S-28S rDNAs, with the possible association of other 'non-rDNA' in the clusters of 18S-28S rDNA genes by the time mammals evolve.

Specific transcription of an Acanthamoeba castellanii 5S RNA gene in homologous nuclear extracts

An RNA polymerase III in vitro transcription system has been developed from the protist Acanthamoeba castellanii. The system is dependent on a cloned 5S RNA gene and utilizes a nuclear extract which contains all the necessary protein components. The system is assembled from completely homologous components. Primer extension and RNA sequencing analysis confirm that the in vitro 5S RNA transcript is identical to the 5S RNA isolated from cells. The transcription complex forms unusually rapidly on the 5S RNA gene and is stable to challenge by excess competitor templates. Several 5' deletion mutants were constructed and indicate that the region upstream of -33 is dispensable. Deletion to +16 show the region between -33 and +16 to be required for transcription, a region outside the canonical internal control region.

Organization and expression of 5S rRNA genes in the parasitic nematode, Brugia malayi

DNA sequence analysis of genes encoding 5S rRNA in the human parasitic nematode Brugia malayi (B. malayi) indicates a surprising degree of heterogeneity. This variation in coding sequence is not accompanied by corresponding heterogeneity in flanking regions which are highly conserved. Six out of eight potential 5S coding regions differed; of these sequence variants, two were abundant in the B. malayi genome. Direct RNA sequence analysis indicated that one of these abundant variants accounts for most if not all of expressed 5S RNA at two stages of development.

Genomic organization of human 5 S rDNA and sequence of one tandem repeat

An organization of human 5 S rDNA repeats is inferred from Southern analyses of restriction digests of genomic DNA fractionated by pulsed-field and conventional gel electrophoreses. A single unit of 2.2 kb is repeated approximately 90 times within a 200-kb fragment (defined by enzymes that do not cleave within individual units, i.e., EcoR1, BglII, HindIII, and PvuII); a comparable number of 5 S sequences are scattered elsewhere in the genome. A lambda clone containing six complete 5 S repeats was obtained from a human placental DNA library. One repeat contains 2231 bp and includes poly(dG-dT).(dC-dA), tracts of polypyrimidine, and an Alu sequence in the spacer region. Also, 5-S-hybridizing clones, containing DNA inserts with an average size of 250 kb, have been obtained as yeast artificial chromosomes. Thus far, four clones have been partially characterized and shown to be 5 S sequences from loci separate from the tandem repeat units.

Visualization of RNA binding proteins by sequential gel shift and ultraviolet cross-linking

RNA binding proteins partially constitute the ribonucleoprotein or protein machinery for RNA processing (splicing, polyadenylation and 3' end formation), transport, and storage. We have devised a novel method for the detection of RNA binding proteins in vitro. The template for transcription is a cloned Drosophila melanogaster 5S rRNA gene. The method is a two-dimensional gel analysis involving: in vitro transcription of 32P-labeled 5S rRNA using a cellular S-100; resolution of labeled RNA protein complexes from unbound RNA on a first-dimension mobility shift gel; cross-linking of RNA to protein in gel by ultraviolet irradiation; degradation of the RNA by RNase A and T1; and analysis of 32P-protein patterns on a second-dimension discontinuous SDS gel by autoradiography. The pattern of proteins associated with 32P-5S rRNA is obtained by covalent transfer of 32P-nucleotides from RNA to the proteins with which the RNA was bound. This method could be useful in the analysis of RNA maturation and processing pathways.

Transcription of the Drosophila melanogaster 5S RNA gene requires an upstream promoter and four intragenic sequence elements

Linker-scanning (LS) mutations were constructed spanning the length of the Drosophila melanogaster 5S RNA gene. In vitro transcription analysis of the LS 5S DNAs revealed five transcription control regions. One control region essential for transcription initiation was identified in the 5'-flanking sequence. The major sequence determinants of this upstream promoter region were located between coordinates -39 and -26 (-30 region), but important sequences extended to the transcription start site at position 1. Since mutations in the upstream promoter did not alter the ability of 5S DNA to sequester transcription factors into a stable transcription complex, it appears that this control region involved the interaction of RNA polymerase III. Active 5S DNA transcription additionally required the four intragenic control regions (ICRs) located between coordinates 3 and 18 (ICR I), 37 and 44 (ICR II), 48 and 61 (ICR III), and 78 and 98 (ICR IV). LS mutations in each ICR decreased the ability of 5S DNA to sequester transcription factors. ICR III, ICR IV, and the spacer sequence between were similar in sequence and position to the determinant elements of the multipartite ICR of Xenopus 5S DNA. The importance of ICR III and ICR IV in transcription initiation and in sequestering transcription factors suggests the presence of an activity in D. melanogaster similar to transcription factor TFIIIA of Xenopus laevis and HeLa cells. Transcription initiation of Drosophila 5S DNA was not eliminated by LS mutations in the spacer region even though these mutations reduced the ability of the TFIIIA-like activity to bind. The previously unidentified control regions ICR I and ICR II appear to be important for the interaction of a transcription factor activity, or multiple-factor activities, distinct from the TFIIIA-like activity. The interaction of this activity with ICR I directed the selection of the transcription start site.

Bipartite structure of the 5S ribosomal gene family in a Drosophila melanogaster strain, and its evolutionary implications

Knowledge of multigenic family organization should provide insight into their mode of evolution. Accordingly, we characterized the 5S ribosomal gene family in the Drosophila melanogaster strain ry506. The 5S genes in this strain display a striking HindIII restriction difference compared to the "standard" D. melanogaster 5S genes. The sequence of three ry506 5S genes was determined. We show that the HindIII restriction site heterogeneity within the ry506 5S family most probably results from the same point mutation, suggesting that a single 5S variant was propagated into the 5S cluster of this strain. Furthermore, we demonstrate that the structural organization of the 5S genes in ry506 is a bipartite structure, i.e., that about 40% of the 5S genes constitute a HindIII+/HindIII- mixed cluster, while those remaining constitute an homogeneous HindIII- cluster. The events which might lead to such an heterogeneous pattern are discussed from an evolutionary point of view.

Transcription of the Drosophila melanogaster 5S RNA gene requires an upstream promoter and four intragenic sequence elements

Linker-scanning (LS) mutations were constructed spanning the length of the Drosophila melanogaster 5S RNA gene. In vitro transcription analysis of the LS 5S DNAs revealed five transcription control regions. One control region essential for transcription initiation was identified in the 5'-flanking sequence. The major sequence determinants of this upstream promoter region were located between coordinates -39 and -26 (-30 region), but important sequences extended to the transcription start site at position 1. Since mutations in the upstream promoter did not alter the ability of 5S DNA to sequester transcription factors into a stable transcription complex, it appears that this control region involved the interaction of RNA polymerase III. Active 5S DNA transcription additionally required the four intragenic control regions (ICRs) located between coordinates 3 and 18 (ICR I), 37 and 44 (ICR II), 48 and 61 (ICR III), and 78 and 98 (ICR IV). LS mutations in each ICR decreased the ability of 5S DNA to sequester transcription factors. ICR III, ICR IV, and the spacer sequence between were similar in sequence and position to the determinant elements of the multipartite ICR of Xenopus 5S DNA. The importance of ICR III and ICR IV in transcription initiation and in sequestering transcription factors suggests the presence of an activity in D. melanogaster similar to transcription factor TFIIIA of Xenopus laevis and HeLa cells. Transcription initiation of Drosophila 5S DNA was not eliminated by LS mutations in the spacer region even though these mutations reduced the ability of the TFIIIA-like activity to bind. The previously unidentified control regions ICR I and ICR II appear to be important for the interaction of a transcription factor activity, or multiple-factor activities, distinct from the TFIIIA-like activity. The interaction of this activity with ICR I directed the selection of the transcription start site.

5S-rRNA genes in rice embryos

The 5S-rRNA from the ungerminated and 48-h-germinated rice embryos differs from the wheat, rye and maize by two nucleotides. The 48-h-germinated embryos contain another species of 5S-rRNA which differs by 3 nucleotides from the ungerminated embryos, thereby showing the expression of two 5S-rRNA genes during germination. The 5S-rRNA genes are present in tandem repeats of a 0.3-kb sequence with some length heterogeneity in the rice genome. The 5S-rRNA gene that was sequenced is identical to that of wheat and maize, except for two nucleotides, C and T, which are interchanged at positions 107 and 117. The insert of continuous 5S-rRNA gene in pBR322 was transcribed in vitro much more efficiently than the discontinuous gene. There was no homology between the 184-bp spacer sequence of 5S-rRNA genes in rice and other systems except the presence of the oligo(T) transcription terminator sequence.

Formation of an active transcription complex in the Drosophila melanogaster 5S RNA gene is dependent on an upstream region

We constructed deletion-substitution and linker-scanning mutations in the 5'-flanking region of the Drosophila melanogaster 5S RNA gene. In vitro transcription of these templates in Drosophila and HeLa cell extracts revealed the presence of an essential control region (-30 region) located between nucleotides -39 and -26 upstream of the transcription initiation site: deletion of sequences upstream of nucleotide position -39 had no detectable effect on the wild-type level of in vitro transcription, whereas mutations extending between positions -39 and 1 resulted in templates with decreased transcriptional levels; specifically, deletion and linker-scanning mutations in the -34 to -26 region (-30 region) resulted in loss of transcription. The -30 region is essential for transcription and therefore forms part of the Drosophila 5S RNA gene transcription promoter. Compared with the activity of the wild-type gene, mutant 5S DNAs exhibited no impairment in the ability to sequester limiting transcription factors in a template exclusion competition assay. While we do not know which transcription factor(s) interacts with the -30 region, the possible involvement of RNA polymerase III at this region is discussed.

A model for the interaction of nucleic acids with transcription factor IIIA

Based on published biochemical evidence which examines the interaction of Xenopus transcription factor IIIA (TFIIIA) with 5 S RNA genes and 5 S RNA, this paper proposes that the formation of a 5 S RNA type stem-loop structure in the DNA occurs during the binding of TFIIIA to 5 S genes.

Formation of an active transcription complex in the Drosophila melanogaster 5S RNA gene is dependent on an upstream region

We constructed deletion-substitution and linker-scanning mutations in the 5'-flanking region of the Drosophila melanogaster 5S RNA gene. In vitro transcription of these templates in Drosophila and HeLa cell extracts revealed the presence of an essential control region (-30 region) located between nucleotides -39 and -26 upstream of the transcription initiation site: deletion of sequences upstream of nucleotide position -39 had no detectable effect on the wild-type level of in vitro transcription, whereas mutations extending between positions -39 and 1 resulted in templates with decreased transcriptional levels; specifically, deletion and linker-scanning mutations in the -34 to -26 region (-30 region) resulted in loss of transcription. The -30 region is essential for transcription and therefore forms part of the Drosophila 5S RNA gene transcription promoter. Compared with the activity of the wild-type gene, mutant 5S DNAs exhibited no impairment in the ability to sequester limiting transcription factors in a template exclusion competition assay. While we do not know which transcription factor(s) interacts with the -30 region, the possible involvement of RNA polymerase III at this region is discussed.

Structural analysis of a triple complex between the histone octamer, a Xenopus gene for 5S RNA and transcription factor IIIA

This paper reports three experiments concerning the structural relationship between the Xenopus transcription factor IIIA (TFIIIA), the histone octamer and the Xenopus somatic gene for 5S RNA. Quantitative footprinting methods have been used in order to discover where and how TFIIIA and the histone octamer bind to the same gene independently and also in a triple complex. First, DNaseI and DNaseII protection experiments show that TFIIIA binds to positions 45-97 within the gene, in agreement with other workers. Second, the histone octamer takes up a unique, well-defined position with respect to DNA sequence. The nucleosome core extends to position 78 of the gene and therefore overlaps the TFIIIA binding region by approximately 35 bp. Third, it is shown that a triple complex can be formed between TFIIIA, the histone octamer and the 5S RNA gene. TFIIIA displaces the DNA from the histone surface in the 35-bp region of overlap. This has led to a three-dimensional model which explains how RNA polymerase III could interact simultaneously with transcription factors bound at the internal control region of the 5S RNA gene and the start point of transcription. The model also explains how histone H1 could repress transcription of 5S RNA genes.

Characterization of the Trypanosoma brucei 5S ribosomal RNA gene and transcript: the 5S rRNA is a spliced-leader-independent species

Recent studies have shown that transcription occurs discontinuously for many genes in Trypanosoma brucei. To further investigate details of transcription in trypanosomes, the genes for the 5S ribosomal RNA from Trypanosoma brucei rhodesiense and Trypanosoma brucei brucei were cloned. Sequence analysis and Southern blotting showed the genes to be arranged in highly conserved tandem repeats of approx. 740 bp, which have no relation to the conserved 35-base spliced-leader repeat element. The genes contain internal control regions similar to 5S genes of other species, and studies of the 5S gene transcript show that it does not contain the conserved 35-base spliced-leader found at the 5' end of other trypanosome transcripts. Moreover, the 5S rRNA can be capped by guanylyltransferase from vaccinia virus, indicating that it has a 5' di- or triphosphate terminus. These results strongly suggest that the spliced-leader does not take part in the transcription of the 5S gene and that discontinuous transcription may be limited to particular classes of transcripts determined, as in other species, by the type of RNA polymerase used in their transcription. The DNA sequences of the 5S gene repeat from T.b. brucei and T.b. rhodesiense are presented, and their evolutionary significance is discussed.