The differential expression of ribosomal 18S RNA paralog genes from the chaetognath Spadella cephaloptera

The Role of Sequence Duplication in Transcriptional Regulation and Genome Evolution

Sequence duplication is nowadays recognized as an important mechanism that underlies the evolution of eukaryote genomes, being indeed one of the most powerful strategies for the generation of adaptive diversity by modulating transcriptional activity. The evolutionary novelties simultaneously associated with sequence duplication and differential gene expression can be collectively referred to as duplication-mediated transcriptional regulation. In the last years, evidence has emerged supporting the idea that sequence duplication and functionalization represent important evolutionary strategies acting at the genome level, and both coding and non-coding sequences have been found to be targets of such events. Moreover, it has been proposed that deleterious effects of sequence duplication might be potentially silenced by endogenous cell machinery (i.e., RNA interference, epigenetic repressive marks, etc). Along these lines, our aim is to highlight the role of sequence duplication on transcriptional activity and the importance of both in genome evolution.

Highly divergent 18S rRNA gene paralogs in a Cryptosporidium genotype from eastern chipmunks (Tamias striatus)

Cryptosporidium is an apicomplexan parasite that causes the disease cryptosporidiosis in humans, livestock, and other vertebrates. Much of the knowledge on Cryptosporidium diversity is derived from 18S rRNA gene (18S rDNA) phylogenies. Eukaryote genomes generally have multiple 18S rDNA copies that evolve in concert, which is necessary for the accurate inference of phylogenetic relationships. However, 18S rDNA copies in some genomes evolve by a birth-and-death process that can result in sequence divergence among copies. Most notably, divergent 18S rDNA paralogs in the apicomplexan Plasmodium share only 89-95% sequence similarity, encode structurally distinct rRNA molecules, and are expressed at different life cycle stages. In the present study, Cryptosporidium 18S rDNA was amplified from 28/72 (38.9%) eastern chipmunks (Tamias striatus). Phylogenetic analyses showed the co-occurrence of two 18S rDNA types, Type A and Type B, in 26 chipmunks, and Type B clustered with a sequence previously identified as Cryptosporidium chipmunk genotype II. Types A and B had a sister group relationship but shared less than 93% sequence similarity. In contrast, actin and heat shock protein 70 gene sequences were homogeneous in samples with both Types A and B present. It was therefore concluded that Types A and B are divergent 18S rDNA paralogs in Cryptosporidium chipmunk genotype II. Substitution patterns in Types A and B were consistent with functionally constrained evolution; however, Type B evolved more rapidly than Type A and had a higher G+C content (46.3% versus 41.0%). Oocysts of Cryptosporidium chipmunk genotype II measured 4.17 μm (3.73-5.04 μm) × 3.94 μm (3.50-4.98 μm) with a length-to-width ratio of 1.06 ± 0.06 μm, and infection occurred naturally in the jejunum, cecum, and colon of eastern chipmunks. The findings of this study have implications for the use of 18S rDNA sequences to infer phylogenetic relationships.

Careful with understudied phyla: the case of chaetognath

Background

A recent study by Barthélémy et al. described a set of ribosomal protein (RP) genes extracted from a collection of expressed sequence tags (ESTs) of the chaetognath (arrow worm) Spadella cephaloptera. Three main conclusions were drawn in this paper. First, the authors stated that RP genes present paralogous copies, which have arisen through allopolyploidization. Second, they reported two alternate nucleotide stretches conserved within the 5' untranslated regions (UTR) of multiple ribosomal cDNAs and they suggested that these motifs are involved in the differential transcriptional regulation of paralogous RP genes. Third, they claimed that the phylogenetic position of chaetognaths could not be accurately inferred from a RP dataset because of the persistence of two problems: a long branch attraction (LBA) artefact and a compositional bias.

Results

We reconsider here the results described in Barthélémy et al. and question the evidence on which they are based. We find that their evidence for paralogous copies relies on faulty PCR experiments since they attempted to amplify DNA fragments absent from the genomic template. Our PCR experiments proved that the conserved motifs in 5'UTRs that they targeted in their amplifications are added post-transcriptionally by a trans-splicing mechanism. Then, we showed that the lack of phylogenetic resolution observed by these authors is due to limited taxon sampling and not to LBA or to compositional bias. A ribosomal protein dataset thus fully supports the position of chaetognaths as sister group of all other protostomes. This reinterpretation demonstrates that the statements of Barthélémy et al. should be taken with caution because they rely on inaccurate evidence.

Conclusion

The genomic study of an unconventional model organism is a meaningful approach to understand the evolution of animals. However, the previous study came to incorrect conclusions on the basis of experiments that omitted validation procedures.

Transcriptome Analysis of ESTs from a Chaetognath Reveals a Deep-Branching Clade of Retrovirus-Like Retrotransposons

Chaetognaths constitute a small marine phylum exhibiting several characteristic which are highly unusual in animal genomes, including two classes of both rRNA and protein ribosomal genes. As in this phylum presence of retrovirus-like elements has never been documented, analysis of a published expressed sequence tag (EST) collection of the chaetognath Spadella cephaloptera has been made. Twelve sequences representing transcript sections of reverse transcriptase domain of active retrotransposons were isolated from~11,000 ESTs. Five of them are originated from Gypsy retrovirus-like elements, whereas the other are transcripts from a Bel-Pao LTR-retrotransposon, a Penelope-like element and LINE retrotransposons. Moreover, a part of a putative integrase has also been found. Phylogenetic analyses suggest a deep-branching clade of the retrovirus-like elements, which is in agreement with the probably Cambrian origin of the phylum. Moreover, retrotransposons have not been found in telomeric-like transcripts which are probably constituted by both vertebrate and arthropod canonical repeats.

Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression

Background

Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studies.

Results

This analysis has allowed us to determine the complete primary structures of 23 out of 32 RPs from the small ribosomal subunit (SSU) and 32 out of 47 RPs from the large ribosomal subunit (LSU). Ten proteins are partially determined and 14 proteins are missing. Phylogenetic analyses of concatenated RPs from six animals (chaetognath, echinoderm, mammalian, insect, mollusc and sponge) and one fungal taxa do not resolve the chaetognath phylogenetic position, although each mega-sequence comprises approximately 5,000 amino acid residues. This is probably due to the extremely biased base composition and to the high evolutionary rates in chaetognaths. However, the analysis of chaetognath RP genes revealed three unique features in the animal Kingdom. First, whereas generally in animals one RP appeared to have a single type of mRNA, two or more genes are generally transcribed for one RP type in chaetognath. Second, cDNAs with complete 5'-ends encoding a given protein sequence can be divided in two sub-groups according to a short region in their 5'-ends: two novel and highly conserved elements have been identified (5'-TAATTGAGTAGTTT-3' and 5'-TATTAAGTACTAC-3') which could correspond to different transcription factor binding sites on paralog RP genes. And, third, the overall number of deduced paralogous RPs is very high compared to those published for other animals.

Conclusion

These results suggest that in chaetognaths the deleterious effects of the presence of paralogous RPs, such as apoptosis or cancer are avoided, and also that in each protein family, some of the members could have tissue-specific and extra-ribosomal functions. These results are congruent with the hypotheses of an allopolyploid origin of this phylum and of a ribosome heterogeneity.