Structure and organization of the peridinin-chlorophyll a-binding protein gene in Gonyaulax polyedra

Abstract

We have identified a major 32-kDa protein in the dinoflagellate Gonyaulax polyedra as a peridinin-chlorophyll a-binding protein (PCP), based on micro-sequence data and immunological cross-reaction with antibodies raised against PCP from another dinoflagellate species. A cDNA for this protein, identified by a PCR-based cloning strategy, encoded all 68 of the amino acids microsequenced, thus confirming the identity of the clone. The PCP gene is highly expressed at both the mRNA and protein levels, and only PCP transcripts corresponding in size to the cDNA sequence were detected. Slot blot analyses show that there are roughly 5000 copies of the PCP gene in Gonyaulax, making this gene one of the most highly repeated protein-coding genes ever reported, yet the sequence of the different gene copies in the genome appears extraordinarily well conserved as judged by Southern blot analyses. The gene, as indicated by Southern blot and PCR data, is suggested to be present in 5000 intronless copies arranged head to tail in the genome, separated by conserved 1-kb spacers. Based on the conserved sequence of the spacer region, its presence next to each of the PCP coding sequences, and the uniform size of the PCP transcript, we propose that this region represents a dinoflagellate transcriptional promoter. This putative promoter region contains none of the sequence elements for DNA-binding proteins involved in transcriptional initiation reported in other organisms.

Thermal Stress Triggers Broad Pocillopora damicornis Transcriptomic Remodeling, while Vibrio coralliilyticus Infection Induces a More Targeted Immuno-Suppression Response

“…Assembled genomes for the two partners in the symbiosis are lacking, and dinoflagellate genomes are known to contain numerous copies of orthologous genes, which can be divergent. The latter factor increases the complexity of the transcriptome [49]–[52] and can make assignment difficult. In addition, our transcriptome probably contained xeno-contaminant sequences from bacteria, eukaryotic species and RNA viruses [53], which are part of the coral holobiont [54].…”

Hyperdiversity of Genes Encoding Integral Light-Harvesting Proteins in the Dinoflagellate Symbiodinium sp

“…Gene duplication is a well documented feature in dinoflagellates [71], [72], [73] which presumably has given rise to polyproteins in addition to increasing the copy number of highly expressed genes [24]. Information on the organisation of dinoflagellate genomes is limited, but there is evidence that subsets of genes are arranged in repeated tandem arrays and result in polycistronic messages carrying multiple copies of a single gene [24].…”

The transcriptome of the novel dinoflagellate Oxyrrhis marina (Alveolata: Dinophyceae): response to salinity examined by 454 sequencing

“…The precise structure and the extent of these tandem gene arrays remains to be investigated in O. marina ; regardless, it is now increasingly clear that gene duplication is extensive in dinoflagellates more generally, and results in complex gene arrangements (e.g. [13,39]. Understanding the mechanisms promoting such expansions is an important focus for dinoflagellate genome biologists.…”

“…More generally, dinoflagellate genomes remain poorly-characterised due to several genomic characteristics. For example, dinoflagellates typically possess large genomes [7,11,12] that contain numerous genes arranged in repetitive tandem-arrays [13]; further, they have potentially complex transcriptomes composed of multiple transcript variants for many genes [14]. The occurrence of such traits in O. marina remains only partially characterised: the genome appears to be large [15], and a number of genes occur as multiple transcribed variants [16], but whether these genes are present as tandem-arrays has not been demonstrated.…”