The recent discovery of a diverse phylogenetic assemblage of picoeukaryotes from environments such as oceans, salt marshes and acidic habitats, has expanded the debates about the extent and origin of microbial eukaryotes. However, the diversity of these eukaryote microorganisms, that overlap bacteria in size, and their environmental and biogeographical ubiquity remains poorly understood. Here we survey picoeukaryotes (microbial eukaryotes of 0.2-5 microm in size) from an oligotrophic (nutrient deficient) freshwater habitat using ribosomal RNA gene sequences. Three taxonomic groups the Heterokonta, Cryptomonads and the Alveolata dominated the detected diversity. Most sequences represented previously unsampled species, with several being unassignable to known taxonomic groups and plausibly represent new or unsampled phyla. Many freshwater phylogenetic groups identified in this study appeared unrelated to picoeukaryotic sequences identified in marine ecosystems, suggesting that aspects of eukaryote microbial diversity are specific to certain aquatic environments. Conversely, at least five phylogenetic clusters comprised sequences from freshwater and globally dispersed and often contrasting environments, supporting the concept that a number of picoeukaryotic lineages are widely distributed.
A self-splicing group I intron has been found in the gene for a leucine transfer RNA in two species of Anabaena, a filamentous nitrogen-fixing cyanobacterium. The intron is similar to one that is found at the identical position in the same transfer RNA gene of chloroplasts of land plants. Because cyanobacteria were the progenitors of chloroplasts, it is likely that group I introns predated the endosymbiotic association of these eubacteria with eukaryotic cells.
Many tRNA UAALeu genes from plastids contain a group I intron. An intron is also inserted in the same gene at the same position in cyanobacteria, the bacterial progenitors of plastids, suggesting an ancient bacterial origin for this intron. A group I intron has also been found in the tRNA fMet gene of some cyanobacteria but not in plastids, suggesting a more recent origin for this intron. In this study, we investigate the phylogenetic distributions of the two introns among cyanobacteria, from the earliest branching to the more derived species. The phylogenetic distribution of the tRNA UAA Leu intron follows the clustering of rRNA sequences, being either absent or present in clades of closely related species, with only one exception in the Pseudanabaena group. Our data support the notion that the tRNA UAA Leu intron was inherited by cyanobacteria and plastids through a common ancestor. Conversely, the tRNA fMet intron has a sporadic distribution, implying that many gains and losses occurred during cyanobacterial evolution. Interestingly, a phylogenetic tree inferred from intronic sequences clearly separates the different tRNA introns, suggesting that each family has its own evolutionary history.Ever since their discovery, the origin of introns has been a subject of controversy. One view, the introns-late hypothesis, proposes that introns are recent invaders and that split genes arose by late insertion of introns into originally uninterrupted genes (28). In that scenario, horizontal transfer and transposition of introns are frequent events, accounting for the scattered phylogenetic distribution of introns. Although the debate has focused on spliceosomal introns, such a scenario could apply as well to other types of introns, some of which are known to be mobile (22). In contrast, the introns-early view implies that introns are very ancient, being present in the progenote (universal ancestor) (7). The demonstration that some members of group I and group II introns are capable of in vitro autocatalytic activity (19,29,39) lends further support to the presence of these introns at an early stage of evolution, maybe as early as the putative precellular RNA world (13). In such a scenario, the observed phylogenetic distribution of introns could be explained by multiple losses in different lineages during evolution (7) and by their mobility, which is assumed to be a derived feature (2). A major obstacle for the introns-early hypothesis was the apparent absence of introns in eubacteria, although this was tentatively rationalized by pressure to streamline the genome in rapidly dividing bacteria (7). Discovery of group I introns in bacteriophages of gram-positive and gram-negative bacteria did not help to resolve the issue, due to uncertainties concerning the origin of the bacteriophages themselves (see discussion in reference 35). The recent discovery of both group I and group II introns in divergent eubacteria (4,11,12,20,31,44) was acclaimed as a breakthrough by introns-early proponents. In most cases, however, the relatio...
In the filamentous cyanobacterium Anabaena, the gene for the small subunit (rbcS) of ribulose-1,5-bisphosphate carboxylase is linked to and transcribed together with the gene encoding the large subunit (rbcL) of the same enzyme. The two genes are separated by a spacer of 545 base pairs (bp) that does not contain an open reading frame. Both genes hybridize with a predominant 3.1-kilobase transcript that initiates 414 bp upstream from the rbcL coding region. The nucleotide sequence 14-8 bp preceding the transcription start site resembles a good Escherichia coli promoter, but the sequence in the -35 region does not. There is no obvious relationship between the sequence flanking the amino terminus of the cyanobacterial small subunit gene and the transit peptide of eukaryotic small subunit genes. The Anabaena rbcS gene is 61% homologous at the amino acid level with the gene from the unicellular cyanobacterium Anacystis and 37-38% homologous with the corresponding nuclear genes from eukaryotes. In contrast, the Anabaena rbcL gene is -86% homologous at the amino acid level with the rbcL genes from plant chloroplasts. Cotranscription satisfies one of the requirements for coordinate expression of the two genes whose products are needed in equimolar amounts in the mature enzyme. The rbcL-rbcS transcript is equally abundant in Anabaena azollae grown in the light or on fructose in the dark.
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