Group II Introns Break New Boundaries: Presence in a Bilaterian's Genome

Group II introns are ribozymes, removing themselves from their primary transcripts, as well as mobile genetic elements, transposing via an RNA intermediate, and are thought to be the ancestors of spliceosomal introns. Although common in bacteria and most eukaryotic organelles, they have never been reported in any bilaterian animal genome, organellar or nuclear. Here we report the first group II intron found in the mitochondrial genome of a bilaterian worm. This location is especially surprising, since animal mitochondrial genomes are generally distinct from those of plants, fungi, and protists by being small and compact, and so are viewed as being highly streamlined, perhaps as a result of strong selective pressures for fast replication while establishing germ plasm during early development. This intron is found in the mtDNA of an annelid worm, (an undescribed species of Nephtys), where the complete sequence revealed a 1819 bp group II intron inside the cox1 gene. We infer that this intron is the result of a recent horizontal gene transfer event from a viral or bacterial vector into the mitochondrial genome of Nephtys sp. Our findings hold implications for understanding mechanisms, constraints, and selective pressures that account for patterns of animal mitochondrial genome evolutio

Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect \u3ci\u3eChlorella\u3c/i\u3e Pbi

Viruses MT325 and FR483, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella Pbi. The 314,335-bp genome of MT325 and the 321,240-bp genome of FR483 are the first viruses that infect Chlorella Pbi to have their genomes sequenced and annotated. Furthermore, these genomes are the two smallest chlorella virus genomes sequenced to date, MT325 has 331 putative protein-encoding and 10 tRNA-encoding genes and FR483 has 335 putative protein-encoding and 9 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Approximately 40% of the viral gene products resemble entries in public databases, including some that are the first of their kind to be detected in a virus. For example, these unique gene products include an aquaglyceroporin in MT325, a potassium ion transporter protein and an alkyl sulfatase in FR483, and a dTDP–glucose pyrophosphorylase in both viruses. Comparison of MT325 and FR483 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that approximately 82% of the genes are present in all three viruses. Supplementary data to accompany this article is archived in this repository as 4 separate documents

Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect \u3ci\u3eChlorella\u3c/i\u3e Pbi

Viruses MT325 and FR483, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella Pbi. The 314,335-bp genome of MT325 and the 321,240-bp genome of FR483 are the first viruses that infect Chlorella Pbi to have their genomes sequenced and annotated. Furthermore, these genomes are the two smallest chlorella virus genomes sequenced to date, MT325 has 331 putative protein-encoding and 10 tRNA-encoding genes and FR483 has 335 putative protein-encoding and 9 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Approximately 40% of the viral gene products resemble entries in public databases, including some that are the first of their kind to be detected in a virus. For example, these unique gene products include an aquaglyceroporin in MT325, a potassium ion transporter protein and an alkyl sulfatase in FR483, and a dTDP–glucose pyrophosphorylase in both viruses. Comparison of MT325 and FR483 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that approximately 82% of the genes are present in all three viruses. Supplementary data to accompany this article is archived in this repository as 4 separate documents

Sequence and annotation of the 288-kb ATCV-1 virus that infects an endosymbiotic chlorella strain of the heliozoon \u3ci\u3eAcanthocystis turfacea\u3c/i\u3e

Acanthocystis turfacea chlorella virus (ATCV-1), a prospective member of the family Phycodnaviridae, genus Chlorovirus, infects a unicellular, eukaryotic, chlorella-like green alga, Chlorella SAG 3.83, that is a symbiont in the heliozoon A. turfacea. The 288,047-bp ATCV-1 genome is the first virus to be sequenced that infects Chlorella SAG 3.83. ATCV-1 contains 329 putative protein-encoding and 11 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands and intergenic space is minimal. Thirty-four percent of the viral gene products resemble entries in the public databases, including some that are unexpected for a virus. For example, these unique gene products include ribonucleoside-triphosphate reductase, dTDP-D-glucose 4,6 dehydratase, potassium ion transporter, aquaglyceroporin, and mucindesulfating sulfatase. Comparison of ATCV-1 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that about 80% of the ATCV-1 genes are present in PBCV-1

Intricate RNA : RNA Interactions in U12-Dependent Nuclear Pre-mRNA Splicing

Coding regions or exons of most human genes are interrupted by noncoding intervening regions or introns. Removal of nuclear precursor messenger RNA (pre-mRNA) introns by RNA splicing is an essential step in eukaryotic gene expression. Two types of nuclear pre-mRNA introns are known as U2-dependent or major type and U12-dependent or minor type. Nuclear pre-mRNA introns are removed by two distinct sets of ribonucleoprotein complexes or spliceosomes, which are formed by five small nuclear RNAs (snRNAs) for each spliceosome. U6atac and U12 snRNAs are central to U12-dependent spliceosome and play essential roles in the removal of U12-dependent introns. U6atac and U12 snRNAs bind to the 5\u27 splice site and branch site, respectively of an U12-dependent intron. In addition, it has been predicted that, U6atac and U12 snRNAs interact inter-molecularly to form helix I structure, which appears to be an essential element of the minor spliceosome. We have been studying U6atac and U12 inter-molecular base-pairing interaction using an in vivo mutation suppression assay. In this study, we have characterized U6atac and U12 mediated helix I intermolecular interactions and have shown in vivo existence of the predicted structure. In addition, we have also identified a region of U6atac snRNA which appears to be a structural analog of U12 snRNA stem III element. This element is important for the function of U12 snRNA and functions by binding to a RNA binding 65K protein, which is unique to minor spliceosome. We show that, analogous stem-loop of U6atac snRNA also interacts with 65K - RNA binding protein. However, functional significance of this interaction remained unclear. In summation, we have characterized sequential and dynamic RNA-RNA interactions between U4atac-U6atac and U6atac-U12 snRNAs. Our data show that, extensive and obligatory RNA-RNA interactions are critical to the splicing of U12-dependent intron

The \u3ci\u3ePhycodnaviridae\u3c/i\u3e: The Story of How Tiny Giants Rule the World

The family Phycodnaviridae encompasses a diverse and rapidly expanding collection of large icosahedral, dsDNA viruses that infect algae. These lytic and lysogenic viruses have genomes ranging from 160 to 560 kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect them with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV).The phycodnaviruses have diverse genome structures, some with large regions of noncoding sequence and others with regions of ssDNA. The genomes of members in three genera in the Phycodnaviridae have been sequenced. The genome analyses have revealed more than 1000 unique genes, with only 14 homologous genes in common among the three genera of phycodnaviruses sequenced to date. Thus, their gene diversity far exceeds the number of so-called core genes. Not much is known about the replication of these viruses, but the consequences of these infections on phytoplankton have global affects, including influencing geochemical cycling and weather patterns

The \u3ci\u3ePhycodnaviridae\u3c/i\u3e: The Story of How Tiny Giants Rule the World

The family Phycodnaviridae encompasses a diverse and rapidly expanding collection of large icosahedral, dsDNA viruses that infect algae. These lytic and lysogenic viruses have genomes ranging from 160 to 560 kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect them with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV).The phycodnaviruses have diverse genome structures, some with large regions of noncoding sequence and others with regions of ssDNA. The genomes of members in three genera in the Phycodnaviridae have been sequenced. The genome analyses have revealed more than 1000 unique genes, with only 14 homologous genes in common among the three genera of phycodnaviruses sequenced to date. Thus, their gene diversity far exceeds the number of so-called core genes. Not much is known about the replication of these viruses, but the consequences of these infections on phytoplankton have global affects, including influencing geochemical cycling and weather patterns

Chlorella Viruses

Chlorella viruses or chloroviruses are large, icosahedral, plaque-forming, double-stranded-DNA-containing viruses that replicate in certain strains of the unicellular green alga Chlorella. DNA sequence analysis of the 330-kbp genome of Paramecium bursaria chlorella virus 1 (PBCV-1), the prototype of this virus family (Phycodnaviridae), predict ∼366 protein-encoding genes and 11 tRNA genes. The predicted gene products of ∼500f these genes resemble proteins of known function, including many that are completely unexpected for a virus. In addition, the chlorella viruses have several features and encode many gene products that distinguish them from most viruses. These products include: (1) multiple DNA methyltransferases and DNA site-specific endonucleases, (2) the enzymes required to glycosylate their proteins and synthesize polysaccharides such as hyaluronan and chitin, (3) a virus-encoded K+ channel (called Kcv) located in the internal membrane of the virions, (4) a SET domain containing protein (referred to as vSET) that dimethylates Lys27 in histone 3, and (5) PBCV-1 has three types of introns; a self-splicing intron, a spliceosomal processed intron, and a small tRNA intron. Accumulating evidence indicates that the chlorella viruses have a very long evolutionary history. This review mainly deals with research on the virion structure, genome rearrangements, gene expression, cell wall degradation, polysaccharide synthesis, and evolution of PBCV-1 as well as other related viruses

An investigation of genetic variation within northwest Atlantic Porphyra (Bangiales, Rhodophyta) with specific phylogeographic analysis of the common, rocky intertidal species, Porphyra umbilicalis

To investigate the phylogeography of the rocky intertidal red alga, Porphyra umbilicalis Kutzing, a restriction fragment polymorphism assay (RFLP) of the ribulose bisphosphate carboxylase large subunit ( rbcL) was developed to accurately distinguish P. umbilicalis from the other morphologically similar species in the North Atlantic. Initial screening of ∼800 Porphyra specimens resulted in the additional discovery of a cryptic Porphyra taxon. The presence and variability of group-I introns of the ribosomal small subunit (SSU) were screened in North Atlantic species of Porphyra in order to assess whether they could be biogeographically informative. In an initial screening for the helix 50 intron, using flanking primers with the Polymerase Chain Reaction, the intron was detected in some, but not all, individuals within populations and across species. The amplified intron also exhibited variable sizes between and within species. Sequence analysis of the helix 50 introns revealed conserved blocks of nucleotides between introns of different species and highly variable regions that were species-specific. Additional screenings of the ribosomal small subunit (SSU) from a collection of Northwest Atlantic Porphyra were conducted for the presence of the helices 21 and 50 introns. However, instead of using two flanking primers, the second screening used an internal primer (located within either the helix 50 or helix 21 intron) and a nearby flanking primer in the SSU. Using these primers the frequency of detecting the intron in individual algal samples increased significantly (\u3e90%). Although phylogenetic analysis of the helix 50 intron in select Northwest Atlantic Porphyra are generally similar to previously reported SSU phylogenies, some differences in topology suggest that horizontal transmission of the intron between species may have occurred. In contrast to previous studies in which the helix 50 intron was detected only in fraction of the accessions, an intraspecific survey using combined external and internal primers detected the helix 50 intron in all 28 samples of Porphyra umbilicalis collected across the geographic range of the species. A survey of P. umbilicalis also revealed that the helix 50 introns were present in two different sizes (710 bp and 1188 bp). The sequence of the larger version of the helix 50 intron encodes a His-Cys open reading frame that has been associated with mobility of group-I introns in other organisms. (Abstract shortened by UMI.)