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1.
RNA ; 29(5): 531-550, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-36737103

RESUMEN

Premessenger RNA splicing is catalyzed by the spliceosome, a multimegadalton RNA-protein complex that assembles in a highly regulated process on each intronic substrate. Most studies of splicing and spliceosomes have been carried out in human or S. cerevisiae model systems. There exists, however, a large diversity of spliceosomes, particularly in organisms with reduced genomes, that suggests a means of analyzing the essential elements of spliceosome assembly and regulation. In this review, we characterize changes in spliceosome composition across phyla, describing those that are most frequently observed and highlighting an analysis of the reduced spliceosome of the red alga Cyanidioschyzon merolae We used homology modeling to predict what effect splicing protein loss would have on the spliceosome, based on currently available cryo-EM structures. We observe strongly correlated loss of proteins that function in the same process, for example, in interacting with the U1 snRNP (which is absent in C. merolae), regulation of Brr2, or coupling transcription and splicing. Based on our observations, we predict splicing in C. merolae to be inefficient, inaccurate, and post-transcriptional, consistent with the apparent trend toward its elimination in this lineage. This work highlights the striking flexibility of the splicing pathway and the spliceosome when viewed in the context of eukaryotic diversity.


Asunto(s)
Proteínas de Saccharomyces cerevisiae , Empalmosomas , Humanos , Empalmosomas/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Empalme del ARN , Intrones , Ribonucleoproteína Nuclear Pequeña U1/genética , Precursores del ARN/genética , Precursores del ARN/metabolismo , ARN Helicasas/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
2.
J Eukaryot Microbiol ; : e13051, 2024 Jul 30.
Artículo en Inglés | MEDLINE | ID: mdl-39079911

RESUMEN

Microsporidia are intracellular parasites that all possess a unique infection apparatus involving a polar tube. Upon contact with a host cell, this tube forms the conduit through which the parasite enters the host. Infecting mostly animals, microsporidian species can be transmitted vertically or horizontally, and exert various effects on their hosts: infections range from being relatively benign to lethal. Microsporidian genomes possess highly divergent sequences and are often substantially reduced in size. Their divergent sequences and unique morphology created early challenges to our understanding of their phylogenetic position within the tree of eukaryotes. Over the last couple of decades, advances in both sequencing technology and phylogenetic methodology supported a clear relationship between microsporidia and fungi. However, the specifics of this relationship were muddied by the lack of known microsporidian relatives. With increased taxon discovery and the morphological and molecular characterization of microsporidia-like taxa, rozellids and aphelids, a better resolved picture is emerging. Here we review the history of microsporidian taxonomy and current status of genomics of microsporidia and their nearest relatives, with an aim to understand their morphological and metabolic differences, along with their evolutionary relationships.

3.
BMC Biol ; 21(1): 137, 2023 06 06.
Artículo en Inglés | MEDLINE | ID: mdl-37280585

RESUMEN

BACKGROUND: Intracellular symbionts often undergo genome reduction, losing both coding and non-coding DNA in a process that ultimately produces small, gene-dense genomes with few genes. Among eukaryotes, an extreme example is found in microsporidians, which are anaerobic, obligate intracellular parasites related to fungi that have the smallest nuclear genomes known (except for the relic nucleomorphs of some secondary plastids). Mikrocytids are superficially similar to microsporidians: they are also small, reduced, obligate parasites; however, as they belong to a very different branch of the tree of eukaryotes, the rhizarians, such similarities must have evolved in parallel. Since little genomic data are available from mikrocytids, we assembled a draft genome of the type species, Mikrocytos mackini, and compared the genomic architecture and content of microsporidians and mikrocytids to identify common characteristics of reduction and possible convergent evolution. RESULTS: At the coarsest level, the genome of M. mackini does not exhibit signs of extreme genome reduction; at 49.7 Mbp with 14,372 genes, the assembly is much larger and gene-rich than those of microsporidians. However, much of the genomic sequence and most (8075) of the protein-coding genes code for transposons, and may not contribute much of functional relevance to the parasite. Indeed, the energy and carbon metabolism of M. mackini share several similarities with those of microsporidians. Overall, the predicted proteome involved in cellular functions is quite reduced and gene sequences are extremely divergent. Microsporidians and mikrocytids also share highly reduced spliceosomes that have retained a strikingly similar subset of proteins despite having reduced independently. In contrast, the spliceosomal introns in mikrocytids are very different from those of microsporidians in that they are numerous, conserved in sequence, and constrained to an exceptionally narrow size range (all 16 or 17 nucleotides long) at the shortest extreme of known intron lengths. CONCLUSIONS: Nuclear genome reduction has taken place many times and has proceeded along different routes in different lineages. Mikrocytids show a mix of similarities and differences with other extreme cases, including uncoupling the actual size of a genome with its functional reduction.


Asunto(s)
Microsporidios , Microsporidios/genética , Filogenia , Evolución Molecular , Genoma , Intrones , Eucariontes/genética
4.
J Eukaryot Microbiol ; 70(1): e12927, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-35662328

RESUMEN

The Cyanidiales are a group of mostly thermophilic and acidophilic red algae that thrive near volcanic vents. Despite their phylogenetic relationship, the reduced genomes of Cyanidioschyzon merolae and Galdieria sulphuraria are strikingly different with respect to pre-mRNA splicing, a ubiquitous eukaryotic feature. Introns are rare and spliceosomal machinery is extremely reduced in C. merolae, in contrast to G. sulphuraria. Previous studies also revealed divergent spliceosomes in the mesophilic red alga Porphyridium purpureum and the red algal derived plastid of Guillardia theta (Cryptophyta), along with unusually high levels of unspliced transcripts. To further examine the evolution of splicing in red algae, we compared C. merolae and G. sulphuraria, investigating splicing levels, intron position, intron sequence features, and the composition of the spliceosome. In addition to identifying 11 additional introns in C. merolae, our transcriptomic analysis also revealed typical eukaryotic splicing in G. sulphuraria, whereas most transcripts in C. merolae remain unspliced. The distribution of intron positions within their host genes was examined to provide insight into patterns of intron loss in red algae. We observed increasing variability of 5' splice sites and branch donor regions with increasing intron richness. We also found these relationships to be connected to reductions in and losses of corresponding parts of the spliceosome. Our findings highlight patterns of intron and spliceosome evolution in related red algae under the pressures of genome reduction.


Asunto(s)
Precursores del ARN , Rhodophyta , Precursores del ARN/genética , Precursores del ARN/metabolismo , Filogenia , Empalme del ARN , Empalmosomas/genética , Empalmosomas/metabolismo , Rhodophyta/genética , Intrones/genética , Eucariontes/genética , Criptófitas/genética
5.
J Eukaryot Microbiol ; 68(3): e12844, 2021 05.
Artículo en Inglés | MEDLINE | ID: mdl-33569840

RESUMEN

Pre-mRNA splicing is a highly conserved eukaryotic process, but our understanding of it is limited by a historical focus on well-studied organisms such as humans and yeast. There is considerable diversity in mechanisms and components of pre-mRNA splicing, especially in lineages that have evolved under the pressures of genome reduction. The ancestor of red algae is thought to have undergone genome reduction prior to the lineage's radiation, resulting in overall gene and intron loss in extant groups. Previous studies on the extremophilic red alga Cyanidioschyzon merolae revealed an intron-sparse genome with a highly reduced spliceosome. To determine whether these features applied to other red algae, we investigated multiple aspects of pre-mRNA splicing in the mesophilic red alga Porphyridium purpureum. Through strand-specific RNA-Seq, we observed high levels of intron retention across a large number of its introns, and nearly half of the transcripts for these genes are not spliced at all. We also discovered a relationship between variability of 5' splice site sequences and levels of splicing. To further investigate the connections between intron retention and splicing machinery, we bioinformatically assembled the P. purpureum spliceosome, and biochemically verified the presence of snRNAs. While most other core spliceosomal components are present, our results suggest highly divergent or missing U1 snRNP proteins, despite the presence of an uncharacteristically long U1 snRNA. These unusual aspects highlight the diverse nature of pre-mRNA splicing that can be seen in lesser-studied eukaryotes, raising the importance of investigating fundamental eukaryotic processes outside of model organisms.


Asunto(s)
Porphyridium , Rhodophyta , Humanos , Intrones/genética , Precursores del ARN/genética , Precursores del ARN/metabolismo , Empalme del ARN , Rhodophyta/genética , Saccharomyces cerevisiae , Empalmosomas/genética , Empalmosomas/metabolismo
6.
PLoS Biol ; 13(2): e1002061, 2015 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-25668728

RESUMEN

Small RNA pathways act at the front line of defence against transposable elements across the Eukaryota. In animals, Piwi interacting small RNAs (piRNAs) are a crucial arm of this defence. However, the evolutionary relationships among piRNAs and other small RNA pathways targeting transposable elements are poorly resolved. To address this question we sequenced small RNAs from multiple, diverse nematode species, producing the first phylum-wide analysis of how small RNA pathways evolve. Surprisingly, despite their prominence in Caenorhabditis elegans and closely related nematodes, piRNAs are absent in all other nematode lineages. We found that there are at least two evolutionarily distinct mechanisms that compensate for the absence of piRNAs, both involving RNA-dependent RNA polymerases (RdRPs). Whilst one pathway is unique to nematodes, the second involves Dicer-dependent RNA-directed DNA methylation, hitherto unknown in animals, and bears striking similarity to transposon-control mechanisms in fungi and plants. Our results highlight the rapid, context-dependent evolution of small RNA pathways and suggest piRNAs in animals may have replaced an ancient eukaryotic RNA-dependent RNA polymerase pathway to control transposable elements.


Asunto(s)
Proteínas de Caenorhabditis elegans/genética , Caenorhabditis elegans/genética , MicroARNs/genética , Nematodos/genética , Filogenia , ARN Interferente Pequeño/genética , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Evolución Biológica , Caenorhabditis elegans/inmunología , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/metabolismo , Metilación de ADN , Elementos Transponibles de ADN/inmunología , Drosophila melanogaster/genética , Drosophila melanogaster/inmunología , Drosophila melanogaster/metabolismo , Regulación de la Expresión Génica , Humanos , MicroARNs/metabolismo , Datos de Secuencia Molecular , Nematodos/clasificación , Nematodos/inmunología , Nematodos/metabolismo , ARN Interferente Pequeño/metabolismo , ARN Polimerasa Dependiente del ARN/genética , ARN Polimerasa Dependiente del ARN/metabolismo , Ribonucleasa III/genética , Ribonucleasa III/metabolismo
7.
Nature ; 492(7427): 59-65, 2012 Dec 06.
Artículo en Inglés | MEDLINE | ID: mdl-23201678

RESUMEN

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.


Asunto(s)
Núcleo Celular/genética , Cercozoos/genética , Criptófitas/genética , Evolución Molecular , Genoma/genética , Mosaicismo , Simbiosis/genética , Proteínas Algáceas/genética , Proteínas Algáceas/metabolismo , Empalme Alternativo/genética , Cercozoos/citología , Cercozoos/metabolismo , Criptófitas/citología , Criptófitas/metabolismo , Citosol/metabolismo , Duplicación de Gen/genética , Transferencia de Gen Horizontal/genética , Genes Esenciales/genética , Genoma Mitocondrial/genética , Genoma de Planta/genética , Genoma de Plastidios/genética , Datos de Secuencia Molecular , Filogenia , Transporte de Proteínas , Proteoma/genética , Proteoma/metabolismo , Transcriptoma/genética
8.
Proc Natl Acad Sci U S A ; 112(11): E1191-200, 2015 Mar 17.
Artículo en Inglés | MEDLINE | ID: mdl-25733880

RESUMEN

The human spliceosome is a large ribonucleoprotein complex that catalyzes pre-mRNA splicing. It consists of five snRNAs and more than 200 proteins. Because of this complexity, much work has focused on the Saccharomyces cerevisiae spliceosome, viewed as a highly simplified system with fewer than half as many splicing factors as humans. Nevertheless, it has been difficult to ascribe a mechanistic function to individual splicing factors or even to discern which are critical for catalyzing the splicing reaction. We have identified and characterized the splicing machinery from the red alga Cyanidioschyzon merolae, which has been reported to harbor only 26 intron-containing genes. The U2, U4, U5, and U6 snRNAs contain expected conserved sequences and have the ability to adopt secondary structures and form intermolecular base-pairing interactions, as in other organisms. C. merolae has a highly reduced set of 43 identifiable core splicing proteins, compared with ∼90 in budding yeast and ∼140 in humans. Strikingly, we have been unable to find a U1 snRNA candidate or any predicted U1-associated proteins, suggesting that splicing in C. merolae may occur without the U1 small nuclear ribonucleoprotein particle. In addition, based on mapping the identified proteins onto the known splicing cycle, we propose that there is far less compositional variability during splicing in C. merolae than in other organisms. The observed reduction in splicing factors is consistent with the elimination of spliceosomal components that play a peripheral or modulatory role in splicing, presumably retaining those with a more central role in organization and catalysis.


Asunto(s)
Rhodophyta/metabolismo , Empalmosomas/metabolismo , Proteínas Algáceas/genética , Proteínas Algáceas/metabolismo , Emparejamiento Base/genética , Humanos , Inmunoprecipitación , Intrones/genética , Modelos Biológicos , Conformación de Ácido Nucleico , Precursores del ARN/genética , Precursores del ARN/metabolismo , Empalme del ARN/genética , Estabilidad del ARN/genética , ARN Nuclear Pequeño/química , ARN Nuclear Pequeño/genética , ARN Nuclear Pequeño/metabolismo , Rhodophyta/genética
9.
RNA Biol ; 12(11): 1-8, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-26400738

RESUMEN

Pre-mRNA splicing has been considered one of the hallmarks of eukaryotes, yet its diversity is astonishing: the number of substrate introns for splicing ranges from hundreds of thousands in humans to a mere handful in certain parasites. The catalytic machinery that carries out splicing, the spliceosome, is similarly diverse, with over 300 associated proteins in humans to a few tens in other organisms. In this Point of View, we discuss recent work characterizing the reduced spliceosome of the acidophilic red alga Cyanidioschyzon merolae, which further highlights the diversity of splicing in that it does not possess the U1 snRNP that is characteristically responsible for 5' splice site recognition. Comparisons to other organisms with reduced spliceosomes, such as microsporidia, trypanosomes, and Giardia, help to identify the most highly conserved splicing factors, pointing to the essential core of this complex machine. These observations argue for increased exploration of important biochemical processes through study of a wider ranger of organisms.


Asunto(s)
Empalme del ARN/genética , Rhodophyta/genética , Rhodophyta/metabolismo , Empalmosomas/metabolismo , Animales , Catálisis , Evolución Molecular , Giardia lamblia/genética , Giardia lamblia/metabolismo , Humanos , Intrones , Precursores del ARN/genética , ARN Nuclear Pequeño/química , ARN Nuclear Pequeño/genética
10.
BMC Genomics ; 14: 207, 2013 Mar 28.
Artículo en Inglés | MEDLINE | ID: mdl-23537046

RESUMEN

BACKGROUND: The microsporidian Encephalitozoon cuniculi possesses one of the most reduced and compacted eukaryotic genomes. Reduction in this intracellular parasite has affected major cellular machinery, including the loss of over fifty core spliceosomal components compared to S. cerevisiae. To identify expression changes throughout the parasite's life cycle and also to assess splicing in the context of this reduced system, we examined the transcriptome of E. cuniculi using Illumina RNA-seq. RESULTS: We observed that nearly all genes are expressed at three post-infection time-points examined. A large fraction of genes are differentially expressed between the first and second (37.7%) and first and third (43.8%) time-points, while only four genes are differentially expressed between the latter two. Levels of intron splicing are very low, with 81% of junctions spliced at levels below 50%. This is dramatically lower than splicing levels found in two other fungal species examined. We also describe the first case of alternative splicing in a microsporidian, an unexpected complexity given the reduction in spliceosomal components. CONCLUSIONS: Low levels of splicing observed are likely the result of an inefficient spliceosome; however, at least in one case, splicing appears to be playing a functional role. Although several RNA decay genes are encoded in E. cuniculi, the lack of a few key players could be reducing decay levels and therefore increasing the proportion of unspliced transcripts. Significant proportions of genes are differentially expressed in the first forty-eight hours but not after, indicative of genetic changes that precede the intracellular to infective stage transition.


Asunto(s)
Encephalitozoon cuniculi/genética , Perfilación de la Expresión Génica , ARN Mensajero/metabolismo , Genoma Fúngico , Intrones , Sistemas de Lectura Abierta , Empalme del ARN , ARN Mensajero/genética , Análisis de Secuencia de ARN , Empalmosomas/metabolismo
11.
J Eukaryot Microbiol ; 60(6): 601-8, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23869987

RESUMEN

Microsporidia are intracellular parasites considered to be ubiquitous in the environment. Yet the true extent of their diversity in soils, sand, and compost remains unclear. We examined microsporidian diversity found in the common urban environments of soil, sand, and compost. We retrieved 22 novel microsporidian sequences and only four from described species. Their distribution was generally restricted to a single site and sample type. Surprisingly, one novel microsporidian showed a wide distribution, and high prevalence, as it was detected in five different compost samples and in soil samples collected over 200 km apart. These results suggest that the majority of Microsporidia appear to have a narrow distribution. Our phylogenetic analysis indicated that the Microsporidia detected in this study include representatives from four of the five major microsporidian groups. Furthermore, the addition of our new sequences calls into question the cohesiveness of microsporidian clade II. These results highlight the importance of increasing our knowledge of microsporidian diversity to better understand the phylogenetic relationships and evolutionary history of this important group of emerging parasites.


Asunto(s)
Biodiversidad , Microsporidios/clasificación , Microsporidios/aislamiento & purificación , Microbiología del Suelo , Análisis por Conglomerados , ADN de Hongos/química , ADN de Hongos/genética , ADN Ribosómico/química , ADN Ribosómico/genética , Genes de ARNr , Microsporidios/genética , Datos de Secuencia Molecular , Noroeste de Estados Unidos , Filogenia , ARN de Hongos/genética , ARN Ribosómico 18S/genética , Análisis de Secuencia de ADN , Dióxido de Silicio , Suelo
12.
Curr Biol ; 33(18): R936-R938, 2023 09 25.
Artículo en Inglés | MEDLINE | ID: mdl-37751700

RESUMEN

In this Quick guide, Thomas Whelan and Naomi Fast introduce the microsporidia: obligate intracellular parasites with the most extremely reduced genomes known in eukaryotes.


Asunto(s)
Microsporidios , Microsporidios/genética , Eucariontes
13.
Curr Biol ; 33(24): R1280-R1281, 2023 12 18.
Artículo en Inglés | MEDLINE | ID: mdl-38113835

RESUMEN

Spliceosomal introns evolved early in eukaryogenesis, originating from self-splicing group II introns that invaded the proto-eukaryotic genome1. Elements of these ribozymes, now called snRNAs (U1, U2, U4, U5, U6), were co-opted to excise these invasive elements. Prior to eukaryotic diversification, the spliceosome is predicted to have accumulated hundreds of proteins2. This early complexification has obscured our understanding of spliceosomal evolution. Reduced systems with few introns and tiny spliceosomes give insights into the plasticity of the splicing reaction and provide an opportunity to study the evolution of the spliceosome3,4. Microsporidia are intracellular parasites possessing extremely reduced genomes that have lost many, and in some instances all, introns5. In the purportedly intron-lacking genome of the microsporidian Pseudoloma neurophilia6, we identified two introns that are spliced at high levels. Furthermore, with only 14 predicted proteins, the P. neurophilia spliceosome could be the smallest known. Intriguingly, the few proteins retained are divergent compared to canonical orthologs. Even the central spliceosomal protein Prp8, which originated from the proteinaceous component of group II introns, is extremely divergent. This is unusual given that Prp8 is highly conserved across eukaryotes, including other microsporidia. All five P. neurophilia snRNAs are present, and all but U2 have diverged extensively, likely resulting from the loss of interacting proteins. Despite this divergence, U1 and U2 are predicted to pair with intron sequences more extensively than previously described. The P. neurophilia spliceosome is retained to splice a mere two introns and, with few proteins and reliance on RNA-RNA interactions, could function in a manner more reminiscent of presumed ancestral splicing.


Asunto(s)
Microsporidios , Empalmosomas , Empalmosomas/genética , Empalmosomas/metabolismo , Intrones/genética , Empalme del ARN , ARN Nuclear Pequeño/genética , ARN Nuclear Pequeño/metabolismo , Microsporidios/genética , Microsporidios/metabolismo
14.
Mol Biol Evol ; 27(9): 1979-82, 2010 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-20360213

RESUMEN

The 2.9-Mbp genome of the microsporidian Encephalitozoon cuniculi is severely reduced and compacted, possessing only 16 known tiny spliceosomal introns. Based on motif and expression data, intron profiles were constructed to screen the genome. Twenty additional introns were predicted and verified, doubling the previous estimate. We further predict that accurate 3' splice site (3'SS) selection is accomplished via a scanning mechanism with specificity achieved by maintaining a constrained variable length between the branch point motif and 3'SS. Only introns in ribosomal protein genes exhibit positional bias, and we hypothesize that splicing could be regulating expression of these genes. The large set of new introns in non-ribosomal protein genes suggests that current models of intron loss are unlikely sufficient to explain the distribution of introns. Together, these results extend our understanding of the role of intron loss in genome evolution and contribute to a novel model for splice site selection.


Asunto(s)
Encephalitozoon cuniculi/genética , Intrones/genética , Evolución Molecular , Genoma Fúngico/genética
15.
Mol Biol Evol ; 27(7): 1579-84, 2010 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-20167610

RESUMEN

Microsporidia are a diverse group of highly derived fungal relatives that are intracellular parasites of many animals. Both transcription and introns have been shown to be unusual in microsporidia: The complete genome of the human parasite Encephalitozoon cuniculi has only a few very short introns, and two distantly related microsporidian spores have been shown to harbor transcripts encoding several genes that overlap on different strands. However, microsporidia alternate between two life stages: the intracellular proliferative stage and the extracellular and largely metabolically dormant infectious spore. To date, most studies have focused on the spore. Here, we have compared transcription profiles for a number of genes from both life stages of microsporidia and found major differences in both the prevalence of overlapping transcription and splicing. Specifically, spore transcripts in E. cuniculi have longer 5' untranslated regions, overlap more frequently with upstream genes, and have a significantly higher number of transcription initiation sites compared with intracellular transcripts from the same species. In addition, we demonstrate that splicing occurs exclusively in the intracellular stage and not in spore messenger RNAs (mRNAs) in both E. cuniculi and the distantly related Antonospora locustae. These differences between the microsporidian life stages raise questions about the functional importance of transcripts in the spore. We hypothesize that at least some transcripts in spores are a product of the cell's transition into a dormant state and that these unusual mRNAs could play a structural role rather than an informational one.


Asunto(s)
Biomarcadores/metabolismo , Microsporidios/crecimiento & desarrollo , Microsporidios/genética , Empalme del ARN/genética , Esporas Fúngicas/fisiología , Transcripción Genética , Regiones no Traducidas 5'/genética , Perfilación de la Expresión Génica , Análisis de Secuencia por Matrices de Oligonucleótidos , ARN Mensajero/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
16.
J Eukaryot Microbiol ; 58(1): 68-74, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-21182561

RESUMEN

Encephalitozoon cuniculi, a eukaryotic intracellular parasite belonging to the group Microsporidia, has a highly reduced and compacted genome. Its mRNA transcripts have been found to differ between the two life stages, the spore and meront, of the parasite. Spore transcripts generally have more transcription start sites, longer 5' untranslated regions (UTRs), and overlap more frequently with upstream genes than those of meronts. A previous analysis of 31 meront gene transcripts showed that most have short 5'UTRs, and intron-containing genes, mostly ribosomal protein genes, exclusively have very short 5'UTRs. Here we analyzed a larger set of transcripts from meronts, and we find a pattern of 5'UTR length distribution similar to other reduced genomes. There is an abundance of very short 5'UTRs that are <20 bp in length, and very few 5'UTRs that are much longer. We also find a relationship between gene categories and 5'UTR length: intron-containing genes and ribosomal protein genes have exclusively short 5'UTRs. We suggest that the abundance of short 5'UTRs may be related to a class of highly expressed genes that benefit the parasite's growth cycle. Also, the longer 5'UTRs may be playing a role in down-regulating expression of genes that require temporal or environment-induced expression.


Asunto(s)
Regiones no Traducidas 5' , Encephalitozoon cuniculi/genética , Regulación Fúngica de la Expresión Génica , Empalme del ARN , Transcripción Genética , Animales , Encephalitozoon cuniculi/aislamiento & purificación , Encephalitozoon cuniculi/metabolismo , Encefalitozoonosis/microbiología , Encefalitozoonosis/veterinaria , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Riñón/microbiología , Datos de Secuencia Molecular , Conejos/microbiología
17.
Curr Biol ; 31(14): R912-R914, 2021 07 26.
Artículo en Inglés | MEDLINE | ID: mdl-34314721

RESUMEN

Whereas most eukaryotic genes are interrupted by introns removed by the U2 (major) spliceosome, U12-type introns are extremely rare. New work uncovers a case of extensive U12-type intron gain, and an unexpectedly flexible and efficient U12 (minor) spliceosome.


Asunto(s)
Empalme del ARN , Empalmosomas , Intrones/genética , Empalme del ARN/genética , Empalmosomas/genética , Empalmosomas/metabolismo
18.
Genome Biol Evol ; 11(1): 263-269, 2019 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-30496512

RESUMEN

Spliceosomal introns are ubiquitous features of eukaryotic genomes, but the mechanisms responsible for their loss and gain are difficult to identify. Microsporidia are obligate intracellular parasites that have significantly reduced genomes and, as a result, have lost many if not all of their introns. In the microsporidian Encephalitozoon cuniculi, a relatively long intron was identified and was spliced at higher levels than the remaining introns. This long intron is part of a set of unique introns in two unrelated genes that show high levels of sequence conservation across diverse microsporidia. The introns possess a unique internal conserved region, which overlaps with a shared, predicted stem-loop structure. The unusual similarity and retention of these long introns in reduced microsporidian genomes could indicate that these introns function similarly, are homologous, or both. Regardless, the significant genome reduction in microsporidia provides a rare opportunity to understand intron evolution.


Asunto(s)
Encephalitozoon cuniculi/genética , Genoma Fúngico , Intrones , Tamaño del Genoma , Secuencias Invertidas Repetidas , Poli A
19.
BMC Genomics ; 9: 296, 2008 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-18570666

RESUMEN

BACKGROUND: Microsporidia are a group of parasites related to fungi that infect a wide variety of animals and have gained recognition from the medical community in the past 20 years due to their ability to infect immuno-compromised humans. Microsporidian genomes range in size from 2.3 to 19.5 Mbp, but almost all of our knowledge comes from species that have small genomes (primarily from the human parasite Encephalitozoon cuniculi and the locust parasite Antonospora locustae). We have conducted an EST survey of the mosquito parasite Edhazardia aedis, which has an estimated genome size several times that of more well-studied species. The only other microsporidian EST project is from A. locustae, and serves as a basis for comparison with E. aedis. RESULTS: The spore transcriptomes of A. locustae and E. aedis were compared and the numbers of unique transcripts that belong to each COG (Clusters of Orthologous Groups of proteins) category differ by at most 5%. The transcripts themselves have widely varying start sites and encode a number of proteins that have not been found in other microsporidia examined to date. However, E. aedis seems to lack the multi-gene transcripts present in A. locustae and E. cuniculi. We also present the first documented case of transcription of a transposable element in microsporidia. CONCLUSION: Although E. aedis and A. locustae are distantly related, have very disparate life cycles and contain genomes estimated to be vastly different sizes, their patterns of transcription are similar. The architecture of the ancestral microsporidian genome is unknown, but the presence of genes in E. aedis that have not been found in other microsporidia suggests that extreme genome reduction and compaction is lineage specific and not typical of all microsporidia.


Asunto(s)
Etiquetas de Secuencia Expresada , Microsporidios/crecimiento & desarrollo , Microsporidios/genética , Esporas Fúngicas/genética , Transcripción Genética , Regiones no Traducidas 3' , Regiones no Traducidas 5' , Animales , Emparejamiento Base , Culicidae/parasitología , Elementos Transponibles de ADN/genética , Proteínas Fúngicas/genética , Genoma Fúngico , Interacciones Huésped-Parásitos , Intrones , Larva/fisiología , Estadios del Ciclo de Vida , Microsporidios/fisiología , Filogenia , Especificidad de la Especie , Esporas Fúngicas/citología , Esporas Fúngicas/fisiología , Sintenía
20.
BMC Genomics ; 9: 200, 2008 Apr 29.
Artículo en Inglés | MEDLINE | ID: mdl-18445287

RESUMEN

BACKGROUND: Microsporidia are well known models of extreme nuclear genome reduction and compaction. The smallest microsporidian genomes have received the most attention, but genomes of different species range in size from 2.3 Mb to 19.5 Mb and the nature of the larger genomes remains unknown. RESULTS: Here we have undertaken genome sequence surveys of two diverse microsporidia, Brachiola algerae and Edhazardia aedis. In both species we find very large intergenic regions, many transposable elements, and a low gene-density, all in contrast to the small, model microsporidian genomes. We also find no recognizable genes that are not also found in other surveyed or sequenced microsporidian genomes. CONCLUSION: Our results demonstrate that microsporidian genome architecture varies greatly between microsporidia. Much of the genome size difference could be accounted for by non-coding material, such as intergenic spaces and retrotransposons, and this suggests that the forces dictating genome size may vary across the phylum.


Asunto(s)
Apansporoblastina/genética , Evolución Molecular , Genoma Fúngico , Microsporidios/genética , Aedes/microbiología , Animales , Elementos Transponibles de ADN , Orden Génico
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