A compensatory base change in human U2 snRNA can suppress a branch site mutation.

ABSTRACTThe genusEuduboscquellais one of a few described genera within the syndinean dinoflagellates, an enigmatic lineage with abundant diversity in marine environmental clone libraries based on small subunit (SSU) rRNA. The region composed of the SSU through to the partial large subunit (LSU) rRNA was determined from 40 individual tintinnid ciliate loricae infected withEuduboscquellasampled from eight surface water sites in the Northern Hemisphere, producing seven distinct SSU sequences. The corresponding host SSU rRNA region was also amplified from eight host species. The SSU tree ofEuduboscquellaand syndinean group I sequences from environmental clones had seven well-supported clades and one poorly supported clade across data sets from 57 to 692 total sequences. The genusEuduboscquellaconsistently formed a supported monophyletic clade within a single subclade of group I sequences. For most parasites with identical SSU sequences, the more variable internal transcribed spacer (ITS) to LSU rRNA regions were polymorphic at 3 to 10 sites. However, inE. cachonithere was variation between ITS to LSU copies at up to 20 sites within an individual, while in a parasite ofTintinnopsisspp., variation between different individuals ranged up to 19 polymorphic sites. However, applying the compensatory base change model to the ITS2 sequences suggested no compensatory changes within or between individuals with the same SSU sequence, while one to four compensatory changes between individuals with similar but not identical SSU sequences were found. Comparisons between host and parasite phylogenies do not suggest a simple pattern of host or parasite specificity.

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An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene

Molecular and Cellular Biology ◽

10.1128/mcb.13.9.5613-5619.1993 ◽

1993 ◽

Vol 13 (9) ◽

pp. 5613-5619

Author(s):

Y Takahashi ◽

S Urushiyama ◽

T Tani ◽

Y Ohshima

Keyword(s):

Mrna Splicing ◽

Small Nuclear Rna ◽

U2 Snrna ◽

U6 Snrna ◽

Branch Site ◽

Snrna Gene ◽

Nuclear Rna ◽

Catalytic Role ◽

Mrna Precursor ◽

Site Recognition

Splicing an mRNA precursor requires multiple factors involving five small nuclear RNA (snRNA) species called U1, U2, U4, U5, and U6. The presence of mRNA-type introns in the U6 snRNA genes of some yeasts led to the hypothesis that U6 snRNA may play a catalytic role in pre-mRNA splicing and that the U6 introns occurred through reverse splicing of an intron from an mRNA precursor into a catalytic site of U6 snRNA. We characterized the U2 snRNA gene of the yeast Rhodotorula hasegawae, which has four mRNA-type introns in the U6 snRNA gene, and found an mRNA-type intron of 60 bp. The intron of the U2 snRNA gene is present in the highly conserved region immediately downstream of the branch site recognition domain. Interestingly, we found that this region can form a novel base pairing with U6 snRNA. We discuss the possible implications of these findings for the mechanisms of intron acquisition and for the role of U2 snRNA in pre-mRNA splicing.

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Multiple functional domains of human U2 small nuclear RNA: strengthening conserved stem I can block splicing.

Molecular and Cellular Biology ◽

10.1128/mcb.12.12.5464 ◽

1992 ◽

Vol 12 (12) ◽

pp. 5464-5473 ◽

Cited By ~ 10

Author(s):

J Wu ◽

J L Manley

Keyword(s):

Simian Virus 40 ◽

Suppressor Gene ◽

Simian Virus ◽

T Antigen ◽

Compensatory Mutation ◽

Base Pairing ◽

Recognition Sequence ◽

Site Mutation ◽

U6 Snrna ◽

Branch Site

We showed previously that a branch site mutation in simian virus 40 early pre-mRNA that prevented small t antigen mRNA splicing could be efficiently suppressed by a compensatory mutation in a coexpressed U2 small nuclear (sn) RNA gene. We have now generated second-site mutations in this suppressor gene to investigate regions of U2 RNA required for function. A number of mutations in a putative stem at the 5' end of the molecule inhibited splicing, indicating that bases in this region are important for activity. However, several lines of evidence suggested that formation of the entire stem is not essential for splicing. Indeed, mutations that strengthen the stem actually inhibited splicing, and evidence that this prevents a required base-pairing interaction with U6 snRNA is presented. These results suggest that the relative stabilities of competing intra- and intermolecular base-pairing interactions play an important role in the splicing reaction. Mutations in a conserved single-stranded region immediately 3' to the branch site recognition sequence all inhibited splicing, indicating that this region is required for U2 function, although its exact role remains unknown. Finally, two mutations in the loop of stem IV at the 3' end of the molecule, which destroy the binding site of U2 sn ribonucleoprotein B", prevented small t splicing; this finding contrasts with previous studies which utilized different assay systems. Analysis of the accumulation and subcellular localization of all of the mutant RNAs showed that they were similar to those of the parental suppressor U2 RNA, indicating that the effects observed indeed reflect defects in splicing.

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The use of compensatory base change analysis of ITS2 as a tool in the phylogeny of Mucorales, illustrated by the Mucor circinelloides complex

Organisms Diversity & Evolution ◽

10.1007/s13127-013-0139-1 ◽

2013 ◽

Vol 13 (4) ◽

pp. 497-502 ◽

Cited By ~ 2

Author(s):

Julia Pawłowska ◽

Grit Walther ◽

Mateusz Wilk ◽

Sybren de Hoog ◽

Marta Wrzosek

Keyword(s):

Mucor Circinelloides ◽

Base Change ◽

Change Analysis ◽

Compensatory Base Change

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A branch site mutation leading to aberrant splicing of the human tyrosine hydroxylase gene in a child with a severe extrapyramidal movement disorder

Annals of Human Genetics ◽

10.1046/j.1469-1809.2000.6450375.x ◽

2000 ◽

Vol 64 (5) ◽

pp. 375-382 ◽

Cited By ~ 34

Author(s):

R. J. R. J. JANSSEN ◽

R. A. WEVERS ◽

M. HAUSSLER ◽

J. A. F. M. LUYTEN ◽

G. C. H. STEENBERGEN-SPANJERS ◽

...

Keyword(s):

Tyrosine Hydroxylase ◽

Movement Disorder ◽

Site Mutation ◽

Aberrant Splicing ◽

Tyrosine Hydroxylase Gene ◽

Branch Site ◽

Hydroxylase Gene

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New finding of green algae with potential for algal biotechnology, Chlorococcum oleofaciens and its molecular investigation

Regulatory Mechanisms in Biosystems ◽

10.15421/021782 ◽

2017 ◽

Vol 8 (4) ◽

pp. 532-539 ◽

Cited By ~ 3

Author(s):

Y. I. Maltsev ◽

T. V. Konovalenko

Keyword(s):

Light Microscopy ◽

Molecular Genetic ◽

Taxonomic Status ◽

Forest Litter ◽

Base Change ◽

Compensatory Base Change ◽

Algal Biotechnology ◽

The Status ◽

Biochemical Research ◽

Different Strains

The practice of soil algology shows that algae from the order Chlamydomonadales are among the most poorly studied and difficult to identify due to the high heterogeneity of their morphology and ultrastructure. Only the involvement of molecular genetic methods usually makes it possible to determine their taxonomic status with high accuracy. At the same time, in the algae flora of Ukraine there are more than 250 species from the order Chlamydomonadales, the status of which in most cases is established exclusively on the basis of light microscopy. This work is devoted to the study of the biotechnologically promising green alga Chlorococcum oleofaciens, taking into account the modern understanding of its taxonomic status. Two new strains of this species, separated from samples of forest litter and oak forest soil (the Samara Forest, Dnipropetrovsk region), are described. The strains were studied at the morphological level by using light microscopy methods, as well as using molecular genetic methods based on the studies of the nucleotide genes sequences of the 18S ribosomal DNA (rDNA) and chloroplast rbcL genes, the topology of secondary structures of internal transcribed spacer 2 (ITS2). The obtained results helped to confirm the presence of C. oleofaciens in the algae flora of Ukraine. Also, the authors of the article discuss the differences in the secondary structure of ITS2 in different strains of C. oleofaciens associated with the presence of compensatory base change (CBC), hemi-CBC in helices I and II, as well as deletions in helix IV and providing a basis for the hypothesis of the existence of cryptic species within C. oleofaciens. The obtained data can be used at the stage of preliminary selection of biochemical research objects.

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An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene.

Molecular and Cellular Biology ◽

10.1128/mcb.13.9.5613 ◽

1993 ◽

Vol 13 (9) ◽

pp. 5613-5619 ◽

Cited By ~ 12

Author(s):

Y Takahashi ◽

S Urushiyama ◽

T Tani ◽

Y Ohshima

Keyword(s):

Mrna Splicing ◽

Small Nuclear Rna ◽

U2 Snrna ◽

U6 Snrna ◽

Branch Site ◽

Snrna Gene ◽

Nuclear Rna ◽

Catalytic Role ◽

Mrna Precursor ◽

Site Recognition

Splicing an mRNA precursor requires multiple factors involving five small nuclear RNA (snRNA) species called U1, U2, U4, U5, and U6. The presence of mRNA-type introns in the U6 snRNA genes of some yeasts led to the hypothesis that U6 snRNA may play a catalytic role in pre-mRNA splicing and that the U6 introns occurred through reverse splicing of an intron from an mRNA precursor into a catalytic site of U6 snRNA. We characterized the U2 snRNA gene of the yeast Rhodotorula hasegawae, which has four mRNA-type introns in the U6 snRNA gene, and found an mRNA-type intron of 60 bp. The intron of the U2 snRNA gene is present in the highly conserved region immediately downstream of the branch site recognition domain. Interestingly, we found that this region can form a novel base pairing with U6 snRNA. We discuss the possible implications of these findings for the mechanisms of intron acquisition and for the role of U2 snRNA in pre-mRNA splicing.

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New cyanobacterium Aliterella vladivostokensis sp. nov. (Aliterellaceae, Chroococcidiopsidales), isolated from temperate monsoon climate zone (Vladivostok, Russia)

Phytotaxa ◽

10.11646/phytotaxa.527.3.7 ◽

2021 ◽

Vol 527 (3) ◽

pp. 221-233

Author(s):

SHAMIL R. ABDULLIN ◽

ARTHUR YU. NIKULIN ◽

VERONIKA B. BAGMET ◽

VYACHESLAV YU. NIKULIN ◽

ANDREY A. GONTCHAROV

Keyword(s):

Phylogenetic Analyses ◽

Base Change ◽

Rrna Gene ◽

High Similarity ◽

16S Rrna Gene Sequences ◽

Monsoon Climate ◽

Compensatory Base Change ◽

Internal Transcribed Spacer Sequences ◽

A New Species ◽

The 16S Rrna Gene

A new coccoid cyanobacterium Aliterella vladivostokensis sp. nov. was described from an urban aerophytic habitat in a temperate monsoon climate (Vladivostok, Russia) using a polyphasic approach. Phylogenetic analyses based on the 16S rRNA gene sequences confirmed that our isolate was a member of the Aliterella genus clade. Aliterella species are hardly distinguishable from each other morphologically and were described from highly contrasting natural and artificial environments with only a few records from several continents. Despite high similarity of morphometric data for A. vladivostokensis and A. antarctica cells and a compensatory base change in the D1–D1′ helix shared by these species; high percent of dissimilarity (11.6±1.3) between their 16S–23S internal transcribed spacer sequences with at least 5 autapomorphic mutations in the D1–D1′ and Box-B helices, and distinct folding patterns of the Box-B helix allowed us to erect a new species.

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trans-spliceosomal U6 RNAs of Crithidia fasciculata and Leptomonas seymouri: deviation from the conserved ACAGAG sequence and potential base pairing with spliced leader RNA.

Molecular and Cellular Biology ◽

10.1128/mcb.14.7.4565 ◽

1994 ◽

Vol 14 (7) ◽

pp. 4565-4570 ◽

Cited By ~ 17

Author(s):

G L Xu ◽

B Wieland ◽

A Bindereif

Keyword(s):

Splice Site ◽

Base Change ◽

Trna Genes ◽

Rna Sequences ◽

Compensatory Base Change ◽

Crithidia Fasciculata ◽

Spliced Leader ◽

Rna Genes ◽

Spliced Leader Rna ◽

U6 Rna

U6 RNA genes from the trypanosomatids Crithidia fasciculata and Leptomonas seymouri have been isolated and sequenced. As in Trypanosoma brucei, the U6 RNA genes in both C. fasciculata and L. seymouri are arranged in close linkage with upstream tRNA genes. The U6 RNA sequences from C. fasciculata and L. seymouri deviate in five and three positions, respectively, from the published T. brucei sequence. Interestingly, both C. fasciculata U6 RNA genes carry a C-->T change at the second position of the ACAGAG hexanucleotide sequence, which is important for splicing function and has been considered phylogenetically invariable. A compensatory base change of the C. fasciculata spliced leader RNA at the highly conserved 5' splice site position +5, G-->A, suggests that an interaction between the 5' splice site region and U6 RNA recently proposed for the yeast cis-splicing system may also occur in trans splicing.

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