scholarly journals Frameshift suppression at tandem AGA and AGG codons by cloned tRNA genes: assigning a codon toargUtRNA and T4 tRNAArg

1990 ◽  
Vol 18 (17) ◽  
pp. 5031-5036 ◽  
Author(s):  
R.A. Spanjaard ◽  
K. Chen ◽  
J.R. Walker ◽  
J. van Duin
Keyword(s):  
Trna Genes ◽  
Frameshift Suppression

scholarly journals FRAMESHIFT SUPPRESSION IN SACCHAROMYCES CEREVISIAE VI. COMPLETE GENETIC MAP OF TWENTY-FIVE SUPPRESSOR GENES

Genetics ◽  
1983 ◽  
Vol 103 (3) ◽  
pp. 389-407
Author(s):  
Richard F Gaber ◽  
Lorilee Mathison ◽  
Irv Edelman ◽  
Michael R Culbertson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Map ◽  
Suppressor Gene ◽  
Yeast Genome ◽  
Trna Genes ◽  
Suppressor Genes ◽  
Genomic Distribution ◽  
Frameshift Suppression ◽  
Approximate Location ◽  
Yeast Genetic

ABSTRACT Five previously unmapped frameshift suppressor genes have been located on the yeast genetic map. In addition, we have further characterized the map positions of two suppressors whose approximate locations were determined in an earlier study. These results represent the completion of genetic mapping studies on all 25 of the known frameshift suppressor genes in yeast.—The approximate location of each suppressor gene was initially determined through the use of a set of mapping strains containing 61 signal markers distributed throughout the yeast genome. Standard meiotic linkage was assayed in crosses between strains carrying the suppressors and the mapping strains. Subsequent to these approximate linkage determinations, each suppressor gene was more precisely located in multi-point crosses. The implications of these mapping results for the genomic distribution of frameshift suppressor genes, which include both glycine and proline tRNA genes, are discussed.

Complete genome of mangrove-derived anti-MRSA streptomycete, Streptomyces pluripotens MUSC 135T

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Kok-Gan Chan ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Bey-Hing Goh ◽  
...  
Keyword(s):  
Complete Genome ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Gene Clusters ◽  
Salmonella Typhi ◽  
Bacteriocin Production ◽  
Trna Genes ◽  
Genus Streptomyces ◽  
Mining Tool ◽  
Bioactive Potential ◽  
Effective Drugs

Microorganisms serve as attractive resources, owing to their ability to synthesize structurally-diverse substanceswith various bioactivities. Within the Bacteria domain, members of the genus Streptomyces have demonstrated remarkableability to produce clinically useful, secondary metabolites such as anticancer, antioxidants, antivirals and antibacterials.Streptomyces pluripotens MUSC 135T was isolated as novel strain from mangrove forest in Malaysia. This strain exhibitedbroad spectrum bacteriocin against several pathogens including methicillin-resistant Staphylococcus aureus (MRSA) strainATCC BAA-44, Salmonella typhi ATCC 19430T and Aeromonas hydrophila ATCC 7966T. Thus, the strain was selected forwhole genome sequencing as an attempt to explore its bioactive potential. Here we report the first complete genome of S.pluripotens MUSC 135T genome which comprise of 7.35 Mbp with G+C content of 69.9 %. A total of 6,404 open readingframes (ORFs) were predicted, along with 18 rRNA and 69 tRNA genes. Using bacteriocin mining tool, BAGEL detectedeights gene clusters associated with bacteriocin production including lanthipeptides and linear azol(in)e-containing peptides(LAPs). Members of Streptomyces have contributed greatly towards improving lives, particularly against deadly infectionsand chronic diseases. The availability of S. pluripotens MUSC 135T genome sequence has opened new window for drugdiscovery, particularly for effective drugs against harmful pathogens such as MRSA and certainly deserves further detailedstudy.

scholarly journals Mitochondrial genome evolution in pelagophyte algae

2021 ◽  
Author(s):  
Shannon J Sibbald ◽  
Maggie Lawton ◽  
John M Archibald
Keyword(s):  
Mitochondrial Genome ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
23S Rrna ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Unique Region ◽  
Long Read ◽  
Genomic Studies ◽  
Aureoumbra Lagunensis

Abstract The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756) and five strains of A. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984 and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 base-pairs (bp) (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five A. anophagefferens strains varied slightly in length (42,401 bp—42,621 bp) and were 99.4%-100.0% identical. Gene content and order was highly conserved between the A. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in A. anophagefferens containing DNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. While the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five A. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to non-bloom-forming species.

scholarly journals The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1517
Author(s):  
Se-Hwan Cheon ◽  
Min-Ah Woo ◽  
Sangjin Jo ◽  
Young-Kee Kim ◽  
Ki-Joong Kim
Keyword(s):  
Northeast Asia ◽  
Single Copy ◽  
Rrna Genes ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Protein Coding ◽  
Tropical Regions ◽  
Relationship Of ◽  
The Relationship ◽  
Simple Sequence

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

scholarly journals Frequent tRNA gene translocation towards the boundaries with control regions contributes to the highly dynamic mitochondrial genome organization of the parasitic lice of mammals

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wen-Ge Dong ◽  
Yalun Dong ◽  
Xian-Guo Guo ◽  
Renfu Shao
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Genome Organization ◽  
Trna Gene ◽  
Trna Genes ◽  
Single Chromosome ◽  
Gene Translocation ◽  
Sucking Lice ◽  
Different Types ◽  
Mt Genome

Abstract Background The typical single-chromosome mitochondrial (mt) genome of animals has fragmented into multiple minichromosomes in the lineage Mitodivisia, which contains most of the parasitic lice of eutherian mammals. These parasitic lice differ from each other even among congeneric species in mt karyotype, i.e. the number of minichromosomes, and the gene content and gene order in each minichromosome, which is in stark contrast to the extremely conserved single-chromosome mt genomes across most animal lineages. How fragmented mt genomes evolved is still poorly understood. We use Polyplax sucking lice as a model to investigate how tRNA gene translocation shapes the dynamic mt karyotypes. Results We sequenced the full mt genome of the Asian grey shrew louse, Polyplax reclinata. We then inferred the ancestral mt karyotype for Polyplax lice and compared it with the mt karyotypes of the three Polyplax species sequenced to date. We found that tRNA genes were entirely responsible for mt karyotype variation among these three species of Polyplax lice. Furthermore, tRNA gene translocation observed in Polyplax lice was only between different types of minichromosomes and towards the boundaries with the control region. A similar pattern of tRNA gene translocation can also been seen in other sucking lice with fragmented mt genomes. Conclusions We conclude that inter-minichromosomal tRNA gene translocation orientated towards the boundaries with the control region is a major contributing factor to the highly dynamic mitochondrial genome organization in the parasitic lice of mammals.

scholarly journals Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure–Function Map

2021 ◽  
Vol 89 (1-2) ◽  
pp. 103-116
Author(s):  
Julie Baker Phillips ◽  
David H. Ardell
Keyword(s):  
Structure Function ◽  
Metal Ion ◽  
Binding Pocket ◽  
Trna Synthetase ◽  
Heterologous Gene ◽  
Multigene Families ◽  
Ion Binding ◽  
Trna Genes ◽  
Structural Factors ◽  
Trna Structure

AbstractThe evolution of tRNA multigene families remains poorly understood, exhibiting unusual phenomena such as functional conversions of tRNA genes through anticodon shift substitutions. We improved FlyBase tRNA gene annotations from twelve Drosophila species, incorporating previously identified ortholog sets to compare substitution rates across tRNA bodies at single-site and base-pair resolution. All rapidly evolving sites fell within the same metal ion-binding pocket that lies at the interface of the two major stacked helical domains. We applied our tRNA Structure–Function Mapper (tSFM) method independently to each Drosophila species and one outgroup species Musca domestica and found that, although predicted tRNA structure–function maps are generally highly conserved in flies, one tRNA Class-Informative Feature (CIF) within the rapidly evolving ion-binding pocket—Cytosine 17 (C17), ancestrally informative for lysylation identity—independently gained asparaginylation identity and substituted in parallel across tRNAAsn paralogs at least once, possibly multiple times, during evolution of the genus. In D. melanogaster, most tRNALys and tRNAAsn genes are co-arrayed in one large heterologous gene cluster, suggesting that heterologous gene conversion as well as structural similarities of tRNA-binding interfaces in the closely related asparaginyl-tRNA synthetase (AsnRS) and lysyl-tRNA synthetase (LysRS) proteins may have played a role in these changes. A previously identified Asn-to-Lys anticodon shift substitution in D. ananassae may have arisen to compensate for the convergent and parallel gains of C17 in tRNAAsn paralogs in that lineage. Our results underscore the functional and evolutionary relevance of our tRNA structure–function map predictions and illuminate multiple genomic and structural factors contributing to rapid, parallel and compensatory evolution of tRNA multigene families.

scholarly journals Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sajjad Asaf ◽  
Abdul Latif Khan ◽  
Muhammad Numan ◽  
Ahmed Al-Harrasi
Keyword(s):  
Chloroplast Genome ◽  
Related Species ◽  
Evolutionary Genetics ◽  
Single Copy ◽  
Avicennia Marina ◽  
Pairwise Distance ◽  
Trna Genes ◽  
Evolutionary Divergence ◽  
Mangrove Tree ◽  
High Degree

AbstractAvicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.

scholarly journals Transcription of eukaryotic tRNA genes in vitro. II. Formation of stable complexes.

1983 ◽  
Vol 258 (4) ◽  
pp. 2447-2453 ◽  
Author(s):  
J Schaack ◽  
S Sharp ◽  
T Dingermann ◽  
D Söll
Keyword(s):  
Trna Genes
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