scholarly journals PlantRNA 2.0 : an updated database dedicated to tRNAs of photosynthetic eukaryotes

2021 ◽  
Author(s):  
Valerie Cognat ◽  
Gael Pawlak ◽  
David Pflieger ◽  
Laurence Drouard
Keyword(s):  
Transcription Initiation ◽  
Transfer Rna ◽  
Biological Information ◽  
Trna Genes ◽  
Photosynthetic Organisms ◽  
Photosynthetic Eukaryotes ◽  
Basal Group ◽  
Flanking Sequences ◽  
Rna Genes

PlantRNA (http://plantrna.ibmp.cnrs.fr/) is a comprehensive database of transfer RNA (tRNA) gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. In the first release (PlantRNA 1.0), tRNA genes from 11 organisms were annotated. In this second version, the annotation was implemented to 48 photosynthetic species covering the whole phylogenetic tree of photosynthetic organisms, from the most basal group of Archeplastida, the glaucophyte Cyanophora paradoxa, to various land plants. Transfer RNA genes from lower photosynthetic organisms such as streptophyte algae or lycophytes as well as extremophile photosynthetic species such as Eutrema parvulum were incorporated in the database. As a whole, circa 35 000 tRNA genes were accurately annotated. In the frame of the tRNA genes annotation from the genome of the Rhodophyte Chondrus crispus, putative unconventional splicing sites in the D- or T- regions of tRNA molecules were experimentally determined to strengthen the quality of the database. As for PlantRNA 1.0, comprehensive biological information including flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences and tRNA mitochondrial import are included.

Transfer RNA genes and their significance to codon usage in the Pseudomonas aeruginosa lamboid bacteriophage D3

1999 ◽  
Vol 45 (9) ◽  
pp. 791-796 ◽  
Author(s):  
Andrew M Kropinski ◽  
Mary Jo Sibbald
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Codon Usage ◽  
Transfer Rna ◽  
Trna Genes ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Early Region ◽  
Phage Proteins ◽  
Rna Genes

Using tRNAscan-SE and FAStRNA we have identified four tRNA genes in the delayed early region of the bacteriophage D3 genome (GenBank accession No. AF077308). These are specific for methionine (AUG), glycine (GGA), asparagine (AAC), and threonine (ACA). The D3 Thr- and Gly-tRNAs recognize codons, which are rarely used in Pseudomonas aeruginosa and presumably, influence the rate of translation of phage proteins. BLASTN searches revealed that the D3 tRNA genes have homology to tRNA genes from Gram-positive bacteria. Analysis of codon usage in the 91 ORFs discovered in D3 indicates patterns of codon usage reminiscent of Escherichia coli or P. aeruginosa.Key words: bacteriophage, Pseudomonas, D3, tRNA, codon usage.

scholarly journals Genetic characterization of mitochondrial genome of the small intestinal fluke, Haplorchis taichui (Trematoda: Heterophyidae), Vietnamese sample

2016 ◽  
Vol 14 (2) ◽  
pp. 215-224
Author(s):  
Lê Thanh Hòa ◽  
Nguyễn Thị Khuê ◽  
Nguyễn Thị Bích Nga ◽  
Đỗ Thị Roan ◽  
Đỗ Trung Dũng ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Transfer Rna ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Mtdna Sequence ◽  
Small Intestinal ◽  
Haplorchis Taichui ◽  
Rna Genes

The small intestinal fluke, Haplorchis taichui Nishigori, 1924, belonging to genus Haplorchis (family Heterophyidae, class Trematoda, phylum Platyhelminthes), is a zoonotic pathogen causing disease in humans and animals. Complete mitochondrial genome (mtDNA) of H. taichui (strain HTAQT, collected from Quang Tri) was obtained and characterized for structural genomics providing valuable data for studies on epidemiology, species identification, diagnosis, classification, molecular phylogenetic relationships and prevention of the disease. The entire nucleotide mtDNA sequence of H. taichui (HTAQT) is 15.119 bp in length, containing 36 genes, including 12 protein-coding genes (cox1, cox2, cox3, nad1, nad2, nad3, nad4L, nad4, nad5, nad6, atp6 and cob); 2 ribosomal RNA genes, rrnL (16S) and rrnS (12S); 22 transfer RNA genes (tRNA or trn), and a non-coding region (NR), divided into two sub-regions of short non-coding (short, SNR) and long non-coding (long, LNR). LNR region, 1.692 bp in length, located between the position of trnG (transfer RNA-Glycine) and trnE (Glutamic acid), contains 6 tandem repeats (TR), arranged as TR1A, TR2A, TR1B, TR2B, TR3A, TR3B, respectively. Each protein coding gene (overall, 12 genes), ribosomal rRNA (2 genes) and tRNA (22 genes) were analyzed, in particular, protein-coding genes were defined in length, start and stop codons, and rRNA and tRNA genes for secondary structure.

scholarly journals The Complete Mitochondrial Genome Sequences of the Philomycus bilineatus (Stylommatophora: Philomycidae) and Phylogenetic Analysis

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 198 ◽  
Author(s):  
Tiezhu Yang ◽  
Guolyu Xu ◽  
Bingning Gu ◽  
Yanmei Shi ◽  
Hellen Lucas Mzuka ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Transfer Rna ◽  
Amino Acid Sequences ◽  
Start Codon ◽  
Trna Genes ◽  
Rna Genes

The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (A + T-rich region). There were 15 overlap locations and 18 intergenic spacer regions found throughout the mitogenome of P. bilineatus. The A + T content in the mitogenome was 72.11%. All PCGs used a standard ATN as a start codon, with the exception of cytochrome c oxidase 1 (cox1) and ATP synthase F0 subunit 8 (atp8) with TTG and GTG. Additionally, TAA or TAG was identified as the typical stop codon. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except for trnS1 (AGC), trnS2 (TCA), and trnK (TTT). A phylogenetic analysis with another 37 species of gastropods was performed using Bayesian inference, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that P. bilineatus shares a close ancestry with Meghimatium bilineatum. It seems more appropriate to reclassify it as Arionoidea rather than Limacoidea, as previously thought. Our research may provide a new meaningful insight into the evolution of P. bilineatus.

scholarly journals Cloning and nucleotide sequence analysis of transfer RNA genes from Mycoplasma mycoides

1985 ◽  
Vol 232 (1) ◽  
pp. 223-228 ◽  
Author(s):  
T Samuelsson ◽  
P Elias ◽  
F Lustig ◽  
Y S Guindy
Keyword(s):  
Sequence Analysis ◽  
Nucleotide Sequence ◽  
Trna Gene ◽  
Transfer Rna ◽  
Nucleotide Sequences ◽  
Transcriptional Unit ◽  
Nucleotide Sequence Analysis ◽  
Trna Genes ◽  
Mycoplasma Mycoides ◽  
Rna Genes

As part of an investigation of the tRNA genes of Mycoplasma mycoides, two HindIII fragments of mycoplasma DNA comprising 0.4 and 2.5 kilobases (kb), respectively, were cloned in pBR322 and their nucleotide sequences determined. Only one tRNA gene was found in the 0.4 kb fragment, the gene for tRNAArg with the anticodon TCT, while the 2.5 kb fragment contained nine different tRNA genes arranged in a cluster which presumably constitutes a transcriptional unit. The clustered tRNA genes, with their respective anticodons, were as follows: Arg (ACG), Pro (TGG), Ala (TGC), Met (CAT), Ile (CAT), Ser (TGA), fMet (CAT), Asp (GTC), and Phe (GAA).

Transcription initiation of eucaryotic transfer RNA Genes

Cell ◽  
1982 ◽  
Vol 29 (1) ◽  
pp. 3-5 ◽  
Author(s):  
Benjamin D. Hall ◽  
Stuart G. Clarkson ◽  
Glauco Tocchini-Valentini
Keyword(s):  
Transcription Initiation ◽  
Transfer Rna ◽  
Rna Genes

A discrete region centered 22 base pairs upstream of the initiation site modulates transcription of Drosophila tRNAAsn genes

1988 ◽  
Vol 8 (10) ◽  
pp. 4441-4449
Author(s):  
A K Lofquist ◽  
A D Garcia ◽  
S J Sharp
Keyword(s):  
Transcription Initiation ◽  
In Vitro Transcription ◽  
Initiation Site ◽  
Trna Genes ◽  
Selection Mechanism ◽  
Base Pairs ◽  
Discrete Region ◽  
Flanking Sequences ◽  
Actual Sequence

We have studied the mechanism by which 5'-flanking sequences modulate the in vitro transcription of eucaryotic tRNA genes. Using deletion and linker substitution mutagenesis, we have found that the 5'-flanking sequences responsible for the different in vitro transcription levels of three Drosophila tRNA5Asn genes are contained within a discrete region centered 22 nucleotides upstream from the transcription initiation site. In conjunction with the A-box intragenic control region, this upstream transcription-modulatory region functions in the selection mechanism for the site of transcription initiation. Since the transcription-modulatory region directs the position of the start site and the actual sequence of the transcription-modulatory region determines the level of tRNAAsn gene transcription, the possibility is raised that the transcription-modulatory region directs a transcription initiation event similar to open complex formation at procaryotic promoters.

scholarly journals tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes

2019 ◽  
Author(s):  
Patricia P. Chan ◽  
Brian Y. Lin ◽  
Allysia J. Mak ◽  
Todd M. Lowe
Keyword(s):  
Gene Prediction ◽  
Transfer Rna ◽  
Trna Genes ◽  
Training Set ◽  
Covariance Models ◽  
Rna Genes ◽  
Eukaryotic Genomes ◽  
Annotation Strategy ◽  
Model Annotation

ABSTRACTtRNAscan-SE has been widely used for whole-genome transfer RNA gene prediction for nearly two decades. With the increased availability of new genomes, a vastly larger training set has enabled creation of nearly one hundred specialized isotype-specific models, greatly improving tRNAscan-SE’s ability to identify and classify both typical and atypical tRNAs. We employ a new multi-model annotation strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models. A post-filtering feature also better identifies tRNA-derived SINEs that are abundant in many eukaryotic genomes, and provides a “high confidence” tRNA gene set which improves upon prior pseudogene prediction. These new enhancements of tRNAscan-SE will provide researchers more accurate detection and more comprehensive annotation for tRNA genes.

scholarly journals A discrete region centered 22 base pairs upstream of the initiation site modulates transcription of Drosophila tRNAAsn genes.

1988 ◽  
Vol 8 (10) ◽  
pp. 4441-4449 ◽  
Author(s):  
A K Lofquist ◽  
A D Garcia ◽  
S J Sharp
Keyword(s):  
Transcription Initiation ◽  
In Vitro Transcription ◽  
Initiation Site ◽  
Trna Genes ◽  
Selection Mechanism ◽  
Base Pairs ◽  
Discrete Region ◽  
Flanking Sequences ◽  
Actual Sequence

We have studied the mechanism by which 5'-flanking sequences modulate the in vitro transcription of eucaryotic tRNA genes. Using deletion and linker substitution mutagenesis, we have found that the 5'-flanking sequences responsible for the different in vitro transcription levels of three Drosophila tRNA5Asn genes are contained within a discrete region centered 22 nucleotides upstream from the transcription initiation site. In conjunction with the A-box intragenic control region, this upstream transcription-modulatory region functions in the selection mechanism for the site of transcription initiation. Since the transcription-modulatory region directs the position of the start site and the actual sequence of the transcription-modulatory region determines the level of tRNAAsn gene transcription, the possibility is raised that the transcription-modulatory region directs a transcription initiation event similar to open complex formation at procaryotic promoters.

Characterization of mutant mitochondrial plasmids of Neurospora spp. that have incorporated tRNAs by reverse transcription

1989 ◽  
Vol 9 (2) ◽  
pp. 678-691
Author(s):  
R A Akins ◽  
R L Kelley ◽  
A M Lambowitz
Keyword(s):  
Mitochondrial Dna ◽  
Reverse Transcription ◽  
Transcription Initiation ◽  
Consensus Sequence ◽  
Trna Genes ◽  
Wild Type ◽  
Mitochondrial Trna ◽  
Mitochondrial Plasmids ◽  
Circular Dnas ◽  
Mitochondrial Introns

The Mauriceville and Varkud mitochondrial plasmids of Neurospora spp. are closely related, closed-circular DNAs (3.6 and 3.7 kilobases, respectively) whose nucleotide sequences and genetic organization suggest relationships to mitochondrial introns and retroelements. We have characterized nine suppressive mutants of these plasmids that outcompete mitochondrial DNA and lead to impaired growth. All nine suppressive plasmids contain small insertions, corresponding to or including a mitochondrial tRNA (tRNATrp, tRNAGly, or tRNAVal) or a tRNA-like sequence. The insertions are located at the position corresponding to the 5' end of the major plasmid transcript or 24 nucleotides downstream near a cognate of the sequence at the major 5' RNA end. The structure of the suppressive plasmids suggests that the tRNAs were inserted via an RNA intermediate. The 3' end of the wild-type plasmid transcript can itself be folded into a secondary structure which has tRNA-like characteristics, similar to the tRNA-like structures at the 3' ends of plant viral RNAs. This structure may play a role in replication of the plasmids by reverse transcription. Major transcripts of the suppressive plasmids begin at the 5' end of the inserted mitochondrial tRNA sequence and are present in 25- to 100-fold-higher concentrations than are transcripts of wild-type plasmids. Mapping of 5' RNA ends within the inserted mtDNA sequences identifies a short consensus sequence (PuNPuAG) which is present at the 5' ends of a subset of mitochondrial tRNA genes. This sequence, together with sequences immediately upstream in the plasmids, forms a longer consensus sequence, which is similar to sequences at transcription initiation sites in Neurospora mitochondrial DNA. The suppressive behavior of the plasmids is likely to be directly related to the insertion of tRNAs leading to overproduction of plasmid transcripts.

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