(Q33778713)

29 July 2017

Dynamic evolution of translation initiation mechanisms in prokaryotes (English)

1 reference

29 July 2017

0 references

4

Takashi Gojobori

1 reference

29 July 2017

So Nakagawa

1

0 references

author name string

Yoshihito Niimura

series ordinal

2

1 reference

PubMed ID

20308567

29 July 2017

Kin-ichiro Miura

series ordinal

3

1 reference

PubMed ID

20308567

29 July 2017

language of work or name

English

0 references

publication date

22 March 2010

1 reference

29 July 2017

6

1 reference

Proceedings of the National Academy of Sciences of the United States of America

inferred from page(s)

published in

1 reference

29 July 2017

107

1 reference

29 July 2017

14

1 reference

29 July 2017

6382-6387

1 reference

What recent ribosome structures have revealed about the mechanism of translation

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Structure-function insights into prokaryotic and eukaryotic translation initiation.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Coding-sequence determinants of gene expression in Escherichia coli

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Questionable 16S ribosomal RNA gene annotations are frequent in completed microbial genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS).

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Mycoplasmas: a distinct cytoskeleton for wall-less bacteria

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Predicting Shine-Dalgarno sequence locations exposes genome annotation errors

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

A leaderless mRNA can bind to mammalian 80S ribosomes and direct polypeptide synthesis in the absence of translation initiation factors

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

DINAMelt web server for nucleic acid melting prediction

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Evolution of translational initiation: new insights from the archaea

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

AU-rich sequences within 5' untranslated leaders enhance translation and stabilize mRNA in Escherichia coli.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Prospects for inferring very large phylogenies by using the neighbor-joining method

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

WebLogo: A Sequence Logo Generator

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Evidence against an Interaction between the mRNA downstream box and 16S rRNA in translation initiation.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Translation during cold adaptation does not involve mRNA-rRNA base pairing through the downstream box.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

The COG database: a tool for genome-scale analysis of protein functions and evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Enhancement of translation by the downstream box does not involve base pairing of mRNA with the penultimate stem sequence of 16S rRNA.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Initiation of translation in prokaryotes and eukaryotes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

The mosaic nature of the eukaryotic nucleus

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Ancient ciphers: translation in Archaea

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Structure and functions of ribosomal protein S1.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Influence of the codon following the AUG initiation codon on the expression of a modified lacZ gene in Escherichia coli

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Translation initiation in Escherichia coli: old and new questions

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Codon choice and potential complementarity between mRNA downstream of the initiation codon and bases 1471 –1480 in 16S ribosomal RNA affects expression ofglnS

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

The location of mRNA in the ribosomal 30S initiation complex; site-directed cross-linking of mRNA analogues carrying several photo-reactive labels simultaneously on either side of the AUG start codon

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Unusual ribosome binding properties of mRNA encoding bacteriophage lambda repressor.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Determinant of cistron specificity in bacterial ribosomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

A blocked structure at the 5′ terminus of mRNA from cytoplasmic polyhedrosis virus

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

On the origin of the cap-dependent initiation of translation in eukaryotes.

4 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1002036107

Evidence for the translation initiation of leaderless mRNAs by the intact 70 S ribosome without its dissociation into subunits in eubacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1002036107

In vivo studies on putative Shine-Dalgarno sequences of the halophilic archaeon Halobacterium salinarum

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1002036107

Quantitative correlation between mRNA secondary structure around the region downstream of the initiation codon and translational efficiency in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1002036107

Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1002036107

[Diverse molecular mechanisms for translation initiation in prokaryotes]

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Bacterial features in the genome of Methanococcus jannaschii in terms of gene composition and biased base composition in ORFs and their surrounding regions.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2851962

Influence of single base change in Shine-Dalgarno sequence on the stability of B. subtilis plasmid PSM604

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20308567

12 December 2020

inferred from PubMed ID database lookup

Correlation between Shine--Dalgarno sequence conservation and codon usage of bacterial genes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20308567

12 December 2020

inferred from PubMed ID database lookup

Bacillus subtilis Requires a "Stringent" Shine-Dalgarno Region for Gene Expression

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20308567

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1073/PNAS.1002036107

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference

PubMed ID

20308567