(Q21256431)

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Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases

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Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases (English)

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structural biology

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2

object named as

Eugene V Koonin

author given names

Eugene V

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Koonin

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Dimensions Publication ID

18 August 2022

object named as

L Aravind

3

author given names

L

author last names

Aravind

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Dimensions Publication ID

18 August 2022

Lakshminarayan M. Iyer

1

object named as

Lakshminarayan M Iyer

author given names

Lakshminarayan M

author last names

Iyer

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Dimensions Publication ID

18 August 2022

language of work or name

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publication date

28 January 2003

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BMC Structural Biology

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3

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1

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1

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MicroRNAs in plants

1 reference

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19 March 2017

Comparative genomics and evolution of proteins involved in RNA metabolism

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Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution

1 reference

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Micro-RNAs: small is plentiful

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Common origin of four diverse families of large eukaryotic DNA viruses

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Identification of novel small RNAs using comparative genomics and microarrays

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19 March 2017

DNA-binding proteins and evolution of transcription regulation in the archaea

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19 March 2017

Structure and interactions of the translation initiation factor eIF1

1 reference

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The universal ancestor

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Dali/FSSP classification of three-dimensional protein folds

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Non–coding RNA genes and the modern RNA world

1 reference

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Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution

1 reference

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19 March 2017

Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution

1 reference

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19 March 2017

Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution

1 reference

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19 March 2017

Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription

1 reference

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A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases

1 reference

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Structure of the RNA polymerase domain of E. coli primase

1 reference

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1 reference

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1 reference

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High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases

1 reference

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Structure of the oligomerization and L-arginine binding domain of the arginine repressor of Escherichia coli

1 reference

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Identification of novel genes coding for small expressed RNAs

1 reference

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1 reference

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1 reference

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19 March 2017

Touring protein fold space with Dali/FSSP

1 reference

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19 March 2017

A novel subunit of yeast RNA polymerase III interacts with the TFIIB-related domain of TFIIIB70.

1 reference

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19 March 2017

Novel predicted RNA-binding domains associated with the translation machinery

1 reference

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19 March 2017

A microRNA in a multiple-turnover RNAi enzyme complex

1 reference

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19 March 2017

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1 reference

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19 March 2017

A species of small antisense RNA in posttranscriptional gene silencing in plants

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19 March 2017

Classification and evolution of P-loop GTPases and related ATPases

1 reference

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7 April 2017

RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals

1 reference

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Prediction of protein secondary structure at better than 70% accuracy

1 reference

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7 April 2017

Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA

1 reference

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7 April 2017

Endogenous and silencing-associated small RNAs in plants

1 reference

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7 April 2017

On the role of RNA amplification in dsRNA-triggered gene silencing

1 reference

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7 April 2017

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1 reference

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7 April 2017

A mechanism for all polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

7 April 2017

Telomerase catalytic subunit homologs from fission yeast and human

1 reference

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7 April 2017

Reverse transcriptase motifs in the catalytic subunit of telomerase

1 reference

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7 April 2017

Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

7 April 2017

Identification of four conserved motifs among the RNA-dependent polymerase encoding elements

1 reference

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7 April 2017

A workbench for multiple alignment construction and analysis

1 reference

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7 April 2017

Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

7 April 2017

Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches

1 reference

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7 April 2017

Trends in protein evolution inferred from sequence and structure analysis.

1 reference

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12 September 2017

RNA-dependent RNA polymerases, viruses, and RNA silencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA.

1 reference

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12 September 2017

RNAi (Nematodes: Caenorhabditis elegans).

1 reference

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12 September 2017

Quelling in Neurospora crassa

1 reference

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12 September 2017

RNAi in Dictyostelium: the role of RNA-directed RNA polymerases and double-stranded RNase

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12 September 2017

Multisubunit RNA polymerases

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12 September 2017

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12 September 2017

SCOP database in 2002: refinements accommodate structural genomics

1 reference

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12 September 2017

A short primer on RNAi: RNA-directed RNA polymerase acts as a key catalyst

1 reference

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12 September 2017

Eukaryotic DNA polymerases: proposal for a revised nomenclature.

1 reference

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12 September 2017

Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains.

1 reference

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12 September 2017

Mechanism and regulation of transcription in archaea

1 reference

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12 September 2017

The expanding polymerase universe

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

GGDEF domain is homologous to adenylyl cyclase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Post-transcriptional gene silencing across kingdoms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Bacterial homologs of the small subunit of eukaryotic DNA primase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Transgene silencing in monocots

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

RNA degradation and models for post-transcriptional gene-silencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

The role of transcription factor B in transcription initiation and promoter clearance in the archaeon Sulfolobus acidocaldarius.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

N-ethylmaleimide-sensitive fusion protein (NSF) and CDC48 confirmed as members of the double-psi beta-barrel aspartate decarboxylase/formate dehydrogenase family

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Posttranscriptional gene silencing of gn1 in tobacco triggers accumulation of truncated gn1-derived RNA species

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

RNA-triggered gene silencing

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Did DNA replication evolve twice independently?

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12 September 2017

A six-stranded double-psi beta barrel is shared by several protein superfamilies.

1 reference

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12 September 2017

DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history

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12 September 2017

AT-hook motifs identified in a wide variety of DNA-binding proteins

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12 September 2017

Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Protein sequence similarity searches using patterns as seeds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

How far divergent evolution goes in proteins

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12 September 2017

SEALS: a system for easy analysis of lots of sequences.

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12 September 2017

Extracting protein alignment models from the sequence database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Gibbs motif sampling: detection of bacterial outer membrane protein repeats

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

A baculovirus gene involved in late gene expression predicts a large polypeptide with a conserved motif of RNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

PHD--an automatic mail server for protein secondary structure prediction

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Non-globular domains in protein sequences: automated segmentation using complexity measures

1 reference

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12 September 2017

Transcription: new insights from studies on Archaea.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

Prokaryotic and eukaryotic RNA polymerases have homologous core subunits

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

A sequence motif in many polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

12 September 2017

The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

27 September 2017

A universally conserved region of the largest subunit participates in the active site of RNA polymerase III

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

27 September 2017

An attempt to unify the structure of polymerases

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

27 September 2017

Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

30 May 2018

Identification of genes encoding late expression factors located between 56.0 and 65.4 map units of the Autographa californica nuclear polyhedrosis virus genome

1 reference

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30 May 2018

Characterization of the RNA-dependent RNA polymerase of tobacco leaves

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

30 May 2018

Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

29 November 2018

MicroRNAs: deviants no longer.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

29 November 2018

Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

29 November 2018

Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

29 November 2018

Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

29 November 2018

Identification of the primase active site of the herpes simplex virus type 1 helicase-primase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

29 November 2018

RNA-directed RNA polymerase from tomato leaves. I. Purification and physical properties.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

29 November 2018

DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=151600

29 November 2018

Similarity of Protein G and Ubiquitin

1 reference

https://pubmed.ncbi.nlm.nih.gov/12553882

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Familiar strangers

1 reference

https://pubmed.ncbi.nlm.nih.gov/12553882

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A polymerase I palm in adenylyl cyclase?

1 reference

https://pubmed.ncbi.nlm.nih.gov/12553882

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The brave new world of RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/12553882

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Small RNAs in Rickettsia: are they functional?

1 reference

https://pubmed.ncbi.nlm.nih.gov/12553882

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RNA-dependent RNA-polymerase in Brassica chinensis L

1 reference

https://pubmed.ncbi.nlm.nih.gov/12553882

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RNA-dependent RNA polymerase in Chinese cabbage

1 reference

https://pubmed.ncbi.nlm.nih.gov/12553882

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1472-6807-3-1

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Dimensions Publication ID

0 references

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PubMed publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

ResearchGate publication ID

0 references

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