TGD | Gene Details

Identifiers and Description

Gene Model Identifier
TTHERM_01109990

Standard Name
PDD3 (Programmed DNA Degradation 3)

Aliases
PreTt17969 | 239.m00048 | 3802.m00189

Description
Programmed DNA degradation 3 protein; developmentally regulated chromodomain protein; localizes to DNA elimination structures during programmed DNA elimination; binds methylated Lys-9 of histone H3

Genome Browser (Macronucleus)

Genome Browser (Micronucleus)

Gene Ontology Annotations

Cellular Component
macronucleus (IDA) | GO:0031039 | Ref:10805754
Molecular Function
methylated histone binding (IDA) | GO:0035064 | Ref:12297044

Domains

No Data fetched for Domains

Gene Expression Profile

Tetrahymena Functional Genomics Database:

Change in Gene Expression

TMHMM

TMHMM

Signal Peptide

Signal Peptide Present?: No
Presense Probability: 14%

TetraMine Data

TTHERM_01109990

WebApollo

Fullscreen View

Tetrahymena Stock Center

( SD01326 ) Micronucleus: PDD3 replaced by neo2 Macronucleus: PDD3 replaced by neo2

Homologs (v.2006 protein sequences)

Source Identifier Score Description

Tetrahymena borealis EI9_41369.1 1.0000943968537097e-101 hypothetical protein (367 aa)

Source	Identifier	Score	Description
Tetrahymena borealis	EI9_41369.1	1.0000943968537097e-101	hypothetical protein (367 aa)

General Information

Paragraph No Gene Name Paragraph Text
2 TWI1,
HHT2,
PDD1,
PDD3,
DCL1 A proposed model for the mechanism of programmed DNA elimination in Tetrahymena is based on the timing of expression, cellular distribution, mutant phenotypes, and predicted functions of the protein and RNA components involved. In this model, both strands of the micronuclear genome (or perhaps only the portions containing internal eliminated sequences) are transcribed early in conjugation to produce large non-genic, double-stranded RNAs. This transcription is likely performed by RNA Polymerase II, based on the localization of its subunit Rpb3p to the micronucleus during this time. These transcripts pass to the cytoplasm where they are processed into short (~28 nucleotide) scan RNAs (scnRNA) by the dicer-like protein Dcl1p, similar to the production of the small inhibitory RNAs (siRNA) central to the RNA interference (RNAi) pathway of other eukaryotes. The scnRNAs complex with Twi1p, a member of the PPD (PAZ and Piwi Domain) protein family, whose members are commonly involved in RNAi and related processes. The scnRNA/Twi1p complexes enter the old macronucleus, where scnRNAs homologous to DNA sequences found there are degraded. The remaining scnRNAs, comprised of micronuclear-restricted sequences, are transferred to the developing macronucleus. There, histone H3 proteins (Hht1p, Hht2p) that are bound to sections of the genome sharing identity to the scnRNAs are methylated on lysine-9. This modification, which is often associated with the formation of heterochromatin, is recognized by one or more of the chromodomains belonging to Pdd1p and Pdd3p. Regions of DNA associated with these modified histones are eliminated from the developing macronuclear genome.

Associated Literature

Ref:12297044: Taverna SD, Coyne RS, Allis CD (2002) Methylation of histone h3 at lysine 9 targets programmed DNA elimination in tetrahymena. Cell 110(6):701-11
Ref:10805754: Nikiforov MA, Gorovsky MA, Allis CD (2000) A novel chromodomain protein, pdd3p, associates with internal eliminated sequences during macronuclear development in Tetrahymena thermophila. Molecular and cellular biology 20(11):4128-34

Sequences

>TTHERM_01109990(coding)
ATGCTAAGTATTGCTTTGATAAAGTTAGAATAAAACTGCTTTGAAGTTAAAAGAATTGCT
GATGATATGCAATAGTAAGTTGAGTAAGTAAAAAGTAGCTATAAGATTATATAAATAAAT
AGAGACCTCAAGACAGCATAGCTTTCAAAAGATTAAATGCAGAATATACTATTAGAATTC
TAGCAAAAGCTGAGTTATTTGGAATGCATGATGAATCAAATTATGGGATTAAAAGATATA
TTTACTTTTAATTTAAATCAACTATTAGAATCAGAATTGAATGATAGCTAAAAGAGTTAC
AACTAAAAGAGTCCGAATGTCCATATAGAGTATTACTTGGAGAGAGATTAAAAATAAAAT
TAAAATGATATTAAAATTGAAGAAAATCAATTTGATGATAATAAAATATTTTATTCTTCT
TTCTCCTCTTCTAAAAAGAAAAGTAATAATGATTCAATTTAAAAGGAGCAAACTGATCAA
AAAAATTAAGATGAATAAGTGCAAGAGTTCGATGATGATTACTTATTTGAAAGTGGGAGT
AAATTACCTTAAGATACTCAAAAACCTAATTTAAATTTAAATGAAAATGAATAGTATTCT
CATCTTAATTTATTCAATCGTAAGATTGTTAAGAAACAACCTTACAAAGTCCCAGAAAAA
ATTCTTGATGAAAAAATTTAACACTATAGTATAAAAAATTTGTATGATGCTAATGTTTTT
GACATGGATTAGAGCAAGTTGAGAAAGTAAAAAGATAATAAAAAATTTTCAAATGATTCG
ATAGCTCAATGCATAGATTACTTGTAAAAAAATAAATAAATTGATTGGGGAAAAGTTTAT
GAAAGTTGGAGATAGTTAGAATAAATATCAAAAATGAAAATTCCTAACTATTTTTACACA
GCAGATTTTAGAAATAACTTAAAAATTAAAGGAGTCACATCAAATCTTTCAAAGTAGGAG
ATTCTCGATCTTTTTGAATTATCTAAACTTTTTAGGAGCCAATCAGCTTTTTCAAAATTT
TTATAGCTTTCTAGAGATTAAATTGGCAAAATGTTTAAGAGAAAACTCGGGGTAAAGTTA
GTTGAGTAAAAATCAATTTTCTAATGTTTCAATTAAAAATGA

>TTHERM_01109990(protein)
MLSIALIKLEQNCFEVKRIADDMQQQVEQVKSSYKIIQINRDLKTAQLSKDQMQNILLEF
QQKLSYLECMMNQIMGLKDIFTFNLNQLLESELNDSQKSYNQKSPNVHIEYYLERDQKQN
QNDIKIEENQFDDNKIFYSSFSSSKKKSNNDSIQKEQTDQKNQDEQVQEFDDDYLFESGS
KLPQDTQKPNLNLNENEQYSHLNLFNRKIVKKQPYKVPEKILDEKIQHYSIKNLYDANVF
DMDQSKLRKQKDNKKFSNDSIAQCIDYLQKNKQIDWGKVYESWRQLEQISKMKIPNYFYT
ADFRNNLKIKGVTSNLSKQEILDLFELSKLFRSQSAFSKFLQLSRDQIGKMFKRKLGVKL
VEQKSIFQCFNQK

>TTHERM_01109990(gene)
ATGCTAAGTATTGCTTTGATAAAGTTAGAATAAAACTGCTTTGAAGTTAAAAGAATTGCT
GATGATATGCAATAGTAAGTTGAGTAAGTAAAAAGTAGCTATAAGATTATATAAATAAAT
AGAGACCTCAAGACAGCATAGCTTTCAAAAGATTAAATGCAGAATATACTATTAGAATTC
TAGCAAAAGCTGAGTTATTTGGAATGCATGATGAATCAAATTATGGGATTAAAAGATATA
TTTACTTTTAATTTAAATCAACTATTAGAATCAGAATTGAATGATAGCTAAAAGAGTTAC
AACTAAAAGAGTCCGAATGTCCATATAGAGTATTACTTGGAGAGAGATTAAAAATAAAAT
TAAAATGATATTAAAATTGAAGAAAATCAATTTGATGATAATAAAATATTTTATTCTTCT
TTCTCCTCTTCTAAAAAGAAAAGTAATAATGATTCAATTTAAAAGGAGCAAACTGATCAA
AAAAATTAAGATGAATAAGTGCAAGAGTTCGATGATGATTACTTATTTGAAAGTGGGAGT
AAATTACCTTAAGATACTCAAAAACCTAATTTAAATTTAAATGAAAATGAATAGTATTCT
CATCTTAATTTATTCAATCGTAAGATTGTTAAGAAACAACCTTACAAAGTCCCAGAAAAA
ATTCTTGATGAAAAAATTTAACACTATAGTATAAAAAATTTGTATGATGCTAATGTTTTT
GACATGGATTAGAGCAAGTTGAGAAAGTAAAAAGATAATAAAAAATTTTCAAATGATTCG
ATAGCTCAATGCATAGATTACTTGTAAAAAAATAAATAAATTGATTGGGGAAAAGTTTAT
GAAAGTTGGAGATAGTTAGAATAAATATCAAAAATGAAAATTCCTAACTATTTTTACACA
GCAGATTTTAGAAATAACTTAAAAATTAAAGGAGTCACATCAAATCTTTCAAAGTAGGAG
ATTCTCGATCTTTTTGAATTATCTAAACTTTTTAGGAGCCAATCAGCTTTTTCAAAATTT
TTATAGCTTTCTAGAGATTAAATTGGCAAAATGTTTAAGAGAAAACTCGGGGTAAAGTTA
GTTGAGTAAAAATCAATTTTCTAATGTTTCAATTAAAAATGA

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Identifiers and Description

Gene Model Identifier

Standard Name

Aliases

Description

Genome Browser (Macronucleus)

Genome Browser (Micronucleus)

Gene Ontology Annotations

Cellular Component

Molecular Function

Domains

Gene Expression Profile

Change in Gene Expression

TMHMM

TMHMM

Signal Peptide

TetraMine Data

WebApollo

Tetrahymena Stock Center

Homologs (v.2006 protein sequences)

General Information

Associated Literature

Sequences

Wiki Links

External Links

Paragraph No	Gene Name	Paragraph Text
2	TWI1, HHT2, PDD1, PDD3, DCL1	A proposed model for the mechanism of programmed DNA elimination in Tetrahymena is based on the timing of expression, cellular distribution, mutant phenotypes, and predicted functions of the protein and RNA components involved. In this model, both strands of the micronuclear genome (or perhaps only the portions containing internal eliminated sequences) are transcribed early in conjugation to produce large non-genic, double-stranded RNAs. This transcription is likely performed by RNA Polymerase II, based on the localization of its subunit Rpb3p to the micronucleus during this time. These transcripts pass to the cytoplasm where they are processed into short (~28 nucleotide) scan RNAs (scnRNA) by the dicer-like protein Dcl1p, similar to the production of the small inhibitory RNAs (siRNA) central to the RNA interference (RNAi) pathway of other eukaryotes. The scnRNAs complex with Twi1p, a member of the PPD (PAZ and Piwi Domain) protein family, whose members are commonly involved in RNAi and related processes. The scnRNA/Twi1p complexes enter the old macronucleus, where scnRNAs homologous to DNA sequences found there are degraded. The remaining scnRNAs, comprised of micronuclear-restricted sequences, are transferred to the developing macronucleus. There, histone H3 proteins (Hht1p, Hht2p) that are bound to sections of the genome sharing identity to the scnRNAs are methylated on lysine-9. This modification, which is often associated with the formation of heterochromatin, is recognized by one or more of the chromodomains belonging to Pdd1p and Pdd3p. Regions of DNA associated with these modified histones are eliminated from the developing macronuclear genome.