User:Nkuldell/mtDNA pt3 - Revision history

Nkuldell at 15:24, 20 June 2007

Nkuldell — Wed, 20 Jun 2007 15:24:53 GMT

←Older revision		Revision as of 15:24, 20 June 2007
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	====Gen'l info about RNases families====		====Gen'l info about RNases families====
	From Current Opinion in Structural Biology 2007 17:77 by [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS6-4MWGYGP-3&_user=501045&_coverDate=02%2F28%2F2007&_rdoc=13&_fmt=full&_orig=browse&_srch=doc-info(%23toc%236254%232007%23999829998%23644320%23FLA%23display%23Volume)&_cdi=6254&_sort=d&_docanchor=&view=c&_ct=21&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=8c18217696d86ae6eda73ed528ffcad7 James M Berger and Christoph W Müller] "A particularly interesting family of ribonucleases that specifically cleave double-stranded RNA serves as the topic of the review by MacRae and Doudna. The RNase III group of RNA-processing enzymes currently attracts broad attention, because two family members, Dicer and Drosha, are responsible for processing RNA transcripts into microRNA (miRNAs) and short interfering RNAs (siRNAs). RNase III proteins are often multifunctional or multisubunit assemblies, and can be classified based on domain composition. Class I RNase III enzymes function as dimers, in which the RNase domains also act as dimerization domains, whereas class II and III family members are monomeric, forming a functional RNase from the internal fusion of two class I RNase III monomers. Comparing RNase III enzymes across a wide range of species leads the authors to conclude that RNase III enzymes use accessory domains as determinants of substrate specificity. For Dicer and Drosha, these accessory domains are the PAZ domain and the additional DGCR8 protein, respectively. Substrate specificity and catalytic domains are spatially separated and, in some instances, it appears that the RNase can precisely measure the distance between the RNA recognition and cleavage sites by using an internal scaffold element that functions as a molecular ruler. Given the number of different types of small RNAs and their importance in gene regulation and other cellular processes, there are sure to be many fundamental insights that will arise from the continued study of this essential protein family."		From Current Opinion in Structural Biology 2007 17:77 by [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS6-4MWGYGP-3&_user=501045&_coverDate=02%2F28%2F2007&_rdoc=13&_fmt=full&_orig=browse&_srch=doc-info(%23toc%236254%232007%23999829998%23644320%23FLA%23display%23Volume)&_cdi=6254&_sort=d&_docanchor=&view=c&_ct=21&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=8c18217696d86ae6eda73ed528ffcad7 James M Berger and Christoph W Müller] "A particularly interesting family of ribonucleases that specifically cleave double-stranded RNA serves as the topic of the review by MacRae and Doudna. The RNase III group of RNA-processing enzymes currently attracts broad attention, because two family members, Dicer and Drosha, are responsible for processing RNA transcripts into microRNA (miRNAs) and short interfering RNAs (siRNAs). RNase III proteins are often multifunctional or multisubunit assemblies, and can be classified based on domain composition. Class I RNase III enzymes function as dimers, in which the RNase domains also act as dimerization domains, whereas class II and III family members are monomeric, forming a functional RNase from the internal fusion of two class I RNase III monomers. Comparing RNase III enzymes across a wide range of species leads the authors to conclude that RNase III enzymes use accessory domains as determinants of substrate specificity. For Dicer and Drosha, these accessory domains are the PAZ domain and the additional DGCR8 protein, respectively. Substrate specificity and catalytic domains are spatially separated and, in some instances, it appears that the RNase can precisely measure the distance between the RNA recognition and cleavage sites by using an internal scaffold element that functions as a molecular ruler. Given the number of different types of small RNAs and their importance in gene regulation and other cellular processes, there are sure to be many fundamental insights that will arise from the continued study of this essential protein family."
-	====S. cerevisiae RNases====	+	====S. cerevisiae RNases/nucleases====
	[[Image:Macintosh HD-Users-nkuldell-Desktop-Rnt1pN-termXtal EMBO04.png\|thumb\| N-term Rnt1p struct. from EMBO 2004]]		[[Image:Macintosh HD-Users-nkuldell-Desktop-Rnt1pN-termXtal EMBO04.png\|thumb\| N-term Rnt1p struct. from EMBO 2004]]
	* [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=nuc1 NUC1] from SGD: "major mitochondrial nuclease, has RNAse and DNA endo- and exonucleolytic activities; has roles in mitochondrial recombination, apoptosis and maintenance of polyploidy"		* [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=nuc1 NUC1] from SGD: "major mitochondrial nuclease, has RNAse and DNA endo- and exonucleolytic activities; has roles in mitochondrial recombination, apoptosis and maintenance of polyploidy"
		+	* Bacterial endonucleases (EcoRI, BamHI and PstI) can be [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16120308&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum\| expressed from the yeast nuclear genome and sent to mt]
	====Rnt1p====		====Rnt1p====
	*[http://www.ihop-net.org/UniPub/iHOP/gs/35375.html seq/struc link]		*[http://www.ihop-net.org/UniPub/iHOP/gs/35375.html seq/struc link]

Nkuldell at 13:53, 20 June 2007

Nkuldell — Wed, 20 Jun 2007 13:53:43 GMT

←Older revision		Revision as of 13:53, 20 June 2007
Line 12:		Line 12:
	====S. cerevisiae RNases====		====S. cerevisiae RNases====
	[[Image:Macintosh HD-Users-nkuldell-Desktop-Rnt1pN-termXtal EMBO04.png\|thumb\| N-term Rnt1p struct. from EMBO 2004]]		[[Image:Macintosh HD-Users-nkuldell-Desktop-Rnt1pN-termXtal EMBO04.png\|thumb\| N-term Rnt1p struct. from EMBO 2004]]
		+	* [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=nuc1 NUC1] from SGD: "major mitochondrial nuclease, has RNAse and DNA endo- and exonucleolytic activities; has roles in mitochondrial recombination, apoptosis and maintenance of polyploidy"
	====Rnt1p====		====Rnt1p====
	*[http://www.ihop-net.org/UniPub/iHOP/gs/35375.html seq/struc link]		*[http://www.ihop-net.org/UniPub/iHOP/gs/35375.html seq/struc link]

Nkuldell at 13:43, 20 June 2007

Nkuldell — Wed, 20 Jun 2007 13:43:33 GMT

←Older revision		Revision as of 13:43, 20 June 2007
Line 37:		Line 37:
	*lysine tRNA CUU (tRK1) encoded by nuclear genome and delivered to mitochondrial matrix [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17560369&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum described almost exclusively in the work of Ivan Tarassov]. Other lysine tRNAs are nuclear encoded-tRK2 which decodes UUU as lysine in the cytoplasm and mitochondrially encoded-tRK3 which decodes UUU for lysine in the mitochondria.		*lysine tRNA CUU (tRK1) encoded by nuclear genome and delivered to mitochondrial matrix [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17560369&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum described almost exclusively in the work of Ivan Tarassov]. Other lysine tRNAs are nuclear encoded-tRK2 which decodes UUU as lysine in the cytoplasm and mitochondrially encoded-tRK3 which decodes UUU for lysine in the mitochondria.
	*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=14576278&ordinalpos=21&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The mitochondrial proteome] includes ~750 proteins from nuclear genome, approx 1/2 (320/750) have mitochondrial pre-sequences and ~1/3 (225/750) have predicted transmembrane domains		*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=14576278&ordinalpos=21&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The mitochondrial proteome] includes ~750 proteins from nuclear genome, approx 1/2 (320/750) have mitochondrial pre-sequences and ~1/3 (225/750) have predicted transmembrane domains
-	*Current method for [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16118422&ordinalpos=9&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum yeast mt isolation]	+

	===Experimental checkpoints for regulated expression===		===Experimental checkpoints for regulated expression===
Line 46:		Line 46:
	*microarray induced/uninduced to look for effect of RNase in mt.		*microarray induced/uninduced to look for effect of RNase in mt.
	** Note: mt directed [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=39310 Barnase] leads to resp- cells when expressed at low level (YPEG from GALS promoter on pMT416GalS) and is toxic at high levels (SC-U/Gal), unless simultanously express mtBARSTAR inhibitor protein ([http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=20148763 "BARSTM"]) [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12928865&dopt=Abstract Mireau, Arnal and Fox in Mol Gen Genomics 2003 270:1-8]. Barnase is ssRNA ribonuclease whereas Rnt1p is dsRNA directed, and structure not seq dep.		** Note: mt directed [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=39310 Barnase] leads to resp- cells when expressed at low level (YPEG from GALS promoter on pMT416GalS) and is toxic at high levels (SC-U/Gal), unless simultanously express mtBARSTAR inhibitor protein ([http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=20148763 "BARSTM"]) [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12928865&dopt=Abstract Mireau, Arnal and Fox in Mol Gen Genomics 2003 270:1-8]. Barnase is ssRNA ribonuclease whereas Rnt1p is dsRNA directed, and structure not seq dep.
		+	* delete C-term nuclear localization signal on mt-directed copy
	====Part 2: guide RNAs in mt====		====Part 2: guide RNAs in mt====
		+	*Current method for [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16118422&ordinalpos=9&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum yeast mt isolation]
	====Gene regulation in mt====		====Gene regulation in mt====

Nkuldell at 13:42, 20 June 2007

Nkuldell — Wed, 20 Jun 2007 13:42:15 GMT

←Older revision		Revision as of 13:42, 20 June 2007
Line 34:		Line 34:

	====Cell components needed for moving guide RNA to mt====		====Cell components needed for moving guide RNA to mt====
-	*piggy back	+	*piggy back on existing import system
		+	*lysine tRNA CUU (tRK1) encoded by nuclear genome and delivered to mitochondrial matrix [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17560369&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum described almost exclusively in the work of Ivan Tarassov]. Other lysine tRNAs are nuclear encoded-tRK2 which decodes UUU as lysine in the cytoplasm and mitochondrially encoded-tRK3 which decodes UUU for lysine in the mitochondria.
		+	*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=14576278&ordinalpos=21&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The mitochondrial proteome] includes ~750 proteins from nuclear genome, approx 1/2 (320/750) have mitochondrial pre-sequences and ~1/3 (225/750) have predicted transmembrane domains
		+	*Current method for [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16118422&ordinalpos=9&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum yeast mt isolation]

	===Experimental checkpoints for regulated expression===		===Experimental checkpoints for regulated expression===

Nkuldell at 11:31, 20 June 2007

Nkuldell — Wed, 20 Jun 2007 11:31:02 GMT

←Older revision		Revision as of 11:31, 20 June 2007
Line 20:		Line 20:

	*RNT1 is not essential but null shows [http://www.molbiolcell.org/cgi/content/full/15/7/3015 defects in cell cycle progression and cell morphology]. This paper also demonstrates Rnt1p localization to the nucleus even when overexpressed.		*RNT1 is not essential but null shows [http://www.molbiolcell.org/cgi/content/full/15/7/3015 defects in cell cycle progression and cell morphology]. This paper also demonstrates Rnt1p localization to the nucleus even when overexpressed.
		+
		+	*processes 3' end of noncoding RNAs [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15337846&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum , e.g. in Henras et al. RNA (2004) 10: 1572]

	*rnt1 and ts rnt1 strain were examined by microarray to look for coding mRNAs that might be affected by mutation and the glucose-sensitive repressor Mig2 was [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4FB230R-W&_user=10&_coverDate=01%2F26%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7c687a52c573b01f935765ab90d629be#fig1 found to be upregulated in the mutants]		*rnt1 and ts rnt1 strain were examined by microarray to look for coding mRNAs that might be affected by mutation and the glucose-sensitive repressor Mig2 was [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4FB230R-W&_user=10&_coverDate=01%2F26%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7c687a52c573b01f935765ab90d629be#fig1 found to be upregulated in the mutants]

Nkuldell at 03:18, 20 June 2007

Nkuldell — Wed, 20 Jun 2007 03:18:06 GMT

←Older revision		Revision as of 03:18, 20 June 2007
Line 19:		Line 19:
	*[http://www.nature.com/emboj/journal/v23/n13/abs/7600260a.html EMBO 2004, NMR and x-ray xtal structure of dsRBD with N-term extension]		*[http://www.nature.com/emboj/journal/v23/n13/abs/7600260a.html EMBO 2004, NMR and x-ray xtal structure of dsRBD with N-term extension]

-	*RNT1 is not essential but null shows [http://www.molbiolcell.org/cgi/content/full/15/7/3015 defects in cell cycle progression and cell morphology]	+	*RNT1 is not essential but null shows [http://www.molbiolcell.org/cgi/content/full/15/7/3015 defects in cell cycle progression and cell morphology]. This paper also demonstrates Rnt1p localization to the nucleus even when overexpressed.

	*rnt1 and ts rnt1 strain were examined by microarray to look for coding mRNAs that might be affected by mutation and the glucose-sensitive repressor Mig2 was [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4FB230R-W&_user=10&_coverDate=01%2F26%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7c687a52c573b01f935765ab90d629be#fig1 found to be upregulated in the mutants]		*rnt1 and ts rnt1 strain were examined by microarray to look for coding mRNAs that might be affected by mutation and the glucose-sensitive repressor Mig2 was [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4FB230R-W&_user=10&_coverDate=01%2F26%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7c687a52c573b01f935765ab90d629be#fig1 found to be upregulated in the mutants]

Nkuldell at 03:13, 20 June 2007

Nkuldell — Wed, 20 Jun 2007 03:13:40 GMT

←Older revision		Revision as of 03:13, 20 June 2007
Line 13:		Line 13:
	[[Image:Macintosh HD-Users-nkuldell-Desktop-Rnt1pN-termXtal EMBO04.png\|thumb\| N-term Rnt1p struct. from EMBO 2004]]		[[Image:Macintosh HD-Users-nkuldell-Desktop-Rnt1pN-termXtal EMBO04.png\|thumb\| N-term Rnt1p struct. from EMBO 2004]]
	====Rnt1p====		====Rnt1p====
-	[http://www.ihop-net.org/UniPub/iHOP/gs/35375.html seq/struc link]	+	*[http://www.ihop-net.org/UniPub/iHOP/gs/35375.html seq/struc link]

-	Like bacterial RNaseIII, Rnt1p has two distinct domains and functions: N-terminal nuclease domain and C-terminal dsRBD [http://mcb.asm.org/cgi/content/full/20/4/1104?view=full&pmid=10648595 as well as non-bacterial kind of N-term extension for efficiency] <br>	+	*Like bacterial RNaseIII, Rnt1p has two distinct domains and functions: N-terminal nuclease domain and C-terminal dsRBD [http://mcb.asm.org/cgi/content/full/20/4/1104?view=full&pmid=10648595 as well as non-bacterial kind of N-term extension for efficiency] <br>

-	[http://www.nature.com/emboj/journal/v23/n13/abs/7600260a.html EMBO 2004, NMR and x-ray xtal structure of dsRBD with N-term extension]	+	*[http://www.nature.com/emboj/journal/v23/n13/abs/7600260a.html EMBO 2004, NMR and x-ray xtal structure of dsRBD with N-term extension]

-	RNT1 is not essential but null shows [http://www.molbiolcell.org/cgi/content/full/15/7/3015 defects in cell cycle progression and cell morphology]	+	*RNT1 is not essential but null shows [http://www.molbiolcell.org/cgi/content/full/15/7/3015 defects in cell cycle progression and cell morphology]
		+
		+	*rnt1 and ts rnt1 strain were examined by microarray to look for coding mRNAs that might be affected by mutation and the glucose-sensitive repressor Mig2 was [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4FB230R-W&_user=10&_coverDate=01%2F26%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7c687a52c573b01f935765ab90d629be#fig1 found to be upregulated in the mutants]

Nkuldell at 02:51, 20 June 2007

Nkuldell — Wed, 20 Jun 2007 02:51:01 GMT

←Older revision		Revision as of 02:51, 20 June 2007
Line 18:		Line 18:

	[http://www.nature.com/emboj/journal/v23/n13/abs/7600260a.html EMBO 2004, NMR and x-ray xtal structure of dsRBD with N-term extension]		[http://www.nature.com/emboj/journal/v23/n13/abs/7600260a.html EMBO 2004, NMR and x-ray xtal structure of dsRBD with N-term extension]
		+
		+	RNT1 is not essential but null shows [http://www.molbiolcell.org/cgi/content/full/15/7/3015 defects in cell cycle progression and cell morphology]

Nkuldell at 16:40, 18 June 2007

Nkuldell — Mon, 18 Jun 2007 16:40:03 GMT

←Older revision		Revision as of 16:40, 18 June 2007
Line 11:		Line 11:
	From Current Opinion in Structural Biology 2007 17:77 by [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS6-4MWGYGP-3&_user=501045&_coverDate=02%2F28%2F2007&_rdoc=13&_fmt=full&_orig=browse&_srch=doc-info(%23toc%236254%232007%23999829998%23644320%23FLA%23display%23Volume)&_cdi=6254&_sort=d&_docanchor=&view=c&_ct=21&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=8c18217696d86ae6eda73ed528ffcad7 James M Berger and Christoph W Müller] "A particularly interesting family of ribonucleases that specifically cleave double-stranded RNA serves as the topic of the review by MacRae and Doudna. The RNase III group of RNA-processing enzymes currently attracts broad attention, because two family members, Dicer and Drosha, are responsible for processing RNA transcripts into microRNA (miRNAs) and short interfering RNAs (siRNAs). RNase III proteins are often multifunctional or multisubunit assemblies, and can be classified based on domain composition. Class I RNase III enzymes function as dimers, in which the RNase domains also act as dimerization domains, whereas class II and III family members are monomeric, forming a functional RNase from the internal fusion of two class I RNase III monomers. Comparing RNase III enzymes across a wide range of species leads the authors to conclude that RNase III enzymes use accessory domains as determinants of substrate specificity. For Dicer and Drosha, these accessory domains are the PAZ domain and the additional DGCR8 protein, respectively. Substrate specificity and catalytic domains are spatially separated and, in some instances, it appears that the RNase can precisely measure the distance between the RNA recognition and cleavage sites by using an internal scaffold element that functions as a molecular ruler. Given the number of different types of small RNAs and their importance in gene regulation and other cellular processes, there are sure to be many fundamental insights that will arise from the continued study of this essential protein family."		From Current Opinion in Structural Biology 2007 17:77 by [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS6-4MWGYGP-3&_user=501045&_coverDate=02%2F28%2F2007&_rdoc=13&_fmt=full&_orig=browse&_srch=doc-info(%23toc%236254%232007%23999829998%23644320%23FLA%23display%23Volume)&_cdi=6254&_sort=d&_docanchor=&view=c&_ct=21&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=8c18217696d86ae6eda73ed528ffcad7 James M Berger and Christoph W Müller] "A particularly interesting family of ribonucleases that specifically cleave double-stranded RNA serves as the topic of the review by MacRae and Doudna. The RNase III group of RNA-processing enzymes currently attracts broad attention, because two family members, Dicer and Drosha, are responsible for processing RNA transcripts into microRNA (miRNAs) and short interfering RNAs (siRNAs). RNase III proteins are often multifunctional or multisubunit assemblies, and can be classified based on domain composition. Class I RNase III enzymes function as dimers, in which the RNase domains also act as dimerization domains, whereas class II and III family members are monomeric, forming a functional RNase from the internal fusion of two class I RNase III monomers. Comparing RNase III enzymes across a wide range of species leads the authors to conclude that RNase III enzymes use accessory domains as determinants of substrate specificity. For Dicer and Drosha, these accessory domains are the PAZ domain and the additional DGCR8 protein, respectively. Substrate specificity and catalytic domains are spatially separated and, in some instances, it appears that the RNase can precisely measure the distance between the RNA recognition and cleavage sites by using an internal scaffold element that functions as a molecular ruler. Given the number of different types of small RNAs and their importance in gene regulation and other cellular processes, there are sure to be many fundamental insights that will arise from the continued study of this essential protein family."
	====S. cerevisiae RNases====		====S. cerevisiae RNases====
-	====[http://www.ihop-net.org/UniPub/iHOP/gs/35375.html ~~Rnt1p,~~ seq/~~struct~~ link]~~====~~	+	[[Image:Macintosh HD-Users-nkuldell-Desktop-Rnt1pN-termXtal EMBO04.png\|thumb\| N-term Rnt1p struct. from EMBO 2004]]
-	Like bacterial RNaseIII, Rnt1p has two distinct domains and functions: N-terminal nuclease domain and C-terminal dsRBD [http://mcb.asm.org/cgi/content/full/20/4/1104?view=full&pmid=10648595 as well as non-bacterial kind of N-term extension for efficiency]	+	====Rnt1p====
		+	[http://www.ihop-net.org/UniPub/iHOP/gs/35375.html seq/struc link]
		+
		+	Like bacterial RNaseIII, Rnt1p has two distinct domains and functions: N-terminal nuclease domain and C-terminal dsRBD [http://mcb.asm.org/cgi/content/full/20/4/1104?view=full&pmid=10648595 as well as non-bacterial kind of N-term extension for efficiency] <br>
		+
		+	[http://www.nature.com/emboj/journal/v23/n13/abs/7600260a.html EMBO 2004, NMR and x-ray xtal structure of dsRBD with N-term extension]
		+
		+
		+

	===Part 2: Guide RNAs===		===Part 2: Guide RNAs===
		+	[[Image:Macintosh HD-Users-nkuldell-Desktop-RNARnt1pCleavageInVitro.png\|thumb\| RNAs that can be cleaved by Rnt1p in vitro[http://www.plosone.org/article/fetchArticle.action;jsessionid=52A54F60AD8F8DBEB598BBCBDBD16464?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000472 PLoS one 2007]]]
	====Structural requirements for guide RNAs====		====Structural requirements for guide RNAs====
-	In vitro requirements shown in ~~[[Image:Macintosh HD-Users-nkuldell-Desktop-RNARnt1pCleavageInVitro.png\|thumb\| RNAs that can be cleaved by Rnt1p in vitro~~[http://www.plosone.org/article/fetchArticle.action;jsessionid=52A54F60AD8F8DBEB598BBCBDBD16464?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000472 PLoS one 2007]]]	+	In vitro requirements shown in [http://www.plosone.org/article/fetchArticle.action;jsessionid=52A54F60AD8F8DBEB598BBCBDBD16464?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000472 PLoS one 2007]

	====Cell components needed for moving guide RNA to mt====		====Cell components needed for moving guide RNA to mt====

Nkuldell at 10:14, 18 June 2007

Nkuldell — Mon, 18 Jun 2007 10:14:28 GMT

←Older revision		Revision as of 10:14, 18 June 2007
Line 7:		Line 7:

	===Part 1: [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=rnt1 Rnt1p]===		===Part 1: [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=rnt1 Rnt1p]===
-	[[Image:Macintosh HD-Users-nkuldell-Desktop-Rnt1p dsRBD snR47RNAhairpin.png\|thumb\| Rnt1p dsRBD in complex with snR47 RNA hairpin]]	+	[[Image:Macintosh HD-Users-nkuldell-Desktop-Rnt1p dsRBD snR47RNAhairpin.png\|thumb\| Rnt1p dsRBD in complex with snR47 RNA hairpin[http://structure.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=27928 Feigon PNAS 1997]]]
	====Gen'l info about RNases families====		====Gen'l info about RNases families====
	From Current Opinion in Structural Biology 2007 17:77 by [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS6-4MWGYGP-3&_user=501045&_coverDate=02%2F28%2F2007&_rdoc=13&_fmt=full&_orig=browse&_srch=doc-info(%23toc%236254%232007%23999829998%23644320%23FLA%23display%23Volume)&_cdi=6254&_sort=d&_docanchor=&view=c&_ct=21&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=8c18217696d86ae6eda73ed528ffcad7 James M Berger and Christoph W Müller] "A particularly interesting family of ribonucleases that specifically cleave double-stranded RNA serves as the topic of the review by MacRae and Doudna. The RNase III group of RNA-processing enzymes currently attracts broad attention, because two family members, Dicer and Drosha, are responsible for processing RNA transcripts into microRNA (miRNAs) and short interfering RNAs (siRNAs). RNase III proteins are often multifunctional or multisubunit assemblies, and can be classified based on domain composition. Class I RNase III enzymes function as dimers, in which the RNase domains also act as dimerization domains, whereas class II and III family members are monomeric, forming a functional RNase from the internal fusion of two class I RNase III monomers. Comparing RNase III enzymes across a wide range of species leads the authors to conclude that RNase III enzymes use accessory domains as determinants of substrate specificity. For Dicer and Drosha, these accessory domains are the PAZ domain and the additional DGCR8 protein, respectively. Substrate specificity and catalytic domains are spatially separated and, in some instances, it appears that the RNase can precisely measure the distance between the RNA recognition and cleavage sites by using an internal scaffold element that functions as a molecular ruler. Given the number of different types of small RNAs and their importance in gene regulation and other cellular processes, there are sure to be many fundamental insights that will arise from the continued study of this essential protein family."		From Current Opinion in Structural Biology 2007 17:77 by [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS6-4MWGYGP-3&_user=501045&_coverDate=02%2F28%2F2007&_rdoc=13&_fmt=full&_orig=browse&_srch=doc-info(%23toc%236254%232007%23999829998%23644320%23FLA%23display%23Volume)&_cdi=6254&_sort=d&_docanchor=&view=c&_ct=21&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=8c18217696d86ae6eda73ed528ffcad7 James M Berger and Christoph W Müller] "A particularly interesting family of ribonucleases that specifically cleave double-stranded RNA serves as the topic of the review by MacRae and Doudna. The RNase III group of RNA-processing enzymes currently attracts broad attention, because two family members, Dicer and Drosha, are responsible for processing RNA transcripts into microRNA (miRNAs) and short interfering RNAs (siRNAs). RNase III proteins are often multifunctional or multisubunit assemblies, and can be classified based on domain composition. Class I RNase III enzymes function as dimers, in which the RNase domains also act as dimerization domains, whereas class II and III family members are monomeric, forming a functional RNase from the internal fusion of two class I RNase III monomers. Comparing RNase III enzymes across a wide range of species leads the authors to conclude that RNase III enzymes use accessory domains as determinants of substrate specificity. For Dicer and Drosha, these accessory domains are the PAZ domain and the additional DGCR8 protein, respectively. Substrate specificity and catalytic domains are spatially separated and, in some instances, it appears that the RNase can precisely measure the distance between the RNA recognition and cleavage sites by using an internal scaffold element that functions as a molecular ruler. Given the number of different types of small RNAs and their importance in gene regulation and other cellular processes, there are sure to be many fundamental insights that will arise from the continued study of this essential protein family."
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	===Part 2: Guide RNAs===		===Part 2: Guide RNAs===
	====Structural requirements for guide RNAs====		====Structural requirements for guide RNAs====
-	In vitro requirements shown in [[Image:Macintosh HD-Users-nkuldell-Desktop-RNARnt1pCleavageInVitro.png\|thumb\| RNAs that can be cleaved by Rnt1p in vitro]][http://www.plosone.org/article/fetchArticle.action;jsessionid=52A54F60AD8F8DBEB598BBCBDBD16464?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000472 PLoS one 2007]	+	In vitro requirements shown in [[Image:Macintosh HD-Users-nkuldell-Desktop-RNARnt1pCleavageInVitro.png\|thumb\| RNAs that can be cleaved by Rnt1p in vitro[http://www.plosone.org/article/fetchArticle.action;jsessionid=52A54F60AD8F8DBEB598BBCBDBD16464?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000472 PLoS one 2007]]]

	====Cell components needed for moving guide RNA to mt====		====Cell components needed for moving guide RNA to mt====