Jump to content

DCL1: Difference between revisions

Add links
From Wikipedia, the free encyclopedia
Browse history interactively
← Previous editNext edit →
Content deleted Content added
VisualWikitext
m Sdrqaz moved page Dcl to DCL1 over redirect: Requested by Tevildo at WP:RM/TR: Correct name for gene (upper-case with number). Lower-case version without number is not mentioned on the page or supported in the references. Move over redirect.
AimerD (talk | contribs)
30 edits
Protein structure, function description and recent-literature review as well as an extension beyond Arabidopsis focus
Line 1: Line 1:
{{Infobox nonhuman protein
{{Infobox nonhuman protein
| Name = Endoribonuclease Dicer homolog 1
| Name = Endoribonuclease Dicer homolog 1
| image = https://cdn.rcsb.org/images/structures/7eld_assembly-1.jpeg
| image =
| width =
| width =
| caption =
| caption =
Line 7: Line 7:
| TaxID = 3702
| TaxID = 3702
| Symbol = DCL1
| Symbol = DCL1
| AltSymbols =
| AltSymbols = AT1G01040
| ATC_prefix =
| ATC_prefix =
| ATC_suffix =
| ATC_suffix =
Line 16: Line 16:
| EntrezGene =
| EntrezGene =
| HomoloGene =
| HomoloGene =
| PDB = 2LRS
| PDB = 7ELD
| RefSeqmRNA =
| RefSeqmRNA =
| RefSeqProtein =
| RefSeqProtein =
| UniProt = Q9SP32
| UniProt = Q9SP32
| ECnumber =
| ECnumber = EC:3.1.26
| Chromosome =
| Chromosome = 1
| EntrezChromosome =
| EntrezChromosome =
| GenLoc_start =
| GenLoc_start = 23416
| GenLoc_end =
| GenLoc_end = 31120
}}
}}
[[File:Cartoon representation of Arabidopsis DCL1 in complex with pri-miRNA 166f (elucidated by Cryo-EM in Wei X. et al. Nat. Plants. 2021).gif|alt=Cartoon representation of Arabidopsis DCL1 in complex with pri-miRNA 166f. The figure shows the single chain of DCL1 in light purple catalyzing the cleavage of pri-miRNA-166f into pre-miRNA-166f, before one more cleavage step to finally release miRNA-166f.|thumb|Cartoon representation of Arabidopsis DCL1 in complex with pri-miRNA 166f (elucidated by Cryo-EM in Wei X. et al. Nat. Plants. 2021).<ref name=":0">{{Cite journal |last=Wei |first=Xiaobin |last2=Ke |first2=Huanhuan |last3=Wen |first3=Aijia |last4=Gao |first4=Bo |last5=Shi |first5=Jing |last6=Feng |first6=Yu |date=2021-10 |title=Structural basis of microRNA processing by Dicer-like 1 |url=https://pubmed.ncbi.nlm.nih.gov/34593993 |journal=Nature Plants |volume=7 |issue=10 |pages=1389–1396 |doi=10.1038/s41477-021-01000-1 |issn=2055-0278 |pmid=34593993}}</ref> MicroRNAs (miRNAs) in plants are processed from hairpin-containing primary transcripts (pri-miRNA) into miRNAs by a single protein, DCL1, which also process the intermediary step pri-mIRNA to pre-miRNAs or precursor-miRNAs, a double strand palindromic structure typically call hairpin. The figure shows the single chain of DCL1 in light purple catalyzing the cleavage of pri-miRNA-166f into pre-miRNA-166f, before one more cleavage step to finally release miRNA-166f. ]]
'''DCL1''' (an abbreviation of '''Dicer-like 1''') is a [[gene]] in [[plant]]s that codes for the DCL1 [[protein]], a [[ribonuclease III]] [[enzyme]] involved in processing [[double-stranded RNA]] (dsRNA) and [[microRNA]] (miRNA).<ref name="schauer" /> Although DCL1, also called Endoribonuclease Dicer homolog 1, is named for its [[homology (biology)|homology]] with the [[metazoan]] protein [[Dicer]], its role in miRNA biogenesis is somewhat different, due to substantial differences in miRNA maturation processes between plants and animals<ref name="axtell" />, as well due to additional downstream plant-specific pathways, where DCL1 paralogs like DCL4 participate, such [[Trans-acting siRNA]] biogenesis.


=== DCL1 function ===
'''DCL1''' (an abbreviation of '''Dicer-like 1''') is a [[gene]] in [[plant]]s that codes for the DCL1 [[protein]], a [[ribonuclease III]] [[enzyme]] involved in processing [[microRNA]] (miRNA).<ref name=schauer /> Although DCL1 is named for its [[homology (biology)|homology]] with the [[metazoan]] protein [[Dicer]], its role in miRNA biogenesis is somewhat different, due to substantial differences in miRNA maturation processes between plants and animals.<ref name=axtell /> Unlike Dicer, DCL1 is localized to the [[cell nucleus]], where it initiates miRNA processing as the catalytic component of the so-called Dicing complex, which also contains [[HYL1]], a [[double-stranded RNA]] [[RNA-binding protein|binding protein]], and a [[zinc-finger protein]] known as SE or [[SERRATE]]. Within the nucleus, Dicing complexes co-localize in Dicing bodies or D-bodies. In plants, DCL1 is responsible both for processing a [[primary miRNA]] to a pre-miRNA, and for then processing the pre-miRNA to a mature miRNA.<ref name=fang /> In animals, the equivalents of these two steps are carried out by different proteins; pri-miRNA processing takes place in the nucleus by the ribonuclease [[Drosha]] as part of the [[Microprocessor complex]], and processing to a mature miRNA takes place in the [[cytoplasm]] by [[Dicer]] to yield a mature miRNA.<ref name=axtell />
DCL1 is localized exclusively in the plant [[cell nucleus]] <ref name=":1">{{Cite journal |last=Tomassi |first=Ariel H. |last2=Re |first2=Delfina A. |last3=Romani |first3=Facundo |last4=Cambiagno |first4=Damian A. |last5=Gonzalo |first5=Lucía |last6=Moreno |first6=Javier E. |last7=Arce |first7=Agustin L. |last8=Manavella |first8=Pablo A. |date=2020-07-07 |title=The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity |url=https://doi.org/10.1104/pp.20.00258 |journal=Plant Physiology |volume=184 |issue=1 |pages=316–329 |doi=10.1104/pp.20.00258 |issn=0032-0889 |pmc=PMC7479909 |pmid=32636339}}</ref>, together with the [[double-stranded RNA]] [[RNA-binding protein|binding protein]] HYPONASTIC LEAVES1 ([[HYL1]]), CTD-PHOSPHATASE-LIKE1 (CPL1) and the zinc finger protein [[SERRATE]] (SE), form nuclear dicing bodies or D-bodies. In these membraneless organelles, pri-miRNAs are recognized and processes into pre-miRNAs and subsecuently into mature miRNA duplexes, by the binding of additional proteins such as CONSTITUTIVE ALTERATIONS IN THE SMALL RNAS PATHWAYS9 (CARP9)<ref name=":1" />. In plants, DCL1 is responsible both for processing a [[primary miRNA]] to a pre-miRNA, and for then processing the pre-miRNA to a mature miRNA.<ref name="fang" /><ref name=":0" /> In animals, the equivalents of these two steps are carried out by different proteins; First, pri-miRNA processing takes place in the nucleus by the ribonuclease [[Drosha]] as part of the [[Microprocessor complex]]. Second and finally processing to a mature miRNA takes place in the [[cytoplasm]] by [[Dicer]] to yield a mature miRNA.<ref name="axtell" />


=== PAZ domain plasticity ===
Although DCL1 is responsible for the majority of the miRNA processing in plants, most plants contain an additional three members of the same family ([[DCL2]], [[DCL3]], [[DCL4]]) with related roles in RNA processing.<ref name=parent /><ref name=nagano />
In animals, hairpin-containing primary transcripts (pri-miRNAs) are cleaved by [[Drosha]] to generate precursor-miRNAs, a double strand palindromic structure typically call hairpin pre-miRNAs, which are subsequently cleaved by Dicer to generate mature [[MicroRNA|miRNAs]]. Instead of being cleaved by two different enzymes, both cleavages in plants are performed by Dicer-like 1 (DCL1), despite of a similar domain architecuture between both homologgous enzymes.<ref name=":0" /> Recent single-particle cryo-electron microscopy structures of both complexs of dsRNA structures ([https://www.rcsb.org/structure/7ELD pri-RNA] and [https://www.rcsb.org/structure/7ELE pre-miRNA]) as ligand of Arabidopsis DCL1, in cleavege-competent state, suggest that PAZ domain plasticity allow its to get involved in pri-miRNA and pre-miRNA recognition, posibilited by an internal loop binding groove of this protein domain, which serves as an engine that transfers the substrate between two sequential cleavage events.<ref name=":0" />
[[File:DCL1-HYL-SE-CARP9_scaffolding_and_miRNA_maturation_in_plants.jpg|thumb|A model for DCL1-HYL-SE scaffolding for the pri-miRNA to pre-miRNA maturation process, as well for the pre-miRNA to miRNA maturation step helped by CARP9 binding into the DICER-Complex <ref>{{Cite journal |last=Tomassi |first=Ariel H. |last2=Re |first2=Delfina A. |last3=Romani |first3=Facundo |last4=Cambiagno |first4=Damian A. |last5=Gonzalo |first5=Lucía |last6=Moreno |first6=Javier E. |last7=Arce |first7=Agustin L. |last8=Manavella |first8=Pablo A. |date=2020-07-07 |title=The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity |url=https://doi.org/10.1104/pp.20.00258 |journal=Plant Physiology |volume=184 |issue=1 |pages=316–329 |doi=10.1104/pp.20.00258 |issn=0032-0889 |pmc=PMC7479909 |pmid=32636339}}</ref>]]

== Other Dicer-Like proteins ==


Although DCL1 is responsible for the majority of the miRNA processing in plants, most plants contain an additional set of DCLs proteins with related roles in RNA processing,<ref name="parent" /> the number of additional members of the same family depends on the plant familiy. For instance, in [[Brassicaceae]] there are 5 additional [[paralog]] genes to DLC1, [[DCL2]], [[DCL3]], [[DCL4]] and two RNASE II-LIKE genes RTL1 and RTL2;<ref>{{Cite journal |last=Belal |first=Mohammad A. |last2=Ezzat |first2=Mohamed |last3=Zhang |first3=Yuanqiang |last4=Xu |first4=Ziang |last5=Cao |first5=Yunpeng |last6=Han |first6=Yuepeng |date=2022 |title=Integrative Analysis of the DICER-like (DCL) Genes From Peach (Prunus persica): A Critical Role in Response to Drought Stress |url=https://www.frontiersin.org/articles/10.3389/fevo.2022.923166 |journal=Frontiers in Ecology and Evolution |volume=10 |doi=10.3389/fevo.2022.923166 |issn=2296-701X}}</ref><ref name="nagano" /> Howeversome dicots such as ''[[Populus trichocarpa]]''<ref>{{Cite journal |last=Moura |first=Marianna O. |last2=Fausto |first2=Anna Karoline S. |last3=Fanelli |first3=Amanda |last4=Guedes |first4=Fernanda A. de F. |last5=Silva |first5=Tatiane da F. |last6=Romanel |first6=Elisson |last7=Vaslin |first7=Maite F. S. |date=2019-11-15 |title=Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars |url=https://doi.org/10.1186/s12870-019-2112-4 |journal=BMC Plant Biology |volume=19 |issue=1 |pages=503 |doi=10.1186/s12870-019-2112-4 |issn=1471-2229 |pmc=PMC6858778 |pmid=31729948}}</ref> as well the majority of monocots plants have five to six DCLs, where DCL2 and DCL3 suffered an additional duplication into the genes DCL2a and DCL2. DCL3's duplication is monocot-specifict, generating the genes DCL3a and DCL3b, also called DCL3 and [[DCL5]] respectively.<ref>{{Cite web |url=https://academic.oup.com/nar/article/50/8/4669/6563722 |access-date=2022-11-06 |website=academic.oup.com |doi=10.1093/nar/gkac223 |pmc=PMC9071481 |pmid=35380679}}</ref><ref>{{Cite journal |last=Belal |first=Mohammad A. |last2=Ezzat |first2=Mohamed |last3=Zhang |first3=Yuanqiang |last4=Xu |first4=Ziang |last5=Cao |first5=Yunpeng |last6=Han |first6=Yuepeng |date=2022 |title=Integrative Analysis of the DICER-like (DCL) Genes From Peach (Prunus persica): A Critical Role in Response to Drought Stress |url=https://www.frontiersin.org/articles/10.3389/fevo.2022.923166 |journal=Frontiers in Ecology and Evolution |volume=10 |doi=10.3389/fevo.2022.923166 |issn=2296-701X}}</ref>


== References ==
== References ==
Line 44: Line 54:


{{protein-stub}}
{{protein-stub}}
{{DEFAULTSORT:Dicer-like 1 (DCL1)}}

Revision as of 18:10, 6 November 2022

Endoribonuclease Dicer homolog 1
Identifiers
OrganismArabidopsis thaliana
SymbolDCL1
Alt. symbolsAT1G01040
PDB7ELD
UniProtQ9SP32
Other data
EC numberEC:3.1.26
Chromosome1: 0.02 - 0.03 Mb
Search for
StructuresSwiss-model
DomainsInterPro
Cartoon representation of Arabidopsis DCL1 in complex with pri-miRNA 166f. The figure shows the single chain of DCL1 in light purple catalyzing the cleavage of pri-miRNA-166f into pre-miRNA-166f, before one more cleavage step to finally release miRNA-166f.
Cartoon representation of Arabidopsis DCL1 in complex with pri-miRNA 166f (elucidated by Cryo-EM in Wei X. et al. Nat. Plants. 2021).[1] MicroRNAs (miRNAs) in plants are processed from hairpin-containing primary transcripts (pri-miRNA) into miRNAs by a single protein, DCL1, which also process the intermediary step pri-mIRNA to pre-miRNAs or precursor-miRNAs, a double strand palindromic structure typically call hairpin. The figure shows the single chain of DCL1 in light purple catalyzing the cleavage of pri-miRNA-166f into pre-miRNA-166f, before one more cleavage step to finally release miRNA-166f.

DCL1 (an abbreviation of Dicer-like 1) is a gene in plants that codes for the DCL1 protein, a ribonuclease III enzyme involved in processing double-stranded RNA (dsRNA) and microRNA (miRNA).[2] Although DCL1, also called Endoribonuclease Dicer homolog 1, is named for its homology with the metazoan protein Dicer, its role in miRNA biogenesis is somewhat different, due to substantial differences in miRNA maturation processes between plants and animals[3], as well due to additional downstream plant-specific pathways, where DCL1 paralogs like DCL4 participate, such Trans-acting siRNA biogenesis.

DCL1 function

DCL1 is localized exclusively in the plant cell nucleus [4], together with the double-stranded RNA binding protein HYPONASTIC LEAVES1 (HYL1), CTD-PHOSPHATASE-LIKE1 (CPL1) and the zinc finger protein SERRATE (SE), form nuclear dicing bodies or D-bodies. In these membraneless organelles, pri-miRNAs are recognized and processes into pre-miRNAs and subsecuently into mature miRNA duplexes, by the binding of additional proteins such as CONSTITUTIVE ALTERATIONS IN THE SMALL RNAS PATHWAYS9 (CARP9)[4]. In plants, DCL1 is responsible both for processing a primary miRNA to a pre-miRNA, and for then processing the pre-miRNA to a mature miRNA.[5][1] In animals, the equivalents of these two steps are carried out by different proteins; First, pri-miRNA processing takes place in the nucleus by the ribonuclease Drosha as part of the Microprocessor complex. Second and finally processing to a mature miRNA takes place in the cytoplasm by Dicer to yield a mature miRNA.[3]

PAZ domain plasticity

In animals, hairpin-containing primary transcripts (pri-miRNAs) are cleaved by Drosha to generate precursor-miRNAs, a double strand palindromic structure typically call hairpin pre-miRNAs, which are subsequently cleaved by Dicer to generate mature miRNAs. Instead of being cleaved by two different enzymes, both cleavages in plants are performed by Dicer-like 1 (DCL1), despite of a similar domain architecuture between both homologgous enzymes.[1] Recent single-particle cryo-electron microscopy structures of both complexs of dsRNA structures (pri-RNA and pre-miRNA) as ligand of Arabidopsis DCL1, in cleavege-competent state, suggest that PAZ domain plasticity allow its to get involved in pri-miRNA and pre-miRNA recognition, posibilited by an internal loop binding groove of this protein domain, which serves as an engine that transfers the substrate between two sequential cleavage events.[1]

A model for DCL1-HYL-SE scaffolding for the pri-miRNA to pre-miRNA maturation process, as well for the pre-miRNA to miRNA maturation step helped by CARP9 binding into the DICER-Complex [6]

Other Dicer-Like proteins

Although DCL1 is responsible for the majority of the miRNA processing in plants, most plants contain an additional set of DCLs proteins with related roles in RNA processing,[7] the number of additional members of the same family depends on the plant familiy. For instance, in Brassicaceae there are 5 additional paralog genes to DLC1, DCL2, DCL3, DCL4 and two RNASE II-LIKE genes RTL1 and RTL2;[8][9] Howeversome dicots such as Populus trichocarpa[10] as well the majority of monocots plants have five to six DCLs, where DCL2 and DCL3 suffered an additional duplication into the genes DCL2a and DCL2. DCL3's duplication is monocot-specifict, generating the genes DCL3a and DCL3b, also called DCL3 and DCL5 respectively.[11][12]

References

  1. ^ a b c d Wei, Xiaobin; Ke, Huanhuan; Wen, Aijia; Gao, Bo; Shi, Jing; Feng, Yu (2021-10). "Structural basis of microRNA processing by Dicer-like 1". Nature Plants. 7 (10): 1389–1396. doi:10.1038/s41477-021-01000-1. ISSN 2055-0278. PMID 34593993. {{cite journal}}: Check date values in: |date= (help)
  2. ^ Schauer SE, Jacobsen SE, Meinke DW, Ray A (November 2002). "DICER-LIKE1: blind men and elephants in Arabidopsis development". Trends in Plant Science. 7 (11): 487–91. doi:10.1016/s1360-1385(02)02355-5. PMID 12417148.
  3. ^ a b Axtell MJ, Westholm JO, Lai EC (2011). "Vive la différence: biogenesis and evolution of microRNAs in plants and animals". Genome Biology. 12 (4): 221. doi:10.1186/gb-2011-12-4-221. PMC 3218855. PMID 21554756.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  4. ^ a b Tomassi, Ariel H.; Re, Delfina A.; Romani, Facundo; Cambiagno, Damian A.; Gonzalo, Lucía; Moreno, Javier E.; Arce, Agustin L.; Manavella, Pablo A. (2020-07-07). "The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity". Plant Physiology. 184 (1): 316–329. doi:10.1104/pp.20.00258. ISSN 0032-0889. PMC 7479909. PMID 32636339.{{cite journal}}: CS1 maint: PMC format (link)
  5. ^ Fang X, Cui Y, Li Y, Qi Y (June 2015). "Transcription and processing of primary microRNAs are coupled by Elongator complex in Arabidopsis". Nature Plants. 1 (6): 15075. doi:10.1038/nplants.2015.75. PMID 27250010.
  6. ^ Tomassi, Ariel H.; Re, Delfina A.; Romani, Facundo; Cambiagno, Damian A.; Gonzalo, Lucía; Moreno, Javier E.; Arce, Agustin L.; Manavella, Pablo A. (2020-07-07). "The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity". Plant Physiology. 184 (1): 316–329. doi:10.1104/pp.20.00258. ISSN 0032-0889. PMC 7479909. PMID 32636339.{{cite journal}}: CS1 maint: PMC format (link)
  7. ^ Parent JS, Bouteiller N, Elmayan T, Vaucheret H (January 2015). "Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing". The Plant Journal. 81 (2): 223–32. doi:10.1111/tpj.12720. PMID 25376953.
  8. ^ Belal, Mohammad A.; Ezzat, Mohamed; Zhang, Yuanqiang; Xu, Ziang; Cao, Yunpeng; Han, Yuepeng (2022). "Integrative Analysis of the DICER-like (DCL) Genes From Peach (Prunus persica): A Critical Role in Response to Drought Stress". Frontiers in Ecology and Evolution. 10. doi:10.3389/fevo.2022.923166. ISSN 2296-701X.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  9. ^ Nagano H, Fukudome A, Hiraguri A, Moriyama H, Fukuhara T (February 2014). "Distinct substrate specificities of Arabidopsis DCL3 and DCL4". Nucleic Acids Research. 42 (3): 1845–56. doi:10.1093/nar/gkt1077. PMC 3919572. PMID 24214956.
  10. ^ Moura, Marianna O.; Fausto, Anna Karoline S.; Fanelli, Amanda; Guedes, Fernanda A. de F.; Silva, Tatiane da F.; Romanel, Elisson; Vaslin, Maite F. S. (2019-11-15). "Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars". BMC Plant Biology. 19 (1): 503. doi:10.1186/s12870-019-2112-4. ISSN 1471-2229. PMC 6858778. PMID 31729948.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  11. ^ academic.oup.com. doi:10.1093/nar/gkac223. PMC 9071481. PMID 35380679 https://academic.oup.com/nar/article/50/8/4669/6563722. Retrieved 2022-11-06. {{cite web}}: Missing or empty |title= (help)CS1 maint: PMC format (link)
  12. ^ Belal, Mohammad A.; Ezzat, Mohamed; Zhang, Yuanqiang; Xu, Ziang; Cao, Yunpeng; Han, Yuepeng (2022). "Integrative Analysis of the DICER-like (DCL) Genes From Peach (Prunus persica): A Critical Role in Response to Drought Stress". Frontiers in Ecology and Evolution. 10. doi:10.3389/fevo.2022.923166. ISSN 2296-701X.{{cite journal}}: CS1 maint: unflagged free DOI (link)
Stub icon

This protein-related article is a stub. You can help Wikipedia by expanding it.

Retrieved from "https://en.wikipedia.org/w/index.php?title=DCL1&oldid=1120379502"