DHX38
Pre-iRNK-faktor prerade ATP-ovisne RNK helikaze PRP16 je enzim koji je kod ljudi kodiran genom DHX38.[5][6][7] Gross (2018) mapirao je gen DHX38 u hromosom 16, sekvenca q22.2, na osnovu poravnanja DHX38 sekvence (GenBank BC004235) sa genomskom sekvencom (GRCh38).
Prerada pre-iRNK zahtijeva stvaranje niza splajsosomnih kompleksa koji se okupljaju redom E, A, B i C. U C kompleksu postoje dva koraka katalitske prerade. DHX38 je faktor prerade, bitan za katalitički korak II.[8]
DEAD kutija proteina, koju karakterizira konzervirani motiv Asp-Glu-Ala-Asp (DEAD), obuhvata navodne RNK-helikaze. Uključeni su u brojne ćelijske procese promjene sekundarne strukture RNK, poput inicijacije translacije, jedare, mitohondrijske ribosomne prerade i prerade splajsosoma. Na osnovu njihovih obrazaca raspodjele, vjeruje se da su neki članovi ove porodice uključeni u embriogenezu, spermatogenezu i ćelijski rast i diobu. Protein kodiran od ovog gena član je porodice faktora prerade RNK DEAD/H. Ovaj protein sličniji je kvaščevom Prp16 više nego ostali članovi ove porodice. To je ATPaza , bitna je za katalitski korak II u procesu prerade pre-iRNK.[7]
Aminokiselinska sekvenca
[uredi | uredi izvor]Dužina polipeptidnog lanca je 1.227 aminokiselina, a molekulska težina 140.503 Da.[9].
| 10 | 20 | 30 | 40 | 50 | ||||
|---|---|---|---|---|---|---|---|---|
| MGDTSEDASI | HRLEGTDLDC | QVGGLICKSK | SAASEQHVFK | APAPRPSLLG | ||||
| LDLLASLKRR | EREEKDDGED | KKKSKVSSYK | DWEESKDDQK | DAEEEGGDQA | ||||
| GQNIRKDRHY | RSARVETPSH | PGGVSEEFWE | RSRQRERERR | EHGVYASSKE | ||||
| EKDWKKEKSR | DRDYDRKRDR | DERDRSRHSS | RSERDGGSER | SSRRNEPESP | ||||
| RHRPKDAATP | SRSTWEEEDS | GYGSSRRSQW | ESPSPTPSYR | DSERSHRLST | ||||
| RDRDRSVRGK | YSDDTPLPTP | SYKYNEWADD | RRHLGSTPRL | SRGRGRREEG | ||||
| EEGISFDTEE | ERQQWEDDQR | QADRDWYMMD | EGYDEFHNPL | AYSSEDYVRR | ||||
| REQHLHKQKQ | KRISAQRRQI | NEDNERWETN | RMLTSGVVHR | LEVDEDFEED | ||||
| NAAKVHLMVH | NLVPPFLDGR | IVFTKQPEPV | IPVKDATSDL | AIIARKGSQT | ||||
| VRKHREQKER | KKAQHKHWEL | AGTKLGDIMG | VKKEEEPDKA | VTEDGKVDYR | ||||
| TEQKFADHMK | RKSEASSEFA | KKKSILEQRQ | YLPIFAVQQE | LLTIIRDNSI | ||||
| VIVVGETGSG | KTTQLTQYLH | EDGYTDYGMI | GCTQPRRVAA | MSVAKRVSEE | ||||
| MGGNLGEEVG | YAIRFEDCTS | ENTLIKYMTD | GILLRESLRE | ADLDHYSAII | ||||
| MDEAHERSLN | TDVLFGLLRE | VVARRSDLKL | IVTSATMDAE | KFAAFFGNVP | ||||
| IFHIPGRTFP | VDILFSKTPQ | EDYVEAAVKQ | SLQVHLSGAP | GDILIFMPGQ | ||||
| EDIEVTSDQI | VEHLEELENA | PALAVLPIYS | QLPSDLQAKI | FQKAPDGVRK | ||||
| CIVATNIAET | SLTVDGIMFV | IDSGYCKLKV | FNPRIGMDAL | QIYPISQANA | ||||
| NQRSGRAGRT | GPGQCFRLYT | QSAYKNELLT | TTVPEIQRTN | LANVVLLLKS | ||||
| LGVQDLLQFH | FMDPPPEDNM | LNSMYQLWIL | GALDNTGGLT | STGRLMVEFP | ||||
| LDPALSKMLI | VSCDMGCSSE | ILLIVSMLSV | PAIFYRPKGR | EEESDQIREK | ||||
| FAVPESDHLT | YLNVYLQWKN | NNYSTIWCND | HFIHAKAMRK | VREVRAQLKD | ||||
| IMVQQRMSLA | SCGTDWDIVR | KCICAAYFHQ | AAKLKGIGEY | VNIRTGMPCH | ||||
| LHPTSSLFGM | GYTPDYIVYH | ELVMTTKEYM | QCVTAVDGEW | LAELGPMFYS | ||||
| VKQAGKSRQE | NRRRAKEEAS | AMEEEMALAE | EQLRARRQEQ | EKRSPLGSVR | ||||
| STKIYTPGRK | EQGEPMTPRR | TPARFGL |
- Simboli
C: Cistein
D: Asparaginska kiselina
E: Glutaminska kiselina
F: Fenilalanin
G: Glicin
H: Histidin
I: Izoleucin
K: Lizin
L: Leucin
M: Metionin
N: Asparagin
P: Prolin
Q: Glutamin
R: Arginin
S: Serin
T: Treonin
V: Valin
W: Triptofan
Y: Tirozin
Kloniranje i ekspresija
[uredi | uredi izvor]Pretragom baza podataka o sekvencama za homologe kvasca Prp16 i Prp17, koji su uključeni u katalitski korak II, praćenom PCR-om, Zhou i Reed (1998) izolirali su cDNK koja kodira ljudskee PRP16 i PRP17. Predviđeni protein PRP16 sa 1.227 aminokiselina, koji je 41% identičan kvašćevom Prp16, sadrži konzerviranini motiv koji veže NTP i šest motiva RNK-helikaza, koji su tipski za porodicu kutija DEAH navodnih RNK-helikaza. PRP16 se razlikuje od svog homologa kvasca na N-kraju, gdje ima REDS-bogatu regiju koje nema u kvaščevom Prp16. Analizom komplementacije, utvrđeno je da PRP16 nije mogao spasiti nokaut Prp16 kvasca, osim kao himera s 298 N-terminalnih ostataka kvasca Prp16, što sugerira da regija bogata REDS-om ne može funkcionirati u sustavu kvasca, dok su faktori DEAH okvira ključni. Western blot analiza otkrila je jedarni protein od 140 kD koji se pojavio kasnije od SF3B3 i povezan je sa splajsosomom prije katalitskog koraka II. Studije imunoosirošivanje/dodavanja u ljudskim jedarnim ekstraktima pokazale su da je PRP16 općeniti faktor prerade, bitan za katalitski korak II.
Molekulska genetika
[uredi | uredi izvor]Sekvenciranjem egzona u pakistanskoj porodici srodnika s ranim početkom retinitis pigmentosa i makulskog koloboma, u kojem je bilo sugestivne veze sa hromosomom 16 (višestruka ocjena loda od 2,65 za marker rs11646282), Ajmal et al. (2014) identificirali su homozigotnost zbog misens mutacije u genu DHX38 (G332D) koja se odvojila od fenotipa u porodici. Varijanta nije pronađena u 180 etnički podudarnih kontrola ili u Exome Variant Serveru, projektu 1000 Genomes ili u bazama podataka dbSNP. Nisu izvedene funkcionalne studije varijante. U dva pogođena člana srodničke pakistanske porodice (MA88 i MA157) s retinitis pigmentosa s ranim početkom, Latif et al. (2018) identificirali su homozigotnost za istu misense mutaciju u genu DHX38 (R324Q). Sekvenciranje gena kod tri člana svake porodice sa normalnim vidom nije identificiralo mutaciju. Varijanta nije bila prisutna ni u jednom od 30.766 južnoazijskih alela u bazi podataka gnomAD. Nisu izvedene funkcionalne studije varijante.[10][11]
Reference
[uredi | uredi izvor]- ^ a b c GRCh38: Ensembl release 89: ENSG00000140829 - Ensembl, maj 2017
- ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000037993 - Ensembl, maj 2017
- ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ Zhou Z, Reed R (Jun 1998). "Human homologs of yeast prp16 and prp17 reveal conservation of the mechanism for catalytic step II of pre-mRNA splicing". EMBO J. 17 (7): 2095–106. doi:10.1093/emboj/17.7.2095. PMC 1170554. PMID 9524131.
- ^ Nagase T, Seki N, Ishikawa K, Ohira M, Kawarabayasi Y, Ohara O, Tanaka A, Kotani H, Miyajima N, Nomura N (maj 1997). "Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain". DNA Res. 3 (5): 321–9, 341–54. doi:10.1093/dnares/3.5.321. PMID 9039502.
- ^ a b "Entrez Gene: DHX38 DEAH (Asp-Glu-Ala-His) box polypeptide 38".
- ^ (Zhou i Reed, 1998). Zhou, Z., Reed, R. Human homologs of yeast Prp16 and Prp17 reveal conservation of the mechanism for catalytic step II of pre-mRNA splicing. EMBO J. 17: 2095-2106, 1998. PubMed: 9524131
- ^ "UniProt, Q92620". Pristupljeno 4. 7. 2021.
- ^ Ajmal, M., Khan, M. I., Neveling, K., Khan, Y. M., Azam, M., Waheed, N. K., Hamel, C. P., Ben-Yosef, T., De Baere, E., Koenekoop, R. K., Collin, R. W. J., Qamar, R., Cremers, F. P. M. A missense mutation in the splicing factor gene DHX38 is associated with early-onset retinitis pigmentosa with macular coloboma. J. Med. Genet. 51: 444-448, 2014. [PubMed[: 24737827
- ^ Latif, Z., Chakchouk, I., Schrauwen, I., Lee, K., Santos-Cortez, R. L. P., Abbe, I., Acharya, A., Jarral, A., Ali, I., Ullah, E., Khan, M. N., Ali, G., Tahir, T. H., Bamshad, M. J., Nickerson, D. A., Ahmad, W., Ansar, M., Leal, S. M. Confirmation of the role of DHX38 in the etiology of early-onset retinitis pigmentosa. Invest. Ophthal. Vis. Sci. 59: 4552-4557, 2018. [PubMed]: 30208423
Dopunska literatura
[uredi | uredi izvor]- Schwer B, Guthrie C (1991). "PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome". Nature. 349 (6309): 494–9. doi:10.1038/349494a0. PMID 1825134. S2CID 4281489.
- Bonaldo MF, Lennon G, Soares MB (1997). "Normalization and subtraction: two approaches to facilitate gene discovery". Genome Res. 6 (9): 791–806. doi:10.1101/gr.6.9.791. PMID 8889548.
- Hillier LD, Lennon G, Becker M, et al. (1997). "Generation and analysis of 280,000 human expressed sequence tags". Genome Res. 6 (9): 807–28. doi:10.1101/gr.6.9.807. PMID 8889549.
- Gee S, Krauss SW, Miller E, et al. (1997). "Cloning of mDEAH9, a putative RNA helicase and mammalian homologue of Saccharomyces cerevisiae splicing factor Prp43". Proc. Natl. Acad. Sci. U.S.A. 94 (22): 11803–7. doi:10.1073/pnas.94.22.11803. PMC 23596. PMID 9342318.
- Wang Y, Guthrie C (1998). "PRP16, a DEAH-box RNA helicase, is recruited to the spliceosome primarily via its nonconserved N-terminal domain". RNA. 4 (10): 1216–29. doi:10.1017/S1355838298980992. PMC 1369694. PMID 9769096.
- Orphanides G, Wu WH, Lane WS, et al. (1999). "The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins". Nature. 400 (6741): 284–8. doi:10.1038/22350. PMID 10421373. S2CID 4300397.
- Loftus BJ, Kim UJ, Sneddon VP, et al. (1999). "Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q". Genomics. 60 (3): 295–308. doi:10.1006/geno.1999.5927. PMID 10493829.
- Jurica MS, Licklider LJ, Gygi SR, et al. (2002). "Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis". RNA. 8 (4): 426–39. doi:10.1017/S1355838202021088. PMC 1370266. PMID 11991638.
- Chagnon P, Michaud J, Mitchell G, et al. (2003). "A missense mutation (R565W) in cirhin (FLJ14728) in North American Indian childhood cirrhosis". Am. J. Hum. Genet. 71 (6): 1443–9. doi:10.1086/344580. PMC 378590. PMID 12417987.
- Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
- Obuse C, Yang H, Nozaki N, et al. (2004). "Proteomics analysis of the centromere complex from HeLa interphase cells: UV-damaged DNA binding protein 1 (DDB-1) is a component of the CEN-complex, while BMI-1 is transiently co-localized with the centromeric region in interphase". Genes Cells. 9 (2): 105–20. doi:10.1111/j.1365-2443.2004.00705.x. PMID 15009096. S2CID 21813024.
- Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.
- Ewing RM, Chu P, Elisma F, et al. (2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931.