Home LiteratureArticle Details
PMID: 23990920 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Human RNase H1 is associated with protein P32 and is involved in mitochondrial pre-rRNA processing.

PloS one ·Vol. 8 ·No. 8 ·2013-00-00 ·Pages e71006

Wu H, Sun H, Liang X, Lima WF, Crooke ST

Abstract

Mammalian RNase H1 has been implicated in mitochondrial DNA replication and RNA processing and is required for embryonic development. We identified the mitochondrial protein P32 that binds specifically to human RNase H1, but not human RNase H2. P32 binds human RNase H1 via the hybrid-binding domain of the enzyme at an approximately 1∶1 ratio. P32 enhanced the cleavage activity of RNase H1 by reducing the affinity of the enzyme for the heteroduplex substrate and enhancing turnover, but had no effect on the cleavage pattern. RNase H1 and P32 were partially co-localized in mitochondria and reduction of P32 or RNase H1 levels resulted in accumulation of mitochondrial pre ribosomal RNA [12S/16S] in HeLa cells. P32 also co-immunoprecipitated with MRPP1, a mitochondrial RNase P protein required for mitochondrial pre-rRNA processing. The P32-RNase H1 complex was shown to physically interact with mitochondrial DNA and pre-rRNA. These results expand the potential roles for RNase H1 to include assuring proper transcription and processing of guanosine-cytosine rich pre-ribosomal RNA in mitochondria. Further, the results identify P32 as a member of the 'RNase H1 degradosome' and the key P32 enhances the enzymatic efficiency of human RNase H1.

MeSH Terms
Carrier Proteins Cell Line Gene Expression Regulation, Enzymologic HEK293 Cells HeLa Cells Humans Hydrolysis Mass Spectrometry Microscopy, Fluorescence Mitochondria/metabolism Mitochondrial Proteins/metabolism RNA Interference RNA Precursors/metabolism RNA Processing, Post-Transcriptional RNA, Ribosomal/metabolism Ribonuclease H/metabolism
Chemicals
C1QBP protein, human Carrier Proteins Mitochondrial Proteins RNA Precursors RNA, Ribosomal Ribonuclease H ribonuclease HI
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Wu Hongjiang
Department of Core Antisense Research, Isis Pharmaceuticals, Inc., Carlsbad, California, United States of America.
Sun Hong
Liang Xuehai
Lima Walt F
Crooke Stanley T
References (62)
62 references, click to expand
  1. Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes.
    FEBS J. 2009 Mar;276(6):1482-93 PMID: 19228197
  2. NMR structure of the N-terminal domain of Saccharomyces cerevisiae RNase HI reveals a fold with a strong resemblance to the N-terminal domain of ribosomal protein L9.
    J Mol Biol. 1999 Aug 20;291(3):661-9 PMID: 10448044
  3. Functional expression of cloned human splicing factor SF2: homology to RNA-binding proteins, U1 70K, and Drosophila splicing regulators.
    Cell. 1991 Jul 26;66(2):383-94 PMID: 1830244
  4. Determination of the role of the human RNase H1 in the pharmacology of DNA-like antisense drugs.
    J Biol Chem. 2004 Apr 23;279(17):17181-9 PMID: 14960586
  5. Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein.
    Science. 1990 Sep 21;249(4975):1398-405 PMID: 2169648
  6. Enzyme from calf thymus degrading the RNA moiety of DNA-RNA Hybrids: effect on DNA-dependent RNA polymerase.
    Science. 1969 Oct 17;166(3903):393-5 PMID: 5812039
  7. The multiligand-binding protein gC1qR, putative C1q receptor, is a mitochondrial protein.
    J Immunol. 1998 Apr 1;160(7):3534-42 PMID: 9531316
  8. Coupling transcription, splicing and mRNA export.
    Curr Opin Cell Biol. 2003 Jun;15(3):326-31 PMID: 12787775
  9. Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice.
    Mol Cell. 2003 Mar;11(3):807-15 PMID: 12667461
  10. Cloning, expression, and mapping of ribonucleases H of human and mouse related to bacterial RNase HI.
    Genomics. 1998 Nov 1;53(3):300-7 PMID: 9799596
  11. Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD.
    EMBO J. 2008 Apr 9;27(7):1172-81 PMID: 18337749
  12. Expression, purification, and characterization of a recombinant ribonuclease H from Thermus thermophilus HB8.
    J Biol Chem. 1992 May 15;267(14):10184-92 PMID: 1315754
  13. On the molecular weight and subunit composition of calf thymus ribonuclease H1.
    Biochemistry. 1990 Jan 16;29(2):383-9 PMID: 2154245
  14. GRP78 and Cripto form a complex at the cell surface and collaborate to inhibit transforming growth factor beta signaling and enhance cell growth.
    Mol Cell Biol. 2008 Jan;28(2):666-77 PMID: 17991893
  15. Importance of the positive charge cluster in Escherichia coli ribonuclease HI for the effective binding of the substrate.
    J Biol Chem. 1991 Jun 25;266(18):11621-7 PMID: 1646812
  16. Replication and transcription of mammalian mitochondrial DNA.
    Exp Physiol. 2003 Jan;88(1):41-56 PMID: 12525854
  17. Efficient and specific knockdown of small non-coding RNAs in mammalian cells and in mice.
    Nucleic Acids Res. 2011 Feb;39(3):e13 PMID: 21062825
  18. Protein kinase C [micro] is regulated by the multifunctional chaperon protein p32.
    J Biol Chem. 2000 Aug 11;275(32):24601-7 PMID: 10831594
  19. Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
    Mol Cell. 2006 Apr 7;22(1):5-13 PMID: 16600865
  20. A general two-metal-ion mechanism for catalytic RNA.
    Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6498-502 PMID: 8341661
  21. Molecular cloning of a ribonuclease H (RNase HI) gene from an extreme thermophile Thermus thermophilus HB8: a thermostable RNase H can functionally replace the Escherichia coli enzyme in vivo.
    Nucleic Acids Res. 1991 Aug 25;19(16):4443-9 PMID: 1653414
  22. Transcription and replication of mitochondrial DNA.
    Hum Reprod. 2000 Jul;15 Suppl 2:11-7 PMID: 11041509
  23. PCNA directs type 2 RNase H activity on DNA replication and repair substrates.
    Nucleic Acids Res. 2011 May;39(9):3652-66 PMID: 21245041
  24. Cloning of the cDNA encoding the large subunit of human RNase HI, a homologue of the prokaryotic RNase HII.
    Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):12872-7 PMID: 9789007
  25. Three-dimensional structure of ribonuclease H from E. coli.
    Nature. 1990 Sep 20;347(6290):306-9 PMID: 1698262
  26. Mitochondrial/cell-surface protein p32/gC1qR as a molecular target in tumor cells and tumor stroma.
    Cancer Res. 2008 Sep 1;68(17):7210-8 PMID: 18757437
  27. How does RNase H recognize a DNA.RNA hybrid?
    Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11535-9 PMID: 1662398
  28. Investigating the structure of human RNase H1 by site-directed mutagenesis.
    J Biol Chem. 2001 Jun 29;276(26):23547-53 PMID: 11319219
  29. Human RNase H1 activity is regulated by a unique redox switch formed between adjacent cysteines.
    J Biol Chem. 2003 Apr 25;278(17):14906-12 PMID: 12473655
  30. Purification, subunit structure, and serologicai analysis of calf thymus ribonuclease H I.
    J Biol Chem. 1980 Oct 10;255(19):9434-43 PMID: 6251088
  31. Human p32 is a novel FOXC1-interacting protein that regulates FOXC1 transcriptional activity in ocular cells.
    Invest Ophthalmol Vis Sci. 2008 Dec;49(12):5243-9 PMID: 18676636
  32. RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme.
    Cell. 2008 Oct 31;135(3):462-74 PMID: 18984158
  33. Ribonuclease H from K562 human erythroleukemia cells. Purification, characterization, and substrate specificity.
    J Biol Chem. 1991 Apr 5;266(10):6472-9 PMID: 1706718
  34. Substrate specificity of human RNase H1 and its role in excision repair of ribose residues misincorporated in DNA.
    Biochimie. 1993;75(1-2):123-6 PMID: 8389211
  35. Ribonuclease H: the enzymes in eukaryotes.
    FEBS J. 2009 Mar;276(6):1494-505 PMID: 19228196
  36. Splicing factor 2-associated protein p32 participates in ribosome biogenesis by regulating the binding of Nop52 and fibrillarin to preribosome particles.
    Mol Cell Proteomics. 2011 Aug;10(8):M110.006148 PMID: 21536856
  37. Human RNase H1 uses one tryptophan and two lysines to position the enzyme at the 3'-DNA/5'-RNA terminus of the heteroduplex substrate.
    J Biol Chem. 2003 Dec 12;278(50):49860-7 PMID: 14506260
  38. RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability.
    Mol Cell. 2011 Dec 23;44(6):978-88 PMID: 22195970
  39. Adenovirus core protein V interacts with p32--a protein which is associated with both the mitochondria and the nucleus.
    J Gen Virol. 1998 Jul;79 ( Pt 7):1677-85 PMID: 9680131
  40. Contributions of the two accessory subunits, RNASEH2B and RNASEH2C, to the activity and properties of the human RNase H2 complex.
    Nucleic Acids Res. 2009 Jan;37(1):96-110 PMID: 19015152
  41. Properties of cloned and expressed human RNase H1.
    J Biol Chem. 1999 Oct 1;274(40):28270-8 PMID: 10497183
  42. Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability.
    Cell. 2005 Aug 12;122(3):365-78 PMID: 16096057
  43. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.
    Cell. 2005 Jul 1;121(7):1005-16 PMID: 15989951
  44. The non-RNase H domain of Saccharomyces cerevisiae RNase H1 binds double-stranded RNA: magnesium modulates the switch between double-stranded RNA binding and RNase H activity.
    RNA. 1995 May;1(3):246-59 PMID: 7489497
  45. Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutières syndrome and mimic congenital viral brain infection.
    Nat Genet. 2006 Aug;38(8):910-6 PMID: 16845400
  46. Junction ribonuclease: an activity in Okazaki fragment processing.
    Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2244-9 PMID: 9482870
  47. The cytoplasmic tail peptide sequence of membrane type-1 matrix metalloproteinase (MT1-MMP) directly binds to gC1qR, a compartment-specific chaperone-like regulatory protein.
    FEBS Lett. 2002 Sep 11;527(1-3):51-7 PMID: 12220632
  48. Selective cloning of genes encoding RNase H from Salmonella typhimurium, Saccharomyces cerevisiae and Escherichia coli rnh mutant.
    Mol Gen Genet. 1991 Jul;227(3):438-45 PMID: 1650910
  49. Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription.
    Mol Cell. 2007 Oct 26;28(2):264-76 PMID: 17964265
  50. Human p32, interacts with B subunit of the CCAAT-binding factor, CBF/NF-Y, and inhibits CBF-mediated transcription activation in vitro.
    Nucleic Acids Res. 2004 Jul 08;32(12):3632-41 PMID: 15243141
  51. Identification of the genes encoding Mn2+-dependent RNase HII and Mg2+-dependent RNase HIII from Bacillus subtilis: classification of RNases H into three families.
    Biochemistry. 1999 Jan 12;38(2):605-18 PMID: 9888800
  52. Molecular cloning and expression of cDNA for human RNase H.
    Antisense Nucleic Acid Drug Dev. 1998 Feb;8(1):53-61 PMID: 9512096
  53. RNase H2 of Saccharomyces cerevisiae is a complex of three proteins.
    Nucleic Acids Res. 2004 Jan 20;32(2):407-14 PMID: 14734815
  54. Junction ribonuclease activity specified in RNases HII/2.
    FEBS J. 2008 Nov;275(21):5444-55 PMID: 18959768
  55. Human Dicer binds short single-strand and double-strand RNA with high affinity and interacts with different regions of the nucleic acids.
    J Biol Chem. 2009 Jan 23;284(4):2535-48 PMID: 19017633
  56. Trex1 prevents cell-intrinsic initiation of autoimmunity.
    Cell. 2008 Aug 22;134(4):587-98 PMID: 18724932
  57. p32/gC1qR is indispensable for fetal development and mitochondrial translation: importance of its RNA-binding ability.
    Nucleic Acids Res. 2012 Oct;40(19):9717-37 PMID: 22904065
  58. Eukaryotic RNases H1 act processively by interactions through the duplex RNA-binding domain.
    Nucleic Acids Res. 2005 Apr 14;33(7):2166-75 PMID: 15831789
  59. RNA processing in human mitochondria.
    Cell Cycle. 2011 Sep 1;10(17):2904-16 PMID: 21857155
  60. Yeast pre-rRNA processing and modification occur cotranscriptionally.
    Mol Cell. 2010 Mar 26;37(6):809-20 PMID: 20347423
  61. Structural requirements at the catalytic site of the heteroduplex substrate for human RNase H1 catalysis.
    J Biol Chem. 2004 Aug 27;279(35):36317-26 PMID: 15205459
  62. The contribution of gC1qR/p33 in infection and inflammation.
    Immunobiology. 2007;212(4-5):333-42 PMID: 17544818
Article Info
Journal
PloS one
Abbr.
PLoS One
ISSN
1932-6203
Published
2013-00-00
Epub
2013-00-22
Pages
e71006
Language
English
Region
United States
NLM ID
101285081
PMCID
PMC3750045
Subset
IM
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com