Biogenesis; Genetics; Molecular Biology; Ribonucleoproteins; Radiation Oncology; RNA Helicases; Genes, rRNA; Biochemical Processes
Molecular Biophysics and Biochemistry: Baserga Lab
Therapeutic Radiology: Radiobiology
Of Yeast and Ribosome Biogenesis: Ribosome biogenesis is a complex process requiring the coordinated expression of rRNA and protein moieties and their assembly in the eukaryotic nucleolus. In order to better understand each aspect of this process, we are using an array of genetic, biochemical, and cell biological techniques in the yeast Saccharomyces cerevisiae. My laboratory focuses on the role of the ribonucleoprotein and protein complexes involved in generating the mature rRNAs.
Specialized Terms: Ribosome biogenesis; RRNA processing; U3 RNP structure and function; RNA helicases; Polymerase I transcription and processing
Extensive Research Description
Study of RNA helicases required for ribosome biogenesis and their cofactors
investigations into the role of ribosome biogenesis in cell cycle regulation
discovery of a subset of SSU processome proteins that are associated with the rDNA and are required for rDNA transcription
subcomplexes of the SSU processome and deciphering the direct
protein-protein and protein-RNA interactions that mediate their assembly
purification and electron microscopy to visualize pre-ribosomes
characterization of an essential new protein-protein interaction motif found in RNA processing RNPs
developing a method to identify individual proteins in chromatin spreads.
Using innovative proteomics techniques, my laboratory has recently
identified the protein components of a large nucleolar
ribonucleoprotein that is required for processing of the 18S small
subunit rRNA. This RNP, which we termed the SSU processome, is composed
of the U3 snoRNA and 40 proteins. Currently, projects in the lab are
aimed at determining the architecture of this RNP and the functions of
individual proteins in 18S processing. We approach this question from
several perspectives, using genetic and biochemical methods to identify
direct interactions between components, and cryo electron microscopy to
visualize the complex in three dimensions.
Through these studies we
have discovered and characterized several unique protein motifs and
their specific roles in rRNA processing. We have recently discovered
that a subset of the SSU processome proteins are associated with the
rDNA and are required for rDNA transcription. Stemming from this idea,
we are interested in studying the proteins which regulate transcription
of the rDNA by Pol I and initiate the processing of the rRNA. We have
learned that these steps are intimately linked, and endeavor to
describe this complex process in detail. Seventeen putative RNA
helicases have been shown to be required for processing of the small
and large ribosomal subunit RNAs, perhaps by remodeling the rRNA to
allow access to cleavage sites. Ongoing genetic and biochemical studies
in the lab examine the roles of each putative RNA helicase and test its
ability to unwind RNA. Through these projects, we strive to ascertain
how and why the helicases are required at each step in ribosome
biogenesis. Because ribosomes are essential to cell growth via the
production of new proteins, we are studying the role of ribosome
biogenesis in cell cycle regulation.
We have previously shown that rRNA
maturation by the SSU processome is required for cell cycle
progression, indicating that the production of ribosomes has a distinct
influence on the cell cycle. Specifically, we seek to find the
ribosome-regulated trigger that allows the cell to progress through the
cell cycle, grow in size, and divide. Transcription of the rDNA and
processing of the rRNA can be visualized in Miller chromatin spreads,
as shown here. In a, the SSU processome corresponds to the terminal
knobs at the end of each rRNA branching off the rDNA. When components
of the SSU processome are depleted (the U3 snoRNA in b, or the Utp7
protein in c), the knobs are no longer present, due to incomplete
formation of the SSU processome.
A protein interaction map of the LSU processome.
McCann KL, Charette JM, Vincent NG, Baserga SJ. A protein interaction map of the LSU processome. Genes & Development 2015, 29:862-75.
The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome.
McCann KL, Teramoto T, Zhang J, Tanaka Hall TM, Baserga SJ. The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome. ELife 2016, 5.
Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs.
Yip WS, Shigematsu H, Taylor DW, Baserga SJ. Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs. Nucleic Acids Research 2016, 44:8976-8989.
Nop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA.
Zhang J, McCann KL, Qiu C, Gonzalez LE, Baserga SJ, Hall TM. Nop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA. Nature Communications 2016, 7:13085.
The nucleolar protein Esf2 interacts directly with the DExD/H box RNA helicase, Dbp8, to stimulate ATP hydrolysis.
Granneman S, Lin C, Champion EA, Nandineni MR, Zorca C, Baserga SJ. The nucleolar protein Esf2 interacts directly with the DExD/H box RNA helicase, Dbp8, to stimulate ATP hydrolysis. Nucleic Acids Research 2006, 34:3189-99.
Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis.
Robson A, Owens ND, Baserga SJ, Khokha MK, Griffin JN. Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis. BMC Developmental Biology 2016, 16:38.
Determinants of mammalian nucleolar architecture.
Farley KI, Surovtseva Y, Merkel J, Baserga SJ. Determinants of mammalian nucleolar architecture. Chromosoma 2015, 124:323-31.
The Contributions of the Ribosome Biogenesis Protein Utp5/WDR43 to Craniofacial Development.
Sondalle SB, Baserga SJ, Yelick PC. The Contributions of the Ribosome Biogenesis Protein Utp5/WDR43 to Craniofacial Development. Journal Of Dental Research 2016, 95:1214-20.
Probing the mechanisms underlying human diseases in making ribosomes.
Farley KI, Baserga SJ. Probing the mechanisms underlying human diseases in making ribosomes. Biochemical Society Transactions 2016, 44:1035-44.
Full List of PubMed Publications
- Frankowski KJ, Wang C, Patnaik S, Schoenen FJ, Southall N, Li D, Teper Y, Sun W, Kandela I, Hu D, Dextras C, Knotts Z, Bian Y, Norton J, Titus S, Lewandowska MA, Wen Y, Farley KI, Griner LM, Sultan J, Meng Z, Zhou M, Vilimas T, Powers AS, Kozlov S, Nagashima K, Quadri HS, Fang M, Long C, Khanolkar O, Chen W, Kang J, Huang H, Chow E, Goldberg E, Feldman C, Xi R, Kim HR, Sahagian G, Baserga SJ, Mazar A, Ferrer M, Zheng W, Shilatifard A, Aubé J, Rudloff U, Marugan JJ, Huang S: Metarrestin, a perinucleolar compartment inhibitor, effectively suppresses metastasis. Sci Transl Med. 2018 May 16. PMID: 29769289
- Farley-Barnes KI, McCann KL, Ogawa LM, Merkel J, Surovtseva YV, Baserga SJ: Diverse Regulators of Human Ribosome Biogenesis Discovered by Changes in Nucleolar Number. Cell Rep. 2018 Feb 13. PMID: 29444442
- Vincent NG, Charette JM, Baserga SJ: The SSU processome interactome in Saccharomyces cerevisiae reveals novel protein subcomplexes. RNA. 2018 Jan; 2017 Oct 20. PMID: 29054886
- Boyden LM, Vincent NG, Zhou J, Hu R, Craiglow BG, Bayliss SJ, Rosman IS, Lucky AW, Diaz LA, Goldsmith LA, Paller AS, Lifton RP, Baserga SJ, Choate KA: Mutations in KDSR Cause Recessive Progressive Symmetric Erythrokeratoderma. Am J Hum Genet. 2017 Jun 1. PMID: 28575652
- Sondalle SB, Baserga SJ: Ribosomes Need Straight A's to Sleep. Cell. 2017 May 4. PMID: 28475888
- Paolini NA, Attwood M, Sondalle SB, Vieira CMDS, van Adrichem AM, di Summa FM, O'Donohue MF, Gleizes PE, Rachuri S, Briggs JW, Fischer R, Ratcliffe PJ, Wlodarski MW, Houtkooper RH, von Lindern M, Kuijpers TW, Dinman JD, Baserga SJ, Cockman ME, MacInnes AW: A Ribosomopathy Reveals Decoding Defective Ribosomes Driving Human Dysmorphism. Am J Hum Genet. 2017 Mar 2. PMID: 28257692
- Robson A, Owens ND, Baserga SJ, Khokha MK, Griffin JN: Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis. BMC Dev Biol. 2016 Oct 26; 2016 Oct 26. PMID: 27784267
- Yip WS, Shigematsu H, Taylor DW, Baserga SJ: Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs. Nucleic Acids Res. 2016 Oct 14; 2016 Jun 24. PMID: 27342279
- Zhang J, McCann KL, Qiu C, Gonzalez LE, Baserga SJ, Hall TM: Nop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA. Nat Commun. 2016 Oct 11; 2016 Oct 11. PMID: 27725644
- Farley KI, Baserga SJ: Probing the mechanisms underlying human diseases in making ribosomes. Biochem Soc Trans. 2016 Aug 15. PMID: 27528749
- McCann KL, Teramoto T, Zhang J, Tanaka Hall TM, Baserga SJ: The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome. Elife. 2016 Apr 14; 2016 Apr 14. PMID: 27077951
- Farley KI, Surovtseva Y, Merkel J, Baserga SJ: Determinants of mammalian nucleolar architecture. Chromosoma. 2015 Sep; 2015 Feb 12. PMID: 25670395
- McCann KL, Charette JM, Vincent NG, Baserga SJ: A protein interaction map of the LSU processome. Genes Dev. 2015 Apr 15; 2015 Apr 15. PMID: 25877921
- Griffin JN, Sondalle SB, Del Viso F, Baserga SJ, Khokha MK: The ribosome biogenesis factor Nol11 is required for optimal rDNA transcription and craniofacial development in Xenopus. PLoS Genet. 2015 Mar; 2015 Mar 10. PMID: 25756904
- Qiu C, McCann KL, Wine RN, Baserga SJ, Hall TM: A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization. Proc Natl Acad Sci U S A. 2014 Dec 30; 2014 Dec 15. PMID: 25512524
- Sondalle SB, Baserga SJ: Human diseases of the SSU processome. Biochim Biophys Acta. 2014 Jun; 2013 Nov 12. PMID: 24240090
- McCann KL, Baserga SJ: Genetics. Mysterious ribosomopathies. Science. 2013 Aug 23. PMID: 23970686
- Yip WS, Vincent NG, Baserga SJ: Ribonucleoproteins in archaeal pre-rRNA processing and modification. Archaea. 2013; 2013 Mar 10. PMID: 23554567
- McCann KL, Baserga SJ: Long noncoding RNAs as sinks in Prader-Willi syndrome. Mol Cell. 2012 Oct 26. PMID: 23102265
- Bower-Phipps KR, Taylor DW, Wang HW, Baserga SJ: The box C/D sRNP dimeric architecture is conserved across domain Archaea. RNA. 2012 Aug; 2012 Jun 29. PMID: 22753779
- Rawling DC, Baserga SJ: In vivo approaches to dissecting the function of RNA helicases in eukaryotic ribosome assembly. Methods Enzymol. 2012. PMID: 22713326
- Freed EF, Prieto JL, McCann KL, McStay B, Baserga SJ: NOL11, implicated in the pathogenesis of North American Indian childhood cirrhosis, is required for pre-rRNA transcription and processing. PLoS Genet. 2012; 2012 Aug 16. PMID: 22916032
- Dutca LM, Gallagher JE, Baserga SJ: The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Res. 2011 Jul; 2011 Feb 23. PMID: 21349877
- Lim YH, Charette JM, Baserga SJ: Assembling a protein-protein interaction map of the SSU processome from existing datasets. PLoS One. 2011 Mar 10; 2011 Mar 10. PMID: 21423703
- Phipps KR, Charette J, Baserga SJ: The small subunit processome in ribosome biogenesis—progress and prospects. Wiley Interdiscip Rev RNA. 2011 Jan-Feb. PMID: 21318072
- Bleichert F, Baserga SJ: Dissecting the role of conserved box C/D sRNA sequences in di-sRNP assembly and function. Nucleic Acids Res. 2010 Dec; 2010 Aug 6. PMID: 20693534
- Charette JM, Baserga SJ: The DEAD-box RNA helicase-like Utp25 is an SSU processome component. RNA. 2010 Nov; 2010 Sep 30. PMID: 20884785
- Bleichert F, Baserga SJ: Ribonucleoprotein multimers and their functions. Crit Rev Biochem Mol Biol. 2010 Oct. PMID: 20572804
- Freed EF, Baserga SJ: The C-terminus of Utp4, mutated in childhood cirrhosis, is essential for ribosome biogenesis. Nucleic Acids Res. 2010 Aug; 2010 Apr 12. PMID: 20385600
- Freed EF, Bleichert F, Dutca LM, Baserga SJ: When ribosomes go bad: diseases of ribosome biogenesis. Mol Biosyst. 2010 Mar; 2010 Jan 11. PMID: 20174677
- Bleichert F, Gagnon KT, Brown BA 2nd, Maxwell ES, Leschziner AE, Unger VM, Baserga SJ: A dimeric structure for archaeal box C/D small ribonucleoproteins. Science. 2009 Sep 11. PMID: 19745151
- Champion EA, Kundrat L, Regan L, Baserga SJ: A structural model for the HAT domain of Utp6 incorporating bioinformatics and genetics. Protein Eng Des Sel. 2009 Jul; 2009 Jun 10. PMID: 19515729
- Champion EA, Lane BH, Jackrel ME, Regan L, Baserga SJ: A direct interaction between the Utp6 half-a-tetratricopeptide repeat domain and a specific peptide in Utp21 is essential for efficient pre-rRNA processing. Mol Cell Biol. 2008 Nov; 2008 Aug 25. PMID: 18725399
- Bleichert F, Baserga SJ: The long unwinding road of RNA helicases. Mol Cell. 2007 Aug 3. PMID: 17679086
- Bernstein KA, Bleichert F, Bean JM, Cross FR, Baserga SJ: Ribosome biogenesis is sensed at the Start cell cycle checkpoint. Mol Biol Cell. 2007 Mar; 2006 Dec 27. PMID: 17192414
- Bleichert F, Granneman S, Osheim YN, Beyer AL, Baserga SJ: The PINc domain protein Utp24, a putative nuclease, is required for the early cleavage steps in 18S rRNA maturation. Proc Natl Acad Sci U S A. 2006 Jun 20; 2006 Jun 12. PMID: 16769905
- Granneman S, Lin C, Champion EA, Nandineni MR, Zorca C, Baserga SJ: The nucleolar protein Esf2 interacts directly with the DExD/H box RNA helicase, Dbp8, to stimulate ATP hydrolysis. Nucleic Acids Res. 2006; 2006 Jun 13. PMID: 16772403
- Bernstein KA, Granneman S, Lee AV, Manickam S, Baserga SJ: Comprehensive mutational analysis of yeast DEXD/H box RNA helicases involved in large ribosomal subunit biogenesis. Mol Cell Biol. 2006 Feb. PMID: 16449635
- Granneman S, Bernstein KA, Bleichert F, Baserga SJ: Comprehensive mutational analysis of yeast DEXD/H box RNA helicases required for small ribosomal subunit synthesis. Mol Cell Biol. 2006 Feb. PMID: 16449634
- Granneman S, Nandineni MR, Baserga SJ: The putative NTPase Fap7 mediates cytoplasmic 20S pre-rRNA processing through a direct interaction with Rps14. Mol Cell Biol. 2005 Dec. PMID: 16287850
- Granneman S, Baserga SJ: Crosstalk in gene expression: coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing. Curr Opin Cell Biol. 2005 Jun. PMID: 15901498
- Bernstein KA, Gallagher JE, Mitchell BM, Granneman S, Baserga SJ: The small-subunit processome is a ribosome assembly intermediate. Eukaryot Cell. 2004 Dec. PMID: 15590835
- Bernstein KA, Baserga SJ: The small subunit processome is required for cell cycle progression at G1. Mol Biol Cell. 2004 Nov; 2004 Sep 8. PMID: 15356263
- Gallagher JE, Dunbar DA, Granneman S, Mitchell BM, Osheim Y, Beyer AL, Baserga SJ: RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components. Genes Dev. 2004 Oct 15. PMID: 15489292
- Granneman S, Baserga SJ: Ribosome biogenesis: of knobs and RNA processing. Exp Cell Res. 2004 May 15. PMID: 15120992
- Gallagher JE, Baserga SJ: Two-hybrid Mpp10p interaction-defective Imp4 proteins are not interaction defective in vivo but do confer specific pre-rRNA processing defects in Saccharomyces cerevisiae. Nucleic Acids Res. 2004; 2004 Feb 27. PMID: 14990745
- Granneman S, Baserga SJ: Probing the yeast proteome for RNA-processing factors. Genome Biol. 2003; 2003 Sep 22. PMID: 14519190
- Wehner KA, Gallagher JE, Baserga SJ: Components of an interdependent unit within the SSU processome regulate and mediate its activity. Mol Cell Biol. 2002 Oct. PMID: 12242301
- Wehner KA, Ayala L, Kim Y, Young PJ, Hosler BA, Lorson CL, Baserga SJ, Francis JW: Survival motor neuron protein in the nucleolus of mammalian neurons. Brain Res. 2002 Aug 2. PMID: 12126878
- Dragon F, Gallagher JE, Compagnone-Post PA, Mitchell BM, Porwancher KA, Wehner KA, Wormsley S, Settlage RE, Shabanowitz J, Osheim Y, Beyer AL, Hunt DF, Baserga SJ: A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature. 2002 Jun 27; 2002 Jun 9. PMID: 12068309
- Wehner KA, Baserga SJ: The sigma(70)-like motif: a eukaryotic RNA binding domain unique to a superfamily of proteins required for ribosome biogenesis. Mol Cell. 2002 Feb. PMID: 11864606