Jeffrey S. Smith
Associate Professor of Biochemistry & Molecular Genetics
Ph.D., University of Medicine and Dentistry of New Jersey
Chromatin Mediated Transcriptional Silencing


Transcription and silencing at the yeast rDNA locus My lab has a long-standing interest in the ribosomal DNA (rDNA) genes, which are transcribed by RNA polymerase I in the nucleolus to produce the large ribosomal RNAs that are ultimately assembled into ribosomes. We use the budding yeast, Saccharomyces cerevisiae, to study how the rDNA genes are transcriptionally regulated in response to changes in nutrient levels, with an emphasis on chromatin effectors. Interestingly, RNA polymerase II also has the capacity to transcribe within the rDNA locus, but is prevented from doing so by a silencing mechanism mediated by the highly conserved NAD+-dependent histone deacetylase, Sir2. In addition to silencing Pol II transcription in the rDNA, Sir2 also suppresses recombination between the repeated rDNA genes. Current studies in the lab are focused on dissecting the mechanism of how Sir2 silences within the rDNA, how the silent chromatin structure is propagated, and how RNA polymerase I transcription contributes to the silencing process.

NAD+ biosynthesis and the regulation of Sirtuins Sir2 and other members of the Sirtuin protein family are deacetylases that hydrolyze NAD+ as part of their catalytic mechanism, releasing nicotinamide as one of the byproducts. Nicotinamide is a strong Sirtuin inhibitor, so to prevent it from accumulating, yeast cells recycle it back into NAD+ though a salvage pathway. This salvage pathway is critical not only limiting nicotinamide concentration, but also for maintaining a cellular NAD+ concentration that is sufficiently high to promote silencing and other Sirtuin-mediated processes. We are interested in genetically elucidating new components of the NAD+ biosynthesis and salvage pathways, and determining how they impact on silencing and other Sirtuin regulated processes in yeast such as aging (see below) and thiamine biosynthesis. Information gained from the yeast system is then used as a guide for the investigation of Sirtuin biology in mammalian cells.

Yeast as a model system for aging and caloric restriction Caloric restriction (CR) is a dietary regimen that extends the lifespan of almost every eukaryotic organism that has been tested, including Saccharomyces cerevisiae. To calorie restrict yeast, we simply reduce the glucose concentration in the growth medium from 2% to 0.5%. This change is sufficient to extend both the replicative lifespan (RLS) and chronological lifespan (CLS) of this organism, where RLS is the number of times that a mother cell divides, and CLS is the number of days that a non-dividing cell remains viable. SIR2 is required for maintaining replicative longevity via its role in controlling rDNA recombination, but is not required for maintaining chronological longevity. We have therefore been utilizing yeast genetics and genomics tools to identify novel genes and cellular pathways that are involved in the control of chronological aging, especially those that are required for the lifespan-extending effects of CR. Such genes and pathways that are conserved in mammals have the potential to be targets for therapeutics in the treatment of age-associated diseases.

Selected References

Li M, Petteys BJ, McClure JM, Valsakumar V, Bekiranov S, Frank EL, Smith JS. (2010) "Thiamine biosynthesis in Saccharomyces cerevisiae is regulated by the NAD+-dependent histone deacetylase Hst1." Mol Cell Biol. 30(13):3329-41. Epub 2010 May 3. [PubMed]

Matecic M, Smith DL, Pan X, Maqani N, Bekiranov S, Boeke JD, Smith JS. (2010) "A microarray-based genetic screen for yeast chronological aging factors." PLoS Genet. Apr 6:e1000921. [PubMed]

Smith DL Jr, Li C, Matecic M, Maqani N, Bryk M, Smith JS. (2009) "Calorie restriction effects on silencing and recombination at the yeast rDNA." Aging Cell. 8:633-42. Epub 2009 Sep 2. [PubMed]

Hontz RD, Niederer RO, Johnson JM, Smith JS. (2009) "Genetic identification of factors that modulate ribosomal DNA transcription in Saccharomyces cerevisiae." Genetics. 182:105-19. Epub 2009 Mar 6. [PubMed]

McClure JM, Gallo CM, Smith DL Jr, Matecic M, Hontz RD, Buck SW, Racette FG,Smith JS. (2008) "Pnc1p-mediated nicotinamide clearance modifies the epigenetic properties of rDNA silencing in Saccharomyces cerevisiae." Genetics. 180:797-810. Epub 2008 Sep 9. [PubMed]

Hontz RD, French SL, Oakes ML, Tongaonkar P, Nomura M, Beyer AL, Smith JS. (2008) "Transcription of multiple yeast ribosomal DNA genes requires targeting of UAF to the promoter by Uaf30." Mol Cell Biol. 28(21):6709-19. Epub 2008 Sep 2. [PubMed]

Smith DL Jr, McClure JM, Matecic M, Smith JS. (2007) "Calorie restriction extends the chronological lifespan of Saccharomyces cerevisiae independently of the Sirtuins." Aging Cell. 6:649-62. Epub 2007 Aug 15. [PubMed]

Belenky P, Racette FG, Bogan KL, McClure JM, Smith JS, Brenner C. (2007) "Nicotinamide riboside promotes Sir2 silencing and extends lifespan via Nrk and Urh1/Pnp1/Meu1 pathways to NAD+." Cell. May 129:473-84. [PubMed]