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Smith, Jeffrey

Jeffrey Smith

Primary Appointment

Biochemistry and Molecular Genetics

Contact Information

1340 JPA Pinn Hall Room 6229A
Charlottesville, VA 22908
Telephone: 434-243-5864
Fax: 434-924-5069
Email: jss5y@virginia.edu

Research Interests

Transcriptional Silencing and Aging in Yeast

Research Description

Transcriptional silencing Understanding how chromatin structure influences DNA-mediated processes has become a fundamental problem in cellular biology. Chromatin is known to influence the regulation of eukaryotic gene expression, DNA replication, DNA repair, and recombination. Chromatin effects on gene expression can be either localized (gene-specific) or more regional. The classic example of a regional chromatin effect is silencing, the epigenetic transcriptional repression of large heterochromatic chromosomal loci. Regions of silent chromatin in the budding yeast Saccharomyces cerevisiae include the HML and HMR cryptic mating-type loci, telomeres, and the ribosomal DNA (rDNA). Silencing at each of these loci requires the Silent Information Regulator 2 (SIR2) gene, which encodes the founding member of a large, phylogenetically conserved family of NAD+-dependent protein deacetylases known as the Sirtuins. Sir2 is recruited to the silenced loci in yeast through interactions with other proteins that bind to specific cis-acting silencer elements. Once recruited to chromatin, Sir2 deacetylates lysines on the N-terminal tails of histones H3 and H4, a critical step in the formation of silent chromatin. One of the research projects in our lab is to dissect the mechanism of silencing at the yeast rDNA locus, which was originally defined as the SIR2-dependent repression of Pol II-transcribed reporter genes positioned within the rDNA tandem array. More recently, SIR2 was also found to silence the transcription of endogenous Pol II-transcribed genes and non-coding RNAs embedded in the rDNA. The silent chromatin structure set up by Sir2 also plays a role in suppressing recombination between the rDNA repeats. Interestingly, transcription of the rDNA genes by Pol I (the classic function of the rDNA is to produce rRNA for ribosomes) is required for silencing of Pol II transcription. We are using genetic and biochemical approaches aimed at 1) determining how Pol I transcription promotes silencing of Pol II genes at the rDNA, 2) identifying new genes that function in rDNA silencing, and 3) using rDNA silencing as a model for the study of heterochromatin spreading and boundary element function. In a related project, the lab has been investigating how chromatin modifying enzymes and rDNA chromatin structure, in turn, regulate Pol I-mediated transcription of the rDNA genes. Regulation of rDNA transcription has important implications for diseases such as cancer and cardiac hypertrophy, both of which involve uncontrolled cell growth and require high ribosome translational capacity. NAD+ biosynthesis and the regulation of Sirtuins Sir2 and the other Sirtuins are protein deacetylases that hydrolyze NAD+ as part of their catalytic mechanism. For every deacetylation reaction, one molecule of NAD+ is consumed. The byproducts are nicotinamide and 2'-O-acetyl-ADP ribose, with nicotinamide acting as a strong feedback inhibitor of the reaction. To prevent nicotinamide accumulation and Sirtuin inhibition, yeast cells recycle it into NAD+ though a salvage pathway. This salvage pathway is critical not only for detoxifying the nicotinamide, but to also maintain a cellular NAD+ concentration that is sufficiently high to promote silencing and other Sirtuin-mediated processes. Another area of research in the lab is focused on 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. This is critical because mammalian Sirtuins have been implicated in the regulation of aging-associated diseases including diabetes, cancer, and forms of neurodegeneration. Yeast as a model system for aging and caloric restriction Caloric restriction (CR) is a dietary regiment 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 Publications

Fine RD, Maqani N, Li M, Franck E, Smith JS, Depletion of Limiting rDNA Structural Complexes Triggers Chromosomal Instability and Replicative Aging of Saccharomyces cerevisiae., 2019; Genetics. 212(1) 75-91 PMID: 30842210 | PMCID: PMC6499517

Maqani N, Fine RD, Shahid M, Li M, Enriquez-Hesles E, Smith JS, Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK., 2018; Microbial cell (Graz, Austria). 5(5) 233-248 PMID: 29796388 | PMCID: PMC5961917

Wierman MB, Maqani N, Strickler E, Li M, Smith JS, Caloric Restriction Extends Yeast Chronological Life Span by Optimizing the Snf1 (AMPK) Signaling Pathway., 2017; Molecular and cellular biology. 37(13) PMID: 28373292 | PMCID: PMC5472825

Buck SW, Maqani N, Matecic M, Hontz RD, Fine RD, Li M, Smith JS, RNA Polymerase I and Fob1 contributions to transcriptional silencing at the yeast rDNA locus., 2016; Nucleic acids research. 44(13) 6173-84 PMID: 27060141 | PMCID: PMC5291248

Gartenberg MR, Smith JS, The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae., 2016; Genetics. 203(4) 1563-99 PMID: 27516616 | PMCID: PMC4981263

Wierman MB, Matecic M, Valsakumar V, Li M, Smith DL, Bekiranov S, Smith JS, Functional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations., 2015; Aging. 7(3) 177-94 PMID: 25769345 | PMCID: PMC4394729

Johnson JM, Smith JS, Schneider DA, A User's Guide to the Ribosomal DNA in Saccharomyces cerevisiae., 2014; Methods in molecular biology (Clifton, N.J.). 1205() 303-28 PMID: 25213252 |

Wierman MB, Smith JS, Yeast sirtuins and the regulation of aging., 2013; FEMS yeast research. 14(1) 73-88 PMID: 24164855 | PMCID: PMC4365911

Johnson JM, French SL, Osheim YN, Li M, Hall L, Beyer AL, Smith JS, Rpd3- and spt16-mediated nucleosome assembly and transcriptional regulation on yeast ribosomal DNA genes., 2013; Molecular and cellular biology. 33(14) 2748-59 PMID: 23689130 | PMCID: PMC3700123

Li M, Valsakumar V, Poorey K, Bekiranov S, Smith JS, Genome-wide analysis of functional sirtuin chromatin targets in yeast., 2013; Genome biology. 14(5) R48 PMID: 23710766 | PMCID: PMC4053722

McClure JM, Wierman MB, Maqani N, Smith JS, Isonicotinamide enhances Sir2 protein-mediated silencing and longevity in yeast by raising intracellular NAD+ concentration., 2012; The Journal of biological chemistry. 287(25) 20957-66 PMID: 22539348 | PMCID: PMC3375519

French SL, Sikes ML, Hontz RD, Osheim YN, Lambert TE, El Hage A, Smith MM, Tollervey D, Smith JS, Beyer AL, Distinguishing the roles of Topoisomerases I and II in relief of transcription-induced torsional stress in yeast rRNA genes., 2010; Molecular and cellular biology. 31(3) 482-94 PMID: 21098118 | PMCID: PMC3028620

Matecic M, Smith DL, Pan X, Maqani N, Bekiranov S, Boeke JD, Smith JS, A microarray-based genetic screen for yeast chronological aging factors., 2010; PLoS genetics. 6(4) e1000921 PMID: 20421943 | PMCID: PMC2858703

Smith DL, Li C, Matecic M, Maqani N, Bryk M, Smith JS, Calorie restriction effects on silencing and recombination at the yeast rDNA., 2009; Aging cell. 8(6) 633-42 PMID: 19732044 | PMCID: PMC3163344

Biswas M, Maqani N, Rai R, Kumaran SP, Iyer KR, Sendinc E, Smith JS, Laloraya S, Limiting the extent of the RDN1 heterochromatin domain by a silencing barrier and Sir2 protein levels in Saccharomyces cerevisiae., 2009; Molecular and cellular biology. 29(10) 2889-98 PMID: 19289503 | PMCID: PMC2682026

Hontz RD, French SL, Oakes ML, Tongaonkar P, Nomura M, Beyer AL, Smith JS, Transcription of multiple yeast ribosomal DNA genes requires targeting of UAF to the promoter by Uaf30., 2008; Molecular and cellular biology. 28(21) 6709-19 PMID: 18765638 | PMCID: PMC2573240

McClure JM, Gallo CM, Smith DL, Matecic M, Hontz RD, Buck SW, Racette FG, Smith JS, Pnc1p-mediated nicotinamide clearance modifies the epigenetic properties of rDNA silencing in Saccharomyces cerevisiae., 2008; Genetics. 180(2) 797-810 PMID: 18780747 | PMCID: PMC2567381

Eisinger-Mathason TS, Andrade J, Groehler AL, Clark DE, Muratore-Schroeder TL, Pasic L, Smith JA, Shabanowitz J, Hunt DF, Macara IG, Lannigan DA, Codependent functions of RSK2 and the apoptosis-promoting factor TIA-1 in stress granule assembly and cell survival., 2008; Molecular cell. 31(5) 722-36 PMID: 18775331 | PMCID: PMC2654589