Tharun Sundaresan, Ph.D.

Tharun Sundaresan, Ph.D.

tharun sundaresan

Name: Tharun Sundaresan, Ph.D.

Department of Primary Appointment: Biochemistry
Position: USU Faculty
Title: Associate Professor

Affiliated Departments: Molecular & Cell Biology,

Research Interests:
Role of Sm-like proteins in mRNA decay in yeast

Email: tharun.sundaresan@usuhs.edu (link sends e-mail)
Office Phone: (301) 295-9423
Lab Phone: (301) 295-3576
Fax Number: (301) 295-3512
Room: B4072

Links
PubMed Listing

Profile

Profile

  • Ph.D in Life Sciences: Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India (affiliated to Jawaharlal Nehru University, New Delhi, India).
  • Post-doctoral research: Department of Molecular and Cellular Biology and Howard Hughes Medical Institute (HHMI), University of Arizona, Tucson, Arizona.

Research Interests

Role of Sm-like proteins in mRNA decay.

The long term goal of our lab is to understand the mechanism of mRNA decay in eukaryotes using the budding yeast S. cerevisiae as the model system.  mRNA decay is a critical determinant of gene expression and deregulation of mRNA decay is known to be the cause of several human diseases including cancer. 

The mRNA decay pathways and decay factors are well conserved in all eukaryotes from yeast to humans.  Two major pathways of mRNA decay exist in eukaryotes.  Both pathways are initiated by poly(A) shortening of the mRNA.  In the 5’ to 3’ pathway, this is followed by decapping which then permits the 5’ to 3’ exonucleolytic degradation of the message body.  In the 3’ to 5’ decay pathway, deadenylated mRNAs are degraded in a 3’ to 5’ exonucleolytic manner.

In the 5’ to 3’ pathway, decapping is a crucial precisely controlled step affected by numerous factors.  Oligoadenylated mRNAs but not polyadenylated mRNAs are selectively targeted for decapping in the 5’ to 3’ decay pathway resulting in the deadenylation dependence of decapping in this pathway.  While translation initiation factors are antagonistic to the decapping enzyme, several other factors enhance the decapping enzyme function in vivo. 

The Lsm1p-7p-Pat1p complex (made up of seven Sm-like proteins, Lsm1 through Lsm7 which are characterized by the presence of the Sm-domain and the Pat1 subunit) is a key activator of decapping needed for normal rates of decapping in vivo.  It is conserved in all eukaryotes and interacts with several decay factors and with the mRNA in vivo.  Interestingly, this complex selectively associates with oligoadenylated mRNPs targeted for decapping in vivo.

We purified the native Lsm1-7-Pat1 complex from yeast and showed that it intrinsically has a higher affinity for oligoadenylated RNA over polyadenylated RNAs in vitro.  Importantly loss of such ability to recognize the oligo(A) tail due to mutations in the Sm domain of Lsm1 impairs mRNA decay function of this complex in vivo.  By studying multiple lsm1 mutants we also showed that decapping activation by the Lsm1-7-Pat1 complex in vivo requires both the binding of that complex to the mRNA and facilitation of one or more (unknown) post-binding events. 

As mentioned above the residues in the Sm-domain of Lsm1 are crucial for the in vivo functions and unique in vitro RNA binding properties of the Lsm1-7-Pat1 complex.  However, unlike many other Sm-like proteins, yeast Lsm1 has a long C-terminal domain (CTD) following its Sm-domain and this feature is conserved in human Lsm1 also.  Interestingly our studies showed that the CTD of Lsm1 is also necessary (in addition to the Sm-domain of Lsm1) for the in vivo functions and the RNA binding activity of the Lsm1-7-Pat1 complex.  Further, the CTD of Lsm1 could even act in trans to support the function of the Lsm1-7-Pat1 complex in vivo suggesting that it folds as a separate domain in the Lsm1 subunit.  Thus Lsm1 is a unique Sm-like protein whose functions are determined not just by its Sm-domain but also residues outside the Sm-domain.

Additional studies showed that the Pat1 subunit is also critical for the in vivo functions and unique in vitro RNA binding properties of the Lsm1-7-Pat1 complex like the Lsm1 subunit and that the RNA binding surface(s) of the Lsm1-7-Pat1 complex are probably composite including residues from both the Lsm1-7 assembly and the Pat1 subunit. 

The Lsm1-7-Pat1 complex has also been implicated in viral RNA translation.  Our recent studies using lsm1 mutants and the yeast system for replication of Brome Mosaic Virus (BMV) have revealed that the Lsm1-7-Pat1 complex binds to different regions of the BMV genomic RNAs and promote their translation and recruitment out of translation to replication via different mechanisms.

Funding support:

  • NIH RO1 grant (GM072718).
  • USUHS exploratory grant (R071JX).

Relevant publications

Chowdhury, A, Swathi Kalurupalle, S, Tharun, S. 2016. Mutagenic Analysis of the C-Terminal Extension of Lsm1. PLoS ONE, 11: e0158876.

Jungfleisch, J, Chowdhury, A, Alves-Rodrigues, I, Tharun, S.*, Díez, J. 2015. The Lsm1-7- Pat1 complex promotes viral RNA translation and replication by differential mechanisms. RNA, 21:1469–1479 (*Corresponding author).

Chowdhury, A., Kalurupalle, S., and Tharun, S. 2014. Pat1 contributes to the RNA binding activity of the Lsm1-7- Pat1 complex. RNA, 20:1465–1475.

Chowdhury, A., Raju, KK., Kalurupalle, S., and Tharun, S. 2012. Both Sm-domain and C-terminal extension of Lsm1 are important for the RNA-binding activity of the Lsm1–7–Pat1 complex. RNA, 18:936–944.

Chowdhury, A., and Tharun, S. 2009. Activation of decapping involves binding of the mRNA and facilitation of the post-binding steps by the Lsm1-7- Pat1 complex. RNA, 15:1837–1848.

Tharun, S. 2009. Lsm1-7- Pat1 complex: A link between 3’ and 5’-ends in mRNA decay? RNA Biology, 6(3):228-232.

Tharun, S. 2009. Roles of eukaryotic Lsm proteins in the regulation of mRNA function. International Review of Cell & Molecular Biology, 272:149-89.

Tharun, S. 2008. Purification and analysis of the decapping activator Lsm1p-7p- Pat1p complex from yeast. Methods in Enzymology, 448:41-55.

Chowdhury, A., and Tharun, S. 2008. lsm1 mutations impairing the ability of the Lsm1p-7p- Pat1p complex to preferentially bind to oligoadenylated RNA affect mRNA decay in vivo. RNA, 14:2149-2158.

Chowdhury, A., Mukhopadhyay, J., Tharun, S. 2007. The decapping activator Lsm1p-7p- Pat1p complex has the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs. RNA, 13:998-1016.

Tharun, S.*., Muhlrad D., Chowdhury A, Parker R. 2005. Mutations in the Saccharomyces cerevisiae LSM1 gene that affect mRNA decapping and 3' end protection. Genetics, 170:33-46 (*Corresponding author).

Tharun, S.*, and Parker R. 2001. Targeting an mRNA for decapping: Displacement of translation factors and association of the Lsm1p-7p complex on deadenylated yeast mRNAs. Molecular Cell, 8:1075-1083 (*Corresponding author).

Tharun, S., He, W., Meyes, A., Lennertz, P., Beggs, J., and Parker, R. 2000. Yeast Sm-like proteins function in mRNA decapping and decay. Nature, 404:515-518.

Tharun, S., and Parker, R. 1999. Analysis of mutations in the yeast mRNA decapping enzyme. Genetics, 151:1273-1285.