Date of Award

Spring 5-2020

Degree Type


Degree Name


Degree Program

Integrative Biology


Biological Sciences

Major Professor

Liu, Zhengchang

Second Advisor

Schluchter, Wendy

Third Advisor

Clancy, Mary

Fourth Advisor

Atallah, Joel


Budding yeast has been used as a powerful model organism to study the network that communicate functions of nucleus, cytoplasm and mitochondria. Depending upon environmental cues, yeast cells regulate their metabolic programming, for example, presence of glucose repress utilization of alternate carbon source to produce energy. This phenomenon is called carbon catabolite repression, which is relieved when glucose is limiting, and alternate carbon source utilization is achieved by an increase in mitochondrial biogenesis (oxidative catabolism) and the upregulation of TCA cycle and gluconeogenesis. Most of genes involved in alternate carbon source utilization are encoded in the nucleus and undergo tight control to fine tune metabolic requirements.

In this study, we have used biochemical, genetic, and molecular biology approaches to understand carbon source dependent regulation of mitochondrial biogenesis and gluconeogenesis in yeast. In Chapter I, we show that casein kinase I protein Hrr25 negatively regulates Puf3 by mediating its phosphorylation to support mitochondrial biogenesis under low glucose conditions. In the presence of glucose, Puf3 (mRNA binding protein) specifically binds to many mRNAs encoding mitochondrial proteins for their target degradation. On switching to a non-fermentable carbon source, Puf3 is hyperphosphorylated which coorelates with increased mitochondrial biogenesis. Hrr25 inactivates Puf3 by phosphorylating it, which makes Hrr25 a positive regulator of mitochondrial biogenesis.

In Chapter II, we characterized the function of a new zinc-cluster transcription factor, Gsm1, which has redundant functions with Cat8 in supporting cell growth on non-fermentable carbon source. Gsm1 regulates expression of gluconeogenic genes (FBP1, PCK1), genes involved in transport of metabolites into mitochondria (SFC1, YAT1), and genes involved in other cellular pathways. The reduction in Gsm1 target gene expression correlates with growth defects of gsm1∆ cat8∆ strain, and overexpression of GSM1 suppresses growth defects of cat8∆ strain on lactate medium.

In Chapter III, we determined the function of mitochondrial proteins, Aim11 and Iai11, which are transcriptionally regulated by Fkh1/2 transcription factors. In the presence of glucose, AIM11 is negatively regulated by mRNA binding protein, Puf3. Cells carrying deletion of AIM11 and IAI11 have severe growth defects on lactate medium which coorelates with reduction in mitochondrial proteins in aim11∆ iai11∆ cells.


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