Identification of Genes Modulating Mitochondrial Biogenesis in Caenorhabditis elegans

Since Altmann recognized ubiquitously distributed "bioblasts" in 1890, understanding of mitochondria has evolved from "elementary organisms" living inside cells and carrying out vital functions, over the Harman's "free radical theory" in 1956, to one of the driving forces of aging and cause of multiple associated diseases impacting society today. While a tremendous amount of work has contributed to the understanding of mitochondrial biology in different model organisms, the precise molecular mechanisms of basic mitochondrial function have yet to be deciphered. By employing an RNA interference mediated screen in Caenorhabditis elegans, we identified two transcription factors: SPTF-3, a member of Sp1 family, and an uncharacterized, nematode specific W04D2.4. We propose that both proteins modulate expression of many genes with regard to mitochondrial function including mitochondrial single-stranded binding protein encoded by mtss-1, whose promoter was used as transcriptional reporter in the screen. Further, RNA sequencing data indicate that W04D2.4 indirectly regulates expression of mitochondrial DNA via control of genes functionally related to mitochondrial replication and translation machineries. We also demonstrate that from all interventions targeting cytosolic translation, MTSS-1 levels are elevated only upon knockdown of genes encoding cytosolic ribosomal proteins. Reduction of ribosomes leads to increased sptf-3 translation, most likely in an internal ribosome entry side (IRES) mediated manner, eventually inducing mtss-1 expression. Moreover, we identify a novel role for SPTF-3 in the regulation of mitochondrial unfolded stress response (UPRmt) activation, but not endoplasmatic reticulum or oxidative stress responses. Taken together, this study identifies two transcription factors previously not associated with mitochondrial biogenesis and UPRmt in C. elegans, establishing a basis for further investigation of mito-nuclear interactions.

Inhibition of nonsense-mediated mRNA decay by the cytoplasmic poly(A)-binding protein

The expression of a gene from transcription of the DNA into pre-messenger RNA (pre-mRNA) over translation of messenger RNA (mRNA) into protein is constantly monitored for errors. This quality control is necessary to guarantee successful gene expression. One quality control mechanism important to this thesis is called nonsense-mediated mRNA decay (NMD). NMD is a cellular process that eliminates mRNA transcripts harboring premature translation termination codons (PTCs). Furthermore, NMD is known to regulate certain transcripts with long 3′ UTRs. However, some mRNA transcripts are known to evade NMD. The mechanism of NMD activation has been subjected to many studies whereas NMD evasion or suppression still remains rather elusive. It has previously been shown that the cytoplasmic poly(A)-binding protein (PABPC1) is able to suppress NMD of certain transcripts. In this study I show that PABPC1 is able to suppress NMD of a long 3′ UTR-carrying reporter when tethered immediately downstream of the termination codon. I further am able to show the importance of the interaction between PABPC1 and eIF4G for NMD suppression, whereas the interaction between PABPC1 and eRF3a seems dispensable. These results indicate an involvement of efficient translation termination and potentially ribosome recycling in NMD suppression. I am able to show that if PABPC1 is too far removed from the terminating ribosome NMD is activated. After showing the importance of PABPC1 recruitment directly downstream of a terminating ribosome in NMD suppression, I am further able to demonstrate several different methods by which PABPC1 can be recruited. Fold-back of the poly(A)-tail mediated by two interacting proteins on opposite ends of a 3′ UTR manages to bring PABPC1 bound to the poly(A)-tail into close proximity of the terminating ribosome and therefore suppress NMD. Furthermore, small PAM2 peptides that are known to interact with the MLLE domain of PABPC1 are able to strongly suppress NMD initiated by either a long 3′ UTR or an EJC. I am also able to show the NMD antagonizing power of recruited PABPC1 for the known endogenous NMD target β-globin PTC39, which is responsible for the disease β-thalassemia. This shows the potential medical implications and application of suppressing NMD by recruiting PABPC1 into close proximity of a terminating ribosome.