Characterization of Npl3 as a 5'- and 3'- quality control factorDoctoral thesis
Date of Examination:2023-09-05
Date of issue:2023-09-11
Advisor:Prof. Dr. Heike Krebber
Referee:Prof. Dr. Heike Krebber
Referee:Prof. Dr. Stefanie Pöggeler
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EnglishMaturation of RNA polymerase II transcripts consists of 5’-capping, splicing, cleavage and 3’-polyadenylation. These processes can generate faulty transcripts that have to be retained in the nucleus to be degraded. An mRNA should get exported into the cytoplasm only after having completed processing successfully, so that a proper translation is ensured. In Saccharomyces cerevisiae, the SR-like guard proteins Gbp2 and Hrb1 control splicing and retain unspliced transcripts in the nucleus while Hrp1 controls the cleavage reaction. The guard Nab2 controls the quality of the 3’-poly(A) tail in a similar way. On correct transcripts, all guard proteins recruit the export receptor Mex67-Mtr2. Only mRNAs which are sufficiently covered with Mex67-Mtr2 can pass through the nuclear pore complex (NPC). The passage is controlled by Mlp1, which is a part of the NPC. For the SR-like protein Npl3, which is highly homologous to Hrp1, Gbp2 and Hrb1, no particular function as a guard protein has been reported so far. Here we show that it acts as a guard in 5’-capping. Npl3 retains uncapped transcripts in the nucleus, interacts with the 5’-3’-end degradation factor Rai1 on the mRNA and recruits Rat1 to the transcript. Most importantly, faulty mRNAs are not retained in the nucleus for degradation but escape retention and leak into the cytoplasm when NPL3 is deleted. On correct pre-mRNAs Npl3 interacts with the cap binding complex (CBC), the indicator of a correct 5’-cap. It binds independently of it and their interaction is lost on uncapped transcripts, suggesting Npl3 can detect its presence. Similar to the other guard proteins, Npl3 recruits Mex67-Mtr2 to correct, quality-controlled transcripts while also interacting with the CBC. The binding of Npl3 to the CBC and Mex67 and its binding to Rai1, which supports the association of Rat1, is mutually exclusive, indicating that it might act as a switch between degradation and export. The fate of the transcript is most probably decided through the contact between Npl3 and the CBC. Rat1 and its cofactor Rai1 also have a role in canonical transcription termination. Here they interact with Rtt103 for the degradation of the RNA overhang that stays attached to RNA polymerase II after cleavage and for torpedo transcription termination. We show that NPL3 genetically and physically interacts with RTT103 and that when Npl3 is missing, Rtt103 shows a reduced binding to RNA overhangs. This indicates that Npl3 is also involved in recruitment of these factors to the RNA overhang. Thus, we have not only shown that Npl3 acts as a quality control factor for 5’-capping, but that it is special in comparison to the other guard proteins as it has a second function on the 5’-end of the remaining RNAP II transcript after the main transcript was cleaved off. This transcript is always degraded, which is supported by Npl3.
Keywords: 5'-capping; Npl3; nuclear mRNA quality control; guard protein; SR-like protein