| 1. |
- Boele, Joost, et al.
(författare)
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PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.
- 2014
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 111:31, s. 11467-11472
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Tidskriftsartikel (refereegranskat)abstract
- Next-generation sequencing experiments have shown that microRNAs (miRNAs) are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found that mature miR-21, the most widely researched miRNA because of its importance in human disease, is produced in two prevalent isomiR forms that differ by 1 nt at their 3' end, and moreover that the 3' end of miR-21 is posttranscriptionally adenylated by the noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase in the miR-21 expression level, suggesting that PAPD5-mediated adenylation of miR-21 leads to its degradation. Exoribonuclease knockdown experiments followed by small-RNA sequencing suggested that PARN degrades miR-21 in the 3'-to-5' direction. In accordance with this model, microarray expression profiling demonstrated that PAPD5 knockdown results in a down-regulation of miR-21 target mRNAs. We found that disruption of the miR-21 adenylation and degradation pathway is a general feature in tumors across a wide range of tissues, as evidenced by data from The Cancer Genome Atlas, as well as in the noncancerous proliferative disease psoriasis. We conclude that PAPD5 and PARN mediate degradation of oncogenic miRNA miR-21 through a tailing and trimming process, and that this pathway is disrupted in cancer and other proliferative diseases.
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| 2. |
- Janasch, Markus
(författare)
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On thermodynamic and kinetic constraints in autotrophic metabolism
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Earth has entered a new geological epoch, the Anthropocene, defined by humanity’s impact on the environment with increased emissions of CO2 due to burning of fossil resource as a major contributor. To ensure a sustainable future, humanity has to move towards a circular economy, where released CO2 is re-captured and turned into resources. Biological CO2 fixation performed by autotrophic microorganisms using renewable energy can thereby play an important role, but requires improvement in capacity and efficiency. To enable targeted improvements, computational methods in systems biology and metabolic engineering were used in this thesis to identify thermodynamic and kinetic constraints of autotrophic microorganisms using the Calvin cycle as their primary CO2 fixation pathway. In Paper I, the different metabolic networks of the photoautotrophic cyanobacterium Synechocystis and the heterotrophic E. coli were compared, revealing network- specific intracellular metabolite concentration ranges and thermodynamic driving forces, causing different capabilities for production of industrially relevant chemicals. For Paper II, a kinetic metabolic model of the Calvin cycle in Synechocystis was developed and analyzed, exposing factors favoring a stable operation, such as a low concentration of Ribulose 1,5-phosphate or low saturation states of many enzymes towards their substrates. It furthermore revealed that control over the reaction rates in the Calvin cycle was distributed, but the CO2 fixation rate could be increased by higher rates through enzymes such as fructose 1,6-bisphosphatase or phosphoglycerate kinase. In Paper III, experimentally determined interactions between metabolites and proteins in several autotrophic microorganisms were tested for their regulatory functions. For Synechocystis, these interactions were interpreted in the metabolic context by integrating them in an expanded kinetic model, revealing significant shifts in metabolome stability when biochemical regulation was added to transketolase, an enzyme central to the Calvin cycle, but only minor effects on flux control. Lastly, for Paper IV the thermodynamic landscape of Cupriavidus necator and its natural capacity of producing the bioplastic PHB were evaluated. Different substrate utilization scenarios and metabolic engineering strategies were simulated using a metabolic model, revealing substrate-independent thermodynamic constraints and contrasting effects of the engineering efforts. This work provides the knowledge for further studies and targeted engineering efforts aiming to alleviate constraints on autotrophic metabolism to improve its performance in transforming CO2 into usable resources.
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