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Fitness Effects of Changing Codon Bias of two genes – mauA and mtdA in Methylobacterium extorquens AM1

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dc.contributor.advisor Agashe, Deepa en_US
dc.contributor.author WALUNJKAR, NILIMA en_US
dc.date.accessioned 2018-04-18T08:22:53Z
dc.date.available 2018-04-18T08:22:53Z
dc.date.issued 2017-04 en_US
dc.identifier.uri http://dr.iiserpune.ac.in:8080/xmlui/handle/123456789/796
dc.description.abstract Organisms have a codon bias i.e. they use certain codons more frequently than others that code for the same amino acid. Studies have shown that changing the codon bias of a gene can have a negative impact on fitness due to decreased mRNA and protein levels. Mechanisms like tRNA-codon imbalance, ribosome pausing and altered mRNA secondary structure have been proposed to explain the fitness effects of altering codon usage. We are studying the fitness effects of changing the codon bias of two genes, mauA and mtdA in Methylobacterium extorquens. Changing the codon bias of fae, another gene in M. extorquens has a negative impact on fitness. By comparing the trends in fitness effects across genes from the same pathway, we may unearth the mechanistic basis of this effect. We generated codon usage variants of mauA and mtdA and quantified their growth rates. Preliminary analysis shows that fitness effects in mauA strains are similar to those of fae. While those seen in mtdA codon usage variants appear to depend on the carbon substrate available, though this may be an artefact of the FLAG tag introduced into the sequence. Also, a previous study in the lab evolved the codon altered fae strains and sequenced them. Here we analyse this sequence data to identify background mutations that could contribute to increasing fitness. Our preliminary data supports the hypothesis that fitness effects of synonymous mutations are context dependent. en_US
dc.language.iso en en_US
dc.subject 2017
dc.subject Biology en_US
dc.subject mauA en_US
dc.subject mtdA en_US
dc.subject Methylobacterium extorquens AM1 en_US
dc.subject Fitness Effects en_US
dc.title Fitness Effects of Changing Codon Bias of two genes – mauA and mtdA in Methylobacterium extorquens AM1 en_US
dc.type Thesis en_US
dc.type.degree BS-MS en_US
dc.contributor.department Dept. of Biology en_US
dc.contributor.registration 20121040 en_US


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  • MS THESES [1705]
    Thesis submitted to IISER Pune in partial fulfilment of the requirements for the BS-MS Dual Degree Programme/MSc. Programme/MS-Exit Programme

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