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Insights into Occurrence and Divergence of Intrinsic Terminators and Studies on Rho-Dependent Termination in Mycobacterium Tuberculosis

Electronic Theses of Indian Institute of Science

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Title Insights into Occurrence and Divergence of Intrinsic Terminators and Studies on Rho-Dependent Termination in Mycobacterium Tuberculosis
 
Creator Mitra, Anirban
 
Subject Mycobacterium Tuberculosis
Mycobacteria - Intrinsic Terminators,
Mycobacterium Tuberculosis -Rho-Dependent Termination -
Intrinsic Termination
Mycobacteria - Transcription Termination
Genetic Transcription - Regulation, Mycobacteria
RHO Proteins - Mycobacterium Tuberculisis
Non-Canonical Intrinsic Terminators
MtbRho
Mycobacterial Genomes
NUS Factors - Intrinsic Termination
Bacterial Transcription Termination
M. tuberculosis - Rho Factor
Mycobacterium tuberculosis - Rho-dependent Terminators
Mycobacterium - Intrinsic Terminators
Bacteriology
 
Description Two mechanisms, intrinsic and factor-dependent, have evolved for accomplishing the termination of transcription in eubacteria. In this thesis, the first chapter is an introduction to the topic that presents what is known about the mechanisms of termination. The properties of the primary and secondary ‘players’- intrinsic terminators, Rho protein, rho-dependent terminators, RNA polymerse and Nus factors - are presented and the known mechanisms by which termination functions are discussed. In Chapter 2, a detailed analysis of intrinsic terminators – their differential distribution, similarity and divergence - has been penned. The database, compiled using the program GeSTer (Genome Scanner for Terminators), comprises ~2000 sequences and is one of the largest of its kind. Furthermore, analyzing the data from over 700 bacteria reveals how different species have fine-tuned intrinsic terminators to suit their cellular needs. Non-canonical intrinsic terminators emerge to be a significant fraction of the observed structures. The conserved structural features of identified intrinsic terminators are discussed and the relationship between the two modes of termination is assessed. Chapter 3 deals with the importance of transcription termination in regulating horizontally acquired DNA. The results show that genomic islands are scarce in intrinsic terminators and thus constitute most likely sites for Rho-dependent termination. Plausible reasons for why such a scenario has evolved are discussed and a generally applicable model is presented. Chapters 4 and 5 focus on Rho protein from Mycobacterium tuberculosis. In silico identification of M. tuberculosisgenes that rely on MtbRho-dependent termination is followed by experimental validation. The data show that Rho-dependent termination is the predominant mechanism in this species.MtbRho is a majorly expressed protein that governs termination of protein-coding and non-protein coding genes. Further, MtbRho can productively interact with RNA that has considerable secondary structure. Such interactions cause conformational changes in the enzyme. Given that MtbRho has to function with a GC-rich transcriptome, the altered properties could have evolved for optimal function.
Taken together, the thesis extends our current understanding of both modes of termination. The importance of non-canonical intrinsic terminators in mycobacteria and other organisms is discussed. The unusual function of Rho and its predominant role in mycobacteria is elucidated. Finally, the inter-relationship between the two modes of termination is also discussed.
 
Contributor Nagaraja, V
 
Date 2018-04-11T16:43:19Z
2018-04-11T16:43:19Z
2018-04-11
2013
 
Type Thesis
 
Identifier http://etd.iisc.ernet.in/2005/3382
http://etd.iisc.ernet.in/abstracts/4248/G25843-Abs.pdf
 
Language en_US
 
Relation G25843