Riboswitch Detection Using Profile Hidden Markov Models

Singh, Payal; Bandyopadhyay, Pradipta; Bhattacharya, Sudha; Krishnamachari, Annangarachari; Sengupta, Supratim

doi:10.1186/1471-2105-10-325

Cited by 35 publications

(31 citation statements)

References 44 publications

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“…A purine riboswitch-specific pHMM7 was used to screen the bacterial genomes. A systematic analysis of the genomic context of purine riboswitches was carried out to identify the genes upstream to which riboswitches occur.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes

Singh

Sengupta

2012

Evol Bioinform Online

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Riboswitches are regulatory RNA that control gene expression by undergoing conformational changes on ligand binding. Using phylogenetic analysis and comparative genomics we have been able to identify the class of genes/operons regulated by the purine riboswitch and obtain a high-resolution map of purine riboswitch distribution across all bacterial groups. In the process, we are able to explain the absence of purine riboswitches upstream to specific genes in certain genomes. We also identify the point of origin of various purine riboswitches and argue that not all purine riboswitches are of primordial origin, and that some purine riboswitches must have originated after the divergence of certain Firmicute orders in the course of evolution. Our study also reveals the role of horizontal transfer events in accounting for the presence of purine riboswitches in some gammaproteobacterial species. Our work provides significant insights into the origin, distribution and regulatory role of purine riboswitches in prokaryotes.

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Section: Methodsmentioning

confidence: 99%

Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes

Singh

Sengupta

2012

Evol Bioinform Online

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“…Thiamine pyrophosphate (TPP) is the most abundant riboswitch and is known to be present even in eukaryotes [37]. It has an intermediate level of sequence conservation [38]. So in many organisms (prokaryotes, algae, plants and fungi), riboswitch has been found to play the role of regulating thiamine biosynthesis [39].…”

Section: Thiamine Pyrophosphate: the Dominant Class Of Riboswitchmentioning

confidence: 99%

The Role of Thiamine in Plants and Current Perspectives in Crop Improvement

Subki¹,

Abidin²,

Yusof³

2018

B Group Vitamins - Current Uses and Perspectives

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Current research is focusing on selecting potential genes that can alleviate stress and produce disease-tolerant crop variety. The novel paradigm is to investigate the potential of thiamine as a crop protection molecule in plants. Thiamine or vitamin B 1 is important for primary metabolism for all living organisms. The active form, thiamine pyrophosphate (TPP), is a cofactor for the enzymes involved in the synthesis of amino acids, tricarboxylic acid cycle and pentose phosphate pathway. Recently, thiamine is shown to have a role in the processes underlying protection of plants against biotic and abiotic stresses. The aim of this chapter is to review the role of thiamine in plant growth and disease protection and also to highlight that TPP and its intermediates are involved in management of stress. The perspectives on its potential for manipulating the biosynthesis pathway in crop improvement will also be discussed.

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“…In contrast, while secondary structure is conserved in the terminator loop of the expression platform in purine riboswitches, there is relatively low sequence conservation (data not shown). While a number of methods exist to computationally predict riboswitch aptamers [31], [32], [33], [34], [35] (and especially INFERNAL [36], which latter is used to predict riboswitch aptamers in Rfam), it is an important biological problem to determine the expression platform, since the structure of the expression platform can suggest whether there is transcriptional regulation via a terminator loop or translational regulation via the sequestration of the Shine-Dalgarno sequence [28]. Determination of the precise location and structure of the expression platform is difficult due to low conserved sequence identity (in-house computations, data not shown).…”

Section: Resultsmentioning

confidence: 99%

Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches

et al. 2012

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Using complex roots of unity and the Fast Fourier Transform, we design a new thermodynamics-based algorithm, FFTbor, that computes the Boltzmann probability that secondary structures differ by base pairs from an arbitrary initial structure of a given RNA sequence. The algorithm, which runs in quartic time and quadratic space , is used to determine the correlation between kinetic folding speed and the ruggedness of the energy landscape, and to predict the location of riboswitch expression platform candidates. A web server is available at http://bioinformatics.bc.edu/clotelab/FFTbor/.

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Riboswitch Detection Using Profile Hidden Markov Models

Cited by 35 publications

References 44 publications

Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes

Phylogenetic Analysis and Comparative Genomics of Purine Riboswitch Distribution in Prokaryotes

The Role of Thiamine in Plants and Current Perspectives in Crop Improvement

Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches

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