Browsing by Author "Swamy, Krishna B. S."

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Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast
(2012-01-10)
Chiang, Sufeng
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Swamy, Krishna B. S.
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Hsu, Ting-Wei
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Tsai, Zing Tsung-Yeh
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Lu, Henry Horng-Shing
It is generally accepted that genes are regulated by the interactions between transcription factors (TFs) and their binding sites (TFBSs). Some studies have demonstrated that nucleotide variants at variable positions in TFBSs affect yeast gene regulation. Furthermore, variable positions in TFBSs in association with distinct accompanying regulatory motifs of other TFs (i.e., co-TFs) can also impact gene regulation in eukaryotes. Given that, even low-affinity IF-DNA interactions are abundant in vivo; we used both low- and high-affinity TFBSs and performed a genome-wide analysis of associations between variable positions and co-TFs. We found that in Saccharomyces cerevisiae, approximately 14% of the variable positions in TFBSs demonstrate such associations. These associations occurred in close proximity on the same promoters (i.e., highly co-localized). Moreover, such associations were highly conserved between sensu stricto yeasts and also influenced gene expression, which were consistent with enriched functional categories. (C) 2011 Elsevier B.V. All rights reserved.
The evolutionary dynamics of tRNA-gene copy number and codon-use in E-coli
(2015-08-19)
McDonald, Michael J.
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Chou, Chih-Hung
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Swamy, Krishna B. S.
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Huang, Hsien-Da
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Leu, Jun-Yi
Background: The introduction of foreign DNA by Lateral Gene Transfer (LGT) can quickly and drastically alter genome composition. Problems can arise if the genes introduced by LGT use codons that are not suited to the host's translational machinery. Here we investigate compensatory adaptation of E. coli in response to the introduction of large volumes of codons that are rarely used by the host genome. Results: We analyze genome sequences from the E. coli/Shigella complex, and find that certain tRNA genes are present in multiple copies in two pathogenic Shigella and O157:H7 subgroups of E. coli. Furthermore, we show that the codons that correspond to these multi-copy number tRNA genes are enriched in the high copy number Selfish Genetic Elements (SGE's) in Shigella and laterally introduced genes in O157:H7. We analyze the duplicate copies and find evidence for the selective retention of tRNA genes introduced by LGT in response to the changed codon content of the genome. Conclusion: These data support a model where the relatively rapid influx of LGT genes and SGE's introduces a large number of genes maladapted to the host's translational machinery. Under these conditions, it becomes advantageous for the host to retain tRNA genes that are required for the incorporation of amino acids at these codons. Subsequently, the increased number of copies of these specific tRNA genes adjusts the cellular tRNA pool to the demands set by global shifts in codon usage.