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Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions

Tatiana V. Karpinets, Margaret F. Romine, Denise D. Schmoyer, Guruprasad H. Kora, Mustafa H. Syed, Michael R. Leuze, Margrethe H. Serres, Byung H. Park, Nagiza F. Samatova, Edward C. Uberbacher
2010 Database: The Journal of Biological Databases and Curation  
The integrated analysis of the data predicted a new type of bacterial transcriptional regulation involving co-transcription of the intergenic region with the downstream gene and suggested a biological  ...  role for co-transcription that likely prevents the binding of a regulator of the upstream gene to the regulator binding site located in the intergenic region.  ...  Acknowledgements We thank members of the Shewanella Federation for their contribution in developing the resource and in data submission. We are especially grateful to Jim Conflict of interest.  ... 
doi:10.1093/database/baq012 pmid:20627862 pmcid:PMC2911847 fatcat:bpto34rdqzc27i63ikcf2mxzzy

Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes

Tatiana V. Karpinets, Anna Y. Obraztsova, Yanbing Wang, Denise D. Schmoyer, Guruprasad H. Kora, Byung H. Park, Margrethe H. Serres, Margaret F. Romine, Miriam L. Land, Terence B. Kothe, Jim K. Fredrickson, Kenneth H. Nealson (+1 others)
2009 Functional & Integrative Genomics  
The second, a bottomup approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network  ...  Our first approach is top-down and involves experimental evaluation and quantification of the species' cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved  ...  Mushegian and other reviewers of the paper for thoughtful suggestions and comments on the study.  ... 
doi:10.1007/s10142-009-0142-y pmid:19802638 pmcid:PMC2834769 fatcat:co23bsd3tfbclkvajkk6jih3ga

Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA

Michael R. Leuze, Tatiana V. Karpinets, Mustafa H. Syed, Alexander S. Beliaev, Edward C. Uberbacher
2012 Gene Regulation and Systems Biology  
We explore the hypothesis that the number of BMs plays an important role in transcriptional regulation, examining empirical data from transcriptional profiling of the CRP and ArcA regulons.  ...  We compare the power of BM counts and of full TFBS characteristics to predict induced transcriptional activity.  ...  Acknowledgements The authors would like to thank Tim Gardner and his group for providing unpublished microarray data on crpmutant strain of S. oneidensis MR-1 for the analysis.  ... 
doi:10.4137/grsb.s9357 pmid:22701314 pmcid:PMC3370831 fatcat:5eli4lf5mjcw7oxzaj5jxkzepq

M. genitalium Whole-cell Model :: Data S1

Jonathan Karr
2012 Figshare  
Supplemental text for Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI & Covert MW. A Whole-Cell Computational Model Predicts Phenotype from Genotype.  ...  While there is a separate set of data for each of the 5 genes, the Transcription process class requires a single probability of transcription for each transcription unit.  ...  For example, the copy number of each gene plays a role in RNA polymerase binding in the Transcription process, and affects the cell's gene expression.  ... 
doi:10.6084/m9.figshare.93256.v1 fatcat:sy5hfikbgfgovflreompaunamq

A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity

Tim McCubbin, R. Axayacatl Gonzalez-Garcia, Robin W. Palfreyman, Chris Stowers, Lars K. Nielsen, Esteban Marcellin
2020 Genes  
Overall, the data provide a platform to explore Propionibacterium metabolism and a tool for the rational design of strains.  ...  Such data also enable a comparative genomic approach to annotation and provide a new opportunity to revisit our understanding of their metabolism.  ...  Acknowledgments: We thank Paul Swanson for his assistance performing and providing the BIOLOG analysis. Conflicts of Interest: The authors declare that they have no competing interests.  ... 
doi:10.3390/genes11101115 pmid:32977700 pmcid:PMC7650540 fatcat:x2sf23ze4vdp7a4s3zhn4rqjai