scholarly journals Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

2004 ◽  
Vol 32 (21) ◽  
pp. 6321-6326 ◽  
Author(s):  
Tobias Doerks ◽  
Christian von Mering ◽  
Peer Bork
Keyword(s):  
Hypothetical Proteins ◽  
Genomic Context ◽  
Context Analysis ◽  
Genomic Context Analysis

scholarly journals Structural basis of terephthalate recognition by solute binding protein TphC

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Trishnamoni Gautom ◽  
Dharmendra Dheeman ◽  
Colin Levy ◽  
Thomas Butterfield ◽  
Guadalupe Alvarez Gonzalez ◽  
...  
Keyword(s):  
Genetic Resource ◽  
Binding Protein ◽  
Structural Basis ◽  
Bacterial Cells ◽  
Ligand Specificity ◽  
Biological Degradation ◽  
Genomic Context ◽  
Context Analysis ◽  
Structural Characterisation ◽  
Genomic Context Analysis

AbstractBiological degradation of Polyethylene terephthalate (PET) plastic and assimilation of the corresponding monomers ethylene glycol and terephthalate (TPA) into central metabolism offers an attractive route for bio-based molecular recycling and bioremediation applications. A key step is the cellular uptake of the non-permeable TPA into bacterial cells which has been shown to be dependent upon the presence of the key tphC gene. However, little is known from a biochemical and structural perspective about the encoded solute binding protein, TphC. Here, we report the biochemical and structural characterisation of TphC in both open and TPA-bound closed conformations. This analysis demonstrates the narrow ligand specificity of TphC towards aromatic para-substituted dicarboxylates, such as TPA and closely related analogues. Further phylogenetic and genomic context analysis of the tph genes reveals homologous operons as a genetic resource for future biotechnological and metabolic engineering efforts towards circular plastic bio-economy solutions.

scholarly journals Evolutionary and functional relationships revealed by the dha regulon predicted by genomic context analysis

2011 ◽  
Vol 12 (S1) ◽  
Author(s):  
Marinalva Martins-Pinheiro ◽  
Wanessa Cristina Lima ◽  
Cláudio A Oller ◽  
Carlos FM Menck
Keyword(s):  
Genomic Context ◽  
Context Analysis ◽  
Functional Relationships ◽  
Genomic Context Analysis ◽  
Dha Regulon

scholarly journals Genomic Context Analysis ofde Novo STXBP1Mutations Identifies Evidence of Splice Site DNA-Motif Associated Hotspots

2018 ◽  
Vol 8 (4) ◽  
pp. 1115-1118 ◽  
Author(s):  
Mohammed Uddin ◽  
Marc Woodbury-Smith ◽  
Ada J. S. Chan ◽  
Ammar Albanna ◽  
Berge Minassian ◽  
...  
Keyword(s):  
Splice Site ◽  
Genomic Context ◽  
Context Analysis ◽  
Dna Motif ◽  
Genomic Context Analysis

scholarly journals Prediction of enzymatic pathways by integrative pathway mapping

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Sara Calhoun ◽  
Magdalena Korczynska ◽  
Daniel J Wichelecki ◽  
Brian San Francisco ◽  
Suwen Zhao ◽  
...  
Keyword(s):  
Structural Biology ◽  
Metabolic Networks ◽  
Mapping Method ◽  
Computational Method ◽  
Molecular Networks ◽  
Genomic Context ◽  
Context Analysis ◽  
Pathway Mapping ◽  
Genomic Context Analysis ◽  
Enzymatic Pathways

The functions of most proteins are yet to be determined. The function of an enzyme is often defined by its interacting partners, including its substrate and product, and its role in larger metabolic networks. Here, we describe a computational method that predicts the functions of orphan enzymes by organizing them into a linear metabolic pathway. Given candidate enzyme and metabolite pathway members, this aim is achieved by finding those pathways that satisfy structural and network restraints implied by varied input information, including that from virtual screening, chemoinformatics, genomic context analysis, and ligand -binding experiments. We demonstrate this integrative pathway mapping method by predicting the L-gulonate catabolic pathway in Haemophilus influenzae Rd KW20. The prediction was subsequently validated experimentally by enzymology, crystallography, and metabolomics. Integrative pathway mapping by satisfaction of structural and network restraints is extensible to molecular networks in general and thus formally bridges the gap between structural biology and systems biology.

scholarly journals Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 1142 ◽  
Author(s):  
Ricardo Martí-Arbona ◽  
Fangping Mu ◽  
Kristy L Nowak-Lovato ◽  
Melinda S Wren ◽  
Clifford J Unkefer ◽  
...  
Keyword(s):  
Experimental Validation ◽  
Transcriptional Regulator ◽  
Genomic Context ◽  
Context Analysis ◽  
Genomic Context Analysis

scholarly journals Evolutionary and Functional Relationships of the dha Regulon by Genomic Context Analysis

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0150772 ◽  
Author(s):  
Marinalva Martins-Pinheiro ◽  
Wanessa C. Lima ◽  
Huma Asif ◽  
Cláudio A. Oller ◽  
Carlos F. M. Menck
Keyword(s):  
Genomic Context ◽  
Context Analysis ◽  
Functional Relationships ◽  
Genomic Context Analysis ◽  
Dha Regulon

scholarly journals Deciphering the Role of Multiple Thioredoxin Fold Proteins of Leptospirillum sp. in Oxidative Stress Tolerance

2020 ◽  
Vol 21 (5) ◽  
pp. 1880 ◽  
Author(s):  
Daniela González ◽  
Pamela Álamos ◽  
Matías Rivero ◽  
Omar Orellana ◽  
Javiera Norambuena ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Carbon Fixation ◽  
Coli Strain ◽  
Genomic Context ◽  
Context Analysis ◽  
Cytochrome C Biogenesis ◽  
Genomic Context Analysis ◽  
Domains Of Life ◽  
Cofactor Biosynthesis ◽  
High Concentrations

Thioredoxin fold proteins (TFPs) form a family of diverse proteins involved in thiol/disulfide exchange in cells from all domains of life. Leptospirillum spp. are bioleaching bacteria naturally exposed to extreme conditions like acidic pH and high concentrations of metals that can contribute to the generation of reactive oxygen species (ROS) and consequently the induction of thiol oxidative damage. Bioinformatic studies have predicted 13 genes that encode for TFP proteins in Leptospirillum spp. We analyzed the participation of individual tfp genes from Leptospirillum sp. CF-1 in the response to oxidative conditions. Genomic context analysis predicted the involvement of these genes in the general thiol-reducing system, cofactor biosynthesis, carbon fixation, cytochrome c biogenesis, signal transduction, and pilus and fimbria assembly. All tfp genes identified were transcriptionally active, although they responded differentially to ferric sulfate and diamide stress. Some of these genes confer oxidative protection to a thioredoxin-deficient Escherichia coli strain by restoring the wild-type phenotype under oxidative stress conditions. These findings contribute to our understanding of the diversity and complexity of thiol/disulfide systems, and of adaptations that emerge in acidophilic microorganisms that allow them to thrive in highly oxidative environments. These findings also give new insights into the physiology of these microorganisms during industrial bioleaching operations.

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