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

Martí-Arbona, Ricardo; Mu, Fangping; Nowak-Lovato, Kristy L.; Wren, Melinda S.; Unkefer, Clifford J.; Unkefer, Pat J.

doi:10.1186/1471-2164-15-1142

Title: Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions

Journal Article · Thu Dec 18 00:00:00 EST 2014 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-15-1142· OSTI ID:1201466

Martí-Arbona, Ricardo ^[1]; Mu, Fangping ^[1]; Nowak-Lovato, Kristy L. ^[1]; Wren, Melinda S. ^[1]; Unkefer, Clifford J. ^[1]; Unkefer, Pat J. ^[1]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

In this study, the clustering of genes in a pathway and the co-location of functionally related genes is widely recognized in prokaryotes. We used these characteristics to predict the metabolic involvement for a Transcriptional Regulator (TR) of unknown function, identified and confirmed its biological activity. software tool that identifies the genes encoded within a defined genomic neighborhood for the subject TR and its homologs was developed. The output lists of genes in the genetic neighborhoods, their annotated functions, the reactants/products, and identifies the metabolic pathway in which the encoded-proteins function. When a set of TRs of known function was analyzed, we observed that their homologs frequently had conserved genomic neighborhoods that co-located the metabolically related genes regulated by the subject TR. We postulate that TR effectors are metabolites in the identified pathways; indeed the known effectors were present. We analyzed Bxe_B3018 from Burkholderia xenovorans, a TR of unknown function and predicted that this TR was related to the glycine, threonine and serine degradation. We tested the binding of metabolites in these pathways and for those that bound, their ability to modulate TR binding to its specific DNA operator sequence. Using rtPCR, we confirmed that methylglyoxal was an effector of Bxe_3018. These studies provide the proof of concept and validation of a systematic approach to the discovery of the biological activity for proteins of unknown function, in this case a TR. Bxe_B3018 is a methylglyoxal responsive TR that controls the expression of an operon composed of a putative efflux system.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1201466

Alternate ID(s):: OSTI ID: 1238661

Report Number(s):: LA-UR-14-20616; PII: 1471-2164-15-1142

Journal Information:: BMC Genomics, Vol. 15, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 2 works

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59 BASIC BIOLOGICAL SCIENCES
comparative genomics
Bxe_B3018
methylglyoxal
transcriptional regulator
anisotropy
EMSA
FAC-MS
rtPCR
Burkholderia xenovorans LB400
protein function discovery
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Title: Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions

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