Publications by authors named "Colbie J Reed"
Article Synopsis
- tRNA modifications are important for ensuring accurate protein synthesis and may help bacteria respond to stress and virulence, yet there's limited understanding of these modifications in intracellular pathogens.
- The study used various advanced methods like genomics and mass spectrometry to identify tRNA modification genes in Bartonella species, which cause cat-scratch disease and trench fever, overcoming challenges such as contamination from host RNA.
- Findings revealed that these bacteria have fewer tRNA modification genes compared to other species, indicating a trend of gene loss and simplification of modifications, suggesting a process of reductive evolution.
Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on specific members of that family. Using a previously gathered dataset of more than 280 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3) family, we evaluated the efficiency of different databases and search tools, and devised a workflow that experimentalists can use to capture the most information published on members of a protein family in the least amount of time. To complement this workflow, web-based platforms allowing for the exploration of protein family members across sequenced genomes or for the analysis of gene neighbourhood information were reviewed for their versatility and ease of use.
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- tRNA modifications are essential for accurate protein synthesis and may also help bacteria respond to stress and infection.
- This study used advanced techniques to identify tRNA modification genes in two intracellular bacteria linked to diseases, despite challenges like host RNA contamination.
- The researchers discovered a reduced set of tRNA modification genes in these pathogens, indicating a trend of gene loss and simplification compared to other bacteria.
Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on specific members of that said family. Using a previously gathered dataset of more than 280 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3), we evaluated the efficiency of different databases and search tools, and devised a workflow that experimentalists can use to capture the most published information on members of a protein family in the least amount of time. To complement this workflow, web-based platforms allowing for the exploration of protein family members across sequenced genomes or for the analysis of gene neighborhood information were reviewed for their versatility and ease of use.
View Article and Find Full Text PDFDihydrouridine (D) is an abundant modified base found in the tRNAs of most living organisms and was recently detected in eukaryotic mRNAs. This base confers significant conformational plasticity to RNA molecules. The dihydrouridine biosynthetic reaction is catalyzed by a large family of flavoenzymes, the dihydrouridine synthases (Dus).
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- * A detailed review of literature and bioinformatics analysis revealed that this labeling may be inaccurate, as the proteins exhibit diverse functions and effects.
- * The study suggests that DUF34 proteins may actually function as metal ion insertases, chaperones, or metallocofactor maturases, which could explain their roles in various biological processes like cell differentiation and pathogen virulence.