A roadmap for the functional annotation of protein families: a community perspective

…, R Amorin de Hegedus, C Arighi, J Babor… - 2022 - academic.oup.com
Over the last 25 years, biology has entered the genomic era and is becoming a science of ‘big
data’. Most interpretations of genomic analyses rely on accurate functional annotations of …

Characterization of the Escherichia coli pyridoxal 5′‐phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability

A Tramonti, MS Ghatge, JT Babor, FN Musayev… - Protein …, 2022 - Wiley Online Library
The pyridoxal 5′‐phosphate (PLP) homeostasis protein (PLPHP) is a ubiquitous member of
the COG0325 family with apparently no catalytic activity. Although the actual cellular role of …

4′-Deoxypyridoxine disrupts vitamin B6 homeostasis in Escherichia coli K12 through combined inhibition of cumulative B6 uptake and PLP-dependent enzyme …

J Babor, A Tramonti, C Nardella… - …, 2023 - microbiologyresearch.org
Pyridoxal 5′-phosphate (PLP) is the active form of vitamin B 6 and a cofactor for many
essential metabolic processes such as amino acid biosynthesis and one carbon metabolism. 4’-…

Are Bacterial Processes Dependent on Global Ribosome Pausing Affected by tRNA Modification Defects?

…, Z Baharoglu, Y Yuan, G Boël, J Babor… - Journal of Molecular …, 2025 - Elsevier
By integrating a literature review with transcriptomic, proteomic, and phenotypic data from
two model bacteria, Escherichia coli and Vibrio cholerae, we put forward the hypothesis that …

Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes

R Denise, J Babor, JA Gerlt… - Microbial …, 2023 - microbiologyresearch.org
Pyridoxal 5’-phosphate or PLP is a cofactor derived from B 6 vitamers and essential for growth
in all known organisms. PLP synthesis and salvage pathways are well characterized in a …

Tandem inactivation of inositol pyrophosphatases Asp1, Siw14, and Aps1 illuminates functional redundancies in inositol pyrophosphate catabolism in fission yeast

B Schwer, I Prucker, AM Sanchez, J Babor, HJ Jessen… - mBio, 2025 - journals.asm.org
Inositol pyrophosphates are key effectors of eukaryal cellular phosphate homeostasis. They
are synthesized by kinases that add a β-phosphate to the 5- or 1-phosphate groups of IP 6 …

The ubiquitous pyridoxal 5′‐phosphate‐binding protein is also an RNA‐binding protein

…, ML di Salvo, I De Cecio, T Colombo, J Babor… - Protein …, 2024 - Wiley Online Library
The pyridoxal 5′‐phosphate binding protein (PLP‐BP) is believed to play a crucial role in
PLP homeostasis, which may explain why it is found in living organisms from all kingdoms. …

Synergistic effects of tRNA modification defects in Escherichia coli K12

JM Bacusmo, J Babor, J Hu, B Cao, S Kellner… - bioRxiv, 2024 - biorxiv.org
tRNAs are the central adaptor molecule in translation and require a wide variety of post-transcriptional
modifications to fulfill their functions. The model gram-negative Escherichia coli K-…

Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families

CJ Reed, R Denise, J Hourihan, J Babor… - Microbial …, 2024 - microbiologyresearch.org
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 …

DrpB (YedR) is a nonessential cell division protein in Escherichia coli

A Yahashiri, JT Babor, AL Anwar, RP Bezy… - Journal of …, 2020 - journals.asm.org
We report that the small Escherichia coli membrane protein DrpB (formerly YedR) is involved
in cell division. We discovered DrpB in a screen for multicopy suppressors of a ΔftsEX …