The ubiquitous pyridoxal 5'-phosphate-binding protein is also an RNA-binding protein.

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. Escherichia coli YggS is the most studied homolog, but human PLP-BP has also attracted much attention because variants of this protein are responsible for a severe form of B-responsive neonatal epilepsy. Yet, how PLP-BP is involved in PLP homeostasis, and thus what its actual function is in cellular metabolism, is entirely unknown.

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

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.

Beyond Blast: Enabling Microbiologists to Better Extract Literature, Taxonomic Distributions and Gene Neighborhood Information for Protein Families.

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.

4'-Deoxypyridoxine disrupts vitamin B homeostasis in K12 through combined inhibition of cumulative B uptake and PLP-dependent enzyme activity.

Pyridoxal 5'-phosphate (PLP) is the active form of vitamin B and a cofactor for many essential metabolic processes such as amino acid biosynthesis and one carbon metabolism. 4'-deoxypyridoxine (4dPN) is a long known B antimetabolite but its mechanism of action was not totally clear. By exploring different conditions in which PLP metabolism is affected in the model organism K12, we showed that 4dPN cannot be used as a source of vitamin B as previously claimed and that it is toxic in several conditions where vitamin B homeostasis is affected, such as in a B auxotroph or in a mutant lacking the recently discovered PLP homeostasis gene, .

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

Pyridoxal 5’-phosphate or PLP is a cofactor derived from B vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B transporters, are still to be identified in many organisms including the model bacteria or . Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes.

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

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 the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages.

DrpB (YedR) Is a Nonessential Cell Division Protein in Escherichia coli.

We report that the small membrane protein DrpB (formerly YedR) is involved in cell division. We discovered DrpB in a screen for multicopy suppressors of a Δ mutation that prevents divisome assembly when cells are plated on low ionic strength medium, such as lysogeny broth without NaCl. Characterization of DrpB revealed that (i) translation initiates at an ATG annotated as codon 22 rather than the GTG annotated as codon 1, (ii) DrpB localizes to the septal ring when cells are grown in medium of low ionic strength but localization is greatly reduced in medium of high ionic strength, (iii) overproduction of DrpB in a Δ mutant background improves recruitment of the septal peptidoglycan synthase FtsI, implying multicopy suppression works by rescuing septal ring assembly, (iv) a Δ mutant divides quite normally, but a Δ Δ double mutant has a strong division and viability defect, albeit only in medium of high ionic strength, and (v) DrpB homologs are found in and a few closely related enteric bacteria, but not outside this group.