Analysis of Spo0M function in Bacillus subtilis.

Spo0M has been previously reported as a regulator of sporulation in Bacillus subtilis; however, little is known about the mechanisms through which it participates in sporulation, and there is no information to date that relates this protein to other processes in the bacterium. In this work we present evidence from proteomic, protein-protein interaction, morphological, subcellular localization microscopy and bioinformatics studies which indicate that Spo0M function is not necessarily restricted to sporulation, and point towards its involvement in other stages of the vegetative life cycle. In the current study, we provide evidence that Spo0M interacts with cytoskeletal proteins involved in cell division, which suggest a function additional to that previously described in sporulation.

Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model.

Background: The goal of most programs developed to find transcription factor binding sites (TFBSs) is the identification of discrete sequence motifs that are significantly over-represented in a given set of sequences where a transcription factor (TF) is expected to bind. These programs assume that the nucleotide conservation of a specific motif is indicative of a selective pressure required for the recognition of a TF for its corresponding TFBS. Despite their extensive use, the accuracies reached with these programs remain low.

RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock.

Background: Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R.

The cation diffusion facilitator protein EmfA of Rhizobium etli belongs to a novel subfamily of Mn(2+)/Fe(2+) transporters conserved in α-proteobacteria.

Manganese (Mn(2+)) plays a key role in important cellular functions such as oxidative stress response and bacterial virulence. The mechanisms of Mn(2+) homeostasis are not fully understood, there are few data regarding the functional and taxonomic diversity of Mn(2+) exporters. Our recent phylogeny of the cation diffusion facilitator (CDF) family of transporters classified the bacterial Mn(2+)-CDF transporters characterized to date, Streptococcus pneumoniae MntE and Deinococcus radiodurans DR1236, into two monophyletic groups.

Phylogenomic analysis of Cation Diffusion Facilitator proteins uncovers Ni2+/Co2+ transporters.

The ubiquitous Cation Diffusion Facilitator proteins (CDF) play a key role in maintaining the cellular homeostasis of essential metal ions. Previous neighbor-joining phylogenetic analysis classified CDF proteins into three substrate-defined groups: Zn(2+), Fe(2+)/Zn(2+) and Mn(2+). These studies were unable to discern substrate-defined clades for Ni(2+), Co(2+), Cd(2+) and Cu(2+) transporters, despite their existence in this family.