Gut microbiota DPP4-like enzymes are increased in type-2 diabetes and contribute to incretin inactivation.

Background: The gut microbiota controls broad aspects of human metabolism and feeding behavior, but the basis for this control remains largely unclear. Given the key role of human dipeptidyl peptidase 4 (DPP4) in host metabolism, we investigate whether microbiota DPP4-like counterparts perform the same function.

Results: We identify novel functional homologs of human DPP4 in several bacterial species inhabiting the human gut, and specific associations between Parabacteroides and Porphyromonas DPP4-like genes and type 2 diabetes (T2D).

The Complement Inhibitor Factor H Generates an Anti-Inflammatory and Tolerogenic State in Monocyte-Derived Dendritic Cells.

The activation of the complement system is a key initiating step in the protective innate immune-inflammatory response against injury, although it may also cause harm if left unchecked. The structurally related soluble complement inhibitors C4b-binding protein (C4BP) and factor H (FH) exert a tight regulation of the classical/lectin and alternative pathways of complement activation, respectively, attenuating the activity of the C3/C5 convertases and, consequently, avoiding serious damage to host tissues. We recently reported that the acute-phase C4BP isoform C4BP lacking the β-chain plays a pivotal role in the modulation of the adaptive immune responses.

Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species.

Background: Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level.

Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases.

Background: RNA post-transcriptional modification is an exciting field of research that has evidenced this editing process as a sophisticated epigenetic mechanism to fine tune the ribosome function and to control gene expression. Although tRNA modifications seem to be more relevant for the ribosome function and cell physiology as a whole, some rRNA modifications have also been seen to play pivotal roles, essentially those located in central ribosome regions. RNA methylation at nucleobases and ribose moieties of nucleotides appear to frequently modulate its chemistry and structure.

Impairing methylations at ribosome RNA, a point mutation-dependent strategy for aminoglycoside resistance: the rsmG case.

Introduction: Aminoglycosides like streptomycin are well-known for binding at specific regions of ribosome RNA and then acting as translation inhibitors. Nowadays, several pathogens have been detected to acquire an undefined strategy involving mutation at non structural ribosome genes like those acting as RNA methylases. rsmG is one of those genes which encodes an AdoMet-dependent methyltransferase responsible for the synthesis of m 7 G527 in the 530 loop of bacterial 16S rRNA.

A practical guide for the computational selection of residues to be experimentally characterized in protein families.

In recent years, numerous biocomputational tools have been designed to extract functional and evolutionary information from multiple sequence alignments (MSAs) of proteins and genes. Most biologists working actively on the characterization of proteins from a single or family perspective use the MSA analysis to retrieve valuable information about amino acid conservation and the functional role of residues in query protein(s). In MSAs, adjustment of alignment parameters is a key point to improve the quality of MSA output.

[Bioinformatics in Colombia: state of the art and perspectives].

Bioinformatics emerged about 50 years ago, but it was developed greatly during the early 1980s by robust databases such as GenBank, EMBL, and DNA Database of Japan (DDBJ). Bioinformatic routines were rapidly adapted once the main algorithms for sequence analysis became available worldwide. As in other science fields, bioinformatics had minimal impact in low-income countries of Latin America until the last decade.

Dissection of functional residues in receptor activity-modifying proteins through phylogenetic and statistical analyses.

Type I and type-II functional divergences have been stated to highlight specific residues carrying out differential functions in evolutionary-divergent protein clusters from a single common ancestor. Briefly, type I analysis is based on residue constraints reflecting a gain of function just in one cluster of an entire family of proteins; while the type-II approach is based on residue constraints showing a different chemical nature in every cluster of a protein family. This last evidence is understood as differential functionality among clusters.