MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems

Abstract

Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated MiST database provides a comprehensive classification of microbial signal transduction systems. This update is a result of a substantial scaling to accommodate constantly growing microbial genomic data. More than 125 000 genomes, 516 million genes and almost 100 million unique protein sequences are currently stored in the database. For each bacterial and archaeal genome, MiST 3.0 provides a complete signal transduction profile, thus facilitating theoretical and experimental studies on signal transduction and gene regulation. New software infrastructure and distributed pipeline implemented in MiST 3.0 enable regular genome updates based on the NCBI RefSeq database. A novel MiST feature is the integration of unique profile HMMs to link complex chemosensory systems with corresponding chemoreceptors in bacterial and archaeal genomes. The data can be explored online or via RESTful API (freely available at https://mistdb.com).

Atypical chemoreceptor arrays accommodate high membrane curvature

“…Based on their evolutionary history and gene cluster organization, the spirochete T. denticola has a single F2 chemotaxis system encoded in its genome 10 . In the M icrobial S ignal T ransduction D atabase version 3 (MiST3) 12 , 306 genomes contain at least 1 CheA of the F2 class (CheA-F2) (Dataset 1). Only three of these genomes were not members of the Spirochaetota phylum and are likely the consequence of lateral gene transfer (see Supplementary Methods).…”

“…The spirochete chemotaxis system belongs to the ‘Flagella class 2’ (F2) category, which has not been investigated with structural methods 14 . To explore the characteristics of chemotaxis proteins in F2 genomes, we analyzed genomes in the Microbial Signal Transduction Database version 3 (MiST3) 15 . All genomes (306) with at least one CheA of the F2 class (CheA-F2) are in the Spirochaetota phylum, with a few exceptions of lateral gene transfer to other phyla (Dataset 1, see Supplementary Methods).…”

“…RAxML v8.2.10 10 was used to perform phylogenetic reconstructions, and low support branches in the phylogenetic trees were collapsed with TreeCollapseCL4 11 . Sequence logos were built using Weblogo 3.7 12 .…”

“…In MiST3 12 , 306 genomes contain at least 1 CheA-F2 (Dataset 1) with three exceptions: two of them belong to Acidobacteriota phylum,and one from Planctomycetota, which suggest that the presence of an F2 system in these genomes (outside of the Spirochaetota phylum) is the consequence of lateral gene transfer. Of the 306 genomes with at least one CheA-F2, only the following lack the CheW-CheR like protein: the three non-Spirochaetota genomes mentioned previously, 40 genomes of the Brachyspirae class, and three genomes from the order Borreliales (Fig.…”

Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens

“…The Hidden Markov Model (HMM) (Eddy 1996) and BLAST (Altschul et al 1997) were used to annotate the TCSs among all the ESKAPEE pathogens. The HMM profile information of HK and RR were collected from MIST3.0 (Gumerov et al 2020) , P2CS (Ortet et al 2015) , and literature. The Pfam profiles of the RR and HK in all ESKAPEE pathogens were downloaded using the Pfam32.0 (El-Gebali et al 2019) .…”