• RNA Thermometers
• Regulated proteolysis
• Bacterial Membrane Biosynthesis
• Bacterial predation behavior
• RNA-SURIBA

RNA Thermometers

Structured RNA regions influence every step in the gene expression program. Many bacterial heat shock and virulence genes are regulated by RNA thermometers (RNATs), which are molecular zippers that control translation initiation. They adopt a structure that blocks the ribosome binding site at low temperatures. A temperature upshift to 37°C (virulence genes) or higher (heat shock genes) destabilizes the structure and permits translation.

Regulated proteolysis

The FtsH protease of E. coli controls important cellular processes like the heat shock response and lipopolysaccharide (LPS) biosynthesis by controlled proteolysis of the responsible key factors. Induction of the heat shock response requires the alternative sigma factor RpoH (Sigma32). Degradation of RpoH under non-stress conditions requires FtsH and the DnaKJ chaperone system. Little is known about proteolysis of LpxC, the key enzyme in LPS biosynthesis. We study how the FtsH protease recognizes its substrate and attempt to identify the turnover elements in RpoH and LpxC by genetic and biochemical approaches.

Bacterial Membrane Biosynthesis

Every living cell is enveloped by at least one membrane, which provides the first line of defense against toxic compounds and harmful conditions. We are interested in the biosynthesis of phosphatidylcholine (PC), an unusual phospholipid in bacteria that plays an important role in stress resistance and host-microbe interactions. We biochemically characterize the enzymes of three different PC biosynthesis pathways that operate either at the phospholipid head group or at the fatty acid site chains.

Bacterial predation behavior

Bacteria have evolved different strategies for surviving in competitive environments. One such strategy is bacterial predation, where predators kill bacteria of another species to use their biomass as an energy source. We study predation behavior of the social soil bacterium Myxococcus xanthus to reveal molecular mechanisms that mediate the specific recognition and lysis of bacterial prey.

RNA-SURIBA

Welcome to the RNA-SURIBA homepage!

The database RNA-SURIBA contains RNA-secondary structure predictions and a set of additional
parameters for all upstream regions of all genes of diverse bacterial genomes.

It can be downloaded free of charge.

Details of the database are published in the article ‘Genome-wide bioinformatic prediction and
experimental evaluation of potential RNA thermometers’
by Waldminghaus, T., Gaubig, L. C., and Narberhaus, F.; Molecular Genetics and Genomics, 2007.

For other articles related to the database see publications.

Download options are specified in the manual.

Any comments and questions should be directed to E-Mail.

Datafiles

• The whole database RNA-SURIBA
• RNA-SURIBA Single Files (Overview)

Please contact us by mail and we will provide you with the datafiles.

Publications

Narberhaus, F., Waldminghaus, T., and Chowdhury, S. (2006) RNA thermometers. FEMS Microbiol Rev 30: 3-16.

Waldminghaus, T., Heidrich, N., Brantl, S. and Narberhaus, F. (2007) FourU – A novel type of RNA thermometer in Salmonella. Mol Microbiol 65(2): 413-24.

Waldminghaus, T., Fippinger, A., Alfsmann, J., and Narberhaus, F. (2005) RNA thermometers are common in alpha - and gamma -proteobacteria. Biol Chem 386: 1279-1286.

Manual

RNA Structures od untranslated Regions in Bacteria

Database description

The database RNA-SURIBA contains RNA-secondary structure predictions and a set of additional parameters for all upstream regions of all genes from 62 bacterial genomes.

Construction and content of the database RNA-SURIBA are described in detail in the article: Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers by Waldminghaus, T., Gaubig, L. C., and Narberhaus, F.; Molecular Genetics and Genomics, 2007.

RNA-SURIBA contains 62 tables, one for each genome. Tables are named according to the bacterial species (see table 1). Each table consists of 36 colums with the structure predictions, sequences, gene annotation data and calculated parameters for each structure (see table 2 for details).


Download RNA-SURIBA

We provide the database RNA-SURIBA in two different formats. First, a SQL-DUMP that allows the simple use of RNA-SURIBA with any SQL-server independently of the platform. Second, ASCII flat files of each table which provide the possibility to download only the dataset of interest and not the whole database. The order of rows in the flat files is consistent with the order in table 2.

Example for installing RNA-SURIBA from the DUMP-file on a postgresql system:

1. Start the SQL-server /usr/bin/pg_ctl -D /home/charly/database/postgresql/data -l /home/charly/tmp/logfile start
2. Create a database with the name RNA-SURIBA shell> /usr/local/pgsql/bin/createdb RNA-SURIBA
3. Read in the DUMP shell> psql RNA-SURIBA RNA-SURIBA.dump
4. Connect to the database RNA-SURIBA shell> psql RNA-SURIBA
   Additional Material

In addition to the database, drawings of the structures in GIF-format of each structure prediction are provided. The drawings are stored in one zip-file for every genome named after the corresponding genome (see table 1). The files are stored in folders named after the corresponding genome (see table 1). Each file is designated according to the start of the gene on the chromosome (column 2 in each RNA-SURIBA table) in combination with the folding number (column 6 in each RNA-SURIBA table).

Example:

For gene thrL from E. coli the gene start is 190 and structure prediction with the lowest energy of -11.0 represents folding 1. The corresponding file is stored as EC/Foldings/190_1.gif.