SPP 2002

Small Proteins in Prokaryotes, an Unexplored World

Motivation:

Small proteins are difficult to detect due to technical limitations but new technologies are emerging to enable their global profiling and systematic investigation of their physiological roles.

We aim to 1) globally identify small proteins in selected prokaryotes using comparative genomics, translatomics and peptidomics, 2) advance novel analytical tools to identify small proteins and their physiological roles, and 3) elucidate the functions and interaction partners of small proteins as well as underlying molecular mechanisms. Exploring the small proteome in Prokaryotes will not only deepen our understanding of gene expression regulation and protein function in general, but may also provide new innovative biotechnological applications and antimicrobial strategies. By disclosing representative functions and mechanisms for the products of this major class of genes in prokaryotic genomes we envisage to uncover novel unique prokaryotic principles in regulation of gene expression and assembly/­disassembly of large (membrane) complexes.

 

Projects:

Archaea:

  1. Functional analysis of small proteins in Methanosarcina mazei focusing on those involved in nitrogen regulation or biofilm formation
    R. Schmitz-Streit
  2. Haloferax volcanii small proteins that contain two CPXCG motifs indicative for one-domain zinc finger proteins
    J. Soppa
  3. Small proteins in Haloferax volcanii: an important part of the proteome
    A. Marchfelder

α-Proteobacteria:

  1. Biological Role of outer membrane vesicle-associated small proteins of the phytopathogen Agrobacterium tumefaciens
    M. Aktas
  2. Small proteins in the soybean symbiont Bradyrhizobium japonicum
    E. Evguenieva-Hackenberg
  3. Role of small proteins in the stress response of alpha-proteobacteria
    G. Klug
  4. Investigation of small arginine-rich proteins of the DUF1127 family from Agrobacterium tumefaciens
    F. Narberhaus

γ-Proteobacteria:

  1. Functional and regulatory interdependence of small proteins during membrane depolarization and persister cell formation in Escherichia coli
    B. Berghoff

Cyanobacteria:

  1. The role of small proteins in metabolic regulation of cyanobacteria
    M. Hagemann
  2. The role of small proteins, peptides and dual function transcripts in cyanobacteria
    W. R. Hess
  3. The role of small single transmembrane helix proteins in cyanobacteria
    M. Nowaczyk

Bacillus subtilis:

  1. Peptide encoding an dual-function sRNAs in Bacillus subtilis
    S. Brantl

Human microbiome related:

  1. Improving prediction and detection of small proteins for functional analysis in a consortium resembling the functions of the human microbiome
    P. F. Stadler and M. von Bergen

Pathogenesis related:

  1. The role of small proteins in the plant pathogen Xanthomonas
    U. Bonas and C. Schmidtke
  2. Functional peptides implicated in the virulence of the enteric pathogen Yersinia pseudotuberculosis
    P. Dersch
  3. Small proteins and dual RNA regulators in Vibrio cholera
    K. Papenfort
  4. Functions of small proteins regulated during Salmonella infection
    J. Vogel
  5. Exploring small proteins in the food-borne pathogen Campylobacter jejuni
    C. M. Sharma

Membrane related:

  1. Identifying and characterizing µ-membrane proteins in prokaryotic terminal oxidases and proteomes
    J. Langer
  2. Small membrane proteins (SMPs) as organizers of the bacterial membrane
    H.-G. Koch

Phages:

  1. Discovery and characterization of prophage-encoded peptides that direct communication between phages
    R. Sorek

Biotechnicals / chemical methods:

  1. NMR and biophysical characterization of structure and dynamics of small proteins and their complexes
    H. Schwalbe
  2. Systematic identification of novel small proteins in bacteria using ribosome profiling data
    Z. Ignatova
  3. Chemo-enzymatic platform for the discovery of natural and functionalized sactipeptides
    H. Kolmar

Z- Projects:

  1. Z1: Proteomics and peptidomics for the identification and functional characterization of sORF encoded proteins
    D. Becher and A. Tholey
  2. Z2: Riboprofiling and Bioinformatics
    C. M. Sharma and R. Backofen