Functional characterization of the RNA chaperone Hfq in the opportunistic human pathogen Stenotrophomonas maltophilia

J Bacteriol. 2012 Nov;194(21):5864-74. doi: 10.1128/JB.00746-12. Epub 2012 Aug 24.


Hfq is an RNA-binding protein known to regulate a variety of cellular processes by interacting with small RNAs (sRNAs) and mRNAs in prokaryotes. Stenotrophomonas maltophilia is an important opportunistic pathogen affecting primarily hospitalized and immunocompromised hosts. We constructed an hfq deletion mutant (Δhfq) of S. maltophilia and compared the behaviors of wild-type and Δhfq S. maltophilia cells in a variety of assays. This revealed that S. maltophilia Hfq plays a role in biofilm formation and cell motility, as well as susceptibility to antimicrobial agents. Moreover, Hfq is crucial for adhesion to bronchial epithelial cells and is required for the replication of S. maltophilia in macrophages. Differential RNA sequencing analysis (dRNA-seq) of RNA isolated from S. maltophilia wild-type and Δhfq strains showed that Hfq regulates the expression of genes encoding flagellar and fimbrial components, transmembrane proteins, and enzymes involved in different metabolic pathways. Moreover, we analyzed the expression of several sRNAs identified by dRNA-seq in wild-type and Δhfq S. maltophilia cells grown in different conditions on Northern blots. The accumulation of two sRNAs was strongly reduced in the absence of Hfq. Furthermore, based on our dRNA-seq analysis we provide a genome-wide map of transcriptional start sites in S. maltophilia.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Anti-Bacterial Agents / pharmacology
  • Bacterial Adhesion
  • Biofilms / growth & development
  • Epithelial Cells / microbiology
  • Gene Deletion
  • Gene Expression Regulation, Bacterial
  • Host Factor 1 Protein / genetics
  • Host Factor 1 Protein / metabolism*
  • Humans
  • Locomotion
  • Macrophages / microbiology
  • Mice
  • Microbial Sensitivity Tests
  • Molecular Chaperones / genetics
  • Molecular Chaperones / metabolism*
  • Molecular Sequence Data
  • RNA, Bacterial / metabolism*
  • Sequence Alignment
  • Stenotrophomonas maltophilia / drug effects
  • Stenotrophomonas maltophilia / genetics
  • Stenotrophomonas maltophilia / pathogenicity
  • Stenotrophomonas maltophilia / physiology*


  • Anti-Bacterial Agents
  • Host Factor 1 Protein
  • Molecular Chaperones
  • RNA, Bacterial