New functions for the ancient DedA membrane protein family

Abstract

The DedA protein family is a highly conserved and ancient family of membrane proteins with representatives in most sequenced genomes, including those of bacteria, archaea, and eukarya. The functions of the DedA family proteins remain obscure. However, recent genetic approaches have revealed important roles for certain bacterial DedA family members in membrane homeostasis. Bacterial DedA family mutants display such intriguing phenotypes as cell division defects, temperature sensitivity, altered membrane lipid composition, elevated envelope-related stress responses, and loss of proton motive force. The DedA family is also essential in at least two species of bacteria: Borrelia burgdorferi and Escherichia coli. Here, we describe the phylogenetic distribution of the family and summarize recent progress toward understanding the functions of the DedA membrane protein family.

Fig 1

Phylogenetic analysis of the DedA protein family. (A) Alignment of E. coli DedA proteins and homologs found in Borrellia burgdorferi, Mycobacterium bovis, and Helicobacter pylori from the NCBI database to illustrate the DedA domain, COG0586 (boxed in region). Predicted transmembrane (TM) domains are highlighted in green, and partial TM regions, possibly amphipathic helixes, are highlighted in blue. The singularly conserved amino acid residue of the DedA domain (glycine) is in bold. Of interest, the only conserved glycine residue is in or near the amphipathic helix for all aligned members. The TM prediction software used was TMHMM (84). (B and C) Bacterial (B) and archaeal (C) domain representative trees are shown. Numbers in red demonstrate the proportion of species lacking a significant DedA homolog (Protein BLAST E value, ≤10⁻⁴) in each bacterial (B) or archaeal (C) phylum. Otherwise, all species of each phylum contain at least one significant DedA homolog (numbers in blue). Phylogenetic trees were constructed with MEGA (85), using a single 16S rRNA sequence from a representative species of each phylum. Previously published phylogenetic trees for both Bacteria (350 species) (10) and Archaea (100 species) (11) were used as a basis for phylogenetic analyses, though additional species were investigated; presented values are solely from published trees. Significant DedA homologs are found within the Thermotogae phylum although not in the five completed genomes analyzed.

Fig 2

Characteristics of DedA family mutants. (A) BC202 (ΔyghB::Kan^r ΔyqjA::Tet^r) grows at 30°C but not at 42°C (5). The ΔyghB and ΔyqjA single mutants grow at all temperatures (not shown) (5, 62). (B) Cell division defects of BC202 are caused by failure to export periplasmic amidases via the twin arginine transport pathway. W3110 (left) and BC202 (right) transformed with plasmid pTB28 expressing AmiC-green fluorescent protein (GFP) fusion protein (31) were grown at 30°C and visualized with differential interference contrast (DIC) and fluorescence microscopy. The bright fluorescence observed in the right panel is due to cytoplasmic accumulation of AmiC-GFP (30). Expression of wild-type yghB from a plasmid restores wild-type appearance and AmiC export to BC202 (not shown) (30). (C) The E. coli DedA family is collectively essential at all temperatures. BAL801 (W3110, ΔydjXYZ::cam ΔyabI772 ΔEcdedA726 ΔyohD762 ΔyqjA785 ΔyqaA770 ΔyghB781::kan pBAD-EcdedA) fails to grow when EcDedA expression from a plasmid is repressed by growth in glucose (6). (D) The sole DedA family member of Borrelia burgdorferi is essential (not shown), and depletion of the protein causes cell division defects (7). B. burgdorferi DXL-01 (Δbb0250, pWTD0250 expressing bb0250 behind a borrelia-optimized lac promoter [86]) was cultured with either 1 mM (top) or 0 mM (bottom) IPTG (isopropyl-β-d-thiogalactopyranoside) for 4 to 5 days and visualized by scanning electron microscopy. Depletion of BB0250 causes membrane bulging (arrow) and cell division defects. Images A to D are reproduced with permission (–7, 30).

Fig 3

Potential physiological roles of E. coli YqjA and YghB. (A) Formation of YqjA homodimer as proposed for LeuT family members (8) transports protons into the cell coupled with symport or antiport of an uncharacterized substrate. The proposed function of YqjA here is similar to that of the Na⁺/K⁺-H⁺ antiporter MdfA (61, 74) with a significant role in pH/PMF homeostasis. Heterodimerization with YghB or an unknown partner is also a possibility here. (B) An alternative model demonstrating an indirect role for YqjA in pH/PMF homeostasis. Regulation of activity or functional modulation of RC (respiratory complexes), ME (metabolic enzymes), or certain classes of transporters (T) such as MdfA, all of which participate in the pH/PMF homeostasis mechanism in E. coli. The topological model of YqjA, comprising 4-transmembrane helices with cytoplasmic N and C termini, is derived from previously published data (87), SOSUI topological prediction software (88), and unpublished observations. IM, inner membrane.