New Functions for the Ancient DedA Membrane Protein Family

Doerrler, William T.; Sikdar, Rakesh; Kumar, Sujeet; Boughner, Lisa A.

doi:10.1128/jb.01006-12

Cited by 75 publications

(106 citation statements)

References 89 publications

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“…These observations show that YqjA plays an important role in providing alkaline tolerance to E. coli. While YghB displays 62% amino acid identity to YqjA and can substitute for YqjA in many processes (8), the ⌬yghB mutant did not display sensitivity to growth under alkaline conditions (see Fig. S1 in the supplemental material).…”

Section: Resultsmentioning

confidence: 99%

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Escherichia coli YqjA, a Member of the Conserved DedA/Tvp38 Membrane Protein Family, Is a Putative Osmosensing Transporter Required for Growth at Alkaline pH

Kumar

Doerrler

2015

J Bacteriol

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The ability to persist and grow under alkaline conditions is an important characteristic of many bacteria. In order to survive at alkaline pH, Escherichia coli must maintain a stable cytoplasmic pH of about 7.6. Membrane cation/proton antiporters play a major role in alkaline pH homeostasis by catalyzing active inward proton transport. The DedA/Tvp38 family is a highly conserved membrane protein family of unknown function present in most sequenced genomes. YqjA and YghB are members of the E. coli DedA family with 62% amino acid identity and partially redundant functions. We have shown that E. coli with ⌬yqjA and ⌬yghB mutations cannot properly maintain the proton motive force (PMF) and is compromised in PMF-dependent drug efflux and other PMF-dependent functions. Furthermore, the functions of YqjA and YghB are dependent upon membrane-embedded acidic amino acids, a hallmark of several families of proton-dependent transporters. Here, we show that the ⌬yqjA mutant (but not ⌬yghB) cannot grow under alkaline conditions (ranging from pH 8.5 to 9.5), unlike the parent E. coli. Overexpression of yqjA restores growth at alkaline pH, but only when more than ϳ100 mM sodium or potassium is present in the growth medium. Increasing the osmotic pressure by the addition of sucrose enhances the ability of YqjA to support growth under alkaline conditions in the presence of low salt concentrations, consistent with YqjA functioning as an osmosensor. We suggest that YqjA possesses proton-dependent transport activity that is stimulated by osmolarity and that it plays a significant role in the survival of E. coli at alkaline pH. IMPORTANCEThe ability to survive under alkaline conditions is important for many species of bacteria. Escherichia coli can grow at pH 5.5 to 9.5 while maintaining a constant cytoplasmic pH of about 7.6. Under alkaline conditions, bacteria rely upon proton-dependent transporters to maintain a constant cytoplasmic pH. The DedA/Tvp38 protein family is a highly conserved but poorly characterized family of membrane proteins. Here, we show that the DedA/Tvp38 protein YqjA is critical for E. coli to survive at pH 8.5 to 9.5. YqjA requires sodium and potassium for this function. At low cation concentrations, osmolytes, including sucrose, can facilitate rescue of E. coli growth by YqjA at high pH. These data are consistent with YqjA functioning as an osmosensing cation-dependent proton transporter. Bacterial alkaline pH tolerance is a key feature of pathogenic, ecological, and industrially important bacteria. Microbes have many naturally occurring alkaline habitats, including the human body (1). Neutralophilic bacteria, including Escherichia coli and Vibrio cholerae, can stay viable in alkaline marine environments and can cause threats to public health (2). They have the ability to maintain their intracellular pH in a range of 7.5 to 7.7 when grown within a wide range of pH values between 5.5 and 9.0. Cytoplasmic pH maintenance is vital for structural integrity and the functions of proteins essential for growth...

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Section: Resultsmentioning

confidence: 99%

“…Inward active transport of protons by these antiporters is coupled with export of cations, such as Na ϩ , K ϩ , and Ca 2ϩ . The DedA/Tvp38 family is a highly conserved membrane protein family, with the corresponding genes present in most sequenced genomes (8). However, the functions of these proteins are not well understood.…”

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confidence: 99%

Escherichia coli YqjA, a Member of the Conserved DedA/Tvp38 Membrane Protein Family, Is a Putative Osmosensing Transporter Required for Growth at Alkaline pH

Kumar

Doerrler

2015

J Bacteriol

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“…The DedA family of membrane proteins is highly conserved and likely essential in many bacterial species (81). E. coli encodes as many as eight DedA family genes, and a distinct phenotype is not observed unless yqjA and yghB are simultaneously deleted (4).…”

Section: Discussionmentioning

confidence: 99%

“…Some are restricted to one or a few closely related species, while others are conserved across diverse phylogenies. The DedA membrane protein family falls into the latter class and is represented in nearly all sequenced bacterial genomes, as well as the genomes of many archaea and eukaryotes (see the accompanying paper by Doerrler et al [81]). At present, there are more than 3,000 members of the DedA family found in the NCBI genome database (2).…”

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Multiple Envelope Stress Response Pathways Are Activated in an Escherichia coli Strain with Mutations in Two Members of the DedA Membrane Protein Family

2013

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We have reported that simultaneous deletion of two Escherichia coli genes, yqjA and yghB, encoding related and conserved inner membrane proteins belonging to the DedA protein family results in a number of intriguing phenotypes, including temperature sensitivity at 42°C, altered membrane lipid composition, and cell division defects. We sought to characterize these and other phenotypes in an effort to establish a function for this protein family in E. coli. Here, using reporter assays, we show that the major envelope stress response pathways Cpx, Psp, Bae, and Rcs are activated in strain BC202 (W3110; ⌬yqjA ⌬yghB) at the permissive growth temperature of 30°C. We previously demonstrated that 10 mM Mg 2؉ , 400 mM NaCl, and overexpression of tatABC are capable of restoring normal growth to BC202 at elevated growth temperatures. Deletion of the cpxR gene from BC202 results in the loss of the ability of these supplements to restore growth at 42°C. Additionally, we report that the membrane potential of BC202 is significantly reduced and that cell division and growth can be restored either by expression of the multidrug transporter MdfA from a multicopy plasmid or by growth at pH 6.0. Together, these results suggest that the DedA family proteins YqjA and YghB are required for general envelope maintenance and homeostasis of the proton motive force under a variety of growth conditions.

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“…For example, mutations of integral membrane proteins of the DedA family cause temperature sensitivity and cell division defects in Escherichia coli (Thompkins et al 2008). Interestingly, proteins from the DedA family have been shown to be essential in at least 2 bacterial species (E. coli and Borrelia burgdorferi), but their homologs are not detected in several thermophilic and hyperthermophilic Thermotogae genomes (Doerrler et al 2013). This suggests that the function provided by DedA either is not needed by these organisms or is being provided by analogous integral membrane proteins, or that their DedA homologs are too divergent to be detected by sequence similarity searches.…”

Section: Thermosipho Japonicus (Ab024932)mentioning

confidence: 99%

Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae

2015

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Thermophiles are extremophiles that grow optimally at temperatures >45°C. To survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperature (mesophiles). At the cellular level, thermophiles have mechanisms for maintaining their membranes, nucleic acids, and other cellular structures. At the protein level, each of their proteins remains stable and retains activity at temperatures that would denature their mesophilic homologs. Conversely, cellular structures and proteins from thermophiles may not function optimally at moderate temperatures. These differences between thermophiles and mesophiles presumably present a barrier for evolutionary transitioning between the 2 lifestyles. Therefore, studying closely related thermophiles and mesophiles can help us determine how such lifestyle transitions may happen. The bacterial phylum Thermotogae contains hyperthermophiles, thermophiles, mesophiles, and organisms with temperature ranges wide enough to span both thermophilic and mesophilic temperatures. Genomic, proteomic, and physiological differences noted between other bacterial thermophiles and mesophiles are evident within the Thermotogae. We argue that the Thermotogae is an ideal group of organisms for understanding of the response to fluctuating temperature and of long-term evolutionary adaptation to a different growth temperature range.Key words: lateral gene transfer, Kosmotoga, Mesotoga, thermostability, stress response. Résumé :Les thermophiles sont des extrémophiles dont la température optimale de croissance se situe au-delà de 45°C. Pour survivre et permettre à leurs biomolécules de bien fonctionner, ils doivent se doter de caractéristiques qu'on ne retrouve pas chez des organismes se développant à des températures intermédiaires (mésophiles). Sur le plan cellulaire, les thermophiles ont des mécanismes permettant de préserver leurs membranes, acides nucléiques et autres structures cellulaires. Au chapitre des protéines, chacune d'entre elles demeure stable et active à des températures qui dénatureraient leurs homologues mésophiles. En revanche, les structures et protéines cellulaires des thermophiles pourraient ne pas fonctionner de manière optimale à des températures intermédiaires. De telles différences entre les thermophiles et les mésophiles auraient tendance à se dresser en travers d'une transition évolutive entre ces deux modes de vie. Par conséquent, l'étude de thermophiles et de mésophiles fortement apparentés pourrait nous permettre d'établir comment surviendraient de telles transitions du mode de vie. Le phylum bactérien Thermotogae regroupe des hyperthermophiles, des thermophiles, des mésophiles et des organismes dont l'intervalle de températures chevauche les plages thermophiles et mésophiles. On observe parmi les Thermotogae des différences sur le plan génomique, protéomique, et physiologique qu'on relève également entre d'autres thermophiles et méso-philes bactériens. Nous soutenons que les Thermot...

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New Functions for the Ancient DedA Membrane Protein Family

Cited by 75 publications

References 89 publications

Escherichia coli YqjA, a Member of the Conserved DedA/Tvp38 Membrane Protein Family, Is a Putative Osmosensing Transporter Required for Growth at Alkaline pH

Escherichia coli YqjA, a Member of the Conserved DedA/Tvp38 Membrane Protein Family, Is a Putative Osmosensing Transporter Required for Growth at Alkaline pH

Multiple Envelope Stress Response Pathways Are Activated in an Escherichia coli Strain with Mutations in Two Members of the DedA Membrane Protein Family

Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae

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