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9.B.27 The Death Effector Domain A (DedA) Family

The ubiquitous DedA family (family UPF0043) includes bacterial, archaeal and eukaryotic proteins. At least some members of the family have lipid (PS and cholesterol) scramblase activities (see below). The bacterial proteins are of about 200-250 residues with probably 6 TMSs. They are related to the DedA protein of E. coli (TC# 9.B.27.2.3) and several functionally unchararcterized proteins in eukaryotes (yeasts, plants and animals).YdjX and YdjZ in E. coli may be involved as dimers in selenite transport (Ledgham et al., 2005). Potential functions of these proteins such as in membrane homeostasis have been summarized by Doerrler et al., (2013). Mutations in DedA proteins exhibit phenotypes such as cell division defects, temperature sensitivity, altered lipid compositions, elevated envelope-related stress responses and loss of the proton motive force. DedA proteins are essential in some bacterial species (Doerrler et al., 2013; Sikdar et al., 2013). Several members of the DedA family (e.g., 9.B.27.1.8) have phospholipid (phosphatidyl serine) and cholesterol scramblase activities (Zhang et al. 2021; Nakao and Nakano 2022). Others may have oxalate transport activity (see TC# 9.B.27.1.7 and the next paragraph). Thus it seems that the DedA domain may be present in several protein of dissimilar function. The different subdomains may have differing topologies although most have a 6 TMS topology in a 3 + 3 TMS arrangement.  TC subfamily 1 has an unusual TMS arrangement of 1 + 2 + 2 + 1 TMS arrangement; subfamilies 2, 4 and 5 probably have 6 TMSs in a 3 + 3 TMS arrangement; subfamily 3 seems to have a 2 + 2 TMS pattern, but it may be 3 + 3. 

An oxalate-fermenting brown rot fungus, Fomitopsis palustris, secretes large amounts of oxalic acid during wood decay. Secretion of oxalic acid is indispensable for the degradation of wood cell walls. Watanabe et al., (2010) characterized an oxalate transporter, FpOAR, using membrane vesicles of F. palustris. FpOAR (Fomitopsis palustris oxalic acid resistance), from F. palustris by functional screening of yeast transformants with cDNAs grown on oxalic acid-containing plates. FpOAR is predicted to be a membrane protein that possesses six TMSs. A yeast transformant possessing FpOAR (FpOAR-transformant) acquired resistance to oxalic acid and contained less oxalate than the control transformant. FpOAR probably plays a role in wood decay by acting as a secondary transporter responsible for secretion of oxalate by F. palustris.

The DedA/Tvp38 family is a highly conserved and ancient family of membrane proteins with representatives in most sequenced genomes (Doerrler et al., 2013). Recent genetic approaches have revealed important roles for certain bacterial DedA family members in membrane homeostasis. Bacterial DedA family mutants display phenotypes such as cell division defects, temperature sensitivity, altered membrane lipid composition, elevated envelope-related stress responses, and loss of the proton motive force. The DedA family is essential in at least two species of bacteria:Borrelia burgdorferi and Escherichia coli under some conditions. Doerrler et al., (2013) described the phylogenetic distribution of the family and summarized progress toward understanding the functions of DedA proteins.

E. coli can normally grow between pH 5.5 and 9.5 while maintaining a 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, YqjA, is critical for E. coli to survive between pH 8.5 and 9.5. YqjA requires sodium and potassium for this function. At low cation concentrations, osmolytes, including sucrose, can facilitate rescue of growth by YqjA at high pH suggesting that YqjA functions as an osmosensing cation-dependent proton transporter (Kumar and Doerrler 2015).

Colistin is a 'last resort' antibiotic for treatment of infections caused by some multidrug resistant Gram-negative bacterial pathogens. Some Gram-negative bacteria such as Burkholderia spp. are intrinsically resistant to high levels of colistin with minimal inhibitory concentrations (MIC) often above 0.5 mg/ml. DedA family proteins YqjA and YghB are conserved membrane transporters required for alkaline tolerance and resistance to several classes of dyes and antibiotics in E. coli. A DedA family protein in Burkholderia thailandensis (DbcA; DedA) is required for resistance to colistin (Panta et al. 2019). Mutation of dbcA results in >100-fold greater sensitivity to colistin. Colistin resistance is often conferred via covalent modification of lipopolysaccharide (LPS) lipid A. Mass spectrometry of lipid A of ΔdbcA showed a sharp reduction of aminoarabinose in lipid A compared to wild type. Complementation of colistin sensitivity of B. thailandensis ΔdbcA was observed by expression of dbcA, E. coli yghB or E. coli yqjA. Many proton-dependent transporters possess charged amino acids in transmembrane domains that take part in the transport mechanism and are essential for function. Site directed mutagenesis of conserved and predicted membrane embedded charged amino acids suggest that DbcA functions as a proton-dependent transporter. Direct measurement of membrane potential shows that B. thailandensis ΔdbcA is partially depolarized suggesting that loss of protonmotive force can lead to alterations in LPS structure and severe colistin sensitivity in this species (Panta et al. 2019).

Proteins containing the Pfam domain PF09335 ('SNARE_ASSOC'/ 'VTT '/'Tvp38') including Tmem41B are involved in early stages of autophagosome formation. They are vital in mouse embryonic development as well as a viral host factor of SARS-CoV-2. Using evolutionary covariance-derived information to construct and validate ab initio models, Mesdaghi et al. 2020 made domain boundary predictions and inferred local structural features. The structural bioinformatics analysis of Tmem41B and its homologues showed that they contain a tandem repeat that is clearly visible in evolutionary covariance data but much less so by sequence analysis. The internal repeat features two-fold rotational symmetry. Local structural features predicted to be present in Tmem41B were also present in Cl-/H+ antiporters. It was suggested that Tmem41B and its homologues are transporters for an as-yet uncharacterised substrate using H+ antiporter activity as its mechanism for energy coupling (Mesdaghi et al. 2020). 

Precursors of peptidoglycan (PG) and other cell surface glycopolymers are synthesized in the cytoplasm and then delivered across the cell membrane bound to the recyclable lipid carrier undecaprenyl phosphate (C55-P). The transporter protein(s) that return C55-P to the cytoplasmic face of the cell membrane have been elusive. Sit et al. 2022 identified the DUF368-containing and DedA transmembrane protein families as candidate C55-P translocases. Gram-negative and -positive bacteria lacking their cognate DUF368-containing protein exhibited alkaline-dependent cell wall and viability defects, along with increased cell surface C55-P levels. pH-dependent synthetic genetic interactions between DUF368-containing proteins and DedA family members suggested that the putative C55-P transporter usage is dynamic and modulated by environmental inputs. C55-P transporter activity was required by the cholera pathogen for growth and cell shape maintenance in the intestine. Sit et al. 2022 proposed that conditional transporter reliance provides resilience in lipid carrier recycling, bolstering microbial fitness within and outside of the host.

References associated with 9.B.27 family:

Boughner, L.A. and W.T. Doerrler. (2012). Multiple deletions reveal the essentiality of the DedA membrane protein family in Escherichia coli. Microbiology 158: 1162-1171. 22301910
Cao, S.Y., Y.S. Liu, X.D. Gao, T. Kinoshita, and M. Fujita. (2023). A lipid scramblase TMEM41B is involved in the processing and transport of GPI-anchored proteins. J Biochem. [Epub: Ahead of Print] 37279648
Daley, D.O., M. Rapp, E. Granseth, K. Melén, D. Drew, and G. von Heijne. (2005). Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321-1323. 15919996
Doerrler, W.T., R. Sikdar, S. Kumar, and L.A. Boughner. (2013). New functions for the ancient DedA membrane protein family. J. Bacteriol. 195: 3-11. 23086209
Gandini, R., T. Reichenbach, O. Spadiut, T.C. Tan, D.C. Kalyani, and C. Divne. (2020). A Transmembrane Crenarchaeal Mannosyltransferase Is Involved in N-Glycan Biosynthesis and Displays an Unexpected Minimal Cellulose-Synthase-like Fold. J. Mol. Biol. [Epub: Ahead of Print] 32569746
Kim, H., T. Kim, B.C. Jeong, I.T. Cho, D. Han, N. Takegahara, T. Negishi-Koga, H. Takayanagi, J.H. Lee, J.Y. Sul, V. Prasad, S.H. Lee, and Y. Choi. (2013). Tmem64 modulates calcium signaling during RANKL-mediated osteoclast differentiation. Cell Metab 17: 249-260. 23395171
Kumar, S. and W.T. Doerrler. (2015). Escherichia coli YqjA, a Member of the Conserved DedA/Tvp38 Membrane Protein Family, Is a Putative Osmosensing Transporter Required for Growth at Alkaline pH. J. Bacteriol. 197: 2292-2300. 25917916
Ledgham, F., B. Quest, T. Vallaeys, M. Mergeay, and J. Covès. (2005). A probable link between the DedA protein and resistance to selenite. Res. Microbiol. 156: 367-374. 15808941
Lin, B., Y. Xue, C. Qi, X. Chen, and W. Mao. (2018). Expression of transmembrane protein 41A is associated with metastasis via the modulation of E‑cadherin in radically resected gastric cancer. Mol Med Rep 18: 2963-2972. 30015937
Mesdaghi, S., D.L. Murphy, F. Sánchez Rodríguez, J.J. Burgos-Mármol, and D.J. Rigden. (2020). In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. F1000Res 9: 1395. 33520197
Morita, K., Y. Hama, T. Izume, N. Tamura, T. Ueno, Y. Yamashita, Y. Sakamaki, K. Mimura, H. Morishita, W. Shihoya, O. Nureki, H. Mano, and N. Mizushima. (2018). Genome-wide CRISPR screen identifies as a gene required for autophagosome formation. J. Cell Biol. 217: 3817-3828. 30093494
Nakao, H. and M. Nakano. (2022). Flip-Flop Promotion Mechanisms by Model Transmembrane Peptides. Chem Pharm Bull (Tokyo) 70: 519-523. 35908916
Panta, P.R., S. Kumar, C.F. Stafford, C.E. Billiot, M.V. Douglass, C.M. Herrera, M.S. Trent, and W.T. Doerrler. (2019). A DedA Family Membrane Protein Is Required for Colistin Resistance. Front Microbiol 10: 2532. 31827463
Shoemaker, C.J., T.Q. Huang, N.R. Weir, N.J. Polyakov, S.W. Schultz, and V. Denic. (2019). CRISPR screening using an expanded toolkit of autophagy reporters identifies TMEM41B as a novel autophagy factor. PLoS Biol 17: e2007044. 30933966
Sikdar, R., A.R. Simmons, and W.T. Doerrler. (2013). Multiple envelope stress response pathways are activated in an Escherichia coli strain with mutations in two members of the DedA membrane protein family. J. Bacteriol. 195: 12-24. 23042993
Thompkins, K., B. Chattopadhyay, Y. Xiao, M.C. Henk, and W.T. Doerrler. (2008). Temperature sensitivity and cell division defects in an Escherichia coli strain with mutations in yghB and yqjA, encoding related and conserved inner membrane proteins. J. Bacteriol. 190: 4489-4500. 18456815
Van Alstyne, M., F. Lotti, A. Dal Mas, E. Area-Gomez, and L. Pellizzoni. (2018). Stasimon/Tmem41b localizes to mitochondria-associated ER membranes and is essential for mouse embryonic development. Biochem. Biophys. Res. Commun. 506: 463-470. 30352685
Watanabe, T., N. Shitan, S. Suzuki, T. Umezawa, M. Shimada, K. Yazaki, and T. Hattori. (2010). Oxalate efflux transporter from the brown rot fungus Fomitopsis palustris. Appl. Environ. Microbiol. 76: 7683-7690. 20889782
Yang, Z., P. Zhao, W. Peng, Z. Liu, G. Xie, X. Ma, Z. An, and F. An. (2022). Cloning, Expression Analysis, and Functional Characterization of Candidate Oxalate Transporter Genes of and from Rubber Tree (). Cells 11:. 36497054
Zhang, T., Y.E. Li, Y. Yuan, X. Du, Y. Wang, X. Dong, H. Yang, and S. Qi. (2021). TMEM41B and VMP1 are phospholipid scramblases. Autophagy 17: 2048-2050. 34074213