2024
A stress biosensor for the production of proteins in the periplasm of Escherichia coli
Cumming AJ, Khananisho D, Liljestrand N, Balka M and Daley DO.
ACS Synthetic Biology (2024), 13(5), 1477-1491.
2023
Tips for efficiently maintaining pET expression plasmids.
Khananisho D, Cumming AJ, Kulakova D, Shilling PJ, Daley DO.
Current Genetics (2023) Nov 8. doi: 10.1007/s00294-023-01276-0. [Link]
Structural and functional insights into the Pseudomonas aeruginosa glycosyltransferase WaaG and the implications for lipopolysaccharide biosynthesis.
Scaletti ER, Pettersson P, Patrick J, Shilling PJ, Westergren RG, Daley DO, Mäler L, Widmalm G, Stenmark P.
Journal of Biological Chemistry (2023) 299(10):105256. doi: 10.1016/j.jbc.2023.105256. [Link]
Application of nanotags and nanobodies for live cell single-molecule imaging of the Z-ring in Escherichia coli.
Westlund E, Bergenstråle A, Pokhrel A, Chan H, Skoglund U, Daley DO, Söderström B.
Current Genetics (2023) 69(2-3):153-163. doi: 10.1007/s00294-023-01266-2. [Link]
Elucidation of the O-antigen structure of Escherichia coli O93 and characterisation of its biosynthetic genes. Furevi A, Ståhle J, Muheim C, Gkotzis S, Daley DO, Udekwu K, Widmalm G.
Glycobiology (2023) 33(4):289-300. doi: 10.1093/glycob/cwac069. [Link]
2022
Signal amplification of araC pBAD using a standardised translation initiation region
Shilling PJ, Khananisho D, Cumming AJ, Söderström B, Daley DO.
Synthetic Biology (2022) doi: 10.1093/synbio/ysac009. [Link]
Antibiotic-Efficient Genetic Cassette for the TEM-1 B-lactamase That Improves Plasmid Performance
Cumming AJ, Khananisho D, Harris R, Bayer CN, Nørholm MHH, Jamshidi S, Ilag LL, Daley DO.
ACS Synthetic Biology (2022) doi: 10.1021/acssynbio.1c00393. [Link]
Assembly dynamics of FtsZ and DamX during infection-related filamentation (IRF) and division of uropathogenic E. coli
Söderström B, Pittorino M, Daley DO, Duggin I.
Nature Communications (2022) doi: 10.1038/s41467-022-31378-1. [Link]
A lead-based fragment library screening of the glycosyltransferase WaaG from Escherichia coli
Riu F, Ruda A, Engström O, Muheim C, Mobarak H, Ståhle J, Kosma P, Carta A, Daley DO, Widmalm G.
Pharmaceuticals (2022) doi: 10.3390/ph15020209. [Link]
2021
Implementing novel designs for transcription and translation in pET expression plasmids
Shilling, P.J. and Daley, D.O.
Bio-protocol (2021) 11(16):e4133. doi: 10.21769/BioProtoc.4133. [Link]
LyGo: A Platform for Rapid Screening of Lytic Polysaccharide Monooxygenase Production
Hernandez-Rollan, C., Falkenberg,K.B., Rennig, M., Bertelsen, A.B., Ipsen, J.O., Brander, S., Daley, D.O., Johansen, K.S and Norholm, M.H.H.
ACS Synthetic Biology (2021) 10(4):897-906. [Link]
2020
Improved designs for pET expression plasmids increase protein production yields in Escherichia coli
Shilling, P.J., Mirzadeh. K., Cumming, A.J., Widesheim, M., Köck, Z. and Daley, D.O.
Communications Biology (2020) 3(1):214. [Link]
This article was chosen as a research highlight by Nature Methods. [Link]
A plasmid from this study received a blue flame award from addgene.
Increased production of periplasmic proteins in Escherichia coli by directed evolution of the translation initiation region
Mirzadeh. K., Shilling, P.J., Elfageih, R., Cumming, A.J., Cui, H.L., Rennig, M., Nørholm, M.H.H. and Daley, D.O.
Microbial Cell Factories (2020) 19(1):85. [Link]
The TIRs developed in this study are patented pending [PCT/SE2021/050083]
An OregonGreen488-labelled D-amino acid for visualizing peptidoglycan by super-resolution STED nanoscopy
Söderström, B., Ruda, A., Widmalm, G. and Daley, D.O.
Microbiology (2020) 166(12):1129-1135. [Link]
Structural analysis of the O-antigen polysaccharide from Escherichia coli O188
Furevi, A., Ståhle, J., Muheim, C., Gkotzis, S., Udekwu, K.I., Daley D.O. and Widmalm, G.
Carbohydrate Research (2020) 498:108051. [Link]
2019
Super-resolution images of the peptidoglycan remodelling enzymes at the division site of Escherichia coli
Söderström. B., Chan, H. and Daley, D.O.
Current Genetics (2019) 65, 99-101. [Link]
2018
Spatial separation of FtsZ and FtsN during cell division
Söderström. B., Chan, H., Shilling, P.J., Skoglund, U. and Daley, D.O.
Molecular Microbiology (2018) 107 (3), 387-401. [Link]
This article was featured on the cover of the journal (see below) and was in the top 5% of all articles tracked by Altmetric (https://www.altmetric.com).
A synbio approach for selection of highly expressed gene variants in Gram-positive bacteria
Ferro, R., Renning, M., Hernandez Rollan, C., Daley, D.O. and Nørholm, M.H.H.
Microbial Cell Factories (2018) 17 (1), 37. [Link]
TARSyn: Tuneable antibiotic resistance devices enabling bacterial synthetic evolution and protein production
Renning, M., Martinez, V., Dunas, F., Rojsater, B., Daley, D.O. and Nørholm, M.H.H.
ACS Synthetic Biology (2018) 7(2), 432-442. [Link]
Selection of highly expressed gene variants in Escherichia coli using translationally coupled antibiotic selection markers
Renning, M., Daley, D.O. and Nørholm, M.H.H.
Methods Molecular Biology (2018) 1671, 259-268. [Link]
2017
Increasing the permeability of Escherichia coli using MAC13243
Muheim, C., Götzke, H., Eriksson, A.U., Lindberg, S. Lauritsen, I., Nørholm, M.H.H. and Daley, D.O.
Scientific Reports (2017) 7 (1): 17629. [Link]
The bacterial divisome: more than a ring?
Söderström, B. and Daley, D.O.
Current Genetics (2017) 63 (2), 161-164. [Link]
2016
FtsZ does not initiate membrane constriction at the onset of cell division
Daley, D.O., Skoglund, U. and Söderström, B.
Scientific Reports (2016) 6:33138. [Link]
Coordinated disassembly of the divisome in Escherichia coli
Söderström, B., Mirzadeh, K., Toddo, S., von Heijne, G., Skoglund, U. and Daley, D.O.
Molecular Microbiology (2016) 101 (3), 425-438. [Link]
This article was featured on the cover of the journal (see below) and recommended twice by the Faculty of 1000. It was the fourth most downloaded paper in Mol. Micro. In 2016 and was in the top 5% of all articles tracked by Altmetric (https://www.altmetric.com).
Codon optimising for increased membrane protein production; A minimalist approach.
Mirzadeh, K., Nørholm, M.H. and Daley, D.O.
Methods Molecular Biology (2016) 1432:53-61. [Link]
Identification of a fragment-based scaffold that inhibits the glycosyltransferase WaaG from Escherichia coli
Muheim, C., Bakali, A., Engström, O., Wieslander, Å., Daley, D.O. and Widmalm, G.
Antibiotics (2016) 28;5(1). [Link]
2015
Enhanced protein production in Escherichia coli by optimization of cloning scars at the vector:coding sequence junction.
Mirzadeh, K., Martinez, V., Toddo, S., Guntur, S., Herrgard, M., Elofsson, A., Nørholm, M.H. and Daley, D.O.
ACS Synthetic Biology (2015) 4(9), 959-965. [Link]
The method developed here has been patented and is being commercialised by CloneOpt AB [EP 3234146 (2019-07-10); US 10,696,963 (2020-06-30)]
Trimeric microsomal glutathione transferase 2 displays one third of the sites reactivity
Ahmad, S., Thulasingam, M., Palombo, I., Daley, D.O., Johnson, K.A., Morgernstern, R., Haeggström, J.Z. and Rinaldo-Matthis, A.
Biochimica Biophysica Acta(2015) 1854(10 Pt A), 1365-1371. [Link]
The Escherichia coli envelope stress sensor CpxA responds to changes in lipid bilayer properties.
Keller, R., Ariöz, C., Hansmeier, N., Stenberg-Bruzell, F., Burstedt, M., Vikström, D., Kelly, A., Wieslander, Å., Daley, D. O. and Hunke, S.
Biochemistry (2015) 54, 3670-3676. [Link]
Identification of putative substrates for the periplasmic chaperone YfgM in Escherichia coli using quantitative proteomics.
Götzke, H., Muheim, C., Altelaar, A.F.M., Heck, A.J.R., Maddalo, G. and Daley, D.O.
Molecular & Cellular Proteomics (2015) 14(1), 216-226. [Link]
2014
Versatile in vitro system to study translocation and functional integration of bacterial outer membrane proteins.
Norell, D., Heuck, A., Tran-Thi, T.A., Götzke, H., Jacob-Dubuisson, F., Clausen, T.,
Daley, D.O., Braun, V. Muller, M. and Fan, E.
Nature Communications (2014) Nov 5;5:5396. [Link]
YfgM is an ancillary subunit of the SecYEG translocon in Escherichia coli.
Götzke, H., Palombo, I., Muheim, C., Perrody, E., Genevaux., P., Kudva, R., Müller, M. and Daley, D.O.
Journal of Biological Chemistry (2014) 289(27) 19089-19097. [Link]
Heterologous overexpression of a monotopic glucosyltransferase (MGS) induces fatty acid remodeling in Escherichia coli membranes.
Ariöz. C., Götzke, H., Lindholm, L., Eriksson, J., Edwards, K., Daley, D.O., Barth., A., Wieslander, Å.
Biochimica Biophysica Acta(2014), 1838(7), 1867-1870. [Link]
Disassembly of the divisome in Escherichia coli: Evidence that FtsZ dissociates before compartmentalisation.
Söderström, B., Skoog, K., Blom., H. Weiss., D.S., von Heijne, G. and Daley, D.O.
Molecular Microbiology (2014), 92 (1), 1-9. [Link]
This article was featured on the cover of the journal (see below) and recommended by the Faculty of 1000.
2013
Improved production of membrane proteins in Escherichia coli by selective codon substitutions.
Norholm, M.H., Toddo, S., Virkki, M.T., Light, S., von Heijne, G., and Daley. D.O.
FEBS Letters (2013) 587 (15), 2352-2358. [Link]
Why is the GMN motif conserved in the CorA/Mrs2/Alr1 superfamily of magnesium transport proteins?
Palombo, I., Daley, D.O. and Rapp. M.
Biochemistry (2013) 52, 4842-4847. [Link]
The outer mitochondrial membrane in higher plants.
Duncan, O., van der Merwe, M.J., Daley, D.O., and Whelan, J.
Trends in Plant Science (2013) 18(4), 207-217. [Link]
2012
Sequential closure of the cytoplasm and then the periplasm during cell division in Escherichia coli.
Skoog, K., Soderstrom, B., Widengren, J., von Heijne, G., and Daley, D.O.
Journal of Bacteriology (2012) 194, 584-586. [Link]
This article was featured in Microbe, a popular science magazine published by the American Society for Microbiology and 'tweeted' by Nature Reviews Microbiology.
The Escherichia coli Cell Division Protein ZipA Forms Homodimers Prior to Association with FtsZ.
Skoog, K., and Daley, D.O.
Biochemistry (2012) 51, 1407-1415. [Link]
Heme incorporation into the cytochrome bo3 occurs at a late stage of assembly.
Palombo, I. and Daley, D.O.
FEBS Letters (2012) 586 (23), 4197-4202. [Link]
Application of split-GFP for topology mapping membrane proteins in Escherichia coli.
Toddo, S., Soderstrom, B., Palombo, I., von Heijne, G., Norholm, M.H.H and Daley. D.O.
Protein Science (2012) 21 (10), 1571-1576. [Link]
The Periplasmic Loop Provides Stability to the Open State of the CorA Magnesium Channel.
Palombo, I., Daley, D.O. and Rapp. M.
Journal of Biological Chemistry (2012) 287, 27547-27555. [Link]
Antiparallel Dimers of the Small Multidrug Resistance Protein EmrE Are More Stable Than Parallel Dimers.
Lloris-Garcera, P., Bianchi, F., Slusky, J. S., Seppala, S., Daley, D.O. and von Heijne. G.
Journal of Biological Chemistry (2012) 287, 26052-26059. [Link]
Manipulating the genetic code for membrane protein production: What have we learnt so far?
Norholm, M. H., Light, S., Virkki, M. T., Elofsson, A., von Heijne, G., and Daley, D.O.
Biochimica Biophysica Acta (2012) 1818, 1091-1096. [Link]
2011
Penicillin-binding protein 5 can form a homo-oligomeric complex in the inner membrane of Escherichia coli.
Skoog, K., Bruzell, F. S., Ducroux, A., Hellberg, M., Johansson, H., Lehtio, J., Hogbom, M., Daley, D.O.
Protein Science (2011) 20, 1520-1529. [Link]
Systematic analysis of native membrane protein complexes in Escherichia coli.
Maddalo, G., Stenberg-Bruzell, F., Gotzke, H., Toddo, S., Bjorkholm, P., Eriksson, H., Chovanec, P., Genevaux, P., Lehtio, J., Ilag, L. L., and Daley, D.O.
Journal of Proteome Research (2011) 10, 1848-1859. [Link]
A reference map of the membrane proteome of Enterococcus faecalis.
Maddalo, G., Chovanec, P., Stenberg-Bruzell, F., Nielsen, H. V., Jensen-Seaman, M. I., Ilag, L. L., Kline, K. A., and Daley, D.O.
Proteomics (2011) 11, 3935-3941. [Link]
2010
Estimating Z-ring radius and contraction in dividing Escherichia coli.
Stromqvist, J., Skoog, K., Daley, D.O., Widengren, J., and von Heijne, G.
Molecular Microbiology (2010) 76, 151-158. [Link]
Cell-free expression profiling of E. coli inner membrane proteins.
Schwarz, D., Daley, D., Beckhaus, T., Dotsch, V., and Bernhard, F.
Proteomics (2010) 10, 1762-1779. [Link]
2009
Exploring the inner membrane proteome of Escherichia coli: which proteins are eluding detection and why?
Bernsel, A., and Daley, D.O.
Trends in Microbiology (2009) 17, 444-449. [Link]
2008
The assembly of membrane proteins into complexes.
Daley, D.O.
Current Opinion in Structural Biology (2008) 18, 420-424. [Link]
Exploring membrane proteomes.
Stenberg, F. and Daley, D.O.
Proteomics sample preparation, eds J. von Hagen, WILEY-VCH.E, (2008) 303-315. [Link]
2007
Assembly of the cytochrome bo3 complex.
Stenberg, F., von Heijne, G., and Daley, D.O.
Journal of Molecular Biology (2007) 371, 765-773. [Link]
Membrane protein structural biology--how far can the bugs take us?
Granseth, E., Seppala, S., Rapp, M., Daley, D. O., and von Heijne, G.
Molecular Membrane Biology (2007) 24, 329-332. [Link]
2006
2005
Protein complexes of the Escherichia coli cell envelope.
Stenberg, F., Chovanec, P., Maslen, S. L., Robinson, C. V., Ilag, L. L., von Heijne, G., and Daley, D.O.
Journal of Biological Chemistry (2005) 280, 34409-34419. [Link]
This article was profiled in Science (Editors choice, 309: 1303) and content was included in a text book, called Membrane Structural Biology (edited by Mary Luckey). Information from the article was also used to annotate entries in the Swiss Prot and Entrez databases.
Experimentally constrained topology models for 51,208 bacterial inner membrane proteins.
Granseth, E., Daley, D. O., Rapp, M., Melen, K., and von Heijne, G.
Journal of Molecular Biology (2005) 352, 489-494. [Link]
Global topology analysis of the Escherichia coli inner membrane proteome.
Daley, D. O., Rapp, M., Granseth, E., Melen, K., Drew, D., and von Heijne, G.
Science (2005) 308, 1321-1323. [Link]
This article was profiled in Nature Methods (Editorial comment, 2: 483) and the Journal of Proteome Research (4: 1045). Content from the article has been included in the text book, Membrane Structural Biology (edited by Mary Luckey) and has been used to annotate hundreds of entries in the Swiss Prot and Entrez databases.
A scalable, GFP-based pipeline for membrane protein overexpression screening and purification.
Drew, D., Slotboom, D. J., Friso, G., Reda, T., Genevaux, P., Rapp, M., Meindl-Beinker, N. M., Lambert, W., Lerch, M., Daley, D. O., Van Wijk, K. J., Hirst, J., Kunji, E., and de Gier, J. W.
Protein Science (2005) 14, 2011-2017. [Link]
Adaptations required for mitochondrial import following mitochondrial to nucleus gene transfer of ribosomal protein S10.
Murcha, M. W., Rudhe, C., Elhafez, D., Adams, K. L., Daley, D. O. and Whelan, J.
Plant Physiology (2005) 138, 2134-2144. [Link]
Why genes persist in organelle genomes.
Daley, D. O., and Whelan, J.
Genome Biology (2005) 6, 110. [Link]
2004
Experimentally based topology models for E. coli inner membrane proteins.
Rapp, M., Drew, D., Daley, D.O., Nilsson, J., Carvalho, T., Melen, K., de Gier J-W., von Heijne, G.
Protei Science (2004) 13, 937-945. [Link]
Plant mitochondrial genome evolution and gene transfer to the nucleus.
Adams, K.L. and Daley, D.O.
Advances in Photosynthesis and Respiration, eds D.A. Day, A.H. Millar and J. Whelan, Kluwer Academic publishers, (2004) 107-120.
2003
Import pathway of nuclear-encoded cytochrome c oxidase subunit 2 using yeast as a model.
Qualmann, S.R., Daley, D.O., Whelan, J. and Pratje, E.
Plant Biology (2003) 5, 481-490.
Respiratory gene expression in soybean cotyledons during post-germinative development.
Daley, D.O., Considine, M.J., Howell, K.A., Millar, A. H., Day, D.A. and Whelan, J.
Plant Molecular Biology (2003) 51, 745 – 755.
2002
Intracellular gene transfer: Reduced hydrophobicity facilitates gene transfer for subunit 2 of cytochrome c oxidase.
Daley, D.O., Clifton, R. and Whelan, J.
PNAS (2002) 99, 10510-10515. [Link]
Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts.
Adams, K.L., Daley, D.O., Whelan, J. and Palmer, J.D.
Plant Cell (2002) 14, 931-943. [Link]
Gene transfer from the mitochondrion to the nucleus: Novel mechanisms of activation from Cox2.
Daley, D.O., Adams, K.L., Clifton, R., Qualmann, S., Millar, A. H., Palmer, J. D., Pratje, E. and Whelan, J.
Plant Journal (2002) 30(1), 11-21. [Link]
2001
The expression of alternative oxidase and uncoupling protein during fruit ripening in mango (Mangifera indica L.).
Considine, M.J., Daley, D.O. and Whelan, J.
Plant Physiology (2001) 126, 1619-1629. [Link]
2000
Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants.
Adams, K.L. Daley, D.O., Qui, Y-L., Whelan, J. and Palmer, J.D.
Nature (2000) 408, 354-357. [Link]
This article was profiled in Nature (News and Views 408: 302-305), Current Opinion in Genetics and Development (Paper alert 11; 7) and Trends in Plant Science (News and Comment 6; 52).
Regulatory, developmental and tissue aspects of mitochondrial biogenesis in plants.
McCabe, T.C., Daley D.O. and Whelan, J.
Plant Biology (2000) 2, 121-135.
1999
The multiple alternative oxidase proteins of soybean.
Tanudji, M., Djajanegara, I.N., Daley, D.O., McCabe, T.C., Finnegan, P.M., Day, D.A. and Whelan. J.
Australian Journal of Plant Physiology (1999) 26, 337-344.
________________________________________________________________
Patents
Selective optimisation of a ribosome binding site for protein production.
Daley DO, Mirzadeh K, Toddo S and Guntur, S
Application number 1451553-0 (Sweden). Filing date 2014-12-16
European patent No. 3234146 (2019-07-10)
US patent No. US 10,696,963 (2020-06-30)
Synthetically evolved DNA constructs for regulating signal peptide performance as well as vectors, host cells and recombinant proteins thereof
Daley DO, Mirzadeh K, Toddo S and Shilling, S
PCT/SE2021/050083
Biosensor nucleotide gene construct for monitoring of protein production in a host cell
Daley DO, Cumming AJ and Khananisho D
Patent application number EP23193337.5