{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T14:13:30Z","timestamp":1788963210606,"version":"build-2803163510"},"posted":{"date-parts":[[2026,5,28]]},"group-title":"Biochemistry","reference-count":74,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T00:00:00Z","timestamp":1779926400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["R35GM122535"],"award-info":[{"award-number":["R35GM122535"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R24GM146107"],"award-info":[{"award-number":["R24GM146107"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The\n                  <jats:italic>E. coli<\/jats:italic>\n                  aerotaxis receptor Aer is a bacterial chemoreceptor that senses intracellular redox changes via an N-terminal PAS domain bound to a flavin adenine dinucleotide (FAD) cofactor. Distinct from canonical methyl-accepting chemotaxis proteins (MCPs) such as Tar\/Tsr, Aer lacks a periplasmic ligand-binding domain and adaptive methylation, transmitting conformational signals laterally from the PAS domain to the HAMP domain and the methylation helix-like cap (MHL-cap) of the kinase control domain (KCD). To elucidate the Aer signalling mechanism, we determined cryo-electron microscopy (cryo-EM) structures of full-length Aer in oxidized flavin quinone (kinase-on) and reduced semiquinone (kinase-off) states. Structural comparison reveals redox-linked rearrangements of the FAD-binding pocket, reorientation of PAS\u2013HAMP interactions, and strikingly altered MHL-cap stability. PAS\u2013MHL-cap contact in the oxidized state compresses the receptor and stabilized proximal KCD helices, whereas reduction disrupts these contacts, increasing KCD flexibility. To probe distal effects on KCD architecture, we performed nanodisc reconstitution and pulse dipolar ESR spectroscopy on spin-labelled positions along the four-helix bundle. Distance distributions indicate redox-dependent changes in helix separation, particularly at the C-terminal MHL2 region, consistent with PAS-driven loosening of KCD packing in kinase-off states. These data support a model in which FAD redox chemistry reorganizes flavin pocket residues that in turn subtly alter PAS conformation to influence PAS-HAMP and PAS-MHL-cap packing and hence KCD conformational stability. The findings reveal an Aer-specific signaling axis distinct from periplasmic-ligand binding MCPs that has adapted MCP architecture for lateral PAS input and cytoplasmic redox sensing.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Significance<\/jats:title>\n                  <jats:p>\n                    Transmembrane energy receptors, such as\n                    <jats:italic>E. coli<\/jats:italic>\n                    Aer, interpret metabolic signals to optimally position bacteria in their environment. We apply cryo-EM and pulse-diplolar ESR spectroscopy to characterize the structural landscape of full-length Aer in oxidized and reduced states to reveal a signal transmission mechanism distinct from that of canonical methyl-accepting chemotaxis proteins (MCPs). This work establishes Aer as a specialized MCP variant adapted for cytoplasmic redox sensing through a flavin-containing PAS domain that yet displays features of conformational propagation long suspected to be critical for signaling by the greater family of MCP transmembrane receptors. These findings open possibilities for engineering redox- and light-responsive receptors and targeting energy taxis pathways in pathogens.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.05.25.727702","type":"posted-content","created":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T23:15:14Z","timestamp":1780010114000},"source":"Crossref","is-referenced-by-count":0,"title":["Signaling mechanism of the transmembrane energy receptor Aer"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1877-5985","authenticated-orcid":false,"given":"Flory A.","family":"Olsthoorn","sequence":"first","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853"},{"name":"Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands, 3584 CG"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8695-3221","authenticated-orcid":false,"given":"Alise R.","family":"Muok","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7938-0792","authenticated-orcid":false,"given":"Zachary A.","family":"Maschmann","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853"},{"name":"Department of Molecular Biology, Princeton University, Princeton, NJ 08544"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yajie","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siddarth","family":"Chandrasekaran","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853"},{"name":"Intrepid Labs, Toronto, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7531-6913","authenticated-orcid":false,"given":"Robert","family":"Dunleavy","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8234-9991","authenticated-orcid":false,"given":"Brian R.","family":"Crane","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026090906400912000_2026.05.25.727702v2.1","doi-asserted-by":"publisher","DOI":"10.1038\/nrm1524"},{"key":"2026090906400912000_2026.05.25.727702v2.2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.039214-0"},{"key":"2026090906400912000_2026.05.25.727702v2.3","doi-asserted-by":"publisher","DOI":"10.1007\/s00203-010-0575-7"},{"key":"2026090906400912000_2026.05.25.727702v2.4","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.53.1.103"},{"key":"2026090906400912000_2026.05.25.727702v2.5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.20.10541"},{"key":"2026090906400912000_2026.05.25.727702v2.6","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.100118697"},{"key":"2026090906400912000_2026.05.25.727702v2.7","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00381-26"},{"key":"2026090906400912000_2026.05.25.727702v2.8","doi-asserted-by":"publisher","DOI":"10.1128\/jb.00278-22"},{"key":"2026090906400912000_2026.05.25.727702v2.9","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.22.7556-7563.2004"},{"key":"2026090906400912000_2026.05.25.727702v2.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2015.03.003"},{"key":"2026090906400912000_2026.05.25.727702v2.11","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.112408.134215"},{"key":"2026090906400912000_2026.05.25.727702v2.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbamem.2019.183030"},{"key":"2026090906400912000_2026.05.25.727702v2.13","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3179"},{"key":"2026090906400912000_2026.05.25.727702v2.14","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2007.05889.x"},{"key":"2026090906400912000_2026.05.25.727702v2.15","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.12.3730-3737.2004"},{"key":"2026090906400912000_2026.05.25.727702v2.16","doi-asserted-by":"publisher","DOI":"10.1089\/15230860152665037"},{"key":"2026090906400912000_2026.05.25.727702v2.17","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.63.2.479-506.1999"},{"key":"2026090906400912000_2026.05.25.727702v2.18","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01028-10"},{"key":"2026090906400912000_2026.05.25.727702v2.19","doi-asserted-by":"publisher","DOI":"10.1128\/JB.188.10.3477-3486.2006"},{"key":"2026090906400912000_2026.05.25.727702v2.20","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.20.6782-6791.2004"},{"key":"2026090906400912000_2026.05.25.727702v2.21","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.02732-23"},{"key":"2026090906400912000_2026.05.25.727702v2.22","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00973-19"},{"key":"2026090906400912000_2026.05.25.727702v2.23","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.08419"},{"key":"2026090906400912000_2026.05.25.727702v2.24","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002204"},{"key":"2026090906400912000_2026.05.25.727702v2.25","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00953-10"},{"key":"2026090906400912000_2026.05.25.727702v2.26","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2009.06819.x"},{"key":"2026090906400912000_2026.05.25.727702v2.27","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1721554115"},{"key":"2026090906400912000_2026.05.25.727702v2.28","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2204161119"},{"key":"2026090906400912000_2026.05.25.727702v2.29","doi-asserted-by":"publisher","DOI":"10.1016\/S1874-6047(06)80014-4"},{"key":"2026090906400912000_2026.05.25.727702v2.30","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1721554115"},{"key":"2026090906400912000_2026.05.25.727702v2.31","doi-asserted-by":"publisher","DOI":"10.1128\/JB.188.3.894-901.2006"},{"key":"2026090906400912000_2026.05.25.727702v2.32","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.C116.757492"},{"key":"2026090906400912000_2026.05.25.727702v2.33","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2022.102598"},{"key":"2026090906400912000_2026.05.25.727702v2.34","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-60623-6"},{"key":"2026090906400912000_2026.05.25.727702v2.35","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2000.01910.x"},{"key":"2026090906400912000_2026.05.25.727702v2.36","doi-asserted-by":"publisher","DOI":"10.1021\/bi0620407"},{"key":"2026090906400912000_2026.05.25.727702v2.37","doi-asserted-by":"crossref","unstructured":"Vaidya, A. T. , Chen, C. , Dunlap, J. C. , Loros, J. J. & Crane, B. R . Structure of a light-activated LOV protein dimer that regulates transcription in Neurospora crassa. (2011) Submitted.","DOI":"10.1126\/scisignal.2001945"},{"key":"2026090906400912000_2026.05.25.727702v2.38","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.1633"},{"key":"2026090906400912000_2026.05.25.727702v2.39","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0806401105"},{"key":"2026090906400912000_2026.05.25.727702v2.40","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2010.07231.x"},{"key":"2026090906400912000_2026.05.25.727702v2.41","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.13308"},{"key":"2026090906400912000_2026.05.25.727702v2.42","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.21.7440-7449.2004"},{"key":"2026090906400912000_2026.05.25.727702v2.43","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.06.058"},{"key":"2026090906400912000_2026.05.25.727702v2.44","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2011.01.006"},{"key":"2026090906400912000_2026.05.25.727702v2.45","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01069-10"},{"key":"2026090906400912000_2026.05.25.727702v2.46","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2010.01.013"},{"key":"2026090906400912000_2026.05.25.727702v2.47","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2011.07577.x"},{"key":"2026090906400912000_2026.05.25.727702v2.48","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.12443"},{"key":"2026090906400912000_2026.05.25.727702v2.49","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.12516"},{"key":"2026090906400912000_2026.05.25.727702v2.50","doi-asserted-by":"publisher","DOI":"10.1128\/JB.188.6.2154-2162.2006"},{"key":"2026090906400912000_2026.05.25.727702v2.51","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2025.169614"},{"key":"2026090906400912000_2026.05.25.727702v2.52","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2014.03.015"},{"key":"2026090906400912000_2026.05.25.727702v2.53","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M111.284067"},{"key":"2026090906400912000_2026.05.25.727702v2.54","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001479"},{"key":"2026090906400912000_2026.05.25.727702v2.55","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2017.02.037"},{"key":"2026090906400912000_2026.05.25.727702v2.56","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac387"},{"key":"2026090906400912000_2026.05.25.727702v2.57","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.21.7456-7459.2004"},{"key":"2026090906400912000_2026.05.25.727702v2.58","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00274-15"},{"key":"2026090906400912000_2026.05.25.727702v2.59","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.1633"},{"key":"2026090906400912000_2026.05.25.727702v2.60","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01858-07"},{"key":"2026090906400912000_2026.05.25.727702v2.61","doi-asserted-by":"publisher","DOI":"10.1021\/bi801727m"},{"key":"2026090906400912000_2026.05.25.727702v2.62","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA119.009865"},{"key":"2026090906400912000_2026.05.25.727702v2.63","doi-asserted-by":"publisher","DOI":"10.1021\/bi901020d"},{"key":"2026090906400912000_2026.05.25.727702v2.64","doi-asserted-by":"publisher","DOI":"10.1021\/bi500657v"},{"key":"2026090906400912000_2026.05.25.727702v2.65","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2505872122"},{"key":"2026090906400912000_2026.05.25.727702v2.66","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4169"},{"key":"2026090906400912000_2026.05.25.727702v2.67","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-00990-8"},{"key":"2026090906400912000_2026.05.25.727702v2.68","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4792"},{"key":"2026090906400912000_2026.05.25.727702v2.69","doi-asserted-by":"publisher","DOI":"10.1107\/s2059798318002425"},{"key":"2026090906400912000_2026.05.25.727702v2.70","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3791"},{"key":"2026090906400912000_2026.05.25.727702v2.71","doi-asserted-by":"publisher","DOI":"10.1107\/S2059798322010026"},{"key":"2026090906400912000_2026.05.25.727702v2.72","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3330"},{"key":"2026090906400912000_2026.05.25.727702v2.73","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpca.8b07673"},{"key":"2026090906400912000_2026.05.25.727702v2.74","doi-asserted-by":"publisher","DOI":"10.1128\/JB.187.1.193-201.2005"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.05.25.727702","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T13:40:19Z","timestamp":1788961219000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.05.25.727702"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,28]]},"references-count":74,"URL":"https:\/\/doi.org\/10.64898\/2026.05.25.727702","relation":{},"subject":[],"published":{"date-parts":[[2026,5,28]]},"subtype":"preprint"}}