Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi

Seppälä, Susanna; Gierke, Taylor; Schauer, Elizabeth E.; Brown, Jennifer L.; O'Malley, Michelle A.

doi:10.1002/pro.4730

Title: Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi

Journal Article · 21 August 2023 · Protein Science

DOI: https://doi.org/10.1002/pro.4730 · OSTI ID:1996299

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Department of Chemical Engineering University of California Santa Barbara Santa Barbara California USA
Department of Chemical Engineering University of California Santa Barbara Santa Barbara California USA, Bioengineering Program University of California Santa Barbara California USA, Joint BioEnergy Institute (JBEI) Emeryville California USA

Abstract Membrane‐embedded transporters impart essential functions to cells as they mediate sensing and the uptake and extrusion of nutrients, waste products, and effector molecules. Promiscuous multidrug exporters are implicated in resistance to drugs and antibiotics and are highly relevant for microbial engineers who seek to enhance the tolerance of cell factory strains to hydrophobic bioproducts. Here, we report on the identification of small multidrug resistance (SMR) transporters in early‐branching anaerobic fungi (Neocallimastigomycetes). The SMR class of transporters is commonly found in bacteria but has not previously been reported in eukaryotes. In this study, we show that SMR transporters from anaerobic fungi can be produced heterologously in the model yeast Saccharomyces cerevisiae , demonstrating the potential of these proteins as targets for further characterization. The discovery of these novel anaerobic fungal SMR transporters offers a promising path forward to enhance bioproduction from engineered microbial strains.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint Bionergy Institute (JBEI)

Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF); US Army Research Office (ARO); USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1996299

Journal Information:: Protein Science, Journal Name: Protein Science Journal Issue: 9 Vol. 32; ISSN 0961-8368

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

References (56)

UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals O’ Donnell, Michelle M.; Harris, Hugh M. B.; Ross, R. Paul MicrobiologyOpen, Vol. 6, Issue 5 https://doi.org/10.1002/mbo3.509	journal	August 2017
Progress toward heterologous expression of active G-protein-coupled receptors in Saccharomyces cerevisiae : Linking cellular stress response with translocation and trafficking O'Malley, Michelle A.; Mancini, J. Dominic; Young, Carissa L. Protein Science, Vol. 18, Issue 11 https://doi.org/10.1002/pro.246	journal	November 2009
Anaerobic fungi Theodorou, Michael K.; Brookman, Jayne; Trinci, Anthony P. J. Methods in Gut Microbial Ecology for Ruminants https://doi.org/10.1007/1-4020-3791-0_5	book	January 2006
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Small multidrug resistance proteins: A multidrug transporter family that continues to grow Bay, Denice C.; Rommens, Kenton L.; Turner, Raymond J. Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1778, Issue 9 https://doi.org/10.1016/j.bbamem.2007.08.015	journal	September 2008
Enhancing the tolerance of Clostridium saccharoperbutylacetonicum to lignocellulosic-biomass-derived inhibitors for efficient biobutanol production by overexpressing efflux pumps genes from Pseudomonas putida Jiménez-Bonilla, Pablo; Zhang, Jie; Wang, Yifen Bioresource Technology, Vol. 312 https://doi.org/10.1016/j.biortech.2020.123532	journal	September 2020
Getting pumped: membrane efflux transporters for enhanced biomolecule production Boyarskiy, Sergey; Tullman-Ercek, Danielle Current Opinion in Chemical Biology, Vol. 28 https://doi.org/10.1016/j.cbpa.2015.05.019	journal	October 2015
Transporter engineering in microbial cell factories: the ins, the outs, and the in-betweens van der Hoek, Steven A.; Borodina, Irina Current Opinion in Biotechnology, Vol. 66 https://doi.org/10.1016/j.copbio.2020.08.002	journal	December 2020
Quasi-symmetry in the Cryo-EM Structure of EmrE Provides the Key to Modeling its Transmembrane Domain Fleishman, Sarel J.; Harrington, Susan E.; Enosh, Angela Journal of Molecular Biology, Vol. 364, Issue 1 https://doi.org/10.1016/j.jmb.2006.08.072	journal	November 2006
Heterologous transporters from anaerobic fungi bolster fluoride tolerance in Saccharomyces cerevisiae Seppälä, Susanna; Yoo, Justin I.; Yur, Daniel Metabolic Engineering Communications, Vol. 9 https://doi.org/10.1016/j.mec.2019.e00091	journal	December 2019
Structure, mechanism and cooperation of bacterial multidrug transporters Du, Dijun; van Veen, Hendrik W.; Murakami, Satoshi Current Opinion in Structural Biology, Vol. 33 https://doi.org/10.1016/j.sbi.2015.07.015	journal	August 2015
Transportome-wide engineering of Saccharomyces cerevisiae Wang, Guokun; Møller-Hansen, Iben; Babaei, Mahsa Metabolic Engineering, Vol. 64 https://doi.org/10.1016/j.ymben.2021.01.007	journal	March 2021
A SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast Podolsky, Igor A.; Seppälä, Susanna; Xu, Haiqing Metabolic Engineering, Vol. 66 https://doi.org/10.1016/j.ymben.2021.04.009	journal	July 2021
An Integrating Vector for Tunable, High Copy, Stable Integration into the Dispersed Ty δ Sites of Saccharomyces cerevisiae Parekh, R. N.; Shaw, M. R.; Wittrup, K. D. Biotechnology Progress, Vol. 12, Issue 1 https://doi.org/10.1021/bp9500627	journal	February 1996
Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues vonHeijne, Gunnar Nature, Vol. 341, Issue 6241 https://doi.org/10.1038/341456a0	journal	October 1989
Engineering microbial biofuel tolerance and export using efflux pumps Dunlop, Mary J.; Dossani, Zain Y.; Szmidt, Heather L. Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.21	journal	January 2011
A parts list for fungal cellulosomes revealed by comparative genomics Haitjema, Charles H.; Gilmore, Sean P.; Henske, John K. Nature Microbiology, Vol. 2, Issue 8 https://doi.org/10.1038/nmicrobiol.2017.87	journal	May 2017
GFP-based optimization scheme for the overexpression and purification of eukaryotic membrane proteins in Saccharomyces cerevisiae Drew, David; Newstead, Simon; Sonoda, Yo Nature Protocols, Vol. 3, Issue 5 https://doi.org/10.1038/nprot.2008.44	journal	April 2008
Membrane-protein topology von Heijne, Gunnar Nature Reviews Molecular Cell Biology, Vol. 7, Issue 12 https://doi.org/10.1038/nrm2063	journal	December 2006
Identification and evolution of dual-topology membrane proteins Rapp, Mikaela; Granseth, Erik; Seppälä, Susanna Nature Structural & Molecular Biology, Vol. 13, Issue 2 https://doi.org/10.1038/nsmb1057	journal	January 2006
The structural basis of promiscuity in small multidrug resistance transporters Kermani, Ali A.; Macdonald, Christian B.; Burata, Olive E. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-19820-8	journal	November 2020
Structure and dynamics of the drug-bound bacterial transporter EmrE in lipid bilayers Shcherbakov, Alexander A.; Hisao, Grant; Mandala, Venkata S. Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-020-20468-7	journal	January 2021
High-pH structure of EmrE reveals the mechanism of proton-coupled substrate transport Shcherbakov, Alexander A.; Spreacker, Peyton J.; Dregni, Aurelio J. Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-28556-6	journal	February 2022
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes Peng, Xuefeng; Wilken, St. Elmo; Lankiewicz, Thomas S. Nature Microbiology, Vol. 6, Issue 4 https://doi.org/10.1038/s41564-020-00861-0	journal	February 2021
ColabFold: making protein folding accessible to all Mirdita, Milot; Schütze, Konstantin; Moriwaki, Yoshitaka Nature Methods, Vol. 19, Issue 6 https://doi.org/10.1038/s41592-022-01488-1	journal	May 2022
High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae Newstead, Simon; Kim, Hyun; von Heijne, Gunnar Proceedings of the National Academy of Sciences, Vol. 104, Issue 35 https://doi.org/10.1073/pnas.0704546104	journal	August 2007
Quality control of overexpressed membrane proteins Geertsma, Eric R.; Groeneveld, Maarten; Slotboom, Dirk-Jan Proceedings of the National Academy of Sciences, Vol. 105, Issue 15 https://doi.org/10.1073/pnas.0802190105	journal	April 2008
Guanidinium export is the primal function of SMR family transporters Kermani, Ali A.; Macdonald, Christian B.; Gundepudi, Roja Proceedings of the National Academy of Sciences, Vol. 115, Issue 12 https://doi.org/10.1073/pnas.1719187115	journal	March 2018
Asymmetric protonation of glutamate residues drives a preferred transport pathway in EmrE Li, Jianping; Sae Her, Ampon; Traaseth, Nathaniel J. Proceedings of the National Academy of Sciences, Vol. 118, Issue 41 https://doi.org/10.1073/pnas.2110790118	journal	October 2021
Antiparallel Dimers of the Small Multidrug Resistance Protein EmrE Are More Stable Than Parallel Dimers Lloris-Garcerá, Pilar; Bianchi, Frans; Slusky, Joanna S. G. Journal of Biological Chemistry, Vol. 287, Issue 31 https://doi.org/10.1074/jbc.M112.357590	journal	June 2012
Protter: interactive protein feature visualization and integration with experimental proteomic data Omasits, Ulrich; Ahrens, Christian H.; Müller, Sebastian Bioinformatics, Vol. 30, Issue 6 https://doi.org/10.1093/bioinformatics/btt607	journal	October 2013
The InterPro protein families and domains database: 20 years on Blum, Matthias; Chang, Hsin-Yu; Chuguransky, Sara Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa977	journal	November 2020
Database resources of the national center for biotechnology information Sayers, Eric W.; Bolton, Evan E.; Brister, J. Rodney Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1112	journal	December 2021
UniProt: the Universal Protein Knowledgebase in 2023 Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1052	journal	November 2022
MycoCosm portal: gearing up for 1000 fungal genomes Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1183	journal	December 2013
Analysis Tool Web Services from the EMBL-EBI McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt376	journal	May 2013
GenBank Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1276	journal	November 2015
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides Tsirigos, Konstantinos D.; Peters, Christoph; Shu, Nanjiang Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv485	journal	May 2015
One major facilitator superfamily transporter is responsible for propionic acid tolerance in Pseudomonas putida KT2440 Ma, Chao; Mu, Qingxuan; Xue, Yubin Microbial Biotechnology, Vol. 14, Issue 2 https://doi.org/10.1111/1751-7915.13597	journal	May 2020
Control of Membrane Protein Topology by a Single C-Terminal Residue Seppala, S.; Slusky, J. S.; Lloris-Garcera, P. Science, Vol. 328, Issue 5986 https://doi.org/10.1126/science.1188950	journal	May 2010
Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes Solomon, Kevin V.; Haitjema, Charles H.; Henske, John K. Science, Vol. 351, Issue 6278 https://doi.org/10.1126/science.aad1431	journal	February 2016
Few Conserved Amino Acids in the Small Multidrug Resistance Transporter EmrE Influence Drug Polyselectivity Saleh, Marwah; Bay, Denice C.; Turner, Raymond J. Antimicrobial Agents and Chemotherapy, Vol. 62, Issue 8 https://doi.org/10.1128/AAC.00461-18	journal	August 2018
Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage Murphy, Chelsea L.; Youssef, Noha H.; Hanafy, Radwa A. Applied and Environmental Microbiology, Vol. 85, Issue 15 https://doi.org/10.1128/AEM.00988-19	journal	May 2019
Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity Higgins, Douglas A.; Gladden, John M.; Kimbrel, Jeff A. Journal of Bacteriology, Vol. 201, Issue 13 https://doi.org/10.1128/JB.00069-19	journal	April 2019
Riboswitch-Associated Guanidinium-Selective Efflux Pumps Frequently Transmitted on Proteobacterial Plasmids Increase Escherichia coli Biofilm Tolerance to Disinfectants Slipski, Carmine J.; Jamieson, Taylor R.; Zhanel, George G. Journal of Bacteriology, Vol. 202, Issue 23 https://doi.org/10.1128/JB.00104-20	journal	November 2020
Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus Wilken, St. Elmo; Monk, Jonathan M.; Leggieri, Patrick A. mSystems, Vol. 6, Issue 1 https://doi.org/10.1128/mSystems.00002-21	journal	February 2021
Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes Wang, Yan; Youssef, Noha H.; Couger, Matthew Brian mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/msystems.00247-19	journal	August 2019
Transporter engineering for improved tolerance against alkane biofuels in Saccharomyces cerevisiae Chen, Binbin; Ling, Hua; Chang, Matthew Wook Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-21	journal	January 2013
Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters Seppälä, Susanna; Solomon, Kevin V.; Gilmore, Sean P. Microbial Cell Factories, Vol. 15, Issue 1 https://doi.org/10.1186/s12934-016-0611-7	journal	December 2016
High-yield production of l-serine through a novel identified exporter combined with synthetic pathway in Corynebacterium glutamicum Zhang, Xiaomei; Gao, Yujie; Chen, Ziwei Microbial Cell Factories, Vol. 19, Issue 1 https://doi.org/10.1186/s12934-020-01374-5	journal	May 2020
Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates Brown, Jennifer L.; Swift, Candice L.; Mondo, Stephen J. Biotechnology for Biofuels, Vol. 14, Issue 1 https://doi.org/10.1186/s13068-021-02083-w	journal	December 2021
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants Xie, Fei; Jin, Wei; Si, Huazhe Microbiome, Vol. 9, Issue 1 https://doi.org/10.1186/s40168-021-01078-x	journal	June 2021
Application of Transcriptomics to Compare the Carbohydrate Active Enzymes That Are Expressed by Diverse Genera of Anaerobic Fungi to Degrade Plant Cell Wall Carbohydrates Gruninger, Robert J.; Nguyen, Thi T. M.; Reid, Ian D. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01581	journal	July 2018
A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics Malla, Sailesh; van der Helm, Eric; Darbani, Behrooz Frontiers in Microbiology, Vol. 13 https://doi.org/10.3389/fmicb.2022.855736	journal	April 2022
Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates Kermani, Ali A.; Burata, Olive E.; Koff, B. Ben eLife, Vol. 11 https://doi.org/10.7554/eLife.76766	journal	March 2022

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59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
anaerobic fungi
bioprocessing
membrane proteins
small multidrug resistance transporters
yeast

Title: Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi

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