1
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Kienlein M, Zacharias M. How arginine inhibits substrate-binding domain 2 elucidated using molecular dynamics simulations. Protein Sci 2024; 33:e5077. [PMID: 38888275 PMCID: PMC11184577 DOI: 10.1002/pro.5077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024]
Abstract
The substrate-binding domain 2 (SBD2) is an important part of the bacterial glutamine (GLN) transporter and mediates binding and delivery of GLN to the transporter translocation subunit. The SBD2 consists of two domains, D1 and D2, that bind GLN in the space between domains in a closed structure. In the absence of ligand, the SBD2 adopts an open conformation with larger space between domains. The GLN binding and closing are essential for the subsequent transport into the cell. Arginine (ARG) can also bind to SBD2 but does not induce closing and inhibits GLN transport. We use atomistic molecular dynamics (MD) simulations in explicit solvent to study ARG binding in the presence of the open SBD2 structure and observed reversible binding to the native GLN binding site with similar contacts but no transition to a closed SBD2 state. Absolute binding free energy simulations predict a considerable binding affinity of ARG and GLN to the binding site on the D1 domain. Free energy simulations to induce subsequent closing revealed a strong free energy penalty in case of ARG binding in contrast to GLN binding that favors the closed SBD2 state but still retains a free energy barrier for closing. The simulations allowed the identification of the molecular origin of the closing penalty in case of bound ARG and suggested a mutation of lysine at position 373 to alanine that strongly reduced the penalty and allowed closing even in the presence of bound ARG. The study offers an explanation of the molecular mechanism of how ARG competitively inhibits GLN from binding to SBD2 and from triggering the transition to a closed conformation. The proposed Lys373Ala mutation shows promise as a potential tool to validate whether a conformational mismatch between open SBD2 and the translocator is responsible for preventing ARG uptake to the cell.
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Affiliation(s)
- Maximilian Kienlein
- Center for Functional Protein Assemblies (CPA)Technical University of MunichGarchingGermany
| | - Martin Zacharias
- Center for Functional Protein Assemblies (CPA)Technical University of MunichGarchingGermany
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2
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Han S, Lu Y, Peng L, Dong X, Zhu L, Han Y. Transcriptomics Reveals the Mechanism of Purpureocillium lilacinum GZAC18-2JMP in Degrading Keratin Material. Curr Microbiol 2024; 81:227. [PMID: 38879855 DOI: 10.1007/s00284-024-03757-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/03/2024] [Indexed: 07/21/2024]
Abstract
Microbial degradation of keratin is characterized by its inherent safety, remarkable efficiency, and the production of copious degradation products. All these attributes contribute to the effective management of waste materials at high value-added and in a sustainable manner. Microbial degradation of keratin materials remains unclear, however, with variations observed in the degradation genes and pathways among different microorganisms. In this study, we sequenced the transcriptome of Purpureocillium lilacinum GZAC18-2JMP mycelia on control medium and the medium containing 1% feather powder, analyzed the differentially expressed genes, and revealed the degradation mechanism of chicken feathers by P. lilacinum GZAC18-2JMP. The results showed that the chicken feather degradation rate of P. lilacinum GZAC18-2JMP reached 64% after 216 h of incubation in the fermentation medium, reaching a peak value of 148.9 μg·mL-1 at 192 h, and the keratinase enzyme activity reached a peak value of 211 U·mL-1 at 168 h, which revealed that P. lilacinum GZAC18-2JMP had a better keratin degradation effect. A total of 1001 differentially expressed genes (DEGs) were identified from the transcriptome database, including 475 upregulated genes and 577 downregulated genes. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis of the DEGs revealed that the metabolic pathways related to keratin degradation were mainly sulfur metabolism, ABC transporters, and amino acid metabolism. Therefore, the results of this study provide an opportunity to gain further insight into keratin degradation and promote the biotransformation of feather wastes.
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Affiliation(s)
- Shumei Han
- Institute of Fungus Resource, College of Life Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yingxia Lu
- Institute of Fungus Resource, College of Life Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Lan Peng
- Institute of Fungus Resource, College of Life Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xuan Dong
- Institute of Fungus Resource, College of Life Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Liping Zhu
- Institute of Fungus Resource, College of Life Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yanfeng Han
- Institute of Fungus Resource, College of Life Science, Guizhou University, Guiyang, 550025, Guizhou, China.
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3
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Smith OB, Frkic RL, Rahman MG, Jackson CJ, Kaczmarski JA. Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides. Biochemistry 2024; 63:1322-1334. [PMID: 38696389 DOI: 10.1021/acs.biochem.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Periplasmic solute-binding proteins (SBPs) are key ligand recognition components of bacterial ATP-binding cassette (ABC) transporters that allow bacteria to import nutrients and metabolic precursors from the environment. Periplasmic SBPs comprise a large and diverse family of proteins, of which only a small number have been empirically characterized. In this work, we identify a set of 610 unique uncharacterized proteins within the SBP_bac_5 family that are found in conserved operons comprising genes encoding (i) ABC transport systems and (ii) putative amidases from the FmdA_AmdA family. From these uncharacterized SBP_bac_5 proteins, we characterize a representative periplasmic SBP from Mesorhizobium sp. A09 (MeAmi_SBP) and show that MeAmi_SBP binds l-amino acid amides but not the corresponding l-amino acids. An X-ray crystal structure of MeAmi_SBP bound to l-serinamide highlights the residues that impart distinct specificity for l-amino acid amides and reveals a structural Ca2+ binding site within one of the lobes of the protein. We show that the residues involved in ligand and Ca2+ binding are conserved among the 610 SBPs from experimentally uncharacterized FmdA_AmdA amidase-associated ABC transporter systems, suggesting these homologous systems are also likely to be involved in the sensing, uptake, and metabolism of l-amino acid amides across many Gram-negative nitrogen-fixing soil bacteria. We propose that MeAmi_SBP is involved in the uptake of such solutes to supplement pathways such as the citric acid cycle and the glutamine synthetase-glutamate synthase pathway. This work expands our currently limited understanding of microbial interactions with l-amino acid amides and bacterial nitrogen utilization.
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Affiliation(s)
- Oliver B Smith
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Rebecca L Frkic
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Marina G Rahman
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Joe A Kaczmarski
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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4
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Xie Z, Nie Y, Dong M, Nie M, Tang J. Integrated physio-biochemical and transcriptomic analysis reveals the joint toxicity mechanisms of two typical antidepressants fluoxetine and sertraline on Microcystis aeruginosa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171802. [PMID: 38508265 DOI: 10.1016/j.scitotenv.2024.171802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/20/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Selective serotonin reuptake inhibitor (SSRI) antidepressants are of increasing concern worldwide due to their ubiquitous occurrence and detrimental effects on aquatic organisms. However, little is known regarding their effects on the dominant bloom-forming cyanobacterium, Microcystis aeruginosa. Here, we investigated the individual and joint effects of two typical SSRIs fluoxetine (FLX) and sertraline (SER) on M. aeruginosa at physio-biochemical and molecular levels. Results showed that FLX and SER had strong growth inhibitory effects on M. aeruginosa with the 96-h median effect concentrations (EC50s) of 362 and 225 μg/L, respectively. Besides, the mixtures showed an additive effect on microalgal growth. Meanwhile, both individual SSRIs and their mixtures can inhibit photosynthetic pigment synthesis, cause oxidative damage, destroy cell membrane, and promote microcystin-leucine-arginine (MC-LR) synthesis and release. Moreover, the mixtures enhanced the damage to photosynthesis, antioxidant system, and cell membrane and facilitated MC-LR synthesis and release compared to individuals. Furthermore, transcriptomic analysis revealed that the dysregulation of the key genes related to transport, photosystem, protein synthesis, and non-ribosomal peptide structures was the fundamental molecular mechanism underlying the physio-biochemical responses of M. aeruginosa. These findings provide a better understanding of the toxicity mechanisms of SSRIs to microalgae and their risks to aquatic ecosystems.
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Affiliation(s)
- Zhengxin Xie
- School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Yunfan Nie
- School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Mingyue Dong
- School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Meng Nie
- School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Jun Tang
- School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
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5
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Li B, Wang XQ, Li QY, Xu D, Li J, Hou WT, Chen Y, Jiang YL, Zhou CZ. Allosteric regulation of nitrate transporter NRT via the signaling protein PII. Proc Natl Acad Sci U S A 2024; 121:e2318320121. [PMID: 38457518 PMCID: PMC10945777 DOI: 10.1073/pnas.2318320121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/10/2024] [Indexed: 03/10/2024] Open
Abstract
Coordinated carbon and nitrogen metabolism is crucial for bacteria living in the fluctuating environments. Intracellular carbon and nitrogen homeostasis is maintained by a sophisticated network, in which the widespread signaling protein PII acts as a major regulatory hub. In cyanobacteria, PII was proposed to regulate the nitrate uptake by an ABC (ATP-binding cassette)-type nitrate transporter NrtABCD, in which the nucleotide-binding domain of NrtC is fused with a C-terminal regulatory domain (CRD). Here, we solved three cryoelectron microscopy structures of NrtBCD, bound to nitrate, ATP, and PII, respectively. Structural and biochemical analyses enable us to identify the key residues that form a hydrophobic and a hydrophilic cavity along the substrate translocation channel. The core structure of PII, but not the canonical T-loop, binds to NrtC and stabilizes the CRD, making it visible in the complex structure, narrows the substrate translocation channel in NrtB, and ultimately locks NrtBCD at an inhibited inward-facing conformation. Based on these results and previous reports, we propose a putative transport cycle driven by NrtABCD, which is allosterically inhibited by PII in response to the cellular level of 2-oxoglutarate. Our findings provide a distinct regulatory mechanism of ABC transporter via asymmetrically binding to a signaling protein.
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Affiliation(s)
- Bo Li
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Xiao-Qian Wang
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Qin-Yao Li
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Da Xu
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Jing Li
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Wen-Tao Hou
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Yuxing Chen
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Yong-Liang Jiang
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Cong-Zhao Zhou
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
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6
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Fang T, Szklarczyk D, Hachilif R, von Mering C. Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration. Sci Rep 2024; 14:6009. [PMID: 38472223 PMCID: PMC10933411 DOI: 10.1038/s41598-024-55655-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Protein-protein interactions (PPIs) play essential roles in most biological processes. The binding interfaces between interacting proteins impose evolutionary constraints that have successfully been employed to predict PPIs from multiple sequence alignments (MSAs). To construct MSAs, critical choices have to be made: how to ensure the reliable identification of orthologs, and how to optimally balance the need for large alignments versus sufficient alignment quality. Here, we propose a divide-and-conquer strategy for MSA generation: instead of building a single, large alignment for each protein, multiple distinct alignments are constructed under distinct clades in the tree of life. Coevolutionary signals are searched separately within these clades, and are only subsequently integrated using machine learning techniques. We find that this strategy markedly improves overall prediction performance, concomitant with better alignment quality. Using the popular DCA algorithm to systematically search pairs of such alignments, a genome-wide all-against-all interaction scan in a bacterial genome is demonstrated. Given the recent successes of AlphaFold in predicting direct PPIs at atomic detail, a discover-and-refine approach is proposed: our method could provide a fast and accurate strategy for pre-screening the entire genome, submitting to AlphaFold only promising interaction candidates-thus reducing false positives as well as computation time.
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Affiliation(s)
- Tao Fang
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Damian Szklarczyk
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Radja Hachilif
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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7
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To KKW, Huang Z, Zhang H, Ashby CR, Fu L. Utilizing non-coding RNA-mediated regulation of ATP binding cassette (ABC) transporters to overcome multidrug resistance to cancer chemotherapy. Drug Resist Updat 2024; 73:101058. [PMID: 38277757 DOI: 10.1016/j.drup.2024.101058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/27/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024]
Abstract
Multidrug resistance (MDR) is one of the primary factors that produces treatment failure in patients receiving cancer chemotherapy. MDR is a complex multifactorial phenomenon, characterized by a decrease or abrogation of the efficacy of a wide spectrum of anticancer drugs that are structurally and mechanistically distinct. The overexpression of the ATP-binding cassette (ABC) transporters, notably ABCG2 and ABCB1, are one of the primary mediators of MDR in cancer cells, which promotes the efflux of certain chemotherapeutic drugs from cancer cells, thereby decreasing or abolishing their therapeutic efficacy. A number of studies have suggested that non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play a pivotal role in mediating the upregulation of ABC transporters in certain MDR cancer cells. This review will provide updated information about the induction of ABC transporters due to the aberrant regulation of ncRNAs in cancer cells. We will also discuss the measurement and biological profile of circulating ncRNAs in various body fluids as potential biomarkers for predicting the response of cancer patients to chemotherapy. Sequence variations, such as alternative polyadenylation of mRNA and single nucleotide polymorphism (SNPs) at miRNA target sites, which may indicate the interaction of miRNA-mediated gene regulation with genetic variations to modulate the MDR phenotype, will be reviewed. Finally, we will highlight novel strategies that could be used to modulate ncRNAs and circumvent ABC transporter-mediated MDR.
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Affiliation(s)
- Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region.
| | - Zoufang Huang
- Department of Hematology, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Hang Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Charles R Ashby
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, United States
| | - Liwu Fu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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8
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Liang J, Yang X, Hu T, Gao Y, Yang Q, Yang H, Peng W, Zhou X, Guddat LW, Zhang B, Rao Z, Liu F. Structural insights into trehalose capture and translocation by mycobacterial LpqY-SugABC. Structure 2023; 31:1158-1165.e3. [PMID: 37619560 DOI: 10.1016/j.str.2023.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/25/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023]
Abstract
The human pathogen, Mycobacterium tuberculosis (Mtb) relies heavily on trehalose for both survival and pathogenicity. The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the only trehalose import pathway in Mtb. Conformational dynamics of ABC transporters is an important feature to explain how they operate, but experimental structures are determined in a static environment. Therefore, a detailed transport mechanism cannot be elucidated because there is a lack of intermediate structures. Here, we used single-particle cryo-electron microscopy (cryo-EM) to determine the structure of the Mycobacterium smegmatis (M. smegmatis) trehalose-specific importer LpqY-SugABC complex in five different conformations. These structures have been classified and reconstructed from a single cryo-EM dataset. This study allows a comprehensive understanding of the trehalose recycling mechanism in Mycobacteria and also demonstrates the potential of single-particle cryo-EM to explore the dynamic structures of other ABC transporters and molecular machines.
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Affiliation(s)
- Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Tianyu Hu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qi Yang
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wei Peng
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Xiaoting Zhou
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, QLD, Australia
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing, China; Laboratory of Structural Biology, Tsinghua University, Beijing, China.
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China.
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9
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Huo X, Pan A, Lei M, Song Z, Chen Y, Wang X, Gao Y, Zhang J, Wang S, Zhao Y, Wang F, Zhang J. Genome-Wide Characterization and Functional Analysis of ABCG Subfamily Reveal Its Role in Cutin Formation in Cotton. Int J Mol Sci 2023; 24:ijms24032379. [PMID: 36768702 PMCID: PMC9916852 DOI: 10.3390/ijms24032379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
ATP-binding cassette transporter G (ABCG) has been shown to be engaged in export of broad-spectrum compounds with structural differences, but little is known concerning its role in cutin formation of cotton (Gossypium spp.). In this study, we conduct a genome-wide survey and detected 69, 71, 124 and 131 ABCG genes within G. arboretum, G. raimondii, G. hirsutum and G. barbadense, separately. The above ABCGs could be divided into four groups (Ia, Ib, Ic, II). Some ABCG genes such as GhABCG15, whose homologous gene transports cuticular lipid in Arabidopsis, was preferentially expressed in the development of fiber. A weighted gene co-expression network analysis (WGCNA) demonstrated that GhABCG expression was significantly associated with the amount of 16-Hydroxypalmitate (a main component of cutin precursor) in cotton fibers. Further, silencing of GhABCG15 by virus-induced gene silencing (VIGS) in cotton generated brightened and crinkled leaves as well as reduced thickness of cuticle and increased permeability. Chemical composition analysis showed the cutin content in GhABCG15-silenced leaves had decreased while the wax content had increased. Our results provide an insight for better understanding of the role of the Gossypium ABCG family and revealed the essential role of GhABCGs in cotton cutin formation.
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Affiliation(s)
- Xuehan Huo
- Life Science College, Shandong Normal University, Jinan 250358, China
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ao Pan
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Mingyang Lei
- Life Science College, Shandong Normal University, Jinan 250358, China
| | - Zhangqiang Song
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xin Wang
- Life Science College, Shandong Normal University, Jinan 250358, China
| | - Yang Gao
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Shengli Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yanxiu Zhao
- Life Science College, Shandong Normal University, Jinan 250358, China
- Correspondence: (Y.Z.); (J.Z.)
| | - Furong Wang
- Life Science College, Shandong Normal University, Jinan 250358, China
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jun Zhang
- Life Science College, Shandong Normal University, Jinan 250358, China
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- Correspondence: (Y.Z.); (J.Z.)
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10
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Hirota R, Katsuura ZI, Momokawa N, Murakami H, Watanabe S, Ishida T, Ikeda T, Funabashi H, Kuroda A. Gatekeeper Residue Replacement in a Phosphite Transporter Enhances Mutational Robustness of the Biocontainment Strategy. ACS Synth Biol 2022; 11:3397-3404. [PMID: 36202772 DOI: 10.1021/acssynbio.2c00296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Biocontainment is a key methodology to reduce environmental risk through the deliberate release of genetically modified microorganisms. Previously, we developed a phosphite (HPO32-)-dependent biocontainment strategy, by expressing a phosphite-specific transporter HtxBCDE and phosphite dehydrogenase in bacteria devoid of their indigenous phosphate (HPO42-) transporters. This strategy did not allow Escherichia coli to generate escape mutants (EMs) in growth media containing phosphate as a phosphorus source using an assay with a detection limit of 1.9 × 10-13. In this study, we found that the coexistence of a high dose of phosphate (>0.5 mM) with phosphite in the growth medium allows the phosphite-dependent E. coli strain to generate EMs at a frequency of approximately 5.4 × 10-10. In all EMs, the mutation was a single amino acid substitution of phenylalanine to cysteine or serine at position 210 of HtxC, the transmembrane domain protein of the phosphorus compound transporter HtxBCDE. Replacement of the HtxC F210 residue with the other 17 amino acids revealed that HtxC F210 is crucial in determining substrate specificity of HtxBCDE. Based on the finding of the role of HtxC F210 as a "gatekeeper" residue for this transporter, we demonstrate that the replacement of HtxC F210 with amino acids resulting from codons that require two simultaneous point mutations to generate phosphate permissive HtxC mutants can reduce the rate of EM generation to an undetectable level. These findings also provide novel insights into the functional classification of HtxBCDE as a noncanonical ATP-binding cassette transporter in which the transmembrane domain protein participates in substrate recognition.
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Affiliation(s)
- Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Zen-Ichiro Katsuura
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Naoki Momokawa
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hiroki Murakami
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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11
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Aller SG, Segrest JP. The regulatory domains of the lipid exporter ABCA1 form domain swapped latches. PLoS One 2022; 17:e0262746. [PMID: 35120130 PMCID: PMC8815970 DOI: 10.1371/journal.pone.0262746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/04/2022] [Indexed: 12/19/2022] Open
Abstract
ABCA1 and ABCA4 are enigmatic because they transport substrates in opposite directions yet share >50% amino acid identity. ABCA4 imports lipid conjugates but ABCA1 exports lipids. Both hydrolyze ATP to drive transport, and both contain cytoplasmic regulatory domains (RDs) following nucleotide-binding domains (NBDs) in the primary structure. The tertiary structures of several ABC importers, including ABCA4, show that each RD forms a domain-swapped latch that locks onto the opposing RD and holds the NBDs close together. Crucially, sequences encoding the RDs and their bridges are among the most conserved in the entire ABC-A subfamily. In the original cryo-EM structure of ABCA1, the RDs were modeled without crossover. After close inspection of that cryo-EM density map and the recent structure of ABCA4, we propose that the RDs of ABCA1 also form a domain-swapped latch. A refined ABCA1 model containing latches exhibited significantly improved overall protein geometry. Critically, the conserved crossover sequence leading to the RD-domain swap is directly supported by the original cryo-EM density map of ABCA1 and appears to have been overlooked. Our refined ABCA1 model suggests the possibility that ABCA1, despite being an exporter, has highly restrained NBDs that suggest a transport mechanism that is distinct from 'alternating access'.
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Affiliation(s)
- Stephen G. Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jere P. Segrest
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
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12
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MURATA K, KAWAI S, HASHIMOTO W. Bacteria with a mouth: Discovery and new insights into cell surface structure and macromolecule transport. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:529-552. [PMID: 36504195 PMCID: PMC9751261 DOI: 10.2183/pjab.98.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
A bacterium with a "mouth"-like pit structure isolated for the first time in the history of microbiology was a Gram-negative rod, containing glycosphingolipids in the cell envelope, and named Sphingomonas sp. strain A1. The pit was dynamic, with repetitive opening and closing during growth on alginate, and directly included alginate concentrated around the pit, particularly by flagellins, an alginate-binding protein localized on the cell surface. Alginate incorporated into the periplasm was subsequently transferred to the cytoplasm by cooperative interactions of periplasmic solute-binding proteins and an ATP-binding cassette transporter in the cytoplasmic membrane. The mechanisms of assembly, functions, and interactions between the above-mentioned molecules were clarified using structural biology. The pit was transplanted into other strains of sphingomonads, and the pitted recombinant cells were effectively applied to the production of bioethanol, bioremediation for dioxin removal, and other tasks. Studies of the function of the pit shed light on the biological significance of cell surface structures and macromolecule transport in bacteria.
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Affiliation(s)
| | - Shigeyuki KAWAI
- Research Institute for Bioresource and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Wataru HASHIMOTO
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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13
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Wang JQ, Wu ZX, Yang Y, Teng QX, Li YD, Lei ZN, Jani KA, Kaushal N, Chen ZS. ATP-binding cassette (ABC) transporters in cancer: A review of recent updates. J Evid Based Med 2021; 14:232-256. [PMID: 34388310 DOI: 10.1111/jebm.12434] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023]
Abstract
The ATP-binding cassette (ABC) transporter superfamily is one of the largest membrane protein families existing in wide spectrum of organisms from prokaryotes to human. ABC transporters are also known as efflux pumps because they mediate the cross-membrane transportation of various endo- and xenobiotic molecules energized by ATP hydrolysis. Therefore, ABC transporters have been considered closely to multidrug resistance (MDR) in cancer, where the efflux of structurally distinct chemotherapeutic drugs causes reduced itherapeutic efficacy. Besides, ABC transporters also play other critical biological roles in cancer such as signal transduction. During the past decades, extensive efforts have been made in understanding the structure-function relationship, transportation profile of ABC transporters, as well as the possibility to overcome MDR via targeting these transporters. In this review, we discuss the most recent knowledge regarding ABC transporters and cancer drug resistance in order to provide insights for the development of more effective therapies.
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Affiliation(s)
- Jing-Quan Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York
| | - Zhuo-Xun Wu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York
| | - Yuqi Yang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York
| | - Qiu-Xu Teng
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York
| | - Yi-Dong Li
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York
| | - Zi-Ning Lei
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York
- School of Public Health, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Khushboo A Jani
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York
| | - Neeraj Kaushal
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York
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14
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Cho CH, Jang S, Choi BY, Hong D, Choi DS, Choi S, Kim H, Han SK, Kim S, Kim M, Palmgren M, Sohn KH, Yoon HS, Lee Y. Phylogenetic analysis of ABCG subfamily proteins in plants: functional clustering and coevolution with ABCGs of pathogens. PHYSIOLOGIA PLANTARUM 2021; 172:1422-1438. [PMID: 31828796 PMCID: PMC8359288 DOI: 10.1111/ppl.13052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/19/2019] [Indexed: 05/02/2023]
Abstract
ABCG subfamily proteins are highly enriched in terrestrial plants. Many of these proteins secrete secondary metabolites that repel or inhibit pathogens. To establish why the ABCG subfamily proteins proliferated extensively during evolution, we constructed phylogenetic trees from a broad range of eukaryotic organisms. ABCG proteins were massively duplicated in land plants and in oomycetes, a group of agronomically important plant pathogens, which prompted us to hypothesize that plant and pathogen ABCGs coevolved. Supporting this hypothesis, full-size ABCGs in host plants (Arabidopsis thaliana and Glycine max) and their pathogens (Hyaloperonospora arabidopsidis and Phytophthora sojae, respectively) had similar divergence times and patterns. Furthermore, generalist pathogens with broad ranges of host plants have diversified more ABCGs than their specialist counterparts. The hypothesis was further tested using an example pair of ABCGs that first diverged during multiplication in a host plant and its pathogen: AtABCG31 of A. thaliana and HpaP802307 of H. arabidopsidis. AtABCG31 expression was activated following infection with H. arabidopsidis, and disrupting AtABCG31 led to increased susceptibility to H. arabidopsidis. Together, our results suggest that ABCG genes in plants and their oomycete pathogens coevolved in an arms race, to extrude secondary metabolites involved in the plant's defense response against pathogens.
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Affiliation(s)
- Chung Hyun Cho
- Department of Biological SciencesSungkyunkwan UniversitySuwonKorea
| | - Sunghoon Jang
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
| | - Bae Young Choi
- Division of Integrative Bioscience and BiotechnologyPOSTECHPohang37673Korea
| | - Daewoong Hong
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
| | - Du Seok Choi
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
- Present address:
GreenBio Center, Corporate R&D, LG Chem, LtdSeoul07796Korea
| | - Sera Choi
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
| | - Haseong Kim
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
| | - Seong Kyu Han
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
| | - Sanguk Kim
- Division of Integrative Bioscience and BiotechnologyPOSTECHPohang37673Korea
| | - Min‐Sung Kim
- Division of Integrative Bioscience and BiotechnologyPOSTECHPohang37673Korea
| | - Michael Palmgren
- Department of Plant and Environmental ScienceUniversity of CopenhagenDK‐1871FrederiksbergDenmark
| | - Kee Hoon Sohn
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
- Division of Integrative Bioscience and BiotechnologyPOSTECHPohang37673Korea
| | - Hwan Su Yoon
- Department of Biological SciencesSungkyunkwan UniversitySuwonKorea
| | - Youngsook Lee
- Department of Life SciencePohang University of Science and Technology (POSTECH)Pohang37673Korea
- Division of Integrative Bioscience and BiotechnologyPOSTECHPohang37673Korea
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15
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Arines FM, Hamlin AJ, Yang X, Liu YYJ, Li M. A selective transmembrane recognition mechanism by a membrane-anchored ubiquitin ligase adaptor. J Cell Biol 2021; 220:211632. [PMID: 33351099 PMCID: PMC7759299 DOI: 10.1083/jcb.202001116] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 09/10/2020] [Accepted: 10/30/2020] [Indexed: 12/30/2022] Open
Abstract
While it is well-known that E3 ubiquitin ligases can selectively ubiquitinate membrane proteins in response to specific environmental cues, the underlying mechanisms for the selectivity are poorly understood. In particular, the role of transmembrane regions, if any, in target recognition remains an open question. Here, we describe how Ssh4, a yeast E3 ligase adaptor, recognizes the PQ-loop lysine transporter Ypq1 only after lysine starvation. We show evidence of an interaction between two transmembrane helices of Ypq1 (TM5 and TM7) and the single transmembrane helix of Ssh4. This interaction is regulated by the conserved PQ motif. Strikingly, recent structural studies of the PQ-loop family have suggested that TM5 and TM7 undergo major conformational changes during substrate transport, implying that transport-associated conformational changes may determine the selectivity. These findings thus provide critical information concerning the regulatory mechanism through which transmembrane domains can be specifically recognized in response to changing environmental conditions.
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Affiliation(s)
- Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Aaron Jeremy Hamlin
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Yun-Yu Jennifer Liu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
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16
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Jiang R, Xiang M, Chen W, Zhang P, Wu X, Zhu G, Tu T, Jiang D, Yao X, Luo Y, Yang Z, Chen D, Wang Y. Biofilm characteristics and transcriptomic analysis of Haemophilus parasuis. Vet Microbiol 2021; 258:109073. [PMID: 33984794 DOI: 10.1016/j.vetmic.2021.109073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/13/2021] [Indexed: 12/27/2022]
Abstract
Haemophilus parasuis (H. parasuis) is a conditional pathogen with the ability to form biofilms which can lead to ineffective drug treatment and severe chronic infections resulting in significant economic losses to the pig industry. Currently, knowledge of biofilm formation by H. parasuis is not well developed. The objective of this study was to investigate the three-dimensional morphology of biofilms and perform transcriptomic analysis on H. parasuis cells in biofilm versus planktonic forms. The results showed that proteins and DNA accounted for a large proportion of the H. parasuis biofilm extracellular matrix. Here, we have traced the entire biofilm formation process of H. parasuis from beginning to end for the first time. These biofilms grew rapidly in the first 48 h and became stable at 60 h. According to GO and KEGG analysis, the differentially expressed genes (DEG) artM, artQ, ssrS, pflA and HutX were implicated as being involved in bacterial colonisation and adhesion; these are the most likely genes to affect biofilm formation. Most functional gene enrichments were of those involved in metabolic pathways, biosynthesis of secondary metabolites, ATP-binding cassette (ABC) transporters, and starch and sucrose metabolism. Thus, in the present pilot study, the composition and characteristics of these biofilms were explored, and the genes related to biofilm formation were screened for. This research lays the foundation for further studies on mechanisms regulating biofilm formation, in order to find new drug targets and develop new therapeutic drugs against H. parasuis.
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Affiliation(s)
- Ruijiao Jiang
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People's Republic of China
| | - Mingyuan Xiang
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Wanting Chen
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Pengfei Zhang
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Xulong Wu
- Branch of Animal Husbandry and Veterinary Medicine, Chengdu Agricultural College, Chengdu 611130, China
| | - Guangheng Zhu
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Teng Tu
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Dike Jiang
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Xueping Yao
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Luo
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zexiao Yang
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Dishi Chen
- Sichuan Animal Disease Prevention and Control Center, Chengdu 610047, China.
| | - Yin Wang
- Sichuan Provincial Key Laboratory of Animal Diseases and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
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17
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Soliman A, Rampitsch C, Tambong JT, Daayf F. Secretome Analysis of Clavibacter nebraskensis Strains Treated with Natural Xylem Sap In Vitro Predicts Involvement of Glycosyl Hydrolases and Proteases in Bacterial Aggressiveness. Proteomes 2021; 9:1. [PMID: 33435483 PMCID: PMC7839047 DOI: 10.3390/proteomes9010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 12/30/2020] [Indexed: 11/16/2022] Open
Abstract
The Gram-positive bacterium Clavibacter nebraskensis (Cn) causes Goss's wilt and leaf blight on corn in the North American Central Plains with yield losses as high as 30%. Cn strains vary in aggressiveness on corn, with highly aggressive strains causing much more serious symptoms and damage to crops. Since Cn inhabits the host xylem, we investigated differences in the secreted proteomes of Cn strains to determine whether these could account for phenotypic differences in aggressiveness. Highly and a weakly aggressive Cn strains (Cn14-15-1 and DOAB232, respectively) were cultured, in vitro, in the xylem sap of corn (CXS; host) and tomato (TXS; non-host). The secretome of the Cn strains were extracted and processed, and a comparative bottom-up proteomics approach with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to determine their identities and concentration. Relative quantitation of peptides was based on precursor ion intensities to measure protein abundances. In total, 745 proteins were identified in xylem sap media. In CXS, a total of 658 and 396 proteins were identified in strains Cn14-5-1 and DOAB232, respectively. The unique and the differentially abundant proteins in the secretome of strain Cn14-5-1 were higher in either sap medium compared to DOAB232. These proteins were sorted using BLAST2GO and assigned to 12 cellular functional processes. Virulence factors, e.g., cellulase, β-glucosidase, β-galactosidase, chitinase, β-1,4-xylanase, and proteases were generally higher in abundance in the aggressive Cn isolate. This was corroborated by enzymatic activity assays of cellulase and protease in CXS. These proteins were either not detected or detected at significantly lower abundance levels in Cn strains grown in non-host xylem sap (tomato), suggesting potential factors involved in Cn-host (corn) interactions.
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Affiliation(s)
- Atta Soliman
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
- Department of Genetics, Faculty of Agriculture, University of Tanta, Tanta, Gharbiya 31111, Egypt
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Christof Rampitsch
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada;
| | | | - Fouad Daayf
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
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18
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Riley EP, Lopez-Garrido J, Sugie J, Liu RB, Pogliano K. Metabolic differentiation and intercellular nurturing underpin bacterial endospore formation. SCIENCE ADVANCES 2021; 7:eabd6385. [PMID: 33523946 PMCID: PMC10670878 DOI: 10.1126/sciadv.abd6385] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Despite intensive research, the role of metabolism in bacterial sporulation remains poorly understood. Here, we demonstrate that Bacillus subtilis sporulation entails a marked metabolic differentiation of the two cells comprising the sporangium: the forespore, which becomes the dormant spore, and the mother cell, which dies as sporulation completes. Our data provide evidence that metabolic precursor biosynthesis becomes restricted to the mother cell and that the forespore becomes reliant on mother cell-derived metabolites for protein synthesis. We further show that arginine is trafficked between the two cells and that proposed proteinaceous channels mediate small-molecule intercellular transport. Thus, sporulation entails the profound metabolic reprogramming of the forespore, which is depleted of key metabolic enzymes and must import metabolites from the mother cell. Together, our results provide a bacterial example analogous to progeny nurturing.
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Affiliation(s)
- Eammon P Riley
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Joseph Sugie
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Roland B Liu
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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19
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Sidiq KR, Chow MW, Zhao Z, Daniel RA. Alanine metabolism in Bacillus subtilis. Mol Microbiol 2020; 115:739-757. [PMID: 33155333 DOI: 10.1111/mmi.14640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/30/2022]
Abstract
Both isomeric forms of alanine play a crucial role in bacterial growth and viability; the L-isomer of this amino acid is one of the building blocks for protein synthesis, and the D-isomer is incorporated into the bacterial cell wall. Despite a long history of genetic manipulation of Bacillus subtilis using auxotrophic markers, the genes involved in alanine metabolism have not been characterized fully. In this work, we genetically characterized the major enzymes involved in B. subtilis alanine biosynthesis and identified an alanine permease, AlaP (YtnA), which we show has a major role in the assimilation of D-alanine from the environment. Our results provide explanations for the puzzling fact that growth of B. subtilis does not result in the significant accumulation of extracellular D-alanine. Interestingly, we find that in B. subtilis, unlike E. coli where multiple enzymes have a biochemical activity that can generate alanine, the primary synthetic enzyme for alanine is encoded by alaT, although a second gene, dat, can support slow growth of an L-alanine auxotroph. However, our results also show that Dat mediates the synthesis of D-alanine and its activity is influenced by the abundance of L-alanine. This work provides valuable insights into alanine metabolism that suggests that the relative abundance of D- and L-alanine might be linked with cytosolic pool of D and L-glutamate, thereby coupling protein and cell envelope synthesis with the metabolic status of the cell. The results also suggest that, although some of the purified enzymes involved in alanine biosynthesis have been shown to catalyze reversible reactions in vitro, most of them function unidirectionally in vivo.
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Affiliation(s)
- Karzan R Sidiq
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Man W Chow
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Zhao Zhao
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Richard A Daniel
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
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20
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Hase K, Contu VR, Kabuta C, Sakai R, Takahashi M, Kataoka N, Hakuno F, Takahashi SI, Fujiwara Y, Wada K, Kabuta T. Cytosolic domain of SIDT2 carries an arginine-rich motif that binds to RNA/DNA and is important for the direct transport of nucleic acids into lysosomes. Autophagy 2020; 16:1974-1988. [PMID: 31944164 PMCID: PMC7595612 DOI: 10.1080/15548627.2020.1712109] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/25/2019] [Accepted: 12/30/2019] [Indexed: 12/26/2022] Open
Abstract
RNautophagy and DNautophagy (RDA) are unconventional autophagic pathways where nucleic acids are directly transported through the lysosomal membrane, then degraded inside lysosomes. We have previously shown that bitopic protein LAMP2C and putative RNA transporter SIDT2, both lysosomal membrane proteins, mediate the direct transport of nucleic acids into lysosomes and that LAMP2C interacts with the nucleic acids and functions as a receptor during RDA. Because SIDT2-mediated RDA occurs in isolated lysosomes that lack LAMP2C, in this study, we tested the hypothesis that SIDT2 itself could also interact with the nucleic acids. Our results show that SIDT2 directly binds RNA and DNA through an arginine-rich motif (ARM) located within its main cytosolic domain, and disruption of this motif dramatically impairs SIDT2-mediated RNautophagic activity. We also found that SIDT2 interacts with exon 1 of HTT (huntingtin) transcript through the ARM in a CAG-dependent manner. Moreover, overexpression of SIDT2 promoted degradation of HTT mRNA and reduced the levels of polyglutamine-expanded HTT aggregates, hallmarks of Huntington disease. In addition, a comparative analysis of LAMP2C and SIDT2 functions at the cellular level revealed that the two proteins exert a synergistic effect on RNautophagic activity and that the ARMs which mediate the interactions of SIDT2 and LAMP2C with RNA are essential for the synergy. Together, our results point out the importance of nucleic acid-binding capacity of SIDT2 for its function in translocating nucleic acids through the lipid bilayer and suggests a potential application of RNautophagy activation to reduce the expression levels of disease-causing toxic proteins. Abbreviations: ACTB/β-actin: actin beta; ARM: arginine-rich motif; CBB: Coomassie Brilliant Blue; CD: cytosolic domain; COX4I1/COX4: cytochrome c oxidase subunit 4I1; E. coli: Escherichia coli; EGFP: enhanced green fluorescent protein; EtBr: ethidium bromide; FITC: fluorescein isothiocyanate; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GOLGA2/GM130: golgin A2; GST: glutathione S-transferase; HRP: horseradish peroxidase; HSPA5/GRP78: heat shock protein family A (Hsp70) member 5; HTT: huntingtin; HTTex1: exon 1 of the HTT gene; LAMP2: lysosomal associated membrane protein 2; LMNA: lamin A/C; PAGE: polyacrylamide gel electrophoresis; PBS: phosphate-buffered saline; PEI: polyethyleneimine; polyQ: polyglutamine; qPCR: quantitative PCR; RAB5A: RAB5A, member RAS oncogene family; RDA: RNautophagy and DNautophagy; SCARB2/LIMP2: scavenger receptor class B member 2; SDS: sodium dodecyl sulfate; SID-1: systemic RNA interference deficient-1; SIDT2: SID1 transmembrane family member 2; WT: wild type.
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Affiliation(s)
- Katsunori Hase
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
- Department of Animal Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Viorica Raluca Contu
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Chihana Kabuta
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Ryohei Sakai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Masayuki Takahashi
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Naoyuki Kataoka
- Department of Animal Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Fumihiko Hakuno
- Department of Animal Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Shin-Ichiro Takahashi
- Department of Animal Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Yuuki Fujiwara
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Keiji Wada
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Tomohiro Kabuta
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
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21
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Ford RC, Hellmich UA. What monomeric nucleotide binding domains can teach us about dimeric ABC proteins. FEBS Lett 2020; 594:3857-3875. [PMID: 32880928 DOI: 10.1002/1873-3468.13921] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
The classic conceptualization of ATP binding cassette (ABC) transporter function is an ATP-dependent conformational change coupled to transport of a substrate across a biological membrane via the transmembrane domains (TMDs). The binding of two ATP molecules within the transporter's two nucleotide binding domains (NBDs) induces their dimerization. Despite retaining the ability to bind nucleotides, isolated NBDs frequently fail to dimerize. ABC proteins without a TMD, for example ABCE and ABCF, have NBDs tethered via elaborate linkers, further supporting that NBD dimerization does not readily occur for isolated NBDs. Intriguingly, even in full-length transporters, the NBD-dimerized, outward-facing state is not as frequently observed as might be expected. This leads to questions regarding what drives NBD interaction and the role of the TMDs or linkers. Understanding the NBD-nucleotide interaction and the subsequent NBD dimerization is thus pivotal for understanding ABC transporter activity in general. Here, we hope to provide new insights into ABC protein function by discussing the perplexing issue of (missing) NBD dimerization in isolation and in the context of full-length ABC proteins.
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Affiliation(s)
- Robert C Ford
- Faculty of Biology Medicine and Health, The University of Manchester, UK
| | - Ute A Hellmich
- Department of Chemistry, Johannes Gutenberg-University, Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt, Germany
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22
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de Boer M, Cordes T, Poolman B. Kinetic Modelling of Transport Inhibition by Substrates in ABC Importers. J Mol Biol 2020; 432:5565-5576. [PMID: 32800784 DOI: 10.1016/j.jmb.2020.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/05/2020] [Accepted: 08/09/2020] [Indexed: 12/11/2022]
Abstract
Prokaryotic ATP-binding cassette (ABC) importers require a substrate-binding protein (SBP) for the capture and delivery of the cognate substrate to the transmembrane domain (TMD) of the transporter. Various biochemical compounds have been identified that bind to the SBP but are not transported. The mechanistic basis for the "non-cognate" substrates not being transported differs. Some non-cognate substrates fail to trigger the appropriate conformational change in the SBP, resulting in loss of affinity for the TMD or the inability to allosterically activate transport. In another mechanism, the SBP cannot release the bound non-cognate substrate. Here, we used rate equations to derive the steady-state transport rate of cognate substrates of an ABC importer and investigated how non-cognate substrates influence this rate. We found that under limiting non-cognate substrate concentrations, the transport rate remains unaltered for each of the mechanisms. In contrast, at saturating substrate and SBP concentrations, the effect of the non-cognate substrate depends heavily on the respective mechanism. For instance, the transport rate becomes zero when the non-cognate substrate cannot be released by the SBP. Yet it remains unaffected when substrate release is possible but the SBP cannot dock onto the TMDs. Our work shows how the different mechanisms of substrate inhibition impact the transport kinetics, which is relevant for understanding and manipulating solute fluxes and hence the propagation of cells in nutritionally complex milieus.
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Affiliation(s)
- Marijn de Boer
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands; Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands; Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr, 2-4, 82152 Planegg-Martinsried, Germany
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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23
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High-yield production of L-serine through a novel identified exporter combined with synthetic pathway in Corynebacterium glutamicum. Microb Cell Fact 2020; 19:115. [PMID: 32471433 PMCID: PMC7260847 DOI: 10.1186/s12934-020-01374-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/25/2020] [Indexed: 01/08/2023] Open
Abstract
Background l-Serine has wide and increasing applications in industries with fast-growing market demand. Although strategies for achieving and improving l-serine production in Corynebacterium glutamicum (C. glutamicum) have focused on inhibiting its degradation and enhancing its biosynthetic pathway, l-serine yield has remained relatively low. Exporters play an essential role in the fermentative production of amino acids. To achieve higher l-serine yield, l-serine export from the cell should be improved. In C. glutamicum, ThrE, which can export l-threonine and l-serine, is the only identified l-serine exporter so far. Results In this study, a novel l-serine exporter NCgl0580 was identified and characterized in C. glutamicum ΔSSAAI (SSAAI), and named as SerE (encoded by serE). Deletion of serE in SSAAI led to a 56.5% decrease in l-serine titer, whereas overexpression of serE compensated for the lack of serE with respect to l-serine titer. A fusion protein with SerE and enhanced green fluorescent protein (EGFP) was constructed to confirm that SerE localized at the plasma membrane. The function of SerE was studied by peptide feeding approaches, and the results showed that SerE is a novel exporter for l-serine and l-threonine in C. glutamicum. Subsequently, the interaction of a known l-serine exporter ThrE and SerE was studied, and the results suggested that SerE is more important than ThrE in l-serine export in SSAAI. In addition, probe plasmid and electrophoretic mobility shift assays (EMSA) revealed NCgl0581 as the transcriptional regulator of SerE. Comparative transcriptomics between SSAAI and the NCgl0581 deletion strain showed that NCgl0581 is a positive regulator of NCgl0580. Finally, by overexpressing the novel exporter SerE, combined with l-serine synthetic pathway key enzyme serAΔ197, serC, and serB, the resulting strain presented an l-serine titer of 43.9 g/L with a yield of 0.44 g/g sucrose, which is the highest l-serine titer and yield reported so far in C. glutamicum. Conclusions This study provides a novel target for l-serine and l-threonine export engineering as well as a new global transcriptional regulator NCgl0581 in C. glutamicum.
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24
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Tamura K, Sugita Y. Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T. J Phys Chem Lett 2020; 11:2824-2829. [PMID: 32202796 PMCID: PMC10961826 DOI: 10.1021/acs.jpclett.0c00547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The heme ATP-binding cassette (ABC) transporter BhuUV-T of bacterial pathogen Burkholderia cenocepacia is required to transport heme across the inner cell membrane. The current hypothesis is that the binding of two ATPs to the nucleotide-binding domains of the transporter drives the initial steps of the transport cycle in which the empty transport sites are reoriented from the cytosol to the periplasm. Molecular details are missing because the structure of a key occluded intermediate remains hypothetical. Here we perform molecular simulations to analyze the free energy surface (FES) of the first step of the reorientation, namely the transition from an open inward-facing (IF) transport site to an occluded (Occ) conformation. We have modeled the latter structure in silico in a previous study. A simple annealing procedure removes residual bias originating from non-equilibrium targeted molecular dynamics. The calculated FES reveals the role of the ATPs in inducing the IF → Occ conformational change and validates the modeled Occ conformation.
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Affiliation(s)
- Koichi Tamura
- Computational Biophysics
Research
Team, RIKEN Center for Computational Science, 6-7-1 minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Computational Biophysics
Research
Team, RIKEN Center for Computational Science, 6-7-1 minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Laboratory for Biomolecular Function
Simulation, RIKEN Center for Biosystems
Dynamics Research, 6-7-1
minatojima-Minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
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25
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Abstract
Energy-coupling factor (ECF)-type ATP-binding cassette (ABC) transporters catalyze membrane transport of micronutrients in prokaryotes. Crystal structures and biochemical characterization have revealed that ECF transporters are mechanistically distinct from other ABC transport systems. Notably, ECF transporters make use of small integral membrane subunits (S-components) that are predicted to topple over in the membrane when carrying the bound substrate from the extracellular side of the bilayer to the cytosol. Here, we review the phylogenetic diversity of ECF transporters as well as recent structural and biochemical advancements that have led to the postulation of conceptually different mechanistic models. These models can be described as power stroke and thermal ratchet. Structural data indicate that the lipid composition and bilayer structure are likely to have great impact on the transport function. We argue that study of ECF transporters could lead to generic insight into membrane protein structure, dynamics, and interaction.
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Affiliation(s)
- S Rempel
- Gr oningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands; , ,
| | - W K Stanek
- Gr oningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands; , ,
| | - D J Slotboom
- Gr oningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands; , , .,Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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26
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Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica. Sci Rep 2019; 9:12158. [PMID: 31434915 PMCID: PMC6704131 DOI: 10.1038/s41598-019-47994-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/24/2019] [Indexed: 12/22/2022] Open
Abstract
Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of these microbial populations, the type of metabolism and the biogeochemical cycles. Three ecosystems can be differentiated in glaciers: supraglacial, subglacial and englacial ecosystems. Firstly, the supraglacial ecosystem, sunlit and oxygenated, is predominantly populated by photoautotrophic microorganisms. Secondly, the subglacial ecosystem contains a majority of chemoautotrophs that are fed on the mineral salts of the rocks and basal soil. Lastly, the englacial ecosystem is the least studied and the one that contains the smallest number of microorganisms. However, these unknown englacial microorganisms establish a food web and appear to have an active metabolism. In order to study their metabolic potentials, samples of englacial ice were taken from an Antarctic glacier. Microorganisms were analyzed by a polyphasic approach that combines a set of -omic techniques: 16S rRNA sequencing, culturomics and metaproteomics. This combination provides key information about diversity and functions of microbial populations, especially in rare habitats. Several whole essential proteins and enzymes related to metabolism and energy production, recombination and translation were found that demonstrate the existence of cellular activity at subzero temperatures. In this way it is shown that the englacial microorganisms are not quiescent, but that they maintain an active metabolism and play an important role in the glacial microbial community.
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27
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de Boer M, Gouridis G, Vietrov R, Begg SL, Schuurman-Wolters GK, Husada F, Eleftheriadis N, Poolman B, McDevitt CA, Cordes T. Conformational and dynamic plasticity in substrate-binding proteins underlies selective transport in ABC importers. eLife 2019; 8:44652. [PMID: 30900991 PMCID: PMC6450668 DOI: 10.7554/elife.44652] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/22/2019] [Indexed: 12/20/2022] Open
Abstract
Substrate-binding proteins (SBPs) are associated with ATP-binding cassette importers and switch from an open to a closed conformation upon substrate binding, providing specificity for transport. We investigated the effect of substrates on the conformational dynamics of six SBPs and the impact on transport. Using single-molecule FRET, we reveal an unrecognized diversity of plasticity in SBPs. We show that a unique closed SBP conformation does not exist for transported substrates. Instead, SBPs sample a range of conformations that activate transport. Certain non-transported ligands leave the structure largely unaltered or trigger a conformation distinct from that of transported substrates. Intriguingly, in some cases, similar SBP conformations are formed by both transported and non-transported ligands. In this case, the inability for transport arises from slow opening of the SBP or the selectivity provided by the translocator. Our results reveal the complex interplay between ligand-SBP interactions, SBP conformational dynamics and substrate transport.
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Affiliation(s)
- Marijn de Boer
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Giorgos Gouridis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.,Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Ruslan Vietrov
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Stephanie L Begg
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Gea K Schuurman-Wolters
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Florence Husada
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.,Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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28
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Maruyama Y, Hashimoto W, Murata K. Structural studies on bacterial system used in the recognition and uptake of the macromolecule alginate. Biosci Biotechnol Biochem 2019; 83:794-802. [PMID: 30744540 DOI: 10.1080/09168451.2019.1578642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alginate is an acidic heteropolysaccharide produced by brown seaweed and certain kinds of bacteria. The cells of Sphingomonas sp. strain A1, a gram-negative bacterium, have several alginate-degrading enzymes in their cytoplasm and efficiently utilize this polymer for their growth. Sphingomonas sp. strain A1 cells can directly incorporate alginate into their cytoplasm through a transport system consisting of a "pit" on their cell surface, substrate-binding proteins in their periplasm, and an ATP-binding cassette transporter in their inner membrane. This review deals with the structural and functional aspects of bacterial systems necessary for the recognition and uptake of alginate.
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Affiliation(s)
- Yukie Maruyama
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Uji, Kyoto , Japan.,b Department of Life Science, Faculty of Science and Engineering , Setsunan University , Neyagawa, Osaka , Japan
| | - Wataru Hashimoto
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Uji, Kyoto , Japan
| | - Kousaku Murata
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Uji, Kyoto , Japan.,b Department of Life Science, Faculty of Science and Engineering , Setsunan University , Neyagawa, Osaka , Japan
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29
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Evidence from Mutational Analysis for a Single Transmembrane Substrate Binding Site in the Histidine ATP-Binding Cassette Transporter of Salmonella enterica Serovar Typhimurium. J Bacteriol 2018; 201:JB.00521-18. [PMID: 30348830 DOI: 10.1128/jb.00521-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/14/2018] [Indexed: 11/20/2022] Open
Abstract
The histidine ATP-binding cassette (ABC) transporter of Salmonella enterica serovar Typhimurium is among the best-studied type I ABC import systems. The transporter consists of two transmembrane subunits, HisQ and HisM, and a homodimer of the nucleotide-binding subunit, HisP. Substrates are delivered by two periplasmic solute binding proteins, HisJ and LAO, with preferences for histidine and for lysine, arginine, and ornithine, respectively. A homology model was built by using the arginine-bound crystal structure of the closely related Art(QN)2 transporter of Thermoanaerobacter tengcongensis as the template. In the homodimeric Art(QN)2, one substrate molecule is bound to each of the ArtQ subunits, whereas the structural model and sequence alignments predict only one substrate molecule in contact with HisM. To address the question whether one or two binding sites exist in heterodimeric HisQM, we have studied the functional consequences of mutations by monitoring (i) the complementation of growth on d-histidine of auxotrophic tester strains, (ii) the growth of tester strains on arginine as a nitrogen source, and (iii) ATPase activity of purified variants in a lipid environment. Our results demonstrate that two negatively charged residues, namely, HisM-E166 and HisQ-D61, are indispensable for function. Furthermore, the complete reconstruction of an ArtQ-like binding site in HisQ resulted in an inactive transporter. Likewise, switching the positions of both negatively charged residues between HisQ and HisM caused transport-deficient phenotypes. Thus, we propose that one substrate molecule is primarily liganded by residues of HisM while HisQ-D61 forms a crucial salt bridge with the α-amino group of the substrate.IMPORTANCE Canonical ATP-binding cassette (ABC) importers are major players in the translocation of numerous nutrients, vitamins, and growth factors to the cytoplasm of prokaryotes. Moreover, some ABC importers have been identified as virulence factors in bacterial pathogenesis. Thus, a full understanding of their mode of action is considered a prerequisite, among others, for the development of novel antibacterial drugs. However, mainly owing to the lack of structural information, the knowledge of the chemical nature and number of substrate binding sites formed by the transmembrane subunits of ABC importers is scarce. Here, we provide evidence from mutational analyses that, in contrast to homologous homodimeric systems, the heterodimeric histidine transporter of Salmonella enterica serovar Typhimurium is liganding only one substrate molecule between its transmembrane subunits, HisM and HisQ.
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30
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Noncanonical role for the binding protein in substrate uptake by the MetNI methionine ATP Binding Cassette (ABC) transporter. Proc Natl Acad Sci U S A 2018; 115:E10596-E10604. [PMID: 30352853 PMCID: PMC6233128 DOI: 10.1073/pnas.1811003115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The high-affinity methionine importer MetNI belongs to the ATP Binding Cassette (ABC) family of transporters that carry out the ATP-dependent uptake of substrates into cells. As with other ABC importers, MetNI requires a soluble binding protein (MetQ) that in the canonical mechanistic model delivers substrates to the transporter. We made the unexpected observation that a MetQ variant with significantly impaired ligand-binding properties supports d-selenomethionine uptake at a higher rate than wild-type MetQ. A crystal structure of MetNIQ in the outward-facing conformation reveals access channels through the binding protein to the transmembrane translocation pathway. These studies support a noncanonical role for the binding protein in facilitating the uptake of certain substrates directly through the transporter–binding protein complex. The Escherichia coli methionine ABC transporter MetNI exhibits both high-affinity transport toward l-methionine and broad specificity toward methionine derivatives, including d-methionine. In this work, we characterize the transport of d-methionine derivatives by the MetNI transporter. Unexpectedly, the N229A substrate-binding deficient variant of the cognate binding protein MetQ was found to support high MetNI transport activity toward d-selenomethionine. We determined the crystal structure at 2.95 Å resolution of the ATPγS-bound MetNIQ complex in the outward-facing conformation with the N229A apo MetQ variant. This structure revealed conformational changes in MetQ providing substrate access through the binding protein to the transmembrane translocation pathway. MetQ likely mediates uptake of methionine derivatives through two mechanisms: in the methionine-bound form delivering substrate from the periplasm to the transporter (the canonical mechanism) and in the apo form by facilitating ligand binding when complexed to the transporter (the noncanonical mechanism). This dual role for substrate-binding proteins is proposed to provide a kinetic strategy for ABC transporters to transport both high- and low-affinity substrates present in a physiological concentration range.
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31
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One Intact Transmembrane Substrate Binding Site Is Sufficient for the Function of the Homodimeric Type I ATP-Binding Cassette Importer for Positively Charged Amino Acids Art(MP) 2 of Geobacillus stearothermophilus. J Bacteriol 2018; 200:JB.00092-18. [PMID: 29581409 DOI: 10.1128/jb.00092-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/20/2018] [Indexed: 02/04/2023] Open
Abstract
ATP-binding cassette (ABC) transport systems comprise two transmembrane domains/subunits that form a translocation path and two nucleotide-binding domains/subunits that bind and hydrolyze ATP. Prokaryotic canonical ABC import systems require an extracellular substrate-binding protein for function. Knowledge of substrate-binding sites within the transmembrane subunits is scarce. Recent crystal structures of the ABC importer Art(QN)2 for positively charged amino acids of Thermoanerobacter tengcongensis revealed the presence of one substrate molecule in a defined binding pocket in each of the transmembrane subunits, ArtQ (J. Yu, J. Ge, J. Heuveling, E. Schneider, and M. Yang, Proc Natl Acad Sci U S A 112:5243-5248, 2015, https://doi.org/10.1073/pnas.1415037112). This finding raised the question of whether both sites must be loaded with substrate prior to initiation of the transport cycle. To address this matter, we first explored the role of key residues that form the binding pocket in the closely related Art(MP)2 transporter of Geobacillus stearothermophilus, by monitoring consequences of mutations in ArtM on ATPase and transport activity at the level of purified proteins embedded in liposomes. Our results emphasize that two negatively charged residues (E153 and D160) are crucial for wild-type function. Furthermore, the variant Art[M(L67D)P]2 exhibited strongly impaired activities, which is why it was considered for construction of a hybrid complex containing one intact and one impaired substrate-binding site. Activity assays clearly revealed that one intact binding site was sufficient for function. To our knowledge, our study provides the first biochemical evidence on transmembrane substrate-binding sites of an ABC importer.IMPORTANCE Canonical prokaryotic ATP-binding cassette importers mediate the uptake of a large variety of chemicals, including nutrients, osmoprotectants, growth factors, and trace elements. Some also play a role in bacterial pathogenesis, which is why full understanding of their mode of action is of the utmost importance. One of the unsolved problems refers to the chemical nature and number of substrate binding sites formed by the transmembrane subunits. Here, we report that a hybrid amino acid transporter of G. stearothermophilus, encompassing one intact and one impaired transmembrane binding site, is fully competent in transport, suggesting that the binding of one substrate molecule is sufficient to trigger the translocation process.
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32
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Protein Linkers Provide Limits on the Domain Interactions in the ABC Importer GlnPQ and Determine the Rate of Transport. J Mol Biol 2018; 430:1249-1262. [PMID: 29486154 DOI: 10.1016/j.jmb.2018.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 01/28/2023]
Abstract
GlnPQ is an ATP-binding cassette importer with a unique domain organization and intricate transport behavior. The protein has two extracytoplamic substrate-binding domains (SBDs) per membrane subunit, each with different specificity for amino acids and different spacing to the translocator domain. We determined the effect of the length and structure of the linkers, which connect the SBDs to each other and to the membrane-embedded translocator domain, on the transport by GlnPQ. We reveal that varying the linker length impacts transport in a dual manner that depends on the conformational dynamics of the SBD. Varying the linker length not only changes the time for the SBD to find the translocator (docking) but also changes the probability to release the substrate again, thus altering the transport efficiency. On the basis of the experimental data and mathematical modeling, we calculate the docking efficiency as function of linker length and lifetime of the closed conformation. Importantly, not only linker length but also features in the sequence are important for efficient delivery of substrate from SBD to the translocator. We show that the linkers provide a platform for SBD docking and are not merely flexible structures.
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33
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Wu S, Fu L. Tyrosine kinase inhibitors enhanced the efficacy of conventional chemotherapeutic agent in multidrug resistant cancer cells. Mol Cancer 2018; 17:25. [PMID: 29455646 PMCID: PMC5817862 DOI: 10.1186/s12943-018-0775-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/01/2018] [Indexed: 01/24/2023] Open
Abstract
Multidrug resistance (MDR) triggered by ATP binding cassette (ABC) transporter such as ABCB1, ABCC1, ABCG2 limited successful cancer chemotherapy. Unfortunately, no commercial available MDR modulator approved by FDA was used in clinic. Tyrosine kinase inhibitors (TKIs) have been administrated to fight against cancer for decades. Almost TKI was used alone in clinic. However, drug combinations acting synergistically to kill cancer cells have become increasingly important in cancer chemotherapy as an approach for the recurrent resistant disease. Here, we summarize the effect of TKIs on enhancing the efficacy of conventional chemotherapeutic drug in ABC transporter-mediated MDR cancer cells, which encourage to further discuss and study in clinic.
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Affiliation(s)
- Shaocong Wu
- State Key Laboratory of Oncology in South China, Guangdong Esophageal Cancer Institute; Cancer Center, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Liwu Fu
- State Key Laboratory of Oncology in South China, Guangdong Esophageal Cancer Institute; Cancer Center, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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34
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Barreto-Ojeda E, Corradi V, Gu RX, Tieleman DP. Coarse-grained molecular dynamics simulations reveal lipid access pathways in P-glycoprotein. J Gen Physiol 2018; 150:417-429. [PMID: 29437858 PMCID: PMC5839720 DOI: 10.1085/jgp.201711907] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/17/2018] [Indexed: 12/13/2022] Open
Abstract
P-glycoprotein (P-gp) exports a broad range of dissimilar compounds, including drugs, lipids, and lipid-like molecules. Because of its substrate promiscuity, P-gp is a key player in the development of cancer multidrug resistance. Although P-gp is one of the most studied ABC transporters, the mechanism by which its substrates access the cavity remains unclear. In this study, we perform coarse-grained molecular dynamics simulations to explore possible lipid access pathways in the inward-facing conformation of P-gp embedded in bilayers of different lipid compositions. In the inward-facing orientation, only lipids from the lower leaflet access the cavity of the transporter. We identify positively charged residues at the portals of P-gp that favor lipid entrance to the cavity, as well as lipid-binding sites at the portals and within the cavity, which is in good agreement with previous experimental studies. This work includes several examples of lipid pathways for phosphatidylcholine and phosphatidylethanolamine lipids that help elucidate the molecular mechanism of lipid binding in P-gp.
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Affiliation(s)
- Estefania Barreto-Ojeda
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| | - Valentina Corradi
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| | - Ruo-Xu Gu
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
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Haferkamp I. Crossing the border - Solute entry into the chlamydial inclusion. Int J Med Microbiol 2017; 308:41-48. [PMID: 28864236 DOI: 10.1016/j.ijmm.2017.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/10/2017] [Accepted: 08/17/2017] [Indexed: 10/19/2022] Open
Abstract
Chlamydiales comprise important human and animal pathogens as well as endosymbionts of amoebae. Generally, these obligate intracellular living bacteria are characterized by a biphasic developmental cycle, a reduced genome and a restricted metabolic capacity. Because of their metabolic impairment, Chlamydiales essentially rely on the uptake of diverse metabolites from their hosts. Chlamydiales thrive in a special compartment, the inclusion, and hence are surrounded by an additional membrane. Solutes might enter the inclusion through pores and open channels or by redirection of host vesicles, which fuse with the inclusion membrane and release their internal cargo. Recent investigations shed new light on the chlamydia-host interaction and identified an additional way for nutrient uptake into the inclusion. Proteome studies and targeting analyses identified chlamydial and host solute carriers in inclusions of Chlamydia trachomatis infected cells. These transporters are involved in the provision of UDP-glucose and biotin, and probably deliver further metabolites to the inclusion. By the controlled recruitment of specific solute carriers to the inclusion, the chlamydial resident thus can actively manipulate the metabolite availability and composition in the inclusion. This review summarizes recent findings and new ideas on carrier mediated solute uptake into the chlamydial inclusion in the context of the bacterial and host metabolism.
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Affiliation(s)
- Ilka Haferkamp
- Universität Kaiserslautern, Pflanzenphysiologie, Erwin-Schrödinger Str. 22, 67663 Kaiserslautern, Germany.
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Teichmann L, Chen C, Hoffmann T, Smits SHJ, Schmitt L, Bremer E. From substrate specificity to promiscuity: hybrid ABC transporters for osmoprotectants. Mol Microbiol 2017; 104:761-780. [PMID: 28256787 DOI: 10.1111/mmi.13660] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/25/2017] [Accepted: 02/27/2017] [Indexed: 01/03/2023]
Abstract
The ABC-transporters OpuB and OpuC from Bacillus subtilis function as osmoprotectant import systems. Their structural genes have most likely evolved through a duplication event but the two transporters are remarkably different in their substrate profile. OpuB possesses narrow substrate specificity, while OpuC is promiscuous. We assessed the functionality of hybrids between these two ABC-transporters by reciprocally exchanging the coding regions for the OpuBC and OpuCC substrate-binding proteins between the corresponding opuB and opuC operons. Substantiating the critical role of the binding protein in setting the substrate specificity of ABC transporters, OpuB::OpuCC turned into a promiscuous system, while OpuC::OpuBC now exhibited narrow substrate specificity. Both hybrid transporters possessed a high affinity for their substrates but the transport capacity of the OpuB::OpuCC system was moderate due to the synthesis of only low amounts of the xenogenetic OpuCC protein. Suppressor mutations causing single amino acid substitutions in the GbsR repressor controlling the choline to glycine betaine biosynthesis pathway greatly improved OpuB::OpuCC-mediated compatible solute import through transcriptional up-regulation of the hybrid opuB::opuCC operon. Collectively, we demonstrate for the first time that one can synthetically switch the substrate specificity of a given ABC transporter by combining its core components with a xenogenetic ligand-binding protein.
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Affiliation(s)
- Laura Teichmann
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, Marburg, D-35043, Germany
| | - Chiliang Chen
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, Marburg, D-35043, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerweinstr. 6, Marburg, D-35043, Germany
| | - Tamara Hoffmann
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, Marburg, D-35043, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, Düsseldorf D-40225, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, Düsseldorf D-40225, Germany
| | - Erhard Bremer
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, Marburg, D-35043, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerweinstr. 6, Marburg, D-35043, Germany
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Crystal Structure of the Substrate-Binding Domain from Listeria monocytogenes Bile-Resistance Determinant BilE. CRYSTALS 2016. [DOI: 10.3390/cryst6120162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Culurgioni S, Harris G, Singh AK, King SJ, Walsh MA. Structural Basis for Regulation and Specificity of Fructooligosaccharide Import in Streptococcus pneumoniae. Structure 2016; 25:79-93. [PMID: 27939783 PMCID: PMC5222590 DOI: 10.1016/j.str.2016.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/28/2016] [Accepted: 11/07/2016] [Indexed: 12/16/2022]
Abstract
Streptococcus pneumoniae is dependent on carbohydrate uptake for colonization and pathogenesis, and dedicates over a third of its transport systems to their uptake. The ability of the pneumococcus to utilize fructooligosaccharides (FOSs) is attributed to the presence of one of two types of FOS ATP-binding cassette (ABC) transporters. Strains encoding SfuABC are only able to utilize short-chain FOSs, while strains encoding FusABC can utilize both short- and long-chain FOSs. The crystal structures of the substrate-binding protein FusA in its open and closed conformations bound to FOSs, and solution scattering data of SfuA, delineate the structural basis for import of short- and long-chain FOSs. The structure of FusA identifies an EF hand-like calcium-binding motif. This is shown to be essential for translocation of FOSs in FusABC and forms the basis for the definition of a new class of substrate-binding proteins that regulate substrate translocation by calcium.
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Affiliation(s)
- Simone Culurgioni
- Diamond House, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Gemma Harris
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Anirudh K Singh
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Samantha J King
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Martin A Walsh
- Diamond House, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
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Marty L, Vigouroux A, Aumont-Nicaise M, Dessaux Y, Faure D, Moréra S. Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens. J Biol Chem 2016; 291:22638-22649. [PMID: 27609514 DOI: 10.1074/jbc.m116.745562] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/31/2016] [Indexed: 11/06/2022] Open
Abstract
Agrobacterium tumefaciens pathogens genetically modify their host plants to drive the synthesis of opines in plant tumors. Opines are either sugar phosphodiesters or the products of condensed amino acids with ketoacids or sugars. They are Agrobacterium nutrients and imported into the bacterial cell via periplasmic-binding proteins (PBPs) and ABC-transporters. Mannopine, an opine from the mannityl-opine family, is synthesized from an intermediate named deoxy-fructosyl-glutamine (DFG), which is also an opine and abundant Amadori compound (a name used for any derivative of aminodeoxysugars) present in decaying plant materials. The PBP MotA is responsible for mannopine import in mannopine-assimilating agrobacteria. In the nopaline-opine type agrobacteria strain, SocA protein was proposed as a putative mannopine binding PBP, and AttC protein was annotated as a mannopine binding-like PBP. Structural data on mannityl-opine-PBP complexes is currently lacking. By combining affinity data with analysis of seven x-ray structures at high resolution, we investigated the molecular basis of MotA, SocA, and AttC interactions with mannopine and its DFG precursor. Our work demonstrates that AttC is not a mannopine-binding protein and reveals a specific binding pocket for DFG in SocA with an affinity in nanomolar range. Hence, mannopine would not be imported into nopaline-type agrobacteria strains. In contrast, MotA binds both mannopine and DFG. We thus defined one mannopine and two DFG binding signatures. Unlike mannopine-PBPs, selective DFG-PBPs are present in a wide diversity of bacteria, including Actinobacteria, α-,β-, and γ-proteobacteria, revealing a common role of this Amadori compound in pathogenic, symbiotic, and opportunistic bacteria.
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Affiliation(s)
- Loïc Marty
- From the Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette 91198, France
| | - Armelle Vigouroux
- From the Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette 91198, France
| | - Magali Aumont-Nicaise
- From the Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette 91198, France
| | - Yves Dessaux
- From the Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette 91198, France
| | - Denis Faure
- From the Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette 91198, France
| | - Solange Moréra
- From the Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette 91198, France
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He Z, Huang Z, Zhou W, Tang Z, Ma R, Liang J. Anti-biofilm Activities from Resveratrol against Fusobacterium nucleatum. Front Microbiol 2016; 7:1065. [PMID: 27458454 PMCID: PMC4932316 DOI: 10.3389/fmicb.2016.01065] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/24/2016] [Indexed: 11/24/2022] Open
Abstract
Fusobacterium nucleatum is a Gram-negative, anaerobic bacterium that plays an important role in dental plaque biofilm formation. In this study, we evaluate the effect of resveratrol, a phytoalexin compound, on F. nucleatum biofilm formation. The effects of different concentrations of resveratrol on biofilms formed on 96-well microtiter plates at different time points were determined by the MTT assay. The structures and thicknesses of the biofilm were observed by confocal laser scanning microscopy (CLSM), and gene expression was investigated by real-time PCR. The results showed that resveratrol at sub-MIC levels can significantly decrease biofilm formation, whereas it does not affect the bacterial growth rate. It was observed by CLSM images that the biofilm was visually decreased with increasing concentrations of resveratrol. Gene expression was down regulated in the biofilm in the presence of resveratrol. Our results revealed that resveratrol can effectively inhibit biofilm formation.
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Affiliation(s)
- Zhiyan He
- Department of Endodontics, Shanghai Research Institute of Stomatology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology Shanghai, China
| | - Zhengwei Huang
- Department of Endodontics, Shanghai Research Institute of Stomatology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology Shanghai, China
| | - Wei Zhou
- Department of Endodontics, Shanghai Research Institute of Stomatology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology Shanghai, China
| | - Zisheng Tang
- Department of Endodontics, Shanghai Research Institute of Stomatology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology Shanghai, China
| | - Rui Ma
- Department of Endodontics, Shanghai Research Institute of Stomatology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology Shanghai, China
| | - Jingping Liang
- Department of Endodontics, Shanghai Research Institute of Stomatology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology Shanghai, China
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