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Chen Y, Sewsurn S, Amand S, Kunz C, Pietrancosta N, Calabro K, Buisson D, Mann S. Metabolic Investigation and Auxiliary Enzyme Modelization of the Pyrrocidine Pathway Allow Rationalization of Paracyclophane-Decahydrofluorene Formation. ACS Chem Biol 2024; 19:886-895. [PMID: 38576157 DOI: 10.1021/acschembio.3c00684] [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: 04/06/2024]
Abstract
Fungal paracyclophane-decahydrofluorene-containing natural products are complex polycyclic metabolites derived from similar hybrid PKS-NRPS pathways. Herein we studied the biosynthesis of pyrrocidines, one representative of this family, by gene inactivation in the producer Sarocladium zeae coupled to thorough metabolic analysis and molecular modeling of key enzymes. We characterized nine pyrrocidines and analogues as well as in mutants a variety of accumulating metabolites with new structures including rare cis-decalin, cytochalasan, and fused 6/15/5 macrocycles. This diversity highlights the extraordinary plasticity of the pyrrocidine biosynthetic gene cluster. From accumulating metabolites, we delineated the scenario of pyrrocidine biosynthesis. The ring A of the decahydrofluorene is installed by PrcB, a membrane-bound cyclizing isomerase, on a PKS-NRPS-derived pyrrolidone precursor. Docking experiments in PrcB allowed us to characterize the active site suggesting a mechanism triggered by arginine-mediated deprotonation at the terminal methyl of the substrate. Next, two integral membrane proteins, PrcD and PrcE, each predicted as a four-helix bundle, perform hydroxylation of the pyrrolidone ring and paracyclophane formation, respectively. Modelization of PrcE highlights a topological homology with vitamin K oxido-reductase and the presence of a disulfide bond. Our results suggest a previously unsuspected coupling mechanism via a transient loss of aromaticity of tyrosine residue to form the strained paracyclophane motif. Finally, the lipocalin-like protein PrcX drives the exo-cycloaddition yielding ring B and C of the decahydrofluorene to afford pyrrocidine A, which is transformed by a reductase PrcI to form pyrrocidine B. These insights will greatly facilitate the microbial production of pyrrocidine analogues by synthetic biology.
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Affiliation(s)
- Youwei Chen
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Steffi Sewsurn
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Séverine Amand
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Caroline Kunz
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 927, F-75005 Paris, France
| | - Nicolas Pietrancosta
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, PSL University, CNRS, F-75005 Paris, France
- Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, INSERM, CNRS, F-75005 Paris, France
| | - Kevin Calabro
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Didier Buisson
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
| | - Stéphane Mann
- Laboratoire Molécules de Communication et Adaptation des Micro-organismes UMR 7245, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Universités; CP54, 57 rue Cuvier, 75005 Paris, France
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Herrera-Quiterio GA, Encarnación-Guevara S. The transmembrane proteins (TMEM) and their role in cell proliferation, migration, invasion, and epithelial-mesenchymal transition in cancer. Front Oncol 2023; 13:1244740. [PMID: 37936608 PMCID: PMC10627164 DOI: 10.3389/fonc.2023.1244740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/11/2023] [Indexed: 11/09/2023] Open
Abstract
Transmembrane proteins (TMEM) are located in the different biological membranes of the cell and have at least one passage through these cellular compartments. TMEM proteins carry out a wide variety of functions necessary to maintain cell homeostasis TMEM165 participates in glycosylation protein, TMEM88 in the development of cardiomyocytes, TMEM45A in epidermal keratinization, and TMEM74 regulating autophagy. However, for many TMEM proteins, their physiological function remains unknown. The role of these proteins is being recently investigated in cancer since transcriptomic and proteomic studies have revealed that exits differential expression of TMEM proteins in different neoplasms concerning cancer-free tissues. Among the cellular processes in which TMEM proteins have been involved in cancer are the promotion or suppression of cell proliferation, epithelial-mesenchymal transition, invasion, migration, intravasation/extravasation, metastasis, modulation of the immune response, and response to antineoplastic drugs. Inclusive data suggests that the participation of TMEM proteins in these cellular events could be carried out through involvement in different cell signaling pathways. However, the exact mechanisms not clear. This review shows a description of the involvement of TMEM proteins that promote or decrease cell proliferation, migration, and invasion in cancer cells, describes those TMEM proteins for which both a tumor suppressor and a tumor promoter role have been identified, depending on the type of cancer in which the protein is expressed. As well as some TMEM proteins involved in chemoresistance. A better characterization of these proteins is required to improve the understanding of the tumors in which their expression and function are altered; in addition to improving the understanding of the role of these proteins in cancer will show those TMEM proteins be potential candidates as biomarkers of response to chemotherapy or prognostic biomarkers or as potential therapeutic targets in cancer.
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Affiliation(s)
| | - Sergio Encarnación-Guevara
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Chen H, Lv P, Liu Z, Chen W, Yao Y, Liu C, Cao Q, Zhou H. Preliminary study on the function of TMEM50A and its correlation with the RH genes. Transfus Med 2021; 31:277-285. [PMID: 33899290 DOI: 10.1111/tme.12778] [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: 06/04/2020] [Revised: 03/03/2021] [Accepted: 04/11/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVES The purpose of this study was to investigate the association and impact of TMEM50A on RH genes activity and function. BACKGROUND SMP1 is located on chromosome 1p36.11 in the RH gene locus, between the RHD and RHCE gene, where its position may be linked to RH haplotypes and contribute to selective pressures regarding certain RH haplotypes. TMEM50A is encoded by the SMP1 located in the intergenic region of RH, its influence on the function of the RH genes remains unclear. METHODS The expression of TMEM50A was regulated by transfection of plasmid and siRNA in K562 cell model. Western blot and real-time PCR were used to detect possible expression changes in the RH. The ammonium transport function of cells was monitored using pH-sensitive dye, while transcriptome sequencing was used to predict the potential function of TMEM50A. RESULTS The overexpression of TMEM50A significantly up-regulated RHCE gene activity (63.56%). The inhibition of TMEM50A resulted in significantly decreased RHCE (41.82%) and RHD expression (27.35%). Compared to control group, there was no significant change in the NH4 + transport function of cells in the overexpressed TMEM50A group. Transcriptome analysis showed that TMEM50A not only affected the transcription of target gene through splicing activities, but also played a role in the development of embryonic nervous system. CONCLUSIONS TMEM50A may regulate the expression of RH gene by affecting the stability of RH mRNA through splicing function. It speculates that TMEM50A may play an important role in the development of embryonic nervous system.
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Affiliation(s)
- Hongtian Chen
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Piao Lv
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ziwei Liu
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wanjun Chen
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuan Yao
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chixiang Liu
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qiong Cao
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Huayou Zhou
- Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Flores SK, Deng Y, Cheng Z, Zhang X, Tao S, Saliba A, Chu I, Burnichon N, Gimenez-Roqueplo AP, Wang E, Aguiar RCT, Dahia PLM. Functional Characterization of TMEM127 Variants Reveals Novel Insights into Its Membrane Topology and Trafficking. J Clin Endocrinol Metab 2020; 105:dgaa396. [PMID: 32575117 PMCID: PMC7414969 DOI: 10.1210/clinem/dgaa396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/17/2020] [Indexed: 02/08/2023]
Abstract
CONTEXT TMEM127 is a poorly known tumor suppressor gene associated with pheochromocytomas, paragangliomas, and renal carcinomas. Our incomplete understanding of TMEM127 function has limited our ability to predict variant pathogenicity. PURPOSE To better understand the function of the transmembrane protein TMEM127 we undertook cellular and molecular evaluation of patient-derived germline variants. DESIGN Subcellular localization and steady-state levels of tumor-associated, transiently expressed TMEM127 variants were compared to the wild-type protein using immunofluorescence and immunoblot analysis, respectively, in cells genetically modified to lack endogenous TMEM127. Membrane topology and endocytic mechanisms were also assessed. RESULTS We identified 3 subgroups of mutations and determined that 71% of the variants studied are pathogenic or likely pathogenic through loss of membrane-binding ability, stability, and/or internalization capability. Investigation into an N-terminal cluster of missense variants uncovered a previously unrecognized transmembrane domain, indicating that TMEM127 is a 4- transmembrane, not a 3-transmembrane domain-containing protein. Additionally, a C-terminal variant with predominant plasma membrane localization revealed an atypical, extended acidic, dileucine-based motif required for TMEM127 internalization through clathrin-mediated endocytosis. CONCLUSION We characterized the functional deficits of several germline TMEM127 variants and identified novel structure-function features of TMEM127. These findings will assist in determining pathogenicity of TMEM127 variants and will help guide future studies investigating the cellular role of TMEM127.
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Affiliation(s)
- Shahida K Flores
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
| | - Yilun Deng
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
| | - Ziming Cheng
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
| | - Xingyu Zhang
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
- Central South University Xiangya School of Medicine, Changsha, Hunan, China
| | - Sifan Tao
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
- Central South University Xiangya School of Medicine, Changsha, Hunan, China
| | - Afaf Saliba
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
| | - Irene Chu
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
| | - Nelly Burnichon
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Européen Georges Pompidou, Genetics Department, Paris, France
- Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue contre le Cancer, Paris, France
| | - Anne-Paule Gimenez-Roqueplo
- Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Européen Georges Pompidou, Genetics Department, Paris, France
- Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue contre le Cancer, Paris, France
| | - Exing Wang
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, Texas
| | - Ricardo C T Aguiar
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
- Mays Cancer Center, UT Health San Antonio, San Antonio, Texas
- South Texas Veterans Health Care System, Audie Murphy VA Hospital, San Antonio, Texas
| | - Patricia L M Dahia
- Division of Hematology and Medical Oncology, Department of Medicine, UT Health San Antonio
- Mays Cancer Center, UT Health San Antonio, San Antonio, Texas
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Attwood MM, Schiöth HB. Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. Front Cell Dev Biol 2020; 7:386. [PMID: 32039202 PMCID: PMC6987440 DOI: 10.3389/fcell.2019.00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/19/2019] [Indexed: 11/13/2022] Open
Abstract
As the structure and functions of proteins are correlated, investigating groups of proteins with the same gross structure may provide important insights about their functional roles. Trispanins, proteins that contain three alpha-helical transmembrane (3TM) regions, have not been previously studied considering their transmembrane features. Our comprehensive identification and classification using bioinformatic methods describe 152 3TM proteins. These proteins are frequently involved in membrane biosynthesis and lipid biogenesis, protein trafficking, catabolic processes, and in particular signal transduction due to the large ionotropic glutamate receptor family. Proteins that localize to intracellular compartments are overrepresented in the dataset in comparison to the entire human transmembrane proteome, and nearly 45% localize specifically to the endoplasmic reticulum (ER). Furthermore, nearly 20% of the trispanins function in lipid metabolic processes and transport, which are also overrepresented. Nearly one-third of trispanins are identified as being targeted by drugs and/or being associated with diseases. A high number of 3TMs have unknown functions and based on this analysis we speculate on the functional involvement of uncharacterized trispanins in relationship to disease or important cellular activities. This first overall study of trispanins provides a unique analysis of a diverse group of membrane proteins.
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Affiliation(s)
- Misty M. Attwood
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B. Schiöth
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
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Abstract
The eutherian connexins were characterized as protein constituents of gap junctions implicated in cell-cell communications between adjoining cells in multiple cell types, regulation of major physiological processes and disease pathogeneses. However, conventional connexin gene and protein classifications could be regarded as unsuitable in descriptions of comprehensive eutherian connexin gene data sets, due to ambiguities and inconsistencies in connexin gene and protein nomenclatures. Using eutherian comparative genomic analysis protocol and 35 public eutherian reference genomic sequence data sets, the present analysis attempted to update and revise comprehensive eutherian connexin gene data sets, and address and resolve major discrepancies in their descriptions. Among 631 potential coding sequences, the tests of reliability of eutherian public genomic sequences annotated, in aggregate, 349 connexin complete coding sequences. The most comprehensive curated eutherian connexin gene data set described 21 major gene clusters, 4 of which included evidence of differential gene expansions. For example, the present gene annotations initially described human CXNK1 gene and annotated 22 human connexin genes. Phylogenetic tree calculations and calculations of pairwise nucleotide sequence identity patterns proposed revised and updated phylogenetic classification of eutherian connexin genes. Therefore, the present study integrating gene annotations, phylogenetic analysis and protein molecular evolution analysis proposed new nomenclature of eutherian connexin genes and proteins.
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Wang Y, Bugge K, Kragelund BB, Lindorff-Larsen K. Role of protein dynamics in transmembrane receptor signalling. Curr Opin Struct Biol 2018; 48:74-82. [DOI: 10.1016/j.sbi.2017.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/16/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
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Farwell SLN, Slee JB, Li Y, Lowe-Krentz LJ. Using a GFP-tagged TMEM184A Construct for Confirmation of Heparin Receptor Identity. J Vis Exp 2017. [PMID: 28287514 DOI: 10.3791/55053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
When novel proteins are identified through affinity-based isolation and bioinformatics analysis, they are often largely uncharacterized. Antibodies against specific peptides within the predicted sequence allow some localization experiments. However, other possible interactions with the antibodies often cannot be excluded. This situation provided an opportunity to develop a set of assays dependent on the protein sequence. Specifically, a construct containing the gene sequence coupled to the GFP coding sequence at the C-terminal end of the protein was obtained and employed for these purposes. Experiments to characterize localization, ligand affinity, and gain of function were originally designed and carried out to confirm the identification of TMEM184A as a heparin receptor1. In addition, the construct can be employed for studies addressing membrane topology questions and detailed protein-ligand interactions. The present report presents a range of experimental protocols based on the GFP-TMEM184A construct expressed in vascular cells that could easily be adapted for other novel proteins.
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Affiliation(s)
| | | | - Yaqiu Li
- Department of Biological Sciences, Lehigh University
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