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Kang Y, Lehmann KS, Vanegas J, Long H, Jefferson A, Freeman M, Clark S. Structural basis of bulk lipid transfer by bridge-like lipid transfer protein LPD-3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600134. [PMID: 38948693 PMCID: PMC11213131 DOI: 10.1101/2024.06.21.600134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Bridge-like lipid transport proteins (BLTPs) are an evolutionarily conserved family of proteins that localize to membrane contact sites and are thought to mediate the bulk transfer of lipids from a donor membrane, typically the endoplasmic reticulum (ER), to an acceptor membrane, such as a that of the cell or an organelle 1 . Despite the fundamental importance of BLTPs for cellular function, the architecture, composition, and lipid transfer mechanisms remain poorly characterized. Here, we present the subunit composition and the cryo-electron microscopy structure of the native LPD-3 BLTP complex isolated from transgenic C. elegans . LPD-3 folds into an elongated, rod-shaped tunnel whose interior is filled with ordered lipid molecules that are coordinated by a track of ionizable residues that line one side of the tunnel. LPD-3 forms a complex with two previously uncharacterized proteins, here named "Intake" and "Spigot", both of which interact with the N-terminal end of LPD-3 where lipids enter the tunnel. Intake has three transmembrane helices, one of which borders the entrance to the tunnel; Spigot has one transmembrane helix and extends 80 Å along the cytosolic surface of LPD-3. Experiments in multiple model systems indicate that Spigot plays a conserved role in ER-PM contact site formation. Our LPD-3 complex structural data, together with molecular dynamics simulations of the transmembrane region in a lipid bilayer, reveal protein-lipid interactions that suggest a model for how the native LPD-3-complex mediates bulk lipid transport and provide a foundation for mechanistic studies of BLTPs.
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Wang J, Sun M, Liu X, Yan Q, Gao Q, Ni K, Yang J, Zhang S, Zhang C, Shan C. Transcriptome analysis identifies genetic risk markers and explores the pathogenesis for inflammatory bowel disease. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167013. [PMID: 38199515 DOI: 10.1016/j.bbadis.2023.167013] [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: 09/16/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]
Abstract
Inflammatory bowel disease (IBD) is an incurable and disabling bowel disease driven by multiple risk factors that severely limit patients' quality of life. We integrated the RNA-sequencing data of 1238 IBD patients, and investigated the pathogenesis of IBD by combining transcriptional element prediction analysis and immune-related analysis. Here, we first determined that KIAA1109 is inhibited in IBD patients. The expression of KIAA1109 and NOD2, the key receptor of NOD-like receptors, showed a negative correlation. The NOD-like receptor signaling pathway is activated and exerts transcriptional regulation on the chemokines CXCL1 and CXCL2 through the activation of the transcription factors NFκB and AP1. Analysis of immune infiltration revealed that the expression of chemokines CXCL1 and CXCL2 may regulate the inflammatory response induced by immune cells. These findings suggest that the KIAA1109-NOD2-NFκB/AP1-CXCL1/CXCL2 regulatory axis is the molecular mechanism of IBD pathogenesis, which will provide a new perspective for the diagnosis, treatment and management of IBD patients.
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Affiliation(s)
- Jiyan Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Mingming Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Xu Liu
- Endoscopy Center, Tianjin Union Medical Center, Tianjin 300121, China
| | - Qi Yan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Qingle Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Kemin Ni
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Juze Yang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Shuai Zhang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China; Tianjin Institute of Coloproctology, Tianjin 300121, China.
| | - Changliang Shan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China.
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Pandey T, Zhang J, Wang B, Ma DK. Bridge-Like Lipid Transfer Proteins (BLTPs) in C. elegans: From Genetics to Structures and Functions. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231186489. [PMID: 37455813 PMCID: PMC10345909 DOI: 10.1177/25152564231186489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023]
Abstract
In eukaryotic cells, lipid transfer can occur at membrane contact sites (MCS) to facilitate the exchange of various lipids between two adjacent cellular organelle membranes. Lipid transfer proteins (LTPs), including shuttle LTP or bridge-like LTP (BLTP), transport lipids at MCS and are critical for diverse cellular processes, including lipid metabolism, membrane trafficking, and cell signaling. BLTPs (BLTP1-5, including the ATG2 and VPS13 family proteins) contain lipid-accommodating hydrophobic repeating β-groove (RBG) domains that allow the bulk transfer of lipids through MCS. Compared with vesicular lipid transfer and shuttle LTP, BLTPs have been only recently identified. Their functions and regulatory mechanisms are currently being unraveled in various model organisms and by diverse approaches. In this review, we summarize the genetics, structural features, and biological functions of BLTP in the genetically tractable model organism C. elegans. We discuss our recent studies and findings on C. elegans LPD-3, a prototypical megaprotein ortholog of BLTP1, with identified lipid transfer functions that are evolutionarily conserved in multicellular organisms and in human cells. We also highlight areas for future research of BLTP using C. elegans and complementary model systems and approaches. Given the emerging links of BLTP to several human diseases, including Parkinson's disease and Alkuraya-Kučinskas syndrome, discovering evolutionarily conserved roles of BLTPs and their mechanisms of regulation and action should contribute to new advances in basic cell biology and potential therapeutic development for related human disorders.
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Affiliation(s)
- Taruna Pandey
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA
| | - Jianxiu Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bingying Wang
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA
| | - Dengke K. Ma
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA
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Taylor MB, Skophammer R, Warwick AR, Geck RC, Boyer JM, Walson M, Large CRL, Hickey ASM, Rowley PA, Dunham MJ. yEvo: experimental evolution in high school classrooms selects for novel mutations that impact clotrimazole resistance in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2022; 12:jkac246. [PMID: 36173330 PMCID: PMC9635649 DOI: 10.1093/g3journal/jkac246] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022]
Abstract
Antifungal resistance in pathogenic fungi is a growing global health concern. Nonpathogenic laboratory strains of Saccharomyces cerevisiae are an important model for studying mechanisms of antifungal resistance that are relevant to understanding the same processes in pathogenic fungi. We have developed a series of laboratory modules in which high school students used experimental evolution to study antifungal resistance by isolating azole-resistant S. cerevisiae mutants and examining the genetic basis of resistance. We have sequenced 99 clones from these experiments and found that all possessed mutations previously shown to impact azole resistance, validating our approach. We additionally found recurrent mutations in an mRNA degradation pathway and an uncharacterized mitochondrial protein (Csf1) that have possible mechanistic connections to azole resistance. The scale of replication in this initiative allowed us to identify candidate epistatic interactions, as evidenced by pairs of mutations that occur in the same clone more frequently than expected by chance (positive epistasis) or less frequently (negative epistasis). We validated one of these pairs, a negative epistatic interaction between gain-of-function mutations in the multidrug resistance transcription factors Pdr1 and Pdr3. This high school-university collaboration can serve as a model for involving members of the broader public in the scientific process to make meaningful discoveries in biomedical research.
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Affiliation(s)
- Matthew Bryce Taylor
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Program in Biology, Loras College, Dubuque, IA 52001, USA
| | | | - Alexa R Warwick
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Josephine M Boyer
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - yEvo Students
- Westridge School, Pasadena, CA 91105, USA
- Moscow High School, Moscow, ID 83843, USA
| | - Margaux Walson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christopher R L Large
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- UW Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Angela Shang-Mei Hickey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Present address: Department of Genetics, Stanford University, Biomedical Innovations Building, Palo Alto, CA 94304, USA
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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Shah K, Sanghavi N, Viswanathan A, Kumar A, Kumar N, Kaushik P, Kumari BSA, Appaji L. Optic pathway tumor in an infant with KIAA1109 variants. Pediatr Blood Cancer 2022; 69:e29701. [PMID: 35377517 DOI: 10.1002/pbc.29701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Krunal Shah
- Pediatric Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - Niyati Sanghavi
- Medical Oncology, HealthCare Global Hospital Bangalore, Bangalore, Karnataka, India
| | - Aarthi Viswanathan
- Pediatric Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - Arun Kumar
- Department of Pediatric Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - Nuthan Kumar
- Department of Pediatric Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - Prakruthi Kaushik
- Department of Pediatric Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - B S Aruna Kumari
- Department of Pediatric Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
| | - L Appaji
- Department of Pediatric Oncology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, India
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Neuman SD, Levine TP, Bashirullah A. A novel superfamily of bridge-like lipid transfer proteins. Trends Cell Biol 2022; 32:962-974. [PMID: 35491307 PMCID: PMC9588498 DOI: 10.1016/j.tcb.2022.03.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 01/21/2023]
Abstract
Lipid transfer proteins mediate nonvesicular transport of lipids at membrane contact sites to regulate the lipid composition of organelle membranes. Recently, a new type of bridge-like lipid transfer protein has emerged; these proteins contain a long hydrophobic groove and can mediate bulk transport of lipids between organelles. Here, we review recent insights into the structure of these proteins and identify a repeating modular unit that we propose to name the repeating β-groove (RBG) domain. This new structural understanding conceptually unifies all the RBG domain-containing lipid transfer proteins as members of an RBG protein superfamily. We also examine the biological functions of these lipid transporters in normal physiology and disease and speculate on the evolutionary origins of RBG proteins in bacteria.
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Affiliation(s)
- Sarah D Neuman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA
| | - Tim P Levine
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK.
| | - Arash Bashirullah
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA.
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Yue L, Jin M, Wang X, Wang J, Chen L, Jia R, Yang Z, Yang F, Li J, Chen C, Zheng H, Yang H. Compound Heterozygous Variants in a Surviving Patient With Alkuraya-Kučinskas Syndrome: A New Case Report and a Review of the Literature. Front Pediatr 2022; 10:806752. [PMID: 35311058 PMCID: PMC8931281 DOI: 10.3389/fped.2022.806752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Alkuraya-Kučinskas syndrome is an autosomal recessive disorder characterized by brain abnormalities associated with cerebral parenchymal underdevelopment, arthrogryposis, club foot, and global developmental delay. Most reported cases were cases of premature termination of pregnancies or neonatal deaths. To date, limited studies of nine surviving patients with global developmental delay and intellectual disability have been reported. In this study, we report another surviving patient. METHODS Whole-exome sequencing was utilized for the proband, and variants were filtered, annotated, and classified. Candidate variants were validated by Sanger sequencing of the proband and his family. The literature was reviewed; the prognosis among different regions and the variant type was analyzed. RESULTS A non-synonymous variant [NM_015312.3: exon29: c.4892C>G (p.Pro1631Arg)] was identified and validated in the patient's father. A frameshift duplication [NM_015312.3: exon62: c.10872dupA (p.Arg3625Lysfs*5)] that caused early translation termination was identified in his mother. The literature was reviewed, variants were classified into three regions of KIAA1109, and their survival status was summarized. CONCLUSION We reported another survival proband with Alkuraya-Kučinskas syndrome driven by KIAA1109. Our case expands the genotypic spectrum of Alkuraya-Kučinskas syndrome and explored the relationship between the variant region and survival.
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Affiliation(s)
- Ling Yue
- Department of Neurological Rehabilitation, Children's Hospital of Hebei Province, Hebei, China
| | - Mei Jin
- Electrophysiology Room, Children's Hospital of Hebei Province, Hebei, China
| | - Xin Wang
- Department of Neurology, Children's Hospital of Hebei Province, Hebei, China
| | - Jing Wang
- Department of Neurology, Children's Hospital of Hebei Province, Hebei, China
| | - Ling Chen
- Department of Neurological Rehabilitation, Children's Hospital of Hebei Province, Hebei, China
| | - Rong Jia
- Department of Neurological Rehabilitation, Children's Hospital of Hebei Province, Hebei, China
| | | | | | - Jingman Li
- Department of Neurological Rehabilitation, Children's Hospital of Hebei Province, Hebei, China
| | - Cuiying Chen
- Department of Neurological Rehabilitation, Children's Hospital of Hebei Province, Hebei, China
| | - Huacheng Zheng
- Department of Neurological Rehabilitation, Children's Hospital of Hebei Province, Hebei, China
| | - Huafang Yang
- Department of Neurological Rehabilitation, Children's Hospital of Hebei Province, Hebei, China
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Can leaky splicing and evasion of premature termination codon surveillance contribute to the phenotypic variability in Alkuraya-Kucinskas syndrome? Eur J Med Genet 2022; 65:104427. [DOI: 10.1016/j.ejmg.2022.104427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 12/28/2021] [Accepted: 01/15/2022] [Indexed: 11/19/2022]
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