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Sun M, Lou J, Xinghe W, Zhao Y, Dai Y, Liu S, Yan T. Hb H disease associated with compound heterozygosity for -- SEA deletion and a novel alpha globin chain variant ( HBA2:c.175C>A) on the distal histidine in a Chinese family. Hematology 2024; 29:2339559. [PMID: 38626234 DOI: 10.1080/16078454.2024.2339559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
OBJECTIVES In clinical practice, the majority of α-thalassaemia cases arise from deletions of the α-globin genes. However, a subset of cases is attributed to rare haemoglobin variants, which can manifest with borderline or normal screening results, potentially leading to missed diagnoses in clinical practice. METHODS Blood samples were collected from family members and underwent haematological, DNA and RNA analysis. RESULTS The five-month-old proband presented a haematological phenotype consistent with Hb H disease. The mother's haematology profile was consistent with an α-thalassaemia carrier, while the father exhibited a borderline reduction in MCV and MCH. MALDI-TOF identified an abnormal α-chain in the proband. DNA analysis revealed a novel α-globin variant (HBA2:c.175C>A, α58His>Asn, Hb DG-Nancheng) affecting the distal histidine in the family. The father and the mother had α-genotype of --SEA/αα and αDG-Nanchengα/αα, respectively; while the proband inherited both mutant alleles (--SEA/αDG-Nanchengα). Sequencing of cDNA from HBA2 gene identified an equal ratio of normal and mutant alleles. CONCLUSION This rare case highlighted the importance of identifying rare haemoglobin variant during prenatal screening. The clinical and genetic data provides useful information on the pathogenicity of this variant and further insight into the role of distal histidine residue of α-globin.
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Affiliation(s)
- Manna Sun
- Department of Obstetrics & Gynecolog, Dongguan Maternal and Children Hospital, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Maternal and Fetal Medicine, Dongguan, People's Republic of China
| | - Jiwu Lou
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Reproduction and Birth Defects Prevention and Control, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Genetic Disorder Prenatal Testing Precision medicine, Dongguan, People's Republic of China
| | - Wang Xinghe
- Department of Obstetrics & Gynecolog, Dongguan Maternal and Children Hospital, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Maternal and Fetal Medicine, Dongguan, People's Republic of China
| | - Ying Zhao
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Reproduction and Birth Defects Prevention and Control, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Genetic Disorder Prenatal Testing Precision medicine, Dongguan, People's Republic of China
| | - Yunshi Dai
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Reproduction and Birth Defects Prevention and Control, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Genetic Disorder Prenatal Testing Precision medicine, Dongguan, People's Republic of China
| | - Shuangai Liu
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Reproduction and Birth Defects Prevention and Control, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Genetic Disorder Prenatal Testing Precision medicine, Dongguan, People's Republic of China
| | - Tizhen Yan
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Reproduction and Birth Defects Prevention and Control, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Genetic Disorder Prenatal Testing Precision medicine, Dongguan, People's Republic of China
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Choi BH, Lee CJ, Kim TH, Kim DNJ, Park YS, Choi JM, Park JS. pH Dependence of HSF1 trimerization is shaped by intramolecular interactions. Biochem Biophys Res Commun 2024; 709:149824. [PMID: 38537598 DOI: 10.1016/j.bbrc.2024.149824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/04/2024] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
Abstract
Heat shock factor 1 (HSF1) primarily regulates various cellular stress responses. Previous studies have shown that low pH within the physiological range directly activates HSF1 function in vitro. However, the detailed molecular mechanisms remain unclear. This study proposes a molecular mechanism based on the trimerization behavior of HSF1 at different pH values. Extensive mutagenesis of human and goldfish HSF1 revealed that the optimal pH for trimerization depended on the identity of residue 103. In particular, when residue 103 was occupied by tyrosine, a significant increase in the optimal pH was observed, regardless of the rest of the sequence. This behavior can be explained by the protonation state of the neighboring histidine residues, His101 and His110. Residue 103 plays a key role in trimerization by forming disulfide or non-covalent bonds with Cys36. If tyrosine resides at residue 103 in an acidic environment, its electrostatic interactions with positively charged histidine residues prevent effective trimerization. His101 and His110 are neutralized at a higher pH, which releases Tyr103 to interact with Cys36 and drives the effective trimerization of HSF1. This study showed that the protonation state of a histidine residue can regulate the intramolecular interactions, which consequently leads to a drastic change in the oligomerization behavior of the entire protein.
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Affiliation(s)
- Bo-Hee Choi
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea
| | - Chang-Ju Lee
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea
| | - Tae Hwan Kim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea
| | - David Nahm-Joon Kim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea; Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Young-Shang Park
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea.
| | - Jang-Su Park
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea.
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Mekonen B, Dugassa S, Feleke SM, Dufera B, Gidisa B, Adamu A, Mandefro A, Tasew G, Golassa L. Widespread pfhrp2/3 deletions and HRP2-based false-negative results in southern Ethiopia. Malar J 2024; 23:108. [PMID: 38632640 PMCID: PMC11025231 DOI: 10.1186/s12936-024-04904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Rapid diagnostic tests (RDTs) play a significant role in expanding case management in peripheral healthcare systems. Histidine-rich protein-2 (HRP2) antigen detection RDTs are predominantly used to diagnose Plasmodium falciparum infection. However, the evolution and spread of P. falciparum parasite strains with deleted hrp2/3 genes, causing false-negative results, have been reported. This study assessed the diagnostic performance of HRP2-detecting RDTs for P. falciparum cases and the prevalence of pfhrp2/3 deletions among symptomatic patients seeking malaria diagnosis at selected health facilities in southern Ethiopia. METHODS A multi-health facilities-based cross-sectional study was conducted on self-presenting febrile patients seeking treatment in southern Ethiopia from July to September 2022. A purposive sampling strategy was used to enroll patients with microscopically confirmed P. falciparum infections. A capillary blood sample was obtained to prepare a blood film for microscopy and a RDT using the SD Bioline™ Malaria Pf/Pv Test. Dried blood spot samples were collected for further molecular analysis. DNA was extracted using gene aid kits and amplification was performed using nested PCR assay. Exon 2 of hrp2 and hrp3, which are the main protein-coding regions, was used to confirm its deletion. The diagnostic performance of RDT was evaluated using PCR as the gold standard test for P. falciparum infections. RESULTS Of 279 P. falciparum PCR-confirmed samples, 249 (89.2%) had successful msp-2 amplification, which was then genotyped for hrp2/3 gene deletions. The study revealed that pfhrp2/3 deletions were common in all health centres, and it was estimated that 144 patients (57.8%) across all health facilities had pfhrp2/3 deletions, leading to false-negative PfHRP2 RDT results. Deletions spanning exon 2 of hrp2, exon 2 of hrp3, and double deletions (hrp2/3) accounted for 68 (27.3%), 76 (30.5%), and 33 (13.2%) of cases, respectively. The study findings revealed the prevalence of P. falciparum parasites lacking a single pfhrp2-/3-gene and that both genes varied across the study sites. This study also showed that the sensitivity of the SD Bioline PfHRP2-RDT test was 76.5% when PCR was used as the reference test. CONCLUSION This study confirmed the existence of widespread pfhrp2/3- gene deletions, and their magnitude exceeded the WHO-recommended threshold (> 5%). False-negative RDT results resulting from deletions in Pfhrp2/3- affect a country's attempts at malaria control and elimination. Therefore, the adoption of non-HRP2-based RDTs as an alternative measure is required to avoid the consequences associated with the continued use of HRP-2-based RDTs, in the study area in particular and in Ethiopia in general.
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Affiliation(s)
- Bacha Mekonen
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
- Malaria and NTDs Research Team, Bacterial, Parasitic, and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
| | - Sisay Dugassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sindew Mekasha Feleke
- Malaria and NTDs Research Team, Bacterial, Parasitic, and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Boja Dufera
- Malaria and NTDs Research Team, Bacterial, Parasitic, and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Bedasa Gidisa
- Malaria and NTDs Research Team, Armeur Hansen Research Institute, Addis Ababa, Ethiopia
| | - Aderaw Adamu
- Department of Medical Laboratory Science, College of Medicine and Health Science, Wollo University, Dessie, Ethiopia
| | - Aynalem Mandefro
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Geremew Tasew
- Malaria and NTDs Research Team, Bacterial, Parasitic, and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
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Oh MW, Lin J, Chong SY, Lew SQ, Alam T, Lau GW. Time-resolved RNA-seq analysis to unravel the in vivo competence induction by Streptococcus pneumoniae during pneumonia-derived sepsis. Microbiol Spectr 2024; 12:e0305023. [PMID: 38305162 PMCID: PMC10913500 DOI: 10.1128/spectrum.03050-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024] Open
Abstract
Competence development in Streptococcus pneumoniae (pneumococcus) is tightly intertwined with virulence. In addition to genes encoding genetic transformation machinery, the competence regulon also regulates the expression of allolytic factors, bacteriocins, and cytotoxins. Pneumococcal competence system has been extensively interrogated in vitro where the short transient competent state upregulates the expression of three distinct phases of "early," "late," and "delayed" genes. Recently, we have demonstrated that the pneumococcal competent state develops naturally in mouse models of pneumonia-derived sepsis. To unravel the underlying adaptive mechanisms driving the development of the competent state, we conducted a time-resolved transcriptomic analysis guided by the spatiotemporal live in vivo imaging system of competence induction during pneumonia-derived sepsis. Mouse lungs infected by the serotype 2 strain D39 expressing a competent state-specific reporter gene (D39-ssbB-luc) were subjected to RNA sequencing guided by monitoring the competence development at 0, 12, 24, and, at the moribund state, >40 hours post-infection (hpi). Transcriptomic analysis revealed that the competence-specific gene expression patterns in vivo were distinct from those under in vitro conditions. There was significant upregulation of early, late, and some delayed phase competence-specific genes as early as 12 hpi, suggesting that the pneumococcal competence regulon is important for adaptation to the lung environment. Additionally, members of the histidine triad (pht) gene family were sharply upregulated at 12 hpi followed by a steep decline throughout the rest of the infection cycle, suggesting that Pht proteins participate in the early adaptation to the lung environment. Further analysis revealed that Pht proteins execute a metal ion-dependent regulatory role in competence induction.IMPORTANCEThe induction of pneumococcal competence for genetic transformation has been extensively studied in vitro but poorly understood during lung infection. We utilized a combination of live imaging and RNA sequencing to monitor the development of a competent state during acute pneumonia. Upregulation of competence-specific genes was observed as early as 12 hour post-infection, suggesting that the pneumococcal competence regulon plays an important role in adapting pneumococcus to the stressful lung environment. Among others, we report novel finding that the pneumococcal histidine triad (pht) family of genes participates in the adaptation to the lung environment and regulates pneumococcal competence induction.
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Affiliation(s)
- Myung Whan Oh
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jingjun Lin
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sook Yin Chong
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Shi Qian Lew
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Tauqeer Alam
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gee W. Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Hutton AE, Foster J, Crawshaw R, Hardy FJ, Johannissen LO, Lister TM, Gérard EF, Birch-Price Z, Obexer R, Hay S, Green AP. A non-canonical nucleophile unlocks a new mechanistic pathway in a designed enzyme. Nat Commun 2024; 15:1956. [PMID: 38438341 PMCID: PMC10912507 DOI: 10.1038/s41467-024-46123-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
Directed evolution of computationally designed enzymes has provided new insights into the emergence of sophisticated catalytic sites in proteins. In this regard, we have recently shown that a histidine nucleophile and a flexible arginine can work in synergy to accelerate the Morita-Baylis-Hillman (MBH) reaction with unrivalled efficiency. Here, we show that replacing the catalytic histidine with a non-canonical Nδ-methylhistidine (MeHis23) nucleophile leads to a substantially altered evolutionary outcome in which the catalytic Arg124 has been abandoned. Instead, Glu26 has emerged, which mediates a rate-limiting proton transfer step to deliver an enzyme (BHMeHis1.8) that is more than an order of magnitude more active than our earlier MBHase. Interestingly, although MeHis23 to His substitution in BHMeHis1.8 reduces activity by 4-fold, the resulting His containing variant is still a potent MBH biocatalyst. However, analysis of the BHMeHis1.8 evolutionary trajectory reveals that the MeHis nucleophile was crucial in the early stages of engineering to unlock the new mechanistic pathway. This study demonstrates how even subtle perturbations to key catalytic elements of designed enzymes can lead to vastly different evolutionary outcomes, resulting in new mechanistic solutions to complex chemical transformations.
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Affiliation(s)
- Amy E Hutton
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Jake Foster
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Rebecca Crawshaw
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Florence J Hardy
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Thomas M Lister
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Emilie F Gérard
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Zachary Birch-Price
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Richard Obexer
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK.
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Rredhi A, Petersen J, Wagner V, Vuong T, Li W, Li W, Schrader L, Mittag M. The UV-A Receptor CRY-DASH1 Up- and Downregulates Proteins Involved in Different Plastidial Pathways. J Mol Biol 2024; 436:168271. [PMID: 37699454 DOI: 10.1016/j.jmb.2023.168271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023]
Abstract
Algae encode up to five different types of cryptochrome photoreceptors. So far, relatively little is known about the biological functions of the DASH (Drosophila, Arabidopsis, Synechocystis and Homo)-type cryptochromes. The green alga Chlamydomonas reinhardtii encodes two of them. CRY-DASH1 also called DCRY1 has its maximal absorption peak in the UV-A range. It is localized in the chloroplast and plays an important role in balancing the photosynthetic machinery. Here, we performed a comparative analysis of chloroplast proteins from wild type and a knockout mutant of CRY-DASH1 named cry-dash1mut, using label-free quantitative proteomics as well as immunoblotting. Our results show upregulation of enzymes involved in specific pathways in the mutant including key enzymes of chlorophyll and carotenoid biosynthesis consistent with increased levels of photosynthetic pigments in cry-dash1mut. There is also an increase in certain redox as well as photosystem I and II proteins, including D1. Strikingly, CRY-DASH1 is coregulated in a D1 deletion mutant, where its amount is increased. In contrast, key proteins of the central carbon metabolism, including glycolysis/gluconeogenesis, dark fermentation and the oxidative pentose phosphate pathway are downregulated in cry-dash1mut. Similarly, enzymes of histidine biosynthesis are downregulated in cry-dash1mut leading to a reduction in the amount of free histidine. Yet, transcripts encoding for several of these proteins are at a similar level in the wild type and cry-dash1mut or even opposite. We show that CRY-DASH1 can bind to RNA, taking the psbA RNA encoding D1 as target. These data suggest that CRY-DASH1 regulates plastidial metabolic pathways at the posttranscriptional level.
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Affiliation(s)
- Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany. https://twitter.com/1anPetersen
| | - Volker Wagner
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Trang Vuong
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany. https://twitter.com/trangha593
| | - Wenshuang Li
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Wei Li
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Laura Schrader
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany.
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Rani NV, Baig MS, Pathak B, Kapoor N, Krishnan A. Mutation of conserved histidine residues of dengue virus envelope protein impairs viral like particle maturation and secretion. Biochim Biophys Acta Mol Cell Res 2024; 1871:119682. [PMID: 38301907 DOI: 10.1016/j.bbamcr.2024.119682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/03/2024]
Abstract
Dengue virus (DENV) envelope protein plays crucial role in virus entry and maturation of virus during infection. Maturation of DENV occurs in the trans Golgi network at slightly acidic pH which is close to pKa of histidine. When exposed to the acidic environment of the late secretory pathway, dengue virus particles go through a significant conformational change, whereby interactions of structural proteins envelope (E) and prM proteins are reorganised and enable furin protease to cleave prM resulting in mature virus. In order to study the role of histidine of E protein in DENV maturation, we mutated 7 conserved histidine residues of envelope protein and assessed the percent of budding using viral like particle (VLP) system. Histidine mutants; H144A, H244A, H261A and H282A severely disrupted VLP formation without any significant change in expression in cell and its oligomerization ability. Treatment with acidotropic amine reversed the defect for all 4 mutants suggesting that these histidines could be involved in maturation and release. Over expression of capsid protein slightly enhanced VLP release of H244A and H261A. Similarly, furin over expression increased VLP release of these mutants. Co-immunoprecipitation studies revealed that prM and E interaction is lost for H244A, H261A and H282A mutants at acidic pH but not at neutral pH indicating that they could be involved in histidine switch during maturation at acidic pH. Detailed analysis of the mutants could provide novel insights on the interplay of envelop protein during maturation and aid in target for drug development.
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Affiliation(s)
- N Veena Rani
- School of Sciences, IGNOU, New Delhi 110068, India
| | - Mirza Sarwar Baig
- Centre for Virology, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi 110062, India
| | - Bharti Pathak
- Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi 110062, India
| | - Neera Kapoor
- School of Sciences, IGNOU, New Delhi 110068, India
| | - Anuja Krishnan
- Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi 110062, India.
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Nana RRD, Ngum NL, Makoge V, Amvongo-Adja N, Hawadak J, Singh V. Rapid diagnostic tests for malaria diagnosis in Cameroon: impact of histidine rich protein 2/3 deletions and lactate dehydrogenase gene polymorphism. Diagn Microbiol Infect Dis 2024; 108:116103. [PMID: 37944271 DOI: 10.1016/j.diagmicrobio.2023.116103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023]
Abstract
Malaria rapid diagnostic tests (mRDT) play a vital role in malaria control in endemic areas. In this study, histidine-rich protein (hrp) and lactate dehydrogenase (ldh) genes were genotyped in Plasmodium falciparum (Pf) and Plasmodium ovale (Po) spp. isolates. Deletions in P. falciparum hrp2/3 (pfhrp2/3) proteins and single nucleotide polymorphisms (SNPs) were analyzed. Twenty-four samples were analyzed for pfhrp2/3 gene deletions and 25 for SNPs in ldh gene (18 Pf and 7 Po spp.). Deletions in pfhrp2/3 genes were observed in 1.9% malaria positive isolates. The pfldh gene sequences showed one SNP at codon 272 (D272N) in 22.2% of samples while in Po spp., sequences were 100% similar to P. ovale curtisi but when compared to P. ovale wallikeri reference sequence, SNPs at positions 143 (P143S), 168 (K168N), 204 (V204I) were found. Findings suggest low prevalence in pfhrp2/3 genes and highlight the circulation of P. ovale curtisi in the studies areas.
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Affiliation(s)
- Rodrigue Roman Dongang Nana
- Institute of Medical Research and Medicinal Plants studies (IMPM), P.O Box 13033 Yaoundé, Cameroon; Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi 110077, India..
| | - Ngum Lesly Ngum
- Institute of Medical Research and Medicinal Plants studies (IMPM), P.O Box 13033 Yaoundé, Cameroon
| | - Valerie Makoge
- Institute of Medical Research and Medicinal Plants studies (IMPM), P.O Box 13033 Yaoundé, Cameroon
| | - Nathalie Amvongo-Adja
- Institute of Medical Research and Medicinal Plants studies (IMPM), P.O Box 13033 Yaoundé, Cameroon
| | - Joseph Hawadak
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi 110077, India
| | - Vineeta Singh
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi 110077, India..
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Beetham CM, Schuster CF, Kviatkovski I, Santiago M, Walker S, Gründling A. Histidine transport is essential for the growth of Staphylococcus aureus at low pH. PLoS Pathog 2024; 20:e1011927. [PMID: 38227607 PMCID: PMC10817146 DOI: 10.1371/journal.ppat.1011927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/26/2024] [Accepted: 12/28/2023] [Indexed: 01/18/2024] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen capable of causing many different human diseases. During colonization and infection, S. aureus will encounter a range of hostile environments, including acidic conditions such as those found on the skin and within macrophages. However, little is known about the mechanisms that S. aureus uses to detect and respond to low pH. Here, we employed a transposon sequencing approach to determine on a genome-wide level the genes required or detrimental for growth at low pH. We identified 31 genes that were essential for the growth of S. aureus at pH 4.5 and confirmed the importance of many of them through follow up experiments using mutant strains inactivated for individual genes. Most of the genes identified code for proteins with functions in cell wall assembly and maintenance. These data suggest that the cell wall has a more important role than previously appreciated in promoting bacterial survival when under acid stress. We also identified several novel processes previously not linked to the acid stress response in S. aureus. These include aerobic respiration and histidine transport, the latter by showing that one of the most important genes, SAUSA300_0846, codes for a previously uncharacterized histidine transporter. We further show that under acid stress, the expression of the histidine transporter gene is increased in WT S. aureus. In a S. aureus SAUSA300_0846 mutant strain expression of the histidine biosynthesis genes is induced under acid stress conditions allowing the bacteria to maintain cytosolic histidine levels. This strain is, however, unable to maintain its cytosolic pH to the same extent as a WT strain, revealing an important function specifically for histidine transport in the acid stress response of S. aureus.
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Affiliation(s)
- Catrin M. Beetham
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Christopher F. Schuster
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Igor Kviatkovski
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Marina Santiago
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Angelika Gründling
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
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10
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Bagyinszky E, Kim M, Park YH, An SSA, Kim S. PSEN1 His214Asn Mutation in a Korean Patient with Familial EOAD and the Importance of Histidine-Tryptophan Interactions in TM-4 Stability. Int J Mol Sci 2023; 25:116. [PMID: 38203287 PMCID: PMC10778985 DOI: 10.3390/ijms25010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
A pathogenic mutation in presenilin-1 (PSEN1), His214Asn, was found in a male patient with memory decline at the age of 41 in Korea for the first time. The proband patient was associated with a positive family history from his father, paternal aunt, and paternal grandmother without genetic testing. He was diagnosed with early onset Alzheimer's disease (EOAD). PSEN1 His214Asn was initially reported in an Italian family, where the patient developed phenotypes similar to the current proband patient. Magnetic resonance imaging (MRI) scans revealed a mild hippocampal atrophy. The amyloid positron emission tomography (amyloid-PET) was positive, along with the positive test results of the increased amyloid ß (Aβ) oligomerization tendency with blood. The PSEN1 His214 amino acid position plays a significant role in the gamma-secretase function, especially from three additional reported mutations in this residue: His214Asp, His214Tyr, and His214Arg. The structure prediction model revealed that PSEN1 protein His214 may interact with Trp215 of His-Trp cation-π interaction, and the mutations of His214 would destroy this interaction. The His-Trp cation-π interaction between His214 and Trp215 would play a crucial structural role in stabilizing the 4th transmembrane domain of PSEN1 protein, especially when aromatic residues were often reported in the membrane interface of the lipid-extracellular region of alpha helices or beta sheets. The His214Asn would alter the cleavage dynamics of gamma-secretase from the disappeared interactions between His214 and Trp215 inside of the helix, resulting in elevated amyloid production. Hence, the increased Aβ was reflected in the increased Aβ oligomerization tendency and the accumulations of Aβ in the brain from amyloid-PET, leading to EOAD.
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Affiliation(s)
- Eva Bagyinszky
- Department of Industrial and Environmental Engineering, Graduate School of Environment, Gachon University, Seongnam 13120, Republic of Korea;
| | - Minju Kim
- Department of Neurology, Seoul National University College of Medicine & Clinical Neuroscience Center, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea; (M.K.); (Y.H.P.)
| | - Young Ho Park
- Department of Neurology, Seoul National University College of Medicine & Clinical Neuroscience Center, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea; (M.K.); (Y.H.P.)
| | - Seong Soo A. An
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Seongnam 13120, Republic of Korea
| | - SangYun Kim
- Department of Neurology, Seoul National University College of Medicine & Clinical Neuroscience Center, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea; (M.K.); (Y.H.P.)
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11
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Forsten E, Finger M, Scholand T, Deitert A, Kauffmann K, Büchs J. Inoculum cell count influences separation efficiency and variance in Ames plate incorporation and Ames RAMOS test. Sci Total Environ 2023; 905:167035. [PMID: 37709100 DOI: 10.1016/j.scitotenv.2023.167035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The Ames test is one of the most applied tools in mutagenicity testing of chemicals ever since its introduction by Ames et al. in the 1970s. Its principle is based on histidine auxotrophic bacteria that regain prototrophy through reverse mutations. In the presence of a mutagen, more reverse mutations occur that become visible as increased bacterial growth on medium without histidine. Many miniaturized formats of the Ames test have emerged to enable the testing of environmental water samples, increase experimental throughput, and lower the required amounts of test substances. However, most of these formats still rely on endpoint determinations. In contrast, the recently introduced Ames RAMOS test determines mutagenicity through online monitoring of the oxygen transfer rate. In this study, the oxygen transfer rate of Salmonella typhimurium TA100 during the Ames plate incorporation test was monitored and compared to the Ames RAMOS test to prove its validity further. Furthermore, the Ames RAMOS test in 96-well scale is newly introduced. For both the Ames plate incorporation and the Ames RAMOS test, the influence of the inoculum cell count on the negative control was highlighted: A lower inoculum cell count led to a higher coefficient of variation. However, a lower inoculum cell count also led to a higher separation efficiency in the Ames RAMOS test and, thus, to better detection of a mutagenic substance at lower concentrations.
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Affiliation(s)
- Eva Forsten
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Maurice Finger
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Theresa Scholand
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Alexander Deitert
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Kira Kauffmann
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany.
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12
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Tarama CW, Soré H, Siribié M, Débé S, Kinda R, Nonkani WG, Tiendrebeogo F, Bantango W, Yira K, Hien EY, Guelbéogo MW, Traoré Y, Ménard D, Gansané A. Assessing the histidine-rich protein 2/3 gene deletion in Plasmodium falciparum isolates from Burkina Faso. Malar J 2023; 22:363. [PMID: 38017455 PMCID: PMC10685617 DOI: 10.1186/s12936-023-04796-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Dual hrp2/hrp3 genes deletions in P. falciparum isolates are increasingly reported in malaria-endemic countries and can produce false negative RDT results leading to inadequate case management. Data on the frequency of hrp2/hrp3 deleted parasites are rarely available and it has become necessary to investigate the issue in Burkina Faso. METHODS Plasmodium falciparum-positive dried blood spots were collected during a cross-sectional household survey of the malaria asymptomatic children from Orodara, Gaoua, and Banfora. Amplicons from the target regions (exon 2 of hrp2 and hrp3 genes) were generated using multiplexed nested PCR and sequenced according to Illumina's MiSeq protocol. RESULTS A total of 251 microscopically positive parasite isolates were sequenced to detect hrp2 and hrp3 gene deletions. The proportion of RDTs negative cases among microscopy positive slides was 12.7% (32/251). The highest prevalence of negative RDTs was found in Orodara 14.3% (5/35), followed by Gaoua 13.1%(24/183), and Banfora 9.1% (3/33). The study found that 95.6% of the parasite isolates were wild type hrp2/ hrp3 while 4.4% (11/251) had a single hrp2 deletion. Of the 11 hrp2 deletion samples, 2 samples were RDT negative (mean parasitaemia was 83 parasites/ μL) while 9 samples were RDT positive with a mean parasitaemia of 520 parasites /μL (CI95%: 192-1239). The highest frequency of hrp2 deletion 4/35 (11.4%) was found in Orodara, while it was similar in the other two sites (< 3.5%). No single deletion of the hrp3 or dual deletion hrp2/3 gene was detected in this study. CONCLUSION These results demonstrate that P. falciparum isolates lacking hrp2 genes are present in 4.4% of samples obtained from the asymptomatic children population in three sites in Burkina Faso. These parasites are circulating and causing malaria, but they are also still detectable by HRP2-based RTDs due to the presence of the intact pfhrp3 gene.
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Affiliation(s)
| | - Harouna Soré
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Mafama Siribié
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Siaka Débé
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Réné Kinda
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Wendyam Gérard Nonkani
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Farida Tiendrebeogo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Winnie Bantango
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Kassoum Yira
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | | | | | - Yves Traoré
- Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
| | - Didier Ménard
- Institut Pasteur, Université Paris Cité, Malaria Genetic and Resistance Unit, INSERM U1201, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Malaria Parasite Biology and Vaccines, F-75015, Paris, France
- Institute of Parasitology and Tropical Diseases, Université de Strasbourg, UR7292 Dynamics of Host-Pathogen Interactions, 67000, Strasbourg, France
- Laboratory of Parasitology and Medical Mycology, CHU Strasbourg, 67000, Strasbourg, France
| | - Adama Gansané
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso.
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13
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Xue F, Zhao Z, Gu S, Chen M, Xu J, Luo X, Li J, Tian C. The transcriptional factor Clr-5 is involved in cellulose degradation through regulation of amino acid metabolism in Neurospora crassa. BMC Biotechnol 2023; 23:50. [PMID: 38031036 PMCID: PMC10687990 DOI: 10.1186/s12896-023-00823-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Filamentous fungi are efficient degraders of plant biomass and the primary producers of commercial cellulolytic enzymes. While the transcriptional regulation mechanisms of cellulases have been continuously explored in lignocellulolytic fungi, the induction of cellulase production remains a complex multifactorial system, with several aspects still largely elusive. RESULTS In this study, we identified a Zn2Cys6 transcription factor, designated as Clr-5, which regulates the expression of cellulase genes by influencing amino acid metabolism in Neurospora crassa during growth on cellulose. The deletion of clr-5 caused a significant decrease in secreted protein and cellulolytic enzyme activity of N. crassa, which was partially alleviated by supplementing with yeast extract. Transcriptomic profiling revealed downregulation of not only the genes encoding main cellulases but also those related to nitrogen metabolism after disruption of Clr-5 under Avicel condition. Clr-5 played a crucial role in the utilization of multiple amino acids, especially leucine and histidine. When using leucine or histidine as the sole nitrogen source, the Δclr-5 mutant showed significant growth defects on both glucose and Avicel media. Comparative transcriptomic analysis revealed that the transcript levels of most genes encoding carbohydrate-active enzymes and those involved in the catabolism and uptake of histidine, branched-chain amino acids, and aromatic amino acids, were remarkably reduced in strain Δclr-5, compared with the wild-type N. crassa when grown in Avicel medium with leucine or histidine as the sole nitrogen source. These findings underscore the important role of amino acid metabolism in the regulation of cellulase production in N. crassa. Furthermore, the function of Clr-5 in regulating cellulose degradation is conserved among ascomycete fungi. CONCLUSIONS These findings regarding the novel transcription factor Clr-5 enhance our comprehension of the regulatory connections between amino acid metabolism and cellulase production, offering fresh prospects for the development of fungal cell factories dedicated to cellulolytic enzyme production in bio-refineries.
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Affiliation(s)
- Fanglei Xue
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zhen Zhao
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Shuying Gu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Meixin Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jing Xu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Xuegang Luo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jingen Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
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14
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van der Voorn SM, van Drie E, Proost V, Dimitrova K, Ernst RF, James CA, Tichnell C, Murray B, Calkins H, Saguner AM, Duru F, Ellinor PT, Bezzina CR, Jurgens SJ, van Tintelen JP, van Veen TAB. Lack of Evidence for the Role of the p.(Ser96Ala) Polymorphism in Histidine-Rich Calcium Binding Protein as a Secondary Hit in Cardiomyopathies. Int J Mol Sci 2023; 24:15931. [PMID: 37958923 PMCID: PMC10648441 DOI: 10.3390/ijms242115931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/17/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Inherited forms of arrhythmogenic and dilated cardiomyopathy (ACM and DCM) are characterized by variable disease expression and age-related penetrance. Calcium (Ca2+) is crucially important for proper cardiac function, and dysregulation of Ca2+ homeostasis seems to underly cardiomyopathy etiology. A polymorphism, c.286T>G p.(Ser96Ala), in the gene encoding the histidine-rich Ca2+ binding (HRC) protein, relevant for sarcoplasmic reticulum Ca2+ cycling, has previously been associated with a marked increased risk of life-threatening arrhythmias among idiopathic DCM patients. Following this finding, we investigated whether p.(Ser96Ala) affects major cardiac disease manifestations in carriers of the phospholamban (PLN) c.40_42delAGA; p.(Arg14del) pathogenic variant (cohort 1); patients diagnosed with, or predisposed to, ACM (cohort 2); and DCM patients (cohort 3). We found that the allele frequency of the p.(Ser96Ala) polymorphism was similar across the general European-American population (control cohort, 40.3-42.2%) and the different cardiomyopathy cohorts (cohorts 1-3, 40.9-43.9%). Furthermore, the p.(Ser96Ala) polymorphism was not associated with life-threatening arrhythmias or heart failure-related events across various patient cohorts. We therefore conclude that there is a lack of evidence supporting the important role of the HRC p.(Ser96Ala) polymorphism as a modifier in cardiomyopathy, refuting previous findings. Further research is required to identify bona fide genomic predictors for the stratification of cardiomyopathy patients and their risk for life-threatening outcomes.
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Affiliation(s)
- Stephanie M. van der Voorn
- Department of Medical Physiology, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands (K.D.)
| | - Esmée van Drie
- Department of Genetics, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands
- Netherlands Heart Institute, 3511 EP Utrecht, The Netherlands
| | - Virginnio Proost
- Departments of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers Location Academic Medical Center, 1105 AZ Amsterdam, The Netherlands (C.R.B.)
| | - Kristina Dimitrova
- Department of Medical Physiology, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands (K.D.)
| | | | - Robert F. Ernst
- Department of Genetics, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands
| | - Cynthia A. James
- Department of Medicine, Division Cardiology, Johns Hopkins University, Baltimore, MD 21218, USA (C.T.)
| | - Crystal Tichnell
- Department of Medicine, Division Cardiology, Johns Hopkins University, Baltimore, MD 21218, USA (C.T.)
| | - Brittney Murray
- Department of Medicine, Division Cardiology, Johns Hopkins University, Baltimore, MD 21218, USA (C.T.)
| | - Hugh Calkins
- Department of Medicine, Division Cardiology, Johns Hopkins University, Baltimore, MD 21218, USA (C.T.)
| | - Ardan M. Saguner
- Department of Cardiology, University Heart Center Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Firat Duru
- Department of Cardiology, University Heart Center Zurich, University Hospital Zurich, 8091 Zurich, Switzerland
- Center for Integrative Human Physiology (ZIHP), University of Zurich, 8091 Zurich, Switzerland
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Connie R. Bezzina
- Departments of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers Location Academic Medical Center, 1105 AZ Amsterdam, The Netherlands (C.R.B.)
| | - Sean J. Jurgens
- Departments of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers Location Academic Medical Center, 1105 AZ Amsterdam, The Netherlands (C.R.B.)
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J. Peter van Tintelen
- Department of Genetics, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands
- Netherlands Heart Institute, 3511 EP Utrecht, The Netherlands
| | - Toon A. B. van Veen
- Department of Medical Physiology, Division Heart & Lungs, University Medical Center Utrecht, 3584 CM Utrecht, The Netherlands (K.D.)
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15
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Kong X, Yu J, Zhu Z, Wang C, Zhang R, Qi J, Wang Y, Wang X, Pan S, Liu L, Feng R. Causal associations of histidine and 12 site-specific cancers: a bidirectional Mendelian randomization study. Mol Genet Genomics 2023; 298:1331-1341. [PMID: 37498357 DOI: 10.1007/s00438-023-02057-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/19/2023] [Indexed: 07/28/2023]
Abstract
An increasing number of studies indicate that cancer patients' histidine (HIS) circulating levels have changed. However, the causality between HIS and cancer is still not well established. Thus, to ascertain the causal link between HIS and cancers, we performed a bidirectional Mendelian randomization (MR) analysis. Summary-level data are derived from publicly available genome-wide association studies (GWAS). The causal effects were mainly estimated using the inverse-variance weighted method (IVW). The weighted-median (WM) method and MR-Egger regression were conducted as sensitivity analyses. In the forward-MR, we found malignant neoplasm of respiratory system and intrathoracic organs (OR: 1.020; 95% CI: 1.006-1.035; pIVW = 0.007) genetically associated with circulating HIS. And there was no significant genetic correlation between HIS and another 11 site-specific cancers using IVW method. In the reversed-MR, we did not observe the causal relationship between HIS and 12 site-specific cancers. Our findings help clarify that HIS, as a biomarker for malignant neoplasms of respiratory system and intrathoracic organs, is causal rather than a secondary biomarker of the cancerous progression. The mechanism between histidine and cancer progression deserves further investigation.
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Affiliation(s)
- Xiangju Kong
- Department of Gynaecology, First Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Jiaying Yu
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Nan Gang District, 157 Baojian Road, Harbin, 150086, People's Republic of China
| | - Zhuolin Zhu
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Nan Gang District, 157 Baojian Road, Harbin, 150086, People's Republic of China
| | - Cheng Wang
- Department of Environmental Hygiene, Public Health College, Harbin Medical University, Harbin, People's Republic of China
| | - Runan Zhang
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Nan Gang District, 157 Baojian Road, Harbin, 150086, People's Republic of China
| | - Jiayue Qi
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Nan Gang District, 157 Baojian Road, Harbin, 150086, People's Republic of China
| | - Yiran Wang
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Nan Gang District, 157 Baojian Road, Harbin, 150086, People's Republic of China
| | - Xiaoxin Wang
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Nan Gang District, 157 Baojian Road, Harbin, 150086, People's Republic of China
| | - Sijia Pan
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Nan Gang District, 157 Baojian Road, Harbin, 150086, People's Republic of China
| | - Liyan Liu
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Nan Gang District, 157 Baojian Road, Harbin, 150086, People's Republic of China.
| | - Rennan Feng
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Nan Gang District, 157 Baojian Road, Harbin, 150086, People's Republic of China.
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16
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Xu P, Li X, Fan J, Tian S, Cao M, Lin A, Gao Q, Xiao K, Wang C, Kuang H, Lian H. An arginine-to-histidine mutation in flavanone-3-hydroxylase results in pink strawberry fruits. Plant Physiol 2023; 193:1849-1865. [PMID: 37477940 DOI: 10.1093/plphys/kiad424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023]
Abstract
Fruit color is a very important external commodity factor for consumers. Compared to the most typical red octoploid strawberry (Fragaria × ananassa), the pink strawberry often sells for a more expensive price and has a higher economic benefit due to its outstanding color. However, few studies have examined the molecular basis of pink-colored strawberry fruit. Through an EMS mutagenesis of woodland strawberry (Fragaria vesca), we identified a mutant with pink fruits and green petioles. Bulked-segregant analysis sequencing analysis and gene function verification confirmed that the responsible mutation resides in a gene encoding flavanone-3-hydroxylase (F3H) in the anthocyanin synthesis pathway. This nonsynonymous mutation results in an arginine-to-histidine change at position 130 of F3H. Molecular docking experiments showed that the arginine-to-histidine mutation results in a reduction of intermolecular force-hydrogen bonding between the F3H protein and its substrates. Enzymatic experiments showed a greatly reduced ability of the mutated F3H protein to catalyze the conversion of the substrates and hence a blockage of the anthocyanin synthesis pathway. The discovery of a key residue in the F3H gene controlling anthocyanin synthesis provides a clear target of modification for the molecular breeding of strawberry varieties with pink-colored fruits, which may be of great commercial value.
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Affiliation(s)
- Pengbo Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinyu Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junmiao Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuhua Tian
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Minghao Cao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Ecology, Lishui University, Lishui 323000, China
| | - Anqi Lin
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qinhua Gao
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Kun Xiao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Horticultural Science, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China
| | - Chong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyun Kuang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences 201403, Shanghai, China
| | - Hongli Lian
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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17
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Shimazu T, Yoshimoto R, Kotoshiba K, Suzuki T, Matoba S, Hirose M, Akakabe M, Sohtome Y, Sodeoka M, Ogura A, Dohmae N, Shinkai Y. Histidine N1-position-specific methyltransferase CARNMT1 targets C3H zinc finger proteins and modulates RNA metabolism. Genes Dev 2023; 37:724-742. [PMID: 37612136 PMCID: PMC10546975 DOI: 10.1101/gad.350755.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023]
Abstract
Histidine (His) residues are methylated in various proteins, but their roles and regulation mechanisms remain unknown. Here, we show that carnosine N-methyltransferase 1 (CARNMT1), a known His methyltransferase of dipeptide carnosine (βAla-His), is a major His N1-position-specific methyltransferase. We found that 52 His sites in 20 proteins underwent CARNMT1-mediated methylation. The consensus methylation site for CARNMT1 was identified as Cx(F/Y)xH, a C3H zinc finger (C3H ZF) motif. CARNMT1-deficient and catalytically inactive mutant mice showed embryonic lethality. Among the CARNMT1 target C3H ZF proteins, RNA degradation mediated by Roquin and tristetraprolin (TTP) was affected by CARNMT1 and its enzymatic activity. Furthermore, the recognition of the 3' splice site of the CARNMT1 target C3H ZF protein U2AF1 was perturbed, and pre-mRNA alternative splicing (AS) was affected by CARNMT1 deficiency. These findings indicate that CARNMT1-mediated protein His methylation, which is essential for embryogenesis, plays roles in diverse aspects of RNA metabolism by targeting C3H ZF-type RNA-binding proteins and modulating their functions, including pre-mRNA AS and mRNA degradation regulation.
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Affiliation(s)
- Tadahiro Shimazu
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan;
| | - Rei Yoshimoto
- Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Kaoru Kotoshiba
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shogo Matoba
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Michiko Hirose
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Mai Akakabe
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Yoshihiro Sohtome
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan;
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18
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Batth TS, Simonsen JL, Hernández-Rollán C, Brander S, Morth JP, Johansen KS, Nørholm MHH, Hoof JB, Olsen JV. A seven-transmembrane methyltransferase catalysing N-terminal histidine methylation of lytic polysaccharide monooxygenases. Nat Commun 2023; 14:4202. [PMID: 37452022 PMCID: PMC10349129 DOI: 10.1038/s41467-023-39875-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes that help break down lignocellulose, making them highly attractive for improving biomass utilization in industrial biotechnology. The catalytically essential N-terminal histidine (His1) of LPMOs is post-translationally modified by methylation in filamentous fungi to protect them from auto-oxidative inactivation, however, the responsible methyltransferase enzyme is unknown. Using mass-spectrometry-based quantitative proteomics in combination with systematic CRISPR/Cas9 knockout screening in Aspergillus nidulans, we identify the N-terminal histidine methyltransferase (NHMT) encoded by the gene AN4663. Targeted proteomics confirm that NHMT was solely responsible for His1 methylation of LPMOs. NHMT is predicted to encode a unique seven-transmembrane segment anchoring a soluble methyltransferase domain. Co-localization studies show endoplasmic reticulum residence of NHMT and co-expression in the industrial production yeast Komagataella phaffii with LPMOs results in His1 methylation of the LPMOs. This demonstrates the biotechnological potential of recombinant production of proteins and peptides harbouring this specific post-translational modification.
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Affiliation(s)
- Tanveer S Batth
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen Denmark, Copenhagen, Denmark.
| | - Jonas L Simonsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen Denmark, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Cristina Hernández-Rollán
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brander
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Jakob B Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen Denmark, Copenhagen, Denmark.
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19
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Freeman ADJ, Déclais AC, Wilson TJ, Lilley DJ. Biochemical and mechanistic analysis of the cleavage of branched DNA by human ANKLE1. Nucleic Acids Res 2023; 51:5743-5754. [PMID: 37216589 PMCID: PMC10287932 DOI: 10.1093/nar/gkad416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/28/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
ANKLE1 is a nuclease that provides a final opportunity to process unresolved junctions in DNA that would otherwise create chromosomal linkages blocking cell division. It is a GIY-YIG nuclease. We have expressed an active domain of human ANKLE1 containing the GIY-YIG nuclease domain in bacteria, that is monomeric in solution and when bound to a DNA Y-junction, and unilaterally cleaves a cruciform junction. Using an AlphaFold model of the enzyme we identify the key active residues, and show that mutation of each leads to impairment of activity. There are two components in the catalytic mechanism. Cleavage rate is pH dependent, corresponding to a pKa of 6.9, suggesting an involvement of the conserved histidine in proton transfer. The reaction rate depends on the nature of the divalent cation, likely bound by glutamate and asparagine side chains, and is log-linear with the metal ion pKa. We propose that the reaction is subject to general acid-base catalysis, using a combination of tyrosine and histidine acting as general base and water directly coordinated to the metal ion as general acid. The reaction is temperature dependent; activation energy Ea = 37 kcal mol-1, suggesting that cleavage is coupled to opening of DNA in the transition state.
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Affiliation(s)
- Alasdair D J Freeman
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anne-Cécile Déclais
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Timothy J Wilson
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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20
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Taylor CJ, Hardy FJ, Burke AJ, Bednar RM, Mehl RA, Green AP, Lovelock SL. Engineering mutually orthogonal PylRS/tRNA pairs for dual encoding of functional histidine analogues. Protein Sci 2023; 32:e4640. [PMID: 37051694 PMCID: PMC10127257 DOI: 10.1002/pro.4640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 04/14/2023]
Abstract
The availability of an expanded genetic code opens exciting new opportunities in enzyme design and engineering. In this regard histidine analogues have proven particularly versatile, serving as ligands to augment metalloenzyme function and as catalytic nucleophiles in designed enzymes. The ability to genetically encode multiple functional residues could greatly expand the range of chemistry accessible within enzyme active sites. Here, we develop mutually orthogonal translation components to selectively encode two structurally similar histidine analogues. Transplanting known mutations from a promiscuous Methanosarcina mazei pyrrolysyl-tRNA synthetase (MmPylRSIFGFF ) into a single domain PylRS from Methanomethylophilus alvus (MaPylRSIFGFF ) provided a variant with improved efficiency and specificity for 3-methyl-L-histidine (MeHis) incorporation. The MaPylRSIFGFF clone was further characterized using in vitro biochemical assays and x-ray crystallography. We subsequently engineered the orthogonal MmPylRS for activity and selectivity for 3-(3-pyridyl)-L-alanine (3-Pyr), which was used in combination with MaPylRSIFGFF to produce proteins containing both 3-Pyr and MeHis. Given the versatile roles played by histidine in enzyme mechanisms, we anticipate that the tools developed within this study will underpin the development of enzymes with new and enhanced functions.
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Affiliation(s)
- Christopher J. Taylor
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Florence J. Hardy
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Ashleigh J. Burke
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Riley M. Bednar
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
| | - Ryan A. Mehl
- Department of Biochemistry and BiophysicsOregon State UniversityCorvallisOregonUSA
| | - Anthony P. Green
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
| | - Sarah L. Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of ManchesterManchesterUK
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21
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Justin GA, Girach A, Maldonado RS. Antisense oligonucleotide therapy for proline-23-histidine autosomal dominant retinitis pigmentosa. Curr Opin Ophthalmol 2023; 34:226-231. [PMID: 36924362 DOI: 10.1097/icu.0000000000000947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
PURPOSE OF REVIEW To discuss antisense oligonucleotide (ASON) therapy for autosomal dominant retinitis pigmentosa (adRP) caused by the proline-23-histidine (P23H) mutation in the rhodopsin gene. RECENT FINDINGS Viral and nonviral therapies to treat adRP are currently under investigation. A promising therapeutic option is a nonviral approach using ASONs. This form of genetic therapy has demonstrated a dose-dependent and highly selective reduction of P23H mutant rhodopsin mRNA in animal models, and it is currently being investigated as a human phase 1/2 clinical trial. SUMMARY There are promising new therapies to treat adRP. ASON has shown encouraging results in animal models and has undergone a phase 1 clinical trial. ASON does not use a viral vector, is delivered with standard intravitreal injection, and its effects are reversible.
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Affiliation(s)
- Grant A Justin
- Department of Ophthalmology, Duke University, Durham, North Carolina, USA
| | | | - Ramiro S Maldonado
- Department of Ophthalmology, Duke University, Durham, North Carolina, USA
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22
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Cheung JW, Kinney WD, Wesalo JS, Reed M, Nicholson EM, Deiters A, Cropp TA. Genetic Encoding of a Photocaged Histidine for Light-Control of Protein Activity. Chembiochem 2023; 24:e202200721. [PMID: 36642698 PMCID: PMC10407765 DOI: 10.1002/cbic.202200721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/17/2023]
Abstract
The use of light to control protein function is a critical tool in chemical biology. Here we describe the addition of a photocaged histidine to the genetic code. This unnatural amino acid becomes histidine upon exposure to light and allows for the optical control of enzymes that utilize active-site histidine residues. We demonstrate light-induced activation of a blue fluorescent protein and a chloramphenicol transferase. Further, we genetically encoded photocaged histidine in mammalian cells. We then used this approach in live cells for optical control of firefly luciferase and, Renilla luciferase. This tool should have utility in manipulating and controlling a wide range of biological processes.
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Affiliation(s)
- Jenny W Cheung
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - William D Kinney
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Joshua S Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Megan Reed
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Eve M Nicholson
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - T Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
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23
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Brown W, Galpin JD, Rosenblum C, Tsang M, Ahern CA, Deiters A. Chemically Acylated tRNAs are Functional in Zebrafish Embryos. J Am Chem Soc 2023; 145:2414-2420. [PMID: 36669466 PMCID: PMC10155198 DOI: 10.1021/jacs.2c11452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Genetic code expansion has pushed protein chemistry past the canonical 22 amino acids. The key enzymes that make this possible are engineered aminoacyl tRNA synthetases. However, as the number of genetically encoded amino acids has increased over the years, obvious limits in the type and size of novel side chains that can be accommodated by the synthetase enzyme become apparent. Here, we show that chemically acylating tRNAs allow for robust, site-specific incorporation of unnatural amino acids into proteins in zebrafish embryos, an important model organism for human health and development. We apply this approach to incorporate a unique photocaged histidine analogue for which synthetase engineering efforts have failed. Additionally, we demonstrate optical control over different enzymes in live embryos by installing photocaged histidine into their active sites.
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Affiliation(s)
- Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Carolyn Rosenblum
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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24
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Abstract
The systematic evolution of ligands by exponential enrichment (SELEX) enables the identification of ssDNA or RNA sequences binding to different target molecules, highly specific and with high affinity. In this chapter, we describe a selection strategy with ssDNA for a histidine-tagged protein that could be either performed hands-on manually or fully automated by an appropriate robotic selection platform.
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Affiliation(s)
- Stefan Breuers
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
- Center of Aptamer Research and Development, University of Bonn, Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
- Center of Aptamer Research and Development, University of Bonn, Bonn, Germany.
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25
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Msafiri Makene A, Liu JL. Association between CARD14 gene polymorphisms and psoriasis vulgaris in Hainan Han population based on exon sequencing: A case-control study. Medicine (Baltimore) 2022; 101:e30890. [PMID: 36221432 PMCID: PMC9542912 DOI: 10.1097/md.0000000000030890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Psoriasis is a serious non-communicable, chronic immune-inflammatory mediated disease affecting about 125 million people worldwide. Its effects go beyond skin manifestation. Through genome-wide association studies, the caspase recruitment domain family member 14 (CARD14) gene and other gene variants have been implicated to have an association with Psoriasis, and as we move towards individualized therapy the discovery of single nucleotide polymorphism (SNP) is of great importance. This study aimed to determine whether the CARD14 gene is a susceptible gene for psoriasis vulgaris. In this study, 101 psoriasis patients and 79 healthy controls were subjected to exome sequencing. The CARD14 gene regions upstream and downstream of 1kb were sequenced. SNP-based association analysis and haplotype-based association analysis were performed in SNPs with minimum allele frequency (MAF) greater than 1%. Bioinformatic methods were used to predict the impact of risk loci on gene function. A total of 32 polymorphisms were identified in this study, of which 3 SNPs (1 in exon and 2 in intron) were susceptible to psoriasis (P < .05, OR = 0.19~0.53, 95%CI = 0.05~0.70). Bioinformatics analysis showed that rs144475004 located on the exon led to an amino acid change from aspartate to histidine. On the other hand, results of haplotype-based association analysis showed that 2 haplotypes (CARD14-1 and CARD14-2) were protective haplotypes of the disease (P < .05, OR = 0.18~0.38, 95%CI = 0.05~0.88), the frequencies in healthy controls and patients was 6.96% and 1.49%, respectively. CARD14 gene is associated with susceptibility to psoriasis vulgaris in the Hainan Han population.
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Affiliation(s)
- Antonia Msafiri Makene
- Department of Dermatology and Venereology. The Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Jun-lin Liu
- Department of Dermatology and Venereology. The Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
- *Correspondence: Jun-lin Liu, The Second Affiliated Hospital of Hainan Medical University No.368, Yehai Av., Haikou, Hainan 570311, China (e-mail: )
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26
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Rogier E, McCaffery JN, Mohamed MA, Herman C, Nace D, Daniels R, Lucchi N, Jones S, Goldman I, Aidoo M, Cheng Q, Kemenang EA, Udhayakumar V, Cunningham J. Plasmodium falciparum pfhrp2 and pfhrp3 Gene Deletions and Relatedness to Other Global Isolates, Djibouti, 2019-2020. Emerg Infect Dis 2022; 28:2043-2050. [PMID: 36148905 PMCID: PMC9514350 DOI: 10.3201/eid2810.220695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Deletions of pfhrp2 and paralogue pfhrp3 (pfhrp2/3) genes threaten Plasmodium falciparum diagnosis by rapid diagnostic test. We examined 1,002 samples from suspected malaria patients in Djibouti City, Djibouti, to investigate pfhrp2/3 deletions. We performed assays for Plasmodium antigen carriage, pfhrp2/3 genotyping, and sequencing for 7 neutral microsatellites to assess relatedness. By PCR assay, 311 (31.0%) samples tested positive for P. falciparum infection, and 296 (95.2%) were successfully genotyped; 37 (12.5%) samples were pfhrp2+/pfhrp3+, 51 (17.2%) were pfhrp2+/pfhrp3-, 5 (1.7%) were pfhrp2-/pfhrp3+, and 203 (68.6%) were pfhrp2-/pfhrp3-. Histidine-rich protein 2/3 antigen concentrations were reduced with corresponding gene deletions. Djibouti P. falciparum is closely related to Ethiopia and Eritrea parasites (pairwise GST 0.68 [Ethiopia] and 0.77 [Eritrea]). P. falciparum with deletions in pfhrp2/3 genes were highly prevalent in Djibouti City in 2019-2020; they appear to have arisen de novo within the Horn of Africa and have not been imported.
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27
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Ha CV, Mostofa MG, Nguyen KH, Tran CD, Watanabe Y, Li W, Osakabe Y, Sato M, Toyooka K, Tanaka M, Seki M, Burritt DJ, Anderson CM, Zhang R, Nguyen HM, Le VP, Bui HT, Mochida K, Tran LSP. The histidine phosphotransfer AHP4 plays a negative role in Arabidopsis plant response to drought. Plant J 2022; 111:1732-1752. [PMID: 35883014 DOI: 10.1111/tpj.15920] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Cytokinin plays an important role in plant stress responses via a multistep signaling pathway, involving the histidine phosphotransfer proteins (HPs). In Arabidopsis thaliana, the AHP2, AHP3 and AHP5 proteins are known to affect drought responses; however, the role of AHP4 in drought adaptation remains undetermined. In the present study, using a loss-of-function approach we showed that AHP4 possesses an important role in the response of Arabidopsis to drought. This is evidenced by the higher survival rates of ahp4 than wild-type (WT) plants under drought conditions, which is accompanied by the downregulated AHP4 expression in WT during periods of dehydration. Comparative transcriptome analysis of ahp4 and WT plants revealed AHP4-mediated expression of several dehydration- and/or abscisic acid-responsive genes involved in modulation of various physiological and biochemical processes important for plant drought acclimation. In comparison with WT, ahp4 plants showed increased wax crystal accumulation in stems, thicker cuticles in leaves, greater sensitivity to exogenous abscisic acid at germination, narrow stomatal apertures, heightened leaf temperatures during dehydration, and longer root length under osmotic stress. In addition, ahp4 plants showed greater photosynthetic efficiency, lower levels of reactive oxygen species, reduced electrolyte leakage and lipid peroxidation, and increased anthocyanin contents under drought, when compared with WT. These differences displayed in ahp4 plants are likely due to upregulation of genes that encode enzymes involved in reactive oxygen species scavenging and non-enzymatic antioxidant metabolism. Overall, our findings suggest that AHP4 plays a crucial role in plant drought adaptation.
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Affiliation(s)
- Chien Van Ha
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Donald Danforth Plant Science Center, 975 N Warson Rd, Saint Louis, Missouri, 63132, USA
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, Texas, 79409, USA
| | - Mohammad Golam Mostofa
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, Texas, 79409, USA
| | - Kien Huu Nguyen
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, 100000, Vietnam
| | - Cuong Duy Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, 100000, Vietnam
| | - Yasuko Watanabe
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Weiqiang Li
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Jilin Da'an Agro-ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Yuriko Osakabe
- School of Life Science and Technology, Tokyo Institute of Technology, J2-12, 4259 Nagatsuda-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Mayuko Sato
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Kiminori Toyooka
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
| | - David J Burritt
- Department of Botany, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | | | - Ru Zhang
- Donald Danforth Plant Science Center, 975 N Warson Rd, Saint Louis, Missouri, 63132, USA
| | - Huong Mai Nguyen
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, Texas, 79409, USA
| | - Vy Phuong Le
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, Texas, 79409, USA
| | - Hien Thuy Bui
- Division of Plant Science and Technology, Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Keiichi Mochida
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- School of Information and Data Science, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan
| | - Lam-Son Phan Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, 2500 Broadway, Lubbock, Texas, 79409, USA
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Wang L, Liu X, Li Q, Xu N, He C. A lineage-specific arginine in POS1 is required for fruit size control in Physaleae (Solanaceae) via gene co-option. Plant J 2022; 111:183-204. [PMID: 35481627 DOI: 10.1111/tpj.15786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Solanaceae have important economic value mainly due to their edible fruits. Physalis organ size 1/cytokinin response factor 3 (POS1/CRF3), a unique gene in Solanaceae, is involved in fruit size variation in Physalis but not in Solanum. However, the underlying mechanisms remain elusive. Here, we found that POS1/CRF3 was likely created via the fusion of CRF7 and CRF8 duplicates. Multiple genetic manipulations revealed that only POS1 and Capsicum POS1 (CaPOS1) functioned in fruit size control via the positive regulation of cell expansion. Comparative studies in a phylogenetic framework showed the directional enhancement of POS1-like expression in the flowers and fruits of Physaleae and the specific gain of certain interacting proteins associated with cell expansion by POS1 and CaPOS1. A lineage-specific single nucleotide polymorphism (SNP) caused the 68th amino acid histidine in the POS1 orthologs of non-Physaleae (Nicotiana and Solanum) to change to arginine in Physaleae (Physalis and Capsicum). Substituting the arginine in Physaleae POS1-like by histidine completely abolished their function in the fruits and the protein-protein interaction (PPI) with calreticulin-3. Transcriptomic comparison revealed the potential downstream pathways of POS1, including the brassinosteroid biosynthesis pathway. However, POS1-like may have functioned ancestrally in abiotic stress within Solanaceae. Our work demonstrated that heterometric expression and a SNP caused a single amino acid change to establish new PPIs, which contributed to the co-option of POS1 in multiple regulatory pathways to regulate cell expansion and thus fruit size in Physaleae. These results provide new insights into fruit morphological evolution and fruit yield control.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
| | - Xueyang Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Qiaoru Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Nan Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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29
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Yap A, Talasz H, Lindner H, Würzner R, Haas H. Ambient Availability of Amino Acids, Proteins, and Iron Impacts Copper Resistance of Aspergillus fumigatus. Front Cell Infect Microbiol 2022; 12:847846. [PMID: 35531339 PMCID: PMC9072627 DOI: 10.3389/fcimb.2022.847846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/23/2022] [Indexed: 12/02/2022] Open
Abstract
The transition metals iron and copper are required by virtually all organisms but are toxic in excess. Acquisition of both metals and resistance to copper excess have previously been shown to be important for virulence of the most common airborne human mold pathogen, Aspergillus fumigatus. Here we demonstrate that the ambient availability of amino acids and proteins increases the copper resistance of A. fumigatus wild type and particularly of the ΔcrpA mutant that lacks export-mediated copper detoxification. The highest-protecting activity was found for L-histidine followed by L-asparagine, L-aspartate, L-serine, L-threonine, and L-tyrosine. Other amino acids and proteins also displayed significant but lower protection. The protecting activity of non-proteinogenic D-histidine, L-histidine-mediated growth inhibition in the absence of high-affinity copper uptake, determination of cellular metal contents, and expression analysis of copper-regulated genes suggested that histidine inhibits low-affinity but not high-affinity copper acquisition by extracellular copper complexation. An increase in the cellular copper content was found to be accompanied by an increase in the iron content, and, in agreement, iron starvation increased copper susceptibility, which underlines the importance of cellular metal balancing. Due to the role of iron and copper in nutritional immunity, these findings are likely to play an important role in the host niche.
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Affiliation(s)
- Annie Yap
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Heribert Talasz
- Protein Micro-Analysis Facility, Institute of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Herbert Lindner
- Protein Micro-Analysis Facility, Institute of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Reinhard Würzner
- Institute of Hygiene and Medical Microbiology, Department of Hygiene, Microbiology, and Public Health, Medical University of Innsbruck, Innsbruck, Austria
| | - Hubertus Haas
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
- *Correspondence: Hubertus Haas,
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30
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Aljazi MB, Gao Y, Wu Y, He J. SMYD5 is a histone H3-specific methyltransferase mediating mono-methylation of histone H3 lysine 36 and 37. Biochem Biophys Res Commun 2022; 599:142-147. [PMID: 35182940 PMCID: PMC8896656 DOI: 10.1016/j.bbrc.2022.02.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/10/2022] [Indexed: 12/15/2022]
Abstract
Although post-translational modifications (-PTMs) of some histone H3 lysine residues are well studied, the PTMs of histone H3 lysine 37 in mammalian cells remain largely unknown. In this study, we provide evidence to show that SMYD family member 5 (SMYD5) is a histone H3-specfic methyltransferase that catalyzes mono-methylation of H3 lysine 36 and 37 (H3K36/K37me1) in vitro. The site-mutagenesis analysis shows that a species-conserved histidine in its catalytic SET domain is required for its histone methyltransferase activity. Genetic deletion of Smyd5 in murine embryonic stem cells (mESCs) partially reduces the global histone H3K37me1 level in cells, suggesting SMYD5 is one of histone methyltransferases catalyzing histone H3K37me1 in vivo. Hence, our study reveals that SMYD5 is a histone H3-specific methyltransferase that mediates histone H3K36/K37me1, which provides a biochemical basis for further studying its functions in mammalian cells.
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Affiliation(s)
- Mohammad B Aljazi
- Department of Biochemistry & Molecular Biology, College of Nature Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Yuen Gao
- Department of Biochemistry & Molecular Biology, College of Nature Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Yan Wu
- Department of Biochemistry & Molecular Biology, College of Nature Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Jin He
- Department of Biochemistry & Molecular Biology, College of Nature Sciences, Michigan State University, East Lansing, MI, 48824, USA.
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31
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Panichsillaphakit E, Kwanbunbumpen T, Chomtho S, Visuthranukul C. Copper-histidine therapy in an infant with novel splice-site variant in the ATP7A gene of Menkes disease: the first experience in South East Asia and literature review. BMJ Case Rep 2022; 15:e247937. [PMID: 35393273 PMCID: PMC8991052 DOI: 10.1136/bcr-2021-247937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2022] [Indexed: 11/03/2022] Open
Abstract
Menkes disease (MD) is an X linked recessive multi-systemic disorder of copper metabolism, resulting from an ATP7A gene mutation. We report a male infant aged 4 months who presented with kinky hair, hypopigmented skin, epilepsy and delayed development. Magnetic resonance imaging (MRI) of brain demonstrated multiple tortuosities of intracranial vessels and brain atrophy. Investigation had showed markedly decreased serum copper and ceruloplasmin. The novel c.2172+1G>T splice-site mutation in the ATP7A gene confirmed MD. He was treated with subcutaneous administration of locally prepared copper-histidine (Cu-His). Following the therapy, hair manifestation was restored and serum ceruloplasmin was normalised 1 month later. Despite the treatment, epilepsy, neurodevelopment and osteoporosis still progressed. He died from severe respiratory tract infection at the age of 9.5 months. These findings suggest that the benefit of Cu-His in our case is limited which might be related to severe presentations and degree of ATP7A mutation.
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Affiliation(s)
- Ekkarit Panichsillaphakit
- Division of Nutrition, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Tanisa Kwanbunbumpen
- Division of Nutrition, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Sirinuch Chomtho
- Pediatric Nutrition Research Unit, Division of Nutrition, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, The Thai Red Cross Society, Bangkok, Thailand
| | - Chonnikant Visuthranukul
- Pediatric Nutrition Research Unit, Division of Nutrition, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, The Thai Red Cross Society, Bangkok, Thailand
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32
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López-Pliego L, González-Acocal V, García-González DL, Reyes-Nicolau JI, Sánchez-Cuapio Z, Meneses-Carbajal AS, Fuentes-Ramírez LE, Castañeda M. HrgS (Avin 34990), a novel histidine-kinase related to GacS, regulates alginate synthesis in Azotobacter vinelandii. FEMS Microbiol Lett 2022; 369:6546211. [PMID: 35266527 DOI: 10.1093/femsle/fnac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/31/2022] [Accepted: 03/08/2022] [Indexed: 11/14/2022] Open
Abstract
Azotobacter vinelandii is a soil bacterium that produces alginates, a family of polymers of biotechnological interest. In A. vinelandii, alginate production is controlled by the two-component system GacS/GacA. GacS/GacA, in turn, regulates the Rsm post-transcriptional regulatory system establishing a cascade that regulates alginate biosynthesis by controlling the expression of the algD biosynthetic gene. In Pseudomonas aeruginosa, GacS/GacA is influenced by other histidine-kinases constituting a multicomponent signal transduction system. In this study, we explore the presence of GacS-related histidine-kinases in A. vinelandii and discover a novel histidine-kinase (Avin_34990, renamed HrgS). This histidin-kinase acts as a negative regulator of alginate synthesis by controlling the transcription of the sRNAs belonging to the Rsm post-transcriptional regulatory system, for which a functional GacS is required.
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Affiliation(s)
- Liliana López-Pliego
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Verónica González-Acocal
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Diana Laura García-González
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Jimena Itzel Reyes-Nicolau
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Zaira Sánchez-Cuapio
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Alan Shared Meneses-Carbajal
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Luis Ernesto Fuentes-Ramírez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
| | - Miguel Castañeda
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla. IC-11 Ciudad Universitaria Puebla, Pue., C.P. 72000, México
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33
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Truelsen SF, Missel JW, Gotfryd K, Pedersen PA, Gourdon P, Lindorff-Larsen K, Hélix-Nielsen C. The role of water coordination in the pH-dependent gating of hAQP10. Biochim Biophys Acta Biomembr 2022; 1864:183809. [PMID: 34699768 DOI: 10.1016/j.bbamem.2021.183809] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/23/2022]
Abstract
Human aquaporin 10 (hAQP10) is an aquaglyceroporin that assists in maintaining glycerol flux in adipocytes during lipolysis at low pH. Hence, a molecular understanding of the pH-sensitive glycerol conductance may open up for drug development in obesity and metabolically related disorders. Control of hAQP10-mediated glycerol flux has been linked to the cytoplasmic end of the channel, where a unique loop is regulated by the protonation status of histidine 80 (H80). Here, we performed unbiased molecular dynamics simulations of three protonation states of H80 to unravel channel gating. Strikingly, at neutral pH, we identified a water coordination pattern with an inverted orientation of the water molecules in vicinity of the loop. Protonation of H80 results in a more hydrophobic loop conformation, causing loss of water coordination and leaving the pore often dehydrated. Our results indicate that the loss of such water interaction network may be integral for the destabilization of the loop in the closed configuration at low pH. Additionally, a residue unique to hAQP10 (F85) reveals structural importance by flipping into the channel in correlation with loop movements, indicating a loop-stabilizing role in the closed configuration. Taken together, our simulations suggest a unique gating mechanism combining complex interaction networks between water molecules and protein residues at the loop interface. Considering the role of hAQP10 in adipocytes, the detailed molecular insights of pH-regulation presented here will help to understand glycerol pathways in these cells and may assist in drug discovery for better management of human adiposity and obesity.
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Affiliation(s)
- Sigurd Friis Truelsen
- Technical University of Denmark, Department of Environmental Engineering, Bygningstorvet Building 115, DK-2800 Kgs Lyngby, Denmark
| | - Julie Winkel Missel
- University of Copenhagen, Department of Biomedical Sciences, Nørre Allé 14, DK-2200 Copenhagen N, Denmark
| | - Kamil Gotfryd
- University of Copenhagen, Department of Biomedical Sciences, Nørre Allé 14, DK-2200 Copenhagen N, Denmark
| | - Per Amstrup Pedersen
- University of Copenhagen, Department of Biology, Universitetsparken 13, DK-2100 Copenhagen OE, Denmark
| | - Pontus Gourdon
- Lund University, Department of Experimental Medical Science, Sölvegatan 19, SE-221 84 Lund, Sweden; Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Claus Hélix-Nielsen
- Technical University of Denmark, Department of Environmental Engineering, Bygningstorvet Building 115, DK-2800 Kgs Lyngby, Denmark; University of Maribor, Faculty of Chemistry and Chemical Engineering, Smetanova 17, SI-2000 Maribor, Slovenia.
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34
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Cantrell MS, Wall JD, Pu X, Turner M, Woodbury L, Fujise K, McDougal OM, Warner LR. Expression and purification of a cleavable recombinant fortilin from Escherichia coli for structure activity studies. Protein Expr Purif 2022; 189:105989. [PMID: 34626801 PMCID: PMC8557625 DOI: 10.1016/j.pep.2021.105989] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/11/2021] [Accepted: 10/04/2021] [Indexed: 01/03/2023]
Abstract
Complications related to atherosclerosis account for approximately 1 in 4 deaths in the United States and treatment has focused on lowering serum LDL-cholesterol levels with statins. However, approximately 50% of those diagnosed with atherosclerosis have blood cholesterol levels within normal parameters. Human fortilin is an anti-apoptotic protein and a factor in macrophage-mediated atherosclerosis and is hypothesized to protect inflammatory macrophages from apoptosis, leading to subsequent cardiac pathogenesis. Fortilin is unique because it provides a novel drug target for atherosclerosis that goes beyond lowering cholesterol and utilization of a solution nuclear magnetic resonance (NMR) spectroscopy, structure-based drug discovery approach requires milligram quantities of pure, bioactive, recombinant fortilin. Here, we designed expression constructs with different affinity tags and protease cleavage sites to find optimal conditions to obtain the quantity and purity of protein necessary for structure activity relationship studies. Plasmids encoding fortilin with maltose binding protein (MBP), 6-histidine (6His) and glutathione-S-transferase (GST), N- terminal affinity tags were expressed and purified from Escherichia coli (E. coli). Cleavage sites with tobacco etch virus (TEV) protease and human rhinovirus (HRV) 3C protease were assessed. Despite high levels of expression of soluble protein, the fusion constructs were resistant to proteinases without the inclusion of amino acids between the cleavage site and N-terminus. We surveyed constructs with increasing lengths of glycine/serine (GGS) linkers between the cleavage site and fortilin and found that inclusion of at least one GGS insert led to successful protease cleavage and pure fortilin with conserved binding to calcium as measured by NMR.
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Affiliation(s)
- Maranda S Cantrell
- Biomolecular Sciences Ph.D. Program, Boise State University, Boise, ID, 83725, USA; Department of Chemistry and Biochemistry, Boise State University, Boise, ID, 83725, USA
| | - Jackson D Wall
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID, 83725, USA
| | - Xinzhu Pu
- Biomolecular Research Center, Boise State University, Boise, ID, 83725, USA
| | - Matthew Turner
- Biomolecular Research Center, Boise State University, Boise, ID, 83725, USA
| | - Luke Woodbury
- Biomolecular Research Center, Boise State University, Boise, ID, 83725, USA
| | - Ken Fujise
- Harborview Medical Center, University of Washington, Seattle, WA, 98104-2499, USA
| | - Owen M McDougal
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID, 83725, USA
| | - Lisa R Warner
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID, 83725, USA.
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35
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Ghosh S, Banerjee-Ghosh K, Levy D, Riven I, Naaman R, Haran G. Substrates Modulate Charge-Reorganization Allosteric Effects in Protein-Protein Association. J Phys Chem Lett 2021; 12:2805-2808. [PMID: 33710900 PMCID: PMC8041378 DOI: 10.1021/acs.jpclett.1c00437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein function may be modulated by an event occurring far away from the functional site, a phenomenon termed allostery. While classically allostery involves conformational changes, we recently observed that charge redistribution within an antibody can also lead to an allosteric effect, modulating the kinetics of binding to target antigen. In the present work, we study the association of a polyhistidine tagged enzyme (phosphoglycerate kinase, PGK) to surface-immobilized anti-His antibodies, finding a significant Charge-Reorganization Allostery (CRA) effect. We further observe that PGK's negatively charged nucleotide substrates modulate CRA substantially, even though they bind far away from the His-tag-antibody interaction interface. In particular, binding of ATP reduces CRA by more than 50%. The results indicate that CRA is affected by the binding of charged molecules to a protein and provide further insight into the significant role that charge redistribution can play in protein function.
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36
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Hsiue EHC, Wright KM, Douglass J, Hwang MS, Mog BJ, Pearlman AH, Paul S, DiNapoli SR, Konig MF, Wang Q, Schaefer A, Miller MS, Skora AD, Azurmendi PA, Murphy MB, Liu Q, Watson E, Li Y, Pardoll DM, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B, Gabelli SB, Zhou S. Targeting a neoantigen derived from a common TP53 mutation. Science 2021; 371:eabc8697. [PMID: 33649166 PMCID: PMC8208645 DOI: 10.1126/science.abc8697] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/30/2020] [Accepted: 02/05/2021] [Indexed: 12/12/2022]
Abstract
TP53 (tumor protein p53) is the most commonly mutated cancer driver gene, but drugs that target mutant tumor suppressor genes, such as TP53, are not yet available. Here, we describe the identification of an antibody highly specific to the most common TP53 mutation (R175H, in which arginine at position 175 is replaced with histidine) in complex with a common human leukocyte antigen-A (HLA-A) allele on the cell surface. We describe the structural basis of this specificity and its conversion into an immunotherapeutic agent: a bispecific single-chain diabody. Despite the extremely low p53 peptide-HLA complex density on the cancer cell surface, the bispecific antibody effectively activated T cells to lyse cancer cells that presented the neoantigen in vitro and in mice. This approach could in theory be used to target cancers containing mutations that are difficult to target in conventional ways.
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Affiliation(s)
- Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Katharine M Wright
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Brian J Mog
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexander H Pearlman
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Suman Paul
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sarah R DiNapoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maximilian F Konig
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Qing Wang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Complete Omics, Baltimore, MD 21227, USA
| | - Annika Schaefer
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michelle S Miller
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Andrew D Skora
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - P Aitana Azurmendi
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | | | - Qiang Liu
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Evangeline Watson
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yana Li
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, MD 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
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Kung WM, Lin MS. The NFκB Antagonist CDGSH Iron-Sulfur Domain 2 Is a Promising Target for the Treatment of Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22020934. [PMID: 33477809 PMCID: PMC7832822 DOI: 10.3390/ijms22020934] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/01/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023] Open
Abstract
Proinflammatory response and mitochondrial dysfunction are related to the pathogenesis of neurodegenerative diseases (NDs). Nuclear factor κB (NFκB) activation has been shown to exaggerate proinflammation and mitochondrial dysfunction, which underlies NDs. CDGSH iron-sulfur domain 2 (CISD2) has been shown to be associated with peroxisome proliferator-activated receptor-β (PPAR-β) to compete for NFκB and antagonize the two aforementioned NFκB-provoked pathogeneses. Therefore, CISD2-based strategies hold promise in the treatment of NDs. CISD2 protein belongs to the human NEET protein family and is encoded by the CISD2 gene (located at 4q24 in humans). In CISD2, the [2Fe-2S] cluster, through coordinates of 3-cysteine-1-histidine on the CDGSH domain, acts as a homeostasis regulator under environmental stress through the transfer of electrons or iron-sulfur clusters. Here, we have summarized the features of CISD2 in genetics and clinics, briefly outlined the role of CISD2 as a key physiological regulator, and presented modalities to increase CISD2 activity, including biomedical engineering or pharmacological management. Strategies to increase CISD2 activity can be beneficial for the prevention of inflammation and mitochondrial dysfunction, and thus, they can be applied in the management of NDs.
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Affiliation(s)
- Woon-Man Kung
- Department of Exercise and Health Promotion, College of Kinesiology and Health, Chinese Culture University, Taipei 11114, Taiwan;
| | - Muh-Shi Lin
- Division of Neurosurgery, Department of Surgery, Kuang Tien General Hospital, Taichung 43303, Taiwan
- Department of Biotechnology and Animal Science, College of Bioresources, National Ilan University, Yilan 26047, Taiwan
- Department of Biotechnology, College of Medical and Health Care, Hung Kuang University, Taichung 43302, Taiwan
- Department of Health Business Administration, College of Medical and Health Care, Hung Kuang University, Taichung 43302, Taiwan
- Correspondence: ; Tel.: +886-4-2665-1900
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Niblett D, Nelson C, Leung CS, Rexroad G, Cozy J, Zhou J, Lancaster L, Noller HF. Mutations in domain IV of elongation factor EF-G confer -1 frameshifting. RNA 2021; 27:40-53. [PMID: 33008838 PMCID: PMC7749637 DOI: 10.1261/rna.077339.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/24/2020] [Indexed: 05/25/2023]
Abstract
A recent crystal structure of a ribosome complex undergoing partial translocation in the absence of elongation factor EF-G showed disruption of codon-anticodon pairing and slippage of the reading frame by -1, directly implicating EF-G in preservation of the translational reading frame. Among mutations identified in a random screen for dominant-lethal mutations of EF-G were a cluster of six that map to the tip of domain IV, which has been shown to contact the codon-anticodon duplex in trapped translocation intermediates. In vitro synthesis of a full-length protein using these mutant EF-Gs revealed dramatically increased -1 frameshifting, providing new evidence for a role for domain IV of EF-G in maintaining the reading frame. These mutations also caused decreased rates of mRNA translocation and rotational movement of the head and body domains of the 30S ribosomal subunit during translocation. Our results are in general agreement with recent findings from Rodnina and coworkers based on in vitro translation of an oligopeptide using EF-Gs containing mutations at two positions in domain IV, who found an inverse correlation between the degree of frameshifting and rates of translocation. Four of our six mutations are substitutions at positions that interact with the translocating tRNA, in each case contacting the RNA backbone of the anticodon loop. We suggest that EF-G helps to preserve the translational reading frame by preventing uncoupled movement of the tRNA through these contacts; a further possibility is that these interactions may stabilize a conformation of the anticodon that favors base-pairing with its codon.
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Affiliation(s)
- Dustin Niblett
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Charlotte Nelson
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Calvin S Leung
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Gillian Rexroad
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Jake Cozy
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Jie Zhou
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Laura Lancaster
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Harry F Noller
- Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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Sugisawa C, Ono M, Kashimada K, Hasegawa T, Narumi S. Inactivation of a Frameshift TSH Receptor Variant Val711Phefs*18 is Due to Acquisition of a Hydrophobic Degron. J Clin Endocrinol Metab 2021; 106:e265-e272. [PMID: 33108452 DOI: 10.1210/clinem/dgaa772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Indexed: 11/19/2022]
Abstract
CONTEXT Inactivating variants of thyrotropin (thyroid-stimulating hormone; TSH) receptor (TSHR) cause congenital hypothyroidism. More than 60 such variants have been reported so far, most of which were located in the extracellular or transmembrane domain. OBJECTIVE We report the identification and characterization of a frameshift TSHR variant in the intracytoplasmic C-tail region. METHODS Sequencing of TSHR was performed in a patient with congenital hypothyroidism. The functionality of the identified variants was assessed by expressing TSHR in HEK293 cells and measuring TSH-dependent activation of the cAMP-response element-luciferase reporter. A series of systematic mutagenesis experiments were performed to characterize the frameshifted amino acid sequence. RESULTS The proband was heterozygous for a known TSHR variant (p.Arg519His) and a novel frameshift TSHR variant (p.Val711Phefs*18), which removed 54 C-terminal residues and added a 17-amino acid frameshifted sequence. The loss of function of Val711Phefs*18-TSHR was confirmed in vitro, but the function of Val711*-TSHR was found to be normal. Western blotting showed the low protein expression of Val711Phefs*18-TSHR. Fusion of the frameshift sequence to green fluorescent protein or luciferase induced inactivation of them, indicating that the sequence acted as a degron. A systematic mutagenesis study revealed that the density of hydrophobic residues in the frameshift sequence determined the stability. Eight additional frameshift TSHR variants that covered all possible shifted frames in C-tail were created, and another frameshift variant (Thr748Profs*27) with similar effect was found. CONCLUSIONS We characterized a naturally occurring frameshift TSHR variant located in C-tail, and provided a unique evidence that hydrophobicity in the C-terminal region of the receptor affects protein stability.
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Affiliation(s)
- Chiho Sugisawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Showa University Fujigaoka Hospital, Kanagawa, Japan
| | - Makoto Ono
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Pediatrics, Tokyo Bay Urayasu Ichikawa Medical Center, Chiba, Japan
| | - Kenichi Kashimada
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Satoshi Narumi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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Naulin PA, Lozano B, Fuentes C, Liu Y, Schmidt C, Contreras JE, Barrera NP. Polydisperse molecular architecture of connexin 26/30 heteromeric hemichannels revealed by atomic force microscopy imaging. J Biol Chem 2020; 295:16499-16509. [PMID: 32887797 PMCID: PMC7864052 DOI: 10.1074/jbc.ra119.012128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 08/31/2020] [Indexed: 11/06/2022] Open
Abstract
Connexin (Cx) protein forms hemichannels and gap junctional channels, which play diverse and profound roles in human physiology and diseases. Gap junctions are arrays of intercellular channels formed by the docking of two hemichannels from adjacent cells. Each hexameric hemichannel contains the same or different Cx isoform. Although homomeric Cxs forms have been largely described functionally and structurally, the stoichiometry and arrangement of heteromeric Cx channels remain unknown. The latter, however, are widely expressed in human tissues and variation might have important implications on channel function. Investigating properties of heteromeric Cx channels is challenging considering the high number of potential subunit arrangements and stoichiometries, even when only combining two Cx isoforms. To tackle this problem, we engineered an HA tag onto Cx26 or Cx30 subunits and imaged hemichannels that were liganded by Fab-epitope antibody fragments via atomic force microscopy. For Cx26-HA/Cx30 or Cx30-HA/Cx26 heteromeric channels, the Fab-HA binding distribution was binomial with a maximum of three Fab-HA bound. Furthermore, imaged Cx26/Cx30-HA triple liganded by Fab-HA showed multiple arrangements that can be derived from the law of total probabilities. Atomic force microscopy imaging of ringlike structures of Cx26/Cx30-HA hemichannels confirmed these findings and also detected a polydisperse distribution of stoichiometries. Our results indicate a dominant subunit stoichiometry of 3Cx26:3Cx30 with the most abundant subunit arrangement of Cx26-Cx26-Cx30-Cx26-Cx30-Cx30. To our knowledge, this is the first time that the molecular architecture of heteromeric Cx channels has been revealed, thus providing the basis to explore the functional effect of these channels in biology.
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Affiliation(s)
- Pamela A Naulin
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Benjamin Lozano
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christian Fuentes
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Yu Liu
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Carla Schmidt
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jorge E Contreras
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Khristin AM, Zabelin AA, Fufina TY, Khatypov RA, Proskuryakov II, Shuvalov VA, Shkuropatov AY, Vasilieva LG. Mutation H(M202)L does not lead to the formation of a heterodimer of the primary electron donor in reaction centers of Rhodobacter sphaeroides when combined with mutation I(M206)H. Photosynth Res 2020; 146:109-121. [PMID: 32125564 DOI: 10.1007/s11120-020-00728-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
In photosynthetic reaction centers (RCs) of purple bacteria, conserved histidine residues [His L173 and His M202 in Rhodobacter (Rba.) sphaeroides] are known to serve as fifth axial ligands to the central Mg atom of the bacteriochlorophyll (BChl) molecules (PA and PB, respectively) that constitute the homodimer (BChl/BChl) primary electron donor P. In a number of previous studies, it has been found that replacing these residues with leucine, which cannot serve as a ligand to the Mg ion of BChl, leads to the assembly of heterodimer RCs with P represented by the BChl/BPheo pair. Here, we show that a homodimer P is assembled in Rba. sphaeroides RCs if the mutation H(M202)L is combined with the mutation of isoleucine to histidine at position M206 located in the immediate vicinity of PB. The resulting mutant H(M202)L/I(M206)H RCs are characterized using pigment analysis, redox titration, and a number of spectroscopic methods. It is shown that, compared to wild-type RCs, the double mutation causes significant changes in the absorption spectrum of the P homodimer and the electronic structure of the radical cation P+, but has only minor effect on the pigment composition, the P/P+ midpoint potential, and the initial electron-transfer reaction. The results are discussed in terms of the nature of the axial ligand to the Mg of PB in mutant H(M202)L/I(M206)H RCs and the possibility of His M202 participation in the previously proposed through-bond route for electron transfer from the excited state P* to the monomeric BChl BA in wild-type RCs.
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Affiliation(s)
- Anton M Khristin
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290, Moscow, Russian Federation
| | - Alexey A Zabelin
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290, Moscow, Russian Federation
| | - Tatiana Yu Fufina
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290, Moscow, Russian Federation
| | - Ravil A Khatypov
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290, Moscow, Russian Federation
| | - Ivan I Proskuryakov
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290, Moscow, Russian Federation
| | - Vladimir A Shuvalov
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290, Moscow, Russian Federation
| | - Anatoly Ya Shkuropatov
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290, Moscow, Russian Federation
| | - Lyudmila G Vasilieva
- Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, 142290, Moscow, Russian Federation.
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Liu J, Zuo Z, Zou M, Finkel T, Liu S. Identification of the transcription factor Miz1 as an essential regulator of diphthamide biosynthesis using a CRISPR-mediated genome-wide screen. PLoS Genet 2020; 16:e1009068. [PMID: 33057331 PMCID: PMC7591051 DOI: 10.1371/journal.pgen.1009068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/27/2020] [Accepted: 08/20/2020] [Indexed: 12/15/2022] Open
Abstract
Diphthamide is a unique post-translationally modified histidine residue (His715 in all mammals) found only in eukaryotic elongation factor-2 (eEF-2). The biosynthesis of diphthamide represents one of the most complex modifications, executed by protein factors conserved from yeast to humans. Diphthamide is not only essential for normal physiology (such as ensuring fidelity of mRNA translation), but is also exploited by bacterial ADP-ribosylating toxins (e.g., diphtheria toxin) as their molecular target in pathogenesis. Taking advantage of the observation that cells defective in diphthamide biosynthesis are resistant to ADP-ribosylating toxins, in the past four decades, seven essential genes (Dph1 to Dph7) have been identified for diphthamide biosynthesis. These technically unsaturated screens raise the question as to whether additional genes are required for diphthamide biosynthesis. In this study, we performed two independent, saturating, genome-wide CRISPR knockout screens in human cells. These screens identified all previously known Dph genes, as well as further identifying the BTB/POZ domain-containing transcription factor Miz1. We found that Miz1 is absolutely required for diphthamide biosynthesis via its role in the transcriptional regulation of Dph1 expression. Mechanistically, Miz1 binds to the Dph1 proximal promoter via an evolutionarily conserved consensus binding site to activate Dph1 transcription. Therefore, this work demonstrates that Dph1-7, along with the newly identified Miz1 transcription factor, are likely to represent the essential protein factors required for diphthamide modification on eEF2. Diphthamide is a unique post-translationally modified histidine residue (His699 in yeast, His715 in all mammals) found only in eukaryotic elongation factor-2 (eEF-2). Mice that are deficient in diphthamide biosynthesis are embryonic lethal, attesting to the importance of diphthamide in normal physiology. It has taken four decades to identify the seven non-redundant genes in diphthamide biosynthesis, but whether additional factors are required and how the pathway is regulated remained elusive. To address these issues, we performed two saturating, independent, and unbiased genome-wide CRISPR knockout screens. The screens concluded independently that Dph1-Dph7 and additionally transcription factor Miz1 are the key factors required for diphthamide biosynthesis. Mechanistically, Miz1 binds to the Dph1 proximal promoter via an evolutionarily conserved consensus binding site to activate Dph1 transcription. While diphthamide biosynthesis machinery (Dph1-Dph7) exists across eukaryotes, Miz1 orthologues do not exist in lower species such as yeast, C. elegans, and Drosophila, indicating that the regulation of diphthamide modification by Miz1 emerged much later in evolution. The work opens a new avenue for understanding the role that diphthamide modification plays in normal physiology and bacterial toxin pathogenesis.
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Affiliation(s)
- Jie Liu
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
- Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Zehua Zuo
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
| | - Meijuan Zou
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
| | - Toren Finkel
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
- Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Shihui Liu
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- * E-mail:
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Chioccioli S, Del Duca S, Vassallo A, Castronovo LM, Fani R. Exploring the role of the histidine biosynthetic hisF gene in cellular metabolism and in the evolution of (ancestral) genes: from LUCA to the extant (micro)organisms. Microbiol Res 2020; 240:126555. [PMID: 32673985 DOI: 10.1016/j.micres.2020.126555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/29/2020] [Accepted: 07/06/2020] [Indexed: 01/14/2023]
Abstract
Histidine biosynthesis is an ancestral pathway that was assembled before the appearance of the Last Universal Common Ancestor; afterwards, it remained unaltered in all the extant histidine-synthesizing (micro)organisms. It is a metabolic cross-road interconnecting histidine biosynthesis to nitrogen metabolism and the de novo synthesis of purines. This interconnection is due to the reaction catalyzed by the products of hisH and hisF genes. The latter gene is an excellent model to study which trajectories have been followed by primordial cells to build the first metabolic routes, since its evolution is the result of different molecular rearrangement events, i.e. gene duplication, gene fusion, gene elongation, and domain shuffling. Additionally, this review summarizes data concerning the involvement of hisF and its product in other different cellular processes, revealing that HisF very likely plays a role also in cell division control and involvement in virulence and nodule development in different bacteria. From the metabolic viewpoint, these results suggest that HisF plays a central role in cellular metabolism, highlighting the interconnections of different metabolic pathways.
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Affiliation(s)
- Sofia Chioccioli
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Sara Del Duca
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Alberto Vassallo
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | | | - Renato Fani
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy.
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Yoder N, Gouaux E. The His-Gly motif of acid-sensing ion channels resides in a reentrant 'loop' implicated in gating and ion selectivity. eLife 2020; 9:e56527. [PMID: 32496192 PMCID: PMC7308080 DOI: 10.7554/elife.56527] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/03/2020] [Indexed: 12/18/2022] Open
Abstract
Acid-sensing ion channels (ASICs) are proton-gated members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed throughout the central and peripheral nervous systems. The homotrimeric splice variant ASIC1a has been implicated in nociception, fear memory, mood disorders and ischemia. Here, we extract full-length chicken ASIC1 (cASIC1) from cell membranes using styrene maleic acid (SMA) copolymer, elucidating structures of ASIC1 channels in both high pH resting and low pH desensitized conformations by single-particle cryo-electron microscopy (cryo-EM). The structures of resting and desensitized channels reveal a reentrant loop at the amino terminus of ASIC1 that includes the highly conserved 'His-Gly' (HG) motif. The reentrant loop lines the lower ion permeation pathway and buttresses the 'Gly-Ala-Ser' (GAS) constriction, thus providing a structural explanation for the role of the His-Gly dipeptide in the structure and function of ASICs.
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Affiliation(s)
- Nate Yoder
- Vollum Institute, Oregon Health & Science UniversityPortlandUnited States
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science UniversityPortlandUnited States
- Howard Hughes Medical Institute, Oregon Health & Science UniversityPortlandUnited States
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Kielkopf CL, Bauer W, Urbatsch IL. Purification of Polyhistidine-Tagged Proteins by Immobilized Metal Affinity Chromatography. Cold Spring Harb Protoc 2020; 2020:102194. [PMID: 32482902 DOI: 10.1101/pdb.prot102194] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Immobilized metal affinity chromatography (IMAC) is based on the affinity of polyhistidine tracts for divalent metal cations (usually Ni2+) immobilized as transition metal chelate complexes on a chromatography resin. The main protocol here is optimized for use of Ni2+-NTA resin to purify soluble 6xHis-tagged proteins by a straightforward batch method during the binding step, followed by gravity flow for washes and elution. This protocol does not require any specialized equipment other than a simple glass or plastic column. IMAC resins can be used in multiple formats, including batch, gravity flow, centrifuge columns, and fast performance liquid chromatography (FPLC) systems. FPLC systems are designed specifically for the chromatographic separations of proteins and other biomolecules. These systems typically contain multiple pumps, an in-line UV absorption monitor, conductivity meter, pH meter, fraction collector, and other options that allow for the simultaneous purification, analysis, and fractionation of the sample. When linked with the appropriate instruments, an FPLC can become a high-precision, automated instrument that separates proteins at a high resolution. An alternative protocol is included here that describes 6xHis-tagged protein purification using FPLC. Procedures for the cleaning and regeneration of the IMAC resin for reuse are also described, and, finally, considerations for storing purified proteins are discussed.
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Chakraborty A, Lin WC, Lin YT, Huang KJ, Wang PY, Chang IYF, Wang HI, Ma KT, Wang CY, Huang XR, Lee YH, Chen BC, Hsieh YJ, Chien KY, Lin TY, Liu JL, Sung LY, Yu JS, Chang YS, Pai LM. SNAP29 mediates the assembly of histidine-induced CTP synthase filaments in proximity to the cytokeratin network. J Cell Sci 2020; 133:jcs240200. [PMID: 32184263 DOI: 10.1242/jcs.240200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
Under metabolic stress, cellular components can assemble into distinct membraneless organelles for adaptation. One such example is cytidine 5'-triphosphate synthase (CTPS, for which there are CTPS1 and CTPS2 forms in mammals), which forms filamentous structures under glutamine deprivation. We have previously demonstrated that histidine (His)-mediated methylation regulates the formation of CTPS filaments to suppress enzymatic activity and preserve the CTPS protein under glutamine deprivation, which promotes cancer cell growth after stress alleviation. However, it remains unclear where and how these enigmatic structures are assembled. Using CTPS-APEX2-mediated in vivo proximity labeling, we found that synaptosome-associated protein 29 (SNAP29) regulates the spatiotemporal filament assembly of CTPS along the cytokeratin network in a keratin 8 (KRT8)-dependent manner. Knockdown of SNAP29 interfered with assembly and relaxed the filament-induced suppression of CTPS enzymatic activity. Furthermore, APEX2 proximity labeling of keratin 18 (KRT18) revealed a spatiotemporal association of SNAP29 with cytokeratin in response to stress. Super-resolution imaging suggests that during CTPS filament formation, SNAP29 interacts with CTPS along the cytokeratin network. This study links the cytokeratin network to the regulation of metabolism by compartmentalization of metabolic enzymes during nutrient deprivation.
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Affiliation(s)
- Archan Chakraborty
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Wei-Cheng Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Yu-Tsun Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Kuang-Jing Huang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Pei-Yu Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 33302, Taiwan
| | - Hsiang-Iu Wang
- Bioinformatics Core Laboratory, Chang Gung University, Taoyuan 33302, Taiwan
| | - Kung-Ting Ma
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Chun-Yen Wang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Xuan-Rong Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Yen-Hsien Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Ya-Ju Hsieh
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Kun-Yi Chien
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Clinical Proteomics Core laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Tzu-Yang Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ji-Long Liu
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Li-Ying Sung
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Li-Mei Pai
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
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47
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Hu L, Zhang H, Xie C, Wang J, Zhang J, Wang H, Weng Y, Chen P, Li Y. A mutation in CsHD encoding a histidine and aspartic acid domain-containing protein leads to yellow young leaf-1 (yyl-1) in cucumber (Cucumis sativus L.). Plant Sci 2020; 293:110407. [PMID: 32081257 DOI: 10.1016/j.plantsci.2020.110407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 05/24/2023]
Abstract
Leaf color mutants are an ideal tool to study chlorophyll biosynthesis, chloroplast development and photosynthesis. In this study, we identified an EMS-induced yellow young leaf mutant C777. The mutant exhibited yellow cotyledons and emerging true leaves with stay-green dots that turn green gradually with leaf growth. Segregation analysis in several populations indicated that the mutant C777 was controlled by a recessive gene yyl-1. Fine mapping delimited the yyl-1 locus to a 45.3 kb region harboring 8 putative genes, but only one SNP (G to A) was identified between C777 and its wild-type parental line in this region which occurred in the 13th exon of CsHD that encodes a histidine and aspartic acid (HD) domain containing protein. This nonsense mutation introduced a stop codon and thus a premature protein. Uniqueness of this mutant allele was verified in 515 cucumber lines. Quantitative real-time PCR revealed significantly reduced expression of CsHD gene in the mutant. Further, silencing the NbHD gene by VIGS in tobacco resulted in virescent young leaves and significantly down-regulated expression of HD gene. These results strongly supported the association of the CsHD gene with the virescent young leaf phenotype in C777. This is the first report to clone and characterize the CsHD gene in the horticultural crops. The results may help understand the functions of the HD gene in chloroplast development and chlorophyll biosynthesis in plants.
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Affiliation(s)
- Liangliang Hu
- College of Horticulture, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Haiqiang Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Chen Xie
- College of Horticulture, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Jin Wang
- College of Horticulture, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Jiayu Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Hui Wang
- College of Horticulture, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Yiqun Weng
- USDA-ARS, Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, Shanxi, 712100, China.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, Shanxi, 712100, China.
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48
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Thadani NN, Yang J, Moyo B, Lee CM, Chen MY, Bao G, Suh J. Site-Specific Post-translational Surface Modification of Adeno-Associated Virus Vectors Using Leucine Zippers. ACS Synth Biol 2020; 9:461-467. [PMID: 32068391 PMCID: PMC7323921 DOI: 10.1021/acssynbio.9b00341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Adeno-associated virus (AAV) is widely favored as a gene therapy vector, tested in over 200 clinical trials internationally. To improve targeted delivery a variety of genetic capsid modifications, such as insertion of targeting proteins/peptides into the capsid shell, have been explored with some success but larger insertions often have unpredictable deleterious impacts on capsid formation and gene delivery. Here, we demonstrate a modular platform for the integration of exogenous peptides and proteins onto the AAV capsid post-translationally while preserving vector functionality. We decorated the AAV capsid with leucine-zipper coiled-coil binding motifs that exhibit specific noncovalent heterodimerization. AAV capsids successfully display hexahistidine tagged-peptides using this approach, as demonstrated through nickel column affinity. This protein display platform may facilitate the incorporation of biological moieties on the AAV surface, expanding possibilities for vector enhancement and engineering.
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Affiliation(s)
- Nicole N Thadani
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Joanna Yang
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Buhle Moyo
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Maria Y Chen
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Junghae Suh
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
- Department of Biosciences, Rice University, Houston, Texas 77030, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77030, United States
- Systems, Synthetic and Physical Biology Program, Rice University, Houston, Texas 77030, United States
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49
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Seniya SP, Yadav P, Jain V. Construction of E. coli-Mycobacterium shuttle vectors with a variety of expression systems and polypeptide tags for gene expression in mycobacteria. PLoS One 2020; 15:e0230282. [PMID: 32160243 PMCID: PMC7065818 DOI: 10.1371/journal.pone.0230282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 02/25/2020] [Indexed: 01/23/2023] Open
Abstract
Cloning and expression of a desired gene is indispensable in molecular biology studies. Expression vectors, in this regard, should offer much needed flexibility and choice of cloning strategies for both in vivo and in vitro protein expression experiments. Furthermore, availability of option to choose from various reporter tags allows one to be flexible during designing of an experiment in a more relevant manner. Thus, the need of a versatile expression system cannot be ignored. Although several different expression vectors are available for gene expression in mycobacteria, they lack the required versatility of expression and the inclusion of reporter tags. We here present the construction of a set of nine E. coli-Mycobacterium shuttle plasmids, which offer a combination of three mycobacterial promoter systems (heat shock inducible-hsp60, tetracycline-, and acetamide-inducible) along with three polypeptide tags (Green Fluorescent Protein (GFP), Glutathione S-transferase (GST) and hexa-histidine tag). These vectors offer the cloning of a target gene in all the nine given vectors in parallel, thus allowing the generation of recombinant plasmids that will express the target gene from different promoters with different tags. Here, while the hexa-histidine and GST tags can be used for protein purification and pull-down experiments, the GFP-tag can be used for protein localization within the cell. Additionally, the vectors also offer the choice of positioning of the reporter tag either at the N-terminus or at the C-terminus of the expressed protein, which is achieved by cloning of the gene at any of the two blunt-end restriction enzyme sites available in the vector. We believe that these plasmids will be extremely useful in the gene expression studies in mycobacteria by offering the choices of promoters and reporters. Our work also paves the way to developing more such plasmids with other tags and promoters that may find use in mycobacterial biology.
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Affiliation(s)
- Surya Pratap Seniya
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Priya Yadav
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, India
- * E-mail:
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50
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Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P. Structural basis of second-generation HIV integrase inhibitor action and viral resistance. Science 2020. [PMID: 32001525 DOI: 10.1126/science.aay4919/suppl_file/papv2.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
Abstract
Although second-generation HIV integrase strand-transfer inhibitors (INSTIs) are prescribed throughout the world, the mechanistic basis for the superiority of these drugs is poorly understood. We used single-particle cryo-electron microscopy to visualize the mode of action of the advanced INSTIs dolutegravir and bictegravir at near-atomic resolution. Glutamine-148→histidine (Q148H) and glycine-140→serine (G140S) amino acid substitutions in integrase that result in clinical INSTI failure perturb optimal magnesium ion coordination in the enzyme active site. The expanded chemical scaffolds of second-generation compounds mediate interactions with the protein backbone that are critical for antagonizing viruses containing the Q148H and G140S mutations. Our results reveal that binding to magnesium ions underpins a fundamental weakness of the INSTI pharmacophore that is exploited by the virus to engender resistance and provide a structural framework for the development of this class of anti-HIV/AIDS therapeutics.
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Affiliation(s)
- Nicola J Cook
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Wen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Dénes Berta
- Department of Chemistry, King's College London, London SE1 1DB, UK
| | - Magd Badaoui
- Department of Chemistry, King's College London, London SE1 1DB, UK
| | | | - Andrea Nans
- Structural Biology Science Technology Platform, Francis Crick Institute, London NW1 1AT, UK
| | - Abhay Kotecha
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, 5651 GG, Netherlands
| | - Edina Rosta
- Department of Chemistry, King's College London, London SE1 1DB, UK
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK.
- Department of Infectious Disease, Imperial College London, St Mary's Campus, London W2 1PG, UK
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