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Brunßen D, Suter B. Effects of unstable β-PheRS on food avoidance, growth, and development are suppressed by the appetite hormone CCHa2. Fly (Austin) 2024; 18:2308737. [PMID: 38374657 PMCID: PMC10880493 DOI: 10.1080/19336934.2024.2308737] [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: 08/07/2023] [Accepted: 01/18/2024] [Indexed: 02/21/2024] Open
Abstract
Amino acyl-tRNA synthetases perform diverse non-canonical functions aside from their essential role in charging tRNAs with their cognate amino acid. The phenylalanyl-tRNA synthetase (PheRS/FARS) is an α2β2 tetramer that is needed for charging the tRNAPhe for its translation activity. Fragments of the α-subunit have been shown to display an additional, translation-independent, function that activates growth and proliferation and counteracts Notch signalling. Here we show in Drosophila that overexpressing the β-subunit in the context of the complete PheRS leads to larval roaming, food avoidance, slow growth, and a developmental delay that can last several days and even prevents pupation. These behavioural and developmental phenotypes are induced by PheRS expression in CCHa2+ and Pros+ cells. Simultaneous expression of β-PheRS, α-PheRS, and the appetite-inducing CCHa2 peptide rescued these phenotypes, linking this β-PheRS activity to the appetite-controlling pathway. The fragmentation dynamic of the excessive β-PheRS points to β-PheRS fragments as possible candidate inducers of these phenotypes. Because fragmentation of human FARS has also been observed in human cells and mutations in human β-PheRS (FARSB) can lead to problems in gaining weight, Drosophila β-PheRS can also serve as a model for the human phenotype and possibly also for obesity.
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Affiliation(s)
| | - Beat Suter
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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Li B, Liu F, Chen X, Chen T, Zhang J, Liu Y, Yao Y, Hu W, Zhang M, Wang B, Liu L, Chen K, Wu Y. FARS2 Deficiency Causes Cardiomyopathy by Disrupting Mitochondrial Homeostasis and the Mitochondrial Quality Control System. Circulation 2024; 149:1268-1284. [PMID: 38362779 PMCID: PMC11017836 DOI: 10.1161/circulationaha.123.064489] [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: 03/17/2023] [Accepted: 12/13/2023] [Indexed: 02/17/2024]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is a common heritable heart disease. Although HCM has been reported to be associated with many variants of genes involved in sarcomeric protein biomechanics, pathogenic genes have not been identified in patients with partial HCM. FARS2 (the mitochondrial phenylalanyl-tRNA synthetase), a type of mitochondrial aminoacyl-tRNA synthetase, plays a role in the mitochondrial translation machinery. Several variants of FARS2 have been suggested to cause neurological disorders; however, FARS2-associated diseases involving other organs have not been reported. We identified FARS2 as a potential novel pathogenic gene in cardiomyopathy and investigated its effects on mitochondrial homeostasis and the cardiomyopathy phenotype. METHODS FARS2 variants in patients with HCM were identified using whole-exome sequencing, Sanger sequencing, molecular docking analyses, and cell model investigation. Fars2 conditional mutant (p.R415L) or knockout mice, fars2-knockdown zebrafish, and Fars2-knockdown neonatal rat ventricular myocytes were engineered to construct FARS2 deficiency models both in vivo and in vitro. The effects of FARS2 and its role in mitochondrial homeostasis were subsequently evaluated using RNA sequencing and mitochondrial functional analyses. Myocardial tissues from patients were used for further verification. RESULTS We identified 7 unreported FARS2 variants in patients with HCM. Heart-specific Fars2-deficient mice presented cardiac hypertrophy, left ventricular dilation, progressive heart failure accompanied by myocardial and mitochondrial dysfunction, and a short life span. Heterozygous cardiac-specific Fars2R415L mice displayed a tendency to cardiac hypertrophy at age 4 weeks, accompanied by myocardial dysfunction. In addition, fars2-knockdown zebrafish presented pericardial edema and heart failure. FARS2 deficiency impaired mitochondrial homeostasis by directly blocking the aminoacylation of mt-tRNAPhe and inhibiting the synthesis of mitochondrial proteins, ultimately contributing to an imbalanced mitochondrial quality control system by accelerating mitochondrial hyperfragmentation and disrupting mitochondrion-related autophagy. Interfering with the mitochondrial quality control system using adeno-associated virus 9 or specific inhibitors mitigated the cardiac and mitochondrial dysfunction triggered by FARS2 deficiency by restoring mitochondrial homeostasis. CONCLUSIONS Our findings unveil the previously unrecognized role of FARS2 in heart and mitochondrial homeostasis. This study may provide new insights into the molecular diagnosis and prevention of heritable cardiomyopathy as well as therapeutic options for FARS2-associated cardiomyopathy.
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Affiliation(s)
- Bowen Li
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics (B.L., X.C., T.C., J.Z., Y.L., Y.Y., W.H., M.Z., Y.W.), Air Force Medical University, Xi'an, China
| | - Fangfang Liu
- Department of Neurobiology (F.L.), Air Force Medical University, Xi'an, China
| | - Xihui Chen
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics (B.L., X.C., T.C., J.Z., Y.L., Y.Y., W.H., M.Z., Y.W.), Air Force Medical University, Xi'an, China
| | - Tangdong Chen
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics (B.L., X.C., T.C., J.Z., Y.L., Y.Y., W.H., M.Z., Y.W.), Air Force Medical University, Xi'an, China
| | - Juan Zhang
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics (B.L., X.C., T.C., J.Z., Y.L., Y.Y., W.H., M.Z., Y.W.), Air Force Medical University, Xi'an, China
| | - Yifeng Liu
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics (B.L., X.C., T.C., J.Z., Y.L., Y.Y., W.H., M.Z., Y.W.), Air Force Medical University, Xi'an, China
| | - Yan Yao
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics (B.L., X.C., T.C., J.Z., Y.L., Y.Y., W.H., M.Z., Y.W.), Air Force Medical University, Xi'an, China
| | - Weihong Hu
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics (B.L., X.C., T.C., J.Z., Y.L., Y.Y., W.H., M.Z., Y.W.), Air Force Medical University, Xi'an, China
| | - Mengjie Zhang
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics (B.L., X.C., T.C., J.Z., Y.L., Y.Y., W.H., M.Z., Y.W.), Air Force Medical University, Xi'an, China
| | - Bo Wang
- School of Basic Medicine, Department of Ultrasound, Xijing Hypertrophic Cardiomyopathy Center, Xijing Hospital (B.W., L.L.), Air Force Medical University, Xi'an, China
| | - Liwen Liu
- School of Basic Medicine, Department of Ultrasound, Xijing Hypertrophic Cardiomyopathy Center, Xijing Hospital (B.W., L.L.), Air Force Medical University, Xi'an, China
| | - Kun Chen
- Department of Anatomy, Histology and Embryology and K.K. Leung Brain Research Center (K.C.), Air Force Medical University, Xi'an, China
| | - Yuanming Wu
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics (B.L., X.C., T.C., J.Z., Y.L., Y.Y., W.H., M.Z., Y.W.), Air Force Medical University, Xi'an, China
- Department of Clinical Laboratory, Tangdu Hospital (Y.W.), Air Force Medical University, Xi'an, China
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Zhang X, Xiang F, Li D, Yang F, Yu S, Wang X. Adult-onset combined oxidative phosphorylation deficiency type 14 manifests as epileptic status: a new phenotype and literature review. BMC Neurol 2024; 24:15. [PMID: 38166857 PMCID: PMC10759640 DOI: 10.1186/s12883-023-03480-4] [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: 05/24/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Combined oxidative phosphorylation deficiency (COXPD) is a severe disorder with early onset and autosomal recessive inheritance, and has been divided into 51 types (COXPD1-COXPD51). COXPD14 is caused by a mutation in the FARS2 gene, which encodes mitochondrial phenylalanyl-tRNA synthetase (mt-PheRS), an enzyme that transfers phenylalanine to its cognate tRNA in mitochondria. Since the first case was reported in 2012, an increasing number of FARS2 variations have been subsequently identified, which present three main phenotypic manifestations: early onset epileptic encephalopathy, hereditary spastic paraplegia, and juvenile-onset epilepsy. To our knowledge, no adult cases have been reported in the literature. METHODS We report in detail a case of genetically confirmed COXPD14 and review the relevant literature. RESULTS Approximately 58 subjects with disease-causing variants of FARS2 have been reported, including 31 cases of early onset epileptic encephalopathy, 16 cases of hereditary spastic paraplegia, 3 cases of juvenile-onset epilepsy, and 8 cases of unknown phenotype. We report a case of autosomal recessive COXPD14 in an adult with status epilepticus as the only manifestation with a good prognosis, which is different from that in neonatal or infant patients reported in the literature. c.467C > T (p.T156M) has been previously reported, while c.119_120del (p.E40Vfs*87) is novel, and, both mutations are pathogenic. CONCLUSIONS This case of autosomal recessive COXPD14 in an adult only presented as status epilepticus, which is different from the patients reported previously. Our study expands the mutation spectrum of FARS2, and we tended to define the phenotypes based on the clinical manifestation rather than the age of onset.
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Affiliation(s)
- Xu Zhang
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China
| | - Feng Xiang
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China
| | - Desheng Li
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China
| | - Fei Yang
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China
| | - Shengyuan Yu
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China
| | - Xiangqing Wang
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China.
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Chen W, Rehsi P, Thompson K, Yeo M, Stals K, He L, Schimmel P, Chrzanowska-Lightowlers ZMA, Wakeling E, Taylor RW, Kuhle B. Clinical and molecular characterization of novel FARS2 variants causing neonatal mitochondrial disease. Mol Genet Metab 2023; 140:107657. [PMID: 37523899 DOI: 10.1016/j.ymgme.2023.107657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/22/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023]
Abstract
FARS2 encodes the mitochondrial phenylalanyl-tRNA synthetase (mtPheRS), which is essential for charging mitochondrial (mt-) tRNAPhe with phenylalanine for use in intramitochondrial translation. Many biallelic, pathogenic FARS2 variants have been described previously, which are mostly associated with two distinct clinical phenotypes; an early onset epileptic mitochondrial encephalomyopathy or a later onset spastic paraplegia. In this study, we report on a patient who presented at 3 weeks of age with tachypnoea and poor feeding, which progressed to severe metabolic decompensation with lactic acidosis and seizure activity followed by death at 9 weeks of age. Rapid trio whole exome sequencing identified compound heterozygous FARS2 variants including a pathogenic exon 2 deletion on one allele and a rare missense variant (c.593G > T, p.(Arg198Leu)) on the other allele, necessitating further work to aid variant classification. Assessment of patient fibroblasts demonstrated severely decreased steady-state levels of mtPheRS, but no obvious defect in any components of the oxidative phosphorylation system. To investigate the potential pathogenicity of the missense variant, we determined its high-resolution crystal structure, demonstrating a local structural destabilization in the catalytic domain. Moreover, the R198L mutation reduced the thermal stability and impaired the enzymatic activity of mtPheRS due to a lower binding affinity for tRNAPhe and a slower turnover rate. Together these data confirm the pathogenicity of this FARS2 variant in causing early-onset mitochondrial epilepsy.
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Affiliation(s)
- Wenqian Chen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Preeya Rehsi
- Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
| | - Mildrid Yeo
- Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne NE1 4LP, UK
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; The Scripps Florida Research Institute at the University of Florida, Jupiter, FL 33458, USA
| | - Zofia M A Chrzanowska-Lightowlers
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
| | - Emma Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne NE1 4LP, UK.
| | - Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen 37073, Germany.
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Guo R, Chen Y, Hu X, Qi Z, Guo J, Li Y, Hao C. Phenylalanyl-tRNA synthetase deficiency caused by biallelic variants in FARSA gene and literature review. BMC Med Genomics 2023; 16:245. [PMID: 37833669 PMCID: PMC10571242 DOI: 10.1186/s12920-023-01662-0] [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: 05/15/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Aminoacyl-tRNA synthetases (ARSs) are indispensable enzymes for protein biosynthesis in cells. The phenylalanyl-tRNA synthetase (FARS1) located in cytoplasm which consists of two FARS alpha subunits (FARSA) and two FARS beta subunits (FARSB). Autosomal recessive inheritance of pathogenic variants of FARSA or FARSB can result in defective FARS1 which are characterized by interstitial lung disease, liver disease, brain abnormalities, facial dysmorphism and growth restriction. METHODS Exome sequencing was used to detect the candidate variants. The in silico prediction and expressional level analysis were performed to evaluate the pathogenicity of the variations. Additionally, we presented the patient's detailed clinical information and compared the clinical feature with other previously reported patients with FARSA-deficiency. RESULTS We identified compound heterozygous rare missense variants (c.1172 T > C/ p.Leu391Pro and c.1211G > A/ p.Arg404His) in FARSA gene in a Chinese male patient. The protein structure prediction and the analysis of levels of FARSA and FARSB subunits indicated both variants pathogenic. Clinical feature review indicated inflammatory symptoms in young infants may be an additional key feature. Thyroid dysfunction should be considered as a phenotype with variable penetrance. CONCLUSIONS Our results expanded the current phenotypic and genetic spectrum of FARSA-deficiency.
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Affiliation(s)
- Ruolan Guo
- Beijing Key Laboratory for Genetics of Birth Defects, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Yuanying Chen
- Beijing Key Laboratory for Genetics of Birth Defects, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Xuyun Hu
- Beijing Key Laboratory for Genetics of Birth Defects, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Zhan Qi
- Beijing Key Laboratory for Genetics of Birth Defects, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Jun Guo
- Beijing Key Laboratory for Genetics of Birth Defects, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Yuchuan Li
- Outpatient Department, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China.
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China.
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Oswald SL, Steinbrücker K, Achleitner MT, Göschl E, Bittner RE, Schmidt WM, Tiefenthaler E, Hammerl E, Eisl A, Mayr D, Mayr JA, Wortmann SB. Treatment of Mitochondrial Phenylalanyl-tRNa-Synthetase Deficiency (FARS2) with Oral Phenylalanine. Neuropediatrics 2023; 54:351-355. [PMID: 36603837 DOI: 10.1055/a-2008-4230] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE By loading transfer RNAs with their cognate amino acids, aminoacyl-tRNA synthetases (ARS) are essential for protein translation. Both cytosolic ARS1-deficiencies and mitochondrial ARS2 deficiencies can cause severe diseases. Amino acid supplementation has shown to positively influence the clinical course of four individuals with cytosolic ARS1 deficiencies. We hypothesize that this intervention could also benefit individuals with mitochondrial ARS2 deficiencies. METHODS This study was designed as a N-of-1 trial. Daily oral L-phenylalanine supplementation was used in a 3-year-old girl with FARS2 deficiency. A period without supplementation was implemented to discriminate the effects of treatment from age-related developments and continuing physiotherapy. Treatment effects were measured through a physiotherapeutic testing battery, including movement assessment battery for children, dynamic gait index, gross motor function measure 66, and quality of life questionnaires. RESULTS The individual showed clear improvement in all areas tested, especially in gross motor skills, movement abilities, and postural stability. In the period without supplementation, she lost newly acquired motor skills but regained these upon restarting supplementation. No adverse effects and good tolerance of treatment were observed. INTERPRETATION AND CONCLUSION Our positive results encourage further studies both on L-phenylalanine for other individuals with FARS2 deficiency and the exploration of this treatment rationale for other ARS2 deficiencies. Additionally, treatment costs were relatively low at 1.10 €/day.
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Affiliation(s)
- Susanne L Oswald
- University Children's Hospital, Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Katja Steinbrücker
- University Children's Hospital, Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Melanie T Achleitner
- University Children's Hospital, Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | | | - Reginald E Bittner
- Neuromuscular Research Department, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang M Schmidt
- Neuromuscular Research Department, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Elke Tiefenthaler
- University Children's Hospital, Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Emma Hammerl
- University Children's Hospital, Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Anna Eisl
- University Children's Hospital, Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Doris Mayr
- University Children's Hospital, Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Johannes A Mayr
- University Children's Hospital, Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Saskia B Wortmann
- University Children's Hospital, Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
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Han Z, Wang X, Wu Z, Li C. Study of the Allosteric Mechanism of Human Mitochondrial Phenylalanyl-tRNA Synthetase by Transfer Entropy via an Improved Gaussian Network Model and Co-evolution Analyses. J Phys Chem Lett 2023; 14:3452-3460. [PMID: 37010935 DOI: 10.1021/acs.jpclett.3c00366] [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: 06/19/2023]
Abstract
We propose an improved transfer entropy approach called the dynamic version of the force constant fitted Gaussian network model based on molecular dynamics ensemble (dfcfGNMMD) to explore the allosteric mechanism of human mitochondrial phenylalanyl-tRNA synthetase (hmPheRS), one of the aminoacyl-tRNA synthetases that play a crucial role in translation of the genetic code. The dfcfGNMMD method can provide reliable estimates of the transfer entropy and give new insights into the role of the anticodon binding domain in driving the catalytic domain in aminoacylation activity and into the effects of tRNA binding and residue mutation on the enzyme activity, revealing the causal mechanism of the allosteric communication in hmPheRS. In addition, we incorporate the residue dynamic and co-evolutionary information to further investigate the key residues in hmPheRS allostery. This study sheds light on the mechanisms of hmPheRS allostery and can provide important information for related drug design.
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Affiliation(s)
- Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Xiaoli Wang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Zhixiang Wu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
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Mo L, Li R, He C, Chen Q, Xu C, Shen L, Chen K, Wu Y. Hedgehog pathway is negatively regulated during the development of Drosophila melanogaster PheRS-m (Drosophila homologs gene of human FARS2) mutants. Hum Cell 2023; 36:121-131. [PMID: 36205831 DOI: 10.1007/s13577-022-00796-0] [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: 07/20/2022] [Accepted: 09/17/2022] [Indexed: 01/20/2023]
Abstract
Hereditary spastic paraplegia (HSP) is a neurodegeneration disease, one of the reasons is caused by autosomal recessive missense mutation of the karyogene that encodes phenylalanyl-tRNA synthetase 2, mitochondrial (FARS2). However, the molecular mechanism underlying FARS2-mediated HSP progression is unknown. Mitochondrial phenylalanyl-tRNA synthetase gene (PheRS-m) is the Drosophila melanogaster homolog gene of human FARS2. This study constructed a Drosophila HSP missense mutation model and a PheRS-m knockout model. Some of the mutant fly phenotypes included developmental delay, shortened lifespan, wing-structure abnormalities and decreased mobility. RNA-sequencing results revealed a relationship between abnormal phenotypes and the hedgehog (Hh) pathway. A qRT-PCR assay was used to determine the key genes (ptc, hib, and slmb) of the Hh pathway that exhibited increased expression during different developmental stages. We demonstrated that Hh signaling transduction is negatively regulated during the developmental stages of PheRS-m mutants but positively regulated during adulthood. By inducing the agonist and inhibitor of Hh pathway in PheRS-m larvae, the developmental delay in mutants can be partly salvaged or postponed. Collectively, our findings indicate that Hh signaling negatively regulates the development of PheRS-m mutants, subsequently leading to developmental delay.
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Affiliation(s)
- Lidangzhi Mo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
- Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Rui Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
- Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Chunxia He
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Qi Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
- Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Changwei Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
- Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Liangliang Shen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.
- Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.
| | - Kun Chen
- Department of Anatomy, Histology and Embryology and K.K. Leung Brain Research Centre, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.
| | - Yuanming Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.
- Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.
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9
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Ho MT, Lu J, Vazquez-Pianzola P, Suter B. α-Phenylalanyl tRNA synthetase competes with Notch signaling through its N-terminal domain. PLoS Genet 2022; 18:e1010185. [PMID: 35486661 PMCID: PMC9094542 DOI: 10.1371/journal.pgen.1010185] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 05/11/2022] [Accepted: 04/04/2022] [Indexed: 02/07/2023] Open
Abstract
The alpha subunit of the cytoplasmic Phenylalanyl tRNA synthetase (α-PheRS, FARSA in humans) displays cell growth and proliferation activities and its elevated levels can induce cell fate changes and tumor-like phenotypes that are neither dependent on the canonical function of charging tRNAPhe with phenylalanine nor on stimulating general translation. In intestinal stem cells of Drosophila midguts, α-PheRS levels are naturally slightly elevated and human FARSA mRNA levels are elevated in multiple cancers. In the Drosophila midgut model, elevated α-PheRS levels caused the accumulation of many additional proliferating cells resembling intestinal stem cells (ISCs) and enteroblasts (EBs). This phenotype partially resembles the tumor-like phenotype described as Notch RNAi phenotype for the same cells. Genetic interactions between α-PheRS and Notch suggest that their activities neutralize each other and that elevated α-PheRS levels attenuate Notch signaling when Notch induces differentiation into enterocytes, type II neuroblast stem cell proliferation, or transcription of a Notch reporter. These non-canonical functions all map to the N-terminal part of α-PheRS which accumulates naturally in the intestine. This truncated version of α-PheRS (α-S) also localizes to nuclei and displays weak sequence similarity to the Notch intracellular domain (NICD), suggesting that α-S might compete with the NICD for binding to a common target. Supporting this hypothesis, the tryptophan (W) residue reported to be key for the interaction between the NICD and the Su(H) BTD domain is not only conserved in α-PheRS and α-S, but also essential for attenuating Notch signaling. Aminoacyl tRNA synthetases charge tRNAs with their cognate amino acid to ensure proper decoding of the genetic code during translation. Independent of its aminoacylation function, the alpha subunit of Drosophila cytoplasmic Phenylalanyl tRNA synthetase (α-PheRS, FARSA in humans) has an additional activity that promotes growth and proliferation. Here we describe that elevated α-PheRS levels also induce cell fate changes and tumorous phenotypes in Drosophila midguts. Excessive proliferating cells with stem and progenitor cell characteristics accumulate and the composition of the terminally differentiated cells changes, too. This phenotype together with observed genetic interactions between α-PheRS and Notch levels show that α-PheRS counteracts Notch signaling in many different tissues and developmental stages. This novel activity of α-PheRS maps to its N-terminal part, which is naturally produced. The fragment contains a DNA binding domain, translocates into nuclei, and displays essential similarities to a Notch domain that binds to the downstream transcription factor. This suggests that it might be competing with Notch for binding to a common target. Not only because Notch plays important roles in many tumors, but also because FARSA mRNA levels are considerably upregulated in many tumors, this novel activity deserves more attention for cancer research.
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Affiliation(s)
- Manh Tin Ho
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Jiongming Lu
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | | | - Beat Suter
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- * E-mail:
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10
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Roux CJ, Barcia G, Schiff M, Sissler M, Levy R, Dangouloff-Ros V, Desguerre I, Edvardson S, Elpeleg O, Rötig A, Munnich A, Boddaert N. Phenotypic diversity of brain MRI patterns in mitochondrial aminoacyl-tRNA synthetase mutations. Mol Genet Metab 2021; 133:222-229. [PMID: 33972171 DOI: 10.1016/j.ymgme.2021.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 11/23/2020] [Revised: 02/15/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND PURPOSE Mitochondrial aminoacyl-tRNA synthetases-encoded by ARS2 genes-are evolutionarily conserved enzymes that catalyse the attachment of amino acids to their cognate tRNAs, ensuring the accuracy of the mitochondrial translation process. ARS2 gene mutations are associated with a wide range of clinical presentations affecting the CNS. METHODS Two senior neuroradiologists analysed brain MRI of 25 patients (age range: 3 d-25 yrs.; 11 males; 14 females) with biallelic pathogenic variants of 11 ARS2 genes in a retrospective study conducted between 2002 and 2019. RESULTS Though several combinations of brain MRI anomalies were highly suggestive of specific aetiologies (DARS2, EARS2, AARS2 and RARS2 mutations), our study detected no MRI pattern common to all patients. Stroke-like lesions were associated with pathogenic SARS2 and FARS2 variants. We also report early onset cerebellar atrophy and calcifications in AARS2 mutations, early white matter involvement in RARS2 mutations, and absent involvement of thalami in EARS2 mutations. Finally, our findings show that normal brain MRI results do not exclude the presence of ARS2 mutations: 5 patients with normal MRI images were carriers of pathogenic IARS2, YARS2, and FARS2 variants. CONCLUSION Our study extends the spectrum of brain MRI anomalies associated with pathogenic ARS2 variants and suggests ARS2 mutations are largely underdiagnosed.
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Affiliation(s)
- Charles-Joris Roux
- Department of Paediatric Radiology, Hôpital Necker-Enfants Malades, Paris, France.
| | - Giulia Barcia
- Department of Genetics, Hospital Necker-Enfants Malades, Paris, France
| | - Manuel Schiff
- Institut Imagine, INSERM UMR 1163, Paris, France; Necker Hospital, APHP, Reference Center for Inborn Error of Metabolism, Pediatrics Department, University of Paris, Paris, France
| | - Marie Sissler
- Institut Européen de Chimie et Biologie, INSERM U1212, CNRS UMR 5320, University of Bordeaux, Pessac, France
| | - Raphaël Levy
- Department of Paediatric Radiology, Hôpital Necker-Enfants Malades, Paris, France
| | | | - Isabelle Desguerre
- Department of Neurology and Metabolism, Hôpital Necker-Enfants Malades, Paris, France
| | - Shimon Edvardson
- Department of Genetics, Hadassah University Hospital, Jerusalem, Israel
| | - Orli Elpeleg
- Department of Genetics, Hadassah University Hospital, Jerusalem, Israel
| | - Agnès Rötig
- Institut Imagine, INSERM UMR 1163, Paris, France
| | - Arnold Munnich
- Department of Genetics, Hospital Necker-Enfants Malades, Paris, France; Institut Imagine, INSERM UMR 1163, Paris, France
| | - Nathalie Boddaert
- Department of Paediatric Radiology, Hôpital Necker-Enfants Malades, Paris, France; Institut Imagine, INSERM UMR 1163, Paris, France
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11
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Aburaya S, Yamauchi Y, Hashimoto T, Minakuchi H, Aoki W, Ueda M. Neuronal subclass-selective proteomic analysis in Caenorhabditis elegans. Sci Rep 2020; 10:13840. [PMID: 32792517 PMCID: PMC7426821 DOI: 10.1038/s41598-020-70692-w] [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: 04/27/2020] [Accepted: 08/03/2020] [Indexed: 12/24/2022] Open
Abstract
Neurons are categorised into many subclasses, and each subclass displays different morphology, expression patterns, connectivity and function. Changes in protein synthesis are critical for neuronal function. Therefore, analysing protein expression patterns in individual neuronal subclass will elucidate molecular mechanisms for memory and other functions. In this study, we used neuronal subclass-selective proteomic analysis with cell-selective bio-orthogonal non-canonical amino acid tagging. We selected Caenorhabditis elegans as a model organism because it shows diverse neuronal functions and simple neural circuitry. We performed proteomic analysis of all neurons or AFD subclass neurons that regulate thermotaxis in C. elegans. Mutant phenylalanyl tRNA synthetase (MuPheRS) was selectively expressed in all neurons or AFD subclass neurons, and azido-phenylalanine was incorporated into proteins in cells of interest. Azide-labelled proteins were enriched and proteomic analysis was performed. We identified 4,412 and 1,834 proteins from strains producing MuPheRS in all neurons and AFD subclass neurons, respectively. F23B2.10 (RING-type domain-containing protein) was identified only in neuronal cell-enriched proteomic analysis. We expressed GFP under the control of the 5' regulatory region of F23B2.10 and found GFP expression in neurons. We expect that more single-neuron specific proteomic data will clarify how protein composition and abundance affect characteristics of neuronal subclasses.
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Affiliation(s)
- Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Japan Society for the Promotion of Science, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yuji Yamauchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takashi Hashimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | | | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
- JST, Precursory Research for Embryonic Science and Technology (PREST), 7 Goban-cho, Chiyoda-ku, Tokyo, 102-0076, Japan.
- JST, Core Research for Evolutionary Science and Technology (CREST), 7 Goban-cho, Chiyoda-ku, Tokyo, 102-0076, Japan.
- Kyoto Integrated Science and Technology Bio-Analysis Center, 134 Chudoji Minamimachi, Simogyo-ku, Kyoto, 600-8813, Japan.
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- JST, Core Research for Evolutionary Science and Technology (CREST), 7 Goban-cho, Chiyoda-ku, Tokyo, 102-0076, Japan
- Kyoto Integrated Science and Technology Bio-Analysis Center, 134 Chudoji Minamimachi, Simogyo-ku, Kyoto, 600-8813, Japan
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12
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Teramoto H, Iga M, Tsuboi H, Nakajima K. Characterization and Scaled-Up Production of Azido-Functionalized Silk Fiber Produced by Transgenic Silkworms with an Expanded Genetic Code. Int J Mol Sci 2019; 20:E616. [PMID: 30708986 PMCID: PMC6387213 DOI: 10.3390/ijms20030616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 12/21/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 11/17/2022] Open
Abstract
The creation of functional materials from renewable resources has attracted much interest. We previously reported on the genetic code expansion of the domesticated silkworm Bombyx mori to functionalize silk fiber with synthetic amino acids such as 4-azido-L-phenylalanine (AzPhe). The azido groups act as selective handles for biorthogonal chemical reactions. Here we report the characterization and scaled-up production of azido-functionalized silk fiber for textile, healthcare, and medical applications. To increase the productivity of azido-functionalized silk fiber, the original transgenic line was hybridized with a high silk-producing strain. The F₁ hybrid produced circa 1.5 times more silk fibroin than the original transgenic line. The incorporation efficiency of AzPhe into silk fibroin was retained after hybridization. The tensile properties of the azido-functionalized silk fiber were equal to those of normal silk fiber. Scaled-up production of the azido-functionalized silk fiber was demonstrated by rearing circa 1000 transgenic silkworms. Differently-colored fluorescent silk fibers were successfully prepared by click chemistry reactions, demonstrating the utility of the azido-functionalized silk fiber for developing silk-based materials with desired functions.
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Affiliation(s)
- Hidetoshi Teramoto
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Ibaraki 305-8518, Japan.
| | - Masatoshi Iga
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Ibaraki 305-8518, Japan.
| | - Hiromi Tsuboi
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Ibaraki 305-8518, Japan.
| | - Kenichi Nakajima
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Ibaraki 305-8518, Japan.
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13
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Almannai M, Wang J, Dai H, El-Hattab AW, Faqeih EA, Saleh MA, Al Asmari A, Alwadei AH, Aljadhai YI, AlHashem A, Tabarki B, Lines MA, Grange DK, Benini R, Alsaman AS, Mahmoud A, Katsonis P, Lichtarge O, Wong LJC. FARS2 deficiency; new cases, review of clinical, biochemical, and molecular spectra, and variants interpretation based on structural, functional, and evolutionary significance. Mol Genet Metab 2018; 125:281-291. [PMID: 30177229 DOI: 10.1016/j.ymgme.2018.07.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 02/07/2023]
Abstract
An increasing number of mitochondrial diseases are found to be caused by pathogenic variants in nuclear encoded mitochondrial aminoacyl-tRNA synthetases. FARS2 encodes mitochondrial phenylalanyl-tRNA synthetase (mtPheRS) which transfers phenylalanine to its cognate tRNA in mitochondria. Since the first case was reported in 2012, a total of 21 subjects with FARS2 deficiency have been reported to date with a spectrum of disease severity that falls between two phenotypes; early onset epileptic encephalopathy and a less severe phenotype characterized by spastic paraplegia. In this report, we present an additional 15 individuals from 12 families who are mostly Arabs homozygous for the pathogenic variant Y144C, which is associated with the more severe early onset phenotype. The total number of unique pathogenic FARS2 variants known to date is 21 including three different partial gene deletions reported in four individuals. Except for the large deletions, all variants but two (one in-frame deletion of one amino acid and one splice-site variant) are missense. All large deletions and the single splice-site variant are in trans with a missense variant. This suggests that complete loss of function may be incompatible with life. In this report, we also review structural, functional, and evolutionary significance of select FARS2 pathogenic variants reported here.
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Affiliation(s)
- Mohammed Almannai
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Julia Wang
- Medical Scientist Training Program and Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatric Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Eissa A Faqeih
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Mohammed A Saleh
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Al Asmari
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali H Alwadei
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Yaser I Aljadhai
- Department of Neuroimaging and Intervention, Medical Imaging Administration, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Amal AlHashem
- Department of Pediatric, Prince Sultan Medical Military City, Riyadh, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Brahim Tabarki
- Divisions of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Matthew A Lines
- Division of Metabolics and Newborn Screening, Children's Hospital of Eastern Ontario, Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Dorothy K Grange
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ruba Benini
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Abdulaziz S Alsaman
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Adel Mahmoud
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lee-Jun C Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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14
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Vantroys E, Larson A, Friederich M, Knight K, Swanson MA, Powell CA, Smet J, Vergult S, De Paepe B, Seneca S, Roeyers H, Menten B, Minczuk M, Vanlander A, Van Hove J, Van Coster R. New insights into the phenotype of FARS2 deficiency. Mol Genet Metab 2017; 122:172-181. [PMID: 29126765 PMCID: PMC5734183 DOI: 10.1016/j.ymgme.2017.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/12/2022]
Abstract
Mutations in FARS2 are known to cause dysfunction of mitochondrial translation due to deficient aminoacylation of the mitochondrial phenylalanine tRNA. Here, we report three novel mutations in FARS2 found in two patients in a compound heterozygous state. The missense mutation c.1082C>T (p.Pro361Leu) was detected in both patients. The mutations c.461C>T (p.Ala154Val) and c.521_523delTGG (p.Val174del) were each detected in one patient. We report abnormal in vitro aminoacylation assays as a functional validation of the molecular genetic findings. Based on the phenotypic data of previously reported subjects and the two subjects reported here, we conclude that FARS2 deficiency can be associated with two phenotypes: (i) an epileptic phenotype, and (ii) a spastic paraplegia phenotype.
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Affiliation(s)
- Elise Vantroys
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Austin Larson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Marisa Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kaz Knight
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Michael A Swanson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Christopher A Powell
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Joél Smet
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Boel De Paepe
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Sara Seneca
- Center for Medical Genetics, UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Herbert Roeyers
- Department of Experimental Clinical and Health Psychology, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Arnaud Vanlander
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Johan Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rudy Van Coster
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium.
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15
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Kwon I, Choi ES. Forced Ambiguity of the Leucine Codons for Multiple-Site-Specific Incorporation of a Noncanonical Amino Acid. PLoS One 2016; 11:e0152826. [PMID: 27028506 PMCID: PMC4814082 DOI: 10.1371/journal.pone.0152826] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 11/02/2015] [Accepted: 03/03/2016] [Indexed: 11/24/2022] Open
Abstract
Multiple-site-specific incorporation of a noncanonical amino acid into a recombinant protein would be a very useful technique to generate multiple chemical handles for bioconjugation and multivalent binding sites for the enhanced interaction. Previously combination of a mutant yeast phenylalanyl-tRNA synthetase variant and the yeast phenylalanyl-tRNA containing the AAA anticodon was used to incorporate a noncanonical amino acid into multiple UUU phenylalanine (Phe) codons in a site-specific manner. However, due to the less selective codon recognition of the AAA anticodon, there was significant misincorporation of a noncanonical amino acid into unwanted UUC Phe codons. To enhance codon selectivity, we explored degenerate leucine (Leu) codons instead of Phe degenerate codons. Combined use of the mutant yeast phenylalanyl-tRNA containing the CAA anticodon and the yPheRS_naph variant allowed incorporation of a phenylalanine analog, 2-naphthylalanine, into murine dihydrofolate reductase in response to multiple UUG Leu codons, but not to other Leu codon sites. Despite the moderate UUG codon occupancy by 2-naphthylalaine, these results successfully demonstrated that the concept of forced ambiguity of the genetic code can be achieved for the Leu codons, available for multiple-site-specific incorporation.
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Affiliation(s)
- Inchan Kwon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
| | - Eun Sil Choi
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea
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16
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Bullwinkle TJ, Reynolds NM, Raina M, Moghal A, Matsa E, Rajkovic A, Kayadibi H, Fazlollahi F, Ryan C, Howitz N, Faull KF, Lazazzera BA, Ibba M. Oxidation of cellular amino acid pools leads to cytotoxic mistranslation of the genetic code. eLife 2014. [PMID: 24891238 DOI: 10.7554/elife.02501.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 02/07/2023] Open
Abstract
Aminoacyl-tRNA synthetases use a variety of mechanisms to ensure fidelity of the genetic code and ultimately select the correct amino acids to be used in protein synthesis. The physiological necessity of these quality control mechanisms in different environments remains unclear, as the cost vs benefit of accurate protein synthesis is difficult to predict. We show that in Escherichia coli, a non-coded amino acid produced through oxidative damage is a significant threat to the accuracy of protein synthesis and must be cleared by phenylalanine-tRNA synthetase in order to prevent cellular toxicity caused by mis-synthesized proteins. These findings demonstrate how stress can lead to the accumulation of non-canonical amino acids that must be excluded from the proteome in order to maintain cellular viability.
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Affiliation(s)
- Tammy J Bullwinkle
- Department of Microbiology, Ohio State University, Columbus, United States
| | - Noah M Reynolds
- Department of Microbiology, Ohio State University, Columbus, United States
| | - Medha Raina
- Center for RNA Biology, Ohio State University, Columbus, United States
| | - Adil Moghal
- Center for RNA Biology, Ohio State University, Columbus, United States
| | - Eleftheria Matsa
- Department of Microbiology, Ohio State University, Columbus, United States
| | - Andrei Rajkovic
- Center for RNA Biology, Ohio State University, Columbus, United States
| | - Huseyin Kayadibi
- Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, United States
| | - Farbod Fazlollahi
- Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, United States
| | - Christopher Ryan
- Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, United States
| | - Nathaniel Howitz
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Kym F Faull
- Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, United States
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, United States
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17
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Senter E, Sheikh S, Dotu I, Ponty Y, Clote P. Using the fast fourier transform to accelerate the computational search for RNA conformational switches. PLoS One 2012; 7:e50506. [PMID: 23284639 PMCID: PMC3526635 DOI: 10.1371/journal.pone.0050506] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 10/26/2012] [Indexed: 01/12/2023] Open
Abstract
Using complex roots of unity and the Fast Fourier Transform, we design a new thermodynamics-based algorithm, FFTbor, that computes the Boltzmann probability that secondary structures differ by base pairs from an arbitrary initial structure of a given RNA sequence. The algorithm, which runs in quartic time and quadratic space , is used to determine the correlation between kinetic folding speed and the ruggedness of the energy landscape, and to predict the location of riboswitch expression platform candidates. A web server is available at http://bioinformatics.bc.edu/clotelab/FFTbor/.
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Affiliation(s)
- Evan Senter
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Saad Sheikh
- Computer Science Department, University of Florida, Gainesville, Florida, United States of America
| | - Ivan Dotu
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Yann Ponty
- Laboratoire d'Informatique, Ecole Polytechnique, Palaiseau, France
| | - Peter Clote
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail:
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18
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Yao Y, Gao G, Li D. [Cloning, expression, purification and activity assay of Trypanosoma brucei phenylalanyl-tRNA synthetase in Escherichia coli]. Sheng Wu Gong Cheng Xue Bao 2010; 26:130-135. [PMID: 20353103] [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] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Phenylalany--tRNA synthetase is a key enzyme for protein synthesis in Trypanosoma. Its validation as an inhibition. target will enable the development of a new generation of anti-Trypanosoma drugs. However, little is known about the isolation of the Trypanosoma Phenylalanyl-tRNA synthetase. Here we report the cloning, expression, purification, and activity assay of Phenylalanyl-tRNA synthetase from Trypanosoma brucei in Escherichia coli host. We co-cloned the alpha-subunit and beta-subunit of Phenylalanyl-tRNA synthetase from Trypanosoma brucei genomic DNA into the co-expression vector pCOLADuet. We successfully expressed the Trypanosoma brucei Phenylalanyl-tRNA synthetase in E. coli host, purified the whole enzyme by Ni-Hind affinity column and verified it by Western blotting. In addition, we tested its enzymatic activity by isotope labeling. The whole work laid a solid foundation for in vitro the screening and optimization of Trypanosoma brucei phenylalanyl-tRNA synthetase inhibitors.
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Affiliation(s)
- Ying Yao
- School of Pharmacy, Shanghai Jiaotong University, Shanghai 200240, China
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19
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Barrett AR, Kang Y, Inamasu KS, Son MS, Vukovich JM, Hoang TT. Genetic tools for allelic replacement in Burkholderia species. Appl Environ Microbiol 2008; 74:4498-508. [PMID: 18502918 PMCID: PMC2493169 DOI: 10.1128/aem.00531-08] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [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: 03/04/2008] [Accepted: 05/13/2008] [Indexed: 11/20/2022] Open
Abstract
Allelic replacement in the Burkholderia genus has been problematic due to the lack of appropriate counter-selectable and selectable markers. The counter-selectable marker sacB, commonly used in gram-negative bacteria, is nonselective on sucrose in many Burkholderia species. In addition, the use of antibiotic resistance markers of clinical importance for the selection of desirable genetic traits is prohibited in the United States for two potential bioterrorism agents, Burkholderia mallei and Burkholderia pseudomallei. Here, we engineered a mutated counter-selectable marker based on the B. pseudomallei PheS (the alpha-subunit of phenylalanyl tRNA synthase) protein and tested its effectiveness in three different Burkholderia species. The mutant PheS protein effectively killed 100% of the bacteria in the presence of 0.1% p-chlorophenylalanine. We assembled the mutant pheS on several allelic replacement vectors, in addition to constructing selectable markers based on tellurite (Tel(r)) and trimethoprim (Tp(r)) resistance that are excisable by flanking unique FLP recombination target (FRT) sequences. As a proof of concept, we utilized one of these gene replacement vectors (pBAKA) and the Tel(r)-FRT cassette to produce a chromosomal mutation in the Burkholderia thailandensis betBA operon, which codes for betaine aldehyde dehydrogenase and choline dehydrogenase. Chromosomal resistance markers could be excised by the introduction of pFLP-AB5 (Tp(r)), which is one of two constructed flp-containing plasmids, pFLP-AB4 (Tel(r)) and pFLP-AB5 (Tp(r)). These flp-containing plasmids harbor the mutant pheS gene and allow self curing on media that contain p-chlorophenylalanine after Flp-FRT excision. The characterization of the Delta betBA::Tel(r)-FRT and Delta betBA::FRT mutants indicated a defect in growth with choline as a sole carbon source, while these mutants grew as well as the wild type with succinate and glucose as alternative carbon sources.
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Affiliation(s)
- Ashley R Barrett
- Department of Microbiology, College of Natural Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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20
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Scheirlinck I, Van der Meulen R, Van Schoor A, Vancanneyt M, De Vuyst L, Vandamme P, Huys G. Influence of geographical origin and flour type on diversity of lactic acid bacteria in traditional Belgian sourdoughs. Appl Environ Microbiol 2007; 73:6262-9. [PMID: 17675431 PMCID: PMC2075033 DOI: 10.1128/aem.00894-07] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [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: 11/20/2022] Open
Abstract
A culture-based approach was used to investigate the diversity of lactic acid bacteria (LAB) in Belgian traditional sourdoughs and to assess the influence of flour type, bakery environment, geographical origin, and technological characteristics on the taxonomic composition of these LAB communities. For this purpose, a total of 714 LAB from 21 sourdoughs sampled at 11 artisan bakeries throughout Belgium were subjected to a polyphasic identification approach. The microbial composition of the traditional sourdoughs was characterized by bacteriological culture in combination with genotypic identification methods, including repetitive element sequence-based PCR fingerprinting and phenylalanyl-tRNA synthase (pheS) gene sequence analysis. LAB from Belgian sourdoughs belonged to the genera Lactobacillus, Pediococcus, Leuconostoc, Weissella, and Enterococcus, with the heterofermentative species Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus plantarum, and Lactobacillus pontis as the most frequently isolated taxa. Statistical analysis of the identification data indicated that the microbial composition of the sourdoughs is mainly affected by the bakery environment rather than the flour type (wheat, rye, spelt, or a mixture of these) used. In conclusion, the polyphasic approach, based on rapid genotypic screening and high-resolution, sequence-dependent identification, proved to be a powerful tool for studying the LAB diversity in traditional fermented foods such as sourdough.
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Affiliation(s)
- Ilse Scheirlinck
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
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21
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Scheirlinck I, Van der Meulen R, Van Schoor A, Huys G, Vandamme P, De Vuyst L, Vancanneyt M. Lactobacillus crustorum sp. nov., isolated from two traditional Belgian wheat sourdoughs. Int J Syst Evol Microbiol 2007; 57:1461-1467. [PMID: 17625176 DOI: 10.1099/ijs.0.64836-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [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: 11/18/2022] Open
Abstract
A polyphasic taxonomic study of the lactic acid bacteria (LAB) population in three traditional Belgian sourdoughs, sampled between 2002 and 2004, revealed a group of isolates that could not be assigned to any recognized LAB species. Initially, sourdough isolates were screened by means of (GTG)5-PCR fingerprinting. Four isolates displaying unique (GTG)5-PCR patterns were further investigated by means of phenylalanyl-tRNA synthase (pheS) gene sequence analysis and represented a bifurcated branch that could not be allocated to any LAB species present in the in-house pheS database. Their phylogenetic affiliation was determined using 16S rRNA gene sequence analysis and showed that the four sourdough isolates belong to the Lactobacillus plantarum group with Lactobacillus mindensis, Lactobacillus farciminis and Lactobacillus nantensis as closest relatives. Further genotypic and phenotypic studies, including whole-cell protein analysis (SDS-PAGE), amplified fragment length polymorphism (AFLP) fingerprinting, DNA–DNA hybridization, DNA G+C content analysis, growth characteristics and biochemical features, demonstrated that the new sourdough isolates represent a novel Lactobacillus species for which the name Lactobacillus crustorum sp. nov. is proposed. The type strain of the new species is LMG 23699T (=CCUG 53174T).
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MESH Headings
- Bacterial Proteins/analysis
- Bacterial Proteins/genetics
- Bacterial Typing Techniques
- Base Composition
- Belgium
- Bread/microbiology
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Polyacrylamide Gel
- Genes, rRNA
- Genotype
- Lactobacillus/chemistry
- Lactobacillus/classification
- Lactobacillus/genetics
- Lactobacillus/isolation & purification
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phenylalanine-tRNA Ligase/genetics
- Phylogeny
- Polymerase Chain Reaction/methods
- Proteome/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Ilse Scheirlinck
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Roel Van der Meulen
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Ann Van Schoor
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Geert Huys
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Marc Vancanneyt
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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22
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Scheirlinck I, Van der Meulen R, Van Schoor A, Cleenwerck I, Huys G, Vandamme P, De Vuyst L, Vancanneyt M. Lactobacillus namurensis sp. nov., isolated from a traditional Belgian sourdough. Int J Syst Evol Microbiol 2007; 57:223-227. [PMID: 17267954 DOI: 10.1099/ijs.0.64607-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [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: 11/18/2022] Open
Abstract
A biodiversity study on lactic acid bacteria (LAB) occurring in traditional Belgian sourdoughs resulted in the isolation of two Lactobacillus isolates, LMG 23583T and LMG 23584, that could not be assigned to any recognized LAB species. The two isolates were initially investigated by means of phenylalanyl-tRNA synthase (pheS) gene sequence analysis and were found to occupy a separate position relative to recognized Lactobacillus species present in the pheS database. Subsequently, their phylogenetic affiliation was determined by 16S rRNA gene sequence analysis, indicating that the two isolates belong to the Lactobacillus buchneri species group with Lactobacillus zymae, Lactobacillus acidifarinae and Lactobacillus spicheri as closest relatives. Whole-cell protein analysis (SDS-PAGE) and amplified fragment length polymorphism fingerprinting of whole genomes confirmed their separate taxonomic status. DNA–DNA hybridization experiments, DNA G+C content, growth characteristics and biochemical features demonstrated that the two isolates represent a novel Lactobacillus species, for which the name Lactobacillus namurensis sp. nov. is proposed. The type strain is LMG 23583T (=CCUG 52843T).
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MESH Headings
- Bacterial Proteins/analysis
- Bacterial Typing Techniques
- Base Composition
- Belgium
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Polyacrylamide Gel
- Flour/microbiology
- Food Microbiology
- Genes, rRNA/genetics
- Lactobacillus/classification
- Lactobacillus/genetics
- Lactobacillus/isolation & purification
- Lactobacillus/physiology
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phenylalanine-tRNA Ligase/genetics
- Phylogeny
- Polymorphism, Restriction Fragment Length
- Proteome/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Ilse Scheirlinck
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Roel Van der Meulen
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Ann Van Schoor
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Geert Huys
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Marc Vancanneyt
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Naser SM, Vancanneyt M, Snauwaert C, Vrancken G, Hoste B, De Vuyst L, Swings J. Reclassification of Lactobacillus amylophilus LMG 11400 and NRRL B-4435 as Lactobacillus amylotrophicus sp. nov. Int J Syst Evol Microbiol 2006; 56:2523-2527. [PMID: 17082384 DOI: 10.1099/ijs.0.64463-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [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: 11/18/2022] Open
Abstract
The taxonomic position of six Lactobacillus amylophilus strains isolated from swine waste-corn fermentations was reinvestigated. All strains were included in a multilocus sequence analysis (MLSA) study for species identification of Lactobacillus using the genes encoding the phenylalanyl-tRNA synthase alpha subunit (pheS) and RNA polymerase alpha subunit (rpoA). Partial pheS and rpoA gene sequences showed that strains LMG 11400 and NRRL B-4435 represent a separate lineage that is distantly related to the type strain of L. amylophilus, LMG 6900T, and to three other strains of the species. The MLSA data showed that the two strains LMG 11400 and NRRL B-4435 constituted a distinct cluster, sharing 100 % pheS and rpoA gene sequence similarity. The other reference strains clustered together with the type strain of L. amylophilus, LMG 6900T, and were clearly differentiated from strains LMG 11400 and NRRL B-4435 (80 and 89 % pheS and rpoA gene sequence similarity, respectively). The 16S rRNA gene sequences of the latter two strains are 100 % identical, with the nearest phylogenetic neighbour L. amylophilus LMG 6900T showing only 97.2 % 16S rRNA gene sequence similarity. Further polyphasic taxonomic study based on whole-cell protein fingerprinting, DNA–DNA hybridization and biochemical features demonstrated that the two strains represent a single, novel Lactobacillus species, for which the name Lactobacillus amylotrophicus sp. nov. is proposed. The type strain is LMG 11400T (=NRRL B-4436T=DSM 20534T).
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MESH Headings
- Animal Husbandry
- Bacterial Proteins/genetics
- Bacterial Typing Techniques
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA-Directed RNA Polymerases/genetics
- Electrophoresis, Polyacrylamide Gel
- Genes, rRNA
- Industrial Waste
- Lactobacillus/classification
- Lactobacillus/cytology
- Lactobacillus/isolation & purification
- Lactobacillus/physiology
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phenylalanine-tRNA Ligase/genetics
- Phylogeny
- Protein Subunits/genetics
- Proteome/analysis
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Sabri M Naser
- BCCM™/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Marc Vancanneyt
- BCCM™/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Cindy Snauwaert
- BCCM™/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Gino Vrancken
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Bart Hoste
- BCCM™/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Jean Swings
- BCCM™/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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24
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Naser SM, Vancanneyt M, Hoste B, Snauwaert C, Swings J. Lactobacillus cypricasei Lawson et al. 2001 is a later heterotypic synonym of Lactobacillus acidipiscis Tanasupawat et al. 2000. Int J Syst Evol Microbiol 2006; 56:1681-1683. [PMID: 16825650 DOI: 10.1099/ijs.0.64229-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [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: 11/18/2022] Open
Abstract
The applicability of a multilocus sequence analysis (MLSA)-based identification system for lactobacilli was evaluated. Two housekeeping genes that code for the phenylalanyl-tRNA synthase alpha-subunit (pheS) and RNA polymerase alpha-subunit (rpoA) were sequenced and analysed for members of the Lactobacillus salivarius species group. The type strains of Lactobacillus acidipiscis and Lactobacillus cypricasei were investigated further using a third gene that encodes the alpha-subunit of ATP synthase (atpA). The MLSA data revealed close relatedness between L. acidipiscis and L. cypricasei, with 99.8-100 % pheS, rpoA and atpA gene sequence similarities. Comparison of the 16S rRNA gene sequences of the type strains of the two species confirmed the close relatedness (99.8 % gene sequence similarity) between the two taxa. Similar phenotypes and high DNA-DNA binding values in the range of 84 to 97.5 % confirmed that L. acidipiscis and L. cypricasei are synonymous species. On the basis of the present study, it is proposed that Lactobacillus cypricasei is a later heterotypic synonym of Lactobacillus acidipiscis.
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Affiliation(s)
- Sabri M Naser
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Marc Vancanneyt
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Bart Hoste
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Cindy Snauwaert
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Jean Swings
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
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25
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Roy H, Ibba M. Phenylalanyl-tRNA synthetase contains a dispensable RNA-binding domain that contributes to the editing of noncognate aminoacyl-tRNA. Biochemistry 2006; 45:9156-62. [PMID: 16866361 DOI: 10.1021/bi060549w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [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: 11/29/2022]
Abstract
Phenylalanyl-tRNA synthetase (PheRS) is a multidomain (alphabeta)2 heterotetrameric protein responsible for synthesizing Phe-tRNA(Phe) during protein synthesis. Previous studies showed that the alpha subunit forms the catalytic core of the enzyme, while the beta subunit contains a number of autonomous structural modules with a wide range of functions including tRNA anticodon binding and editing of the misaminoacylated species Tyr-tRNA(Phe). The B2 domain of the beta subunit is a structural homologue of the EMAPII/OB fold, which has been shown in other systems to contribute to tRNA binding. Structural studies of PheRS indicated that the B2 domain is distant from bound tRNA(Phe), leaving the role of this module in question. On the basis of homology modeling with other EMAPII domain-containing proteins, the 110 amino acid B2 domain was deleted to produce PheRS deltaB2. Full-length PheRS and PheRS deltaB2 showed comparable kinetics for in vitro aminoacylation, and both enzymes complemented a defect in phenylalanylation in vivo. PheRS deltaB2 showed a 2-fold drop compared to full-length PheRS in the catalytic efficiency (kcat/KM) of Tyr-tRNA(Phe) hydrolysis, suggesting a role for the B2 domain in post-transfer editing. A comparison of tRNA binding by full-length PheRS and PheRS deltaB2 indicated that the B2 domain acts as a secondary tRNA-binding site that could contribute to editing by promoting the translocation of mischarged tRNA to the editing site of PheRS. This proposed role for the B2 domain of PheRS is consistent with previous studies, suggesting that the highly conserved EMAPII fold is able to modulate the affinity of tRNA for its primary binding site.
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MESH Headings
- Amino Acid Sequence
- Binding Sites/physiology
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phenylalanine/metabolism
- Phenylalanine-tRNA Ligase/chemistry
- Phenylalanine-tRNA Ligase/genetics
- Phenylalanine-tRNA Ligase/metabolism
- Protein Folding
- Protein Structure, Tertiary
- RNA Editing/genetics
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Tyr/genetics
- RNA, Transfer, Tyr/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Thermus thermophilus/enzymology
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Affiliation(s)
- Hervé Roy
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
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26
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Vancanneyt M, Naser SM, Engelbeen K, De Wachter M, Van der Meulen R, Cleenwerck I, Hoste B, De Vuyst L, Swings J. Reclassification of Lactobacillus brevis strains LMG 11494 and LMG 11984 as Lactobacillus parabrevis sp. nov. Int J Syst Evol Microbiol 2006; 56:1553-1557. [PMID: 16825629 DOI: 10.1099/ijs.0.64215-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [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: 11/18/2022] Open
Abstract
A polyphasic study revealed taxonomic heterogeneity among reference strains of the species Lactobacillus brevis. Representative strains of L. brevis and related taxa were investigated by partial sequence analysis of the housekeeping gene encoding the alpha-subunit of phenylalanyl-tRNA synthase (pheS). Species-specific clusters were delineated for all taxa studied except for two L. brevis strains, LMG 11494 and LMG 11984, respectively isolated from cheese and wheat, which occupied a distinct position. Their phylogenetic affiliation was determined using 16S rRNA gene sequence analysis and it was found that both strains (with 99.9 % gene sequence similarity between them) belonged to the Lactobacillus buchneri group, with nearest neighbours Lactobacillus hammesii and L. brevis (gene sequence similarities of 99.2 and 98.1 %, respectively). Further genotypic and phenotypic studies, including fluorescent amplified fragment length polymorphism, DNA–DNA hybridization and DNA G+C content, clearly demonstrated that the two strains represent a single novel taxon for which the name Lactobacillus parabrevis sp. nov. is proposed (type strain LMG 11984T=ATCC 53295T).
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Affiliation(s)
- Marc Vancanneyt
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Sabri M Naser
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Katrien Engelbeen
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Marjan De Wachter
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Roel Van der Meulen
- Research Group of Industrial Microbiology, Fermentation Technology and Downstream Processing (IMDO), Department of Applied Biological Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Bart Hoste
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology, Fermentation Technology and Downstream Processing (IMDO), Department of Applied Biological Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Jean Swings
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Kotik-Kogan O, Moor N, Tworowski D, Safro M. Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase. Structure 2006; 13:1799-807. [PMID: 16338408 DOI: 10.1016/j.str.2005.08.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 08/17/2005] [Accepted: 08/18/2005] [Indexed: 11/18/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) exert control over the faithful transfer of amino acids onto cognate tRNAs. Since chemical structures of various amino acids closely resemble each other, it is difficult to discriminate between them. Editing activity has been evolved by certain aaRSs to resolve the problem. In this study, we determined the crystal structures of complexes of T. thermophilus phenylalanyl-tRNA synthetase (PheRS) with L-tyrosine, p-chloro-phenylalanine, and a nonhydrolyzable tyrosyl-adenylate analog. The structures demonstrate plasticity of the synthetic site capable of binding substrates larger than phenylalanine and provide a structural basis for the proofreading mechanism. The editing site is localized at the B3/B4 interface, 35 A from the synthetic site. Glubeta334 plays a crucial role in the specific recognition of the Tyr moiety in the editing site. The tyrosyl-adenylate analog binds exclusively in the synthetic site. Both structural data and tyrosine-dependent ATP hydrolysis enhanced by tRNA(Phe) provide evidence for a preferential posttransfer editing pathway in the phenylalanine-specific system.
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Affiliation(s)
- Olga Kotik-Kogan
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
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28
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Jurkovic D, Krizková L, Sojka M, Belicová A, Dusinský R, Krajcovic J, Snauwaert C, Naser S, Vandamme P, Vancanneyt M. Molecular identification and diversity of enterococci isolated from Slovak Bryndza cheese. J GEN APPL MICROBIOL 2006; 52:329-37. [PMID: 17325446 DOI: 10.2323/jgam.52.329] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [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: 11/03/2022]
Abstract
Three hundred and eight presumed enterococcal isolates were recovered from Bryndza, a soft sheep milk cheese. The cheese samples were obtained from five different commercial distributors in Slovakia and were taken at three different seasonal intervals. All isolates were identified to the species level using genotypic tools. Species-specific PCR using ddl genes highlighted the predominance of Enterococcus faecium (176 isolates) and assigned 50 isolates to the species Enterococcus faecalis. The remaining 82 isolates were classified using repetitive element sequence-based polymerase chain reaction (PCR) with primer (GTG)(5)-(GTG)(5)-PCR, in combination with phenylalanyl-tRNA synthase gene (pheS) sequence analysis and by whole-cell protein analysis (SDS-PAGE). These strains were identified as Enterococcus durans (59 strains), Enterococcus italicus (8 strains), Enterococcus casseliflavus (3 strains), Enterococcus gallinarum (3 strains), Enterococcus hirae (1 strain), and 8 strains were members of the species Lactococcus lactis. Of the seven enterococcal species isolated, three of them, E. durans, E. faecalis and E. faecium were present in all samples studied, with E. faecium as the predominant one. The precise identification of enterococci in Bryndza cheese is an essential step in the process of evaluation of their functional properties which will be further studied and assessed.
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Affiliation(s)
- Dusan Jurkovic
- Institute of Cell Biology, Faculty of Natural Sciences, Mlynská dolina, Bratislava, Slovak Republic
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29
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Švec P, Vancanneyt M, Devriese LA, Naser SM, Snauwaert C, Lefebvre K, Hoste B, Swings J. Enterococcus aquimarinus sp. nov., isolated from sea water. Int J Syst Evol Microbiol 2005; 55:2183-2187. [PMID: 16166729 DOI: 10.1099/ijs.0.63722-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [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: 11/18/2022] Open
Abstract
Two enterococcal strains LMG 16607(T) and LMG 16612 originating from sea water were analysed in a polyphasic taxonomic study. Both strains, assigned as Enterococcus sp. in the BCCM/LMG culture collection, possessed analogous protein profiles, but these were different from all other enterococcal species. 16S rRNA gene sequence analysis of one strain showed the highest similarity, 96.9-96.1%, with its closest phylogenetic neighbours Enterococcus saccharolyticus, Enterococcus sulfureus, Enterococcus saccharominimus and Enterococcus italicus. Further genomic analysis by (GTG)(5)-PCR fingerprinting and sequence analysis of the housekeeping gene phenylalanyl-tRNA synthase (pheS) and distinct biochemical features confirmed that the two strains represent a novel enterococcal species for which the name Enterococcus aquimarinus sp. nov. is proposed. The type strain is LMG 16607(T) (=CCM 7283(T)).
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Affiliation(s)
- Pavel Švec
- Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Tvrdého 14, 602 00 Brno, Czech Republic
| | - Marc Vancanneyt
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc A Devriese
- Laboratory of Veterinary Bacteriology and Mycology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Sabri M Naser
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Cindy Snauwaert
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Karen Lefebvre
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Bart Hoste
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Jean Swings
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
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30
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Abstract
A designed polypeptide scaffold contains a surface immobilization domain and a target capture domain for flexible protein arraying.
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31
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Abstract
An artificial polypeptide scaffold composed of surface anchor and protein capture domains was designed and expressed in vivo. By using a mutant E. coli phenylalanyl-tRNA synthetase, the photoreactive amino acid para-azidophenylalanine was incorporated into the surface anchor domain. Octyltrichlorosilane-treated surfaces were functionalized with this polypeptide by spin coating and photocrosslinking. The resulting protein films were shown to immobilize recombinant proteins through association of coiled coil heterodimer.
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Affiliation(s)
- Kechun Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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32
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Roy H, Ling J, Irnov M, Ibba M. Post-transfer editing in vitro and in vivo by the beta subunit of phenylalanyl-tRNA synthetase. EMBO J 2004; 23:4639-48. [PMID: 15526031 PMCID: PMC533057 DOI: 10.1038/sj.emboj.7600474] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2004] [Accepted: 10/13/2004] [Indexed: 11/09/2022] Open
Abstract
Translation of the genetic code requires attachment of tRNAs to their cognate amino acids. Errors during amino-acid activation and tRNA esterification are corrected by aminoacyl-tRNA synthetase-catalyzed editing reactions, as extensively described for aliphatic amino acids. The contribution of editing to aromatic amino-acid discrimination is less well understood. We show that phenylalanyl-tRNA synthetase misactivates tyrosine and that it subsequently corrects such errors through hydrolysis of tyrosyl-adenylate and Tyr-tRNA(Phe). Structural modeling combined with an in vivo genetic screen identified the editing site in the B3/B4 domain of the beta subunit, 40 angstroms from the active site in the alpha subunit. Replacements of residues within the editing site had no effect on Phe-tRNA(Phe) synthesis, but abolished hydrolysis of Tyr-tRNA(Phe) in vitro. Expression of the corresponding mutants in Escherichia coli significantly slowed growth, and changed the activity of a recoded beta-galactosidase variant by misincorporating tyrosine in place of phenylalanine. This loss in aromatic amino-acid discrimination in vivo revealed that editing by phenylalanyl-tRNA synthetase is essential for faithful translation of the genetic code.
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Affiliation(s)
- Hervé Roy
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Jiqiang Ling
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Michael Irnov
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
- Department of Microbiology, The Ohio State University, 556 Bioscience Building, 484 West 12th Avenue, Columbus, OH 43210-1292, USA. Tel.: +1 614 292 2120; Fax: +1 614 292 8120; E-mail:
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33
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Shiraki K, Tsuji M, Hashimoto Y, Fujimoto K, Fujiwara S, Takagi M, Imanaka T. Genetic, enzymatic, and structural analyses of phenylalanyl-tRNA synthetase from Thermococcus kodakaraensis KOD1. J Biochem 2004; 134:567-74. [PMID: 14607984 DOI: 10.1093/jb/mvg175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 11/14/2022] Open
Abstract
Phenylalanyl-tRNA synthetase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (Tk-PheRS) was cloned. The open reading frames for both the alpha-subunit (Tk-pheRSA) and beta-subunit (Tk-pheRSB) genes were 1,503 bp (501 amino acids) and 1,722 bp (574 amino acids), respectively. Tk-pheRSB located 879 bp downstream from Tk-pheRSA with a putative TATA box, suggesting that these two subunits are transcribed and regulated independently in KOD1 cells. Tk-PheRS and its respective subunits were expressed in Escherichia coli cells and the proteins were purified. Tk-PheRS showed an optimum enzymatic activity at around 95 degrees C and retained its tertiary structure at 98 degrees C. The estimated isoelectric point (pI) for the alpha-subunit is 9.4 and that for the beta-subunit is 4.6, the largest difference among the 12 kinds of PheRSs reported. The considerable thermostability of Tk-PheRS may be responsible for the electrostatic interaction between the alpha- and beta-subunits.
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Affiliation(s)
- Kentaro Shiraki
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Ishikawa 923-1292
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34
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Bentin T, Hamzavi R, Salomonsson J, Roy H, Ibba M, Nielsen PE. Photoreactive bicyclic amino acids as substrates for mutant Escherichia coli phenylalanyl-tRNA synthetases. J Biol Chem 2004; 279:19839-45. [PMID: 15004015 DOI: 10.1074/jbc.m401278200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [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: 11/06/2022] Open
Abstract
Unnatural amino acids carrying reactive groups that can be selectively activated under non-invasive biologically benign conditions are of interest in protein engineering as biological tools for the analysis of protein-protein and protein-nucleic acids interactions. The double ring system phenylalanine analogues benzofuranylalanine and benzotriazolylalanine were synthesized, and their photolability was tested by UV irradiation at 254, 320, and 365 nm. Although both showed photo reactivity, benzofuranylalanine appeared as the most promising compound because this amino acid was activated by UVA (long wavelength) irradiation. These amino acids were also tested for in vitro charging of tRNA(Phe) and for protein mutagenesis via the phenylalanyl-tRNA synthetase variant alphaA294G that is able to facilitate in vivo protein synthesis using a range of para-substituted phenylalanine analogues. The results demonstrate that benzofuranylalanine, but not benzotriazolylalanine, is a substrate for phenylalanine tRNA synthetase alphaA294G, and matrix-assisted laser desorption ionization time-of-flight analysis showed it to be incorporated into a model protein with high efficiency. The in vivo incorporation into a target protein of a bicyclic phenylalanine analogue, as described here, demonstrates the applicability of phenylalanine tRNA synthetase variants in expanding the scope of protein engineering.
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Affiliation(s)
- Thomas Bentin
- Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, 2200 Copenhagen N, Denmark
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35
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Lin J, Huang JF. Evolution of phenylalanyl-tRNA synthetase by domain losing. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 2003; 35:1061-5. [PMID: 14673495] [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] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The gene duplication, fusion and horizontal transfer are the frequent events during evolution of many proteins, including the aminoacyl-tRNA synthetases (AARSs). However, in this work, it was shown that the main event during evolution of phenylalanyl-tRNA synthetase (PheRS) is a domain loss, and the function/activity of PheRS is not affected by domain losing. Generally, the size of genome and number of genes are increased during evolution from bacteria to eukaryote, but the interesting thing is that the type and number of PheRS domains in eukaryote are obviously less than those in bacteria. The evolution of PheRS by domain losing seems to be related to the functional evolution of some AARSs from the multiple specificities to the single specificity.
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Affiliation(s)
- Jun Lin
- Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China
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36
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Moor N, Lavrik O, Favre A, Safro M. Prokaryotic and eukaryotic tetrameric phenylalanyl-tRNA synthetases display conservation of the binding mode of the tRNA(Phe) CCA end. Biochemistry 2003; 42:10697-708. [PMID: 12962494 DOI: 10.1021/bi034732q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [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: 11/30/2022]
Abstract
The interaction of human phenylalanyl-tRNA synthetase, a eukaryotic prototype with an unknown three-dimensional structure, with the tRNA(Phe) acceptor end was studied by s(4)U-induced affinity cross-linking with human tRNA(Phe) derivatives site-specifically substituted at the single-stranded 3' end. Two different subunits of the enzyme bind two adjacent nucleotides of the tRNA(Phe) 3' end: nucleotide 76 is associated with the catalytic alpha subunit, while nucleotide 75 is in contact with the beta subunit. The binding mode is similar to that revealed previously in structural and affinity cross-linking studies of the prokaryotic Thermus thermophilus phenylalanyl-tRNA synthetase. Our results suggest that the distinctive features of tRNA(Phe) acceptor end binding are conserved for the eukaryotic and prokaryotic tetrameric phenylalanyl-tRNA synthetases despite their significant differences in the domain composition of the beta subunits. The data from affinity cross-linking experiments with human phenylalanyl-tRNA synthetase complexed with small ligands (ATP and/or phenylalanine or a stable synthetic analogue of phenylalanyl adenylate) reveal that the location of the tRNA(Phe) acceptor end varies with the presence and nature of other substrates. The lack of substrate activity of human tRNA(Phe) substituted with s(4)U at the 3'-terminal position suggests that base-specific interactions of the terminal adenosine are critically important for a productive interaction. The conformational rearrangement of the tRNA 3' end induced by the other substrates and dictated by base-specific contacts of the terminal nucleotide is an additional means of ensuring the phenylalanylation specificity in both prokaryotic and eukaryotic systems.
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Affiliation(s)
- Nina Moor
- Novosibirsk Institute of Bioorganic Chemistry, 630090 Novosibirsk, Russia.
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37
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Page WJ, Mehrotra M, Vande Woestyne M, Tindale AE, Kujat Choy SL, Macyk AS, Leskiw BK. Iron-regulated phenylalanyl-tRNA synthetase activity in Azotobacter vinelandii. FEMS Microbiol Lett 2003; 218:15-21. [PMID: 12583892 DOI: 10.1111/j.1574-6968.2003.tb11492.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [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: 12/01/2022] Open
Abstract
Azotobacter vinelandii strain UA22 was produced by pTn5luxAB mutagenesis, such that the promoterless luxAB genes were transcribed in an iron-repressible manner. Tn5luxAB was localized to a fragment of chromosomal DNA encoding the thrS, infC, rpmI, rplT, pheS and pheT genes, with Tn5 inserted in the 3'-end of pheS. The isolation of this mutation in an essential gene was possible because of polyploidy in Azotobacter, such that strain UA22 carried both wild-type and mutant alleles of pheS. Phenylalanyl-tRNA synthetase activity and PHES::luxAB reporter activity was partially repressed under iron-sufficient conditions and fully derepressed under iron-limited conditions. The ferric uptake regulator (Fur) bound to a DNA sequence immediately upstream of luxAB, within the pheS gene, but PHES::luxAB reporter activity was not affected by phenylalanine availability. This suggests there is novel regulation of pheST in A. vinelandii by iron availability.
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Affiliation(s)
- William J Page
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9.
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38
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Affiliation(s)
- Nigel J Saunders
- Bacterial Pathogenesis and Functional Genomics Group, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford. OX1 3RE, 1
| | - Lori A S Snyder
- Bacterial Pathogenesis and Functional Genomics Group, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford. OX1 3RE, 1
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39
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Mittenhuber G. A phylogenomic study of the general stress response sigma factor sigmaB of Bacillus subtilis and its regulatory proteins. J Mol Microbiol Biotechnol 2002; 4:427-52. [PMID: 12125823] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Regulation of expression of the general stress regulon of Bacillus subtilis is mediated by the activation of the alternative sigma factor sigmaB. Activation of sigmaB is accomplished by a complex regulatory network involving protein-protein interactions and reversible protein phosphorylation. PSI-BLAST searches were performed and phylogenetic trees for sigmaB and its regulatory proteins were constructed. Occurrence of sigmaB is restricted to a small group of gram-positive bacteria (Bacillus, Staphylococcus, Listeria). Related sigma factors also involved in stress responses are present in Mycobacterium tuberculosis, Streptomyces species and even in cyanobacteria (Synechocystis species). Putative regulatory proteins found in several other bacterial species can be broadly catagorized into three categories: Anti sigma factors, anti-anti sigma factors and phosphatases. Anti sigma factors are able to bind to sigma factors and are also kinases of anti sigma factor antagonists. Only in their nonphosphorylated state, these antagonists are able to bind to the anti sigma factor. Phosphorylated antagonists can be dephosphorylated by PP2C phosphatases. These phosphatases are of pivotal importance for activation of the sigma factor. Different phosphatases identified in this search contain a wide variety of domains found in signal transducing proteins (PAS/PAC, GAF, REC, HATase_c, HAMP). The HATPase_c domain found in several phosphatases most probably constitutes a serine/threonine kinase domain of anti sigma factors. Such proteins are most probably bifunctional anti-anti sigma factor kinases and phosphatases. The regulatory network of anti-anti sigma factors anti sigma factors and phosphatases is probably ancient and most likely evolved from a structurally similar network found in the Deinococcus radiodurans genome. In completely sequenced genomes of several bacterial species, some elements of the network are missing. The N-terminus of RsbU, a phosphatase activated in response to environmental stress exhibits similarities to a region in the beta chain of phenylalanyl-tRNA synthetases.
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40
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Datta D, Wang P, Carrico IS, Mayo SL, Tirrell DA. A designed phenylalanyl-tRNA synthetase variant allows efficient in vivo incorporation of aryl ketone functionality into proteins. J Am Chem Soc 2002; 124:5652-3. [PMID: 12010034 DOI: 10.1021/ja0177096] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.4] [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: 11/30/2022]
Abstract
Incorporation of non-natural amino acids into proteins in vivo expands the scope of protein synthesis and design. p-Acetylphenylalanine was incorporated into recombinant dihydrofolate reductase (DHFR) in Escherichia coli via a computationally designed mutant form of the phenylalanyl-tRNA synthetase of the host. DHFR outfitted with ketone functionality can be chemoselectively ligated with hydrazide reagents under mild conditions.
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Affiliation(s)
- Deepshikha Datta
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA
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41
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Moor N, Linshiz G, Safro M. Cloning and expression of human phenylalanyl-tRNA synthetase in Escherichia coli: comparative study of purified recombinant enzymes. Protein Expr Purif 2002; 24:260-7. [PMID: 11858721 DOI: 10.1006/prep.2001.1560] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [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: 11/22/2022]
Abstract
Human phenylalanyl-tRNA synthetase (PheRS) was cloned and expressed in Escherichia coli. The cDNAs of the alpha and beta subunits were cloned into pET-21b(+) and pET-28b(+) vectors. The 6x histidine-tagged (HT) plasmids pET-21_HTbeta, pET-28_HTalpha, and pET-28_HTbeta were constructed. Three different types of (alphabeta)(2) heterodimers of human PheRS carrying HT at the N-terminus of either of two alpha or beta subunits or simultaneously on both of them were overproduced and purified. The heterodimeric protein with HT appended to the N-terminus of the beta subunit revealed no activity in the aminoacylation reaction as opposed to those with HT on the alpha subunit. It is known from the structure of the Thermus thermophilus Phe system that the N-terminal coiled-coil domain of the alpha subunit is involved in the binding of cognate tRNA(Phe). Our data demonstrate that a histidine-tagged N-terminal extension appended to the alpha subunit does not affect the kinetic parameters of tRNA(Phe) aminoacylation. Elimination of the HT from the alpha subunit by thrombin cleavage leads to nonspecific splitting of the enzyme that occurs in parallel to the main reaction. In addition to the tagged proteins the properly assembled heterodimer containing intact alpha and beta subunits free of HT was overproduced and purified. Aminoacylation activity of the overproduced human PheRS in the crude bacterial extract is two orders of magnitude higher than the corresponding activity in human placenta and the yield of the recombinant enzyme overproduced in E. coli is five times higher.
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Affiliation(s)
- Nina Moor
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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42
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Abstract
Prokaryotes have been at the forefront of the genome sequencing revolution. Many genomes have been completely sequenced, revealing much about bacterial and archaeal genome content and organization. Yet, a meaningful evolutionary picture of prokaryotes still eludes us. Much of the problem lies in understanding the mode and tempo of genome evolution. Here phenylalanyl-tRNA synthetase is used as an example of the complex interplay among lateral gene transfer, operon recombination, and gene recruitment in the evolution of some prokaryotic genes. Promising new approaches to genomic analyses, which could add to our understanding prokaryotic evolution and help in their classification, are discussed.
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Affiliation(s)
- J R Brown
- Microbial Bioinformatics Department, Division of Bioinformatics, Glaxo SmithKline Pharmaceuticals, 1250 South Collegeville Road, P.O. Box 5089, UP1345, Collegeville, Pennsylvania 19426-0989, USA.
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43
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Savopoulos JW, Hibbs M, Jones EJ, Mensah L, Richardson C, Fosberry A, Downes R, Fox SG, Brown JR, Jenkins O. Identification, cloning, and expression of a functional phenylalanyl-tRNA synthetase (pheRS) from Staphylococcus aureus. Protein Expr Purif 2001; 21:470-84. [PMID: 11281723 DOI: 10.1006/prep.2001.1407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [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: 11/22/2022]
Abstract
Phenylalanyl-tRNA synthetase (pheRS) is unique among aminoacyl tRNA synthetases in that it is a heterotetrameric enzyme composed of two alpha-subunits and two larger beta-subunits. In prokaryotes, the alpha- and beta-subunits of pheRS are encoded by the genes pheS and pheT, respectively. In this report we describe the isolation of a DNA fragment (3.52 kb) containing the pheS and pheT genes from a Staphylococcus aureus (WCUH29) genomic DNA library. Both genes, found as a part of transcriptional operon, were predicted to encode polypeptides which showed strong primary and structural similarity to prokaryotic phenylalanyl-tRNA synthetase alpha- and beta- subunits. We describe the high-level overexpression and purification of recombinant S. aureus pheRS using pheS and pheT genes as part of an artificial operon in Escherichia coli. For comparative analysis we also report a procedure for the purification of native pheRS from S. aureus (Oxford Strain) and demonstrate that Michaelis-Menten parameters for both recombinant and native enzyme, at least for phenylalanine tRNA aminoacylation are comparable.
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Affiliation(s)
- J W Savopoulos
- GlaxoSmithkline Pharmaceuticals, New Frontiers Science Park (North), Coldharbour Road, Harlow, Essex CM19 5AD, United Kingdom
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44
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Abstract
The phenylalanyl-tRNA synthetase (FRS) from Thermus thermophilus has previously been shown to bind DNA. We demonstrate that the "winged" helix-turn-helix motifs in the duplicate domains B5 are the relevant structural elements for this DNA-binding property. By altering particular amino acids in the "wing", the affinity of the FRS to DNA was significantly reduced. Based on experimental data, which indicate that the FRS prefers a certain DNA structure rather than a particular consensus sequence, we propose a novel loop model for the DNA-binding mode of the FRS. In our model we assume that two segments of the same DNA molecule are bound simultaneously by both B5 domains and are aligned in parallel, while the intervening DNA forms a loop. Due to the limited flexibility of the DNA, loop formation is only possible if the respective intervening DNA stretch exceeds a certain length. Several lines of evidence support this model. (1) We demonstrate by gel retardation assays that the DNA requires a minimal number of ca 80 base-pairs to be bound by the FRS. (2) In the presence of the FRS, DNA longer than ca 80 base-pairs has a significantly increased DNase I accessibility. This agrees well with its known preferential cleavage at positions where the minor grove is on the outside of looped-out DNA molecules. (3) The initial cleavage by DNase I of >80 bp long DNA occurs in the middle of the fragment. In a looped molecule this is the position with the highest accessibility to DNase I. The function of the FRS related to DNA binding is still unknown. Since the FRS exists in the nucleus of rapidly growing mammalian cells, and protein-induced DNA bending or looping contributes to several transcription, replication, and recombination systems in both prokaryotes and eukaryotes, it is likely that the FRS, in addition to its aminoacylation function, influences common cellular processes via DNA binding.
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Affiliation(s)
- X Dou
- Laboratorium für Biochemie, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
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45
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Abstract
Myxococcus xanthus responds to blue light by producing carotenoids. Several regulatory genes are known that participate in the light action mechanism, which leads to the transcriptional activation of the carotenoid genes. We had already reported the isolation of a carotenoid-less, Tn5-induced strain (MR508), whose mutant site was unlinked to the indicated regulatory genes. Here, we show that OmegaMR508::Tn5 affects all known light-inducible promoters in different ways. It blocks the activation of two of them by light but makes the activity of a third one light independent. The OmegaMR508 locus has been cloned and sequenced. The mutation had occurred at the promoter of a gene we propose is the M. xanthus ortholog of ihfA. This encodes the alpha subunit of the histone-like integration host factor protein. An in-frame deletion within ihfA causes the same effects as the OmegaMR508::Tn5 insertion. Like other IhfA proteins, the deduced amino acid sequence of M. xanthus IhfA shows much similarity to HU, another histone-like protein. Sequence comparison data, however, and the finding that the M. xanthus gene is preceded by gene pheT, as happens in other gram-negative bacteria, strongly argue for the proposed orthology relationship. The M. xanthus ihfA gene shows some unusual features, both from structural and physiological points of view. In particular, the protein is predicted to have a unique, long acidic extension at the carboxyl terminus, and it appears to be necessary for normal cell growth and even vital for a certain wild-type strain of M. xanthus.
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Affiliation(s)
- A J Moreno
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
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46
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Abstract
We have identified two polarity-defective (pod) mutants in Aspergillus nidulans from a collection of heat-sensitive lethal mutants. At restrictive temperature, these mutants are capable of nuclear division but are unable to establish polar hyphal growth. We cloned the two pod genes by complementation of their heat-sensitive lethal phenotypes. The libraries used to clone the pod genes are under the control of the bidirectional niaD and niiA promoters. Complementation of the pod mutants is dependent on growth on inducing medium. We show that rescue of the heat-sensitive phenotype on inducing media is independent of the orientation of the gene relative to the niaD or niiA promoters, demonstrating that the intergenic region between the niaD and the niiA genes functions as an orientation-independent enhancer and repressor that is capable of functioning over long distances. The products of the podG and the podH genes were identified as homologues of the alpha subunit of yeast mitochondrial phenylalanyl--tRNA synthetase and transcription factor IIF interacting component of the CTD phosphatase. Neither of these gene products would have been predicted to produce a pod mutant phenotype based on studies of cellular polarity mutants in other organisms. The implications of these results are discussed.
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Affiliation(s)
- N Osherov
- Division of Pathology and Laboratory Medicine, The University of Texas, M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
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47
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Abstract
Artificial proteins can be engineered to exhibit interesting solid state, liquid crystal or interfacial properties and may ultimately serve as important alternatives to conventional polymeric materials. The utility of protein-based materials is limited, however, by the availability of just the 20 amino acids that are normally recognized and utilized by biological systems; many desirable functional groups cannot be incorporated directly into proteins by biosynthetic means. In this study, we incorporate para-bromophenylalanine (p-Br-phe) into a model target protein, mouse dihydrofolate reductase (DHFR), by using a bacterial phenylalanyl-tRNA synthetase (PheRS) variant with relaxed substrate specificity. Coexpression of the mutant PheRS and DHFR in a phenylalanine auxotrophic Escherichia coli host strain grown in p-Br-phe-supplemented minimal medium resulted in 88% replacement of phenylalanine residues by p-Br-phe; variation in the relative amounts of phe and p-Br-phe in the medium allows control of the degree of substitution by the analog. Protein expression yields of 20-25 mg/l were obtained from cultures supplemented with p-Br-phe; this corresponds to about two-thirds of the expression levels characteristic of cultures supplemented with phe. The aryl bromide function is stable under the conditions used to purify DHFR and creates new opportunities for post-translational derivatization of brominated proteins via metal-catalyzed coupling reactions. In addition, bromination may be useful in X-ray studies of proteins via the multiwavelength anomalous diffraction (MAD) technique.
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Affiliation(s)
- N Sharma
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA
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48
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Abstract
Phenylalanyl-tRNA synthetase from the methanogenic archaeon Methanobacterium thermoautotrophicum was purified to apparent homogeneity. The catalytically active enzyme is a heterotetramer composed of two subunits, alpha and beta. N-terminal sequence data were obtained for both subunits and the open reading frames MT770 and MT742 of the genome sequence of M. thermoautotrophicum were identified as coding for these proteins. Two ORFs with similarity to non-archaeal PheRSs alpha-subunits had previously been found in the genome sequence, but these results show that only one of them, MT742, is part of the active PheRS.
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Affiliation(s)
- R Das
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114 USA
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49
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Tumbula D, Vothknecht UC, Kim HS, Ibba M, Min B, Li T, Pelaschier J, Stathopoulos C, Becker H, Söll D. Archaeal aminoacyl-tRNA synthesis: diversity replaces dogma. Genetics 1999; 152:1269-76. [PMID: 10430557 PMCID: PMC1460689 DOI: 10.1093/genetics/152.4.1269] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [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: 11/14/2022] Open
Abstract
Accurate aminoacyl-tRNA synthesis is essential for faithful translation of the genetic code and consequently has been intensively studied for over three decades. Until recently, the study of aminoacyl-tRNA synthesis in archaea had received little attention. However, as in so many areas of molecular biology, the advent of archaeal genome sequencing has now drawn researchers to this field. Investigations with archaea have already led to the discovery of novel pathways and enzymes for the synthesis of numerous aminoacyl-tRNAs. The most surprising of these findings has been a transamidation pathway for the synthesis of asparaginyl-tRNA and a novel lysyl-tRNA synthetase. In addition, seryl- and phenylalanyl-tRNA synthetases that are only marginally related to known examples outside the archaea have been characterized, and the mechanism of cysteinyl-tRNA formation in Methanococcus jannaschii and Methanobacterium thermoautotrophicum is still unknown. These results have revealed completely unexpected levels of complexity and diversity, questioning the notion that aminoacyl-tRNA synthesis is one of the most conserved functions in gene expression. It has now become clear that the distribution of the various mechanisms of aminoacyl-tRNA synthesis in extant organisms has been determined by numerous gene transfer events, indicating that, while the process of protein biosynthesis is orthologous, its constituents are not.
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Affiliation(s)
- D Tumbula
- Department of Molecular Biophysics and Biochemistry, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8114, USA
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50
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Abstract
Using the sequence information from nine completely sequenced bacterial genomes, we extract 32 protein families that are thought to contain orthologous proteins from each genome. The alignments of these 32 families are used to construct a phylogeny with the neighbor-joining algorithm. This tree has several topological features that are different from the conventional phylogeny, yet it is highly reliable according to its bootstrap values. Upon closer study of the individual families used, it is clear that the strong phylogenetic signal comes from three families, at least two of which are good candidates for horizontal transfer. The tree from the remaining 29 families consists almost entirely of noise at the level of bacterial phylum divisions, indicating that, even with large amounts of data, it may not be possible to reconstruct the prokaryote phylogeny using standard sequence-based methods.
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Affiliation(s)
- S A Teichmann
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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