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Zhao B, Deng J, Ma M, Li N, Zhou J, Li X, Luan T. Environmentally relevant concentrations of 2,3,7,8-TCDD induced inhibition of multicellular alternative splicing and transcriptional dysregulation. Sci Total Environ 2024; 919:170892. [PMID: 38346650 DOI: 10.1016/j.scitotenv.2024.170892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Alternative splicing (AS), found in approximately 95 % of human genes, significantly amplifies protein diversity and is implicated in disease pathogenesis when dysregulated. However, the precise involvement of AS in the toxic mechanisms induced by TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) remains incompletely elucidated. This study conducted a thorough global AS analysis in six human cell lines following TCDD exposure. Our findings revealed that environmentally relevant concentration (0.1 nM) of TCDD significantly suppressed AS events in all cell types, notably inhibiting diverse splicing events and reducing transcript diversity, potentially attributed to modifications in the splicing patterns of the inhibitory factor family, particularly hnRNP. And we identified 151 genes with substantial AS alterations shared among these cell types, particularly enriched in immune and metabolic pathways. Moreover, TCDD induced cell-specific changes in splicing patterns and transcript levels, with increased sensitivity notably in THP-1 monocyte, potentially linked to aberrant expression of pivotal genes within the spliceosome pathway (DDX5, EFTUD2, PUF60, RBM25, SRSF1, and CRNKL1). This study extends our understanding of disrupted alternative splicing and its relation to the multisystem toxicity of TCDD. It sheds light on how environmental toxins affect post-transcriptional regulatory processes, offering a fresh perspective for toxicology and disease etiology investigations.
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Affiliation(s)
- Bilin Zhao
- Guangdong Provincial Laboratory of Chemistry and Fine Chemical Engineering Jieyang Center, Jieyang 515200, China; Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Jiewei Deng
- Guangdong Provincial Laboratory of Chemistry and Fine Chemical Engineering Jieyang Center, Jieyang 515200, China; School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China; Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China
| | - Mei Ma
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Na Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Junlin Zhou
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Xinyan Li
- Guangdong Provincial Laboratory of Chemistry and Fine Chemical Engineering Jieyang Center, Jieyang 515200, China; School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China; Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China.
| | - Tiangang Luan
- Guangdong Provincial Laboratory of Chemistry and Fine Chemical Engineering Jieyang Center, Jieyang 515200, China; Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China; Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China
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Zheng X, Sun X, Xiang W, Ni H, Zou L, Long ZE. Expression of Staphylococcus aureus translation elongation factor P is regulated by a stress-inducible promotor. Antonie Van Leeuwenhoek 2024; 117:54. [PMID: 38489110 DOI: 10.1007/s10482-024-01954-0] [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: 09/04/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Translation elongation factor P, expressed by the efp gene, is a conserved protein closely related to bacterial virulence and environmental stress regulation responses, however, little is known about the efp gene expression regulations. Here, the strain of Staphylococcus aureus subsp. aureus NCTC 8325 was taken as the research object and cultured under different conditions, including different culture temperatures, pH, and antibiotics, to study the expression of the efp gene in S. aureus by qRT-PCR, the results showed that the expression of the efp gene is upregulated under high temperature (40 °C), acidic (pH 5.4) or alkaline (pH 9.4) culture conditions, but upregulated early and downregulated later under the conditions of 0.5 MIC antibiotics (chloramphenicol at the final concentration of 2 μg/mL and vancomycin at the final concentration of 0.25 μg/mL), indicating that the efp promoter in S. aureus is inducible. The efp promoter sequence and structure in S. aureus were predicted by bioinformatics methods, and the predicted promoter was validated by constructing a promoter-probe vector and a series of promoter mutants, the results showed that the efp promoter sequence in S. aureus, named Pro, located in 1,548,179-1,548,250 of the S. aureus genome (NC_007795.1), and the sequence of - 10 element is CCTTATAGT, - 35 element is TTTACT. The results above could lay a foundation for screening transcription factors involved in the expression of the efp gene and then exploring the transcriptional regulation mechanism of EF-P in S. aureus.
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Affiliation(s)
- Xingxing Zheng
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xiuhui Sun
- Chongren County Center for Disease Prevention and Control, Chongren, 344203, China
| | - Weiwei Xiang
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Haiyan Ni
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Long Zou
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhong-Er Long
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
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Wu S, Han J, Duan G, Xue J, Huang R, Wu L, Yan X, Pi H, Yang X. Prenatal Diagnosis of Fetal Micrognathia at 11-20 Weeks of Gestation: A Prospective Observation Study. J Ultrasound Med 2024; 43:491-499. [PMID: 38164991 DOI: 10.1002/jum.16379] [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] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVE To prospectively evaluate the prognosis of fetuses diagnosed with micrognathia using prenatal ultrasound screening. METHODS Between January 2019 and December 2022, a normal range of IFA to evaluate the facial profile in fetuses with micrognathia in a Chinese population between 11 and 20 gestational weeks was established, and the pregnancy outcomes of fetal micrognathia were described. The medical records of these pregnancies were collected, including family history, maternal demographics, sonographic findings, genetic testing results, and pregnancy outcomes. RESULTS Ultrasound identified 25 patients with fetal micrognathia, with a mean IFA value of 43.6°. All cases of isolated fetal micrognathia in the initial scans were non-isolated in the following scans. A total of 78.9% (15/19) cases had a genetic cause confirmed, including 12 with chromosomal abnormalities and 3 with monogenic disorders. Monogenic disorders were all known causes of micrognathia, including two cases of campomelic dysplasia affected by SOX9 mutations and one case of mandibulofacial dysostosis with an EFTUD2 mutation. In the end, 19 cases were terminated, 1 live birth was diagnosed as Pierre Robin syndrome, and 5 cases were lost to follow-up. CONCLUSION IFA is a useful indicator and three-dimensional ultrasound is a significant support technique for fetal micrognathia prenatal diagnosis. Repeat ultrasound monitoring and genetic testing are crucial, with CMA recommended and Whole exome sequencing performed when normal arrays are reported. Isolated fetal micrognathia may be an early manifestation of monogenic disorders.
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Affiliation(s)
- Siqi Wu
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Jin Han
- Department of Prenatal Diagnosis, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Guanhua Duan
- Department of Ultrasonics, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Jiaxin Xue
- Department of Obstetrics, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Ruchun Huang
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Liping Wu
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Xiuyan Yan
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Huichun Pi
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Xin Yang
- Department of Medical Genetics and Prenatal Diagnosis, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
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Quinzi V, De Luca C, Giovannetti F, Splendiani A, Cocciadiferro D, Capolino R, Brancati F, Marzo G. First and second branchial arch involvement in mandibulofacial dysostosis Guion-Almeida type. Eur J Paediatr Dent 2023; 24:334-336. [PMID: 38015115 DOI: 10.23804/ejpd.2023.24.04.03] [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: 11/29/2023]
Abstract
BACKGROUND Mandibulofacial dysostosis Guion-Almeida Type (MFDGA; OMIM#610536) is a rare autosomal dominant genetic disorder caused by heterozygous pathogenic variants in the EFTUD2 gene. Mandibulofacial dysostoses are characterised by the core triad malar hypoplasia, maxillary hypoplasia and dysplastic ears, all derived by the impaired development of the first and second branchial arches. Differential diagnosis is often challenging. The early genetic diagnosis is extremely useful, not only for the correct management of cranial malformations, but also for the early diagnosis and treatment of the comorbidities associated to the disease, which greatly benefit from early treatment.
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Affiliation(s)
- V Quinzi
- Department of Life, Health and Environmental Sciences, Postgraduate School of Orthodontics, University of L'Aquila, Italy
| | - C De Luca
- Human Genetics Laboratory, Department of Life, Health and Environmental Sciences, University of L'Aquila, Italy
| | - F Giovannetti
- Maxillofacial Surgery, Department of Life, Health and Environmental Sciences, University of L'Aquila, Italy
| | - A Splendiani
- Radiology Unit, Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Italy
| | - D Cocciadiferro
- Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - R Capolino
- Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - F Brancati
- Human Genetics Laboratory, Department of Life, Health and Environmental Sciences, University of L'Aquila, Italy - San Raffaele Roma IRCCS, Rome, Italy
| | - G Marzo
- Department of Life, Health and Environmental Sciences, Postgraduate School of Orthodontics, University of L'Aquila, Italy
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Han Z, Moore GA, Mitter R, Lopez Martinez D, Wan L, Dirac Svejstrup AB, Rueda DS, Svejstrup JQ. DNA-directed termination of RNA polymerase II transcription. Mol Cell 2023; 83:3253-3267.e7. [PMID: 37683646 PMCID: PMC7615648 DOI: 10.1016/j.molcel.2023.08.007] [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: 03/23/2023] [Revised: 06/27/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
RNA polymerase II (RNAPII) transcription involves initiation from a promoter, transcriptional elongation through the gene, and termination in the terminator region. In bacteria, terminators often contain specific DNA elements provoking polymerase dissociation, but RNAPII transcription termination is thought to be driven entirely by protein co-factors. We used biochemical reconstitution, single-molecule studies, and genome-wide analysis in yeast to study RNAPII termination. Transcription into natural terminators by pure RNAPII results in spontaneous termination at specific sequences containing T-tracts. Single-molecule analysis indicates that termination involves pausing without backtracking. The "torpedo" Rat1-Rai1 exonuclease (XRN2 in humans) greatly stimulates spontaneous termination but is ineffectual on other paused RNAPIIs. By contrast, elongation factor Spt4-Spt5 (DSIF) suppresses termination. Genome-wide analysis further indicates that termination occurs by transcript cleavage at the poly(A) site exposing a new 5' RNA-end that allows Rat1-Rai1 loading, which then catches up with destabilized RNAPII at specific termination sites to end transcription.
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Affiliation(s)
- Zhong Han
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - George A Moore
- Single Molecule Imaging group, MRC-London Institute of Medical Sciences, and Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Lopez Martinez
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Li Wan
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - A Barbara Dirac Svejstrup
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David S Rueda
- Single Molecule Imaging group, MRC-London Institute of Medical Sciences, and Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Jesper Q Svejstrup
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Meng S, Liu X, Zhu S, Xie P, Fang H, Pan Q, Fang K, Li F, Zhang J, Che Z, Zhang Q, Mao G, Wang Y, Hu P, Chen K, Sun F, Xie W, Luo Z, Lin C. Young LINE-1 transposon 5' UTRs marked by elongation factor ELL3 function as enhancers to regulate naïve pluripotency in embryonic stem cells. Nat Cell Biol 2023; 25:1319-1331. [PMID: 37591949 DOI: 10.1038/s41556-023-01211-y] [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] [Received: 07/14/2022] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
LINE-1s are the major clade of retrotransposons with autonomous retrotransposition activity. Despite the potential genotoxicity, LINE-1s are highly activated in early embryos. Here we show that a subset of young LINE-1s, L1Md_Ts, are marked by the RNA polymerase II elongation factor ELL3, and function as enhancers in mouse embryonic stem cells. ELL3 depletion dislodges the DNA hydroxymethylase TET1 and the co-repressor SIN3A from L1Md_Ts, but increases the enrichment of the Bromodomain protein BRD4, leading to loss of 5hmC, gain of H3K27ac, and upregulation of the L1Md_T nearby genes. Specifically, ELL3 occupies and represses the L1Md_T-based enhancer located within Akt3, which encodes a key regulator of AKT pathway. ELL3 is required for proper ERK activation and efficient shutdown of naïve pluripotency through inhibiting Akt3 during naïve-primed transition. Our study reveals that the enhancer function of a subset of young LINE-1s controlled by ELL3 in transcription regulation and mouse early embryo development.
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Affiliation(s)
- Siyan Meng
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Xiaoxu Liu
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Shiqi Zhu
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Peng Xie
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haitong Fang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Qingyun Pan
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Ke Fang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Fanfan Li
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jin Zhang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zhuanzhuan Che
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Guangyao Mao
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Fei Sun
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Wei Xie
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zhuojuan Luo
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, China.
- Shenzhen Research Institute, Southeast University, Shenzhen, China.
| | - Chengqi Lin
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.
- Shenzhen Research Institute, Southeast University, Shenzhen, China.
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, China.
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Setlur AS, K C, Bhattacharjee R, Kumar J, Niranjan V. Deciphering the interaction mechanism of natural actives against larval proteins of Aedes aegypti to identify potential larvicides: a computational biology analysis. J Biomol Struct Dyn 2023; 41:12480-12502. [PMID: 36688316 DOI: 10.1080/07391102.2023.2166993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/04/2023] [Indexed: 01/24/2023]
Abstract
Aedes aegypti is the target for repellents to curb incidences of vector-borne diseases. Stopping breeding of this mosquito species at its larval stages helps in controlling spread of insect-borne diseases. Therefore, the present study focused on deciphering the mechanism of interaction of selected natural actives against larval proteins of A. aegypti to identify potential natural alternative larvicides. 65 larval proteins were identified from literature, whose structures were modelled and validated using RaptorX and ProCheck. 11 natural actives were selected for predicting their ligand properties and toxicities via Toxicity Estimation Software Tool and ProTox-II. Molecular docking studies were carried out using POAP followed by 100 ns molecular dynamic simulation studies for top three best docked complexes to better understand the robustness of docking, complex stabilities and molecular mechanisms of interactions. Toxicity predictions revealed that 6 molecules belonged to toxicity class 4, and five to toxicity class 5, implying that they were all safe to use. Complexes goniothalamin-translation elongation factor (-10 kcal/mol), andrographolide-acetyl-CoA C-myristoyltransferase (-9.2 kcal/mol) and capillin-translation elongation factor (-8.4 kcal/mol) showed best binding energies. When simulated, capillin-translation elongation factor showed most stability, while the remaining two also evidenced robust docking. Evolutionary studies for top two larval proteins disclosed 100 other insect species in which these proteins can be targeted using various larvicides. Protein-protein interaction network analysis revealed several protein pathways that might be affected due to aforesaid naturals. Therefore, this study provides computational insights into the molecular interaction of naturals against larval proteins, acting as potential natural larvicides.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anagha S Setlur
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
| | - Chandrashekar K
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
| | | | - Jitendra Kumar
- Bangalore Bio-innovation Centre (BBC), Helix Biotech Park, Electronic City Phase-I, Bangalore, Karnataka, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
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Duan Y, Kang L, He Y, Li M, Li T, Wen Z, Chen L. A pilot study on identifying gene signatures as markers for predicting patient response to antiseizure medications. Neurol Sci 2023; 44:2137-2148. [PMID: 36658410 DOI: 10.1007/s10072-023-06605-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023]
Abstract
The majority of the biomarkers were associated with the diagnosis of epilepsy and few of them can be applied to predict the response to antiseizure medications (ASMs). In this study, we identified 26 significantly up-regulated genes and 32 down-regulated genes by comparing the gene expression profiles of patients with epilepsy that responded to valproate with those without applying any ASM. The results of gene set enrichment analysis indicated that the ferroptosis pathway was significantly impacted (p = 0.0087) in patients who responded to valproate. Interestingly, the gene NCOA4 in this pathway exhibited significantly different expression levels between the two groups, indicating that NCOA4 could serve as a potential biomarker to better understand the mechanism of valproate resistance. In addition, six up-regulated genes SF3A2, HMGN2, PABPN1, SSBP3, EFTUD2, and CREB3L2 as well as six down-regulated genes ZFP36L1, ACRC, SUB1, CALM2, TLK1, and STX2 also showed significantly different expression patterns between the two groups. Moreover, based on the gene expression profiles of the patients with the treatment of valproate, carbamazepine, and phenytoin, we proposed a strategy for predicting the response to the ASMs by using the Connectivity Map scoring method. Our findings could be helpful for better understanding the mechanisms of drug resistance of ASMs and improving the clinical treatment of epilepsy.
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Affiliation(s)
- Yifei Duan
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, Sichuan, China
| | - Liyuan Kang
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Yujie He
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Ting Li
- University of Arkansas at Little Rock and University of Arkansas for Medical Sciences Joint Bioinformatics Program, Little Rock, AK, 72204, USA
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
- Medical Big Data Center, Sichuan University, Chengdu, 610064, Sichuan, China.
| | - Lei Chen
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, Sichuan, China.
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Zhang C, Zhang KF, Chen FJ, Chen YH, Yang X, Cai ZH, Jiang YB, Wang XB, Zhang GP, Wang FY. Deoxynivalenol triggers porcine intestinal tight junction disorder: Insights from mitochondrial dynamics and mitophagy. Ecotoxicol Environ Saf 2022; 248:114291. [PMID: 36395652 DOI: 10.1016/j.ecoenv.2022.114291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Deoxynivalenol (DON) is universally detected trichothecene in most cereal commodities, which is considered as a major hazardous material for human and animal health. Intestine is the most vulnerable organ with higher concentration of DON than other organs, owing to the first defense barrier function to exogenous substances. However, the underling mechanisms about DON-induced intestinal toxicity remain poorly understood. Here, DON poisoning models of IPEC-J2 cells was established to explore adverse effect and the potential mechanism of DON-induced enterotoxicity. Results showed that DON exposure destroyed IPEC-J2 cells morphology. Results showed that DON exposure destroyed IPEC-J2 cells morphology. Intestinal epithelial barrier injury was caused by DON with increasing LDH release, decreasing cell viability as well decreasing tight junction protein expressions (Occludin, N-Cad, ZO-1, Claudin-1 and Claudin-3). Moreover, DON caused mitochondrial dysfunction by opening mitochondrial permeability transition pore and eliminating mitochondrial membrane potential. DON exposure upregulated protein and mRNA expression of mitochondrial fission factors (Drp1, Fis1, MIEF1 and MFF) and mitophagy factors (PINK1, Parkin and LC3), downregulated mitochondrial fusion factors (Mfn1, Mfn2, except OPA1), resulting in mitochondrial dynamics imbalance and mitophagy. Overall, these findings suggested that DON induced tight junction dysfunction in IPEC-J2 cells was related to mitochondrial dynamics-mediated mitophagy.
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Affiliation(s)
- Cong Zhang
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China; International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Ke-Fei Zhang
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China
| | - Feng-Juan Chen
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China
| | - Yun-He Chen
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China
| | - Xu Yang
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China; International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Zi-Hui Cai
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China
| | - Yi-Bao Jiang
- College of Animal Science and Technology, Henan Agricultural University, 450046, Zhengzhou, Henan, China
| | - Xue-Bing Wang
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China
| | - Gai-Ping Zhang
- College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China; International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Fang-Yu Wang
- Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China.
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10
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Cantanhede IG, Liu H, Liu H, Balbuena Rodriguez V, Shiwen X, Ong VH, Denton CP, Ponticos M, Xiong G, Lima-Filho JL, Abraham D, Abu-Hanna J, Taanman JW. Exploring metabolism in scleroderma reveals opportunities for pharmacological intervention for therapy in fibrosis. Front Immunol 2022; 13:1004949. [PMID: 36304460 PMCID: PMC9592691 DOI: 10.3389/fimmu.2022.1004949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022] Open
Abstract
Background Recent evidence has indicated that alterations in energy metabolism play a critical role in the pathogenesis of fibrotic diseases. Studies have suggested that ‘metabolic reprogramming’ involving the glycolysis and oxidative phosphorylation (OXPHOS) in cells lead to an enhanced generation of energy and biosynthesis. The aim of this study was to assess the molecular basis of changes in fibrotic metabolism in systemic sclerosis (Scleroderma; SSc) and highlight the most appropriate targets for anti-fibrotic therapies. Materials and methods Dermal fibroblasts were isolated from five SSc patients and five healthy donors. Cells were cultured in medium with/without TGF-β1 and with/without ALK5, pan-PIM or ATM kinase inhibitors. Extracellular flux analyses were performed to evaluate glycolytic and mitochondrial respiratory function. The mitochondrial network in TMRM-stained cells was visualized by confocal laser-scanning microscopy, followed by semi-automatic analysis on the ImageJ platform. Protein expression of ECM and fibroblast components, glycolytic enzymes, subunits of the five OXPHOS complexes, and dynamin-related GTPases and receptors involved in mitochondrial fission/fusion were assessed by western blotting. Results Enhanced mitochondrial respiration coupled to ATP production was observed in SSc fibroblasts at the expense of spare respiratory capacity. Although no difference was found in glycolysis when comparing SSc with healthy control fibroblasts, levels of phophofructokinase-1 isoform PFKM were significantly lower in SSc fibroblasts (P<0.05). Our results suggest that the number of respirasomes is decreased in the SSc mitochondria; however, the organelles formed a hyperfused network, which is thought to increase mitochondrial ATP production through complementation. The increased mitochondrial fusion correlated with a change in expression levels of regulators of mitochondrial morphology, including decreased levels of DRP1, increased levels of MIEF2 and changes in OPA1 isoform ratios. TGF-β1 treatment strongly stimulated glycolysis and mitochondrial respiration and induced the expression of fibrotic markers. The pan-PIM kinase inhibitor had no effect, whereas both ALK5 and ATM kinase inhibition abrogated TGF-β1-mediated fibroblast activation, and upregulation of glycolysis and respiration. Conclusions Our data provide evidence for a novel mechanism(s) by which SSc fibroblasts exhibit altered metabolic programs and highlight changes in respiration and dysregulated mitochondrial morphology and function, which can be selectively targeted by small molecule kinase inhibitors.
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Affiliation(s)
- Isabella Gomes Cantanhede
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, University College London, London, United Kingdom
- Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco, Recife, Brazil
| | - Huan Liu
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, University College London, London, United Kingdom
- Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - Huan Liu
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, University College London, London, United Kingdom
| | - Vestaen Balbuena Rodriguez
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, University College London, London, United Kingdom
| | - Xu Shiwen
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, University College London, London, United Kingdom
| | - Voo H. Ong
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, University College London, London, United Kingdom
| | - Christopher P. Denton
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, University College London, London, United Kingdom
| | - Markella Ponticos
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, University College London, London, United Kingdom
| | - Guo Xiong
- Health Science Center, Xi’an Jiaotong University, Xi’an, China
| | - José Luiz Lima-Filho
- Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco, Recife, Brazil
| | - David Abraham
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, University College London, London, United Kingdom
- *Correspondence: David Abraham, ; Jan-Willem Taanman,
| | - Jeries Abu-Hanna
- Centre for Rheumatology and Connective Tissue Diseases, Division of Medicine, University College London, London, United Kingdom
| | - Jan-Willem Taanman
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, United Kingdom
- *Correspondence: David Abraham, ; Jan-Willem Taanman,
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11
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Li Z, Wu M, Liu S, Liu X, Huan Y, Ye Q, Yang X, Guo H, Liu A, Huang X, Yang X, Ding F, Xu H, Zhou J, Liu P, Liu S, Jin Y, Xuan K. Apoptotic vesicles activate autophagy in recipient cells to induce angiogenesis and dental pulp regeneration. Mol Ther 2022; 30:3193-3208. [PMID: 35538661 PMCID: PMC9552912 DOI: 10.1016/j.ymthe.2022.05.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 12/14/2021] [Revised: 04/19/2022] [Accepted: 05/07/2022] [Indexed: 11/16/2022] Open
Abstract
Extracellular vesicles (EVs) derived from living cells play important roles in donor cell-induced recipient tissue regeneration. Although numerous studies have found that cells undergo apoptosis after implantation in an ischemic-hypoxic environment, the roles played by the EVs released by apoptotic cells are largely unknown. In this study, we obtained apoptotic vesicles (apoVs) derived from human deciduous pulp stem cells and explored their effects on the dental pulp regeneration process. Our work showed that apoVs were ingested by endothelial cells (ECs) and elevated the expression of angiogenesis-related genes, leading to pulp revascularization and tissue regeneration. Furthermore, we found that, at the molecular level, apoV-carried mitochondrial Tu translation elongation factor was transported and regulated the angiogenic activation of ECs via the transcription factor EB-autophagy pathway. In a beagle model of dental pulp regeneration in situ, apoVs recruited endogenous ECs and facilitated the formation of dental-pulp-like tissue rich in blood vessels. These findings revealed the significance of apoptosis in tissue regeneration and demonstrated the potential of using apoVs to promote angiogenesis in clinical applications.
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Affiliation(s)
- Zihan Li
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China; State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Meiling Wu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Siying Liu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Xuemei Liu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China; State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Yu Huan
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Qingyuan Ye
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China; State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Department of Periodontology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Xiaoxue Yang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Hao Guo
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Anqi Liu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Xiaoyao Huang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Xiaoshan Yang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China; Stomatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Feng Ding
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Haokun Xu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Jun Zhou
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Peisheng Liu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China
| | - Shiyu Liu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China.
| | - Yan Jin
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China.
| | - Kun Xuan
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Clinical Research Center for Oral Diseases, Department of Preventive Dentistry, School of Stomatology, The Fourth Military Medical University, 145West Changle Road, Xi'an, Shaanxi, China.
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12
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Dąbrowska J, Biedziak B, Szponar-Żurowska A, Budner M, Jagodziński PP, Płoski R, Mostowska A. Identification of novel susceptibility genes for non-syndromic cleft lip with or without cleft palate using NGS-based multigene panel testing. Mol Genet Genomics 2022; 297:1315-1327. [PMID: 35778651 DOI: 10.1007/s00438-022-01919-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/12/2022] [Indexed: 01/02/2023]
Abstract
For non-syndromic cleft lip with or without cleft palate (ns-CL/P), the proportion of heritability explained by the known risk loci is estimated to be about 30% and is captured mainly by common variants identified in genome-wide association studies. To contribute to the explanation of the "missing heritability" problem for orofacial clefts, a candidate gene approach was taken to investigate the potential role of rare and private variants in the ns-CL/P risk. Using the next-generation sequencing technology, the coding sequence of a set of 423 candidate genes was analysed in 135 patients from the Polish population. After stringent multistage filtering, 37 rare coding and splicing variants of 28 genes were identified. 35% of these genetic alternations that may play a role of genetic modifiers influencing an individual's risk were detected in genes not previously associated with the ns-CL/P susceptibility, including COL11A1, COL17A1, DLX1, EFTUD2, FGF4, FGF8, FLNB, JAG1, NOTCH2, SHH, WNT5A and WNT9A. Significant enrichment of rare alleles in ns-CL/P patients compared with controls was also demonstrated for ARHGAP29, CHD7, COL17A1, FGF12, GAD1 and SATB2. In addition, analysis of panoramic radiographs of patients with identified predisposing variants may support the hypothesis of a common genetic link between orofacial clefts and dental abnormalities. In conclusion, our study has confirmed that rare coding variants might contribute to the genetic architecture of ns-CL/P. Since only single predisposing variants were identified in novel cleft susceptibility genes, future research will be required to confirm and fully understand their role in the aetiology of ns-CL/P.
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Affiliation(s)
- Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland
| | - Barbara Biedziak
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Szponar-Żurowska
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Margareta Budner
- Eastern Poland Burn Treatment and Reconstructive Center, Leczna, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781, Poznan, Poland.
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13
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Zhao S, Mai RM, Zhang T, Feng XZ, Li WT, Wang WX, Luo XM, Feng JX. Simultaneous manipulation of transcriptional regulator CxrC and translational elongation factor eEF1A enhances the production of plant-biomass-degrading enzymes of Penicillium oxalicum. Bioresour Technol 2022; 351:127058. [PMID: 35339654 DOI: 10.1016/j.biortech.2022.127058] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Genetic engineering is an efficient approach to improve fungal bioproducts, but the specific targets are limited. In this study, it was found that the key transcription repressor CxrC of Penicillium oxalicum could physically interact with the translational elongation factor eEF1A that positively regulated the production of plant-biomass-degrading enzymes by the fungus under Avicel induction. Simultaneously deletion of the cxrC and overexpression of the eEF1A in the strain Δku70 resulted in 55.4%-314.6% higher production of cellulase, xylanase and raw-starch-degrading enzymes than that of the start strain Δku70. Transcript abundance of the genes encoding predominant cellulases, xylanases and raw-starch-degrading enzymes were significantly upregulated in the mutant ΔcxrC::eEF1A. The ΔcxrC::eEF1A enhanced saccharification efficiency of raw cassava flour by 9.3%-15.5% at early-middle stage of hydrolysis in comparison with Δku70. The obtained knowledges expanded the sources used as effective targets for increased production of plant-biomass-degrading enzymes by fungi.
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Affiliation(s)
- Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Rong-Ming Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xiang-Zhao Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Wen-Tong Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Wen-Xuan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China.
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14
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Das JK, Ren Y, Kumar A, Peng HY, Wang L, Xiong X, Alaniz RC, de Figueiredo P, Ren X, Liu X, Ryazonov AG, Yang JM, Song J. Elongation factor-2 kinase is a critical determinant of the fate and antitumor immunity of CD8 + T cells. Sci Adv 2022; 8:eabl9783. [PMID: 35108044 PMCID: PMC8809536 DOI: 10.1126/sciadv.abl9783] [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] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
eEF-2K has important roles in stress responses and cellular metabolism. We report here a previously unappreciated but critical role of eEF-2K in regulating the fate and cytocidal activity of CD8+ T cells. CD8+ T cells from eEF-2K KO mice were more proliferative but had lower survival than their wild-type counterparts after their activation, followed by occurrence of premature senescence and exhaustion. eEF-2K KO CD8+ T cells were more metabolically active and showed hyperactivation of the Akt-mTOR-S6K pathway. Loss of eEF-2K substantially impaired the activity of CD8+ T cells. Furthermore, the antitumor efficacy and tumor infiltration of the CAR-CD8+ T cells lacking eEF-2K were notably reduced as compared to the control CAR-CD8+ T cells. Thus, eEF-2K is critically required for sustaining the viability and function of cytotoxic CD8+ T cells, and therapeutic augmentation of this kinase may be exploited as a novel approach to reinforcing CAR-T therapy against cancer.
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Affiliation(s)
- Jugal Kishore Das
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77843, USA
| | - Yijie Ren
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77843, USA
| | - Anil Kumar
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77843, USA
| | - Hao-Yun Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77843, USA
| | - Liqing Wang
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77843, USA
| | - Xiaofang Xiong
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77843, USA
| | - Robert C. Alaniz
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77843, USA
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77843, USA
- Norman Borlaug Center, Texas A&M University, College Station, TX 77843, USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Xingcong Ren
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Alexey G. Ryazonov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Jin-Ming Yang
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Jianxun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77843, USA
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15
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李 晓, 洪 梦, 戴 朴, 袁 永. [Clinical case analysis and literature review of mandibulofacial dysostosis with microcephaly syndrome]. Lin Chuang Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2022; 36:36-40. [PMID: 34979617 PMCID: PMC10128212 DOI: 10.13201/j.issn.2096-7993.2022.01.008] [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] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Indexed: 06/14/2023]
Abstract
Objective:To explore the clinical diagnosis, otological treatment and molecular etiology in a rare syndromic hearing loss case characterized by mandibulofacial dysostosis with microcephaly(MFDM). Methods: The proband underwent detailed history collection, systematic physical examination and phenotypic analysis, as well as audiological examination, chest X-ray, temporal bone CT and brain MRI and other imaging examinations. The blood DNA of the proband and his parents was extracted and tested by the whole exom sequencing. The EFTUD2-related-MFDM literatures published by the end of 2020 were searched and sifted in PubMed and CNKI databases,the clinical characteristics of MFDM were summarized. Results:In this study, the patient presented with hypoplasia of auricle, micrognathia, microcephaly, developmental retardation, severe sensorineural hearing loss in both ears, and developmental malformation of middle and inner ear. Genetic analysis revealed a de novo deletion c.623_624delAT in EFTUD2 gene. According to the clinical features and genetic test results, the patient was diagnosed as MFDM. In order to solve the problem of hearing loss, the patient was further performed bilateral cochlear implantation, and part of the electrodes responded well during and after operation. Conclusion:This is the first domestic reported case of MFDM caused by EFTUD2 gene mutation. The key problem of cochlear implantation for this kind of patient is to avoid damaging the malformed facial nerve during the operation.The effect of speech rehabilitation after cochlear implant operation is related to many factors such as intelligence development of the patients.
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Affiliation(s)
- 晓雨 李
- 国家耳鼻咽喉疾病临床医学研究中心 解放军总医院第六医学中心耳鼻咽喉头颈外科医学部 解放军总医院第六医学中心耳显微外科(北京,100048)National Clinical Research Center for Otolaryngologic Diseases, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Department of Otomicrosurgery, Sixth Medical Center of the PLA General Hospital, Beijing, 100048, China
| | - 梦迪 洪
- 解放军总医院第一医学中心耳鼻咽喉头颈外科听觉植入中心Auditory Implant Center, Department of Otolaryngology Head and Neck Surgery, First Medical Center of the PLA General Hospital
| | - 朴 戴
- 国家耳鼻咽喉疾病临床医学研究中心 解放军总医院第六医学中心耳鼻咽喉头颈外科医学部 解放军总医院第六医学中心耳显微外科(北京,100048)National Clinical Research Center for Otolaryngologic Diseases, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Department of Otomicrosurgery, Sixth Medical Center of the PLA General Hospital, Beijing, 100048, China
| | - 永一 袁
- 国家耳鼻咽喉疾病临床医学研究中心 解放军总医院第六医学中心耳鼻咽喉头颈外科医学部 解放军总医院第六医学中心耳显微外科(北京,100048)National Clinical Research Center for Otolaryngologic Diseases, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Department of Otomicrosurgery, Sixth Medical Center of the PLA General Hospital, Beijing, 100048, China
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16
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Abstract
In ribosomal translation, peptidyl transfer occurs between P-site peptidyl-tRNA and A-site aminoacyl-tRNA, followed by translocation of the resulting P-site deacylated-tRNA and A-site peptidyl-tRNA to E and P site, respectively, mediated by EF-G. Here, we report that mistranslocation of P-site peptidyl-tRNA and A-site aminoacyl-tRNA toward E and A site occurs when high concentration of EF-G triggers the migration of two tRNAs prior to completion of peptidyl transfer. Consecutive incorporation of less reactive amino acids, such as Pro and d-Ala, makes peptidyl transfer inefficient and thus induces the mistranslocation event. Consequently, the E-site peptidyl-tRNA drops off from ribosome to give a truncated peptide lacking the C-terminal region. The P-site aminoacyl-tRNA allows for reinitiation of translation upon accommodation of a new aminoacyl-tRNA at A site, leading to synthesis of a truncated peptide lacking the N-terminal region, which we call the ‘reinitiated peptide’. We also revealed that such a drop-off-reinitiation event can be alleviated by EF-P that promotes peptidyl transfer of Pro. Moreover, this event takes place both in vitro and in cell, showing that reinitiated peptides during protein synthesis could be accumulated in this pathway in cells.
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Affiliation(s)
- Kenya Tajima
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Hiroaki Suga
- To whom correspondence should be addressed. Tel: +81 3 5841 8372; Fax: +81 3 5841 8372;
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17
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Chen X, He L, Xu M, Yang J, Li J, Zhang T, Liao Q, Zhang H, Yang J, Chen J. Binding between elongation factor 1A and the 3'-UTR of Chinese wheat mosaic virus is crucial for virus infection. Mol Plant Pathol 2021; 22:1383-1398. [PMID: 34405507 PMCID: PMC8518580 DOI: 10.1111/mpp.13120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 05/06/2023]
Abstract
The Chinese wheat mosaic virus (CWMV) genome consists of two positive-strand RNAs that are required for CWMV replication and translation. The eukaryotic translation elongation factor (eEF1A) is crucial for the elongation of protein translation in eukaryotes. Here, we show that silencing eEF1A expression in Nicotiana benthamiana plants by performing virus-induced gene silencing can greatly reduce the accumulation of CWMV genomic RNAs, whereas overexpression of eEF1A in plants increases the accumulation of CWMV genomic RNAs. In vivo and in vitro assays showed that eEF1A does not interact with CWMV RNA-dependent RNA polymerase. Electrophoretic mobility shift assays revealed that eEF1A can specifically bind to the 3'-untranslated region (UTR) of CWMV genomic RNAs. By performing mutational analyses, we determined that the conserved region in the 3'-UTR of CWMV genomic RNAs is necessary for CWMV replication and translation, and that the sixth stem-loop (SL-6) in the 3'-UTR of CWMV genomic RNAs plays a key role in CWMV infection. We conclude that eEF1A is an essential host factor for CWMV infection. This finding should help us to develop new strategies for managing CWMV infections in host plants.
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Affiliation(s)
- Xuan Chen
- College of Plant ProtectionNorthwest Agriculture and Forestry UniversityYanglingChina
- State Key Laboratory for Quality and Safety of Agro‐productsInstitute of Plant Virology of Ningbo UniversityNingboChina
- Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Long He
- State Key Laboratory for Quality and Safety of Agro‐productsInstitute of Plant Virology of Ningbo UniversityNingboChina
| | - Miaoze Xu
- State Key Laboratory for Quality and Safety of Agro‐productsInstitute of Plant Virology of Ningbo UniversityNingboChina
| | - Jin Yang
- College of Plant ProtectionNorthwest Agriculture and Forestry UniversityYanglingChina
- State Key Laboratory for Quality and Safety of Agro‐productsInstitute of Plant Virology of Ningbo UniversityNingboChina
| | - Juan Li
- State Key Laboratory for Quality and Safety of Agro‐productsInstitute of Plant Virology of Ningbo UniversityNingboChina
| | - Tianye Zhang
- State Key Laboratory for Quality and Safety of Agro‐productsInstitute of Plant Virology of Ningbo UniversityNingboChina
| | - Qiansheng Liao
- College of Life ScienceZhejiang SCI‐Tech UniversityHangzhouChina
| | - Hengmu Zhang
- Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro‐productsInstitute of Plant Virology of Ningbo UniversityNingboChina
- Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Jianping Chen
- College of Plant ProtectionNorthwest Agriculture and Forestry UniversityYanglingChina
- State Key Laboratory for Quality and Safety of Agro‐productsInstitute of Plant Virology of Ningbo UniversityNingboChina
- Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouChina
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18
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Reina J. [Plitidepsin, an inhibitor of the cell elongation factor eEF1a, and molnupiravir an analogue of the ribonucleoside cytidine, two new chemical compounds with intense activity against SARS-CoV-2]. Rev Esp Quimioter 2021; 34:402-407. [PMID: 33902254 PMCID: PMC8638831 DOI: 10.37201/req/042.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/14/2021] [Accepted: 03/21/2021] [Indexed: 11/10/2022]
Abstract
The knowledge of the replicative cycle of SARS-CoV-2 and its interactions with cellular proteins has opened a new therapeutic possibility based on blocking those essential for the virus. The cellular protein elongation factor eEF1A could be a good target. Among its natural inhibitors are didemnins and their related chemical compounds such as plitidepsin. In human cell culture, this compound is capable of inhibiting the virus with a potency 27,5 times that of remdesivir. It must be administered intravenously. Of the ribonucleoside analogues, molnupiravir (MK-4483/EIDD-2801) (hydroxy-cytidine) determines a lethal mutagenesis on SARS-CoV-2. In animals, after oral administration, the pulmonary viral load decreases 25,000 times and when administered as prophylaxis, approximately 100,000 times. It prevents the transmission of the virus and eliminates its presence in the oropharynx. Both chemicals have started Phase I / II human clinical trials.
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Affiliation(s)
- J Reina
- Jordi Reina, Unidad de Virología, Hospital Universitario Son Espases. Facultad de Medicina UIB. Carretera de Valldemossa 79, 07120 Palma de Mallorca. Spain.
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19
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Marković SM, Živančev D, Horvat D, Torbica A, Jovankić J, Djukić NH. Correlation of elongation factor 1A accumulation with photosynthetic pigment content and yield in winter wheat varieties under heat stress conditions. Plant Physiol Biochem 2021; 166:572-581. [PMID: 34175812 DOI: 10.1016/j.plaphy.2021.06.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Heat stress is one of the most important environmental factors that influences wheat growth and development, leading to significant losses in grain yield and has become a significant detrimental factor for worldwide wheat production. In recent years, several studies suggested that eukaryotic elongation factor 1A (eEF1A), may contribute to heat tolerance in plants, therefore the aim of this study was: to investigate the accumulation of eEF1A in wheat under conditions of moderate and high air temperatures; to determine the amount of photosynthetic pigments and to determine the yield traits; and to examine whether there is a correlation between eEF1A accumulation, photosynthetic pigments, and yield in different wheat varieties. The results showed that heat stress induced accumulation of eEF1A significantly different among wheat varieties and showed that varieties with a higher accumulation of eEF1A under heat stress are characterized by a smaller decrease in the photosynthetic pigments. A correlation between higher accumulation of eEF1A under heat stress and yield traits was found. Analyzed parameters from two growing seasons, indicated that the higher accumulation of eEF1A and a smaller decrease in photosynthetic pigments distinguishes the varieties more resistant to heat stress. The analysis of the molecular mechanisms by immunoblot, under conditions of high and moderate air temperatures in two growing seasons, aims to develop agricultural strategy and develop wheat varieties tolerant to heat stress.
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Affiliation(s)
- Stefan M Marković
- University of Kragujevac, Faculty of Science, Department of Biology and Ecology, Radoja Domanovića 12, 34000, Kragujevac, Serbia.
| | - Dragan Živančev
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
| | - Daniela Horvat
- Agricultural Institute Osijek, Agrochemical Laboratory, Južno Predgrađe 17, 31000, Osijek, Croatia
| | - Aleksandra Torbica
- University of Novi Sad, Institute of Food Technology, Bulevar Cara Lazara 1, 21000, Novi Sad, Serbia
| | - Jovana Jovankić
- University of Kragujevac, Faculty of Science, Department of Biology and Ecology, Radoja Domanovića 12, 34000, Kragujevac, Serbia
| | - Nevena H Djukić
- University of Kragujevac, Faculty of Science, Department of Biology and Ecology, Radoja Domanovića 12, 34000, Kragujevac, Serbia
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20
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Gijsbers A, Montagut DC, Méndez-Godoy A, Altamura D, Saviano M, Siliqi D, Sánchez-Puig N. Interaction of the GTPase Elongation Factor Like-1 with the Shwachman-Diamond Syndrome Protein and Its Missense Mutations. Int J Mol Sci 2018; 19:E4012. [PMID: 30545121 PMCID: PMC6321010 DOI: 10.3390/ijms19124012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
The Shwachman-Diamond Syndrome (SDS) is a disorder arising from mutations in the genes encoding for the Shwachman-Bodian-Diamond Syndrome (SBDS) protein and the GTPase known as Elongation Factor Like-1 (EFL1). Together, these proteins remove the anti-association factor eIF6 from the surface of the pre-60S ribosomal subunit to promote the formation of mature ribosomes. SBDS missense mutations can either destabilize the protein fold or affect surface epitopes. The molecular alterations resulting from the latter remain largely unknown, although some evidence suggest that binding to EFL1 may be affected. We further explored the effect of these SBDS mutations on the interaction with EFL1, and showed that all tested mutations disrupted the binding to EFL1. Binding was either severely weakened or almost abolished, depending on the assessed mutation. In higher eukaryotes, SBDS is essential for development, and lack of the protein results in early lethality. The existence of patients whose only source of SBDS consists of that with surface missense mutations highlights the importance of the interaction with EFL1 for their function. Additionally, we studied the interaction mechanism of the proteins in solution and demonstrated that binding consists of two independent and cooperative events, with domains 2⁻3 of SBDS directing the initial interaction with EFL1, followed by docking of domain 1. In solution, both proteins exhibited large flexibility and consisted of an ensemble of conformations, as demonstrated by Small Angle X-ray Scattering (SAXS) experiments.
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Affiliation(s)
- Abril Gijsbers
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Diana Carolina Montagut
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Alfonso Méndez-Godoy
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Davide Altamura
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Michele Saviano
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Dritan Siliqi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Nuria Sánchez-Puig
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
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21
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Tan QKG, Cope H, Spillmann RC, Stong N, Jiang YH, McDonald MT, Rothman JA, Butler MW, Frush DP, Lachman RS, Lee B, Bacino CA, Bonner MJ, McCall CM, Pendse AA, Walley N, Shashi V, Pena LDM. Further evidence for the involvement of EFL1 in a Shwachman-Diamond-like syndrome and expansion of the phenotypic features. Cold Spring Harb Mol Case Stud 2018; 4:a003046. [PMID: 29970384 PMCID: PMC6169826 DOI: 10.1101/mcs.a003046] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022] Open
Abstract
Recent evidence has implicated EFL1 in a phenotype overlapping Shwachman-Diamond syndrome (SDS), with the functional interplay between EFL1 and the previously known causative gene SBDS accounting for the similarity in clinical features. Relatively little is known about the phenotypes associated with pathogenic variants in the EFL1 gene, but the initial indication was that phenotypes may be more severe, when compared with SDS. We report a pediatric patient who presented with a metaphyseal dysplasia and was found to have biallelic variants in EFL1 on reanalysis of trio whole-exome sequencing data. The variant had not been initially reported because of the research laboratory's focus on de novo variants. Subsequent phenotyping revealed variability in her manifestations. Although her metaphyseal abnormalities were more severe than in the original reported cohort with EFL1 variants, the bone marrow abnormalities were generally mild, and there was equivocal evidence for pancreatic insufficiency. Despite the limited number of reported patients, variants in EFL1 appear to cause a broader spectrum of symptoms that overlap with those seen in SDS. Our report adds to the evidence of EFL1 being associated with an SDS-like phenotype and provides information adding to our understanding of the phenotypic variability of this disorder. Our report also highlights the value of exome data reanalysis when a diagnosis is not initially apparent.
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Affiliation(s)
- Queenie K-G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York 10032, USA
| | - Yong-Hui Jiang
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Marie T McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jennifer A Rothman
- Department of Pediatrics, Division of Hematology-Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Megan W Butler
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Donald P Frush
- Department of Radiology, Division of Pediatric Radiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Ralph S Lachman
- Cedars-Sinai Medical Center, International Skeletal Dysplasia Registry, Los Angeles, California 90048, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Melanie J Bonner
- Department of Psychiatry and Behavioral Sciences, Division of Child and Family Mental Health and Developmental Neuroscience, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Chad M McCall
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Avani A Pendse
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Nicole Walley
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Loren D M Pena
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, Ohio 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, USA
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22
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Abstract
Transcription is a discontinuous process, where each nucleotide incorporation cycle offers a decision between elongation, pausing, halting, or termination. Many cis-acting regulatory RNAs, such as riboswitches, exert their influence over transcription elongation. Through such mechanisms, certain RNA elements can couple physiological or environmental signals to transcription attenuation, a process where cis-acting regulatory RNAs directly influence formation of transcription termination signals. However, through another regulatory mechanism called processive antitermination (PA), RNA polymerase can bypass termination sites over much greater distances than transcription attenuation. PA mechanisms are widespread in bacteria, although only a few classes have been discovered overall. Also, although traditional, signal-responsive riboswitches have not yet been discovered to promote PA, it is increasingly clear that small RNA elements are still oftentimes required. In some instances, small RNA elements serve as loading sites for cellular factors that promote PA. In other instances, larger, more complicated RNA elements participate in PA in unknown ways, perhaps even acting alone to trigger PA activity. These discoveries suggest that what is now needed is a systematic exploration of PA in bacteria, to determine how broadly these transcription elongation mechanisms are utilized, to reveal the diversity in their molecular mechanisms, and to understand the general logic behind their cellular applications. This review covers the known examples of PA regulatory mechanisms and speculates that they may be broadly important to bacteria.
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Affiliation(s)
- Jonathan R. Goodson
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD 20742
| | - Wade C. Winkler
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD 20742
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23
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Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ. Mechanism of eIF6 release from the nascent 60S ribosomal subunit. Nat Struct Mol Biol 2015; 22:914-9. [PMID: 26479198 PMCID: PMC4871238 DOI: 10.1038/nsmb.3112] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [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: 08/04/2015] [Accepted: 09/17/2015] [Indexed: 12/20/2022]
Abstract
SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eIF6 from nascent 60S ribosomal subunits. However, the mechanism is completely unknown. Here, we present cryo-EM structures of human SBDS and SBDS-EFL1 bound to Dictyostelium discoideum 60S ribosomal subunits with and without endogenous eIF6. SBDS assesses the integrity of the peptidyl (P) site, bridging uL16 (mutated in T-cell acute lymphoblastic leukemia) with uL11 at the P-stalk base and the sarcin-ricin loop. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit. Our data reveal the conserved mechanism of eIF6 release, which is corrupted in both inherited and sporadic leukemias.
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Affiliation(s)
- Félix Weis
- Cambridge Institute for Medical Research, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Emmanuel Giudice
- Université de Rennes 1, Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 6290, Institut de Génétique et Développement de Rennes, Rennes, France
| | - Mark Churcher
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Li Jin
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Christine Hilcenko
- Cambridge Institute for Medical Research, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Chi C Wong
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - David Traynor
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Robert R Kay
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Alan J Warren
- Cambridge Institute for Medical Research, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge Research Unit, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
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24
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Priya P, Venkatachalam P, Thulaseedharan A. Differential expression pattern of rubber elongation factor (REF) mRNA transcripts from high and low yielding clones of rubber tree (Hevea brasiliensis Muell. Arg.). Plant Cell Rep 2007; 26:1833-8. [PMID: 17632724 DOI: 10.1007/s00299-007-0402-z] [Citation(s) in RCA: 30] [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] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 06/13/2007] [Accepted: 06/23/2007] [Indexed: 05/16/2023]
Abstract
In Hevea tree, rubber elongation factor (REF) is a key gene involved in rubber biosynthesis. Since the immaturity period for Hevea is 6 years, identification of molecular marker for latex yield potential will be beneficial for early selection of high yielding clones. The main objective of this research is to study the expression pattern of the REF gene in contrasting latex yield rubber clones (high and low yielding) by Northern blot as well as RT-PCR analysis. Accumulation of REF mRNA transcripts was significantly higher in latex cells compared to other cells of seedlings and mature Hevea trees. Northern results revealed that the level of REF gene expression in latex cells of high yielding rubber clones was significantly higher than in low yielders. According to RT-PCR results, the abundance of REF mRNA transcripts in latex cells was fivefold higher in the RRII105 clone, one of the most high yielding rubber clones. It is evident from the results that both tapping and ethephon treatment had a direct effect on induction of REF gene expression. Results demonstrate a positive correlation between REF gene expression pattern and latex yield.
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Affiliation(s)
- P Priya
- Biotechnology Division, Rubber Research Institute of India, Kottayam 686009, India
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25
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Cresawn SG, Prins C, Latner DR, Condit RC. Mapping and phenotypic analysis of spontaneous isatin-beta-thiosemicarbazone resistant mutants of vaccinia virus. Virology 2007; 363:319-32. [PMID: 17336362 PMCID: PMC1950264 DOI: 10.1016/j.virol.2007.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 02/05/2007] [Accepted: 02/05/2007] [Indexed: 11/22/2022]
Abstract
Treatment of wild type vaccinia virus infected cells with the anti-poxviral drug isatin-beta-thiosemicarbazone (IBT) induces the viral postreplicative transcription apparatus to synthesize longer-than-normal mRNAs through an unknown mechanism. Previous studies have shown that virus mutants resistant to or dependent on IBT affect genes involved in control of viral postreplicative transcription elongation. This study was initiated in order to identify additional viral genes involved in control of vaccinia postreplicative transcription elongation. Eight independent, spontaneous IBT resistant mutants of vaccinia virus were isolated. Marker rescue experiments mapped two mutants to gene G2R, which encodes a previously characterized postreplicative gene positive transcription elongation factor. Three mutants mapped to the largest subunit of the viral RNA polymerase, rpo147, the product of gene J6R. One mutant contained missense mutations in both G2R and A24R (rpo132, the second largest subunit of the RNA polymerase). Two mutants could not be mapped, however sequence analysis demonstrated that neither of these mutants contained mutations in previously identified IBT resistance or dependence genes. Phenotypic and biochemical analysis of the mutants suggests that they possess defects in transcription elongation that compensate for the elongation enhancing effects of IBT. The results implicate the largest subunit of the RNA polymerase (rpo147) in the control of elongation, and suggest that there exist additional gene products which mediate intermediate and late transcription elongation in vaccinia virus.
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Affiliation(s)
| | | | | | - Richard C. Condit
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610
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26
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Abstract
The purpose of this review is to provide an overview of the unique mechanism by which mammalian selenoprotein synthesis occurs. Selenoprotein synthesis requires translational recoding of the UGA codon from a stop signal to a selenocysteine insertion signal (SECIS). Dedicated factors directly involved in this translation process include specific secondary structure in the mRNA (SECIS), a unique tRNA (Sec-tRNA(Sec)), an RNA binding protein (SBP2), and a specialized elongation factor (EFsec). Regulation of this process is discussed along with physiologic and clinical issues regarding selenoprotein synthesis, including the side effects associated with statin drugs.
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Affiliation(s)
- Peter R Hoffmann
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA.
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27
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Pereira CM, Sattlegger E, Jiang HY, Longo BM, Jaqueta CB, Hinnebusch AG, Wek RC, Mello LEAM, Castilho BA. IMPACT, a protein preferentially expressed in the mouse brain, binds GCN1 and inhibits GCN2 activation. J Biol Chem 2005; 280:28316-23. [PMID: 15937339 DOI: 10.1074/jbc.m408571200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [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: 12/17/2022] Open
Abstract
Translational control directed by the eukaryotic translation initiation factor 2 alpha-subunit (eIF2alpha) kinase GCN2 is important for coordinating gene expression programs in response to nutritional deprivation. The GCN2 stress response, conserved from yeast to mammals, is critical for resistance to nutritional deficiencies and for the control of feeding behaviors in rodents. The mouse protein IMPACT has sequence similarities to the yeast YIH1 protein, an inhibitor of GCN2. YIH1 competes with GCN2 for binding to a positive regulator, GCN1. Here, we present evidence that IMPACT is the functional counterpart of YIH1. Overexpression of IMPACT in yeast lowered both basal and amino acid starvation-induced levels of phosphorylated eIF2alpha, as described for YIH1 (31). Overexpression of IMPACT in mouse embryonic fibroblasts inhibited phosphorylation of eIF2alpha by GCN2 under leucine starvation conditions, abolishing expression of its downstream target genes, ATF4 (CREB-2) and CHOP (GADD153). IMPACT bound to the minimal yeast GCN1 segment required for interaction with yeast GCN2 and YIH1 and to native mouse GCN1. At the protein level, IMPACT was detected mainly in the brain. IMPACT was found to be abundant in the majority of hypothalamic neurons. Scattered neurons expressing this protein at higher levels were detected in other regions such as the hippocampus and piriform cortex. The abundance of IMPACT correlated inversely with phosphorylated eIF2alpha levels in different brain areas. These results suggest that IMPACT ensures constant high levels of translation and low levels of ATF4 and CHOP in specific neuronal cells under amino acid starvation conditions.
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Affiliation(s)
- Cátia M Pereira
- Departamentos de Microbiologia, Imunologia, e Parasitologia and Fisiologia, Universidade Federal de São Paulo, São Paulo SP 04023-062, Brazil
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28
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Sattlegger E, Hinnebusch AG. Polyribosome Binding by GCN1 Is Required for Full Activation of Eukaryotic Translation Initiation Factor 2α Kinase GCN2 during Amino Acid Starvation. J Biol Chem 2005; 280:16514-21. [PMID: 15722345 DOI: 10.1074/jbc.m414566200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [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: 11/06/2022] Open
Abstract
The protein kinase GCN2 mediates translational control of gene expression in amino acid-starved cells by phosphorylating eukaryotic translation initiation factor 2alpha. In Saccharomyces cerevisiae, activation of GCN2 by uncharged tRNAs in starved cells requires its direct interaction with both the GCN1.GCN20 regulatory complex and ribosomes. GCN1 also interacts with ribosomes in cell extracts, but it was unknown whether this activity is crucial for its ability to stimulate GCN2 function in starved cells. We describe point mutations in two conserved, noncontiguous segments of GCN1 that lead to reduced polyribosome association by GCN1.GCN20 in living cells without reducing GCN1 expression or its interaction with GCN20. Mutating both segments simultaneously produced a greater reduction in polyribosome binding by GCN1.GCN20 and a stronger decrease in eukaryotic translation initiation factor 2alpha phosphorylation than did mutating in one segment alone. These findings provide strong evidence that ribosome binding by GCN1 is required for its role as a positive regulator of GCN2. A particular mutation in the GCN1 domain, related in sequence to translation elongation factor 3 (eEF3), decreased GCN2 activation much more than it reduced ribosome binding by GCN1. Hence, the eEF3-like domain appears to have an effector function in GCN2 activation. This conclusion supports the model that an eEF3-related activity of GCN1 influences occupancy of the ribosomal decoding site by uncharged tRNA in starved cells.
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Affiliation(s)
- Evelyn Sattlegger
- Laboratory of Gene Regulation and Development, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA
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Sattlegger E, Swanson MJ, Ashcraft EA, Jennings JL, Fekete RA, Link AJ, Hinnebusch AG. YIH1 Is an Actin-binding Protein That Inhibits Protein Kinase GCN2 and Impairs General Amino Acid Control When Overexpressed. J Biol Chem 2004; 279:29952-62. [PMID: 15126500 DOI: 10.1074/jbc.m404009200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [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: 11/06/2022] Open
Abstract
The general amino acid control (GAAC) enables yeast cells to overcome amino acid deprivation by activation of the alpha subunit of translation initiation factor 2 (eIF2alpha) kinase GCN2 and consequent induction of GCN4, a transcriptional activator of amino acid biosynthetic genes. Binding of GCN2 to GCN1 is required for stimulation of GCN2 kinase activity by uncharged tRNA in starved cells. Here we show that YIH1, when overexpressed, dampens the GAAC response (Gcn- phenotype) by suppressing eIF2alpha phosphorylation by GCN2. The overexpressed YIH1 binds GCN1 and reduces GCN1-GCN2 complex formation, and, consistent with this, the Gcn- phenotype produced by YIH1 overexpression is suppressed by GCN2 overexpression. YIH1 interacts with the same GCN1 fragment that binds GCN2, and this YIH1-GCN1 interaction requires Arg-2259 in GCN1 in vitro and in full-length GCN1 in vivo, as found for GCN2-GCN1 interaction. However, deletion of YIH1 does not increase eIF2alpha phosphorylation or derepress the GAAC, suggesting that YIH1 at native levels is not a general inhibitor of GCN2 activity. We discovered that YIH1 normally resides in a complex with monomeric actin, rather than GCN1, and that a genetic reduction in actin levels decreases the GAAC response. This Gcn- phenotype was partially suppressed by deletion of YIH1, consistent with YIH1-mediated inhibition of GCN2 in actin-deficient cells. We suggest that YIH1 resides in a YIH1-actin complex and may be released for inhibition of GCN2 and stimulation of protein synthesis under specialized conditions or in a restricted cellular compartment in which YIH1 is displaced from monomeric actin.
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Affiliation(s)
- Evelyn Sattlegger
- Laboratory of Gene Regulation and Development, NICHD, National Institutes of Health, Bethesda, Maryland 20892-2427, USA
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Min B, Kitabatake M, Polycarpo C, Pelaschier J, Raczniak G, Ruan B, Kobayashi H, Namgoong S, Söll D. Protein synthesis in Escherichia coli with mischarged tRNA. J Bacteriol 2003; 185:3524-6. [PMID: 12775689 PMCID: PMC156233 DOI: 10.1128/jb.185.12.3524-3526.2003] [Citation(s) in RCA: 34] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two types of aspartyl-tRNA synthetase exist: the discriminating enzyme (D-AspRS) forms only Asp-tRNA(Asp), while the nondiscriminating one (ND-AspRS) also synthesizes Asp-tRNA(Asn), a required intermediate in protein synthesis in many organisms (but not in Escherichia coli). On the basis of the E. coli trpA34 missense mutant transformed with heterologous ND-aspS genes, we developed a system with which to measure the in vivo formation of Asp-tRNA(Asn) and its acceptance by elongation factor EF-Tu. While large amounts of Asp-tRNA(Asn) are detrimental to E. coli, smaller amounts support protein synthesis and allow the formation of up to 38% of the wild-type level of missense-suppressed tryptophan synthetase.
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Affiliation(s)
- Bokkee Min
- Department of Molecular Biophysics, Yale University, New Haven, Connecticut 06520-8114, USA
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31
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Abstract
The (11;19)(q23;p13.1) translocation in acute leukemia results in the formation of a chimeric MLL-ELL fusion protein. ELL is an RNA Polymerase II (Pol II) transcriptional elongation factor that interacts with the recently identified EAF1 protein. Here, we show that ELL and EAF1 are components of Cajal bodies (CBs). Although ELL and EAF1 colocalize with p80 coilin, the signature protein of CBs, ELL and EAF1 do not exhibit a direct physical interaction with p80 coilin. Treatment of cells with actinomycin D, DRB, or alpha-amanitin, specific inhibitors of Pol II, disperses ELL and EAF1 from CBs, indicating that localization of ELL and EAF1 in CBs is dependent on active transcription by Pol II. The concentration of ELL and EAF1 in CBs links the transcriptional elongation activity of ELL to the RNA processing functions previously identified in CBs. Strikingly, CBs are disrupted in MLL-ELL leukemia. EAF1 and p80 coilin are delocalized from CBs in murine MLL-ELL leukemia cells and in HeLa cells transiently transfected with MLL-ELL. Nuclear and cytoplasmic fractionation revealed diminished expression of p80 coilin and EAF1 in the nuclei of MLL-ELL leukemia cells [corrected]. These studies are the first demonstration of a direct role of CB components in leukemogenesis.
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MESH Headings
- Autoantigens
- Cell Line
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 19/genetics
- Coiled Bodies/metabolism
- DNA-Binding Proteins/metabolism
- HeLa Cells
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Myeloid-Lymphoid Leukemia Protein
- Neoplasm Proteins
- Nuclear Proteins/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Peptide Elongation Factors
- Phosphoproteins/metabolism
- RNA/biosynthesis
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribonucleoproteins, Small Nuclear/metabolism
- Transcription Factors/metabolism
- Transcriptional Elongation Factors
- Transfection
- Translocation, Genetic
- snRNP Core Proteins
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Affiliation(s)
- Paul E Polak
- University of Chicago Section of Hematology/Oncology, Chicago, Illinois 60637-1470, USA
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Yamamoto K, Nagata K, Tsurukubo Y, Inagaki K, Ono R, Taki T, Hayashi Y, Hamaguchi H. Translocation (8;12)(q13;p13) during disease progression in acute myelomonocytic leukemia with t(11;19)(q23;p13.1). Cancer Genet Cytogenet 2002; 137:64-7. [PMID: 12377416 DOI: 10.1016/s0165-4608(02)00555-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here the first case of acute myelomonocytic leukemia (AMMoL) with both t(8;12)(q13;p13) and t(11;19)(q23;p13.1). A 75-year-old woman was initially diagnosed as having AMMoL with t(11;19) (q23;p13) as a sole abnormality. At the second relapse, G-banding analysis of the bone marrow cells showed 46,XX,t(11;19)(q23;p13)/46,XX,t(8;12)(q13;p13),t(11;19)(q23;p13). Fluorescence in situ hybridization analysis with chromosome-specific painting probes confirmed both the der(8)t(8;12) and the der(12)t(8;12). Reverse transcription-polymerase chain reaction analysis detected the MLL/ELL fusion transcript, indicating that the breakpoint on chromosome 19 was 19p13.1. Leukemic cells at the second relapse were positive for CD2, CD13, CD33, and CD34 but negative for CD14 and HLA-DR. The patient died within 2 months after a subclone with t(8;12)(q13;p13) had appeared. In the literature, t(8;12)(q12;p13) has been observed in two cases of myelodysplastic syndrome and one case of acute myeloblastic leukemia. Our results indicated that t(8;12)(q13;p13) may be one of the recurrent aberrations in myeloid malignancies, although molecular heterogeneity of the breakpoints might exist. Furthermore, it is suggested that t(8;12)(q13;p13) may play an important role in the progression of the disease and lead to the poor prognosis.
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MESH Headings
- Aged
- Amino Acid Sequence
- Base Sequence
- Chromosome Banding
- Chromosome Mapping
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 12
- Chromosomes, Human, Pair 19
- Chromosomes, Human, Pair 8
- DNA Primers
- DNA-Binding Proteins/genetics
- Disease Progression
- Exons
- Female
- Histone-Lysine N-Methyltransferase
- Humans
- Immunophenotyping
- In Situ Hybridization, Fluorescence
- Karyotyping
- Leukemia, Myelomonocytic, Acute/genetics
- Leukemia, Myelomonocytic, Acute/pathology
- Molecular Sequence Data
- Myeloid-Lymphoid Leukemia Protein
- Neoplasm Proteins
- Peptide Elongation Factors
- Polymerase Chain Reaction
- Proto-Oncogenes
- Recombinant Fusion Proteins/genetics
- Transcription Factors/genetics
- Transcription, Genetic
- Transcriptional Elongation Factors
- Translocation, Genetic
- Zinc Fingers
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Affiliation(s)
- Katsuya Yamamoto
- Department of Hematology, Musashino Red Cross Hospital, 1-26-1 Kyonan-cho, Musashino, 180-8610, Tokyo, Japan
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De Sanctis V, La Terra S, Bianchi A, Shore D, Burderi L, Di Mauro E, Negri R. In vivo topography of Rap1p-DNA complex at Saccharomyces cerevisiae TEF2 UAS(RPG) during transcriptional regulation. J Mol Biol 2002; 318:333-49. [PMID: 12051841 DOI: 10.1016/s0022-2836(02)00110-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [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: 10/27/2022]
Abstract
We have analyzed in detail the structure of RAP1-UAS(RPG) complexes in Saccharomyces cerevisiae cells using multi-hit KMnO(4), UV and micrococcal nuclease high-resolution footprinting. Three copies of the Rap1 protein are bound to the promoter simultaneously in exponentially growing cells, as shown by KMnO(4) multi-hit footprinting analysis, causing extended and diagnostic changes in the DNA structure of the region containing the UAS(RPG). Amino acid starvation does not cause loss of Rap1p from the complex; however, in vivo UV-footprinting reveals the occurrence of structural modifications of the complex. Moreover, low-resolution micrococcal nuclease digestion shows that the chromatin of the entire region is devoid of positioned nucleosomes but is susceptible to changes in accessibility to the nuclease upon amino acid starvation. The implications of these results for the mechanism of Rap1p action are discussed.
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Affiliation(s)
- Veronica De Sanctis
- Fondazione "Istituto Pasteur-Fondazione Cenci-Bolognetti", c/o Dipartimento di Genetica e Biologia Molecolare, Università di Roma, La Sapienza, Rome, Italy
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Carr-Schmid A, Pfund C, Craig EA, Kinzy TG. Novel G-protein complex whose requirement is linked to the translational status of the cell. Mol Cell Biol 2002; 22:2564-74. [PMID: 11909951 PMCID: PMC133728 DOI: 10.1128/mcb.22.8.2564-2574.2002] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2001] [Revised: 11/14/2001] [Accepted: 01/11/2002] [Indexed: 11/20/2022] Open
Abstract
G proteins, which bind and hydrolyze GTP, are involved in regulating a variety of critical cellular processes, including the process of protein synthesis. Many members of the subfamily of elongation factor class G proteins interact with the ribosome and function to regulate discrete steps during the process of protein synthesis. Despite sequence similarity to factors involved in translation, a role for the yeast Hbs1 protein has not been defined. In this work we have identified a genetic relationship between genes encoding components of the translational apparatus and HBS1. HBS1, while not essential for viability, is important for efficient growth and protein synthesis under conditions of limiting translation initiation. The identification of an Hbs1p-interacting factor, Dom34p, which shares a similar genetic relationship with components of the translational apparatus, suggests that Hbs1p and Dom34p may function as part of a complex that facilitates gene expression. Dom34p contains an RNA binding motif present in several ribosomal proteins and factors that regulate translation of specific mRNAs. Thus, Hbs1p and Dom34p may function together to help directly or indirectly facilitate the expression either of specific mRNAs or under certain cellular conditions.
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Affiliation(s)
- Anne Carr-Schmid
- Department of Molecular Genetics and Microbiology, UMDNJ Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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35
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Abstract
Structural features of the tRNAPhe molecule upon ternary complex formation with the bacterial elongation factor Tu were investigated. Phosphodiester bonds at positions 18 and 34 were found to be labilized in bound tRNA. Conversely, a higher stability of the phosphodiester links at positions 20, 21 and 36 was detected. Using ethylnitrosourea as a chemical probe a conformational change occurring at phosphate position 53 was observed in complexed tRNA. These results are interpreted by a structural rearrangement of the nucleic acid induced by complex formation.
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36
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Abstract
Phosphorylation of the alpha-subunit of eukaryotic initiation factor 2 (eIF2alpha) is a conserved mechanism regulating protein synthesis in response to various stresses. A screening for negative factors in yeast salt stress tolerance has led to the identification of Gcn2p, the single yeast eIF2alpha kinase that is activated by amino acid starvation in the general amino acid control response. Mutation of other components of this regulatory circuit such as GCN1 and GCN3 also resulted in improved NaCl tolerance. The gcn2 phenotype was not accompanied by changes in sodium or potassium homeostasis. NaCl induced a Gcn2p-dependent phosphorylation of eIF2alpha and translational activation of Gcn4p, the transcription factor that mediates the general amino acid control response. Mutations that activate Gcn4p function, such as gcd7-201, cpc2, and deletion of the translational regulatory region of the GCN4 gene, also cause salt sensitivity. It can be postulated that sodium activation of the Gcn2p pathway has toxic effects on growth under NaCl stress and that this novel mechanism of sodium toxicity may be of general significance in eukaryotes.
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Affiliation(s)
- A Goossens
- Instituto de Biologia Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C., Camino de Vera s/n, 46022 Valencia, Spain
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Gopal B, Papavinasasundaram KG, Colston MJ, Dodson G, Haire LF. Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance A (NusA) from Mycobacterium tuberculosis. Acta Crystallogr D Biol Crystallogr 2001; 57:1187-8. [PMID: 11468414 DOI: 10.1107/s0907444901009970] [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] [Subscribe] [Scholar Register] [Received: 05/14/2001] [Accepted: 06/15/2001] [Indexed: 11/11/2022]
Abstract
N-utilizing substance A (NusA) is a protein which performs several roles as a cofactor of DNA-dependent RNA polymerase. Its acts as an elongation factor and facilitates pausing, termination and the formation of a complex assembly that mediates transcription antitermination in eubacteria. Biochemical and biophysical data in the literature suggest that this protein performs these functions by binding to the core RNA polymerase, other protein factors and certain RNA fragments having specific signal sequences. The NusA of Mycobacterium tuberculosis has been cloned and overexpressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method. The space group is P3(1)21, with unit-cell parameters a = b = 78.1, c = 180.3 A. A native data set complete to 1.7 A resolution has been collected from a single crystal.
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Affiliation(s)
- B Gopal
- Division of Protein Structure, The National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, England
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38
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Luo RT, Lavau C, Du C, Simone F, Polak PE, Kawamata S, Thirman MJ. The elongation domain of ELL is dispensable but its ELL-associated factor 1 interaction domain is essential for MLL-ELL-induced leukemogenesis. Mol Cell Biol 2001; 21:5678-87. [PMID: 11463848 PMCID: PMC87288 DOI: 10.1128/mcb.21.16.5678-5687.2001] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [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: 11/20/2022] Open
Abstract
The MLL-ELL chimeric gene is the product of the (11;19)(q23p13.1) translocation associated with de novo and therapy-related acute myeloid leukemias (AML). ELL is an RNA polymerase II elongation factor that interacts with the recently identified EAF1 (ELL associated factor 1) protein. EAF1 contains a limited region of homology with the transcriptional activation domains of three other genes fused to MLL in leukemias, AF4, LAF4, and AF5q31. Using an in vitro transformation assay of retrovirally transduced myeloid progenitors, we conducted a structure-function analysis of MLL-ELL. Whereas the elongation domain of ELL was dispensable, the EAF1 interaction domain of ELL was critical to the immortalizing properties of MLL-ELL in vitro. To confirm these results in vivo, we transplanted mice with bone marrow transduced with MLL fused to the minimal EAF1 interaction domain of ELL. These mice all developed AML, with a longer latency than mice transplanted with the wild-type MLL-ELL fusion. Based on these results, we generated a heterologous MLL-EAF1 fusion gene and analyzed its transforming potential. Strikingly, we found that MLL-EAF1 immortalized myeloid progenitors in the same manner as that of MLL-ELL. Furthermore, transplantation of bone marrow transduced with MLL-EAF1 induced AML with a shorter latency than mice transplanted with the MLL-ELL fusion. Taken together, these results indicate that the leukemic activity of MLL-ELL requires the EAF1 interaction domain of ELL, suggesting that the recruitment by MLL of a transactivation domain similar to that in EAF1 or the AF4/LAF4/AF5q31 family may be a critical common feature of multiple 11q23 translocations. In addition, these studies support a critical role for MLL partner genes and their protein-protein interactions in 11q23 leukemogenesis.
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Affiliation(s)
- R T Luo
- Section of Hematology/Oncology, University of Chicago, Chicago, Illinois 60637, USA
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Torres M, Condon C, Balada JM, Squires C, Squires CL. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J 2001; 20:3811-20. [PMID: 11447122 PMCID: PMC125540 DOI: 10.1093/emboj/20.14.3811] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.7] [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: 11/14/2022] Open
Abstract
Escherichia coli ribosomal RNA (rRNA) operons contain antitermination motifs necessary for forming terminator-resistant transcription complexes. In preliminary work, we isolated 'antiterminating' transcription complexes and identified four new proteins potentially involved in rRNA transcription antitermination: ribosomal (r-) proteins S4, L3, L4 and L13. We show here that these r-proteins and Nus factors lead to an 11-fold increase in terminator read-through in in vitro transcription reactions. A significant portion of the effect was a result of r-protein S4. We show that S4 acted as a general antitermination factor, with properties very similar to NusA. It retarded termination and increased read-through at Rho-dependent terminators, even in the absence of the rRNA antiterminator motif. High concentrations of NusG showed reduced antitermination by S4. Like rrn antitermination, S4 selectively antiterminated at Rho-dependent terminators. Lastly, S4 tightly bound RNA polymerase in vivo. Our results suggest that, like NusA, S4 is a general transcription antitermination factor that associates with RNA polymerase during normal transcription and is also involved in rRNA operon antitermination. A model for key r-proteins playing a regulatory role in rRNA synthesis is presented.
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Affiliation(s)
| | - Ciarán Condon
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA and
CNRS UPR9073, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France Corresponding author e-mail:
| | | | | | - Catherine L. Squires
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA and
CNRS UPR9073, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, France Corresponding author e-mail:
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Simone F, Polak PE, Kaberlein JJ, Luo RT, Levitan DA, Thirman MJ. EAF1, a novel ELL-associated factor that is delocalized by expression of the MLL-ELL fusion protein. Blood 2001; 98:201-9. [PMID: 11418481 DOI: 10.1182/blood.v98.1.201] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The (11;19)(q23;p13.1) translocation in acute leukemia leads to the generation of a chimeric protein that fuses MLL to the transcriptional elongation factor ELL. A novel protein was isolated from a yeast 2-hybrid screen with ELL that was named EAF1 for ELL-associated factor 1. Using specific antibodies, the endogenous EAF1 and ELL proteins were coimmunoprecipitated from multiple cell lines. In addition, endogenous EAF1 also exhibited the capacity to interact with ELL2. Database comparisons with EAF1 identified a region with a high content of serine, aspartic acid, and glutamic acid residues that exhibited homology with the transcriptional activation domains of several translocation partner proteins of MLL, including AF4, LAF4, and AF5q31. A similar transcriptional activation domain has been identified in this region of EAF1. By confocal microscopy, endogenous EAF1 and ELL colocalized in a distinct nuclear speckled pattern. Transfection of the MLL-ELL fusion gene delocalized EAF1 from its nuclear speckled distribution to a diffuse nucleoplasmic pattern. In leukemic cell lines derived from mice transplanted with MLL-ELL-transduced bone marrow, EAF1 speckles were not detected. Taken together, these data suggest that expression of the MLL-ELL fusion protein may have a dominant effect on the normal protein-protein interactions of ELL.
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Affiliation(s)
- F Simone
- Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA
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41
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Zhou Y, Mah TF, Yu YT, Mogridge J, Olson ER, Greenblatt J, Friedman DI. Interactions of an Arg-rich region of transcription elongation protein NusA with NUT RNA: implications for the order of assembly of the lambda N antitermination complex in vivo. J Mol Biol 2001; 310:33-49. [PMID: 11419935 DOI: 10.1006/jmbi.2001.4722] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [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: 11/22/2022]
Abstract
The E. coli NusA transcription elongation protein (NusA(Ec)), identified because of its requirement for transcription antitermination by the N protein, has an Arg-rich S1 RNA-binding domain. A complex of N and NusA with other host factors binding at NUT sites in the RNA renders RNA polymerase termination-resistant. An E. coli haploid for nusA944, having nine different codons replacing four normally found in the Arg-rich region, is defective in support of N action. Another variant, haploid for the nusAR199A allele, with a change in a highly conserved Arg codon in the S1 domain, effectively supports N-mediated antitermination. However, nusAR199A is recessive to nusA944, while nusA(Ec) is dominant to nusA944 for support of N-mediated antitermination, suggesting a competition between NusA944 and NusAR199A during complex formation. Complex formation with the variant NusA proteins was assessed by mobility gel shifts. NusAR199A, unlike NusA(Ec) and NusA944, fails to form a complex with N and NUT RNA. However, while NusAR199A, like wild-type NusA, forms an enlarged complex with NUT RNA, N, RNA polymerase, and other host proteins required for efficient N-mediated antitermination, NusA944 does not form this enlarged complex. Consistent with the in vivo results, NusA944 prevents NusAR199A but not NusA(Ec) from forming the enlarged complex. The simplest conclusion from these dominance studies is that in the formation of the complete active antitermination complex in vivo, NusA and N binding to the newly synthesized NUT RNA precedes addition of the other factors. Alternative less effective routes to the active complex that allows bypass of this preferred pathway may also exist.
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Affiliation(s)
- Y Zhou
- Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI 48109-0620, USA
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42
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Elmendorf BJ, Shilatifard A, Yan Q, Conaway JW, Conaway RC. Transcription factors TFIIF, ELL, and Elongin negatively regulate SII-induced nascent transcript cleavage by non-arrested RNA polymerase II elongation intermediates. J Biol Chem 2001; 276:23109-14. [PMID: 11259417 DOI: 10.1074/jbc.m101445200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [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: 11/06/2022] Open
Abstract
TFIIF, ELL, and Elongin belong to a class of RNA polymerase II transcription factors that function similarly to activate the rate of elongation by suppressing transient pausing by polymerase at many sites along DNA templates. SII is a functionally distinct RNA polymerase II elongation factor that promotes elongation by reactivating arrested polymerase. Studies of the mechanism of SII action have shown (i) that arrest of RNA polymerase II results from irreversible displacement of the 3'-end of the nascent transcript from the polymerase catalytic site and (ii) that SII reactivates arrested polymerase by inducing endonucleolytic cleavage of the nascent transcript by the polymerase catalytic site thereby creating a new transcript 3'-end that is properly aligned with the catalytic site and can be extended. SII also induces nascent transcript cleavage by paused but non-arrested RNA polymerase II elongation intermediates, leading to the proposal that pausing may result from reversible displacement of the 3'-end of nascent transcripts from the polymerase catalytic site. On the basis of evidence consistent with the model that TFIIF, ELL, and Elongin suppress pausing by preventing displacement of the 3'-end of the nascent transcript from the polymerase catalytic site, we investigated the possibility of cross-talk between SII and transcription factors TFIIF, ELL, and Elongin. These studies led to the discovery that TFIIF, ELL, and Elongin are all capable of inhibiting SII-induced nascent transcript cleavage by non-arrested RNA polymerase II elongation intermediates. Here we present these findings, which bring to light a novel activity associated with TFIIF, ELL, and Elongin and suggest that these transcription factors may expedite elongation not only by increasing the forward rate of nucleotide addition by RNA polymerase II, but also by inhibiting SII-induced nascent transcript cleavage by non-arrested RNA polymerase II elongation intermediates.
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Affiliation(s)
- B J Elmendorf
- Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
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43
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Abstract
The crystal structure of Thermotoga maritima NusA, a transcription factor involved in pausing, termination, and antitermination processes, reveals a four-domain, rod-shaped molecule. An N-terminal alpha/beta portion, a five-stranded beta-barrel (S1 domain), and two K-homology (KH) modules create a continuous spine of positive electrostatic potential, suitable for nonspecific mRNA attraction. Homology models suggest how, in addition, specific mRNA regulatory sequences can be recognized by the S1 and KH motifs. An arrangement of multiple S1 and KH domains mediated by highly conserved residues is seen, creating an extended RNA binding surface, a paradigm for other proteins with similar domain arrays. Structural and mutational analyses indicate that the motifs cooperate, modulating strength and specificity of RNA binding.
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Affiliation(s)
- M Worbs
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152, Martinsried, Germany
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44
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Kamura T, Burian D, Khalili H, Schmidt SL, Sato S, Liu WJ, Conrad MN, Conaway RC, Conaway JW, Shilatifard A. Cloning and characterization of ELL-associated proteins EAP45 and EAP20. a role for yeast EAP-like proteins in regulation of gene expression by glucose. J Biol Chem 2001; 276:16528-33. [PMID: 11278625 DOI: 10.1074/jbc.m010142200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [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: 11/06/2022] Open
Abstract
RNA polymerase II elongation factor ELL was recently purified from rat liver as a component of a multiprotein complex containing ELL and three ELL-associated proteins (EAPs) of approximately 45 (EAP45), approximately 30 (EAP30), and approximately 20 (EAP20) kDa (Shilatifard, A. (1998) J. Biol. Chem. 273, 11212-11217). Cloning of cDNA encoding the EAP30 protein revealed that it shares significant sequence similarity with the product of the Saccharomyces cerevisiae SNF8 gene (Schmidt, A. E., Miller, T., Schmidt, S. L., Shiekhattar, R., and Shilatifard, A. (1999) J. Biol. Chem. 274, 21981-21985), which is required for efficient derepression of glucose-repressed genes. Here we report the cloning of cDNAs encoding the EAP45 and EAP20 proteins. In addition, we identify the S. cerevisiae VPS36 and YJR102c genes as potential orthologs of EAP45 and EAP20 and show that they are previously uncharacterized SNF genes with properties very similar to SNF8.
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Affiliation(s)
- T Kamura
- Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
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45
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Abstract
When starved for a single amino acid, the budding yeast Saccharomyces cerevisiae activates the eukaryotic initiation factor 2alpha (eIF2alpha) kinase GCN2 in a GCN1-dependent manner. Phosphorylated eIF2alpha inhibits general translation but selectively derepresses the synthesis of the transcription factor GCN4, which leads to coordinated induction of genes involved in biosynthesis of various amino acids, a phenomenon called general control response. We recently demonstrated that this response requires binding of GCN1 to the GI domain occurring at the N terminus of GCN2 (Kubota, H., Sakaki, Y., and Ito, T. (2000) J. Biol. Chem. 275, 20243-20246). Here we provide the first evidence for the involvement of GCN1-GCN2 interaction in activation of GCN2 per se. We identified a C-terminal segment of GCN1 sufficient to bind the GI domain and used a novel dual bait two-hybrid method to identify mutations rendering GCN1 incapable of interacting with GCN2. The yeast bearing such an allele, gcn1-F2291L, fails to display derepression of GCN4 translation and hence general control response, as does a GI domain mutant, gcn2-Y74A, defective in association with GCN1. Furthermore, we demonstrated that phosphorylation of eIF2alpha is impaired in both mutants. Since GCN2 is the sole eIF2alpha kinase in yeast, these findings indicate a critical role of GCN1-GCN2 interaction in activation of the kinase in vivo.
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Affiliation(s)
- H Kubota
- Division of Genome Biology, Cancer Research Institute, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-0934, Japan
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46
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Abstract
DNA, RNA, and regulatory molecules control gene expression through interactions with RNA polymerase (RNAP). We show that a short alpha helix at the tip of the flaplike domain that covers the RNA exit channel of RNAP contacts a nascent RNA stem-loop structure (hairpin) that inhibits transcription, and that this flap-tip helix is required for activity of the regulatory protein NusA. Protein-RNA cross-linking, molecular modeling, and effects of alterations in RNAP and RNA all suggest that a tripartite interaction of RNAP, NusA, and the hairpin inhibits nucleotide addition in the active site, which is located 65 angstroms away. These findings favor an allosteric model for regulation of transcript elongation.
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Affiliation(s)
- I Toulokhonov
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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47
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Johnstone RW, Gerber M, Landewe T, Tollefson A, Wold WS, Shilatifard A. Functional analysis of the leukemia protein ELL: evidence for a role in the regulation of cell growth and survival. Mol Cell Biol 2001; 21:1672-81. [PMID: 11238904 PMCID: PMC86713 DOI: 10.1128/mcb.21.5.1672-1681.2001] [Citation(s) in RCA: 29] [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: 11/20/2022] Open
Abstract
The ELL gene encodes an RNA polymerase II transcription factor that frequently undergoes translocation with the MLL gene in acute human myeloid leukemia. Here, we report that ELL can regulate cell proliferation and survival. In order to better understand the physiological role of the ELL protein, we have developed an ELL-inducible cell line. Cells expressing ELL were uniformly inhibited for growth by a loss of the G(1) population and an increase in the G(2)/M population. This decrease in cell growth is followed by the condensation of chromosomal DNA, activation of caspase 3, poly(ADP ribose) polymerase cleavage, and an increase in sub-G(1) population, which are all indicators of the process of programmed cell death. In support of the role of ELL in induction of cell death, expression of an ELL antisense RNA or addition of the caspase inhibitor ZVAD-fmk results in a reversal of ELL-mediated death. We have also demonstrated that the C-terminal domain of ELL, which is conserved among the ELL family of proteins that we have cloned (ELL, ELL2, and ELL3), is required for ELL's activity in the regulation of cell growth. These novel results indicate that ELL can regulate cell growth and survival and may explain how ELL translocations result in the development of human malignancies.
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MESH Headings
- Amino Acid Chloromethyl Ketones/pharmacology
- Antigens, Differentiation
- Apoptosis
- Blotting, Western
- Caspase 3
- Caspase Inhibitors
- Caspases/metabolism
- Cell Cycle Proteins
- Cell Death
- Cell Division
- Cell Line
- Cell Survival
- Cysteine Proteinase Inhibitors/pharmacology
- DNA/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Enzyme Activation
- Enzyme Inhibitors/pharmacology
- Flow Cytometry
- G1 Phase
- G2 Phase
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Microscopy, Fluorescence
- Microscopy, Phase-Contrast
- Mitosis
- Neoplasm Proteins
- Oligonucleotides, Antisense/metabolism
- Peptide Elongation Factors
- Plasmids/metabolism
- Poly(ADP-ribose) Polymerases/metabolism
- Propidium/pharmacology
- Protein Phosphatase 1
- Proteins/metabolism
- RNA, Messenger/metabolism
- Time Factors
- Transcription Factors/genetics
- Transcription Factors/physiology
- Transcriptional Elongation Factors
- Transfection
- Translocation, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- R W Johnstone
- The Peter MacCallum Cancer Institute, Gene Regulation Laboratory, Cancer Immunology Division, East Melbourne, 3002 Victoria, Australia
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48
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Abstract
BACKGROUND Type I myosin is highly conserved among eukaryotes, and apparently plays important roles in a number of cellular processes. In the budding yeast, two myosin I species have been identified and their role in F-actin assembly has been inferred. RESULTS We cloned the fission yeast myo1 gene, which apparently encoded a myosin I protein. Disruption of myo1 was not lethal, but it caused growth retardation at high and low temperatures, sensitivity to a high concentration of KCl, and aberrance in cell morphology associated with an abnormal distribution of F-actin patches. An abnormal deposition of cell wall materials was also seen. Homothallic myo1Delta cells could mate, but heterothallic myo1Delta cells were poor in conjugation. Myo1p was necessary for the encapsulation of spores. The tail domain of Myo1p was pivotal for its function. Calmodulin could bind to Myo1p through the IQ domain at the neck. CONCLUSIONS Myo1p appears to control the redistribution of F-actin patches during the cell cycle. Loss of Myo1p function is likely to slow down the actin assembly/disassembly process, which results in a failure of the actin cycle to catch up with other events in both the mitotic and meiotic cell cycles, including extension of the conjugation tubes.
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Affiliation(s)
- M Toya
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan
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49
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Abstract
Proper completion of mitosis requires careful coordination of numerous cellular events. It is crucial, for example, that cells do not initiate spindle disassembly and cytokinesis until chromosomes have been properly segregated. Cells have developed numerous safeguards or checkpoints to delay exit from mitosis and initiation of the next cell cycle in response to defects in late mitosis. In this review, we discuss recent work on two homologous signaling pathways in budding and fission yeast, termed the mitotic exit network (MEN) and septation initiation network (SIN), respectively, that are essential for coordinating completion of mitosis and cytokinesis with other mitotic events.
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Affiliation(s)
- D McCollum
- Dept of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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50
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Sattlegger E, Hinnebusch AG. Separate domains in GCN1 for binding protein kinase GCN2 and ribosomes are required for GCN2 activation in amino acid-starved cells. EMBO J 2000; 19:6622-33. [PMID: 11101534 PMCID: PMC305848 DOI: 10.1093/emboj/19.23.6622] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.1] [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] [Indexed: 11/13/2022] Open
Abstract
GCN2 stimulates GCN4 translation in amino acid-starved cells by phosphorylating the alpha-subunit of translation initiation factor 2. GCN2 function in vivo requires the GCN1/GCN20 complex, which binds to the N-terminal domain of GCN2. A C-terminal segment of GCN1 (residues 2052-2428) was found to be necessary and sufficient for binding GCN2 in vivo and in vitro. Overexpression of this fragment in wild-type cells impaired association of GCN2 with native GCN1 and had a dominant Gcn(-) phenotype, dependent on Arg2259 in the GCN1 fragment. Substitution of Arg2259 with Ala in full-length GCN1 abolished complex formation with native GCN2 and destroyed GCN1 regulatory function. Consistently, the Gcn(-) phenotype of gcn1-R2259A, but not that of gcn1Delta, was suppressed by overexpressing GCN2. These findings prove that GCN2 binding to the C-terminal domain of GCN1, dependent on Arg2259, is required for high level GCN2 function in vivo. GCN1 expression conferred sensitivity to paromomycin in a manner dependent on its ribosome binding domain, supporting the idea that GCN1 binds near the ribosomal acceptor site to promote GCN2 activation by uncharged tRNA.
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Affiliation(s)
- E Sattlegger
- Laboratory of Eukaryotic Gene Regulation, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Building 6A, Room B1A-13, Bethesda, MD 20892-2759, USA
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