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He Z, Li X, Zhang X, Ouyang Q, Hu J, Hu S, He H, Li L, Liu H, Wang J. Effects of rearing systems (cage versus floor) on the microbial composition and transcriptome of goose ileum. Front Vet Sci 2024; 11:1394290. [PMID: 38846790 PMCID: PMC11155456 DOI: 10.3389/fvets.2024.1394290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
There is a gradual transition from water to dryland rearing of geese. In this study, we performed 16S rRNA sequencing (16S rRNA-seq) and transcriptome sequencing (RNA-seq) to reveal the effects of cage rearing (CR) and floor rearing (FR) systems on the microbial composition and transcriptome of the goose ileum. Through 16S rRNA-seq, Linear Discriminant Analysis Effect Size (LEfSe) analysis identified 2 (hgcI_clade and Faecalibacterium) and 14 (Bacteroides, Proteiniphilum, Proteiniclasticum, etc.) differential microbiota in CR and FR, respectively. The rearing system influenced 4 pathways including biosynthesis of amino acids in ileal microbiota. Moreover, we identified 1,198 differentially expressed genes (DEGs) in the ileum mucosa, with 957 genes up-regulated in CR and 241 genes up-regulated in FR. In CR, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the significant enrichment (p < 0.05) of 28 KEGG pathways, most of which were associated with amino acid metabolism. In FR, up-regulated DEGs were mainly enriched in KEGG pathways associated with cellular processes, including apoptosis, necroptosis, and cellular senescence. Spearman correlation analysis of differential microbiota and amino acid metabolism-related DEGs in CR showed a significant positive correlation. Additionally, differential microbiota of FR, Phascolarctobacterium and Sutterella, were positively correlated with FGF10 (p < 0.05) and PIK3R1 (p < 0.01), respectively. In conclusion, there might be differences in ileal amino acid metabolism levels between CR and FR geese, and the observed increase in harmful bacterial species in FR might impact the activity of ileal cells.
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Affiliation(s)
- Zhiyu He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xuejian Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xi Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingyuan Ouyang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiwei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Lejeune C, Cornu D, Sago L, Redeker V, Virolle MJ. The stringent response is strongly activated in the antibiotic producing strain, Streptomyces coelicolor. Res Microbiol 2024; 175:104177. [PMID: 38159786 DOI: 10.1016/j.resmic.2023.104177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
S. lividans and S. coelicolor are phylogenetically closely related strains with different abilities to produce the same specialized metabolites. Previous studies revealed that the strong antibiotic producer, S. coelicolor, had a lower ability to assimilate nitrogen and phosphate than the weak producer, Streptomyces lividans, and this resulted into a lower growth rate. A comparative proteomic dataset was used to establish the consequences of these nutritional stresses on the abundance of proteins of the translational apparatus of these strains, grown in low and high phosphate availability. Our study revealed that most proteins of the translational apparatus were less abundant in S. coelicolor than in S. lividans whereas it was the opposite for ET-Tu 3 and a TrmA-like methyltransferase. The expression of the latter being known to be under the positive control of the stringent response whereas that of the other ribosomal proteins is under its negative control, this indicated the occurrence of a strong activation of the stringent response in S. coelicolor. Furthermore, in S. lividans, ribosomal proteins were more abundant in phosphate proficiency than in phosphate limitation suggesting that a limitation in phosphate, that was also shown to trigger RelA expression, contributes to the induction of the stringent response.
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Affiliation(s)
- Clara Lejeune
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - David Cornu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Laila Sago
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Virginie Redeker
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France; Institut Francois Jacob, Molecular Imaging Center (MIRCen), Laboratory of Neurodegenerative Diseases, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique, Université Paris-Saclay, Fontenay-aux-Roses, France.
| | - Marie-Joelle Virolle
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
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Yin M, Wu Y, Li D, Zhang Y, Bian X, Li J, Pei Y, Cui Y, Li J. Non-filamentous bulking of activated sludge induced by graphene oxide: Insights from extracellular polymeric substances. BIORESOURCE TECHNOLOGY 2024; 399:130574. [PMID: 38471631 DOI: 10.1016/j.biortech.2024.130574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/03/2024] [Accepted: 03/09/2024] [Indexed: 03/14/2024]
Abstract
Widespread use of nanomaterials raises concerns. The underlying mechanism by which graphene oxide (GO) nanoparticles causes poor settleability of activated sludge remains unclear. To explore this mechanism, three reactors with different GO concentrations were established. Extended Derjaguin-Landau-Verwey-Overbeek theory indicated that GO destroyed the property of extracellular polymeric substances (EPS), increasing the energy barrier between bacteria. Low levels of uronic acid and hydrogen bonding in exopolysaccharide weakened the EPS gelation increasing aggregation repulsion. Lager amounts of hydrophilic amino acid and looser structure of extracellular proteins for exposing inner hydrophilic groups significantly contributed to the hydrophilicity of EPS. Both changes implied deterioration in EPS structure under GO stress. Metagenome demonstrated a decrease in genes responsible for capsular polysaccharide colonization and genes regulated the translocation of loose proteins were increased, which increased repulsion between bacteria. This study elucidated that changes in EPS secretion under GO exposure are the underlying causes of poor settleability.
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Affiliation(s)
- Muchen Yin
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yaodong Wu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Dongyue Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yanzhuo Zhang
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xueying Bian
- BGI Engineering Consultants Ltd., Beijing 100038, China
| | - Jiarui Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yanxue Pei
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yanan Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Jun Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
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Barai P, Chen J. Beyond protein synthesis: non-translational functions of threonyl-tRNA synthetases. Biochem Soc Trans 2024; 52:661-670. [PMID: 38477373 PMCID: PMC11088916 DOI: 10.1042/bst20230506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
Aminoacyl-tRNA synthetases (AARSs) play an indispensable role in the translation of mRNAs into proteins. It has become amply clear that AARSs also have non-canonical or non-translational, yet essential, functions in a myriad of cellular and developmental processes. In this mini-review we discuss the current understanding of the roles of threonyl-tRNA synthetase (TARS) beyond protein synthesis and the underlying mechanisms. The two proteins in eukaryotes - cytoplasmic TARS1 and mitochondrial TARS2 - exert their non-canonical functions in the regulation of gene expression, cell signaling, angiogenesis, inflammatory responses, and tumorigenesis. The TARS proteins utilize a range of biochemical mechanisms, including assembly of a translation initiation complex, unexpected protein-protein interactions that lead to activation or inhibition of intracellular signaling pathways, and cytokine-like signaling through cell surface receptors in inflammation and angiogenesis. It is likely that new functions and novel mechanisms will continue to emerge for these multi-talented proteins.
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Affiliation(s)
- Pallob Barai
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Jie Chen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
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Suo L, Liang X, Zhang W, Gao M, Ma T, Hu D, Song Y, Gao Z. Potential prognostic biomarkers of hepatocellular carcinoma based on 4D label-free quantitative proteomics analysis pilot investigation. Int J Biol Markers 2024; 39:59-69. [PMID: 37956648 DOI: 10.1177/03936155231212925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
BACKGROUND Hepatocellular carcinoma carries a poor prognosis and poses a serious threat to global health. Currently, there are few potential prognostic biomarkers available for the prognosis of hepatocellular carcinoma. METHODS This pilot study used 4D label-free quantitative proteomics to compare the proteomes of hepatocellular carcinoma and adjacent non-tumor tissue. A total of 66,075 peptides, 6363 identified proteins, and 772 differentially expressed proteins were identified in specimens from three hepatocellular carcinoma patients. Through functional enrichment analysis of differentially expressed proteins by Gene Ontology, KEGG pathway, and protein domain, we identified proteins with similar functions. RESULTS Twelve differentially expressed proteins (RPL17, RPL27, RPL27A, RPS5, RPS16, RSL1D1, DDX18, RRP12, TARS2, YARS2, MARS2, and NARS1) were selected for identification and validation by parallel reaction monitoring. Subsequent Western blotting confirmed overexpression of RPL27, RPS16, and TARS2 in hepatocellular carcinoma compared to non-tumor tissue in 16 pairs of clinical samples. Analysis of The Cancer Genome Atlas datasets associated the increased expression of these proteins with poor prognosis. Tissue microarray revealed a negative association between high expression of RPL27 and TARS2 and the prognosis of hepatocellular carcinoma patients, although RPS16 was not significant. CONCLUSIONS These data suggest that RPL27 and TARS2 play an important role in hepatocellular carcinoma progression and may be potential prognostic biomarkers of overall survival in hepatocellular carcinoma patients.
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Affiliation(s)
- Lida Suo
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Xiangnan Liang
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Weibin Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Mingwei Gao
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Taiheng Ma
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Daosheng Hu
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Yilin Song
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
| | - Zhenming Gao
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, China
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Yang H, Ma L, Deng W, Fu B, Nie J, Liu X. Prognostic biomarker DARS2 correlated with immune infiltrates in bladder tumor. Front Immunol 2024; 14:1301945. [PMID: 38299141 PMCID: PMC10827901 DOI: 10.3389/fimmu.2023.1301945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024] Open
Abstract
Background DARS2 is a pivotal member of the Aminoacyl-tRNA synthetases family that is critical for regulating protein translation. However, the biological role of DARS2 in bladder cancer remains elusive. Methods We analyzed the correlation between DARS2 expression and prognosis, tumor stage, and immune infiltration in bladder cancer using The Cancer Genome Atlas (TCGA) database. We validated findings in clinical samples from The First Affiliated Hospital of Nanchang University and explored the biological functions of DARS2 using cell and animal models. Results We found DARS2 to be upregulated in bladder cancer, associated with tumor progression and poor prognosis. Immune infiltration analysis suggested that DARS2 may facilitate immune evasion by modulating PD-L1. Cell and animal experiments validated that DARS2 knockdown and overexpress can inhibit or increase cancer cell proliferation, metastasis, tumorigenesis, immune escape, and PD-L1 levels. Conclusions Our study reveals DARS2 as a potential prognostic biomarker and immunotherapy target in BLCA.
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Affiliation(s)
- Hailang Yang
- Department of Urology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Li Ma
- Department of Pathology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Wen Deng
- Department of Urology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Bin Fu
- Department of Urology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Jianqiang Nie
- Department of Urology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xiaoqiang Liu
- Department of Urology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
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Zeb A, Liu W, Ali N, Shi R, Lian Y, Wang Q, Wang J, Li J, Zheng Z, Liu J, Yu M, Liu J. Integrating metabolomics and high-throughput sequencing to investigate the effects of tire wear particles on mung bean plants and soil microbial communities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122872. [PMID: 37926408 DOI: 10.1016/j.envpol.2023.122872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023]
Abstract
Tire wear particles (TWPs) generated by vehicle tires are ubiquitous in soil ecosystems, while their impact on soil biota remains poorly understood. In this study, we investigated the effects of TWPs (0.1%, 0.7%, and 1.5% of dry soil weight) on the growth and metabolism of mung bean (Vigna radiata) plants over 32 days in soil pots. We found that TWPs-treated soils had high levels of heavy metals and polycyclic aromatic hydrocarbons (PAHs). However, there was no significant impact of TWPs exposure on plant growth, suggesting that mung bean plants have a degree of tolerance to TWPs. Despite the lack of impact on plant growth, exposure to TWPs had significant effects on soil enzyme activities, with a decrease of over 50% in urease and dehydrogenase activity. Furthermore, TWPs exposure resulted in marked changes in the plant metabolite profile, including altered levels of sugars, carboxylic acids, and amino acids, indicating altered nitrogen and amino acid-related metabolic pathways. TWPs exposure also disrupted the rhizospheric and bulk soil microbiota, with a decrease in the abundance of bacterial (Blastococcus) and fungal (Chaetomium) genera involved in nitrogen cycles and suppressing plant diseases. In summary, our study provides new insights into the effects of TWPs on plants and soil, highlighting the potential ecological consequences of TWPs pollution in terrestrial ecosystems and underscoring the need for further research in this area.
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Affiliation(s)
- Aurang Zeb
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
| | - Weitao Liu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China.
| | - Nouman Ali
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
| | - Ruiying Shi
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
| | - Yuhang Lian
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
| | - Qi Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
| | - Jianling Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
| | - Jiantao Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
| | - Zeqi Zheng
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
| | - Jinzheng Liu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
| | - Miao Yu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
| | - Jianv Liu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin, 300350, China
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Kuan J, Hansen A, Wang H. Case Report: A new case of YARS1-associated autosomal recessive disorder with compound heterozygous and concurrent 47, XXY. Front Pediatr 2023; 11:1282253. [PMID: 38125821 PMCID: PMC10731953 DOI: 10.3389/fped.2023.1282253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Aminoacyl-tRNA synthetases play a pivotal role in catalyzing the precise coupling of amino acids with their corresponding tRNAs. Among them, Tyrosyl tRNA synthetase, encoded by the YARS1 gene, facilitates the aminoacylation of tyrosine to its designated tRNA. Heterozygous variants in the YARS1 gene have been linked to autosomal dominant Charcot-Marie-Tooth type C, while recent findings have unveiled biallelic YARS1 variants leading to an autosomal recessive multisystemic disorder in several cases. In this report, we present a novel case characterized by dysmorphic facies, and multisystemic symptoms, prominently encompassing neurological issues and a microarray conducted shortly after birth revealed 47, XXY. Utilizing whole exome sequencing, we uncovered a paternally inherited likely pathogenic variant (c.1099C > T, p.Arg367Trp), previously reported, coinciding with the father's history of hearing loss and neurological symptoms. Additionally, a maternally inherited variant of uncertain significance (c.782T > G, p.Leu261Arg), previously unreported, was identified within the YARS1 gene. The observed phenotypes and the presence of compound heterozygous results align with the diagnosis of an autosomal recessive disorder associated with YARS1. Through our cases, the boundaries of this emerging clinical entity are broadened. This instance underscores the significance of comprehensive genetic testing in patients exhibiting intricate phenotypes.
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Affiliation(s)
- Janene Kuan
- Department of Pediatrics, University of California, San Francisco, CA, United States
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, United States
| | - Ashleigh Hansen
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, United States
- Neurosciences Department, Cedars-Sinai, Los Angeles, CA, United States
| | - Hua Wang
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, United States
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Hosseini E, Amirjannati N, Henkel R, Bazrafkan M, Moghadasfar H, Gilany K. Targeted Amino Acids Profiling of Human Seminal Plasma from Teratozoospermia Patients Using LC-MS/MS. Reprod Sci 2023; 30:3285-3295. [PMID: 37264261 DOI: 10.1007/s43032-023-01272-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/13/2023] [Indexed: 06/03/2023]
Abstract
Identifying the metabolome of human seminal plasma (HSP) is a new research area to screen putative biomarkers of infertility. This case-control study was performed on HSP specimens of 15 infertile patients with teratozoospermia (defined as normal sperm morphology < 4%) and 12 confirmed fertile normozoospermic men as the control group to investigate the seminal metabolic signature and whether there are differences in the metabolome between two groups. HSPs were subjected to LC-MS-MS analysis. MetaboAnalyst5.0 software was utilized for statistical analysis. Different univariate and multivariate analyses were used, including T-tests, fold change analysis, random forest (RF), and metabolite set enrichment analysis (MSEA). Teratozoospermic samples contained seventeen significantly different amino acids. Upregulated metabolites include glutamine, asparagine, and glycylproline, whereas downregulated metabolites include cysteine, γ-aminobutyric acid, histidine, hydroxylysine, hydroxyproline, glycine, proline, methionine, ornithine, tryptophan, aspartic acid, argininosuccinic acid, α-aminoadipic acid, and β-aminoisobutyric acid. RF algorithm defined a set of 15 metabolites that constitute the significant features of teratozoospermia. In particular, increased glutamine, asparagine, and decreased cysteine, tryptophan, glycine, and valine were strong predictors of teratozoospemia. The most affected metabolic pathways in teratozoospermic men are the aminoacyl-tRNA, arginine, valine-leucine, and isoleucine biosynthesis. Altered metabolites detected in teratozoospermia were responsible for various roles in sperm functions that classified into four subgroups as follows: related metabolites to antioxidant function, energy production, sperm function, and spermatogenesis. The altered amino acid metabolome identified in this study may be related to the etiology of teratozoospermia, and may provide novel insight into potential biomarkers of male infertility for therapeutic targets.
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Affiliation(s)
- Elham Hosseini
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
- Department of Obstetrics and Gynecology, Mousavi Hospital, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Naser Amirjannati
- Department of Andrology and Embryology, Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Ralf Henkel
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa
- LogixX Pharma, Theale, Berkshire, UK
| | - Mahshid Bazrafkan
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Hanieh Moghadasfar
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Kambiz Gilany
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
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Gupta S, Jani J, Vijayasurya, Mochi J, Tabasum S, Sabarwal A, Pappachan A. Aminoacyl-tRNA synthetase - a molecular multitasker. FASEB J 2023; 37:e23219. [PMID: 37776328 DOI: 10.1096/fj.202202024rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
Aminoacyl-tRNA synthetases (AaRSs) are valuable "housekeeping" enzymes that ensure the accurate transmission of genetic information in living cells, where they aminoacylated tRNA molecules with their cognate amino acid and provide substrates for protein biosynthesis. In addition to their translational or canonical function, they contribute to nontranslational/moonlighting functions, which are mediated by the presence of other domains on the proteins. This was supported by several reports which claim that AaRS has a significant role in gene transcription, apoptosis, translation, and RNA splicing regulation. Noncanonical/ nontranslational functions of AaRSs also include their roles in regulating angiogenesis, inflammation, cancer, and other major physio-pathological processes. Multiple AaRSs are also associated with a broad range of physiological and pathological processes; a few even serve as cytokines. Therefore, the multifunctional nature of AaRSs suggests their potential as viable therapeutic targets as well. Here, our discussion will encompass a range of noncanonical functions attributed to Aminoacyl-tRNA Synthetases (AaRSs), highlighting their links with a diverse array of human diseases.
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Affiliation(s)
- Swadha Gupta
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Jaykumar Jani
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Vijayasurya
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Jigneshkumar Mochi
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
| | - Saba Tabasum
- Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Akash Sabarwal
- Harvard Medical School, Boston, Massachusetts, USA
- Boston Children's Hospital, Boston, Massachusetts, USA
| | - Anju Pappachan
- School of Life Sciences, Central University of Gujarat, Gandhinagar, India
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11
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Gill B, Schwecht I, Rahman N, Dhawan T, Verschoor C, Nazli A, Kaushic C. Metabolic signature for a dysbiotic microbiome in the female genital tract: A systematic review and meta-analysis. Am J Reprod Immunol 2023; 90:e13781. [PMID: 37766408 DOI: 10.1111/aji.13781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/06/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The vaginal microbiome (VMB) is a critical determinant of reproductive health, where a microbial shift towards a dysbiotic environment has implications for susceptibility to, and clinical presentation of sexually transmitted infections (STIs). Metabolomic profiling of the vaginal microenvironment has led to the identification of metabolic responses to clinical conditions of dysbiosis. However, no studies have examined metabolic markers that are common across conditions and can serve as a signature for vaginal dysbiosis. METHOD OF STUDY We have conducted a comprehensive systematic review and meta-analysis to identify consistently deregulated metabolites along with their impact on host and microbial metabolism during dysbiosis. We employed two complementary approaches including a vote counting analysis for all eligible studies identified in the systematic review, in addition to a meta-analysis for a subset of studies with sufficient available data. Significantly deregulated metabolites were then selected for pathway enrichment analysis. RESULTS Our results revealed a total of 502 altered metabolites reported across 10 dysbiotic conditions from 16 studies. Following a rigorous, collective analysis, six metabolites which were consistently downregulated and could be generalized to all dysbiotic conditions were identified. In addition, five downregulated and one upregulated metabolite was identified from a bacterial vaginosis (BV) focused sub-analysis. These metabolites have the potential to serve as a metabolic signature for vaginal dysbiosis. Their role in eight altered metabolic pathways indicates a disruption of amino acid, carbohydrate, and energy metabolism during dysbiosis. CONCLUSION Based on this analysis, we propose a schematic model outlining the common metabolic perturbations associated with vaginal dysbiosis, which can be potential targets for therapeutics and prophylaxis.
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Affiliation(s)
- Biban Gill
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Ingrid Schwecht
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Nuzhat Rahman
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Tushar Dhawan
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Chris Verschoor
- Health Sciences North Research Institute, Northern Ontario School of Medicine, Sudbury, ON, Canada
| | - Aisha Nazli
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Charu Kaushic
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
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12
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Castillo KD, Chapa ED, Lamb TM, Gangopadhyay M, Bell-Pedersen D. Circadian clock control of tRNA synthetases in Neurospora crassa. F1000Res 2023; 11:1556. [PMID: 37841830 PMCID: PMC10576190 DOI: 10.12688/f1000research.125351.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/31/2023] [Indexed: 10/17/2023] Open
Abstract
Background: In Neurospora crassa, the circadian clock controls rhythmic mRNA translation initiation through regulation of the eIF2α kinase CPC-3 (the homolog of yeast and mammalian GCN2). Active CPC-3 phosphorylates and inactivates eIF2α, leading to higher phosphorylated eIF2α (P-eIF2α) levels and reduced translation initiation during the subjective day. This daytime activation of CPC-3 is driven by its binding to uncharged tRNA, and uncharged tRNA levels peak during the day under control of the circadian clock. The daily rhythm in uncharged tRNA levels could arise from rhythmic amino acid levels or aminoacyl-tRNA synthetase (aaRSs) levels. Methods: To determine if and how the clock potentially controls rhythms in aspartyl-tRNA synthetase (AspRS) and glutaminyl-tRNA synthetase (GlnRS), both observed to be rhythmic in circadian genomic datasets, transcriptional and translational fusions to luciferase were generated. These luciferase reporter fusions were examined in wild type (WT), clock mutant Δ frq, and clock-controlled transcription factor deletion strains. Results: Translational and transcriptional fusions of AspRS and GlnRS to luciferase confirmed that their protein levels are clock-controlled with peak levels at night. Moreover, clock-controlled transcription factors NCU00275 and ADV-1 drive robust rhythmic protein expression of AspRS and GlnRS, respectively. Conclusions: These data support a model whereby coordinate clock control of select aaRSs drives rhythms in uncharged tRNAs, leading to rhythmic CPC-3 activation, and rhythms in translation of specific mRNAs.
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Affiliation(s)
- Kathrina D. Castillo
- Biology, Texas A&M University, College Station, TX, 77843, USA
- Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Emily D. Chapa
- Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Teresa M. Lamb
- Biology, Texas A&M University, College Station, TX, 77843, USA
- Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Madhusree Gangopadhyay
- Biology, Texas A&M University, College Station, TX, 77843, USA
- Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Deborah Bell-Pedersen
- Biology, Texas A&M University, College Station, TX, 77843, USA
- Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
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13
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Sung Y, Yu YC, Han JM. Nutrient sensors and their crosstalk. Exp Mol Med 2023; 55:1076-1089. [PMID: 37258576 PMCID: PMC10318010 DOI: 10.1038/s12276-023-01006-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/22/2023] [Accepted: 03/13/2023] [Indexed: 06/02/2023] Open
Abstract
The macronutrients glucose, lipids, and amino acids are the major components that maintain life. The ability of cells to sense and respond to fluctuations in these nutrients is a crucial feature for survival. Nutrient-sensing pathways are thus developed to govern cellular energy and metabolic homeostasis and regulate diverse biological processes. Accordingly, perturbations in these sensing pathways are associated with a wide variety of pathologies, especially metabolic diseases. Molecular sensors are the core within these sensing pathways and have a certain degree of specificity and affinity to sense the intracellular fluctuation of each nutrient either by directly binding to that nutrient or indirectly binding to its surrogate molecules. Once the changes in nutrient levels are detected, sensors trigger signaling cascades to fine-tune cellular processes for energy and metabolic homeostasis, for example, by controlling uptake, de novo synthesis or catabolism of that nutrient. In this review, we summarize the major discoveries on nutrient-sensing pathways and explain how those sensors associated with each pathway respond to intracellular nutrient availability and how these mechanisms control metabolic processes. Later, we further discuss the crosstalk between these sensing pathways for each nutrient, which are intertwined to regulate overall intracellular nutrient/metabolic homeostasis.
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Affiliation(s)
- Yulseung Sung
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, 21983, South Korea
| | - Ya Chun Yu
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, 21983, South Korea
| | - Jung Min Han
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, 21983, South Korea.
- Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, 03722, South Korea.
- POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, 37673, South Korea.
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14
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Shirouchi B, Kawahara Y, Kutsuna Y, Higuchi M, Okumura M, Mitsuta S, Nagao N, Tanaka K. Oral Administration of Chaetoceros gracilis—A Marine Microalga—Alleviates Hepatic Lipid Accumulation in Rats Fed a High-Sucrose and Cholesterol-Containing Diet. Metabolites 2023; 13:metabo13030436. [PMID: 36984876 PMCID: PMC10051878 DOI: 10.3390/metabo13030436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Microalgae are attracting attention as a next-generation alternative source of protein and essential fatty acids that do not consume large amounts of water or land. Chaetoceros gracilis (C. gracilis)—a marine microalga—is rich in proteins, fucoxanthin, and eicosapentaenoic acid (EPA). Growing evidence indicates that dietary fucoxanthin and EPA have beneficial effects in humans. However, none of these studies have shown that dietary C. gracilis has beneficial effects in mammals. In this study, we investigated the effects of dietary C. gracilis on lipid abnormalities in Sprague-Dawley rats fed a high-sucrose cholesterol-containing diet. Dried C. gracilis was added to the control diet at a final dose of 2 or 5% (w/w). After four weeks, the soleus muscle weights were found to be dose-responsive to C. gracilis and showed a tendency to increase. The hepatic triglyceride and total cholesterol levels were significantly reduced by C. gracilis feeding compared to those in the control group. The activities of FAS and G6PDH, which are related to fatty acid de novo synthesis, were found to be dose-responsive to C. gracilis and tended to decrease. The hepatic glycerol content was also significantly decreased by C. gracilis feeding, and the serum HDL cholesterol levels were significantly increased, whereas the serum levels of cholesterol absorption markers (i.e., campesterol and β-sitosterol) and the hepatic mRNA levels of Scarb1 were significantly decreased. Water-soluble metabolite analysis showed that the muscular contents of several amino acids, including leucine, were significantly increased by C. gracilis feeding. The tendency toward an increase in the weight of the soleus muscle as a result of C. gracilis feeding may be due to the enhancement of muscle protein synthesis centered on leucine. Collectively, these results show that the oral administration of C. gracilis alleviates hepatic lipid accumulation in rats fed a high-sucrose and cholesterol-containing diet, indicating the potential use of C. gracilis as a food resource.
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Affiliation(s)
- Bungo Shirouchi
- Department of Nutrition Science, Faculty of Nursing and Nutrition, University of Nagasaki, Siebold, 1-1-1 Manabino, Nagayo-cho, Nishi-Sonogi-gun, Nagasaki 851-2195, Japan
- Correspondence: ; Tel.: +81-95-813-5734
| | - Yuri Kawahara
- Department of Nutrition Science, Faculty of Nursing and Nutrition, University of Nagasaki, Siebold, 1-1-1 Manabino, Nagayo-cho, Nishi-Sonogi-gun, Nagasaki 851-2195, Japan
| | - Yuka Kutsuna
- Department of Nutrition Science, Faculty of Nursing and Nutrition, University of Nagasaki, Siebold, 1-1-1 Manabino, Nagayo-cho, Nishi-Sonogi-gun, Nagasaki 851-2195, Japan
| | - Mina Higuchi
- Department of Nutrition Science, Faculty of Nursing and Nutrition, University of Nagasaki, Siebold, 1-1-1 Manabino, Nagayo-cho, Nishi-Sonogi-gun, Nagasaki 851-2195, Japan
| | - Mai Okumura
- Department of Nutrition Science, Faculty of Nursing and Nutrition, University of Nagasaki, Siebold, 1-1-1 Manabino, Nagayo-cho, Nishi-Sonogi-gun, Nagasaki 851-2195, Japan
| | - Sarasa Mitsuta
- Department of Nutrition Science, Faculty of Nursing and Nutrition, University of Nagasaki, Siebold, 1-1-1 Manabino, Nagayo-cho, Nishi-Sonogi-gun, Nagasaki 851-2195, Japan
| | - Norio Nagao
- Blue Scientific Shinkamigoto Co., Ltd., 770 Kogushi, Shin-Kamigoto, Minami-Matsuura, Nagasaki 857-4601, Japan
| | - Kazunari Tanaka
- Regional Partnership Center, University of Nagasaki, Siebold, 1-1-1 Manabino, Nagayo-cho, Nishi-Sonogi-gun, Nagasaki 851-2195, Japan
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15
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Yan T, Shi L, Xu K, Bai J, Wen R, Liao X, Dai X, Wu Q, Zeng L, Peng W, Wang Y, Yan H, Dang S, Liu X. Habitual intakes of sugar-sweetened beverages associated with gut microbiota-related metabolites and metabolic health outcomes in young Chinese adults. Nutr Metab Cardiovasc Dis 2023; 33:359-368. [PMID: 36577637 DOI: 10.1016/j.numecd.2022.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/05/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND AND AIMS Reducing consumption of sugar-sweetened beverages (SSBs) is a global public health priority because of their limited nutritional value and associations with increased risk of obesity and metabolic diseases. Gut microbiota-related metabolites emerged as quintessential effectors that may mediate impacts of dietary exposures on the modulation of host commensal microbiome and physiological status. METHODS AND RESULTS This study assessed the associations among SSBs, circulating microbial metabolites, and gut microbiota-host co-metabolites, as well as metabolic health outcomes in young Chinese adults (n = 86), from the Carbohydrate Alternatives and Metabolic Phenotypes study in Shaanxi Province. Five principal component analysis-derived beverage drinking patterns were determined on self-reported SSB intakes, which were to a varying degree associated with 143 plasma levels of gut microbiota-related metabolites profiled by untargeted metabolomics. Moreover, carbonated beverages, fruit juice, energy drinks, and bubble tea exhibited positive associations with obesity-related markers and blood lipids, which were further validated in an independent cohort of 16,851 participants from the Regional Ethnic Cohort Study in Northwest China in Shaanxi Province. In contrast, presweetened coffee was negatively associated with the obesity-related traits. A total of 79 metabolites were associated with both SSBs and metabolic markers, particularly obesity markers. Pathway enrichment analysis identified the branched-chain amino acid catabolism and aminoacyl-tRNA biosynthesis as linking SSB intake with metabolic health outcomes. CONCLUSION Our findings demonstrate the associations between habitual intakes of SSBs and several metabolic markers relevant to noncommunicable diseases, and highlight the critical involvement of gut microbiota-related metabolites in mediating such associations.
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Affiliation(s)
- Tao Yan
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi' an, Shaanxi, China
| | - Lin Shi
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi' an, Shaanxi, China; Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Kun Xu
- Global Health Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Jinyu Bai
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi' an, Shaanxi, China
| | - Ruixue Wen
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi' an, Shaanxi, China
| | - Xia Liao
- Department of Nutrition, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaoshuang Dai
- BGI Institute of Applied Agriculture, BGI-Agro, Shenzhen, China
| | - Qian Wu
- Global Health Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Lingxia Zeng
- Global Health Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Wen Peng
- Nutrition and Health Promotion Center, Department of Public Health, Medical College, Qinghai University, Xining, Qinghai, China
| | - Youfa Wang
- Global Health Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China; School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Hong Yan
- Global Health Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Shaonong Dang
- Global Health Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.
| | - Xin Liu
- Global Health Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.
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16
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Nguyen TTT, Choi YH, Lee WK, Ji Y, Chun E, Kim YH, Lee JE, Jung HS, Suh JH, Kim S, Jin M. Tryptophan-dependent and -independent secretions of tryptophanyl- tRNA synthetase mediate innate inflammatory responses. Cell Rep 2023; 42:111905. [PMID: 36640342 DOI: 10.1016/j.celrep.2022.111905] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/29/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
While cytoplasmic tryptophanyl-tRNA synthetase (WARS1) ligates tryptophan (Trp) to its cognate tRNAs for protein synthesis, it also plays a role as an innate immune activator in extracellular space. However, its secretion mechanism remains elusive. Here, we report that in response to stimuli, WARS1 can be secreted via two distinct pathways: via Trp-dependent secretion of naked protein and via Trp-independent plasma-membrane-derived vesicles (PMVs). In the direct pathway, Trp binding to WARS1 induces a "closed" conformation, generating a hydrophobic surface and basic pocket. The Trp-bound WARS1 then binds stable phosphatidylinositol (4,5)-biphosphate and inner plasma membrane leaflet, passing across the membrane. In the PMV-mediated secretion, WARS1 recruits calpain 2, which is activated by calcium. WARS1 released from PMVs induces inflammatory responses in vivo. These results provide insights into the secretion mechanisms of WARS1 and improve our understanding of how WARS1 is involved in the control of local and systemic inflammation upon infection.
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Affiliation(s)
- Tram Thuy Thuy Nguyen
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Korea
| | - Yun Hui Choi
- Department of Microbiology, College of Medicine, Gachon University, Incheon 21999, Korea; Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Korea
| | - Won-Kyu Lee
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju 28160, Korea
| | - Yeounjung Ji
- Department of Microbiology, College of Medicine, Gachon University, Incheon 21999, Korea; Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Korea
| | - Eunho Chun
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Korea
| | - Yi Hyo Kim
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Korea
| | - Joo-Eun Lee
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, Korea
| | - Hyun Suk Jung
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, Korea
| | - Ji Hun Suh
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Korea
| | - Mirim Jin
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Korea; Department of Microbiology, College of Medicine, Gachon University, Incheon 21999, Korea; Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Korea.
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17
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Sugar-Sweetened Beverages and Metabolic Risk in Children and Adolescents with Obesity: A Narrative Review. Nutrients 2023; 15:nu15030702. [PMID: 36771409 PMCID: PMC9918944 DOI: 10.3390/nu15030702] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
Sugar-sweetened beverages (SSBs) are major contributors of free sugars to the diet. A strong relationship between SSB intake and weight gain is described. METHODS we performed a narrative review to present an overview of the role of SSBs as a pivotal contributor in the development of obesity and metabolism-related complications. RESULTS different factors influence SSB consumption in children, including economic variables, individual attributes and behaviors to environmental factors, parent features and parents' behaviors. Data suggest that SSB intake has a negative effect on weight and obesity-related diseases. The leading mechanism linking SSB intake to the risk of gaining weight is decreased satiety and incomplete compensatory reduction in energy intake at meals following ingestion of liquid calories. Additionally, the effects of SSBs on gut microbiota and on eating behaviors were also reported. An association between SSB intake, weight gain and cardiometabolic risks is evident. Consumption of SSBs had a significant impact on the prevalence of obesity and related metabolic risks, including insulin resistance, type 2 diabetes, hypertension and metabolic syndrome. CONCLUSIONS Limiting consumption of SSBs and increasing knowledge of the effect of SSBs on early metabolic and cardiovascular disorders will be useful in developing strategies to counteract the problem and to prevent obesity and related complications.Key future research areas for which further studies are needed include investigating the long-term effects of SSBs on health outcomes as well as analyzing the health effects of sugar consumed in solid compared to liquid forms and further elucidating the biological mechanisms of sugar addiction and energy compensation.
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18
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Rawat J, Bhambri A, Pandey U, Banerjee S, Pillai B, Gadgil M. Amino acid abundance and composition in cell culture medium affects trace metal tolerance and cholesterol synthesis. Biotechnol Prog 2023; 39:e3298. [PMID: 36053936 DOI: 10.1002/btpr.3298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/02/2022] [Accepted: 08/21/2022] [Indexed: 11/05/2022]
Abstract
Amino acid compositions of cell culture media are empirically designed to enhance cell growth and productivity and vary both across media formulations and over the course of culture due to imbalance in supply and consumption. The interconnected nature of the amino acid transporters and metabolism suggests that changes in amino acid composition can affect cell physiology. In this study, we explore the effect of a step change in amino acid composition from a DMEM: F12-based medium to a formulation varying in relative abundances of all amino acids, evaluated at two amino acid concentrations (lean LAA vs. rich HAA). Cell growth was inhibited in LAA but not HAA. In addition to the expected effects on expression of the cell cycle, amino acid response and mTOR pathway genes in LAA, we observed an unanticipated effect on zinc uptake and efflux genes. This was accompanied by a lower tolerance to zinc supplementation in LAA but not in the other formulations. Histidine was sufficient but not necessary to prevent such zinc toxicity. Additionally, an unanticipated downregulation of genes in the cholesterol synthesis pathway was observed in HAA, accompanied by an increase in cellular cholesterol content, which may depend on the relative abundances of glutamine and other amino acids. This study shows that changes in the amino acid composition without any evident effect on growth may have profound effects on metabolism. Such analyses can help rationalize the designing of medium and feed formulations for bioprocess applications beyond replenishment of consumed components.
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Affiliation(s)
- Jyoti Rawat
- Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Ghaziabad, India
| | - Aksheev Bhambri
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Ghaziabad, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Ujjiti Pandey
- Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Ghaziabad, India
| | - Sanchita Banerjee
- Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, India
| | - Beena Pillai
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Mugdha Gadgil
- Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Ghaziabad, India
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19
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Liu Y, Yu Y, Li S, Sun M, Li F. Comparative transcriptomic analysis of gill reveals genes belonging to mTORC1 signaling pathway associated with the resistance trait of shrimp to VP AHPND. Front Immunol 2023; 14:1150628. [PMID: 37143674 PMCID: PMC10151482 DOI: 10.3389/fimmu.2023.1150628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Selective breeding for acute hepatopancreatic necrosis disease (AHPND) resistant shrimp is an effective way to deal with heavy losses to shrimp aquaculture caused by AHPND. However, knowledge about the molecular mechanism of susceptibility or resistance to AHPND is very limited. We herein performed a comparative transcriptomic analysis of gill tissue between AHPND susceptible and resistant families of the white Pacific shrimp Litopenaeus vannamei during Vibrio parahaemolyticus (VPAHPND) infection. A total of 5,013 genes that were differentially expressed between the two families at 0 and 6 h post-infection, and 1,124 DEGs were shared for both two time points. Both GO and KEGG analyses in each or two time point's comparisons showed DEGs involved in endocytosis, protein synthesis and cell inflammation were significantly enriched. Several immune DEGs including PRRs, antioxidants and AMPs were also identified. The susceptible shrimp showed enhanced endocytosis, higher aminoacyl-tRNA ligase activity and occurrence of inflammatory response, while the resistant shrimp had much more strong ability in ribosome biogenesis, antioxidant activity and pathogen recognition and clearance. These genes and processes were mostly associated with mTORC1 signaling pathway, which could reflect differences in cell growth, metabolism and immune response between the two families. Our findings indicate a close link between mTORC1 signaling-related genes and Vibrio-resistance phenotype of shrimp, and provide new clues for further research on resistance strategy of shrimp to AHPND.
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Affiliation(s)
- Yuan Liu
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yang Yu
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shihao Li
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Mingzhe Sun
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Fuhua Li
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- *Correspondence: Fuhua Li,
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20
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Zhao WB, An JX, Hu YM, Li AP, Zhang SY, Zhang BQ, Zhang ZJ, Luo XF, Bian Q, Ma Y, Ding YY, Wang R, Liu YQ. Tavaborole-Induced Inhibition of the Aminoacyl-tRNA Biosynthesis Pathway against Botrytis cinerea Contributes to Disease Control and Fruit Quality Preservation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12297-12309. [PMID: 36149871 DOI: 10.1021/acs.jafc.2c03441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The inhibitory effect of tavaborole on the invasion of Botrytis cinerea in grapes and tomatoes, as well as the potential mechanism involved, was discovered in this study. Our findings showed that tavaborole inhibited Botrytis cinerea spore germination and mycelial expansion in vitro and that the control efficiency in vivo on fruit decay was dose-dependent, which was effective in reducing disease severity and maintaining the organoleptic quality of the fruit, such as reducing weight loss and retaining fruit hardness and titratable acid contents during storage. Furthermore, the precise mechanism of action was investigated further. Propidium iodide staining revealed that Botrytis cinerea treated with tavaborole lost membrane integrity. For further validation, cytoplasmic malondialdehyde accumulation and leakage of cytoplasmic constituents were determined. Notably, the inhibitory effect was also dependent on inhibiting the activities of aminoacyl-tRNA synthetases involved in the aminoacyl-tRNA biosynthesis pathway in Botrytis cinerea. The above findings concluded that tavaborole was effective against Botrytis cinerea infection in postharvest fruit, and a related mechanism was also discussed, which may provide references for the drug repurposing of tavaborole as a postharvest fungicide.
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Affiliation(s)
- Wen-Bin Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Jun-Xia An
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yong-Mei Hu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - An-Ping Li
- Gansu Institute for Drug Control, Lanzhou 730000, P. R. China
| | - Shao-Yong Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
| | - Bao-Qi Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Zhi-Jun Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Xiong-Fei Luo
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Qiang Bian
- National Pesticide Engineering Research Center (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yue Ma
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yan-Yan Ding
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Rui Wang
- Key Laboratory of Biochemistry and Molecular Biology in Universities of Shandong Province, Weifang University, Weifang 261061, China
| | - Ying-Qian Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, People's Republic of China
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou 730000, China
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21
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Bögershausen N, Krawczyk HE, Jamra RA, Lin SJ, Yigit G, Hüning I, Polo AM, Vona B, Huang K, Schmidt J, Altmüller J, Luppe J, Platzer K, Dörgeloh BB, Busche A, Biskup S, Mendes MI, Smith DEC, Salomons GS, Zibat A, Bültmann E, Nürnberg P, Spielmann M, Lemke JR, Li Y, Zenker M, Varshney GK, Hillen HS, Kratz CP, Wollnik B. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Hum Mutat 2022; 43:1454-1471. [PMID: 35790048 DOI: 10.1002/humu.24430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023]
Abstract
Aminoacylation of transfer RNA (tRNA) is a key step in protein biosynthesis, carried out by highly specific aminoacyl-tRNA synthetases (ARSs). ARSs have been implicated in autosomal dominant and autosomal recessive human disorders. Autosomal dominant variants in tryptophanyl-tRNA synthetase 1 (WARS1) are known to cause distal hereditary motor neuropathy and Charcot-Marie-Tooth disease, but a recessively inherited phenotype is yet to be clearly defined. Seryl-tRNA synthetase 1 (SARS1) has rarely been implicated in an autosomal recessive developmental disorder. Here, we report five individuals with biallelic missense variants in WARS1 or SARS1, who presented with an overlapping phenotype of microcephaly, developmental delay, intellectual disability, and brain anomalies. Structural mapping showed that the SARS1 variant is located directly within the enzyme's active site, most likely diminishing activity, while the WARS1 variant is located in the N-terminal domain. We further characterize the identified WARS1 variant by showing that it negatively impacts protein abundance and is unable to rescue the phenotype of a CRISPR/Cas9 wars1 knockout zebrafish model. In summary, we describe two overlapping autosomal recessive syndromes caused by variants in WARS1 and SARS1, present functional insights into the pathogenesis of the WARS1-related syndrome and define an emerging disease spectrum: ARS-related developmental disorders with or without microcephaly.
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Affiliation(s)
- Nina Bögershausen
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Hannah E Krawczyk
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Rami A Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Irina Hüning
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Anna M Polo
- MVZ Labor Krone, Filialpraxis für Humangenetik, Bielefeld, Germany
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Julia Schmidt
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Johannes Luppe
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Beate B Dörgeloh
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Andreas Busche
- Institut für Humangenetik, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Saskia Biskup
- CeGaT GmbH, Center for Genomics and Transcriptomics, Tübingen, Germany
| | - Marisa I Mendes
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Desiree E C Smith
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Gajja S Salomons
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Arne Zibat
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Eva Bültmann
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Malte Spielmann
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Yun Li
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Martin Zenker
- Institute of Human Genetics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Hauke S Hillen
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable cells" (MBExC), University of Göttingen, Göttingen, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
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22
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Jiang Y, You J, Wu C, Kang Y, Chen F, Chen L, Wu W. High expression of DARS2 indicates poor prognosis in lung adenocarcinoma. J Clin Lab Anal 2022; 36:e24691. [PMID: 36085578 PMCID: PMC9550967 DOI: 10.1002/jcla.24691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 01/25/2023] Open
Abstract
Background DARS2 was overexpressed in multiple tumor types, but the biological role of DARS2 in lung adenocarcinoma (LUAD) have not been elucidated. Methods Firstly, the DARS2 expression in LUAD was explored using The Cancer Genome Atlas (TCGA). Then, qRT‐PCR and Western blot were performed to confirm DARS2 expression in LUAD. Next, Cox regression and Kaplan–Meier methods were utilized to evaluate whether DARS2 expression can affect the overall survival. The relationships between DARS2 expression and clinicopathological characteristics were investigated by TCGA database. Moreover, we utilized Gene Set Enrichment Analysis (GSEA) to detect DARS2‐related signaling pathways in LUAD. Finally, the special function of DARS2 in cell proliferation, invasion and apoptosis was assessed in vitro. Results The higher expression of DARS2 was found in LUAD compared to para‐carcinoma tissues and significantly related to tumor stage, T stage, and M stage. The survival analysis indicated that DARS2 overexpression was related to poor prognosis in LUAD. Multivariate analysis suggested that DARS2 expression was a prognostic indicator. GSEA revealed that DARS2 was primarily involved in cell cycle‐related pathways. In addition, upregulation of DARS2 facilitated LUAD cell proliferation, migration, invasion and inhabited apoptosis, DARS2 knockdown showed an opposite result. Conclusion DARS2 modulates the proliferation, invasion and apoptosis of LUAD cells, and sever as a promising therapeutic target for LUAD.
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Affiliation(s)
- Yingfeng Jiang
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Jianbin You
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Chuncai Wu
- Department of Clinical Laboratory, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
| | - Yanli Kang
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Falin Chen
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Liangyuan Chen
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Wenbing Wu
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
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23
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Liu Q, Lin F. Lentivirus-induced knockdown of IARS2 expression inhibits the proliferation and promotes the apoptosis of human osteosarcoma cells. Oncol Lett 2022; 24:262. [PMID: 35765273 PMCID: PMC9219035 DOI: 10.3892/ol.2022.13382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/09/2022] [Indexed: 11/19/2022] Open
Abstract
Isoleucyl-tRNA synthetase 2 (IARS2), distributed in mitochondria, is an IARS involved in protein synthesis. Notably, IARS2 has been reported to be associated with tumor progression; however, the relationship between osteosarcoma (OS) and IARS2 remains unclear. To investigate the role of IARS2 in human OS, the expression and relationship of IARS2 with survival were firstly analyzed using the Gene Expression Profiling Interactive Analysis 2 database. Subsequently, an IARS2-short hairpin RNA lentiviral vector was established and used to infect the MNNG/HOS and U2OS cell lines. Reverse transcription-quantitative PCR (RT-qPCR) and western blotting were applied to determine the efficiency of IARS2 knockdown. The effects of IARS2 knockdown on cell proliferation, colony formation and apoptosis were evaluated by Celigo, MTT assays, colony formation assays and flow cytomeric analysis. In the present study, IARS2 tends to be high expressed in OS tissue and was associated with survival but this was not significant. The results of RT-qPCR and western blotting showed that the expression of IARS2 was effectively knocked down in the MNNG/HOS and U2OS cell lines. Celigo, MTT and colony formation assays showed that IARS2 knockdown in MNNG/HOS and U2OS cell lines inhibited cell proliferation and colony formation compared with in the control group. Flow cytometric analysis revealed that IARS2 knockdown increased apoptosis. These results suggested that IARS2 may be critical for the proliferation and apoptosis of OS cells.
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Affiliation(s)
- Qi Liu
- Department of Oncology, The Eighth People's Hospital of Shanghai, Shanghai 200235, P.R. China
| | - Feng Lin
- Department of Oncology, The Eighth People's Hospital of Shanghai, Shanghai 200235, P.R. China
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24
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Dang JT, Mocanu V, Park H, Laffin M, Hotte N, Karmali S, Birch DW, Madsen KL. Roux-en-Y gastric bypass and sleeve gastrectomy induce substantial and persistent changes in microbial communities and metabolic pathways. Gut Microbes 2022; 14:2050636. [PMID: 35316158 PMCID: PMC8942407 DOI: 10.1080/19490976.2022.2050636] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bariatric surgery induces significant microbial and metabolomic changes, however, links between microbial and metabolic pathways have not been fully elucidated. The objective of this study was to conduct a comprehensive investigation of the microbial, metabolomic, and inflammatory changes that occur following Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG). A prospective clinical trial was conducted with participants undergoing RYGB, SG, and non-operative controls (CTRL). Clinical parameters, blood samples, and fecal samples were collected pre-intervention and at 3 and 9 months. A multi-omics approach was used to perform integrated microbial-metabolomic analysis to identify functional pathways in which weight loss and metabolic changes occur after surgery. RYGB led to profound microbial changes over time that included reductions in alpha-diversity, increased Proteobacteria and Verrucomicrobiota, decreased Firmicutes, and numerous changes at the genera level. These changes were associated with a reduction in inflammation and significant weight loss. A reduction in Romboutsia genera correlated strongly with weight loss and integrated microbial-metabolomic analysis revealed the importance of Romboutsia. Its obliteration correlated with improved weight loss and insulin resistance, possibly through decreases in glycerophospholipids. In contrast, SG was associated with no changes in alpha-diversity, and only a small number of changes in microbial genera. A cluster of Firmicutes genera including Butyriciccocus, Eubacterium ventriosum, and Monoglobus was decreased, which correlated with decreased weight, insulin resistance, and systemic inflammation. This work represents comprehensive analyses of microbial-metabolomic changes that occur following bariatric surgery and identifies several pathways that are associated with beneficial metabolic effects of surgery.
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Affiliation(s)
- Jerry T. Dang
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada,CONTACT Jerry T. Dang Division of General Surgery, Department of Surgery, University of Alberta, University of Alberta Hospital, 8440 112 Street NW, Edmonton, AB, CanadaT6G 2B7
| | - Valentin Mocanu
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Heekuk Park
- Department of Medicine, Columbia University, New York, New York, USA
| | - Michael Laffin
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Naomi Hotte
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Shahzeer Karmali
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel W. Birch
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Karen L. Madsen
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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25
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Gupta A, Rangarajan PN. Histidine is essential for growth of Komagataella phaffii cultured in YPA medium. FEBS Open Bio 2022; 12:1241-1252. [PMID: 35416413 PMCID: PMC9157411 DOI: 10.1002/2211-5463.13408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/26/2022] [Accepted: 04/12/2022] [Indexed: 11/08/2022] Open
Abstract
Komagataella phaffii (a.k.a. Pichia pastoris) requires histidine for optimal growth when cultured in a medium containing yeast extract, peptone (YP) and acetate (YPA). We demonstrate that HIS4-deficient, K. phaffii strain GS115 exhibits a growth defect on YP-media containing acetate, but not on other carbon sources. K. phaffii X33, a prototroph, grows better than K. phaffii GS115 (his4), a histidine auxotroph in YPA. Normal growth of GS115 is restored either by the expression of HIS4 or by culturing in YPA containing ≥0.6 mM histidine. In presence of histidine, expression of several genes is altered including those encoding key subunits of mitochondrial ATP synthase, transporters of amino acids and nutrients, as well as biosynthetic enzymes. Thus, histidine should be included as an essential component for optimal growth of K.phaffii histidine auxotrophs cultured in YPA.
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Affiliation(s)
- Aditi Gupta
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Pundi N Rangarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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26
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Tryptophan depletion results in tryptophan-to-phenylalanine substitutants. Nature 2022; 603:721-727. [PMID: 35264796 PMCID: PMC8942854 DOI: 10.1038/s41586-022-04499-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Activated T cells secrete interferon-γ, which triggers intracellular tryptophan shortage by upregulating the indoleamine 2,3-dioxygenase 1 (IDO1) enzyme1-4. Here we show that despite tryptophan depletion, in-frame protein synthesis continues across tryptophan codons. We identified tryptophan-to-phenylalanine codon reassignment (W>F) as the major event facilitating this process, and pinpointed tryptophanyl-tRNA synthetase (WARS1) as its source. We call these W>F peptides 'substitutants' to distinguish them from genetically encoded mutants. Using large-scale proteomics analyses, we demonstrate W>F substitutants to be highly abundant in multiple cancer types. W>F substitutants were enriched in tumours relative to matching adjacent normal tissues, and were associated with increased IDO1 expression, oncogenic signalling and the tumour-immune microenvironment. Functionally, W>F substitutants can impair protein activity, but also expand the landscape of antigens presented at the cell surface to activate T cell responses. Thus, substitutants are generated by an alternative decoding mechanism with potential effects on gene function and tumour immunoreactivity.
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27
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Gupta A, Galinski MR, Voit EO. Dynamic Control Balancing Cell Proliferation and Inflammation is Crucial for an Effective Immune Response to Malaria. Front Mol Biosci 2022; 8:800721. [PMID: 35242812 PMCID: PMC8886244 DOI: 10.3389/fmolb.2021.800721] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria has a complex pathology with varying manifestations and symptoms, effects on host tissues, and different degrees of severity and ultimate outcome, depending on the causative Plasmodium pathogen and host species. Previously, we compared the peripheral blood transcriptomes of two macaque species (Macaca mulatta and Macaca fascicularis) in response to acute primary infection by Plasmodium knowlesi. Although these two species are very closely related, the infection in M. mulatta is fatal, unless aggressively treated, whereas M. fascicularis develops a chronic, but tolerable infection in the blood. As a reason for this stark difference, our analysis suggests delayed pathogen detection in M. mulatta followed by extended inflammation that eventually overwhelms this monkey’s immune response. By contrast, the natural host M. fascicularis detects the pathogen earlier and controls the inflammation. Additionally, M. fascicularis limits cell proliferation pathways during the log phase of infection, presumably in an attempt to control inflammation. Subsequent cell proliferation suggests a cell-mediated adaptive immune response. Here, we focus on molecular mechanisms underlying the key differences in the host and parasite responses and their coordination. SICAvar Type 1 surface antigens are highly correlated with pattern recognition receptor signaling and important inflammatory genes for both hosts. Analysis of pathogen detection pathways reveals a similar signaling mechanism, but with important differences in the glutamate G-protein coupled receptor (GPCR) signaling pathway. Furthermore, differences in inflammasome assembly processes suggests an important role of S100 proteins in balancing inflammation and cell proliferation. Both differences point to the importance of Ca2+ homeostasis in inflammation. Additionally, the kynurenine-to-tryptophan ratio, a known inflammatory biomarker, emphasizes higher inflammation in M. mulatta during log phase. Transcriptomics-aided metabolic modeling provides a functional method for evaluating these changes and understanding downstream changes in NAD metabolism and aryl hydrocarbon receptor (AhR) signaling, with enhanced NAD metabolism in M. fascicularis and stronger AhR signaling in M. mulatta. AhR signaling controls important immune genes like IL6, IFNγ and IDO1. However, direct changes due to AhR signaling could not be established due to complicated regulatory feedback mechanisms associated with the AhR repressor (AhRR). A complete understanding of the exact dynamics of the immune response is difficult to achieve. Nonetheless, our comparative analysis provides clear suggestions of processes that underlie an effective immune response. Thus, our study identifies multiple points of intervention that are apparently responsible for a balanced and effective immune response and thereby paves the way toward future immune strategies for treating malaria.
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Affiliation(s)
- Anuj Gupta
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Mary R. Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA, United States
| | - Eberhard O. Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
- *Correspondence: Eberhard O. Voit,
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28
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Fu Z, Han F, Huang K, Zhang J, Qin JG, Chen L, Li E. Impact of imidacloprid exposure on the biochemical responses, transcriptome, gut microbiota and growth performance of the Pacific white shrimp Litopenaeus vannamei. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127513. [PMID: 34687996 DOI: 10.1016/j.jhazmat.2021.127513] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/01/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The widespread use of neonicotinoid insecticides, such as imidacloprid, in agriculture is one of the key factors for the drop in the survival of invertebrates, including decapod crustaceans. However, there is currently a lack of comprehensive studies on the chronic toxicity mechanisms in decapod crustaceans. Here, the concentration-dependent effects of imidacloprid on the physiology and biochemistry, gut microbiota and transcriptome of L. vannamei , and the interaction between imidacloprid, gut microbiota and genes were studied. Imidacloprid caused oxidative stress, leading to reduced growth and to immunity and tissue damage in L. vannamei . Imidacloprid increased the gut pathogenic microbiota abundance and broke the steady state of the gut microbiota interaction network, resulting in microbiota function disorders. Chronic imidacloprid exposure induced overall transcriptome changes in L. vannamei . Specifically, imidacloprid caused a large number of differentially expressed genes (DEGs) to be significantly downregulated. The inhibition of autophagy-related pathways revealed the toxic process of imidacloprid to L. vannamei . The changes in phase I and II detoxification gene expression clarified the formation of a detoxification mechanism in L. vannamei . The disturbance of circadian rhythm (CLOCK) caused by imidacloprid is one of the reasons for the increase in gut pathogenic microbiota abundance.
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Affiliation(s)
- Zhenqiang Fu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Fenglu Han
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Kaiqi Huang
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Jiliang Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Jian G Qin
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Liqiao Chen
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Erchao Li
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China.
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Wang L, Qi H, Li D, Liu L, Chen D, Gao X. METTL3 is a key regulator of milk synthesis in mammary epithelial cells. Cell Biol Int 2021; 46:359-369. [PMID: 34865263 DOI: 10.1002/cbin.11733] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/31/2021] [Accepted: 11/28/2021] [Indexed: 12/15/2022]
Abstract
The enzyme m6 A methyltransferase-like 3 (METTL3) catalyzes N6 -methyladenosine (m6 A) modification in eukaryotic messenger RNAs (mRNAs). However, the physiological function and molecular mechanism of METTL3 in mammalian cells have not been fully understood. Here we showed that METTL3 was highly expressed in mouse mammary gland of the lactation period. METTL3 was located in the nucleus of bovine mammary epithelial cells (MECs), and methionine (Met) and β-estrodial (E2) upregulated METTL3 protein level. METTL3 knockdown decreased milk protein and fat synthesis, whereas its overexpression had the opposite effects. METTL3 overexpression stimulated mRNA expression and protein phosphorylation of the mechanistic target of rapamycin (mTOR) and mRNA and protein expression of sterol regulatory element binding protein 1 (SREBP1), whereas METTL3 knockdown blocked the stimulatory effects of Met and E2 on these processes. Furthermore, METTL3 overexpression led to increased mRNA m6 A methylation of mTOR and SREBP1, whereas METTL3 knockdown suppressed the stimulatory effects of Met and E2 on these processes. The interaction between METTL3 and glycyl-tRNA synthetase (GlyRS) was confirmed by Co-immunoprecipitation and fluorescence resonance energy transfer approaches, and colocalization observation further showed that Met and E2 treatment increased this interaction. GlyRS knockdown abolished METTL3 protein levels upregulated by Met and E2, and METTL3 knockdown markedly decreased the effects of GlyRS overexpression on mTOR expression and phosphorylation and SREBP1 expression. In summary, we demonstrate that METTL3 is a key positive regulator of Met and E2-stimulated and GlyRS-mediated mTOR and SREBP1 signaling pathways and milk protein and fat synthesis in mammary epithelial cells.
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Affiliation(s)
- Lulu Wang
- College of Animal Science, Yangtze University, Jingzhou, China.,College of Life Science, Northeast Agricultural University, Harbin, China
| | - Hao Qi
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Dong Li
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Lijie Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Dongying Chen
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Xuejun Gao
- College of Animal Science, Yangtze University, Jingzhou, China
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tRNA Biology in the Pathogenesis of Diabetes: Role of Genetic and Environmental Factors. Int J Mol Sci 2021; 22:ijms22020496. [PMID: 33419045 PMCID: PMC7825315 DOI: 10.3390/ijms22020496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 02/07/2023] Open
Abstract
The global rise in type 2 diabetes results from a combination of genetic predisposition with environmental assaults that negatively affect insulin action in peripheral tissues and impair pancreatic β-cell function and survival. Nongenetic heritability of metabolic traits may be an important contributor to the diabetes epidemic. Transfer RNAs (tRNAs) are noncoding RNA molecules that play a crucial role in protein synthesis. tRNAs also have noncanonical functions through which they control a variety of biological processes. Genetic and environmental effects on tRNAs have emerged as novel contributors to the pathogenesis of diabetes. Indeed, altered tRNA aminoacylation, modification, and fragmentation are associated with β-cell failure, obesity, and insulin resistance. Moreover, diet-induced tRNA fragments have been linked with intergenerational inheritance of metabolic traits. Here, we provide a comprehensive review of how perturbations in tRNA biology play a role in the pathogenesis of monogenic and type 2 diabetes.
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