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Stewart RK, Nguyen P, Laederach A, Volkan PC, Sawyer JK, Fox DT. Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation. Nat Commun 2024; 15:5270. [PMID: 38902233 PMCID: PMC11190236 DOI: 10.1038/s41467-024-48344-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/25/2024] [Indexed: 06/22/2024] Open
Abstract
Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, we identify the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent mRNA stability in neurons. Using RNA sequencing, we reveal that Orb2-upregulated mRNAs in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, we demonstrate that rare-codon enrichment is important for mRNA stability and social behavior function of the metabotropic glutamate receptor (mGluR). Our findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA stability and protein expression.
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Affiliation(s)
- Rebeccah K Stewart
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Patrick Nguyen
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jessica K Sawyer
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Donald T Fox
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA.
- Duke Regeneration Center, Duke University, Durham, NC, USA.
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2
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Potera K, Tomala K. Using yeasts for the studies of nonfunctional factors in protein evolution. Yeast 2024. [PMID: 38895906 DOI: 10.1002/yea.3970] [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: 01/31/2024] [Revised: 05/08/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024] Open
Abstract
The evolution of protein sequence is driven not only by factors directly related to protein function and shape but also by nonfunctional factors. Such factors in protein evolution might be categorized as those connected to energetic costs, synthesis efficiency, and avoidance of misfolding and toxicity. A common approach to studying them is correlational analysis contrasting them with some characteristics of the protein, like amino acid composition, but these features are interdependent. To avoid possible bias, empirical studies are needed, and not enough work has been done to date. In this review, we describe the role of nonfunctional factors in protein evolution and present an experimental approach using yeast as a suitable model organism. The focus of the proposed approach is on the potential negative impact on the fitness of mutations that change protein properties not related to function and the frequency of mutations that change these properties. Experimental results of testing the misfolding avoidance hypothesis as an explanation for why highly expressed proteins evolve slowly are inconsistent with correlational research results. Therefore, more efforts should be made to empirically test the effects of nonfunctional factors in protein evolution and to contrast these results with the results of the correlational analysis approach.
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Affiliation(s)
- Katarzyna Potera
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Katarzyna Tomala
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
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3
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Choi SW, Nam JW. Optimal design of synthetic circular RNAs. Exp Mol Med 2024:10.1038/s12276-024-01251-w. [PMID: 38871815 DOI: 10.1038/s12276-024-01251-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 06/15/2024] Open
Abstract
Circular RNAs are an unusual class of single-stranded RNAs whose ends are covalently linked via back-splicing. Due to their versatility, the need to express circular RNAs in vivo and in vitro has increased. Efforts have been made to efficiently and precisely synthesize circular RNAs. However, a review on the optimization of the processes of circular RNA design, synthesis, and delivery is lacking. Our review highlights the multifaceted aspects considered when producing optimal circular RNAs and summarizes the available options for each step of exogenous circular RNA design and synthesis, including circularization strategies. Additionally, this review describes several potential applications of circular RNAs.
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Affiliation(s)
- Seo-Won Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
- Bio-BigData Center, Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Seoul, 04763, Republic of Korea.
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4
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Hassan MM, Tenazas F, Williams A, Chiu JW, Robin C, Russell DA, Golz JF. Minimizing IP issues associated with gene constructs encoding the Bt toxin - a case study. BMC Biotechnol 2024; 24:37. [PMID: 38825715 PMCID: PMC11145813 DOI: 10.1186/s12896-024-00864-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 05/27/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND As part of a publicly funded initiative to develop genetically engineered Brassicas (cabbage, cauliflower, and canola) expressing Bacillus thuringiensis Crystal (Cry)-encoded insecticidal (Bt) toxin for Indian and Australian farmers, we designed several constructs that drive high-level expression of modified Cry1B and Cry1C genes (referred to as Cry1BM and Cry1CM; with M indicating modified). The two main motivations for modifying the DNA sequences of these genes were to minimise any licensing cost associated with the commercial cultivation of transgenic crop plants expressing CryM genes, and to remove or alter sequences that might adversely affect their activity in plants. RESULTS To assess the insecticidal efficacy of the Cry1BM/Cry1CM genes, constructs were introduced into the model Brassica Arabidopsis thaliana in which Cry1BM/Cry1CM expression was directed from either single (S4/S7) or double (S4S4/S7S7) subterranean clover stunt virus (SCSV) promoters. The resulting transgenic plants displayed a high-level of Cry1BM/Cry1CM expression. Protein accumulation for Cry1CM ranged from 5.18 to 176.88 µg Cry1CM/g dry weight of leaves. Contrary to previous work on stunt promoters, we found no correlation between the use of either single or double stunt promoters and the expression levels of Cry1BM/Cry1CM genes, with a similar range of Cry1CM transcript abundance and protein content observed from both constructs. First instar Diamondback moth (Plutella xylostella) larvae fed on transgenic Arabidopsis leaves expressing the Cry1BM/Cry1CM genes showed 100% mortality, with a mean leaf damage score on a scale of zero to five of 0.125 for transgenic leaves and 4.2 for wild-type leaves. CONCLUSIONS Our work indicates that the modified Cry1 genes are suitable for the development of insect resistant GM crops. Except for the PAT gene in the USA, our assessment of the intellectual property landscape of components presents within the constructs described here suggest that they can be used without the need for further licensing. This has the capacity to significantly reduce the cost of developing and using these Cry1M genes in GM crop plants in the future.
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Affiliation(s)
- Md Mahmudul Hassan
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Francis Tenazas
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Adam Williams
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jing-Wen Chiu
- School of Agriculture, Food and Ecosystem Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Charles Robin
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Derek A Russell
- Melbourne Veterinary School, University of Melbourne, Parkville, VIC, 3010, Australia
| | - John F Golz
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia.
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5
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Jiang C, Zhao G, Wang H, Zheng W, Zhang R, Wang L, Zheng Z. Comparative genomics analysis and transposon mutagenesis provides new insights into high menaquinone-7 biosynthetic potential of Bacillus subtilis natto. Gene 2024; 907:148264. [PMID: 38346457 DOI: 10.1016/j.gene.2024.148264] [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: 10/06/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
This research combined Whole-Genome sequencing, intraspecific comparative genomics and transposon mutagenesis to investigate the menaquinone-7 (MK-7) synthesis potential in Bacillus subtilis natto. First, Whole-Genome sequencing showed that Bacillus subtilis natto BN-P15-11-1 contains one single circular chromosome in size of 3,982,436 bp with a GC content of 43.85 %, harboring 4,053 predicted coding genes. Next, the comparative genomics analysis among strain BN-P15-11-1 with model Bacillus subtilis 168 and four typical Bacillus subtilis natto strains proves that the closer evolutionary relationship Bacillus subtilis natto BN-P15-11-1 and Bacillus subtilis 168 both exhibit strong biosynthetic potential. To further dig for MK-7 biosynthesis latent capacity of BN-P15-11-1, we constructed a mutant library using transposons and a high throughput screening method using microplates. We obtained a YqgQ deficient high MK-7 yield strain F4 with a yield 3.02 times that of the parent strain. Experiments also showed that the high yield mutants had defects in different transcription and translation regulatory factor genes, indicating that regulatory factor defects may affect the biosynthesis and accumulation of MK-7 by altering the overall metabolic level. The findings of this study will provide more novel insights on the precise identification and rational utilization of the Bacillus subtilis subspecies for biosynthesis latent capacity.
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Affiliation(s)
- Chunxu Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Genhai Zhao
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Han Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Wenqian Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Rui Zhang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Li Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Zhiming Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
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6
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Shan KJ, Wu C, Tang X, Lu R, Hu Y, Tan W, Lu J. Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad003. [PMID: 38862422 DOI: 10.1093/gpbjnl/qzad003] [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: 06/28/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
The monkeypox virus (mpox virus, MPXV) epidemic in 2022 has posed a significant public health risk. Yet, the evolutionary principles of MPXV remain largely unknown. Here, we examined the evolutionary patterns of protein sequences and codon usage in MPXV. We first demonstrated the signal of positive selection in OPG027, specifically in the Clade I lineage of MPXV. Subsequently, we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 outbreak. Furthermore, we showed strong epistasis between amino acid substitutions located in different genes. The codon adaptation index (CAI) analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes, and the CAI decreased over time and diverged between clades, with Clade I > IIa and IIb-A > IIb-B. While the decrease in fatality rate among the three groups aligned with the CAI pattern, it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality rates. This study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.
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Affiliation(s)
- Ke-Jia Shan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Changcheng Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Roujian Lu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Yaling Hu
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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7
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You J, Wang Y, Wang K, Du Y, Zhang X, Zhang X, Yang T, Pan X, Rao Z. Utilizing 5' UTR Engineering Enables Fine-Tuning of Multiple Genes within Operons to Balance Metabolic Flux in Bacillus subtilis. BIOLOGY 2024; 13:277. [PMID: 38666889 PMCID: PMC11047901 DOI: 10.3390/biology13040277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
The application of synthetic biology tools to modulate gene expression to increase yield has been thoroughly demonstrated as an effective and convenient approach in industrial production. In this study, we employed a high-throughput screening strategy to identify a 5' UTR sequence from the genome of B. subtilis 168. This sequence resulted in a 5.8-fold increase in the expression level of EGFP. By utilizing the 5' UTR sequence to overexpress individual genes within the rib operon, it was determined that the genes ribD and ribAB serve as rate-limiting enzymes in the riboflavin synthesis pathway. Constructing a 5' UTR library to regulate EGFP expression resulted in a variation range in gene expression levels exceeding 100-fold. Employing the same 5' UTR library to regulate the expression of EGFP and mCherry within the operon led to a change in the expression ratio of these two genes by over 10,000-fold. So, employing a 5' UTR library to modulate the expression of the rib operon gene and construct a synthetic rib operon resulted in a 2.09-fold increase in riboflavin production. These results indicate that the 5' UTR sequence identified and characterized in this study can serve as a versatile synthetic biology toolkit for achieving complex metabolic network reconstruction. This toolkit can facilitate the fine-tuning of gene expression to produce target products.
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Affiliation(s)
- Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (J.Y.); (K.W.); (Y.D.); (X.Z.); (X.Z.); (T.Y.)
- Yixing Institute of Food and Biotechnology Co., Ltd., Yixing 214200, China
| | - Yifan Wang
- Department of Food Science and Technology, Texas A & M University, College Station, TX 77843, USA;
| | - Kang Wang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (J.Y.); (K.W.); (Y.D.); (X.Z.); (X.Z.); (T.Y.)
| | - Yuxuan Du
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (J.Y.); (K.W.); (Y.D.); (X.Z.); (X.Z.); (T.Y.)
| | - Xiaoling Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (J.Y.); (K.W.); (Y.D.); (X.Z.); (X.Z.); (T.Y.)
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (J.Y.); (K.W.); (Y.D.); (X.Z.); (X.Z.); (T.Y.)
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (J.Y.); (K.W.); (Y.D.); (X.Z.); (X.Z.); (T.Y.)
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (J.Y.); (K.W.); (Y.D.); (X.Z.); (X.Z.); (T.Y.)
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (J.Y.); (K.W.); (Y.D.); (X.Z.); (X.Z.); (T.Y.)
- Yixing Institute of Food and Biotechnology Co., Ltd., Yixing 214200, China
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8
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Khomarbaghi Z, Ngan WY, Ayan GB, Lim S, Dechow-Seligmann G, Nandy P, Gallie J. Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens SBW25. Nucleic Acids Res 2024; 52:2446-2462. [PMID: 38296823 PMCID: PMC10954465 DOI: 10.1093/nar/gkae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
The complement of tRNA genes within a genome is typically considered to be a (relatively) stable characteristic of an organism. Here, we demonstrate that bacterial tRNA gene set composition can be more flexible than previously appreciated, particularly regarding tRNA gene copy number. We report the high-rate occurrence of spontaneous, large-scale, tandem duplication events in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The identified duplications are up to ∼1 Mb in size (∼15% of the wildtype genome) and are predicted to change the copy number of up to 917 genes, including several tRNA genes. The observed duplications are inherently unstable: they occur, and are subsequently lost, at extremely high rates. We propose that this unusually plastic type of mutation provides a mechanism by which tRNA gene set diversity can be rapidly generated, while simultaneously preserving the underlying tRNA gene set in the absence of continued selection. That is, if a tRNA set variant provides no fitness advantage, then high-rate segregation of the duplication ensures the maintenance of the original tRNA gene set. However, if a tRNA gene set variant is beneficial, the underlying duplication fragment(s) may persist for longer and provide raw material for further, more stable, evolutionary change.
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Affiliation(s)
- Zahra Khomarbaghi
- Microbial Evolutionary Dynamics Research Group, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Wing Y Ngan
- Microbial Evolutionary Dynamics Research Group, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Gökçe B Ayan
- Microbial Evolutionary Dynamics Research Group, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Sungbin Lim
- Microbial Evolutionary Dynamics Research Group, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Gunda Dechow-Seligmann
- Microbial Evolutionary Dynamics Research Group, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Pabitra Nandy
- Microbial Evolutionary Dynamics Research Group, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Jenna Gallie
- Microbial Evolutionary Dynamics Research Group, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
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9
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Uddin A. Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04091-x. [PMID: 38488980 DOI: 10.1007/s12035-024-04091-x] [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: 11/04/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024]
Abstract
Codon usage bias (CUB) is the phenomenon of non-uniform usage of synonymous codons in which some codons are more used than others and it helps in understanding the molecular organization of genome. Bioinformatic approach was used to analyze the protein-coding sequences of genes associated with Parkinson's disease (PD) to explore compositional features and codon usage pattern as no details work was reported yet. The average improved effective number of codons (Nc) and Nc prime were 42.74 and 44.26 respectively, indicated that CUB was low in these genes. In most of the genes, the overall GC content was almost 50% and GC content at the 1st codon position was the highest while GC content at the 2nd codon position was lowest. Relative synonymous codon usage (RSCU) analysis elucidated over-represented (p > 1.6) and under-represented codons (p < 0.6). The GTG (Val) is the only codon over-represented in all genes. Over-represented codons except (GTG) were A or T ending while under-represented codons (except ACT) were G or C ending. The codons namely TTA (Leu), CTA (Leu), ATC (Ile), ATA (Ile), AGT (Ser), AAC (Asn), TGT (Cys), TGC (Cys), CGC (Arg), AGA (Arg), and AGG (Arg) were absent in SNCA1 to SNCA8 genes. The codon TCG (Ser) was absent in all genes except UCHL1 and PINK1. Correspondence analysis (COA) revealed that the pattern of codon usage differs among genes associated with PD. Neutrality plot analysis indicated some of the points are diagonal distribution suggested that mutation pressure influenced the CUB in genes associated with PD.
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Affiliation(s)
- Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi-788150, Assam, India.
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10
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Ghashghaei M, Liu Y, Ettles J, Bombaci G, Ramkumar N, Liu Z, Escano L, Miko SS, Kim Y, Waldron JA, Do K, MacPherson K, Yuen KA, Taibi T, Yue M, Arsalan A, Jin Z, Edin G, Karsan A, Morin GB, Kuchenbauer F, Perna F, Bushell M, Vu LP. Translation efficiency driven by CNOT3 subunit of the CCR4-NOT complex promotes leukemogenesis. Nat Commun 2024; 15:2340. [PMID: 38491013 PMCID: PMC10943099 DOI: 10.1038/s41467-024-46665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Protein synthesis is frequently deregulated during tumorigenesis. However, the precise contexts of selective translational control and the regulators of such mechanisms in cancer is poorly understood. Here, we uncovered CNOT3, a subunit of the CCR4-NOT complex, as an essential modulator of translation in myeloid leukemia. Elevated CNOT3 expression correlates with unfavorable outcomes in patients with acute myeloid leukemia (AML). CNOT3 depletion induces differentiation and apoptosis and delayed leukemogenesis. Transcriptomic and proteomic profiling uncovers c-MYC as a critical downstream target which is translationally regulated by CNOT3. Global analysis of mRNA features demonstrates that CNOT3 selectively influences expression of target genes in a codon usage dependent manner. Furthermore, CNOT3 associates with the protein network largely consisting of ribosomal proteins and translation elongation factors in leukemia cells. Overall, our work elicits the direct requirement for translation efficiency in tumorigenesis and propose targeting the post-transcriptional circuitry via CNOT3 as a therapeutic vulnerability in AML.
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Affiliation(s)
- Maryam Ghashghaei
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Yilin Liu
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, Canada
| | - James Ettles
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Giuseppe Bombaci
- Department of Medicine, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
| | - Niveditha Ramkumar
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Zongmin Liu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Leo Escano
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Sandra Spencer Miko
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Yerin Kim
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
- Bioinformatics program, University of British Columbia, Vancouver, Canada
| | - Joseph A Waldron
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kim Do
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyle MacPherson
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Katie A Yuen
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Thilelli Taibi
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Marty Yue
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Aaremish Arsalan
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Zhen Jin
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Glenn Edin
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Aly Karsan
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Gregg B Morin
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Florian Kuchenbauer
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Fabiana Perna
- Department of Medicine, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Moffit Cancer Center, Tampa, FL, USA
| | - Martin Bushell
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ly P Vu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada.
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11
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Baghdassarian HM, Lewis NE. Resource allocation in mammalian systems. Biotechnol Adv 2024; 71:108305. [PMID: 38215956 PMCID: PMC11182366 DOI: 10.1016/j.biotechadv.2023.108305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
Cells execute biological functions to support phenotypes such as growth, migration, and secretion. Complementarily, each function of a cell has resource costs that constrain phenotype. Resource allocation by a cell allows it to manage these costs and optimize their phenotypes. In fact, the management of resource constraints (e.g., nutrient availability, bioenergetic capacity, and macromolecular machinery production) shape activity and ultimately impact phenotype. In mammalian systems, quantification of resource allocation provides important insights into higher-order multicellular functions; it shapes intercellular interactions and relays environmental cues for tissues to coordinate individual cells to overcome resource constraints and achieve population-level behavior. Furthermore, these constraints, objectives, and phenotypes are context-dependent, with cells adapting their behavior according to their microenvironment, resulting in distinct steady-states. This review will highlight the biological insights gained from probing resource allocation in mammalian cells and tissues.
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Affiliation(s)
- Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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12
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Khandia R, Pandey MK, Khan AA, Baklanov I, Alanazi AM, Nepali P, Gurjar P, Choudhary OP. Synthetic biology approach revealed enhancement in haeme oxygenase-1 gene expression by codon pair optimization while reduction by codon deoptimization. Ann Med Surg (Lond) 2024; 86:1359-1369. [PMID: 38463112 PMCID: PMC10923308 DOI: 10.1097/ms9.0000000000001465] [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: 09/13/2023] [Accepted: 10/23/2023] [Indexed: 03/12/2024] Open
Abstract
Haem oxygenase-1 (HO-1) is a ubiquitously expressed gene involved in cellular homoeostasis, and its imbalance in expression results in various disorders. To alleviate such disorders, HO-1 gene expression needs to be modulated. Codon usage bias results from evolutionary forces acting on any nucleotide sequence and determines the gene expression. Like codon usage bias, codon pair bias also exists, playing a role in gene expression. In the present study, HO-1 gene was recoded by manipulating codon and codon pair bias, and four such constructs were made through codon/codon pair deoptimization and codon/codon pair optimization to reduce and enhance the HO-1 gene expression. Codon usage analysis was done for these constructs for four tissues brain, heart, pancreas and liver. Based on codon usage in different tissues, gene expression of these tissues was determined in terms of the codon adaptation index. Based on the codon adaptation index, minimum free energy, and translation efficiency, constructs were evaluated for enhanced or decreased HO-1 expression. The analysis revealed that for enhancing gene expression, codon pair optimization, while for reducing gene expression, codon deoptimization is efficacious. The recoded constructs developed in the study could be used in gene therapy regimens to cure HO-1 over or underexpression-associated disorders.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, MP, India
| | - Megha Katare Pandey
- Translational Medicine Center, All India Institute of Medical Sciences, Bhopal, MP, India
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Igor Baklanov
- Department of Philosophy, North Caucasus Federal University, Pushkina, Stavropol, Russia
| | - Amer M. Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Prakash Nepali
- Bhimad Primary Health Care Center, Government of Nepal, Tanahun, Nepal
| | - Pankaj Gurjar
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Rampura Phul, Bathinda, Punjab, India
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13
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Jung M, Jung JS, Pfeifer J, Hartmann C, Ehrhardt T, Abid CL, Kintzel J, Puls A, Navarrete Santos A, Hollemann T, Riemann D, Rujescu D. Neuronal Stem Cells from Late-Onset Alzheimer Patients Show Altered Regulation of Sirtuin 1 Depending on Apolipoprotein E Indicating Disturbed Stem Cell Plasticity. Mol Neurobiol 2024; 61:1562-1579. [PMID: 37728850 PMCID: PMC10896791 DOI: 10.1007/s12035-023-03633-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023]
Abstract
Late-onset Alzheimer's disease (AD) is a complex multifactorial disease. The greatest known risk factor for late-onset AD is the E4 allele of the apolipoprotein E (APOE), while increasing age is the greatest known non-genetic risk factor. The cell type-specific functions of neural stem cells (NSCs), in particular their stem cell plasticity, remain poorly explored in the context of AD pathology. Here, we describe a new model that employs late-onset AD patient-derived induced pluripotent stem cells (iPSCs) to generate NSCs and to examine the role played by APOE4 in the expression of aging markers such as sirtuin 1 (SIRT1) in comparison to healthy subjects carrying APOE3. The effect of aging was investigated by using iPSC-derived NSCs from old age subjects as healthy matched controls. Transcript and protein analysis revealed that genes were expressed differently in NSCs from late-onset AD patients, e.g., exhibiting reduced autophagy-related protein 7 (ATG7), phosphatase and tensin homolog (PTEN), and fibroblast growth factor 2 (FGF2). Since SIRT1 expression differed between APOE3 and APOE4 NSCs, the suppression of APOE function in NSCs also repressed the expression of SIRT1. However, the forced expression of APOE3 by plasmids did not recover differently expressed genes. The altered aging markers indicate decreased plasticity of NSCs. Our study provides a suitable in vitro model to investigate changes in human NSCs associated with aging, APOE4, and late-onset AD.
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Affiliation(s)
- Matthias Jung
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany.
| | - Juliane-Susanne Jung
- Institute of Anatomy and Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, 06118, Halle (Saale), Germany
| | - Jenny Pfeifer
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Carla Hartmann
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Toni Ehrhardt
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Chaudhry Luqman Abid
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Jenny Kintzel
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Anne Puls
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Anne Navarrete Santos
- Institute of Anatomy and Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, 06118, Halle (Saale), Germany
| | - Thomas Hollemann
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Dagmar Riemann
- Department Medical Immunology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Magdeburger Strasse 2, 06112, Halle (Saale), Germany
| | - Dan Rujescu
- Department of Psychiatry and Psychotherapy, Division of General Psychiatry, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
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14
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Mao Y, Qian SB. Making sense of mRNA translational "noise". Semin Cell Dev Biol 2024; 154:114-122. [PMID: 36925447 PMCID: PMC10500040 DOI: 10.1016/j.semcdb.2023.03.004] [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: 03/16/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023]
Abstract
The importance of translation fidelity has been apparent since the discovery of genetic code. It is commonly believed that translation deviating from the main coding region is to be avoided at all times inside cells. However, ribosome profiling and mass spectrometry have revealed pervasive noncanonical translation. Both the scope and origin of translational "noise" are just beginning to be appreciated. Although largely overlooked, those translational "noises" are associated with a wide range of cellular functions, such as producing unannotated protein products. Furthermore, the dynamic nature of translational "noise" is responsive to stress conditions, highlighting the beneficial effect of translational "noise" in stress adaptation. Mechanistic investigation of translational "noise" will provide better insight into the mechanisms of translational regulation. Ultimately, they are not "noise" at all but represent a signature of cellular activities under pathophysiological conditions. Deciphering translational "noise" holds the therapeutic and diagnostic potential in a wide spectrum of human diseases.
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Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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15
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Truong NH, T. Vo N, Nguyen BT, Huynh ST, Nguyen HD. Analyzing the correlation between protein expression and sequence-related features of mRNA and protein in Escherichia coli K-12 MG1655 model. PLoS One 2024; 19:e0288526. [PMID: 38324614 PMCID: PMC10849221 DOI: 10.1371/journal.pone.0288526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/27/2023] [Indexed: 02/09/2024] Open
Abstract
It was necessary to have a tool that could predict the amount of protein and optimize the gene sequences to produce recombinant proteins efficiently. The Transim model published by Tuller et al. in 2018 can calculate the translation rate in E. coli using features on the mRNA sequence, achieving a Spearman correlation with the amount of protein per mRNA of 0.36 when tested on the dataset of operons' first genes in E. coli K-12 MG1655 genome. However, this Spearman correlation was not high, and the model did not fully consider the features of mRNA and protein sequences. Therefore, to enhance the prediction capability, our study firstly tried expanding the testing dataset, adding genes inside the operon, and using the microarray of the mRNA expression data set, thereby helping to improve the correlation of translation rate with the amount of protein with more than 0.42. Next, the applicability of 6 traditional machine learning models to calculate a "new translation rate" was examined using initiation rate and elongation rate as inputs. The result showed that the SVR algorithm had the most correlated new translation rates, with Spearman correlation improving to R = 0.6699 with protein level output and to R = 0.6536 with protein level per mRNA. Finally, the study investigated the degree of improvement when combining more features with the new translation rates. The results showed that the model's predictive ability to produce a protein per mRNA reached R = 0.6660 when using six features, while the correlation of this model's final translation rate to protein level was up to R = 0.6729. This demonstrated the model's capability to predict protein expression of a gene, rather than being limited to predicting expression by an mRNA and showed the model's potential for development into gene expression predicting tools.
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Affiliation(s)
- Nhat H.M. Truong
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Nam T. Vo
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam
| | - Binh T. Nguyen
- Vietnam National University, Ho Chi Minh City, Vietnam
- Department of Computer Science, University of Science, Ho Chi Minh City, Vietnam
| | - Son T. Huynh
- Vietnam National University, Ho Chi Minh City, Vietnam
- Department of Computer Science, University of Science, Ho Chi Minh City, Vietnam
| | - Hoang D. Nguyen
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
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16
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Dunuweera AN, Dunuweera SP, Ranganathan K. A Comprehensive Exploration of Bioluminescence Systems, Mechanisms, and Advanced Assays for Versatile Applications. Biochem Res Int 2024; 2024:8273237. [PMID: 38347947 PMCID: PMC10861286 DOI: 10.1155/2024/8273237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/10/2023] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
Bioluminescence has been a fascinating natural phenomenon of light emission from living creatures. It happens when the enzyme luciferase facilitates the oxidation of luciferin, resulting in the creation of an excited-state species that emits light. Although there are many bioluminescent systems, few have been identified. D-luciferin-dependent systems, coelenterazine-dependent systems, Cypridina luciferin-based systems, tetrapyrrole-based luciferins, bacterial bioluminescent systems, and fungal bioluminescent systems are natural bioluminescent systems. Since different bioluminescence systems, such as various combinations of luciferin-luciferase pair reactions, have different light emission wavelengths, they benefit industrial applications such as drug discovery, protein-protein interactions, in vivo imaging in small animals, and controlling neurons. Due to the expression of luciferase and easy permeation of luciferin into most cells and tissues, bioluminescence assays are applied nowadays with modern technologies in most cell and tissue types. It is a versatile technique in a variety of biomedical research. Furthermore, there are some investigated blue-sky research projects, such as bioluminescent plants and lamps. This review article is mainly based on the theory of diverse bioluminescence systems and their past, present, and future applications.
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Affiliation(s)
| | | | - K. Ranganathan
- Department of Botany, University of Jaffna, Jaffna 40000, Sri Lanka
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17
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Chai N, Stachon T, Berger T, Li Z, Seitz B, Langenbucher A, Szentmáry N. Short-Term Effect of Rose Bengal Photodynamic Therapy (RB-PDT) on Collagen I, Collagen V, NF-κB, LOX, TGF-β and IL-6 Expression of Human Corneal Fibroblasts, In Vitro. Curr Eye Res 2024; 49:150-157. [PMID: 37921272 DOI: 10.1080/02713683.2023.2276057] [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: 07/31/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
PURPOSE To investigate collagen I, collagen V, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), lysyl oxidase (LOX), transforming growth factor β1 (TGF-β1) and interleukin-6 (IL-6) expression in healthy and keratoconus human corneal fibroblasts (HCFs and KC-HCFs), 24 h after Rose Bengal photodynamic therapy (RB-PDT). METHODS HCFs were isolated from healthy human corneal donors (n = 5) and KC-HCFs from elective penetrating keratoplasties (n = 5). Both cell cultures underwent RB-PDT (0.001% RB concentration, 0.17 J/cm2 fluence) and 24 h later collagen I, collagen V, NF-κB, LOX, TGF-β1 and IL-6 mRNA and protein expression have been determined using qPCR and Western blot, IL-6 concentration in the cell culture supernatant by ELISA. RESULTS TGF-β1 mRNA expression was significantly lower (p = 0.02) and IL-6 mRNA expression was significantly higher in RB-PDT treated HCFs (p = 0.01), than in HCF controls. COL1A1, COL5A1 and TGF-β1 mRNA expression was significantly lower (p = 0.04; p = 0.02 and p = 0.003) and IL-6 mRNA expression was significantly higher (p = 0.02) in treated KC-HCFs, than in KC-HCF controls. TGF-β1 protein expression in treated HCFs was significantly higher than in HCF controls (p = 0.04). IL-6 protein concentration in the HCF and KC-HCF culture supernatant after RB-PDT was significantly higher than in controls (p = 0.02; p = 0.01). No other analyzed mRNA and protein expression differed significantly between the RB-PDT treated and untreated groups. CONCLUSIONS Our study demonstrates that RB-PDT reduces collagen I, collagen V and TGF-β1 mRNA expression, while increasing IL-6 mRNA and protein expression in KC-HCFs. In HCFs, RB-PDT increases TGF-β1 and IL-6 protein level after 24 h.
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Affiliation(s)
- Ning Chai
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg, Saar, Germany
| | - Tanja Stachon
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg, Saar, Germany
| | - Tim Berger
- Department of Ophthalmology, Saarland University Medical Center, Homburg, Saar, Germany
| | - Zhen Li
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg, Saar, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, Homburg, Saar, Germany
| | | | - Nóra Szentmáry
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg, Saar, Germany
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
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18
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Connor A, Zha RH, Koffas M. Production and secretion of recombinant spider silk in Bacillus megaterium. Microb Cell Fact 2024; 23:35. [PMID: 38279170 PMCID: PMC10821235 DOI: 10.1186/s12934-024-02304-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/12/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Silk proteins have emerged as versatile biomaterials with unique chemical and physical properties, making them appealing for various applications. Among them, spider silk, known for its exceptional mechanical strength, has attracted considerable attention. Recombinant production of spider silk represents the most promising route towards its scaled production; however, challenges persist within the upstream optimization of host organisms, including toxicity and low yields. The high cost of downstream cell lysis and protein purification is an additional barrier preventing the widespread production and use of spider silk proteins. Gram-positive bacteria represent an attractive, but underexplored, microbial chassis that may enable a reduction in the cost and difficulty of recombinant silk production through attributes that include, superior secretory capabilities, frequent GRAS status, and previously established use in industry. RESULTS In this study, we explore the potential of gram-positive hosts by engineering the first production and secretion of recombinant spider silk in the Bacillus genus. Using an industrially relevant B. megaterium host, it was found that the Sec secretion pathway enables secretory production of silk, however, the choice of signal sequence plays a vital role in successful secretion. Attempts at increasing secreted titers revealed that multiple translation initiation sites in tandem do not significantly impact silk production levels, contrary to previous findings for other gram-positive hosts and recombinant proteins. Notwithstanding, targeted amino acid supplementation in minimal media was found to increase production by 135% relative to both rich media and unaltered minimal media, yielding secretory titers of approximately 100 mg/L in flask cultures. CONCLUSION It is hypothesized that the supplementation strategy addressed metabolic bottlenecks, specifically depletion of ATP and NADPH within the central metabolism, that were previously observed for an E. coli host producing the same recombinant silk construct. Furthermore, this study supports the hypothesis that secretion mitigates the toxicity of the produced silk protein on the host organism and enhances host performance in glucose-based minimal media. While promising, future research is warranted to understand metabolic changes more precisely in the Bacillus host system in response to silk production, optimize signal sequences and promoter strengths, investigate the mechanisms behind the effect of tandem translation initiation sites, and evaluate the performance of this system within a bioreactor.
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Affiliation(s)
- Alexander Connor
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - R Helen Zha
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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19
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Giguère S, Wang X, Huber S, Xu L, Warner J, Weldon SR, Hu J, Phan QA, Tumang K, Prum T, Ma D, Kirsch KH, Nair U, Dedon P, Batista FD. Antibody production relies on the tRNA inosine wobble modification to meet biased codon demand. Science 2024; 383:205-211. [PMID: 38207021 PMCID: PMC10954030 DOI: 10.1126/science.adi1763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 11/27/2023] [Indexed: 01/13/2024]
Abstract
Antibodies are produced at high rates to provide immunoprotection, which puts pressure on the B cell translational machinery. Here, we identified a pattern of codon usage conserved across antibody genes. One feature thereof is the hyperutilization of codons that lack genome-encoded Watson-Crick transfer RNAs (tRNAs), instead relying on the posttranscriptional tRNA modification inosine (I34), which expands the decoding capacity of specific tRNAs through wobbling. Antibody-secreting cells had increased I34 levels and were more reliant on I34 for protein production than naïve B cells. Furthermore, antibody I34-dependent codon usage may influence B cell passage through regulatory checkpoints. Our work elucidates the interface between the tRNA pool and protein production in the immune system and has implications for the design and selection of antibodies for vaccines and therapeutics.
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Affiliation(s)
- Sophie Giguère
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Xuesong Wang
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Sabrina Huber
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Liling Xu
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - John Warner
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Stephanie R. Weldon
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Jennifer Hu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Quynh Anh Phan
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Katie Tumang
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Thavaleak Prum
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Duanduan Ma
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kathrin H. Kirsch
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Usha Nair
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Peter Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Facundo D. Batista
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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20
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He J, Huang Y, Li L, Lin S, Ma M, Wang Y, Lin S. Novel Plastid Genome Characteristics in Fugacium kawagutii and the Trend of Accelerated Evolution of Plastid Proteins in Dinoflagellates. Genome Biol Evol 2024; 16:evad237. [PMID: 38155596 PMCID: PMC10781511 DOI: 10.1093/gbe/evad237] [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: 10/31/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023] Open
Abstract
Typical (peridinin-containing) dinoflagellates possess plastid genomes composed of small plasmids named "minicircles". Despite the ecological importance of dinoflagellate photosynthesis in corals and marine ecosystems, the structural characteristics, replication dynamics, and evolutionary forcing of dinoflagellate plastid genomes remain poorly understood. Here, we sequenced the plastid genome of the symbiodiniacean species Fugacium kawagutii and conducted comparative analyses. We identified psbT-coding minicircles, features previously not found in Symbiodiniaceae. The copy number of F. kawagutii minicircles showed a strong diel dynamics, changing between 3.89 and 34.3 copies/cell and peaking in mid-light period. We found that F. kawagutii minicircles are the shortest among all dinoflagellates examined to date. Besides, the core regions of the minicircles are highly conserved within genus in Symbiodiniaceae. Furthermore, the codon usage bias of the plastid genomes in Heterocapsaceae, Amphidiniaceae, and Prorocentraceae species are greatly influenced by selection pressure, and in Pyrocystaceae, Symbiodiniaceae, Peridiniaceae, and Ceratiaceae species are influenced by both natural selection pressure and mutation pressure, indicating a family-level distinction in codon usage evolution in dinoflagellates. Phylogenetic analysis using 12 plastid-encoded proteins and five nucleus-encoded plastid proteins revealed accelerated evolution trend of both plastid- and nucleus-encoded plastid proteins in peridinin- and fucoxanthin-dinoflagellate plastids compared to plastid proteins of nondinoflagellate algae. These findings shed new light on the structure and evolution of plastid genomes in dinoflagellates, which will facilitate further studies on the evolutionary forcing and function of the diverse dinoflagellate plastids. The accelerated evolution documented here suggests plastid-encoded sequences are potentially useful for resolving closely related dinoflagellates.
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Affiliation(s)
- Jiamin He
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yulin Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Sitong Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Minglei Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yujie Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
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21
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Wang Y, Chi C, Zhang J, Zhang K, Deng D, Zheng W, Chen N, Meurens F, Zhu J. Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype. Microb Genom 2024; 10:001186. [PMID: 38270515 PMCID: PMC10868601 DOI: 10.1099/mgen.0.001186] [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: 11/16/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
African swine fever (ASF) is a severe haemorrhagic disease caused by the African swine fever virus (ASFV), transmitted by ticks, resulting in high mortality among domestic pigs and wild boars. The global spread of ASFV poses significant economic threats to the swine industry. This study employs diverse analytical methods to explore ASFV's evolution and host adaptation, focusing on codon usage patterns and associated factors. Utilizing phylogenetic analysis methods including neighbour-joining and maximum-likelihood, 64 ASFV strains were categorized into four clades. Codon usage bias (CUB) is modest in ASFV coding sequences. This research identifies multiple factors - such as nucleotide composition, mutational pressures, natural selection and geographical diversity - contributing to the formation of CUB in ASFV. Analysis of relative synonymous codon usage reveals CUB variations within clades and among ASFVs and their hosts. Both Codon Adaptation Index and Similarity Index analyses confirm that ASFV strains are highly adapted to soft ticks (Ornithodoros moubata) but less so to domestic pigs, which could be a result of the long-term co-evolution of ASFV with ticks. This study sheds light on the factors influencing ASFV's codon usage and fitness dynamics, enriching our understanding of its evolution, adaptation and host interactions.
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Affiliation(s)
- Yuening Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Chenglin Chi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Jiajia Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Kaili Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Dafu Deng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Wanglong Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Nanhua Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - François Meurens
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, St. Hyacinthe, QC, J2S 2M2, Canada
- Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Jianzhong Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
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22
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Irshad IU, Sharma AK. Decoding stoichiometric protein synthesis in E. coli through translation rate parameters. BIOPHYSICAL REPORTS 2023; 3:100131. [PMID: 37789867 PMCID: PMC10542608 DOI: 10.1016/j.bpr.2023.100131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
Abstract
E. coli is one of the most widely used organisms for understanding the principles of cellular and molecular genetics. However, we are yet to understand the origin of several experimental observations related to the regulation of gene expression in E. coli. One of the prominent examples in this context is the proportional synthesis in multiprotein complexes where all of their obligate subunits are produced in proportion to their stoichiometry. In this work, by combining the next-generation sequencing data with the stochastic simulations of protein synthesis, we explain the origin of proportional protein synthesis in multicomponent complexes. We find that the estimated initiation rates for the translation of all subunits in those complexes are proportional to their stoichiometry. This constraint on protein synthesis kinetics enforces proportional protein synthesis without requiring any feedback mechanism. We also find that the translation initiation rates in E. coli are influenced by the coding sequence length and the enrichment of A and C nucleotides near the start codon. Thus, this study rationalizes the role of conserved and nonrandom features of genes in regulating the translation kinetics and unravels a key principle of the regulation of protein synthesis.
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Affiliation(s)
| | - Ajeet K. Sharma
- Department of Physics, Indian Institute of Technology Jammu, Jammu, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, Jammu, India
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23
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Yimyaem M, Jitobaom K, Auewarakul P. A small stretch of poor codon usage at the beginning of dengue virus open reading frame may act as a translational checkpoint. BMC Res Notes 2023; 16:359. [PMID: 38053139 DOI: 10.1186/s13104-023-06615-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
OBJECTIVE Rare codons were previously shown to be enriched at the beginning of the dengue virus (DENV) open reading frame. However, the role of rare codons in regulating translation efficiency and replication of DENV remains unclear. The present study aims to clarify the significance of rare codon usage at the beginning of DENV transcripts using the codon adaptation index (CAI). METHODOLOGY CAIs of the whole starting regions of DENV transcripts as well as 18-codon sliding windows of the regions were analyzed. RESULTS One of the intriguing findings is that those rare codons do not typically result in uniformly low CAI in the starting region with rare codons. However, it shows a notable local drop in CAI around the 50th codon in all dengue serotypes. This suggests that there may be a translational checkpoint at this site and that the rare codon usage upstream to this checkpoint may not be related to translational control.
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Affiliation(s)
- Maneenop Yimyaem
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Kunlakanya Jitobaom
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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24
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Bajaj P, Bhasin M, Varadarajan R. Molecular bases for strong phenotypic effects of single synonymous codon substitutions in the E. coli ccdB toxin gene. BMC Genomics 2023; 24:732. [PMID: 38049728 PMCID: PMC10694988 DOI: 10.1186/s12864-023-09817-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/18/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Single synonymous codon mutations typically have only minor or no effects on gene function. Here, we estimate the effects on cell growth of ~ 200 single synonymous codon mutations in an operonic context by mutating almost all positions of ccdB, the 101-residue long cytotoxin of the ccdAB Toxin-Antitoxin (TA) operon to most degenerate codons. Phenotypes were assayed by transforming the mutant library into CcdB sensitive and resistant E. coli strains, isolating plasmid pools, and subjecting them to deep sequencing. Since autoregulation is a hallmark of TA operons, phenotypes obtained for ccdB synonymous mutants after transformation in a RelE toxin reporter strain followed by deep sequencing provided information on the amount of CcdAB complex formed. RESULTS Synonymous mutations in the N-terminal region involved in translation initiation showed the strongest non-neutral phenotypic effects. We observe an interplay of numerous factors, namely, location of the codon, codon usage, t-RNA abundance, formation of anti-Shine Dalgarno sequences, predicted transcript secondary structure, and evolutionary conservation in determining phenotypic effects of ccdB synonymous mutations. Incorporation of an N-terminal, hyperactive synonymous mutation, in the background of the single synonymous codon mutant library sufficiently increased translation initiation, such that mutational effects on either folding or termination of translation became more apparent. Introduction of putative pause sites not only affects the translational rate, but might also alter the folding kinetics of the protein in vivo. CONCLUSION In summary, the study provides novel insights into diverse mechanisms by which synonymous mutations modulate gene function. This information is useful in optimizing heterologous gene expression in E. coli and understanding the molecular bases for alteration in gene expression that arise due to synonymous mutations.
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Affiliation(s)
- Priyanka Bajaj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
- Present address: Department of Bioengineering and Therapeutic Sciences, University of CA - San Francisco, San Francisco, CA, 94158, USA
| | - Munmun Bhasin
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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25
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Davyt M, Bharti N, Ignatova Z. Effect of mRNA/tRNA mutations on translation speed: Implications for human diseases. J Biol Chem 2023; 299:105089. [PMID: 37495112 PMCID: PMC10470029 DOI: 10.1016/j.jbc.2023.105089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Recent discoveries establish tRNAs as central regulators of mRNA translation dynamics, and therefore cotranslational folding and function of the encoded protein. The tRNA pool, whose composition and abundance change in a cell- and tissue-dependent manner, is the main factor which determines mRNA translation velocity. In this review, we discuss a group of pathogenic mutations, in the coding sequences of either protein-coding genes or in tRNA genes, that alter mRNA translation dynamics. We also summarize advances in tRNA biology that have uncovered how variations in tRNA levels on account of genetic mutations affect protein folding and function, and thereby contribute to phenotypic diversity in clinical manifestations.
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Affiliation(s)
- Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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26
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Stewart RK, Nguyen P, Laederach A, Volkan PC, Sawyer JK, Fox DT. Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550700. [PMID: 37546801 PMCID: PMC10402044 DOI: 10.1101/2023.07.26.550700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, we identify the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent expression in neurons. Using RNA sequencing, we reveal that Orb2-upregulated mRNAs in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, we demonstrate that rare-codon enrichment is important for expression control and social behavior function of the metabotropic glutamate receptor (mGluR). Our findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA and protein expression.
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27
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Ju D, Li L, Xie Y. Homeostatic regulation of ribosomal proteins by ubiquitin-independent cotranslational degradation. Proc Natl Acad Sci U S A 2023; 120:e2306152120. [PMID: 37459537 PMCID: PMC10372694 DOI: 10.1073/pnas.2306152120] [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: 05/09/2023] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
Ribosomes are the workplace for protein biosynthesis. Protein production required for normal cell function is tightly linked to ribosome abundance. It is well known that ribosomal genes are actively transcribed and ribosomal messenger RNAs (mRNAs) are rapidly translated, and yet ribosomal proteins have relatively long half-lives. These observations raise questions as to how homeostasis of ribosomal proteins is controlled. Here, we show that ribosomal proteins, while posttranslationally stable, are subject to high-level cotranslational protein degradation (CTPD) except for those synthesized as ubiquitin (Ub) fusion precursors. The N-terminal Ub moiety protects fused ribosomal proteins from CTPD. We further demonstrate that cotranslational folding efficiency and expression level are two critical factors determining CTPD of ribosomal proteins. Different from canonical posttranslational degradation, we found that CTPD of all the ribosomal proteins tested in this study does not require prior ubiquitylation. This work provides insights into the regulation of ribosomal protein homeostasis and furthers our understanding of the mechanism and biological significance of CTPD.
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Affiliation(s)
- Donghong Ju
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI48201
- Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI48201
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI48201
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI48201
| | - Li Li
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI48201
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI48201
| | - Youming Xie
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI48201
- Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI48201
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28
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Riley AT, Robson JM, Green AA. Generative and predictive neural networks for the design of functional RNA molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549043. [PMID: 37503279 PMCID: PMC10370010 DOI: 10.1101/2023.07.14.549043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
RNA is a remarkably versatile molecule that has been engineered for applications in therapeutics, diagnostics, and in vivo information-processing systems. However, the complex relationship between the sequence and structural properties of an RNA molecule and its ability to perform specific functions often necessitates extensive experimental screening of candidate sequences. Here we present a generalized neural network architecture that utilizes the sequence and structure of RNA molecules (SANDSTORM) to inform functional predictions. We demonstrate that this approach achieves state-of-the-art performance across several distinct RNA prediction tasks, while learning interpretable abstractions of RNA secondary structure. We paired these predictive models with generative adversarial RNA design networks (GARDN), allowing the generative modelling of novel mRNA 5' untranslated regions and toehold switch riboregulators exhibiting a predetermined fitness. This approach enabled the design of novel toehold switches with a 43-fold increase in experimentally characterized dynamic range compared to those designed using classic thermodynamic algorithms. SANDSTORM and GARDN thus represent powerful new predictive and generative tools for the development of diagnostic and therapeutic RNA molecules with improved function.
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Affiliation(s)
- Aidan T. Riley
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - James M. Robson
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA 02215, USA
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29
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Bhakta S, Bhattacharya A. In silico evolutionary and structural analysis of cAMP response proteins (CARPs) from Leishmania major. Arch Microbiol 2023; 205:125. [PMID: 36941487 DOI: 10.1007/s00203-023-03463-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023]
Abstract
With unidentified chemical triggers and novel-effectors, cAMP signaling is broadly noncanonical in kinetoplastida parasites. Though novel protein kinase A regulatory subunits (PKAR) have been identified earlier, cAMP Response Proteins (CARPs) have been identified as a unique and definite cAMP effector of trypanosomatids. CARP1-CARP4 emerged as critical regulatory components of cAMP signaling pathway in Trypanosoma with evidences that CARP3 can directly interact with a flagellar adenylate cyclase (AC). CARP-mediated regulations, identified so far, reflects the mechanistic diversity of cAMP signaling. Albeit the function of the orthologous is not yet delineated, in kinetoplastids like Leishmania, presence of CARP1, 2 and 4 orthologues suggests existence of conserved effector mechanisms. Targeting CARP orthologues in Leishmania, a comprehensive evolutionary analysis of CARPs have been aimed in this study which revealed phylogenetic relationship, codon adaptation and structural heterogeneity among the orthologues, warranting functional analysis in future to explore their involvement in infectivity.
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Affiliation(s)
- Swarnav Bhakta
- Department of Biotechnology, Adamas University, Barasat-Barrackpore Rd., Kolkata, 700126, India
| | - Arijit Bhattacharya
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd., Kolkata, 700126, India.
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30
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Murakami K, Furuya H, Hokutan K, Goodison S, Pagano I, Chen R, Shen CH, Chan MWY, Ng CF, Kobayashi T, Ogawa O, Miyake M, Thornquist M, Shimizu Y, Hayashi K, Wang Z, Yu H, Rosser CJ. Association of SNPs in the PAI1 Gene with Disease Recurrence and Clinical Outcome in Bladder Cancer. Int J Mol Sci 2023; 24:4943. [PMID: 36902377 PMCID: PMC10003630 DOI: 10.3390/ijms24054943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
PURPOSE Bladder cancer (BCa) is one of the most common cancer types worldwide and is characterized by a high rate of recurrence. In previous studies, we and others have described the functional influence of plasminogen activator inhibitor-1 (PAI1) in bladder cancer development. While polymorphisms in PAI1 have been associated with increased risk and worsened prognosis in some cancers, the mutational status of PAI1 in human bladder tumors has not been well defined. METHODS In this study, we evaluated the mutational status of PAI1 in a series of independent cohorts, comprised of a total of 660 subjects. RESULTS Sequencing analyses identified two clinically relevant 3' untranslated region (UTR) single nucleotide polymorphisms (SNPs) in PAI1 (rs7242; rs1050813). Somatic SNP rs7242 was present in human BCa cohorts (overall incidence of 72%; 62% in Caucasians and 72% in Asians). In contrast, the overall incidence of germline SNP rs1050813 was 18% (39% in Caucasians and 6% in Asians). Furthermore, Caucasian patients with at least one of the described SNPs had worse recurrence-free survival and overall survival (p = 0.03 and p = 0.03, respectively). In vitro functional studies demonstrated that SNP rs7242 increased the anti-apoptotic effect of PAI1, and SNP rs1050813 was related to a loss of contact inhibition associated with cellular proliferation when compared to wild type. CONCLUSION Further investigation of the prevalence and potential downstream influence of these SNPs in bladder cancer is warranted.
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Affiliation(s)
- Kaoru Murakami
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hideki Furuya
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kanani Hokutan
- Clinical and Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Steve Goodison
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Ian Pagano
- Population Sciences in the Pacific Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Runpu Chen
- Department of Microbiology and Immunology, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Cheng-Huang Shen
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan
| | - Michael W. Y. Chan
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi 621, Taiwan
| | - Chi Fai Ng
- SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong
| | - Takashi Kobayashi
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Osamu Ogawa
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Makito Miyake
- Department of Urology, Nara Medical University, Nara 6348522, Japan
| | - Mark Thornquist
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yoshiko Shimizu
- Clinical and Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Kazukuni Hayashi
- Clinical and Translational Research Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Zhangwei Wang
- Population Sciences in the Pacific Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Herbert Yu
- Population Sciences in the Pacific Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Charles J. Rosser
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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31
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Raval PK, Ngan WY, Gallie J, Agashe D. The layered costs and benefits of translational redundancy. eLife 2023; 12:81005. [PMID: 36862572 PMCID: PMC9981150 DOI: 10.7554/elife.81005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/25/2023] [Indexed: 03/03/2023] Open
Abstract
The rate and accuracy of translation hinges upon multiple components - including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules - many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on growth rate. However, we lack empirical measurements of the fitness costs and benefits of redundancy, and we have poor a understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of Escherichia coli by deleting 28 tRNA genes, 3 tRNA modifying systems, and 4 rRNA operons in various combinations. We find that redundancy in tRNA pools is beneficial when nutrients are plentiful and costly under nutrient limitation. This nutrient-dependent cost of redundant tRNA genes stems from upper limits to translation capacity and growth rate, and therefore varies as a function of the maximum growth rate attainable in a given nutrient niche. The loss of redundancy in rRNA genes and tRNA modifying enzymes had similar nutrient-dependent fitness consequences. Importantly, these effects are also contingent upon interactions across translation components, indicating a layered hierarchy from copy number of tRNA and rRNA genes to their expression and downstream processing. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species' evolutionary history with feasts and famines.
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Affiliation(s)
- Parth K Raval
- National Centre for Biological Sciences (NCBS-TIFR)BengaluruIndia
| | - Wing Yui Ngan
- Max Plank Institute for Evolutionary BiologyPlönGermany
| | - Jenna Gallie
- Max Plank Institute for Evolutionary BiologyPlönGermany
| | - Deepa Agashe
- National Centre for Biological Sciences (NCBS-TIFR)BengaluruIndia
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32
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A dynamical stochastic model of yeast translation across the cell cycle. Heliyon 2023; 9:e13101. [PMID: 36793957 PMCID: PMC9922973 DOI: 10.1016/j.heliyon.2023.e13101] [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: 03/18/2022] [Revised: 01/04/2023] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Translation is a central step in gene expression, however its quantitative and time-resolved regulation is poorly understood. We developed a discrete, stochastic model for protein translation in S. cerevisiae in a whole-transcriptome, single-cell context. A "base case" scenario representing an average cell highlights translation initiation rates as the main co-translational regulatory parameters. Codon usage bias emerges as a secondary regulatory mechanism through ribosome stalling. Demand for anticodons with low abundancy is shown to cause above-average ribosome dwelling times. Codon usage bias correlates strongly both with protein synthesis rates and elongation rates. Applying the model to a time-resolved transcriptome estimated by combining data from FISH and RNA-Seq experiments, it could be shown that increased total transcript abundance during the cell cycle decreases translation efficiency at single transcript level. Translation efficiency grouped by gene function shows highest values for ribosomal and glycolytic genes. Ribosomal proteins peak in S phase while glycolytic proteins rank highest in later cell cycle phases.
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33
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Zhang M, Song J, Xiao J, Jin J, Nomura CT, Chen S, Wang Q. Engineered multiple translation initiation sites: a novel tool to enhance protein production in Bacillus licheniformis and other industrially relevant bacteria. Nucleic Acids Res 2022; 50:11979-11990. [PMID: 36382403 PMCID: PMC9723656 DOI: 10.1093/nar/gkac1039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
Gram-positive bacteria are a nascent platform for synthetic biology and metabolic engineering that can provide new opportunities for the production of biomolecules. However, the lack of standardized methods and genetic parts is a major obstacle towards attaining the acceptance and widespread use of Gram-positive bacterial chassis for industrial bioproduction. In this study, we have engineered a novel mRNA leader sequence containing more than one ribosomal binding site (RBS) which could initiate translation from multiple sites, vastly enhancing the translation efficiency of the Gram-positive industrial strain Bacillus licheniformis. This is the first report elucidating the impact of more than one RBS to initiate translation and enhance protein output in B. licheniformis. We also explored the application of more than one RBS for both intracellular and extracellular protein production in B. licheniformis to demonstrate its efficiency, consistency and potential for biotechnological applications. Moreover, we applied these concepts for use in other industrially relevant Gram-positive bacteria, such as Bacillus subtilis and Corynebacterium glutamicum. In all, a highly efficient and robust broad-host expression element has been designed to strengthen and fine-tune the protein outputs for the use of bioproduction in microbial cell factories.
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Affiliation(s)
- Manyu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan 430062, China
| | | | - Jun Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan 430062, China
| | - Jingjie Jin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Christopher T Nomura
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, USA
| | - Shouwen Chen
- Correspondence may also be addressed to Shouwen Chen.
| | - Qin Wang
- To whom correspondence should be addressed. Tel: +86 18507140137;
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34
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Sharma P, Mondal K, Kumar S, Tamang S, Najar IN, Das S, Thakur N. RNA thermometers in bacteria: Role in thermoregulation. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194871. [DOI: 10.1016/j.bbagrm.2022.194871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 04/09/2023]
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35
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Komarova ES, Dontsova OA, Pyshnyi DV, Kabilov MR, Sergiev PV. Flow-Seq Method: Features and Application in Bacterial Translation Studies. Acta Naturae 2022; 14:20-37. [PMID: 36694903 PMCID: PMC9844084 DOI: 10.32607/actanaturae.11820] [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: 10/04/2022] [Accepted: 11/11/2022] [Indexed: 01/22/2023] Open
Abstract
The Flow-seq method is based on using reporter construct libraries, where a certain element regulating the gene expression of fluorescent reporter proteins is represented in many thousands of variants. Reporter construct libraries are introduced into cells, sorted according to their fluorescence level, and then subjected to next-generation sequencing. Therefore, it turns out to be possible to identify patterns that determine the expression efficiency, based on tens and hundreds of thousands of reporter constructs in one experiment. This method has become common in evaluating the efficiency of protein synthesis simultaneously by multiple mRNA variants. However, its potential is not confined to this area. In the presented review, a comparative analysis of the Flow-seq method and other alternative approaches used for translation efficiency evaluation of mRNA was carried out; the features of its application and the results obtained by Flow-seq were also considered.
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Affiliation(s)
- E. S. Komarova
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - O. A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119234 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437 Russia
| | - D. V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M. R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - P. V. Sergiev
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119234 Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119234 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
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36
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Tayşi N, Kaymaz Y, Ateş D, Sari H, Toker C, Tanyolaç MB. Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris. Sci Rep 2022; 12:15068. [PMID: 36064865 PMCID: PMC9445179 DOI: 10.1038/s41598-022-17877-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/02/2022] [Indexed: 12/05/2022] Open
Abstract
Lens is a member of the Papilionoideae subfamily of Fabaceae and is generally used as a source of vegetable protein as part of human diets in many regions worldwide. Chloroplast (cp) genomes are highly active genetic components of plants and can be utilized as molecular markers for various purposes. As one of the wild lentil species, the Lens ervoides cp genome has been sequenced for the first time in this study using next-generation sequencing. The de novo assembly of the cp genome resulted in a single 122,722 bp sequence as two separate coexisting structural haplotypes with similar lengths. Results indicated that the cp genome of L. ervoides belongs to the inverted repeat lacking clade. Several noteworthy divergences within the coding regions were observed in ndhB, ndhF, rbcL, rpoC2, and ycf2 genes. Analysis of relative synonymous codon usage showed that certain genes, psbN, psaI, psbI, psbE, psbK, petD, and ndhC, preferred using biased codons more often and therefore might have elevated expression and translation efficiencies. Overall, this study exhibited the divergence level between the wild-type and cultured lentil cp genomes and pointed to certain regions that can be utilized as distinction markers for various goals.
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Affiliation(s)
- Nurbanu Tayşi
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Yasin Kaymaz
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Duygu Ateş
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Hatice Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Cengiz Toker
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - M Bahattin Tanyolaç
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey.
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37
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Design of 5′-UTR to Enhance Keratinase Activity in Bacillus subtilis. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8090426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Keratinase is an important industrial enzyme, but its application performance is limited by its low activity. A rational design of 5′-UTRs that increases translation efficiency is an important approach to enhance protein expression. Herein, we optimized the 5′-UTR of the recombinant keratinase KerZ1 expression element to enhance its secretory activity in Bacillus subtilis WB600 through Spacer design, RBS screening, and sequence simplification. First, the A/U content in Spacer was increased by the site-directed saturation mutation of G/C bases, and the activity of keratinase secreted by mutant strain B. subtilis WB600-SP was 7.94 times higher than that of KerZ1. Subsequently, the keratinase activity secreted by the mutant strain B. subtilis WB600-SP-R was further increased to 13.45 times that of KerZ1 based on the prediction of RBS translation efficiency and the multi-site saturation mutation screening. Finally, the keratinase activity secreted by the mutant strain B. subtilis WB600-SP-R-D reached 204.44 KU mL−1 by reducing the length of the 5′ end of the 5′-UTR, which was 19.70 times that of KerZ1. In a 5 L fermenter, the keratinase activity secreted by B. subtilis WB600-SP-R-D after 25 h fermentation was 797.05 KU mL−1, which indicated its high production intensity. Overall, the strategy of this study and the obtained keratinase mutants will provide a good reference for the expression regulation of keratinase and other industrial enzymes.
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38
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Zhang Y, Su D, Zhu J, Wang M, Zhang Y, Fu Q, Zhang S, Lin H. Oxygen level regulates N-terminal translation elongation of selected proteins through deoxyhypusine hydroxylation. Cell Rep 2022; 39:110855. [PMID: 35613595 DOI: 10.1016/j.celrep.2022.110855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 03/19/2022] [Accepted: 05/02/2022] [Indexed: 11/15/2022] Open
Abstract
Hypusine is a post-translational modification on eukaryotic translation initiation factor 5A (eIF5A). The last step of hypusine biosynthesis, deoxyhypusine hydroxylation, is an oxygen-dependent reaction. Here we show that deletion of the deoxyhypusine hydroxylase Lia1 compromises yeast respiration through translation downregulation of selected proteins in the respiration pathway. The translation suppression, because of the lack of deoxyhypusine hydroxylation, mainly affects translation of the N termini of the proteins, independent of the presence of proline residues but likely dependent on the interaction between the N-terminal nascent peptide and the ribosomal peptide exit tunnel. Proteomics and biochemical studies reveal that Lia1 deletion decreases N-terminal translation of proteins involved in mitochondrial respiration, oxidative stress response, and protein folding. Our work uncovers functions of the hypusine modification by considering the substrate requirement of the post-translational modification, highlights the unique challenges of translating the N termini of proteins, and reveals an oxygen-sensing mechanism in eukaryotic cells.
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Affiliation(s)
- Yugang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dan Su
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Julia Zhu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Miao Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Yandong Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Qin Fu
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, NY 14853, USA
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, NY 14853, USA
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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39
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Olasunkanmi OI, Mageto J, Avala Ntsigouaye J, Yi M, Fei Y, Chen Y, Chen S, Xu W, Lin L, Zhao W, Wang Y, Zhong ZH. Novel Antiviral Activity of Ethyl 3-Hydroxyhexanoate Against Coxsackievirus B Infection. Front Microbiol 2022; 13:875485. [PMID: 35495645 PMCID: PMC9048257 DOI: 10.3389/fmicb.2022.875485] [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: 02/14/2022] [Accepted: 03/14/2022] [Indexed: 01/26/2023] Open
Abstract
Coxsackievirus group B (CVB) is a member of the genus Enterovirus in the family Picornaviridae. CVB infection has been implicated as a major etiologic agent of viral myocarditis, dilated cardiomyopathy, meningitis, and pancreatitis among children and young adults. Until date, no antiviral agent has been licensed for the treatment of Coxsackievirus infection. In an effort to identify antiviral agents against diseases caused by the CVB, we found that ethyl 3-hydroxyhexanoate (EHX), a volatile compound present in fruits and food additives, is a potent antiviral compound. In this study, we demonstrated that EHX treatment significantly inhibits CVB replication both in vivo and in vitro. Furthermore, EHX possesses antiviral activity at 50% effective concentration (EC50) of 1.2 μM and 50% cytotoxicity (CC50) of 25.6 μM, yielding a selective index (SI) value as high as 20.8. Insights into the mechanism of antiviral activity of EHX showed that it acts at the step of viral RNA replication. Since EHX has received approval as food additives, treatment of CVB-related infections with EHX might be a safe therapeutic option and may be a promising strategy for the development of semi-synthetic antiviral drugs for viral diseases.
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Affiliation(s)
| | - James Mageto
- Department of Microbiology, Harbin Medical University, Harbin, China
| | | | - Ming Yi
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yanru Fei
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yang Chen
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Sijia Chen
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Weizhen Xu
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Lexun Lin
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Wenran Zhao
- Department of Cell Biology, Harbin Medical University, Harbin, China
| | - Yan Wang
- Department of Cell Biology, Harbin Medical University, Harbin, China
| | - Zhao-Hua Zhong
- Department of Microbiology, Harbin Medical University, Harbin, China
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40
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Attaluri S, Arora M, Madhu LN, Kodali M, Shuai B, Melissari L, Upadhya R, Rao X, Bates A, Mitra E, Ghahfarouki KR, Ravikumar MNV, Shetty AK. Oral Nano-Curcumin in a Model of Chronic Gulf War Illness Alleviates Brain Dysfunction with Modulation of Oxidative Stress, Mitochondrial Function, Neuroinflammation, Neurogenesis, and Gene Expression. Aging Dis 2022; 13:583-613. [PMID: 35371600 PMCID: PMC8947830 DOI: 10.14336/ad.2021.0829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/29/2021] [Indexed: 12/14/2022] Open
Abstract
Unrelenting cognitive and mood impairments concomitant with incessant oxidative stress and neuroinflammation are among the significant symptoms of chronic Gulf War Illness (GWI). Curcumin (CUR), an antiinflammatory compound, has shown promise to alleviate brain dysfunction in a model of GWI following intraperitoneal administrations at a high dose. However, low bioavailability after oral treatment has hampered its clinical translation. Therefore, this study investigated the efficacy of low-dose, intermittent, oral polymer nanoparticle encapsulated CUR (nCUR) for improving brain function in a rat model of chronic GWI. Intermittent administration of 10 or 20 mg/Kg nCUR for 8 weeks in the early phase of GWI improved brain function and reduced oxidative stress (OS) and neuroinflammation. We next examined the efficacy of 12-weeks of intermittent nCUR at 10 mg/Kg in GWI animals, with treatment commencing 8 months after exposure to GWI-related chemicals and stress, mimicking treatment for the persistent cognitive and mood dysfunction displayed by veterans with GWI. GWI rats receiving nCUR exhibited better cognitive and mood function associated with improved mitochondrial function and diminished neuroinflammation in the hippocampus. Improved mitochondrial function was evident from normalized expression of OS markers, antioxidants, and mitochondrial electron transport genes, and complex proteins. Lessened neuroinflammation was noticeable from reductions in astrocyte hypertrophy, NF-kB, activated microglia with NLRP3 inflammasomes, and multiple proinflammatory cytokines. Moreover, nCUR treated animals displayed enhanced neurogenesis with a normalized expression of synaptophysin puncta, and multiple genes linked to cognitive dysfunction. Thus, low-dose, intermittent, oral nCUR therapy has promise for improving brain function in veterans with GWI.
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Affiliation(s)
- Sahithi Attaluri
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
| | - Meenakshi Arora
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, USA
| | - Leelavathi N Madhu
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
| | - Maheedhar Kodali
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
| | - Bing Shuai
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
| | - Laila Melissari
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
| | - Raghavendra Upadhya
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
| | - Xiaolan Rao
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
| | - Adrian Bates
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
| | - Eeshika Mitra
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
| | - Keyhan R Ghahfarouki
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
| | - M. N. V Ravikumar
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, USA
| | - Ashok K Shetty
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, Texas, USA.
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41
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Neumann T, Tuller T. Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data. Nucleic Acids Res 2022; 50:1297-1316. [PMID: 35100399 PMCID: PMC8860609 DOI: 10.1093/nar/gkac021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 12/31/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Translation Complex Profile Sequencing (TCP-seq), a protocol that was developed and implemented on Saccharomyces cerevisiae, provides the footprints of the small subunit (SSU) of the ribosome (with additional factors) across the entire transcriptome of the analyzed organism. In this study, based on the TCP-seq data, we developed for the first-time a predictive model of the SSU density and analyzed the effect of transcript features on the dynamics of the SSU scan in the 5′UTR. Among others, our model is based on novel tools for detecting complex statistical relations tailored to TCP-seq. We quantitatively estimated the effect of several important features, including the context of the upstream AUG, the upstream ORF length and the mRNA folding strength. Specifically, we suggest that around 50% of the variance related to the read counts (RC) distribution near a start codon can be attributed to the AUG context score. We provide the first large scale direct quantitative evidence that shows that indeed AUG context affects the small sub-unit movement. In addition, we suggest that strong folding may cause the detachment of the SSU from the mRNA. We also identified a number of novel sequence motifs that can affect the SSU scan; some of these motifs affect transcription factors and RNA binding proteins. The results presented in this study provide a better understanding of the biophysical aspects related to the SSU scan along the 5′UTR and of translation initiation in S. cerevisiae, a fundamental step toward a comprehensive modeling of initiation.
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Affiliation(s)
- Tamar Neumann
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel
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42
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Stein KC, Morales-Polanco F, van der Lienden J, Rainbolt TK, Frydman J. Ageing exacerbates ribosome pausing to disrupt cotranslational proteostasis. Nature 2022; 601:637-642. [PMID: 35046576 DOI: 10.1038/s41586-021-04295-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 12/01/2021] [Indexed: 02/04/2023]
Abstract
Ageing is accompanied by a decline in cellular proteostasis, which underlies many age-related protein misfolding diseases1,2. Yet, how ageing impairs proteostasis remains unclear. As nascent polypeptides represent a substantial burden on the proteostasis network3, we hypothesized that altered translational efficiency during ageing could help to drive the collapse of proteostasis. Here we show that ageing alters the kinetics of translation elongation in both Caenorhabditis elegans and Saccharomyces cerevisiae. Ribosome pausing was exacerbated at specific positions in aged yeast and worms, including polybasic stretches, leading to increased ribosome collisions known to trigger ribosome-associated quality control (RQC)4-6. Notably, aged yeast cells exhibited impaired clearance and increased aggregation of RQC substrates, indicating that ageing overwhelms this pathway. Indeed, long-lived yeast mutants reduced age-dependent ribosome pausing, and extended lifespan correlated with greater flux through the RQC pathway. Further linking altered translation to proteostasis collapse, we found that nascent polypeptides exhibiting age-dependent ribosome pausing in C. elegans were strongly enriched among age-dependent protein aggregates. Notably, ageing increased the pausing and aggregation of many components of proteostasis, which could initiate a cycle of proteostasis collapse. We propose that increased ribosome pausing, leading to RQC overload and nascent polypeptide aggregation, critically contributes to proteostasis impairment and systemic decline during ageing.
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Affiliation(s)
- Kevin C Stein
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | | | | | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA. .,Department of Genetics, Stanford University, Stanford, CA, USA.
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43
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Ho AT, Hurst LD. Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage. Mol Biol Evol 2022; 39:msab326. [PMID: 34751397 PMCID: PMC8789281 DOI: 10.1093/molbev/msab326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3'untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Laurence D Hurst
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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44
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Ristau J, Watt K, Oertlin C, Larsson O. Polysome Fractionation for Transcriptome-Wide Studies of mRNA Translation. Methods Mol Biol 2022; 2418:223-241. [PMID: 35119669 DOI: 10.1007/978-1-0716-1920-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein synthesis and degradation determine the relationship between mRNA and corresponding protein amounts. This relationship can change in a dynamic and selective fashion when translational efficiencies of transcript subsets are altered downstream of, for example, translation factors and/or RNA binding proteins. Notably, even transcription factors such as estrogen receptor alpha (ERα) can modulate mRNA translation in a transcript-selective manner. Yet, despite ample evidence suggesting a key role for mRNA translation in shaping the proteome in health and disease, it remains largely unexplored. Here, we present a guide for the extraction of mRNA engaged in translation using polysome fractionation with linear and optimized sucrose gradients. The isolated polysome-associated RNA is then quantified, in parallel with total mRNA from the same conditions, using methods such as RNA sequencing; and the resulting data set is analyzed to derive transcriptome-wide insights into how mRNA translation is modulated. The methods we describe are applicable to cultured cells, small numbers of FACS-isolated primary cells, and small tissue samples from biobanks or animal studies. Accordingly, this approach can be applied to study in detail how ERα and other factors control gene expression by selectively modulating mRNA translation both in vitro and in vivo.
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Affiliation(s)
- Johannes Ristau
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Kathleen Watt
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Christian Oertlin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden.
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45
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Nelakurti DD, Rossetti T, Husbands AY, Petreaca RC. Arginine Depletion in Human Cancers. Cancers (Basel) 2021; 13:cancers13246274. [PMID: 34944895 PMCID: PMC8699593 DOI: 10.3390/cancers13246274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Thousands of cancer genomes are now publicly available which has led to new insights into the underlying features of cancers. These include the identification of mutational signatures at both nucleotide and amino acid levels. Here, we discuss C > T transitions as a key nucleotide-level mutational signature that leads to a dramatic overrepresentation of arginine substitutions in cancers. We propose that this underlying C > T mutational signature canalizes possible arginine substitution outcomes, favoring histidine, cysteine, glutamine, and tryptophan. This initial asymmetry is then acted on at the amino acid level by purifying selection. Thus, a model of “sequential selection” could explain the documented bias towards arginine substitutions in multiple cancers. Abstract Arginine is encoded by six different codons. Base pair changes in any of these codons can have a broad spectrum of effects including substitutions to twelve different amino acids, eighteen synonymous changes, and two stop codons. Four amino acids (histidine, cysteine, glutamine, and tryptophan) account for over 75% of amino acid substitutions of arginine. This suggests that a mutational bias, or “purifying selection”, mechanism is at work. This bias appears to be driven by C > T and G > A transitions in four of the six arginine codons, a signature that is universal and independent of cancer tissue of origin or histology. Here, we provide a review of the available literature and reanalyze publicly available data from the Catalogue of Somatic Mutations in Cancer (COSMIC). Our analysis identifies several genes with an arginine substitution bias. These include known factors such as IDH1, as well as previously unreported genes, including four cancer driver genes (FGFR3, PPP6C, MAX, GNAQ). We propose that base pair substitution bias and amino acid physiology both play a role in purifying selection. This model may explain the documented arginine substitution bias in cancers.
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Affiliation(s)
- Devi D. Nelakurti
- Biomedical Science Undergraduate Program, The Ohio State University Medical School, Columbus, OH 43210, USA;
| | - Tiffany Rossetti
- Biology Undergraduate Program, The Ohio State University, Marion, OH 43302, USA;
| | - Aman Y. Husbands
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43215, USA
- Correspondence: (A.Y.H.); (R.C.P.)
| | - Ruben C. Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
- Cancer Biology Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH 43210, USA
- Correspondence: (A.Y.H.); (R.C.P.)
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Yang X, Yu H, Sun W, Ding L, Li J, Cheema J, Ramirez-Gonzalez R, Zhao X, Martín AC, Lu F, Liu B, Uauy C, Ding Y, Zhang H. Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry. Genome Biol 2021; 22:326. [PMID: 34847934 PMCID: PMC8638558 DOI: 10.1186/s13059-021-02549-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/19/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Polyploidy, especially allopolyploidy, which entails merging divergent genomes via hybridization and whole-genome duplication (WGD), is a major route to speciation in plants. The duplication among the parental genomes (subgenomes) often leads to one subgenome becoming dominant over the other(s), resulting in subgenome asymmetry in gene content and expression. Polyploid wheats are allopolyploids with most genes present in two (tetraploid) or three (hexaploid) functional copies, which commonly show subgenome expression asymmetry. It is unknown whether a similar subgenome asymmetry exists during translation. We aim to address this key biological question and explore the major contributing factors to subgenome translation asymmetry. RESULTS Here, we obtain the first tetraploid wheat translatome and reveal that subgenome expression asymmetry exists at the translational level. We further perform in vivo RNA structure profiling to obtain the wheat RNA structure landscape and find that mRNA structure has a strong impact on translation, independent of GC content. We discover a previously uncharacterized contribution of RNA structure in subgenome translation asymmetry. We identify 3564 single-nucleotide variations (SNVs) across the transcriptomes between the two tetraploid wheat subgenomes, which induce large RNA structure disparities. These SNVs are highly conserved within durum wheat cultivars but are divergent in both domesticated and wild emmer wheat. CONCLUSIONS We successfully determine both the translatome and in vivo RNA structurome in tetraploid wheat. We reveal that RNA structure serves as an important modulator of translational subgenome expression asymmetry in polyploids. Our work provides a new perspective for molecular breeding of major polyploid crops.
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Affiliation(s)
- Xiaofei Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Haopeng Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wenqing Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Ling Ding
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Ji Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Jitender Cheema
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Azahara C Martín
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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Kang YJ, Li JY, Ke L, Jiang S, Yang DC, Hou M, Gao G. Quantitative model suggests both intrinsic and contextual features contribute to the transcript coding ability determination in cells. Brief Bioinform 2021; 23:6445106. [PMID: 34849565 DOI: 10.1093/bib/bbab483] [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: 07/12/2021] [Revised: 10/18/2021] [Accepted: 10/23/2021] [Indexed: 11/13/2022] Open
Abstract
Gene transcription and protein translation are two key steps of the 'central dogma.' It is still a major challenge to quantitatively deconvolute factors contributing to the coding ability of transcripts in mammals. Here, we propose ribosome calculator (RiboCalc) for quantitatively modeling the coding ability of RNAs in human genome. In addition to effectively predicting the experimentally confirmed coding abundance via sequence and transcription features with high accuracy, RiboCalc provides interpretable parameters with biological information. Large-scale analysis further revealed a number of transcripts with a variety of coding ability for distinct types of cells (i.e. context-dependent coding transcripts), suggesting that, contrary to conventional wisdom, a transcript's coding ability should be modeled as a continuous spectrum with a context-dependent nature.
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Affiliation(s)
- Yu-Jian Kang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jing-Yi Li
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Lan Ke
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Shuai Jiang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - De-Chang Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Mei Hou
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ge Gao
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
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Ferreira M, Ventorim R, Almeida E, Silveira S, Silveira W. Protein Abundance Prediction Through Machine Learning Methods. J Mol Biol 2021; 433:167267. [PMID: 34563548 DOI: 10.1016/j.jmb.2021.167267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/09/2021] [Accepted: 09/17/2021] [Indexed: 10/20/2022]
Abstract
Proteins are responsible for most physiological processes, and their abundance provides crucial information for systems biology research. However, absolute protein quantification, as determined by mass spectrometry, still has limitations in capturing the protein pool. Protein abundance is impacted by translation kinetics, which rely on features of codons. In this study, we evaluated the effect of codon usage bias of genes on protein abundance. Notably, we observed differences regarding codon usage patterns between genes coding for highly abundant proteins and genes coding for less abundant proteins. Analysis of synonymous codon usage and evolutionary selection showed a clear split between the two groups. Our machine learning models predicted protein abundances from codon usage metrics with remarkable accuracy, achieving strong correlation with experimental data. Upon integration of the predicted protein abundance in enzyme-constrained genome-scale metabolic models, the simulated phenotypes closely matched experimental data, which demonstrates that our predictive models are valuable tools for systems metabolic engineering approaches.
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Affiliation(s)
- Mauricio Ferreira
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil. https://twitter.com/@mauriciomyces
| | - Rafaela Ventorim
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
| | - Eduardo Almeida
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil. https://twitter.com/@elm_almeida
| | - Sabrina Silveira
- Department of Computer Science, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil. https://twitter.com/@sabrina_as
| | - Wendel Silveira
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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Chen M, Long Q, Borrie MS, Sun H, Zhang C, Yang H, Shi D, Gartenberg MR, Deng W. Nucleoporin TPR promotes tRNA nuclear export and protein synthesis in lung cancer cells. PLoS Genet 2021; 17:e1009899. [PMID: 34793452 PMCID: PMC8639082 DOI: 10.1371/journal.pgen.1009899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/02/2021] [Accepted: 10/21/2021] [Indexed: 12/26/2022] Open
Abstract
The robust proliferation of cancer cells requires vastly elevated levels of protein synthesis, which relies on a steady supply of aminoacylated tRNAs. Delivery of tRNAs to the cytoplasm is a highly regulated process, but the machinery for tRNA nuclear export is not fully elucidated. In this study, using a live cell imaging strategy that visualizes nascent transcripts from a specific tRNA gene in yeast, we identified the nuclear basket proteins Mlp1 and Mlp2, two homologs of the human TPR protein, as regulators of tRNA export. TPR expression is significantly increased in lung cancer tissues and correlated with poor prognosis. Consistently, knockdown of TPR inhibits tRNA nuclear export, protein synthesis and cell growth in lung cancer cell lines. We further show that NXF1, a well-known mRNA nuclear export factor, associates with tRNAs and mediates their transport through nuclear pores. Collectively, our findings uncover a conserved mechanism that regulates nuclear export of tRNAs, which is a limiting step in protein synthesis in eukaryotes.
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Affiliation(s)
- Miao Chen
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Qian Long
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Melinda S. Borrie
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Haohui Sun
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Changlin Zhang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Han Yang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Dingbo Shi
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Marc R. Gartenberg
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
- The Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Wuguo Deng
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
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50
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Gillen SL, Waldron JA, Bushell M. Codon optimality in cancer. Oncogene 2021; 40:6309-6320. [PMID: 34584217 PMCID: PMC8585667 DOI: 10.1038/s41388-021-02022-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 12/14/2022]
Abstract
A key characteristic of cancer cells is their increased proliferative capacity, which requires elevated levels of protein synthesis. The process of protein synthesis involves the translation of codons within the mRNA coding sequence into a string of amino acids to form a polypeptide chain. As most amino acids are encoded by multiple codons, the nucleotide sequence of a coding region can vary dramatically without altering the polypeptide sequence of the encoded protein. Although mutations that do not alter the final amino acid sequence are often thought of as silent/synonymous, these can still have dramatic effects on protein output. Because each codon has a distinct translation elongation rate and can differentially impact mRNA stability, each codon has a different degree of 'optimality' for protein synthesis. Recent data demonstrates that the codon preference of a transcriptome matches the abundance of tRNAs within the cell and that this supply and demand between tRNAs and mRNAs varies between different cell types. The largest observed distinction is between mRNAs encoding proteins associated with proliferation or differentiation. Nevertheless, precisely how codon optimality and tRNA expression levels regulate cell fate decisions and their role in malignancy is not fully understood. This review describes the current mechanistic understanding on codon optimality, its role in malignancy and discusses the potential to target codon optimality therapeutically in the context of cancer.
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Affiliation(s)
- Sarah L Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
| | - Joseph A Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK, G61 1QH.
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