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Komar AA, Samatova E, Rodnina MV. Translation Rates and Protein Folding. J Mol Biol 2024; 436:168384. [PMID: 38065274 DOI: 10.1016/j.jmb.2023.168384] [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: 10/20/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023]
Abstract
The mRNA coding sequence defines not only the amino acid sequence of the protein, but also the speed at which the ribosomes move along the mRNA while making the protein. The non-uniform local kinetics - denoted as translational rhythm - is similar among mRNAs coding for related protein folds. Deviations from this conserved rhythm can result in protein misfolding. In this review we summarize the experimental evidence demonstrating how local translation rates affect cotranslational protein folding, with the focus on the synonymous codons and patches of charged residues in the nascent peptide as best-studied examples. Alterations in nascent protein conformations due to disturbed translational rhythm can persist off the ribosome, as demonstrated by the effects of synonymous codon variants of several disease-related proteins. Charged amino acid patches in nascent chains also modulate translation and cotranslational protein folding, and can abrogate translation when placed at the N-terminus of the nascent peptide. During cotranslational folding, incomplete nascent chains navigate through a unique conformational landscape in which earlier intermediate states become inaccessible as the nascent peptide grows. Precisely tuned local translation rates, as well as interactions with the ribosome, guide the folding pathway towards the native structure, whereas deviations from the natural translation rhythm may favor pathways leading to trapped misfolded states. Deciphering the 'folding code' of the mRNA will contribute to understanding the diseases caused by protein misfolding and to rational protein design.
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Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; Department of Biochemistry and Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Ekaterina Samatova
- Max Planck Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, 37077 Goettingen, Germany
| | - Marina V Rodnina
- Max Planck Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, 37077 Goettingen, Germany.
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2
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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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3
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Zhang S, Lin R, Cui L, Jiang T, Shi J, Lu C, Li P, Zhou M. Alter codon bias of the P. pastoris genome to overcome a bottleneck in codon optimization strategy development and improve protein expression. Microbiol Res 2024; 282:127629. [PMID: 38330819 DOI: 10.1016/j.micres.2024.127629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/27/2023] [Accepted: 01/21/2024] [Indexed: 02/10/2024]
Abstract
Apart from its role in translation, codon bias is also an important mechanism to regulate mRNA levels. The traditional frequency-based codon optimization strategy is rather efficient in organisms such as N. crassa, but much less in yeast P. pastoris which is a popular host for heterologous protein expression. This is because that unlike N. crassa, the preferred codons of P. pastoris are actually AU-rich and hence codon optimization for extremely low GC content comes with issues of pre-mature transcriptional termination or low RNA stability in spite of translational advantages. To overcome this bottleneck, we focused on three reporter genes in P. pastoris first and confirmed the great advantage of GC-prone codon optimization on mRNA levels. Then we altered the codon bias profile of P. pastoris by introducing additional rare tRNA gene copies. Prior to that we constructed IPTG-regulated tRNA species to enable chassis cells to switch between different codon bias status. As demonstrated again with reporter genes, protein yield of luc and 0788 was successfully increased by 4-5 folds in chassis cells. In summary, here we provide an alternative codon optimization strategy for genes with unsatisfactory performance under traditional codon frequency-based optimization.
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Affiliation(s)
- Siyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ru Lin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Luyao Cui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Tianyi Jiang
- China Innovation Center of Roche, Shanghai 201203, China
| | - Jiacheng Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chaoyu Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pengfei Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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4
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Zhang H, Zhou Z, Guo J. The Function, Regulation, and Mechanism of Protein Turnover in Circadian Systems in Neurospora and Other Species. Int J Mol Sci 2024; 25:2574. [PMID: 38473819 DOI: 10.3390/ijms25052574] [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: 12/27/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Circadian clocks drive a large array of physiological and behavioral activities. At the molecular level, circadian clocks are composed of positive and negative elements that form core oscillators generating the basic circadian rhythms. Over the course of the circadian period, circadian negative proteins undergo progressive hyperphosphorylation and eventually degrade, and their stability is finely controlled by complex post-translational pathways, including protein modifications, genetic codon preference, protein-protein interactions, chaperon-dependent conformation maintenance, degradation, etc. The effects of phosphorylation on the stability of circadian clock proteins are crucial for precisely determining protein function and turnover, and it has been proposed that the phosphorylation of core circadian clock proteins is tightly correlated with the circadian period. Nonetheless, recent studies have challenged this view. In this review, we summarize the research progress regarding the function, regulation, and mechanism of protein stability in the circadian clock systems of multiple model organisms, with an emphasis on Neurospora crassa, in which circadian mechanisms have been extensively investigated. Elucidation of the highly complex and dynamic regulation of protein stability in circadian clock networks would greatly benefit the integrated understanding of the function, regulation, and mechanism of protein stability in a wide spectrum of other biological processes.
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Affiliation(s)
- Haoran Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zengxuan Zhou
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jinhu Guo
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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5
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Xie P, Xie X, Ye C, Dean KM, Laothamatas I, Taufique SKT, Takahashi J, Yamazaki S, Xu Y, Liu Y. Mammalian circadian clock proteins form dynamic interacting microbodies distinct from phase separation. Proc Natl Acad Sci U S A 2023; 120:e2318274120. [PMID: 38127982 PMCID: PMC10756265 DOI: 10.1073/pnas.2318274120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) underlies diverse biological processes. Because most LLPS studies were performed in vitro using recombinant proteins or in cells that overexpress protein, the physiological relevance of LLPS for endogenous protein is often unclear. PERIOD, the intrinsically disordered domain-rich proteins, are central mammalian circadian clock components and interact with other clock proteins in the core circadian negative feedback loop. Different core clock proteins were previously shown to form large complexes. Circadian clock studies often rely on experiments that overexpress clock proteins. Here, we show that when Per2 transgene was stably expressed in cells, PER2 protein formed nuclear phosphorylation-dependent slow-moving LLPS condensates that recruited other clock proteins. Super-resolution microscopy of endogenous PER2, however, revealed formation of circadian-controlled, rapidly diffusing nuclear microbodies that were resistant to protein concentration changes, hexanediol treatment, and loss of phosphorylation, indicating that they are distinct from the LLPS condensates caused by protein overexpression. Surprisingly, only a small fraction of endogenous PER2 microbodies transiently interact with endogenous BMAL1 and CRY1, a conclusion that was confirmed in cells and in mice tissues, suggesting an enzyme-like mechanism in the circadian negative feedback process. Together, these results demonstrate that the dynamic interactions of core clock proteins are a key feature of mammalian circadian clock mechanism and the importance of examining endogenous proteins in LLPS and circadian clock studies.
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Affiliation(s)
- Pancheng Xie
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX75390
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu215123, China
| | - Xiaowen Xie
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Congrong Ye
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Kevin M. Dean
- Lyda Hill Department of Bioinformatics and Cecil H. and Ida Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Isara Laothamatas
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
| | - S. K. Tahajjul Taufique
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
| | - Joseph Takahashi
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
| | - Shin Yamazaki
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
| | - Ying Xu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu215123, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX75390
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6
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Xie P, Xie X, Ye C, Dean KM, Laothamatas I, Taufique SKT, Takahashi J, Yamazaki S, Xu Y, Liu Y. Mammalian circadian clock proteins form dynamic interacting microbodies distinct from phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563153. [PMID: 37961341 PMCID: PMC10634710 DOI: 10.1101/2023.10.19.563153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Liquid-liquid phase separation (LLPS) underlies diverse biological processes. Because most LLPS studies were performed in vitro or in cells that overexpress protein, the physiological relevance of LLPS is unclear. PERIOD proteins are central mammalian circadian clock components and interact with other clock proteins in the core circadian negative feedback loop. Different core clock proteins were previously shown to form large complexes. Here we show that when transgene was stably expressed, PER2 formed nuclear phosphorylation-dependent LLPS condensates that recruited other clock proteins. Super-resolution microscopy of endogenous PER2, however, revealed formation of circadian-controlled, rapidly diffusing microbodies that were resistant to protein concentration changes, hexanediol treatment, and loss of phosphorylation, indicating that they are distinct from the LLPS condensates caused by overexpression. Surprisingly, only a small fraction of endogenous PER2 microbodies transiently interact with endogenous BMAL1 and CRY1, a conclusion that was confirmed in cells and in mice tissues, suggesting an enzyme-like mechanism in the circadian negative feedback process. Together, these results demonstrate that the dynamic interactions of core clock proteins is a key feature of mammalian circadian clock mechanism and the importance of examining endogenous proteins in LLPS and circadian studies.
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Affiliation(s)
- Pancheng Xie
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Cambridge-Su Genomic Resource Center, Soochow University; Suzhou, Jiangsu 215123, China
| | - Xiaowen Xie
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Congrong Ye
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kevin M. Dean
- Lyda Hill Department of Bioinformatics and Cecil H. and Ida Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isara Laothamatas
- Department of Neuroscience and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9111, USA
| | - S K Tahajjul Taufique
- Department of Neuroscience and Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9111, USA
| | - Joseph Takahashi
- Department of Neuroscience and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9111, USA
| | - Shin Yamazaki
- Department of Neuroscience and Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9111, USA
| | - Ying Xu
- Cambridge-Su Genomic Resource Center, Soochow University; Suzhou, Jiangsu 215123, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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7
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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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8
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Halder R, Nissley DA, Sitarik I, Jiang Y, Rao Y, Vu QV, Li MS, Pritchard J, O'Brien EP. How soluble misfolded proteins bypass chaperones at the molecular level. Nat Commun 2023; 14:3689. [PMID: 37344452 DOI: 10.1038/s41467-023-38962-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2023] [Indexed: 06/23/2023] Open
Abstract
Subpopulations of soluble, misfolded proteins can bypass chaperones within cells. The extent of this phenomenon and how it happens at the molecular level are unknown. Through a meta-analysis of the experimental literature we find that in all quantitative protein refolding studies there is always a subpopulation of soluble but misfolded protein that does not fold in the presence of one or more chaperones, and can take days or longer to do so. Thus, some misfolded subpopulations commonly bypass chaperones. Using multi-scale simulation models we observe that the misfolded structures that bypass various chaperones can do so because their structures are highly native like, leading to a situation where chaperones do not distinguish between the folded and near-native-misfolded states. More broadly, these results provide a mechanism by which long-time scale changes in protein structure and function can persist in cells because some misfolded states can bypass components of the proteostasis machinery.
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Affiliation(s)
- Ritaban Halder
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniel A Nissley
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yiyun Rao
- Molecular, Cellular and Integrative Biosciences Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Quyen V Vu
- Institute of Physics, Polish Academy of Sciences; Al. Lotnikow 32/46, 02-668, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences; Al. Lotnikow 32/46, 02-668, Warsaw, Poland
- Institute for Computational Sciences and Technology; Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Justin Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, State College, PA, 16802, USA
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, 16802, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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Li M, Li S, Zhang L. Phosphorylation Promotes the Accumulation of PERIOD Protein Foci. RESEARCH (WASHINGTON, D.C.) 2023; 6:0139. [PMID: 37223461 PMCID: PMC10202380 DOI: 10.34133/research.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/17/2023] [Indexed: 05/25/2023]
Abstract
Circadian clock drives the 24-h rhythm in our behavior and physiology. The molecular clock consists of a series of transcriptional/translational feedback loops operated by a number of clock genes. A very recent study reported that the clock protein PERIOD (PER) is organized into discrete foci at the nuclear envelope in fly circadian neurons, which is believed to be important for controlling the subcellular localization of clock genes. Loss of inner nuclear membrane protein lamin B receptor (LBR) leads to disruption of these foci, but how they are regulated is yet unknown. Here, we found that PER foci are likely phase-separated condensates, the formation of which is mediated by intrinsically disordered region in PER. Phosphorylation promotes the accumulation of these foci. Protein phosphatase 2A, which is known to dephosphorylate PER, hampers the accumulation of the foci. On the other hand, the circadian kinase DOUBLETIME (DBT) which phosphorylates PER enhances the accumulation of the foci. LBR likely facilitates PER foci accumulation by destabilizing the catalytic subunit of protein phosphatase 2A, MICROTUBULE STAR (MTS). In conclusion, here, we demonstrate a key role for phosphorylation in promoting the accumulation of PER foci, while LBR modulates this process by impinging on the circadian phosphatase MTS.
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Affiliation(s)
- Mengna Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shujing Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Department of Life Sciences, Bengbu Medical College, Bengbu, Anhui 233030, China
| | - Luoying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, Hubei 430022, China
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Leca I, Phillips AW, Ushakova L, Cushion TD, Keays DA. Codon modification of Tuba1a alters mRNA levels and causes a severe neurodevelopmental phenotype in mice. Sci Rep 2023; 13:1215. [PMID: 36681692 PMCID: PMC9867703 DOI: 10.1038/s41598-023-27782-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
The tubulinopathies are an umbrella of rare diseases that result from mutations in tubulin genes and are frequently characterised by severe brain malformations. The characteristics of a given disease reflect the expression pattern of the transcript, the function of a given tubulin gene, and the role microtubules play in a particular cell type. Mouse models have proved to be valuable tools that have provided insight into the molecular and cellular mechanisms that underlie the disease state. In this manuscript we compare two Tuba1a mouse models, both of which express wild-type TUBA1A protein but employ different codon usage. We show that modification of the Tuba1a mRNA sequence results in homozygous lethality and a severe neurodevelopmental phenotype. This is associated with a decrease in the number of post-mitotic neurons, PAX6 positive progenitors, and an increase in the number of apoptotic cells. We attribute this to a decrease in the stability of the modified Tuba1a transcript, and the absence of compensation by the other neurogenic tubulins. Our findings highlight the importance of maintaining the wild-type coding sequence when engineering mouse lines and the impact of synonymous genetic variation.
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Affiliation(s)
- Ines Leca
- Vienna Biocenter (VBC), Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Alexander William Phillips
- Vienna Biocenter (VBC), Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
- Department of Biology, Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
| | - Lyubov Ushakova
- Vienna Biocenter (VBC), Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Thomas David Cushion
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
| | - David Anthony Keays
- Vienna Biocenter (VBC), Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.
- Department of Biology, Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany.
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The role of spatiotemporal organization and dynamics of clock complexes in circadian regulation. Curr Opin Cell Biol 2022; 78:102129. [PMID: 36126370 DOI: 10.1016/j.ceb.2022.102129] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/26/2022] [Accepted: 08/19/2022] [Indexed: 01/31/2023]
Abstract
Circadian clocks are cell autonomous timekeepers that regulate ∼24-h oscillations in the expression of many genes and control rhythms in nearly all our behavior and physiology. Almost every cell in the human body has a molecular clock and networks of cells containing clock proteins orchestrate daily rhythms in many physiological processes, from sleep-wake cycles to metabolism to immunity. All eukaryotic circadian clocks are based on transcription-translation delayed negative feedback loops in which activation of core clock genes is negatively regulated by their cognate protein products. Our current understanding of circadian clocks has been accumulated from decades of genetic and biochemical experiments, however, what remains poorly understood is how clock proteins, genes, and mRNAs are spatiotemporally organized within live clock cells and how such subcellular organization affects circadian rhythms at the single cell level. Here, we review recent progress in understanding how clock proteins and genes are spatially organized within clock cells over the circadian cycle and the role of such organization in generating circadian rhythms and highlight open questions for future studies.
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Moreno García CA, Zhou H, Altimira D, Dynes R, Gregorini P, Jayathunga S, Maxwell TMR, Hickford J. The glutamate metabotropic receptor 5 (GRM5) gene is associated with beef cattle home range and movement tortuosity. J Anim Sci Biotechnol 2022; 13:111. [PMID: 36104821 PMCID: PMC9476267 DOI: 10.1186/s40104-022-00755-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022] Open
Abstract
Background The grazing behaviour of herbivores and their grazing personalities might in part be determined genetically, but there are few studies in beef cattle illustrating this. In this study, we investigated for first time the genetic variation within a candidate ‘grazing gene’, the glutamate metabotropic receptor 5 gene (GRM5), and tested associations between variation in that gene and variation in grazing personality behaviours (GP-behaviours) displayed by free-ranging cows during winter grazing in the steep and rugged rangelands of New Zealand. Mature beef cows (n = 303, from 3 to 10 years of age) were tracked with global positioning system (GPS) and, with 5-minutes (min) relocation frequency, various GP-behaviours were calculated. These included horizontal and vertical distances travelled, mean elevation, elevation range, elevation gain, slope, home range and movement tortuosity, variously calculated using daily relocation trajectories with repeated measurements (i.e., 7 to 24 days (d)) and satellite-derived digital elevation models (DEM). The different GP-behaviours were fitted into mixed models to ascertain their associations with variant sequences and genotypes of GRM5. Results We discovered three GRM5 variants (A, B and C) and identified the six possible genotypes in the cattle studied. The mixed models revealed that A was significantly associated with elevation range, home range and movement tortuosity. Similarly, GRM5 genotypes were associated (P < 0.05) to home range and movement tortuosity, while trends suggesting association (P < 0.1) were also revealed for elevation range and horizontal distance travelled. Most GP-behaviour models were improved by correcting for cow age-class as a fixed factor. The analysis of GP-behaviours averaged per cow age-class suggests that grazing personality is fully established as beef cows reached 4 years of age. Home range and movement tortuosity were not only associated with GRM5 variation, but also negatively correlated with each other (r = − 0.27, P < 0.001). Conclusions There seems to be a genetically determined trade-off between home range and movement tortuosity that may be useful in beef cattle breeding programmes aiming to improve the grazing distribution and utilisation of steep and rugged rangelands. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00755-7.
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Nissley DA, Jiang Y, Trovato F, Sitarik I, Narayan KB, To P, Xia Y, Fried SD, O’Brien EP. Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional. Nat Commun 2022; 13:3081. [PMID: 35654797 PMCID: PMC9163053 DOI: 10.1038/s41467-022-30548-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 05/05/2022] [Indexed: 01/12/2023] Open
Abstract
Some misfolded protein conformations can bypass proteostasis machinery and remain soluble in vivo. This is an unexpected observation, as cellular quality control mechanisms should remove misfolded proteins. Three questions, then, are: how do long-lived, soluble, misfolded proteins bypass proteostasis? How widespread are such misfolded states? And how long do they persist? We address these questions using coarse-grain molecular dynamics simulations of the synthesis, termination, and post-translational dynamics of a representative set of cytosolic E. coli proteins. We predict that half of proteins exhibit misfolded subpopulations that bypass molecular chaperones, avoid aggregation, and will not be rapidly degraded, with some misfolded states persisting for months or longer. The surface properties of these misfolded states are native-like, suggesting they will remain soluble, while self-entanglements make them long-lived kinetic traps. In terms of function, we predict that one-third of proteins can misfold into soluble less-functional states. For the heavily entangled protein glycerol-3-phosphate dehydrogenase, limited-proteolysis mass spectrometry experiments interrogating misfolded conformations of the protein are consistent with the structural changes predicted by our simulations. These results therefore provide an explanation for how proteins can misfold into soluble conformations with reduced functionality that can bypass proteostasis, and indicate, unexpectedly, this may be a wide-spread phenomenon.
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Affiliation(s)
- Daniel A. Nissley
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA
| | - Yang Jiang
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA
| | - Fabio Trovato
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA
| | - Ian Sitarik
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA
| | - Karthik B. Narayan
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA
| | - Philip To
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Yingzi Xia
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Stephen D. Fried
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA ,grid.21107.350000 0001 2171 9311Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Edward P. O’Brien
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA ,grid.29857.310000 0001 2097 4281Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 USA ,grid.29857.310000 0001 2097 4281Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802 USA
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14
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Cope AL, Gilchrist MA. Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach. BMC Genomics 2022; 23:408. [PMID: 35637464 PMCID: PMC9153123 DOI: 10.1186/s12864-022-08635-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/03/2022] [Indexed: 11/28/2022] Open
Abstract
Background Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate translation, mRNA secondary structure, and/or protein folding. Given the critical link between protein folding and protein function, numerous studies have analyzed the relationship between codon usage and protein structure. The results from these studies have often been contradictory, likely reflecting the differing methods used for measuring codon usage and the failure to appropriately control for confounding factors, such as differences in amino acid usage between protein structures and changes in the frequency of different structures with gene expression. Results Here we take an explicit population genetics approach to quantify codon-specific shifts in natural selection related to protein structure in S. cerevisiae and E. coli. Unlike other metrics of codon usage, our approach explicitly separates the effects of natural selection, scaled by gene expression, and mutation bias while naturally accounting for a region’s amino acid usage. Bayesian model comparisons suggest selection on codon usage varies only slightly between helix, sheet, and coil secondary structures and, similarly, between structured and intrinsically-disordered regions. Similarly, in contrast to prevous findings, we find selection on codon usage only varies slightly at the termini of helices in E. coli. Using simulated data, we show this previous work indicating “non-optimal” codons are enriched at the beginning of helices in S. cerevisiae was due to failure to control for various confounding factors (e.g. amino acid biases, gene expression, etc.), and rather than selection to modulate cotranslational folding. Conclusions Our results reveal a weak relationship between codon usage and protein structure, indicating that differences in selection on codon usage between structures are slight. In addition to the magnitude of differences in selection between protein structures being slight, the observed shifts appear to be idiosyncratic and largely codon-specific rather than systematic reversals in the nature of selection. Overall, our work demonstrates the statistical power and benefits of studying selective shifts on codon usage or other genomic features from an explicitly evolutionary approach. Limitations of this approach and future potential research avenues are discussed. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08635-0).
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Affiliation(s)
- Alexander L Cope
- Genome Science and Technology, University of Tennessee, Knoxville, United States.,Current Address: Department of Genetics, Rutgers University, Piscataway, United States
| | - Michael A Gilchrist
- Genome Science and Technology, University of Tennessee, Knoxville, United States. .,National Institute for Mathematical and Biological Synthesis, Knoxville, TN, United States. .,Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, United States.
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15
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Zhao S, Cui H, Hu Z, Du L, Ran X, Wen X. Senecavirus A Enhances Its Adaptive Evolution via Synonymous Codon Bias Evolution. Viruses 2022; 14:v14051055. [PMID: 35632797 PMCID: PMC9146685 DOI: 10.3390/v14051055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 12/10/2022] Open
Abstract
Synonymous codon bias in the viral genome affects protein translation and gene expression, suggesting that the synonymous codon mutant plays an essential role in influencing virulence and evolution. However, how the recessive mutant form contributes to virus evolvability remains elusive. In this paper, we characterize how the Senecavirus A (SVA), a picornavirus, utilizes synonymous codon mutations to influence its evolution, resulting in the adaptive evolution of the virus to adverse environments. The phylogenetic tree and Median-joining (MJ)-Network of these SVA lineages worldwide were constructed to reveal SVA three-stage genetic development clusters. Furthermore, we analyzed the codon bias of the SVA genome of selected strains and found that SVA could increase the GC content of the third base of some amino acid synonymous codons to enhance the viral RNA adaptive evolution. Our results highlight the impact of recessive mutation of virus codon bias on the evolution of the SVA and uncover a previously underappreciated evolutionary strategy for SVA. They also underline the importance of understanding the genetic evolution of SVA and how SVA adapts to the adverse effects of external stress.
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Affiliation(s)
- Simiao Zhao
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
| | - Huiqi Cui
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenru Hu
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
| | - Li Du
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
| | - Xuhua Ran
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
- Correspondence: (X.R.); (X.W.)
| | - Xiaobo Wen
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
- Correspondence: (X.R.); (X.W.)
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16
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Allen SR, Stewart RK, Rogers M, Ruiz IJ, Cohen E, Laederach A, Counter CM, Sawyer JK, Fox DT. Distinct responses to rare codons in select Drosophila tissues. eLife 2022; 11:e76893. [PMID: 35522036 PMCID: PMC9116940 DOI: 10.7554/elife.76893] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Codon usage bias has long been appreciated to influence protein production. Yet, relatively few studies have analyzed the impacts of codon usage on tissue-specific mRNA and protein expression. Here, we use codon-modified reporters to perform an organism-wide screen in Drosophila melanogaster for distinct tissue responses to codon usage bias. These reporters reveal a cliff-like decline of protein expression near the limit of rare codon usage in endogenously expressed Drosophila genes. Near the edge of this limit, however, we find the testis and brain are uniquely capable of expressing rare codon-enriched reporters. We define a new metric of tissue-specific codon usage, the tissue-apparent Codon Adaptation Index (taCAI), to reveal a conserved enrichment for rare codon usage in the endogenously expressed genes of both Drosophila and human testis. We further demonstrate a role for rare codons in an evolutionarily young testis-specific gene, RpL10Aa. Optimizing RpL10Aa codons disrupts female fertility. Our work highlights distinct responses to rarely used codons in select tissues, revealing a critical role for codon bias in tissue biology.
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Affiliation(s)
- Scott R Allen
- Department of Cell Biology, Duke UniversityDurhamUnited States
| | - Rebeccah K Stewart
- Department of Pharmacology and Cancer Biology, Duke UniversityDurhamUnited States
| | - Michael Rogers
- Department of Pharmacology and Cancer Biology, Duke UniversityDurhamUnited States
| | - Ivan Jimenez Ruiz
- Department of Biology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Erez Cohen
- Department of Cell Biology, Duke UniversityDurhamUnited States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel HillChapel HillUnited States
| | | | - Jessica K Sawyer
- Department of Pharmacology and Cancer Biology, Duke UniversityDurhamUnited States
| | - Donald T Fox
- Department of Cell Biology, Duke UniversityDurhamUnited States
- Department of Pharmacology and Cancer Biology, Duke UniversityDurhamUnited States
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17
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Ramazzotti D, Angaroni F, Maspero D, Mauri M, D’Aliberti D, Fontana D, Antoniotti M, Elli EM, Graudenzi A, Piazza R. Large-Scale Analysis of SARS-CoV-2 Synonymous Mutations Reveals the Adaptation to the Human Codon Usage During the Virus Evolution. Virus Evol 2022; 8:veac026. [PMID: 35371557 PMCID: PMC8971538 DOI: 10.1093/ve/veac026] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/11/2022] [Accepted: 03/22/2022] [Indexed: 11/27/2022] Open
Abstract
Many large national and transnational studies have been dedicated to the analysis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome, most of which focused on missense and nonsense mutations. However, approximately 30 per cent of the SARS-CoV-2 variants are synonymous, therefore changing the target codon without affecting the corresponding protein sequence. By performing a large-scale analysis of sequencing data generated from almost 400,000 SARS-CoV-2 samples, we show that silent mutations increasing the similarity of viral codons to the human ones tend to fixate in the viral genome overtime. This indicates that SARS-CoV-2 codon usage is adapting to the human host, likely improving its effectiveness in using the human aminoacyl-tRNA set through the accumulation of deceitfully neutral silent mutations. One-Sentence Summary. Synonymous SARS-CoV-2 mutations related to the activity of different mutational processes may positively impact viral evolution by increasing its adaptation to the human codon usage.
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Affiliation(s)
- Daniele Ramazzotti
- Dept. of Medicine and Surgery, Università degli Studi di Milano-Bicocca; Monza, Italy
| | - Fabrizio Angaroni
- Dept. of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca; Milan, Italy
| | - Davide Maspero
- Dept. of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca; Milan, Italy
- Inst. of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche (IBFM-CNR); Segrate, Milan, Italy
| | - Mario Mauri
- Dept. of Medicine and Surgery, Università degli Studi di Milano-Bicocca; Monza, Italy
| | - Deborah D’Aliberti
- Dept. of Medicine and Surgery, Università degli Studi di Milano-Bicocca; Monza, Italy
| | - Diletta Fontana
- Dept. of Medicine and Surgery, Università degli Studi di Milano-Bicocca; Monza, Italy
| | - Marco Antoniotti
- Dept. of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca; Milan, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Center – B4; Milan, Italy
| | - Elena Maria Elli
- Dept. of Medicine and Surgery, Università degli Studi di Milano-Bicocca; Monza, Italy
- Hematology and Clinical Research Unit, San Gerardo Hospital, Monza, Italy
| | - Alex Graudenzi
- Inst. of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche (IBFM-CNR); Segrate, Milan, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Center – B4; Milan, Italy
| | - Rocco Piazza
- Dept. of Medicine and Surgery, Università degli Studi di Milano-Bicocca; Monza, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Center – B4; Milan, Italy
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18
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Liu K, Ouyang Y, Lin R, Ge C, Zhou M. Strong negative correlation between codon usage bias and protein structural disorder impedes protein expression after codon optimization. J Biotechnol 2022; 343:15-24. [PMID: 34763006 DOI: 10.1016/j.jbiotec.2021.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/14/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022]
Abstract
As a common phenomenon existing in almost all genomes, codon usage bias has been studied for a long time. Codon optimization is a frequently used strategy to accelerate protein synthesis rate. Besides regulating protein translation speed, codon usage bias has also be reported to affect co-translation folding and transcription. P. pastoris is a well-developed expression system, whose efficiency is tightly correlated with commercial value. However, few studies focus on the role of codon usage bias in affecting protein expression in P. pastoris. Besides, many genes in P. pastoris genome show significant negative correlation between codon usage bias and protein structural disorder tendency. It's not known whether this feature is important for their expression. In order to answer these questions, we picked 4P. pastoris gene candidates with strong negative correlation between codon usage bias and protein structural disorder. We then performed full-length codon optimization which completely eliminated the correlation. Protein and RNA assays were then used to compare protein and mRNA levels before and after codon optimization. As a result, codon optimization failed to elevate their protein expression levels, and even resulted in a decrease. As represented by the trypsin sensitivity assays, codon optimization also altered the protein structure of 0616 and 0788. Besides protein, codon optimization also affected mRNA levels. Shown by in vitro and in vivo RNA degradation assays, the mRNA stability of 0616, 0788 and 0135 were also altered by codon optimization. For each gene, the detailed effect may be related with its specific sequence and protein structure. Our results suggest that codon usage bias is an important factor to regulate gene expression level, as well as mRNA and protein stabilities in P. pastoris. "Extreme" codon optimization in genes with strong negative correlation between codon usage bias and protein structural disorder tendency may not be favored. Compromised strategies should be tried if expression is not successful. Besides, codon optimization may affect protein structural conformation more severely in structural disordered proteins.
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Affiliation(s)
- Kunshan Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yaqi Ouyang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ru Lin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chenyu Ge
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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19
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Lyu X, Yang Q, Zhao F, Liu Y. Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed. Nucleic Acids Res 2021; 49:9404-9423. [PMID: 34417614 PMCID: PMC8450115 DOI: 10.1093/nar/gkab729] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/26/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022] Open
Abstract
Essential cellular functions require efficient production of many large proteins but synthesis of large proteins encounters many obstacles in cells. Translational control is mostly known to be regulated at the initiation step. Whether translation elongation process can feedback to regulate initiation efficiency is unclear. Codon usage bias, a universal feature of all genomes, plays an important role in determining gene expression levels. Here, we discovered that there is a conserved but codon usage-dependent genome-wide negative correlation between protein abundance and CDS length. The codon usage effects on protein expression and ribosome flux on mRNAs are influenced by CDS length; optimal codon usage preferentially promotes production of large proteins. Translation of mRNAs with long CDS and non-optimal codon usage preferentially induces phosphorylation of initiation factor eIF2α, which inhibits translation initiation efficiency. Deletion of the eIF2α kinase CPC-3 (GCN2 homolog) in Neurospora preferentially up-regulates large proteins encoded by non-optimal codons. Surprisingly, CPC-3 also inhibits translation elongation rate in a codon usage and CDS length-dependent manner, resulting in slow elongation rates for long CDS mRNAs. Together, these results revealed a codon usage and CDS length-dependent feedback mechanism from translation elongation to regulate both translation initiation and elongation kinetics.
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Affiliation(s)
- Xueliang Lyu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.,State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qian Yang
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Fangzhou Zhao
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
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20
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Xiao Y, Yuan Y, Jimenez M, Soni N, Yadlapalli S. Clock proteins regulate spatiotemporal organization of clock genes to control circadian rhythms. Proc Natl Acad Sci U S A 2021; 118:e2019756118. [PMID: 34234015 PMCID: PMC8285898 DOI: 10.1073/pnas.2019756118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Circadian clocks regulate ∼24-h oscillations in gene expression, behavior, and physiology. While the genetic and molecular mechanisms of circadian rhythms are well characterized, what remains poorly understood are the intracellular dynamics of circadian clock components and how they affect circadian rhythms. Here, we elucidate how spatiotemporal organization and dynamics of core clock proteins and genes affect circadian rhythms in Drosophila clock neurons. Using high-resolution imaging and DNA-fluorescence in situ hybridization techniques, we demonstrate that Drosophila clock proteins (PERIOD and CLOCK) are organized into a few discrete foci at the nuclear envelope during the circadian repression phase and play an important role in the subnuclear localization of core clock genes to control circadian rhythms. Specifically, we show that core clock genes, period and timeless, are positioned close to the nuclear periphery by the PERIOD protein specifically during the repression phase, suggesting that subnuclear localization of core clock genes might play a key role in their rhythmic gene expression. Finally, we show that loss of Lamin B receptor, a nuclear envelope protein, leads to disruption of PER foci and per gene peripheral localization and results in circadian rhythm defects. These results demonstrate that clock proteins play a hitherto unexpected role in the subnuclear reorganization of core clock genes to control circadian rhythms, revealing how clocks function at the subcellular level. Our results further suggest that clock protein foci might regulate dynamic clustering and spatial reorganization of clock-regulated genes over the repression phase to control circadian rhythms in behavior and physiology.
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Affiliation(s)
- Yangbo Xiao
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Ye Yuan
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Mariana Jimenez
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Neeraj Soni
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Swathi Yadlapalli
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109;
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21
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Pintó RM, Bosch A. The codon usage code for co-translational folding of viral capsids. Genome Biol Evol 2021; 13:6259148. [PMID: 33914886 PMCID: PMC8410136 DOI: 10.1093/gbe/evab089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2021] [Indexed: 12/25/2022] Open
Abstract
Codon bias is common to all organisms and is the result of mutation, drift, and selection. Selection for the efficiency and accuracy of translation is well recognized as a factor shaping the codon usage. In contrast, fewer studies report the control of the rate of translation as an additional selective pressure influencing the codon usage of an organism. Experimental molecular evolution using RNA virus populations is a powerful tool for the identification of mechanisms underlying the codon bias. Indeed, the role of deoptimized codons on the cotranslational folding has been proven in the capsids of two fecal-orally transmitted picornaviruses, poliovirus, and the hepatitis A virus, emphasizing the role of the frequency of codons in determining the phenotype. However, most studies on virus codon usage rely only on computational analyses, and experimental studies should be encouraged to clearly define the role of selection on codon evolution.
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Affiliation(s)
- Rosa M Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
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22
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Xu Y, Liu K, Han Y, Xing Y, Zhang Y, Yang Q, Zhou M. Codon usage bias regulates gene expression and protein conformation in yeast expression system P. pastoris. Microb Cell Fact 2021; 20:91. [PMID: 33902585 PMCID: PMC8077831 DOI: 10.1186/s12934-021-01580-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/13/2021] [Indexed: 11/30/2022] Open
Abstract
Background Protein synthesis is one of the extremely important anabolic pathways in the yeast expression system Pichia pastoris. Codon optimization is a commonly adopted strategy for improved protein expression, although unexpected failures did appear sometimes waiting for further exploration. Recently codon bias has been studied to regulate protein folding and activity in many other organisms. Results Here the codon bias profile of P. pastoris genome was examined first and a direct correlation between codon translation efficiency and usage frequency was identified. By manipulating the codon choices of both endogenous and heterologous signal peptides, secretion abilities of N-terminal signal peptides were shown to be tolerant towards codon changes. Then two gene candidates with different levels of structural disorder were studied, and full-length codon optimization was found to affect their expression profiles differentially. Finally, more evidences were provided to support possible protein conformation change brought by codon optimization in structurally disordered proteins. Conclusion Our results suggest that codon bias regulates gene expression by modulating several factors including transcription and translation efficiency, protein folding and activity. Because of sequences difference, the extent of affection may be gene specific. For some genes, special codon optimization strategy should be adopted to ensure appropriate expression and conformation. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01580-9.
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Affiliation(s)
- Yichun Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Kunshan Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yu Han
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yanzi Xing
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Qiuying Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, 430062, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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23
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Liu Y, Yang Q, Zhao F. Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding. Annu Rev Biochem 2021; 90:375-401. [PMID: 33441035 DOI: 10.1146/annurev-biochem-071320-112701] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Codon usage bias, the preference for certain synonymous codons, is found in all genomes. Although synonymous mutations were previously thought to be silent, a large body of evidence has demonstrated that codon usage can play major roles in determining gene expression levels and protein structures. Codon usage influences translation elongation speed and regulates translation efficiency and accuracy. Adaptation of codon usage to tRNA expression determines the proteome landscape. In addition, codon usage biases result in nonuniform ribosome decoding rates on mRNAs, which in turn influence the cotranslational protein folding process that is critical for protein function in diverse biological processes. Conserved genome-wide correlations have also been found between codon usage and protein structures. Furthermore, codon usage is a major determinant of mRNA levels through translation-dependent effects on mRNA decay and translation-independent effects on transcriptional and posttranscriptional processes. Here, we discuss the multifaceted roles and mechanisms of codon usage in different gene regulatory processes.
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Affiliation(s)
- Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
| | - Qian Yang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
| | - Fangzhou Zhao
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
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24
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Abstract
The identification and characterization of rhythmically expressed mRNAs have been an active area of research over the past 20 years, as these mRNAs are believed to produce the daily rhythms in a wide range of biological processes. Circadian transcriptome studies have used mature mRNA as a primary readout and focused largely on rhythmic RNA synthesis as a regulatory mechanism underlying rhythmic mRNA expression. However, RNA synthesis, RNA degradation, or a combination of both must be rhythmic to drive rhythmic RNA profiles, and it is still unclear to what extent rhythmic synthesis leads to rhythmic RNA profiles. In addition, circadian RNA expression is also often tissue specific. Although a handful of genes cycle in all or most tissues, others are rhythmic only in certain tissues, even though the same core clock mechanism is believed to control the rhythmic RNA profiles in all tissues. This review focuses on the dynamics of rhythmic RNA synthesis and degradation and discusses how these steps collectively determine the rhythmicity, phase, and amplitude of RNA accumulation. In particular, we highlight a possible role of RNA degradation in driving tissue-specific RNA rhythms. By unifying findings from experimental and theoretical studies, we will provide a comprehensive overview of how rhythmic gene expression can be achieved and how each regulatory step contributes to tissue-specific circadian transcriptome output in mammals.
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Affiliation(s)
| | - Shihoko Kojima
- To whom all correspondence should be addressed: Shihoko Kojima, Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA; .
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Nonoptimal Codon Usage Is Critical for Protein Structure and Function of the Master General Amino Acid Control Regulator CPC-1. mBio 2020; 11:mBio.02605-20. [PMID: 33051373 PMCID: PMC7554675 DOI: 10.1128/mbio.02605-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Under amino acid starvation conditions, eukaryotic organisms activate a general amino acid control response. In Neurospora crassa, Cross Pathway Control Protein 1 (CPC-1), the ortholog of the Saccharomyces cerevisiae bZIP transcription factor GCN4, functions as the master regulator of the general amino acid control response. Codon usage biases are a universal feature of eukaryotic genomes and are critical for regulation of gene expression. Although codon usage has also been implicated in the regulation of protein structure and function, genetic evidence supporting this conclusion is very limited. Here, we show that Neurospora cpc-1 has a nonoptimal NNU-rich codon usage profile that contrasts with the strong NNC codon preference in the genome. Although substitution of the cpc-1 NNU codons with synonymous NNC codons elevated CPC-1 expression in Neurospora, it altered the CPC-1 degradation rate and abolished its amino acid starvation-induced protein stabilization. The codon-manipulated CPC-1 protein also exhibited different sensitivity to limited protease digestion. Furthermore, CPC-1 functions in rescuing the cell growth of the cpc-1 deletion mutant and activation of the expression of its target genes were impaired by the synonymous codon changes. Together, these results reveal the critical role of codon usage in regulation of CPC-1 expression and function and establish a genetic example of the importance of codon usage in protein folding.IMPORTANCE The general amino acid control response is critical for adaptation of organisms to amino acid starvation conditions. The preference to use certain synonymous codons is a universal feature of all genomes. Synonymous codon changes were previously thought to be silent mutations. In this study, we showed that the Neurospora cpc-1 gene has an unusual codon usage profile compared to other genes in the genome. We found that codon optimization of the cpc-1 gene without changing its amino acid sequence resulted in elevated CPC-1 expression, an altered protein degradation rate, and impaired protein functions due to changes in protein structure. Together, these results reveal the critical role of synonymous codon usage in regulation of CPC-1 expression and function and establish a genetic example of the importance of codon usage in protein structure.
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26
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Nieuwkoop T, Finger-Bou M, van der Oost J, Claassens NJ. The Ongoing Quest to Crack the Genetic Code for Protein Production. Mol Cell 2020; 80:193-209. [PMID: 33010203 DOI: 10.1016/j.molcel.2020.09.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/10/2020] [Accepted: 09/10/2020] [Indexed: 01/05/2023]
Abstract
Understanding the genetic design principles that determine protein production remains a major challenge. Although the key principles of gene expression were discovered 50 years ago, additional factors are still being uncovered. Both protein-coding and non-coding sequences harbor elements that collectively influence the efficiency of protein production by modulating transcription, mRNA decay, and translation. The influences of many contributing elements are intertwined, which complicates a full understanding of the individual factors. In natural genes, a functional balance between these factors has been obtained in the course of evolution, whereas for genetic-engineering projects, our incomplete understanding still limits optimal design of synthetic genes. However, notable advances have recently been made, supported by high-throughput analysis of synthetic gene libraries as well as by state-of-the-art biomolecular techniques. We discuss here how these advances further strengthen understanding of the gene expression process and how they can be harnessed to optimize protein production.
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Affiliation(s)
- Thijs Nieuwkoop
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Max Finger-Bou
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
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27
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A Crosstalk on Codon Usage in Genes Associated with Leukemia. Biochem Genet 2020; 59:235-255. [PMID: 32989646 DOI: 10.1007/s10528-020-10000-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023]
Abstract
Leukemia is the outcome of aggregation of damaged white blood cells. Several genes were reported to be associated with the pathogenesis of leukemia. These genes were computationally analyzed to decipher their codon usage bias (CUB) and to identify the prime factors influencing the codon usage profile as no work was reported yet. The mean values of synonymous codon usage order (SCUO) parameter indicated low CUB of the genes. Significant positive association of SCUO with overall GC and positional GCs might signal the presence of mutational pressure. However, neutrality plot suggested the dominant role of natural selection across the genes. Along with natural selection, the role of mutation pressure was also prominent and that might be responsible for lower CUB (SCUO = 0.19) of genes. Low translational speed might permit accuracy in the process. A strong inverse relationship of translational rate was observed with CUB of genes and folding energy.
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28
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Liu Y. A code within the genetic code: codon usage regulates co-translational protein folding. Cell Commun Signal 2020; 18:145. [PMID: 32907610 PMCID: PMC7488015 DOI: 10.1186/s12964-020-00642-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/10/2020] [Indexed: 01/05/2023] Open
Abstract
The genetic code is degenerate, and most amino acids are encoded by two to six synonymous codons. Codon usage bias, the preference for certain synonymous codons, is a universal feature of all genomes examined. Synonymous codon mutations were previously thought to be silent; however, a growing body evidence now shows that codon usage regulates protein structure and gene expression through effects on co-translational protein folding, translation efficiency and accuracy, mRNA stability, and transcription. Codon usage regulates the speed of translation elongation, resulting in non-uniform ribosome decoding rates on mRNAs during translation that is adapted to co-translational protein folding process. Biochemical and genetic evidence demonstrate that codon usage plays an important role in regulating protein folding and function in both prokaryotic and eukaryotic organisms. Certain protein structural types are more sensitive than others to the effects of codon usage on protein folding, and predicted intrinsically disordered domains are more prone to misfolding caused by codon usage changes than other domain types. Bioinformatic analyses revealed that gene codon usage correlates with different protein structures in diverse organisms, indicating the existence of a codon usage code for co-translational protein folding. This review focuses on recent literature on the role and mechanism of codon usage in regulating translation kinetics and co-translational protein folding. Video abstract
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Affiliation(s)
- Yi Liu
- Department of Physiology, ND13.214A, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9040, USA.
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29
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Reshetniak S, Ußling JE, Perego E, Rammner B, Schikorski T, Fornasiero EF, Truckenbrodt S, Köster S, Rizzoli SO. A comparative analysis of the mobility of 45 proteins in the synaptic bouton. EMBO J 2020; 39:e104596. [PMID: 32627850 PMCID: PMC7429486 DOI: 10.15252/embj.2020104596] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 02/01/2023] Open
Abstract
Many proteins involved in synaptic transmission are well known, and their features, as their abundance or spatial distribution, have been analyzed in systematic studies. This has not been the case, however, for their mobility. To solve this, we analyzed the motion of 45 GFP‐tagged synaptic proteins expressed in cultured hippocampal neurons, using fluorescence recovery after photobleaching, particle tracking, and modeling. We compared synaptic vesicle proteins, endo‐ and exocytosis cofactors, cytoskeleton components, and trafficking proteins. We found that movement was influenced by the protein association with synaptic vesicles, especially for membrane proteins. Surprisingly, protein mobility also correlated significantly with parameters as the protein lifetimes, or the nucleotide composition of their mRNAs. We then analyzed protein movement thoroughly, taking into account the spatial characteristics of the system. This resulted in a first visualization of overall protein motion in the synapse, which should enable future modeling studies of synaptic physiology.
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Affiliation(s)
- Sofiia Reshetniak
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany.,International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Jan-Eike Ußling
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany
| | - Eleonora Perego
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Burkhard Rammner
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas Schikorski
- Department of Neuroscience, Universidad Central del Caribe, Bayamon, PR, USA
| | - Eugenio F Fornasiero
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany
| | - Sven Truckenbrodt
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany.,International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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30
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Chakraborty S, Barbhuiya PA, Paul S, Uddin A, Choudhury Y, Ahn Y, Cho YS. Codon usage trend in genes associated with obesity. Biotechnol Lett 2020; 42:1865-1875. [PMID: 32488444 DOI: 10.1007/s10529-020-02931-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/29/2020] [Indexed: 11/29/2022]
Abstract
Obesity is not only a social menace but also an economic burden as it reduces productivity and increases health care cost. We used bioinformatic tools to analyze the CUB of obesity associated genes and compared with housekeeping genes (control) to explore the similarities and differences between two data sets as no work was reported yet. The mean effective number of codons (ENC) in genes associated with obesity and housekeeping gene was 50.45 and 52.03 respectively, indicating low CUB. The relative synonymous codon usage (RSCU) suggested that codons namely CTG and GTG were over-represented in both obesity and housekeeping genes while under-represented codons were TCG, TTA, CTA, CCG, CAA, CGT, ATA, ACG, GTA and GCG in obesity genes and TCG, TTA, CCG, ATA, ACG, GTA, and GCG in housekeeping genes. t test analysis suggested that 11 codons namely TTA (Leu), TTG (Leu), CCG (Pro), CAC (His), CAA (Gln), CAG (Gln), CGT (Arg), AGA (Arg), ATA (Ile), ATT (Ile) and GCG (Ala) were significantly differed (p < 0.05 or p < 0.01) between obesity and housekeeping genes. Highly significant correlation was observed between GC12 and GC3 in obesity and housekeeping genes i.e. r = 0.580** and r = 0.498** (p < 0.01) respectively indicating the effect of directional mutation pressure present in all codon positions.
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Affiliation(s)
- Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, Assam, 788011, India.
| | - Parvin A Barbhuiya
- Department of Biotechnology, Assam University, Silchar, Assam, 788011, India
| | - Sunanda Paul
- Department of Biotechnology, Assam University, Silchar, Assam, 788011, India
| | - Arif Uddin
- Department of Biotechnology, Assam University, Silchar, Assam, 788011, India
| | - Yashmin Choudhury
- Department of Biotechnology, Assam University, Silchar, Assam, 788011, India
| | - Yeongseon Ahn
- Department of Biomedical Science, Hallym University, Hallymdachak-gil, Chuncheon, 24252, Gangwon-do, Korea
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Hallymdachak-gil, Chuncheon, 24252, Gangwon-do, Korea.
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31
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Castelo-Szekely V, Gatfield D. Emerging Roles of Translational Control in Circadian Timekeeping. J Mol Biol 2020; 432:3483-3497. [PMID: 32246961 DOI: 10.1016/j.jmb.2020.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/07/2023]
Abstract
A large part of mammalian physiology and behaviour shows regular daily variations. This temporal organisation is driven by the activity of an endogenous circadian clock, whose molecular basis consists of diurnal waves in gene expression. Circadian transcription is the major driver of these rhythms, yet post-transcriptional mechanisms, some of which occur in response to systemic cues and in a tissue-specific fashion, have central roles in ultimately establishing the oscillatory gene expression programme as well. Regulatory control that occurs at the level of translation is emerging as an important player in the generation and modulation of protein accumulation rhythms. As a mechanism, translation lies at a privileged position to integrate genetically encoded rhythmic signals with other, external and internal stimuli, including nutrient-derived cues. In this review, we summarise our current knowledge of how diurnal control of translation affects both bulk protein levels and gene-specific protein biosynthesis. We discuss mechanisms of regulation, in particular with regard to the complex interplay between circadian cycles and feeding/fasting cycles, as well as emerging roles for upstream open reading frames in clock control.
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Affiliation(s)
- Violeta Castelo-Szekely
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland.
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32
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Liu XY, Li Y, Ji KK, Zhu J, Ling P, Zhou T, Fan LY, Xie SQ. Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in Cuscuta australis. Genomics 2020; 112:2695-2702. [PMID: 32145379 DOI: 10.1016/j.ygeno.2020.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/05/2020] [Accepted: 03/03/2020] [Indexed: 11/28/2022]
Abstract
The protein-coding genes and pseudogenes of Cuscuta australis had the diverse contribution to the formation and evolution of parasitism. The codon usage pattern analysis of these two type genes could be used to understand the gene transcription and translation. In this study, we systematically analyzed the codon usage patterns of protein-coding sequences and pseudogenes sequences in C. australis. The results showed that the high frequency codons of protein coding sequences and pseudogenes had the same A/U bias in the third position. However, these two sequences had converse bias at the third base in optimal codons: the protein coding sequences preferred G/C-ending codons while pseudogene sequences preferred A/U-ending codons. Neutrality plot and effective number of codons plot revealed that natural selection played a more important role than mutation pressure in two sequences codon usage bias. Furthermore, the gene expression level had a significant positive correlation with codon usage bias in C. australis. Highly-expressed protein coding genes exhibited a higher codon bias than lowly-expressed genes. Meanwhile, the high-expression genes tended to use G/C-ending synonymous codons. This result further verified the optimal codons usage bias and its correlation with the gene expression in C. australis.
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Affiliation(s)
- Xu-Yuan Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Yu Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Kai-Kai Ji
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Jie Zhu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Peng Ling
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Tao Zhou
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou 570228, China
| | - Lan-Ying Fan
- Shanxi Academy of Forestry Sciences, Taiyuan 030012, China.
| | - Shang-Qian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou 570228, China.
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33
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Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps. Proc Natl Acad Sci U S A 2020; 117:1485-1495. [PMID: 31911473 DOI: 10.1073/pnas.1913207117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Many large proteins suffer from slow or inefficient folding in vitro. It has long been known that this problem can be alleviated in vivo if proteins start folding cotranslationally. However, the molecular mechanisms underlying this improvement have not been well established. To address this question, we use an all-atom simulation-based algorithm to compute the folding properties of various large protein domains as a function of nascent chain length. We find that for certain proteins, there exists a narrow window of lengths that confers both thermodynamic stability and fast folding kinetics. Beyond these lengths, folding is drastically slowed by nonnative interactions involving C-terminal residues. Thus, cotranslational folding is predicted to be beneficial because it allows proteins to take advantage of this optimal window of lengths and thus avoid kinetic traps. Interestingly, many of these proteins' sequences contain conserved rare codons that may slow down synthesis at this optimal window, suggesting that synthesis rates may be evolutionarily tuned to optimize folding. Using kinetic modeling, we show that under certain conditions, such a slowdown indeed improves cotranslational folding efficiency by giving these nascent chains more time to fold. In contrast, other proteins are predicted not to benefit from cotranslational folding due to a lack of significant nonnative interactions, and indeed these proteins' sequences lack conserved C-terminal rare codons. Together, these results shed light on the factors that promote proper protein folding in the cell and how biomolecular self-assembly may be optimized evolutionarily.
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34
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Yang Q, Yu CH, Zhao F, Dang Y, Wu C, Xie P, Sachs MS, Liu Y. eRF1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons. Nucleic Acids Res 2019; 47:9243-9258. [PMID: 31410471 PMCID: PMC6755126 DOI: 10.1093/nar/gkz710] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 12/16/2022] Open
Abstract
Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and plays an important role in regulating gene expression levels. A major role of codon usage is thought to regulate protein expression levels by affecting mRNA translation efficiency, but the underlying mechanism is unclear. By analyzing ribosome profiling results, here we showed that codon usage regulates translation elongation rate and that rare codons are decoded more slowly than common codons in all codon families in Neurospora. Rare codons resulted in ribosome stalling in manners both dependent and independent of protein sequence context and caused premature translation termination. This mechanism was shown to be conserved in Drosophila cells. In both Neurospora and Drosophila cells, codon usage plays an important role in regulating mRNA translation efficiency. We found that the rare codon-dependent premature termination is mediated by the translation termination factor eRF1, which recognizes ribosomes stalled on rare sense codons. Silencing of eRF1 expression resulted in codon usage-dependent changes in protein expression. Together, these results establish a mechanism for how codon usage regulates mRNA translation efficiency.
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Affiliation(s)
- Qian Yang
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Chien-Hung Yu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.,Department of Biochemistry and Molecular Biology, National Cheng Kung University, Tainan 701, Taiwan
| | - Fangzhou Zhao
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yunkun Dang
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.,State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - Pancheng Xie
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.,Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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35
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Sanguinetti M, Iriarte A, Amillis S, Marín M, Musto H, Ramón A. A pair of non-optimal codons are necessary for the correct biosynthesis of the Aspergillus nidulans urea transporter, UreA. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190773. [PMID: 31827830 PMCID: PMC6894576 DOI: 10.1098/rsos.190773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
In both prokaryotic and eukaryotic genomes, synonymous codons are unevenly used. Such differential usage of optimal or non-optimal codons has been suggested to play a role in the control of translation initiation and elongation, as well as at the level of transcription and mRNA stability. In the case of membrane proteins, codon usage has been proposed to assist in the establishment of a pause necessary for the correct targeting of the nascent chains to the translocon. By using as a model UreA, the Aspergillus nidulans urea transporter, we revealed that a pair of non-optimal codons encoding amino acids situated at the boundary between the N-terminus and the first transmembrane segment are necessary for proper biogenesis of the protein at 37°C. These codons presumably regulate the translation rate in a previously undescribed fashion, possibly contributing to the correct interaction of ureA-translating ribosome-nascent chain complexes with the signal recognition particle and/or other factors, while the polypeptide has not yet emerged from the ribosomal tunnel. Our results suggest that the presence of the pair of non-optimal codons would not be functionally important in all cellular conditions. Whether this mechanism would affect other proteins remains to be determined.
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Affiliation(s)
- Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, Uruguay
- Laboratorio de Organización y Evolución del Genoma, Unidad de Genómica Evolutiva, Departamento de Evolución, Facultad de Ciencias, UdelaR, Montevideo, Uruguay
| | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Athens, Hellas, Greece
| | - Mónica Marín
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Organización y Evolución del Genoma, Unidad de Genómica Evolutiva, Departamento de Evolución, Facultad de Ciencias, UdelaR, Montevideo, Uruguay
| | - Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
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36
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Honey bee predisposition of resistance to ubiquitous mite infestations. Sci Rep 2019; 9:7794. [PMID: 31127129 PMCID: PMC6534585 DOI: 10.1038/s41598-019-44254-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/07/2019] [Indexed: 11/18/2022] Open
Abstract
Host-parasite co-evolution history is lacking when parasites switch to novel hosts. This was the case for Western honey bees (Apis mellifera) when the ectoparasitic mite, Varroa destructor, switched hosts from Eastern honey bees (Apis cerana). This mite has since become the most severe biological threat to A. mellifera worldwide. However, some A. mellifera populations are known to survive infestations, largely by suppressing mite population growth. One known mechanism is suppressed mite reproduction (SMR), but the underlying genetics are poorly understood. Here, we take advantage of haploid drones, originating from one queen from the Netherlands that developed Varroa-resistance, whole exome sequencing and elastic-net regression to identify genetic variants associated with SMR in resistant honeybees. An eight variants model predicted 88% of the phenotypes correctly and identified six risk and two protective variants. Reproducing and non-reproducing mites could not be distinguished using DNA microsatellites, which is in agreement with the hypothesis that it is not the parasite but the host that adapted itself. Our results suggest that the brood pheromone-dependent mite oogenesis is disrupted in resistant hosts. The identified genetic markers have a considerable potential to contribute to a sustainable global apiculture.
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37
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CodSeqGen: A tool for generating synonymous coding sequences with desired GC-contents. Genomics 2019; 112:237-242. [PMID: 30738198 PMCID: PMC7127556 DOI: 10.1016/j.ygeno.2019.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/29/2019] [Accepted: 02/02/2019] [Indexed: 11/30/2022]
Abstract
Identification of regulatory elements is essential for understanding the mechanism behind regulating gene expression. These regulatory elements—located in or near gene—bind to proteins called transcription factors to initiate the transcription process. Their occurrences are influenced by the GC-content or nucleotide composition. For generating synthetic coding sequences with pre-specified amino acid sequence and desired GC-content, there exist two stochastic methods, multinomial and maximum entropy. Both methods rely on the probability of choosing the codon synonymous for usage in regard to a specific amino acid. In spite the latter exhibited unbiased manner, the produced sequences are not exactly obeying the GC-content constraint. In this paper, we present an algorithmic solution to produce coding sequences that follow exactly a primary amino acid sequence and a desired GC-content. The proposed tool, namely CodSeqGen, depends on random selection for smaller subsets to be traversed using the backtracking approach. Generating random coding sequence is computationally expensive. For proteins of length n, we need to test 6n coding sequences to find those satisfying GC-content constraints. CodSeqGen uses smart backtracking, and produces synonymous coding sequences with the exact desired GC-contents. Experiments show CodSeqGen produces sequences with GC-contents that satisfy the constraints while NullSeq does not.
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38
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Li YH, Liu X, Vanselow JT, Zheng H, Schlosser A, Chiu JC. O-GlcNAcylation of PERIOD regulates its interaction with CLOCK and timing of circadian transcriptional repression. PLoS Genet 2019; 15:e1007953. [PMID: 30703153 PMCID: PMC6372208 DOI: 10.1371/journal.pgen.1007953] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/12/2019] [Accepted: 01/10/2019] [Indexed: 11/18/2022] Open
Abstract
Circadian clocks coordinate time-of-day-specific metabolic and physiological processes to maximize organismal performance and fitness. In addition to light and temperature, which are regarded as strong zeitgebers for circadian clock entrainment, metabolic input has now emerged as an important signal for clock entrainment and modulation. Circadian clock proteins have been identified to be substrates of O-GlcNAcylation, a nutrient sensitive post-translational modification (PTM), and the interplay between clock protein O-GlcNAcylation and other PTMs is now recognized as an important mechanism by which metabolic input regulates circadian physiology. To better understand the role of O-GlcNAcylation in modulating clock protein function within the molecular oscillator, we used mass spectrometry proteomics to identify O-GlcNAcylation sites of PERIOD (PER), a repressor of the circadian transcriptome and a critical biochemical timer of the Drosophila clock. In vivo functional characterization of PER O-GlcNAcylation sites indicates that O-GlcNAcylation at PER(S942) reduces interactions between PER and CLOCK (CLK), the key transcriptional activator of clock-controlled genes. Since we observe a correlation between clock-controlled daytime feeding activity and higher level of PER O-GlcNAcylation, we propose that PER(S942) O-GlcNAcylation during the day functions to prevent premature initiation of circadian repression phase. This is consistent with the period-shortening behavioral phenotype of per(S942A) flies. Taken together, our results support that clock-controlled feeding activity provides metabolic signals to reinforce light entrainment to regulate circadian physiology at the post-translational level. The interplay between O-GlcNAcylation and other PTMs to regulate circadian physiology is expected to be complex and extensive, and reach far beyond the molecular oscillator.
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Affiliation(s)
- Ying H. Li
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States of America
| | - Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States of America
| | - Jens T. Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ, United States of America
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States of America
- * E-mail:
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39
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Mandad S, Rahman RU, Centeno TP, Vidal RO, Wildhagen H, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Kirli K, Benito E, Fischer A, Yousefi RY, Dennerlein S, Rehling P, Feussner I, Urlaub H, Bonn S, Rizzoli SO, Fornasiero EF. The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. Sci Rep 2018; 8:16913. [PMID: 30443017 PMCID: PMC6237891 DOI: 10.1038/s41598-018-35277-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
The homeostasis of the proteome depends on the tight regulation of the mRNA and protein abundances, of the translation rates, and of the protein lifetimes. Results from several studies on prokaryotes or eukaryotic cell cultures have suggested that protein homeostasis is connected to, and perhaps regulated by, the protein and the codon sequences. However, this has been little investigated for mammals in vivo. Moreover, the link between the coding sequences and one critical parameter, the protein lifetime, has remained largely unexplored, both in vivo and in vitro. We tested this in the mouse brain, and found that the percentages of amino acids and codons in the sequences could predict all of the homeostasis parameters with a precision approaching experimental measurements. A key predictive element was the wobble nucleotide. G-/C-ending codons correlated with higher protein lifetimes, protein abundances, mRNA abundances and translation rates than A-/U-ending codons. Modifying the proportions of G-/C-ending codons could tune these parameters in cell cultures, in a proof-of-principle experiment. We suggest that the coding sequences are strongly linked to protein homeostasis in vivo, albeit it still remains to be determined whether this relation is causal in nature.
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Affiliation(s)
- Sunit Mandad
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, 37077, Göttingen, Germany
| | - Raza-Ur Rahman
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Tonatiuh Pena Centeno
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - Ramon O Vidal
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - Hanna Wildhagen
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Burkhard Rammner
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Sarva Keihani
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Felipe Opazo
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Inga Urban
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, 37073, Göttingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University, 37073, Göttingen, Germany
| | - Koray Kirli
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, 37073, Göttingen, Germany
| | - Eva Benito
- Laboratory of Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - André Fischer
- Laboratory of Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Roya Y Yousefi
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
- Max Planck Institute for Biophysical Chemistry, 37073, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University, 37073, Göttingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, 37077, Göttingen, Germany
| | - Stefan Bonn
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany.
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany.
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany.
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075, Göttingen, Germany.
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany.
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CK1α Collaborates with DOUBLETIME to Regulate PERIOD Function in the Drosophila Circadian Clock. J Neurosci 2018; 38:10631-10643. [PMID: 30373768 DOI: 10.1523/jneurosci.0871-18.2018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 10/05/2018] [Accepted: 10/21/2018] [Indexed: 11/21/2022] Open
Abstract
The animal circadian timing system interprets environmental time cues and internal metabolic status to orchestrate circadian rhythms of physiology, allowing animals to perform necessary tasks in a time-of-day-dependent manner. Normal progression of circadian rhythms is dependent on the daily cycling of core transcriptional factors that make up cell-autonomous molecular oscillators. In Drosophila, PERIOD (PER), TIMELESS (TIM), CLOCK (CLK), and CYCLE (CYC) are core clock proteins that function in a transcriptional-translational feedback mechanism to regulate the circadian transcriptome. Posttranslational modifications of core clock proteins provide precise temporal control over when they are active as regulators of clock-controlled genes. In particular, phosphorylation is a key regulatory mechanism that dictates the subcellular localization, stability, and transcriptional activity of clock proteins. Previously, casein kinase 1α (CK1α) has been identified as a kinase that phosphorylates mammalian PER1 and modulates its stability, but the mechanisms by which it modulates PER protein stability is still unclear. Using Drosophila as a model, we show that CK1α has an overall function of speeding up PER metabolism and is required to maintain the 24 h period of circadian rhythms. Our results indicate that CK1α collaborates with the key clock kinase DOUBLETIME (DBT) in both the cytoplasm and the nucleus to regulate the timing of PER-dependent repression of the circadian transcriptome. Specifically, we observe that CK1α promotes PER nuclear localization by antagonizing the activity of DBT to inhibit PER nuclear translocation. Furthermore, CK1α enhances DBT-dependent PER phosphorylation and degradation once PER moves into the nucleus.SIGNIFICANCE STATEMENT Circadian clocks are endogenous timers that integrate environmental signals to impose temporal control over organismal physiology over the 24 h day/night cycle. To maintain the 24 h period length of circadian clocks and to ensure that circadian rhythms are in synchrony with the external environment, key proteins that make up the molecular oscillator are extensively regulated by phosphorylation to ensure that they perform proper time-of-day-specific functions. Casein kinase 1α (CK1α) has previously been identified as a kinase that phosphorylates mammalian PERIOD (PER) proteins to promote their degradation, but the mechanism by which it modulates PER stability is unclear. In this study, we characterize the mechanisms by which CK1α interacts with DOUBLETIME (DBT) to achieve the overall function of speeding up PER metabolism and to ensure proper time-keeping.
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41
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Fu J, Dang Y, Counter C, Liu Y. Codon usage regulates human KRAS expression at both transcriptional and translational levels. J Biol Chem 2018; 293:17929-17940. [PMID: 30275015 DOI: 10.1074/jbc.ra118.004908] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/17/2018] [Indexed: 12/14/2022] Open
Abstract
KRAS and HRAS are highly homologous oncogenic Ras GTPase family members that are mutated in a wide spectrum of human cancers. Despite having high amino acid identity, KRAS and HRAS have very different codon usage biases: the HRAS gene contains many common codons, and KRAS is enriched for rare codons. Rare codons in KRAS suppress its protein expression, which has been shown to affect both normal and cancer biology in mammals. Here, using HRAS or KRAS expression in different human cell lines and in vitro transcription and translation assays, we show that KRAS rare codons inhibit both translation efficiency and transcription and that the contribution of these two processes varies among different cell lines. We observed that codon usage regulates mRNA translation efficiency such that WT KRAS mRNA is poorly translated. On the other hand, common codons increased transcriptional rates by promoting activating histone modifications and recruitment of transcriptional coactivators. Finally, we found that codon usage also influences KRAS protein conformation, likely because of its effect on co-translational protein folding. Together, our results reveal that codon usage has multidimensional effects on protein expression, ranging from effects on transcription to protein folding in human cells.
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Affiliation(s)
- Jingjing Fu
- From the Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Christopher Counter
- Department of Pharmacology and Cancer Biology, School of Medicine, Duke University, Durham, North Carolina 27708
| | - Yi Liu
- From the Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235.
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42
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Castellana S, Mazza T, Capocefalo D, Genov N, Biagini T, Fusilli C, Scholkmann F, Relógio A, Hogenesch JB, Mazzoccoli G. Systematic Analysis of Mouse Genome Reveals Distinct Evolutionary and Functional Properties Among Circadian and Ultradian Genes. Front Physiol 2018; 9:1178. [PMID: 30190679 PMCID: PMC6115496 DOI: 10.3389/fphys.2018.01178] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/06/2018] [Indexed: 02/02/2023] Open
Abstract
In living organisms, biological clocks regulate 24 h (circadian) molecular, physiological, and behavioral rhythms to maintain homeostasis and synchrony with predictable environmental changes, in particular with those induced by Earth’s rotation on its axis. Harmonics of these circadian rhythms having periods of 8 and 12 h (ultradian) have been documented in several species. In mouse liver, harmonics of the 24-h period of gene transcription hallmarked genes oscillating with a frequency two or three times faster than circadian periodicity. Many of these harmonic transcripts enriched pathways regulating responses to environmental stress and coinciding preferentially with subjective dawn and dusk. At this time, the evolutionary history of genes with rhythmic expression is still poorly known and the role of length-of-day changes due to Earth’s rotation speed decrease over the last four billion years is totally ignored. We hypothesized that ultradian and stress anticipatory genes would be more evolutionarily conserved than circadian genes and background non-oscillating genes. To investigate this issue, we performed broad computational analyses of genes/proteins oscillating at different frequency ranges across several species and showed that ultradian genes/proteins, especially those oscillating with a 12-h periodicity, are more likely to be of ancient origin and essential in mice. In summary, our results show that genes with ultradian transcriptional patterns are more likely to be phylogenetically conserved and associated with the primeval and inevitable dawn/dusk transitions.
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Affiliation(s)
- Stefano Castellana
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Daniele Capocefalo
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Nikolai Genov
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin and Humboldt University of Berlin, Berlin, Germany.,Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tommaso Biagini
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Caterina Fusilli
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Felix Scholkmann
- Research Office for Complex Physical and Biological Systems (ROCoS), Zürich, Switzerland.,Department of Neonatology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin and Humboldt University of Berlin, Berlin, Germany.,Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - John B Hogenesch
- Divisions of Human Genetics and Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Gianluigi Mazzoccoli
- Division of Internal Medicine and Chronobiology Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
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Zhou Z, Dang Y, Zhou M, Yuan H, Liu Y. Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation. eLife 2018; 7:33569. [PMID: 29547124 PMCID: PMC5869017 DOI: 10.7554/elife.33569] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022] Open
Abstract
Codon usage biases are found in all genomes and influence protein expression levels. The codon usage effect on protein expression was thought to be mainly due to its impact on translation. Here, we show that transcription termination is an important driving force for codon usage bias in eukaryotes. Using Neurospora crassa as a model organism, we demonstrated that introduction of rare codons results in premature transcription termination (PTT) within open reading frames and abolishment of full-length mRNA. PTT is a wide-spread phenomenon in Neurospora, and there is a strong negative correlation between codon usage bias and PTT events. Rare codons lead to the formation of putative poly(A) signals and PTT. A similar role for codon usage bias was also observed in mouse cells. Together, these results suggest that codon usage biases co-evolve with the transcription termination machinery to suppress premature termination of transcription and thus allow for optimal gene expression.
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Affiliation(s)
- Zhipeng Zhou
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Haiyan Yuan
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, United States
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44
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Lu YW, Chiu TS. Factors affecting synonymous codon usage of housekeeping genes in Drosophila melanogaster. ACTA BIOLOGICA HUNGARICA 2018; 69:58-71. [PMID: 29575916 DOI: 10.1556/018.68.2018.1.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Housekeeping genes (HK genes) are required for cell survival and the maintenance of basic cellular functions. The investigation of factors affecting codon usage patterns in HK genes of insects can help in understanding the molecular evolution of insects and aid the development of insect pest management strategies. In this study, we employed bioinformatics approaches to analyze the codon usage bias (CUB) of HK genes in the insect model organism, Drosophila melanogaster. A comparison of CUB between 1107 HK genes and 1084 high tissue specificity genes suggested that HK genes have higher CUB in D. melanogaster. In addition, we found that CUB inversely correlates with the non-synonymous substitution rate of HK genes. Therefore, we attempted to identify the factors that potentially influence the codon usage pattern of HK genes. Our results suggest that mutation pressure and natural selection highly correlate with CUB in the HK genes of D. melanogaster and that two topological properties of HK proteins (proportion of protein interacting length and protein connectivity) also correlate with CUB in the HK genes of D. melanogaster. This study provides insight into CUB in the HK genes of D. melanogaster, and the results can support future investigations of potential applications in agricultural and biomedical field.
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Affiliation(s)
- Yi Wen Lu
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Tai Sheng Chiu
- Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
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45
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Zhao F, Yu CH, Liu Y. Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells. Nucleic Acids Res 2017; 45:8484-8492. [PMID: 28582582 PMCID: PMC5737824 DOI: 10.1093/nar/gkx501] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/26/2017] [Indexed: 11/14/2022] Open
Abstract
Codon usage biases are found in all eukaryotic and prokaryotic genomes and have been proposed to regulate different aspects of translation process. Codon optimality has been shown to regulate translation elongation speed in fungal systems, but its effect on translation elongation speed in animal systems is not clear. In this study, we used a Drosophila cell-free translation system to directly compare the velocity of mRNA translation elongation. Our results demonstrate that optimal synonymous codons speed up translation elongation while non-optimal codons slow down translation. In addition, codon usage regulates ribosome movement and stalling on mRNA during translation. Finally, we show that codon usage affects protein structure and function in vitro and in Drosophila cells. Together, these results suggest that the effect of codon usage on translation elongation speed is a conserved mechanism from fungi to animals that can affect protein folding in eukaryotic organisms.
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Affiliation(s)
- Fangzhou Zhao
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Chien-Hung Yu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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46
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Seligmann H, Warthi G. Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes. Comput Struct Biotechnol J 2017; 15:412-424. [PMID: 28924459 PMCID: PMC5591391 DOI: 10.1016/j.csbj.2017.08.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/20/2017] [Accepted: 08/05/2017] [Indexed: 12/14/2022] Open
Abstract
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5'-ZXX-3'/5'-XXZ-3').
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Affiliation(s)
- Hervé Seligmann
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France
- Dept. Ecol Evol Behav, Alexander Silberman Inst Life Sci, The Hebrew University of Jerusalem, IL-91904 Jerusalem, Israel
| | - Ganesh Warthi
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France
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47
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Millius A, Ueda HR. Systems Biology-Derived Discoveries of Intrinsic Clocks. Front Neurol 2017; 8:25. [PMID: 28220104 PMCID: PMC5292584 DOI: 10.3389/fneur.2017.00025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/17/2017] [Indexed: 12/19/2022] Open
Abstract
A systems approach to studying biology uses a variety of mathematical, computational, and engineering tools to holistically understand and model properties of cells, tissues, and organisms. Building from early biochemical, genetic, and physiological studies, systems biology became established through the development of genome-wide methods, high-throughput procedures, modern computational processing power, and bioinformatics. Here, we highlight a variety of systems approaches to the study of biological rhythms that occur with a 24-h period-circadian rhythms. We review how systems methods have helped to elucidate complex behaviors of the circadian clock including temperature compensation, rhythmicity, and robustness. Finally, we explain the contribution of systems biology to the transcription-translation feedback loop and posttranslational oscillator models of circadian rhythms and describe new technologies and "-omics" approaches to understand circadian timekeeping and neurophysiology.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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