1
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Kroll A, Rousset Y, Hu XP, Liebrand NA, Lercher MJ. Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning. Nat Commun 2023; 14:4139. [PMID: 37438349 DOI: 10.1038/s41467-023-39840-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
The turnover number kcat, a measure of enzyme efficiency, is central to understanding cellular physiology and resource allocation. As experimental kcat estimates are unavailable for the vast majority of enzymatic reactions, the development of accurate computational prediction methods is highly desirable. However, existing machine learning models are limited to a single, well-studied organism, or they provide inaccurate predictions except for enzymes that are highly similar to proteins in the training set. Here, we present TurNuP, a general and organism-independent model that successfully predicts turnover numbers for natural reactions of wild-type enzymes. We constructed model inputs by representing complete chemical reactions through differential reaction fingerprints and by representing enzymes through a modified and re-trained Transformer Network model for protein sequences. TurNuP outperforms previous models and generalizes well even to enzymes that are not similar to proteins in the training set. Parameterizing metabolic models with TurNuP-predicted kcat values leads to improved proteome allocation predictions. To provide a powerful and convenient tool for the study of molecular biochemistry and physiology, we implemented a TurNuP web server.
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Affiliation(s)
- Alexander Kroll
- Institute for Computer Science and Department of Biology, Heinrich Heine University, D-40225, Düsseldorf, Germany
| | - Yvan Rousset
- Institute for Computer Science and Department of Biology, Heinrich Heine University, D-40225, Düsseldorf, Germany
| | - Xiao-Pan Hu
- Institute for Computer Science and Department of Biology, Heinrich Heine University, D-40225, Düsseldorf, Germany
| | - Nina A Liebrand
- Institute for Computer Science and Department of Biology, Heinrich Heine University, D-40225, Düsseldorf, Germany
| | - Martin J Lercher
- Institute for Computer Science and Department of Biology, Heinrich Heine University, D-40225, Düsseldorf, Germany.
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2
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Morohoshi K, Yamazaki T, Kito K, Sato B, Kang W, Hibino T, Yoshida M, Yoshida K, Iwamoto T, Yamada M, Miyado K, Kawano N. Identification of an antibacterial polypeptide in mouse seminal vesicle secretions. J Reprod Immunol 2021; 148:103436. [PMID: 34700103 DOI: 10.1016/j.jri.2021.103436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022]
Abstract
In both men and women, pathogenic bacteria enter the reproductive tract and cause harmful symptoms. Intrauterine and oviductal inflammation after copulation may have severe effects, such as infertility, implantation failure, oviduct obstruction, and robust life-threatening bacterial infection. Human seminal plasma is considered to be protective against bacterial infection. Among its components, Semenogelin-I/-II proteins are digested to function as bactericidal factors; however, their sequences are not conserved in mammals. Therefore, alternative antibacterial (bactericidal and/or bacteriostatic) systems may exist across mammals. In this study, we examined the antibacterial activity in the seminal plasma of mice lacking a gene cluster encoding Semenogelin-I/-II counterparts. Even in the absence of the majority of seminal proteins, antibacterial activity remained in the seminal plasma. Moreover, a combination of gel chromatography and liquid chromatography coupled with tandem mass spectrometry revealed that the prostate and testis expressed 4 protein as a novel antibacterial (specifically, bacteriostatic) protein, the sequence of which is broadly conserved across mammals. Our results provide the first evidence of a bacteriostatic protein that is widely present in the mammalian seminal plasma.
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Affiliation(s)
- Kazunori Morohoshi
- Laboratory of Regulatory Biology, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama, Kawasaki, Kanagawa, 214-8571, Japan
| | - Takeo Yamazaki
- Laboratory of Regulatory Biology, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama, Kawasaki, Kanagawa, 214-8571, Japan
| | - Keiji Kito
- Laboratory of Proteomics, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama, Kawasaki, Kanagawa, 214-8571, Japan
| | - Ban Sato
- Laboratory of Regulatory Biology, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama, Kawasaki, Kanagawa, 214-8571, Japan
| | - Woojin Kang
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Taku Hibino
- Faculty of Education, Saitama University, 255 Shimo-Okubo, Sakura, Saitama City, Saitama, 338-8570, Japan
| | - Manabu Yoshida
- Misaki Marine Biological Station, School of Science, the University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa, 238-0225, Japan
| | - Kaoru Yoshida
- Faculty of Biomedical Engineering, Toin University of Yokohama, 1614 Kurogane, Aoba, Yokohama, Kanagawa, 225-8503, Japan
| | - Teruaki Iwamoto
- Division of Male Infertility, Center for Human Reproduction, Sanno Hospital, International University of Health and Welfare, 8-10-21 Akasaka, Minato, Tokyo, 107-0052, Japan
| | - Mitsutoshi Yamada
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Kenji Miyado
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Natsuko Kawano
- Laboratory of Regulatory Biology, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama, Kawasaki, Kanagawa, 214-8571, Japan.
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3
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Xiberras J, Klein M, Prosch C, Malubhoy Z, Nevoigt E. Anaplerotic reactions active during growth of Saccharomyces cerevisiae on glycerol. FEMS Yeast Res 2021; 20:5672635. [PMID: 31821485 DOI: 10.1093/femsyr/foz086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/09/2019] [Indexed: 02/01/2023] Open
Abstract
Anaplerotic reactions replenish TCA cycle intermediates during growth. In Saccharomyces cerevisiae, pyruvate carboxylase and the glyoxylate cycle have been experimentally identified to be the main anaplerotic routes during growth on glucose (C6) and ethanol (C2), respectively. The current study investigates the importance of the two isoenzymes of pyruvate carboxylase (PYC1 and PYC2) and one of the key enzymes of the glyoxylate cycle (ICL1) for growth on glycerol (C3) as a sole carbon source. As the wild-type strains of the CEN.PK family are unable to grow in pure synthetic glycerol medium, a reverse engineered derivative showing a maximum specific growth rate of 0.14 h-1 was used as the reference strain. While the deletion of PYC1 reduced the maximum specific growth rate by about 38%, the deletion of PYC2 had no significant impact, neither in the reference strain nor in the pyc1Δ mutant. The deletion of ICL1 only marginally reduced growth of the reference strain but further decreased the growth rate of the pyc1 deletion strain by 20%. Interestingly, the triple deletion (pyc1Δ pyc2Δ icl1Δ) did not show any growth. Therefore, both the pyruvate carboxylase and the glyoxylate cycle are involved in anaplerosis during growth on glycerol.
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Affiliation(s)
- Joeline Xiberras
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Celina Prosch
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Zahabiya Malubhoy
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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4
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Chang AYF, Liao BY. Reduced Translational Efficiency of Eukaryotic Genes after Duplication Events. Mol Biol Evol 2021; 37:1452-1461. [PMID: 31904835 DOI: 10.1093/molbev/msz309] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Control of gene expression has been found to be predominantly determined at the level of protein translation. However, to date, reduced expression from duplicated genes in eukaryotes for dosage maintenance has only been linked to transcriptional control involving epigenetic mechanisms. Here, we hypothesize that dosage maintenance following gene duplication also involves regulation at the protein level. To test this hypothesis, we compared transcriptome and proteome data of yeast models, Saccharomyces cerevisiae and Schizosaccharomyces pombe, and worm models, Caenorhabditis elegans and Caenorhabditis briggsae, to investigate lineage-specifically duplicated genes. Duplicated genes in both eukaryotic models exhibited a reduced protein-to-mRNA abundance ratio. Moreover, dosage sensitive genes, represented by genes encoding protein complex subunits, reduced their protein-to-mRNA abundance ratios more significantly than the other genes after duplication events. An analysis of ribosome profiling (Ribo-Seq) data further showed that reduced translational efficiency was more prominent for dosage sensitive genes than for the other genes. Meanwhile, no difference in protein degradation rate was associated with duplication events. Translationally repressed duplicated genes were also more likely to be inhibited at the level of transcription. Taken together, these results suggest that translation-mediated dosage control is partially contributed by natural selection and it enhances transcriptional control in maintaining gene dosage after gene duplication events during eukaryotic genome evolution.
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Affiliation(s)
- Andrew Ying-Fei Chang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan, Republic of China
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan, Republic of China
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5
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Dai X, Zhu M. Coupling of Ribosome Synthesis and Translational Capacity with Cell Growth. Trends Biochem Sci 2020; 45:681-692. [DOI: 10.1016/j.tibs.2020.04.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/11/2020] [Accepted: 04/27/2020] [Indexed: 12/31/2022]
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Proteomics insights into the responses of Saccharomyces cerevisiae during mixed-culture alcoholic fermentation with Lachancea thermotolerans. FEMS Microbiol Ecol 2019; 95:5550729. [DOI: 10.1093/femsec/fiz126] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 08/14/2019] [Indexed: 01/25/2023] Open
Abstract
ABSTRACT
The response of Saccharomyces cerevisiae to cocultivation with Lachancea thermotolerans during alcoholic fermentations has been investigated using tandem mass tag (TMT)-based proteomics. At two key time-points, S. cerevisiae was sorted from single S. cerevisiae fermentations and from mixed fermentations using flow cytometry sorting. Results showed that the purity of sorted S. cerevisiae was above 96% throughout the whole mixed-culture fermentation, thereby validating our sorting methodology. By comparing protein expression of S. cerevisiae with and without L. thermotolerans, 26 proteins were identified as significantly regulated proteins at the early death phase (T1), and 32 significantly regulated proteins were identified at the late death phase (T2) of L. thermotolerans in mixed cultures. At T1, proteins involved in endocytosis, increasing nutrient availability, cell rescue and resistance to stresses were upregulated, and proteins involved in proline synthesis and apoptosis were downregulated. At T2, proteins involved in protein synthesis and stress responses were up- and downregulated, respectively. These data indicate that S. cerevisiae was stressed by the presence of L. thermotolerans at T1, using both defensive and fighting strategies to keep itself in a dominant position, and that it at T2 was relieved from stress, perhaps increasing its enzymatic machinery to ensure better survival.
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Xiberras J, Klein M, Nevoigt E. Glycerol as a substrate for Saccharomyces cerevisiae based bioprocesses - Knowledge gaps regarding the central carbon catabolism of this 'non-fermentable' carbon source. Biotechnol Adv 2019; 37:107378. [PMID: 30930107 DOI: 10.1016/j.biotechadv.2019.03.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/14/2022]
Abstract
Glycerol is an interesting alternative carbon source in industrial bioprocesses due to its higher degree of reduction per carbon atom compared to sugars. During the last few years, significant progress has been made in improving the well-known industrial platform organism Saccharomyces cerevisiae with regard to its glycerol utilization capability, particularly in synthetic medium. This provided a basis for future metabolic engineering focusing on the production of valuable chemicals from glycerol. However, profound knowledge about the central carbon catabolism in synthetic glycerol medium is a prerequisite for such incentives. As a matter of fact, the current assumptions about the actual in vivo fluxes active on glycerol as the sole carbon source have mainly been based on omics data collected in complex media or were even deduced from studies with other non-fermentable carbon sources, such as ethanol or acetate. A number of uncertainties have been identified which particularly regard the role of the glyoxylate cycle, the subcellular localization of the respective enzymes, the contributions of mitochondrial transporters and the active anaplerotic reactions under these conditions. The review scrutinizes the current knowledge, highlights the necessity to collect novel experimental data using cells growing in synthetic glycerol medium and summarizes the current state of the art with regard to the production of valuable fermentation products from a carbon source that has been considered so far as 'non-fermentable' for the yeast S. cerevisiae.
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Affiliation(s)
- Joeline Xiberras
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany.
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8
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Tsukada T, Isowa Y, Kito K, Yoshida S, Toneri S, Horiguchi K, Fujiwara K, Yashiro T, Kato T, Kato Y. Identification of TGFβ-induced proteins in non-endocrine mouse pituitary cell line TtT/GF by SILAC-assisted quantitative mass spectrometry. Cell Tissue Res 2019; 376:281-293. [DOI: 10.1007/s00441-018-02989-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 12/29/2018] [Indexed: 01/04/2023]
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9
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Eguchi Y, Makanae K, Hasunuma T, Ishibashi Y, Kito K, Moriya H. Estimating the protein burden limit of yeast cells by measuring the expression limits of glycolytic proteins. eLife 2018; 7:34595. [PMID: 30095406 PMCID: PMC6086662 DOI: 10.7554/elife.34595] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/01/2018] [Indexed: 11/30/2022] Open
Abstract
The ultimate overexpression of a protein could cause growth defects, which are known as the protein burden. However, the expression limit at which the protein-burden effect is triggered is still unclear. To estimate this limit, we systematically measured the overexpression limits of glycolytic proteins in Saccharomyces cerevisiae. The limits of some glycolytic proteins were up to 15% of the total cellular protein. These limits were independent of the proteins’ catalytic activities, a finding that was supported by an in silico analysis. Some proteins had low expression limits that were explained by their localization and metabolic perturbations. The codon usage should be highly optimized to trigger the protein-burden effect, even under strong transcriptional induction. The S–S-bond-connected aggregation mediated by the cysteine residues of a protein might affect its expression limit. Theoretically, only non-harmful proteins could be expressed up to the protein-burden limit. Therefore, we established a framework to distinguish proteins that are harmful and non-harmful upon overexpression. If a cell makes too much of a given protein, it can sometimes cause problems and impair the cell’s growth. Overproducing some proteins may deplete the cell’s limited resources, meaning it does not have enough to make other more essential proteins. This phenomenon is known as the protein burden effect. Theoretically, only harmless proteins can be overproduced up to a level where growth would be impaired in this way. Conversely, if an overproduced protein causes harm before it becomes a burden on resources, scientists must consider other mechanisms to explain the cell’s problems, namely that the protein itself is harmful. Knowing the ultimate level of protein production that could cause the protein burden effect – the protein burden limit – would allow scientists to distinguish between harmful and non-harmful proteins. However, to date, this limit had not been defined for any cell. Eguchi et al. have now tried to estimate the protein burden limit for budding yeast – one of the best-studied experimental organisms. The experiments first focused on enzymes involved in alcoholic fermentation because they were expected to be non-harmful. Some of these enzymes were overproduced to the level were the made up 15% of all the cell’s proteins before they started to cause growth defects. The same results were seen with versions of the enzymes that had been mutated to be less active, leading Eguchi et al. to conclude that this level is the protein burden limit. In other experiments, harmful enzymes could only be overproduced to levels that were far less than this proposed protein burden limit. These enzymes caused problems for the yeast in several ways, including interfering with biochemical reactions and forming large aggregates in the cell. Lastly, Eguchi et al. looked at the yeast’s genetic code and saw that most of its genes seemed to have evolved to specifically limit the production of proteins to a level that would avoid the unwanted protein burden effect. Together these findings establish a framework to clearly distinguish between harmful and non-harmful proteins. This framework will be useful to understand the different reasons why the overproduction of certain proteins, which is seen in neurodegenerative diseases and cancer cells, can cause problems for cells.
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Affiliation(s)
- Yuichi Eguchi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Koji Makanae
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Yuko Ishibashi
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Hisao Moriya
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.,Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
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Marsit S, Leducq JB, Durand É, Marchant A, Filteau M, Landry CR. Evolutionary biology through the lens of budding yeast comparative genomics. Nat Rev Genet 2017; 18:581-598. [DOI: 10.1038/nrg.2017.49] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Okada M, Kusunoki S, Ishibashi Y, Kito K. Proteomics analysis for asymmetric inheritance of preexisting proteins between mother and daughter cells in budding yeast. Genes Cells 2017; 22:591-601. [PMID: 28503907 DOI: 10.1111/gtc.12497] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/29/2017] [Indexed: 11/28/2022]
Abstract
In budding yeast, a mother cell can produce a finite number of daughter cells over its life. The accumulation of a variety of types of damaged components has an impact on the aging process. Asymmetrical inheritance during cell division causes these aberrant intracellular constituents to be retained in mother cells and prevents them from segregating to daughter cells. However, the understanding of asymmetrical inheritance of individual proteins that are damaged or old age, and their relevance to the aging process, has been limited. The aim of this study is to propose a proteomics strategy for asymmetrical inheritance of preexisting proteins between mother and daughter cells. During synchronous culture for one generation, newly synthesized proteins were labeled with stable isotope amino acids to discriminate preexisting proteins originally expressed in mother cells, followed by separation of mother and daughter cells using a conventional method based on biotin labeling. Isotope incorporation ratios for individual proteins were quantified using mass spectrometry. We successfully identified 21 proteins whose preexisting versions were asymmetrically inherited in mother cells, including plasma membrane transporter involved in the aging process and organelle-anchoring proteins related to the stress response to misfolded proteins. Thus, our approach would be useful for making catalog of asymmetrically inherited proteins.
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Affiliation(s)
- Mitsuhiro Okada
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Shunta Kusunoki
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Yuko Ishibashi
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
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12
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Iñiguez LP, Hernández G. The Evolutionary Relationship between Alternative Splicing and Gene Duplication. Front Genet 2017; 8:14. [PMID: 28261262 PMCID: PMC5306129 DOI: 10.3389/fgene.2017.00014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/02/2017] [Indexed: 01/23/2023] Open
Abstract
The protein diversity that exists today has resulted from various evolutionary processes. It is well known that gene duplication (GD) along with the accumulation of mutations are responsible, among other factors, for an increase in the number of different proteins. The gene structure in eukaryotes requires the removal of non-coding sequences, introns, to produce mature mRNAs. This process, known as cis-splicing, referred to here as splicing, is regulated by several factors which can lead to numerous splicing arrangements, commonly designated as alternative splicing (AS). AS, producing several transcripts isoforms form a single gene, also increases the protein diversity. However, the evolution and manner for increasing protein variation differs between AS and GD. An important question is how are patterns of AS affected after a GD event. Here, we review the current knowledge of AS and GD, focusing on their evolutionary relationship. These two processes are now considered the main contributors to the increasing protein diversity and therefore their relationship is a relevant, yet understudied, area of evolutionary study.
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Affiliation(s)
- Luis P Iñiguez
- Programa de Genómica Funcional de Eucariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, México
| | - Georgina Hernández
- Programa de Genómica Funcional de Eucariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, México
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Kito K, Okada M, Ishibashi Y, Okada S, Ito T. A strategy for absolute proteome quantification with mass spectrometry by hierarchical use of peptide-concatenated standards. Proteomics 2016; 16:1457-73. [DOI: 10.1002/pmic.201500414] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/18/2016] [Accepted: 03/24/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Keiji Kito
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Mitsuhiro Okada
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Yuko Ishibashi
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Satoshi Okada
- Department of Biochemistry; Kyushu University Graduate School of Medical Science; Fukuoka Japan
| | - Takashi Ito
- Department of Biochemistry; Kyushu University Graduate School of Medical Science; Fukuoka Japan
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