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AYKANAT S, TÜRKTAŞ M. Divergent proteomic profiles of opium poppy cultivars. Turk J Biol 2024; 48:80-90. [PMID: 38665780 PMCID: PMC11042869 DOI: 10.55730/1300-0152.2684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/27/2024] [Accepted: 02/06/2024] [Indexed: 04/28/2024] Open
Abstract
We examined the proteomic profiles of three registered opium poppy cultivars (Papaver somniferum L.) with varying alkaloid contents. The study was conducted on both the stem and capsule organs. A high number of differentially expressed proteins (DEPs) were identified between the cultivars and the organs. We analyzed DEPs for their contribution in GO terms and KEGG pathways. The upregulated DEPs were significantly enriched in photosynthesis and translation for morphine-rich and noscapine-rich cultivars, respectively. The data indicated that photosynthesis is crucial for benzylisoquinoline alkaloid (BIA) biosynthesis, but different processes are also effective in morphine and noscapine biosynthesis, which occur at different branches in the biosynthetic pathway. The proteomics profiles revealed that energy demand is more effective in morphine biosynthesis, while translational control plays a leading role in noscapine biosynthesis. This study represents the first report demonstrating organ-based and cultivar-based protein expression differences in mature poppy plants.
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Affiliation(s)
- Setenay AYKANAT
- Department of Biology, Faculty of Science, Gazi University, Ankara,
Turkiye
| | - Mine TÜRKTAŞ
- Department of Biology, Faculty of Science, Gazi University, Ankara,
Turkiye
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2
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Goldkamp AK, Hagen DE. Implications of tRNA abundance on translation elongation across bovine tissues. Front Genet 2023; 14:1308048. [PMID: 38174049 PMCID: PMC10763252 DOI: 10.3389/fgene.2023.1308048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction: Translation is a crucial stage of gene expression. It may also act as an additional layer of regulation that plays an important role in gene expression and function. Highly expressed genes are believed to be codon-biased to support increased protein production, in which quickly translated codons correspond to highly abundant tRNAs. Synonymous SNPs, considered to be silent due to the degeneracy of the genetic code, may shift protein abundance and function through alterations in translational efficiency and suboptimal pairing to lowly abundant tRNAs. Methods: Here, we applied Quantitative Mature tRNA sequencing (QuantM-tRNAseq) and ribosome profiling across bovine tissues in order to investigate the relationship between tRNA expression and slowed translation. Results: Moreover, we have identified genes modulated at transcriptional and/or translational levels underlying tissue-specific biological processes. We have also successfully defined pausing sites that depict the regulatory information encoded within the open reading frame of transcripts, which could be related to translation rate and facilitate proper protein folding. This work offers an atlas of distinctive pausing sites across three bovine tissues, which provides an opportunity to predict codon optimality and understand tissue-specific mechanisms of regulating protein synthesis.
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Affiliation(s)
| | - Darren E. Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, United States
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Kejiou NS, Ilan L, Aigner S, Luo E, Tonn T, Ozadam H, Lee M, Cole G, Rabano I, Rajakulendran N, Yee BA, Najafabadi H, Moraes T, Angers S, Yeo G, Cenik C, Palazzo A. Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling. Nucleic Acids Res 2023; 51:6461-6478. [PMID: 37224531 PMCID: PMC10325899 DOI: 10.1093/nar/gkad440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023] Open
Abstract
In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we asked whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic survey of spatially regulated polysome interacting proteins, we identified the glycolytic enzyme Pyruvate Kinase M (PKM) as a cytosolic (i.e. ER-excluded) polysome interactor and investigated how it influences mRNA translation. We discovered that the PKM-polysome interaction is directly regulated by ADP levels-providing a link between carbohydrate metabolism and mRNA translation. By performing enhanced crosslinking immunoprecipitation-sequencing (eCLIP-seq), we found that PKM crosslinks to mRNA sequences that are immediately downstream of regions that encode lysine- and glutamate-enriched tracts. Using ribosome footprint protection sequencing, we found that PKM binding to ribosomes causes translational stalling near lysine and glutamate encoding sequences. Lastly, we observed that PKM recruitment to polysomes is dependent on poly-ADP ribosylation activity (PARylation)-and may depend on co-translational PARylation of lysine and glutamate residues of nascent polypeptide chains. Overall, our study uncovers a novel role for PKM in post-transcriptional gene regulation, linking cellular metabolism and mRNA translation.
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Affiliation(s)
- Nevraj S Kejiou
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Lena Ilan
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Enching Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Muyoung Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Gregory B Cole
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Ines Rabano
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Stephane Angers
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
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Burke PC, Park H, Subramaniam AR. A nascent peptide code for translational control of mRNA stability in human cells. Nat Commun 2022; 13:6829. [PMID: 36369503 PMCID: PMC9652226 DOI: 10.1038/s41467-022-34664-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 11/02/2022] [Indexed: 11/13/2022] Open
Abstract
Stability of eukaryotic mRNAs is associated with their codon, amino acid, and GC content. Yet, coding sequence motifs that predictably alter mRNA stability in human cells remain poorly defined. Here, we develop a massively parallel assay to measure mRNA effects of thousands of synthetic and endogenous coding sequence motifs in human cells. We identify several families of simple dipeptide repeats whose translation triggers mRNA destabilization. Rather than individual amino acids, specific combinations of bulky and positively charged amino acids are critical for the destabilizing effects of dipeptide repeats. Remarkably, dipeptide sequences that form extended β strands in silico and in vitro slowdown ribosomes and reduce mRNA levels in vivo. The resulting nascent peptide code underlies the mRNA effects of hundreds of endogenous peptide sequences in the human proteome. Our work suggests an intrinsic role for the ribosome as a selectivity filter against the synthesis of bulky and aggregation-prone peptides.
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Affiliation(s)
- Phillip C. Burke
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA ,grid.34477.330000000122986657Department of Microbiology, University of Washington, Seattle, WA 98195 USA
| | - Heungwon Park
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - Arvind Rasi Subramaniam
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA ,grid.34477.330000000122986657Department of Microbiology, University of Washington, Seattle, WA 98195 USA
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Leininger SE, Rodriguez J, Vu QV, Jiang Y, Li MS, Deutsch C, O'Brien EP. Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force. Biochemistry 2021; 60:3223-3235. [PMID: 34652913 DOI: 10.1021/acs.biochem.1c00507] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The speed of protein synthesis can dramatically change when consecutively charged residues are incorporated into an elongating nascent protein by the ribosome. The molecular origins of this class of allosteric coupling remain unknown. We demonstrate, using multiscale simulations, that positively charged residues generate large forces that move the P-site amino acid away from the A-site amino acid. Negatively charged residues generate forces of similar magnitude but move the A- and P-sites closer together. These conformational changes, respectively, increase and decrease the transition state barrier height to peptide bond formation, explaining how charged residues mechanochemically alter translation speed. This mechanochemical mechanism is consistent with in vivo ribosome profiling data exhibiting proportionality between translation speed and the number of charged residues, experimental data characterizing nascent chain conformations, and a previously published cryo-EM structure of a ribosome-nascent chain complex containing consecutive lysines. These results expand the role of mechanochemistry in translation and provide a framework for interpreting experimental results on translation speed.
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Affiliation(s)
- Sarah E Leininger
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Judith Rodriguez
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, United States
| | - Quyen V Vu
- Institute of Physics, Polish Academy of Sciences, Warsaw 02-668, Poland
| | - Yang Jiang
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw 02-668, Poland.,Institute for Computational Sciences and Technology, Ho Chi Minh City 700000, Vietnam
| | - Carol Deutsch
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Edward P O'Brien
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States.,Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, United States.,Institute for Computational and Data Sciences, Penn State University, University Park, Pennsylvania 16802, United States
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Patriarca EJ, Cermola F, D’Aniello C, Fico A, Guardiola O, De Cesare D, Minchiotti G. The Multifaceted Roles of Proline in Cell Behavior. Front Cell Dev Biol 2021; 9:728576. [PMID: 34458276 PMCID: PMC8397452 DOI: 10.3389/fcell.2021.728576] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Herein, we review the multifaceted roles of proline in cell biology. This peculiar cyclic imino acid is: (i) A main precursor of extracellular collagens (the most abundant human proteins), antimicrobial peptides (involved in innate immunity), salivary proteins (astringency, teeth health) and cornifins (skin permeability); (ii) an energy source for pathogenic bacteria, protozoan parasites, and metastatic cancer cells, which engage in extracellular-protein degradation to invade their host; (iii) an antistress molecule (an osmolyte and chemical chaperone) helpful against various potential harms (UV radiation, drought/salinity, heavy metals, reactive oxygen species); (iv) a neural metabotoxin associated with schizophrenia; (v) a modulator of cell signaling pathways such as the amino acid stress response and extracellular signal-related kinase pathway; (vi) an epigenetic modifier able to promote DNA and histone hypermethylation; (vii) an inducer of proliferation of stem and tumor cells; and (viii) a modulator of cell morphology and migration/invasiveness. We highlight how proline metabolism impacts beneficial tissue regeneration, but also contributes to the progression of devastating pathologies such as fibrosis and metastatic cancer.
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Affiliation(s)
| | | | | | | | | | | | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics “A. Buzzati Traverso”, Consiglio Nazionale delle Ricerche, Naples, Italy
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