Codon usage bias controls mRNA and protein abundance in trypanosomatids
Protein abundance differs from a few to millions of copies per cell. Trypanosoma brucei presents an excellent model for studies on codon bias and differential gene expression because transcription is broadly unregulated and uniform across the genome. T. brucei is also a major human and animal protoz...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2018-03-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/32496 |
| _version_ | 1797693149348364288 |
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| author | Laura Jeacock Joana Faria David Horn |
| author_facet | Laura Jeacock Joana Faria David Horn |
| author_sort | Laura Jeacock |
| collection | DOAJ |
| description | Protein abundance differs from a few to millions of copies per cell. Trypanosoma brucei presents an excellent model for studies on codon bias and differential gene expression because transcription is broadly unregulated and uniform across the genome. T. brucei is also a major human and animal protozoal pathogen. Here, an experimental assessment, using synthetic reporter genes, revealed that GC3 codons have a major positive impact on both mRNA and protein abundance. Our estimates of relative expression, based on coding sequences alone (codon usage and sequence length), are within 2-fold of the observed values for the majority of measured cellular mRNAs (n > 7000) and proteins (n > 2000). Our estimates also correspond with expression measures from published transcriptome and proteome datasets from other trypanosomatids. We conclude that codon usage is a key factor affecting global relative mRNA and protein expression in trypanosomatids and that relative abundance can be effectively estimated using only protein coding sequences. |
| first_indexed | 2024-03-12T02:39:24Z |
| format | Article |
| id | doaj.art-79e9ebb5253f460ebae2af929051bfef |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-03-12T02:39:24Z |
| publishDate | 2018-03-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-79e9ebb5253f460ebae2af929051bfef2023-09-04T09:06:44ZengeLife Sciences Publications LtdeLife2050-084X2018-03-01710.7554/eLife.32496Codon usage bias controls mRNA and protein abundance in trypanosomatidsLaura Jeacock0Joana Faria1David Horn2https://orcid.org/0000-0001-5173-9284Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United KingdomWellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United KingdomWellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United KingdomProtein abundance differs from a few to millions of copies per cell. Trypanosoma brucei presents an excellent model for studies on codon bias and differential gene expression because transcription is broadly unregulated and uniform across the genome. T. brucei is also a major human and animal protozoal pathogen. Here, an experimental assessment, using synthetic reporter genes, revealed that GC3 codons have a major positive impact on both mRNA and protein abundance. Our estimates of relative expression, based on coding sequences alone (codon usage and sequence length), are within 2-fold of the observed values for the majority of measured cellular mRNAs (n > 7000) and proteins (n > 2000). Our estimates also correspond with expression measures from published transcriptome and proteome datasets from other trypanosomatids. We conclude that codon usage is a key factor affecting global relative mRNA and protein expression in trypanosomatids and that relative abundance can be effectively estimated using only protein coding sequences.https://elifesciences.org/articles/32496Leishmaniapost-transcriptionsynonymoustranslationTrypanosomabrucei |
| spellingShingle | Laura Jeacock Joana Faria David Horn Codon usage bias controls mRNA and protein abundance in trypanosomatids eLife Leishmania post-transcription synonymous translation Trypanosoma brucei |
| title | Codon usage bias controls mRNA and protein abundance in trypanosomatids |
| title_full | Codon usage bias controls mRNA and protein abundance in trypanosomatids |
| title_fullStr | Codon usage bias controls mRNA and protein abundance in trypanosomatids |
| title_full_unstemmed | Codon usage bias controls mRNA and protein abundance in trypanosomatids |
| title_short | Codon usage bias controls mRNA and protein abundance in trypanosomatids |
| title_sort | codon usage bias controls mrna and protein abundance in trypanosomatids |
| topic | Leishmania post-transcription synonymous translation Trypanosoma brucei |
| url | https://elifesciences.org/articles/32496 |
| work_keys_str_mv | AT laurajeacock codonusagebiascontrolsmrnaandproteinabundanceintrypanosomatids AT joanafaria codonusagebiascontrolsmrnaandproteinabundanceintrypanosomatids AT davidhorn codonusagebiascontrolsmrnaandproteinabundanceintrypanosomatids |