Elongation factor P (-like) protein and polyproline motifs
Аутори
Parr, MarinaSieber, Alin
Frishman, Dmitrij
Lassak, Jürgen
Остала ауторства
Morić, IvanaĐorđević, Valentina
Конференцијски прилог (Објављена верзија)
,
© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
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Two or more consecutive prolines induce ribosome stalling during translation. In bacteria
the elongation factor P (EF-P) efficiently rescues the ribosome stalling and allows the
protein biosynthesis to continue. A seven amino acids long loop between beta-strands
β3/β4 is crucial for EF-P function. The residue at the tip of the loop is subjected to the
post-translational modifications: lysine is lysylated or arginine is rhamnosylated. We have
demonstrated that only those enzymes that are needed for specific post-translational
modification of the tip are coded in the bacterial genome (EpmA, EpmB and EpmC
proteins for EF-P with lysine and EarP- for those with arginine). Phylogenetic analysis
has also unveiled an invariant proline in the -2 position of the tip of the loop in EF-Ps that
utilize lysine modifications such as Escherichia coli. Bacteria with the arginine modification
like Pseudomonas putida on the contrary have selected against it. Combining these
observations with e...xperimental evidence, we conclude that β3/β4 loop composition is
important for functionalization of EF-P by chemically distinct modifications.
Some bacterial genomes also code the elongation factor P-like (EfpL) protein that shares
the same domain architecture with EF-P and has an extended loop of eight amino acid
residues long. The evolution, sequence and the structure of EfpL protein have been
extensively characterized. Using the assay based on luminescence emission and ribosomal
profiles we have shown that EfpL can also relieve the arrest of the ribosome induced by
polyproline motifs.
We have also observed the negative correlation between the occurrence of the motif in
the proteome of Escherichia coli and its stalling strength measured in luminescence assay.
We hypothesize that motifs that cause strong ribosome stalling are disfavored in the
protein sequences during evolution due to their impact on the dynamics of translation.
Кључне речи:
polyproline motifs / translation / post-translational modifications / evolution / ribosome profiling / ribosome stallingИзвор:
4th Belgrade Bioinformatics Conference, 2023, 4, 73-73Издавач:
- Belgrade : Institute of molecular genetics and genetic engineering
Напомена:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Колекције
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Parr, Marina AU - Sieber, Alin AU - Frishman, Dmitrij AU - Lassak, Jürgen PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2013 AB - Two or more consecutive prolines induce ribosome stalling during translation. In bacteria the elongation factor P (EF-P) efficiently rescues the ribosome stalling and allows the protein biosynthesis to continue. A seven amino acids long loop between beta-strands β3/β4 is crucial for EF-P function. The residue at the tip of the loop is subjected to the post-translational modifications: lysine is lysylated or arginine is rhamnosylated. We have demonstrated that only those enzymes that are needed for specific post-translational modification of the tip are coded in the bacterial genome (EpmA, EpmB and EpmC proteins for EF-P with lysine and EarP- for those with arginine). Phylogenetic analysis has also unveiled an invariant proline in the -2 position of the tip of the loop in EF-Ps that utilize lysine modifications such as Escherichia coli. Bacteria with the arginine modification like Pseudomonas putida on the contrary have selected against it. Combining these observations with experimental evidence, we conclude that β3/β4 loop composition is important for functionalization of EF-P by chemically distinct modifications. Some bacterial genomes also code the elongation factor P-like (EfpL) protein that shares the same domain architecture with EF-P and has an extended loop of eight amino acid residues long. The evolution, sequence and the structure of EfpL protein have been extensively characterized. Using the assay based on luminescence emission and ribosomal profiles we have shown that EfpL can also relieve the arrest of the ribosome induced by polyproline motifs. We have also observed the negative correlation between the occurrence of the motif in the proteome of Escherichia coli and its stalling strength measured in luminescence assay. We hypothesize that motifs that cause strong ribosome stalling are disfavored in the protein sequences during evolution due to their impact on the dynamics of translation. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Elongation factor P (-like) protein and polyproline motifs EP - 73 SP - 73 VL - 4 DO - 978-86-82679-14-1 ER -
@conference{ author = "Parr, Marina and Sieber, Alin and Frishman, Dmitrij and Lassak, Jürgen", year = "2023", abstract = "Two or more consecutive prolines induce ribosome stalling during translation. In bacteria the elongation factor P (EF-P) efficiently rescues the ribosome stalling and allows the protein biosynthesis to continue. A seven amino acids long loop between beta-strands β3/β4 is crucial for EF-P function. The residue at the tip of the loop is subjected to the post-translational modifications: lysine is lysylated or arginine is rhamnosylated. We have demonstrated that only those enzymes that are needed for specific post-translational modification of the tip are coded in the bacterial genome (EpmA, EpmB and EpmC proteins for EF-P with lysine and EarP- for those with arginine). Phylogenetic analysis has also unveiled an invariant proline in the -2 position of the tip of the loop in EF-Ps that utilize lysine modifications such as Escherichia coli. Bacteria with the arginine modification like Pseudomonas putida on the contrary have selected against it. Combining these observations with experimental evidence, we conclude that β3/β4 loop composition is important for functionalization of EF-P by chemically distinct modifications. Some bacterial genomes also code the elongation factor P-like (EfpL) protein that shares the same domain architecture with EF-P and has an extended loop of eight amino acid residues long. The evolution, sequence and the structure of EfpL protein have been extensively characterized. Using the assay based on luminescence emission and ribosomal profiles we have shown that EfpL can also relieve the arrest of the ribosome induced by polyproline motifs. We have also observed the negative correlation between the occurrence of the motif in the proteome of Escherichia coli and its stalling strength measured in luminescence assay. We hypothesize that motifs that cause strong ribosome stalling are disfavored in the protein sequences during evolution due to their impact on the dynamics of translation.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Elongation factor P (-like) protein and polyproline motifs", pages = "73-73", volume = "4", doi = "978-86-82679-14-1" }
Parr, M., Sieber, A., Frishman, D.,& Lassak, J.. (2023). Elongation factor P (-like) protein and polyproline motifs. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 73-73. https://doi.org/978-86-82679-14-1
Parr M, Sieber A, Frishman D, Lassak J. Elongation factor P (-like) protein and polyproline motifs. in 4th Belgrade Bioinformatics Conference. 2023;4:73-73. doi:978-86-82679-14-1 .
Parr, Marina, Sieber, Alin, Frishman, Dmitrij, Lassak, Jürgen, "Elongation factor P (-like) protein and polyproline motifs" in 4th Belgrade Bioinformatics Conference, 4 (2023):73-73, https://doi.org/978-86-82679-14-1 . .