Duplication of Drosophila melanogaster mitochondrial EF-Tu: pre-adaptation to T-arm truncation and exclusion of bulky aminoacyl residues

Translation elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA (aa-tRNA) to ribosomes in protein synthesis. EF-Tu generally recognizes aminoacyl moieties and acceptor- and T-stems of aa-tRNAs. However, nematode mitochondrial (mt) tRNAs frequently lack all or part of the T-arm that is recognized by canonical EF-Tu. We previously reported that two distinct EF-Tu species, EF-Tu1 and EF-Tu2, respectively, recognize mt tRNAs lacking T-arms and D-arms in the mitochondria of the chromadorean nematode Caenorhabditis elegans. C. elegans EF-Tu2 specifically recognizes the seryl moiety of serylated D-armless tRNAs. Mitochondria of the enoplean nematode Trichinella possess three structural types of tRNAs: T-armless tRNAs, D-armless tRNAs, and cloverleaf tRNAs with a short T-arm. Trichinella mt EF-Tu1 binds to all three types and EF-Tu2 binds only to D-armless Ser-tRNAs, showing an evolutionary intermediate state from canonical EF-Tu to chromadorean nematode (e.g. C. elegans) EF-Tu species. We report here that two EF-Tu species also participate in Drosophila melanogaster mitochondria. Both D. melanogaster EF-Tu1 and EF-Tu2 bound to cloverleaf and D-armless tRNAs. D. melanogaster EF-Tu1 has the ability to recognize T-armless tRNAs that do not evidently exist in D. melanogaster mitochondria, but do exist in related arthropod species. In addition, D. melanogaster EF-Tu2 preferentially bound to aa-tRNAs carrying small amino acids, but not to aa-tRNAs carrying bulky amino acids. These results suggest that the Drosophila mt translation system could be another intermediate state between the canonical and nematode mitochondria-type translation systems.

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Translation elongation factor EF1α1 interacts with ZAD domains of transcription factors from Drosophila melanogaster

Molecular Biology ◽

10.1134/s002689331606025x ◽

2016 ◽

Vol 50 (6) ◽

pp. 895-899

Author(s):

N. A. Zolotarev ◽

O. G. Maksimenko ◽

Yu. V. Shidlovskii ◽

P. G. Georgiev ◽

A. N. Bonchuk

Keyword(s):

Drosophila Melanogaster ◽

Transcription Factors ◽

Elongation Factor ◽

Translation Elongation Factor ◽

Translation Elongation

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Engineering Translation Components Improve Incorporation of Exotic Amino Acids

International Journal of Molecular Sciences ◽

10.3390/ijms20030522 ◽

2019 ◽

Vol 20 (3) ◽

pp. 522 ◽

Cited By ~ 4

Author(s):

Takayuki Katoh ◽

Hiroaki Suga

Keyword(s):

Amino Acids ◽

Genetic Code ◽

Active Site ◽

Structural Characteristics ◽

Elongation Factor ◽

Lower Affinity ◽

Nonsense Codon ◽

Nascent Chain ◽

Translation Systems ◽

Incorporation Efficiency

Methods of genetic code manipulation, such as nonsense codon suppression and genetic code reprogramming, have enabled the incorporation of various nonproteinogenic amino acids into the peptide nascent chain. However, the incorporation efficiency of such amino acids largely varies depending on their structural characteristics. For instance, l-α-amino acids with artificial, bulky side chains are poorer substrates for ribosomal incorporation into the nascent peptide chain, mainly owing to the lower affinity of their aminoacyl-tRNA toward elongation factor-thermo unstable (EF-Tu). Phosphorylated Ser and Tyr are also poorer substrates for the same reason; engineering EF-Tu has turned out to be effective in improving their incorporation efficiencies. On the other hand, exotic amino acids such as d-amino acids and β-amino acids are even poorer substrates owing to their low affinity to EF-Tu and poor compatibility to the ribosome active site. Moreover, their consecutive incorporation is extremely difficult. To solve these problems, the engineering of ribosomes and tRNAs has been executed, leading to successful but limited improvement of their incorporation efficiency. In this review, we comprehensively summarize recent attempts to engineer the translation systems, resulting in a significant improvement of the incorporation of exotic amino acids.

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Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction

Nature Communications ◽

10.1038/s41467-021-27399-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Hongxia Zhao ◽

Wenlong Ding ◽

Jia Zang ◽

Yang Yang ◽

Chao Liu ◽

...

Keyword(s):

Amino Acids ◽

Unnatural Amino Acids ◽

Background Activity ◽

Trna Synthetase ◽

Translation System ◽

Aminoacyl Trna Synthetase ◽

E Coli ◽

Natural Amino Acids ◽

Translation Systems ◽

Cognate Trna

AbstractSite-specific incorporation of unnatural amino acids (UAAs) with similar incorporation efficiency to that of natural amino acids (NAAs) and low background activity is extremely valuable for efficient synthesis of proteins with diverse new chemical functions and design of various synthetic auxotrophs. However, such efficient translation systems remain largely unknown in the literature. Here, we describe engineered chimeric phenylalanine systems that dramatically increase the yield of proteins bearing UAAs, through systematic engineering of the aminoacyl-tRNA synthetase and its respective cognate tRNA. These engineered synthetase/tRNA pairs allow single-site and multi-site incorporation of UAAs with efficiencies similar to those of NAAs and high fidelity. In addition, using the evolved chimeric phenylalanine system, we construct a series of E. coli strains whose growth is strictly dependent on exogenously supplied of UAAs. We further show that synthetic auxotrophic cells can grow robustly in living mice when UAAs are supplemented.

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Requirements for branched chain amino acids and their interactions in the nematode Caenorhabditis elegans

Nematology ◽

10.1163/156854100509411 ◽

2000 ◽

Vol 2 (5) ◽

pp. 501-506 ◽

Cited By ~ 4

Author(s):

Dalia Perelman ◽

Nancy Lu

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Caenorhabditis Elegans ◽

Branched Chain Amino Acids ◽

Nematode Caenorhabditis Elegans ◽

Optimal Range ◽

C Elegans ◽

Branched Chain Amino Acid ◽

High Concentrations ◽

Branched Chain

AbstractBranched chain amino acid (BCAA) requirements and their interactions were studied in the nematode Caenorhabditis elegans. Optimal, deficiency and toxic levels affecting nematode population growth were determined for each of the three BCAAs. The optimal range for leucine was 0.72-2.8; for isoleucine, 0.86-1.7; and for valine, 0.51-4.1 mg ml-1. Leucine at high concentrations was toxic. When isoleucine and valine were both added at high concentrations, they also exerted a marked toxic effect. The interactions of the branched chain amino acids found among vertebrate animals were not observed in C. elegans. Les besoins relatifs aux amino-acides en chaîne ramifiée et leurs interactions chez le nématode Caenorhabditis elegans - Les besoins relatifs aux amino-acides en chaîne ramifiée (BCAA) et leurs interactions ont été étudiés chez le nématode Caenorhabditis elegans. Les niveaux optimal, de déficience et toxique affectant la croissance de la population du nématode ont été déterminés pour chacune des BCAA. L'optimum est, pour la leucine de 0,72 à 2,8, pour l'isoleucine de 0,86 à 1,7 et pour la valine de 0,51 à 4,1 mg ml-1. A forte concentration la leucine est toxique. Si l'isoleucine et la valine sont ajoutées à forte concentration elles exercent également une action toxique prononcée. Les interactions entre BCAA observées chez les vertébrés ne l'ont pas été chez les C. elegans.

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Protein homeostasis is maintained by proteasomes containing PSMB9 induced by EEF1A2 upon mitochondrial stress

10.1101/2021.12.23.473808 ◽

2021 ◽

Author(s):

Minji Kim ◽

Lukasz Samluk ◽

Tomasz Maciej Stępkowski ◽

Ida Suppanz ◽

Remigiusz Adam Serwa ◽

...

Keyword(s):

Mitochondrial Dysfunction ◽

Elongation Factor ◽

Small Heat Shock Protein ◽

Therapeutic Strategies ◽

Proteasome Activity ◽

Protein Homeostasis ◽

Translation Elongation Factor ◽

Translation Elongation ◽

C Elegans ◽

Age Related

Perturbed proteostasis and mitochondrial dysfunction are often associated with age-related diseases such as Alzheimer′s and Parkinson′s diseases. However, the link between them remains incompletely understood. Mitochondrial dysfunction causes proteostasis imbalance, and cells respond to restore proteostasis by increasing proteasome activity and molecular chaperons in yeast and C. elegans. Here, we demonstrate the presence of similar responses in humans. Mitochondrial dysfunction upregulates a small heat shock protein HSPB1 and an immunoproteasome subunit PSMB9 leading to an increase in proteasome activity. HSPB1 and PSMB9 are required to prevent protein aggregation upon mitochondrial dysfunction. Moreover, PSMB9 expression is dependent on a translation elongation factor EEF1A2, and PSMB9-containing proteasomes are located near mitochondria, enabling fast local degradation of aberrant proteins. Our findings put a step forward in understanding the stress response triggered by mitochondrial dysfunction, and may be useful for therapeutic strategies to prevent or delay the onset of age-related diseases and attenuate their progression.

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A protein extension to shorten RNA: elongated elongation factor-Tu recognizes the D-arm of T-armless tRNAs in nematode mitochondria

Biochemical Journal ◽

10.1042/bj20060781 ◽

2006 ◽

Vol 399 (2) ◽

pp. 249-256 ◽

Cited By ~ 17

Author(s):

Masayuki Sakurai ◽

Yoh-ichi Watanabe ◽

Kimitsuna Watanabe ◽

Takashi Ohtsuki

Keyword(s):

Rna Binding ◽

Rna Binding Proteins ◽

Elongation Factor ◽

Binding Activity ◽

Translation System ◽

Elongation Factor Tu ◽

Mitochondrial Translation ◽

Recognition Mechanism ◽

C Elegans ◽

C Terminus

Nematode mitochondria possess extremely truncated tRNAs. Of 22 tRNAs, 20 lack the entire T-arm. The T-arm is necessary for the binding of canonical tRNAs and EF (elongation factor)-Tu (thermo-unstable). The nematode mitochondrial translation system employs two different EF-Tu factors named EF-Tu1 and EF-Tu2. Our previous study showed that nematode Caenorhabditis elegans EF-Tu1 binds specifically to T-armless tRNA. C. elegans EF-Tu1 has a 57-amino acid C-terminal extension that is absent from canonical EF-Tu, and the T-arm-binding residues of canonical EF-Tu are not conserved. In this study, the recognition mechanism of T-armless tRNA by EF-Tu1 was investigated. Both modification interference assays and primer extension analysis of cross-linked ternary complexes revealed that EF-Tu1 interacts not only with the tRNA acceptor stem but also with the D-arm. This is the first example of an EF-Tu recognizing the D-arm of a tRNA. The binding activity of EF-Tu1 was impaired by deletion of only 14 residues from the C-terminus, indicating that the C-terminus of EF-Tu1 is required for its binding to T-armless tRNA. These results suggest that C. elegans EF-Tu1 recognizes the D-arm instead of the T-arm by a mechanism involving its C-terminal region. This study sheds light on the co-evolution of RNA and RNA-binding proteins in nematode mitochondria.

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Apoptosis and development

Essays in Biochemistry ◽

10.1042/bse0390011 ◽

2003 ◽

Vol 39 ◽

pp. 11-24 ◽

Cited By ~ 6

Author(s):

Justin V McCarthy

Keyword(s):

Drosophila Melanogaster ◽

Mammalian Cells ◽

Cell Number ◽

Model Organisms ◽

Biological Processes ◽

Nematode Caenorhabditis Elegans ◽

Apoptotic Pathway ◽

Genetic Pathways ◽

Evolutionarily Conserved ◽

Multicellular Organisms

Apoptosis is an evolutionarily conserved process used by multicellular organisms to developmentally regulate cell number or to eliminate cells that are potentially detrimental to the organism. The large diversity of regulators of apoptosis in mammalian cells and their numerous interactions complicate the analysis of their individual functions, particularly in development. The remarkable conservation of apoptotic mechanisms across species has allowed the genetic pathways of apoptosis determined in lower species, such as the nematode Caenorhabditis elegans and the fruitfly Drosophila melanogaster, to act as models for understanding the biology of apoptosis in mammalian cells. Though many components of the apoptotic pathway are conserved between species, the use of additional model organisms has revealed several important differences and supports the use of model organisms in deciphering complex biological processes such as apoptosis.

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How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans?

Biochemical Society Transactions ◽

10.1042/bst20190944 ◽

2020 ◽

Vol 48 (3) ◽

pp. 1019-1034 ◽

Cited By ~ 1

Author(s):

Rachel M. Woodhouse ◽

Alyson Ashe

Keyword(s):

Histone Modifications ◽

Molecular Mechanisms ◽

Epigenetic Inheritance ◽

Nematode Caenorhabditis Elegans ◽

Histone Methyltransferases ◽

Transgenerational Epigenetic Inheritance ◽

C Elegans ◽

Recent Developments ◽

Gene Regulatory

Gene regulatory information can be inherited between generations in a phenomenon termed transgenerational epigenetic inheritance (TEI). While examples of TEI in many animals accumulate, the nematode Caenorhabditis elegans has proven particularly useful in investigating the underlying molecular mechanisms of this phenomenon. In C. elegans and other animals, the modification of histone proteins has emerged as a potential carrier and effector of transgenerational epigenetic information. In this review, we explore the contribution of histone modifications to TEI in C. elegans. We describe the role of repressive histone marks, histone methyltransferases, and associated chromatin factors in heritable gene silencing, and discuss recent developments and unanswered questions in how these factors integrate with other known TEI mechanisms. We also review the transgenerational effects of the manipulation of histone modifications on germline health and longevity.

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