Gene organization and phylum-specific attributes of eukaryotic arginyl-tRNA synthetases

Igloi, Gabor L.

doi:10.1016/j.genrep.2020.100778

Cited by 3 publications

(10 citation statements)

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“…This relies on the accessibility of genome-specific parameters which are lacking for most protists so that the data from closely related organisms was used. Considering the extent of N-terminal variability between arginyl-tRNA synthetases from different species (Igloi 2019), this section of the predicted protein sequence must be treated with caution until confirmation from the corresponding transcriptome sequence becomes available. The alternative genetic code for ciliates was used for translating the Trepomonas (Keeling and Doolittle 1997) and Streblomastix (Keeling and Leander 2003) genes.…”

Section: Methodsmentioning

confidence: 99%

“…The parasitic Entamoeba species are remarkable with their mitochondria being reduced to mitosomes and lacking organelle protein biosynthesis. In its multiple protein alignment with other amoebozoa the Archamoeba form a striking outgroup (Igloi 2019). The sequence of the protein quite clearly indicates a mitochondrial origin.…”

Section: Amoebozoamentioning

confidence: 99%

“…Amoebozoa are a major taxonomic group most of whose members possess a mitochondrial genome and consequently perform mitochondrial protein biosynthesis. Their nuclear genome encodes both cytoplasmic and mitochondrial forms of the enzyme (Igloi 2020b). Nevertheless, certain Archamoeba are amitochondrial.…”

Section: Amoebozoamentioning

confidence: 99%

“…Among the genes transferred from the endosymbiont to the nucleus were those of the family of aminoacyl-tRNA synthetases whose products are then imported to participate in mitochondrial protein biosynthesis. However, their subsequent presence in modern eukaryote cells is very variable (Igloi 2020b). The mitochondrial gene of arginyl-tRNA synthetase, for example, has either been retained in the nucleus (e.g., in Metazoans), eliminated such that the cytoplasmic form is imported into the organelle (e.g., in higher plants), or has itself replaced the ancestral nuclear gene (e.g., in Fungi; Karlberg et al 2000;Brindefalk et al 2007;Furukawa et al 2017)).…”

Section: Introductionmentioning

confidence: 99%

“…It constitutes a part of the catalytic site in three dimensions. Although these distinctive features have been confirmed in hundreds of species from numerous phyla (Igloi 2020b), one is aware of the pitfalls in making global generalizations since it is likely that evolutionary niches with diverging characteristics will be found.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms

Igloi

2021

J Mol Evol

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During the endosymbiotic evolution of mitochondria, the genes for aminoacyl-tRNA synthetases were transferred to the ancestral nucleus. A further reduction of mitochondrial function resulted in mitochondrion-related organisms (MRO) with a loss of the organelle genome. The fate of the now redundant ancestral mitochondrial aminoacyl-tRNA synthetase genes is uncertain. The derived protein sequence for arginyl-tRNA synthetase from thirty mitosomal organisms have been classified as originating from the ancestral nuclear or mitochondrial gene and compared to the identity element at position 20 of the cognate tRNA that distinguishes the two enzyme forms. The evolutionary choice between loss and retention of the ancestral mitochondrial gene for arginyl-tRNA synthetase reflects the coevolution of arginyl-tRNA synthetase and tRNA identity elements.

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Section: Methodsmentioning

confidence: 99%

Section: Amoebozoamentioning

confidence: 99%

Section: Amoebozoamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms

Igloi

2021

J Mol Evol

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Evolutionary Adjustment of tRNA Identity Rules in Bacillariophyta for Recognition by an Aminoacyl-tRNA Synthetase Adds a Facet to the Origin of Diatoms

Igloi

2022

J Mol Evol

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Error-free protein synthesis relies on the precise recognition by the aminoacyl-tRNA synthetases of their cognate tRNAs in order to attach the corresponding amino acid. A concept of universal tRNA identity elements requires the aminoacyl-tRNA synthetases provided by the genome of an organism to match the identity elements found in the cognate tRNAs in an evolution-independent manner. Identity elements tend to cluster in the tRNA anticodon and acceptor stem regions. However, in the arginine system, in addition to the anticodon, the importance of nucleotide A20 in the tRNA D-loop for cognate enzyme recognition has been a sustained feature for arginyl-tRNA synthetase in archaea, bacteria and in the nuclear-encoded cytosolic form in mammals and plants. However, nuclear-encoded mitochondrial arginyl-tRNA synthetase, which can be distinguished from its cytosolic form by the presence or absence of signature motifs, dispenses with the A20 requirement. An examination of several hundred non-metazoan organisms and their corresponding tRNAArg substrates has confirmed this general concept to a large extent and over numerous phyla. However, some Stramenopiles, and in particular, Diatoms (Bacillariophyta) present a notable exception. Unusually for non-fungal organisms, the nuclear genome encodes tRNAArg isoacceptors with C or U at position 20. In this case one of two nuclear-encoded cytosolic arginyl-tRNA synthetases has evolved to become insensitive to the nature of the D-loop identity element. The other, with a binding pocket that is compatible with tRNAArg-A20 recognition, is targeted to organelles that encode solely such tRNAs.

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Unraveling the peculiarities and development of novel inhibitors of leishmanial arginyl‐tRNA synthetase

Nasim,

Kumar,

Alvala

et al. 2024

The FEBS Journal

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Aminoacylation by tRNA synthetase is a crucial part of protein synthesis and is widely recognized as a therapeutic target for drug development. Unlike the arginyl‐tRNA synthetases (ArgRSs) reported previously, here, we report an ArgRS of Leishmania donovani (LdArgRS) that can follow the canonical two‐step aminoacylation process. Since a previously uncharacterized insertion region is present within its catalytic domain, we implemented the splicing by overlap extension PCR (SOE–PCR) method to create a deletion mutant (ΔIns‐LdArgRS) devoid of this region to investigate its function. Notably, the purified LdArgRS and ΔIns‐LdArgRS exhibited different oligomeric states along with variations in their enzymatic activity. The full‐length protein showed better catalytic efficiency than ΔIns‐LdArgRS, and the insertion region was identified as the tRNA binding domain. In addition, a benzothiazolo‐coumarin derivative (Comp‐7j) possessing high pharmacokinetic properties was recognized as a competitive and more specific inhibitor of LdArgRS than its human counterpart. Removal of the insertion region altered the mode of inhibition for ΔIns‐LdArgRS and caused a reduction in the inhibitor's binding affinity. Both purified proteins depicted variances in the secondary structural content upon ligand binding and thus, thermostability. Apart from the trypanosomatid‐specific insertion and Rossmann fold motif, LdArgRS revealed typical structural characteristics of ArgRSs, and Comp‐7j was found to bind within the ATP binding pocket. Furthermore, the placement of tRNAArg near the insertion region enhanced the stability and compactness of LdArgRS compared to other ligands. This study thus reports a unique ArgRS with respect to catalytic as well as structural properties, which can be considered a plausible drug target for the derivation of novel anti‐leishmanial agents.

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Gene organization and phylum-specific attributes of eukaryotic arginyl-tRNA synthetases

Cited by 3 publications

References 50 publications

The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms

The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms

Evolutionary Adjustment of tRNA Identity Rules in Bacillariophyta for Recognition by an Aminoacyl-tRNA Synthetase Adds a Facet to the Origin of Diatoms

Unraveling the peculiarities and development of novel inhibitors of leishmanial arginyl‐tRNA synthetase

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