Structural and functional characterization of the TYW3/Taw3 class of SAM-dependent methyltransferases

Currie, Mark A.; Brown, Greg; Wong, Andrew; Ohira, Takayuki; Sugiyama, Kimio; Suzuki, Tsutomu; Yakunin, Alexander F.; Jia, Zongchao

doi:10.1261/rna.057943.116

Cited by 12 publications

(9 citation statements)

References 42 publications

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“…Several genes identified in our analyses encoded RNA binding and processing proteins, including a PPR protein, a nucleotidyltransferase, a NTP_transf_2 domain protein, a NYN domain protein, a class I SAM-dependent methyltransferase and a YbaK/prolyl-tRNA synthetase (Anantharaman and Aravind, 2006 ; Bartholow et al, 2014 ; Yamashita et al, 2014 ; Manna, 2015 ; Currie et al, 2017 ). Notably PPR proteins are involved in RNA splicing, editing, processing and translation.…”

Section: Resultsmentioning

confidence: 98%

Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis

Zhao

Tang

et al. 2018

Front. Plant Sci.

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Arbuscular mycorrhizal fungi (AMF) belong to Glomeromycotina, and are mutualistic symbionts of many land plants. Associated bacteria accompany AMF during their lifecycle to establish a robust tripartite association consisting of fungi, plants and bacteria. Physical association among this trinity provides possibilities for the exchange of genetic materials. However, very few horizontal gene transfer (HGT) from bacteria or plants to AMF has been reported yet. In this study, we complement existing algorithms by developing a new pipeline, Blast2hgt, to efficiently screen for putative horizontally derived genes from a whole genome. Genome analyses of the glomeromycete Rhizophagus irregularis identified 19 fungal genes that had been transferred between fungi and bacteria/plants, of which seven were obtained from bacteria. Another 18 R. irregularis genes were found to be recently acquired from either plants or bacteria. In the R. irregularis genome, gene duplication has contributed to the expansion of three foreign genes. Importantly, more than half of the R. irregularis foreign genes were expressed in various transcriptomic experiments, suggesting that these genes are functional in R. irregularis. Functional annotation and available evidence showed that these acquired genes may participate in diverse but fundamental biological processes such as regulation of gene expression, mitosis and signal transduction. Our study suggests that horizontal gene influx through endosymbiosis is a source of new functions for R. irregularis, and HGT might have played a role in the evolution and symbiotic adaptation of this arbuscular mycorrhizal fungus.

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Section: Resultsmentioning

confidence: 98%

Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis

Zhao

Tang

et al. 2018

Front. Plant Sci.

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“…We propose to name these enzymes Taw3c. In recent work, the crystal structure of putativeTaw3c protein from S. solfataricus was solved and revealed a novel α/β fold, which constitutes a new class of methyltransferases composed of SHS2, RAGNYA fold domains, and an N-terminal extension (PDB 1TLJ, [50], Figure 3). Interestingly, total tRNA isolated from S. cerevisiae tyw3 mutant and possessing yW-86 was not a substrate for SsTaw3c enzyme, clearly distinguishing it from yeast Tyw3 or Pyrococcus Taw3a proteins.…”

Section: Formation Of Img-14 By Taw1 Enzymementioning

confidence: 99%

“…In the aforementioned work [50], the structure of SsTaw3c was compared with the other three Taw3 structures deposited into PDB: Archaeoglobus fulgidus (PDB 2QG3), Pyrococcus horikoshii (PDB 2IT2), and Aeropyrum pernix (PDB 2DVK)). It was shown that all three structures share the same domain architecture and overall fold as SsTaw3.…”

Section: Formation Of Img-14 By Taw1 Enzymementioning

confidence: 99%

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Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea

Urbonavičius

Tauraitė

2020

Biomolecules

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Tricyclic wyosine derivatives are present at position 37 in tRNAPhe of both eukaryotes and archaea. In eukaryotes, five different enzymes are needed to form a final product, wybutosine (yW). In archaea, 4-demethylwyosine (imG-14) is an intermediate for the formation of three different wyosine derivatives, yW-72, imG, and mimG. In this review, current knowledge regarding the archaeal enzymes involved in this process and their reaction mechanisms are summarized. The experiments aimed to elucidate missing steps in biosynthesis pathways leading to the formation of wyosine derivatives are suggested. In addition, the chemical synthesis pathways of archaeal wyosine nucleosides are discussed, and the scheme for the formation of yW-86 and yW-72 is proposed. Recent data demonstrating that wyosine derivatives are present in the other tRNA species than those specific for phenylalanine are discussed.

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“…Finally, also the class I SAM-dependent methyltransferase, which regulates a wide range of biological processes through the modification of biological macromolecules such as DNA, RNA, polysaccharides, and lipids (Currie et al, 2017), enriched those clusters.…”

Section: Discussionmentioning

confidence: 99%

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Structural and functional characterization of the TYW3/Taw3 class of SAM-dependent methyltransferases

Cited by 12 publications

References 42 publications

Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis

Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis

Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea

Table_1.XLSX

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