OB or Not OB: Idiosyncratic utilization of the tRNA‐binding OB‐fold domain in unicellular, pathogenic eukaryotes

Kapps, Delphine; Cela, Marta; Théobald-Dietrich, Anne; Hendrickson, Tamara L.; Frugier, Magali

doi:10.1002/1873-3468.12441

“…MPsome proteins (Fig 6,Tables S3 and S4) suggests that they have some similar functional characteristics which may aid elucidating their specific functions. Variants of the ZF, IDR and OB-fold domains of A3 function in a wide range of critical processes that entail protein and nucleic acid interactions which span DNA replication, repair and telomere maintenance as well as transcription, tRNA and microRNA processing, translation and others (Allison et al 1998;Brevet et al 2003;Theobald et al 2003;Horvath 2011;Nam et al 2011;Kapps et al 2016;Wang et al 2017;Amir et al 2018;Gao et al 2018). Results from this study may contribute the understanding of the roles of these domains in RNA editing and other processes.…”

Section: Scsmentioning

confidence: 82%

Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA Editing Catalytic Complexes inTrypanosoma brucei

Davidge

¹

,

McDermott

²

,

Carnes

³

et al. 2023

Preprint

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The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multi-protein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the ZFs, an intrinsically disordered region (IDR) and several within or near the C-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.

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“…We also found that a few Microgenomates lysyl-tRNA synthetases (KKR67068.1 & KKQ91124.1) have an additional C -terminal domain that is very similar to this B2 domain and predicted α-helix. It is known that aaRS proteins are often fused with an OB domain [41]. The two Klosterneuburg active sludge metagenomic contigs containing the B2-TyrRS fusion genes showed almost identical gene organization and gene sequences, indicating that these two contigs belong to two closely-related bacteria.…”

Section: Resultsmentioning

confidence: 99%

Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria

Mukai

¹

,

Reynolds

²

,

Crnković

³

et al. 2017

Life

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The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNATyr and tRNATrp genes reveal bacterial or archaeal origins. We identified a trace of domain fusion and swapping in the archaeal-type TyrRS gene of a bacterial lineage, suggesting that CPR bacteria may have used this mechanism to create diverse proteins. Archaeal-type TrpRS of bacteria and a few TrpRS species of DPANN archaea represent a new phylogenetic clade (named TrpRS-A). The TrpRS-A open reading frames (ORFs) are always associated with another ORF (named ORF1) encoding an unknown protein without global sequence identity to any known protein. However, our protein structure prediction identified a putative HIGH-motif and KMSKS-motif as well as many α-helices that are characteristic of class I aminoacyl-tRNA synthetase (aaRS) homologs. These results provide another example of the diversity of molecular components that implement the genetic code and provide a clue to the early evolution of life and the genetic code.

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“…S4 ; Supplemental Tables S4, S5 ) suggests that they have some similar functional characteristics which may aid elucidating their specific functions. Variants of the ZF, IDR, and OB-fold domains of A3 function in a wide range of critical processes that entail protein and nucleic acid interactions which span DNA replication, repair and telomere maintenance as well as transcription, tRNA and microRNA processing, translation, and others ( Allison et al 1998 ; Brevet et al 2003 ; Theobald et al 2003 ; Horvath 2011 ; Nam et al 2011 ; Kapps et al 2016 ; Wang et al 2017 ; Amir et al 2018 ; Gao et al 2018 ). Results from this study may contribute the understanding of the roles of these domains in RNA editing and other processes.…”

Section: Discussionmentioning

confidence: 99%

Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes inTrypanosoma brucei

Davidge

¹

,

McDermott

²

,

Carnes

³

et al. 2023

RNA

View full text Add to dashboard Cite

The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multi-protein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the ZFs, an intrinsically disordered region (IDR) and several within or near the C-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.

show abstract

OB or Not OB: Idiosyncratic utilization of the tRNA‐binding OB‐fold domain in unicellular, pathogenic eukaryotes

Cited by 9 publications

References 55 publications

Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA Editing Catalytic Complexes inTrypanosoma brucei

Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA Editing Catalytic Complexes inTrypanosoma brucei

Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria

Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes inTrypanosoma brucei

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