Pentatricopeptide repeat poly(A) binding protein KPAF4 stabilizes mitochondrial mRNAs in Trypanosoma brucei

Mesitov, Mikhail V.; Yu, Tian; Suematsu, Takuma; Sement, François M.; Zhang, Liye; Yu, Clinton; Huang, Lan; Aphasizheva, Inna

doi:10.1038/s41467-018-08137-2

Cited by 14 publications

(28 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The coupling between mRNA editing status, the timing of 3′ extensions, and their distinct roles suggest the existence of a surveillance mechanism that potentially: (i) stimulates addition and enables A-tail's stabilizing function; (ii) monitors editing initiation and completion as sequence changes proceed from the 3′ to the 5′ region and (iii) induces 3′ A/U-tailing upon editing cessation in the 5′ region. These tasks have been attributed to PPR Kinetoplast Polyadenylation Factors KPAF3 ( 6 ), KPAF4 ( 13 ) and KPAF1/2 ( 12 ), respectively. Discovered in land plants ( 14 ), the helix-turn-helix PPR motif recognizes a single nucleoside via side chains occupying cardinal positions 5 and 35 of the repeat (or the last position in a longer repeat).…”

Section: Introductionmentioning

confidence: 99%

Poly(A) binding KPAF4/5 complex stabilizes kinetoplast mRNAs in Trypanosoma brucei

Aphasizheva

Suematsu

et al. 2020

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

Abstract In Trypanosoma brucei, mitochondrial pre-mRNAs undergo 3′-5′ exonucleolytic processing, 3′ adenylation and uridylation, 5′ pyrophosphate removal, and, often, U-insertion/deletion editing. The 3′ modifications are modulated by pentatricopeptide repeat (PPR) Kinetoplast Polyadenylation Factors (KPAFs). We have shown that KPAF3 binding to the 3′ region stabilizes properly trimmed transcripts and stimulates their A-tailing by KPAP1 poly(A) polymerase. Conversely, poly(A) binding KPAF4 shields the nascent A-tail from uridylation and decay thereby protecting pre-mRNA upon KPAF3 displacement by editing. While editing concludes in the 5′ region, KPAF1/2 dimer induces A/U-tailing to activate translation. Remarkably, 5′ end recognition and pyrophosphate hydrolysis by the PPsome complex also contribute to mRNA stabilization. Here, we demonstrate that KPAF4 functions as a heterodimer with KPAF5, a protein lacking discernable motifs. We show that KPAF5 stabilizes KPAF4 to enable poly(A) tail recognition, which likely leads to mRNA stabilization during the editing process and impedes spontaneous translational activation of partially-edited transcripts. Thus, KPAF4/5 represents a poly(A) binding element of the mitochondrial polyadenylation complex. We present evidence that RNA editing substrate binding complex bridges the 5′ end-bound PPsome and 3′ end-bound polyadenylation complexes. This interaction may enable mRNA circularization, an apparently critical element of mitochondrial mRNA stability and quality control.

show abstract

Section: Introductionmentioning

confidence: 99%

Poly(A) binding KPAF4/5 complex stabilizes kinetoplast mRNAs in Trypanosoma brucei

Aphasizheva

Suematsu

et al. 2020

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…Unlike in plants, prior studies of yeast (as well as animal) PPR proteins failed to identify the exact target sequence or a predictable recognition code. The only non-plant PPR proteins with clearly determined target sequences-KRIPP11 and KPAF4 from the protist Trypanosoma brucei, recognize simple polynucleotide repeats of poly(G) and poly(A), respectively (Kamba et al 2018;Mesitov et al 2019).…”

Section: Discussionmentioning

confidence: 99%

“…Similarly, many PPR proteins of trypanosomes were found to be involved in mitochondrial ribosome function and translational control (Pusnik et al 2007;Aphasizhev and Aphasizheva 2013;Aphasizheva et al 2016). In Trypanosoma brucei, two PPR proteins were found to bind poly(A) and poly(G) stretches in mitochondrial RNAs (Kamba et al 2018;Mesitov et al 2019). In spite of overall similarity of secondary structure (and predicted tertiary structure), the yeast and animal PPR motifs differ from their plant counterparts, and are generally more divergent in sequence (Lipinski et al 2011;Rackham and Filipovska 2012;Herbert et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Yeast pentatricopeptide protein Dmr1 (Ccm1) binds a repetitive AU-rich motif in the small subunit mitochondrial ribosomal RNA

Piątkowski

Golik

2020

RNA

View full text Add to dashboard Cite

PPR proteins are a diverse family of RNA binding factors found in all Eukaryotic lineages. They perform multiple functions in the expression of organellar genes, mostly on the post-transcriptional level. PPR proteins are also significant determinants of evolutionary nucleo-organellar compatibility. Plant PPR proteins recognize their RNA substrates using a simple modular code. No target sequences recognized by animal or yeast PPR proteins were identified prior to the present study, making it impossible to assess whether this plant PPR code is conserved in other organisms. Dmr1p (Ccm1p, Ygr150cp) is a S. cerevisiae PPR protein essential for mitochondrial gene expression and involved in the stability of 15S ribosomal RNA. We demonstrate that in vitro Dmr1p specifically binds a motif composed of multiple AUA repeats occurring twice in the 15S rRNA sequence as the minimal 14 nt (AUA) 4 AU or longer (AUA) 7 variant. Short RNA fragments containing this motif are protected by Dmr1p from exoribonucleolytic activity in vitro. Presence of the identified motif in mtDNA of different yeast species correlates with the compatibility between their Dmr1p orthologs and S. cerevisiae mtDNA. RNA recognition by Dmr1p is likely based on a rudimentary form of a PPR code specifying U at every third position, and depends on other factors, like RNA structure.

show abstract

“…Although kinetoplastid mitochondrial mRNAs are not flanked by tRNAs, it was thought that these transcripts were produced by a similar route as animal and fungal mitochondrial mRNAs. However, recent work in the Aphasizhev laboratory revealed the finding that these transcripts in T. brucei are, in fact, individually synthesized and subsequently processed at their 5 ′ and 3 ′ ends to form mature mRNAs (Sement et al 2018;Mesitov et al 2019). The 5 ′ ends are processed by a pyrophosphohydrolase complex termed the PPsome, which is composed of the so-called mitochondrial edited mRNA stability factors 1-3 (MERS1-MERS3).…”

Section: Introductionmentioning

confidence: 99%

“…MERS1 is a 395 residue protein, MERS2, a 946 residue peptatricopeptide repeat polypeptide and MERS3, a 189 amino acid protein with no known motifs (Sement et al 2018). These three proteins also interface with kRNA editing and RNA processing complexes including the RNA-editing substrate-binding complex (RESC) and the kinteoplastid polyadenylation complex (KPAC) (Aphasizhev and Aphasizheva 2011;Ammerman et al 2013;Aphasizheva et al 2014;Suematsu et al 2016;Sement et al 2018;Mesitov et al 2019). MERS1 was shown to be the factor responsible for catalyzing the 5 ′ processing event while MERS2 and MERS3 activates its catalysis (Sement et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Structures of MERS1, the 5′ processing enzyme of mitochondrial mRNAs in Trypanosoma brucei

Schumacher

Henderson

Zhang

2019

RNA

View full text Add to dashboard Cite

Most mitochondrial mRNAs are transcribed as polycistronic precursors that are cleaved by endonucleases to produce mature mRNA transcripts. However, recent studies have shown that mitochondrial transcripts in the kinetoplastid protozoan, Trypanosoma brucei, are transcribed individually. Also unlike most mitochondrial mRNAs, the 5 ′ ′ ′ ′ ′ end of these transcripts harbor a triphosphate that is hydrolyzed. This modification is carried out by a putative Nudix hydrolase called MERS1. The Nudix motif in MERS1 is degenerate, lacking a conserved glutamic acid, thus it is unclear how it may bind its substrates and whether it contains a Nudix fold. To obtain insight into this unusual hydrolase, we determined structures of apo, GTPbound and RNA-bound T. brucei MERS1 to 2.30 Å, 2.45 Å, and 2.60 Å, respectively. The MERS1 structure has a unique fold that indeed contains a Nudix motif. The nucleotide bound structures combined with binding studies reveal that MERS1 shows preference for RNA sequences with a central guanine repeat which it binds in a single-stranded conformation. The apo MERS1 structure indicates that a significant portion of its nucleotide binding site folds upon substrate binding. Finally, a potential interaction region for a binding partner, MERS2, that activates MERS1 was identified. The MERS2like peptide inserts a glutamate near the missing Nudix acidic residue in the RNA binding pocket, suggesting how the enzyme may be activated. Thus, the combined studies reveal insight into the structure and enzyme properties of MERS1 and its substrate-binding activities.

show abstract

Pentatricopeptide repeat poly(A) binding protein KPAF4 stabilizes mitochondrial mRNAs in Trypanosoma brucei

Cited by 14 publications

References 49 publications

Poly(A) binding KPAF4/5 complex stabilizes kinetoplast mRNAs in Trypanosoma brucei

Poly(A) binding KPAF4/5 complex stabilizes kinetoplast mRNAs in Trypanosoma brucei

Yeast pentatricopeptide protein Dmr1 (Ccm1) binds a repetitive AU-rich motif in the small subunit mitochondrial ribosomal RNA

Structures of MERS1, the 5′ processing enzyme of mitochondrial mRNAs in Trypanosoma brucei

Contact Info

Product

Resources

About