PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif

Abstract

PAPD5 is one of the seven members of the family of noncanonical poly(A) polymerases in human cells. PAPD5 was shown to polyadenylate aberrant pre-ribosomal RNAs in vivo, similar to degradation-mediating polyadenylation by the noncanonical poly(A) polymerase Trf4p in yeast. PAPD5 has been reported to be also involved in the uridylation-dependent degradation of histone mRNAs. To test whether PAPD5 indeed catalyzes adenylation as well as uridylation of RNA substrates, we analyzed the in vitro properties of recombinant PAPD5 expressed in mammalian cells as well as in bacteria. Our results show that PAPD5 catalyzes the polyadenylation of different types of RNA substrates in vitro. Interestingly, PAPD5 is active without a protein cofactor, whereas its yeast homolog Trf4p is the catalytic subunit of a bipartite poly(A) polymerase in which a separate RNAbinding subunit is needed for activity. In contrast to the yeast protein, the C terminus of PAPD5 contains a stretch of basic amino acids that is involved in binding the RNA substrate.

Inhibition of polyadenylation reduces inflammatory gene induction

“…There are eight candidate poly(A) polymerase genes in the human genome: PAPa-g (PAPOLA,B,G), PAPD1, PAPD2, PAPD4, PAPD5, and PAPD7 (Hirose and Manley 1998;Wahle and Rüegsegger 1999;Topalian et al 2001;Houseley and Tollervey 2008;Kashiwabara et al 2008;Radford et al 2008;Rammelt et al 2011). They have a variety of substrates and functions, ranging from targeting aberrant transcripts for degradation in the nucleus to stabilizing microRNAs in the cytoplasm (Katoh et al 2009;Shcherbik et al 2010).…”

PAPD5-mediated 3′ adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease

“…In vitro, PAPD5 has previously been shown to be an RNAspecific nucleotidyl transferase that can add adenosine to the 3′ end of a variety of oligoribonucleotides (36). To evaluate if also in cells PAPD5 acts directly on miR-21, we analyzed previously published photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) sequencing data obtained from HEK293 human embryonic kidney cells (36,37).…”

“…To evaluate if also in cells PAPD5 acts directly on miR-21, we analyzed previously published photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) sequencing data obtained from HEK293 human embryonic kidney cells (36,37). These data revealed a statistically significant fraction of miR-21 cross-linking to PAPD5 in two independent replicates (P = 3.7e-4 and P = 0.0072, respectively; SI Materials and Methods and Table S2), suggesting that the decrease in miR-21 adenylation observed in the PAPD5 knockdown libraries is a direct effect.…”

The Nucleic Acid-binding Domain and Translational Repression Activity of a Xenopus Terminal Uridylyl Transferase

“…BRs are present in other rNTases. Human PAPD5, a noncanonical poly(A) polymerase, binds a subset of RNAs likely through a small, lysine-rich stretch of amino acids (52). The basic stretch of PAPD5 is also required for efficient catalytic activity, much like the BR in XTUT7.…”

“…4G) (49 -51). In contrast, a recently identified basic stretch of amino acids in PAPD5, a poly(A) polymerase related to XTUT7, is composed primarily of lysine (52,53). Intriguingly, the ARMs in Rev and Tat, as well as the basic stretch in PAPD5, directly bind RNA (49 -52).…”