1.4.1 General characteristics of poly (A) Polymerase
The first poly(A) polymerase (PAP) was isolated from calf thymus in the beginning of the (Edmonds and Abrams 1960, Mandel et al. 2008). PAP is the enzyme that (A) tail of mRNAs (Zhao and Manley 1996, Martin et al. 2008). PAP activity can be mediated by a variety of enzymes and is present in prokaryotes as well in eukaryotes. In eukaryotes it is present in mitochondria, nucleus, RNPs (ribonucleoprotein particles) and ribosomes (Jacob et al. 1989). PAPs play diverse roles from marking aberrant nuclear transcripts to stabilizing the small non coding RNAs (miRNAs) in cytoplasm (Katoh et al. 2009, Shcherbik et al. 2010). Addition of the A s of an mRNA by PAP in the nucleus is carried out in a processive manner until it reaches a length of ~250 residues (Martin et al. 2004).
1.4.2 Structure of poly (A) polymerases
PAPs belong to the superfamily of the template-independent RNA specific nucleotidyl transferases (rNTrs), which are responsible for the covalent addition of ‘NA M NT and PAPs share a similar active site structure with that of the template dependent DNA P , a DNA repair enzyme, and have sequence similarity to other enzymes in their catalytic domains, such as RNA and DNA polymerases (Martin and Keller 1996, Zhao et al. 1999, Martin et al. 2004, Martin and Keller 2007, Schmidt and Norbury 2010). The nucleotide substrates of rNTRs are a wide range of substrates, from single AMP or UMP residues to the addition of the trinucleotide CCA to tRNA a (Martin et al. 2008). Other members of this group mediate the addition of single to several residues of UMP, these are known as TUTases (terminal uridylyl transferases) (Martin and Keller 2007). The majority of PAPs are conserved among eukaryotes (Zhao et al. 1999).
PAPs in general consist of three main domains: the catalytic domain found near the N terminal, followed by the central and the RNA binding domain near C-terminal NLS (nuclear localization signal), which overlaps with the RNA binding domain
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(Balbo and Bohm 2007). All canonical PAPs share similar catalytic domains at the N terminal, which is connected to the RNA binding domain by the central domain. The
nuclear localization signal (NLS) overlaps with the RNA binding domain. The C-terminal domain (residues 354 530) of canonical PAPs is responsible for binding
the cleavage/polyadenylation subunit Fip1, in which three constant aspartate residues interact with two metals out of three metals of the active site, among which one interacts with the adenine ring. This interaction serves a crucial role in structural selection of ATP by poly(A) polymerase (Martin et al. 2000). Addition of ‘NA OH PAP accomplished by two metal ions in the active site. One binds to RNA while the other one interacts with the phosphate group of the incoming nucleotide and the OH roup of a pre- mRNA. PAP is highly specific for ATP selection (Martin and Keller 2007). Identification of substrate and nucleotide selection by PAP is due to the induced fit mechanism of enzyme (Martin and Keller 2007, Mandel et al. 2008).
1.4.3 Types of PAPs
The PAPs are classified into canonical and non canonical on a structural and functional basis in table 4. The eight identified PAP genes in mammals are PAPOLA
PAPOLB PAPOLG PAPD PAPD PAPD PAPD PAPD7 (PAP associated domain containing 1, 2, 4, 5, 7 respectively) (Wahle and Ruegsegger 1999, Kashiwabara et al. 2008). PAP first identified in mammals, are found in nucleus and are now called canonical PAPs. PAPD4 (GLD-2) (germline development gene), Trf-4/5, PAPD5, MtPAP and POLS were identified later so are known as non canonical rNTrs (Martin and Keller 2007).
GLD-2, Trf-4/5 and other non-canonical PAPs contain a similar catalytic domain to canonical PAPs, but differ in their nucleotide recognition motifs. Non canonical PAPs lack the RRM-like RNA binding domain. TUTase and Mt PAP have different potential RNA binding domains in their N terminus, as indicated in figure 1.7. Most non- canonical PAPs therefore require additional protein factors which recruit them to their target RNAs.
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Figure 1.7: Structural organization of types of RNA specific nucleotidyl transferases:
Three canonical and five non canonical PAPs are shown. Localizations in cells are indicated as C (cytoplasmic), N (nuclear), M (mitochondria) and No (nucleolar). Domains are indicated as: green for catalytic domain, Orange for central domain, pink for RNA binding domain, blue for nucleotide recognition motif in canonical PAPs (NRM type1), dark brown for NRM type 2 in non canonical PAPs, light brown or Tan in U6 TUTase.
Trf4 and Trf5 were initially identified in S.cerevisiae as being part of the TRAMP complex and are involved in transcript quality control and decay in the nucleus (Shcherbik et al. 2010). RNA oligoadenylated by the TRAMP complex becomes a substrate for degradation by the nuclear exosome. In addition to Trf4/5, the TRAMP complex consists of the RNA helicase (Mtr4p) along with RNA binding proteins Air1 and Air2. Complete turnover of RNA requires multiple rounds of oligoadenylation (by the T‘AMP (Martin et al. 2008). PAPs Canonical PAPs Non-canonical PAPs Domain organization PAP PAP PAP GLD2 PAPD5 Pols TUTase MtPAP Localizations NC CN n n CN N No M
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Table 4: Types of mammalian poly (A) polymerases
Types of PAPs Synonyms/homologs Characteristics
PAP-alpha
P
PAPOLA, PAPII
Found predominately in nucleus adds poly (A) tail to the end of an mRNA (Bardwell et al. 1990). Also involved in some cases of cytoplasmic polyadenylation (Hwang et al. 2001, Radford et al. 2008). Different isoforms as a result of APA have been reported. PAP interacts with CPSF-1 and Fip1L by its C-terminal region (Martin and Keller 2007).
PAP- beta
P
PAPOLB, TPAP or
PAPT
Testis-specific cytoplasmic PAP, mediates in polyadenylation of mRNA transcripts for spermatogenesis (Benoit et al. 2008, Kashiwabara et al. 2008) is found in cytoplasm and nucleus both (Lee et al. 2000).
PAP-gamma P PAPOLG, Neo-PAP, SRP RNA 3'-adenylating enzyme Involved in -mRNA by
polyadenylation, interacts with components cleavage and polyadenylation machinery (Martin and Keller 2007). Found in nucleus, very similar to PAP (Topalian et al. 2001). Is 60-75% homologous to amino termini region of PAP Also mediates mono
‘NA U nuclear RNA, signal recognition particle (SRP) RNA, ribosomal 5S RNA and nuclear 7SK RNA (Kyriakopoulou et al. 2001, Perumal et al. 2001).
Gld2 PAP associated domain containing 4 (PAPD4)
Mediates cytoplasmic polyadenylation of CPE containing specific mRNAs upon oocytes maturation in Xenopus as well in Drosophila embryo and also in neurons (Radford et al. 2008). Regulate transition from mitosis to meiosis. Initially identified in C.
Elegans (Stevenson and Norbury 2006), where it
forms a complex with RNA binding protein Gld3 which is recruited it to specific mRNAs (Martin and Keller 2007). Also stabilizes ‘NA end monoadenylation (D'Ambrogio et al. 2012). Involved in spermatogenesis and oogenesis in frog and mice as well in cytoplasmic polyadenylation in somatic cells. XGLD2 an ortholog of GLD-2 in Xenopus found to localized in nucleus and cytoplasm.
Drosophila GLD2 limited to cytoplasm only
54 Papd5
Gld4, Trf4 or 5p (topoisomerase-related
function protein)
Involves in RNA quality control, oligoadenylates RNA by targeting exosome mediated cryptic RNA degradation, component of TRAMP complex, ortholog of S. Cerevisiae, found in nucleus (Fasken et al. 2011, Schmidt et al. 2011). Also involves in polyadenylation of specific mRNAs (Ciais et al. 2008, Houseley and Tollervey 2009, Rammelt et al. 2011). Found to involved in cytoplasmic polyadenylation in the absence of GLD-2 in C. Elegans and expressed in germ cells (Schmid et al. 2009). Role in histone mRNAs uridylation and degradation also involves in turnover of pre-rRNA in nucleus (Schmidt and Norbury 2010, Schmidt et al. 2011). In human fibroblast, it is required for CPEB1 mediated polyadenylation of TP53 mRNA (D'Ambrogio et al. 2013). Pols (DNA polymerase sigma) Trf4/PAP2/ PAPD7
RNA quality control, oligoadenylates RNA by targeting exosome mediated cryptic RNA degradation, component of TRAMP complex, ortholog of S.
Cerevisiae, found in nucleus (Stevenson and Norbury
2006). Also involves in polyadenylation of specific mRNAs (Ciais et al. 2008, Rammelt et al. 2011).
Starpap TUTase, Papd2
Eukaryotic specific U6 snRNA TUTase (terminal RNA
U
of an mRNA (Trippe et al. 2003, Trippe et al. 2006). Role in nuclear phosphoinositides mediated signalling pathways where it polyadenylates specific mRNAs (Schmidt and Norbury 2010).
Mtpap
(mitochondrial poly(A) polymerase)
Mitopap, Papd1
Involves in polyadenylation of transcripts encoded in mitochondria, localize in mitochondria (Nagaike et al. 2008, Chang and Tong 2012). It also oligouridylate s and degrade histone mRNAs in cytoplasm (Bai et al. 2011).