TRAMP complex (Trf4/Air2/Mtr4p Polyadenylation complex) is a multiprotein, heterotrimeric complex having distributive

polyadenylation Polyadenylation is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In euk ...

activity and identifies wide varieties of RNAs produced by polymerases. It was originally discovered in ''Saccharomyces'' ''cerevisiae'' by LaCava et al., Vanacova et al. and Wyers et al. in 2005. TRAMP

It interacts with the

exosome complex The exosome complex (or PM/Scl complex, often just called the exosome) is a multi-protein intracellular complex capable of degrading various types of RNA (ribonucleic acid) molecules. Exosome complexes are found in both eukaryotic cells and a ...

in the

nucleus Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucle ...

eukaryotic Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...

cells and is involved in the 3' end processing and degradation of

ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal ...

and

snoRNA In molecular biology, Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, ...

s. The TRAMP complex trims the poly(A) tails of RNAs destined fo
Rrp6
and the core exosome down to 4-5 adenosines assisting in transcript recognition and

activation. The substrate specificity of exosomes is improved in the presence of TRAMP complex as it acts as a crucial cofactor and helps in maintaining various activities. In this way, TRAMP plays a critical role in ridding the cell of noncoding transcripts generated through pervasive

RNA polymerase II RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryoti ...

transcription, as well as functioning in the

biogenesis Spontaneous generation is a superseded scientific theory that held that living creatures could arise from nonliving matter and that such processes were commonplace and regular. It was hypothesized that certain forms, such as fleas, could arise ...

and turnover of functional coding and noncoding RNAs. TRAMP complex also affects various other RNA processes either directly or indirectly. It is involved in RNA export, Splicing, hetero-chromatic gene silencing and helps in maintaining stability of genome.

Components

Non-Canonical Poly(A) Polymerases

Pol(A) Polymerases showed various genetic interactions with DNA

Topoisomerase DNA topoisomerases (or topoisomerases) are enzymes that catalyze changes in the topological state of DNA, interconverting relaxed and supercoiled forms, linked (catenated) and unlinked species, and knotted and unknotted DNA. Topological issues i ...

s Top1p and hence they were called topoisomerase-related function Trf4p and Trf5p due to this interaction with DNA it has an important part in genomic stability. In the cell Trf4p is in higher concentration as compared to Trf5p and also has a stronger effect on the phenotype. Trf4p is present throughout the nucleus while Trf5p is mainly found mainly in nucleolus. The Trf4p structure consists of a central domain and a catalytic domain which is similar to the structure of canonical polymerases. The non-canonical Poly(A) polymerases (Trf4p or Trf5p) of the TRAMP complex which belong to the Cid1 family do not contain

RNA recognition motif RNA recognition motif, RNP-1 is a putative RNA-binding domain of about 90 amino acids that are known to bind single-stranded RNAs. It was found in many eukaryotic proteins. The largest group of single strand RNA-binding protein is the eukaryoti ...

(RRM) therefore additional proteins like Air1/Air2 are required by the non-canonical polymerases for polyadenylation.

Zinc knuckle proteins

The zinc knuckle proteins Air1p/Air2p (Arginine methyltransferase-interacting RING-finger protein) are mainly involved in the binding of RNAs. There are five CCHC (C stands for Cysteine and H stands for Histidine) zinc knuckle motifs which are present in between the C and N terminals. In Air2p proteins, the fourth and fifth zinc knuckle have different roles. The fourth zinc knuckle have a role in RNA binding while the fifth knuckle is important for protein-protein interactions. Air2p interacts with the central domain of Trf4p and polyadenylation activity of Trf4p is dependent on this interaction as deletion or mutation of the knuckles hinders the polyadenylation activity. Air1p is responsible for inhibiting methylation of Npl3p (a protein which is responsible mRNA export). Air1p/Air2p also direct abnormal mRNPs to TRAMP pathway and bring about their degradation.

Ski2 like helicase Mtr4p

The Ski2 like helicase Mtr4p was discovered during the screening of heat resistant mutants that gather Poly(A) RNA in the nucleus and is mainly involved in unwinding activity. Mtr4p (also called as Dob1p) is an SF2 helicase and belongs to DExH-box RNA helicases family consisting of two RecA like domains. It also consists of WH domain ( Winged Helix domain), an Arch domain (also called as stalk an
KOW domain
yprides, Ouzounis, Woese domain and helical bundle domain. The packing of the WH and helical bundle domains on surface of the helicase core results in the formation of a channel for ssRNA. Mtr4p requires ATP or dATP hydrolysis for RNA duplex unwinding mediated by Q-motif. A single-stranded region 3' to the paired region is also essential for the unwinding activity of Mtr4p. Through direct contact with various components of exosome, Mtr4p helps in proper addition of RNA substrates of TRAMP complex to nuclear exosome.

Difference between canonical and non-canonical polymerases

The difference between non-canonical and canonical Poly(A) Polymerases is that canonical polymerases help in maintaining mRNAs and its activity is regulated by a specific sequence in the mRNA while

of non-canonical polymerases uses a different regulated sequence in the RNA and specifies RNAs for degeneration or processing. Canonical polymerases belong to DNA polymerase β superfamily whereas non-canonical polymerases belong t

https://www.uniprot.org/uniprot/O13833 Cid1] family, another main difference is the length of the poly(A) tail; canonical polymerases can add many adenylates thus the RNA produced has longer poly(A) tails while non-canonical polymerases on the other hand can produce RNAs with shorter length of poly(A) tails as they can add only few adenylates.

Interaction with 3’->5’ exonuclease complex exosome

The TRAMP complex brings about degradation or processing of various RNAs with the help of 3’->5’ exonuclease complex called the exosome. A hexameric ring of RNase PH domain proteins
Rrp41pRrp42pRrp45pRrp46p
an
Mtr3p
comprises the exosome of ''S. cerevisiae''. The exosome can bring about RNA degradation more efficiently in the presence of Rrp6p with the help of TRAMP complex invitro. Also, RNA degradation is enhanced in the presence of various exosome cofactors which are recruited co-transcriptionally. The

Ski complex The Ski complex is a multi-protein complex involved in the 3' end degradation of messenger RNAs in yeast. Structure The complex consists of three main proteins, the RNA helicase ''Ski2'' and the proteins ''Ski3'' and ''Ski8''. This tetramer con ...

consisting of Ski2p, Ski3p, Ski8p is required by cytoplasmic exosome for all mRNA degradation pathways. The cytoplasmic exosome along with the Ski7p protein attaches to various abnormal ribosomes and mRNAs and brings about their degradation.

Inter-relation between components

All the components of the TRAMP complex are inter-related to each other. For the activity of Poly(A) polymerases likeTrf4p/Trf5p, zinc knuckle proteins are essential. In similar way RNA degradation brought about by exosomes is stimulated by unwinding activity of Ski2 like helicases and Mtr4p which acts as a cofactor. The unwinding activity of Mtr4p is improved by the Trf4p/Air2p in the TRAMP complex. Mtr4p also has an important role in maintaining and controlling the length of Poly(A) tails. But destruction or absence of Mtr4p results in hyperadenylation and hinders the length of Poly(A) tails. A complex formed between Trf5p, Air1p and Mtr4p is called as TRAMP5 complex. In ''S. cerevisiae'' there are two types of TRAMP complexes depending on the presence of polymerases. If Trf4p is present, then the complex is called as TRAMP4 and if Trf5p is present then It is called as TRAMP5.

RNA substrates

RNAs produced by all three polymerases (Pol I, II, III) act as substrates for TRAMP complex. TRAMP complex is involved in processing and surveillance of various RNAs and degrade abnormal RNAs. Different type of RNA substrates include

s (rRNAs),

small nucleolar RNA In molecular biology, Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, t ...

s (snoRNAs),

transfer RNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino ac ...

s (tRNAs),

small nuclear RNA Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcribe ...

s (snRNAs), Long transcripts of RNA polymerase II (Pol II) etc. But the mechanism by which TRAMP complex identifies various substrates is unknown. The TRAMP complex works more efficiently in RNA processing by engaging Exosome complex exonuclease RrP6 wherein Nab3(RNA binding protein) plays a crucial role.

Role in maintaining chromatin

Post-transcriptional modifications due to various enzymes like

methyltransferase Methyltransferases are a large group of enzymes that all methylate their substrates but can be split into several subclasses based on their structural features. The most common class of methyltransferases is class I, all of which contain a Rossm ...

Hmt1p (Rmt1p) may have an indirect effect on chromatin maintenance. The chromatin structures are affected when RNA substrates of TRAMP complex are transcribed across the genome. Various TRAMP components interact physically and genetically with various proteins and bring about changes in

chromatin Chromatin is a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important roles in r ...

and DNA metabolism.

Conservation of TRAMP-mediated processes

Components of the TRAMP complex in ''Saccharomyces cerevisiae'' are conserved in other organisms ranging from yeast to mammals. The TRAMP complex components of ''

Schizosaccharomyces pombe ''Schizosaccharomyces pombe'', also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically meas ...

'' including Cid14p, Air1p, and Mtr4p are functionally similar to the components of TRAMP complex in ''S. cerevisiae''.

In humans

The TRAMP complex in humans consists of various components including the helicase hMtr4p, a non-canonical poly(A) polymeras
hPAPD (PAP-associated domain-containing) 5
o
hPAPD7
and a Zinc knuckle protein hZCCHC7, RNA binding protein hRbm7p.{{Cite journal, last1=Lubas, first1=Michal, last2=Christensen, first2=Marianne S., last3=Kristiansen, first3=Maiken S., last4=Domanski, first4=Michal, last5=Falkenby, first5=Lasse G., last6=Lykke-Andersen, first6=Søren, last7=Andersen, first7=Jens S., last8=Dziembowski, first8=Andrzej, last9=Jensen, first9=Torben Heick, date=2011-08-19, title=Interaction profiling identifies the human nuclear exosome targeting complex, journal=Molecular Cell, volume=43, issue=4, pages=624–637, doi=10.1016/j.molcel.2011.06.028, issn=1097-4164, pmid=21855801, url=http://eprints.ibb.waw.pl/227/13/Lubas%20et%20al.%202011.pdf

References

Protein complexes