Non-stop decay

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Diagram of non-stop decay (NSD) process. Nonstopdecay.jpg
Diagram of non-stop decay (NSD) process.

Non-stop decay (NSD) is a cellular mechanism of mRNA surveillance to detect mRNA molecules lacking a stop codon and prevent these mRNAs from translation. The non-stop decay pathway releases ribosomes that have reached the far 3' end of an mRNA and guides the mRNA to the exosome complex, or to RNase R in bacteria for selective degradation. [1] [2] In contrast to Nonsense-mediated decay (NMD), polypeptides do not release from the ribosome, and thus, NSD seems to involve mRNA decay factors distinct from NMD. [3]

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Non-Stop Decay (NSD)

Non-stop decay (NSD) is a cellular pathway that identifies and degrades aberrant mRNA transcripts that do not contain a proper stop codon. Stop codons are signals in messenger RNA that signal for synthesis of proteins to end. Aberrant transcripts are identified during translation when the ribosome translates into the poly A tail at the 3' end of mRNA. A non-stop transcript can occur when point mutations damage the normal stop codon. Moreover, some transcriptional events are more likely to preserve gene expression on a lower scale in particular states.

The NSD pathway discharges ribosomes that have stalled at the 3' end of mRNA and directs the mRNA to the exosome complex in eukaryotes or RNase R in bacteria.  Once directed to their appropriate sites, the transcripts are then degraded. The NSD mechanism requires the interaction of RNA exosome with the Ski complex, a multi-protein structure that includes the Ski2p helicase and (notably) Ski7p.  The combination of these proteins and subsequent complex formation activates the degradation of aberrant mRNAs. Ski7p is thought to bind the ribosome stalled at the 3’ end of the mRNA poly(A) tail and recruit the exosome to degrade the aberrant mRNA. However in mammalian cells, Ski7p is not found, and even the presence of the NSD mechanism itself has remained relatively unclear. The short splicing isoform of HBS1L (HBS1LV3) was found to be the long-sought after human homologue of Ski7p, linking the exosome and SKI complexes. Recently, it has been reported that NSD also occurs in mammalian cells, albeit through a slightly different system.  In mammals, due to the absence of Ski7, the GTPase Hbs1, as well as its binding partner Dom34, were identified as potential regulators of decay.  Together, Hbs1/Dom34 are capable of binding to the 3’ end of a mis-regulated mRNA, facilitating the dissociation of malfunctioning or inactive ribosomes in order to restart the process of translation.  In addition, once the Hbs1/Dom34 complex has dissociated and recycled a ribosome, it has also been shown to recruit the exosome/Ski complex.

Liberation of the Ribosome

In bacteria, trans-translation, a highly conserved mechanism, acts as a direct counter to the accumulation of non-stop RNA, inducing decay and liberating the misregulated ribosome.  Originally discovered in Escherichia coli, the process of trans-translation is made possible by the interactions between transfer-messenger RNA (tmRNA) and the cofactor protein SmpB, which allows for the stable binding of the tmRNA to the stalled ribosome. [4]   The current tmRNA model states that tmRNA and SmpB interact together in order to mimic tRNA. The SmpB protein recognizes the point of stalling, and directs the tmRNA to bind to the ribosomal A site. [4] Once bound, SmpB engages in a transpeptidation reaction with the improperly functioning polypeptide chain through the donation of charged alanine. [4]   Through this process, the stalled and defective mRNA sequence is replaced with the SmpB RNA sequence, which encodes for the addition of an 11 amino acid tag on the C-terminus of the mRNA, which promotes degradation. [4] The modified portion of RNA, along with the amino acid tag, are translated, and demonstrate incomplete characteristics, alerting and allowing for intracellular proteases to remove these harmful protein fragments, causing stalled ribosomes on damaged mRNA to resume function. [4]

mRNA Degradation

Many enzymes and proteins play role in degrading mRNA. For example, in Escherichia coli there are three enzymes: RNase II, PNPase, and RNase R. [3] RNase R is a 3’-5’ exoribonuclease that is recruited to degrade a defective mRNA. [5] RNase R has two structural domains, an N-terminal putative helix-turn-helix (HTH) and a C-terminal lysine(K-rich) domain. [6] These two domains are unique to RNase R, and are attributed as being the determining factors for the selectivity and specificity of the protein. [7] Evidence has been shown that the K-rich domain is involved in the degradation of non-stop mRNA. [6] These domains are not present in other RNases. Both RNase II and RNase R are members of RNR family, and they share a noteworthy similarity in primary sequence and domain architecture. [2] However, RNase R has the ability to efficiently degrade mRNA, while RNase II has less efficiency in the degrading process. Nevertheless, the specific mechanics of degrading mRNA via RNase R has remained a mystery. [5]

See also

Related Research Articles

Messenger RNA RNA that is read by the ribosome to produce a protein

In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein.

Ribosome Intracellular organelle consisting of RNA and protein functioning to synthesize proteins

Ribosomes are macromolecular machines, found within all living cells, that perform biological protein synthesis. Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to form polypeptide chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more ribosomal RNA (rRNA) molecules and many ribosomal proteins. The ribosomes and associated molecules are also known as the translational apparatus.

Translation (biology) Cellular process of protein synthesis

In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or endoplasmic reticulum synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process is called gene expression.

The RNA-induced silencing complex, or RISC, is a multiprotein complex, specifically a ribonucleoprotein, which functions in gene silencing via a variety of pathways at the transcriptional and translational levels. Using single-stranded RNA (ssRNA) fragments, such as microRNA (miRNA), or double-stranded small interfering RNA (siRNA), the complex functions as a key tool in gene regulation. The single strand of RNA acts as a template for RISC to recognize complementary messenger RNA (mRNA) transcript. Once found, one of the proteins in RISC, Argonaute, activates and cleaves the mRNA. This process is called RNA interference (RNAi) and it is found in many eukaryotes; it is a key process in defense against viral infections, as it is triggered by the presence of double-stranded RNA (dsRNA).

Transfer-messenger RNA

Transfer-messenger RNA is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1. In trans-translation, tmRNA and its associated proteins bind to bacterial ribosomes which have stalled in the middle of protein biosynthesis, for example when reaching the end of a messenger RNA which has lost its stop codon. The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. In the majority of bacteria these functions are carried out by standard one-piece tmRNAs. In other bacterial species, a permuted ssrA gene produces a two-piece tmRNA in which two separate RNA chains are joined by base-pairing.

Nonsense-mediated decay Elimination of mRNA with premature stop codons in eukaryotes

Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that exists in all eukaryotes. Its main function is to reduce errors in gene expression by eliminating mRNA transcripts that contain premature stop codons. Translation of these aberrant mRNAs could, in some cases, lead to deleterious gain-of-function or dominant-negative activity of the resulting proteins.

In genetics, attenuation is a proposed mechanism of control in some bacterial operons which results in premature termination of transcription and is based on the fact that, in bacteria, transcription and translation proceed simultaneously. Attenuation involves a provisional stop signal (attenuator), located in the DNA segment that corresponds to the leader sequence of mRNA. During attenuation, the ribosome becomes stalled (delayed) in the attenuator region in the mRNA leader. Depending on the metabolic conditions, the attenuator either stops transcription at that point or allows read-through to the structural gene part of the mRNA and synthesis of the appropriate protein.

Ribosome biogenesis Cellular process

Ribosome biogenesis is the process of making ribosomes. In prokaryotes, this process takes place in the cytoplasm with the transcription of many ribosome gene operons. In eukaryotes, it takes place both in the cytoplasm and in the nucleolus. It involves the coordinated function of over 200 proteins in the synthesis and processing of the three prokaryotic or four eukaryotic rRNAs, as well as assembly of those rRNAs with the ribosomal proteins. Most of the ribosomal proteins fall into various energy-consuming enzyme families including ATP-dependent RNA helicases, AAA-ATPases, GTPases, and kinases. About 60% of a cell's energy is spent on ribosome production and maintenance.

A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence. They are named so because they release new peptides from the ribosome.

Exosome complex Protein complex that degrades RNA

The exosome complex is a multi-protein intracellular complex capable of degrading various types of RNA molecules. Exosome complexes are found in both eukaryotic cells and archaea, while in bacteria a simpler complex called the degradosome carries out similar functions.

RNase R, or Ribonuclease R, is a 3'-->5' exoribonuclease, which belongs to the RNase II superfamily, a group of enzymes that hydrolyze RNA in the 3' - 5' direction. RNase R has been shown to be involved in selective mRNA degradation, particularly of non stop mRNAs in bacteria. RNase R has homologues in many other organisms.

The Ski complex is a multi-protein complex involved in the 3' end degradation of messenger RNAs in yeast. The complex consists of three main proteins, the RNA helicase Ski2 and the proteins Ski3 and Ski8. This tetramer contains a 370 kDa core complex, containing N-terminal arms and C-terminal arms from Ski3. The helicase core of Ski2 is positioned by both the C-terminal of Ski3 and two subunits of Ski8. Helicase activities are initiated by the N-terminal arm and the Ski2 insertion domain. In yeast, the complex guides RNA molecules to the exosome complex for degradation via a fourth protein, called Ski7, which contains a GTPase-like protein. Ski7 involves the 3’ to 5’ degradation of RNA through two different pathways, 3’ poly(A) tail shortening and the binding of the Ski2, Ski3, and Ski8 tetramer and the exosome. The complex consists of three main proteins, the RNA helicase Ski2 and the proteins Ski3 and Ski8. This tetramer contains a 370 kDa core complex, containing N-terminal arms and C-terminal arms from Ski3. Degradation of the 3' mRNA overhang occurs by association with the 80s ribosome. The 3' end of the mRNA is threaded through the ribosome to Ski2, preparing it for the degradation process. The helicase core of Ski2 is positioned by both the C-terminal of Ski3 and two subunits of Ski8. Helicase activities are initiated by the N-terminal arm and the Ski2 insertion domain. Biochemical studies also show that the Ski complex can thread RNA through the exosome complex, thereby coupling the Ski2 protein helicase function with the exoribonuclease activity, leading to degradation of the RNA strand.

TRAMP complex

TRAMP complex is a multiprotein, heterotrimeric complex having distributive polyadenylation activity and identifies wide varieties of RNAs produced by polymerases. It was originally discovered in Saccharomycescerevisiae by LaCava et al., Vanacova et al. and Wyers et al. in 2005.

The degradosome is a multiprotein complex present in most bacteria that is involved in the processing of ribosomal RNA and the degradation of messenger RNA and is regulated by Non-coding RNA. It contains the proteins RNA helicase B, RNase E and Polynucleotide phosphorylase.

SKIV2L

Helicase SKI2W is an enzyme that in humans is encoded by the SKIV2L gene. This enzyme is a human homologue of yeast SKI2, which may be involved in antiviral activity by blocking translation of poly(A) deficient mRNAs. The SKIV2L gene is located in the class III region of the major histocompatibility complex.

mRNA surveillance mechanisms are pathways utilized by organisms to ensure fidelity and quality of messenger RNA (mRNA) molecules. There are a number of surveillance mechanisms present within cells. These mechanisms function at various steps of the mRNA biogenesis pathway to detect and degrade transcripts that have not properly been processed.

Exon junction complex Protein complex assembled on mRNA

An exon junction complex (EJC) is a protein complex which forms on a pre-messenger RNA strand at the junction of two exons which have been joined together during RNA splicing. The EJC has major influences on translation, surveillance and localization of the spliced mRNA. It is first deposited onto mRNA during splicing and is then transported into the cytoplasm. There it plays a major role in post-transcriptional regulation of mRNA. It is believed that exon junction complexes provide a position-specific memory of the splicing event. The EJC consists of a stable heterotetramer core, which serves as a binding platform for other factors necessary for the mRNA pathway. The core of the EJC contains the protein eukaryotic initiation factor 4A-III bound to an adenosine triphosphate (ATP) analog, as well as the additional proteins Magoh and Y14.The binding of these proteins to nuclear speckled domains has been measured recently and it may be regulated by PI3K/AKT/mTOR signaling pathways. In order for the binding of the complex to the mRNA to occur, the eIF4AIII factor is inhibited, stopping the hydrolysis of ATP. This recognizes EJC as an ATP dependent complex. EJC also interacts with a large number of additional proteins; most notably SR proteins. These interactions are suggested to be important for mRNA compaction. The role of EJC in mRNA export is controversial.

Translational regulation refers to the control of the levels of protein synthesized from its mRNA. This regulation is vastly important to the cellular response to stressors, growth cues, and differentiation. In comparison to transcriptional regulation, it results in much more immediate cellular adjustment through direct regulation of protein concentration. The corresponding mechanisms are primarily targeted on the control of ribosome recruitment on the initiation codon, but can also involve modulation of peptide elongation, termination of protein synthesis, or ribosome biogenesis. While these general concepts are widely conserved, some of the finer details in this sort of regulation have been proven to differ between prokaryotic and eukaryotic organisms.

ABCE1

ATP-binding cassette sub-family E member 1 (ABCE1) also known as RNase L inhibitor (RLI) is an enzyme that in humans is encoded by the ABCE1 gene.

Ribonuclease E is a bacterial ribonuclease that participates in the processing of ribosomal RNA and the chemical degradation of bulk cellular RNA.

References

  1. ↑ Vasudevan; Peltz, SW; Wilusz, CJ; et al. (2002). "Non-stop decay--a new mRNA surveillance pathway". BioEssays. 24 (9): 785–8. doi:10.1002/bies.10153. PMID   12210514.
  2. 1 2 Venkataraman, K; Guja, KE; Garcia-Diaz, M; Karzai, AW (2014). "Non-stop mRNA decay: a special attribute of trans-translation mediated ribosome rescue". Frontiers in Microbiology. 5: 93. doi: 10.3389/fmicb.2014.00093 . PMC   3949413 . PMID   24653719.
  3. 1 2 Wu, X; Brewer, G (2012). "The regulation of mRNA stability in mammalian cells: 2.0". Gene. 500 (1): 10–21. doi:10.1016/j.gene.2012.03.021. PMC   3340483 . PMID   22452843.
  4. 1 2 3 4 5 Karzai, A. Wali; Roche, Eric D.; Sauer, Robert T.; (2000).  “The SsrA–SmpB system for protein tagging, directed degradation and ribosome rescue”.  Nature, Structural Biology. 7: 449-455.
  5. 1 2 Alberts, Bruce (2002). Molecular biology of the cell 4th edition. New York: Garland Science. ISBN   978-0-8153-3218-3.
  6. 1 2 Vasudevan, Shobha; Peltz, Stuart W.; Wilusz, Carol J. (September 2002). "Non-stop decay--a new mRNA surveillance pathway". BioEssays. 24 (9): 785–788. doi:10.1002/bies.10153. ISSN   0265-9247. PMID   12210514.
  7. ↑ Ge, Zhiyun; Mehta, Preeti; Richards, Jamie; Wali Karzai, A. (September 27, 2010). "Non‐stop mRNA decay initiates at the ribosome". Molecular Microbiology. 78 (5): 1159–1170. doi:10.1111/j.1365-2958.2010.07396.x. PMC   3056498 . PMID   21091502.
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