Thimet oligopeptidase

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Human thimet oligopeptidase
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EC no. 3.4.24.15
CAS no. 110639-28-6
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Thimet oligopeptidases (EC 3.4.24.15), also known as TOPs, are a type of M3 metallopeptidases. [1] These enzymes can be found in animals and plants, showing distinctive functions. In animals and humans, they are involved in the degradation of peptides, such as bradykinin, neurotensin, angiotensin I, and Aβ peptide, helping to regulate physiological processes. [2] In plants, their role is related to the degradation of targeting peptides and the immune response to pathogens through Salicylic Acid (SA)-dependent stress signaling. In Arabidopsis thaliana —recognized as a model plant for scientific studies [3] —two thimet oligopeptidases, known as TOP1 and TOP2, have been identified as targets for salicylic acid binding in the plant. [4] [5] These TOP enzymes are key components to understand the SA-mediated signaling where interactions exist with different components and most of the pathways are unknown.

Contents

Origin and name

Thimet (from "thiolsensitive metallo") oligopeptidases (peptide-size restriction) [6] have been widely studied in the Kingdom Animalia. The first TOP enzyme was found and purified from rat brain homogenates in 1983. [7] Today, it is known that TOP enzymes are mostly distributed in the pituitary, brain, and testes of humans and rats. [8] In plants, specifically in A. thaliana, the enzymes were more recently discovered as part of the 20S proteasome and SA-binding proteins. [4] [9] [5]

Different names have been used to identify this group of enzymes, such as soluble metalloproteinase, Pz-peptidase, collagenase-like peptidase, thimet peptidase, and endopeptidase 24.15. [6] [10] In 1992 the name "thimet oligopeptidases" was proposed by the International Union of Biochemistry and Molecular Biology (IUBMB), preserving this name. [6]

Family

Thimet oligopeptidases are metallopeptidases that belong to the clan MA, subclan MA (E), family M3 and subfamily M3A. [11] M3 family is composed by eight other members, such as neurolysin (EC 3.4.24.16), saccharolysin (EC:3.4.24.37), oligopeptidase MepB, oligopepetidase A, oligopeptidase F, oligopeptidase PepB, among others. These enzymes perform important functions in both prokaryotic and eukaryotic organisms. [11]

The plant Arabidopsis thaliana contains TOP1, TOP2, and TOPL enzymes. Arabidopsis thaliana.jpg
The plant Arabidopsis thaliana contains TOP1, TOP2, and TOPL enzymes.

Arabidopsis thimet oligopeptidases

There are three types of TOPs found in Arabidopsis thaliana. TOP1 (also known as OOP, organellar oligopeptidase, TOPorg, and thimet metalloendopeptidase 1) is located in the mitochondria and chloroplasts and has the AT5G65620 gene. TOP2 (also known as thimet metalloendopeptidase 2) is located in the cytosol and has the AT5G10540 gene. The distinctive genes of these two enzymes are maintained in fruit fly, mosquito, and rice as well. Finally, TOPL (also known as TOP-like) is located in the cytosol and has the AT1G67690 gene. [12] [13] [9] [4]

These TOPs are similar to those found in mammalian tissues. TOP1 and TOP2 are more similar to the mouse TOP with 28% similarity in the amino acid sequence, whereas TOPL is more similar to the mouse neurolysin with 34% similarity in the amino acid sequence. [9] [5]

Biochemical characteristics

Thimet oligopeptidases are M3 peptidases that possess the conserved sequence His-Glu-X-X-His in the amino acid sequence [1] (as cited in Wang, 2014). [14] The enzymes need the presence of thiol and zinc to be able of performing their functions. [4] From the three recognized thimet oligopeptidases in A. thaliana, only TOP1 and TOP2 are the TOP enzymes involved in SA immune system response. They are able of performing their function in a wide range of pH from 6.5 to 8.5. [15] TOP enzymes have the capacity to bind and form a dimer. They can exist as monomers and dimers. [15]

TOP1 and TOP2 are considered homologs with a 93% similarity in the protein sequence. Their structures have two domains. However, these domains are closer in TOP1 than in TOP2 due to differences in the position of helices α6, α9, and α20 in the domain I. Because of that, TOP1 has a closed form and TOP2 an open form. Unlike TOP1, TOP2 does not contain an N-terminal serine-rich region in its sequence. Based on the localization within the cell, TOP1 is considered an organellar oligopeptidase with dual localization while TOP2 is named as a cytosolic oligopeptidase. [5] [16]

Functions and interactions in plants

Peptide degradation

TOP1 plays a role in the pathway for degradation of unneeded peptides during importation of proteins to mitochondria and chloroplasts. This function can be explained due to changes in the closed conformation of TOP1 structure. The spheroidal shape, generating by the domains I and II, represents the catalytic cavity with a volume of ~3,000 Å3. During the peptide degradation, the substrate binding can occur only if there is a separation of the two domains allowing the access and binding of the free targeting peptides to the cavity (active site). The enzyme substrate complex is maintained by several non-covalent interactions: hydrophobic and polar interactions. The process is limited by the peptide size. Thus, only peptides with approximately the same volume (~3,000 Å3) can be degraded by the enzyme. Peptides that can be cleaved off are between 8 and 23 amino-acid residues. [16]

In addition, it has been suggested that TOP1 takes place in the degradation of other types of peptides. The enzyme is important for the elimination of unfolded or damaged proteins within the organelles mitochondria and chloroplasts. During the cleavage process of the proteins, the enzyme can break down peptide fragments without any strict sequence requirement but only constrained by the peptide size. [16]

TOP2 is part of the proteolytic activity that takes place in the cytosol. In A. thaliana, the enzyme has a role in the response to oxidative stress and degradation of oxidized proteins by breaking down peptides between 5 and 17 amino-acid residues. [9]

Stress signaling and immunity response

Salicylic acid (SA), recognized as a phenolic compound, is involved in different biological processes within plants. This compound, together with other hormones, contributes to growth and development regulation. Additionally, they maintain plant immune response. [17] In order to counter pathogen attacks and stress conditions, SA signaling activates the pathogen triggered immunity (PTI), [18] effector-triggered immunity (ETI), [18] and programmed cell death (PCD). TOP1 and TOP2 have shown a capacity to interact with salicylic acid and mediate SA activity in the system. [15] In vitro experiments have shown that when these enzymes are not present or defective, the vulnerability to pathogen infection is higher. [4] [5]

TOPs proteolytic activity is affected by their monomer/dimer relation. Oxidative environment increases the dimer form and result in proteolytic activity inhibition while reducing environments, stimulate accumulation of monomers and then favor TOP enzymes activity. Under stress condition, the production of reactive oxygen species (ROS) increases, causing damages in the photosynthesis and the PCD. [5] TOP enzymes mediate the response to this unfavorable condition. TOP1 regulates the importation of antioxidant enzymes to the chloroplast. These antioxidant enzymes reduce the ROS levels within the organelle. It has been suggested also that TOP1 allows the importation of enzymes that catalyze SA synthesis. On the other hand, TOP2 controls the amount of signaling peptides, important for PCD, in the cytosol. [15] Oxidative damage, such as cadmium (Cd2+) stress produces oxidized proteins that have to be removed to prevent further damage in the cell. TOP2 helps with the degradation of these damaged proteins. The enzyme degrades peptides by targeting the amino acids residues that are exposed during the stress. [9]

Interaction between exogenous salicylic acid and thimet oligopeptidases

In plants, endogenous SA activation can be carried out by exogenous SA. Low levels of exogenous SA, considered as less than 10 μM, help to reduce the damage caused by abiotic stress and increase photosynthetic activity. In contrast, high levels of exogenous SA reduce photosynthetic activity and result in cell death. This high amount of exogenous SA interacts with TOP enzymes and results in a reduction of their enzymatic activity. TOP1 and TOP2 activity is reduced by approximately 60% in presence of 5 mN exogenous SA. This phenolic compound inhibits TOP enzymes by a non-competitive mechanism where SA binds in a site different to the active site. The type of reaction is characterized for having a decrease in the maximum velocity (Vmax), whereas the Michaelis constant (Km) is maintained unchanged. [4] [5]

Related Research Articles

<span class="mw-page-title-main">Proteolysis</span> Breakdown of proteins into smaller polypeptides or amino acids

Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion.

Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations within or outside the cell. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, the plasma membrane, or to the exterior of the cell via secretion. Information contained in the protein itself directs this delivery process. Correct sorting is crucial for the cell; errors or dysfunction in sorting have been linked to multiple diseases.

<span class="mw-page-title-main">Protease</span> Enzyme that cleaves other proteins into smaller peptides

A protease is an enzyme that catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products. They do this by cleaving the peptide bonds within proteins by hydrolysis, a reaction where water breaks bonds. Proteases are involved in many biological functions, including digestion of ingested proteins, protein catabolism, and cell signaling.

The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amine group is bonded to the carboxylic group of another amino acid, making it a chain. That leaves a free carboxylic group at one end of the peptide, called the C-terminus, and a free amine group on the other end called the N-terminus. By convention, peptide sequences are written N-terminus to C-terminus, left to right (in LTR writing systems). This correlates the translation direction to the text direction, because when a protein is translated from messenger RNA, it is created from the N-terminus to the C-terminus, as amino acids are added to the carboxyl end of the protein.

A metalloproteinase, or metalloprotease, is any protease enzyme whose catalytic mechanism involves a metal. An example is ADAM12 which plays a significant role in the fusion of muscle cells during embryo development, in a process known as myogenesis.

<span class="mw-page-title-main">Systemin</span> Plant peptide hormone

Systemin is a plant peptide hormone involved in the wound response in the family Solanaceae. It was the first plant hormone that was proven to be a peptide having been isolated from tomato leaves in 1991 by a group led by Clarence A. Ryan. Since then, other peptides with similar functions have been identified in tomato and outside of the Solanaceae. Hydroxyproline-rich glycopeptides were found in tobacco in 2001 and AtPeps were found in Arabidopsis thaliana in 2006. Their precursors are found both in the cytoplasm and cell walls of plant cells, upon insect damage, the precursors are processed to produce one or more mature peptides. The receptor for systemin was first thought to be the same as the brassinolide receptor but this is now uncertain. The signal transduction processes that occur after the peptides bind are similar to the cytokine-mediated inflammatory immune response in animals. Early experiments showed that systemin travelled around the plant after insects had damaged the plant, activating systemic acquired resistance, now it is thought that it increases the production of jasmonic acid causing the same result. The main function of systemins is to coordinate defensive responses against insect herbivores but they also affect plant development. Systemin induces the production of protease inhibitors which protect against insect herbivores, other peptides activate defensins and modify root growth. They have also been shown to affect plants' responses to salt stress and UV radiation. AtPEPs have been shown to affect resistance against oomycetes and may allow A. thaliana to distinguish between different pathogens. In Nicotiana attenuata, some of the peptides have stopped being involved in defensive roles and instead affect flower morphology.

In molecular biology, the Signal Peptide Peptidase (SPP) is a type of protein that specifically cleaves parts of other proteins. It is an intramembrane aspartyl protease with the conserved active site motifs 'YD' and 'GxGD' in adjacent transmembrane domains (TMDs). Its sequences is highly conserved in different vertebrate species. SPP cleaves remnant signal peptides left behind in membrane by the action of signal peptidase and also plays key roles in immune surveillance and the maturation of certain viral proteins.

<span class="mw-page-title-main">Prolyl endopeptidase</span>

Prolyl endopeptidase (PE) also known as prolyl oligopeptidase or post-proline cleaving enzyme is an enzyme that in humans is encoded by the PREP gene.

<span class="mw-page-title-main">THOP1</span> Protein-coding gene in the species Homo sapiens

Thimet oligopeptidase is an enzyme that in humans is encoded by the THOP1 gene.

<span class="mw-page-title-main">NLN (gene)</span> Protein-coding gene in the species Homo sapiens

Neurolysin, mitochondrial is a protein that in humans is encoded by the NLN gene. It is a 78-kDa enzyme, widely distributed in mammalian tissues and found in various subcellular locations that vary with cell type. Neurolysin exemplifies the ability of neuropeptidases to target various cleavage site sequences by hydrolyzing them in vitro, and metabolism of neurotensin is the most important role of neurolysin in vivo. Neurolysin has also been implicated in pain control, blood pressure regulation, sepsis, reproduction, cancer biology pathogenesis of stroke, and glucose metabolism.

<span class="mw-page-title-main">NPEPPS</span> Protein-coding gene in the species Homo sapiens

Puromycin-sensitive amino peptidase also known as cytosol alanyl aminopeptidase or alanine aminopeptidase (AAP) is an enzyme that in humans is encoded by the NPEPPS gene. It is used as a biomarker to detect damage to the kidneys, and that may be used to help diagnose certain kidney disorders. It is found at high levels in the urine when there are kidney problems.

<span class="mw-page-title-main">PMPCB</span> Protein-coding gene in humans

Mitochondrial-processing peptidase subunit beta is an enzyme that in humans is encoded by the PMPCB gene. This gene is a member of the peptidase M16 family and encodes a protein with a zinc-binding motif. This protein is located in the mitochondrial matrix and catalyzes the cleavage of the leader peptides of precursor proteins newly imported into the mitochondria, though it only functions as part of a heterodimeric complex.

<span class="mw-page-title-main">PMPCA</span> Protein-coding gene in humans

Mitochondrial-processing peptidase subunit alpha is an enzyme that in humans is encoded by the PMPCA gene. This gene PMPCA encoded a protein that is a member of the peptidase M16 family. This protein is located in the mitochondrial matrix and catalyzes the cleavage of the leader peptides of precursor proteins newly imported into the mitochondria, though it only functions as part of a heterodimeric complex.

Peptide signaling plays a significant role in various aspects of plant growth and development and specific receptors for various peptides have been identified as being membrane-localized receptor kinases, the largest family of receptor-like molecules in plants. Signaling peptides include members of the following protein families.

<span class="mw-page-title-main">Chloroplast DNA</span> DNA located in cellular organelles called chloroplasts

Chloroplast DNA (cpDNA) is the DNA located in chloroplasts, which are photosynthetic organelles located within the cells of some eukaryotic organisms. Chloroplasts, like other types of plastid, contain a genome separate from that in the cell nucleus. The existence of chloroplast DNA was identified biochemically in 1959, and confirmed by electron microscopy in 1962. The discoveries that the chloroplast contains ribosomes and performs protein synthesis revealed that the chloroplast is genetically semi-autonomous. The first complete chloroplast genome sequences were published in 1986, Nicotiana tabacum (tobacco) by Sugiura and colleagues and Marchantia polymorpha (liverwort) by Ozeki et al. Since then, a great number of chloroplast DNAs from various species have been sequenced.

<span class="mw-page-title-main">Oligopeptidase</span>

An Oligopeptidase is an enzyme that cleaves peptides but not proteins. This property is due to its structure: the active site of this enzyme is located at the end of a narrow cavity which can only be reached by peptides.

<span class="mw-page-title-main">Astacin</span>

Astacins are a family of multidomain metalloendopeptidases which are either secreted or membrane-anchored. These metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12A. The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH.

A target peptide is a short peptide chain that directs the transport of a protein to a specific region in the cell, including the nucleus, mitochondria, endoplasmic reticulum (ER), chloroplast, apoplast, peroxisome and plasma membrane. Some target peptides are cleaved from the protein by signal peptidases after the proteins are transported.

Caricain is an enzyme. This enzyme catalyses the following chemical reaction: Hydrolysis of proteins with broad specificity for peptide bonds, similar to those of papain and chymopapain

Chaperones, also called molecular chaperones, are proteins that assist other proteins in assuming their three-dimensional fold, which is necessary for protein function. However, the fold of a protein is sensitive to environmental conditions, such as temperature and pH, and thus chaperones are needed to keep proteins in their functional fold across various environmental conditions. Chaperones are an integral part of a cell's protein quality control network by assisting in protein folding and are ubiquitous across diverse biological taxa. Since protein folding, and therefore protein function, is susceptible to environmental conditions, chaperones could represent an important cellular aspect of biodiversity and environmental tolerance by organisms living in hazardous conditions. Chaperones also affect the evolution of proteins in general, as many proteins fundamentally require chaperones to fold or are naturally prone to misfolding, and therefore mitigates protein aggregation.

References

  1. 1 2 Rawlings ND, Barrett AJ (1995). Evolutionary families of metallopeptidases. Methods in Enzymology. Vol. 248. pp. 183–228. doi:10.1016/0076-6879(95)48015-3. ISBN   9780121821494. PMID   7674922.
  2. ↑ Ray K, Hines CS, Coll-Rodriguez J, Rodgers DW (May 2004). "Crystal structure of human thimet oligopeptidase provides insight into substrate recognition, regulation, and localization". The Journal of Biological Chemistry. 279 (19): 20480–9. doi: 10.1074/jbc.M400795200 . PMID   14998993.
  3. ↑ The Arabidopsis Genome Initiative (December 2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana". Nature. 408 (6814): 796–815. Bibcode:2000Natur.408..796T. doi: 10.1038/35048692 . PMID   11130711.
  4. 1 2 3 4 5 6 Moreau M, Westlake T, Zampogna G, Popescu G, Tian M, Noutsos C, Popescu S (November 2013). "The Arabidopsis oligopeptidases TOP1 and TOP2 are salicylic acid targets that modulate SA-mediated signaling and the immune response". The Plant Journal. 76 (4): 603–14. doi: 10.1111/tpj.12320 . PMID   24004003.
  5. 1 2 3 4 5 6 7 Giulio, Zampogna (2013-06-18). "Arabidopsis Salicylic Acid-Binding Metalloendopeptidases TOP1 and TOP2 Regulate H2O2 Accumulation and Programmed Cell Death during the Immune Response against the Bacterial Pathogen Pseudomonas syringae".{{cite journal}}: Cite journal requires |journal= (help)
  6. 1 2 3 Barrett AJ, Rawlings ND, Woessner JF (2012-10-30). Handbook of Proteolytic Enzymes. Academic Press. ISBN   9780123822208.
  7. ↑ Orlowski M, Michaud C, Chu TG (September 1983). "A soluble metalloendopeptidase from rat brain. Purification of the enzyme and determination of specificity with synthetic and natural peptides". European Journal of Biochemistry. 135 (1): 81–8. doi:10.1111/j.1432-1033.1983.tb07620.x. PMID   6349998.
  8. ↑ Pineau C, McCool S, Glucksman MJ, Jégou B, Pierotti AR (October 1999). "Distribution of thimet oligopeptidase (E.C. 3.4.24.15) in human and rat testes". Journal of Cell Science. 112 ( Pt 20) (20): 3455–62. doi:10.1242/jcs.112.20.3455. PMID   10504294.
  9. 1 2 3 4 5 Polge C, Jaquinod M, Holzer F, Bourguignon J, Walling L, Brouquisse R (December 2009). "Evidence for the Existence in Arabidopsis thaliana of the Proteasome Proteolytic Pathway: ACTIVATION IN RESPONSE TO CADMIUM". The Journal of Biological Chemistry. 284 (51): 35412–24. doi: 10.1074/jbc.M109.035394 . PMC   2790970 . PMID   19822524.
  10. ↑ Tisljar U (February 1993). "Thimet oligopeptidase--a review of a thiol dependent metallo-endopeptidase also known as Pz-peptidase endopeptidase 24.15 and endo-oligopeptidase". Biological Chemistry Hoppe-Seyler. 374 (2): 91–100. PMID   8471182.
  11. 1 2 Barrett AJ, Rawlings ND, Woessner JF (2012-10-30). Handbook of Proteolytic Enzymes. Academic Press. ISBN   9780123822208.
  12. ↑ "AT5G10540 Zincin-like metalloproteases family protein [Arabidopsis thaliana (thale cress)] – Gene – NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-10-01.
  13. ↑ "AT5G65620 Zincin-like metalloproteases family protein [Arabidopsis thaliana (thale cress)] – Gene – NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-10-01.
  14. ↑ Wang R, Rajagopalan K, Sadre-Bazzaz K, Moreau M, Klessig DF, Tong L (May 2014). "Structure of the Arabidopsis thaliana TOP2 oligopeptidase". Acta Crystallographica Section F. 70 (Pt 5): 555–9. doi:10.1107/S2053230X14006128. PMC   4014318 . PMID   24817709.
  15. 1 2 3 4 Westlake TJ, Ricci WA, Popescu GV, Popescu SC (2015). "Dimerization and thiol sensitivity of the salicylic acid binding thimet oligopeptidases TOP1 and TOP2 define their functions in redox-sensitive cellular pathways". Frontiers in Plant Science. 6: 327. doi: 10.3389/fpls.2015.00327 . PMC   4434903 . PMID   26042129.
  16. 1 2 3 Kmiec B, Teixeira PF, Berntsson RP, Murcha MW, Branca RM, Radomiljac JD, Regberg J, Svensson LM, Bakali A, Langel U, Lehtiö J, Whelan J, Stenmark P, Glaser E (October 2013). "Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts". Proceedings of the National Academy of Sciences of the United States of America. 110 (40): E3761–9. Bibcode:2013PNAS..110E3761K. doi: 10.1073/pnas.1307637110 . PMC   3791733 . PMID   24043784.
  17. ↑ Rivas-San Vicente M, Plasencia J (June 2011). "Salicylic acid beyond defence: its role in plant growth and development". Journal of Experimental Botany. 62 (10): 3321–38. doi: 10.1093/jxb/err031 . PMID   21357767.
  18. 1 2 Bigeard J, Colcombet J, Hirt H (April 2015). "Signaling mechanisms in pattern-triggered immunity (PTI)". Molecular Plant. 8 (4): 521–39. doi: 10.1016/j.molp.2014.12.022 . hdl: 10754/347286 . PMID   25744358.
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