Adenylylation

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AMPylator setting up target protein with ATP for AMPylation reaction. AMPylation Before.png
AMPylator setting up target protein with ATP for AMPylation reaction.

Adenylylation, [1] [2] more commonly known as AMPylation, is a process in which an adenosine monophosphate (AMP) molecule is covalently attached to the amino acid side chain of a protein. [3] This covalent addition of AMP to a hydroxyl side chain of the protein is a post-translational modification. [4] Adenylylation involves a phosphodiester bond between a hydroxyl group of the molecule undergoing adenylylation, and the phosphate group of the adenosine monophosphate nucleotide (i.e. adenylic acid). Enzymes that are capable of catalyzing this process are called AMPylators.

Contents

The known amino acids to be targeted in the protein are tyrosine and threonine, and sometimes serine. [5] When charges on a protein undergo a change, it affects the characteristics of the protein, normally by altering its shape via interactions of the amino acids which make up the protein. AMPylation can have various effects on the protein. These are properties of the protein like, stability, enzymatic activity, co-factor binding, and many other functional capabilities of a protein. Another function of adenylylation is amino acids activation, which is catalyzed by tRNA aminoacyl synthetase. [3] The most commonly identified protein to receive AMPylation are GTPases, and glutamine synthetase.

AMPylator having attached the ATP, now an AMP to the targeted protein, completing AMPylation. AMPylation After.png
AMPylator having attached the ATP, now an AMP to the targeted protein, completing AMPylation.

Adenylylators

Enzymes responsible for AMPylation, called AMPylators or Adenylyltransferase, fall into two different families, all depending on their structural properties and mechanism used. AMPylator is created by two catalytic homologous halves. One half is responsible for catalyzing the adenylylation reaction, while the other half catalyzes the phosphorolytic deadenylylation reaction [2] . These two families are the DNA-β-polymerase-like and the Fic family. [6]

DNA-β-polymerase-like, is a family of Nucleotidyltransferase. [4] It more specifically is known as the GlnE family. There is a specific motif that is used to clarify this particular family. The motif consists of a three stranded β-sheet which is part of magnesium ion coordination and phosphate binding. Aspartate is essential for the activity to occur in this family.

The Fic domain belongs to Fido (Fic/Doc) superfamilyFic family, which is a filamentation induced by cyclic AMP domain, is known to perform AMPylation. This term was coined when VopS from Vibrio parahaemolyticus was discovered to modify RhoGTPases with AMP on a serine. This family of proteins are found in all domains of life on earth. It is mediated via a mechanism of ATP-binding-site alpha helix motif. Infectious bacteria use this domain to interrupt phagocytosis and cause cell death. Fic domains are evolutionarily conserved domains in prokaryotes and eukaryotes that belong to the Fido domain superfamily. [4]

AMPylators have been shown to be comparable to kinases due to their ATP hydrolysis activity and reversible transfer of the metabolite to a hydroxyl side chain of the protein substrate. However, AMPylation catalyse a nucleophilic attack on the α-phosphate group, while kinase in the phosphorylation reaction targets γ-phosphate. The nucleophilic attack of AMPylation leads to release Pyrophosphate and the AMP-modified protein are the products of the AMPylation reaction. [5]

The regulation of PII proteins in Glutamine Synthase ( the most example using AMPylation and DeAMPylation) Glutamine synthase regulation by PII proteins.png
The regulation of PII proteins in Glutamine Synthase ( the most example using AMPylation and DeAMPylation)

De-adenylylators

De-AMPylation is the reverse reaction in which the AMP molecule is detached from the amino acid side of a chain protein.

There are three known mechanisms for this reaction. The bacterial GS-ATase (GlnE) encodes a bipartite protein with separate N-terminal AMPylation and C-terminal de-AMPylation domains whose activity is regulated by PII and associated posttranslational modifications. De-AMPylation of its substrate AMPylated glutamine synthetase proceeds by a phosphorolytic reaction between the adenyl-tyrosine of GS and orthophosphate, leading to the formation of ADP and unmodified glutamine synthetase. [4]

SidD, a protein introduced in the host cell by the pathogenic bacteria Legionella pneumophila , de-AMPylates Rab1 a host protein AMPylated by a different Legionella pneumophila enzyme, the AMPylase SidM. Whilst the benefit to the pathogen of introducing these two antagonistic effectors in the host remains unclear, the biochemical reaction carried out by SidD involves the use of a phosphatase-like domain to catalyse the hydrolytic removal of the AMP from tyrosine 77 of the host's Rab1. [7]

In animal cells the removal of AMP from threonine 518 of BiP/Grp78 is catalysed by the same enzyme, FICD, that AMPylates BiP. Unlike the bacterial GS-ATase, FICD carries out both reactions with same catalytic domain. [8]

Prokaryotic

Bacterial homeostasis

AMPylation is involved in bacterial homeostasis. The most famous example is AMPylator GS-ATase (GlnE), which contributes in complex regulation of nitrogen metabolism through AMPylation of glutamine synthetase that was introduced in the AMPylation and DeAMPylation parts.

Another example of AMPylators that play a role in bacterial homeostasis is the class I Fic AMPylators (FicT), which modifies the GyrB subunit of DNA gyrase, the conserved tyrosine residue for ATP binding of ParE subunit at Topoisomerase IV. This DNA gyrase inactivation by AMPylation leads to the activation of SOS response, which is the cellular response to DNA damage. The activity of FicT AMPylation is reversible and only leads to growth arrest, but not cell death. Therefore, FicT AMPylation plays a role in regulating cell stress, which is shown in the Wolbachia bacteria that the level of FicT increases in response to doxycycline.

A Class III Fic AMPylator NmFic of N. meningtidis is also found to modify AMPylate GyrB at the conserved tyrosine for ATP binding. This shows that Fic domains are highly conserved that indicates the important role of AMPylation in regulating cellular stress in bacteria. The regulation of NmFic involves the concentration-dependent monomerization and autoAMPylation for activation of NmFic activity. [5]

Bacterial pathogenicity

Bacteria proteins, also known as effectors, have been shown to use AMPylation. Effectors such as VopS, IbpA, and DrrA, have been shown to AMPylate host GTPases and cause actin cytoskeleton changes. GTPases are common targets of AMPylators. Rho, Rab, and Arf GTPase families are involved in actin cytoskeleton dynamics and vesicular trafficking. They also play roles in cellular control mechanisms such as phagocytosis in the host cell.

The pathogen enhances or prevents its internalization by either inducing or inhibiting host cell phagocytosis [4] . Vibrio parahaemolyticus is a Gram-negative bacterium that causes food poisoning as a result of raw or undercooked seafood consumption in humans. [9] VopS, a type III effector found in Vibrio parahaemolyticus, contains a Fic domain that has a conserved HPFx(D/E)GN(G/K)R motif that contains a histidine residue essential for AMPylation. VopS blocks actin assembly by modifying threonine residue in the switch 1 region of Rho GTPases. The transfer of an AMP moiety using ATP to the threonine residue results in steric hindrance, and thus prevents Rho GTPases from interacting with downstream effectors. VopS also adenylates RhoA and cell division cycle 42 (CDC42), leading to a disaggregation of the actin filament network. [3] [5] As a result, the host cell's actin cytoskeleton control is disabled, leading to cell rounding. [4] [9]

IbpA is secreted into eukaryotic cells from H. somni, a Gram-negative bacterium in cattle that causes respiratory epithelium infection. This effector contains two Fic domains at the C-terminal region. AMPylation of the IbpA Fic domain of Rho family GTPases is responsible for its cytotoxicity. Both Fic domains have similar effects on host cells’ cytoskeleton as VopS. [3] [5] The AMPylation on a tyrosine residue of the switch 1 region blocks the interaction of the GTPases with downstream substrates such as PAK.

DrrA is the Dot/Icm type IV translocation system substrate DrrA from Legionella pneumophila. It is the effector secreted by L. pneumophila to modify GTPases of the host cells. This modification increases the survival of bacteria in host cells. DrrA is composed of Rab1b specific guanine nucleotide exchange factor (GEF) domain, a C-terminal lipid binding domain and an N-terminal domain with unclear cytotoxic properties. Research works show that N-terminal and full-length DrrA shows AMPylators activity toward host's Rab1b protein (Ras related protein), which is also the substrate of Rab1b GEF domain. Rab1b protein is the GTPase Rab to regulate vesicle transportation and membrane fusion. The adenylation by bacteria AMPylators prolong GTP-bound state of Rab1b. Thus, the role of effector DrrA is connected toward the benefits of bacteria's vacuoles for their replication during the infection. [3] [5]

Eukaryotic

Plants and yeasts have no known endogenous AMPylating enzymes, but animal genomes are endowed with a single copy of a gene encoding a Fic-domain AMPylase, [10] that was likely acquired by an early ancestor of animals via horizontal gene transfer from a prokaryote. The human protein referred to commonly as FICD, had been previously identified as Huntingtin associated protein E (HypE; an assignment arising from a yeast two-hybrid screen, but of questionable relevance, as Huntingtin and HypE/FICD are localised to different cellular compartments). CG9523 Homologues in Drosophila melanogaster (CG9523) and C. elegans (Fic-1) have also received attention. In all animals FICD has a similar structure. It is a type II transmembrane domain protein, with a short cytoplasmic domain followed by membrane anchor that holds the protein in the endoplasmic reticulum (ER) and long C-terminal portion that resides in ER and encompasses tetratricopeptide repeats (TPRs) followed by a catalytic Fic domain. [11]

Endoplasmic reticulum

The discovery of an animal cell AMPylase, [10] followed by the discovery of its ER localisation and that BiP is a prominent substrate for its activity [12] were important breakthroughs. BiP (also known as Grp78) had long been known to undergo an inactivating post-translational modification, [13] [14] but it nature remain elusive. Widely assumed to be ADP-ribosylation, it turns out to be FICD-mediated AMPylation, as inactivating the FICD gene in cells abolished all measurable post-translational modification of BiP. [15]

BiP is an ER-localised protein chaperone whose activity is tightly regulated at the transcriptional level via a gene-expression program known as the Unfolded Protein Response (UPR). The UPR is a homeostatic process that couples the transcription rate of BiP (and many other proteins) to the burden of unfolded proteins in the ER (so-called ER stress) to help maintain ER proteostasis. AMPylation adds another rapid post-translational layer of control of BiP's activity, as modification of Thr518 of BiP's substrate-binding domain with an AMP locks the chaperone into an inactive conformation. [16] [17] This modification is selectively deployed as ER stress wanes, to inactivate surplus BiP. However, as ER stress rises again, the same enzyme, FICD, catalyses the opposite reaction, BiP de-AMPylation. [8]

An understanding of the structural basis of BiP AMPylation and de-AMPylation is gradually emerging, [18] [19] as are clues to the allostery that might regulate the switch in FICD's activity [20] but important details of this process as it occurs in cells remain to be discovered.

The role of FICD in BiP AMPylation (and de-AMPylation) on Thr518 is well supported by biochemical and structural studies. Evidence has also been presented that in some circumstances FICD may AMPylate a different residue, Thr366 in BiP's nucleotide binding domain. [12]

Caenorhabditis elegans

Fic-1 is the only Fic protein present in the genetic code of C. elegans. It is primarily found in the ER nuclear envelope of adult germline cells and embryotic cells, but small amounts may be found within the cytoplasm. This extra-ER pool of FICD-1s is credited with AMPylation of core histones and eEF1-A type translation factors within the nematode. [21]

Though varying AMPylation levels did not create any noticeable effects within the nematode's behaviour or physiology, Fic-1 knockout worms were more susceptible to infection by Pseudomonas aeruginosa compared to the counterparts with active Fic-1 domains, implying a link between AMPylation of cellular targets and immune responses within nematodes. [11]

Drosophila melanogaster

Flies lacking in FICD (CG9523) have been described as blind. Initially, this defect was attributed to a role for FICD on the cell surface of capitate projections - a putative site of neurotransmitter recycling [22] however a later study implicated FICD-mediated AMPylation of BiP Thr366 in the visual problem [23]

Clinical significance

The presynaptic protein α-synuclein was found to be a target for FICD AMPylation. During HypE-mediated adenylylation of αSyn, aggregation of αSyn decreases and both neurotoxicity and ER stress were discovered to decrease in vitro. Thus, adenylylation of αSyn is possibly a protective response to ER stress and αSyn aggregation. However, as aSyn and FICD reside in different compartments further research needs to be done confirm the significance of these claims. [24]

Detection

Chemical handles

Chemical handles are used to detect post-translationally modified proteins. Recently, there is a N6pATP that contains an alkynyl tag (propargyl) at the N6 position of the adenine of ATP. This N6pATP combines with the click reaction to detect AMPylated proteins. To detect unrecognized modified protein and label VopS substrates, ATP derivatives with a fluorophore at the adenine N6 NH2 is utilized to do that. [5] [6]

Antibody-based method

Antibody is famous for its high affinity and selectivity, so it is the good way to detect AMPylated proteins. Recently, ɑ- AMP antibodies is used to directly detect and isolate AMPylated proteins (especially AMPylated tyrosine and AMPylated threonine) from cells and cell lysates. AMPylation is a post-translational modification, so it will modify protein properties by giving the polar character of AMP and hydrophobicity. Thus, instead of using antibodies that detect a whole peptide sequence, raising AMP antibodies directly targeted to specific amino acids are preferred. [5] [6]

Mass spectrometry

Previously, many science works used Mass Spectrometry (MS) in different fragmentation modes to detect AMPylated peptides. In responses to the distinctive fragmentation techniques, AMPylated protein sequences disintegrated at different parts of AMP. While electron transfer dissociation (ETD) creates minimum fragments and less complicated spectra, collision-induced dissociation (CID) and high-energy collision (HCD) fragmentation generate characteristic ions suitable for AMPylated proteins identification by generating multiple AMP fragments. Due to AMP's stability, peptide fragmentation spectra is easy to read manually or with search engines. [5] [6]

Inhibitors

Inhibitors of protein AMPylation with inhibitory constant (Ki) ranging from 6 - 50 µM and at least 30-fold selectivity versus HypE have been discovered. [25] [5] [6]

Related Research Articles

<span class="mw-page-title-main">Adenylyl cyclase</span> Enzyme with key regulatory roles in most cells

Adenylate cyclase is an enzyme with systematic name ATP diphosphate-lyase . It catalyzes the following reaction:

<span class="mw-page-title-main">Cyclic adenosine monophosphate</span> Cellular second messenger

Cyclic adenosine monophosphate is a second messenger, or cellular signal occurring within cells, that is important in many biological processes. cAMP is a derivative of adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway.

<span class="mw-page-title-main">G protein-coupled receptor</span> Class of cell surface receptors coupled to G-protein-associated intracellular signaling

G protein-coupled receptors (GPCRs), also known as seven-(pass)-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptors, and G protein-linked receptors (GPLR), form a large group of evolutionarily related proteins that are cell surface receptors that detect molecules outside the cell and activate cellular responses. They are coupled with G proteins. They pass through the cell membrane seven times in the form of six loops of amino acid residues, which is why they are sometimes referred to as seven-transmembrane receptors. Ligands can bind either to the extracellular N-terminus and loops or to the binding site within transmembrane helices. They are all activated by agonists, although a spontaneous auto-activation of an empty receptor has also been observed.

GTPases are a large family of hydrolase enzymes that bind to the nucleotide guanosine triphosphate (GTP) and hydrolyze it to guanosine diphosphate (GDP). The GTP binding and hydrolysis takes place in the highly conserved P-loop "G domain", a protein domain common to many GTPases.

<span class="mw-page-title-main">G protein</span> Type of proteins

G proteins, also known as guanine nucleotide-binding proteins, are a family of proteins that act as molecular switches inside cells, and are involved in transmitting signals from a variety of stimuli outside a cell to its interior. Their activity is regulated by factors that control their ability to bind to and hydrolyze guanosine triphosphate (GTP) to guanosine diphosphate (GDP). When they are bound to GTP, they are 'on', and, when they are bound to GDP, they are 'off'. G proteins belong to the larger group of enzymes called GTPases.

<span class="mw-page-title-main">Kinase</span> Enzyme catalyzing transfer of phosphate groups onto specific substrates

In biochemistry, a kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule donates a phosphate group to the substrate molecule. This transesterification produces a phosphorylated substrate and ADP. Conversely, it is referred to as dephosphorylation when the phosphorylated substrate donates a phosphate group and ADP gains a phosphate group. These two processes, phosphorylation and dephosphorylation, occur four times during glycolysis.

<span class="mw-page-title-main">Phosphorylation</span> Chemical process of introducing a phosphate

In biochemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology. Protein phosphorylation often activates many enzymes.

<span class="mw-page-title-main">Ubiquitin ligase</span> Protein

A ubiquitin ligase is a protein that recruits an E2 ubiquitin-conjugating enzyme that has been loaded with ubiquitin, recognizes a protein substrate, and assists or directly catalyzes the transfer of ubiquitin from the E2 to the protein substrate. In simple and more general terms, the ligase enables movement of ubiquitin from a ubiquitin carrier to another thing by some mechanism. The ubiquitin, once it reaches its destination, ends up being attached by an isopeptide bond to a lysine residue, which is part of the target protein. E3 ligases interact with both the target protein and the E2 enzyme, and so impart substrate specificity to the E2. Commonly, E3s polyubiquitinate their substrate with Lys48-linked chains of ubiquitin, targeting the substrate for destruction by the proteasome. However, many other types of linkages are possible and alter a protein's activity, interactions, or localization. Ubiquitination by E3 ligases regulates diverse areas such as cell trafficking, DNA repair, and signaling and is of profound importance in cell biology. E3 ligases are also key players in cell cycle control, mediating the degradation of cyclins, as well as cyclin dependent kinase inhibitor proteins. The human genome encodes over 600 putative E3 ligases, allowing for tremendous diversity in substrates.

In organic chemistry, a group transfer reaction is a class of the pericyclic reaction where one or more groups of atoms is transferred from one molecule to another. Group transfer reactions can sometimes be difficult to identify when separate reactant molecules combine into a single product molecule. Unlike other pericyclic reaction classes, group transfer reactions do not have a specific conversion of pi bonds into sigma bonds or vice versa, and tend to be less frequently encountered. Like all pericyclic reactions, group transfer reactions must obey the Woodward–Hoffmann rules. Group transfer reactions can be divided into two distinct subcategories: the ene reaction and the diimide reduction. Group transfer reactions have diverse applications in various fields, including protein adenylation, biocatalytic and chemoenzymatic approaches for chemical synthesis, and strengthening skim natural rubber latex.

<span class="mw-page-title-main">Glutamine synthetase</span> Class of enzymes

Glutamine synthetase (GS) is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine:

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

Myristoylation is a lipidation modification where a myristoyl group, derived from myristic acid, is covalently attached by an amide bond to the alpha-amino group of an N-terminal glycine residue. Myristic acid is a 14-carbon saturated fatty acid (14:0) with the systematic name of n-tetradecanoic acid. This modification can be added either co-translationally or post-translationally. N-myristoyltransferase (NMT) catalyzes the myristic acid addition reaction in the cytoplasm of cells. This lipidation event is the most common type of fatty acylation and is present in many organisms, including animals, plants, fungi, protozoans and viruses. Myristoylation allows for weak protein–protein and protein–lipid interactions and plays an essential role in membrane targeting, protein–protein interactions and functions widely in a variety of signal transduction pathways.

<span class="mw-page-title-main">G protein-coupled receptor kinase</span>

G protein-coupled receptor kinases are a family of protein kinases within the AGC group of kinases. Like all AGC kinases, GRKs use ATP to add phosphate to Serine and Threonine residues in specific locations of target proteins. In particular, GRKs phosphorylate intracellular domains of G protein-coupled receptors (GPCRs). GRKs function in tandem with arrestin proteins to regulate the sensitivity of GPCRs for stimulating downstream heterotrimeric G protein and G protein-independent signaling pathways.

Neuromedin B (NMB) is a bombesin-related peptide in mammals. It was originally purified from pig spinal cord, and later shown to be present in human central nervous system and gastrointestinal tract.

The unfolded protein response (UPR) is a cellular stress response related to the endoplasmic reticulum (ER) stress. It has been found to be conserved between mammalian species, as well as yeast and worm organisms.

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

Binding immunoglobulin protein (BiPS) also known as 78 kDa glucose-regulated protein (GRP-78) or heat shock 70 kDa protein 5 (HSPA5) is a protein that in humans is encoded by the HSPA5 gene.

<span class="mw-page-title-main">Protein phosphorylation</span> Process of introducing a phosphate group on to a protein

Protein phosphorylation is a reversible post-translational modification of proteins in which an amino acid residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Phosphorylation alters the structural conformation of a protein, causing it to become activated, deactivated, or otherwise modifying its function. Approximately 13,000 human proteins have sites that are phosphorylated.

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

Rho GTPase-activating protein 32 is a protein that in humans is encoded by the RICS gene. RICS has two known isoforms, RICS that are expressed primarily at neurite growth cones, and at the post synaptic membranes, and PX-RICS which is more widely expressed in the endoplasmic reticulum, Golgi apparatus and endosomes. The only known domain of the RICS is the RhoGAP domain, whilst PX-RICS has an additional Phox homology and SH3 domain.

<span class="mw-page-title-main">Fic/DOC protein family</span>

In molecular biology, the Fic/DOC protein family is a family of proteins which catalyzes the post-translational modification of proteins using phosphate-containing compound as a substrate. Fic domain proteins typically use ATP as a co-factor, but in some cases GTP or UTP is used. Post-translational modification performed by Fic domains is usually NMPylation, however they also catalyze phosphorylation and phosphocholine transfer. This family contains a central conserved motif HPFX[D/E]GNGR in most members and it carries the invariant catalytic histidine. Fic domain was found in bacteria, eukaryotes and archaea and can be found organized in almost hundred different multi-domain assemblies.

<span class="mw-page-title-main">Guanylate-binding protein</span>

In molecular biology, the guanylate-binding proteins family is a family of GTPases that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-KD immunity-related GTPases (IRGs), the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class.

FIC domain protein adenylyltransferase (FICD) is an enzyme in metazoans possessing adenylylation and deadenylylation activity (also known as (de)AMPylation), and is a member of the Fic (filamentation induced by cAMP) domain family of proteins. AMPylation is a reversible post-translational modification that FICD performs on target cellular protein substrates. FICD is the only known Fic domain encoded by the metazoan genome, and is located on chromosome 12 in humans. Catalytic activity is reliant on the enzyme's Fic domain, which catalyzes the addition of an AMP (adenylyl group) moiety to the substrate. FICD has been linked to many cellular pathways, most notably the ATF6 and PERK branches of the UPR (unfolded protein response) pathway regulating ER homeostasis. FICD is present at very low basal levels in most cell types in humans, and its expression is highly regulated. Examples of FICD include HYPE (Huntingtin Yeast Interacting Partner E) in humans, Fic-1 in C. elegans, and dfic in D. melanogaster.

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