Unusual N-terminal Extension Research Articles

Halotolerant carbonic anhydrase with unusual N-terminal extension from marine Hydrogenovibrio marinus as novel biocatalyst for carbon sequestration under high-salt environments

Carbonic anhydrase (CA), an enzyme that catalyzes the carbon dioxide (CO2) hydration, has been suggested as a potentially powerful agent for CO2 capture and utilization. For successful application, CA should withstand the harsh environment presented by CO2-capturing facilities. While there have been intensive efforts to identify and engineer thermostable CAs, other required conditions such as the high salt concentration of CO2 absorbents have often been ignored. Herein, we expressed, purified, and characterized a novel α-type CA (hmCA) possessing an unusual N-terminal extension from the halophilic marine bacterium Hydrogenovibrio marinus. We found that the N-terminal extension strongly influenced the enzyme solubility. Recombinant hmCA showed catalytic efficiency comparable to other bacterial α-type CAs. hmCA was less inhibited by anionic inhibitors showing 1.6- (NO3−), 3.1- (NO2−), and 3.7-fold (Cl−) higher inhibition constants than those of mesophilic bovine CA (bCA), suggesting halotolerance. Recombinant hmCA was markedly stabilized using most of the alkali metal salts tested, showing 19 °C higher melting temperature at 1 M NaCl compared to bCA that was significantly destabilized. The region of N-terminal extension seemed not to be involved in halotolerance. The remarkable halotolerance may be attributed to the uneven distribution of electrostatic potential and the localized negative charge on the hmCA surface. hmCA displayed ∼29-fold longer half-life than that of bCA at 40 °C in potassium carbonate as a practical absorbent, suggesting that halotolerance should be considered another key characteristic in the development of biocatalysts for CO2 capture using high-salt-containing CO2 absorbents.

An Appended Domain Results in an Unusual Architecture for Malaria Parasite Tryptophanyl-tRNA Synthetase

Specific activation of amino acids by aminoacyl-tRNA synthetases (aaRSs) is essential for maintaining fidelity during protein translation. Here, we present crystal structure of malaria parasite Plasmodium falciparum tryptophanyl-tRNA synthetase (Pf-WRS) catalytic domain (AAD) at 2.6 Å resolution in complex with L-tryptophan. Confocal microscopy-based localization data suggest cytoplasmic residency of this protein. Pf-WRS has an unusual N-terminal extension of AlaX-like domain (AXD) along with linker regions which together seem vital for enzymatic activity and tRNA binding. Pf-WRS is not proteolytically processed in the parasites and therefore AXD likely provides tRNA binding capability rather than editing activity. The N-terminal domain containing AXD and linker region is monomeric and would result in an unusual overall architecture for Pf-WRS where the dimeric catalytic domains have monomeric AXDs on either side. Our PDB-wide comparative analyses of 47 WRS crystal structures also provide new mechanistic insights into this enzyme family in context conserved KMSKS loop conformations.

The tumour suppressor DiRas3 interacts with C‐RAF and downregulates MEK activity to restrict cell migration

The mitogenic pathway, composed of RAF kinases, mitogen-activated protein kinase kinases (MEK) and extracellular signal-regulated kinases (ERK), promotes cell proliferation and migration and is upregulated in many tumours. DiRas3 (ARHI, Noey2), a mainly GTP-bound Ras-like protein with an unusual N-terminal extension, is predominantly lost in ovarian and breast cancers. Its re-expression in these tissues impairs cell proliferation, autophagy, apoptosis and cell migration. Further, loss of DiRas3 correlates with an increase in growth factor-induced ERK phosphorylation. Therefore, DIRAS3 proves to be a curious gene with remarkable tumour suppressing capabilities. However, how DiRas3 interferes with ERK phosphorylation, has remained unknown. We demonstrate that DiRas3 associates in vivo with C-RAF and directly binds in vitro to C-RAF, which is upstream of MEK and ERK. Direct binding of DiRas3 to C-RAF is nucleotide independent, and DiRas3's N-terminal extension alone is not sufficient for binding C-RAF. DiRas3 expression inhibits the activating phosphorylations of MEK and ERK. Serum-induced recruitment of DiRas3 to the plasma membrane depends mainly on its N-terminal extension and less on its C-terminus, bound nucleotide or the presence of Ras-GTP. Correspondingly, removal of the N-terminal extension strongly decreases DiRas3's inhibition of MEK and ERK phosphorylations. Tyrosyl-phosphatases do not contribute significantly to reduction of ERK-phosphorylation byDiRas3. Consistently, downregulation of DiRas3 results in a small but significant and persistent increase in MEK and ERK phosphorylation, but does not increase phosphorylation of P38, AKT and c-Jun NH2-terminal kinase. Finally, downregulation of DiRas3 causes increased cell migration, through a mechanism that is MEK dependent. These results support a model in which serum signals induce the recruitment of DiRas3 to the plasma membrane, where it is tethered via its N- and C-termini. At the plasma membrane, DiRas3 interacts with C-RAF to specifically suppress the activating phosphorylations on MEK and ERK, thus restricting migration of non-cancer cells. This effect is relatively small, but it is also persistent, suggesting that it contributes to the maintenance of the non-migratory phenotype of non-cancerous tissues, in which DiRas3 is expressed.

Vaccinia virus anti-apoptotic F1L is a novel Bcl-2-like domain-swapped dimer that binds a highly selective subset of BH3-containing death ligands

Apoptosis is an important part of the host's defense mechanism for eliminating invading pathogens. Some viruses express proteins homologous in sequence and function to mammalian pro-survival Bcl-2 proteins. Anti-apoptotic F1L expressed by vaccinia virus is essential for survival of infected cells, but it bears no discernable sequence homology to proteins other than its immediate orthologues in related pox viruses. Here we report that the crystal structure of F1L reveals a Bcl-2-like fold with an unusual N-terminal extension. The protein forms a novel domain-swapped dimer in which the alpha1 helix is the exchanged domain. Binding studies reveal an atypical BH3-binding profile, with sub-micromolar affinity only for the BH3 peptide of pro-apoptotic Bim and low micromolar affinity for the BH3 peptides of Bak and Bax. This binding interaction is sensitive to F1L mutations within the predicted canonical BH3-binding groove, suggesting parallels between how vaccinia virus F1L and myxoma virus M11L bind BH3 domains. Structural comparison of F1L with other Bcl-2 family members reveals a novel sequence signature that redefines the BH4 domain as a structural motif present in both pro- and anti-apoptotic Bcl-2 members, including viral Bcl-2-like proteins.

The N Terminus of the Anti-apoptotic BCL-2 Homologue MCL-1 Regulates Its Localization and Function

The BCL-2 homologue MCL-1 plays an important role in the regulation of cell fate by blocking apoptosis as well as regulating cell cycle. MCL-1 has an unusual N-terminal extension, which contains a PEST domain and several phosphorylation sites that have been suggested to regulate its turnover. Here we report that the first 79 amino acids of MCL-1 regulate its subcellular localization. Deletion of this domain impairs both its mitochondrial localization and its anti-apoptotic activity. Conversely, expression of the N terminus of MCL-1 promotes both the association of MCL-1 with mitochondria and cell survival in a fashion that is dependent on the presence of endogenous MCL-1. In addition, the N terminus of MCL-1 has an antagonistic effect on proliferation. Although MCL-1 decreases proliferation through binding to proliferating cell nuclear antigen and cyclin-dependent kinase 1 in the nucleus, the N terminus of MCL-1 accelerates cell division. On the other hand, deletion of this region further increases the anti-proliferative activity of MCL-1. These results suggest that the N terminus of MCL-1 plays a major regulatory role, regulating coordinately the mitochondrial (anti-apoptotic) and nuclear (anti-proliferative) functions of MCL-1.

The glucose-6-phosphate dehydrogenase from Trypanosoma cruzi: Its role in the defense of the parasite against oxidative stress

The Trypanosoma cruzi glucose-6-phosphate dehydrogenase (G6PDH) is encoded by several genes located in three of the parasite chromosomes. All the sequences present two possible start codons, 111 bp apart, also present in its Trypanosoma brucei counterpart. As the 37 residues comprised between the two candidate initiator methionines of T. brucei and T. cruzi G6PDHs constitute an unusual N-terminal extension only present in trypanosomatids, two forms of the T. cruzi G6PDH were expressed in Escherichia coli: a long one (Tc-G6PDH-L) translated from the first ATG codon, and a short one (Tc-G6PDH-S) translated from the second. Both were purified and their kinetic constants determined. The apparent K m for glucose-6-phosphate was 189.9, 98.4, and 288 μM, for Tc-G6PDH-L, Tc-G6PDH-S and native Tc-G6PDH, respectively. The apparent K m for NADP was similar for both recombinant proteins. The Tc-G6PDH-L as well as the native enzyme, was inactivated by DTT while the Tc-G6PDH-S was unaffected by the reducing agent. This behavior could be related to the presence of two Cys groups in the N-terminal extension of the Tc-G6PDH-L similarly to the redox regulated G6PDHs from chloroplasts and cyanobacteria. This property, together with a remarkable induction (up to 46-fold) of the T. cruzi G6PDH in metacyclic trypomastigotes under oxidative stress conditions, suggests that the enzyme may play a prominent role in the defense mechanisms of the parasite against oxidative stress becoming an important target for chemotherapy. Western blots using antibodies against the N-terminal extension in Tc-G6PDH-L show that this form is expressed in the parasite.

Role of the N-Terminal Extension of the (βα)8-Barrel Enzyme Indole-3-glycerol Phosphate Synthase for Its Fold, Stability, and Catalytic Activity,

Indole-3-glycerol phosphate synthase (IGPS) catalyzes the fifth step in the biosynthesis of tryptophan. It belongs to the large and versatile family of (betaalpha)(8)-barrel enzymes but has an unusual N-terminal extension of about 40 residues. Limited proteolysis with trypsin of IGPS from both Sulfolobus solfataricus (sIGPS) and Thermotoga maritima (tIGPS) removes about 25 N-terminal residues and one of the two extra helices contained therein. To assess the role of the extension, the N-terminally truncated variants sIGPSDelta(1-26) and tIGPSDelta(1-25) were produced recombinantly in Escherichia coli, purified, and characterized in comparison to the wild-type enzymes. Both sIGPSDelta(1-26) and tIGPSDelta(1-25) have unchanged oligomerization states and turnover numbers. In contrast, their Michaelis constants for the substrate 1-(o-carboxyphenylamino)-1-deoxyribulose 5-phosphate are increased, and their resistance toward unfolding induced by heat and guanidinium chloride is decreased. sIGPSDelta(1-26) was crystallized, and its X-ray structure was solved at 2.8 A resolution. The comparison with the known structure of sIGPS reveals small differences that account for its reduced substrate affinity and protein stability. The structure of the core of sIGPSDelta(1-26) is, however, unchanged compared to sIGPS, explaining its retained catalytic activity and consistent with the idea that it evolved from the same ancestor as the phosphoribosyl anthranilate isomerase and the alpha-subunit of tryptophan synthase. These (betaalpha)(8)-barrel enzymes catalyze the reactions preceding and following IGPS in tryptophan biosynthesis but lack an N-terminal extension.

The Invertase Inhibitor Nt-CIF from Tobacco: A Highly Thermostable Four-helix Bundle with an Unusual N-terminal Extension

Plant invertases are sucrolytic enzymes essential for plant metabolism and development. Enzyme activity is regulated on a posttranslational level via inhibitory proteins, referred to as invertase inhibitors. Ectopic expression of invertase inhibitors in crop plants has high biotechnological potential. However, little biochemical and up to now no detailed structural information is available about this class of plant regulatory proteins. Here, we present the crystal structure of the cell wall-associated invertase inhibitor Nt-CIF from tobacco at a resolution of 1.87Å. The structural model reveals an asymmetric four-helix bundle with an uncommon N-terminal extension that appears to be critical for the structural integrity of the protein. Structure analysis of a second crystal form grown in the presence of CdCl2 reveals two metal binding sites. Nt-CIF is highly thermostable and retains full inhibitory activity after cooling to ambient temperatures. The structure of Nt-CIF provides the first three-dimensional information source for the posttranslational regulation of plant invertases. Based on the recently discovered sequence homology between inhibitors of invertases and pectin methylesterases, our structural model is likely to represent a scaffold also used for the regulation of the latter enzymes, which do not share sequence similarity with invertases. Thus, our structural model sets the 3D-stage for the investigation of posttranslational regulation of invertases as well as pectin methylesterases.

Biochemical and genetic evidence for a family of heterotrimeric G-proteins in Trichomonas vaginalis.

We have cloned a single copy gene from the human parasite Trichomonas vaginalis that encodes a putative protein of 402 amino acids with approximately 35% sequence identity to known alpha subunits of heterotrimeric G-proteins. It contains the characteristic GTP binding domains G-1 to G-5 with the key residues conserved. The new sequence has an unusual N-terminal extension of approximately 70 residues that cannot be aligned to reference G-proteins and which is characterised by proline-rich repeats. To investigate the expression and cellular localisation of the protein we produced specific antisera against a recombinant fusion protein. The antisera recognised a protein of an apparent molecular mass of 51 kDa in protein extracts from T. vaginalis and immunofluorescent microscopy established that the protein is localised to discrete endomembranes. Using a protocol designed to purify mammalian heterotrimeric G-proteins incorporating a GTPgammaS binding assay, we isolated two proteins from Trichomonas that are recognised by an heterologous GA/1 antisera raised to a peptide of the conserved G-1 domain of G-protein alpha subunits. These two proteins have an apparent molecular mass of 61 and 48 kDa, respectively, larger and smaller than the translation product of the cloned gene. Consistent with these results, the GA/1 antisera did not cross-react with the fusion protein produced from the gene we have cloned. These data suggest T. vaginalis possesses more than one heterotrimeric G-protein alpha subunit. Based on the sequence features of the cloned gene and the biochemical properties of the purified proteins, we suggest that these alpha subunits are likely to be part of classic heterotrimeric G-protein complexes.

The Streptomyces coelicolor developmental transcription factor sigmaBldN is synthesized as a proprotein.

bldN is one of a set of genes required for the formation of specialized, spore-bearing aerial hyphae during differentiation in the mycelial bacterium Streptomyces coelicolor. Previous analysis (M. J. Bibb et al., J. Bacteriol. 182:4606-4616, 2000) showed that bldN encodes a member of the extracytoplasmic function subfamily of RNA polymerase sigma factors and that translation from the most strongly predicted start codon (GTG(1)) would give rise to a sigma factor having an unusual N-terminal extension of ca. 86 residues. Here, by using a combination of site-directed mutagenesis and immunoblot analysis, we provide evidence that all bldN translation arises from initiation at GTG(1) and that the primary translation product is a proprotein (pro-sigma(BldN)) that is proteolytically processed to a mature species (sigma(BldN)) by removal of most of the unusual N-terminal extension. A time course taken during differentiation of the wild type on solid medium showed early production of pro-sigma(BldN) and the subsequent appearance of mature sigma(BldN), which was concomitant with aerial mycelium formation and the disappearance of pro-sigma(BldN). Two genes encoding members of a family of metalloproteases that are involved in the regulated proteolytic processing of transcription factors in other organisms were identified in the S. coelicolor genome, but their disruption did not affect differentiation or pro-sigma(BldN) processing.

Structural analysis and antibody response to the extracellular glutathione S-transferases from Onchocerca volvulus.

Onchocerca volvulus is a human pathogenic filarial parasite which, like other parasitic nematodes, is capable of surviving in an immunologically competent host by employing a variety of immune evasion strategies and defense mechanisms including the detoxification and repair mechanisms of the glutathione S-transferases (GSTs). In this study we analyzed the glycosylation pattern and the immunological properties of extracellular O. volvulus GST1a and -1b (OvGST1a and -1b). The enzymes differ in only 10 amino acids, and both are glycoproteins that have cleavable signal peptides and unusual N-terminal extensions. These characteristics have not been described for other GSTs so far. Mass spectrometry analyses indicate that both enzymes carry high-mannose type oligosaccharides on at least four glycosylation sites. Glycosylation sites 1 to 3 of OvGST1a (OvGST1b sites 2 to 4) are occupied by truncated N-glycans (Man(2)GlcNAc2 to Man(5)GlcNAc(2)), and N glycosylation site 4 of OvGST1a (OvGST1b site 5) carries Man(5)GlcNAc2 to Man(9)GlcNAc(2). To analyze the capacity of these secretory GSTs to stimulate host immune responses, we studied the antibody responses of onchocerciasis patients against the native affinity-purified OvGST1a and -1b. By enzyme-linked immunosorbent assay we showed that OvGST1a and -1b are immunodominant antigens, with less than 7% nonresponder patients. A direct comparison of the antibody responses to the glycosylated and deglycosylated forms demonstrates the high immunogenicity of the N-glycans. Analyses of the antibody responses to the unusual N-terminal extension show an enhanced recognition of this portion by patients as opposed to recognition of the recombinant protein without extension.

Sigma(BldN), an extracytoplasmic function RNA polymerase sigma factor required for aerial mycelium formation in Streptomyces coelicolor A3(2).

Sporulation mutants of Streptomyces coelicolor appear white because they are defective in the synthesis of the gray polyketide spore pigment, and such white (whi) mutants have been used to define 13 sporulation loci. whiN, one of five new whi loci identified in a recent screen of NTG (N-methyl-N'-nitro-N-nitrosoguanidine)-induced whi strains (N. J. Ryding et al., J. Bacteriol. 181:5419-5425, 1999), was defined by two mutants, R112 and R650. R650 produced frequent spores that were longer than those of the wild type. In contrast, R112 produced long, straight, undifferentiated hyphae, although rare spore chains were observed, sometimes showing highly irregular septum placement. Subcloning and sequencing showed that whiN encodes a member of the extracytoplasmic function subfamily of RNA polymerase sigma factors and that the sigma factor has an unusual N-terminal extension of approximately 86 residues that is not present in other sigma factors. A constructed whiN null mutant failed to form aerial mycelium (the "bald" phenotype) and, as a consequence, whiN was renamed bldN. This observation was not totally unexpected because, on some media, the R112 point mutant produced substantially less aerial mycelium than its parent, M145. The bldN null mutant did not fit simply into the extracellular signaling cascade proposed for S. coelicolor bld mutants. Expression of bldN was analyzed during colony development in wild-type and aerial mycelium-deficient bld strains. bldN was transcribed from a single promoter, bldNp. bldN transcription was developmentally regulated, commencing approximately at the time of aerial mycelium formation, and depended on bldG and bldH, but not on bldA, bldB, bldC, bldF, bldK, or bldJ or on bldN itself. Transcription from the p1 promoter of the response-regulator gene bldM depended on bldN in vivo, and the bldMp1 promoter was shown to be a direct biochemical target for sigma(BldN) holoenzyme in vitro.

Identification, Characterization, and Crystal Structure of the Omega Class Glutathione Transferases

A new class of glutathione transferases has been discovered by analysis of the expressed sequence tag data base and sequence alignment. Glutathione S-transferases (GSTs) of the new class, named Omega, exist in several mammalian species and Caenorhabditis elegans. In humans, GSTO 1-1 is expressed in most tissues and exhibits glutathione-dependent thiol transferase and dehydroascorbate reductase activities characteristic of the glutaredoxins. The structure of GSTO 1-1 has been determined at 2.0-A resolution and has a characteristic GST fold (Protein Data Bank entry code ). The Omega class GSTs exhibit an unusual N-terminal extension that abuts the C terminus to form a novel structural unit. Unlike other mammalian GSTs, GSTO 1-1 appears to have an active site cysteine that can form a disulfide bond with glutathione.