P-loop GTPases Research Articles

The Universally Conserved Unconventional G Protein YchF Is Critical for Growth and Stress Response.

The ancient guanine nucleotide-binding (G) proteins are a group of critical regulatory and signal transduction proteins, widely involved in diverse cellular processes of all kingdoms of life. YchF is a kind of universally conserved novel unconventional G protein that appears to be crucial for growth and stress response in eukaryotes and bacteria. YchF is able to bind and hydrolyze both adenine nucleoside triphosphate (ATP) and guanosine nucleoside triphosphate (GTP), unlike other members of the P-loop GTPases. Hence, it can transduce signals and mediate multiple biological functions by using either ATP or GTP. YchF is not only a nucleotide-dependent translational factor associated with the ribosomal particles and proteasomal subunits, potentially bridging protein biosynthesis and degradation, but also sensitive to reactive oxygen species (ROS), probably recruiting many partner proteins in response to environmental stress. In this review, we summarize the latest insights into how YchF is associated with protein translation and ubiquitin-dependent protein degradation to regulate growth and maintain proteostasis under stress conditions.

Protection of HSP60 in Myzus persicae Treated with Cry7Ab4 Toxin

Heat shock proteins (HSPs) are essential for the survival and development of animals under various stresses. However, little is known about the function of HSPs in insects response to Bacillus thuringiensis (Bt) toxins treatment. Here, we investigated the role of HSP60 in Myzus persicae (M. persicae) treated with an active Cry7Ab4 toxic core. First, we demonstrated the insensitivity of M. persicae to the Cry7Ab4 toxic core through a membrane capsule method. Then, using protein pull-down assay, several putative Cry7Ab4-binding proteins, including HSP60, were identified in an M. persicae nymph. P-loop GTPase Obg-like ATPase-1 (OLA1) was also found to be a Cry2Ab12-binding protein (unpublished data). Subsequent enzymatic and RT-qPCR assays revealed that highly expressed HSP60 removed the enhanced OLA1 activity caused by Cry7Ab4. ELISA analysis confirmed the binding interactions between Cry7Ab4, HSP60, and OLA1. Interestingly, a combination of ELISA and molecular docking analysis further suggested that HSP60 could block the binding interaction between Cry7Ab4 and OLA1 via higher affinity with Cry7Ab4. Besides, the Jun N-terminal kinase (JNK) pathway was found to be activated. Overall, we proposed the model that HSP60 protects M. persicae from Cry7Ab4 toxin. The study implies that HSP60 can be a crucial factor in insect defense against Cry toxins.

Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.

The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p/Fma1). Deletion of the putative metal transferase in Saccharomyces cerevisiae (ZNG1; formerly YNR029c) leads to defective Map1p function and a Zn-deficiency growth defect. Invitro, Zng1p can transfer Zn2+ or Co2+ to apo-Map1p, but unlike characterized copper chaperones, transfer is dependent on GTP hydrolysis. Proteomics reveal mis-regulation of the Zap1p transcription factor regulon because of loss of ZNG1 and Map1p activity, suggesting that Zng1p is required to avoid a compounding effect of Map1p dysfunction on survival during Zn limitation.

Biochemical Characterization of a Human Septin Octamer.

Septins are part of the cytoskeleton and polymerize into non-polar filaments of heteromeric hexamers or octamers. They belong to the class of P-loop GTPases but the roles of GTP binding and hydrolysis on filament formation and dynamics are not well understood. The basic human septin building block is the septin rod, a hetero-octamer composed of SEPT2, SEPT6, SEPT7, and SEPT9 with a stoichiometry of 2:2:2:2 (2-6-7-9-9-7-6-2). Septin rods polymerize by end-to-end and lateral joining into linear filaments and higher ordered structures such as rings, sheets, and gauzes. We purified a recombinant human septin octamer from E. coli for in vitro experimentation that is able to polymerize into filaments. We could show that the C-terminal region of the central SEPT9 subunit contributes to filament formation and that the human septin rod decreases the rate of in vitro actin polymerization. We provide further first kinetic data on the nucleotide uptake- and exchange properties of human hexameric and octameric septin rods. We could show that nucleotide uptake prior to hydrolysis is a dynamic process and that a bound nucleotide is exchangeable. However, the hydrolyzed γ-phosphate is not released from the native protein complex. We consequently propose that GTP hydrolysis in human septins does not follow the typical mechanism known from other small GTPases.

The Universally Conserved ATPase YchF Regulates Translation of Leaderless mRNA in Response to Stress Conditions.

The universally conserved P-loop GTPases control diverse cellular processes, like signal transduction, ribosome assembly, cell motility, and intracellular transport and translation. YchF belongs to the Obg-family of P-loop GTPases and is one of the least characterized member of this family. It is unique because it preferentially hydrolyses ATP rather than GTP, but its physiological role is largely unknown. Studies in different organisms including humans suggest a possible role of YchF in regulating the cellular adaptation to stress conditions. In the current study, we explored the role of YchF in the model organism Escherichia coli. By western blot and promoter fusion experiments, we demonstrate that YchF levels decrease during stress conditions or when cells enter stationary phase. The decline in YchF levels trigger increased stress resistance and cells lacking YchF are resistant to multiple stress conditions, like oxidative stress, replication stress, or translational stress. By in vivo site directed cross-linking we demonstrate that YchF interacts with the translation initiation factor 3 (IF3) and with multiple ribosomal proteins at the surface of the small ribosomal subunit. The absence of YchF enhances the anti-association activity of IF3, stimulates the translation of leaderless mRNAs, and increases the resistance against the endoribonuclease MazF, which generates leaderless mRNAs during stress conditions. In summary, our data identify YchF as a stress-responsive regulator of leaderless mRNA translation.

Reformulation of an extant ATPase active site to mimic ancestral GTPase activity reveals a nucleotide base requirement for function.

Hydrolysis of nucleoside triphosphates releases similar amounts of energy. However, ATP hydrolysis is typically used for energy-intensive reactions, whereas GTP hydrolysis typically functions as a switch. SpoIVA is a bacterial cytoskeletal protein that hydrolyzes ATP to polymerize irreversibly during Bacillus subtilis sporulation. SpoIVA evolved from a TRAFAC class of P-loop GTPases, but the evolutionary pressure that drove this change in nucleotide specificity is unclear. We therefore reengineered the nucleotide-binding pocket of SpoIVA to mimic its ancestral GTPase activity. SpoIVAGTPase functioned properly as a GTPase but failed to polymerize because it did not form an NDP-bound intermediate that we report is required for polymerization. Further, incubation of SpoIVAGTPase with limiting ATP did not promote efficient polymerization. This approach revealed that the nucleotide base, in addition to the energy released from hydrolysis, can be critical in specific biological functions. We also present data suggesting that increased levels of ATP relative to GTP at the end of sporulation was the evolutionary pressure that drove the change in nucleotide preference in SpoIVA.

The Impact of the Stringent Response on TRAFAC GTPases and Prokaryotic Ribosome Assembly.

Many facets of ribosome biogenesis and function, including ribosomal RNA (rRNA) transcription, 70S assembly and protein translation, are negatively impacted upon induction of a nutrient stress-sensing signalling pathway termed the stringent response. This stress response is mediated by the alarmones guanosine tetra- and penta-phosphate ((p)ppGpp), the accumulation of which leads to a massive cellular response that slows growth and aids survival. The 70S bacterial ribosome is an intricate structure, with assembly both complex and highly modular. Presiding over the assembly process is a group of P-loop GTPases within the TRAFAC (Translation Factor Association) superclass that are crucial for correct positioning of both early and late stage ribosomal proteins (r-proteins) onto the rRNA. Often described as ‘molecular switches’, members of this GTPase superfamily readily bind and hydrolyse GTP to GDP in a cyclic manner that alters the propensity of the GTPase to carry out a function. TRAFAC GTPases are considered to act as checkpoints to ribosome assembly, involved in binding to immature sections in the GTP-bound state, preventing further r-protein association until maturation is complete. Here we review our current understanding of the impact of the stringent response and (p)ppGpp production on ribosome maturation in prokaryotic cells, focusing on the inhibition of (p)ppGpp on GTPase-mediated subunit assembly, but also touching upon the inhibition of rRNA transcription and protein translation.

Cellular roles of the human Obg-like ATPase 1 (hOLA1) and its YchF homologs.

P-loop NTPases comprise one of the major superfamilies of nucleotide binding proteins, which mediate a variety of cellular processes, such as mRNA translation, signal transduction, cell motility, and growth regulation. In this review, we discuss the structure and function of two members of the ancient Obg-related family of P-loop GTPases: human Obg-like ATPase 1 (hOLA1), and its bacterial/plant homolog, YchF. After a brief discussion of nucleotide binding proteins in general and the classification of the Obg-related family in particular, we discuss the sequence and structural features of YchF and hOLA1. We then explore the various functional roles of hOLA1 in mammalian cells during stress response and cancer progression, and of YchF in bacterial cells. Finally, we directly compare and contrast the structure and function of hOLA1 with YchF before summarizing the future perspectives of hOLA1 research. This review is timely, given the variety of recent studies aimed at understanding the roles of hOLA1 and YchF in such critical processes as cellular-stress response, oncogenesis, and protein synthesis.

Genome analysis of urease positive Serratia marcescens, co-producing SRT-2 and AAC(6′)-Ic with multidrug efflux pumps for antimicrobial resistance

In this study, we present the genome sequence of Serratia marcescens SM03, recovered from a human gut in India. The final assembly consists of 26 scaffolds (4620 coding DNA sequences, 5.08 Mb, 59.6% G + C ratio) and 79 tRNA genes. Analysis identified novel genes associated with lactose utilization, virulence, P-loop GTPases involved in urease production, CFA/I fimbriae apparatus and Yersinia – type CRISPR proteins. Antibiotic susceptibility testing indicated drug tolerant phenotype and inhibition assays demonstrated involvement of extrusion in resistance. Presence of enzymes SRT-2, AAC(6′)-Ic, with additional Ybh transporter and EamA-like efflux pumps signifies the genetic plasticity observed in S. marcescens SM03.

Initial Cluster Analysis.

We study a simple abstract problem motivated by a variety of applications in protein sequence analysis. Consider a string of 0s and 1s of length L, and containing D 1s. If we believe that some or all of the 1s may be clustered near the start of the sequence, which subset is the most significantly so clustered, and how significant is this clustering? We approach this question using the minimum description length principle and illustrate its application by analyzing residues that distinguish translational initiation and elongation factor guanosine triphosphatases (GTPases) from other P-loop GTPases. Within a structure of yeast elongation factor 1nalphan, these residues form a significant cluster centered on a region implicated in guanine nucleotide exchange. Various biomedical questions may be cast as the abstract problem considered here.

Inferring joint sequence-structural determinants of protein functional specificity.

Residues responsible for allostery, cooperativity, and other subtle but functionally important interactions remain difficult to detect. To aid such detection, we employ statistical inference based on the assumption that residues distinguishing a protein subgroup from evolutionarily divergent subgroups often constitute an interacting functional network. We identify such networks with the aid of two measures of statistical significance. One measure aids identification of divergent subgroups based on distinguishing residue patterns. For each subgroup, a second measure identifies structural interactions involving pattern residues. Such interactions are derived either from atomic coordinates or from Direct Coupling Analysis scores, used as surrogates for structural distances. Applying this approach to N-acetyltransferases, P-loop GTPases, RNA helicases, synaptojanin-superfamily phosphatases and nucleases, and thymine/uracil DNA glycosylases yielded results congruent with biochemical understanding of these proteins, and also revealed striking sequence-structural features overlooked by other methods. These and similar analyses can aid the design of drugs targeting allosteric sites.

Abstract 419: OLA1 Regulates GSK3β/eIF2-alpha Signaling Axis in Angiotensin II-treated Human Ventricular Cardiomyocytes

Pathological cardiac hypertrophy in response to stress or disease such as hypertension, myocardial infarction, valvular disease or neurohomonal dysregulation often result in heart failure. Cardiac hypertrophy is associated with changes in key molecular features including protein synthesis, sarcomeric organization, fibrogenesis, cell death and energy metabolism. OBG like ATPase 1 (OLA1) belongs to the translation factor-related (TRAFAC) class, Obg family, and YchF subfamily of P-loop GTPases that play a crucial role in the regulation of diverse cellular processes including protein translation, intracellular transport, signal transduction and growth. Recent study has shown that OLA1 functions as an intrinsic regulator in cellular stress responses, such as oxidative stress and heat shock. However, its role in cardiac hypertrophy is unknown so far. Here, we investigated the effect of OLA1 deficiency on angiotensin II (ANG II)-induced hypertrophic signaling response in immortalized human ventricular cardiomyocytes (hCM) and in heart tissue from OLA1 knockout mice. We observed that ANG II-induced increase in cardiomyocyte cell size was lower in OLA1 knockdown hCM cells as compared to control transfected cells. Interestingly, OLA1 knockdown inhibits the above effect and increases phosphorylation of GSK3β and eIF2α (inactive state). Furthermore, OLA1 homozygous knockout mice showed increase in phosphorylation of GSK3β. Taken together, these findings show that OLA1 deficiency decreases ANG II-induced hypertrophy signaling response in ventricular cardiomyocytes. This study provides the first evidence for the role of OLA1 in ANG II-induced hypertrophic response of human ventricular cardiomyocytes.

The relationship between folding and activity in UreG, an intrinsically disordered enzyme

A growing body of literature on intrinsically disordered proteins (IDPs) led scientists to rethink the structure-function paradigm of protein folding. Enzymes are often considered an exception to the rule of intrinsic disorder (ID), believed to require a unique structure for catalysis. However, recent studies revealed the presence of disorder in several functional native enzymes. In the present work, we address the importance of dynamics for catalysis, by investigating the relationship between folding and activity in Sporosarcina pasteurii UreG (SpUreG), a P-loop GTPase and the first discovered native ID enzyme, involved in the maturation of the nickel-containing urease. The effect of denaturants and osmolytes on protein structure and activity was analyzed using circular dichroism (CD), Site-Directed Spin Labeling (SDSL) coupled to EPR spectroscopy, and enzymatic assays. Our data show that SpUreG needs a “flexibility window” to be catalytically competent, with both too low and too high mobility being detrimental for its activity.

Structural and biochemical analysis of Escherichia coli ObgE, a central regulator of bacterial persistence

The Obg protein family belongs to the TRAFAC (translation factor) class of P-loop GTPases and is conserved from bacteria to eukaryotes. Essential roles in many different cellular processes have been suggested for the Obg protein from Escherichia coli (ObgE), and we recently showed that it is a central regulator of bacterial persistence. Here, we report the first crystal structure of ObgE at 1.85-Å resolution in the GDP-bound state, showing the characteristic N-terminal domain and a central G domain that are common to all Obg proteins. ObgE also contains an intrinsically disordered C-terminal domain, and we show here that this domain specifically contributed to GTP binding, whereas it did not influence GDP binding or GTP hydrolysis. Biophysical analysis, using small angle X-ray scattering and multi-angle light scattering experiments, revealed that ObgE is a monomer in solution, regardless of the bound nucleotide. In contrast to recent suggestions, our biochemical analyses further indicate that ObgE is neither activated by K+ ions nor by homodimerization. However, the ObgE GTPase activity was stimulated upon binding to the ribosome, confirming the ribosome-dependent GTPase activity of the Obg family. Combined, our data represent an important step toward further unraveling the detailed molecular mechanism of ObgE, which might pave the way to further studies into how this GTPase regulates bacterial physiology, including persistence.

The iron-type nitrile hydratase activator protein is a GTPase.

The Fe-type nitrile hydratase activator protein from Rhodococcus equi TG328-2 (ReNHase TG328-2) was successfully expressed and purified. Sequence analysis and homology modeling suggest that it is a G3E P-loop guanosine triphosphatase (GTPase) within the COG0523 subfamily. Kinetic studies revealed that the Fe-type activator protein is capable of hydrolyzing GTP to GDP with a kcat value of 1.2 × 10-3 s-1 and a Km value of 40 μM in the presence of 5 mM MgCl2 in 50 mM 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid at a pH of 8.0. The addition of divalent metal ions, such as Co(II), which binds to the ReNHase TG328-2 activator protein with a Kd of 2.9 μM, accelerated the rate of GTP hydrolysis, suggesting that GTP hydrolysis is potentially connected to the proposed metal chaperone function of the ReNHase TG328-2 activator protein. Circular dichroism data reveal a significant conformational change upon the addition of GTP, which may be linked to the interconnectivity of the cofactor binding sites, resulting in an activator protein that can be recognized and can bind to the NHase α-subunit. A combination of these data establishes, for the first time, that the ReNHase TG328-2 activator protein falls into the COG0523 subfamily of G3E P-loop GTPases, many of which play a role in metal homeostasis processes.

The C-terminal α-helix of YsxC is essential for its binding to 50S ribosome and rRNAs

YsxC is an essential P-loop GTPase that interacts with the 50S subunit of the ribosome. The putative implication in ribosome binding of two basic clusters of YsxC, a conserved positively charged patch including R31, R116, H117 and K146 lying adjacent to the nucleotide-binding site, and the C-terminal alpha helix, was investigated. C-terminal truncation variants of YsxC were unable to bind to both ribosome and rRNAs, whereas mutations in the other cluster did not affect YsxC binding. Our results indicate that the basic C-terminal region of YsxC is required for its binding to the 50S ribosomal subunit.

Interaction between Bacillus subtilis YsxC and ribosomes (or rRNAs)

YsxC is an essential P-loop GTPase, that binds to the 50S ribosomal subunit, and is required for the proper assembly of the ribosome. The aim of this study was to characterize YsxC ribosome interactions.The stoichiometry of YsxC ribosome subunit complex was evaluated. We showed that YsxC binding to the 50S ribosomal subunit is not affected by GTP, but in the presence of GDP the stoichiometry of YsxC-ribosome is decreased. YsxC GTPase activity was stimulated upon 50S ribosomal subunit binding. In addition, it is shown for the first time that YsxC binds both 16S and 23S ribosomal RNAs.

Plant DrgProteins are Cytoplasmic Small GTPase-ObgHomologue

The Obg/Era proteins of P-loop GTPase superclass are conserved in various prokaryotic and eukaryotic organisms. Some of these proteins are critical regulators of many aspects of basic cellular processes, including ribosome biogenesis, translation and signal transduction. However, a genome-wide overview of the Obg/EraGTPase genes in plants is not available. Recentlystudies on comprehensive genomic analyses of Arabidopsis thaliana identified 11 Obg-Hflx like GTPase genes that are divided into nine families/subfamilies: Archaea-related Drg and Nog1, and Eubacteria-related Obg, EngB, HflX, Era, TrmE, EngA, and EngD. In this study we found that Arabidopsis has 3 (three) Drg homologue proteins, namely AtDrg1-1, AtDrg1-2 and AtDrg1-3. Subcellular localization analysis of Arabidopsis Obg-Hflx homologues revealed that Archaea-derived Drg proteins are mainly targeted to cytoplasm, except Drg1-3 was detected not only in cytoplasm but also in nucleus. Furthermore, based on expression pattern profiling indicates that Drg1-1 and Drg1-2 were expressed constitutively trough plant development. On the other hand, Drg1-3 was detected in dry seed and under stress plant.

Abstract 3784: Role of OBG like ATPase 1 (OLA1) in F-actin polymerization and cell adhesion.

Abstract Cell adhesion and migration, driven by actin cytoskeletal dynamics, are the fundamental phenomenon in cancer metastasis. However, the molecular nature that underlies the coordination of actin cytoskeleton at sites of focal adhesions remains elusive. Obg like ATPase (OLA1) belongs to the YchF subfamily of Obg like P-loop GTPases. YchF proteins are highly conserved from yeast to humans, and believed to be regulatory proteins that interact with their client protein(s) by the conformational switch between the ADP and ATP bound forms. However, the actual physiological functions of OLA1 are poorly understood. In our previous studies we reported that OLA1 functions as a negative regulator in antioxidant response and knockdown of OLA1 inhibits migration and invasion of breast cancer cells in vitro. In this study, we have examined the mechanism underlying the anti-migratory role of OLA1. Expression of OLA1 was silenced by siRNA transfection (siOLA1) in human breast cancer cells MDA-MB-231 and human embryonic lung fibroblast cells WI-38, and the rate of attachment of suspended cells was evaluated against control siRNA-transfected cells. After plating into fibronectin or laminin coated plates, siOLA1 cells were attached and spread significantly faster than the control cells. At the end of 60 min siOLA1 MDA-MB-231 cells showed profound F-actin fibers on fibronectin coated plates. Immunofluorescence staining further revealed the co-localization of vinculin with actin at the spherical leading edges in control siRNA-transfected cells, which proclaimed that these cells are still trying to spread. In contrast, siOLA1 cells were fully spread and immensely polymerized actin fibers were completely dissociated from vinculin. Due to the augmented actin polymerization, siOLA1 cells are rendered with impaired depolymerization, a process required for an efficient actin disassembly. Furthermore, levels of S-glutathionylation, a form of redox sensitive and reversible posttranslational modification, were measured in these cells by immunoblot analysis. Consistently, glutathionylation of actin was found increased significantly in siOLA1 MDA-MB-231 cells at various adherent growth conditions, as well as in the form of single cell suspension immediately before the cells were plated. Since earlier studies have established the impacts of actin glutathionylation in impaired actin depolymerization and cell adhesion processes, we reason that heavier glutathionylation on actin attributes to the altered actin dynamics in siOLA1 cells. These studies provide evidence that focal adhesions are more stable in the absence of OLA1 and suggest that OLA1 regulates cell adhesion and migration in part by actin polymerization and S-glutathionylation of actin. Further studies are warranted to explore molecular mechanisms by which OLA1 modulates protein S-glutathionylation either globally or specifically on cytoskeleton molecules such as actin. Citation Format: Prince V. Jeyabal, Valentina Rubio, Jiawei Zhang, Zheng-Zheng Shi. Role of OBG like ATPase 1 (OLA1) in F-actin polymerization and cell adhesion. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3784. doi:10.1158/1538-7445.AM2013-3784

ATP hydrolysis by a domain related to translation factor GTPases drives polymerization of a static bacterial morphogenetic protein

The assembly of static supramolecular structures is a culminating event of developmental programs. One such structure, the proteinaceous shell (called the coat) that surrounds spores of the bacterium Bacillus subtilis, is composed of about 70 different proteins and represents one of the most durable biological structures known. The coat is built atop a basement layer that contains an ATPase (SpoIVA) that forms a platform required for coat assembly. Here, we show that SpoIVA belongs to the translation factors class of P-loop GTPases and has evolutionarily lost the ability to bind GTP; instead, it uses ATP hydrolysis to drive its self-assembly into static filaments. We demonstrate that ATP hydrolysis is required by every subunit for incorporation into the growing polymer by inducing a conformational change that drives polymerization of a nucleotide-free filament. SpoIVA therefore differs from other self-organizing polymers (dynamic cytoskeletal structures and static intermediate filaments) in that it uses ATP hydrolysis to self-assemble, not disassemble, into a static polymer. We further show that polymerization requires a critical concentration that we propose is only achieved once SpoIVA is recruited to the surface of the developing spore, thereby ensuring that SpoIVA polymerization only occurs at the correct subcellular location during spore morphogenesis.