Two-domain arginine kinase from the deep-sea clam Calyptogena kaikoi--evidence of two active domains

The characterization of novel monomeric creatine kinases in the early branching Alveolata species, Perkinsus marinus: Implications for phosphagen kinase evolution

The genome of the unicellular molluscan parasite Perkinsus marinus contains at least five genes coding for putative creatine kinases (CK), a phosphoryl transfer enzyme which plays a key role in cellular energy transactions. Expression and kinetic analyses of three of the P. marinus CKs revealed them to be true CKs with catalytic properties in the range of typical metazoan CKs. A sequence comparison of the P. marinus CKs with a range of CK dimers and other dimeric phosphoryl transfer enzymes in this family (phosphagen kinases) showed that the P. marinus CKs lacked some of the critical residues involved in dimer stabilization, a trait all previously characterized CKs share. Size exclusion chromatography of all three expressed P. marinus CK constructs indicated they are monomeric, consistent with the observed lack of some critical dimer stabilizing residues. Phylogenetic analyses of the P. marinus CKs and putative dinoflagellate CKs with a broad range of monomeric and dimeric phosphagen kinases revealed that the Perkinsus CKs form a distinct, well-supported clade with dinoflagellate CKs which also lack the dimer stabilizing residues. Analysis of the genomic data for P. marinus showed the presence of putative genes for the two enzymes associated with creatine biosynthesis. CK in higher organisms plays a critical role in energy buffering in cell types displaying high and variable rates of ATP turnover. The presence of multiple CKs and the creatine biosynthetic pathway in P. marinus indicates that this unicellular parasite has the full complement of molecular machinery for CK-mediated energy buffering.

Structure and functional analysis reveal an important regulated role of arginine kinase in Patinopecten yessoensis under low pH stress

Arginine kinase (AK), an important member of the phosphokinase family, is involved in temporal and spatial adenosine triphosphate (ATP) buffering systems. AK plays an important role in physiological function and metabolic regulations, in particular tissues with high and fluctuating energy demands. In present study, four AK genes were firstly identified from Yesso scallop (Patinopecten yessoensis) genome, respectively named PyAK1-4. PyAKs have highly conserved structures with a six-exon/five-exon structure, except for PyAK3. PyAK3 contains an unusual two-domain structure and a "bridge intron" between the two domains, which may originate from gene duplication and subsequent fusion. Phylogenetic analysis showed that all PyAKs belonged to an AK supercluster together with other AK proteins from Mollusca, Platyhelminthes, Arthropoda, and Nematode. A transcriptome database demonstrated that PyAK3 and PyAK4 were the main functional executors with high expression level during larval development and in adult tissues, while PyAK1 and PyAK2 were expressed at a low level. Furthermore, both PyAK2 and PyAK3 showed notably high expression in the male gonad, and PyAK4 was broadly expressed in almost all tissues with the highest level in striated muscle, indicating a tissue-specific expression pattern of PyAKs. In addition, quantitative real-time PCR results demonstrated that the expression of PyAK2, PyAK3 and PyAK4 were significantly upregulated in response to pH stress, especially in an extremely acidifying condition (pH 6.5), revealing the possible involvement of PyAKs in energetic homeostasis during environmental changes. Collectively, a comprehensive analysis of PyAKs was conducted in P. yessoensis. The diversity of PyAKs and their specific expression patterns promote a better understanding of energy metabolism in the growth, development and environmental response of P. yessoensis.

Natural Products Containing 'Rare' Organophosphorus Functional Groups

Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.

Positive selection adaptation of two-domain arginine kinase (AK) from cold seep Vesicomyidae clams

Arginine kinase (AK) is an important member of Phosphagen kinases which engage in energy metabolism process, and AKs from cold seep clams may develop an effective mechanism to adapt a special habitat (e.g. low temperature). Three Vesicomyidae clams and seven Veneridae clams (belong to the same Order Veneroida) were chosen to analyze the evolution of two-domain AKs. In the present study, ten two-domain AKs were identified and Neighbor-joining tree showed that AKs were divided into two groups. Branch-site model indicated that two-domain AKs were subjected to strong positive selection (ω_2a = 17.5058). 16 positively selective sites were detected and five of them showed posterior probabilities of 0.95 or more. Comparative analysis found that domain 2 might be suffered from more evolutionary selection pressure than domain 1, as most positively sites were located at domain 2. Residue Pro (positively selective site) (587P in ApAK) in domain 2 from all Vesicomyidae AKs might participate in change of the synergism and in the function of its cold-adapted characteristics. In conclusion, our studies provide evidence of positive Darwinian selection in the two-domain AKs family of Vesicomyidae clams, and may contribute to a better understanding of its adaptation mechanisms to cold seep habitats.

The substrate-free and -bound crystal structures of the duplicated taurocyamine kinase from the human parasite Schistosoma mansoni

The taurocyamine kinase from the blood fluke Schistosoma mansoni (SmTK) belongs to the phosphagen kinase (PK) family and catalyzes the reversible Mg(2+)-dependent transfer of a phosphoryl group between ATP and taurocyamine. SmTK is derived from gene duplication, as are all known trematode TKs. Our crystallographic study of SmTK reveals the first atomic structure of both a TK and a PK with a bilobal structure. The two unliganded lobes present a canonical open conformation and interact via their respective C- and N-terminal domains at a helix-mediated interface. This spatial arrangement differs from that observed in true dimeric PKs, in which both N-terminal domains make contact. Our structures of SmTK complexed with taurocyamine or l-arginine compounds explain the mechanism by which an arginine residue of the phosphagen specificity loop is crucial for substrate specificity. An SmTK crystal was soaked with the dead end transition state analog (TSA) components taurocyamine-NO3 (2-)-MgADP. One SmTK monomer was observed with two bound TSAs and an asymmetric conformation, with the first lobe semiclosed and the second closed. However, isothermal titration calorimetry and enzyme kinetics experiments showed that the two lobes function independently. A small angle x-ray scattering model of SmTK-TSA in solution with two closed active sites was generated.

Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains

Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

Gene structure of the two-domain taurocyamine kinase from Paragonimus westermani: evidence for a distinct lineage of trematode phosphagen kinases

Taurocyamine kinase (TK) is an enzyme that catalyzes the reversible transfer of a phosphate between ATP and taurocyamine. Annelid TKs were suggested to have evolved from a CK ancestor. However, TKs from the lung fluke Paragonimus westermani comprised another lineage. Construction of phylogenetic tree and comparison of exon/intron organization showed that P. westermani TK and other trematode TKs evolved from a molluscan arginine kinase (AK) gene. Exon shuffling probably caused the changes in amino acid sequence thereby changing the affinity from AK to TK. The present study provides new insights on the evolution of phosphagen kinases found in trematodes.

Cold-adapted features of arginine kinase from the deep-sea clam Calyptogena kaikoi

The heterodont clam Calyptogena kaikoi, which inhabits depths exceeding 3,500 m where low ambient temperatures prevail, has an unusual two-domain arginine kinase (AK) with molecular mass of 80 kDa, twice that of typical AKs. The purpose of this work is to investigate the nature of the adaptations of this AK for functioning at low temperatures. Recombinant C. kaikoi AK constructs were expressed, and their two-substrate kinetic constants (k(cat), K(a), and K(ia)) were determined at 10°C and 25°C, respectively. When measured at 25°C, the K(ia) values were tenfold larger than those for corresponding K(a) values, while at 10°C, the K(ia) values decreased remarkably, but the K (a) values were almost unchanged. The Calyptogena two-domain enzyme has threefold higher catalytic efficiency, calculated by k (cat)/(K(a)(ARG)·K(ia)(ATP) ), at 10°C, than that at 25°C, reflecting adaptation for function at reduced ambient temperatures. The activation energy (E(a)) and thermodynamic parameters were determined for Calyptogena two-domain enzyme and compared with those of two-domain enzymes from mesophilic Corbicula and Anthopleura. The value for E(a) of Calyptogena enzyme were about half of those for mesophilic enzymes, and a larger decrease in entropy was observed in Calyptogena AK reaction. Although large decrease in entropy increases the ΔG(o‡) value and consequently lowers the k(cat) value, this is compensated with its lower E(a) value thereby minimizing the reduction in its k(cat) value. These thermodynamic properties, together with the kinetic ones, are also present in the separated domain 2 of the Calyptogena two-domain enzyme.

A diverse array of creatine kinase and arginine kinase isoform genes is present in the starlet sea anemone Nematostella vectensis, a cnidarian model system for studying developmental evolution

Phosphagen (guanidino) kinases (PK) constitute a family of homologous phosphotransferases catalyzing the reversible transfer of the high-energy phosphoryl group of ATP to naturally occurring guanidine compounds. Prior work has shown that PKs can be phylogenetically separated into two distinct groups- an arginine kinase (AK) subfamily and a creatine kinase (CK) subfamily. The latter includes three CK isoforms- cytoplasmic CK (CyCK), mitochondrial CK (MiCK) and three-domain flagellar CK (fCK). In the present study we identified six unique PK genes from the draft genome sequence of the starlet sea anemone Nematostella vectensis, a well-known model organism for understanding metazoan developmental evolution. Using reverse transcription polymerase chain reaction (RTPCR) methods, full length cDNAs were amplified for all of these PKs. These cDNAs were cloned and expressed in Escherichia coli as 6x His-tagged fusion proteins. The six PKs were identified as the three typical CK isoforms (CyCK, MiCK and fCK), two unusual AKs (a two-domain AK (2DAK) and a three-domain AK (3DAK)) and a PK which phosphorylated arginine. The latter enzyme had a very low AK activity (its apparent V(max) value being less than 0.2% that of 3DAK), lacks several key residues necessary for AK enzyme activity, and was tentatively designated as AK1. As far as we know, this constitutes the first report of an AK with the three fused AK domains. The Bayesian tree suggested that the third domain of 3DAK likely evolved from the gene for domain 2 of typical two-domain AK found widely in cnidarians. Construction of phylogenetic trees and comparison of exon-intron organizations of their respective genes indicated that the N. vectensis three-domain fCK and 3DAK evolved independently, and both enzymes are likely to be targeted to cell membranes since they have a myristoylation signal at their respective N-termini. These results complement prior work on other basal invertebrates showing that multiple CK and AK isoform genes were present at the dawn of the radiation of metazoans. The presence of isoform diversity in an organism lacking in structural complexity reflects an early imperative for targeting of PKs to particular cellular contexts such as muscle fibers, neurons, ciliated/flagellated epithelia and spermatozoa.

Biochemical and mutational analyses of a multidomain cellulase/mannanase from Caldicellulosiruptor bescii

Thermophilic cellulases and hemicellulases are of significant interest to the biofuel industry due to their perceived advantages over their mesophilic counterparts. We describe here biochemical and mutational analyses of Caldicellulosiruptor bescii Cel9B/Man5A (CbCel9B/Man5A), a highly thermophilic enzyme. As one of the highly secreted proteins of C. bescii, the enzyme is likely to be critical to nutrient acquisition by the bacterium. CbCel9B/Man5A is a modular protein composed of three carbohydrate-binding modules flanked at the N terminus and the C terminus by a glycoside hydrolase family 9 (GH9) module and a GH5 module, respectively. Based on truncational analysis of the polypeptide, the cellulase and mannanase activities within CbCel9B/Man5A were assigned to the N- and C-terminal modules, respectively. CbCel9B/Man5A and its truncational mutants, in general, exhibited a pH optimum of ∼5.5 and a temperature optimum of 85°C. However, at this temperature, thermostability was very low. After 24 h of incubation at 75°C, the wild-type protein maintained 43% activity, whereas a truncated mutant, TM1, maintained 75% activity. The catalytic efficiency with phosphoric acid swollen cellulose as a substrate for the wild-type protein was 7.2 s(-1) ml/mg, and deleting the GH5 module led to a mutant (TM1) with a 2-fold increase in this kinetic parameter. Deletion of the GH9 module also increased the apparent k(cat) of the truncated mutant TM5 on several mannan-based substrates; however, a concomitant increase in the K(m) led to a decrease in the catalytic efficiencies on all substrates. These observations lead us to postulate that the two catalytic activities are coupled in the polypeptide.

Gene profiling and characterization of arginine kinase-1 (MrAK-1) from freshwater giant prawn (Macrobrachium rosenbergii)

Arginine kinase-1 (MrAK-1) was sequenced from the freshwater prawn Macrobrachium rosenbergii using Illumina Solexa Genome Analyzer Technique. MrAK-1 consisted of 1068 bp nucleotide encoded 355 polypeptide with an estimated molecular mass of 40 kDa. MrAK-1 sequence contains a potential ATP:guanido phosphotransferases active domain site. The deduced amino acid sequence of MrAK-1 was compared with other 7 homologous arginine kinase (AK) and showed the highest identity (96%) with AK-1 from cherry shrimp Neocaridina denticulate. The qRT-PCR analysis revealed a broad expression of MrAK-1 with the highest expression in the muscle and the lowest in the eyestalk. The expression of MrAK-1 after challenge with the infectious hypodermal and hematopoietic necrosis virus (IHHNV) was tested in muscle. In addition, MrAK-1 was expressed in Escherichia coli by prokaryotic expression plasmid pMAL-c2x. The optimum temperature (30 °C) and pH (8.5) was determined for the enzyme activity assay. MrAK-1 showed significant (P < 0.05) activity towards 10-50 mM ATP concentration. The enzyme activity was inhibited by α-ketoglutarate, glucose and ATP at the concentration of 10, 50 and 100 mM respectively. Conclusively, the findings of this study indicated that MrAK-1 might play an important role in the coupling of energy production and utilization and the immune response in shrimps.

Cloning, expression, characterization and phylogenetic analysis of arginine kinase from greasyback shrimp (Metapenaeus ensis)

Arginine kinase (AK) plays an important role in cellular energy metabolism in invertebrate. The encoding AK gene from Shrimp Metapenaeus ensis (M. ensis) was cloned in prokaryotic expression plasmid pET-28a, and it was then expressed in Escherichia coil in dissoluble form. The recombinant protein was purified by following three chromatography steps in turn: CM-Cellulose cation-exchange, Sephacryl S-100HR gel filtrate and DEAE-Sepharose anion-exchange. The purified AK's apparent K(m) was 2.33+/-0.1 and 1.59+/-0.2 mM for ATP and l-arginine, respectively, while its optimum pH and temperature was 8.5 and 30 degrees C in the process of forward reaction, respectively. Phylogenetic analysis of cDNA-derived amino acid sequences for the AKs indicated a close affinity of M. ensis and another shrimp (Litopenaeus vannamei).

A novel arginine kinase from the shrimp Neocaridina denticulata: the fourth arginine kinase gene lineage

Arginine kinases (AK) evolved independently at least three times: first at an early stage of phosphagen kinase evolution (typical AK), second from the cytoplasmic creatine kinase (CK) gene later in metazoan evolution (Stichopus AK) and third from the mitochondrial CK gene in the course of annelid radiation (Sabellastarte AK). Here, we present a possible fourth AK lineage. We amplified cDNA encoding three AKs (AK1, AK2 and AK3) from the shrimp Neocaridina denticulata, and determined their amino acid sequences (355-356 residues). Each cDNA sequence was cloned in a pET plasmid and the corresponding recombinant kinase was expressed in E. coli. The AKs showed monomeric nature similar to typical AKs on an analytical gel filtration column. While the amino acid sequence of AK2 corresponded to that of typical AK, containing the conserved key residues established in Limulus AK for the substrate binding site, those of AK1 and AK3 lacked some of these key residues, indicating a similar evolution to Stichopus and Sabellastarte AKs. Moreover, phylogenetic analysis of phosphagen kinases indicated that Neocaridina AK1 and AK3 diverged at the deepest branching point close to the root of the tree and formed a distinct cluster outside the typical AK cluster, which included Neocaridina AK2. Kinetic constants of Neocaridina AKs were similar to those of other AKs. However, activation energy (E(a)) for the transition state of AK1 and AK3 was about 1.5-fold larger than that of AK2. The DeltaH(o++) values for AK1 and AK3 were also about 1.5-fold larger than that for AK2, but all three DeltaG(o++) values were very similar (71-72 kJ/mol); this results in similar reaction velocities for the three AK reactions due to a lower decrease in entropy in the activated complexes of AK1 and AK3 reactions compared to that of AK2. These findings suggest that Neocaridina AK1 and AK3 are unique from the known three AK gene lineages and therefore comprises a fourth AK lineage.