Characterization and origin of bacterial arginine kinases

An emerging field: Post-translational modification in microbiome

Post-translational modifications (PTMs) play an essential role in most biological processes. PTMs on human proteins have been extensively studied. Studies on bacterial PTMs are emerging, which demonstrate that bacterial PTMs are different from human PTMs in their types, mechanisms and functions. Few PTM studies have been done on the microbiome. Here, we reviewed several studied PTMs in bacteria including phosphorylation, acetylation, succinylation, glycosylation, and proteases. We discussed the enzymes responsible for each PTM and their functions. We also summarized the current methods used to study microbiome PTMs and the observations demonstrating the roles of PTM in the microbe-microbe interactions within the microbiome and their interactions with the environment or host. Although new methods and tools for PTM studies are still needed, the existing technologies have made great progress enabling a deeper understanding of the functional regulation of the microbiome. Large-scale application of these microbiome-wide PTM studies will provide a better understanding of the microbiome and its roles in the development of human diseases.

Knockdown or inhibition of arginine kinases enhances susceptibility of Tribolium castaneum to deltamethrin

Metabolism of insecticides is an energy-consuming process. As an important component of the intracellular energy buffering system, arginine kinase (AK) plays an important role in insect cellular energy homeostasis and environmental stress response, but the involvement of AKs in the response to chemical stressors (insecticides) remains largely unknown. In this study, using Tribolium castaneum as a model organism, we found that deltamethrin treatment significantly upregulated the expression of TcAK1 and TcAK2 and decreased the whole body ATP content. The knockdown of TcAK1 or TcAK2 significantly enhances the deltamethrin-induced ATP depletion and increase the susceptibility of T. castaneum to deltamethrin. In addition, pretreatment with two AK inhibitors, rutin and quercetin, significantly decreased the lifespan of beetles treated with deltamethrin. These results suggest that AKs might be involved in detoxification of insecticides by regulating cellular energy balance.

Diversity of phosphagen kinases in annelids: The first sequence report for a putative opheline kinase

Opheline kinase (OK) is one of the phosphagen kinases (PKs) restricted to annelids, but the amino acid sequence has not been determined yet. The OK enzyme was isolated in 1966 from the polychaete Ophelia neglecta (Opheliidae) and shown to have somewhat broader activities for the various substrates opheline, lombricine and taurocyamine. To determine the OK sequence, we analyzed the RNA sequencing data for Ophelina sp. and Thoracophelia sp., belonging to Opheliidae. Four PK sequences, namely, taurocyamine kinase (TK), creatine kinase (CK), mitochondrial CK (MiCK) and putative OK, were identified in both species, and the recombinant Ophelina enzymes were expressed in E. coli and purified. Since the substrate opheline was not commercially available, we used the partial activity toward taurocyamine to infer the enzyme specificity. The putative Ophelina OK showed lower activity to taurocyamine with a V_max/K_m nearly identical to a previously published value for an OK from a related species Ophelia neglecta. Under the same conditions, the true Ophelina TK showed much higher activity. Thus, the putative Ophelina enzyme was determined to be OK. The amino acid sequence alignment indicated that Ophelina and Thoracophelia OKs have five amino acid deletions in the GS region, like those of LKs and AKs, and the guanidino substrate specific residue was Lys, the same as LKs. In the phylogenetic tree constructed from annelid PK amino acid sequences, the OK sequences formed a distinct cluster, and it was placed near the TK and lombricine kinase (LK) clusters. This is the first report of the amino acid sequence for the OK enzyme.

Broad-complex transcription factor mediates opposing hormonal regulation of two phylogenetically distant arginine kinase genes in Tribolium castaneum

The phosphoarginine-arginine kinase shuttle system plays a critical role in maintaining insect cellular energy homeostasis. Insect molting and metamorphosis are coordinated by fluctuations of the ecdysteroid and juvenile hormone. However, the hormonal regulation of insect arginine kinases remain largely elusive. In this report, we comparatively characterized two arginine kinase genes, TcAK1 and TcAK2, in Tribolium castaneum. Functional analysis using RNAi showed that TcAK1 and TcAK2 play similar roles in adult fertility and stress response. TcAK1 was detected in cytoplasm including mitochondria, whereas TcAK2 was detected in cytoplasm excluding mitochondria. Interestingly, TcAK1 expression was negatively regulated by 20-hydroxyecdysone and positively by juvenile hormone, whereas TcAK2 was regulated by the opposite pattern. RNAi, dual-luciferase reporter assays and electrophoretic mobility shift assay further revealed that the opposite hormonal regulation of TcAK1 and TcAK2 was mediated by transcription factor Broad-Complex. Finally, relatively stable AK activities were observed during larval-pupal metamorphosis, which was generally consistent with the constant ATP levels. These results provide new insights into the mechanisms underlying the ATP homeostasis in insects by revealing opposite hormonal regulation of two phylogenetically distant arginine kinase genes.

Zhang et al. characterize the functions of two distinct arginine kinase genes in flour beetles. Using RNA interference and electophoretic mobility shift assays, they identify Broad-Complex transcription factor as the mediator of opposing hormonal regulation in these genes.

Quest for the Crypto-phosphoproteome

Protein phosphorylation is one of the most studied post-translational modifications (PTMs). Despite the remarkable advances in phosphoproteomics, a chemically less-stable subset of the phosphosites, which we call the crypto-phosphoproteome, has remained underexplored due to technological challenges. In this Viewpoint, we briefly summarize the current understanding of these elusive protein phosphorylations and identify the missing pieces for future studies.

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.

Bacterial arginine kinases have a highly skewed distribution within the proteobacteria

Phosphagen kinases (PKs) are known to be distributed throughout the animal kingdom, but have recently been discovered in some protozoan and bacterial species. A recent search of the available bacterial genomes revealed 49 unique sequences that appear to code for an arginine kinase (AK). The distribution of sequences was highly skewed with thirty nine out the forty nine sequences being found in six Proteobacteria classes (α, β, δ, γ, ε, and ζ) which represented 46.6% of the 61,335 bacterial genomes available at JGI-IMG/M website. Moreover, twenty one of the unique and metagenome bAK sequences identified were from δ-Proteobacteria despite these representing only 0.88% of the total genomes available. Phylogenetic analyses revealed that the bacterial AK sequences were interpersed between basal species such as cnidarians, sponges and protozoa, displaying an unstable clustering that was dependent upon the parameters chosen for phylogenetic analysis. Three of these putative bacterial AK genes were cloned into the pET45 expression vector, expressed, and biochemically confirmed to be capable of phosphorylating arginine using ATP. Results of the kinetic analyses of the putative bAKs from Ahrensia, D. autotrophicum, and O. profundus show that the catalytic efficiencies with respect to arginine for each enzyme, measured at 10⁴-10⁵ M^-1 s^-1, fall within the range expected for competent arginine kinases.

Structure of McsB, a protein kinase for regulated arginine phosphorylation

Protein phosphorylation regulates key processes in all organisms. In Gram-positive bacteria, protein arginine phosphorylation plays a central role in protein quality control by regulating transcription factors and marking aberrant proteins for degradation. Here, we report structural, biochemical, and in vivo data of the responsible kinase, McsB, the founding member of an arginine-specific class of protein kinases. McsB differs in structure and mechanism from protein kinases that act on serine, threonine, and tyrosine residues and instead has a catalytic domain related to that of phosphagen kinases (PhKs), metabolic enzymes that phosphorylate small guanidino compounds. In McsB, the PhK-like phosphotransferase domain is structurally adapted to target protein substrates and is accompanied by a novel phosphoarginine (pArg)-binding domain that allosterically controls protein kinase activity. The identification of distinct pArg reader domains in this study points to a remarkably complex signaling system, thus challenging simplistic views of bacterial protein phosphorylation.

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.

Arginine Kinases from the Precious Corals Corallium rubrum and Paracorallium japonicum: Presence of Two Distinct Arginine Kinase Gene Lineages in Cnidarians

The cDNA sequence of arginine kinase (AK) from the precious coral Corallium rubrum was assembled from transcriptome sequence data, and the deduced amino acid sequence of 364 residues was shown to conserve the structural features characteristic of AK. Based on the amino acid sequence, the DNA coding C. rubrum AK was synthesized by overlap extension PCR to prepare the recombinant enzyme. The following kinetic parameters were determined for the C. rubrum enzyme: K _a^Arg (0.10 mM), K _ia^Arg (0.79 mM), K _a^ATP (0.23 mM), K _ia^ATP (2.16 mM), and k _cat (74.3 s^-1). These are comparable with the kinetic parameters of other AKs. However, phylogenetic analysis suggested that the C. rubrum AK sequence has a distinct origin from that of other known cnidarian AKs with unusual two-domain structure. Using oligomers designed from the sequence of C. rubrum AK, the coding region of genomic DNA of another coral Paracorallium japonicum AK was successfully amplified. Although the nucleotide sequences differed between the two AKs at 14 positions in the coding region, all involved synonymous substitutions, giving the identical amino acid sequence. The P. japonicum AK gene contained one intron at a unique position compared with other cnidarian AK genes. Together with the observations from phylogenetic analysis, the comparison of exon/intron organization supports the idea that two distinct AK gene lineages are present in cnidarians. The difference in the nucleotide sequence between the coding regions of C. rubrum and P. japonicum AKs was 1.28%, which is twice that (0.54%) of mitochondrial DNA, is consistent with the general observation that the mitochondrial genome evolves slower than the nuclear one in cnidarians.

Arginine kinase from Haemonchus contortus decreased the proliferation and increased the apoptosis of goat PBMCs in vitro

BACKGROUND

Arginine kinase (AK), an important member of phosphagen kinase family has been extensively studied in various vertebrates and invertebrates. Immunologically, AKs are important constituents of different body parts, involved in various biological and cellular functions, and considered as immune-modulator and effector for pro-inflammatory cytokines. However, immunoregulatory changes of host cells triggered by AK protein of Haemonchus contortus, a parasitic nematode of ruminants, are still unknown. The current study was focused on cloning and characterisation of Hc-AK, and its regulatory effects on cytokines level, cell migration, cell proliferation, nitric oxide production and apoptosis of goat peripheral blood mononuclear cells (PBMCs) were observed.

METHODS

The full-length sequence of the Hc-AK gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) and sub-cloned into the prokaryotic expression vector pET-32a. The biochemical characteristics of recombinant protein Hc-AK, which was purified by affinity chromatography, were performed based on the enzymatic assay. Binding of rHc-AK with PBMCs was confirmed by immunofluorescence assay (IFA). Immunohistochemical analysis was used to detect localisation of Hc-AK within adult worms sections. The immunoregulatory effects of rHc-AK on cytokine secretions, cell proliferation, cell migration, nitric oxide production and apoptosis were determined by co-incubation of rHc-AK with goat PBMCs.

RESULTS

The full-length ORF (1080 bp) of the Hc-AK gene was successfully cloned, and His-tagged AK protein was expressed in the Escherichia coli strain BL21. The recombinant protein of Hc-AK (rHc-AK) was about 58.5 kDa together with the fused vector protein of 18 kDa. The biochemical assay showed that the protein encoded by the Hc-ak exhibited enzymatic activity. Western blot analysis confirmed that the rHc-AK was recognised by the sera from rat (rat-antiHc-AK). The IFA results showed that rHc-AK could bind on the surface of goat PBMCs. Immunohistochemically, Hc-AK was localised at the inner and outer membrane as well as in the gut region of adult worms. The binding of rHc-AK to host cells increased the levels of IL-4, IL-10, IL-17, IFN-γ, nitric oxide (NO) production and cell apoptosis of goat PBMCs, whereas, TGF-β1 levels, cell proliferation and PBMCs migration were significantly decreased in a dose dependent manner.

CONCLUSIONS

Our findings suggested that rHc-AK is an important excretory and secretory (ES) protein involved in host immune responses and exhibit distinct immunomodulatory properties during interaction with goat PBMCs.

Activity-Based Profiling Reveals a Regulatory Link between Oxidative Stress and Protein Arginine Phosphorylation

Protein arginine phosphorylation is a recently discovered modification that affects multiple cellular pathways in Gram-positive bacteria. In particular, the phosphorylation of arginine residues by McsB is critical for regulating the cellular stress response. Given that the highly efficient protein arginine phosphatase YwlE prevents arginine phosphorylation under non-stress conditions, we hypothesized that this enzyme negatively regulates arginine phosphorylation and acts as a sensor of cell stress. To evaluate this hypothesis, we developed the first suite of highly potent and specific SO₃-amidine-based YwlE inhibitors. With these protein arginine phosphatase-specific probes, we demonstrated that YwlE activity is suppressed by oxidative stress, which consequently increases arginine phosphorylation, thereby inducing the expression of stress-response genes, which is critical for bacterial virulence. Overall, we predict that these novel chemical tools will be widely used to study the regulation of protein arginine phosphorylation in multiple organisms.

Arginine kinase from Myzostoma cirriferum, a basal member of annelids

We assembled a phosphagen kinase gene from the Expressed Sequence Tags database of Myzostoma cirriferum, a basal member of annelids. The assembled gene sequence was synthesized using an overlap extension polymerase chain reaction method and was expressed in Escherichia coli. The recombinant enzyme (355 residues) exhibited monomeric behavior on a gel filtration column and showed strong activity only for l-arginine. Thus, the enzyme was identified as arginine kinase (AK). The two-substrate kinetic parameters were obtained and compared with other AKs. Phylogenetic analysis of amino acid sequences of phosphagen kinases indicated that the Myzostoma AK gene lineage differed from that of the polychaete Sabellastarte spectabilis AK, which is a dimer of creatine kinase (CK) origin. It is likely that the Myzostoma AK gene lineage was lost at an early stage of annelid evolution and that Sabellastarte AK evolved secondarily from the CK gene. This work contributes to our understanding of the evolution of phosphagen kinases of annelids with marked diversity.

Exploring the diversity of protein modifications: special bacterial phosphorylation systems

Protein modifications not only affect protein homeostasis but can also establish new cellular protein functions and are important components of complex cellular signal sensing and transduction networks. Among these post-translational modifications, protein phosphorylation represents the one that has been most thoroughly investigated. Unlike in eukarya, a large diversity of enzyme families has been shown to phosphorylate and dephosphorylate proteins on various amino acids with different chemical properties in bacteria. In this review, after a brief overview of the known bacterial phosphorylation systems, we focus on more recently discovered and less widely known kinases and phosphatases. Namely, we describe in detail tyrosine- and arginine-phosphorylation together with some examples of unusual serine-phosphorylation systems and discuss their potential role and function in bacterial physiology, and regulatory networks. Investigating these unusual bacterial kinase and phosphatases is not only important to understand their role in bacterial physiology but will help to generally understand the full potential and evolution of protein phosphorylation for signal transduction, protein modification and homeostasis in all cellular life.

Cooperativity and evolution of Tetrahymena two-domain arginine kinase

Tetrahymena pyriformis contains two arginine kinases, a 40-kDa enzyme (AK1) with a myristoylation signal sequence at the N-terminus and a two-domain 80-kDa enzyme (AK2). The former is localized mainly in cilia and the latter is in the cytoplasm. AK1 was successfully synthesized using an insect cell-free protein synthesis system and subjected to peptide mass fingerprinting (PMF) analysis. The masses corresponding to unmodified N-terminal tryptic peptide or N-terminal myristoylated peptide were not observed, suggesting that N-terminal peptides were not ionized in this analysis. We performed PMF analyses for two other phosphagen kinases (PKs) with myristoylation signals, an AK from Nematostella vectensis and a PK from Ectocarpus siliculosus. In both cases, the myristoylated, N-terminal peptides were clearly identified. The differences between the experimental and theoretical masses were within 0.0165-0.0583 Da, supporting the accuracy of the identification. Domains 1 and 2 of Tetrahymena two-domain AK2 were expressed separately in Escherichia coli and the extent of cooperativity was estimated on the basis of their kinetic constants. The results suggested that each of the domains functions independently, namely no cooperativity is displayed between the two domains. This is in sharp contrast to the two-domain AK from Anthopleura.

Characterization of the arginine kinase isoforms in Caenorhabditis elegans

Phosphagen kinases (PKs) are well-studied enzymes involved in energy homeostasis in a wide range of animal, protozoan, and even some bacterial species. Recent genome efforts have allowed comparative work on the PKs to extend beyond the biochemistry of individual proteins to the comparative cellular physiology and examining of the role of all PK family members in an organism. The sequencing of the Caenorhabditis elegans genome and availability of sophisticated genetic tools within that system affords the opportunity to conduct a detailed physiological analysis of the PKs from a well known invertebrate for comparison with the extensive work conducted on vertebrate systems. As a first step in this effort we have carried out a detailed molecular genetic and biochemical characterization of the PKs in C. elegans. Our results reveal that C. elegans has five PK genes encoding arginine kinases that range in catalytic efficiency (kcat/KM(Arg)) from (3.1±0.6)×10(4) to (9±4)×10(5) M(-1) s(-1). This range is generally within the range seen for arginine kinases from a variety of species. Our molecular genetic and phylogenetic analysis reveals that the gene family has undergone extensive intron loss and gain within the suborder Rhabditina. In addition, within C. elegans we find evidence of gene duplication and loss. The analysis described here for the C. elegans AKs represents one of the most complete biochemical and molecular genetic analysis of a PK family within a genetically tractable invertebrate system and opens up the possibility of conducting detailed physiological comparisons with vertebrate systems using the sophisticated tools available with this model invertebrate system.

Arginine kinases from the marine feather star Tropiometra afra macrodiscus: The first finding of a prenylation signal sequence in metazoan phosphagen kinases

Two arginine kinase cDNAs (AK1 and AK2) were isolated from the marine feather star Tropiometra afra macrodiscus, and the gene structure (exon/intron organization) of AK1 was determined. The cDNA-derived amino acid sequences and the exon/intron organization of the Tropiometra AK1 gene were homologous to those of a human creatine kinase (CK) as well as the AK of the sea cucumber Stichopus. Phylogenetic analysis also supports the close relationship between human CKs and echinoderm AKs, indicating that the latter AKs evolved from an ancestral CK gene. We observed that the Tropiometra AK1 gene has a novel C-terminal extension (approximately 50 amino acid residues) encoded by a unique exon. Moreover, a typical prenylation signal sequence (CSLL) was found at the C-terminal end of this extension, suggesting that AK1 is anchored to a membrane. AK2 had no such C-terminal extension. This is the first finding of a prenylation signal in metazoan phosphagen kinases. Recombinant Tropiometra AK1 and AK2 enzymes were successfully expressed in Escherichia coli, and their kinetic constants were determined. Both enzymes showed activity comparable to that of typical invertebrate AKs.

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.

Two arginine kinases of Tetrahymena pyriformis: characterization and localization

Two cDNAs, one coding a typical 40-kDa arginine kinase (AK1) and the other coding a two-domain 80-kDa enzyme (AK2), were isolated from ciliate Tetrahymena pyriformis, and their recombinant enzymes were successfully expressed in Escherichia coli. Both enzymes had an activity comparable to those of typical invertebrate AKs. Interestingly, the amino acid sequence of T. pyriformis AK1, but not AK2, had a distinct myristoylation signal sequence at the N-terminus, suggesting that 40-kDa AK1 targets the membrane. Moreover, Western blot analysis showed that the AK1 is mainly localized in the ciliary fraction. Based on these results, we discuss the phosphoarginine shuttle, which enables a continuous energy flow to dynein for ciliary movement in T. pyriformis, and the role of AK1 in this model.