Biochemical and structural characterization of a novel arginine kinase from the spider<i>Polybetes pythagoricus</i>

Laino, Aldana; López-Zavala, Alonso A.; García-Orozco, Karina D.; Carrasco-Miranda, J.S.; Santana, Marianela; Stojanoff, V.; Sotelo‐Mundo, Rogerio R.; Garcı́a, Carlos

doi:10.7717/peerj.3787

Cited by 15 publications

(10 citation statements)

References 66 publications

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“…The NE2 atom of this residue formed a hydrogen bond with the backbone carbonyl oxygen of A135, as previously reported for the DmAK structure (Figure 5a) [25]. This hydrogen bond is commonly found in many AK structures, such as A131-H224 in Apostichopus japonicus [28] and P135-H227 in Scylla paramamosain [29], P135-H227 in Polybetes pythagoricus [30], P135-H227 in Penaeus vannamei [31] and P135-H227 in Limulus Polyphemus [14], in both the basal and transition states. In the case of the DmAK H227A structure, the hydrogen bond destruction between A135 and H227, resulted in the replacement of one water molecule (WAT684) at the imidazole group of histidine position (Figure 5b).…”

Section: Structural Features Of Dmak H227asupporting

confidence: 78%

Crystal Structure of H227A Mutant of Arginine Kinase in Daphnia magna Suggests the Importance of Its Stability

et al. 2022

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Arginine kinase (AK) plays a crucial role in the survival of Daphnia magna, a water flea and a common planktonic invertebrate sensitive to water pollution, owing to the production of bioenergy. AK from D. magna (DmAK) has four highly conserved histidine residues, namely, H90, H227, H284, and H315 in the amino acid sequence. In contrast to DmAK WT (wild type), the enzyme activity of the H227A mutant decreases by 18%. To identify the structure-function relationship of this H227A mutant enzyme, the crystal 3D X-ray structure has been determined and an unfolding assay using anilino-1-naphthalenesulfonic acid (ANS) fluorescence has been undertaken. The results revealed that when compared to the DmAK WT, the hydrogen bonding between H227 and A135 was broken in the H227A crystal structure. This suggests that H227 residue, closed to the arginine binding site, plays an important role in maintaining the structural stability and maximizing the enzyme activity through hydrogen bonding with the backbone oxygen of A135.

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Section: Structural Features Of Dmak H227asupporting

confidence: 78%

Crystal Structure of H227A Mutant of Arginine Kinase in Daphnia magna Suggests the Importance of Its Stability

et al. 2022

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“…An increase in phospho-L-arginine is also a hallmark of exposure to OA in stage I larvae. This amino acid has an important role in buffering high energy phosphate in invertebrates, acting also as a shuttle mechanism for ATP production when needed [ 64 , 65 ].…”

Section: Discussionmentioning

confidence: 99%

Tolerant Larvae and Sensitive Juveniles: Integrating Metabolomics and Whole-Organism Responses to Define Life-Stage Specific Sensitivity to Ocean Acidification in the American Lobster

et al. 2021

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Bentho-pelagic life cycles are the dominant reproductive strategy in marine invertebrates, providing great dispersal ability, access to different resources, and the opportunity to settle in suitable habitats upon the trigger of environmental cues at key developmental moments. However, free-dispersing larvae can be highly sensitive to environmental changes. Among these, the magnitude and the occurrence of elevated carbon dioxide (CO2) concentrations in oceanic habitats is predicted to exacerbate over the next decades, particularly in coastal areas, reaching levels beyond those historically experienced by most marine organisms. Here, we aimed to determine the sensitivity to elevated pCO2 of successive life stages of a marine invertebrate species with a bentho-pelagic life cycle, exposed continuously during its early ontogeny, whilst providing in-depth insights on their metabolic responses. We selected, as an ideal study species, the American lobster Homarus americanus, and investigated life history traits, whole-organism physiology, and metabolomic fingerprints from larval stage I to juvenile stage V exposed to different pCO2 levels. Current and future ocean acidification scenarios were tested, as well as extreme high pCO2/low pH conditions that are predicted to occur in coastal benthic habitats and with leakages from underwater carbon capture storage (CCS) sites. Larvae demonstrated greater tolerance to elevated pCO2, showing no significant changes in survival, developmental time, morphology, and mineralisation, although they underwent intense metabolomic reprogramming. Conversely, juveniles showed the inverse pattern, with a reduction in survival and an increase in development time at the highest pCO2 levels tested, with no indication of metabolomic reprogramming. Metabolomic sensitivity to elevated pCO2 increased until metamorphosis (between larval and juvenile stages) and decreased afterward, suggesting this transition as a metabolic keystone for marine invertebrates with complex life cycles.

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“…AK is an important allergen, causing asthma, and it has been identified in crustaceans, spiders, and insects (García‐Orozco et al, 2007; Khamtorn et al, 2020; Sookrung et al, 2006). Moreover, AK is widely distributed in other invertebrates (Laino et al, 2017). A total of three AK coding genes were annotated in the genome (Figure 3d), with two genes expressed in VP (Figure 3b).…”

Section: Resultsmentioning

confidence: 99%

Chromosomal‐level genome of a sheet‐web spider provides insight into the composition and evolution of venom

Zhu

Jin

Hou

et al. 2022

Molecular Ecology Resources

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Spiders are the most abundant venomous predators in the world. Previous research related to spider venom has mostly relied on transcriptomes and proteomes, with only a few high-quality genomes available. This is far from consistent with the species diversity of spiders. In this study, we constructed a high-quality chromosome-level genome assembly of Hylyphantes graminicola, which contained 13 chromosomes, with a genome length of 931.68 Mb and scaffold N50 of 77.07 Mb. Integrating genome, transcriptome, and proteome profiling, we identified a total of 59 coding genes among nine toxin gene families. Among them, Group 7 allergen (ALL7) protein was reported in spider venom for the first time. Its coding genes had a predicted signal peptide and maintained high expression levels in the venom, suggesting that ALL7 plays an important role in venom and maybe is a type of newly discovered venom toxin in the spider. By implementing comparative genomics, we found a similar gene number of main toxin gene families in spiders and the scorpion genome with conservative evolutionary rates, indicating that these toxin genes could be an ancient (~400 million years) and a conserved "basic toolkit" for spiders and scorpions to perform primary defence functions. Obtaining high-quality chromosome-level genomes from spiders not only facilitates venom research and toxin resource application, but also can improve comparative genomic analysis in other important traits, like the evolution of silk or behaviour.

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Biochemical and structural characterization of a novel arginine kinase from the spiderPolybetes pythagoricus

Cited by 15 publications

References 66 publications

Crystal Structure of H227A Mutant of Arginine Kinase in Daphnia magna Suggests the Importance of Its Stability

Crystal Structure of H227A Mutant of Arginine Kinase in Daphnia magna Suggests the Importance of Its Stability

Tolerant Larvae and Sensitive Juveniles: Integrating Metabolomics and Whole-Organism Responses to Define Life-Stage Specific Sensitivity to Ocean Acidification in the American Lobster

Chromosomal‐level genome of a sheet‐web spider provides insight into the composition and evolution of venom

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