Gene Expression Detects the Factors Influencing the Reproductive Success and the Survival Rates of Paracentrotus lividus Offspring

The increase in the demand for Paracentrotus lividus roe, a food delicacy, causes increased pressure on its wild stocks. In this scenario, aquaculture facilities will mitigate the effects of anthropogenic pressures on the wild stocks of P. lividus. Consequently, experimental studies should be conducted to enhance techniques to improve efficient aquaculture practices for these animals. Here, we for the first time performed molecular investigations on cultured sea urchins. We aimed at understanding if maternal influences may significantly impact the life of future offspring, and how the culture conditions may impact the development and growth of cultured specimens. Our findings demonstrate that the outcomes of in vitro fertilization of P. lividus are influenced by maternal influences, but these effects are largely determined by culture conditions. In fact, twenty-three genes involved in the response to stress and skeletogenesis, whose expressions were measured by Real Time qPCR, were differently expressed in sea urchins cultured in two experimental conditions, and the results were largely modified in offspring deriving from two groups of females. The findings herein reported will be critical to develop protocols for the larval culture of the most common sea urchin, both for research and industrial production purposes for mass production.     

Family Growth and Survival Response to Two Simulated Water Temperature Environments in the Sea Urchin Strongylocentrotus intermedius

Heat tolerance is a target trait in the selective breeding of the sea urchin Strongylocentrotus intermedius, as it plays an important role in the survival and growth of cultured S. intermedius during summer. We investigated family growth and survival response to two temperature treatments to evaluate the genotype by temperature interaction (GEI) in the family selection of S. intermedius. Sea urchins from 11 families were exposed to two simulated water temperature environments—high temperature (HE) and control temperature (CE)—for 12 months, with each experiment divided into four periods (P1, stress-free period I; P2, stress-full high period; P3, stress-response period; and P4, stress-free period II) based on the temperature changes and the survival. Test diameter (TD), body weight (BW), and survival rate (SR) in HE and CE were measured monthly. Effects of family, temperature, and family-temperature interaction on TD, BW, SR, and specific growth rate (SGR) for BW were examined. In CE, BW differed significantly between families in P2, P3, and P4, while TD differed significantly between families in P3 and P4 (p < 0.05). In HE, family had significant effects on BW in P4, and on TD in P3 and P4, while temperature had significant effects on SR, TD, and BW in P3 and P4 (p < 0.05). GEI effects were not significant for TD or BW; however, family ranking changes revealed the existence of GEI in SR. The GEI results indicate the necessity of applying family selection in CE and HE for SR, but not for TD or BW. These results may provide a guide for aquaculture and selective breeding of S. intermedius under temperature pressure.     

Characterization of Copper/Zinc Superoxide Dismutase Activity on Phascolosoma esculenta (Sipuncula: Phascolosomatidea) and Its Protection from Oxidative Stress Induced by Cadmium

Phascolosoma esculenta, an economically important species inhabiting the high tide areas of the intertidal zone, is particularly sensitive to water pollution. Considering its potential as a bioindicator, studies on the ecotoxicology of P. esculenta are imperative. The toxic effects of cadmium (Cd) were analyzed by exposing P. esculenta to different concentrations of Cd (6, 24, 96 mg/L). In this study, the changes in the antioxidative indexes of total superoxide dismutase (T-SOD), glutathione s-transferase (GST), reduced glutathione (GSH), and microscale malondialdehyde (MDA) were recorded. Copper/zinc superoxide dismutase (Cu/Zn SOD) is one of the most important free radical scavenging members. To reveal the antioxidative function of P. esculenta, an important member of the antioxidative system, designated Pe-Cu/Zn SOD, was cloned and analyzed. Phylogenic analysis revealed that Pe-Cu/Zn SOD was located in the invertebrate evolutionary branch of intracellular Cu/Zn SOD (icCu/Zn SOD). The quantitative real-time polymerase chain reaction results showed that Pe-Cu/Zn SOD messenger ribonucleic acid was widely expressed in all tissues examined. The highest expression levels in coelomic fluid after Cd exposure indicated its function in the stress response. Using a prokaryotic expression system, we obtained a Pe-Cu/Zn SOD recombinant protein, which enhanced the heavy metal tolerance of Escherichia coli. In vivo assays also confirmed that the Pe-Cu/Zn SOD recombinant protein had an antioxidative and free radical scavenging ability. A Cd toxicity experiment, in which purified Pe-Cu/Zn SOD protein was injected into the body cavities of P. esculenta, showed that the reactive oxygen species content in the coelomic fluid of the experimental group was significantly lower compared with the control group. These results suggest that Pe-Cu/Zn SOD played a role in Cd detoxification by chelating heavy metal ions and scavenging reactive oxygen free radicals, and that P. esculenta could be used as a bioindicator to evaluate heavy metal pollution.     

Palatability of Macroalgae that Use Different Types of Chemical Defenses

This study compared algal palatability and chemical defenses from subtropical green algae that may use different types of defense systems that deter feeding by the rock-boring sea urchin Echinometra lucunter. The potential defense systems present include (1) the terpenoid caulerpenyne and its activated products from Caulerpa spp., and (2) dimethylsulfoniopropionate (DMSP)-related defenses in Ulva spp. Secondary metabolites from these chemical groups have been shown to deter feeding by various marine herbivores, including tropical and temperate sea urchins. Live algal multiple-choice feeding assays and assays incorporating algal extracts or isolated metabolites into an artificial diet were conducted. Several green algae, including Ulva lactuca, Caulerpa prolifera, and Cladophora sp., were unpalatable. Nonpolar extracts from U. lactuca deterred feeding, whereas nonpolar extracts from C. prolifera had no effect on feeding. Polar extracts from both species stimulated feeding. Caulerpenyne deterred feeding at approximately 4% dry mass; however, dimethyl sulfide and acrylic acid had no effect at natural and elevated concentrations. E. lucunter is more tolerant than other sea urchins to DMSP-related defenses and less tolerant to caulerpenyne than many reef fish. Understanding the chemical defenses of the algae tested in this study is important because they, and related species, frequently are invasive or form blooms, and can significantly modify marine ecosystems.     

Recent advances in biomolecular process intensification

Escherichia coli has been the most popular cellular biofactory for the production of many biomolecules including recombinant proteins whose bioactivities are not dependent on complicated post-translational modifications such as glycosylation. Despite many advantages of protein production using E. coli, the formation of insoluble inclusion bodies (IBs) poses a major challenge to harnessing E. coli as a host of choice. Furthermore, the complicated processing steps associated with IB extraction, solubilisation of IBs and refolding of the solubilised-denatured IB proteins, which are typically encountered in the traditional IB processing flowsheet, significantly compromise process economics of IB-route protein production using E. coli. In this paper, many recent advances in innovative IB processing technologies are reviewed with a special emphasis on their potential to contribute to process intensification, which is critical to achieve better process economics in the IB-route recombinant protein production using E. coli.     

Synthesis of an Anti-CD7 Recombinant Immunotoxin Based on PE24 in CHO and E. coli Cell-Free Systems

Recombinant immunotoxins (RITs) are an effective class of agents for targeted therapy in cancer treatment. In this article, we demonstrate the straight-forward production and testing of an anti-CD7 RIT based on PE24 in a prokaryotic and a eukaryotic cell-free system. The prokaryotic cell-free system was derived from Escherichia coli BL21 Star^TM (DE3) cells transformed with a plasmid encoding the chaperones groEL/groES. The eukaryotic cell-free system was prepared from Chinese hamster ovary (CHO) cells that leave intact endoplasmic reticulum-derived microsomes in the cell-free reaction mix from which the RIT was extracted. The investigated RIT was built by fusing an anti-CD7 single-chain variable fragment (scFv) with the toxin domain PE24, a shortened variant of Pseudomonas Exotoxin A. The RIT was produced in both cell-free systems and tested for antigen binding against CD7 and cell killing on CD7-positive Jurkat, HSB-2, and ALL-SIL cells. CD7-positive cells were effectively killed by the anti-CD7 scFv-PE24 RIT with an IC₅₀ value of 15 pM to 40 pM for CHO and 42 pM to 156 pM for E. coli cell-free-produced RIT. CD7-negative Raji cells were unaffected by the RIT. Toxin and antibody domain alone did not show cytotoxic effects on either CD7-positive or CD7-negative cells. To our knowledge, this report describes the production of an active RIT in E. coli and CHO cell-free systems for the first time. We provide the proof-of-concept that cell-free protein synthesis allows for on-demand testing of antibody–toxin conjugate activity in a time-efficient workflow without cell lysis or purification required.     

Whole Genome Sequencing and CRISPR/Cas9 Gene Editing of Enterotoxigenic Escherichia coli BE311 for Fluorescence Labeling and Enterotoxin Analyses

Some prevention strategies, including vaccines and antibiotic alternatives, have been developed to reduce enterotoxigenic Escherichia coli proliferation in animal production. In this study, a wild-type strain of BE311 with a virulent heat-stable enterotoxin gene identical to E. coli K99 was isolated for its high potential for gene expression ability. The whole genome of E. coli BE311 was sequenced for gene analyses and editing. Subsequently, the fluorescent gene mCherry was successfully knocked into the genome of E. coli BE311 by CRISPR/Cas9. The E. coli BE311–mCherry strain was precisely quantified through the fluorescence intensity and red colony counting. The inflammatory factors in different intestinal tissues all increased significantly after an E. coli BE311–mCherry challenge in Sprague–Dawley rats (p < 0.05). The heat-stable enterotoxin gene of E. coli BE311 was knocked out, and an attenuated vaccine host E. coli BE311-ST^KO was constructed. Flow cytometry showed apoptotic cell numbers were lower following a challenge of IPEC-J2 cells with E. coli BE311-ST^KO than with E. coli BE311. Therefore, the E. coli BE311–mCherry and E. coli BE311-ST^KO strains that were successfully constructed based on the gene knock-in and knock-out technology could be used as ideal candidates in ETEC challenge models and for the development of attenuated vaccines.     

Are Tropical Herbivores More Resistant Than Temperate Herbivores to Seaweed Chemical Defenses? Diterpenoid Metobolites from Dictyota acutiloba as Feeding Deterrents for Tropical Versus Temperate Fishes and Urchins

Because herbivory is more intense in the tropics, tropical seaweeds may be better defended against herbivory than are temperate seaweeds. A “diffuse” coevolutionary corollary to this hypothesis is that tropical herbivores should be more resistant to seaweed defenses than temperate herbivores because tropical herbivores more commonly encounter heavily defended seaweeds. We begin to test the latter prediction using three newly discovered diterpenoid secondary metabolites from the tropical brown alga Dictyota acutiloba. We tested the feeding deterrent properties of these compounds against common herbivorous fishes and sea urchins from warm-temperate North Carolina versus tropical Guam using standardized laboratory feeding assays. The temperate herbivores were deterred by lower concentrations of secondary metabolites than the tropical herbivores. In no case was a tropical herbivore more deterred by a compound than a temperate herbivore, suggesting that temperate herbivores may be more strongly affected by seaweed chemical defenses. Feeding by the temperate pinfish Lagodon rhomboides was significantly reduced by two of the three diterpenes at a concentration that was only 13–18% of the natural concentration found in the alga. Feeding by four species of tropical fishes (two parrotfishes and two surgeonfishes) was unaffected by metabolite concentrations that deterred the temperate fish. At 100% of natural concentrations, only one of the three compounds deterred the two parrotfishes, and none of the three compounds deterred the surgeonfishes. Contrasts between the temperate sea urchin Arbacia punctulata and the tropical sea urchin Diadema savignyi showed a similar pattern; low concentrations of acutilol A acetate strongly deterred the temperate, but not the tropical, urchin. Tropical herbivores appear more resistant than temperate herbivores to seaweed chemical defenses.     

The changes of phospholipid degradation in sea urchin gonads (Glyptocidaris crenularis) during cold storage at 4°C

Sea urchin gonads (SUGs) are rich in phospholipid (PL) which is easily oxidized and hydrolyzed during cold storage. PL changes were evaluated to clarify the quality changes of sea urchins during 72 h storage at 4°C. During storage at 4°C, PL content decreased, including phosphatidylethanolamine and phosphatidylinositol content decreased significantly and lysophosphatidylcholine (LPC) was detected after 36 h storage. At the same time, phospholipase C and phospholipase D remained active, and the content of free choline and free fatty acids increased, suggesting that PL was hydrolyzed. The addition of n-butanol inhibited the activity of phospholipases C and D, decrease of total PL content, and the production of LPC and free choline, indicating that phospholipase-mediated hydrolysis of PL in gonads occurred during refrigeration. The addition of vitamin E inhibited lipoxygenase, reduced lipid peroxidation (POV), and thiobarbituric acid reactive substances. It indicated that lipoxygenase in SUG mediated the oxidative degradation of PL during cold storage.     

Synthesis and characterization of whitlockite from sea urchin skeleton and investigation of antibacterial activity

In the present study, undoped whitlockite and ZnO doped-Whitlockite, which is the second most abundant inorganic material in bone structure, were synthesized from sea urchin skeleton. The obtained bioceramic materials were characterized by XRD, FT-IR, and SEM and their antibacterial activities were determined using the inhibition zone diameters of Escherichia coli and Pseudomonas aeruginosa as gram negative bacteria and Staphylococcus aureus as gram positive bacterium after 24 h incubation. The characterization studies showed that nano size homogenous biocereamic whitlockite (Ca_2.86Mg_0.14(PO₄)₂) was synthesized from the sea urchin skeleton. After dopping process, the main structure of the whitlockite keeps stable, showing a dopping concentration-independent character. On the other hand, the peaks belonging to ZnO were started to seen in the XRD pattern with increasing the level of ZnO-concentration (after 7 %). All experimental results point out that the obtained whitlockites are viable nominate candidates for bioceramic materials and the results of antibacterial sensitivity prove the inhibitory effect towards Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus for ZnO-doped-whitlockite.     

A Multi-Disulfide Receptor-Binding Domain (RBD) of the SARS-CoV-2 Spike Protein Expressed in E. coli Using a SEP-Tag Produces Antisera Interacting with the Mammalian Cell Expressed Spike (S1) Protein

An Escherichia coli (E. coli) production of the receptor-binding domain (RBD) of the SARS-CoV-2 (isolate Wuhan-Hu-1) spike protein would significantly accelerate the search for anti-COVID-19 therapeutics because of its versatility and low cost. However, RBD contains four disulfide bonds and its expression in E. coli is limited by the formation of aberrant disulfide bonds resulting in inclusion bodies. Here, we show that a solubility-enhancing peptide (SEP) tag containing nine arginine residues (RBD-C9R) attached at the C-terminus can overcome this problem. The SEP-tag increased the expression in the soluble fraction and the final yield by five times (2 mg/L). The folding properties of the E. coli expressed RBD-C9R were demonstrated with biophysical characterization using RP-HPLC, circular dichroism, thermal denaturation, fluorescence, and light scattering. A quartz crystal microbalance (QCM) analysis confirmed the binding activity of RBD-C9R with ACE2, the host cell’s receptor. In addition, RBD-C9R elicited a Th-2 immune response with a high IgG titer in Jcl: ICR mice. The RBD-C9R antisera interacted with both itself and the mammalian-cell expressed spike protein (S1), as demonstrated by ELISA, indicating that the E. coli expressed RBD-C9R harbors native-like epitopes. Overall, these results emphasize the potential of our SEP-tag for the E. coli production of active multi-disulfide-bonded RBD.     

The Esterase PfeE,the Achilles’ Heel in the Battle for Iron between Pseudomonas aeruginosa and Escherichia coli

Bacteria access iron, a key nutrient, by producing siderophores or using siderophores produced by other microorganisms. The pathogen Pseudomonas aeruginosa produces two siderophores but is also able to pirate enterobactin (ENT), the siderophore produced by Escherichia coli. ENT-Fe complexes are imported across the outer membrane of P. aeruginosa by the two outer membrane transporters PfeA and PirA. Iron is released from ENT in the P. aeruginosa periplasm by hydrolysis of ENT by the esterase PfeE. We show here that pfeE gene deletion renders P. aeruginosa unable to grow in the presence of ENT because it is unable to access iron via this siderophore. Two-species co-cultures under iron-restricted conditions show that P. aeruginosa strongly represses the growth of E. coli as long it is able to produce its own siderophores. Both strains are present in similar proportions in the culture as long as the siderophore-deficient P. aeruginosa strain is able to use ENT produced by E. coli to access iron. If pfeE is deleted, E. coli has the upper hand in the culture and P. aeruginosa growth is repressed. Overall, these data show that PfeE is the Achilles’ heel of P. aeruginosa in communities with bacteria producing ENT.     

Effect of Polyhexamethylene Biguanide in Combination with Undecylenamidopropyl Betaine or PslG on Biofilm Clearance

Hospital-acquired infection is a great challenge for clinical treatment due to pathogens’ biofilm formation and their antibiotic resistance. Here, we investigate the effect of antiseptic agent polyhexamethylene biguanide (PHMB) and undecylenamidopropyl betaine (UB) against biofilms of four pathogens that are often found in hospitals, including Gram-negative bacteria Pseudomonas aeruginosa and Escherichia coli, Gram-positive bacteria Staphylococcus aureus, and pathogenic fungus, Candida albicans. We show that 0.02% PHMB, which is 10-fold lower than the concentration of commercial products, has a strong inhibitory effect on the growth, initial attachment, and biofilm formation of all tested pathogens. PHMB can also disrupt the preformed biofilms of these pathogens. In contrast, 0.1% UB exhibits a mild inhibitory effect on biofilm formation of the four pathogens. This concentration inhibits the growth of S. aureus and C. albicans yet has no growth effect on P. aeruginosa or E. coli. UB only slightly enhances the anti-biofilm efficacy of PHMB on P. aeruginosa biofilms. However, pretreatment with PslG, a glycosyl hydrolase that can efficiently inhibit and disrupt P. aeruginosa biofilm, highly enhances the clearance effect of PHMB on P. aeruginosa biofilms. Meanwhile, PslG can also disassemble the preformed biofilms of the other three pathogens within 30 min to a similar extent as UB treatment for 24 h.     

Study of Linkage between Glutathione Pathway and the Antibiotic Resistance of Escherichia coli from Patients’ Swabs

In this work, we focused on the differences between bacterial cultures of E. coli obtained from swabs of infectious wounds of patients compared to laboratory E. coli. In addition, blocking of the protein responsible for the synthesis of glutathione (γ-glutamylcysteine synthase—GCL) using 10 mM buthionine sulfoximine was investigated. Each E. coli showed significant differences in resistance to antibiotics. According to the determined resistance, E. coli were divided into experimental groups based on a statistical evaluation of their properties as more resistant and more sensitive. These groups were also used for finding the differences in a dependence of the glutathione pathway on resistance to antibiotics. More sensitive E. coli showed the same kinetics of glutathione synthesis while blocking GCL (K_m 0.1 µM), as compared to non-blocking. In addition, the most frequent mutations in genes of glutathione synthetase, glutathione peroxidase and glutathione reductase were observed in this group compared to laboratory E.coli. The group of “more resistant” E. coli exhibited differences in K_m between 0.3 and 0.8 µM. The number of mutations compared to the laboratory E. coli was substantially lower compared to the other group.     

RadA,a Key Gene of the Circadian Rhythm of Escherichia coli

Circadian rhythms are present in almost all living organisms, and their activity relies on molecular clocks. In prokaryotes, a functional molecular clock has been defined only in cyanobacteria. Here, we investigated the presence of circadian rhythms in non-cyanobacterial prokaryotes. The bioinformatic approach was used to identify a homologue of KaiC (circadian gene in cyanobacteria) in Escherichia coli. Then, strains of E. coli (wild type and mutants) were grown on blood agar, and sampling was made every 3 h for 24 h at constant conditions. Gene expression was determined by qRT-PCR, and the rhythmicity was analyzed using the Cosinor model. We identified RadA as a KaiC homologue in E. coli. Expression of radA showed a circadian rhythm persisting at least 3 days, with a peak in the morning. The circadian expression of other E. coli genes was also observed. Gene circadian oscillations were lost in radA mutants of E. coli. This study provides evidence of molecular clock gene expression in E. coli with a circadian rhythm. Such a finding paves the way for new perspectives in antibacterial treatment.     

Evolving Escherichia coli Host Strains for Efficient Deuterium Labeling of Recombinant Proteins Using Sodium Pyruvate-d3

Labeling of proteins with deuterium (2H) is often necessary for structural biology techniques, such as neutron crystallography, NMR spectroscopy, and small-angle neutron scattering. Perdeuteration in which all protium (1H) atoms are replaced by deuterium is a costly process. Typically, expression hosts are grown in a defined medium with heavy water as the solvent, which is supplemented with a deuterated carbon source. Escherichia coli, which is the most widely used host for recombinant protein production, can utilize several compounds as a carbon source. Glycerol-d₈ is often used as a carbon source for deuterium labelling due to its lower cost compered to glucose-d₇. In order to expand available options for recombinant protein deuteration, we investigated the possibility of producing a deuterated carbon source in-house. E. coli can utilize pyruvate as a carbon source and pyruvate-d₃ can be made by a relatively simple procedure. To circumvent the very poor growth of E. coli in minimal media with pyruvate as sole carbon source, adaptive laboratory evolution for strain improvement was applied. E. coli strains with enhanced growth in minimal pyruvate medium was subjected to whole genome sequencing and the genetic changes were revealed. One of the evolved strains was adapted for the widely used T7 RNA polymerase overexpression systems. Using the improved strain E. coli DAP1(DE3) and in-house produced deuterated carbon source (pyruvic acid-d₄ and sodium pyruvate-d₃), we produce deuterated (>90%) triose-phosphate isomerase, at quantities sufficient enough for large volume crystal production and subsequent analysis by neutron crystallography.