Gene Designer: a synthetic biology tool for constructing artificial DNA segments

High-level expression of codon-optimized Taq DNA polymerase under the control of rhaBAD promoter

A DNA polymerase from Thermus aquaticus remains the most popular among DNA polymerases. It was widely applied in various fields involving the application of polymerase chain reaction (PCR), implying the high commercial value of this enzyme. For this reason, an attempt to obtain a high yield of Taq DNA polymerase is continuously conducted. In this study, the l-rhamnose-inducible promoter rhaBAD was utilized due to its ability to produce recombinant protein under tight control in E. coli expression system. Instead of full-length Taq polymerase, an N-terminal deletion of Taq polymerase was selected. To obtain a high-level expression, we attempted to optimize the codon by reducing the rare codon and GC content, and in a second attempt, we optimized the culture conditions for protein expression. The production of Taq polymerase using the optimum culture condition improved the level of expression by up to 3-fold. This approach further proved that a high level of recombinant protein expression could be achieved by yielding a purified Taq polymerase of about 8.5 mg/L of culture. This is the first research publication on the production of Taq polymerase with N-terminal deletion in E. coli with the control of the rhaBAD promoter system.

Profiling expression strategies for a type III polyketide synthase in a lysate-based, cell-free system

Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli often results in a myriad of unpredictable issues with regard to protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as a valuable expression platform as a testbed for rapid prototyping expression parameters. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We applied a library of constructs with different combinations of promoters and rppA coding sequences to investigate the synergies between promoter and codon usage. Subsequently, we assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. More importantly, the choice of coding sequences and promoters impact protein expression synergistically, which should be considered for future efforts to use CFE for high-yield protein expression. The promoter strategy when applied to RppA was not completely correlated with that observed with GFP, indicating that different promoter strategies should be applied for different proteins. In vivo experiments suggest that there is correlation, but not complete alignment between expressing in cell free and in vivo. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs, which advances CFE as a tool for natural product research.

An Integer Linear Programming Model to Optimize Coding DNA Sequences By Joint Control of Transcript Indicators

A Coding DNA Sequence (CDS) is a fraction of DNA whose nucleotides are grouped into consecutive triplets called codons, each one encoding an amino acid. Because most amino acids can be encoded by more than one codon, the same amino acid chain can be obtained by a very large number of different CDSs. These synonymous CDSs show different features that, also depending on the organism the transcript is expressed in, could affect translational efficiency and yield. The identification of optimal CDSs with respect to given transcript indicators is in general a challenging task, but it has been observed in recent literature that integer linear programming (ILP) can be a very flexible and efficient way to achieve it. In this article, we add evidence to this observation by proposing a new ILP model that simultaneously optimizes different well-grounded indicators. With this model, we efficiently find solutions that dominate those returned by six existing codon optimization heuristics.

Sustainable production of natural products using synthetic biology: Ginsenosides

Synthetic biology approaches offer potential for large-scale and sustainable production of natural products with bioactive potency, including ginsenosides, providing a means to produce novel compounds with enhanced therapeutic properties. Ginseng, known for its non-toxic and potent qualities in traditional medicine, has been used for various medical needs. Ginseng has shown promise for its antioxidant and neuroprotective properties, and it has been used as a potential agent to boost immunity against various infections when used together with other drugs and vaccines. Given the increasing demand for ginsenosides and the challenges associated with traditional extraction methods, synthetic biology holds promise in the development of therapeutics. In this review, we discuss recent developments in microorganism producer engineering and ginsenoside production in microorganisms using synthetic biology approaches.

Metabolic engineering of high-salinity-induced biosynthesis of γ-aminobutyric acid improves salt-stress tolerance in a glutamic acid-overproducing mutant of an ectoine-deficient Halomonas elongata

A moderately halophilic eubacterium, Halomonas elongata, has been used as cell factory to produce fine chemical 1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (ectoine), which functions as a major osmolyte protecting the cells from high-salinity stress. To explore the possibility of using H. elongata to biosynthesize other valuable osmolytes, an ectoine-deficient salt-sensitive H. elongata deletion mutant strain KA1 (ΔectABC), which only grows well in minimal medium containing up to 3% NaCl, was subjected to an adaptive mutagenesis screening in search of mutants with restored salt tolerance. Consequently, we obtained a mutant, which tolerates 6% NaCl in minimal medium by overproducing L-glutamic acid (Glu). However, this Glu-overproducing (GOP) strain has a lower tolerance level than the wild-type H. elongata, possibly because the acidity of Glu interferes with the pH homeostasis of the cell and hinders its own cellular accumulation. Enzymatic decarboxylation of Glu to γ-aminobutyric acid (GABA) by a Glu decarboxylase (GAD) could restore cellular pH homeostasis; therefore, we introduced an engineered salt-inducible HopgadBmut gene, which encodes a wide pH-range GAD mutant, into the genome of the H. elongata GOP strain. We found that the resulting H. elongata GOP-Gad strain exhibits higher salt tolerance than the GOP strain by accumulating high concentration of GABA as an osmolyte in the cell (176.94 µmol/g cell dry weight in minimal medium containing 7% NaCl). With H. elongata OUT30018 genetic background, H. elongata GOP-Gad strain can utilize biomass-derived carbon and nitrogen compounds as its sole carbon and nitrogen sources, making it a good candidate for the development of GABA-producing cell factories.IMPORTANCEWhile the wild-type moderately halophilic H. elongata can synthesize ectoine as a high-value osmolyte via the aspartic acid metabolic pathway, a mutant H. elongata GOP strain identified in this work opens doors for the biosynthesis of alternative valuable osmolytes via glutamic acid metabolic pathway. Further metabolic engineering to install a GAD system into the H. elongata GOP strain successfully created a H. elongata GOP-Gad strain, which acquired higher tolerance to salt stress by accumulating GABA as a major osmolyte. With the ability to assimilate biomass-derived carbon and nitrogen sources and thrive in high-salinity environment, the H. elongata GOP-Gad strain can be used in the development of sustainable GABA-producing cell factories.

Characterization of exclusively non-commensal Neisseria gonorrhoeae pangenome to prioritize globally conserved and thermodynamically stable vaccine candidates using immune-molecular dynamic simulations

Neisseria gonorrhoeae (Ngo) has emerged as a global threat leading to one of the most common sexually transmitted diseases in the world. It has also become one of the leading antimicrobial resistant organisms, resulting in fewer treatment options and an increased morbidity. Therefore, in recent years, there has been an increased focus on the development of new treatments and preventive strategies to combat its infection. In this study, we have combined the most conserved epitopes from the completely assembled strains of Ngo to develop a universal and a thermodynamically stable vaccine candidate. For our vaccine design, the epitopes were selected for their high immunogenicity, non-allergenicity and non-cytotoxicity, making them the ideal candidates for vaccine development. For the screening process, several reverse vaccinology tools were employed to rigorously extract non-homologous and immunogenic epitopes from the selected proteins. Consequently, a total number of 3 B-cell epitopes and 6 T-cell epitopes were selected and joined by multiple immune-modulating adjuvants and linkers to generate a promiscuous immune response. Additionally, the stability and flexible nature of the vaccine construct was confirmed using various molecular dynamic simulation tools. Overall, the vaccine candidate showed promising binding affinity to various HLA alleles and TLR receptors; however, further studies are needed to assess its efficacy in-vivo. In this way, we have designed a multi-subunit vaccine candidate to potentially combat and control the spread of N. gonorrhoeae.

Profiling Expression Strategies for a Type III Polyketide Synthase in a Lysate-Based, Cell-free System

Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli frequently results in a myriad of unpredictable issues with protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts, such as BGC refactoring, can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as 1) a valuable expression platform for enzymes that are challenging to synthesize in vivo, and as 2) a testbed for rapid prototyping that can improve cellular expression. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We synergistically tune promoter and codon usage to improve flaviolin production from cell-free expressed RppA. We then assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs. By showing the coordinators between CFE versus in vivo expression, this work advances CFE as a tool for natural product research.

Harnessing synthetic biology for advancing RNA therapeutics and vaccine design

Recent global events have drawn into focus the diversity of options for combatting disease across a spectrum of prophylactic and therapeutic approaches. The recent success of the mRNA-based COVID-19 vaccines has paved the way for RNA-based treatments to revolutionize the pharmaceutical industry. However, historical treatment options are continuously updated and reimagined in the context of novel technical developments, such as those facilitated through the application of synthetic biology. When it comes to the development of genetic forms of therapies and vaccines, synthetic biology offers diverse tools and approaches to influence the content, dosage, and breadth of treatment with the prospect of economic advantage provided in time and cost benefits. This can be achieved by utilizing the broad tools within this discipline to enhance the functionality and efficacy of pharmaceutical agent sequences. This review will describe how synthetic biology principles can augment RNA-based treatments through optimizing not only the vaccine antigen, therapeutic construct, therapeutic activity, and delivery vector. The enhancement of RNA vaccine technology through implementing synthetic biology has the potential to shape the next generation of vaccines and therapeutics.

Codon optimization of a gene encoding DNA polymerase from Pyrococcus furiosus and its expression in Escherichia coli

BACKGROUND

DNA polymerase is an essential component in PCR assay for DNA synthesis. Improving DNA polymerase with characteristics indispensable for a powerful assay is crucial because it can be used in wide-range applications. Derived from Pyrococcus furiosus, Pfu DNA polymerase (Pfu pol) is one of the excellent polymerases due to its high fidelity. Therefore, we aimed to develop Pfu pol from a synthetic gene with codon optimization to increase its protein yield in Escherichia coli.

RESULTS

Recombinant Pfu pol was successfully expressed and purified with a two-step purification process using nickel affinity chromatography, followed by anion exchange chromatography. Subsequently, the purified Pfu pol was confirmed by Western blot analysis, resulting in a molecular weight of approximately 90 kDa. In the final purification process, we successfully obtained a large amount of purified enzyme (26.8 mg/L). Furthermore, the purified Pfu pol showed its functionality and efficiency when tested for DNA amplification using the standard PCR.

CONCLUSIONS

Overall, a high-level expression of recombinant Pfu pol was achieved by employing our approach in the present study. In the future, our findings will be useful for studies on synthesizing recombinant DNA polymerase in E. coli expression system.

An exploratory in silico comparison of open-source codon harmonization tools

BACKGROUND

Not changing the native constitution of genes prior to their expression by a heterologous host can affect the amount of proteins synthesized as well as their folding, hampering their activity and even cell viability. Over the past decades, several strategies have been developed to optimize the translation of heterologous genes by accommodating the difference in codon usage between species. While there have been a handful of studies assessing various codon optimization strategies, to the best of our knowledge, no research has been performed towards the evaluation and comparison of codon harmonization algorithms. To highlight their importance and encourage meaningful discussion, we compared different open-source codon harmonization tools pertaining to their in silico performance, and we investigated the influence of different gene-specific factors.

RESULTS

In total, 27 genes were harmonized with four tools toward two different heterologous hosts. The difference in %MinMax values between the harmonized and the original sequences was calculated (ΔMinMax), and statistical analysis of the obtained results was carried out. It became clear that not all tools perform similarly, and the choice of tool should depend on the intended application. Almost all biological factors under investigation (GC content, RNA secondary structures and choice of heterologous host) had a significant influence on the harmonization results and thus must be taken into account. These findings were substantiated using a validation dataset consisting of 8 strategically chosen genes.

CONCLUSIONS

Due to the size of the dataset, no complex models could be developed. However, this initial study showcases significant differences between the results of various codon harmonization tools. Although more elaborate investigation is needed, it is clear that biological factors such as GC content, RNA secondary structures and heterologous hosts must be taken into account when selecting the codon harmonization tool.

Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation

In many species highly expressed genes (HEGs) over-employ the synonymous codons that match the more abundant iso-acceptor tRNAs. Bacterial transgene codon randomization experiments report, however, that enrichment with such "translationally optimal" codons has little to no effect on the resultant protein level. By contrast, consistent with the view that ribosomal initiation is rate limiting, synonymous codon usage following the 5' ATG greatly influences protein levels, at least in part by modifying RNA stability. For the design of bacterial transgenes, for simple codon based in silico inference of protein levels and for understanding selection on synonymous mutations, it would be valuable to computationally determine initiation optimality (IO) scores for codons for any given species. One attractive approach is to characterize the 5' codon enrichment of HEGs compared with the most lowly expressed genes, just as translational optimality scores of codons have been similarly defined employing the full gene body. Here we determine the viability of this approach employing a unique opportunity: for Escherichia coli there is both the most extensive protein abundance data for native genes and a unique large-scale transgene codon randomization experiment enabling objective definition of the 5' codons that cause, rather than just correlate with, high protein abundance (that we equate with initiation optimality, broadly defined). Surprisingly, the 5' ends of native genes that specify highly abundant proteins avoid such initiation optimal codons. We find that this is probably owing to conflicting selection pressures particular to native HEGs, including selection favouring low initiation rates, this potentially enabling high efficiency of ribosomal usage and low noise. While the classical HEG enrichment approach does not work, rendering simple prediction of native protein abundance from 5' codon content futile, we report evidence that initiation optimality scores derived from the transgene experiment may hold relevance for in silico transgene design for a broad spectrum of bacteria.

Insertion sequence transposition inactivates CRISPR-Cas immunity

CRISPR-Cas immunity systems safeguard prokaryotic genomes by inhibiting the invasion of mobile genetic elements. Here, we screened prokaryotic genomic sequences and identified multiple natural transpositions of insertion sequences (ISs) into cas genes, thus inactivating CRISPR-Cas defenses. We then generated an IS-trapping system, using Escherichia coli strains with various ISs and an inducible cas nuclease, to monitor IS insertions into cas genes following the induction of double-strand DNA breakage as a physiological host stress. We identified multiple events mediated by different ISs, especially IS1 and IS10, displaying substantial relaxed target specificity. IS transposition into cas was maintained in the presence of DNA repair machinery, and transposition into other host defense systems was also detected. Our findings highlight the potential of ISs to counter CRISPR activity, thus increasing bacterial susceptibility to foreign DNA invasion.

Automating the design-build-test-learn cycle towards next-generation bacterial cell factories

Automation is playing an increasingly significant role in synthetic biology. Groundbreaking technologies, developed over the past 20 years, have enormously accelerated the construction of efficient microbial cell factories. Integrating state-of-the-art tools (e.g. for genome engineering and analytical techniques) into the design-build-test-learn cycle (DBTLc) will shift the metabolic engineering paradigm from an almost artisanal labor towards a fully automated workflow. Here, we provide a perspective on how a fully automated DBTLc could be harnessed to construct the next-generation bacterial cell factories in a fast, high-throughput fashion. Innovative toolsets and approaches that pushed the boundaries in each segment of the cycle are reviewed to this end. We also present the most recent efforts on automation of the DBTLc, which heralds a fully autonomous pipeline for synthetic biology in the near future.

Effects of solvent polarity on the novel excited-state intramolecular thiol proton transfer and photophysical property compared with the oxygen proton transfer

Recently, the dual-fluorescent phenomena of excited state intramolecular thiol proton transfer (ESIPT) for 3-thiolflavone derivative (3NTF) were reported by Chou and coworkers for the first time [J. Am. Chem. Soc. 143 (2021) 12715-12724], which opened a new chapter in the field of ESIPT. Based on density functional theory (DFT) and time-dependent density functional theory (TDDFT), the proton transfer processes of 3NTF in toluene, dichloromethane and acetonitrile were studied. By optimizing the structure of the ground (S0) state and first excited (S1) state of 3NTF in different solvents, the hydrogen-bond parameters and proton-transfer potential energy curves were calculated. It was shown that although photo-excitation enhanced the intramolecular hydrogen bonding strength and thus promoted the occurrence of ESIPT, the solvent polarities inhibited the enhancement of the hydrogen bond of S1 state, which was not conducive to ESIPT. The electron spectra analyses were consistent with experimental data, which confirmed the rationality of molecular configurations. The time-evolved excited state dynamics simulation was performed based on the optimized structure of 3NTF, indicating that the ESIPT was an ultrafast photochemical reaction less than 180 fs. Moreover, we compared the potential energy surfaces of ESIPT, electronic structures based on natural transition orbitals (NTOs) method and electron-hole isosurfaces for the 3NTF and the traditional flavone molecule (3NHF), concluded that the unusually large Stokes shift fluorescence of 3NTF was mainly caused by the coupling of ESIPT and twisting intramolecular charge transfer (TICT), and the 3NTF isomer had the more nπ* character in the electron transition process. The nπ* ICT significantly increased with the decrease of solvent polarities, affecting the molecular photophysical properties, this made it more widely used in biomedical, photochemical, materials science and other fields.

ICOR: improving codon optimization with recurrent neural networks

BACKGROUND

In protein sequences-as there are 61 sense codons but only 20 standard amino acids-most amino acids are encoded by more than one codon. Although such synonymous codons do not alter the encoded amino acid sequence, their selection can dramatically affect the expression of the resulting protein. Codon optimization of synthetic DNA sequences is important for heterologous expression. However, existing solutions are primarily based on choosing high-frequency codons only, neglecting the important effects of rare codons. In this paper, we propose a novel recurrent-neural-network based codon optimization tool, ICOR, that aims to learn codon usage bias on a genomic dataset of Escherichia coli. We compile a dataset of over 7,000 non-redundant, high-expression, robust genes which are used for deep learning. The model uses a bidirectional long short-term memory-based architecture, allowing for the sequential context of codon usage in genes to be learned. Our tool can predict synonymous codons for synthetic genes toward optimal expression in Escherichia coli.

RESULTS

We demonstrate that sequential context achieved via RNN may yield codon selection that is more similar to the host genome. Based on computational metrics that predict protein expression, ICOR theoretically optimizes protein expression more than frequency-based approaches. ICOR is evaluated on 1,481 Escherichia coli genes as well as a benchmark set of 40 select DNA sequences whose heterologous expression has been previously characterized. ICOR's performance is measured across five metrics: the Codon Adaptation Index, GC-content, negative repeat elements, negative cis-regulatory elements, and codon frequency distribution.

CONCLUSIONS

The results, based on in silico metrics, indicate that ICOR codon optimization is theoretically more effective in enhancing recombinant expression of proteins over other established codon optimization techniques. Our tool is provided as an open-source software package that includes the benchmark set of sequences used in this study.

Making small molecules in plants: A chassis for synthetic biology-based production of plant natural products

Plant natural products have been extensively exploited in food, medicine, flavor, cosmetic, renewable fuel, and other industrial sectors. Synthetic biology has recently emerged as a promising means for the cost-effective and sustainable production of natural products. Compared with engineering microbes for the production of plant natural products, the potential of plants as chassis for producing these compounds is underestimated, largely due to challenges encountered in engineering plants. Knowledge in plant engineering is instrumental for enabling the effective and efficient production of valuable phytochemicals in plants, and also paves the way for a more sustainable future agriculture. In this manuscript, we briefly recap the biosynthesis of plant natural products, focusing primarily on industrially important terpenoids, alkaloids, and phenylpropanoids. We further summarize the plant hosts and strategies that have been used to engineer the production of natural products. The challenges and opportunities of using plant synthetic biology to achieve rapid and scalable production of high-value plant natural products are also discussed.

High-level expression of functional Pfu DNA polymerase recombinant protein by mimicking the enhanced green fluorescence protein gene codon usage

Pfu DNA polymerase is a vital enzyme in PCR-related experiments. However, it is not easy to achieve high-level expression and high purity through one-step purification. This paper illustrates the method to acquire the full-length open reading frame of Pfu DNA polymerase. Without altering its amino acids, we have modified the codon usage, based on that of the enhanced green fluorescence protein (eGFP), and named it rPfu. The synthesized rPfu gene has been subcloned into the pET28a plasmid and expressed in four Escherichia coli strains without the pLysS plasmid. Three strains have expressed a high level of soluble Pfu DNA polymerase. With the aid of Ni-NTA His•Bind^® resin, we could obtain high purity (>95%) soluble recombinant protein. Compared with the commercial, proofreading DNA polymerase, rPfu's bioactivity was 12,987 U/mg; that is, 88,311 U of rPfu could be obtained from 50 mL cultured E. coli. The purified rPfu was able to amplify the length of DNA fragments at least 5.5 kb. The method of increasing soluble protein's yield using the eGFP codon usage may introduce a new possibility to the expression of other soluble recombinant proteins.

Integrated mRNA sequence optimization using deep learning

The coronavirus disease of 2019 pandemic has catalyzed the rapid development of mRNA vaccines, whereas, how to optimize the mRNA sequence of exogenous gene such as severe acute respiratory syndrome coronavirus 2 spike to fit human cells remains a critical challenge. A new algorithm, iDRO (integrated deep-learning-based mRNA optimization), is developed to optimize multiple components of mRNA sequences based on given amino acid sequences of target protein. Considering the biological constraints, we divided iDRO into two steps: open reading frame (ORF) optimization and 5' untranslated region (UTR) and 3'UTR generation. In ORF optimization, BiLSTM-CRF (bidirectional long-short-term memory with conditional random field) is employed to determine the codon for each amino acid. In UTR generation, RNA-Bart (bidirectional auto-regressive transformer) is proposed to output the corresponding UTR. The results show that the optimized sequences of exogenous genes acquired the pattern of human endogenous gene sequence. In experimental validation, the mRNA sequence optimized by our method, compared with conventional method, shows higher protein expression. To the best of our knowledge, this is the first study by introducing deep-learning methods to integrated mRNA sequence optimization, and these results may contribute to the development of mRNA therapeutics.

Discovery and Heterologous Expression of Unspecific Peroxygenases

Since 2004, unspecific peroxygenases, in short UPOs (EC. 1.11.2.1), have been explored. UPOs are closing a gap between P450 monooxygenases and chloroperoxidases. These enzymes are highly active biocatalysts for the selective oxyfunctionalisation of C–H, C=C and C-C bonds. UPOs are secreted fungal proteins and Komagataella phaffii (Pichia pastoris) is an ideal host for high throughput screening approaches and UPO production. Heterologous overexpression of 26 new UPOs by K. phaffii was performed in deep well plate cultivation and shake flask cultivation up to 50 mL volume. Enzymes were screened using colorimetric assays with 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,6-dimethoxyphenol (DMP), naphthalene and 5-nitro-1,3-benzodioxole (NBD) as reporter substrates. The PaDa-I (AaeUPO mutant) and HspUPO were used as benchmarks to find interesting new enzymes with complementary activity profiles as well as good producing strains. Herein we show that six UPOs from Psathyrella aberdarensis, Coprinopsis marcescibilis, Aspergillus novoparasiticus, Dendrothele bispora and Aspergillus brasiliensis are particularly active.

In-silico design and evaluation of an epitope-based serotype-independent promising vaccine candidate for highly cross-reactive regions of pneumococcal surface protein A

BACKGROUND

The pathogenicity of pneumococcus with high morbidity, mortality, and multi-drug resistance patterns has been increasing. The limited coverage of the licensed polysaccharide-based vaccines and the replacement of the non-vaccine serotypes are the main reasons for producing a successful serotype-independent vaccine. Pneumococcal surface protein A (PspA) is an extremely important virulence factor and an interesting candidate for conserved protein-based pneumococcal vaccine classified into two prominent families containing five clades. PspA family-elicited immunity is clade-dependent, and the level of the PspA cross-reactivity is restricted to the same family.

METHODS

To cover and overcome the clade-dependent immunity of the PspAs in this study, we designed and tested a PspA_1-5c+p vaccine candidate composed of the highest immunodominant coverage of B- and T-cell epitope truncated domain of each clade focusing on two cross-reactive B and C regions of the PspAs. The antigenicity, toxicity, physicochemical properties, 3D structure prediction, stability and flexibility of the designed protein using molecular dynamic (MD) simulation, molecular docking of the construct withHLADRB1*(01:01) and human lactoferrin N-lop, and immune simulation were assessed using immunoinformatics tools. In the experimental section, after intraperitoneal immunization of the mice with Alum adjuvanted recombinant PspA_1-5c+p, we evaluated the immune response, cross-reactivity, and functionality of the Anti-PspA_1-5c+p antibody using ELISA, Opsonophagocytic killing activity, and serum bactericidal assay.

RESULTS

For the first time, this work suggested a novel PspA-based vaccine candidate using immunoinformatics tools. The designed PspA_1-5c+p protein is predicted to be highly antigenic, non-toxic, soluble, stable with low flexibility in MD simulation, and able to stimulate both humoral and cellular immune responses. The designed protein also could interact strongly with HLADRB1*(01:01) and human lactoferrin N-lop in the docking study. Our immunoinformatics predictions were validated using experimental data. Results showed that the anti-PspA_1-5c+p IgG not only had a high titer with strong and same cross-reactivity coverage against all pneumococcal serotypes used but also had high and effective bioactivity for pneumococcal clearance using complement system and phagocytic cells.

CONCLUSION

Our findings elucidated the potential application of the PspA_1-5c+p vaccine candidate as a serotype-independent pneumococcal vaccine with a strong cross-reactivity feature. Further in-vitro and in-vivo investigations against other PspA clades should be performed to confirm the full protection of the PspA_1-5c+p vaccine candidate.

Protein Extraction and Purification by Differential Solubilization

The preparation of purified soluble proteins for biochemical studies is essential and the solubility of a protein of interest in various media is central to this process. Selectively altering the solubility of a protein is a rapid and economical step in protein purification and is based on exploiting the inherent physicochemical properties of a polypeptide. Precipitation of proteins, released from cells upon lysis, is often used to concentrate a protein of interest before further purification steps (e.g., ion exchange chromatography, size exclusion chromatography etc).Recombinant proteins may be expressed in host cells as insoluble inclusion bodies due to various influences during overexpression. Such inclusion bodies can often be solubilized to be reconstituted as functional, correctly folded proteins.In this chapter, we examine strategies for extraction/precipitation/solubilization of proteins for protein purification. We also present bioinformatic tools to aid in understanding a protein's propensity to aggregate/solubilize that will be a useful starting point for the development of protein extraction, precipitation, and selective re-solubilization procedures.

Designing multi-epitope monkeypox virus-specific vaccine using immunoinformatics approach

BACKGROUND

Monkeypox virus is an enveloped DNA virus that belongs to Poxviridae family. The virus is transmitted from rodents to primates via infected body fluids, skin lesions, and respiratory droplets. After being infected with virus, the patients experience fever, myalgia, maculopapular rash, and fluid-filled blisters. It is necessary to differentiate monkeypox virus from other poxviruses during diagnosis which can be appropriately envisioned via DNA analysis from swab samples. During small outbreaks, the virus is treated with therapies administered in other orthopoxviruses infections and does not have its own specific therapy and vaccine. Consequently, in this article, two potential peptides have been designed.

METHODS

For the purpose of designing a vaccine, protein sequences were retrieved followed by the prediction of B- and T-cell epitopes. Afterward, vaccine structures were predicted which were docked with toll-like receptors. The docked complexes were analyzed with iMODS. Moreover, vaccine constructs nucleotide sequences were optimized and expressed in silico.

RESULTS

COP-B7R vaccine construct (V1) has antigenicity score of 0.5400, instability index of 29.33, z-score of - 2.11-, and 42.11% GC content whereas COP-A44L vaccine construct (V2) has an antigenicity score of 0.7784, instability index of 23.33, z-score of - 0.61, and 48.63% GC content. It was also observed that COP-A44L can be expressed as a soluble protein in Escherichia coli as compared to COP-B7R which requires a different expression system.

CONCLUSION

The obtained results revealed that both vaccine constructs show satisfactory outcomes after in silico investigation and have significant potential to prevent the monkeypox virus. However, COP-A44L gave better results.

Codon Usage and Context Analysis of Genes Modulated during SARS-CoV-2 Infection and Dental Inflammation

The overexpression of SARS-CoV-2 primary receptors and co-receptors (ACE2, TMPRSS2, FURIN, and CD147) enhance the likeliness of SARS-CoV-2 infection. The genes for same receptors are overexpressed in the periodontal tissues of periodontitis patients. On the other hand, BMAL1 is recognized to play a crucial role in regulating pulmonary inflammation and enhancing susceptibility to viral infection. Silenced BMAL1 disrupts circadian transcriptional regulations, enhances vulnerability to SARS-CoV-2 infections, and may trigger the further production of TNF-α and other pro-inflammatory cytokines that propagate the cytokine storm and exacerbate periodontal inflammation. Therefore ACE2, TMPRSS2, FURIN, CD147, and BMAL1 are the crossroads between SARS-CoV-2 and Periodontitis genes. The enhanced expression of ACE2, TMPRSS2, FURIN, and CD147 and the diminished expression of BMAL1 may be a strategy to check both ailments simultaneously. In gene manipulation techniques, oligos are introduced, which contain all the necessary information to manipulate gene expression. The data are derived from the studies on genes' molecular patterns, including nucleotide composition, dinucleotide patterns, relative synonymous codon usage, codon usage bias, codon context, and rare and abundant codons. Such information may be used to manipulate the overexpression and underexpression of the genes at the time of SARS-CoV-2 infection and periodontitis to mitigate both ailments simultaneously; it can be explored to uncover possible future treatments.

mRNA Treatment Rescues Niemann-Pick Disease Type C1 in Patient Fibroblasts

Messenger RNA (mRNA) holds great potential as a disease-modifying treatment for a wide array of monogenic disorders. Niemann-Pick disease type C1 (NP-C1) is an ultrarare monogenic disease that arises due to loss-of-function mutations in the NPC1 gene, resulting in the entrapment of unesterified cholesterol in the lysosomes of affected cells and a subsequent reduction in their capacity for cholesterol esterification. This causes severe damage to various organs including the brain, liver, and spleen. In this work, we describe the use of NPC1-encoded mRNA to rescue the protein insufficiency and pathogenic phenotype caused by biallelic NPC1 mutations in cultured fibroblasts derived from an NP-C1 patient. We first evaluated engineering strategies for the generation of potent mRNAs capable of eliciting high protein expression across multiple cell types. We observed that "GC3" codon optimization, coupled with N1-methylpseudouridine base modification, yielded an mRNA that was approximately 1000-fold more potent than wild-type, unmodified mRNA in a luciferase reporter assay and consistently superior to other mRNA variants. Our data suggest that the improved expression associated with this design strategy was due in large part to the increased secondary structure of the designed mRNAs. Both codon optimization and base modification appear to contribute to increased secondary structure. Applying these principles to the engineering of NPC1-encoded mRNA, we observed a normalization in NPC1 protein levels after mRNA treatment, as well as a rescue of the mutant phenotype. Specifically, mRNA treatment restored the cholesterol esterification capacity of patient cells to wild-type levels and induced a significant reduction in both unesterified cholesterol levels (>57% reduction compared to Lipofectamine-treated control in a cholesterol esterification assay) and lysosome size (157 μm² reduction compared to Lipofectamine-treated control). These findings show that engineered mRNA can correct the deficit caused by NPC1 mutations. More broadly, they also serve to further validate the potential of this technology to correct diseases associated with loss-of-function mutations in genes coding for large, complex, intracellular proteins.

Expression of Codon-Optimized Gene Encoding Murine Moloney Leukemia Virus Reverse Transcriptase in Escherichia coli

Moloney murine leukemia virus reverse transcriptase (MMLV-RT) is the most frequently used enzyme in molecular biology for cDNA synthesis. To date, reverse transcription coupled with Polymerase Chain Reaction, known as RT-PCR, has been popular as an excellent approach for the detection of SARS-CoV-2 during the COVID-19 pandemic. In this study, we aimed to improve the enzymatic production and performance of MMLV-RT by optimizing both codon and culture conditions in E. coli expression system. By applying the optimized codon and culture conditions, the enzyme was successfully overexpressed and increased at high level based on the result of SDS-PAGE and Western blotting. The total amount of MMLV-RT has improved 85-fold from 0.002 g L^-1 to 0.175 g L^-1 of culture. One-step purification by nickel affinity chromatography has been performed to generate the purified enzyme for further analysis of qualitative and quantitative RT activity. Overall, our investigation provides useful strategies to enhance the recombinant enzyme of MMLV-RT in both production and performance. More importantly, the enzyme has shown promising activity to be used for RT-PCR assay.

Design of typical genes for heterologous gene expression

Heterologous protein expression is an important method for analysing cellular functions of proteins, in genetic circuit engineering and in overexpressing proteins for biopharmaceutical applications and structural biology research. The degeneracy of the genetic code, which enables a single protein to be encoded by a multitude of synonymous gene sequences, plays an important role in regulating protein expression, but substantial uncertainty exists concerning the details of this phenomenon. Here we analyse the influence of a profiled codon usage adaptation approach on protein expression levels in the eukaryotic model organism Saccharomyces cerevisiae. We selected green fluorescent protein (GFP) and human α-synuclein (αSyn) as representatives for stable and intrinsically disordered proteins and representing a benchmark and a challenging test case. A new approach was implemented to design typical genes resembling the codon usage of any subset of endogenous genes. Using this approach, synthetic genes for GFP and αSyn were generated, heterologously expressed and evaluated in yeast. We demonstrate that GFP is expressed at high levels, and that the toxic αSyn can be adapted to endogenous, low-level expression. The new software is publicly available as a web-application for performing host-specific protein adaptations to a set of the most commonly used model organisms ( https://odysseus.motorprotein.de ).

Optimal Design of Synthetic DNA Sequences Without Unwanted Binding Sites

Synthesizing DNA molecules by design has become an essential tool in molecular biology and is expected to become ubiquitous in the coming decade. Successful design of a synthetic DNA molecule often requires satisfying multiple objectives, some of which may conflict with others. One particularly important objective is the elimination of unwanted protein binding sites, which may interfere with the desired function of the synthesized molecule. While most design tools offer this fundamental capability, they do not follow a systematic approach that guarantees elimination of all unwanted sites whenever a feasible solution exists. Furthermore, the algorithms these tools use (when published) are often quite naive and inefficient. We present a formal description of the binding site elimination problem and suggest several efficient algorithms that eliminate unwanted patterns with minimum interference to the desired function of the synthesized sequence. These algorithms are simple, efficient, and flexible and, therefore, can be easily incorporated in all existing DNA design tools, enhancing their design capabilities.

Advances in COVID-19 mRNA vaccine development

To date, the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has determined 399,600,607 cases and 5,757,562 deaths worldwide. COVID-19 is a serious threat to human health globally. The World Health Organization (WHO) has declared COVID-19 pandemic a major public health emergency. Vaccination is the most effective and economical intervention for controlling the spread of epidemics, and consequently saving lives and protecting the health of the population. Various techniques have been employed in the development of COVID-19 vaccines. Among these, the COVID-19 messenger RNA (mRNA) vaccine has been drawing increasing attention owing to its great application prospects and advantages, which include short development cycle, easy industrialization, simple production process, flexibility to respond to new variants, and the capacity to induce better immune response. This review summarizes current knowledge on the structural characteristics, antigen design strategies, delivery systems, industrialization potential, quality control, latest clinical trials and real-world data of COVID-19 mRNA vaccines as well as mRNA technology. Current challenges and future directions in the development of preventive mRNA vaccines for major infectious diseases are also discussed.

Identification of a Potential mRNA-based Vaccine Candidate against the SARS-CoV-2 Spike Glycoprotein: A Reverse Vaccinology Approach

The emergence of the novel coronavirus (SARS-CoV-2) in December 2019 has generated a devastating global consequence which makes the development of a rapidly deployable, effective and safe vaccine candidate an imminent global health priority. The design of most vaccine candidates has been directed at the induction of antibody responses against the trimeric spike glycoprotein of SARS-CoV-2, a class I fusion protein that aids ACE2 (angiotensin-converting enzyme 2) receptor binding. A variety of formulations and vaccinology approaches are being pursued for targeting the spike glycoprotein, including simian and human replication-defective adenoviral vaccines, subunit protein vaccines, nucleic acid vaccines and whole-inactivated SARS-CoV-2. Here, we directed a reverse vaccinology approach towards the design of a nucleic acid (mRNA-based) vaccine candidate. The "YLQPRTFLL" peptide sequence (position 269-277) which was predicted to be a B cell epitope and likewise a strong binder of the HLA*A-0201 was selected for the design of the vaccine candidate, having satisfied series of antigenicity assessments. Through the codon optimization protocol, the nucleotide sequence for the vaccine candidate design was generated and targeted at the human toll-like receptor 7 (TLR7). Bioinformatics analyses showed that the sequence "UACCUGCAGCCGCGUACCUUCCUGCUG" exhibited a strong affinity and likewise was bound to a stable cavity in the TLR7 pocket. This study is therefore expected to contribute to the research efforts directed at securing definitive preventive measures against the SARS-CoV-2 infection.

Overcoming the Solubility Problem in E. coli: Available Approaches for Recombinant Protein Production

Despite the importance of recombinant protein production in the academy and industrial fields, many issues concerning the expression of soluble and homogeneous products are still unsolved. Several strategies were developed to overcome these obstacles; however, at present, there is no magic bullet that can be applied for all cases. Indeed, several key expression parameters need to be evaluated for each protein. Among the different hosts for protein expression, Escherichia coli is by far the most widely used. In this chapter, we review many of the different tools employed to circumvent protein insolubility problems.

CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern

There is a growing appreciation that synonymous codon usage, although historically regarded as phenotypically silent, can instead alter a wide range of mechanisms related to functional protein production, a term we use here to describe the net effect of transcription (mRNA synthesis), mRNA half-life, translation (protein synthesis) and the probability of a protein folding correctly to its active, functional structure. In particular, recent discoveries have highlighted the important role that sub-optimal codons can play in modifying co-translational protein folding. These results have drawn increased attention to the patterns of synonymous codon usage within coding sequences, particularly in light of the discovery that these patterns can be conserved across evolution for homologous proteins. Because synonymous codon usage differs between organisms, for heterologous gene expression it can be desirable to make synonymous codon substitutions to match the codon usage pattern from the original organism in the heterologous expression host. Here we present CHARMING (for Codon HARMonizING), a robust and versatile algorithm to design mRNA sequences for heterologous gene expression and other related codon harmonization tasks. CHARMING can be run as a downloadable Python script or via a web portal at http://www.codons.org.

mRNA codon optimization with quantum computers

Reverse translation of polypeptide sequences to expressible mRNA constructs is a NP-hard combinatorial optimization problem. Each amino acid in the protein sequence can be represented by as many as six codons, and the process of selecting the combination that maximizes probability of expression is termed codon optimization. This work investigates the potential impact of leveraging quantum computing technology for codon optimization. A Quantum Annealer (QA) is compared to a standard genetic algorithm (GA) programmed with the same objective function. The QA is found to be competitive in identifying optimal solutions. The utility of gate-based systems is also evaluated using a simulator resulting in the finding that while current generations of devices lack the hardware requirements, in terms of both qubit count and connectivity, to solve realistic problems, future generation devices may be highly efficient.

Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites

Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann's ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experiments, which utilised Escherichia coli cells to express 11,430 recombinant proteins from over 189 diverse species. On this basis, we develop TIsigner that uses simulated annealing to modify up to the first nine codons of mRNAs with synonymous substitutions. We show that accessibility captures the key propensity beyond the target region (initiation sites in this case), as a modest number of synonymous changes is sufficient to tune the recombinant protein expression levels. We build a stochastic simulation model and show that higher accessibility leads to higher protein production and slower cell growth, supporting the idea of protein cost, where cell growth is constrained by protein circuits during overexpression.

Synthetic Biology in Plants, a Boon for Coming Decades

Recently an enormous expansion of knowledge is seen in various disciplines of science. This surge of information has given rise to concept of interdisciplinary fields, which has resulted in emergence of newer research domains, one of them is 'Synthetic Biology' (SynBio). It captures basics from core biology and integrates it with concepts from the other areas of study such as chemical, electrical, and computational sciences. The essence of synthetic biology is to rewire, re-program, and re-create natural biological pathways, which are carried through genetic circuits. A genetic circuit is a functional assembly of basic biological entities (DNA, RNA, proteins), created using typical design, built, and test cycles. These circuits allow scientists to engineer nearly all biological systems for various useful purposes. The development of sophisticated molecular tools, techniques, genomic programs, and ease of nucleic acid synthesis have further fueled several innovative application of synthetic biology in areas like molecular medicines, pharmaceuticals, biofuels, drug discovery, metabolomics, developing plant biosensors, utilization of prokaryotic systems for metabolite production, and CRISPR/Cas9 in the crop improvement. These applications have largely been dominated by utilization of prokaryotic systems. However, newer researches have indicated positive growth of SynBio for the eukaryotic systems as well. This paper explores advances of synthetic biology in the plant field by elaborating on its core components and potential applications. Here, we have given a comprehensive idea of designing, development, and utilization of synthetic biology in the improvement of the present research state of plant system.

Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation

We present the Infobiotics Workbench (IBW), a user-friendly, scalable, and integrated computational environment for the computer-aided design of synthetic biological systems. It supports an iterative workflow that begins with specification of the desired synthetic system, followed by simulation and verification of the system in high-performance environments and ending with the eventual compilation of the system specification into suitable genetic constructs. IBW integrates modeling, simulation, verification, and biocompilation features into a single software suite. This integration is achieved through a new domain-specific biological programming language, the Infobiotics Language (IBL), which tightly combines these different aspects of in silico synthetic biology into a full-stack integrated development environment. Unlike existing synthetic biology modeling or specification languages, IBL uniquely blends modeling, verification, and biocompilation statements into a single file. This allows biologists to incorporate design constraints within the specification file rather than using decoupled and independent formalisms for different in silico analyses. This novel approach offers seamless interoperability across different tools as well as compatibility with SBOL and SBML frameworks and removes the burden of doing manual translations for standalone applications. We demonstrate the features, usability, and effectiveness of IBW and IBL using well-established synthetic biological circuits.

A unified cost-effective method for the construction of reliable potential energy surfaces for H2S and H2O clusters

A DFT-based methodology has been used to construct the potential energy surface of H2S clusters up to pentamers. Geometrical parameters and energetics show very good agreement with the existing experimental and high-level theoretical results. Distinct stable conformers of three dimers, six trimers, eleven tetramers and twenty-three pentamers have been identified. Both S-HS H-bond and SS interactions are identified in dimers, trimers and pentamers, while no SS interactions could be found in any of the 11 tetramer conformers. The binding energies of the most stable dimer, trimer, tetramer and pentamer are -1.66, -5.21, -8.57 and -12.54 kcal mol-1, respectively. The PES has been found to be exceedingly flat and the energy gap between the most and the least stable conformers was found to be only 0.09, 2.13, 1.65 and 1.13 kcal mol-1, from the dimer to the pentamer, respectively. The proposed method has also been used for water clusters up to the pentamer. The results obtained were found to agree closely with the existing results. Only one conformer was found for the water dimer, whereas four, five and fifteen conformers were obtained for the trimer, tetramer and pentamer, respectively. Atoms in molecular calculations were found to corroborate with the geometric and energetic results for both clusters.

Thermostable cellulose saccharifying microbial enzymes: Characteristics, recent advances and biotechnological applications

Cellulases play a promising role in the bioconversion of renewable lignocellulosic biomass into fermentable sugars which are subsequently fermented to biofuels and other value-added chemicals. Besides biofuel industries, they are also in huge demand in textile, detergent, and paper and pulp industries. Low titres of cellulase production and processing are the main issues that contribute to high enzyme cost. The success of ethanol-based biorefinery depends on high production titres and the catalytic efficiency of cellulases functional at elevated temperatures with acid/alkali tolerance and the low cost. In view of their wider application in various industrial processes, stable cellulases that are active at elevated temperatures in the acidic-alkaline pH ranges, and organic solvents and salt tolerance would be useful. This review provides a recent update on the advances made in thermostable cellulases. Developments in their sources, characteristics and mechanisms are updated. Various methods such as rational design, directed evolution, synthetic & system biology and immobilization techniques adopted in evolving cellulases with ameliorated thermostability and characteristics are also discussed. The wide range of applications of thermostable cellulases in various industrial sectors is described.

Chapter Open for the Excited-State Intramolecular Thiol Proton Transfer in the Room-Temperature Solution

We report here, for the first time, the experimental observation on the excited-state intramolecular proton transfer (ESIPT) reaction of the thiol proton in room-temperature solution. This phenomenon is demonstrated by a derivative of 3-thiolflavone (3TF), namely, 2-(4-(diethylamino)phenyl)-3-mercapto-4H-chromen-4-one (3NTF), which possesses an -S-H···O═ intramolecular H-bond (denoted by the dashed line) and has an S₁ absorption at 383 nm. Upon photoexcitation, 3NTF exhibits a distinctly red emission maximized at 710 nm in cyclohexane with an anomalously large Stokes shift of 12 230 cm^-1. Upon methylation on the thiol group, 3MeNTF, lacking the thiol proton, exhibits a normal Stokes-shifted emission at 472 nm. These, in combination with the computational approaches, lead to the conclusion of thiol-type ESIPT unambiguously. Further time-resolved study renders an unresolvable (<180 fs) ESIPT rate for 3NTF, followed by a tautomer emission lifetime of 120 ps. In sharp contrast to 3NTF, both 3TF and 3-mercapto-2-(4-(trifluoromethyl)phenyl)-4H-chromen-4-one (3FTF) are non-emissive. Detailed computational approaches indicate that all studied thiols undergo thermally favorable ESIPT. However, once forming the proton-transferred tautomer, the lone-pair electrons on the sulfur atom brings non-negligible nπ* contribution to the S₁' state (prime indicates the proton-transferred tautomer), for which the relaxation is dominated by the non-radiative deactivation. For 3NTF, the extension of π-electron delocalization by the diethylamino electron-donating group endows the S₁' state primarily in the ππ* configuration, exhibiting the prominent tautomer emission. The results open a new chapter in the field of ESIPT, covering the non-canonical sulfur intramolecular H-bond and its associated ESIPT at ambient temperature.

Electrical conductivity as a driver of biological and geological spatial heterogeneity in the Puquios, Salar de Llamara, Atacama Desert, Chile

Reputed to be the driest desert in the world, the Atacama Desert in the Central Andes of Northern Chile is an extreme environment with high UV radiation, wide temperature variation, and minimum precipitation. Scarce lagoons associated with salt flats (salars) in this desert are the surface expression of shallow groundwater; these ponds serve as refugia for life and often host microbial communities associated with evaporitic mineral deposition. Results based on multidisciplinary field campaigns and associated laboratory examination of samples collected from the Puquios of the Salar de Llamara in the Atacama Desert during austral summer provide unprecedented detail regarding the spatial heterogeneity of physical, chemical, and biological characteristics of these salar environments. Four main lagoons ('Puquios') and more than 400 smaller ponds occur within an area less than 5 km2, and are characterized by high variability in electrical conductivity, benthic and planktonic biota, microbiota, lagoon bottom type, and style of mineral deposition. Results suggest that electrical conductivity is a driving force of system heterogeneity. Such spatial heterogeneity within the Puquios is likely to be expanded with temporal observations incorporating expected seasonal changes in electrical conductivity. The complexity of these Andean ecosystems may be key to their ability to persist in extreme environments at the edge of habitability.

A bivalent vaccine against avian necrotic enteritis and coccidiosis

AIMS

In this study, we attempted to design a recombinant vaccine harbouring domain with a key role in enterocyte attachment and cell invasion in necrotic enteritis (NE) and coccidiosis.

METHODS AND RESULTS

In this study, we investigated whether a recombinant protein consisting of necrotic enteritis B-like toxin, C-terminal domain of alpha-toxin, apical membrane antigen 1 (AMA1), and Rhoptry neck protein 2 (RON2) which we call "NeCoVac" hereafter, can improve protection against both diseases compared to vaccination with each antigen in previous studies. Birds intestinal lesion scores and specific antibody levels were measured to determine protection after oral gavage challenges with virulent Clostridium perfringens and LIVACOX^® T. Birds immunized with NeCoVac were protected up to 84% against NE and coccidiosis compared to unimmunized and even positive groups (groups treated with LIVACOX^® T [coccidiosis live vaccine] and tylosin as routine veterinary interventions) (p < 0.05).

CONCLUSIONS

Our findings suggest that vaccination with NeCoVac is highly efficient in protecting birds from NE, coccidiosis and a combination of both diseases.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study is the first one to describe the combinatorial use of AMA1 and RON2 against coccidiosis, and the first report using NeCoVac against NE and coccidiosis together.

In Silico Development of Novel Chimeric Lysins with Highly Specific Inhibition against Salmonella by Computer-Aided Design

Four novel chimeric lysins (P361, P362, P371, and P372), which were the fusion of Salmonella phage lysins and novel antimicrobial peptide LeuA-P, were obtained using bioinformatics analysis and in silico design. The recombinant chimeric lysins were expressed in E. coli BL21(DE3) strain and showed highly specific inhibition against Salmonella. The minimal inhibitory concentrations (MICs) of P362 and P372 to S. typhi CMCC 50071 were 8 and 16 μg/mL, respectively. Both 1 × MIC P362 and P372 could increase the outer membrane permeability and cleave the cell wall peptidoglycan, causing the leakage of intracellular nucleic acids and proteins and ultimately killing Salmonella efficiently without drug resistance. The combination of P362, P372, and potassium sorbate reduced more than 3 log CFU/g counts of microorganisms in contaminated chilled chicken and extended the shelf life by 7 days. The strategy of antimicrobial peptide (AMP)-lysin chimera inspired the inability of phage lysin to specifically inhibit Gram-negative bacteria with dense outer membranes in vitro.

Assessing optimal: inequalities in codon optimization algorithms

BACKGROUND

Custom genes have become a common resource in recombinant biology over the last 20 years due to the plummeting cost of DNA synthesis. These genes are often "optimized" to non-native sequences for overexpression in a non-native host by substituting synonymous codons within the coding DNA sequence (CDS). A handful of studies have compared native and optimized CDSs, reporting different levels of soluble product due to the accumulation of misfolded aggregates, variable activity of enzymes, and (at least one report of) a change in substrate specificity. No study, to the best of our knowledge, has performed a practical comparison of CDSs generated from different codon optimization algorithms or reported the corresponding protein yields.

RESULTS

In our efforts to understand what factors constitute an optimized CDS, we identified that there is little consensus among codon-optimization algorithms, a roughly equivalent chance that an algorithm-optimized CDS will increase or diminish recombinant yields as compared to the native DNA, a near ubiquitous use of a codon database that was last updated in 2007, and a high variability of output CDSs by some algorithms. We present a case study, using KRas4B, to demonstrate that a median codon frequency may be a better predictor of soluble yields than the more commonly utilized CAI metric.

CONCLUSIONS

We present a method for visualizing, analyzing, and comparing algorithm-optimized DNA sequences for recombinant protein expression. We encourage researchers to consider if DNA optimization is right for their experiments, and work towards improving the reproducibility of published recombinant work by publishing non-native CDSs.

Pyridoxal kinase PdxY mediated carbon dioxide assimilation to enhance the biomass in Chlamydomonas reinhardtii CC-400

Microalga served as the promising bioresources due to the high efficiency of carbon dioxide conversion. However, the application of microalga is still restricted by low biomass, easier contamination, and high cost of production. To overcome the challenge, engineered Chlamydomonas reinhardtii CC-400 with pyridoxal kinase gene (pdxY) has demonstrated in this study. The results indicated CC-400 with pdxY reached enhanced algal biomass in three different systems, including flask, Two-layer Photo-Reactor (TPR) and airlift Photo-Bioreactor (PBR). The genetic strain PY9 cultured with 1% CO₂ in the PBR showed a significant enhancement of biomass up to 1.442 g/L, a 2-times of that of the wild type. We also found the transcriptional levels of carbonic anhydrase (CA) dropped down in PY9 while higher levels of RuBisCo and pdxY occurred, thus the carbon dioxide assimilation under mixotrophic culture dramatically increased. We proofed that pdxY successfully mediated carbon dioxide utilization in CC-400.

BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts

Synthetic biology seeks to create new biological parts, devices, and systems, and to reconfigure existing natural biological systems for custom-designed purposes. The standardized BioBrick parts are the foundation of synthetic biology. The incomplete and flawed metadata of BioBrick parts, however, are a major obstacle for designing genetic circuit easily, quickly, and accurately. Here, a database termed BioMaster http://www.biomaster-uestc.cn was developed to extensively complement information about BioBrick parts, which includes 47,934 items of BioBrick parts from the international Genetically Engineered Machine (iGEM) Registry with more comprehensive information integrated from 10 databases, providing corresponding information about functions, activities, interactions, and related literature. Moreover, BioMaster is also a user-friendly platform for retrieval and analyses of relevant information on BioBrick parts.

Comparison of Different Signal Peptides for the Efficient Secretion of the Sweet-Tasting Plant Protein Brazzein in Pichia pastoris

Brazzein is a small sweet-tasting protein found in the red berries of a West African evergreen shrub, Pentadiplandra brazzeana Baillon. Brazzein is highly soluble and stable over a large pH range and at high temperatures, which are characteristics that suggest its use as a natural sweetener. However, Pentadiplandra brazzeana culture is difficult at a large scale, limiting the natural source of brazzein. Heterologous expression of brazzein has been established in numerous systems, including bacteria, yeast, and transgenic plants. Brazzein requires four disulfide bonds to be active in eliciting an intense sweet taste, and the yeast Pichia pastoris appears to be one of the best options for obtaining functional brazzein in high quantities. Employing yeast secretion in the culture medium allows us to obtain fully active brazzein and facilitate purification later. To increase yeast secretion, we compared seven different signal peptides to successfully achieve brazzein secretion using the yeast P. pastoris. The brazzein proteins corresponding to these signal peptides elicited activation of the sweet taste receptor functionally expressed in a cellular assay. Among these tested signal peptides, three resulted in the secretion of brazzein at high levels.

Immuno-informatics analysis and expression of a novel multi-domain antigen as a vaccine candidate against glioblastoma

Glioblastoma multiform is the most common of primary malignant brain tumors in adults. Currently, surgical resection of the tumor mass, followed by adjuvant radiotherapy and chemotherapy are standard treatments for glioblastoma multiform but so far are not effective treatments. Thus, the development of a vaccine, as a safe and efficient strategy for prophylactic or therapeutic purposes against glioblastoma multiform is very necessary. The present study aimed to design the multi-domain vaccine for glioblastoma multiform. An in silico approach was used to select the most potent domains of proteins to induce the host's B- and T-cell immune response against glioblastoma multiform. IL-13Rα-2 (amino acid positions 27-144), TNC (amino acid positions 1900-2100), and PTPRZ-1(amino acid positions 731-884) were found to have potent inducible immune responses. So, we considered them for fusing with a linker A(EAAAK)₃A to construct the multi-domain recombinant vaccine. The immuno-informatics analysis of the designed recombinant vaccine construct was performed to evaluate its efficacy. Although the designed recombinant vaccine construct did not show allergen property, its antigenicity was estimated at 0.78. The Physico-chemical properties of the recombinant vaccine construct were characterized and revealed the potency of the vaccine candidate. Then its secondary and tertiary structures, mRNA structure, molecular docking, and immune simulation were predicted using bioinformatics tools. Next, the designed recombinant vaccine construct was synthesized, and cloned into the pET28a vector and expressed in E. coli BL21. Besides, the circular dichroism spectroscopy was utilized for the investigation of the secondary structure changes of the recombinant vaccine construct. The results of the verification assessment of the recombinant vaccine construct expression indicated that in silico analysis was relatively accurate, and relatively change occurred on the protein secondary structure. In our future plan, the vaccine candidate that was confirmed by in silico tools should be validated by further in vitro and in vivo experimental studies.