Screening and cloning of antimicrobial DNA sequences using a vital staining method

A novel method for cloning of coding sequences of highly toxic proteins

BACKGROUND

During standard gene cloning, the recombinant protein appearing in bacteria as the result of expression leakage very often inhibits cell proliferation leading to blocking of the cloning procedure. Although different approaches can reduce transgene basal expression, the recombinant proteins, which even in trace amounts inhibit bacterial growth, can completely prevent the cloning process.

METHODS

Working to solve the problem of DNase II-like cDNA cloning, we developed a novel cloning approach. The method is based on separate cloning of the 5' and 3' fragments of target cDNA into a vector in such a way that the short Multiple Cloning Site insertion remaining between both fragments changes the reading frame and prevents translation of mRNA arising as a result of promoter leakage. Subsequently, to get the vector with full, uninterrupted Open Reading Frame, the Multiple Cloning Site insertion is removed by in vitro restriction/ligation reactions, utilizing the unique restriction site present in native cDNA.

RESULTS

Using this designed method, we cloned a coding sequence of AcDNase II that is extremely toxic for bacteria cells. Then, we demonstrated the usefulness of the construct prepared in this way for overexpression of AcDNase II in eukaryotic cells.

CONCLUSIONS

The designed method allows cloning of toxic protein coding sequences that cannot be cloned by standard methods.

GENERAL SIGNIFICANCE

Cloning of cDNAs encoding toxic proteins is still a troublesome problem that hinders the progress of numerous studies. The method described here is a convenient solution to cloning problems that are common in research on toxic proteins.

Antimicrobial genes from Allium sativum and Pinellia ternata revealed by a Bacillus subtilis expression system

Antimicrobial genes are found in all classes of life. To efficiently isolate these genes, we used Bacillus subtilis and Escherichia coli as target indicator bacteria and transformed them with cDNA libraries. Among thousands of expressed proteins, candidate proteins played antimicrobial roles from the inside of the indicator bacteria (internal effect), contributing to the sensitivity (much more sensitivity than the external effect from antimicrobial proteins working from outside of the cells) and the high throughput ability of screening. We found that B. subtilis is more efficient and reliable than E. coli. Using the B. subtilis expression system, we identified 19 novel, broad-spectrum antimicrobial genes. Proteins expressed by these genes were extracted and tested, exhibiting strong external antibacterial, antifungal and nematicidal activities. Furthermore, these newly isolated proteins could control plant diseases. Application of these proteins secreted by engineered B. subtilis in soil could inhibit the growth of pathogenic bacteria. These proteins are thermally stable and suitable for clinical medicine, as they exhibited no haemolytic activity. Based on our findings, we speculated that plant, animal and human pathogenic bacteria, fungi or even cancer cells might be taken as the indicator target cells for screening specific resistance genes.

Comparative genomics analysis of five families of antimicrobial peptide-like genes in seven ant species

Ants, as eusocial insects, live in dense groups with high connectivity, increasing the risk of pathogen spread and possibly driving the evolution of their antimicrobial immune system. Draft genomes of seven ant species provide a new source to undertake comparative study of their antimicrobial peptides (AMPs), key components of insect innate immunity. By using computational approaches, we analyzed five AMP families that include abaecins, hymenoptaecins, insect defensins, tachystatins, and crustins in ants, which comprise 69 new members. Among them, a new type of proline-rich abaecins was recognized and they are exclusively present in ants. Hymenoptaecins, a family of glycine-rich AMPs from Hymenoptera and Diptera, exhibit variable numbers of intragenic tandem repeats in a lineage-specific manner and all hymenoptaecins in ants have evolved an acidic C-terminal propeptide. In some ant species, insect defensins with the cysteine-stabilized α-helical and β-sheet (CSαβ) fold and tachystatin-like AMPs with the inhibitor cysteine knot (ICK) fold have undergone gene expansion and differential gene loss. Moreover, extensive sequence diversity exists in the C-termini of the defensins and the ICK-type peptides and the n-loop of the defensins. Also, we identified for the first time a crustin-type AMP in ants, which are only known in crustaceans previously. These ant crustins evolutionarily gain an aromatic amino acid-rich insertion when compared with those of crustaceans. Our work not only enlarges the insect AMP resource, but also sheds light on the complexity and dynamic evolution of AMPs in ants.

Plant Essential Oils and Mastitis Disease: Their Potential Inhibitory Effects on Pro-inflammatory Cytokine Production in Response to Bacteria Related Inflammation

This paper highlights the role of plant volatile organic compounds, found in essential oils, for the treatment of bacteria related inflammation. This report is focused on tea tree oil, particularly its main compound terpinen-4-ol. Analysis of the published literature shows that many essential oils have significant antibacterial, antifungal and anti-inflammatory effects. Some of their major components, such as terpinen-4-ol, act by inhibiting pro-inflammatory cytokine expression while stimulating production of anti-inflammatory cytokines. Such observations may be exploited to encourage biotherapy against mastitis. The use of synthetic antibiotics is being increasingly discouraged because their presence in dairy milk may have potential downstream effects on population health and the agri-food chain. In the context of inflammation and related mammalian responses, understanding the interplay between volatile organic compounds, especially terpinen-4-ol, and cytokines during bacteria related inflammation should clarify their mode of action to control mastitis.

Rice dehydrin K-segments have in vitro antibacterial activity

Dehydrins are groups of plant proteins that have been shown to response to various environmental stimuli such as dehydration, elevated salinity, and low temperature. However, their roles in plant defense against microbes have not been demonstrated. In an attempt to discover plant antimicrobial proteins, we have screened a rice cDNA library and isolated several cDNAs coding for dehydrins. Protein extracts from Escherichia coli expressing these cDNAs were tested for their activity against Gram-positive bacteria (Bacillus pumilus, B. subtilis, Staphylococcus aureus, and Sarcina lutea) and Gram-negative bacteria (Escherichia coli and Xanthomonas oryzae pv. oryzae). The results indicate that the crude protein extracts exhibited antibacterial activities against the Gram-positive bacteria. However, dehydrins purified by immunoaffinity chromatography were not active against the bacteria. To pinpoint the dehydrin peptides that were responsible for the bactericidal activity, we expressed DNA sequences coding for truncated dehydrins containing either K- or S-segment and found that K-segment peptides, and not S-segment, were responsible for the antibacterial activities against Gram-positive bacteria. Antibacterial assay with synthetic K-segments indicated that the peptides inhibited growth of B. pumilus with minimum inhibition concentration and minimum bactericidal concentration of 130 and 400 μg/ml, respectively.

Proline-rich antimicrobial peptides: converging to a non-lytic mechanism of action

Proline-rich antimicrobial peptides are a group of cationic host defense peptides of vertebrates and invertebrates characterized by a high content of proline residues, often associated with arginine residues in repeated motifs. Those isolated from some mammalian and insect species, although not evolutionarily related, use a similar mechanism to selectively kill Gram-negative bacteria, with a low toxicity to animals. Unlike other types of antimicrobial peptides, their mode of action does not involve the lysis of bacterial membranes but entails penetration into susceptible cells, where they then act intracellularly. Some aspects of the transport system and cytoplasmic targets have been elucidated. These features make them attractive both as anti-infective lead compounds and as a new class of potential cell-penetrating peptides capable of internalising membrane-impermeant drugs into both bacterial and eukaryotic cells.

Characterization of an abaecin-like antimicrobial peptide identified from a Pteromalus puparum cDNA clone

Abaecin is a major antimicrobial peptide, initially identified from the honeybee. In our effort to discover new antimicrobial peptides from the endoparasitoid wasp Pteromalus puparum, we identified an antibacterial cDNA clone that codes a fragment with high amino acid sequence similarity to abaecin. The proline-rich peptide (YVPPVQKPHPNGPKFPTFP, named PP30) was chemically synthesized and characterized in this study. Antimicrobial assays indicated that the cationic peptide was active against both Gram-negative and positive bacteria, but not active against fungi tested. No hemolytic activity was observed against human erythrocytes after 1h incubation at concentration of 125 microM or below. The antibacterial activity of PP30 against Escherichia coli was attenuated in the presence of increasing concentrations of NaCl. Transmission electron microscopic (TEM) examination of PP30-treated E. coli cells showed morphological changes in the cells and extensive damage to the cell membranes. The circular dichroism (CD) spectroscopy studies indicated that PP30 formed random coil structures in phosphate buffer (pH 7.4), 50% TFE and 25 mM SDS solution. Expression analysis of the gene coding for the peptide indicated that its expression was upregulated upon bacterial infection, indicating that the gene may play a role in preventing potential infection by microorganisms during parasitization in Pieris rapae.

Novel antimicrobial peptides identified from an endoparasitic wasp cDNA library

We screened an endoparasitic wasp (Pteromalus puparum) cDNA library for DNA sequences having antimicrobial activity using a vital dye exclusion assay. Two dozens of clones were isolated that inhibited the growth of host Escherichia coli cells due to expression of the cloned genes. Three peptides (PP13, PP102 and PP113) were synthesized chemically based on the amino acid sequences deduced from these clones and assayed for their antimicrobial activity. These peptides have net positive charges and are active against both Gram-negative and -positive bacteria, but are not active against fungi tested. Their hemolytic activity on human red blood cells was measured, and no hemolytic activity was observed after 1-h incubation at a concentration of 62.5 microM or below. A Blast search indicated that the three peptides have not been previously characterized as antimicrobial peptides (AMPs). Salt-dependency studies revealed that the biocidal activity of these peptides against E. coli decreased with increasing concentration of NaCl. Transmission electron microscopic (TEM) examination of PP13-treated E. coli cells showed extensive damage of cell membranes. The CD spectroscopy studies noted that the enhanced alpha-helical characteristics of PP13 strongly contribute to its higher antimicrobial properties. These results demonstrate the feasibility to identify novel AMPs by screening the expressional cDNA library.

Antimicrobial peptide-like genes in Nasonia vitripennis: a genomic perspective

BACKGROUND

Antimicrobial peptides (AMPs) are an essential component of innate immunity which can rapidly respond to diverse microbial pathogens. Insects, as a rich source of AMPs, attract great attention of scientists in both understanding of the basic biology of the immune system and searching molecular templates for anti-infective drug design. Despite a large number of AMPs have been identified from different insect species, little information in terms of these peptides is available from parasitic insects.

RESULTS

By using integrated computational approaches to systemically mining the Hymenopteran parasitic wasp Nasonia vitripennis genome, we establish the first AMP repertoire whose members exhibit extensive sequence and structural diversity and can be distinguished into multiple molecular types, including insect and fungal defensin-like peptides (DLPs) with the cysteine-stabilized alpha-helical and beta-sheet (CSalphabeta) fold; Pro- or Gly-rich abaecins and hymenoptaecins; horseshoe crab tachystatin-type AMPs with the inhibitor cystine knot (ICK) fold; and a linear alpha-helical peptide. Inducible expression pattern of seven N. vitripennis AMP genes were verified, and two representative peptides were synthesized and functionally identified to be antibacterial. In comparison with Apis mellifera (Hymenoptera) and several non-Hymenopteran model insects, N. vitripennis has evolved a complex antimicrobial immune system with more genes and larger protein precursors. Three classical strategies that are likely responsible for the complexity increase have been recognized: 1) Gene duplication; 2) Exon duplication; and 3) Exon-shuffling.

CONCLUSION

The present study established the N. vitripennis peptidome associated with antimicrobial immunity by using a combined computational and experimental strategy. As the first AMP repertoire of a parasitic wasp, our results offer a basic platform for further studying the immunological and evolutionary significances of these newly discovered AMP-like genes in this class of insects.