From Never Born Proteins to Minimal Living Cells: Two Projects in Synthetic Biology

The Never Born Proteins (NBPs) and the Minimal Cell projects are two currently developed research lines belonging to the field of synthetic biology. The first deals with the investigation of structural and functional properties of de novo proteins with random sequences, selected and isolated using phage display methods. The minimal cell is the simplest cellular construct which displays living properties, such as self-maintenance, self-reproduction and evolvability. The semi-synthetic approach to minimal cells involves the use of extant genes and proteins in order to build a supramolecular construct based on lipid vesicles. Results and outlooks on these two research lines are shortly discussed, mainly focusing on their relevance to the origin of life studies. Presented at: National Workshop on Astrobiology: Search for Life in the Solar System, Capri, Italy 26 to 28 October, 2005.     

A coproofreading Zn(2+)-dependent exonuclease within a bacterial replicase

The proofreading exonucleases of all DNA replicases contain acidic residues that chelate two Mg(2+) ions that participate in catalysis. DNA polymerase III holoenzymes contain their proofreading activity in a separate subunit, epsilon, which binds the polymerase subunit, alpha, through alpha's N-terminal php domain. Here we demonstrate that the alpha php domain contains a novel Zn(2+)-dependent 3' --> 5' exonuclease that preferentially removes mispaired nucleotides, providing the first example of a coediting nuclease.     

Inducible expression of maize polyamine oxidase in the nucleus of MCF-7 human breast cancer cells confers sensitivity to etoposide

Summary. In this study, polyamine oxidase from maize (MPAO), which is involved in the terminal catabolism of spermidine and spermine to produce an aminoaldehyde, 1,3-diaminopropane and H₂O₂, has been conditionally expressed at high levels in the nucleus of MCF-7 human breast cancer cells, with the aim to interfere with polyamine homeostasis and cell proliferation. Recombinant MPAO expression induced accumulation of a high amount of 1,3-diaminopropane, an increase of putrescine levels and no alteration in the cellular content of spermine and spermidine. Furthermore, recombinant MPAO expression did not interfere with cell growth of MCF-7 cells under normal conditions but it did confer higher growth sensitivity to etoposide, a DNA topoisomerase II inhibitor widely used as antineoplastic drug. These data suggest polyamine oxidases as a potential tool to improve the efficiency of antiproliferative agents despite the difficulty to interfere with cellular homeostasis of spermine and spermidine. Authors’ address: Dr. Paraskevi Tavladoraki, Department of Biology, University ‘Roma Tre’, Viale G. Marconi 446, 00146 Rome, Italy     

Fabrication and characterization of electrospun chitosan nanofibers formed via templating with polyethylene oxide

Chitosan is an abundantly common, naturally occurring, polysaccharide biopolymer. Its biocompatible, biodegradable, and antimicrobial properties have led to significant research toward biological applications such as drug delivery, artificial tissue scaffolds for functional tissue engineering, and wound-healing dressings. For applications such as tissue scaffolding, formation of highly porous mats of nanometer-sized fibers, such as those fabricated via electrospinning, may be quite important. Previously, strong acidic solvents and blending with synthetic polymers have been used to achieve electrospun nanofibers containing chitosan. As an alternative approach, in this work, polyethylene oxide (PEO) has been used as a template to fabricate chitosan nanofibers by electrospinning in a core-sheath geometry, with the PEO sheath serving as a template for the chitosan core. Solutions of 3 wt % chitosan (in acetic acid) and 4 wt % PEO (in water) were found to have matching rheological properties that enabled efficient core-sheath fiber formation. After removing the PEO sheath by washing with deionized water, chitosan nanofibers were obtained. Electron microscopy confirmed nanofibers of approximately 250 nm diameter with a clear core-sheath geometry before sheath removal, and chitosan nanofibers of approximately 100 nm diameter after washing. The resultant fibers were characterized with IR spectroscopy and X-ray diffraction, and the mechanical and electrical properties were evaluated.     

Aversive reactions of two invertebrate predators to European red–black insects

Prey species gain protection by imitating signals of unpalatable models in defensive mimicry. Mimics have been traditionally classified as Batesian (palatable mimic resembling an unpalatable model) or Müllerian (unpalatable mimic resembling a similarly unpalatable model). However, recent studies suggest that rather than discrete categories, the phenomenon of mimicry can be better understood as a continuum. The level of unpalatability of defended prey is a key factor in determining the type of mimetic relationship. Herein, we used insects (ladybugs and true bugs) from a putative European “red–black” mimetic complex as experimental models of defended species and crickets as a control prey. We offered the prey to two species of sympatric invertebrate predators (praying mantis and spider) and video recorded the interactions. We tested three alternative hypotheses, namely (i) the three red–black species tested are similarly defended against both predators; (ii) some red–black species are better defended than others against both predator species, and (iii) the effectiveness of the red–black species defenses is predator dependent. Both predators attacked all prey types with a similar frequency. But while all three red–black species similarly elicited aversive behaviors in spiders, the mantises' aversive reactions varied depending on the prey species. Our results provide support to the third hypothesis, suggesting that the same prey species can fall into different parts of the spectrum of palatability–unpalatability depending on the type of predator.     

NMR and photo-CIDNP studies of human proinsulin and prohormone processing intermediates with application to endopeptidase recognition

The proinsulin-insulin system provides a general model for the proteolytic processing of polypeptide hormones. Two proinsulin-specific endopeptidases have been defined, a type I activity that cleaves the B-chain/C-peptide junction (Arg31-Arg32) and a type II activity that cleaves the C-peptide/A-chain junction (Lys64-Arg65). These endopeptidases are specific for their respective dibasic target sites; not all such dibasic sites are cleaved, however, and studies of mutant proinsulins have demonstrated that additional sequence or structural features are involved in determining substrate specificity. To define structural elements required for endopeptidase recognition, we have undertaken comparative 1H NMR and photochemical dynamic nuclear polarization (photo-CIDNP) studies of human proinsulin, insulin, and split proinsulin analogues as models of prohormone processing intermediates. The overall conformation of proinsulin is observed to be similar to that of insulin, and the connecting peptide is largely unstructured. In the 1H NMR spectrum of proinsulin significant variation is observed in the line widths of insulin-specific amide resonances, reflecting exchange among conformational substates; similar exchange is observed in insulin and is not damped by the connecting peptide. The aromatic 1H NMR resonances of proinsulin are assigned by analogy to the spectrum of insulin, and assignments are verified by chemical modification. Unexpectedly, nonlocal perturbations are observed in the insulin moiety of proinsulin, as monitored by the resonances of internal aromatic groups. Remarkably, these perturbations are reverted by site-specific cleavage of the connecting peptide at the CA junction but not the BC junction. These results suggest that a stable local structure is formed at the CA junction, which influences insulin-specific packing interactions. We propose that this structure (designated the "CA knuckle") provides a recognition element for type II proinsulin endopeptidase.     

Resource availability,mating opportunity and sexual selection intensity influence the expression of male alternative reproductive tactics

The expression of alternative reproductive tactics can be plastic and occur simultaneously depending on cues that vary spatially or temporally. For example, variation in resources and sexual selection intensity is expected to influence the pay‐off of each tactic and shape the decision of which tactic to employ. Males of the nuptial gift‐giving spider Pisaura mirabilis can adopt three tactics: offering a genuine prey gift, a ‘worthless’ non‐nutritious gift or no gift. We hypothesized that resources and/or male body condition, and mating opportunity and sexual selection intensity, vary over the course of the mating season to shape the co‐existence of alternative traits. We measured these variables in the field over two seasons, to investigate the predictions that as the mating season progresses, (i) males become more likely to employ a gift‐giving tactic, and (ii) the likelihood of switching from worthless to genuine gifts increases. Prey availability increased over the season and co‐varied with the propensity of males to employ the gift‐giving tactic, but we found no support for condition‐dependent gift giving. Males responded to an increase in female availability by increasing their mating effort (gift production). Furthermore, the frequency of genuine gift use increased with sexual selection intensity, consistent with the assumption that sperm competition intensity increases with time. Our results suggest that the frequency of alternative tactics is shaped by seasonal changes in ecological factors and sexual selection. This leads to relaxed selection for the gift‐giving tactic early in the season when females are less choosy and resources more scarce, and increased selection for genuine gifts later in the season driven by mating opportunity and risk of sperm competition.     

Demonstration of Activity of α‐Galactosidase Secreted by Cucumis sativus L. Cells

A simple, rapid and reproducible procedure for the identification of extracellular cucumber (Cucumis sativus L.) α‐galactosidase is described using callus cultures of seedlings from the tested plant, hairy roots of 2‐day‐old seedlings of cucumber germinating on agar plates as well as cell suspension cultures derived from callus cultures. For the determination of the intracellular and extracellular activities of α‐galactosidase, 6‐bromo‐2‐naphthyl‐α‐D‐galactopyranoside and p‐nitrophenyl‐α‐D‐galactopyranoside, respectively, were used as synthetic substrates. The extracellular α‐galactosidase activity was identified by evaluating the dye‐zones in agar medium. The enzyme from cucumber callus cultures and seedling roots, cultivated on agar plates supplemented with 6‐bromo‐2‐naphthyl‐α‐D‐galactopyranoside, hydrolyzed this substrate releasing 6‐bromo‐2‐naphthol. By simultaneous coupling with hexazonium p‐rosaniline the corresponding azodye was formed. Thus, the extracellular enzyme was detected by the presence of reddish‐brown zones on the agar plates around the plant material. The parallel extracellular and intracellular activities were determined in cell suspension cultures derived from callus cultures. The results show a 44.6% intracellular and 55.4% extracellular distribution of α‐galactosidase activity. The described agar plate method enables a rapid, simple and specific detection of plant producers of extracellular α‐galactosidase.     

Question 7: New Aspects of Interactions Among Vesicles

In this short article I discuss the relevance of two aspects of vesicle reactivity that are germane to understand the role of compartments in the origin of early cells. Studies of vesicle self-reproduction indicate that simple vesicles can grow and divide, maintaining inside most of their content and giving rise to a simple autopoietic system. New aspects of vesicle reactivity are also introduced, such as selection and competition processes within vesicle populations, emphasizing the concepts of vesicle diversity, inter-vesicles and vesicles–environment interactions, intended as synthetic analogs of primitive ‘ecological’ processes. Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.