Rainbow screening: Chromoproteins enable visualized molecular cloning

Molecular cloning facilitates the assembly of heterologous DNA fragments with vectors, resulting in the generation of plasmids that can steadily replicate in host cells. To efficiently and accurately screen out the expected plasmid candidates, various methods, such as blue-white screening, have been developed for visualization. However, these methods typically require additional genetic manipulations and costs. To simplify the process of visualized molecular cloning, here we report Rainbow Screening, a method that combines Gibson Assembly with chromoproteins to distinguish Escherichia coli (E. coli) colonies by naked eyes, eliminating the need for additional genetic manipulations or costs. To illustrate the design, we select both E. coli 16s rRNA and sfGFP expression module as two inserted fragments. Using Rainbow Screening, false positive colonies can be easily distinguished on LB-agar plates. Moreover, both the assembly efficiency and the construct accuracy can exceed 80%. We anticipate that Rainbow Screening will enrich the molecular cloning methodology and expand the application of chromoproteins in biotechnology and synthetic biology.

Expansion and Diversification of Fluorescent Protein Genes in Fifteen Acropora Species during the Evolution of Acroporid Corals

In addition to a purple, non-fluorescent chromoprotein (ChrP), fluorescent proteins (FPs) account for the vivid colors of corals, which occur in green (GFP), cyan (CFP), and red (RFP) FPs. To understand the evolution of the coral FP gene family, we examined the genomes of 15 Acropora species and three confamilial taxa. This genome-wide survey identified 219 FP genes. Molecular phylogeny revealed that the 15 Acropora species each have 9–18 FP genes, whereas the other acroporids examined have only two, suggesting a pronounced expansion of the FP genes in the genus Acropora. The data estimates of FP gene duplication suggest that the last common ancestor of the Acropora species that survived in the period of high sea surface temperature (Paleogene period) has already gained 16 FP genes. Different evolutionary histories of lineage-specific duplication and loss were discovered among GFP/CFPs, RFPs, and ChrPs. Synteny analysis revealed core GFP/CFP, RFP, and ChrP gene clusters, in which a tandem duplication of the FP genes was evident. The expansion and diversification of Acropora FPs may have contributed to the present-day richness of this genus.

Gene cloning of the pink-colored protein from Pleurotus salmoneostramineus (PsPCP) and its species-specific chromoprotein are effective for colorization of the fruit body

Pleurotus salmoneostramineus is a pink mushroom. This pink color is a protein and forms a complex with 3H-indol-3-one. The gene encoding the pink-colored protein from P. salmoneostramineus (PsPCP) was cloned, and its sequence was elucidated as a 681-bp. The ORF encodes 226 amino acid residues. The amino acid sequence of the protein did not show any significant homology in the DDBJ/EMBL/GenBank databases. Recombinant PsPCP was expressed as the soluble form in E. coli. The reaction mixture of purified recombinant PsPCP and 3H-indol-3-one showed a pink color as the native pigment. A real-time PCR analysis revealed the strong expression of PsPCP in the primordium formation stage of the life cycle of the fungus; however, its expression decreased with the maturation of the fruit body. A comparison of PsPCP gene expression profiles between two strains revealed high levels in the dark-colored strain.

[Construction and characterization of a bio-detector for inflammatory bowel disease]

Genetically engineered intestinal microbes could be powerful tools to detect and treat intestine inflammation due to their non-invasive character, low costs, and convenience. Intestinal inflammation is usually detected along with an increasing concentration of thiosulfate and tetrathionate molecules in the intestines. ThsSR and TtrSR are two-component biosensors to detect the presence of thiosulfate and tetrathionate molecules, respectively. In real-life intestinal inflammation detection, sophisticated instruments are needed if using fluorescent proteins as reporters. However, chromoproteins and other colored small molecules, which can be seen by the unaided eye, could extend the use of ThsSR and TtrSR biosensors to detect intestine inflammation. The feasibility of ThsSR and TtrSR systems was tested by monitoring the fluorescence intensity of sfGFP in response to the concentration of thiosulfate and tetrathionate, followed by the incorporation of the two systems into Escherichia coli Top10 and E. coli Nissle 1917. The potential for the real-life application of the two systems was further corroborated by substituting sfGFP with a series of chromoproteins and a protoviolaceinic acid synthesis cassette as reporter genes. The results indicated that signal expression of the new systems had a positive correlation with the concentration of tetrathionate and thiosulfate molecules. Thus, the modified ThsSR and TtrSR system may potentially be applied in the human body for the detection of intestinal inflammation.

The structure of a far-red fluorescent protein, AQ143, shows evidence in support of reported red-shifting chromophore interactions

Engineering fluorescent proteins (FPs) to emit light at longer wavelengths is a significant focus in the development of the next generation of fluorescent biomarkers, as far-red light penetrates tissue with minimal absorption, allowing better imaging inside of biological hosts. Structure-guided design and directed evolution have led to the discovery of red FPs with significant bathochromic shifts to their emission. Here, we present the crystal structure of one of the most bathochromically shifted FPs reported to date, AQ143, a nine-point mutant of aeCP597, a chromoprotein from Actinia equina. The 2.19 Å resolution structure reveals several important chromophore interactions that contribute to the protein's far-red emission and shows dual occupancy of the green and red chromophores.

Characterization of the maduropeptin biosynthetic gene cluster from Actinomadura madurae ATCC 39144 supporting a unifying paradigm for enediyne biosynthesis

The biosynthetic gene cluster for the enediyne antitumor antibiotic maduropeptin (MDP) from Actinomadura madurae ATCC 39144 was cloned and sequenced. Cloning of the mdp gene cluster was confirmed by heterologous complementation of enediyne polyketide synthase (PKS) mutants from the C-1027 producer Streptomyces globisporus and the neocarzinostatin producer Streptomyces carzinostaticus using the MDP enediyne PKS and associated genes. Furthermore, MDP was produced, and its apoprotein was isolated and N-terminal sequenced; the encoding gene, mdpA, was found to reside within the cluster. The biosynthesis of MDP is highlighted by two iterative type I PKSs--the enediyne PKS and a 6-methylsalicylic acid PKS; generation of (S)-3-(2-chloro-3-hydroxy-4-methoxyphenyl)-3-hydroxypropionic acid derived from L-alpha-tyrosine; a unique type of enediyne apoprotein; and a convergent biosynthetic approach to the final MDP chromophore. The results demonstrate a platform for engineering new enediynes by combinatorial biosynthesis and establish a unified paradigm for the biosynthesis of enediyne polyketides.