Loss of Serine-Type D-Ala-D-Ala Carboxypeptidase DacA Enhances Prodigiosin Production in Serratia marcescens

Transcriptome analysis reveals that yeast extract inhibits synthesis of prodigiosin by Serratia marcescens SDSPY-136

Prodigiosin (2-methyl-3-pentyl-6-methoxyprodiginine) is a valuable medicinal and edible natural pigment derived from Serratia marcescens. How prodigiosin synthesis is suppressed by environmental factors has not been investigated. Previous studies described a low level of prodigiosin production in the presence of yeast extracts. However, we have observed that S. marcescens SDSPY-136 did not synthesize prodigiosin in yeast extract culture. In this study, transcriptome sequencing of yeast extract cultures was used to estimate the metabolic control of the synthetic prodigiosin pathway in S. marcescens. Key phosphorylation enzymes in the glycolysis pathway, 6-phosphofructokinase, and glyceraldehyde 3-phosphate dehydrogenase, were downregulated by yeast extract and other carbon metabolism pathway genes were enhanced. Genes related to ribosomes, amino acid metabolism, and aminoacyl-tRNA biosynthesis were also highly up-regulated. The presence of metal ions in yeast extracts and the accumulation of fermentation metabolites alter the two-component signaling system, which regulated metabolism to various degrees. The results of metal ion testing suggested that prodigiosin inhibition could be caused by metal ions, such as zinc ion. The findings indicate that yeast extract may affect metabolism through multiple pathways in S. marcescens. This research sheds light on the mechanism of prodigiosin regulatory inhibition.

Lactic acid bacteria secreted proteins as potential Listeria monocytogenes quorum sensing inhibitors

Listeria monocytogenes is an important human and animal pathogen able to cause an infection named listeriosis and is mainly transmitted through contaminated food. Among its virulence traits, the ability to form biofilms and to survive in harsh environments stand out and lead to the persistence of L. monocytogenes for long periods in food processing environments. Virulence and biofilm formation are phenotypes regulated by quorum sensing (QS) and, therefore, the control of L. monocytogenes through an anti-QS strategy is promising. This study aimed to identify, by in silico approaches, proteins secreted by lactic acid bacteria (LAB) potentially able to interfere with the agr QS system of L. monocytogenes. The genome mining of Lacticaseibacillus rhamnosus GG and Lactobacillus acidophilus NCFM revealed 151 predicted secreted proteins. Concomitantly, the three-dimensional (3D) structures of AgrB and AgrC proteins of L. monocytogenes were modeled and validated, and their active sites were predicted. Through protein-protein docking and molecular dynamic, Serine-type D-Ala-D-Ala carboxypeptidase and L,D-transpeptidase, potentially secreted by L. rhamnosus GG and L. acidophilus NCFM, respectively, were identified with high affinity to AgrB and AgrC proteins, respectively. By inhibiting the translocation of the cyclic autoinducer peptide (cyclic AIP) via AgrB, and its recognition in the active site of AgrC, these LAB proteins could disrupt L. monocytogenes communication by impairing the agr QS system. The application of the QS inhibitors predicted in this study can emerge as a promising strategy in controlling L. monocytogenes in food processing environment and as an adjunct to antibiotic therapy for the treatment of listeriosis.

Improving prodigiosin production by transcription factor engineering and promoter engineering in Serratia marcescens

Prodigiosin (PG), a red linear tripyrrole pigment produced by Serratia marcescens, has attracted attention due to its immunosuppressive, antimicrobial, and anticancer properties. Although many studies have been used to dissect the biosynthetic pathways and regulatory network of prodigiosin production in S. marcescens, few studies have been focused on improving prodigiosin production through metabolic engineering in this strain. In this study, transcription factor engineering and promoter engineering was used to promote the production of prodigiosin in S. marcescens JNB5-1. Firstly, through construing of a Tn5G transposon insertion library of strain JNB5-1, it was found that the DNA-binding response regulator BVG89_19895 (OmpR) can promote prodigiosin synthesis in this strain. Then, using RNA-Seq analysis, reporter green fluorescent protein analysis and RT-qPCR analysis, the promoter P17 (P_RplJ) was found to be a strong constitutive promoter in strain JNB5-1. Finally, the promoter P17 was used for overexpressing of prodigiosin synthesis activator OmpR and PsrA in strain JNB5-1 and a recombinant strain PG-6 was obtained. Shake flask analysis showed that the prodigiosin titer of this strain was increased to 10.25 g/L, which was 1.62-times that of the original strain JNB5-1 (6.33 g/L). Taken together, this is the first well-characterized constitutive promoter library from S. marcescens, and the transcription factor engineering and promoter engineering can be also useful strategies to improve the production of other high value-added products in S. marcescens.

Prodigiosin: a promising biomolecule with many potential biomedical applications

Pigments are among the most fascinating molecules found in nature and used by human civilizations since the prehistoric ages. Although most of the bio-dyes reported in the literature were discovered around the eighties, the necessity to explore novel compounds for new biological applications has made them resurface as potential alternatives. Prodigiosin (PG) is an alkaloid red bio-dye produced by diverse microorganisms and composed of a linear tripyrrole chemical structure. PG emerges as a really interesting tool since it shows a wide spectrum of biological activities, such as antibacterial, antifungal, algicidal, anti-Chagas, anti-amoebic, antimalarial, anticancer, antiparasitic, antiviral, and/or immunosuppressive. However, PG vehiculation into different delivery systems has been proposed since possesses low bioavailability because of its high hydrophobic character (XLogP3-AA = 4.5). In the present review, the general aspects of the PG correlated with synthesis, production process, and biological activities are reported. Besides, some of the most relevant PG delivery systems described in the literature, as well as novel unexplored applications to potentiate its biological activity in biomedical applications, are proposed.

Efficient extracellular production of recombinant proteins in E. coli via enhancing expression of dacA on the genome

D, D-carboxypeptidase DacA plays an important role in the synthesis and stabilization of Escherichia coli cell wall peptidoglycan. The production level of extracellular recombinant proteins in E. coli can be enhanced by high D, D-carboxypeptidase activity. Construction of expression systems under optimal promoters is one of the main strategies to realize high protein production in E. coli. In this study, the promoter P_dacA-3 from DacA on the genome of E. coli BL21 (DE3) was verified to be efficient for recombinant green fluorescent protein using the plasmid mutant pET28a-P_dacA with P_dacA-3. Meanwhile, the promoter P_dacA-3 was engineered to increase the production level of proteins via inserting one or two Shine–Dalgarno (SD) sequences between the promoter P_dacA-3 and the target genes. The expression level of dacA on the genome was increased by the improved transcription of the engineered promoters (especially after inserting one additional SD sequence). The engineered promoters increased cell membrane permeabilities to significantly enhance the secretion production of extracellular recombinant proteins in E. coli. Among them, the extracellular recombinant amylase activities in E. coli BL21::1SD-pET28a-amyK and E. coli BL21::2SD-pET28a-amyK were increased by 2.0- and 1.6-fold that of the control (E. coli BL21-pET28a-amyK), respectively. Promoter engineering also affected the morphology and growth of the E. coli mutants. It was indicated that the engineered promoters enhanced the expression of dacA on the genome to disturb the synthesis and structural stability of cell wall peptidoglycans.

Gaseous NO2 induces various envelope alterations in Pseudomonas fluorescens MFAF76a

Anthropogenic atmospheric pollution and immune response regularly expose bacteria to toxic nitrogen oxides such as NO^• and NO₂. These reactive molecules can damage a wide variety of biomolecules such as DNA, proteins and lipids. Several components of the bacterial envelope are susceptible to be damaged by reactive nitrogen species. Furthermore, the hydrophobic core of the membranes favors the reactivity of nitrogen oxides with other molecules, making membranes an important factor in the chemistry of nitrosative stress. Since bacteria are often exposed to endogenous or exogenous nitrogen oxides, they have acquired protection mechanisms against the deleterious effects of these molecules. By exposing bacteria to gaseous NO₂, this work aims to analyze the physiological effects of NO₂ on the cell envelope of the airborne bacterium Pseudomonas fluorescens MFAF76a and its potential adaptive responses. Electron microscopy showed that exposure to NO₂ leads to morphological alterations of the cell envelope. Furthermore, the proteomic profiling data revealed that these cell envelope alterations might be partly explained by modifications of the synthesis pathways of multiple cell envelope components, such as peptidoglycan, lipid A, and phospholipids. Together these results provide important insights into the potential adaptive responses to NO₂ exposure in P. fluorescens MFAF76a needing further investigations.

Transcriptomic Analysis Reveals Competitive Growth Advantage of Non-pigmented Serratia marcescens Mutants

Serratia marcescens is a common bacterium well-known for the red secondary metabolite prodigiosin. However, color mutants have long been described. Non-pigmented strains can be found to exist both naturally and under laboratory conditions. It is unclear why S. marcescens loses prodigiosin synthesis capacity in certain conditions. In the present study, we find that the spontaneous color mutants arise within a few generations (about five passages) and rapidly replace the wild-type parent cells (about 24 passages), which indicates a growth advantage of the former. Although, the loss of prodigiosin synthesis genes (pigA-N) is frequently reported as the major reason for pigment deficiency, it was unexpected that the whole gene cluster is completely preserved in the different color morphotypes. Comparative transcriptomic analysis indicates a dramatic variation at the transcriptional level. Most of the pig genes are significantly downregulated in the color morphotypes which directly lead to prodigiosin dyssynthesis. Besides, the transcriptional changes of several other genes have been noticed, of which transcriptional regulators, membrane proteins, and nearly all type VI secretion system (T6SS) components are generally downregulated, while both amino acid metabolite and transport systems are activated. In addition, we delete the transcription regulator slyA to generate a non-pigmented mutant. The ΔslyA strain loses prodigiosin synthesis capacity, but has a higher cell density, and surprisingly enhances the virulence as an entomopathogen. These data indicate that S. marcescens shuts down several high-cost systems and activates the amino acid degradation and transport pathways at the transcriptional level to obtain extra resources, which provides new insights into the competitive growth advantage of bacterial spontaneous color mutants.

Identification of Essential Genes Associated With Prodigiosin Production in Serratia marcescens FZSF02

Prodigiosin is a promising secondary metabolite produced mainly by Serratia strains. To study the global regulatory mechanism of prodigiosin biosynthesis, a mutagenesis library containing 23,000 mutant clones was constructed with the EZ-Tn5 transposon, and 114 clones in the library showed altered prodigiosin production ability. For 37 of the 114 clones, transposon insertion occurred on the prodigiosin biosynthetic cluster genes; transposon inserted genes of the 77 clones belonged to 33 different outside prodigiosin biosynthetic cluster genes. These 33 genes can be divided into transcription-regulating genes, membrane protein-encoding genes, and metabolism enzyme-encoding genes. Most of the genes were newly reported to be involved in prodigiosin production. Transcriptional levels of the pigA gene were significantly downregulated in 22 mutants with different inserted genes, which was in accordance with the phenotype of decreased prodigiosin production. Functional confirmation of the mutant genes involved in the pyrimidine nucleotide biosynthesis pathway was carried out by adding orotate and uridylate (UMP) into the medium. Gene complementation confirmed the regulatory function of the EnvZ/OmpR two-component regulatory system genes envZ and ompR in prodigiosin production.

High-level production of microbial prodigiosin: A review

Prodigiosin is a natural red pigment derived primarily from secondary metabolites of microorganisms, especially Serratia marcescens. It can also be chemically synthesized. Prodigiosin has been proven to have antitumor, antibacterial, antimalaria, anti-insect, antialgae, and immunosuppressive activities, and is gaining increasing important in the global market because of its great potential application value in clinical medicine development, environmental treatment, preparation of food additives, and so on. Due to the low efficiency of prodigiosin chemical synthesis, high-level prodigiosin of production by microorganisms are necessary for prodigiosin applications. In this paper, the production of prodigiosin by microorganism in recent decades is reviewed. The methods and strategies for increasing the yield of prodigiosin are discussed from the aspects of medium composition, additives, factors affecting production conditions, strain modification, and fermentation methods.

Construction and Application of an Escherichia coli Strain Lacking 62 Genes Responsible for the Biosynthesis of Enterobacterial Common Antigen and Flagella

The biosynthesis of the enterobacterial common antigen and flagella in Escherichia coli consumes lots of substrates and energy. In this study, 12 genes responsible for the biosynthesis of the enterobacterial common antigen were deleted in E. coli MG1655, resulting in WQM021. WQM021 grew better than MG1655 in both rich LB medium and minimum M9 medium. Compared with MG1655, WQM021 showed higher membrane permeability and higher production efficiency for recombinant proteins, polyhydroxyalkanoate, and l-threonine. Transcriptome analysis revealed that genes relevant to glucose consumption, glycolysis, and flagellar synthesis were significantly upregulated in WQM021. Therefore, 50 genes responsible for flagellar biosynthesis were further deleted in WQM021, resulting in WQM022. WQM022 grew better and could synthesize more polyhydroxyalkanoate and l-threonine than WQM021. The results demonstrate that the productivity of E. coli can be efficiently improved when the enterobacterial common antigen and flagella are eliminated. This strategy has guiding significance in the optimization of other industrial products and microorganisms.

Improved Prodigiosin Production by Relieving CpxR Temperature-Sensitive Inhibition

Prodigiosin (PG) is a typical secondary metabolite mainly produced by Serratia marcescens. CpxR protein is an OmpR family transcriptional regulator in Gram-negative bacteria. Firstly, it was found that insertion mutation of cpxR in S. marcescens JNB 5-1 by a transposon Tn5G increased the production of PG. Results from the electrophoretic mobility shift assay (EMSA) indicated that CpxR could bind to the promoter of the pig gene cluster and repress the transcription levels of genes involved in PG biosynthesis in S. marcescens JNB 5-1. In the ΔcpxR mutant strain, the transcription levels of the pig gene cluster and the genes involved in the pathways of PG precursors, such as proline, pyruvate, serine, methionine, and S-adenosyl methionine, were significantly increased, hence promoting the production of PG. Subsequently, a fusion segment composed of the genes proC, serC, and metH, responsible for proline, serine, and methionine, was inserted into the cpxR gene in S. marcescens JNB 5-1. On fermentation by the resultant engineered S. marcescens, the highest PG titer reached 5.83 g/L and increased by 41.9%, relative to the parental strain. In this study, we revealed the role of CpxR in PG biosynthesis and provided an alternative strategy for the engineering of S. marcescens to enhance PG production.

The production and bioactivity of prodigiosin: quo vadis?

Prodigiosin (PG), a red tripyrrole pigment, belongs to a member of the prodiginine family and is normally secreted by various sources including Serratia marcescens and other Gram-negative bacteria. The studies of PG have received innovative devotion as a result of reported antimicrobial, larvicidal and anti-nematoid immunomodulation and antitumor properties, owing to its antibiotic and cytotoxic activities. This review provides a comprehensive summary of research undertaken toward the isolation and structural elucidation of the prodiginine family of natural products. Additionally, the current evidence-based understanding of the biological activities and medicinal potential of PG is employed to determine the efficacy, with some reports of information related to pharmacokinetics, pharmacodynamics and toxicology.