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Background Transgenic technology has become an important technique for crop genetic improvement. The application of well-characterized promoters is essential for developing a vector system for efficient genetic transformation. Therefore, isolation and functional validation of more alternative constitutive promoters to the CaMV35S promoter is highly desirable. Results In this study, a 2093-bp sequence upstream of the translation initiation codon ATG of AtSCPL30 was isolated as the full-length promoter (PD1). To characterize the AtSCPL30 promoter (PD1) and eight 5′ deleted fragments (PD2-PD9) of different lengths were fused with GUS to produce the promoter::GUS plasmids and were translocated into Nicotiana benthamiana. PD1-PD9 could confer strong and constitutive expression of transgenes in almost all tissues and development stages in Nicotiana benthamiana transgenic plants. Additionally, PD2-PD7 drove transgene expression consistently over twofold higher than the well-used CaMV35S promoter under normal and stress conditions. Among them, PD7 was only 456 bp in length, and its transcriptional activity was comparable to that of PD2-PD6. Moreover, GUS transient assay in the leaves of Nicotiana benthamiana revealed that the 162-bp (− 456~ − 295 bp) and 111-bp (− 294~ − 184 bp) fragments from the AtSCPL30 promoter could increase the transcriptional activity of mini35S up to 16- and 18-fold, respectively. Conclusions As a small constitutive strong promoter of plant origin, PD7 has the advantage of biosafety and reduces the probability of transgene silencing compared to the virus-derived CaMV35S promoter. PD7 would also be an alternative constitutive promoter to the CaMV35S promoter when multigene transformation was performed in the same vector, thereby avoiding the overuse of the CaMV35S promoter and allowing for the successful application of transgenic technology. And, the 162- and 111-bp fragments will also be very useful for synthetic promoter design based on their high enhancer activities.

Salvianic acid A (SAA), a valuable natural product from herbal plant Salvia miltiorrhiza, exhibits excellent antioxidant activities on food industries and efficacious therapeutic potential on cardiovascular diseases. Recently, production of SAA in engineered Escherichia coli was established via the artificial biosynthetic pathway of SAA on the multiple plasmids in our previous work. However, the plasmid-mediated system required to supplement expensive inducers and antibiotics during the fermentation process, restricting scale-up production of SAA. Microbial cell factory would be an attractive approach for constitutive production of SAA by chromosome engineering. The limited enzymatic reactions in SAA biosynthetic pathway from glucose were grouped into three modules, which were sequentially integrated into chromosome of engineered E. coli by λ Red homologous recombination method. With starting strain E. coli BAK5, in which the ptsG, pykF, pykA, pheA and tyrR genes were previously deleted, chassis strain BAK11 was constructed for constitutive production of precursor l-tyrosine by replacing the 17.7-kb mao-paa cluster with module 1 (P lacUV5 -aroG fbr -tyrA fbr -aroE) and the lacI gene with module 2 (P trc -glk-tktA-ppsA). The synthetic 5tacs promoter demonstrated the optimal strength to drive the expression of hpaBC-d-ldh Y52A in module 3, which then was inserted at the position between nupG and speC on the chromosome of strain BAK11. The final strain BKD13 produced 5.6 g/L of SAA by fed-batch fermentation in 60 h from glucose without any antibiotics and inducers supplemented. The plasmid-free and inducer-free strain for SAA production was developed by targeted integration of the constitutive expression of SAA biosynthetic genes into E. coli chromosome. Our work provides the industrial potential for constitutive production of SAA by the indel microbial cell factory and also sets an example of further producing other valuable natural and unnatural products.

A novel sequence that functions as a promoter element for moderate constitutive expression of transgenes, designated as the PtMCP promoter, was isolated from the woody perennial Populus tomentosa. The PtMCP promoter was fused to the GUS reporter gene to characterize its expression pattern in different species. In stable Arabidopsis transformants, transcripts of the GUS reporter gene could be detected by RT-PCR in the root, stem, leaf, flower and silique. Further histochemical and fluorometric GUS activity assays demonstrated that the promoter could direct transgene expression in all tissues and organs, including roots, stems, rosette leaves, cauline leaves and flowers of seedlings and maturing plants. Its constitutive expression pattern was similar to that of the CaMV35S promoter, but the level of GUS activity was significantly lower than in CaMV35S promoter::GUS plants. We also characterized the promoter through transient expression in transgenic tobacco and observed similar expression patterns. Histochemical GUS staining and quantitative analysis detected GUS activity in all tissues and organs of tobacco, including roots, stems, leaves, flower buds and flowers, but GUS activity in PtMCP promoter::GUS plants was significantly lower than in CaMV35S promoter::GUS plants. Our results suggested that the PtMCP promoter from poplar is a constitutive promoter with moderate activity and that its function is presumably conserved in different species. Therefore, the PtMCP promoter may provide a practical choice to direct moderate level constitutive expression of transgenes and could be a valuable new tool in plant genetic engineering.

Rice being the staple food of middle and south India, there is an extensive research undertaken in protecting the species and improving the quality and yield. Several recombinations have been made to the rice genome to impart various qualities which lack in the pure breed. Oryza faces various natural stress, like temperature variance, high salinity, etc., drought is one of the major parameters affecting the growth and yield of the plant. Transgenic rice cultivars can be generated for drought tolerance using the Agrobacterium mediated transformations. The current work aims to impart the gene for drought tolerance in Oryza sativa L. using Agrobacterium mediated transformation. The gene targeted in this context is dehydration response element binding factors (DREB). DREB plays a major role in response to drought mediated stress. Sambha mahsuri (Indica type) and Cotton dora sannalu (Indica type) the two local cultivars have been transformed for the gene AtDREB1A under 35s CaMV promoters (pBIH binary vector) for which the vector used was Agrobacterium. The target plant tissue being used was calli. Optimization of the parameters was performed for a lethal dose of hygromycin, cefotaxime level, and acetosyringone level. PCR amplification was used for the confirmation of the transgenic (T0) species in which 23% and 18% for Sambha mahsuri and Cotton dora sannalu, respectively. Southern blotting was performed for the genomic DNA. Normal growth was shown by the T1 transgenic plants whose expression was confirmed by RT-PCR. The T1 transgenic plants showed good tolerance to drought mediated stress for a total period of one and a half week under greenhouse condition. The study can be concluded by producing a potentially successful drought resistance T1 species produced using Agrobacterium mediated transformation. Keywords: Agrobacterium mediated transformation, Constitutive promoter, Dehydration responsive element, Drought tolerance, Hygromycin, Cefotaxime, Acetosyringone, PCR amplification

Background Streptomycetes attract a lot of attention in metabolic engineering and synthetic biology because of their well-known ability to produce secondary metabolites. However, the available constitutive promoters are rather limited in this genus. Results In this work, constitutive promoters were selected from a pool of promoters whose downstream genes maintained constant expression profiles in various conditions. A total of 941 qualified genes were selected based on systematic analysis of five sets of time-series transcriptome microarray data of Streptomyces coelicolor M145 cultivated under different conditions. Then, 166 putative constitutive promoters were selected by following a rational selection workflow containing disturbance analysis, function analysis, genetic loci analysis, and transcript abundance analysis. Further, eight promoters with different strengths were chosen and subjected to experimental validation by green fluorescent protein reporter and real-time reverse-transcription quantitative polymerase chain reaction in S. coelicolor, Streptomyces venezuelae and Streptomyces albus. The eight promoters drove the stable expression of downstream genes in different conditions, implying that the 166 promoters that we identified might be constitutive under the genus Streptomyces. Four promoters were used in a plug-and-play platform to control the expression of the cryptic cluster of jadomycin B in S. venezuelae ISP5230 and resulted in different levels of the production of jadomycin B that corresponded to promoter strength. Conclusions This work identified and evaluated a set of constitutive promoters with different strengths in streptomycetes, and it enriched the presently available promoter toolkit in this genus. These promoters should be valuable in current platforms of metabolic engineering and synthetic biology for the activation of cryptic biosynthetic clusters and the optimization of pathways for the biosynthesis of important natural products in Streptomyces species. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0351-0) contains supplementary material, which is available to authorized users.

Background Lactobacillus plantarum constitutes a well-recognized food-grade system for the expression of recombinant proteins in the field of industrial and medical biotechnology. For applications in vivo or in biotechnological processes, the level of expression of e.g. antigens or enzymes is often critical, as expression levels should be of a certain effectiveness, yet, without putting too much strain to the overall system. The key factors that control gene expression are promoter strength, gene copy number and translation efficiency. In order to estimate the impact of these adjusting screws in L. plantarum CD033, we have tested several constitutive promoters in combination with high and low copy number plasmid backbones and varying space between the Shine-Dalgarno sequence and the start-codon. Results By combining strong promoters, such as transcription elongation factor promoters, isolated from L. plantarum CD033 and L. buchneri CD034, a synthetic promoter, originally derived from L. plantarum WCSF1 and a heterologous promoter derived from L. buchneri CD034 with a high and a low copy number origin of replication we demonstrated various expression levels of the model protein mCherry. All promoters were feasible for protein expression and in all cases, the high copy number origin of replication increased expression twofold. We found that the optimal spacer between the Shine-Dalgarno sequence and the start codon in L. plantarum consists of 8 nucleotides and elongation as well as shortening this sequence gradually down-regulates gene expression. Conclusions We have evaluated the effects of a set of gene regulatory tools to fine tune recombinant gene expression in L. plantarum CD033. We have thus, provided potential expression vectors useful for constitutive protein expression in lactic acid bacteria ranging from moderate to strong production levels.

Synthetic biology approaches for the synthesis of value-based products provide interesting and potentially fruitful possibilities for generating a wide variety of useful compounds and biofuels. However, industrial production is hampered by the costs associated with the need to supplement large microbial cultures with expensive but necessary co-inducer compounds and antibiotics that are required for up-regulating synthetic gene expression and maintaining plasmid-borne synthetic genes, respectively. To address these issues, a metabolism-based plasmid addiction system, which relies on lipopolysaccharide biosynthesis and maintenance of cellular redox balance for 1-butanol production; and utilizes an active constitutive promoter, was developed in Escherichia coli. Expression of the plasmid is absolutely required for cell viability and 1-butanol production. This system abrogates the need for expensive antibiotics and co-inducer molecules so that plasmid-borne synthetic genes may be expressed at high levels in a cost-effective manner. To illustrate these principles, high level and sustained production of 1-butanol by E. coli was demonstrated under different growth conditions and in semi-continuous batch cultures, in the absence of antibiotics and co-inducer molecules., Highlights • Production of 1-butanol without the need for antibiotics and co-inducer molecules. • Product production relies on a stable metabolism-based plasmid addiction system. • Lipid polysaccharide biosynthesis and redox balance were used as driving forces. • Active constitutive promoter drives gene expression. • 4 g/L of 1-butanol was produced over a 200 h semi-continuous growth period.

The preservative challenge test is a regulatory requirement specified in various pharmacopoeias to determine the efficacy of preservatives. However, such testing is a labour-intensive repetitive task and often requires days before results can be generated. Microbial biosensors have the potential to provide a rapid and automated alternative to the traditional viable counting currently in use. However, the selection of appropriate promoters is essential. The bioluminescent reporter strains used in the current study comprise the Photorhabdus luminescence lux CDABE reporter genes under the control of five individual constitutive Escherichia coli promoters: outer lipoprotein (lpp); twin arginine translocase (tatA); lysine decarboxylase (ldc); lysyl t-RNA (lysS); and ribosomal protein (spc). The promoter plus lux CDABE constructs were cloned, ligated into the plasmid vector pBR322 and transformed into E. coli ATCC 8739. The bioluminescence intensity in the decreasing order of constitutive promoter was lpp > spc> tatA> ldc > lysS. The five biosensor strains tested successfully in PET assays and demonstrated accuracy with a minimum detection limit of 103 CFU/ml, a detection range of 6 orders magnitude, and yielded equivalent results to methods currently recommended by the pharmacopoeias. The bioluminescent biosensors were used to monitor the efficacy of preservatives; sorbic acid at concentrations of 0.031% to 0.2% at pH 5.0, and benzalkonium chloride at concentrations of 0.0062% to 0.00039% alone and in combination with 0.03% EDTA. The 99.9% percentage of bioluminescence reduction of tatA-lux, ldc-lux, lysS-lux, and spc-lux was statistically equivalent to the 3 log10 CFU/ml reduction as required by the Pharmacopeias’. Strong significant correlations between bioluminescence and the methods recommended by the pharmacopoeias were obtained when the biosensor strains were challenged with preservatives, for all except lpp-lux E. coli. The bioluminescence expressed by the lpp-lux biosensor was significantly lower during long-term stationary phase than it was for any of the other biosensors and was also significantly lower than for any of the other biosensors in the presence of preservatives. Since the plasmid copy number and viable counts for lpp-lux did not change under these conditions, it suggests that perhaps lpp-lux was down regulated under stress conditions. There were no statistically significant differences between the results of the bioluminescence assays and the results of the viable count and ATP chemiluminescence assay. Virtual foot printing (using Regulon DB database) demonstrated that two crp binding sites overlapping the -10 regions are located on the negative strand of the lysS promoter sequences and that one crp binding site is located in lpp. The biosensor strains ldc-lux exhibited levels of bioluminescence per cell significantly lower than spc in the presence of preservatives whilst there was a significant increase in bioluminescence per cell by tatA-lux under alkaline conditions (pH 8.9) during long-term stationary phase. Amongst the five biosensor strains tested in the current work, it was determined that the spc-lux strain would be the most attractive candidate for further work, since the bioluminescence expressed per cell was significantly greater, by 10-1000 times, than that expressed by the other four promoters when challenged with the preservatives tested with excellent significant correlations between bioluminescence expression and viable counts in the PET assays with the various preservatives in this study (R2: 8.79-1.00). The bioluminescent biosensor strains showed no statistical differences from the control strains (wildtype E.coli ATCC 8739 and E.coli carrying a promoterless [pBR322.lux] for adneylate energy charge (AEC), plasmid copy number (PCN) bioluminescence or viable counts over 28 days. The emission of bioluminescence by the four bioreporter strains across 28 days is reflected by the stability of PCN with correlations of 0.78-0.90, except for lpp-lux with R2: 0.59. The following promoter elements were found likely to assist greater expression of bioluminescence: an A+T level of approximately 50% between the -40 and -60 regions (the UP element); a G+C level of approximately 50% within the -10 and +1 regions; the extended -10 region and -10 region of consensus sequence RpoD (σ70/D).

More than 300 million people are suffering from diabetes worldwide and the numbers of diabetic patients are increasing. Today´s treatments mainly rely on daily insulin injections. This help people to control blood glucose levels but still many patients suffer from the many complications associated with diabetes. Transplantations of islet cells are an alternative treatment that could help patients to become insulin independent and presumably also delay the development of complications. However, the increasing number of diabetic patients would require large amounts of transplantable insulin producing cells. Due to the fact that islet donor material is a limiting factor for transplantations, human embryonic stem cells (hESCs) could be an alternative source of transplantable insulin producing cells. hESCs have the unique potential to self-renew and to differentiate to many cell types, presumably also beta cells. In order to generate therapeutically relevant beta cells, the scientific community focuses on recapitulating the embryonic processes behind beta cell development. In order to develop protocols that direct differentiation of hESCs along the developmental program of pancreas development, cellular markers and methods that allow the identification and isolation of cells that displays a correct phenotype of each developmental stage are fundamental research tools. Identification of definitive endoderm (DE) - from where pancreas originates, requires analysis methods that can detect multiple markers within individual cells, since many markers expressed in DE are also detected in extraembryonic endoderm. In this thesis, we approached single cell gene expression analysis of hESCs differentiated towards DE to provide insight about expression of a panel of DE markers at the cellular level. Some of these markers have conventionally been measured by gene expression analysis at the population level and little information is available about expression at the cellular level in differentiating hESCs. To differentiate hESCs towards DE three different methods of activin A treatment were used. Single-cell gene expression analysis identified distinct gene expression signatures both between the activinA treated populations and within each population. Within the SOX17+ population, the DE markers CER1 and FOXA2 were co-expressed in the majority cells independent of activin A treatment. By contrast, HHEX, CXCR4, FOXA2, MIXL1 and LIM1/LHX1 were expressed to various extents within the SOX17+ populations of each activin A treatment. These data provides novel insight in DE gene expression at the cellular level of vitro differentiated hESCs and illustrates the usefulness of single-cell gene expression analysis in to identify the molecular signature of in vitro differentiated hESCs. Thus, this technique could be of great help to develop protocols that mimics pancreas development in vivo. Furthermore, this thesis includes work that test the ability of RA and FGF4 alone or in combination to direct differentiation of hESCs towards PDX1+ foregut endoderm. The rationale for this was that both RA and FGF signaling exhibit a patterning effect during endoderm patterning and also supports pancreas specification. By optimizing the timing and concentration of RA and FGF4, it was shown that RA is required to convert activin A-induced hESCs into PDX1+ cells and that part of the underlying mechanism involves FGF signaling. Characterization of the PDX1+ cells suggests that they represent posterior foregut endoderm not yet commited to pancreatic, posterior stomach or duodenal endoderm. Directed differentiation of hESCs would greatly benefit from a deeper understanding of the molecular mechanism that regulate growth and differentiation. To approach these questions, efficient genetic engineering techniques are advantageous tools for controlled expression of genes or to introduce fluorescent reporter genes. Constitutive promoters are useful tools due to their high level of expression in most cell types. Different eukaryotic/mammalian and viral constitutive promoters have been reported to ensure high level and sustained activity in hESCs but a comprehensive study was lacking. In this thesis, we performed a comparative study the activity and stability of five commonly used promoters in undifferentiated hESCs and during differentiation. These data suggested ACTB, EF1α and PGK promoters as the most stable promoters during long term culture of undifferentiated hESCs. During EB differentiation, activities of all five promoters were downregulated and EF1α was the most stable promoter although it was downregulated in 50% of the cells. Gene expression analysis of differentiated cells indicated that promoter activities might be restricted to specific cell lineages, indicating the need to carefully select optimal promoters for constitutive gene expression in differentiated hESCs.

Yeast mitochondrial adenylate kinase (high molecular mass form, gene locus: AKY2) is encoded on chromosome IV of the same DNA strand as histone H2A-1. The nontranslated intergenic region spans 560 bp, the nontranscribed spacer can be estimated to comprise at most 300 bp. The TATA-box sequence is contained in a striking environment consisting of 20 alternating pyrimidines and purines. The AKY2 transcript is made constitutively: (i) the cellular mRNA concentration does not vary significantly with either growth conditions or elapse of the cell cycle; (ii) β-galactosidase activity is about constant in yeast cells grown on various carbon sources after transformation with AKY2-promoter/lacZ fusions; (iii) primer elongation analysis shows that utilization of 5 initiation sites is qualitatively and quantitatively independent of the growth conditions and the carbon source used; (iv) Western blot analysis and adenylate kinase activity measurements indicate the absence of post-transciptional controls as well.