Identification of Salmonella Enterica Serovar Typhi Dna Fragments with Transcriptional Activity under Different Growth Conditions

Salmonella enterica serovar Typhi is a human pathogenic microorganism with a very complex infective cycle, involving the transit of bacteria across different microenvironments; to optimize the performance of attenuated Salmonella strains suitable as live carriers of heterologous antigens, fine tuning of wild type bacteria gene expression is essential. Several DNA fragments were obtained from a Salmonella enterica serovar Typhi (vi+, fim+) blood isolate and 18 clones were selected according to the dimension of the insert (range <0.2-1.6 kb). These fragments showed a transcriptional activity in a promoterless vector cloned in Escherichia coli background, according to homogeneous parameters. The results obtained provide an insight about signals mediating gene activation in vivo, particularly in the microenvironments known to exist during the infectious process, even if the fragments are not promoters sequences. Finally, the functional characterization of several fragments showed that they possessed an efficient and homogeneous transcriptional activity, worth to be further investigated.


INTRODUCTION
Salmonella enterica serovar Typhi is the etiological agent of typhoid fever, a human disease.These bacteria infect the human gastrointestinal tract, penetrate the Peyers patches M cells and local lymph nodes and, through the bloodstream and lymph, reach the cells of the reticuloendothelial system.Here the microorganisms multiply within the phagocytes and the persistent bacteremia causes a systemic dissemination.Infected people develop a syndrome characterized by fever, sensorial ailment, splenomegaly, rash and leukopenia [1].Serovar Typhi is a generalized facultative intracellular parasite and is therefore capable of both extra and intracellular life within the host; S. enterica is also able to exist in environmental conditions and this stage allows the completion of the oral-fecal cycle, making infection possible by ingestion of contaminated food products [1].
During the whole infective cycle, inside and outside of the host, enteric pathogens face variations of many parameters, such as pH, osmolarity, temperature and the availability of nutrients and oxygen [2].In the environmental stage bacteria experience a higher O 2 availability and a temperature that can be sub-optimal with respect to that found in the lumen *Address correspondence to this author at the Università Degli Studi di Genova, Dipartimento di Medicina Sperimentale, DiMeS, Sezione di Anatomia Umana, Di.Me.S., Via De Toni, 14, 16132 Genova, Italy; Tel: +390103537875; E-mail: daniele.saverino@unige.it of the distal ileum, where serovar Typhi begins infection finding a higher temperature and osmolarity, and a lower O 2 tension.When entering the epithelial cells and macrophages, microorganisms encounter a restriction of nutrients, and, in the bloodstream, a low availability of O 2 , as most of it is bound by hemoglobin.The bacterial versatility reflects reversible metabolic changes and can only be achieved by a complex regulatory network which warrants not only a tight transcriptional control in spite of a great diversity of conditions [3,4], but also allows the expression of bacterial virulence (e.g.adherence and invasiveness) [5][6][7][8][9].Due to its ability to colonize and stimulate important immunological niches, Salmonella enterica serovar Typhi has been widely considered as an attractive live vector [10][11][12][13][14][15].However, its use is limited by the instability of multiple-copy plasmid systems encoding the heterologous gene, whose expression can place a metabolic burden and favour a negative selection of the vector; furthermore, maintenance of plasmid expression system requests the problematic use of antibiotic selection markers [16].Moreover, chromosomal integration of the heterologous gene drives an antigen expression that is too low with respect to the ability of generating an effective immune response [17][18][19][20][21].In previous works, in vivo-inducible promoters have been utilized in plasmid vectors to modulate heterologous genes expression in salmonella strains in a manner ideal for bacterial survival and immunological response [22].More recently, it was demonstrated that, by integrating a single copy of a heterologous gene associated with nirB promoter into attenuated Salmonella chromosome, an inducible expression of foreign antigen was achieved [23].A similar approach relies on chromosomal insertion of heterologous genes under the control of in vivo-inducible promoters that allow a selective expression within human macrophages by bacterial carriers Salmonella enterica serovar Typhi [24,25].
A further understanding of genetic mechanisms involved in the regulation of serovar Typhi metabolism and virulence could improve development and immunological efficacy of attenuated live Salmonella employed as carriers of foreign antigens.This work describes the isolation and functional characterization of DNA fragments of a blood culture Salmonella enterica serovar Typhi as putative promoters, activated under different in vivo-mimicking conditions, using Escherichia coli, genera related to Salmonella, as the bacterial recipient, which allowed a solution to be found for the instability of constructs in wild type serovar Typhi and preliminary data to be obtained.

Bacterial Strains and Plasmids
The wild type Salmonella enterica serovar Typhi strain 30 Ty5 (vi +, fim +), isolated from a blood culture, was used for the extraction of total DNA.The Escherichia coli Sure (Stratagene) was used as a recipient for the cloning experiments; this strain was used because most of the constructs were highly unstable in wild type Salmonella, even when passed through an intermediate rec-mod+ Salmonella strain.The plasmid used in this work was pUJ10 [26], a pCB267 derivative.
All the cultures were grown overnight in 250 mL of medium.In order to value the response to different oxygen availability, bacteria were grown at 37 °C in LB broth; the aerobic cultures were achieved in shaking flasks, the microaerophilic cultures were grown with shaking in a 10% CO 2 thermostat and the anaerobic ones were achieved by using a GasPak system (BBL Microbiology Laboratories).To determine the influence of temperature, bacteria were grown under atmospheric O 2 tension in LB broth, at 25°C and 37°C.For the assays under different osmolarities, a low osmolarity medium (73 mmol/l NaCl) [30] was used, the osmolarity was increased, when appropriate, to 0.3 mol/l [30] and the strains were grown at 37°C in presence of atmospheric O 2 tension.Media were supplemented, when indicated, with ampicillin (100 g/ml).

DNA Manipulations
Total DNA and plasmid isolation, restriction endonuclease digestion, dephosphorylation with fetal calf intestinal phosphatase, ligation with T4 DNA ligase, transformation and DNA analysis by agarose gel electrophoresis were performed following standard protocols [17] or as indicated by the manufacturer.Restriction and modification enzymes were purchased from New England Biolabs and Boehringer Mannheim.30 specimens of total DNA of the Salmonella strain 30 Ty5 (vi+, fim+) were partially digested with serial dilutions of Sau3A1 [27], to create small sized fragments.After dephosphorilation with alkaline phosphatase, the DNA fragments were ligated with BamHI-digested pUJ10.The ligation mixture was transformed into the E. coli Sure strain.The size of the positive clones inserts were measured by restriction analysis using Bgl II and Sma I. Primers for sequencing were selected on the two reporter genes and DNA sequencing was performed by the method of Sanger [31] with a Taq Dyedeoxy Terminator Cycle Sequencing Kit (Applied Biosystems) and an automated sequencer (model 310; Applied Biosystems).Three of the putative promoters were sequenced (pCG61, pCG88, pCG93) and homologies with known sequences were searched with BLAST 2.2.12 [32].

Enzymatic Assays
To determine alkaline phosphatase and -galactosidase activity, 1 ml of bacterial culture grown under appropriate conditions were spun down and resuspended in 1 ml of 1 mol/l Tris, pH 8.0 and in 1 mL of Z buffer respectively, to read the optical density at 600 nm (OD 600 ), as described previously [27,28]; 100 μl of the diluited bacterial suspensions were permeabilized with 50 μl of chloroform and 50 μl of sodium dodecyl sulfate (SDS) 0.1%, and 900 μl of 1 mol/l Tris, pH 8.0 for the alkaline phosphatase and with 900 μl of Z-buffer for the -galactosidase determination.After equilibrating for 10 min at room temperature, 100 μl of pnitrophenyl phosphate (PNPP) 0.4% and 200 μl of onitrophenyl -D-galactopiranoside (ONPG) 0.4% were added, and the respective stop solutions were added when a significant yellow colour was observed [27,28].
Alkaline phosphatase and -galactosidase activities of individual clones was measured spectrophotometrically as previously described and compared with the activity of the control, the parental strain containing the promoterless vector.The enzymatic activities were measured in enzyme units (E.U.) that represent the slightest quantity of enzyme capable of releasing 1 mol of p-nitrophenyl phosphate or onitrophenyl -D-galactopyranoside per minute [27,28].
The induction of enzymatic activity in recombinants was considered to have taken place when the OD value doubled following a change in the experimental condition relating to a single parameter (i.e. temperature, medium osmolarity, O 2 tension) and also when a two-fold increase was observed in the recombinant OD value in respect to the value obtained with the control, the promotorless pUJ10.

Cloning of DNA Fragments with Transcriptional Activity
Following partial digestion of Salmonella DNA with Sau3A1, 25 samples with a prevalent fragment size range from 0.1 kb to 2.8 kb were obtained.After ligation of the inserts with a BamHI-digested pUJ10 vector, harboring the promoterless lacZ and phoA reporter genes, and transformation of E. coli Sure bacteria, the analysis of divergent promoters was made by the screening on substrate agar, and 18 positive recombinant clones were obtained (data not shown).The size of inserts, measured by restriction analysis, ranged from <0.2 to 1.6 kb (Table 1).Most of the constructs were highly unstable in wild type Salmonella strains, even when passed through an intermediate rec-mod+ Salmonella strain, suggesting that this instability may be in part due to recombination events.Therefore, transcriptional activation studies were performed using an Escherichia coli strain as recipient, which permitted preliminary results to be extrapolated.

Functional Characterization of DNA Fragments
The effects of incubation temperature on enzymatic activity of the clones were first analyzed: most clones showed a greater alkaline phosphatase activity at 37°C than at 25°C, particularly those harboring plasmids pCG61, pCG78, pCG79 and pCG93; the values of clones harbouring plasmid pCG78 were 3160 and 960 E.U. at 37°C and 25°C, respectively.With regard to -galactosidase activity, only clones harboring plasmids pCG88 and pCG92 showed a significant increment in the enzymatic activity, more than 100% and 30% respectively, when the temperature was raised from 25°C to 37°C.In contrast, clones containing plasmids pCG81 and pCG91 showed higher enzymatic values at 25°C than at 37°C, with regard to the activity of both enzymes (Table 2).Ctr.: control.
The effects of variations in osmolarity and O 2 availability on enzymatic activation were also monitored.Under conditions of hyperosmolarity greater phoA expression was observed for clones harbouring pCG61, pCG72, pCG76 and pCG93, and greater lacZ expression was observed for clones harboring pCG84, pCG88, pCG91 and pCG92 (the alkaline phosphatase values of pCG93 were 620 and 2209 U.E., and the -galactosidase values of pCG88 were 792 and 4766, in low and high osmolarity medium, respectively).The alkaline phosphatase values increased when measured in low osmolarity in clones harboring plasmids pCG77, PCG88 and pCG91 (Table 3).
When clones containing pCG61, pCG78, pCG79 and pCG93 were tested in anaerobiosis the alkaline phosphatase activity increased (the values expressed by clone pCG61 were 1220, 5333 and 3184 U.E. in atmospheric O 2 , anaerobiosis and microaerophilia conditions respectively), and clones containing pCG71, pCG79 and pCG91 showed minimal -galactosidase activity which was otherwise undetectable in aerobic conditions.In contrast, clones harbouring pCG81 and pCG88 showed a minor increase ingalactosidase expression in the presence of atmospheric O 2 and a disappearance in anaerobiosis; a reduction in microaerophilia was only observed in the clone harbouring pCG88 (Table 4).
The 258-bp fragment isolated from clone pCG88 shared a close homology with known Salmonella enterica serovar Typhi Ty2 and CT18 (100%) and Salmonella enterica serovar Paratyphi A (98%) sequences, both coding for a penicillin-binding protein and a rRNA guanine-N1-methyltransferase.The 285 nucleotide from clone pCG93 also showed close identity to known Salmonella enterica serovar Typhi Ty2 and CT18 (99%) and Salmonella enterica serovar Typhimurium LT2 (98%) sequences, both coding for a conserved hypothetical protein.

DISCUSSION
Salmonella enterica serovar Typhi, like other facultative intracellular parasites (e.g.Yersinia, Brucella, Legionella, Listeria monocytogenes and Mycobacterium), encounters multiple microenvironments in vivo, growing and replicating extracellularly or within leukocytes and macrophages.During parasitic life serovar Typhi not only adapts itself to different environments, but is also able to escape from nonspecific host clearance mechanisms, such as complement and phagocytic lysis, through virulence factors.Salmonella has not lost the capacity for a saprophytic life (e.g. in a milk, freshwater or saltwater environment) where habitats are not hostile but nutritional limitations, as well as sub-optimal temperatures, may represent stringent challenges for the survival [1].In a microorganism as versatile as Salmonella enterica serovar Typhi some functions, which are essential (e.g.metabolic), although modulated under different conditions, must be always present; in contrast, other functions are activated only when it is possible and/or necessary, in response to specific signals [2].A coordinate regulation of gene expression allows bacteria to survive and replicate both inside the host and in the environment through sequential signals that, affecting RNA polymerase sigma factors [33][34][35][36] and/or the efficiency of different promoters that regulate a single operon [3,4], permit changes in transcription.It is therefore important to understand and to imitate the natural bacterial versatility to avoid compromising the competitiveness and efficacy of Salmonella when used as vaccine delivery system; this could be developed by selecting wild type promoters up-regulated at different time points or niches during infection, choosing the promoters whose transcriptional activity is the greatest in conditions similar to that which bacteria find in the organism and, particularly, in the antigen presenting cells, and the lowest in the environmental ones, such as during fermentation of vaccine manufacture [37,38].
In this work, we have isolated 18 DNA fragments from Salmonella enterica serovar Typhi whose transcriptional efficacy was valued by inserting them into a promoterless plasmide, encoding lacZ and phoA as reporter genes, and cloning into Escherichia coli background.After growing all the recombinants in seven different conditions, we obtained 23 activations (four low activation, with E. U. value under 100) and six significant increases, relating to 12 clones (Tables 5 and 6).Only four enzymatic activations (related to recombinants pCG72, pCG76, pCG77 and pCG84) were obtained following a single change in the growth parameters, while other activations or increases were obtained for at least two homogeneous conditions, i.e. 37°C, high osmolarity medium and anaerobiosis or 25°C, low osmolarity medium and atmospheric O 2 tension.Four recombinants exhibited increase, relating to the same enzyme, in two experimental conditions similar to that of ileum mucosa and, in particular, two recombinants (pCG78 and pCG79) showed the greatest alkaline phosphatase value at 37°C and in anaerobiosis while two recombinants (pCG88 and pCG92) attained majorgalactosidase activity at 37°C and in high osmolarity medium; finally, it is also interesting to note that clones containing pCG61 and pCG93 showed enzymatic activation or a significant increase at 37°C, in hyperosmolarity and in anaerobiosis (Table 5).Recombinants pCG61, pCG78, pCG79 and pCG93 showed a high baseline activation for a reporter gene, phoA, that has been probably enhanced by a culture condition change.
Different clones showed the opposite behaviour, having the greatest transcriptional activity in the environmental conditions.Growing at 25°C clone pCG81 reached a double value for alkaline phosphatase and a minor increase ingalactosidase, in respect to 37°C, and, in the presence of atmospheric O 2 tension, showed a low activation ofgalactosidase in respect to the anaerobiosis condition.Recombinant pCG91 attained major alkaline phosphatase at 25°C and in low osmolarity medium, whereas it attained major -galactosidase activity at 25°C but also in two conditions similar to that of ileum mucosa, i.e. high osmolarity medium and anaerobiosis.Recombinant pCG88 also showed un-homogeneous behaviour, as -galactosidase was activated by growth at 37°C and in high osmolarity medium as well as in aerobiosis, while alkaline phosphatase was only activated in low osmolarity medium (Table 6).x : activation (enzymatic value higher than 100 E. U. and double in respect to the relating parameter and to the control value).
x-: low activation (enzymatic value under 100 E. U. but double in respect to the relating parameter and to the control value).(x): increase of activity (increasing in enzymatic value but not double in respect to the relating parameter and to the control value).x: activation (enzymatic value higher than 100 E. U. and double in respect to the relating parameter and to the control value).
x-: low activation (enzymatic value under 100 E. U. but double in respect to the relating parameter and to the control value).(x): increase of activity (increasing in enzymatic value but not double in respect to the relating parameter and to the control value).
Although functional characterization of several fragments showed that they possessed an efficient transcriptional activity, and some of these demonstrated homogeneous behaviour in respect to growth parameters, when further investigated by sequence analysis, it emerges that three clones contained sequences which did not correspond to known serovar Typhi promoter sequences; yet, it is clear that they were bacterial DNA fragments, encoding for the beta'-subunit of DNA-directed RNA polymerase and other proteins, which are highly conserved in the genus salmonella.Although they are not promoters, the expression took place as if a suitable promoter was located upstream of the corresponding reporter gene.We intend to perform additional studies in order to fully understand the significance of our findings.
The versatility of Salmonella enterica serovar Typhi and moreover its ability to live in host cells are factors which are difficult to maintain in the genetically-engineered strains.It is necessary to understand and exploit these characteristics, so that the attenuated microorganism does loose its capacity to penetrate the enteric cells and macrophage, in order to obtaine an important advantage for the oral administration of live attenuated bacterial vaccines.

Table 3 . Alcaline Phosphatase and -Galactosidase Activities of Clones Harboring Salmonella enterica Serovar Typhi DNA Fragments with Reference to Different Medium Osmolarities, Measured in Enzymatic
Ctr.: control; H.o.m.: high osmolarity medium; L.o.m.: low osmolarity medium.

Table 5 . Alcaline Phosphatase and -Galactosidase Activities of Clones Harboring Salmonella enterica Serovar Typhi DNA Fragments which Exhibited Preferential Activation in Experimental Conditions Alike to that of Ileum Mucosa
H.o.m.: high osmolarity medium; Anaer.: anaerobiosis.