Identification of mycoplasmal promoters in Escherichia coli using a promoter probe vector with Green Fluorescent Protein as reporter system

In situ real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe Deinococcus radiodurans

A third generation promoter probe shuttle vector pKG was constructed, using the green fluorescent protein as a reporter, for in situ evaluation of Deinococcal promoter activity in Escherichia coli or Deinococcus radiodurans. The construct yielded zero background fluorescence in both the organisms, in the absence of promoter sequences. Fifteen Deinococcal promoters, either harbouring Radiation and Desiccation Response Motif (RDRM) or not, were cloned in vector pKG. Only the RDRM-promoter constructs displayed (i) gamma radiation inducible GFP expression in D. radiodurans, following gamma irradiation, (ii) DdrO-mediated repression of GFP expression in heterologous E. coli, or (iii) abolition in GFP induction following gamma irradiation, in pprI mutant of D. radiodurans. Utility of pKG vector for real-time in situ assessment of Deinococcal promoter function was, thus, successfully demonstrated.

A novel transposon construct expressing PhoA with potential for studying protein expression and translocation in Mycoplasma gallisepticum

BACKGROUND

Mycoplasma gallisepticum is a major poultry pathogen and causes severe economic loss to the poultry industry. In mycoplasmas lipoproteins are abundant on the membrane surface and play a critical role in interactions with the host, but tools for exploring their molecular biology are limited.

RESULTS

In this study we examined whether the alkaline phosphatase gene (phoA ) from Escherichia coli could be used as a reporter in mycoplasmas. The promoter region from the gene for elongation factor Tu (ltuf) and the signal and acylation sequences from the vlhA 1.1 gene, both from Mycoplasma gallisepticum , together with the coding region of phoA , were assembled in the transposon-containing plasmid pISM2062.2 (pTAP) to enable expression of alkaline phosphatase (AP) as a recombinant lipoprotein. The transposon was used to transform M. gallisepticum strain S6. As a control, a plasmid containing a similar construct, but lacking the signal and acylation sequences, was also produced (pTP) and also introduced into M. gallisepticum . Using a colorimetric substrate for detection of alkaline phosphatase activity, it was possible to detect transformed M. gallisepticum . The level of transcription of phoA in organisms transformed with pTP was lower than in those transformed with pTAP, and alkaline phosphatase was not detected by immunoblotting or enzymatic assays in pTP transformants, eventhough alkaline phosphatase expression could be readily detected by both assays in pTAP transformants. Alkaline phosphatase was shown to be located in the hydrophobic fraction of transformed mycoplasmas following Triton X-114 partitioning and in the membrane fraction after differential fractionation. Trypsin proteolysis confirmed its surface exposure. The inclusion of the VlhA lipoprotein signal sequence in pTAP enabled translocation of PhoA and acylation of the amino terminal cysteine moiety, as confirmed by the effect of treatment with globomycin and radiolabelling studies with [14C]palmitate. PhoA could be identified by mass-spectrometry after separation by two-dimensional electrophoresis.

CONCLUSION

This is the first study to express PhoA as a lipoprotein in mycoplasmas. The pTAP plasmid will facilitate investigations of lipoproteins and protein translocation across the cell membrane in mycoplasmas, and the ease of detection of these transformants makes this vector system suitable for the simultaneous screening and detection of cloned genes expressed as membrane proteins in mycoplasmas.

Transcriptional regulation of MG_149, an osmoinducible lipoprotein gene from Mycoplasma genitalium

Transcriptional regulation remains poorly understood in Mycoplasma genitalium, the smallest self-replicating cell and the causative agent of a spectrum of urogenital diseases. Previously, we reported that MG_149, a lipoprotein-encoding gene, was highly induced under physiological hyperosmolarity conditions. In this study we further analysed MG_149 transcription with a focus on the identification of promoter elements and regulatory mechanisms. We established MG_149 as a genuine osmoinducible gene that exhibited the highest transcript abundance compared with other lipoprotein genes. Using genetic approaches, we demonstrated that the -10 region of the MG_149 promoter was essential for osmoinduction. Moreover, we showed that MG_149 osmoinduction was regulated by DNA supercoiling, as the presence of novobiocin decreased MG_149 expression in a dose-dependent manner. Taken together, these results indicate that DNA supercoiling participates in controlling MG_149 expression during in vivo-like conditions.

Selection against spurious promoter motifs correlates with translational efficiency across bacteria

Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the −10 promoter motifs that bind the σ⁷⁰ subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of −10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, −10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers. These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also confirms previous results indicating that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria.

Plasmid Vectors for Testing In Vivo Promoter Activities in Corynebacterium glutamicum and Rhodococcus erythropolis

Novel shuttle promoter-probe vectors replicating in Escherichia coli, Corynebacterium glutamicum, and Rhodococcus erythropolis were constructed on the basis of the C. glutamicum plasmid pCG1. The vectors carry reporter genes coding for fluorescent proteins, which allow the measurement of promoter activities in vivo. The promoter-probe vector pPRE11 contains the rsgfp reporter gene, coding for a variant of green fluorescent protein (GFP) with a red-shifted excitation maximum. To ensure efficient expression of the gfp gene in R. erythropolis from the tested promoters, the promoterless gene gfpuv, with 5' end fusion with the initial six codons of the aph gene and upstream insertion of the aph Shine-Dalgarno sequence, was used as a reporter gene in the promoter-probe vector pEPR1. Insertion of the rfp reference gene, coding for a variant of the red fluorescent protein DsRed.T4 and cloned under the strong constitutive C. glutamicum promoter P-45, into the vector pEPR1 resulted in a new-generation promoter-probe vector (pRAG5). All vectors were tested using a set of mutant P-dapA promoters displaying various transcriptional activities. The vector pRAG5 is suitable for normalized measurements of promoter activities during the growth of bacterial batch cultures because estimation of the GFP-to-red fluorescent protein fluorescence ratio in strains carrying the plasmid pRAG5 with the tested promoters upstream of gfpuv avoids the influence of plasmid copy number variations on the promoter activity assay.

Characterization of the promoter of 1A6/DRIM, a novel cancer-related gene and identification of its transcriptional activator

1A6/DRIM (Down-regulated in Metastasis) has been reported to express at a high level in the gastric cancer tissues and the premalignant lesions implicating the involvement of 1A6/DRIM in cell transformation. Although the information regarding the putative functions and distribution of the 1A6/DRIM in different tissues and cell lines has been increasing recently, its promoter and promoter-regulating factors remain unknown. In this study, the transcription initiation site of 1A6/DRIM was confirmed to be located at 147 bp upstream of the ATG codon using the primer extension analysis. The minimal promoter region of the 1A6/DRIM is located between -47 and +42 of the transcription initiation site measured by luciferase reporter assays using a set of deletion constructs. In addition, an E-box is shown to be an essential element for transcriptional regulation of 1A6/DRIM demonstrated by luciferase assay with different deletion and mutation constructs. Finally, a transcription factor, upstream stimulatory factor 2 (USF2) was found to be an activator of the 1A6/DRIM through binding to the E-box demonstrated by luciferase reporter assay, electrophoretic mobility shift assay, and chromatin immunoprecipitation (ChIP) assay. The structural analysis of the 1A6/DRIM promoter and the identification of its potential regulatory effecter may help us to understand its biological functions in regulating cancer development.

Transcriptional starts for cytadherence-related operons of Mycoplasma genitalium

One mechanism of mycoplasma cytadherence possessed by several mycoplasmas, including Mycoplasma genitalium, necessitates coordination of multiple adhesins and adherence-associated proteins. The genes encoding these adherence-related proteins are located in three different regions of the M. genitalium genome and exhibit an operon-like organization with surrounding genes. To understand whether genes encoding adherence-related proteins in M. genitalium are regulated as operons, we performed transcriptional and reverse transcription-polymerase chain reaction (RT-PCR) analyses on the loci mg191 (encoding major cytadhesin P140 localized at the specialized tip organelle) and mg218 (encoding high molecular mass cytadherence-related protein MG218 required for tip-mediated adherence). Primer extension suggested that transcription of mg191 was under the control of two transcriptional starts, one immediately upstream of mg191 (Prm(MG191)) and the other upstream of mg190 (Prm(MG190)). In contrast, mg218 appeared to be transcribed by a single transcriptional start, located upstream of mg217. RT-PCR indicated that transcription was continuous from mg190 to mg192 and mg217 to mg219, suggesting that these loci constitute true operons. Additional data revealed heretofore undetected similarities between adherence-related operons of M. genitalium and Mycoplasma pneumoniae.

Stability of cytadherence-related proteins P140/P110 in Mycoplasma genitalium requires MG218 and unidentified factors

BACKGROUND

Tip-mediated cytadherence in Mycoplasma genitalium requires the structural and functional stability of the P140 adhesin, its operon-related protein P110, and the high molecular weight protein MG218 (190-kDa). Disruption mutants of mg218 unable to express MG218 exhibit both a non-cytadhering phenotype and P140/P110 instability, while disruption mutants that synthesize a truncated MG218 (160 kDa) retain the stability of P140/P110 and are >95% cytadhering. However, the origin of the MG218 truncated protein in these mutants is unclear. Therefore, we attempted to identify the origin of the truncated MG218 protein and to evaluate whether this truncated protein possessed the C-terminal part of MG218. In addition, we used spontaneous mutants lacking P140 to assess the role of MG218 in the stability of P140/P110.

METHODS

RNA from M. genitalium mutant producing truncated MG218 was subjected to primer extension analysis to identify the origin of expression of truncated MG218. Extracts of this mutant were examined for the presence of the C-terminal region of MG218 by immunoblot. In addition, pulse-chase analysis was performed to assess the role of MG218 in the stability of P140/P110 in spontaneous p140 mutants.

RESULTS

Primer extension analysis identified a transcriptional start point adjacent to the gentamycin-resistance gene in disrupted mg218 mutants. Antibodies directed against the C-terminal region (amino acids 1651-1666) of MG218 bound to truncated MG218 protein from mutants. Spontaneous p140 mutants subjected to pulse chase analysis indicated that solely class I mutants exhibited instability of P140/P110 in the presence of intact MG218.

CONCLUSIONS

Expression of truncated MG218 in M. genitalium mg218 mutants appears to be due to the presence of a putative promoter upstream to the point of mg218 disruption; this truncated protein possesses the C-terminal region of MG218. However, pulse chase results from spontaneously arising, non-cytadhering P140-deficient M. genitalium mutants suggest that the stability of P140 and P110 requires not only MG218 but also additional factors.

Transcription in Mycoplasma pneumoniae

Very little is understood of the structure of mycoplasma promoters, and this limits interpretation of genomic sequence data in these species. In this study the transcriptional start points of 22 genes of Mycoplasma pneumoniae were identified and the regions 5' to the start point compared. Although a strong consensus -10 region could be seen, there was only a weak consensus in the -35 region. A high proportion of transcripts had heterogeneous 5'-ends and characterisation of the sequence of the 5'-ends of two transcripts established that the heterogeneity was derived from initiation of transcription at reduced levels between 1 and 4 bases 5' to the major starting point. In addition to this apparently unique feature, a high proportion of transcripts lacked a 5' untranslated leader region that could contain a ribosomal binding site. Such leaderless transcripts are seen rarely in other bacterial species. Although the promoter regions for a number of members of lipoprotein multigene families were examined, no obvious explanation for regulation of expression was apparent. Using the data from this study an improved matrix for prediction of M.pneumoniae promoters was derived. Application of this matrix to the sequences immediately 3' and 5' to each predicted start codon in the genome suggested that most M. pneumoniae transcriptional start points were likely to occur between 5 and 30 bases 5' to the start codon.

Identification of a small RNA within the pdh gene cluster of Mycoplasma pneumoniae and Mycoplasma genitalium

A highly abundant and heterogeneous small RNA about 205 to 210 bases long named MP200 RNA has been identified in Mycoplasma pneumoniae. It was localized on the genome within a 319-bp-long intergenic space of the pyruvate dehydrogenase (pdh) gene cluster. A database search at the DNA level revealed the highest similarity to a sequence located within the pdh gene cluster of Mycoplasma genitalium that was also shown to be transcribed into two abundant, but smaller RNAs than the ones in Mycoplasma pneumoniae. The RNAs from both M. pneumoniae and M. genitalium have the potential to code for cysteine-rich 29- and 23-amino-acid-long peptides, but so far, these peptides have not been identified experimentally in bacterial protein extracts.

Transcriptional analysis of the hmw gene cluster of Mycoplasma pneumoniae

Mycoplasma pneumoniae adherence to host cells is a multifactorial process that requires the cytadhesin P1 and additional accessory proteins. The hmw gene cluster consists of the genes p30, hmw3, and hmw1, the products of which are known to be essential for cytadherence, the rpsD gene, and six open reading frames of unknown function. Putative transcriptional terminators flank this locus, raising the possibility that these genes are expressed as a single transcriptional unit. However, S1 nuclease protection and primer extension experiments identified probable transcriptional start sites upstream of the p32, p21, p50, and rpsD genes. Each was preceded at the appropriate spacing by the -10-like sequence TTAAAATT, but the -35 regions were not conserved. Analysis of the M. pneumoniae genome sequence indicated that this promoter-like sequence is found upstream of only a limited number of open reading frames, including the genes for P65 and P200, which are structurally related to HMW1 and HMW3. Promoter deletion studies demonstrated that the promoter-like region upstream of p21 was necessary for the expression of p30 and an hmw3-cat fusion in M. pneumoniae, while deletion of the promoter-like region upstream of p32 had no apparent effect. Analysis by reverse transcription-PCR confirmed transcriptional linkage of all the open reading frames in the hmw gene cluster. Taken together, these findings suggest that the genes of this locus constitute an operon expressed from overlapping transcripts.

A plasmid vector for isolation of strong promoters in Escherichia coli

In order to isolate very strong promoters from bacteria and bacteriophage a plasmid named pProm was constructed. It possesses an origin (ORI) for replication in Gram-negative bacteria, an ORI for replication in Gram-positive bacteria, a promoterless ampicillin resistance gene with a multiple cloning site (MCS) in the position formerly occupied by the ampicillin promoter, a tetracycline resistance gene for selection in Gram-negative bacteria and a chloramphenicol resistance gene for selection in Gram-positive bacteria. Insertion in the MCS of DNA fragments of Staphylococcus aureus bacteriophages resulted in isolation of several clones very resistant to ampicillin. The DNA fragments inserted in these recombinant plasmids were sequenced and all of them contained putative promoter motifs. Direct measurement of the penicillinase activity indicated that one of the isolated promoters could be included within a group of the stronger known prokaryotic promoters. According to these results pProm is a powerful tool to perform studies on promoter strength and for industrial applications.

Disruption of gene mg218 of Mycoplasma genitalium through homologous recombination leads to an adherence-deficient phenotype

Although the complete genome of Mycoplasma genitalium has been sequenced, the functional identification of various genes, including those involved in virulence, has not been accomplished. Further compounding these difficulties has been the failure to develop genetic tools in mycoplasmas that permit the assessment of gene and operon function and regulation. To determine whether homologous recombination could be developed as a tool to analyze the function of genes in M. genitalium, a plasmid that replicates in Escherichia coli but not in M. genitalium was constructed to disrupt the cytadherence-related gene mg218 of M. genitalium. The electroporation of this disruption plasmid into wild-type hemadsorption-positive (HA+) M. genitalium cells permitted the isolation of HA- (strain JB1) and partial HA+ (strains JB2 and JB20) transformants. Analysis of the transformants by Southern hybridization indicated that homologous recombination occurred at the mg218 locus by single-crossover events in JB1 and JB2 and by a double-crossover event in JB20. While integration of the disruption construct abolished the expression MG218 in JB1, strains JB2 and JB20 exhibited a truncated MG218 protein (160 kDa), possibly because of in-frame fusion of the disrupted mg218 gene with sequences downstream of the gentamycin-resistance gene present in the disruption construct. Strain JB1, which lacked MG218, displayed a post-translational defect, being unable to maintain the structural integrity of the major adhesin P140 and its operon-related protein P110, in contrast to JB2 and JB20. It appears that MG218 influences the stability of other cytadherence-related proteins in vivo. Thus, targeted gene disruption through homologous recombination will be a powerful and promising tool for investigating the biology and pathogenesis of M. genitalium.