Direct and negative regulation of the sycO-ypkA-ypoJ operon by cyclic AMP receptor protein (CRP) in Yersinia pestis
BMC Microbiology volume 9, Article number: 178 (2009)
Pathogenic yersiniae, including Y. pestis, share a type III secretion system (T3SS) that is composed of a secretion machinery, a set of translocation proteins, a control system, and six Yop effector proteins including YpkA and YopJ. The cyclic AMP receptor protein (CRP), a global regulator, was recently found to regulate the laterally acquired genes (pla and pst) in Y. pestis. The regulation of T3SS components by CRP is unknown.
The sycO, ypkA and yopJ genes constitute a single operon in Y. pestis. CRP specifically binds to the promoter-proximate region of sycO, and represses the expression of the sycO-ypkA-yopJ operon. A single CRP-dependent promoter is employed for the sycO-ypkA-yopJ operon, but two CRP binding sites (site 1 and site 2) are detected within the promoter region. A CRP box homologue is found in site 1 other than site 2. The determination of CRP-binding sites, transcription start site and core promoter element (-10 and -35 regions) promotes us to depict the structural organization of CRP-dependent promoter, giving a map of CRP-promoter DNA interaction for sycO-ypkA-yopJ.
The sycO-ypkA-yopJ operon is under the direct and negative regulation of CRP in Y. pestis. The sycO-ypkA-yopJ promoter-proximate regions are extremely conserved in Y. pestis, Y. pseudotuberculosis and Y. enterocolitica. Therefore, data presented here can be generally applied to the above three pathogenic yersiniae.
Plague, caused by Yesinia pestis, is a zoonotic disease that threatened public health seriously. The three pathogenic Yersinia species, Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica, share a type III secretion system (T3SS) that is composed of a secretion machinery, a set of translocation proteins, a control system, and six Yop effector proteins [1, 2]. Through the T3SS, pathogenic yersiniae inject effectors into the cytosol of eukaryotic cells when docking at the surface of host cell. The injected Yops perturb the signaling cascades that activate the processes of phagocytosis, cytokine release and respiratory burst. As a result, phagocytosis is inhibited, recruitment of PMNs and monocyte-derived macrophages is reduced, and lymphocyte proliferation is prevented.
The cyclic AMP receptor protein (CRP) is a global regulator that controls the transcription initiation for more than 100 bacterial genes/operons . CRP is activated by cyclic AMP (cAMP), forming the cAMP-CRP complex. This complex binds a symmetrical consensus DNA sequence TGTGA-N6-TCACA (known as the CRP box sequence) located within the upstream promoter regions. The CRP-promoter DNA interaction is crucial for the regulation of target genes.
CRP and its homologues are required for virulence and/or expression of virulence genes in several pathogens, including Y. pestis , Y. enterocolitica , Vibrio vulnificus , Vibrio cholerae  and Mycobacterium tuberculosis . The crp disruption in Y. pestis attenuates both in vitro and in vivo growth of the mutant, and leads to a >15,000-fold loss of virulence after subcutaneous infection, but a less than 40-fold increase in LD50 by intravenous inoculation . CRP plays a role in the globally transcriptional regulation of genes including a wide set of virulence genes in Y. pestis . Especially, it directly stimulates the expression of plasminogen activator (Pla) [4, 9], a virulence factor essential for bubonic and primary pneumonic plague [10, 11].
Yersinia protein kinase A (YpkA) and Yersinia outer protein J (YopJ) are encoded by plasmid pCD1-borne ypkA and yopJ genes in Y. pestis, respectively. YpkA/YopO is a serine/threonine protein kinase involved in host actin cytoskeletal rearrangements and in inhibition of phagocytosis , while YopJ/YopP acts as an acetyltransferase inhibiting mitogen-activated protein kinase (MAPK) and the nuclear factor kappaB (NFκB) signaling pathways used in innate immune response . Both of them are the effector proteins of T3SS and essentially contribute to the virulence of Y. pestis [2, 14]. SycO is a T3SS chaperone that increases solubility and secretion efficiency of the effector YpkA/YopO .
In the present work, we disclosed that CRP directly and negatively regulated the sycO-ypkA-yopJ operon in Y. pestis under the calcium-rich condition, by using real-time RT-PCR, LacZ reporter fusion, electrophoretic mobility shift assay (EMSA), and DNase I footprinting assay. Data presented here further validated the important role of CRP in virulence of Y. pestis.
The wild-type (WT) Y. pestis strain 201 belongs to a newly established Y. pestis biovar, Microtus , which was thought to be avirulent to humans, but highly virulent to mice. An in-frame deletion of the crp gene was constructed by using one step inactivation method , generating a mutant strain referred to as Δcrp . Bacteria were grown in Luria-Bertani (LB) broth or chemically defined TMH medium  at 26 or 37°C. E. coli was grown in LB broth at 37°C. When needed, antibiotics were added at the following concentrations: 100 μg/ml for ampicillin, 50 μg/ml for kanamycin, and 34 μg/ml chloramphenicol.
Bacterial growth and RNA isolation
The WT and Δcrp were grown at 26°C in the TMH medium with the addition of 1 mM cAMP (referred to as 'TMH-1mM cAMP') to an OD620 of about 1.0, and then diluted by 20-fold into the fresh 'TMH-1mM cAMP' medium for cultivating at 26°C until an OD620 of about 1.0, and finally transferred to 37°C for 3 h. Bacterial cells were harvested for the isolation of total RNA. Immediately before harvesting, bacterial cultures were mixed with RNAprotect Bacteria Reagent (Qiagen) to minimize RNA degradation. Total RNA was isolated using the MasterPure™ RNA Purification kit (Epicenter). Contaminated DNA in RNA samples was removed by using the Amibion's DNA-free™ Kit. RNA quality was monitored by agarose gel electrophoresis and RNA quantity was measured by spectrophotometer.
Gene-specific primers (Table 1) were designed to produce a 150 to 200 bp amplicon for each gene. cDNAs were generated by using 5 μg of RNA and 3 μg of random hexamer primers. Using three independent cultures and RNA preparations, real-time PCR was performed in triplicate as described previously , through the LightCycler system (Roche) together with the SYBR Green master mix. Based on the standard curve of 16S rRNA expression for each RNA preparation, the relative mRNA level was determined by the classic ΔCt method. 16S rRNA gene was used to normalize that of all the other genes. The transcriptional variation between the WT and Δcrp strains was then calculated for each gene. A mean ratio of two was taken as the cutoff of statistical significance.
LacZ reporter fusion and β-Galactosidase assay
A 408 bp promoter-proximate of cycO (Table 1) was cloned directionally into the Eco RI and Bam HI sites of plasmid pRS551 expressing LacZ, which was verified by DNA sequencing. The recombinant plasmids were introduced into the WT and Δcrp, respectively. The plasmid pRS551 was also transformed as negative control. The resulting strains were grown as described in RNA isolation. β-Galactosidase activity was determined for each strain by using the Promega β-Galactosidase Enzyme Assay System . Assays were performed in triplicate.
Preparation of purified recombinant His-CRP protein, electrophoretic mobility shift assay (EMSA) and DNase I footprinting assay were conducted as described previously . For EMSA, a 468 bp promoter-proximate region of cycO (containing a predicted CRP binding site) or the corresponding cold probe (i.e. unlabeled target DNA) (Table 1) was radioactively labeled, incubated with increasing amounts of purified His-CRP protein, and then subjected to 4% (w/v) polyacrylamide gel electrophoresis. In the DNase I footprinting experiments, coding or noncoding strand (261 bp in length) containing the predicted CRP binding site was labeled with [γ-32P] at the 5' end, then, incubated with increasing amounts of His-CRP; after partial digestion with DNase I, the resulting fragments were analyzed by denaturing gel electrophoresis. Radioactive species were detected by autoradiography.
Primer extension analysis
For the primer extension assay , an oligonucleotide primer (Table 1) complementary to a portion of the RNA transcript of each gene was employed to synthesize cDNAs from the RNA templates. Electrophoresis of primer extension products was performed with a 6% polyacrylamide/8M urea gel. The yield of each primer extension product would indicate the mRNA expression level of the corresponding gene in each strain, and further could be employed to map the 5' terminus of RNA transcript for each gene.
The sycO, ypkA and yopJ genes constitute a single operon
The RT-PCR assay indicated that the sycO, ypkA and yopJ genes (designated as pCD12, pCD13 and pCD14 in Y. pestis 91001 , respectively) were transcribed as a single primary RNA (Fig. 1), and thereby these three genes constituted a single operon in Y. pestis Microtus strain 201.
CRP greatly represses transcription of the sycO-ypkA-yopJ operon
Our previous cDNA microarray analysis showed that the transcription of sycO, ypkA and yopJ was repressed by CRP . Herein, the real-time RT-PCR assays confirmed that these three genes were up-regulated by more than 50 folds in the Δcrp mutant in relative to the WT strain (Fig. 2). Taken together, transcription of the sycO-ypkA-yopJ operon was under the negative control of CRP.
CRP greatly represses promoter activity of sycO-ypkA-yopJ
To test the action of CRP on the sycO-ypkA-yopJ promoter activity, we constructed the sycO::lacZ fusion promoter consisting of a 690 bp promoter-proximate region of sycO and promoterless lacZ, and then transformed into the WT and Δcrp, respectively. Empty vector pRS551 was also introduced into them, respectively, as controls. β-galactosidase activity was measured for evaluating the sycO-ypkA-yopJ promoter activity in each strain. Since the crp mutation had an effect on the copy number of recombinant or empty pRS551 plasmid , a normalized fold change in the activity of each fusion promoter in WT in relative to Δcrp was calculated to avoid the influence of copy number of pRS551 (Table 2).
Accordingly, the β-galactosidase activity in the Δcrp increased compared to the WT when they grew in the 'TMH-1mM cAMP' medium, indicating that CRP greatly repressed the promoter activity of sycO-ypkA-yopJ (Table 2).
CRP binds to promoter-proximate region of sycO-ypkA-yopJ
A CRP box-like sequence was found in the promoter-proximate region of sycO-ypkA-yopJ , indicating the direct association of CRP with the sycO-ypkA-yopJ promoter region. Further EMSA experiments showed that the cAMP-CRP complex bound to the sycO-ypkA-yopJ promoter region in a CRP dose-dependent manner (Fig. 3a). CRP could not bind to the target DNA in the absence of cAMP.
To validate the specificity of CRP-DNA interaction, YPO0180 and YPO1099 [gene IDs in CO92 ] were used as negative controls (Fig. 3b). The PCR-generated upstream DNA of YPO0180 did not harbor the predicted CRP binding site, while the YPO1099 upstream region gave an extremely low score value of 0.96 during the pattern matching analysis using the CRP consensus (sycO gave a score value of 8.57) . Both of them gave negative EMSA result, even the CRP protein was increased to 4 μg in a single reaction mixture (Fig. 3b).
Therefore, CRP specifically bound to the sycO-ypkA-yopJ promoter region and directly repressed the transcription of sycO-ypkA-yopJ.
Structural organization of CRP-dependent sycO-ypkA-yopJ promoter
In order to locate the precise CRP binding site within the sycO-ypkA-yopJ promoter region, DNase I footprinting assay was performed with both coding and non-coding strands. As shown in Fig. 4, CRP protected two distinct DNA regions (sites 1 and 2) against DNase I digestion in a dose-dependent pattern. Only site 1 contained the CRP box-like sequence.
The transcription start site of sycO was determined by primer extension assay. A single primer extension product was detected and thus a single CRP-dependent promoter was transcribed for sycO-ypkA-yopJ (Fig. 5). Compared to the WT, a much stronger primer extension product was detected in the Δcrp. Since the yield of primer extension product would indicate the mRNA expression level of sycO in each strain, data presented here confirmed the repression of sycO-ypkA-yopJ by CRP.
The primer extension results could be also employed to map the 5' terminus of RNA transcript for sycO (i.e. the transcription start site of sycO-ypkA-yopJ) (Fig. 6). The -10 and -35 core promoter elements were predicted accordingly.
The determination of CRP-binding sites, transcription start site, and core promoter element (-10 and -35 regions) promoted us to depict the structural organization of CRP-dependent promoter, giving a map of CRP-promoter DNA interaction for sycO-ypkA-yopJ (Fig. 6).
CRP and the sycO-ypkA-yopJ operon
CRP specifically bound to the sycO promoter-proximate region and directly repressed the expression of sycO-ypkA-yopJ in Y. pestis biovar Microtus strain 201. The sycO-ypkA-yopJ promoter-proximate regions were extremely conserved in Y. pestis (including all the four biovars Antiqua , Mediaevalis , Orientalis  and Microtus ), Y. pseudotuberculosis  and Y. enterocolitica . Therefore, data presented in Y. pestis biovar Microtus can be generally applied to the above three pathogenic yersiniae.
A single CRP-dependent promoter transcribed for the sycO-ypkA-yopJ operon, but two CRP-binding sites (site 1 and site 2) were detected within its promoter region. A CRP box-like sequence (TAGATATCACC) was found in site 1 rather than in site 2. It was speculated that site 2 was a non-specific or non-functional CRP-binding site. Further reporter fusion experiments and/or in vitr o transcription assays, using the sycO promoter-proximate regions with different mutations/deletions within sites 1 and 2, should be done to elucidate the roles of site 1 and site 2 in CRP-mediated regulation of sycO-ypkA-yopJ.
CRP and T3SS
The crp mutation caused a reduced secretion of YOP proteins in both Y. enterocolitica  and Y. pestis  grown under calcium-depleted conditions. This indicated that CRP is a positive regulator for the YOP secretion by Y. pestis. It is well known that the YOP secretion phenotype is only observable under calcium depleted conditions. Herein, the direct and negative regulation of sycO-ypkA-yopJ by CRP was observed at transcriptional level under calcium-rich conditions. How CRP controls T3SS is essentially unclear yet. It needs to investigate the mRNA/protein pools of T3SS that are regulated by CRP under calcium depleted or rich conditions and upon cell contact, and to answer whether CRP has a regulatory action on T3SS in general or on SycO, YpkA and YopJ specifically.
CRP and virulence
The crp deletion attenuated Y. pestis much more greatly by subcutaneous route of infection in relative to an intravenous inoculation, and a reduced in vivo growth phenotype of the crp mutant was observed . CRP seemed more important for the infection at the subcutaneous site and in the lymph other than the later systemic infection, while the reduced in vivo growth of the crp mutant should contribute to its attenuation by intravenous infection. The crp disruption led to a great defect of pla expression . Since Pla specifically promoted Y. pestis dissemination from peripheral infection routes, the defect of pla expression in the crp mutant will contribute to the huge loss of virulence of this mutant strain after subcutaneous infection.
Expression of Pla, Pst, F1 antigen and T3SS are dependent on CRP, and this regulator appears to control a wide set of virulence-related factors in Y. pestis . All the above CRP-regulated genes are harbored in plasmids that are required through horizontal gene transfer. Either the CRP protein itself or the mechanism of CRP-promoter DNA association is extremely conserved between E. coli and Y. pestis. Therefore, the above laterally acquired genes have evolved to integrate themselves into the 'ancestral' CRP regulatory cascade. It has been shown recently that the histone-like protein H-NS mediates the silencing of laterally acquired genes with low G+C contents scattered on the bacterial genome (these H-NS-dependent genes often contribute to virulence or host adaptation in corresponding pathogens) [25, 26]. Herein, regulation (either activation or repression) of foreign genes in plasmids was mediated by the ancient regulator CRP in the host, Y. pestis.
Three T3SS genes, sycO, ypkA and yopJ, constitute a single operon in Y. pestis. The CRP regulator binds to the upstream DNA region of sycO, and represses the expression of the sycO-ypkA-yopJ operon. The sycO promoter-proximate regions are extremely conserved in Y. pestis, Y. pseudotuberculosis and Y. enterocolitica, indicating that the CRP-dependent expression of sycO-ypkA-yopJ can be generally applied to the above three pathogenic yersiniae.
Ramamurthi KS, Schneewind O: Type iii protein secretion in yersinia species. Annu Rev Cell Dev Biol. 2002, 18: 107-133. 10.1146/annurev.cellbio.18.012502.105912.
Trosky JE, Liverman AD, Orth K: Yersinia outer proteins: Yops. Cell Microbiol. 2008, 10 (3): 557-565. 10.1111/j.1462-5822.2007.01109.x.
Zheng D, Constantinidou C, Hobman JL, Minchin SD: Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res. 2004, 32 (19): 5874-5893. 10.1093/nar/gkh908.
Zhan L, Han Y, Yang L, Geng J, Li Y, Gao H, Guo Z, Fan W, Li G, Zhang L: The cyclic AMP receptor protein, CRP, is required for both virulence and expression of the minimal CRP regulon in Yersinia pestis biovar microtus. Infect Immun. 2008, 76 (11): 5028-5037. 10.1128/IAI.00370-08.
Petersen S, Young GM: Essential role for cyclic AMP and its receptor protein in Yersinia enterocolitica virulence. Infect Immun. 2002, 70 (7): 3665-3672. 10.1128/IAI.70.7.3665-3672.2002.
Oh MH, Lee SM, Lee DH, Choi SH: Regulation of the Vibrio vulnificus hupA gene by temperature alteration and cyclic AMP receptor protein and evaluation of its role in virulence. Infect Immun. 2009, 77 (3): 1208-1215. 10.1128/IAI.01006-08.
Skorupski K, Taylor RK: Cyclic AMP and its receptor protein negatively regulate the coordinate expression of cholera toxin and toxin-coregulated pilus in Vibrio cholerae. Proc Natl Acad Sci USA. 1997, 94 (1): 265-270. 10.1073/pnas.94.1.265.
Rickman Lisa, Scott Colin, Debbie Hunt, Hutchinson Thomas, Menendez M Carmen, Whalan Rachael, Hinds Jason, Colston M Joseph, Green J, Buxton RS: A member of the cAMP receptor protein family of transcription regulators in Mycobacterium tuberculosis is required for virulence in mice and controls transcription of the rpfA gene coding for a resuscitation promoting factor. Molecular Microbiology. 2005, 56 (5): 1274-1286. 10.1111/j.1365-2958.2005.04609.x.
Kim TJ, Chauhan S, Motin VL, Goh EB, Igo MM, Young GM: Direct transcriptional control of the plasminogen activator gene of Yersinia pestis by the cyclic AMP receptor protein. J Bacteriol. 2007, 189 (24): 8890-8900. 10.1128/JB.00972-07.
Sebbane F, Jarrett CO, Gardner D, Long D, Hinnebusch BJ: Role of the Yersinia pestis plasminogen activator in the incidence of distinct septicemic and bubonic forms of flea-borne plague. Proceedings of the National Academy of Sciences of the United States of America. 2006, 103 (14): 5526-5530. 10.1073/pnas.0509544103.
Lathem WW, Price PA, Miller VL, Goldman WE: A plasminogen-activating protease specifically controls the development of primary pneumonic plague. Science. 2007, 315 (5811): 509-513. 10.1126/science.1137195.
Park H, Teja K, O'Shea JJ, Siegel RM: The Yersinia effector protein YpkA induces apoptosis independently of actin depolymerization. J Immunol. 2007, 178 (10): 6426-6434.
Mukherjee S, Keitany G, Li Y, Wang Y, Ball HL, Goldsmith EJ, Orth K: Yersinia YopJ acetylates and inhibits kinase activation by blocking phosphorylation. Science. 2006, 312 (5777): 1211-1214. 10.1126/science.1126867.
Viboud GI, Bliska JB: YERSINIA OUTER PROTEINS: Role in Modulation of Host Cell Signaling Responses and Pathogenesis. Annu Rev Microbiol. 2005, 59: 69-89. 10.1146/annurev.micro.59.030804.121320.
Dittmann S, Schmid A, Richter S, Trulzsch K, Heesemann J, Wilharm G: The Yersinia enterocolitica type three secretion chaperone SycO is integrated into the Yop regulatory network and binds to the Yop secretion protein YscM1. BMC Microbiol. 2007, 7: 67-10.1186/1471-2180-7-67.
Zhou D, Tong Z, Song Y, Han Y, Pei D, Pang X, Zhai J, Li M, Cui B, Qi Z: Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus. J Bacteriol. 2004, 186 (15): 5147-5152. 10.1128/JB.186.15.5147-5152.2004.
Datsenko KA, Wanner BL: One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA. 2000, 97 (12): 6640-6645. 10.1073/pnas.120163297.
Straley SC, Bowmer WS: Virulence genes regulated at the transcriptional level by Ca2+ in Yersinia pestis include structural genes for outer membrane proteins. Infect Immun. 1986, 51 (2): 445-454.
Song Y, Tong Z, Wang J, Wang L, Guo Z, Han Y, Zhang J, Pei D, Zhou D, Qin H: Complete genome sequence of Yersinia pestis strain 9 an isolate avirulent to humans. DNA Res. 1001, 11 (3): 179-197. 10.1093/dnares/11.3.179.
Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL: Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 2001, 413 (6855): 523-527. 10.1038/35097083.
Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, Vergez LM, Worsham P, Chu MC, Andersen GL: Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. Journal of bacteriology. 2006, 188 (12): 4453-4463. 10.1128/JB.00124-06.
Deng W, Burland V, Plunkett G, Boutin A, Mayhew GF, Liss P, Perna NT, Rose DJ, Mau B, Zhou S: Genome sequence of Yersinia pestis KIM. J Bacteriol. 2002, 184 (16): 4601-4611. 10.1128/JB.184.16.4601-4611.2002.
Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL: Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci USA. 2004, 101 (38): 13826-13831. 10.1073/pnas.0404012101.
Thomson NR, Howard S, Wren BW, Holden MT, Crossman L, Challis GL, Churcher C, Mungall K, Brooks K, Chillingworth T: The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS Genet. 2006, 2 (12): e206-10.1371/journal.pgen.0020206.
Lucchini S, Rowley G, Goldberg MD, Hurd D, Harrison M, Hinton JC: H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog. 2006, 2 (8): e81-10.1371/journal.ppat.0020081.
Navarre WW, Porwollik S, Wang Y, McClelland M, Rosen H, Libby SJ, Fang FC: Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science. 2006, 313 (5784): 236-238. 10.1126/science.1128794.
Financial support for this work came from the National Natural Science Foundation of China for Distinguished Young Scholars (30525025), the National Natural Science Foundation of China (30771179), and the National Key Program for Infectious Disease of China (2009ZX10004-103 and 2008ZX10004-009).
DZ and RY conceived the study and designed the experiments. LJZ and LY performed all the experiments. LZ, YL and HG contributed to RT-PCR, primer extension assay and DNA binding assays. ZG participated in protein expression and purification. DZ, LFZ, CQ and DZ assisted in computational analysis and figure construction. The manuscript was written by LJZ and DZ, and revised by RY. All the authors read and approved the final manuscript.
Lingjun Zhan, Lei Yang, Lei Zhou contributed equally to this work.
Lingjun Zhan, Lei Yang, Lei Zhou contributed equally to this work.
Authors’ original submitted files for images
About this article
Cite this article
Zhan, L., Yang, L., Zhou, L. et al. Direct and negative regulation of the sycO-ypkA-ypoJ operon by cyclic AMP receptor protein (CRP) in Yersinia pestis. BMC Microbiol 9, 178 (2009). https://doi.org/10.1186/1471-2180-9-178