Role of (p)ppGpp in Viability and Biofilm Formation of Actinobacillus pleuropneumoniae S8
Role of (p)ppGpp in Viability and Biofilm Formation of Actinobacillus pleuropneumoniae S8
Gang Li 0 1
Fang Xie 0 1
Yanhe Zhang 0 1
Janine T. Bossé 0 1
Paul R. Langford 0 1
Chunlai Wang 0 1
0 1 Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Harbin , China , 2 Section of Paediatrics, Department of Medicine, Imperial College London , St. Mary's Campus , London , United Kingdom
1 Editor: Willem van Schaik, University Medical Center Utrecht , NETHERLANDS
Actinobacillus pleuropneumoniae is a Gram-negative bacterium and the cause of porcine pleuropneumonia. When the bacterium encounters nutritional starvation, the relA-dependent (p)ppGpp-mediated stringent response is activated. The modified nucleotides guanosine 5'-diphosphate 3'-diphosphate (ppGpp) and guanosine 5'-triphosphate 3'-diphosphate (pppGpp) are known to be signaling molecules in other prokaryotes. Here, to investigate the role of (p)ppGpp in A. pleuropneumoniae, we created a mutant A. pleuropneumoniae strain, S8ΔrelA, which lacks the (p)ppGpp-synthesizing enzyme RelA, and investigated its phenotype in vitro. S8ΔrelA did not survive after stationary phase (starvation condition) and grew exclusively as non-extended cells. Compared to the wild-type (WT) strain, the S8ΔrelA mutant had an increased ability to form a biofilm. Transcriptional profiles of early stationary phase cultures revealed that a total of 405 bacterial genes were differentially expressed (including 380 up-regulated and 25 down-regulated genes) in S8ΔrelA as compared with the WT strain. Most of the up-regulated genes are involved in ribosomal structure and biogenesis, amino acid transport and metabolism, translation cell wall/membrane/envelope biogenesis. The data indicate that (p)ppGpp coordinates the growth, viability, morphology, biofilm formation and metabolic ability of A. pleuropneumoniae in starvation conditions. Furthermore, S8ΔrelA could not use certain sugars nor produce urease which has been associated with the virulence of A. pleuropneumoniae, suggesting that (p)ppGpp may directly or indirectly affect the pathogenesis of A. pleuropneumoniae during the infection process. In summary, (p)ppGpp signaling represents an essential component of the regulatory network governing stress adaptation and virulence in A. pleuropneumoniae.
Funding: National Natural Science Foundation of
China (No. 31302091, http://www.nsfc.gov.cn), GL,
National Natural Science Foundation of China (No.
31201907, http://www.nsfc.gov.cn), YHZ, National
High Technology Research and Development
Program of China (No. 2011AA10A210, http://www.
863.gov.cn), CLW, Special Fund for Agro-scientific
Research in the Public Interest (No. 201303034,
http://www.moa.gov.cn/), CLW. The funders had no
role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript.
Actinobacillus pleuropneumoniae is a non-motile Gram-negative bacterium causing porcine
pleuropneumonia, a highly contagious respiratory disease that is transmitted through aerosols
Competing Interests: The authors have declared
that no competing interests exist.
or close contact with infected animals including asymptomatic carriers. This disease is often
fatal and characterized by hemorrhagic, fibrinous and necrotic lung lesions; the clinical features
ranging from acute to chronic, and it is an important cause of economic losses worldwide in
the porcine industry .
The stringent response is a broadly conserved bacterial stress response that controls
adaptation to nutrient deprivation, and is activated by a number of different starvation and stress
signals. This response is used by bacteria to determine resource allocation for either reproductive
or cell maintenance functions . It is important for activation of survival strategies such as
the stationary phase, sporulation and biofilm formation [3–5]. The central molecular signals of
this response are the small molecules guanosine 5’-diphosphate 3’-diphosphate (ppGpp) and
guanosine 5’-triphosphate 3’-diphosphate (pppGpp) (together termed (p)ppGpp) [6, 7]. To
regulate the concentration of (p)ppGpp, some bacteria express RelA, which phosphorylates
GDP or GTP to produce (p)ppGpp, or hydrolyzes (p)ppGpp back to GDP or GTP, to allow
growth after nutrient restrictions are alleviated .
The stringent response is also utilized by many bacterial pathogens to regulate their
virulence. Recently, a growing number of studies identified the stringent response as being
important for both virulence and survival in harsh environments [8–11]. The complexity and
multiplicity of the bacterial genes and regulatory pathways affected by the stringent response
suggest that the relationship between the stringent response and virulence could be
considerably more complex than expected and is perhaps unique for each pathogen .
A. pleuropneumoniae can adhere to cells of the lower respiratory tract in a process involving
different adhesins and probably biofilm formation . In this site, A. pleuropneumoniae
causes tissue damage leading to clinical disease and mortality . After successful adherence,
A. pleuropneumoniae requires a variety of nutrients to sustain growth and exert its pathogenic
effects. However, the lower respiratory tract is a nutrient-limited environment .
Subashchandrabose et al.  previously reported that most amino acids were present in lower
concentrations in epithelial lining fluid compared to serum, and some amino acids (lysine and
threonine) were present only at roughly 40 to 50% of the serum level.
Transition between growth in the upper respiratory tract and lung tissue subjects A.
pleuropneumoniae to environmental stresses . However, it is poorly understood how A.
pleuropneumoniae can withstand such stresses. In particular, it is not yet known whether the stringent
response has a role in stress adaption and/or is necessary for virulence traits of A.
pleuropneumoniae within the porcine respiratory tract. In the present study, we have inactivated the relA
gene (required for (p)ppGpp synthesis) in A. pleuropneumoniae strain S8 , and compared
its growth, morphology, metabolic and enzyme activity, viability, ability to form biofilms, and
transcriptome with its wild-type parent. The results suggest that (p)ppGpp directly or
indirectly affects the pathogenesis of A. pleuropneumoniae.
Materials and Methods
Bacterial strains, primers, plasmids and growth conditions
The bacterial strains, primers and plasmids used in this study are described in Table 1. All
A. pleuropneumoniae strains were cultured in Tryptic Soy Broth (TSB) or Tryptic Soy Agar
(TSA) (Becton Dickinson, Franklin Lakes, NJ, USA) supplemented with 10 μg /ml NAD .
Selection of A. pleuropneumoniae ΔrelA transformants was achieved by the addition of
chloramphenicol (5 μg/ml) to TSA. Complemented A. pleuropneumoniae S8ΔrelA HB
was grown in a TSB supplemented with NAD (10 μg/ml), chloramphenicol (5 μg/ml) and
kanamycin (50 μg/ml). For culture of E. coli β2155 (ΔdapA), Luria-Bertani (LB) medium was
A. pleuropneumoniae serovar 7 clinical isolate from the lung of a diseased pig in northern China
Inactivation of S8 (relA) by insertion mutant
The complemented strain of A. pleuropneumoniae S8ΔrelA containing the relA gene
thrB1004 pro thi hsdS lacZ M15 (F’ lacZ M15 lacIq traD36 proA+ proB+)dap::erm (Ermr)
Transconjugation vector based on pBluescript SK with mobRP4, a polycloning site, Cmr, and transcriptional fusion of the
omlA promoter with the sacB gene
Broad-host-range shuttle vector from Haemophilus ducreyi; Strr Smr Kmr
900 bp homologous fragment of relA cloned into pEMOC2 via SalI/NotI sites
pLS88 with a PCR-derived insert containing the relA gene
supplemented with 1 mM diaminopimelic acid (DAP) (Sigma-Aldrich, St. Louis, MO, USA)
and, when required, chloramphenicol (30 μg/ml). All the bacteria were cultured at 37°C.
Construction of a (p)ppGpp synthase deletion mutant and
The strategy used for inactivation of the relA gene in A. pleuropneumoniae was as described
previously . A 900-bp DNA fragment of relA (646 bp-1546 bp, encoding amino acid
residues 216 to 516 of the RelA protein) was amplified from genomic DNA of A.
pleuropneumoniae strain S8 with primers P1 and P2 (Table 1, Fig 1). The PCR product was cloned into the
suicide plasmid pEMOC2 between sites SalI and NotI. The resulting insertional plasmid,
pEMOC2-ΔrelA, was electroporated into A. pleuropneumoniae S8. Recombinants were selected
on TSA plates containing chloramphenicol (5 μg/ml). The ΔrelA strain was verified to have
the plasmid inserted into the relA locus by PCR using primers P3 and P4 and DNA sequencing
of the resulting amplicon. To construct the complemented strain, full-length relA gene with its
signal peptide sequence was amplified from S8 genomic DNA with primers P5 and P6
(Table 1, Fig 1). The PCR product was cloned between the EcoRI and the SacI sites of the
shuttle vector pLS88. The recombinant plasmid, pLSrelA, was confirmed by DNA sequencing and
electroporated into the S8ΔrelA strain. Transformants were selected on TSA plates containing
kanamycin (50 μg/ml) and chloramphenicol (5 μg/ml). The complemented strain was
confirmed by PCR and DNA sequencing of the amplicon, and named S8HB.
Fig 1. Schematic representation of the construction of S8ΔrelA mutant. The figure shows the binding
locations for the oligonucleotide primers used to amplify the homologous regions (from 646 bp to 1556 bp)
used in the construction of the insertion plasmid. The blue area represents the upstream region of the
homologous fragment; the red area represents the downstream region of the homologous fragment.
Detection of intracellular (p)ppGpp
The production of (p)ppGpp in response to minimal medium was assayed as previously described
. The strains were grown over-night in TSB to early stationary phase (12 h), diluted back to an
OD600 of 0.2 with fresh TSB, and incubated in TSB for additional 2 h, at which point all strains
had reached an OD600 of 0.3. For nutrient deprivation, 2 ml of each culture were pelleted by
centrifugation at 12,000 g for 5 min, and washed once with minimal medium (50 mM MOPS
(morpho-linepropanesulfonic acid) pH 7.4, 1 mM MgSO4, 0.25 mM CaCl2, 19 mM glutamic acid, and
0.004 mM biotin, 10 mg NAD) and resuspended in 250 μl of minimal medium, 32P (Perkin
Elmer) was added to 100 μCi/ml, and the culture labeled for 1 h at 37°C. Fifty microliters of
labeled culture were added to an equal volume of 2 M formic acid and placed on ice for at least 15
min. The mixture was centrifuged for 5 min at 16,000 g, and 3 μl of the supernatant were spotted
directly onto polyethyleneimine (PEI) cellulose thin-layer chromatography plates (Sigma), dried,
and developed in 1.5 M KH2PO4 for 2.5 h. Nucleotides were visualized by autoradiography .
All strains (S8, S8ΔrelA and S8HB) were first grown in 2 ml of TSB for 12 h and diluted with
fresh TSB to OD600 of 0.2. The diluted cultures were incubated at 37°C. The OD600 was
determined using an Eppendorf Biophotometer (Eppendorf, Hamburg, Germany) at various time
points. The effect of relA on the viability of A. pleuropneumoniae was determined by counting
the CFU of A. pleuropneumoniae at the indicated time points. One hundred microliter aliquots
of culture were taken and serially diluted in TSB. After plating in duplicate on TSA plates
containing relevant antibiotics and incubated at 37°C for 12 h, the CFU were counted. All
experiments were repeated three times.
Scanning electron microscopy
The pellets of S8, S8ΔrelA and S8HB were harvested by centrifugation at 10,000 g after growth
in TSB broth for 6 h, 12 h, 24 h and 36 h at 37°C. The harvested cells were washed twice with
0.1 M PBS buffer (pH 7.2) and fixed overnight using 2.5% glutaraldehyde at 4°C. Subsequently,
fixed cells were washed three times with 0.1 M PBS (pH 7.2) and dehydrated using increasing
concentrations of ethanol (i.e. washed once with each of 50%, 70%, 85%, 95%, and three times
with 100%). The samples were subjected to critical point drying with CO2 (BAL-TEC CPD030)
and metal-spraying (BAL-TEC SCD005) apparatuses. Finally, the cell morphology of all three
strains was compared by scanning electron microscope (Hitachi SU8010).
Quantitative biofilm assay
The microtiter plate biofilm assay is a static assay particularly useful for examining early events
in biofilm formation . Overnight cultures were diluted 100× with TSB, and 200 μl of the
dilution added to the wells of a sterile 96-well microtiter plate (Costar 3599, Corning, NY,
USA). After incubation for 36 h at 37°C, the wells were washed with 200 μl water to remove
loosely adherent cells. Excess water was removed by inverting plates several times onto new
paper towels. The wells were filled with 100 μl crystal violet (0.1%) and incubated for 2 min at
room temperature. After removal of the crystal violet solution, the wells were washed with
200 μl water and dried in a 37°C incubator for 30 min. Subsequently, 100 μl ethanol (70%) was
added to each well. Absorbance was measured at 590 nm.
Confocal laser scanning microscopy
The biofilm assay protocol mentioned above was used except that after washing off
non-adherent bacteria, instead of adding crystal violet, 200 μl diluted LIVE/DEAD@ BacLightTm Bacterial
Viability Kit solution (Molecular Probes, Eugene, Oregon, USA) were added to stain the
bacterial cells. Plates were incubated for 20 min at room temperature in the dark and washed with
water. The wells were examined with a confocal microscope (TCS SP5, Leica Microsystems,
Hamburg, Germany). SYTO 9 nucleic acid stain was excited at 488 nm and detected using a
520 nm filter. Propidium iodide was excited at 488 nm and detected using a 572 nm filter.
Physiological and biochemical effects of (p)ppGpp
All strains (S8, S8ΔrelA and S8HB) were cultured on TSA plates overnight. Subsequently,
bacteria were harvested using PBS, and centrifuged at 12,000 g for 5 min. Pellets were
re-suspended to an OD600 of 0.2 in the suspension medium provided in the kit. The tests were
performed using API identification systems, including API 50 CH, API 20 E, API 20 NE and
API ZYM, following the manufacturer instructions (BioMerieux).
RNA isolation and qRT-PCR
Total RNA was isolated from A. pleuropneumoniae S8 and S8HB strains grown to early
stationary phase (12 h) in TSB broth for analysis of relA expression. They were harvested by
centrifugation at 10,000 g at 4°C and diluted back to an OD600 of 1.0 with fresh TSB medium. The
RNeasy kit (Qiagen) was used to isolate RNA. RNA concentrations were measured
spectrophotometrically at 260/280 nm (IMPLEN, Germany). Complementary DNA (cDNA) was
synthesized using the PrimeScript RT reagent kit with gDNA Eraser (TaKaRa, Japan) following the
manufacturer’s instructions. Real-time PCR was performed using a Stratagene3000 system
(Agilent Technologies, Germany). The reaction volume was 20 μl, containing 2 μl cDNA
template, 10 μl 2μSYBR Green I (TaKaRa) and 0.8 μM of forward and reverse primers. PCR
reactions were set up in triplicate. For all amplifications, the cycle conditions were 95°C for 2 min,
followed by 40 cycles of 95°C for 15 s and 56°C for 1 min. This experiment was done with three
biological replicates, and the average values were taken as the quantitative result. The gyrA and
recF gene were used as internal control. Reaction mixtures lacking RNA were used as negative
controls for each set of primers. The primers for amplifying cDNAs of gyrA, recF, relA are
presented in Table 1. Relative expression values were calculated as 2−4(CT target − CT reference), where
CT is the fractional threshold cycle .
Cultures of S8 and S8ΔrelA were grown to early-stationary-phase (12 h) in TSB. The cells were
collected at 4°C, the RNeasy kit (Qiagen) was used to isolate RNA, and the Ribo-Zero™ rRNA
Removal Kit for Gram-negative bacteria (EPICENTRE Biotechnologies) used to remove rRNA.
The remaining RNA was quantified and examined for protein and reagent contamination with a
Nanodrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA). RNA samples
showing A260/A280 ratio of 1.8–2.0, and A260/A230 ratio above 1.5 were selected for analysis. A total
of 20 μg of RNAs for both the S8 and S8ΔrelA strains were pooled for cDNA library construction.
Illumina sequencing was performed at the Beijing Genomics Institute (BGI)-Shenzhen in
Shenzhen, China (http://www.genomics.cn/index) following the manufacturer’s instructions
(Illumina, San Diego, CA). The cDNA libraries were constructed according to Illumina’s
protocols and sequenced using the Illumina HiSeq 2000 platform. This experiment was done with
three biological replicates.
Differential expression analysis
The raw sequence reads were filtered using the Illumina pipeline. All of the low-quality reads,
reads with adaptor contamination, and reads with only one copy were excluded from the
analysis. The clean reads remaining were mapped to the reference sequence of A. pleuropneumoniae
S8 (Genbank accession No. ALYN00000000.1).
To identify the genes affected by deletion of relA, the libraries were compared. The number
of reads for each coding region was determined, the number of total reads was normalized
between the libraries and the ratio of S8 to S8ΔrelA reads was calculated. Differentially
expressed genes were detected as previously described , with a false discovery rate (FDR)
threshold of 0.01 . Differences with FDR 0.001 and log2Ratio absolute value 1 were set
as the threshold for significant differences in gene expression.
The Blast2GO program was used to obtain GO annotations for molecular functions,
biological processes and cellular component ontologies (http://www.geneontology.org). The Kyoto
Encyclopedia of Genes and Genomes pathway database (http://www.genome.jp/kegg) was
used for pathway assignments. The BlastN program (http://blast.ncbi.nlm.nih.gov/) was used
to compare sequences with the A. pleuropneumoniae serovar 7 strain AP76 reference sequence
(Genbank accession No. CP001091.1) for annotation.
Basic statistical analyses were conducted with the SPSS software (SPSS, Inc., Chicago, IL, USA).
The Student’s t test was used to determine the significance of the differences in the means
between multiple experimental groups. The data were expressed as the mean +/- standard
deviation, and values of P<0.05 were considered to be significant.
The relA insertion mutant of A. pleuropneumoniae S8, constructed with plasmid
pEMOC2ΔrelA (Fig 1), was confirmed by PCR and DNA sequencing, and designated as S8ΔrelA.
Complementation of the S8ΔrelA mutant was achieved using the plasmid pLSrelA, with
transformants selected on plates containing chloramphenicol and kanamycin. The complemented
mutant was designated S8HB.
To determine whether the ΔrelA mutant produces (p)ppGpp, all strains were subjected to
nutrient deprivation, a condition which had been shown to induce (p)ppGpp [10, 28–30]. S8,
S8ΔrelA and S8HB were incubated in minimal medium with 32P for 1 h. As shown in Fig 2, the
S8 and S8HB strains accumulated significant amounts of (p)ppGpp upon exposure to this
starvation stress. In contrast, there was almost no detectable level in the S8ΔrelA mutant extracts.
Plate counts of parallel bacterial cultures after 1 h incubation in minimal medium showed that
all three strains remained viable during the experiment; thus, the absence of (p)ppGpp
production in the S8ΔrelA strain was not due to bacterial death. This result indicated that the relA
gene product is indispensable for (p)ppGpp production in A. pleuropneumoniae S8, and
disruption of the relA gene results in the absence of (p)ppGpp.
Lack of (p)ppGpp resulted in abnormal growth under nutrient limitation
and decreased viability under starvation conditions
Having ascertained that deletion of relA affects the production of (p)ppGpp in A.
pleuropneumoniae S8, and given the vital role of the stringent response in bacterial survival, we
investigated the impact of (p)ppGpp on cell growth and viability. As shown in Fig 3, OD600
measurements indicated that S8ΔrelA grew slower than S8 when cultured in TSB. The growth
pattern of S8HB was similar to that of S8ΔrelA, indicating lack of complementation of the
slow-growth phenotype by the cloned relA gene. To test whether (p)ppGpp is required for
Fig 2. Accumulation of (p)ppGpp in S8, S8ΔrelA and S8HB. Cells were labeled with [32P]-H3PO4-labelled
in MOPS under starvation conditions, nucleotides were acid extracted, centrifuged, 32Pi-labeled nucleotides
were resolved by polyethyleneimine coated TLC plates followed by autoradiography. (P)ppGpp separated by
TLC are indicated. Strains used are: S8, S8ΔrelA and S8HB.
Fig 3. The growth curves of the S-8 strain, S8ΔrelA mutant and the complemented S8HB strain.
Overnight cultures of S8 (●), S8ΔrelA (&) and S8HB (▲)were diluted into fresh medium and then incubated in
TSB containing different antibiotics (5 μg/ml chloramphenicol and 50 μg/ml kanamycin). Growth was
monitored by OD600 at various time points. Points indicate the mean values, and error bars indicate standard
viability, we determined cell counts for S8, S8ΔrelA and S8HB cultured in TSB over 36 h. As
shown in Fig 4, all strains exhibited a decline in viability from 6 h to 36 h. However, S8 exhibits
a gradual decline in viable counts from 12 h to 36 h, whereas, S8ΔrelA and S8HB showed a
rapid decline during late stationary phase; no viable cells were detected for either strain at 36 h.
The results indicated that the relA gene expressed on plasmid pLSrelA was only able to partially
restore growth of S8ΔrelA in TSB. However, it was unable to complement viability: the number
of colonies decreased approximately seven orders of magnitude relative to the S8 strain. These
results indicated that (p)ppGpp contributed to prolonged survival under conditions of nutrient
While examining the role of (p)ppGpp in morphology, we found that the S8ΔrelA mutant grew
as a homogeneous population of non-extended (i.e. short) rods from 12 to 36 h in liquid
medium (Fig 5). The non-extended phenotype is in sharp contrast to S8, which grew as a
population of significantly longer rods under the same growth conditions. The extended-rod
phenotype was not restored by introduction pLSrelA.
Deletion of (p)ppGpp synthases affects the biofilm formation of A.
We tested whether (p)ppGpp plays a role in biofilm formation by examining the
biofilm-forming ability of S8, S8ΔrelA and S8HB in polystyrene microtiter plates. As shown in Fig 6, S8 and
S8ΔrelA produced minor and dense biofilms, respectively. Biofilm quantification was
confirmed by confocal laser scanning microscopy (Fig 7). These results indicated that (p)ppGpp is
involved in A. pleuropneumoniae biofilm production. The S8HB strain yielded less biofilm
than S8ΔrelA, although it produced much more biofilm than WT S8 strain (Figs 6 and 7). This
Fig 4. The S8ΔrelA mutant has a stationary phase survival defect. S8, S8ΔrelA and S8HB strains were
grown by shaking under the same conditions at 37°C, and numbers of CFU ml-1 were determined at different
time points indicated. A representative assay of at least three experiments is shown. Error bars indicate the
standard deviations of replicate plating.
Fig 5. Scanning electron microscopy. SEM of S8, S8ΔrelA and S8HB. Compared to the S8, cells of the S8ΔrelA mutant and S8HB are of shorter length
and typical of WT cells grown in nutrient conditions.
Fig 6. Polystyrene microtiter plate biofilm assay. Biofilm formation of S8, S8ΔrelA and S8HB in 96-well
polystyrene microtiter plates. The plates were stained with crystal violet. The optical density of the bacterial
biofilm formation was monitored by OD595 after 36 h incubation. Error bars indicate standard deviations.
Metabolic effects of (p)ppGpp in A. pleuropneumoniae S8
tured in API identification systems. The S8 strain utilizes citrate and all the twelve carbon
in reversal to wild-type citrate utilization and production of urease, but the production of
arginine dihydrolase was not restored (Table 2). No other differences in substrate utilization or
Validation of expression level of relA in S8 and S8HB
To compare the expression levels of relA in S8 and S8HB, qRT-PCR analysis was performed
three times for RNA extracts from the three biological replicates. Two internal reference genes
were used to evaluate the expression level. The results indicated that the plasmid encoded relA
Fig 7. (p)ppGpp affects the biofilm formation of A. pleuropneumoniae S8. Biofilm development was monitored by confocal laser scanning microscopy
after 36 h. The cells were stained with LIVE/DEAD@ BacLightTm Bacterial Viability Kit solution. S8 showed a reduction in biofilm formation compared to the
strains S8ΔrelA and S8HB.
−, negative result; +, positive result. All strains produced acid from D-glucose. None of these strains
produced acid from Glycerol, β-methyl-D-xyloside, inositol, α- methyl-D-glucoside, esculin, inulin, glycogen,
D-lyxose, α-methyl-D-mannoside, 5-keto-gluconate, L-sorbose, N-acetylglucosamine, salicin, D-melibiose,
xylitol, D-tagatose, L-arabinitol, D-arabinose, L-xylose, L-rhamnose, sorbitol, Amygdalin, D-cellobiose,
Dgentiobiose, D-fucose, gluconate, L-arabinose, adonitol, dulcitol, D-arabinitol, arbutin, D-trehalose, starch,
D-turanose, L-fucose, 2-keto-gluconate. None of these strains had Akaline phosphatase, Leucine
arylamidase, Chymotrypsin, N-acetylglucosaminidase, lysine decarboxylase, Acid phosphatase,
βglucuronidase, Ornithine decarboxylase, Lipid esterase(C8), Cystine arylamidase, α-glucosidase,
βfucosidase, Tryptophan deaminase, Lipid enzyme(C14), Trypsase, β-D-glucosidase. All strains had
βgalactosidase, Esterase (C4), Valine arylamidase, α-mannosidase, Naphthol-as-bi-phosphate hydrolase,
αgalactosidase. All strains were negative by Bile esculin test, H2S production, Indole test, VP test. All strains
were positive by nitrate reduction and glucose ferment test.
Global gene expression in the early stationary phase is different in A.
pleuropneumoniae S8 strain compared to the relA-deficient mutant
To study the effects of the effector molecule (p)ppGpp on a genome-wide scale, the
transcriptomes of S8 and S8ΔrelA were compared by RNA-seq. The overwhelming majority of the
differentially expressed genes in this strain were upregulated (94%). S1 Table shows the
differentially expressed genes between S8 and its isogenic S8ΔrelA mutant. A total of 405 genes
were found to be differentially expressed in the S8ΔrelA mutant. Among these, 380 genes were
upregulated and 25 genes were downregulated compared to the WT S8. The differently
expressed genes were annotated according to the COG database and are summarized in Fig 9.
The most prominently upregulated transcription was in genes involved in amino acid transport
and metabolism (45/405); cell wall/membrane/envelope biogenesis (45/405); translation,
Fig 8. Confirmation of the differentially expressed of relA gene by real-time RT-PCR. Transcriptional alteration of relA gene was examined by
quantitative analysis of corresponding mRNA expression levels in S8 and S8HB. Total RNA were extracted from S8 and S8HB and reverse transcribed into
cDNA for subsequent analysis via quantitative PCR. Fold change values were calculated according to the 2−44Ct method, using gyrA and recF as internal
reference gene. Error bars represent the standard error of three independent experiments, ** represent p-value<0.01.
ribosomal structure and biogenesis (45/405); replication, recombination and repair (33/405);
carbohydrate transport and metabolism (31/405); energy production and conversion (25/405);
inorganic ion transport and metabolism (24/405). The genes coding for a global anaerobic
regulator (APP7_0696, log2 = 1.04), dimethyl sulfoxide reductase (APP7_1734, log2 = 2.38),
hemoglobin-binding protein (APP7_1103, log2 = 2.26), capsule polysaccharide export protein
(APP7_1644, log2 = 2.01) and autotransporter serine protease (APP7_0385, log2 = 4.03),
which are involved in persistence in the upper respiratory tract; the fimbrial biogenesis
protein (APP7_0937, log2 = 2.96; APP7_0938, log2 = 1.38), tight adherence protein
(APP7_0589, log2 = 1.98), outer membrane protein (APP7_1942, log2 = 2.16; APP7_1512,
log2 = 2.39), which are involved in adhesion to the lower respiratory tract; the ATP-dependent
protease (APP7_0400, log2 = 4.18; APP7_1329, log2 = 2.32), RTX toxin protein (APP7_
1051, log2 = 1.76), which are involved in the induction of lesions and the ferric hydroxamate
receptor (APP7_2103, log2 = 1.87; APP7_1452, log2 = 1.26), hemoglobin-binding protein A
(APP7_1103, log2 = 2.26), iron (chelated) ABC transporter periplasmic-binding protein
(APP7_0274, log2 = 1.56), which are involved in acquisition of essential nutrients, are all
upregulated. All of these genes have been characterized as virulence factors in A. pleuropneumoniae
In a previous study by Lone et al. , genes involved in the stringent response were shown to
be up-regulated in a malT mutant of A pleuropneumoniae grown in porcine bronchoalviolar
Fig 9. Functional categories of A. pleuropneumoniae genes that changed their expression profile in the S8 and S8ΔrelA during stationary phase
growth. Black bars and the white bars indicate the number of genes in each indicated functional category (COG) that was upregulated or downregulated,
respectively. The total number of genes within each COG category is indicated in brackets.
lavage fluid and it was suggested that that this response may play a role in pathogenesis of this
bacterium. However, no further investigations were made regarding the roles of individual
genes. In order to investigate the role of RelA, a stringent response regulatory protein
responsible for synthesis of (p)ppGpp, in A. pleuropneumoniae physiology, we constructed a relA
mutant of the serovar 7 clinical isolate S8 . We confirmed the mutant, S8ΔrelA, to be
deficient in (p)ppGpp production compared to the WT S8 strain when incubated in minimal
medium (Fig 2), and complementation of the mutant by plasmid encoded relA (pLSrelA) was
able to restore WT levels of (p)ppGpp under this growth condition.
The S8ΔrelA mutant had a reduced growth rate in TSB compared to S8 (Fig 3). This is
consistent with previous studies describing relA-deficiency leading to growth limitation .
However, complementation with the relA gene (strain S8HB) only led to partial restoration of
growth limitation, possibly due to differences in expression levels of relA from the plasmid.
Indeed, qRT-PCR analysis of cultures grown in TSB for 12 h revealed that the expression level
of relA in S8HB was less than in S8 (Fig 8), suggesting lower concentrations of (p)ppGpp in the
complemented mutant under these conditions.
It was also found that the viability of S8ΔrelA decreased with prolonged culture in TSB
compared to S8, i.e it had a stationary phase growth defect. At the 24 h time point, the CFU of
S8ΔrelA was seven orders of magnitude less compared to S8. No viable S8ΔrelA were recovered
from the TSB cultures at 36 h when plated on TSA. Other studies have documented that the
availability of (p)ppGpp affects bacterial survival, i.e. relA deficiency results in the death of the
cells. For example, a Bordetella pertussis relA-deficient mutant also lost viability more rapidly
than the wild-type . In addition, (p)ppGpp is reported to be responsible for significant
changes in gene expression, leading to cessation of growth and induction of specific stress
responses [12, 37–40]. Our results indicated that (p)ppGpp contributes to prolonged survival
of A. pleuropneumoniae S8 under conditions of nutrient limitation.
In stationary phase in rich medium (TSB), S8 exhibited a change in morphology such that it
produced prolonged rods and with an increase in volume (Fig 5), as has previously been seen
in other bacteria . Both, S8ΔrelA and S8HB had similar morphology to that of
non-stationary phase S8 cells (i.e. short rods), even at 36 h in TSB. Transcriptome analysis showed that
genes involved in cell wall/membrane/envelope biogenesis were up-regulated in S8ΔrelA
compared to S8, consistent with the morphological changes observed.
More recently, (p)ppGpp has been reported to be involved in a number of non-stringent
processes, including virulence, and biofilm formation [7, 36, 42]. Bacterial biofilm formation is
a complex, multifactorial process requiring genes involved in adherence, metabolism, quorum
sensing, and stress responses. When we tested the ability of S8, S8ΔrelA and S8HB to form
biofilms, we found increased biofilm formation by S8ΔrelA compared to S8, suggesting that (p)
ppGpp negatively regulates biofilm formation of A. pleuropneumoniae S8. These results are in
contrast to those found with Agrobacterium , Vibrio cholerae , E. coli , B. pertussis
, where (p)ppGpp promoted biofilm formation. The reasons for this apparent
discrepenancy are not clear. The transcriptome data revealed that the genes known to be important for
the formation of biofilm (pgaA log2 = 2.73, pgaB log2 = 1.37, pgaC log2 = 2.64) were all
up-regulated in S8ΔrelA. In A. pleuropneumoniae, biofilm formation has been shown to be part of the
extracytoplasmic stress response, with genes of the pga operon positively regulated by ϭE .
In addition, ϭE regulates expression of numerous genes encoding proteins involved in stress
response and in reparation and maintenance of the bacterial envelope, and is itself negatively
regulated by the anti-sigma factor, RseA [45–47]. However, the rseA gene (APP7_0419) was
up-regulated (log2 = 2.04) in S8ΔrelA, suggesting that ϭE was not the only regulator responsible
for biofilm formation in the relA mutant.
The stringent response occurs when bacteria encounter nutrient-limited environment and
initiates changes in gene regulation in order to maximize the utilization of available resources
. In contrast to the growth and morphology results obtained in growth in TSB broth, but in
agreement with the detection of WT levels of (p)ppGpp in the S8HB strain when incubated in
minimal medium, the metabolic defects (including changes in carbon source utilization and all
biochemical characteristics except for arginine dihydrolase; Table 2) in S8ΔrelA were
complemented in S8HB as determined by API analysis, which uses a minimal medium base for
inoculation of the test strips. These results suggest that expression of relA from pLSrelA may be
higher in minimal medium than in late log phase in TSB.
Besides the differently expressed genes involved the metabolism, some virulence-related
genes were also differently expressed (S1 Table). It has been shown that (p)ppGpp has a direct
role in expression of virulence in other pathogenic bacteria [2, 31–33]. Some virulence factors
involved in adhesion, acquisition of essential nutrients, induction of lesions, avoiding the host’s
defense mechanism and persistence have been up-regulated in S8ΔrelA. These results suggest
that the virulence of S8ΔrelA might be higher than S8, however further experiments are
required to validate this.
The gene expression profiles for S8 and S8ΔrelA were also analysed to determine if any of
the differentially regulated genes could explain the various phenotypes in the relA mutant.
Some significantly differentially expressed transcripts were detected. Among these, the genes
involved in ribosomal structure and biogenesis, amino acid transport and metabolism, and
translation cell wall/membrane/envelope biogenesis were all up-regulated in the mutant. This
is consistent with a previous report that cells entering stationary phase without (p)ppGpp
production have a proteomic profile similar to that during growth . This suggests that the
transcriptional program of S8ΔrelA is geared towards exponential growth, and may be poorly
adapted to inducing systems that are required to withstand stress. Also, the (p)ppGpp deficient
strain failed to suppress unnecessary gene expression under nutrient-limiting conditions,
which may contribute to diminished survival. A balanced carbon flux is extremely important
for viability of bacterial cells .
In conclusion, our results show that during stationary-phase growth in TSB, (p)ppGpp is
critical for A. pleuropneumoniae S8 to adapt to the nutrient-limiting conditions. Several
phenotypes were changed owing to the deficiency of (p)ppGpp. By analyzing the transcriptome of a
relA mutant, we have demonstrated a set of genes that may be regulated by A.
pleuropneumoniae during adaptation to changing nutrient levels. Many differently expressed genes have been
identified, and further study will clarify the role of selected genes in the pathogenesis of porcine
pleuropneumonia. Some of the genes identified here may serve as new targets in drug and
relA gene. All the differently expressed genes were categorized according to the COG database.
We thank Dr. Gerald-F. Gerlach (Institute for Microbiology, Department of Infectious
Diseases, University of Veterinary Medicine Hannover, Germany) for the generous donation of E.
tute of Food & Fermentation industries) for technical assistance with the SEM experiments.
We also thank Dr. Du cheng (State Key Laboratory of Veterinary Biotechnology, Harbin
Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China) for
technical assistance with the qRT-PCR experiments.
Conceived and designed the experiments: GL FX CLW. Performed the experiments: GL YHZ.
Analyzed the data: GL YHZ. Contributed reagents/materials/analysis tools: YHZ. Wrote the
paper: GL JTB PRL CLW.
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