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Abstract
A random amplified polymorphic DNA (RAPD) procedure was used to identify a specific 0.6 kb DNA fragment unique to
Dermatophilus congolensis. This 0.6 kb fragment was evaluated as a specific DNA probe and used to design oligonucleotide
primers for polymerase chain reaction (PCR) amplification. The nucleotide sequences adjacent to this DNA fragment were
determined by inverse PCR allowing the identification of a 4.1 kb sequence. Analysis of this revealed a complete open reading
frame (ORF) with a high similarity to an alkaline ceramidase from Pseudomonas aeruginosa. The molecular weight of the
enzyme derived from the predicted amino acid sequence is 74,662 Da, its pI is 9.81. The predicted N-terminal sequence of the
enzyme contains a signal sequence indicating that the enzyme is exported by the bacterium. Since ceramides have important
protective and cell regulatory roles in the epidermis we suggest that this ceramidase may have a role in the pathogenesis of
dermatophilosis. It is the first completely sequenced gene described for D. congolensis.
2003 Elsevier B.V. All rights reserved.
Keywords: Alkaline ceramidase; RAPD; Inverse PCR; Dermatophilus congolensis; agc gene
1. Introduction
Corresponding author. Tel.: +34-927257129;
fax: +34-927257110.
E-mail address: jhermoso@unex.es (J. Hermoso-de-Mendoza).
1 Present address: Scottish Executive Environment and Rural
Affairs Department (SEERAD), The Scottish Executive, Room
440, Pentland House, 47 Robbs Loan, Edinburgh EH14 1TY,
Scotland.
0378-1135/$ see front matter 2003 Elsevier B.V. All rights reserved.
doi:10.1016/j.vetmic.2003.10.028
68
Host species
Origin
Sheep
Cattle
Sheep
Horse
Sheep
Cattle
Horse
Horse
Sheep
Sheep
Cattle
Deer
Sheep
Tortoise
UK
Zimbabwe
Spain
Germany
Spain
Spain
Spain
UK
Australia
Australia
Ghana
UK
Australia
Australia
69
biochemical methods and multiplex PCR amplifying the MPB20 sequence (Cousins et al., 1991) and
RNAr16S (Woese, 1987), a Corynebacterium propinquum field isolate, identified by API-CoryneTM ,
and a Dermatophilus chelonae type strain (ATCC
51576) were digested with the restriction enzyme
PstI, separated by electrophoresis on 0.8% agarose
gel and transferred onto Hybond N + membrane
(BoehringerMannheim).
2.4. PCR conditions
For specific amplification of D. congolensis, two
oligonucleotide primers, ESP1 and ESP2, were designed from the nucleotide sequence of the 0.6 kbRAPD fragment cloned from D. congolensis (NCTC
5175). ESP1 (5 -CTTCAGCAGAAAATTCACCA-3 )
and ESP2 (5 -CGTACATTCCCGGAATCTTC-3 ),
delineating a 438 bp fragment. DNA was amplified in
100 !l of reaction mixture which contained 100 ng of
genomic DNA, 1.5 mM MgCl2 , 1 !M of each primers,
250 !M (each) deoxynucleoside triphosphate (dNTP),
1.5 units of Taq DNA polymerase (BioTaqTM , Bioline), 10 mM TrisHCl, pH 8, 50 mM KCl and 0.1%
Triton 100. PCR conditions were programmed for denaturation at 94 C for 5 min and then for 35 cycles of
1 min at 94 C, 1 min at 55 C, and 1.5 min at 72 C.
To clone the 5 - and 3 -flanking regions of the RAPD
product, amplification by inverse PCR (Moreau et al.,
1997) was performed. Chromosomal DNA from the
type culture strain (NCTC 5175) was digested with
different restriction enzymes PstI, AgeI, EcoRI, BglII
and SmaI (Amersham Biosciences), the restriction endonucleases were then thermally inactivated (80 C,
20 min), and aliquots were incubated with T4 DNA
ligase (Amersham Biosciences) overnight at 16 C.
The resulting self-ligated DNA was precipitated with
ethanol and resuspended in sterile distilled water to
give a final concentration of 10 ng !l1 . Then, it was
used as the template in further PCR reactions with
primers based on the RAPD band sequence.
PCR reactions (100 !l) contained 5 or 10 !l
self-ligated chromosomal DNA, 0.5 mM of each
primer, 0.2 mM concentrations of each deoxynucleotide triphosphate, 1.5 units of Taq DNA polymerase (BioTaq), 1.5 mM MgCl2 , 10 mM TrisHCl,
pH 8, 50 mM KCl and 0.1% Triton 100. The thermocycler was programmed as follows: 5 min warm-up/hold
70
3. Results
The optimal RAPD mixture and amplification conditions with primer A were as follows: PCR reactions
(100 !l) contained 100 ng of genomic DNA, 1 !M of
each primer, 300 !M dNTP, 2.5 units of Taq DNA
polymerase (BioTaq), 2 mM MgCl2 , 10 mM TrisHCl,
pH 8, 50 mM KCl and 0.1% Triton 100. The thermocycler was programmed as follows: 5 min warm-up/hold
at 94 C, followed by 30 cycles of: 15 s at 94 C, 40 s
at annealing temperature (35 C) and 30 s at 72 C,
1, followed by a 15 min step holding at 72 C. With
primer B, the conditions were as follows: PCR reactions (100 !l) contained 100 ng of genomic DNA,
1 !M of each primer, 250 !M dNTP, 1.5 units of Taq
DNA polymerase (BioTaq), 1.5 mM MgCl2 , 10 mM
TrisHCl, pH 8, 50 mM KCl and 0.1% Triton 100.
The thermocycler was programmed as follows: 5 min
warm-up/hold at 94 C, followed by 30 cycles of:
1 min at 94 C, 1 min at annealing temperature (45 C)
and 90 s at 72 C, 1, followed by a 15 min step holding at 72 C. The RAPD amplification patterns obtained with these primers on the DNA extracts of D.
congolensis were reproducible and revealed clearly
marked products of about 0.6 kb (Fig. 1).
The selected DNA fragments were gel purified and
cloned in plasmid vector and the insert were sequenced
from both directions. The DNA sequenced fragments
were searched for homologies with EMBL and GenBank and the band from primer A showed a high degree of homology with a portion of the P. aeruginosa
alkaline ceramidase gene (Okino et al., 1999), whereas
the band from B was nor significantly homologous
with previously characterized gene sequences.
The 0.6 kb DNA fragment was eluted from agarose
gel, labeled with DIG by PCR with the primer A, and
used as a probe against PstI digested total DNAs of
D. congolensis and one isolate of M. bovis, one of
D. chelonae and other of C. propinquum. The results
showed that the 0.6 kb DNA fragment hybridized to
an approximately 3.0 kb PstI fragment in the genomic
DNA of D. congolensis, but not with those of any
other species tested.
Based on this DNA sequence, two oligonucleotides
(ESP1 and ESP2) were used for subsequent PCR amplification tests. To determine the specificity of these
primers, PCRs were carried out with DNA of all of the
strains listed in Table 1, DNA from a M. bovis field isolate and from a C. propinquum field isolate. The PCR
71
Fig. 2. The PCR amplification using ESP1 and ESP2 primers generated an approximately 0.4 kb size amplified DNA fragment in all D.
congolensis strains tested (lanes 415), in addition a minor second band was also observed from isolates of ovine origin. No amplifications
were observed with the M. bovis, C. propinquum and D. chelonae strains tested (lanes 13) (ladder 0.5 kb, Amersham Biosciences).
4. Discussion
In this study, the RAPD procedure was used to find
specific DNA fragments unique to D. congolensis.
A 0.6 kb fragment was evaluated as a specific DNA
probe and used to design oligonucleotide primers for
PCR amplification. The primers amplified a conspicuous 0.43 kb PCR product, from all D. congolensis
isolates tested, the product could be easily visualized
on a standard 0.81% agarose gel. The primers did
not amplify DNA from a selection of related other
pathogenic species, nor from the closely related D.
chelonae. This study demonstrates that the selection
and analysis of taxon-specific bands within patterns of
RAPD offers an effective method of identifying nucleic acid sequences on which to base specific diagnostic primers for conventional high-stringency PCR.
Using the data generated in this study it would now
be straightforward to develop and apply a PCR for diagnosis or detection of D. congolensis.
The nucleotide sequences adjacent to this 0.6 kb
DNA fragment were determined by inverse PCR allowing the identification of the agc gene. Interpretation
72
of the deduced amino acid sequence revealed a conserved alkaline ceramidase domain with around 35%
similarity with the P. aeruginosa and M. tuberculosis
ceramidases (Fig. 3) and a theoretical isoelectric point
of 9.81. Interestingly, the D. congolensis ceramidase
showed a putative signal peptide sequence suggesting
CER2
CER3
CER1
1
50
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~ML
~~~~~~~~~~ ~~~~~~~~~~ ~MSRSAFTAL LLSCVLLALS MPARADDLPY
MTRRTRKITL SKIMAPAVVV ALALPAGTAF AAQPHVVHTS AVKTDGSGAY
CER2
CER3
CER1
51
SVGRGIADIT
RFGLGKADIT
LVGSGMYDIT
--*-*--***
GEAADCGMLG
GEAAEVGMMG
GAAAETGMLG
*-**--**-*
YGKSDQRTAG
YSSLEQKTAG
YAAS.QEVDG
*----*---*
IHQRLRSRAF
IHMRQWARAF
LHMRLYSRAF
-*-*---***
100
VFRDDSQDGD
VI.EEAASG.
VVAD..QKSG
*---------
CER2
CER3
CER1
101
ARLLLIVAEL
RRLVYVNTDL
KRVAMVTTDM
-*--------
PLPMQNVNEE
GMTFQAVHLK
GAMFPSITSA
----------
VLRRLADLYG
VLARLKAKYP
VVAKLQQKFG
*---*-----
DTYSEQNTLI
GVYDENNVML
DKYTPKNVLI
--*---*---
150
TATHTHAGPG
AATHTHSGPG
AATHTHVGNS
-*****-*--
CER2
CER3
CER1
151
GYCGYLLYNL
GFSHYAMYNL
GMSGDRLYQV
*------*--
.....TTSGF
.....SVLGF
AGADSTSAGY
--------*-
RPATFAAIVD
QEKTFNAIVD
DKKNFGTVVN
----*---*-
GIVESVEHAH
GIVRSIERAQ
GIVESISRAH
***-*---*-
200
ADVAPAEVSL
ARLQPGRLFY
TSLAPGTVQR
----*-----
CER2
CER3
CER1
201
SHGELYGASI
GSGELRNASR
SEGELKGATR
--***--*--
NRSPSAF..D
NRSLLSH..L
NRSLPAHRAN
***-------
RNPPADKAFF
KNP..DIAGY
KNPGSE....
-**-------
PKRVDPHTTL
EDGIDPQMSV
...VDSSMTQ
----*-----
250
VR.IDRGEAT
LSFVDANGEL
LEFRRSNGQA
----------
CER2
CER3
CER1
251
VGVIHFFATH
AGAISWFPVH
VGVLNWFAIH
-*----*--*
GTSMTNRNHL
STSMTNANHL
PTSFSRKFTK
-**-------
ISGDNKGFAA
ISPDNKGYAS
LSGDNKGYAS
-*-****-*-
YHWERTVGGA
YHWEHDV...
YMFEKQMGGD
*--*------
300
DYLAGQPDFI
...SRKSGFV
PDKAG..SFV
--------*-
CER2
CER3
CER1
301
AAFAQTNPGD
AAFAQTNAGN
AAFANSAVGD
****----*-
MSP.NVDGPL
LSP.NLN..L
VVPAQGNAHS
--*-------
SPEAPP.DRE
KPGSGPFDNE
APGYGGSSDE
-*-------*
FDNTRRTGLC
FDNTREIGLR
YHNTHVAGEA
--**---*--
350
QFEDAFTQLS
QFAKAY.EIA
QLGKA.RQLW
*---*-----
CER2
CER3
CER1
351
GAT..PIGAG
GQAQEEVLGE
AAQGQAQGGP
----------
IDARFTYVDL
LDSRFRFVDF
VDFRSRHIDL
-*-*----*-
GSVLVRGEYT
TRLPIRPEFT
RNYMVDAKYA
----------
PDGEERRTGR
.DGQPRQLCT
.GGKAVQLCK
--*-------
400
PMFGAGAMAG
AAIGTSLAAG
AARGFSFASG
---*-----*
CER2
CER3
CER1
401
.TDEGPGFH.
STEDGPGPL.
G.ENGPSKIP
----**----
GFRQG..RNP
GLEEG..NNP
GMYEGMTRDS
*---*-----
FW........
FL........
FSISDKIKKV
*---------
..DRLSR...
..SALGG...
IPSALGGLTR
----*-----
450
.AMYRL.ARP
.LLTGVPPQE
LAFAGVSALH
----------
CER2
CER3
CER1
451
TAAAQAPKGI
LVQCQAEKTI
QDKCHAEKPI
-----*-*-*
VMPARLPNRI
LADTG.NKKP
PLPTGA....
----------
HPFVQEIVPV
YPWTPTVLPI
WKMVSSVVQV
----------
QLVRIGRLYL
QMFRIGQLEL
QLVRVGNTAV
*--*-*----
500
IGIPGEPTIV
LGAPAEFTVM
LALPVEPTTV
---*-*-*--
Fig. 3. Alignment of Dermatophilus congolensis CDase (CER1), Mycobacterium CDase (CER2) and Pseudomonas CDase (CER3). Pileup
algorithm (Devereux et al., 1984) was used. Identical amino acid are indicated by a consensus symbol (asterisk). Gaps inserted into the
sequences are indicated by dots.
CER2
CER3
CER1
501
AGLRLRRMV.
AGVRIRRAVQ
ASRRLQERVA
*--*----*-
ASIVGADLAD
AASEAAGIRH
AELAGTGVNR
*---------
VLCVGYTNAY
VVFNGYANAY
VVIAGVANGY
*---*--*-*
IHYVTTPEEY
ASYVTTREEY
NGYLATREEY
--*--*-***
550
LEQRYEGGST
AAQEYEGGST
AAQHYEGAST
--*-***-**
CER2
CER3
CER1
551
LFGRWELCAL
LYGPWTQAAY
EFGPFEFAAF
--*-----*-
MQTVAELAEA
QQLFVDMAVA
EQEAAGLASA
-*-----*-*
MRDGRPV.TL
LRERLPVETS
MKKGAAVSDA
------*---
GRRP.RPTRE
AIAPDLSCCQ
ASPAGSFTAK
----------
600
LSWVRGAPAD
MNFQTGVVAD
TPARPGVLFD
-----*---*
CER2
CER3
CER1
601
....AGSFGA
DPYIGKSFGD
SKPAGQQFGQ
-------**-
VIAEPSATYR
VLQQPRESYR
VLGQPSQSYS
*---*---*-
PGQAVEAVFV
IGDKVTVAFV
AGQVASAVFR
-*------*-
SALPNNDLRR
TGHPKNDLRT
AGHPKNDYRT
---*-**-*-
650
GGTYLEVVR.
EKTFLEVVNI
MGSFLQVQR.
----*-*---
CER2
CER3
CER1
651
.REGASW.VR
GKDGKQTPVT
.QEGGQWK.T
---*------
IADDGDWATS
VATDNDWDTQ
VRTDRDWDTT
---*-**-*-
FRWQRQGRAG
YRWERVGISA
YAWKREGVAF
--*-*-*---
SHVSIRWDVP
SKATISWSIP
SRATVQWRIP
*-----*--*
700
GDTTPGQYRI
PGTEPGHYYI
KGTPAGTYRL
--*--*-*--
CER2
CER3
CER1
701
VHHGTARD.R
RHYGNAKNFW
VQTGDWKNAR
---*------
NGMLTAFSAT
TQKISEIGGS
GGKVSPYVGM
----------
731
TREFTVV~~~ ~
TRSFEVLGTT P
SRSFTVRZ~~ ~
-*-*-*-*** *
73
Fig. 3. (Continued ).
Acknowledgements
This work was supported by a Grant from the European Union Programme INCO-DC Genetic and
Immunological Control on Dermatophilosis contract
no. IC18-CT98-0334 (DGXII-SNRD). Special thanks
to Dr. Alberto Quesada, Department of Biochemistry,
University of Extremadura, for his suggestions for the
characterization of the gene, to Dr. Anne Masters, Department of Agriculture of Western Australia, Animal
Health Laboratories, South Perth, Australia, for the
D. chelonae reference strain and for Australian ovine
74
D. congolensis strains, and to Dr. K.H. Bhm, Institut fur Mikrobiologie und Tierseuchen, Tierarztlichen
Hochschule, Hannover, Germany, for providing German horse isolates of D. congolensis.
References
Altschul, S.F., Gish, W., Miller, W., Myers, W., Lipman, D.J.,
1990. Basic local alignment search tool. J. Mol. Biol. 215,
403410.
Ambrose, N.C., El Jack, M.A., McOrist, S., Boyd, R.,
1997. Electrophoretic and antigenic characterisation of
Dermatophilus congolensis extracellular products. Vet.
Microbiol. 59, 3751.
Ambrose, N.C., Mijinyawa, M.S., Hermoso de Mendoza, J., 1998.
Preliminary characterisation of extracellular serine proteases
of Dermatophilus congolensis isolates from cattle, sheep and
horses. Vet. Microbiol. 62, 321335.
Bos, J.D., Kapsenberg, M.L., Smitt, J.H., 1994. Pathogenesis of
atopic eczema. Lancet 343, 13381341.
Cousins, D.V., Wilton, S.D., Francis, B.R., 1991. Use of DNA
amplification for the rapid identification of Mycobacterium
bovis. Vet. Microbiol. 27, 187195.
Devereux, J., Haeberli, P., Smithies, O., 1984. A comprehensive
set of sequence analysis programs for the VAX. Nucl. Acids
Res. 12, 387395.
Gordon, M.A., 1964. The genus Dermatophilus. J. Bacteriol. 88,
509522.
Hamanaka, S., Asagami, C., Suzuki, M., Inagaki, F.,
Suzuki, A., 1989. Structure determination of glucosyl beta
1-N-omega-O-linoleoyl-acylsphigosines of human epidermis. J.
Biochem. 105, 684690.
Hnel, H., Kalisch, J., Keil, M., Marsch, W.C., Buslau, M., 1991.
Quantification of keratinolytic activity from Dermatophilus
congolensis. Med. Microbiol. Immunol. 180, 4551.
Henrik, N., Engelbrecht, J., Brunak, S., Von Heijne, G., 1997.
Identification of prokaryotic and eukaryotic signal peptides and
prediction of their cleavage sites. Prot. Eng. 10, 16.
Hermoso de Mendoza, J., Arenas, A., Alonso, J.M., Rey, J.M.,
Gil, M.C., Antn, J.M., Hermoso-de-Mendoza, M., 1993.
Enzymatic activities of Dermatophilus congolensis measured
by API ZYM. Vet. Microbiol. 37, 175179.
Imokawa, G., Akasaki, S., Hattori, M., Yoshizuka, N., 1986.
Selective recovery of deranged water-holding properties by
stratum corneum lipids. J. Investig. Dermatol. 87, 758761.
Johansson, M.L., Quednau, M., Molin, G., Ahrne, S., 1995.
Randomly amplified polymorphic DNA (RAPD) for rapid
typing of Lactobacillus plantarum strains. Lett. Appl.
Microbiol. 21, 155159.
Lampe, M.A., Burlingame, A.L., Whitney, J., Williams, M.L.,
Brown, B.E., Roitman, E., Elias, P.M., 1983. Human stratum