J. Biomedical Science and Engineering, 2011, 4, 70-75
doi:10.4236/jbise.2011.41009 Published Online January 2011 (http://www.SciRP.org/journal/jbise/
JBiSE
).
Published Online January 2011 in SciRes. http://www.scirp.org/journal/JBiSE
Analysis of the arginine biosynthetic gene cluster argCJBDFR
of Corynebacterium crenatum
Haitao Jiao1, Yong Yuan2, Yo nghua Xiong2, Xuelan Chen1
1College of life sciences, Jiangxi Normal University, Nanchang, China;
2State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.
Received 8 October 2010; revised 28 October 2010; accepted 8 November 2010.
ABSTRACT
Objective: Corynebacterium crenatum AS1.542, a
Gram-positive bacterium and indigenous nonpatho-
genic corynebacteria, is widely exploited for the in-
dustrial production of amino acids. The objective of
this paper is to clarify the genetic information of the
arginine biosynthetic pathway, and further more
contribute to the improvement of arginine produc-
tion. Methods: Polymerase chain reaction (PCR)
technology was employed for obtaining the arginine
biosynthetic gene sequence and softwares eg. Laser-
gene, BPROM, RNAshapes were used for the analysis
of obtained sequences. Results: Arginine bio-
synethetic gene cluster of C. crenatum, comprising
argJ, argB, argD, argF, argR and part of argC, has
been amplified and sequenced. The gene order has
been established as argCJBDFR, with a entire length
of 6.08kb. Conclusion: An internal promoter was
found in the upstream of argB gene, four argBDFR
ORFs are located in a same transcription unit, and
the transcripiton termination of argC gene is irrele-
vant with the rho-factor. Comparison with ornithine
acetyltransferase (coded by argJ gene) from C. glu-
tamate, ornithine acetyltransferase from C. crenatum
also belongs to the monofunctional enzymes.
Keywords: Corynebacte riu m crenatum; argCJBDFR
Sequence; Ornithine Acetyltransferase; argR Gene
1. INTRODUCTION
Arginine biosynthesis commences with the acetylation
of the amino group of glutamate (Figure 1). Eight en-
zymes coded by eight or nine genes take part in the
process of catalyzation, resulting the biotransformation
of glutamate into arginine [1]. The pathway of arginine
biosynthesis can be divided into two parts according to
two strategies evolved in the removal of the acetyl group.
One is called the “linear” pathway, in which argE gene
coded acetylornithinase catalyses the hydrolysis of
N-acetylornithine into the arginine precursor ornithine
and acetate; the other is called the “economic cyclic”
pathway, in which acetylornithine is catalyzed into or-
nithine and acetyl groups, and recycled with generation
of acetylglutamate by argJ gene coded ornithine acetyl-
transferase [2]. ArgJ has both acetylornithinase (coded
by argE) function and N-acetylglutamate synthase
(coded by argA) functions in the “cyclic” pathway. Lit-
eratures showed that Enterobacteriaceae and Sulfolobus
solfataricus [2,3] adopted the “linear” pathway in which
the metabolic flow is controlled by arginine-mediated
feedback inhibition of the first biosynthetic step； all the
other prokaryotes, including Methanogenic archaea,
Neisseria gonorrboese, members of the genus Bacillus
and the eukaryotic microbes, use the “cyclic” pathway in
which the metabolic flow was controlled by argin-
ine-mediated feedback inhibition of the second biosyn-
thetic step or by orthinine-mediated feedback inhibition
of the fifth step [2]. Although the argJ gene by itself
would thus be able to assure both the first and the fifth
steps of arginine biosynthesis in above mentioned or-
ganisms, there is genetic evidence for the existence of
the cloned ornithine acetyltransferase genes from Pseu-
domonas aeruginosa [4], Saccbaromyces cerevisiae [5],
Streptomyces coelicolor [6] and Corynebacterium glu-
tamicum complementing E. coli argE but not argA mu-
tants.
C. crenatum AS1.542, a Gram-positive bacterium and
indigenous nonpathogenic corynebacteria, is widely ex-
ploited for the industrial production of amino acids. The
genetic information of arginine biosynthetic pathway
was analyzed and clarified in this paper with the aim to
contribute to the improvement of arginine production.
2. MATERIALS AND METHODS
2.1. Reagent
All the primers were synthesized by Shanghai Biotech-

H. T. Jiao et al. / J. Biomedical Science and Engineering 4 (2011) 70-75
71
glutamate
↓ argA acetylglutamate synthase
acetylglutamate
↓ argB N-acetylglutamate kinase
acetylglutamate phosphate
↓ argC N-acetylglutamate semialdehyde dehyogenase
acetylglutamate semialdehyde
↓ argD N-acetyl-ornithine aminotransferase
glutamate
↓ acetyl ornithine
argJ ↓ ↓ argE N-acetylornithine aminotransferase
ornithine
acetylornithine
aminotransferase ↓ argI,F ornithine carbamoyltransferase
citrulline
↓ argG argininosuccinate synthetase
ornithine succinate
↓ argH argininosuccinase
arginine
Figure 1. The “linear” (in E. coli) and the “alternative cyclic” (in B. stearothermophilus
and C. glutamate) arginine biosynthesis pathways.
nology Corporation, China. Gel extraction kit and pGEM-
T-Easy vector were purchased from Promega, USA.
2.2. Bacterial Cultivation
C. crenatum and C. glutamicum were cultured in a rotary
shaker incubator at 150 rpm under 30°C in Luria-Bertani
(LB) medium.
2.3. DNA Manipulation, Amplification,
Sequencing and Analysis
Chromosomal DNA of C. crenatum was isolated as de-
scribed by Shengdong L [7]. Total genomic DNA (50 ng)
was used as a template for PCR amplification of
argCJBDFR gene cluster. The employed primers were
designed using the conserved sequences of C. glutamicum
ATCC 13032, C. diphtheriae gravis NCTC13129, C.
efficiens YS-314 and Mycobacterium tuberculosis CDC
1551. The primers were: sense-1 (5’-TCAAGGTTGCA
ATCGCAGGAGCC-3’), antisense-1 (5’-GCAACTCAC
CAATAAGACCAGTGG-3’), sense-2 (5’-CCGCAGCG
CCGTGTTTACACGTAACC-3’), antisense-2 (5’-GAC
AAGATTGTTGTCGTGAAATATG-3’), sense-3 (5’-AT
CTTTGGAATCATGCCGGAATC-3’), antisense-3 (5’-
TCTTCGTCGGTGATCACCAGCGG-3’), sense-4 (5’-
CATGCCAGATTCTGGCTGATCTGCAG-3’) and an-
tisense-4 (5’-GCAAGAACGATGCGGTTAGTCATG-3’),
respectively. The amplicons were purified using gel ex-
traction kit and sub-cloned into pGEM-T-Easy vector.
The selected clones were subjected to sequencing of
argCJBDFR gene cluster fragments with SP6 and T7
sequencing primers using ABI prism 3730 sequencer.
The sequence data were compiled, aligned and ana-
lyzed using Lasergene software (DNASTAR), Soft-
berry’s BPROM (www.softberry.com) and RNAshapes
WebServices (BiBiServ) et al.
3. RESULTS AND DISCUSSION
3.1. PCR Amplification
The results of PCR amplification were shown in Figure
2. The full-length of amplified DNA, aligned with
SeqMan function of Lasergene software, was 6080 bp.
The full-length DNA sequence alignment of C. crenatum
Figure 2. PCR amplification of tandem ar-
ginine biosynthetic genes (Lane 1: DL2000
Marker; lane 2, 3 4 and 5: argCJ, argJBD,
argDF and argFR, respectively).

H. T. Jiao et al. / J. Biomedical Science and Engineering 4 (2011) 70-75
72
showed a very high homology with the arginine biosyn-
thetic gene cluster: argCJBDFR of C. glutamicum ATCC
13032 by blastn analysis in NCBI. This result indicated
that the 6080 bp sequence of C. crenatum was the argin-
ine biosynthetic gene cluster. The acession number for
the sequence in Genbank is AY509864.
3.2. Sequence Analysis
Analysis of the nucleotide sequence revealed the pres-
ence of five intact open reading frames (ORFs): argJ,
argB, argD, argF, argR, and partial of argC ORF (shown
in Figure 3).
Sequence analysis of the gene cluster indicated that
the argB TAA termination coden was contiguous to the
initiation codon of the argD gene, the distance between
argD and argF was 13 bp, and argF gene was blocked
off argR by 3 bp. This phenomenon suggested that the
four ORFs located in the same transcription unit. Two
relatively long intergenic spacers were found in the
argC/argJ and argJ/argB, and a potential promoter re-
gion existing in the upstream of argB gene was doped
out, but there was no potential promoter existing in the
upstream of argJ gene. The argB upstream sequence was
shown in Figure 4. The interval between Sextama and
Pribnow shown in under-double-line is 15 bp. A pair of
inverse repeat sequence indicated by under-single-line is
presumed to be operator region, also known as Arg box
recognized by control protein.
The Arg box consensus were described as TNTGA
ATWWWWATTCANW in E. coli [8], CATGAATAAAA
ATKCAAK in B. subtilis [9] and AWTGCATRWWYAT
GCAWT in Streptomycetes [10] (where W = A or T, K =
G or T, R = A or G, Y = T or C, N = any base). In Addi-
tion, Binding of ArgR homologs to the sites similar to
ARG boxes has been reported in Salmonella typhi-
murium [13] and other Bacillus species (B. licheniformis
[11] and B. stearothermophilus [12]). The most popular
base of Arg boxes from the strains mentioned above
wereA and T, whereas G and C in C. crenatum (as
shown in Figure 4). The difference might be related with
the control of arginine biosynthesis of corynebacterium
and the distance of cognation.
A stem-loop structure was found in the downstream of
argC gene using RNAshapes tool. Two primary charac-
ters of rho-independent terminator were appeared: a re-
verse repeat sequence and the reverse repeat sequence
mostly composed with G and C. The argC terminator
region was shown in Figure 5. The downstream of rest
genes have no fixed features, which implied that the
transcription termination of the rest genes were relevant
with the rho-factor.
The C. crenatum argJ sequence, compared with blastp
software in NCBI, shares 98.5, 70, 79 and 53% identical
amino acids with the ornithine acetyltransferases
(OATase) of C. glutamicum [2], C. diphtheriae gravis
[14], C. efficiens [15] and M. tuberculosis [16], respec-
tively. Sakanyan et al. reported that the OATase of C.
glutamicum had only acetylorthine amidohydrolase
function but no transacetylation by cloning of argJ gene
for heterologous complementation of argA deficiency in
E. coli [2]. The CLUSTAL alignment indicated that the
similarity covered the whole argJ gene sequence be-
tween C. crenatum and C. glutamicum. The result indi-
cated that C. crenatum argJ coded OATase belongs to
monofunctional enzymes.
The C. glutamicum ArgJ molecular mass is 39.8 kDa,
approximately 3 kDa less than the other known bacterial
bifuctional OATases. Sakanyan et al held that the miss-
ing 11-12 amino acids at the N-terminus was connected
with the transacetylation deficiency via CLUSTAL
alignment among C. glutamicum, B. sterothermophilus,
B. subilis and Neisseria gonorrboeae [2]. In the present
Figure 3. Genetic map of the 6.08 Kb stretch of C. crenatum A.S1.542 DNA. The long ar-
rowheads indicated the orientation and location of the ORFs.
Figure 4. Promoter sequence of arg B gene.

H. T. Jiao et al. / J. Biomedical Science and Engineering 4 (2011) 70-75
73
Figure 5. The characters of transcription termination sequence
of argC gene.
paper, the OATases from 12 strains, containing five
OATases (from C. crenatum, C. glutamicum, C. diphteric,
C. efficiens and Streptomyces clavuligerus) reported no
transacetylation and seven bifunctional OATases, were
found that the absence of 11-12 amino acids at the
N-terminus had nothing to do with the bifunction (shown
in Figure 6).
A Blastp comparison shows that N-acetylglutamate
kinase (AGKase) polypeptide sequence coded by argB
gene of C. crenatum, 313 amino acids with a predicted
molecular mass of 34.6 kDa, shares approximately 95%,
63% and 48% identical amino acids with those gene of C.
glutamicum, Bifidobacterium longum [17] and N. men-
ingitides serogroup[18], respectively. AGKase belongs
to a member of Mg2+ activated superfamily. The locations
of kinases binding-ATP domain are shown in Figure 7.
According to a blastp comparison, N-aetylornithine
aminotransferase (AOATase) polypeptide sequence coded
by argD gene of C. crenatum shares approximately 96,
77.4, 61.5 and 52.2% identical amino acids with those of
C. glutamicum [2], C. efficiens [14], C. diphtheriae [15]
and M. tuberculosis [16], respectively. The C. crenatum
ArgF sequence shares 97.5, 84.95, 75.5 and 58.1% iden-
tical amino acids with the ornithine carbamoyltrans-
ferase from C.glutamicum, C. efficiens, C. diphtheriae
and M. tuberculosis, respectively.
The terminal gene in the cluster corresponds to argR,
which is a transcription factor in arginine metabolism.
The polypeptide sequence is composed with 172 amino
acid residues with a predicted molecular mass of 18.2
kDa. Blastn comparison shows that there are three nu-
cleotide differences between the argR of C. crenatum
and the argR of C. glutamicum, however, the two ArgR
sequences are 100% identical due to the codon degener-
acy. The C. crenatum ArgR sequence shares 71, 89 and
56% identical amino acids with those of C. efficiens, C.
diphtheriae and M. tuberculosis, respectively.
The ArgR, whose interspace configuration is winged
helix-turn-helix (wHTH), consists of a N-terminal
DNA-binding domain and a C-terminal oligomerization
domain joined by a hinge region [17,18]. It was reported
that the E. coli ArgR C-terminal domain contained an
arginine pocket defined in part by two aspartic acid
residues at positions 128 and 129 [13,19]. By CLUSTAL
alignment between the C. crenatum ArgR C-terminus
and the E. coli ArgR C-terminus, it was found that there
were two consecutive aspartic acid residues at positions
146 and 147 and eight sequential highly conserved
amino acid residues around the two aspartic acid resi-
dues in the C. crenatum ArgR C-terminus (shown in
Figure 8). Despite there is only 21.2% identical amino
acids between the Gram-positive C. crenatum ArgR and
the Gram-negative E. coli ArgR, the important conserved
MAE----------KG--ITAPKGFVASATTAGI-KASGNPDMALVVNQGPEFSAAAVFTR 47 C.crenatum OATase
MSS----------RG--VTAPQGFVAAGATAGI-KPSGNKDMALVVNQGPEFVGAAVFTR 47 C.diphteric OATase
MAQ----------TG--ITAPKGFVASATTAGI-KPSGKPDMALVVNQGPEYTAAAVFTR 47 C.efficiens OATase
MAE----------KG--ITAPKGFVASATTAGI-KASGNPDMALVVNQGPEFSAAAVFTR 47 C.glutamcium OATas e
MT---------------VTAPKGSTGGGCRRG-SKESGQPDLALVVNEGPRRAAAGVFTA 44 S. clavuligerus OATase
M----------KEIKGTIASPKGFLADAVHAQL-KYK-NLDLGLILSQVPA-AIAGVFTT 47 Lactococcus lactic OATase
MS---------------VTFAQGFSAAGVAAGISSVEGKKDLALVVNNGPLDAAAGVFTS 45 B. longum OATase
MTITKQTGQVTAVADGTVVTPEGFQAAGVNAGLRYS-KN-DLGVILCDVPA-SAAAVYTQ 57 B.stearothermopbilus OATase
M-IQLSEDQIVKVT-GDVSSPKGFQAKGVHCGLRYS-KK-DLGVIISETPA-VSAAVYTQ 55 B.subtilis OATase
MTDLAGTTRL—LRAQGVTAPAGFRAAGVAAGIKASGAL-DLALVFNEGPDYAAAGVFTR 58 M.tuberculosis OATase
MAVNLTEKTAEQLPDID-----GIALYTAQAGVKKPGHT-DLTLIAVAAGSTVGA-VFTT 54 N.meningitides serogroup OATase
MEIL----------DGKIELPKGFVASGVFAGIKRS-KK-DLALIYSERLANISA-VFTT 48 T.tengcongensis OATase
* * * *
* *
Figure 6. Comparison of N-terminal amino acid sequences of ornithine acetyltransferases by CLUSTAL
alignment. (Stars indicate the identical amino acid of all mentioned strains).

H. T. Jiao et al. / J. Biomedical Science and Engineering 4 (2011) 70-75
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###
C. crenatum-AGKase AVRGGVSAAHVIDGRIAHSVLLELLTMGG IGTMVL 293
C. glutamicum-AGKase AVRGGVSAAHVIDGRIAHSVLLELLTMGG IGTMVL 293
C. efficiens-AGKase AVRGGVNAAHVIDGRIAHSVLLELLTMGG IGTMVL 293
C. diphteric-AGKase AVI HGVSAAHV IDGRVAHSVLLELLTSGGVGTMVV 293
E. coli-AGKase VNADQAATALAATLGADLILLSDVSGILDGKGQRIA 194
M. bovis-AGKase LRAVIGGVPSAHIIDGRVTHCVLVELFTDAGTGTKVV 292
Figure 7. AGKase shows feature of putative ATP-binding domain protein. (# indicates a putative
ATP-binding site).
##
E. coli-ArgR KNLVLDIDYNDAVVVIHTSFGAAQLITARLLDS L GKAEGI LGTI AGDDT
C. crenatum-ArgR DELLVSTDHSGNI AMLRTPPGAAQYLASFI DRRVGLKE-VV GTIAGDDT
Consensus L D T GAAQ A D G E GTIAGDDT
E. coli-ArgR I FTTPANG FTVKALYEAILELFDQEL 156
C. crenatum-ArgR VFVLARDPLTGKELGELLSG- -RTT 171
Consensus F K L E
Figure 8. Comparison of amino acids sequence of C-terminal domain of ArgR between C. cre-
natum and E. coli (# indicates asparagine).
region binding arginine is quite consistent. The result
implied that the two genes originated by a duplication of
some common ancestral gene. Although it was modified
and changed by different host in far-flung evolvement
course, the partial region determining function still kept
highly conservative.
6. ACKNOWLEDGEMENTS
The authors are thankful to the financial support from the National
Natural Science Foundation of China (No. 30960012).
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