Global regulation of gene expression in response to cysteine availability in Clostridium perfringens.
BACKGROUND
Cysteine has a crucial role in cellular physiology and its synthesis is tightly controlled due to its reactivity. However, little is known about the sulfur metabolism and its regulation in clostridia compared with other firmicutes. In Clostridium perfringens, the two-component system, VirR/VirS, controls the expression of the ubiG operon involved in methionine to cysteine conversion in addition to the expression of several toxin genes. The existence of links between the C. perfringens virulence regulon and sulfur metabolism prompted us to analyze this metabolism in more detail.


RESULTS
We first performed a tentative reconstruction of sulfur metabolism in C. perfringens and correlated these data with the growth of strain 13 in the presence of various sulfur sources. Surprisingly, C. perfringens can convert cysteine to methionine by an atypical still uncharacterized pathway. We further compared the expression profiles of strain 13 after growth in the presence of cystine or homocysteine that corresponds to conditions of cysteine depletion. Among the 177 genes differentially expressed, we found genes involved in sulfur metabolism and controlled by premature termination of transcription via a cysteine specific T-box system (cysK-cysE, cysP1 and cysP2) or an S-box riboswitch (metK and metT). We also showed that the ubiG operon was submitted to a triple regulation by cysteine availability via a T-box system, by the VirR/VirS system via the VR-RNA and by the VirX regulatory RNA.In addition, we found that expression of pfoA (theta-toxin), nagL (one of the five genes encoding hyaluronidases) and genes involved in the maintenance of cell redox status was differentially expressed in response to cysteine availability. Finally, we showed that the expression of genes involved in [Fe-S] clusters biogenesis and of the ldh gene encoding the lactate dehydrogenase was induced during cysteine limitation.


CONCLUSIONS
Several key functions for the cellular physiology of this anaerobic bacterium were controlled in response to cysteine availability. While most of the genes involved in sulfur metabolism are regulated by premature termination of transcription, other still uncharacterized mechanisms of regulation participated in the induction of gene expression during cysteine starvation.
André
Gaelle
G
Institut Pasteur, Unité de Génétique des Génomes Bactériens and Unité des Bactéries Anaérobies et Toxines, 28 rue du Docteur Roux, 75015 Paris, France.
Haudecoeur
Elise
E
Monot
Marc
M
Ohtani
Kaori
K
Shimizu
Tohru
T
Dupuy
Bruno
B
Martin-Verstraete
Isabelle
I
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D003016:Clostridium perfringens / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D003545:Cysteine / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D013455:Sulfur / Q000378:metabolism
D001426:Bacterial Proteins; D013455:Sulfur; D003545:Cysteine
J Bacteriol. 2000 Jan;182(1):57-66
10613863
Nucleic Acids Res. 2005 Apr 14;33(7):2141-52
15831787
Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14895-900
11742080
J Bacteriol. 2010 Jul;192(13):3464-73
20418399
Mol Microbiol. 2002 Jan;43(1):257-65
11849553
Microbiol Immunol. 2000;44(6):525-8
10941936
Biochem Biophys Res Commun. 2007 Jan 12;352(2):351-9
17123467
Methods. 2001 Dec;25(4):402-8
11846609
J Bacteriol. 1996 May;178(9):2514-20
8626316
Nucleic Acids Res. 2004 Jun 23;32(11):3340-53
15215334
Nature. 1989 Sep 21;341(6239):245-8
2506452
Appl Environ Microbiol. 1986 Jul;52(1):169-72
16347104
J Bacteriol. 2005 Sep;187(17):6019-30
16109943
Appl Microbiol. 1975 Jan;29(1):1-6
162964
J Mol Microbiol Biotechnol. 2000 Jan;2(1):9-14
10937481
FEMS Microbiol Lett. 2001 Jul 10;201(1):29-35
11445163
Mol Microbiol. 2002 Apr;44(1):171-9
11967077
J Bacteriol. 2002 Sep;184(17):4681-9
12169591
Annu Rev Microbiol. 1998;52:333-60
9891801
J Bacteriol. 2003 Mar;185(6):1942-50
12618458
FEMS Microbiol Lett. 2002 Mar 19;209(1):113-8
12007663
J Bacteriol. 2004 Aug;186(15):4875-84
15262924
J Bacteriol. 2006 Mar;188(6):2184-97
16513748
Front Biosci. 2003 Jan 01;8:d20-31
12456320
FEBS Lett. 2007 Dec 11;581(29):5605-10
18005665
Microbiology (Reading). 2004 Jun;150(Pt 6):1649-1659
15184551
FEBS Lett. 2009 Jan 5;583(1):241-5
19084524
Mol Microbiol. 2009 Jul;73(2):194-211
19508281
J Bacteriol. 2007 Jan;189(1):187-97
17056751
J Bacteriol. 2002 May;184(10):2587-94
11976286
Biotechnol Adv. 2009 Nov-Dec;27(6):764-781
19539744
Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):996-1001
11792842
J Bacteriol. 2007 Oct;189(19):7032-44
17675375
Appl Environ Microbiol. 2009 Feb;75(4):1021-9
19124587
PLoS Genet. 2009 May;5(5):e1000497
19478995
J Bacteriol. 1996 Apr;178(7):1990-5
8606174
FEBS Lett. 2007 Jul 31;581(19):3598-607
17659286
J Biol Chem. 2008 Dec 19;283(51):35551-60
18974048
Microbiol Mol Biol Rev. 2008 Mar;72(1):110-25, table of contents
18322036
Science. 2001 Jul 13;293(5528):297-300
11452124
Microbiology (Reading). 2009 Jan;155(Pt 1):16-24
19118342
Curr Opin Microbiol. 2003 Apr;6(2):191-7
12732311
Curr Microbiol. 1998 Mar;36(3):131-5
9516540
Microbiol Mol Biol Rev. 2009 Mar;73(1):36-61
19258532
Adv Enzymol Relat Areas Mol Biol. 2000;74:129-84
10800595
Nat Chem Biol. 2009 Sep;5(9):625-7
19578333
BMC Genomics. 2008 Jul 14;9:330
18625071
J Bacteriol. 2008 Dec;190(23):7719-27
18790863
Antioxid Redox Signal. 2006 May-Jun;8(5-6):753-62
16771667
Anaerobe. 2010 Jun;16(3):258-64
19835966
Mol Microbiol. 2000 Feb;35(4):854-64
10692162
Nucleic Acids Res. 2003 Jun 15;31(12):3057-62
12799432
J Intern Med. 1999 Nov;246(5):425-54
10583714
Naturwissenschaften. 2006 Jun;93(6):259-66
16555095
Arch Microbiol. 1984 May;138(1):72-8
6742957
RNA. 2008 Apr;14(4):717-35
18359782
Mol Microbiol. 2006 May;60(4):1058-75
16677314
FEBS Lett. 2004 Aug 27;573(1-3):83-92
15327980
Methods. 2003 Dec;31(4):265-73
14597310
Nucleic Acids Res. 2008 Oct;36(18):5955-69
18812398