citB

citB
168

aconitase, trigger enzyme

Locus
BSU_18000
Molecular weight
99.14 kDa
Isoelectric point
4.9
Protein length
Gene length
Function
TCA cycle
Product
aconitase, trigger enzyme
Essential
no
E.C.
4.2.1.3
Synonyms
citB

Genomic Context

List of homologs in different organisms, belongs to COG1048 (Galperin et al., 2021)

This gene is a member of the following regulons

SigA regulon, CcpA regulon, CodY regulon, CcpC regulon, CitB regulon

Gene
Coordinates
1,926,680 1,929,409
Phenotypes of a mutant
glutamate auxotrophy and a defect in sporulation PubMed
The protein
Catalyzed reaction/ biological activity
Citrate --> isocitrate (according to UniProt)
3-hydroxybutane-1,2,3-tricarboxylate --> 2-methyl-cis-aconitate + H2O (according to UniProt)
Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster PubMed
2-methylaconitate --> 2-methyl-isocitrate in the methylcitric acid cycle PubMed
Protein family
aconitase/IPM isomerase family (with LeuC, according to UniProt)
FeS cluster PubMed
Structure
2B3X (PDB) (the human enzyme, 53% identity) PubMed
Additional information
CitB is degraded in the forespore using MdfA as the adaptor protein PubMed
B. subtilis aconitase is both an enzyme and an RNA binding protein (moonlighting protein) PubMed
extensive information on the structure and enzymatic properties of CitB can be found at Proteopedia
belongs to the 100 most abundant proteins PubMed
Expression and Regulation
Operons
Genes
Description
Regulation
expressed upon transition into the stationary phase (AbrB) PubMed, indirect negative regulation by AbrB PubMed
Regulatory mechanism
CodY: repression, PubMed, in codY regulon
CcpC: repression, (molecular inducer: citrate) PubMed PubMed, in ccpC regulon
CcpA: repression, PubMed, in ccpA regulon
Sigma factors
SigA: sigma factor, PubMed, in sigA regulon
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citByneN

2025-07-20 08:02:56

ghost

181

11c3575e19719d9d98495e9324e23aee6d346029

4D8AE4853A402B931A1A3D2C11A2983642117BB6

Other regulations
FsrA: translation repression, PubMed
Biological materials
Mutant
GP1275 (citB::erm), available in Jörg Stülke's lab
GP1441 (citB::spec), available in Jörg Stülke's lab
1A999 (citB::spec), PubMed, available at BGSC
GP2338 (citB::kan, Cre-recombinase is integrated in sacA), available in Jörg Stülke's lab
GP2339 (citB::lox72, Cre-recombinase is integrated in sacA), available in Jörg Stülke's lab
BKE18000 (citB::erm trpC2) available at BGSC, PubMed, upstream reverse: _UP1_CATTCTCCAAAATCCCCCTT, downstream forward: _UP4_TGATGAATCAATAGGAAGAG
BKK18000 (citB::kan trpC2) available at BGSC, PubMed, upstream reverse: _UP1_CATTCTCCAAAATCCCCCTT, downstream forward: _UP4_TGATGAATCAATAGGAAGAG
Expression vectors
pFM1, expression of CitB with a cleavable His6-tag at the C-terminus in E. coli, based on pBAD30, available in Jörg Stülke's lab PubMed
pGP939, expression in E. coli, based on pBluescript, available in Jörg Stülke's lab
pGP1810, expression of Strep-CitB in E. coli, based on pGP172, available in Jörg Stülke's lab
Two-hybrid system
B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab
FLAG-tag construct
GP1144 citB-3xFLAG spc (based on pGP1331), available in Jörg Stülke's lab
GP1145 citB-3xFLAG kan, available in Jörg Stülke's lab
LacZ fusion
pGP700 (cat, based on pAC5]), available in Jörg Stülke's lab
Antibody
available in Linc Sonenshein's lab
GFP fusion
GP1434 (spc, based on pGP1870), available in Jörg Stülke's lab
Labs working on this gene/protein
Linc Sonenshein, Tufts University, Boston, MA, USA Homepage
Jörg Stülke, University of Göttingen, Germany Homepage
References
Reviews
Ul Haq I, Müller P, Brantl SIntermolecular Communication in Bacillus subtilis: RNA-RNA, RNA-Protein and Small Protein-Protein Interactions.Frontiers in molecular biosciences. 2020; 7:178. PMID: 32850966
Volz K The functional duality of iron regulatory protein 1. Current opinion in structural biology. 2008 Feb; 18(1):106-11. doi:10.1016/j.sbi.2007.12.010. PMID:18261896
Commichau FM, Stülke J Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression. Molecular microbiology. 2008 Feb; 67(4):692-702. . PMID:18086213
Kiley PJ, Beinert H The role of Fe-S proteins in sensing and regulation in bacteria. Current opinion in microbiology. 2003 Apr; 6(2):181-5. . PMID:12732309
Switzer RL Non-redox roles for iron-sulfur clusters in enzymes. BioFactors (Oxford, England). 1989 Dec; 2(2):77-86. . PMID:2696478
Original Publications
Riley EP, Lyda JA, Reyes-Matte O, Sugie J, Kasu IR, Enustun E, Armbruster E, Ravishankar S, Isaacson RL, Camp AH, Lopez-Garrido J, Pogliano KDevelopmentally-regulated proteolysis by MdfA and ClpCP mediates metabolic differentiation during Bacillus subtilis sporulation.bioRxiv : the preprint server for biology. 2024 Nov 26; . PMID: 39651166
O'Reilly FJ, Graziadei A, Forbrig C, Bremenkamp R, Charles K, Lenz S, Elfmann C, Fischer L, Stülke J, Rappsilber JProtein complexes in cells by AI-assisted structural proteomics.Molecular systems biology. 2023 Feb 23; :e11544. PMID: 36815589
Reddick JJ, Sirkisoon S, Dahal RA, Hardesty G, Hage NE, Booth WT, Quattlebaum AL, Mills SN, Meadows VG, Adams SLH, Doyle JS, Kiel BE First Biochemical Characterization of a Methylcitric Acid Cycle from Bacillus subtilis strain 168. Biochemistry. 2017 Sep 28; . doi:10.1021/acs.biochem.7b00778. PMID:28956599
Pechter KB, Meyer FM, Serio AW, Stülke J, Sonenshein AL Two roles for aconitase in the regulation of tricarboxylic acid branch gene expression in Bacillus subtilis. Journal of bacteriology. 2013 Apr; 195(7):1525-37. doi:10.1128/JB.01690-12. PMID:23354745
Mittal M, Pechter KB, Picossi S, Kim HJ, Kerstein KO, Sonenshein AL Dual role of CcpC protein in regulation of aconitase gene expression in Listeria monocytogenes and Bacillus subtilis. Microbiology (Reading, England). 2013 Jan; 159(Pt 1):68-76. doi:10.1099/mic.0.063388-0. PMID:23139400
Smaldone GT, Revelles O, Gaballa A, Sauer U, Antelmann H, Helmann JD A global investigation of the Bacillus subtilis iron-sparing response identifies major changes in metabolism. Journal of bacteriology. 2012 May; 194(10):2594-605. doi:10.1128/JB.05990-11. PMID:22389480
Brown CT, Fishwick LK, Chokshi BM, Cuff MA, Jackson JM, Oglesby T, Rioux AT, Rodriguez E, Stupp GS, Trupp AH, Woollcombe-Clarke JS, Wright TN, Zaragoza WJ, Drew JC, Triplett EW, Nicholson WL Whole-genome sequencing and phenotypic analysis of Bacillus subtilis mutants following evolution under conditions of relaxed selection for sporulation. Applied and environmental microbiology. 2011 Oct; 77(19):6867-77. doi:10.1128/AEM.05272-11. PMID:21821766
Albrecht AG, Landmann H, Nette D, Burghaus O, Peuckert F, Seubert A, Miethke M, Marahiel MA The frataxin homologue Fra plays a key role in intracellular iron channeling in Bacillus subtilis. Chembiochem : a European journal of chemical biology. 2011 Sep 05; 12(13):2052-61. doi:10.1002/cbic.201100190. PMID:21744456
Gao W, Dai S, Liu Q, Xu H, Bai Y, Qiao M Effect of site-directed mutagenesis of citB on the expression and activity of Bacillus subtilis aconitase. Mikrobiologiia.; 79(6):774-8. . PMID:21446632
Gao W, Dai S, Liu Q, Xu H, Qiao M CitB mutation increases the alkaline protease productivity in Bacillus subtilis. The Journal of general and applied microbiology. 2010 Oct; 56(5):403-7. . PMID:21099137
Meyer FM, Gerwig J, Hammer E, Herzberg C, Commichau FM, Völker U, Stülke J Physical interactions between tricarboxylic acid cycle enzymes in Bacillus subtilis: evidence for a metabolon. Metabolic engineering. 2011 Jan; 13(1):18-27. doi:10.1016/j.ymben.2010.10.001. PMID:20933603
Chumsakul O, Takahashi H, Oshima T, Hishimoto T, Kanaya S, Ogasawara N, Ishikawa S Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation. Nucleic acids research. 2011 Jan; 39(2):414-28. doi:10.1093/nar/gkq780. PMID:20817675
Albrecht AG, Netz DJ, Miethke M, Pierik AJ, Burghaus O, Peuckert F, Lill R, Marahiel MA SufU is an essential iron-sulfur cluster scaffold protein in Bacillus subtilis. Journal of bacteriology. 2010 Mar; 192(6):1643-51. doi:10.1128/JB.01536-09. PMID:20097860
Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. Proceedings of the National Academy of Sciences of the United States of America. 2008 Aug 19; 105(33):11927-32. doi:10.1073/pnas.0711752105. PMID:18697947
Serio AW, Sonenshein AL Expression of yeast mitochondrial aconitase in Bacillus subtilis. Journal of bacteriology. 2006 Sep; 188(17):6406-10. . PMID:16923908
Serio AW, Pechter KB, Sonenshein AL Bacillus subtilis aconitase is required for efficient late-sporulation gene expression. Journal of bacteriology. 2006 Sep; 188(17):6396-405. . PMID:16923907
Dupuy J, Volbeda A, Carpentier P, Darnault C, Moulis JM, Fontecilla-Camps JC Crystal structure of human iron regulatory protein 1 as cytosolic aconitase. Structure (London, England : 1993). 2006 Jan; 14(1):129-39. . PMID:16407072
Blencke HM, Reif I, Commichau FM, Detsch C, Wacker I, Ludwig H, Stülke J Regulation of citB expression in Bacillus subtilis: integration of multiple metabolic signals in the citrate pool and by the general nitrogen regulatory system. Archives of microbiology. 2006 Mar; 185(2):136-46. . PMID:16395550
Eymann C, Dreisbach A, Albrecht D, Bernhardt J, Becher D, Gentner S, Tam le T, Büttner K, Buurman G, Scharf C, Venz S, Völker U, Hecker M A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics. 2004 Oct; 4(10):2849-76. . PMID:15378759
Blencke HM, Homuth G, Ludwig H, Mäder U, Hecker M, Stülke J Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metabolic engineering. 2003 Apr; 5(2):133-49. . PMID:12850135
Kim HJ, Kim SI, Ratnayake-Lecamwasam M, Tachikawa K, Sonenshein AL, Strauch M Complex regulation of the Bacillus subtilis aconitase gene. Journal of bacteriology. 2003 Mar; 185(5):1672-80. . PMID:12591885
Williams CH, Stillman TJ, Barynin VV, Sedelnikova SE, Tang Y, Green J, Guest JR, Artymiuk PJ E. coli aconitase B structure reveals a HEAT-like domain with implications for protein-protein recognition. Nature structural biology. 2002 Jun; 9(6):447-52. . PMID:11992126
Jourlin-Castelli C, Mani N, Nakano MM, Sonenshein AL CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis. Journal of molecular biology. 2000 Jan 28; 295(4):865-78. . PMID:10656796
Alén C, Sonenshein AL Bacillus subtilis aconitase is an RNA-binding protein. Proceedings of the National Academy of Sciences of the United States of America. 1999 Aug 31; 96(18):10412-7. . PMID:10468622
Nakano MM, Zuber P, Sonenshein AL Anaerobic regulation of Bacillus subtilis Krebs cycle genes. Journal of bacteriology. 1998 Jul; 180(13):3304-11. . PMID:9642180
Craig JE, Ford MJ, Blaydon DC, Sonenshein AL A null mutation in the Bacillus subtilis aconitase gene causes a block in Spo0A-phosphate-dependent gene expression. Journal of bacteriology. 1997 Dec; 179(23):7351-9. . PMID:9393699
Fisher SH, Magasanik B 2-Ketoglutarate and the regulation of aconitase and histidase formation in Bacillus subtilis. Journal of bacteriology. 1984 Apr; 158(1):379-82. . PMID:6143742
Rosenkrantz MS, Dingman DW, Sonenshein AL Bacillus subtilis citB gene is regulated synergistically by glucose and glutamine. Journal of bacteriology. 1985 Oct; 164(1):155-64. . PMID:2413006
Fouet A, Jin SF, Raffel G, Sonenshein AL Multiple regulatory sites in the Bacillus subtilis citB promoter region. Journal of bacteriology. 1990 Sep; 172(9):5408-15. . PMID:2118511
Fouet A, Sonenshein AL A target for carbon source-dependent negative regulation of the citB promoter of Bacillus subtilis. Journal of bacteriology. 1990 Feb; 172(2):835-44. . PMID:2105305

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