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Metabolism

Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation

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  • Author: John E. Cronan1
  • Editors: Valley Stewart2, Tadhg Begley3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Departments of Microbiology and Biochemistry, University of Illinois, Urbana, IL 61801; 2: University of California—Davis, Davis, CA; 3: Texas A&M University, College Station, TX
  • Received 19 November 2012 Accepted 01 November 2013 Published 06 January 2014
  • Address correspondence to John E. Cronan j-cronan@life.uiuc.edu
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  • Abstract:

    Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as “swinging arms” that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like “arm” of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise, and the BioH esterase is responsible for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl acyl carrier protein of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyltransferase followed by sulfur insertion at carbons C-6 and C-8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and, thus, there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate proteins.

  • Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012

Key Concept Ranking

Lipoic Acid Synthesis
0.4891802
Lipoic Acid Synthase
0.4366342
Fatty Acid Biosynthesis
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Amino Acid Synthesis
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Article Version

This article is an updated version of the following content:

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266. Hermes FA, Cronan JE. 2009. Scavenging of cytosolic octanoic acid by mutant LplA lipoate ligases allows growth of Escherichia coli strains lacking the LipB octanoyltransferase of lipoic acid synthesis. J Bacteriol 191:6796–6803. [PubMed][CrossRef]
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/content/journal/ecosalplus/10.1128/ecosalplus.ESP-0001-2012
2014-01-06
2017-05-01

Abstract:

Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as “swinging arms” that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like “arm” of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise, and the BioH esterase is responsible for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl acyl carrier protein of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyltransferase followed by sulfur insertion at carbons C-6 and C-8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and, thus, there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate proteins.

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Figures

Image of Figure 1
Figure 1

(A) All biotin carbon atoms are numbered, as are the relevant carbons of the other molecules. (B) Stereochemistry of biotin and lipoic acid showing that both molecules have nonplanar structures. The lipoic acid dithiolane ring would emerge from and protrude below the plane of the page, whereas biotin has a chair structure (the viewer is looking at the back of the chair). Note that lipoic acid structure is rotated relative to that in panel A to conform with the Cahn-Ingold-Prelog rules, and, since biotin has three chiral centers, the hydrogen atoms attached to carbon atoms 7 and 10 can be depicted as either above or below the plane of the page depending on the chiral center chosen as primary (the ring centers were chosen in this depiction). For simplicity, the stereochemistry will not be given (except as relevant) in the subsequent figures of this review. doi:10.1128/ecosalplus.ESP-0001-2012.f1

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Figure 2

The current pathway of biotin synthesis in doi:10.1128/ecosalplus.ESP-0001-2012.f2

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Figure 3

The BioD reaction. doi:10.1128/ecosalplus.ESP-0001-2012.f3

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Figure 4

For simplicity, only DTB carbon atoms 6, 7, 9, and 10 ( Fig. 1 ) are shown, of which only carbons 6 and 9 are labeled. The reaction is shown as proceeding with the initial attack on C-9 because a derivative of DTB carrying a thiol group on C-9 has been shown to be converted to biotin both in vitro and in vivo ( 56 , 260 ) and the crystal structure ( 24 ) shows C-9 in an appropriate position for the primary sulfur insertion. doi:10.1128/ecosalplus.ESP-0001-2012.f4

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Image of Figure 5
Figure 5

BirA is represented by green ovals, biotin by black circles, the AMP moiety by red pentagons, AccB by dark blue ovals, and AccC by light blue crescents. The arrows denote transcription from the leftward and rightward promoters. (A to C) BirA switches from the biotin ligation function to the repressor function in response to the intracellular biotin requirement, which is monitored by the level of unbiotinylated AccB. If the levels of unbiotinylated AccB are high, the protein functions as a biotin ligase. Once the unbiotinylated AccB has been converted to the biotinylated form, the bio-AMP is no longer consumed and remains bound to BirA. This liganded form of BirA accumulates to levels sufficiently high to form dimers that fully occupy the operator, resulting in transcriptional repression of the biotin biosynthetic genes. (D) Overproduction of AccC ties up unbiotinylated AccB into a complex that is a poor biotinylation substrate. Therefore, high levels of the liganded form of BirA accumulate, resulting in repression of operon transcription. doi:10.1128/ecosalplus.ESP-0001-2012.f5

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Figure 6

(A) The BirA structure is that of the protein liganded with a bio-AMP analogue (which for simplicity was omitted) ( 235 ). (B) The boxed region is the operator to which a BirA dimer binds. and are the promoters of the and transcriptional units, respectively. The −10 and −35 promoter regions are denoted by underlines. doi:10.1128/ecosalplus.ESP-0001-2012.f6

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Figure 7

This is the general reaction of biotin protein ligases ( 38 ). The lipoic acid ligase LplA has the same reaction mechanism given substitution of lipoic acid for biotin. doi:10.1128/ecosalplus.ESP-0001-2012.f7

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Image of Figure 8
Figure 8

(A) The innermost lipoyl domain of PDH. (B) The BCCP biotinyl domain of acetyl-CoA carboxylase. The images are MOLSCRIPT drawings from the NMR data of Jones and coworkers ( 177 ) and the diffraction data of Athappilly and Hendrickson ( 193 ), respectively. doi:10.1128/ecosalplus.ESP-0001-2012.f8

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Image of Figure 9
Figure 9

The thioester linkage of octanoic acid attached to the thiol of the 4′-phosphopantheteine group of ACP (the product of fatty acid synthesis) is attacked by the ε-amino group of the target lysine of a lipoyl domain, resulting in the modified protein plus the free thiol form of ACP. The enzyme also uses lipoyl-ACP, although this is thought to be of no physiological importance. The reaction proceeds through an octanoyl-LipB acyl enzyme intermediate (not shown). doi:10.1128/ecosalplus.ESP-0001-2012.f9

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Image of Figure 10
Figure 10

The rounded rectangle denotes an cell. Exogenous lipoic acid or octanoic acid enters by diffusion and is attached to the 2-oxoacid lipoyl domains and to H protein by LplA. The domains modified with exogenously derived octanoate can be converted to lipoyl domains by LipA, although this is probably not a reaction of physiological significance, because high levels of octanoic acid are required for significant modification by this route. In contrast, LplA-catalyzed attachment of lipoate is very efficient and provides a salvage or scavenging pathway for utilization of exogenous lipoic acid and seems likely to be physiologically significant. The major (and probably sole) route of lipoic acid synthesis is LipB-catalyzed transfer of octanoate from octanoyl-ACP to the 2-oxoacid lipoyl domains and H protein, followed by LipA-catalyzed sulfur insertion to give lipoate. doi:10.1128/ecosalplus.ESP-0001-2012.f10

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Figure 11

The bypass pathway accounting for the growth of mutants on octanoate is shown in the upper-right cartoon. The experimental protocol scheme and mass spectral data for testing the pathway are also shown. In the left cartoon, octanoylation of the lipoyl domain by endogenously synthesized octanoyl moieties is blocked by a mutation, and the cells use LplA and exogenously supplied octanoate to octanoylate the domain. LipA is also blocked so deuterated lipoylated domain is not made. Following accumulation of the deuterated octanoyl domain, LipA function is restored (right cartoon). Following incubation to allow lipoate synthesis, the cells were harvested and the modified domains were purified and then analyzed by electrospray mass spectrometry. Note the accumulation of deuterated lipoylated domain (D-Lip) in the right hand spectrum and that the mass change between deuterated octanoylated domain (D-C8) and D-Lip is 60 mass units, indicating the loss of two deuterons and the gain of two sulfur atoms. For details, see reference 201 . doi:10.1128/ecosalplus.ESP-0001-2012.f11

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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Figure 12

The canonical SAM radical [4Fe-4S] cluster of LipA reduces SAM to generate the deoxyadenosine radical (5′-Ado) as seen previously in the BioB reaction ( Fig. 4 ). The radical then removes a hydrogen atom from the C-6 methylene of the octanoate moiety of an octanoyl domain (Oct-E2 on the figure) ( 229 ) to give a carbon radical that then attacks the lipoyl synthase-specific [4Fe-4S] cluster and abstracts a reduced sulfur atom. This process is repeated at the methyl carbon (C-8) to give lipoyl domain (Lip-E2, probably as the dihydrolipoyl form due to the strongly reducing conditions under which the reaction proceeds). doi:10.1128/ecosalplus.ESP-0001-2012.f12

Citation: Cronan J. 2014. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0001-2012
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