Browsing Pathways

The virB operon is the largest operon within the virulence regulon, consisting of 11 genes, virB1 to virB11, and is responsible for transferring T-DNA and effector proteins from the bacterium into the plant cell during infection. VirB1 encodes a lytic transglycosylase that degrades the bacterial peptidoglycan cell wall, facilitating insertion and assembly of T4SS. virB2 encodes the major pilin subunit, which is processed and polymerized to form the T-pilus, which is essential for DNA transfer to the plant cell. VirB3 encodes an inner membrane protein necessary for T-DNA secretion and it interacts with virb4 to facilitate formation of the T-pilus. virB4 and VirB11 encode ATPases that generates energy necessary for T-DNA transport across the membrane. VirB5 forms the minor pilin subunit of the T-pilus. virB6 encodes an inner mermbrane protein involved in the transport of virulence factors through the T4SS and also stabilizes virB5 and virB3 and virB7 formation. virB7 encodes an outer membrane lipoprotein, which together with virB9 anchor the T4SS to the bacterial outer membrane. VirB8 encodes a membrane protein that serves as a scaffold for T4SS assembly. virB9 encodes an outer membrane-associated protein that is part of the T4SS channel and lastly, virB10 encodes a transmembrane protein that forms part of the channel through which T-DNA as well as virB2 and virB5 factors are translocated.

Cardiolipin (CL) is an important component of the inner mitochondrial membrane where it constitutes about 20% of the total lipid composition. It is essential for the optimal function of numerous enzymes that are involved in mitochondrial energy metabolism (Wikipedia). Cardiolipin biosynthesis occurs mainly in the mitochondria, but there also exists an alternative synthesis route for CDP-diacylglycerol that takes place in the endoplasmic reticulum. This second route may supplement this pathway. All membrane-localized enzymes are coloured dark green in the image. First, dihydroxyacetone phosphate (or glycerone phosphate) from glycolysis is used by the cytosolic enzyme glycerol-3-phosphate dehydrogenase [NAD(+)] to synthesize sn-glycerol 3-phosphate. Second, the mitochondrial outer membrane enzyme glycerol-3-phosphate acyltransferase esterifies an acyl-group to the sn-1 position of sn-glycerol 3-phosphate to form 1-acyl-sn-glycerol 3-phosphate (lysophosphatidic acid or LPA). Third, the enzyme 1-acyl-sn-glycerol-3-phosphate acyltransferase converts LPA into phosphatidic acid (PA or 1,2-diacyl-sn-glycerol 3-phosphate) by esterifying an acyl-group to the sn-2 position of the glycerol backbone. PA is then transferred to the inner mitochondrial membrane to continue cardiolipin synthesis. Fourth, magnesium-dependent phosphatidate cytidylyltransferase catalyzes the conversion of PA into CDP-diacylglycerol. Fifth, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase synthesizes phosphatidylglycerophosphate (PGP). Sixth, phosphatidylglycerophosphatase and protein-tyrosine phosphatase dephosphorylates PGP to form phosphatidylglycerol (PG). Last, cardiolipin synthase catalyzes the synthesis of cardiolipin by transferring a phosphatidyl group from a second CDP-diacylglycerol to PG. It requires a divalent metal cation cofactor.

Cardiolipin (CL) is an important component of the inner mitochondrial membrane where it constitutes about 20% of the total lipid composition. It is essential for the optimal function of numerous enzymes that are involved in mitochondrial energy metabolism (Wikipedia). Cardiolipin biosynthesis occurs mainly in the mitochondria, but there also exists an alternative synthesis route for CDP-diacylglycerol that takes place in the endoplasmic reticulum. This second route may supplement this pathway. All membrane-localized enzymes are coloured dark green in the image. First, dihydroxyacetone phosphate (or glycerone phosphate) from glycolysis is used by the cytosolic enzyme glycerol-3-phosphate dehydrogenase [NAD(+)] to synthesize sn-glycerol 3-phosphate. Second, the mitochondrial outer membrane enzyme glycerol-3-phosphate acyltransferase esterifies an acyl-group to the sn-1 position of sn-glycerol 3-phosphate to form 1-acyl-sn-glycerol 3-phosphate (lysophosphatidic acid or LPA). Third, the enzyme 1-acyl-sn-glycerol-3-phosphate acyltransferase converts LPA into phosphatidic acid (PA or 1,2-diacyl-sn-glycerol 3-phosphate) by esterifying an acyl-group to the sn-2 position of the glycerol backbone. PA is then transferred to the inner mitochondrial membrane to continue cardiolipin synthesis. Fourth, magnesium-dependent phosphatidate cytidylyltransferase catalyzes the conversion of PA into CDP-diacylglycerol. Fifth, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase synthesizes phosphatidylglycerophosphate (PGP). Sixth, phosphatidylglycerophosphatase and protein-tyrosine phosphatase dephosphorylates PGP to form phosphatidylglycerol (PG). Last, cardiolipin synthase catalyzes the synthesis of cardiolipin by transferring a phosphatidyl group from a second CDP-diacylglycerol to PG. It requires a divalent metal cation cofactor.

Cardiolipin (CL) is an important component of the inner mitochondrial membrane where it constitutes about 20% of the total lipid composition. It is essential for the optimal function of numerous enzymes that are involved in mitochondrial energy metabolism (Wikipedia). Cardiolipin biosynthesis occurs mainly in the mitochondria, but there also exists an alternative synthesis route for CDP-diacylglycerol that takes place in the endoplasmic reticulum. This second route may supplement this pathway. All membrane-localized enzymes are coloured dark green in the image. First, dihydroxyacetone phosphate (or glycerone phosphate) from glycolysis is used by the cytosolic enzyme glycerol-3-phosphate dehydrogenase [NAD(+)] to synthesize sn-glycerol 3-phosphate. Second, the mitochondrial outer membrane enzyme glycerol-3-phosphate acyltransferase esterifies an acyl-group to the sn-1 position of sn-glycerol 3-phosphate to form 1-acyl-sn-glycerol 3-phosphate (lysophosphatidic acid or LPA). Third, the enzyme 1-acyl-sn-glycerol-3-phosphate acyltransferase converts LPA into phosphatidic acid (PA or 1,2-diacyl-sn-glycerol 3-phosphate) by esterifying an acyl-group to the sn-2 position of the glycerol backbone. PA is then transferred to the inner mitochondrial membrane to continue cardiolipin synthesis. Fourth, magnesium-dependent phosphatidate cytidylyltransferase catalyzes the conversion of PA into CDP-diacylglycerol. Fifth, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase synthesizes phosphatidylglycerophosphate (PGP). Sixth, phosphatidylglycerophosphatase and protein-tyrosine phosphatase dephosphorylates PGP to form phosphatidylglycerol (PG). Last, cardiolipin synthase catalyzes the synthesis of cardiolipin by transferring a phosphatidyl group from a second CDP-diacylglycerol to PG. It requires a divalent metal cation cofactor.

Cardiolipin (CL) is an important component of the inner mitochondrial membrane where it constitutes about 20% of the total lipid composition. It is essential for the optimal function of numerous enzymes that are involved in mitochondrial energy metabolism (Wikipedia). Cardiolipin biosynthesis occurs mainly in the mitochondria, but there also exists an alternative synthesis route for CDP-diacylglycerol that takes place in the endoplasmic reticulum. This second route may supplement this pathway. All membrane-localized enzymes are coloured dark green in the image. First, dihydroxyacetone phosphate (or glycerone phosphate) from glycolysis is used by the cytosolic enzyme glycerol-3-phosphate dehydrogenase [NAD(+)] to synthesize sn-glycerol 3-phosphate. Second, the mitochondrial outer membrane enzyme glycerol-3-phosphate acyltransferase esterifies an acyl-group to the sn-1 position of sn-glycerol 3-phosphate to form 1-acyl-sn-glycerol 3-phosphate (lysophosphatidic acid or LPA). Third, the enzyme 1-acyl-sn-glycerol-3-phosphate acyltransferase converts LPA into phosphatidic acid (PA or 1,2-diacyl-sn-glycerol 3-phosphate) by esterifying an acyl-group to the sn-2 position of the glycerol backbone. PA is then transferred to the inner mitochondrial membrane to continue cardiolipin synthesis. Fourth, magnesium-dependent phosphatidate cytidylyltransferase catalyzes the conversion of PA into CDP-diacylglycerol. Fifth, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase synthesizes phosphatidylglycerophosphate (PGP). Sixth, phosphatidylglycerophosphatase and protein-tyrosine phosphatase dephosphorylates PGP to form phosphatidylglycerol (PG). Last, cardiolipin synthase catalyzes the synthesis of cardiolipin by transferring a phosphatidyl group from a second CDP-diacylglycerol to PG. It requires a divalent metal cation cofactor.

Phospholipids are membrane components in E. coli. The major phospholipids of E. coli are phosphatidylethanolamine, phosphatidylglycerol, and cardiolipin. All phospholipids contain sn-glycerol-3-phosphate esterified with fatty acids at the sn-1 and sn-2 positions. The reaction starts from a glycerone phosphate (dihydroxyacetone phosphate) produced in glycolysis. The glycerone phosphate is transformed into an sn-glycerol 3-phosphate (glycerol 3 phosphate) by NADPH-driven glycerol-3-phosphate dehydrogenase. sn-Glycerol 3-phosphate is transformed to a 1-acyl-sn-glycerol 3-phosphate (lysophosphatidic acid). This can be achieved by an sn-glycerol-3-phosphate acyltransferase that interacts either with a long-chain acyl-CoA or with an acyl-[acp]. The 1-acyl-sn-glycerol 3-phosphate is transformed into a 1,2-diacyl-sn-glycerol 3-phosphate (phosphatidic acid) through a 1-acylglycerol-3-phosphate O-acyltransferase. This compound is then converted into a CPD-diacylglycerol through a CTP phosphatidate cytididyltransferase. CPD-diacylglycerol can be transformed either into an L-1-phosphatidylserine or an L-1-phosphatidylglycerol-phosphate through a phosphatidylserine synthase or a phosphatidylglycerophosphate synthase, respectively. The L-1-phosphatidylserine transforms into L-1-phosphatidylethanolamine through a phosphatidylserine decarboxylase. On the other hand, L-1-phosphatidylglycerol-phosphate gets transformed into an L-1-phosphatidyl-glycerol through a phosphatidylglycerophosphatase. These 2 products combine to produce a cardiolipin and an ethanolamine. The L-1 phosphatidyl-glycerol can also interact with cardiolipin synthase resulting in a glycerol and a cardiolipin.

The regulation of the kbl, tdh operon. The operon is activated by gcvA (Glycine cleavage system transcriptional activator) and inhibited when gcvR (Glycine cleavage system transcriptional repressor) also binds to the promoter. GcvA binds to the promoter providing the affinity or shape needed for crp to bind to the promoter. When gcvR also binds to the promoter, the conditions for crp to bind are no longer optimal and it cannot transcribe the operon. Glycine concentrations also play a role in whether the operon is inhibited or activated. High concentrations of glycine inhibit the operon, while low concentrations of glycine activate the operon. The products of this operon are two enzymes: kbl (2-amino-3-ketobutyrate coenzyme A ligase) and tdh (L-threonine 3-dehydrogenase). Both enzymes are used in a two step process to degrade threonine to glycine. Tdh is used in the first step to change threonine to (2S)-2-amino-3-oxobutanoate. Kbl is used in the second step to change (2S)-2-amino-3-oxobutanoate to glycine.

The areCBA operon in Acinetobacter sp. strain ADP1 is activated in response to the presence of aromatic compounds, particularly benzyl acetate, which diffuses into the bacterial cell when its extracellular concentration reaches a threshold level. Upon entry into the cell, benzyl acetate serves as an inducer that triggers the transcriptional activation of the operon through the action of the regulatory protein AreR. AreR, a member of the NtrC/XylR family, binds to specific regulatory sequences located upstream of the promoter region of the areCBA operon, enhancing the RNA polymerase recruitment and initiation of transcription. The operon comprises three genes: areA, areB, and areC. The AreA protein, an esterase, catalyzes the hydrolysis of benzyl acetate, converting it into benzyl alcohol and acetic acid, thereby initiating the degradation process. Subsequently, the alcohol is converted into benzaldehyde by the action of AreB, an alcohol dehydrogenase, which facilitates the oxidation of benzyl alcohol to its corresponding aldehyde. Finally, AreC, a dehydrogenase, further processes benzaldehyde into salicylate, which integrates into the β-ketoadipate pathway for subsequent degradation, allowing the bacteria to utilize these aromatic compounds as carbon sources. This structured sequence of reactions, coupled with AreR's regulatory function, ensures efficient catabolism of benzyl alkanoates, allowing Acinetobacter sp. strain ADP1 to thrive in environments rich in these compounds. The coordinate induction of the areCBA operon through AreR exemplifies a finely tuned mechanism that responds dynamically to environmental cues, ultimately facilitating the bacterium's adaptability and metabolic versatility.

The benzoate degradation pathway involves the conversion of benzoate into intermediates that can enter central metabolic pathways such as the TCA cycle. This process is mediated by the catBCIJFD operon, which encodes enzymes responsible for the ortho-cleavage pathway of catechol, a key intermediate in benzoate catabolism. The catBCIJFD operon is made up of 6 genes (catB, catC, catI, catJ, catF and catD). It is regulated by two genes outside of the operon - CatM and an adjacent gene, benM, which encode LysR-type transcriptional regulators that can act both as activators and repressors of the catBCIJFD operon. cis,cis-muconate (CCM), produced from catechol ring cleavage, interacts with the LysR-type transcriptional regulator, to activate expression catBCIJFD operon. catB encodes Muconate cycloisomerase 1, an enzyme that converts cis,cis-muconate (a product of catechol cleavage) into muconolactone, catC encodes Muconolactone Delta-isomerase, which converts muconolactone into beta-ketoadipate enol-lactone, catD encodes β-ketoadipate enol-lactone hydrolase II also referred to as 3-oxoadipate enol-lactonase 2, which catalyzes the formation of beta-ketoadipate from beta-ketoadipate enol-lactone, catI and catJ encode 3-oxoadipate CoA-transferase subunit A and 3-oxoadipate CoA-transferase subunit B, which catalyze conversion of beta-ketoadipate to beta-ketoadipyl-CoA and lastly, catF encodes Beta-ketoadipyl-CoA thiolase, which converts beta-ketoadipyl-CoA into Succinyl-CoA and Acetyl-CoA which can then enter the TCA cycle.

The virB operon is the largest operon within the virulence regulon, consisting of 11 genes, virB1 to virB11, and is responsible for transferring T-DNA and effector proteins from the bacterium into the plant cell during infection. VirB1 encodes a lytic transglycosylase that degrades the bacterial peptidoglycan cell wall, facilitating insertion and assembly of T4SS. virB2 encodes the major pilin subunit, which is processed and polymerized to form the T-pilus, which is essential for DNA transfer to the plant cell. VirB3 encodes an inner membrane protein necessary for T-DNA secretion and it interacts with virb4 to facilitate formation of the T-pilus. virB4 and VirB11 encode ATPases that generates energy necessary for T-DNA transport across the membrane. VirB5 forms the minor pilin subunit of the T-pilus. virB6 encodes an inner mermbrane protein involved in the transport of virulence factors through the T4SS and also stabilizes virB5 and virB3 and virB7 formation. virB7 encodes an outer membrane lipoprotein, which together with virB9 anchor the T4SS to the bacterial outer membrane. VirB8 encodes a membrane protein that serves as a scaffold for T4SS assembly. virB9 encodes an outer membrane-associated protein that is part of the T4SS channel and lastly, virB10 encodes a transmembrane protein that forms part of the channel through which T-DNA as well as virB2 and virB5 factors are translocated.