147
9
plant metabolites are also in place. All these mechanisms allow a tight control of the accumulation of secondary metabolites to balance strategies of survival with growth and
development.
9.3 General Mechanisms for Biosynthesis
Some general mechanisms can be observed in all secondary pathways (. Fig. 9.2a). In all
pathways, some enzymes catalyse the committed step for a pathway. These enzymes are
usually highly regulated by feedback mechanisms and post-translational modifications
(Anarat-Cappillino and Sattely 2014). The plant primary metabolism provides the carbon
backbones for the secondary metabolism, usually via glycolysis, Calvin cycle or TCA cycle
(. Fig. 1.1). The nitrogen groups are mostly derived from amino acids. The most important starter molecules for the basic building blocks, which form the backbone of secondary metabolites, are therefore acetyl-CoA, shikimate, mevalonic acid, 1-deoxyxylulose
5-phosphate and fatty acids. Condensation reactions between compounds or the addition
of groups enlarges these molecules (Dewick 2002). Several kinds of groups can be added
to the carbon backbone. These include one-carbon groups (C1), which are methyl groups
usually donated by S-adenosylmethionine (SAM), leading to methylation or alkylation
reactions. Two-carbon units are supplied by acetyl-CoA, whereas malonyl-CoA supplies
C3 units. C5 carbon groups can be added as isoprene units (prenylation). For forming
carbon-carbon bonds, several condensation reactions occur; the aldol reaction is the
addition of enolates to aldehydes or ketones, and the Claisen reaction is the addition of
enolates to esters (. Fig. 9.2b, c). Both begin with a deprotonation. The difference is that
within the Claisen reaction, an elimination step is needed to generate a β-keto ester.
Nitrogen is incorporated either via aminotransferases (or transaminases), which need
pyridoxal-5′-phosphate (PLP) as a cofactor, or via condensation with amino acids. To
form these carbon-nitrogen bonds also different condensation reactions can occur. When
amines attack the electrophilic carbon atoms of aldehydes and ketones, a C=O double
bond is replaced by a C=N double bond, forming an imine (Schiff base). The Mannich
reaction converts a primary or secondary amine and two carbonyl compounds into a
β-amino carbonyl compound (Mannich base) (. Fig. 9.2d).
Alkanes, which are saturated hydrocarbons, can be transformed into unsaturated
compounds that contain double or triple bonds (alkenes or alkynes), by desaturases
that remove two hydrogen atoms. Unsaturated compounds are usually more reactive and
promote cyclization. Many secondary metabolites undergo several steps of cyclization.
One way to achieve this is via the Diels-Alder reaction, a cycloaddition, where a conjugated diene and a substituted alkene form a cyclic olefin (. Fig. 9.2e). The Pictet-Spengler
reaction converts an amine and an aldehyde or ketone to a protonated imine intermediate,
which then undergoes cyclization (. Fig. 9.2f).
Once the backbone or scaffold is formed, the metabolite complexity and diversity arise
especially from oxygenation/hydroxylation reactions catalysed by oxygenases such as
cytochrome P450 monooxygenases (Cyt P450) and 2-oxoglutarate-dependent dioxygenases (2OGDs) (. Fig. 9.3). Cyt P450s are heme-containing proteins, which are anchored
by their N-terminus to the cytoplasmic side of the endoplasmic reticulum (Barnaba et al.
2017; Groves 2015). In contrast, 2OGDs are non-heme proteins that localize in the cytosol
as soluble proteins. They have iron Fe (II) as a cofactor and require 2-oxoglutarate (2OG)
and molecular oxygen as co-substrates. These so-called tailoring enzymes are not equally
distributed between all species; nevertheless, many genes encoding for these enzymes have
9.3 · General Mechanisms for Biosynthesis
9
plant metabolites are also in place. All these mechanisms allow a tight control of the accumulation of secondary metabolites to balance strategies of survival with growth and
development.
9.3 General Mechanisms for Biosynthesis
Some general mechanisms can be observed in all secondary pathways (. Fig. 9.2a). In all
pathways, some enzymes catalyse the committed step for a pathway. These enzymes are
usually highly regulated by feedback mechanisms and post-translational modifications
(Anarat-Cappillino and Sattely 2014). The plant primary metabolism provides the carbon
backbones for the secondary metabolism, usually via glycolysis, Calvin cycle or TCA cycle
(. Fig. 1.1). The nitrogen groups are mostly derived from amino acids. The most important starter molecules for the basic building blocks, which form the backbone of secondary metabolites, are therefore acetyl-CoA, shikimate, mevalonic acid, 1-deoxyxylulose
5-phosphate and fatty acids. Condensation reactions between compounds or the addition
of groups enlarges these molecules (Dewick 2002). Several kinds of groups can be added
to the carbon backbone. These include one-carbon groups (C1), which are methyl groups
usually donated by S-adenosylmethionine (SAM), leading to methylation or alkylation
reactions. Two-carbon units are supplied by acetyl-CoA, whereas malonyl-CoA supplies
C3 units. C5 carbon groups can be added as isoprene units (prenylation). For forming
carbon-carbon bonds, several condensation reactions occur; the aldol reaction is the
addition of enolates to aldehydes or ketones, and the Claisen reaction is the addition of
enolates to esters (. Fig. 9.2b, c). Both begin with a deprotonation. The difference is that
within the Claisen reaction, an elimination step is needed to generate a β-keto ester.
Nitrogen is incorporated either via aminotransferases (or transaminases), which need
pyridoxal-5′-phosphate (PLP) as a cofactor, or via condensation with amino acids. To
form these carbon-nitrogen bonds also different condensation reactions can occur. When
amines attack the electrophilic carbon atoms of aldehydes and ketones, a C=O double
bond is replaced by a C=N double bond, forming an imine (Schiff base). The Mannich
reaction converts a primary or secondary amine and two carbonyl compounds into a
β-amino carbonyl compound (Mannich base) (. Fig. 9.2d).
Alkanes, which are saturated hydrocarbons, can be transformed into unsaturated
compounds that contain double or triple bonds (alkenes or alkynes), by desaturases
that remove two hydrogen atoms. Unsaturated compounds are usually more reactive and
promote cyclization. Many secondary metabolites undergo several steps of cyclization.
One way to achieve this is via the Diels-Alder reaction, a cycloaddition, where a conjugated diene and a substituted alkene form a cyclic olefin (. Fig. 9.2e). The Pictet-Spengler
reaction converts an amine and an aldehyde or ketone to a protonated imine intermediate,
which then undergoes cyclization (. Fig. 9.2f).
Once the backbone or scaffold is formed, the metabolite complexity and diversity arise
especially from oxygenation/hydroxylation reactions catalysed by oxygenases such as
cytochrome P450 monooxygenases (Cyt P450) and 2-oxoglutarate-dependent dioxygenases (2OGDs) (. Fig. 9.3). Cyt P450s are heme-containing proteins, which are anchored
by their N-terminus to the cytoplasmic side of the endoplasmic reticulum (Barnaba et al.
2017; Groves 2015). In contrast, 2OGDs are non-heme proteins that localize in the cytosol
as soluble proteins. They have iron Fe (II) as a cofactor and require 2-oxoglutarate (2OG)
and molecular oxygen as co-substrates. These so-called tailoring enzymes are not equally
distributed between all species; nevertheless, many genes encoding for these enzymes have
9.3 · General Mechanisms for Biosynthesis