965px-plant_cell_structureZiegler and Facchini (2008) did a review in metabolism and trafficking of alkaloid biosynthesis which is published in Annual Review of Plant Biology. Plant biologist duos present the subcellular compartments like cytosol, plastids, mitochondria, microsomes, endoplasmic reticulum, vacuoles etc., as the sites where occur enzymes involved in various biosynthetic pathways of alkaloids.

An enzyme involved in monoterpenoid indole alkaloids (MIA) biosynthetic pathways such as geraniol 10-hydrosylase (G10H) occurs in internal phloem parenchyma of aerial organs. Other enzymes of same pathway like Tryptophan decarboxylase (TDC), secologanin synthase, and Strictosidine synthase (STR) are found in epidermis of aerial organs, and apical meristem of roots. Still other enzymes  2-oxoglutarate dependent deoxygenase desacetoxyvindoline 4-hydroxylase (D4H), and Acetyl Co-A dependent desacetylvindoline-4-O-acetyltransferase (DAT) localize to the laticifers and idioblasts ofleaves and stems. The subcellular compartments which contain such enzymes are cytosol, vacuole, endoplasmic reticulum, and thylakoids. Cytosol contains TDC, D4H, and DAT while vacuole has STR and the perioxydase. The enzyme strictosidine β-D-glucosidase (SGD) associates with cytoplasmic face of the endoplasmic reticulum. The thylakoid membranes bear the enzymes and integral endomembrane proteins such as P450-dependent monoxygenases G10H, sacologanin synthase (SLS), and T16H and the N-methyltransferase (enzyme involved in vindoline biosynthesis).

The BIA biosynthetic enzymes are associated with a subcellular compartment other than the cytosol. Berberine bridge enzymes (BBE) and P450 monoxygenases (enzymes of sanguinarine branch pathway) localize to microsomes with a density slightly higher than that of typical endoplasmic reticulum. Although BBE is not an integral membrane protein, it is sorted to a vacuolar compartment. Norcoclaurine synthase (NCS) likely occurs in an ER-derived compartment. Enzymes like (S)-N-methylcoclaurine 3′-hydroxylase (Cyp80B3), BBE, and sanguinarine were colocalized with Endoplasmic reticulum in opium poppy cell cultures.

Enzymes of quinolizidine alkaloid biosynthesis occur in mesophyll of legumes. Lysine decarbosylase andquinolizidine skeleton forming enxyme have been detected from chloroplasts of Lupinus polyphyllus. 13-α-hydroxymultifluorine/13 α-hydroxylupanine O-tigloylase is localized to the mitochondrial matrix rather than chloroplasts (where de novo synthesis of quinolizidine alkloid occurs).  

Reference: Ziegle J and Facchini P J. 2008. Alkaloid Biosyntheisi: Metabolism and Trafficking. Annual Review of Plant Biology, 59:735-69.