Guayule (
Parthenium argentatum
) is a perennial shrub in the Asteraceae family and synthesizes a high quality, hypoallergenic
cis
-1,4-polyisoprene (or natural rubber; NR). Despite its potential to be an alternative NR supplier, the enzymes for
cis
-polyisoprene biosynthesis have not been comprehensively studied in guayule. Recently, implications of the protein complex involving
cis
-prenyltransferases (CPTs) and CPT-Binding Proteins (CBPs) in NR biosynthesis were shown in lettuce and dandelion, but such protein complexes have yet to be examined in guayule. Here, we identified four guayule genes – three
PaCPTs
(
PaCPT1-3
) and one
PaCBP
, whose protein products organize PaCPT/PaCBP complexes. Co-expression of both
PaCBP
and each of the
PaCPTs
could complemented the dolichol (a short
cis
-polyisoprene)-deficient yeast, whereas the individual expressions could not. Microsomes from the
PaCPT/PaCBP
-expressing yeast efficiently incorporated
14
C-isopentenyl diphosphate into dehydrodolichyl diphosphates; however, NR with high molecular weight could not be synthesized in
in vitro
assays. Furthermore, co-immunoprecipitation and split-ubiquitin yeast 2-hybrid assays using PaCPTs and PaCBP confirmed the formation of protein complexes. Of the three
PaCPT
s, guayule transcriptomics analysis indicated that the
PaCPT3
is predominantly expressed in stem and induced by cold-stress, suggesting its involvement in NR biosynthesis. The comprehensive analyses of these PaCPTs and PaCBP here provide the foundational knowledge to generate a high NR-yielding guayule.