We have cloned and identified a DNA sequence complementary to the mRNA of creatine kinase (CK) isozyme M, although the mRNA is a minor species of the total mRNA in developing myoblasts. Poly(A)+RNA from breast and thigh muscle of 5-week-old chicks was enriched for CK mRNA by a novel procedure of sucrose gradient centrifugation in the presence of methylmercuric hydroxide. DNA complementary to this mRNA was inserted into pBR322, and colonies containing the recombinant plasmids were screened for the ability of the plasmid DNA to hybridize with and rescue CK mRNA from total muscle mRNA. Three plasmids, pCS195, pCS192, and pM35-4, could specifically rescue CK-M mRNA. CK-M mRNA was detected by in vitro translation and specific immunoprecipitation. The identity of the in vitro translation product was further confirmed by its migration in two-dimensional gels at the isoelectric point and molecular weight ofCK-M. The heterogeneity ofCK-M observed in vivo also was found upon translation of the CK-M mRNA which hybridizes to the plasmid.Differentiation of myoblasts into a functional myotube requires the synthesis not only of abundant contractile proteins but also of minor enzymatic proteins (1-3). Creatine kinase (CK), one such enzyme, is a dimer ofsubunit molecular weight 41,000 and is involved in the synthesis ofATP which is required for muscle contraction (4). One CK isozyme, the BB form, is present in many tissues and in undifferentiated myoblasts, but during myogenesis the synthesis of a second isozyme, the MM form, is induced (5-7). Recent reports have indicated that the MM and BB isozymes contain two subspecies which may be distinguished on high-resolution two-dimensional gels, but the genetic origin of this heterogeneity is unknown (8,9).In order to investigate the mechanisms that control the expression of these enzymes and the switching of isozyme forms, it is necessary first to isolate their genes. The isolation of genes that encode minor but important proteins requires refinements in the recombinant DNA protocols in order to enrich for the mRNAs and allow detection of these sequences.We report here the molecular cloning of DNA sequences complementary to CK-M mRNA. CK is identified by two criteria: its precipitation by specific antibodies against purified CK-M, and its mobility in two-dimensional gels. The heterogeneity that is observed in the subunits of CK-M in vivo is also found in the translation products of mRNA that hybridizes to the cloned plasmid DNA.MATERIALS AND METHODS RNA Isolation and Partial Purification of CK mRNA. Twenty-five grams of frozen thigh and breast muscle from 5-week-old chicks was ground to a powder under liquid nitrogen and was resuspended in 100 ml of 8 M guanidine-HCI (Heico)/ 10 mM Tris-HCl, pH 7.3, by stirring for 10 min at room temperature. An equal volume of H20-saturated phenol was added, the mixture was stirred for 10 min and centrifuged (25 min at 1,020 x g), and the supernatant was mixed with 4 vol of 100% ethanol. The suspension was chilled at -80°C for 1 hr to preci...