The combined structural study of proteins and of their corresponding genes utilizing the methods of both protein and nucleotide chemistry greatly accelerates and considerably simplifies both the nucleotide and protein structure determination and, in particular, enhances the reliability of the analysis. This approach has been successfully applied in the primary structure determination of the fl and j' subunits of Escherichia coli DNAdependent RNA potynierase and of their structural genes, yielding a continuous nucleotide sequence (4714 base pairs) that embraces the entire rpoB gene, the initial part of the rpoC gene and the intercistronic region, together with the total amino acid sequence of the fl subunit, comprising 1342 residues, and the N-terminal sequence of the jl' subunit (1 76 residues).Elucidation of the transcription mechanism requires detailed knowledge of the active-center organization of RNA polymerase at the various stages of the RNA synthesis. This, in turn, can be obtained only after determining the primary and spatial structure of the enzyme.Earlier we had established the amino acid sequence of the x subunit of Escherichiu coli DNA-dependent RNA polymerase by resorting solely to the ordinary methods of protein chemistry [5]. In the case of the fl and p' subunits with their much higher molecular weights (= 155000 and z 165000, respectively) [6], such an approach could no longer suffice, in view of the difficulties in isolating and purifying the resulting fragments and in reconstituting the amino acid sequence via overlapping peptides [7].The progress in DNA sequencing methods and the possibility of using the genetic code to obtain information on the primary protein structure from the nucleotide sequences is an attractive way to circumvent such difficulties; although here, too, there are many pitfalls, requiring considerable caution to avoid possible sources of error.In the first place the mRNA can undergo processing, leading to erroneous deduction of the protein structure. Secondly, the protein itself can be processed. Thirdly, it is often difficult to recognize in the overall DNA structure the beginning of a structural gene. The criterion for this purpose is the presence of an initiating codon together with the adjacent sequences complementary to the 3' end of 16-S RNA [8,9]. Frequently more than one such combination can be found for one and the same protein. insertion) in the DNA sequence determination could lead to a completely erroneous amino acid sequence of the protein. Thus, primary structure determination of DNA cannot serve as a substitute for the direct sequencing of the protein.In view of this, we decided to utilize the methods of both protein and nucleotide chemistries, performing the parallel sequencing of the structural genes rpoB (jl subunit) and rpoC (jl' subunit) and of the corresponding proteins. Knowledge of the nucleotide sequence of the pertinent DNA segments would permit aligning of the peptide fragments from the protein analysis into an uninterrupted polypeptide chain. Such...

The primary structure of the gamma-subunit of cyclic GMP phosphodiesterase was determined by parallel analysis of the amino acid sequence of the protein and nucleotide sequence of the corresponding cDNA. The enzyme gamma-subunit contains 87 amino acid residues, its N-terminal amino group being acetylated.

The ct-subunit primary structure of cyclic GMP phosphodiesterase has been determined by parallel analysis of the protein amino acid sequence and the corresponding cDNA nucleotide sequence. The enzyme ~t-subunit contains 858 amino acid residues, its N-terminal amino group being acetylated. The partial primary structure of the enzyme fl-subunit has also been elucidated. A significant homology has been found between the ct-and fl-subunits of cGMP phosphodiesterase.

The primary structure of the E. coli rpoC gene (5321 base pairs) coding the beta'-subunit of RNA polymerase as well as its adjacent segment have been determined. The structure analysis of the peptides obtained by cleavage of the protein with cyanogen bromide and trypsin has confirmed the amino acid sequence of the beta'-subunit deduced from the nucleotide sequence analysis. The beta'-subunit of E. coli RNA polymerase contains 1407 amino acid residues. Its translation is initiated by codon GUG and terminated by codon TAA. It has been detected that the sequence following the terminating codon is strikingly homologous to known sequences of rho-independent terminators.

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