The complete covalent structure of protein B. The third major protein degraded during germination of Bacillus megaterium spores

Nonsporulating bacterial species contain DNA sequences homologous to the Bacillus spore-specific C-protein gene

Genes for small, acid-soluble spore proteins (SASPs) are ubiquitous among the spore-forming bacteria and are expressed only during sporulation. Although they perform the function of amino acid storage in spores, the members of the SASP-C multigene family probably serve additional functions, so that similar sequences might be present in non-spore-formers. Using the SASP-C gene (ssp-c) as a hybridization probe, restriction digests of whole genomic DNA from seven nonsporulating bacterial species were examined for similar sequences. Hybridization was found in four species: Streptococcus pyogenes, Staphylococcus aureus, Neisseria sicca, and Mycobacterium phlei, indicating the presence of similar sequences in some, but not all, of the non-spore-formers. In each of these positive species, multiple bands hybridized. A 4.5-kb hybridizing fragment from S. pyogenes and a 9.0-kb hybridizing fragment from M. phlei have been cloned and partially sequenced. These fragments show substantial DNA sequence homology to ssp-c and their deduced amino acid sequences show substantial homology to SASP-C.

Cloning and nucleotide sequence of the Bacillus megaterium gene coding for small, acid-soluble spore protein B

The Bacillus megaterium gene coding for small, acid-soluble spore protein (SASP) B was cloned and its nucleotide sequence was determined. The amino acid sequence predicted from the DNA sequence was identical to that determined previously for SASP B, with the exception of the amino-terminal methionine predicted from the gene sequence which is presumably removed posttranslationally and an asparagine residue predicted at position 21 which was originally identified as an aspartate residue. The mRNA encoded by the SASP B gene is synthesized for only a discrete period midway in sporulation, in parallel with mRNAs coding for other SASPs. The small size of the SASP B mRNA (365 nucleotides) indicated that the mRNA is monocistronic. The SASP B gene itself hybridized strongly to only one band in Southern blots of restriction enzyme digests of B. megaterium DNA, suggesting that the SASP B gene is not a member of a highly conserved multigene family, as is the case for other SASP genes.

Genes for Bacillus megaterium small, acid-soluble spore proteins: cloning and nucleotide sequence of three additional genes from this multigene family

Three genes coding for small, acid-soluble spore proteins (SASP) were cloned from Bacillus megaterium, using previously cloned B. megaterium SASP genes (SASP-C and -C-3) as DNA-DNA hybridization probes. One gene (SASP-A) codes for the A protein, a previously identified major SASP. The other two (termed genes for SASP-C-4 and -C-5) are extremely similar in much of their nucleotide sequence to the previously cloned B. megaterium SASP-C-2 gene. The proteins coded for by all these SASP genes had extensive sequence homology with each other and with those coded for by the B. megaterium SASP-C, -C-1, -C-2, and -C-3 genes. Their coding sequences are preceded by strong ribosome-binding sites and are followed by regions of dyad symmetry which presumably are transcription stop sites. The SASP-A, -C-4, and -C-5 genes are expressed in parallel during sporulation, and their transcription start points were localized by the size of the mRNAs produced. The sequences localized 10 and 35 base pairs upstream from the transcription start points show significant homology with the analogous regions of the SASP-C, -C-1, -C-2, and -C-3 genes. The identification of seven closely related SASP genes in B. megaterium indicates that the SASP are the products of a very extensive multigene family.

Transcriptional control of synthesis of acid-soluble proteins in sporulating Bacillus subtilis

The major acid-soluble spore proteins (ASSPs) isolated from mature spores of Bacillus subtilis are designated alpha, beta, and gamma (about 60, 60, and 100 amino acids in length, respectively). Alpha and beta are very similar, and gamma is very similar to a less predominant ASSP called delta (about 115 amino acids). A minor and very basic ASSP called epsilon is the same size as alpha and beta but is unrelated antigenically. These and several minor ASSPs comprise at least three related families of sporulation-specific gene products. Expression of the alpha and beta genes, detectable as functional mRNA in vitro, coincides with the time of synthesis of all of the major ASSPs in vivo. This apparently coordinate expression is dependent on at least the spo0A, spoIIA, and spoIIIA loci, but not on the spoIVA or spoVA loci, consistent with the late stage of this expression (initiating at 3.5 h after the start of sporulation and peaking at 5 h after start of sporulation). A few minor ASSPs may be asynchronously expressed.

Cloning of a small, acid-soluble spore protein gene from Bacillus subtilis and determination of its complete nucleotide sequence

The first Bacillus subtilis small, acid-soluble spore protein (SASP) gene has been cloned by using previously cloned B. megaterium SASP genes as DNA-DNA hybridization probes. Determination of the DNA sequence of the B. subtilis SASP gene showed that it codes for a 72-residue protein (termed SASP-1) containing a single spore protease cleavage site as well as other sequences conserved in Bacillus megaterium SASPs A, C, C-1, C-2, and C-3. The B. subtilis SASP-1 genes's coding sequence is preceded by a potential Bacillus ribosome-binding site, and is followed by a sequence that could form a stem-and-loop structure characteristic of transcription termination sites. Upstream from the coding sequence there are no obvious homologies with other B. subtilis sporulation genes, but similarities with B. megaterium SASP genes are evident. SASP-1 mRNA (290 bases long) is absent from vegetative cells, but appears midway in sporulation and then disappears. The cloned SASP-1 gene hybridizes to three bands other than the SASP-1 gene itself in EcoRI or HindIII digests of B. subtilis DNA. Presumably these other bands represent SASP genes related to the SASP-1 gene, and we have been able to detect at least three such proteins in B. subtilis spores.

Bacillus megaterium spore protein C-3: nucleotide sequence of its gene and the amino acid sequence at its spore protease cleavage site

The nucleotide sequence of the Bacillus megaterium gene coding for spore-specific protein C-3 has been determined. The gene codes for 65 amino acids and the coding sequence is preceded by an efficient ribosome-binding site. The predicted protein C-3 sequence agrees with both the amino acid composition and the amino terminal sequence of protein C-3, and shows homology (approx. 65% of all residues are identical) with the sequences of the analogous proteins A and C of B. megaterium. Protein C-3 is cleaved by the sequence-specific B. megaterium spore protease, and the amino acid sequence at the new amino-terminus generated is identical to that predicted from the gene sequence, and homologous to the spore protease cleavage sites in the A and C proteins. The protein C-3 gene also shares a number of features with the previously sequenced protein C gene in both upstream and downstream flanking sequence.

Complete nucleotide sequence and start sites for transcription and translation of the Bacillus megaterium protein C gene

The nucleotide sequence of the Bacillus megaterium protein C gene, encompassing the coding region and 341 base pairs of flanking regions, has been determined. The gene codes for a 72-residue protein whose predicted amino acid sequence is identical to that previously determined for protein C with the exception of an amino-terminal methionine predicted from the gene sequence, but not found in the mature protein. The translational initiation codon is preceded by an 11-base pair sequence highly complementary to the 3' terminus of B. megaterium 16S rRNA. Protection against S1 nuclease digestion by hybridization of a protein C gene fragment to RNA containing high levels of protein C mRNA localized the transcription initiation site 108 base pairs upstream from the translation start site. Upstream from the transcription initiation site there are no obvious homologies with conserved regions of promoters for previously described B. subtilis vegetative or sporulation genes.

Isolation and characterization of two distinct fractions from the inner membrane of dormant Bacillus megaterium spores

Two distinct membrane bands were obtained after sucrose velocity gradient centrifugation of crude inner membranes from dormant Bacillus megaterium spores disrupted under conditions which minimized endogenous enzyme action. These two inner membrane fractions (termed LD and HD) contained similar amounts of total and individual phospholipid species. However, LD and HD differed significantly in phospholipid/protein ratios (4.3 and 0.47 mg/mg, respectively), equilibrium densities (1.12 and 1.18 g/cm3), NADH oxidase specific activity (less than 0.01 and 0.13 mumol/min X mg), and content of specific proteins. In contrast, crude membranes prepared in identical fashion from germinated spores gave only a single inner membrane band (termed G) on sucrose velocity gradients. G had a phospholipid/protein ratio of 0.98 mg/mg, an equilibrium density of 1.16 g/cm3, and an NADH oxidase specific activity of 2.1 mumol/min X mg. Essentially all of the proteins present in LD or HD or both were found in G, consistent with the latter membrane being derived from a mixture of LD and HD. No evidence was found suggesting that there is significant degradation of dormant spore inner membrane protein upon spore germination.

Cloning of a new low-molecular-weight spore-specific protein gene from Bacillus megaterium

Three EcoRI fragments of Bacillus megaterium DNA hybridized only under nonrestrictive conditions on Southern blots to a probe containing the previously cloned gene for protein C, a small, acid-soluble spore protein (SASP) from B. megaterium. All three fragments were cloned in Escherichia coli cells in plasmid pBR325, and after being transferred to an E. coli expression vector, one of the fragments (C-3) directed the synthesis of a new small, acid-soluble spore protein (termed C-3) immunologically related to protein C. As previously observed with the protein C gene, protein C-3 gene expression in E. coli required an external promoter and suppression of termination of transcription. Protein C-3 was purified from induced E. coli cells, and its immunological properties, electrophoretic mobility, amino acid composition, and amino-terminal sequence were determined. These data indicated that protein C-3 was related, but not identical, to either protein C or the closely related protein A--two of the major small, acid-soluble spore proteins of B. megaterium. Detailed examination of acid extracts of B. megaterium spores showed that they contained a minor protein which comigrated with C-3 on acrylamide gel electrophoresis at low pH and reacted immunologically like C-3.

Structure of dihydrofolate reductase: primary sequence of the bovine liver enzyme

The primary structure of dihydrofolate reductase from bovine liver has been established by Edman degradation of the intact carboxymethylated protein and of peptides obtained from the protein by the action of cyanogen bromide, trypsin, and the protease from Staphylococcus aureus, respectively. Since separation of some of the peptide mixtures by classical methods proved impossible, new systems were developed for the use of high-performance liquid chromatography to separate such mixtures. Some of the cleavage procedures used to obtain peptides gave atypical results at certain peptide bonds. The results are discussed in terms of the residues involved in these unexpectedly resistant or sensitive bonds. The sequence of the bovine liver enzyme is compared with those published for the enzyme from other sources, and known or probable functions of invariant residues are described. Sequences of vertebrate and bacterial reductases are compared and contrasted, and a possible role is considered for the residues which are invariant in bacterial reductases, but different in vertebrate reductases, in determining the selective inhibitory action of trimethoprim on bacterial reductases.

Chemical structure of rat liver cytochrome b5. Isolation of peptides by high-pressure liquid chromatography

The complete amino acid sequence of rat cytochrome b5 has been determined. Isolation of this species of cytochrome b5 in its native form from microsomes by means of detergent solubilization required the inclusion of the protease inhibitor, phenylmethylsulfonyl fluoride, throughout the isolation steps. Omission of the protease inhibitor yielded a 97-residue heme-containing peptide without the membranous segment. The primary structure of the intact molecules was deduced from automated sequence analysis of peptides generated by proteolytic or chemical cleavage and isolated exclusively by reversed-phase HPLC. The blocked amino terminus of cytochrome b5 was identified as N-acetylalanine. The hexosamine content of the cytochrome preparation was less than 0.1 mol/mol protein, indicating an absence of asparaginyl linked oligosaccharide.

Acid-soluble spore proteins of Bacillus subtilis

Acid-soluble spore proteins (ASSPs) comprise about 5% of the total protein of mature spores of different Bacillus subtilis strains. They consist of three abundant species, alpha, beta, and gamma, four less abundant species, and several minor species, alpha, beta, and gamma make up about 18, 18 and 36%, respectively, of the total ASSPs of strain 168, have molecular weights of 5,900, 5,9000, and 11,000, respectively, and resemble the major (A, C, and B) components of Bacillus megaterium ASSPs in several respects, including sensitivity to a specific B. megaterium spore endopeptidase. However, they have pI's of 6.58, 6.67, and 7.96, all lower than those of any of the B. megaterium ASSPs. Although strains varied in the proportions of different ASSPs, to overall patterns seen on gel electrophoresis are constant. ASSPs are located interior to the cortex, presumably in the spore cytoplasm, and are synthesized during sporulation and degraded during germination.

Comparison of various properties of low-molecular-weight proteins from dormant spores of several Bacillus species

Several properties of the major proteins degraded during germination of spores of Bacillus cereus, Bacillus megaterium, and Bacillus subtilis have been compared. All of the proteins had low molecular weights (6,000 to 13,000) and lacked cysteine, cystine, and tryptophan. The proteins could be subdivided into two groups: group I (B. megaterium A and C proteins, B. cereus A protein, and B. subtilis alpha and beta proteins) and group II (B. cereus and B. megaterium B proteins and B. subtilis gamma protein). Species in group II had lower levels of (or lacked) the amino acids isoleucine, leucine, methionine, and proline. Similarly, proteins in each group were more closely related immunologically. However, antisera against a B. megaterium group I protein cross-reacted more strongly with the B. megaterium group II protein than with group I proteins from other spore species, whereas antisera against the B. megaterium group II protein cross-reacted most strongly with B. megaterium group I proteins. Analysis of the primary sequences at the amino termini and in the regions of the B. cereus and B. subtilis proteins cleaved by the B. megaterium spore protease revealed that the B. cereus A protein was most similar to the B. megaterium A and C proteins, and the B. cereus B protein and the B. subtilis gamma protein were most similar to the B. megaterium B protein. However, amino terminal sequences within one group of proteins varied considerably, whereas the spore protease cleavage sites were more highly conserved.