Similar organization of the nusA-infB operon in Bacillus subtilis and Escherichia coli

Abstract

We reported previously the cloning and sequence of the Bacillus subtifis infB gene which encodes the essential IF2 factor required for initiation of translation (K. Shazand, J. Tucker, R. Chiang, K. Stansmore, H. U. Sperling-Petersen, M. Grunberg-Manago, J. C. Rabinowitz, and T. Leighton, J. Bacteriol. 172:2675-2687. The location of the 5' border of the infB operon was investigated by using integrative plasmids carrying various DNA fragments from the region upstream of the inf8 gene. The lethal effect of disruption of the infi transcriptional unit could be suppressed when the integrated plasmid introduced the spac promoter upstream of the inJB operon and transformants were selected in conditions of induction of spac expression. Translation initiation is usually the rate-limiting subreaction in the protein biosynthesis process, and as such, it is the focal point for control of translation efficiency (17). Initiation of protein biosynthesis is a complex process involving ribosome-binding motifs present on the mRNA (the ShineDalgarno sequence as well as additional sequence elements), the 30S ribosomal subunit, formyl-Met-tRNA, GTP, and three protein factors (17,19,23,28). The three ribosomeassociated proteins, initiation factors IF1, IF2, and IF3, play a crucial role in initiation of translation. They are involved in the selection of initiator tRNA (19) and in controlling entry into the elongation cycle (28).The genes encoding the three initiation factors, infA (IFi), infB (IF2), and infC (IF3), were first cloned in Escherichia coli (35,36,38). Recent studies have identified homologs of infA in Bacillus subtilis (4), of infB in B. subtilis (42), Bacillus stearothermophilus (6), and Streptococcus faecium (10), and of infC in B. stearothennophilus (33). The Bacillus infA and infC genes have been shown to belong to operons encoding other ribosomal proteins (4, 33).Only part of the B. subtilis infB operon was cloned previously, and its structure, outside of the infB gene, was not characterized (42). The E. coli infB operon contains the metY gene encoding a minor form of initiator tRNA, three genes encoding proteins of unknown function (P15A, P15B, and P35K), infB itself, and the nusA gene encoding a protein which is involved in termination of transcription (15,20,32,39). To define the genes cotranscribed with infB in B. subtilis and to compare the organization of the infB operon in bacteria belonging to the gram-positive and gram-negative * Corresponding author. lineages, we have cloned the entire B. subtilis infB operon and determined its complete nucleotide sequence. MATERIALS AND METHODSBacterial strains and media. DNA was cloned from B. subtilis 168RS2 provided by J. C. Rabinowitz. Strain JH642 trpC2 pheAl and its derivative M01099 amyE::erm (13), both provided by P. Stragier, were used as recipients for plasmids carrying lacZ fusions. B. subtilis cells were transformed as described previously (1). Antibiotics were added to selection and growth media when required: chloramphenicol (5 pug/ml); and a mixture of eryth...

YbxF, a Protein Associated with Exponential-Phase Ribosomes inBacillus subtilis

“…The ybxF gene has a paralogous counterpart in the B. subtilis genome, the ymxC gene (22% amino acid identity with YbxF). It is situated in the nusA-infB operon, and its function is unknown (26). Similarly as with ybxF, the deletion of ymxC had no effect on B. subtilis viability and/or growth.…”

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops

“…6B) as well as its conserved genomic location do point to an RNA-binding function. ylxQ is found in the autoregulatory nusA/infB operon consisting of ylxS-nusA-ylxRQ-infB-ylxPrbfA (Shazand et al 1993), where it is invariably associated (Winkler 2002) with YlxR, a putative RNA-binding protein (Osipiuk et al 2001). The strong genetic linkage between YlxR and YlxQ and at least one possible occurrence of a YlxR-YlxQ ORF fusion in Geobacter sulfurreducens (Winkler 2002) suggests an intriguing possibility that YlxR and YlxQ associate and YlxQ may bind its cellular RNA target with high affinity once in complex with YlxR.…”

Cloning and Characterization of the str Operon and Elongation Factor Tu Expression in Bacillus stearothermophilus

“…The ymxC gene is organized in the nusA-infB region and codes for a protein of unknown function (7,48). In most of the known archaebacterial genomes, the nusA gene and the ybxF orthologue are organized upstream of the rpsL gene (see, for example, references 8, 24, and 30).…”