Involvement of the nusB gene products in transcription of Escherichia coli tryptophan operon in vitro

Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle

The rumen microbiome is essential for the biological processes involved in the conversion of feed into nutrients that can be utilized by the host animal. In the present research, the influence of the rumen microbiome on feed conversion efficiency, growth rate, and appetite of beef cattle was investigated using metagenomic data. Our aim was to explore the associations between microbial genes and functional pathways, to shed light on the influence of bacterial enzyme expression on host phenotypes. Two groups of cattle were selected on the basis of their high and low feed conversion ratio. Microbial DNA was extracted from rumen samples, and the relative abundances of microbial genes were determined via shotgun metagenomic sequencing. Using partial least squares analyses, we identified sets of 20, 14, 17, and 18 microbial genes whose relative abundances explained 63, 65, 66, and 73% of the variation of feed conversion efficiency, average daily weight gain, residual feed intake, and daily feed intake, respectively. The microbial genes associated with each of these traits were mostly different, but highly correlated traits such as feed conversion ratio and growth rate showed some overlapping genes. Consistent with this result, distinct clusters of a coabundance network were enriched with microbial genes identified to be related with feed conversion ratio and growth rate or daily feed intake and residual feed intake. Microbial genes encoding for proteins related to cell wall biosynthesis, hemicellulose, and cellulose degradation and host-microbiome crosstalk (e.g., aguA, ptb, K01188, and murD) were associated with feed conversion ratio and/or average daily gain. Genes related to vitamin B12 biosynthesis, environmental information processing, and bacterial mobility (e.g., cobD, tolC, and fliN) were associated with residual feed intake and/or daily feed intake. This research highlights the association of the microbiome with feed conversion processes, influencing growth rate and appetite, and it emphasizes the opportunity to use relative abundances of microbial genes in the prediction of these performance traits, with potential implementation in animal breeding programs and dietary interventions.

Insertional disruption of the nusB (ssyB) gene leads to cold-sensitive growth of Escherichia coli and suppression of the secY24 mutation

The Escherichia coli gene ssyB was cloned and sequenced. The ssyB63 (Cs) mutation is an insertion mutation in nusB, while the nusB5 (Cs) mutation suppresses secY24, indicating that inactivation of nusB causes cold-sensitive cell growth as well as phenotypic suppression of secY24. The correct map position of nusB is 9.5 min rather than 11 min as previously assigned. It is located at the distal end of an operon that contains a gene showing significant homology with a Bacillus subtilis gene involved in riboflavin biosynthesis.

Effects of Escherichia coli Nus A protein on transcription termination in vitro are not increased or decreased by DNA sequences sufficient for antitermination in vivo

The ability of Escherichia coli Nus A protein to recognize specific DNA or RNA sequences in vitro was tested by using transcription templates containing a variety of promoters, transcription terminators, and antitermination-conferring regions. We conclude that the effects of Nus A on termination are not qualitatively or quantitatively altered by sequences present in promoters, Rho-dependent terminators, or antitermination-conferring regions. Nus A was also shown to increase termination at the rrnC Rho-independent T1 terminator by a mechanism that is independent of the promoter or sequences involved in antitermination. Altogether, these observations argue against a direct Nus A-nucleic acid interaction affecting termination in vitro. Together with the results described in the accompanying paper [Sigmund, C. D., & Morgan, E. A. (1988) Biochemistry (preceding paper in this issue)], these results suggest that the effects of Nus A on termination in vitro may not be related to the in vivo functions of Nus A.

Differential transcriptional control of the two tRNA(fMet) genes of Escherichia coli K-12

The metZ gene of Escherichia coli, which encodes the tRNA(f1Met), was cloned. Using the nucleotide sequence, in vitro transcription, and S1 nuclease mapping analyses, we identified the promoter region, transcriptional start point, the two tandem tRNA(f1Met) structural genes separated by an intergenic space of 33 bp, and the two Rho-independent transcriptional termination sites, in that order. We compared the promoter region of the metZ gene with that of the metY gene, which encodes the tRNA(f2Met) and is located in the promoter-proximal portion of the nusA operon. A G + C-rich sequence (5'-GCGCATCCAC-3'), similar to the corresponding sequence of the rrn promoters that are under stringent control, was found between the Pribnow box and the transcriptional start point of the metZ promoter, but not in the metY promoter region. We therefore examined the effect of guanosine 3'-diphosphate, 5'-diphosphate (ppGpp), the chemical mediator of stringent control, and found that ppGpp inhibited the transcription of the metZ gene, but not that of the metY gene. These data suggested that the promoters for metZ and metY have different physiological functions and are regulated by different mechanisms.

Multivalent regulation of the nusA operon of Escherichia coli

The rate of synthesis and intracellular content of the NusA protein, a transcription termination factor, were determined for wild-type and nusA and/or nusB mutants of Escherichia coli. Both the rate and content of NusA in wild-type strains were similar to that of the RNA polymerase sigma subunit, a transcription initiation factor, on a molar basis, and about 30%-40% the levels of RNA polymerase beta beta' subunits. At the stationary phase of cell growth, the values increased in parallel for both transcription factors up to approximately the level of the beta beta' subunits. In nus mutants, the rate of synthesis and the content of the sigma subunit were significantly increased. These observations together suggest that the two transcription factors are coordinately regulated.

Purification of the NusB gene product of Escherichia coli K12

The nucleotide sequence of the entire nusB gene of Escherichia coli has recently been determined and the amino acid sequence of its product deduced (Ishii et al. 1984; Swindle et al. 1984). The NusB protein was purified by chromatography on Sephadex G-100, phosphocellulose and hydroxylapatite. Purification of the protein was monitored using 14C-labelled NusB protein, which was synthesized in a maxicell containing an nusB plasmid as a marker. The final product, which was at least 95% pure as judged by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulphate, had a molecular weight of about 16,000 and an isoelectric point of about 7.3. Analytical data on the amino acid composition of the purified protein agreed with that deduced from the DNA sequence and indicated that this protein was indeed the product of the nusB gene.

Isolation and characterization of nucleoid proteins from Escherichia coli

Of the molecular species of proteins associated with the nucleoids of Escherichia coli cells, those with relatively high affinity to bind to DNA were isolated and characterized. Seven classes of nucleoid proteins with molecular weights of 9,000, 17,000 (two molecular species), 22,000, 24,000, 27,000 and 28,000 were isolated at more than 90% purity or were partially purified. On the basis of its amino acid composition and other chemical properties, the 9,000 dalton protein was identified as HLP II (or HU protein or BH2) (Pettijohn 1982; Rouvière-Yaniv and Gros 1975; Varshavsky et al. 1978). The 17 K protein consisted of two molecular species and one of these, 17 K (a) protein, seemed to be identical with HLPI (or protein 1 or BH1) reported previously (Pettijohn 1982; Varshavsky et al. 1977; Varshavsky et al. 1978). The 26 K protein was identical to the 22 K protein (Kishi et al. 1982). The 27 K protein showed immunological cross-reactivity with the antibody for histone H2A and was thus identified as the H protein reported previously (Hübscher et al. 1980). Two basic proteins, 9 K and 17 K(a), showed relatively high binding affinities to DNA, while the 28 K protein showed moderate binding affinity. The biological significance of these nucleoid proteins, which constitute a family of proteins participating in formation of the nucleoid structure, is discussed.

Molecular cloning and nucleotide sequencing of the nusB gene of E. coli

The nusB gene of E. coli has been cloned in plasmid pBR322. Using genetic complementation as an assay for the gene, its location in subclones was analyzed, and the nucleotide sequence of this gene and its flanking regions was determined. The coding region consists of 417 base pairs (bp), which specify a protein of 139 amino acids, and the calculated molecular weight of the nusB protein is 15,702. The nusB protein contains 20 acidic and 21 basic amino acids. A significant promoter sequence was not found to be located in the region upstream from the translational initiation codon. The possibility that the nusB gene consists of an operon is discussed. After the coding region, there is a G-C rich inverted repeat sequence followed by a run of Ts, which could be a transcriptional terminator of the nusB gene.

The nucleotide sequence of the cloned nusA gene and its flanking region of Escherichia coli

The nucleotide sequence of the promoter-proximal portion of the nusA operon including the genes for tRNAMetf2, a 15 kilodalton protein and the initial portion of the nusA gene has been determined previously (1). Here, we report the sequence for the entire nusA gene and its flanking region. The open reading frame, consisting of 1,482 nucleotides, was identified as that of the nusA protein on the basis of agreement of the amino acid sequence deduced from the DNA sequence with the N-terminal sequence of the purified nusA protein. The molecular weight of 54,417 daltons calculated for the 494 amino acid polypeptide is significantly lower than that determined previously by SDS polyacrylamide gel analysis. The nusA gene is immediately followed by another open reading frame encoding a polypeptide of at least 22 amino acids, which was identified as the initial portion of the infB structural gene. In the spacer region of 24 base pairs between the nusA and infB structural genes there is no significant DNA sequence that fits the canonical transcriptional termination signal or promoter sequence. We suggest, therefore, that the genes for tRNAMetf2, a 15 kilodalton protein, the nusA protein and IF2 alpha, aligned in this order, are co-transcribed.

tRNAMetf2 gene in the leader region of the nusA operon in Escherichia coli

The promoter-proximal portion of the operon containing the Escherichia coli nusA gene has been cloned. Its nucleotide sequence shows that genes for tRNAMetf2 and a 15-kilodalton protein of unknown function precede the nusA protein gene. The sequence suggests that the three genes form a single transcription unit. Consistent with this hypothesis, purified RNA polymerase formed full-length transcripts on the cloned DNA in vitro, although transcription was frequently arrested at the intercistronic site(s) between the gene for tRNAMetf2 and the 15-kilodalton protein.

Direct expression of hepatitis B surface antigen gene in E. coli

A 809 bp Sau 3A - Hpa I fragment containing a complete HBsAg gene and fragments 744 bp Hinc II - Hpa I and 712 bp Xba I - Hpa I containing a truncated HBsAg gene lacking the sequence encoding the NH2-terminal hydrophobic domain were prepared from a composite plasmid pHBV933 containing the 3.2 kb Eco RI DNA fragment of the entire HBV/adw genome and inserted into an expression vector pTRP801 to give plasmids pTRP SS-6, pTRP SS-39, and pTRP SS-50, respectively. The growth of a recombinant having pTRP SS-6 was greatly inhibited and the transformant expressed a low level of HBsAg, which is reactive to human anti-HBsAg antibody. Interestingly, the growth of transformants harbouring pTRP SS-39 and pTRP SS-50 was not inhibited and these transformants expressed a considerable level of the HBsAg. Minicells harbouring pTRP SS-6, pTRP SS-39, and pTRP SS-50 formed specific polypeptides of about 24 K, 23 K, and 22 K daltons, respectively.