Transcriptional analysis of Bacillus subtilis rRNA-tRNA operons. I. The tRNA gene cluster of rrnB has an internal promoter.

ABSTRACTThe biosynthetic gene cluster of FK228, an FDA-approved anticancer natural product, was identified and sequenced previously. The genetic organization of this gene cluster has now been delineated through systematic gene deletion and transcriptional analysis. As a result, the gene cluster is redefined to contain 12 genes:depAthroughdepJ,depM, and a newly identified pathway regulatory gene,depR.

Download Full-text

Clone of plipastatin biosynthetic gene cluster by transformation-associated recombination technique and high efficient expression in model organism Bacillus subtilis

Journal of Biotechnology ◽

10.1016/j.jbiotec.2018.10.006 ◽

2018 ◽

Vol 288 ◽

pp. 1-8 ◽

Cited By ~ 7

Author(s):

Yimin Hu ◽

Fang Nan ◽

Sarah Wanjiku Maina ◽

Jia Guo ◽

Shenglu Wu ◽

...

Keyword(s):

Bacillus Subtilis ◽

Gene Cluster ◽

Model Organism ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene ◽

High Efficient ◽

Efficient Expression

Download Full-text

Characterization of a rat tRNA gene cluster containing the genes for tRNAAsp, tRNAGlyand tRNAGhi, and pseudogenes

Nucleic Acids Research ◽

10.1093/nar/10.14.4441 ◽

1982 ◽

Vol 10 (14) ◽

pp. 4441-4448 ◽

Cited By ~ 18

Author(s):

Kyoko Shibuya ◽

Shigeru Noguchi ◽

Susuma Nishimura ◽

Takao Sekiya

Keyword(s):

Gene Cluster ◽

Trna Gene

Download Full-text

Characterization and analysis of an industrial strain of Streptomyces bingchenggensis by genome sequencing and gene microarray

Genome ◽

10.1139/gen-2013-0098 ◽

2013 ◽

Vol 56 (11) ◽

pp. 677-689 ◽

Cited By ~ 7

Author(s):

Xiang-Jing Wang ◽

Bo Zhang ◽

Yi-Jun Yan ◽

Jing An ◽

Ji Zhang ◽

...

Keyword(s):

Natural Products ◽

Gene Cluster ◽

Crop Protection ◽

Gc Content ◽

Gene Clusters ◽

High Expression ◽

Expression Level ◽

Transcriptional Analysis ◽

Streptomyces Bingchenggensis ◽

High Expression Level

Streptomyces bingchenggensis is a soil bacterium that produces milbemycins, a family of macrolide antibiotics that are commercially important in crop protection and veterinary medicine. In addition, S. bingchenggensis produces many other natural products including the polyether nanchangmycin and novel cyclic pentapeptides. To identify the gene clusters involved in the biosynthesis of these compounds, and better clarify the biochemical pathways of these gene clusters, the whole genome of S. bingchenggensis was sequenced, and the transcriptome profile was subsequently investigated by microarray. In comparison with other sequenced genomes in Streptomyces, S. bingchenggensis has the largest linear chromosome consisting of 11 936 683 base pairs (bp), with an average GC content of 70.8%. The 10 023 predicted protein-coding sequences include at least 47 gene clusters correlated with the biosynthesis of known or predicted secondary metabolites. Transcriptional analysis demonstrated an extremely high expression level of the milbemycin gene cluster during the entire growth period and a moderately high expression level of the nanchangmycin gene cluster during the initial hours that subsequently decreased. However, other gene clusters appear to be silent. The genome-wide analysis of the secondary metabolite gene clusters in S. bingchenggensis, coupled with transcriptional analysis, will facilitate the rational development of high milbemycins-producing strains as well as the discovery of new natural products.

Download Full-text

Transcriptional analysis of the gap-pgk-tpi-ppc gene cluster of Corynebacterium glutamicum.

Journal of Bacteriology ◽

10.1128/jb.175.12.3905-3908.1993 ◽

1993 ◽

Vol 175 (12) ◽

pp. 3905-3908 ◽

Cited By ~ 34

Author(s):

J W Schwinde ◽

N Thum-Schmitz ◽

B J Eikmanns ◽

H Sahm

Keyword(s):

Corynebacterium Glutamicum ◽

Gene Cluster ◽

Transcriptional Analysis

Download Full-text

Insight into Energy Conservation via Alternative Carbon Monoxide Metabolism inCarboxydothermus pertinaxRevealed by Comparative Genome Analysis

Applied and Environmental Microbiology ◽

10.1128/aem.00458-18 ◽

2018 ◽

Vol 84 (14) ◽

Cited By ~ 7

Author(s):

Yuto Fukuyama ◽

Kimiho Omae ◽

Yasuko Yoneda ◽

Takashi Yoshida ◽

Yoshihiko Sako

Keyword(s):

Carbon Monoxide ◽

Co Oxidation ◽

Gene Cluster ◽

Genome Analysis ◽

Transcriptional Analysis ◽

Comparative Genome Analysis ◽

Co Dehydrogenase ◽

Comparative Genome ◽

Content Type ◽

Energy Converting

ABSTRACTCarboxydothermusspecies are some of the most studied thermophilic carboxydotrophs. Their varied carboxydotrophic growth properties suggest distinct strategies for energy conservation via carbon monoxide (CO) metabolism. In this study, we used comparative genome analysis of the genusCarboxydothermusto show variations in the CO dehydrogenase-energy-converting hydrogenase gene cluster, which is responsible for CO metabolism with H2production (hydrogenogenic CO metabolism). Indeed, the ability or inability to produce H2with CO oxidation is explained by the presence or absence of this gene cluster inCarboxydothermus hydrogenoformans,Carboxydothermus islandicus, andCarboxydothermus ferrireducens. Interestingly, despite its hydrogenogenic CO metabolism,Carboxydothermus pertinaxlacks the Ni-CO dehydrogenase catalytic subunit (CooS-I) and its transcriptional regulator-encoding genes in this gene cluster, probably due to inversion. Transcriptional analysis inC. pertinaxshowed that the Ni-CO dehydrogenase gene (cooS-II) and distantly encoded energy-converting-hydrogenase-related genes were remarkably upregulated with 100% CO. In addition, when thiosulfate was available as a terminal electron acceptor in 100% CO, the maximum cell density and maximum specific growth rate ofC. pertinaxwere 3.1-fold and 1.5-fold higher, respectively, than when thiosulfate was absent. The amount of H2produced was only 62% of the amount of CO consumed, less than expected according to hydrogenogenic CO oxidation (CO + H2O → CO2+ H2). Accordingly,C. pertinaxwould couple CO oxidation by Ni-CO dehydrogenase II with simultaneous reduction of not only H2O but also thiosulfate when grown in 100% CO.IMPORTANCEAnaerobic hydrogenogenic carboxydotrophs are thought to fill a vital niche by scavenging potentially toxic CO and producing H2as an available energy source for thermophilic microbes. This hydrogenogenic carboxydotrophy relies on a Ni-CO dehydrogenase-energy-converting hydrogenase gene cluster. This feature is thought to be common to these organisms. However, the hydrogenogenic carboxydotrophCarboxydothermus pertinaxlacks the gene for the Ni-CO dehydrogenase catalytic subunit encoded in the gene cluster. Here, we performed a comparative genome analysis of the genusCarboxydothermus, a transcriptional analysis, and a cultivation study in 100% CO to prove the hydrogenogenic CO metabolism. Results revealed thatC. pertinaxcould couple Ni-CO dehydrogenase II alternatively to the distal energy-converting hydrogenase. Furthermore,C. pertinaxrepresents an example of the functioning of Ni-CO dehydrogenase that does not always correspond to its genomic context, owing to the versatility of CO metabolism and the low redox potential of CO.

Download Full-text

Novel tRNA gene organization in the 16S-23S intergenic spacer of the Streptococcus pneumoniae rRNA gene cluster.

Journal of Bacteriology ◽

10.1128/jb.173.13.4234-4236.1991 ◽

1991 ◽

Vol 173 (13) ◽

pp. 4234-4236 ◽

Cited By ~ 36

Author(s):

C M Bacot ◽

R H Reeves

Keyword(s):

Streptococcus Pneumoniae ◽

Gene Cluster ◽

Trna Gene ◽

Intergenic Spacer ◽

Gene Organization ◽

Rrna Gene

Download Full-text

Fur-Dam Regulatory Interplay at an Internal Promoter of the Enteroaggregative Escherichia coli Type VI Secretion sci1 Gene Cluster

Journal of Bacteriology ◽

10.1128/jb.00075-20 ◽

2020 ◽

Vol 202 (10) ◽

Cited By ~ 3

Author(s):

Yannick R. Brunet ◽

Christophe S. Bernard ◽

Eric Cascales

Keyword(s):

Escherichia Coli ◽

Gene Cluster ◽

Gene Clusters ◽

Secretion System ◽

Target Cells ◽

Type Vi Secretion System ◽

Content Type ◽

Internal Promoter ◽

E Coli ◽

Type Vi Secretion

ABSTRACT The type VI secretion system (T6SS) is a weapon for delivering effectors into target cells that is widespread in Gram-negative bacteria. The T6SS is a highly versatile machine, as it can target both eukaryotic and prokaryotic cells, and it has been proposed that T6SSs are adapted to the specific needs of each bacterium. The expression of T6SS gene clusters and the activation of the secretion apparatus are therefore tightly controlled. In enteroaggregative Escherichia coli (EAEC), the sci1 T6SS gene cluster is subject to a complex regulation involving both the ferric uptake regulator (Fur) and DNA adenine methylase (Dam)-dependent DNA methylation. In this study, an additional, internal, promoter was identified within the sci1 gene cluster using +1 transcriptional mapping. Further analyses demonstrated that this internal promoter is controlled by a mechanism strictly identical to that of the main promoter. The Fur binding box overlaps the −10 transcriptional element and a Dam methylation site, GATC-32. Hence, the expression of the distal sci1 genes is repressed and the GATC-32 site is protected from methylation in iron-rich conditions. The Fur-dependent protection of GATC-32 was confirmed by an in vitro methylation assay. In addition, the methylation of GATC-32 negatively impacted Fur binding. The expression of the sci1 internal promoter is therefore controlled by iron availability through Fur regulation, whereas Dam-dependent methylation maintains a stable ON expression in iron-limited conditions. IMPORTANCE Bacteria use weapons to deliver effectors into target cells. One of these weapons, the type VI secretion system (T6SS), assembles a contractile tail acting as a spring to propel a toxin-loaded needle. Its expression and activation therefore need to be tightly regulated. Here, we identified an internal promoter within the sci1 T6SS gene cluster in enteroaggregative E. coli. We show that this internal promoter is controlled by Fur and Dam-dependent methylation. We further demonstrate that Fur and Dam compete at the −10 transcriptional element to finely tune the expression of T6SS genes. We propose that this elegant regulatory mechanism allows the optimum production of the T6SS in conditions where enteroaggregative E. coli encounters competing species.

Download Full-text