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The Journal of Biological Chemistry Dec 2017Genome sequencing analysis has revealed at least 35 clusters of likely biosynthetic genes for secondary metabolites in Disruption of encoding a global regulator (AdpA)...
Genome sequencing analysis has revealed at least 35 clusters of likely biosynthetic genes for secondary metabolites in Disruption of encoding a global regulator (AdpA) resulted in the failure of nikkomycin production, whereas other antibacterial activities against , , and were observed with the fermentation broth of ΔadpA but not with that of the wild-type strain. Transcriptional analysis showed that a cryptic gene cluster (), which shows high identity with an oviedomycin biosynthetic gene cluster (), was activated in ΔadpA. The corresponding product of was characterized as oviedomycin by MS and NMR spectroscopy. To understand the molecular mechanism of activation, the roles of six regulatory genes situated in the cluster were investigated. Among them, proteins encoded by co-transcribed genes and are positive regulators of AdpA directly represses the transcription of and Co-overexpression of and can relieve the repression of AdpA on transcription and effectively activate oviedomycin biosynthesis. The promoter of is identified as the direct target of OvmZ and OvmW. This is the first report that AdpA can simultaneously activate nikkomycin biosynthesis but repress oviedomycin biosynthesis in one strain. Our findings provide an effective strategy that is able to activate cryptic secondary metabolite gene clusters by genetic manipulation of global regulatory genes.
Topics: Aminoglycosides; Ethers, Cyclic; Genes, Bacterial; Genes, Regulator; Multigene Family; Streptomyces
PubMed: 28972184
DOI: 10.1074/jbc.M117.809145 -
Journal of Dental Research Aug 2016Analytic approaches confined to fold-change comparisons of gene expression patterns between states of health and disease are unable to distinguish between primary causal...
Analytic approaches confined to fold-change comparisons of gene expression patterns between states of health and disease are unable to distinguish between primary causal disease drivers and secondary noncausal events. Genome-wide reverse engineering approaches can facilitate the identification of candidate genes that may distinguish between causal and associative interactions and may account for the emergence or maintenance of pathologic phenotypes. In this work, we used the algorithm for the reconstruction of accurate cellular networks (ARACNE) to analyze a large gene expression profile data set (313 gingival tissue samples from a cross-sectional study of 120 periodontitis patients) obtained from clinically healthy (n = 70) or periodontitis-affected (n = 243) gingival sites. The generated transcriptional regulatory network of the gingival interactome was subsequently interrogated with the master regulator inference algorithm (MARINA) and gene expression signature data from healthy and periodontitis-affected gingiva. Our analyses identified 41 consensus master regulator genes (MRs), the regulons of which comprised between 25 and 833 genes. Regulons of 7 MRs (HCLS1, ZNF823, XBP1, ZNF750, RORA, TFAP2C, and ZNF57) included >500 genes each. Gene set enrichment analysis indicated differential expression of these regulons in gingival health versus disease with a type 1 error between 2% and 0.5% and with >80% of the regulon genes in the leading edge. Ingenuity pathway analysis showed significant enrichment of 36 regulons for several pathways, while 6 regulons (those of MRs HCLS1, IKZF3, ETS1, NHLH2, POU2F2, and VAV1) were enriched for >10 pathways. Pathways related to immune system signaling and development were the ones most frequently enriched across all regulons. The unbiased analysis of genome-wide regulatory networks can enhance our understanding of the pathobiology of human periodontitis and, after appropriate validation, ultimately identify target molecules of diagnostic, prognostic, or therapeutic value.
Topics: Adult; Algorithms; Case-Control Studies; Chronic Periodontitis; Cross-Sectional Studies; Genes, Regulator; Gingiva; Humans; Periodontitis; Transcriptome
PubMed: 27302879
DOI: 10.1177/0022034516653588 -
The conserved role and divergent regulation of foxa, a pan-eumetazoan developmental regulatory gene.Developmental Biology Sep 2011Foxa is a forkhead transcription factor that is expressed in the endoderm lineage across metazoans. Orthologs of foxa are expressed in cells that intercalate, polarize,... (Review)
Review
Foxa is a forkhead transcription factor that is expressed in the endoderm lineage across metazoans. Orthologs of foxa are expressed in cells that intercalate, polarize, and form tight junctions in the digestive tracts of the mouse, the sea urchin, and the nematode and in the chordate notochord. The loss of foxa expression eliminates these morphogenetic processes. The remarkable similarity in foxa phenotypes in these diverse organisms raises the following questions: why is the developmental role of Foxa so highly conserved? Is foxa transcriptional regulation as conserved as its developmental role? Comparison of the regulation of foxa orthologs in sea urchin and in Caenorhabditis elegans shows that foxa transcriptional regulation has diverged significantly between these two organisms, particularly in the cells that contribute to the C. elegans pharynx formation. We suggest that the similarity of foxa phenotype is due to its role in an ancestral gene regulatory network that controlled intercalation followed by mesenchymal-to-epithelial transition. foxa transcriptional regulation had evolved to support the developmental program in each species so foxa would play its role controlling morphogenesis at the necessary embryonic address.
Topics: Animals; Caenorhabditis elegans; Conserved Sequence; Forkhead Transcription Factors; Gene Expression Regulation, Developmental; Genes, Developmental; Genes, Regulator; Humans; Mesenchymal Stem Cells
PubMed: 21130759
DOI: 10.1016/j.ydbio.2010.11.027 -
PloS One 2022Synthetic biology has successfully advanced our ability to design and implement complex, time-varying genetic circuits to control the expression of recombinant proteins....
Synthetic biology has successfully advanced our ability to design and implement complex, time-varying genetic circuits to control the expression of recombinant proteins. However, these circuits typically require the production of regulatory genes whose only purpose is to coordinate expression of other genes. When designing very small genetic constructs, such as viral genomes, we may want to avoid introducing such auxiliary gene products while nevertheless encoding complex expression dynamics. To this end, here we demonstrate that varying only the placement and strengths of promoters, terminators, and RNase cleavage sites in a computational model of a bacteriophage genome is sufficient to achieve solutions to a variety of basic gene expression patterns. We discover these genetic solutions by computationally evolving genomes to reproduce desired gene expression time-course data. Our approach shows that non-trivial patterns can be evolved, including patterns where the relative ordering of genes by abundance changes over time. We find that some patterns are easier to evolve than others, and comparable expression patterns can be achieved via different genetic architectures. Our work opens up a novel avenue to genome engineering via fine-tuning the balance of gene expression and gene degradation rates.
Topics: Gene Expression; Gene Regulatory Networks; Genes, Regulator; Promoter Regions, Genetic; Synthetic Biology
PubMed: 35617346
DOI: 10.1371/journal.pone.0268883 -
Microbial Cell Factories Feb 2018The deep-sea-derived microbe Streptomyces koyangensis SCSIO 5802 produces neoabyssomicins A-B (1-2) and abyssomicins 2 (3) and 4 (4). Neoabyssomicin A (1) augments human...
BACKGROUND
The deep-sea-derived microbe Streptomyces koyangensis SCSIO 5802 produces neoabyssomicins A-B (1-2) and abyssomicins 2 (3) and 4 (4). Neoabyssomicin A (1) augments human immunodeficiency virus-1 (HIV-1) replication whereas abyssomicin 2 (3) selectively reactivates latent HIV and is also active against Gram-positive pathogens including methicillin-resistant Staphylococcus aureus (MRSA). Structurally, neoabyssomicins A-B constitute a new subtype within the abyssomicin family and feature unique structural traits characteristic of extremely interesting biosynthetic transformations.
RESULTS
In this work, the biosynthetic gene cluster (BGC) for the neoabyssomicins and abyssomicins, composed of 28 opening reading frames, was identified in S. koyangensis SCSIO 5802, and its role in neoabyssomicin/abyssomicin biosynthesis was confirmed via gene inactivation and heterologous expression experiments. Bioinformatics and genomics analyses enabled us to propose a biosynthetic pathway for neoabyssomicin/abyssomicin biosynthesis. Similarly, a protective export system by which both types of compounds are secreted from the S. koyangensis producer was identified, as was a four-component ABC transporter-based import system central to neoabyssomicin/abyssomicin biosynthesis. Furthermore, two regulatory genes, abmI and abmH, were unambiguously shown to be positive regulators of neoabyssomicin/abyssomicin biosynthesis. Consistent with their roles as positive regulatory genes, the overexpression of abmI and abmH (independent of each other) was shown to improve neoabyssomicin/abyssomicin titers.
CONCLUSIONS
These studies provide new insight into the biosynthesis of the abyssomicin class of natural products, and highlight important exploitable features of its BGC for future efforts. Elucidation of the neoabyssomicin/abyssomicin BGC now enables combinatorial biosynthetic initiatives aimed at improving both the titers and pharmaceutical properties of these important natural products-based drug leads.
Topics: Biosynthetic Pathways; Genes, Regulator; Multigene Family; Streptomyces
PubMed: 29463238
DOI: 10.1186/s12934-018-0875-1 -
PloS One 2023In systems biology, the accurate reconstruction of Gene Regulatory Networks (GRNs) is crucial since these networks can facilitate the solving of complex biological...
In systems biology, the accurate reconstruction of Gene Regulatory Networks (GRNs) is crucial since these networks can facilitate the solving of complex biological problems. Amongst the plethora of methods available for GRN reconstruction, information theory and fuzzy concepts-based methods have abiding popularity. However, most of these methods are not only complex, incurring a high computational burden, but they may also produce a high number of false positives, leading to inaccurate inferred networks. In this paper, we propose a novel hybrid fuzzy GRN inference model called MICFuzzy which involves the aggregation of the effects of Maximal Information Coefficient (MIC). This model has an information theory-based pre-processing stage, the output of which is applied as an input to the novel fuzzy model. In this preprocessing stage, the MIC component filters relevant genes for each target gene to significantly reduce the computational burden of the fuzzy model when selecting the regulatory genes from these filtered gene lists. The novel fuzzy model uses the regulatory effect of the identified activator-repressor gene pairs to determine target gene expression levels. This approach facilitates accurate network inference by generating a high number of true regulatory interactions while significantly reducing false regulatory predictions. The performance of MICFuzzy was evaluated using DREAM3 and DREAM4 challenge data, and the SOS real gene expression dataset. MICFuzzy outperformed the other state-of-the-art methods in terms of F-score, Matthews Correlation Coefficient, Structural Accuracy, and SS_mean, and outperformed most of them in terms of efficiency. MICFuzzy also had improved efficiency compared with the classical fuzzy model since the design of MICFuzzy leads to a reduction in combinatorial computation.
Topics: Algorithms; Computational Biology; Gene Regulatory Networks; Systems Biology; Genes, Regulator; Models, Genetic
PubMed: 37418430
DOI: 10.1371/journal.pone.0288174 -
Applied and Environmental Microbiology Dec 2023Central metabolism plays a key role in the control of growth and antibiotic production in streptomycetes. Specifically, aminosugars act as signaling molecules that...
Central metabolism plays a key role in the control of growth and antibiotic production in streptomycetes. Specifically, aminosugars act as signaling molecules that affect development and antibiotic production, via metabolic interference with the global repressor DasR. While aminosugar metabolism directly connects to other major metabolic routes such as glycolysis and cell wall synthesis, several important aspects of their metabolism are yet unresolved. Accumulation of -acetylglucosamine 6-phosphate or glucosamine 6-phosphate is lethal to many bacteria, a yet unresolved phenomenon referred to as "aminosugar sensitivity." We made use of this concept by selecting for suppressors in genes related to glucosamine toxicity in mutants, which showed that the gene pair of -family regulatory gene and major facilitator superfamily transporter gene sco1448 forms a cryptic rescue mechanism. Inactivation of resulted in the expression of sco1448, which then prevents the toxicity of amino sugar-derived metabolites in . The systems biology of RokL6 and its transcriptional control of sco1448 shed new light on aminosugar metabolism in streptomycetes and on the response of bacteria to aminosugar toxicity.
Topics: Streptomyces coelicolor; Glucosamine; Streptomyces; Amino Sugars; Anti-Bacterial Agents; Genes, Regulator; Bacterial Proteins; Gene Expression Regulation, Bacterial
PubMed: 37982622
DOI: 10.1128/aem.01674-23 -
Proceedings of the National Academy of... Nov 1982GAL4 is a classically defined positive regulatory gene controlling the five inducible structural genes of galactose/melibiose utilization in yeast. The positive...
GAL4 is a classically defined positive regulatory gene controlling the five inducible structural genes of galactose/melibiose utilization in yeast. The positive regulatory function of the GAL4 gene product in turn is controlled by the product of another gene, the negative regulator GAL80. We have cloned a 3.1-kilobase fragment containing GAL4 by homologous complementation using the multicopy chimeric vector YEp24 and demonstrated that multiple copies of GAL4 in yeast have pronounced dosage effects on the expression of the structural genes. Yeast transformed with GAL4-bearing plasmid become constitutive for expression of the galactose/melibiose genes, even in normally repressing (glucose) medium. Multiple copies of the GAL4 plasmid also increase expression of the structural genes in inducing (galactose) medium and can partially overcome the effects of a dominant super-repressor mutant, GAL80S. Using an internal deletion in GAL4, we have demonstrated that these dosage effects are due to overproduction of GAL4 positive regulatory product rather than an effect of the flanking sequences titrating out a negative regulator. These results point to the importance of competitive interplay between the positive and negative regulatory proteins in the control of this system. We have also used the dosage effect of GAL4 plasmid in combination with different GAL4 and GAL80 alleles to create new phenotypes. We interpret these phenotypes as indicating that (i) the repressing effects of glucose, at least in part, are mediated by the product of the negative regulatory gene, GAL80, and (ii) the GAL80 protein may have specific interactions with the control regions of the structural genes.
Topics: Cloning, Molecular; DNA Restriction Enzymes; DNA Transposable Elements; DNA, Fungal; Disaccharides; Escherichia coli; Galactose; Genes, Regulator; Melibiose; Plasmids; Saccharomyces cerevisiae
PubMed: 6294669
DOI: 10.1073/pnas.79.22.6971 -
Genetics Oct 1991A trans-acting regulatory gene, Inr-a, that alters the level of expression of the white eye color locus as an inverse function of the number of its functional copies is...
A trans-acting regulatory gene, Inr-a, that alters the level of expression of the white eye color locus as an inverse function of the number of its functional copies is described. Several independent lines of evidence demonstrate that this regulatory gene interacts with white via the promoter sequences. Among these are the observations that the inverse regulatory effect is conferred to the Adh gene when fused to the white promoter and that cis-regulatory mutants of white fail to respond. The phenotypic response to Inr-a is found in all tissues in which white is expressed, and mutants of the regulator exhibit a recessive lethality during larval periods. Increased white messenger RNA levels in pupal stages are found in Inr-a/+ individuals versus +/+ and a coordinate response is observed for mRNA levels from the brown and scarlet loci. All are structurally related and participate in pigment deposition. These experiments demonstrate that a single regulatory gene can exert an inverse effect on a target structural locus, a situation postulated from segmental aneuploid studies of gene expression and dosage compensation.
Topics: Alcohol Dehydrogenase; Alleles; Animals; Crosses, Genetic; Drosophila; Female; Gene Expression Regulation; Genes, Lethal; Genes, Regulator; Genetic Complementation Test; Male; Mutation; Organ Specificity; Phenotype; Pigmentation; RNA, Messenger; Restriction Mapping
PubMed: 1743487
DOI: 10.1093/genetics/129.2.463 -
Molecular and Cellular Biology Aug 1988The positively acting regulatory gene amdR of Aspergillus nidulans coordinately regulates the expression of four unlinked structural genes involved in acetamide (amdS),...
The positively acting regulatory gene amdR of Aspergillus nidulans coordinately regulates the expression of four unlinked structural genes involved in acetamide (amdS), omega amino acid (gatA and gabA), and lactam (lamA) catabolism. By the use of DNA-mediated transformation of A. nidulans, the amdR regulatory gene was cloned from a genomic cosmid library. Southern blot analysis of DNA from various loss-of-function amdR mutants revealed the presence of four detectable DNA rearrangements, including a deletion, an insertion, and a translocation. No detectable DNA rearrangements were found in several constitutive amdRc mutants. Analysis of the fate of amdR-bearing plasmids in transformants showed that 10 to 20% of the transformation events were homologous integrations or gene conversions, and this phenomenon was exploited in developing a strategy by which amdRc and amdR- alleles can be readily cloned and analyzed. Examination of the transcription of amdR by Northern blot (RNA blot) analysis revealed the presence of two mRNAs (2.7 and 1.8 kilobases) which were constitutively synthesized at a very low level. In addition, amdR transcription did not appear to depend on the presence of a functional amdR product nor was it altered in amdRc mutants. The dosage effects of multiple copies of amdR in transformants were examined, and it was shown that such transformants exhibited stronger growth than did the wild type on acetamide and pyrrolidinone media, indicating increased expression of the amdS and lamA genes, respectively. These results were used to formulate a model for amdR-mediated regulation of gene expression in which the low constitutive level of amdR product sets the upper limits of basal and induced transcription of the structural genes. Multiple copies of 5' sequences from the amdS gene can result in reduced growth on substrates whose utilization is dependent on amdR-controlled genes. This has been attributed to titration of limiting amdR gene product. Strong support for this proposal was obtained by showing that multiple copies of the amdR gene can reverse this phenomenon (antititration).
Topics: Aspergillus nidulans; Cloning, Molecular; Genes; Genes, Fungal; Genes, Regulator; Genotype; Mutation; Plasmids; Transcription, Genetic
PubMed: 3062382
DOI: 10.1128/mcb.8.8.3532-3541.1988