Relevant bibliographies by topics / Operonic regulation

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Operonic regulation'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Operonic regulation"

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Lewis, Janina P., Konrad Plata, Fan Yu, Adriana Rosato, and Cecilia Anaya. "Transcriptional organization, regulation and role of the Porphyromonas gingivalis W83 hmu haemin-uptake locus." Microbiology 152, no. 11 (November 1, 2006): 3367–82. http://dx.doi.org/10.1099/mic.0.29011-0.

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Porphyromonas gingivalis, an oral bacterium associated with periodontal disease, requires haemin for growth. Although several multigenic clusters encoding haemin-uptake systems are present on the genome of P. gingivalis, little is known regarding their transcriptional organization and expression. This study identified a 23 kDa iron-regulated haemin-binding protein encoded by a larger than previously reported variant of hmuY. It was shown that the hmu locus is larger than previously reported and is composed of six genes, hmuYRSTUV, encoding a novel hybrid haemin-uptake system. The locus has an operonic organization and the transcriptional start site is located 292 bp upstream of hmuY. The data indicate that the regulation of the operon is iron-dependent. Interestingly, differential regulation within the operon was demonstrated, resulting in excess of the hmuYR message encoding the outer-membrane proteins when compared to the full-length transcript. In addition, the hmuY transcript is more prevalent than the hmuR transcript. Secondary structure analysis of the hmuYRSTUV mRNA predicted the formation of several potential stem–loops in the 5′ ends of hmuR- and hmuS-specific mRNAs, consistent with the differential regulation observed. Finally, it was demonstrated that haemin binding and uptake are elevated in iron-depleted conditions and are reduced 45 % and 70 %, respectively, in an hmu-deficient strain when compared to the parental strain, indicating that the hmu locus plays a major role in haemin acquisition in P. gingivalis. Since homologues of the hmu locus were also found in Bacteroides fragilis, Bacteroides thetaiotaomicron and Prevotella intermedia, these findings may have implications for a better understanding of haemin acquisition in those organisms as well.
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Browne, Patrick D., and Hinsby Cadillo-Quiroz. "Contribution of Transcriptomics to Systems-Level Understanding of MethanogenicArchaea." Archaea 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/586369.

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Methane-producingArchaeaare of interest due to their contribution to atmospheric change and for their roles in technological applications including waste treatment and biofuel production. Although restricted to anaerobic environments, methanogens are found in a wide variety of habitats, where they commonly live in syntrophic relationships with bacterial partners. Owing to tight thermodynamic constraints of methanogenesis alone or in syntrophic metabolism, methanogens must carefully regulate their catabolic pathways including the regulation of RNA transcripts. The transcriptome is a dynamic and important control point in microbial systems. This paper assesses the impact of mRNA (transcriptome) studies on the understanding of methanogenesis with special consideration given to how methanogenesis is regulated to cope with nutrient limitation, environmental variability, and interactions with syntrophic partners. In comparison with traditional microarray-based transcriptome analyses, next-generation high-throughput RNA sequencing is greatly advantageous in assessing transcription start sites, the extent of 5′ untranslated regions, operonic structure, and the presence of small RNAs. We are still in the early stages of understanding RNA regulation but it is already clear that determinants beyond transcript abundance are highly relevant to the lifestyles of methanogens, requiring further study.
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Lakhova, Tatiana N., Fedor V. Kazantsev, Aleksey M. Mukhin, Nikolay A. Kolchanov, Yury G. Matushkin, and Sergey A. Lashin. "Algorithm for the Reconstruction of Mathematical Frame Models of Bacterial Transcription Regulation." Mathematics 10, no. 23 (November 28, 2022): 4480. http://dx.doi.org/10.3390/math10234480.

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Transcription regulation plays an important role in bacterial activity. The operon concept coined by François Jacob and Jacques Monod has had a considerable effect on investigations into gene expression regulation, including modeling. However, most such studies have considered the regulation models devised manually for one or several operons. For that reason, the objective of the present study was automated genome model reconstruction for different bacteria. The suggested algorithm accounted for all possible interactions of transcription factors and their binding sites in an operon’s promoter region. Transcription factor enumeration was performed using the deep-first search technique. The obtained models are of interest for those involved in the research of transcription factor regulatory effects on bacterial gene expression in microbiology and biotechnology.
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Brandis, Gerrit, Sha Cao, and Diarmaid Hughes. "Operon Concatenation Is an Ancient Feature That Restricts the Potential to Rearrange Bacterial Chromosomes." Molecular Biology and Evolution 36, no. 9 (May 27, 2019): 1990–2000. http://dx.doi.org/10.1093/molbev/msz129.

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Abstract The last common ancestor of the Gammaproteobacteria carried an important 40-kb chromosome section encoding 51 proteins of the transcriptional and translational machinery. These genes were organized into eight contiguous operons (rrnB-tufB-secE-rpoBC-str-S10-spc-alpha). Over 2 Gy of evolution, in different lineages, some of the operons became separated by multigene insertions. Surprisingly, in many Enterobacteriaceae, much of the ancient organization is conserved, indicating a strong selective force on the operons to remain colinear. Here, we show for one operon pair, tufB-secE in Salmonella, that an interruption of contiguity significantly reduces growth rate. Our data show that the tufB-secE operons are concatenated by an interoperon terminator–promoter overlap that plays a significant role regulating gene expression. Interrupting operon contiguity interferes with this regulation, reducing cellular fitness. Six operons of the ancestral chromosome section remain contiguous in Salmonella (tufB-secE-rpoBC and S10-spc-alpha) and, strikingly, each of these operon pairs is also connected by an interoperon terminator–promoter overlap. Accordingly, we propose that operon concatenation is an ancient feature that restricts the potential to rearrange bacterial chromosomes and can select for the maintenance of a colinear operon organization over billions of years.
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Aseev, Leonid V., Ludmila S. Koledinskaya, and Irina V. Boni. "Regulation of Ribosomal Protein OperonsrplM-rpsI,rpmB-rpmG, andrplU-rpmAat the Transcriptional and Translational Levels." Journal of Bacteriology 198, no. 18 (July 5, 2016): 2494–502. http://dx.doi.org/10.1128/jb.00187-16.

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ABSTRACTIt is widely assumed that in the best-characterized model bacteriumEscherichia coli, transcription units encoding ribosomal proteins (r-proteins) and regulation of their expression have been already well defined. However, transcription start sites for severalE. colir-protein operons have been established only very recently, so that information concerning the regulation of these operons at the transcriptional or posttranscriptional level is still missing. This paper describes for the first time thein vivoregulation of three r-protein operons,rplM-rpsI,rpmB-rpmG, andrplU-rpmA. The results demonstrate that transcription of all three operons is subject to ppGpp/DksA-dependent negative stringent control under amino acid starvation, in parallel with the rRNA operons. By using single-copy translational fusions with the chromosomallacZgene, we show here that at the translation level only one of these operons,rplM-rpsI, is regulated by the mechanism of autogenous repression involving the 5′ untranslated region (UTR) of the operon mRNA, whilerpmB-rpmGandrplU-rpmAare not subject to this type of regulation. This may imply that translational feedback control is not a general rule for modulating the expression ofE. colir-protein operons. Finally, we report that L13, a primary protein in 50S ribosomal subunit assembly, serves as a repressor ofrplM-rpsIexpressionin vivo, acting at a target within therplMtranslation initiation region. Thus, L13 represents a novel example of regulatory r-proteins in bacteria.IMPORTANCEIt is important to obtain a deeper understanding of the regulatory mechanisms responsible for coordinated and balanced synthesis of ribosomal components. In this paper, we highlight the major role of a stringent response in regulating transcription of three previously unexplored r-protein operons, and we show that only one of them is subject to feedback regulation at the translational level. Improved knowledge of the regulatory pathways controlling ribosome biogenesis may promote the development of novel antibacterial agents.
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Gaballa, Ahmed, and John D. Helmann. "Identification of a Zinc-Specific Metalloregulatory Protein, Zur, Controlling Zinc Transport Operons inBacillus subtilis." Journal of Bacteriology 180, no. 22 (November 15, 1998): 5815–21. http://dx.doi.org/10.1128/jb.180.22.5815-5821.1998.

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ABSTRACT Zinc is an essential nutrient for all cells, but remarkably little is known regarding bacterial zinc transport and its regulation. We have identified three of the key components acting to maintain zinc homeostasis in Bacillus subtilis. Zur is a metalloregulatory protein related to the ferric uptake repressor (Fur) family of regulators and is required for the zinc-specific repression of two operons implicated in zinc uptake, yciC andycdHIyceA. A zur mutant overexpresses the 45-kDa YciC membrane protein, and purified Zur binds specifically, and in a zinc-responsive manner, to an operator site overlapping theyciC control region. A similar operator precedes theycdH-containing operon, which encodes an ABC transporter. Two lines of evidence suggest that the ycdH operon encodes a high-affinity zinc transporter whereas YciC may function as part of a lower-affinity pathway. First, a ycdH mutant is impaired in growth in low-zinc medium, and this growth defect is exacerbated by the additional presence of a yciC mutation. Second, mutation ofycdH, but not yciC, alters the regulation of both the yciC and ycdH operons such that much higher levels of exogenous zinc are required for repression. We conclude that Zur is a Fur-like repressor that controls the expression of two zinc homeostasis operons in response to zinc. Thus, Fur-like regulators control zinc homeostasis in addition to their previously characterized roles in regulating iron homeostasis, acid tolerance responses, and oxidative stress functions.
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He, Hongjun, Holly A. Snyder, and Steven Forst. "Unique organization and regulation of the mrx fimbrial operon in Xenorhabdus nematophila." Microbiology 150, no. 5 (May 1, 2004): 1439–46. http://dx.doi.org/10.1099/mic.0.26853-0.

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Xenorhabdus nematophila, a Gram-negative bacterium belonging to the Proteus clade of the family Enterobacteriaceae, forms a mutualistic association with the soil nematode Steinernema carpocapsae. The nematode invades insects and releases Xenorhabdus into the haemolymph, where it participates in insect killing. To begin to understand the role of fimbriae in the unique life cycle of Xenorhabdus, the organization and expression of the mrx fimbrial operon was analysed. The mrx operon contained only five structural genes (mrxACDGH), making it one of the smallest chaperone-usher fimbrial operons studied to date. Unlike the mrp operon of Proteus mirabilis, a site-specific recombinase was not linked to the mrx operon. The intergenic region between the major fimbrial gene (mrxA) and the usher gene (mrxC) lacked a mrpB-like gene, but contained three tandem inverted repeat sequences located downstream of mrxA. A 940 nt mrxA-containing mRNA was the major transcript produced in cells growing on agar, while an mrx polycistronic mRNA was produced at low levels. A canonical σ 70 promoter, identified upstream of mrxA, was not subject to promoter inversion. Fimbriae were not produced in an lrp-mutant strain, suggesting that the leucine-responsive regulatory protein, Lrp, plays a role in the regulation of the mrx operon. These findings show that the genetic organization and regulation of the mrx operon is in several respects distinct from other chaperone-usher fimbrial operons.
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Schrader, Jared M., Gene-Wei Li, W. Seth Childers, Adam M. Perez, Jonathan S. Weissman, Lucy Shapiro, and Harley H. McAdams. "Dynamic translation regulation inCaulobactercell cycle control." Proceedings of the National Academy of Sciences 113, no. 44 (October 17, 2016): E6859—E6867. http://dx.doi.org/10.1073/pnas.1614795113.

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Progression of theCaulobactercell cycle requires temporal and spatial control of gene expression, culminating in an asymmetric cell division yielding distinct daughter cells. To explore the contribution of translational control, RNA-seq and ribosome profiling were used to assay global transcription and translation levels of individual genes at six times over the cell cycle. Translational efficiency (TE) was used as a metric for the relative rate of protein production from each mRNA. TE profiles with similar cell cycle patterns were found across multiple clusters of genes, including those in operons or in subsets of operons. Collections of genes associated with central cell cycle functional modules (e.g., biosynthesis of stalk, flagellum, or chemotaxis machinery) have consistent but different TE temporal patterns, independent of their operon organization. Differential translation of operon-encoded genes facilitates precise cell cycle-timing for the dynamic assembly of multiprotein complexes, such as the flagellum and the stalk and the correct positioning of regulatory proteins to specific cell poles. The cell cycle-regulatory pathways that produce specific temporal TE patterns are separate from—but highly coordinated with—the transcriptional cell cycle circuitry, suggesting that the scheduling of translational regulation is organized by the same cyclical regulatory circuit that directs the transcriptional control of theCaulobactercell cycle.
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Swanson, J. A., J. T. Mulligan, and S. R. Long. "Regulation of syrM and nodD3 in Rhizobium meliloti." Genetics 134, no. 2 (June 1, 1993): 435–44. http://dx.doi.org/10.1093/genetics/134.2.435.

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Abstract The early steps of symbiotic nodule formation by Rhizobium on plants require coordinate expression of several nod gene operons, which is accomplished by the activating protein NodD. Three different NodD proteins are encoded by Sym plasmid genes in Rhizobium meliloti, the alfalfa symbiont. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to host plant inducers. The third, NodD3, is an inducer-independent activator of nod operons. We previously observed that nodD3 carried on a multicopy plasmid required another closely linked gene, syrM, for constitutive nod operon expression. Here, we show that syrM activates expression of the nodD3 gene, and that nodD3 activates expression of syrM. The two genes constitute a self-amplifying positive regulatory circuit in both cultured Rhizobium and cells within the symbiotic nodule. We find little effect of plant inducers on the circuit or on expression of nodD3 carried on pSyma. This regulatory circuit may be important for regulation of nod genes within the developing nodule.
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Miguel-Arribas, Andrés, Ling Juan Wu, Claudia Michaelis, Ken-ichi Yoshida, Elisabeth Grohmann, and Wilfried J. J. Meijer. "Conjugation Operons in Gram-Positive Bacteria with and without Antitermination Systems." Microorganisms 10, no. 3 (March 8, 2022): 587. http://dx.doi.org/10.3390/microorganisms10030587.

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Genes involved in the same cellular process are often clustered together in an operon whose expression is controlled by an upstream promoter. Generally, the activity of the promoter is strictly controlled. However, spurious transcription undermines this strict regulation, particularly affecting large operons. The negative effects of spurious transcription can be mitigated by the presence of multiple terminators inside the operon, in combination with an antitermination system. Antitermination systems modify the transcription elongation complexes and enable them to bypass terminators. Bacterial conjugation is the process by which a conjugative DNA element is transferred from a donor to a recipient cell. Conjugation involves many genes that are mostly organized in one or a few large operons. It has recently been shown that many conjugation operons present on plasmids replicating in Gram-positive bacteria possess a bipartite antitermination system that allows not only many terminators inside the conjugation operon to be bypassed, but also the differential expression of a subset of genes. Here, we show that some conjugation operons on plasmids belonging to the Inc18 family of Gram-positive broad host-range plasmids do not possess an antitermination system, suggesting that the absence of an antitermination system may have advantages. The possible (dis)advantages of conjugation operons possessing (or not) an antitermination system are discussed.
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Dissertations / Theses on the topic "Operonic regulation"

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Patterson, Kathryn Grace. "Gene regulation in the lac operon." Thesis, Montana State University, 2009. http://etd.lib.montana.edu/etd/2009/patterson/PattersonK0809.pdf.

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The lac operon, a jointly controlled series of genes in the bacteria E. coli, has been studied extensively since the 1940's. The lac operon genes are transcribed and then translated into proteins necessary for transport and digestion of lactose. The operon is activated in the presence of lactose after glucose, the preferred carbon source, has been expended. In this thesis, we introduce a biophysical model using the Shea-Ackers framework for modeling promoter dynamics. The model spans two scales: the inputs are biophysical parameters of molecular interactions and the result is a level of gene expression - a macroscopic behavior of the cell. We include all experimentally suggested control mechanisms into the model, even though the experimental evidence is stronger for some of these mechanisms than others. We compare our model to experimental data and explore the individual contribution of the proposed mechanisms by removing them one by one and testing the reduced model's fit to the data. Finally, we find a minimal model which faithfully represents the available data, yet includes only the minimal number of control mechanisms.
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Lazarus, Linda Ruth. "The role of FIS in tyrT transcriptional regulation." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259766.

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Vichivanives, Padungsri. "Transcriptional regulation of the Rhodobacter Capsulatus CO? fixation operons /." The Ohio State University, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=osu1488205318510482.

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Nold, Niklas. "Untersuchungen zur Regulation des sol-Operons in Clostridium acetobutylicum." [S.l. : s.n.], 2008. http://nbn-resolving.de/urn:nbn:de:bsz:289-vts-65443.

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Clarke, Simon Richard. "Regulation of the bla operon in Staphylococcus aureus." Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326077.

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Min, Kyung-Tai. "Regulation of the spoIIA operon in Bacillus subtilis." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333440.

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Low, Yuen Li. "Metal regulation of the E. faecalis efaCBA operon." Thesis, University of Bath, 2002. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.760823.

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Dole, Sudhanshu. "Multiple level regulation of the Escherichia coli bgl operon." [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=963645978.

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Davies, Ian J. "Transcriptional regulation of the qua operon of Escherichia coli." Thesis, University of Southampton, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314696.

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Yuen, Hiu-fung. "A study of the catabolite repression of the dehalogenase IVa gene of Burkholderia cepacia MBA4." Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B30682113.

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Books on the topic "Operonic regulation"

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Keen, Jennifer Emily Jane. The regulation of the Escherichia Coli melibiose operon. Birmingham: University of Birmingham, 1997.

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Maguire, M. The regulation of the three chaperonin operons of Rhizobium leguminosarum. Birmingham: University of Birmingham, 2000.

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Gould, Phillip Spencer. Regulation and role of the three chaperonin operons of Rhizobium leguminosarum. Birmingham: University of Birmingham, 2002.

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Wu, Hui-Chung. Co-regulation of transcription at the Escherichia coli nir operon promoter. Birmingham: University of Birmingham, 1998.

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Lee, See-Lai. Studies on regulation of expression of the verotoxin operon and of the 39K replication protein of plasmid pFA3 using gene and operon fusions to lac Z. Ottawa: National Library of Canada, 1990.

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Nilles, Matthew L. Regulation of the acrAB operon of Escherichia coli. 1995.

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Li, Suzanne C. Control elements within the ribosomal RNA operons of E. coli. 1985.

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Peacock, Susan Louise. In vitro studies on the regulation of gene expression in RNA polymerase operons of Escherichia coli. 1985.

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Saltman, Laura Herschaft. The kilA operon of promiscuous plasmid RK2: Effects of the klaA gene on Escherichia coli growth and bacteriophage [lambda] development. 1991.

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Climie, Shane Christopher. mRNA secondary structure and feedback regulation of the L10 ribosomal protein operon of "Escherichia coli". 1988.

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Book chapters on the topic "Operonic regulation"

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Adhya, Sankar. "The lac and gal Operons Today." In Regulation of Gene Expression in Escherichia coli, 181–200. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4684-8601-8_9.

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Brot, N., S. Peacock, and H. Weissbach. "Regulation of the Escherichia coli L10 Operon." In Springer Series in Molecular Biology, 749–65. New York, NY: Springer New York, 1986. http://dx.doi.org/10.1007/978-1-4612-4884-2_44.

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Pinto, Marcelo Cezar, Luciana Foss, José Carlos Merino Mombach, and Leila Ribeiro. "Modeling and Property Verification of Lactose Operon Regulation." In Advances in Bioinformatics and Computational Biology, 95–106. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11532323_11.

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Ajdic, Dragana, and Joseph J. Ferretti. "Regulation of the Galactose Operon of Streptococcus mutans." In Streptococci and the Host, 1015–18. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4899-1825-3_239.

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Tian, Tianhai, and Kevin Burrage. "A Mathematical Model for Genetic Regulation of the Lactose Operon." In Computational Science and Its Applications – ICCSA 2005, 1245–53. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11424826_132.

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Nakazawa, Teruko, Sachiye Inouye, and Atsushi Nakazawa. "Positive Regulation and Transcription Initiation of XYL Operons on TOL Plasmid." In Plasmids in Bacteria, 415–29. Boston, MA: Springer US, 1985. http://dx.doi.org/10.1007/978-1-4613-2447-8_30.

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Wallington, Emma J., J. Allan Downie, and Peter A. Lund. "Distinct Modes of Regulation in Two of the Three Chaperonin Operons of Rhizobium leguminosarum." In Biological Nitrogen Fixation for the 21st Century, 158. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-011-5159-7_62.

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Alberti, Sebastian, and Michael R. Wessels. "Regulation of Hyaluronic Acid Capsule Production by the has Operon Promoter in Group A Streptococci." In Streptococci and the Host, 975–78. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4899-1825-3_229.

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Zengel, Janice M., and Lasse Lindahl. "Regulation of the Eleven Gene S10 Ribosomal Protein Operon by the 50S Subunit Protein L4." In The Translational Apparatus, 131–38. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2407-6_13.

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Parveen, Sadiya, William R. Bishai, and John R. Murphy. "Corynebacterium diphtheriae: Diphtheria Toxin, the tox Operon, and Its Regulation by Fe2+ Activation of apo-DtxR." In Gram-Positive Pathogens, 1154–64. Washington, DC, USA: ASM Press, 2019. http://dx.doi.org/10.1128/9781683670131.ch69.

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Conference papers on the topic "Operonic regulation"

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"Automatic annotation of operons responsible for O-antigen synthesis." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-086.

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Gao, Ling, Yutian Lin, Huibin Lin, Xiaoyi Jia, Jianqun Lin, and Jianqiang Lin. "Mathematical modeling of lac operon regulation dynamics." In International conference on Human Health and Medical Engineering. Southampton, UK: WIT Press, 2014. http://dx.doi.org/10.2495/hhme130611.

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"The secondary structure model of the transcriptional terminator of the C. glutamicum inbc operon proved by mutational analysis of the operon gene expression and valine production." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-333.

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Suen, Garret, and Christian Jacob. "A Symbolic and Graphical Gene Regulation Model of the lac Operon." In Proceedings of the Fifth International Mathematica Symposium. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2003. http://dx.doi.org/10.1142/9781848161313_0010.

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Yang, Xiaoli, Yifan Cai, and Charles Tseng. "Visualizing Bacterial Gene Regulation with an Interactive Computer Program: The Trp Operon." In 2015 15th International Conference on Computational Science and Its Applications (ICCSA). IEEE, 2015. http://dx.doi.org/10.1109/iccsa.2015.12.

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Liaudanskaya, Anastasia, Katsiaryna Verameyenka, and Natalia Maksimova. "PCR analysis of phenazine operon transcriptional regulation in pseudomonas Chlororaphis Subsp. Aurantiaca." In National Scientific Symposium With International Participation: Modern Biotechnologies – Solutions to the Challenges of the Contemporary World. Institute of Microbiology and Biotechnology, Republic of Moldova, 2021. http://dx.doi.org/10.52757/imb21.084.

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"PFNA operon of bifidobacteria: Role of bioinformatics in the discovery, structural and functional characterization, and possible application in biotechnology." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-285.

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Lu, Lili, and Hongwei Lou. "Mathematical Description of the Lac Operon Regulation in Diauxic and Non-Diauxic Growth on Glucose and Lactose." In 2009 3rd International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2009. http://dx.doi.org/10.1109/icbbe.2009.5163028.

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Sun, Yaqin, Xiaojia Mu, Zheng Li, Hu Teng, and ZhiLong Xiu. "Robustness and Nonlinear Dynamic Analysis for Trp Operon and Optimization of Tryptophan Production: An Integrated Model Considering Gene Regulation, Genes Interaction and Product Excretion." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5517954.

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10

Pannekok, H., A. J. Van Zonneveid, C. J. M. de vries, M. E. MacDonald, H. Veerman, and F. Blasi. "FUNCTIONAL PROPERTIES OF DELETION-MUTANTS OF TISSUE-TYPE PLASMINOGEN ACTIVATOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643724.

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Over the past twenty-five years, genetic methods have generated a wealth of information on the regulation and the structure-function relationship of bacterial genes.These methods are based on the introduction of random mutations in a gene to alter its function. Subsequently, genetic techniques cure applied to localize the mutation, while the nature of the impairedfunction could be determined using biochemical methods. Classic examples of this approach is now considered to be the elucidation of the structure and function of genes, constituting the Escherichia coli lactose (lac) and tryptophan (trp) operons,and the detailed establishment of the structure and function of the repressor (lacl) of the lac operon. Recombinant DNA techniques and the development of appropriate expression systems have provided the means both to study structure and functionof eukaryotic (glyco-) proteins and to create defined mutations with a predestinedposition. The rationale for the construction of mutant genes should preferentiallyrely on detailed knowledge of the three-dimensional structure of the gene product.Elegant examples are the application of in vitro mutagenesis techniques to substitute amino-acid residues near the catalytic centre of subtilisin, a serine proteasefrom Bacillus species and to substituteanamino acid in the reactive site (i.e. Pi residue; methionine) of α-antitrypsin, a serine protease inhibitor. Such substitutions have resulted into mutant proteins which are less susceptible to oxidation and, in some cases, into mutant proteins with a higher specific activity than the wild-type protein.If no data are available on the ternary structure of a protein, other strategies have to be developed to construct intelligent mutants to study the relation between the structure and the function of a eukaryotic protein. At least for a number of gene families, the gene structure is thought to be created by "exon shuffling", an evolutionary recombinational process to insert an exon or a set of exons which specify an additional structural and/or functional domain into a pre-existing gene. Both the structure of the tissue-type plasminogen activator protein(t-PA) and the t-PA gene suggest that this gene has evolved as a result of exon shuffling. As put forward by Gilbert (Science 228 (1985) 823), the "acid test"to prove the validity of the exon shuffling theory is either to delete, insert or to substitute exon(s) (i.e. in the corresponding cDNA) and toassay the properties of the mutant proteins to demonstrate that an exon or a set of adjacent exons encode (s) an autonomousfunction. Indeed, by the construction of specific deletions in full-length t-PA cDNA and expression of mutant proteins intissue-culture cells, we have shown by this approach that exon 2 of thet-PA gene encodes the function required forsecretion, exon 4 encodes the "finger" domain involved in fibrin binding(presumably on undegraded fibrin) and the set of exons 8 and 9 specifies kringle 2, containing a lysine-binding sit(LBS) which interacts with carboxy-terminal lysines, generated in fibrin after plasmic digestion. Exons 10 through 14 encode the carboxy-ter-minal light chain of t-PA and harbor the catalytic centre of the molecule and represents the predominant "target site" for the fast-acting endothelial plasminogen activator inhibitor (PAI-1).As a follow-up of this genetic approach to construct deletion mutants of t-PA, we also created substitution mutants of t-PA. Different mutants were constructed to substitute cDNA encoding thelight chain of t-PA by cDNA encoding the B-chain of urokinase (u-PA), in order to demonstrate that autonomous structural and functional domains of eitherone of the separate molecules are able toexert their intrinsic properties in a different context (C.J.M. de Vries et al., this volume). The possibilities and the limitations of this approach to study the structure and the function of t-PA and of other components of the fibrinolytic process will be outlined.
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Reports on the topic "Operonic regulation"

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Kapulnik, Yoram, and Donald A. Phillips. Isoflavonoid Regulation of Root Bacteria. United States Department of Agriculture, January 1996. http://dx.doi.org/10.32747/1996.7570561.bard.

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The overall objective of this project was to develop a conceptual framework for enhancing root colonization by beneficial bacteria. To accomplish this aim we tested the hypothesis that production and excretion of the plant phytoalexin medicarpin can be used for creation of a special niche along the legume roots, where beneficial microorganism, such as rhizobium, will have a selective advantage. On the Israeli side it was shown that higher medicarpin levels are exuded following the application of Rhizobium meliloti to the rhizosphere but the specific biochemical pathway governing medicarpin production was not induced significantly enough to support a constant production and excretion of this molecule to the rhizosphere. Furthermore, pathogenic bacteria and chemical elicitors were found to induce higher levels of this phytoalexin and it became important to test its natural abundance in field grown plants. On the US side, the occurrence of flavonoids and nucleosides in agricultural soils has been evaluated and biologically significant quantities of these molecules were identified. A more virulent Agrobacterium tumefaciens strain was isolated from alfalfa (Medicago sativa L.) which forms tumors on a wide range of plant species. This isolate contains genes that increase competitive colonization abilities on roots by reducing the accumulation of alfalfa isoflavonoids in the bacterial cells. Following gene tagging efforts the US lab found that mutation in the bacterial efflux pump operons of this isolate reduced its competitive abilities. This results support our original hypothesis that detoxification activity of isoflavenoids molecules, based on bacterial gene(s), is an important selection mechanism in the rhizosphere. In addition, we focused on biotin as a regulatory element in the rhizosphere to support growth of some rhizosphere microorganisms and designed a bacterial gene construct carrying the biotin-binding protein, streptavidin. Expressing this gene in tobacco roots did not affect the biotin level but its expression in alfalfa was lethal. In conclusion, the collaborative combination of basic and applied approaches toward the understanding of rhizosphere activity yielded new knowledge related to the colonization of roots by beneficial microorganisms in the presence of biological active molecules exuded from the plant roots.
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Sessa, Guido, and Gregory Martin. role of FLS3 and BSK830 in pattern-triggered immunity in tomato. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604270.bard.

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Pattern-recognition receptors (PRRs) located on the plant cell surface initiate immune responses by perceiving conserved pathogen molecules known as pathogen-associated molecular patterns (PAMPs). PRRs typically function in multiprotein complexes that include transmembrane and cytoplasmickinases and contribute to the initiation and signaling of pattern-triggered immunity (PTI). An important challenge is to identify molecular components of PRR complexes and downstream signaling pathways, and to understand the molecular mechanisms that mediate their function. In research activities supported by BARD-4931, we studied the role of the FLAGELLIN SENSING 3 (FLS3) PRR in the response of tomato leaves to flagellin-derivedPAMPs and PTI. In addition, we investigated molecular properties of the tomato brassinosteroid signaling kinase 830 (BSK830) that physically interacts with FLS3 and is a candidate for acting in the FLS3 signaling pathway. Our investigation refers to the proposal original objectives that were to: 1) Investigate the role of FLS3 and its interacting proteins in PTI; 2) Investigate the role of BSK830 in PTI; 3) Examine molecular and phosphorylation dynamics of the FLS3-BSK830 interaction; 4) Examine the possible interaction of FLS3 and BSK830 with Pstand Xcveffectors. We used CRISPR/Cas9 techniques to develop plants carrying single or combined mutations in the FLS3 gene and in the paralogsFLS2.1 and FLS2.2 genes, which encode the receptor FLAGELLIN SENSING2 (FLS2), and analyzed their function in PTI. Domain swapping analysis of the FLS2 and FLS3 receptors revealed domains of the proteins responsible for PAMP detection and for the different ROS response initiated by flgII-28/FLS3 as compared to flg22/FLS2. In addition, in vitro kinase assays and point mutations analysis identified FLS2 and FLS3 domains required for kinase activity and ATP binding. In research activities on tomato BSK830, we found that it interacts with PRRs and with the co-receptor SERK3A and PAMP treatment affects part of these interactions. CRISPR/Cas9 bsk830 mutant plants displayed enhanced pathogen susceptibility and reduced ROS production upon PAMP treatment. In addition, BSK830 interacted with 8 Xanthomonastype III secreted effectors. Follow up analysis revealed that among these effectors XopAE is part of an operon, is translocated into plant cells, and displays E3 ubiquitinligase activity. Our investigation was also extended to other Arabidopsis and tomato BSK family members. Arabidopsis BSK5 localized to the plant cell periphery, interacted with receptor-like kinases, and it was phosphorylatedin vitro by the PEPR1 and EFRPRRs. bsk5 mutant plants displayed enhanced susceptibility to pathogens and were impaired in several, but not all, PAMP-induced responses. Conversely, BSK5 overexpression conferred enhanced disease resistance and caused stronger PTI responses. Genetic complementation suggested that proper localization, kinase activity, and phosphorylation by PRRs are critical for BSK5 function. BSK7 and BSK8 specifically interacted with the FLS2 PRR, their respective mutant plants were more susceptible to B. cinereaand displayed reduced flg22-induced responses. The tomato BSK Mai1 was found to interact with the M3KMAPKKK, which is involved in activation of cell death associated with effector-triggered immunity. Silencing of Mai1 in N. benthamianaplants compromised cell death induced by a specific class of immune receptors. In addition, co-expression of Mai1 and M3Kin leaves enhanced MAPKphosphorylation and cell death, suggesting that Mai1 acts as a molecular link between pathogen recognition and MAPK signaling. Finally, We identified the PP2C phosphatase Pic1 that acts as a negative regulator of PTI by interacting with and dephosphorylating the receptor-like cytoplasmickinase Pti1, which is a positive regulator of plant immunity. The results of this investigation shed new light on the molecular characteristics and interactions of components of the immune system of crop plants providing new knowledge and tools for development of novel strategies for disease control.
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