• Microbiology and Biotechnology Letters
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• v.49 no.4
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• pp.478-484
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• 2021

Cellular resources including transcriptional and translational machineries in bacteria are limited, yet microorganisms depend upon them to maximize cellular fitness. Bacteria have evolved strategies for using resources economically. Regulatory networks for the gene expression system enable the cell to synthesize proteins only when necessary. At the same time, regulatory interactions enable the cell to limit losses when the system cannot make a cellular profit due to fake substrates. Also, the architecture of the gene expression flow can be advantageous for clustering functionally related products, thus resulting in effective interactions among molecules. In addition, cellular systems modulate the investment of proteomes, depending upon nutrient qualities, and fast-growing cells spend more resources on the synthesis of ribosomes, whereas nonribosomal proteins are synthesized in nutrient-limited conditions. A deeper understanding of cellular mechanisms underlying the optimal allocation of cellular resources can be used for biotechnological purposes, such as designing complex genetic circuits and constructing microbial cell factories.

• Molecules and Cells
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• v.42 no.2
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• pp.166-174
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• 2019

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

• BMB Reports
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• v.38 no.2
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• pp.121-127
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• 2005

Drosophila protects itself from infection by microbial organisms by means of its pivotal defense, the so-called innate immunity system. This is its sole defense as it lacks an adaptive immunity system such as is found in mammals. The strong conservation of innate immunity systems in organisms from Drosophila to mammals, and the ease with which Drosophila can be manipulated genetically, makes this fly a good model system for investigating the mechanisms of virulence of a number of medically important pathogens. Potentially damaging endogenous and/or exogenous challenges sensed by specific receptors initiate signals via the Toll and/or Imd signaling pathways. These in turn activate the transcription factors Dorsal, Dorsal-related immune factor (Dif) and Relish, culminating in transcription of genes involved in the production of antimicrobial peptides, melanization, phagocytosis, and the cytoskeletal rearrangement required for appropriate responses. Clarifying the regulatory interactions between the various pathways involved is very important for understanding the specificity and termination mechanism of the immune response.

• Journal of Microbiology and Biotechnology
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• v.30 no.1
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• pp.127-135
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• 2020

Small RNAs (sRNAs) are widespread and play major roles in regulation circuits in bacteria. Previously, we have demonstrated that transcription of esrE is under the control of its own promoter. However, the regulatory elements involved in EsrE sRNA expression are still unknown. In this study, we found that different cis-regulatory elements exist in the promoter region of esrE. We then screened and analyzed seven potential corresponding trans-regulatory elements by using pull-down assays based on DNA affinity chromatography. Among these candidate regulators, we investigated the relationship between the ferric uptake regulator (Fur) and the EsrE sRNA. Electrophoresis mobility shift assays (EMSAs) and β-galactosidase activity assays demonstrated that Fur can bind to the promoter region of esrE, and positively regulate EsrE sRNA expression in the presence of Fe²⁺.

• BMB Reports
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• v.46 no.12
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• pp.567-574
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• 2013

Liver plays a major role in maintaining glucose homeostasis in mammals. Under fasting conditions, hepatic glucose production is critical as a source of fuel to maintain the basic functions in other tissues, including skeletal muscle, red blood cells, and the brain. Fasting hormones glucagon and cortisol play major roles during the process, in part by activating the transcription of key enzyme genes in the gluconeogenesis such as phosphoenol pyruvate carboxykinase (PEPCK) and glucose 6 phosphatase catalytic subunit (G6Pase). Conversely, gluconeogenic transcription is repressed by pancreatic insulin under feeding conditions, which effectively inhibits transcriptional activator complexes by either promoting post-translational modifications or activating transcriptional inhibitors in the liver, resulting in the reduction of hepatic glucose output. The transcriptional regulatory machineries have been highlighted as targets for type 2 diabetes drugs to control glycemia, so understanding of the complex regulatory mechanisms for transcription circuits for hepatic gluconeogenesis is critical in the potential development of therapeutic tools for the treatment of this disease. In this review, the current understanding regarding the roles of two key transcriptional activators, CREB and FoxO1, in the regulation of hepatic gluconeogenic program is discussed.

• Clinical and Experimental Pediatrics
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• v.48 no.2
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• pp.126-137
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• 2005

New insights in the complex metabolic pathways and its control mechanism for energy homeostasis have refined our understanding of the pathophysiology of obesity. It is now recognized that there are several additional regulatory mechanism such as peripheral signals including leptin, ghrelin, GLP-1 and PYY and cellular signals including uncoupling proteins and ${\beta}$ Adrenergic receptors, which contribute to the regulation of food intake and energy expenditure, respectively. In addition, the function of adipocyte as an endocrine organ in energy homeostasis has been recently emphasized. Recent findings suggest that elevated levels of adipokines, such as leptin, adiponectin, resistin and TNF-${\alpha}$, in addition to increased free fatty acid level could be related to the pathophysiology of insulin resistance in obesity. For effective treatments and prevention of obesity, further studies on the circuits of neural and endocrine interactions in the regulation of energy homeostasis are needed.

• Journal of Microbiology and Biotechnology
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• v.29 no.10
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• pp.1522-1542
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• 2019

To adapt to environmental changes and to maintain cellular homeostasis, microorganisms adjust the intracellular concentrations of biochemical compounds, including metal ions; these are essential for the catalytic function of many enzymes in cells, but excessive amounts of essential metals and heavy metals cause cellular damage. Metal-responsive transcriptional regulators play pivotal roles in metal uptake, pumping out, sequestration, and oxidation or reduction to a less toxic status via regulating the expression of the detoxification-related genes. The sensory and regulatory functions of the metalloregulators have made them as attractive biological parts for synthetic biology, and the exceptional sensitivity and selectivity of metalloregulators toward metal ions have been used in heavy metal biosensors to cope with prevalent heavy metal contamination. Due to their importance, substantial efforts have been made to characterize heavy metal-responsive transcriptional regulators and to develop heavy metal-sensing biosensors. In this review, we summarize the biochemical data for the two major metalloregulator families, SmtB/ArsR and MerR, to describe their metal-binding sites, specific chelating chemistry, and conformational changes. Based on our understanding of the regulatory mechanisms, previously developed metal biosensors are examined to point out their limitations, such as high background noise and a lack of well-characterized biological parts. We discuss several strategies to improve the functionality of the metal biosensors, such as reducing the background noise and amplifying the output signal. From the perspective of making heavy metal biosensors, we suggest that the characterization of novel metalloregulators and the fabrication of exquisitely designed genetic circuits will be required.

• BMB Reports
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• v.43 no.7
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• pp.451-460
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• 2010

Starting with the first publication of lacZ gene fusion in 1980, reporter genes have just entered their fourth decade. Initial studies relied on the simple fusion of a promoter or gene with a particular reporter gene of interest. Such constructs were then used to determine the promoter activity under specific conditions or within a given cell or organ. Although this protocol was, and still is, very effective, current research shows a paradigm shift has occurred in the use of reporter systems. With the advent of innovative cloning and synthetic biology techniques and microfluidic/nanodroplet systems, reporter genes and their proteins are now finding themselves used in increasingly intricate and novel applications. For example, researchers have used fluorescent proteins to study biofilm formation and discovered that microchannels develop within the biofilm. Furthermore, there has recently been a "fusion" of art and science; through the construction of genetic circuits and regulatory systems, researchers are using bacteria to "paint" pictures based upon external stimuli. As such, this review will discuss the past and current trends in reporter gene applications as well as some exciting potential applications and models that are being developed based upon these remarkable proteins.

• Animal cells and systems
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• v.6 no.1
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• pp.1-12
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• 2002

A role of Src family protein Tyrosine kinases (SFK) as mediators of receptor-ligand initiated responses is well established. Well documented, but less well understood is the role of SFK in cellular reaction to stresses. Evidence from the wide variety of experimental systems indicates that SFK mediate responses to all major classes of stress, including oxidation, DNA damage, mechanical impacts, and protein denaturing. SFK may be activated by stresses directly or via regulatory circuits whose identity is not yet fully understood. Depending on the cell type and the nature of activating stimulus, SFK may activate known downstream signaling cascades leading to cell survival, proliferation, cytoskeletal rearrangement, and apoptosis; the identity of these cascades is discussed. As in the case of receptor-initiated signaling, roles of individual SFK in various stress response may be redundant or non-redundant. Although signals generated by different stresses are generally transduced via distinct SFK pathways, these pathways may overlap or exhibit crosstalk. In some cell types stress-induced activation of SFK promotes survival and inhibits apoptosis, whereas the opposite may be true for other cell types. Stress responses constitute a new and rapidly developing area of SFK-mediated signaling.

• BMB Reports
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• v.44 no.1
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• pp.1-10
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• 2011

Inter-cellular communication via diffusible small molecules is a defining character not only of multicellular forms of life but also of single-celled organisms. A large number of bacterial genes are regulated by the change of chemical milieu mediated by the local population density of its own species or others. The cell density-dependent "autoinducer" molecules regulate the expression of those genes involved in genetic competence, biofilm formation and persistence, virulence, sporulation, bioluminescence, antibiotic production, and many others. Recent innovations in recombinant DNA technology and micro-/nano-fluidics systems render the genetic circuitry responsible for cell-to-cell communication feasible to and malleable via synthetic biological approaches. Here we review the current understanding of the molecular biology of bacterial intercellular communication and the novel experimental protocols and platforms used to investigate this phenomenon. A particular emphasis is given to the genetic regulatory circuits that provide the standard building blocks which constitute the syntax of the biochemical communication network. Thus, this review gives focus to the engineering principles necessary for rewiring bacterial chemo-communication for various applications, ranging from population-level gene expression control to the study of host-pathogen interactions.