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1
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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Alcántara, Cristina, Luz Adriana Sarmiento-Rubiano, Vicente Monedero, Josef Deutscher, Gaspar Pérez-Martínez, and María J. Yebra. "Regulation of Lactobacillus casei Sorbitol Utilization Genes Requires DNA-Binding Transcriptional Activator GutR and the Conserved Protein GutM." Applied and Environmental Microbiology 74, no. 18 (August 1, 2008): 5731–40. http://dx.doi.org/10.1128/aem.00230-08.
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ABSTRACT Sequence analysis of the five genes (gutRMCBA) downstream from the previously described sorbitol-6-phosphate dehydrogenase-encoding Lactobacillus casei gutF gene revealed that they constitute a sorbitol (glucitol) utilization operon. The gutRM genes encode putative regulators, while the gutCBA genes encode the EIIC, EIIBC, and EIIA proteins of a phosphoenolpyruvate-dependent sorbitol phosphotransferase system (PTSGut). The gut operon is transcribed as a polycistronic gutFRMCBA messenger, the expression of which is induced by sorbitol and repressed by glucose. gutR encodes a transcriptional regulator with two PTS-regulated domains, a galactitol-specific EIIB-like domain (EIIBGat domain) and a mannitol/fructose-specific EIIA-like domain (EIIAMtl domain). Its inactivation abolished gut operon transcription and sorbitol uptake, indicating that it acts as a transcriptional activator. In contrast, cells carrying a gutB mutation expressed the gut operon constitutively, but they failed to transport sorbitol, indicating that EIIBCGut negatively regulates GutR. A footprint analysis showed that GutR binds to a 35-bp sequence upstream from the gut promoter. A sequence comparison with the presumed promoter region of gut operons from various firmicutes revealed a GutR consensus motif that includes an inverted repeat. The regulation mechanism of the L. casei gut operon is therefore likely to be operative in other firmicutes. Finally, gutM codes for a conserved protein of unknown function present in all sequenced gut operons. A gutM mutant, the first constructed in a firmicute, showed drastically reduced gut operon expression and sorbitol uptake, indicating a regulatory role also for GutM.
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Maeda, Shin-Ichi, Yuriko Kawaguchi, Taka-Aki Ohe, and Tatsuo Omata. "cis-Acting Sequences Required for NtcB-Dependent, Nitrite-Responsive Positive Regulation of the Nitrate Assimilation Operon in the Cyanobacterium Synechococcus sp. Strain PCC 7942." Journal of Bacteriology 180, no. 16 (August 15, 1998): 4080–88. http://dx.doi.org/10.1128/jb.180.16.4080-4088.1998.
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ABSTRACT There are three binding sites for NtcA (nirI,nirII, and nirIII), the global nitrogen regulator of cyanobacteria, in the DNA region between the two divergently transcribed operons (nirA andnirB operons) involved in nitrate assimilation inSynechococcus sp. strain PCC 7942. Using theluxAB reporter system, we showed that nirI andnirIII, which are located 23 bp upstream from the −10 promoter element of nirA and nirB, respectively, are required for induction by nitrogen depletion of thenirA and nirB operons, respectively. The induction of nirA operon transcription was a prerequisite for the nitrite-responsive positive regulation of the transcription by NtcB, a LysR-type protein. The NtcA-binding sitenirII, located in the middle of the nirA-nirBintergenic region, and a potential binding site for a LysR-type protein (TGCAN5TGCA; designated L1), located betweennirI and nirII, were required for the nitrite-responsive, NtcB-dependent enhancement of nirAoperon transcription. Although the requirement for the L1 site was consistent with the involvement of the LysR family protein NtcB in transcriptional regulation, NtcB did not bind to the nirAregulatory region in vitro in the presence of nitrite and NtcA, suggesting the involvement of some additional factor(s) in the regulation. An L1-like inverted repeat with the consensus sequence TGCN7GCA was conserved in the nirA promoter region of cyanobacteria, being centered at position −23 with respect to the NtcA-binding site corresponding to nirI, which suggested the common occurrence of nitrite-responsive regulation of the nitrate assimilation operon among cyanobacteria.
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Takeda, Yasuo, Kazuma Takase, Ichiro Yamato, and Keietsu Abe. "Sequencing and Characterization of the xyl Operon of a Gram-Positive Bacterium, Tetragenococcus halophila." Applied and Environmental Microbiology 64, no. 7 (July 1, 1998): 2513–19. http://dx.doi.org/10.1128/aem.64.7.2513-2519.1998.
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ABSTRACT The xyl operon of a gram-positive bacterium,Tetragenococcus halophila (previously calledPediococcus halophilus), was cloned and sequenced. The DNA was about 7.7 kb long and contained genes for a ribose binding protein and part of a ribose transporter, xylR (a putative regulatory gene), and the xyl operon, along with its regulatory region and transcription termination signal, in this order. The DNA was AT rich, the GC content being 35.8%, consistent with the GC content of this gram-positive bacterium. The xyl operon consisted of three genes, xylA, encoding a xylose isomerase, xylB, encoding a xylulose kinase, andxylE, encoding a xylose transporter, with predicted molecular weights of 49,400, 56,400, and 51,600, respectively. The deduced amino acid sequences of the XylR, XylA, XylB, and XylE proteins were similar to those of the corresponding proteins in other gram-positive and -negative bacteria, the similarities being 37 to 64%. Each polypeptide of XylB and XylE was expressed functionally inEscherichia coli. XylE transported d-xylose in a sodium ion-dependent manner, suggesting that it is the first described xylose/Na+ symporter. The XylR protein contained a consensus sequence for binding catabolites of glucose, such as glucose-6-phosphate, which has been discovered in glucose and fructose kinases in bacteria. Correspondingly, the regulatory region of this operon contained a putative binding site of XylR with a palindromic structure. Furthermore, it contained a consensus sequence, CRE (catabolite-responsive element), for binding CcpA (catabolite control protein A). We speculate that the transcriptional regulation of this operon resembles the regulation of catabolite-repressible operons such as the amy, lev, xyl, andgnt operons in various gram-positive bacteria. We discuss the significance of the regulation of gene expression of this operon inT. halophila.
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Kalyuzhnaya, Marina G., and Mary E. Lidstrom. "QscR-Mediated Transcriptional Activation of Serine Cycle Genes in Methylobacterium extorquens AM1." Journal of Bacteriology 187, no. 21 (November 1, 2005): 7511–17. http://dx.doi.org/10.1128/jb.187.21.7511-7517.2005.
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ABSTRACT QscR, a LysR-type regulator, is the major regulator of assimilatory C1 metabolism in Methylobacterium extorquens AM1. It has been shown to interact with the promoters of the two operons that encode the majority of the serine cycle enzymes (sga-hpr-mtdA-fch for the qsc1 operon and mtkA-mtkB-ppc-mclA for the qsc2 operon), as well as with the promoter of glyA and its own promoter. To obtain further insights into the mechanisms of this regulation, we mapped transcriptional start sites for the qsc1 and qsc2 operons and for glyA via primer extension analysis. We also identified the specific binding sites for QscR upstream of the qsc1 and qsc2 operons and glyA by DNase I footprinting. The QscR protected areas were located at nucleotides −216 to −165, nucleotides −59 to −26, and nucleotides −72 to −39 within the promoter-regulatory regions upstream of transcriptional starts of, respectively, qsc1, qsc2 and glyA. To examine the nature of the metabolic signal that may influence QscR-mediated regulation of the serine cycle genes, Pqsc1::xylE translational fusions were constructed and expression of XylE monitored in the wild-type strain, as well as in knockout mutants defective in a variety of methylotrophy functions. The data from these experiments pointed toward formyl-H4F being a coinducer of QscR and possibly the major signal in the regulation of the serine cycle in M. extorquens AM1. The ability of formyl-H4F to enhance the binding of QscR to a specific region upstream of one of the serine cycle operons was demonstrated in gel retardation experiments.
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White-Ziegler, Christine A., Anuradha Villapakkam, Karla Ronaszeki, and Sarah Young. "H-NS Controls pap and daaFimbrial Transcription in Escherichia coli in Response to Multiple Environmental Cues." Journal of Bacteriology 182, no. 22 (November 15, 2000): 6391–400. http://dx.doi.org/10.1128/jb.182.22.6391-6400.2000.
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ABSTRACT A comparative study was completed to determine the influence of various environmental stimuli on the transcription of three different fimbrial operons in Escherichia coli and to determine the role of the histone-like protein H-NS in this environmental regulation. The fimbrial operons studied included the pap operon, which encodes pyelonephritis-associated pili (P pili), the daaoperon, which encodes F1845 fimbriae, and the fan operon, which encodes K99 fimbriae. Using lacZYA transcriptional fusions within each of the fimbrial operons, we tested temperature, osmolarity, carbon source, rich medium, oxygen levels, pH, amino acids, solid medium, and iron concentration for their effects on fimbrial gene expression. Low temperature, high osmolarity, glucose as a carbon source, and rich medium repressed transcription of all three operons. High iron did not alter transcription of any of the operons tested, whereas the remaining stimuli had effects on individual operons. For the pap and daa operons, introduction of thehns651 mutation relieved the repression, either fully or partially, due to low temperature, glucose as a carbon source, rich medium, and high osmolarity. Taken together, these data indicate that there are common environmental cues that regulate fimbrial transcription in E. coli and that H-NS is an important environmental regulator for fimbrial transcription in response to several stimuli.
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Darwin, Andrew J., Eva C. Ziegelhoffer, Patricia J. Kiley, and Valley Stewart. "Fnr, NarP, and NarL Regulation of Escherichia coli K-12 napF (Periplasmic Nitrate Reductase) Operon Transcription In Vitro." Journal of Bacteriology 180, no. 16 (August 15, 1998): 4192–98. http://dx.doi.org/10.1128/jb.180.16.4192-4198.1998.
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ABSTRACT The expression of several Escherichia coli operons is activated by the Fnr protein during anaerobic growth and is further controlled in response to nitrate and nitrite by the homologous response regulators, NarL and NarP. Among these operons, thenapF operon, encoding a periplasmic nitrate reductase, has unique features with respect to its Fnr-, NarL-, and NarP-dependent regulation. First, the Fnr-binding site is unusually located compared to the control regions of most other Fnr-activated operons, suggesting different Fnr-RNA polymerase contacts during transcriptional activation. Second, nitrate and nitrite activation is solely dependent on NarP but is antagonized by the NarL protein. In this study, we used DNase I footprint analysis to confirm our previous assignment of the unusual location of the Fnr-binding site in the napFcontrol region. In addition, the in vivo effects of Fnr-positive control mutations on napF operon expression indicate that the napF promoter is atypical with respect to Fnr-mediated activation. The transcriptional regulation of napF was successfully reproduced in vitro by using a supercoiled plasmid template and purified Fnr, NarL, and NarP proteins. These in vitro transcription experiments demonstrate that, in the presence of Fnr, the NarP protein causes efficient transcription activation whereas the NarL protein does not. This suggests that Fnr and NarP may act synergistically to activate napF operon expression. As observed in vivo, this activation by Fnr and NarP is antagonized by the addition of NarL in vitro.
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Turnbough, Charles L., and Robert L. Switzer. "Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors." Microbiology and Molecular Biology Reviews 72, no. 2 (June 2008): 266–300. http://dx.doi.org/10.1128/mmbr.00001-08.
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SUMMARY DNA-binding repressor proteins that govern transcription initiation in response to end products generally regulate bacterial biosynthetic genes, but this is rarely true for the pyrimidine biosynthetic (pyr) genes. Instead, bacterial pyr gene regulation generally involves mechanisms that rely only on regulatory sequences embedded in the leader region of the operon, which cause premature transcription termination or translation inhibition in response to nucleotide signals. Studies with Escherichia coli and Bacillus subtilis pyr genes reveal a variety of regulatory mechanisms. Transcription attenuation via UTP-sensitive coupled transcription and translation regulates expression of the pyrBI and pyrE operons in enteric bacteria, whereas nucleotide effects on binding of the PyrR protein to pyr mRNA attenuation sites control pyr operon expression in most gram-positive bacteria. Nucleotide-sensitive reiterative transcription underlies regulation of other pyr genes. With the E. coli pyrBI, carAB, codBA, and upp-uraA operons, UTP-sensitive reiterative transcription within the initially transcribed region (ITR) leads to nonproductive transcription initiation. CTP-sensitive reiterative transcription in the pyrG ITRs of gram-positive bacteria, which involves the addition of G residues, results in the formation of an antiterminator RNA hairpin and suppression of transcription attenuation. Some mechanisms involve regulation of translation rather than transcription. Expression of the pyrC and pyrD operons of enteric bacteria is controlled by nucleotide-sensitive transcription start switching that produces transcripts with different potentials for translation. In Mycobacterium smegmatis and other bacteria, PyrR modulates translation of pyr genes by binding to their ribosome binding site. Evidence supporting these conclusions, generalizations for other bacteria, and prospects for future research are presented.
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Duca, Sara Del, Giulia Semenzato, Antonia Esposito, Pietro Liò, and Renato Fani. "The Operon as a Conundrum of Gene Dynamics and Biochemical Constraints: What We Have Learned from Histidine Biosynthesis." Genes 14, no. 4 (April 21, 2023): 949. http://dx.doi.org/10.3390/genes14040949.
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Operons represent one of the leading strategies of gene organization in prokaryotes, having a crucial influence on the regulation of gene expression and on bacterial chromosome organization. However, there is no consensus yet on why, how, and when operons are formed and conserved, and many different theories have been proposed. Histidine biosynthesis is a highly studied metabolic pathway, and many of the models suggested to explain operons origin and evolution can be applied to the histidine pathway, making this route an attractive model for the study of operon evolution. Indeed, the organization of his genes in operons can be due to a progressive clustering of biosynthetic genes during evolution, coupled with a horizontal transfer of these gene clusters. The necessity of physical interactions among the His enzymes could also have had a role in favoring gene closeness, of particular importance in extreme environmental conditions. In addition, the presence in this pathway of paralogous genes, heterodimeric enzymes and complex regulatory networks also support other operon evolution hypotheses. It is possible that histidine biosynthesis, and in general all bacterial operons, may result from a mixture of several models, being shaped by different forces and mechanisms during evolution.
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Wang, Xing-Guo, Bo Lin, J. Michael Kidder, Samuel Telford, and Linden T. Hu. "Effects of Environmental Changes on Expression of the Oligopeptide Permease (opp) Genes of Borrelia burgdorferi." Journal of Bacteriology 184, no. 22 (November 15, 2002): 6198–206. http://dx.doi.org/10.1128/jb.184.22.6198-6206.2002.
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ABSTRACT We analyzed expression of a putative oligopeptide permease (Opp) of Borrelia burgdorferi. Unlike the opp operons of other bacteria for which there is a single substrate binding protein, B. burgdorferi codes for three substrate binding proteins (OppA-I to -III) in its opp operon and an additional two homologs on plasmids (OppA-IV and -V). Instead of a single promoter region regulating transcription of the entire operon, as seen in other bacterial opp operons, it appears that among oppA-I, -II, and -III, as well as oppA-IV and -V, each has a potential upstream promoter region. We tested the function of these putative promoter sequences by fusion to a promoterless β-galactosidase reporter gene in pCB182. Each of the promoter regions was found to be active. The level of activity in the reporter constructs closely paralleled the level of expression of each gene in in vitro-grown B. burgdorferi. Changes in carbon and nitrogen availability differentially affected individual promoters, but no changes in promoter activity were seen when Escherichia coli bacteria (with the promoter constructs) were grown in various concentrations of phosphate and leucine and changes in pH. Expression of specific oppA genes with B. burgdorferi varied significantly between its mouse and fed and unfed tick hosts. Differences in regulation of opp gene expression suggest a potential role in environmental response by the organism.
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Vu-Khac, Hung, and Kurt W. Miller. "Regulation of Mannose Phosphotransferase System Permease and Virulence Gene Expression in Listeria monocytogenes by the EIItMan Transporter." Applied and Environmental Microbiology 75, no. 21 (September 4, 2009): 6671–78. http://dx.doi.org/10.1128/aem.01104-09.
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ABSTRACT The EIIt Man phosphotransferase system (PTS) permease encoded by the mpt operon is the principal glucose transporter in Listeria monocytogenes. EIIt Man participates in glucose-mediated carbon catabolite repression (CCR) and downregulation of virulence gene expression, and it is the receptor for class IIa bacteriocins. The regulation of this important protein and its roles in gene control were examined using derivatives of strain EGD-e in which the mpt operon or its regulatory genes, manR and lmo0095, were deleted. Real-time reverse transcription-PCR analysis showed that the mpt mRNA level was 10- and 100-fold lower in the lmo0095 and manR deletion strains, respectively. The manR mRNA level was higher in the mpt deletion mutant in medium lacking glucose, possibly due to disruption of a regulatory process that normally downregulates manR transcription in the absence of this sugar. Analysis of the mpt deletion mutant also showed that EIIt Man participates to various degrees in glucose-mediated CCR of PTS operons. CCR of the lmo0027 gene, which encodes a β-glucoside PTS transporter, required expression of EIIt Man. In contrast, genes in two mannose PTS operons (lmo0024, lmo1997, and lmo2002) were repressed by glucose even when EIIt Man was not synthesized. A third mannose PTS operon, mpo, was not regulated by glucose or by the level of EIIt Man. Finally, the mRNA levels for five genes in the prfA virulence gene cluster were two- to fourfold higher in the mpt deletion mutant. The results show that EIIt Man participates to various extents in glucose-mediated CCR of PTS operons and makes a small, albeit significant, contribution to downregulation of virulence gene transcription by glucose in strain EGD-e.
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Poulsen, Tim S., Ying-Ying Chang, and Bjarne Hove-Jensen. "d-Allose Catabolism ofEscherichia coli: Involvement of alsI and Regulation of als Regulon Expression by Allose and Ribose." Journal of Bacteriology 181, no. 22 (November 15, 1999): 7126–30. http://dx.doi.org/10.1128/jb.181.22.7126-7130.1999.
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ABSTRACT Genes involved in allose utilization of Escherichia coli K-12 are organized in at least two operons,alsRBACE and alsI, located next to each other on the chromosome but divergently transcribed. Mutants defective inalsI (allose 6-phosphate isomerase gene) andalsE (allulose 6-phosphate epimerase gene) were Als−. Transcription of the two allose operons, measured as β-galactosidase activity specified byalsI-lacZ + oralsE-lacZ + operon fusions, was induced by allose. Ribose also caused derepression of expression of the regulon under conditions in which ribose phosphate catabolism was impaired.
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Collado-Vides, Julio, Gabriel Moreno-Hagelsieb, and Arturo Medrano-Soto. "Microbial computational genomics of gene regulation." Pure and Applied Chemistry 74, no. 6 (January 1, 2002): 899–905. http://dx.doi.org/10.1351/pac200274060899.
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Escherichia coli is a free-living bacterium that condensates a large legacy of knowledge as a result of years of experimental work in molecular biology. It represents a point of departure for analyses and comparisons with the ever-increasing number of finished microbial genomes. For years, we have been gathering knowledge from the literature on transcriptional regulation and operon organization in E. coli K-12, and organizing it in a relational database, RegulonDB. RegulonDB contains information of 2025 % of the expected total sets of regulatory interactions at the level of transcription initiation. We have used this knowledge to generate computational methods to predict the missing sets in the genome of E. coli, focusing on prediction of promoters, regulatory sites, regulatory proteins, operons, and transcription units. These predictions constitute separate pieces of a single puzzle. By putting them all together, we shall be able to predict the complete set of regulatory interactions and transcription unit organization of E. coli. Orthologous genes in other genomes of known co-regulated sets of genes in E. coli, along with their corresponding predicted operons, and their predicted transcriptional regulators, shall permit the extension of the previous goal to many more microbial genomes.
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Delorme, C., S. D. Ehrlich, and P. Renault. "Regulation of Expression of the Lactococcus lactis Histidine Operon." Journal of Bacteriology 181, no. 7 (April 1, 1999): 2026–37. http://dx.doi.org/10.1128/jb.181.7.2026-2037.1999.
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ABSTRACT In Lactococcus lactis, the his operon contains all the genes necessary for histidine biosynthesis. It is transcribed from a unique promoter, localized 300 bp upstream of the first gene. The region corresponding to the untranslated 5′ end of the transcript, named the his leader region, displays the typical features of the T box transcriptional attenuation mechanism which is involved in the regulation of many amino acid biosynthetic operons and tRNA synthetase genes in gram-positive bacteria. Here we describe the regulation of transcription of the his operon by the level of histidine in the growth medium. In the absence of histidine, two transcripts are present. One covers the entire operon, while the other stops at a terminator situated about 250 bp downstream of the transcription start point. DNA sequences implicated in regulation of the his operon were identified by transcriptional fusion with luciferase genes and site-directed mutagenesis. In addition to the previously defined sequences necessary for effective T-box-mediated regulation, new essential regions were identified. Eighteen percent of the positions of the hisleader region were found to differ in seven distantly related strains of L. lactis. Analysis of the variable positions supports the folding model of the central part of the his leader region. Lastly, in addition to the T-box-mediated regulation, the operon is regulated at the level of initiation of transcription, which is repressed in the presence of histidine. An operator site, necessary for full repression, overlaps the terminator involved in the T box attenuation mechanism. The functionality of the operator is altered on plasmids with low and high copy numbers, suggesting that supercoiling may play a role in the expression of the his operon. The extents of regulation at the levels of initiation and attenuation of transcription are 6- to 8-fold and 14-fold, respectively. Together, the two levels of control allow a 120-fold range of regulation of theL. lactis operon by histidine.
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Li, Xiangkai, and Lee R. Krumholz. "Regulation of Arsenate Resistance in Desulfovibrio desulfuricans G20 by an arsRBCC Operon and an arsC Gene." Journal of Bacteriology 189, no. 10 (March 2, 2007): 3705–11. http://dx.doi.org/10.1128/jb.01913-06.
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ABSTRACT Desulfovibrio desulfuricans G20 grows and reduces 20 mM arsenate to arsenite in lactate-sulfate media. Sequence analysis and experimental data show that D. desulfuricans G20 has one copy of arsC and a complete arsRBCC operon in different locations within the genome. Two mutants of strain G20 with defects in arsenate resistance were generated by nitrosoguanidine mutagenesis. The arsRBCC operons were intact in both mutant strains, but each mutant had one point mutation in the single arsC gene. Mutants transformed with either the arsC1 gene or the arsRBCC operon displayed wild-type arsenate resistance, indicating that the two arsC genes were equivalently functional in the sulfate reducer. The arsC1 gene and arsRBCC operon were also cloned into Escherichia coli DH5α independently, with either DNA fragment conferring increased arsenate resistance. The recombinant arsRBCC operon allowed growth at up to 50 mM arsenate in LB broth. Quantitative PCR analysis of mRNA products showed that the single arsC1 was constitutively expressed, whereas the operon was under the control of the arsR repressor protein. We suggest a model for arsenate detoxification in which the product of the single arsC1 is first used to reduce arsenate. The arsenite formed is then available to induce the arsRBCC operon for more rapid arsenate detoxification.
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Maouche, Rim, Hector L. Burgos, Laetitia My, Julie P. Viala, Richard L. Gourse, and Emmanuelle Bouveret. "Coexpression of Escherichia coli obgE, Encoding the Evolutionarily Conserved Obg GTPase, with Ribosomal Proteins L21 and L27." Journal of Bacteriology 198, no. 13 (May 2, 2016): 1857–67. http://dx.doi.org/10.1128/jb.00159-16.
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ABSTRACTMultiple essential small GTPases are involved in the assembly of the ribosome or in the control of its activity. Among them, ObgE (CgtA) has been shown recently to act as a ribosome antiassociation factor that binds to ppGpp, a regulator whose best-known target is RNA polymerase. The present study was aimed at elucidating the expression ofobgEinEscherichia coli. We show thatobgEis cotranscribed with ribosomal protein genesrplUandrpmAand with a gene of unknown function,yhbE. We show here that about 75% of the transcripts terminate beforeobgE, because there is a transcriptional terminator betweenrpmAandyhbE. As expected for ribosomal protein operons, expression was highest during exponential growth, decreased during entry into stationary phase, and became almost undetectable thereafter. Expression of the operon was derepressed in mutants lacking ppGpp or DksA. However, regulation by these factors appears to occur post-transcription initiation, since no effects of ppGpp and DksA onrplUpromoter activity were observedin vitro.IMPORTANCEThe conserved and essential ObgE GTPase binds to the ribosome and affects its assembly. ObgE has also been reported to impact chromosome segregation, cell division, resistance to DNA damage, and, perhaps most interestingly, persister formation and antibiotic tolerance. However, it is unclear whether these effects are related to its role in ribosome formation. Despite its importance, no studies on ObgE expression have been reported. We demonstrate here thatobgEis expressed from an operon encoding two ribosomal proteins, that the operon's expression varies with the growth phase, and that it is dependent on the transcription regulators ppGpp and DksA. Our results thus demonstrate thatobgEexpression is coupled to ribosomal gene expression.
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Hayes, S., and H. J. Bull. "Translational frameshift sites within bacteriophage lambda genes rexA and cI." Acta Biochimica Polonica 46, no. 4 (December 31, 1999): 879–84. http://dx.doi.org/10.18388/abp.1999_4109.
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Phage lambda's cI-rexA-rexB operon displays an intriguing example of regulation by an unexplained mechanism of polarity. We have identified three potential -1 translational frameshift sites and present a model for translational frameshift suppression by lambda's CI repressor as a mechanism of regulating operon polarity, implying an additional role for CI self-regulation.
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Martínez-Pérez, O., E. Moreno-Ruiz, B. Floriano, and E. Santero. "Regulation of Tetralin Biodegradation and Identification of Genes Essential for Expression of thn Operons." Journal of Bacteriology 186, no. 18 (September 15, 2004): 6101–9. http://dx.doi.org/10.1128/jb.186.18.6101-6109.2004.
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ABSTRACT The tetralin biodegradation genes of Sphingomonas macrogolitabida strain TFA are clustered in two closely linked and divergent operons. To analyze expression of both operons under different growth conditions, transcriptional and translational gene fusions of the first genes of each operon to lacZ have been constructed in plasmids unable to replicate in Sphingomonas and integrated by recombination into the genome of strain TFA. Expression analysis indicated that the transcription of both genes is induced in similar ways by the presence of tetralin. Gene expression in both operons is also subjected to overimposed catabolic repression. Two additional genes named thnR and thnY have been identified downstream of thnCA3A4 genes. ThnR is similar to LysR-type regulators, and mutational analysis indicated that ThnR is strictly required for expression of the thn operons. Unlike other LysR-type regulators, ThnR does not repress its own synthesis. In fact, ThnR activates its own expression, since thnR is cotranscribed with the thnCA3A4 genes. ThnY is similar to the ferredoxin reductase components of dioxygenase systems and shows the fer2 domain, binding a Cys4[2Fe-2S] iron sulfur center, and the FAD-binding domain, common to those reductases. However, it lacks the NAD-binding domain. Intriguingly, ThnY has a regulatory role, since it is also strictly required for expression of the thn operons. Given the similarity of ThnY to reductases and the possibility of its being present in the two redox states, it is tempting to speculate that ThnY is a regulatory component connecting expression of the thn operons to the physiological status of the cell.
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Allenby, Nicholas E. E., Nicola O'Connor, Zoltán Prágai, Noel M. Carter, Marcus Miethke, Susanne Engelmann, Michael Hecker, Anil Wipat, Alan C. Ward, and Colin R. Harwood. "Post-transcriptional regulation of the Bacillus subtilis pst operon encoding a phosphate-specific ABC transporter." Microbiology 150, no. 8 (August 1, 2004): 2619–28. http://dx.doi.org/10.1099/mic.0.27126-0.
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During phosphate starvation, Bacillus subtilis regulates genes in the PhoP regulon to reduce the cell's requirement for this essential substrate and to facilitate the recovery of inorganic phosphate from organic sources such as teichoic and nucleic acids. Among the proteins that are highly induced under these conditions is PstS, the phosphate-binding lipoprotein component of a high-affinity ABC-type phosphate transporter. PstS is encoded by the first gene in the pst operon, the other four members of which encode the integral membrane and cytoplasmic components of the transporter. The transcription of the pst operon was analysed using a combination of methods, including transcriptional reporter gene technology, Northern blotting and DNA arrays. It is shown that the primary transcript of the pst operon is processed differentially to maintain higher concentrations of PstS relative to other components of the transporter. The comparative studies have revealed limitations in the use of reporter gene technology for analysing the transcription of operons in which the messenger RNA transcript is differentially processed.
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Mortera, Pablo, Martín Espariz, Cristian Suárez, Guillermo Repizo, Josef Deutscher, Sergio Alarcón, Víctor Blancato, and Christian Magni. "Fine-Tuned Transcriptional Regulation of Malate Operons in Enterococcus faecalis." Applied and Environmental Microbiology 78, no. 6 (January 13, 2012): 1936–45. http://dx.doi.org/10.1128/aem.07280-11.
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ABSTRACTInEnterococcus faecalis, themaelocus is constituted by two putative divergent operons,maePEandmaeKR. The first operon encodes a putative H+/malate symporter (MaeP) and a malic enzyme (MaeE) previously shown to be essential for malate utilization in this bacterium. ThemaeKRoperon encodes two putative proteins with significant similarity to two-component systems involved in sensing malate and activating its assimilation in bacteria. Our transcriptional and genetic assays showed thatmaePEandmaeKRare induced in response to malate by the response regulator MaeR. In addition, we observed that both operons were partially repressed in the presence of glucose. Accordingly, the cometabolism of this sugar and malate was detected. The binding of the complex formed by CcpA and its corepressor P-Ser-HPr to acresite located in themaeregion was demonstratedin vitroand explains the carbon catabolite repression (CCR) observed for themaePEoperon. However, our results also provide evidence for a CcpA-independent CCR mechanism regulating the expression of both operons. Finally, a biomass increment of 40 or 75% was observed compared to the biomass of cells grown only on glucose or malate, respectively. Cells cometabolizing both carbon sources exhibit a higher rate of glucose consumption and a lower rate of malate utilization. The growth improvement achieved byE. faecalisduring glucose-malate cometabolism might explain why this microorganism employs different regulatory systems to tightly control the assimilation of both carbon sources.
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Melior, Hendrik, Siqi Li, Ramakanth Madhugiri, Maximilian Stötzel, Saina Azarderakhsh, Susanne Barth-Weber, Kathrin Baumgardt, John Ziebuhr, and Elena Evguenieva-Hackenberg. "Transcription attenuation-derived small RNA rnTrpL regulates tryptophan biosynthesis gene expression in trans." Nucleic Acids Research 47, no. 12 (April 17, 2019): 6396–410. http://dx.doi.org/10.1093/nar/gkz274.
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Abstract Ribosome-mediated transcription attenuation is a basic posttranscriptional regulation mechanism in bacteria. Liberated attenuator RNAs arising in this process are generally considered nonfunctional. In Sinorhizobium meliloti, the tryptophan (Trp) biosynthesis genes are organized into three operons, trpE(G), ppiD-trpDC-moaC-moeA, and trpFBA-accD-folC, of which only the first one, trpE(G), contains a short ORF (trpL) in the 5′-UTR and is regulated by transcription attenuation. Under conditions of Trp sufficiency, transcription is terminated between trpL and trpE(G), and a small attenuator RNA, rnTrpL, is produced. Here, we show that rnTrpL base-pairs with trpD and destabilizes the polycistronic trpDC mRNA, indicating rnTrpL-mediated downregulation of the trpDC operon in trans. Although all three trp operons are regulated in response to Trp availability, only in the two operons trpE(G) and trpDC the Trp-mediated regulation is controlled by rnTrpL. Together, our data show that the trp attenuator coordinates trpE(G) and trpDC expression posttranscriptionally by two fundamentally different mechanisms: ribosome-mediated transcription attenuation in cis and base-pairing in trans. Also, we present evidence that rnTrpL-mediated regulation of trpDC genes expression in trans is conserved in Agrobacterium and Bradyrhizobium, suggesting that the small attenuator RNAs may have additional conserved functions in the control of bacterial gene expression.
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Voronina, Olga L., Marina S. Kunda, Natalia N. Ryzhova, Ekaterina I. Aksenova, Andrey N. Semenov, Yulia M. Romanova, and Alexandr L. Gintsburg. "Burkholderia contaminansBiofilm Regulating Operon and Its Distribution in Bacterial Genomes." BioMed Research International 2016 (2016): 1–13. http://dx.doi.org/10.1155/2016/6560534.
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Biofilm formation byBurkholderiaspp. is a principal cause of lung chronic infections in cystic fibrosis patients. A “lacking biofilm production” (LBP) strainB. contaminansGIMC4587:Bct370-19 has been obtained by insertion modification of clinical strain with plasposon mutagenesis. It has an interrupted transcriptional response regulator (RR) gene. The focus of our investigation was a two-component signal transduction system determination, including this RR.B. contaminansclinical and LBP strains were analyzed by whole genome sequencing and bioinformatics resources. A four-component operon (BiofilmReg) has a key role in biofilm formation. The relative location (i.e., by being separated by another gene) of RR and histidine kinase genes is unique in BiofilmReg. Orthologs were found in other members of the Burkholderiales order. Phylogenetic analysis of strains containing BiofilmReg operons demonstrated evidence for earlier inheritance of a three-component operon. During further evolution one lineage acquired a fourth gene, whereas others lost the third component of the operon. Mutations in sensor domains have created biodiversity which is advantageous for adaptation to various ecological niches. Different speciesBurkholderiaandAchromobacterstrains all demonstrated similar BiofilmReg operon structure. Therefore, there may be an opportunity to develop a common drug which is effective for treating all these causative agents.
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Wang, Henian, and Robert P. Gunsalus. "Coordinate Regulation of the Escherichia coli Formate Dehydrogenase fdnGHI and fdhF Genes in Response to Nitrate, Nitrite, and Formate: Roles for NarL and NarP." Journal of Bacteriology 185, no. 17 (September 1, 2003): 5076–85. http://dx.doi.org/10.1128/jb.185.17.5076-5085.2003.
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ABSTRACT Escherichia coli possesses three distinct formate dehydrogenase enzymes encoded by the fdnGHI, fdhF, and fdoGHI operons. To examine how two of the formate dehyrogenase operons (fdnGHI and fdhF) are expressed anaerobically in the presence of low, intermediate, and high levels of nitrate, nitrite, and formate, chemostat culture techniques were employed with fdnG-lacZ and fdhF-lacZ reporter fusions. Complementary patterns of gene expression were seen. Optimal fdhF-lacZ expression occurred only at low to intermediate levels of nitrate, while high nitrate levels caused up to 10-fold inhibition of gene expression. In contrast, fdnG-lacZ expression was induced 25-fold in the presence of intermediate to high nitrate concentrations. Consistent with prior reports, NarL was able to induce fdnG-lacZ expression. However, NarP could not induce expression; rather, it functioned as an antagonist of fdnG-lacZ expression under low-nitrate conditions (i.e., it was a negative regulator). Nitrite, a reported signal for the Nar sensory system, was unable to stimulate or suppress expression of either formate dehydrogenase operon via NarL and NarP. The different gene expression profiles of the alternative formate dehydrogenase operons suggest that the two enzymes have complementary physiological roles under environmental conditions when nitrate and formate levels are changing. Revised regulatory schemes for NarL- and NarP-dependent nitrate control are presented for each operon.
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Goh, Ee-Been, Peggy J. Bledsoe, Li-Ling Chen, Prasad Gyaneshwar, Valley Stewart, and Michele M. Igo. "Hierarchical Control of Anaerobic Gene Expression in Escherichia coli K-12: the Nitrate-Responsive NarX-NarL Regulatory System Represses Synthesis of the Fumarate-Responsive DcuS-DcuR Regulatory System." Journal of Bacteriology 187, no. 14 (July 2005): 4890–99. http://dx.doi.org/10.1128/jb.187.14.4890-4899.2005.
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ABSTRACT Hierarchical control ensures that facultative bacteria preferentially use the available respiratory electron acceptor with the most positive standard redox potential. Thus, nitrate is used before other electron acceptors such as fumarate for anaerobic respiration. Nitrate regulation is mediated by the NarX-NarL two-component system, which activates the transcription of operons encoding nitrate respiration enzymes and represses the transcription of operons for other anaerobic respiratory enzymes, including enzymes involved in fumarate respiration. These are fumarate reductase (encoded by the frdABCD operon), fumarase B, which generates fumarate from malate, and the DcuB permease for fumarate, malate, and aspartate. The transcription of the corresponding structural genes is activated by the DcuS-DcuR two-component system in response to fumarate or its dicarboxylate precursors. We report results from preliminary transcription microarray experiments that revealed two previously unknown members of the NarL regulon: the aspA gene encoding aspartate-ammonia lyase, which generates fumarate; and the dcuSR operon encoding the dicarboxylate-responsive regulatory system. We measured beta-galactosidase expression from monocopy aspA-lacZ, frdA-lacZ, and dcuS-lacZ operon fusions in response to added nitrate and fumarate and with respect to the dcuR and narL genotypes. Nitrate, acting through the NarX-NarL regulatory system, repressed the transcription of all three operons. Only frdA-lacZ expression, however, was responsive to added fumarate or a dcuR + genotype. Phospho-NarL protein protected operator sites in the aspA and dcuS promoter regions from DNase I cleavage in vitro. The overall results are consistent with the hypothesis that nitrate represses frdA operon transcription not only directly, by repressing frdA promoter activity, but also indirectly, by repressing dcuS promoter activity.
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Miguel-Arribas, Andrés, Jorge Val-Calvo, César Gago-Córdoba, José M. Izquierdo, David Abia, Ling Juan Wu, Jeff Errington, and Wilfried J. J. Meijer. "A novel bipartite antitermination system widespread in conjugative elements of Gram-positive bacteria." Nucleic Acids Research 49, no. 10 (May 17, 2021): 5553–67. http://dx.doi.org/10.1093/nar/gkab360.
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Abstract Transcriptional regulation allows adaptive and coordinated gene expression, and is essential for life. Processive antitermination systems alter the transcription elongation complex to allow the RNA polymerase to read through multiple terminators in an operon. Here, we describe the discovery of a novel bipartite antitermination system that is widespread among conjugative elements from Gram-positive bacteria, which we named conAn. This system is composed of a large RNA element that exerts antitermination, and a protein that functions as a processivity factor. Besides allowing coordinated expression of very long operons, we show that these systems allow differential expression of genes within an operon, and probably contribute to strict regulation of the conjugation genes by minimizing the effects of spurious transcription. Mechanistic features of the conAn system are likely to decisively influence its host range, with important implications for the spread of antibiotic resistance and virulence genes.
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Boston, T., and T. Atlung. "FNR-Mediated Oxygen-Responsive Regulation of the nrdDG Operon of Escherichia coli." Journal of Bacteriology 185, no. 17 (September 1, 2003): 5310–13. http://dx.doi.org/10.1128/jb.185.17.5310-5313.2003.
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ABSTRACT Transcription of the nrdDG operon, which encodes the class III nucleotide reductase, which is only active under anaerobic conditions, was strongly induced after a shift to anaerobiosis. The induction was completely dependent on the transcriptional activator FNR and was independent of the ArcA-ArcB two-component response regulator system. The nrdD transcript start site was mapped to a position immediately downstream of two FNR binding sites. Transcription of the other two nucleotide reductase operons, nrdAB and nrdEF, did not respond to oxygen conditions in a wild-type background, but nrdAB expression was increased in the fnr mutant under anaerobic conditions.
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Tzeng, Yih-Ling, John S. Swartley, Yoon K. Miller, Rachel E. Nisbet, Li-Jun Liu, Jay H. Ahn, and David S. Stephens. "Transcriptional Regulation of Divergent Capsule Biosynthesis and Transport Operon Promoters in Serogroup BNeisseria meningitidis." Infection and Immunity 69, no. 4 (April 1, 2001): 2502–11. http://dx.doi.org/10.1128/iai.69.4.2502-2511.2001.
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ABSTRACT The clinically important serogroups B, C, Y, and W-135 ofNeisseria meningitidis produce sialic acid capsules that are critical in pathogenesis. In each of these serogroups, the capsule transport (ctrABCD) and capsule biosynthesis (synABCD) operons are divergently transcribed from putative promoters located in a 134-bp intergenic region (J. S. Swartley, J. H. Ahn, L. J. Liu, C. M. Kahler, and D. S. Stephens, J. Bacteriol. 178:4052–4059, 1996). In this study we further assessed the role of the intergenic sequence in the transcriptional regulation of the sialic acid capsules of N. meningitidis. Insertional mutagenesis or deletions of the 134-bp sequence in the serogroup B meningococcal strain NMB resulted in a marked reduction or elimination of ctrABCD and synABCDtranscription, with a concomitant loss of encapsulation. Chromosomal transcriptional lacZ-ermC reporter fusions ofsyn and ctr promoters were constructed through allelic exchange. Using these constructs, both operons were found to be constitutively transcribed in meningococci, the biosynthesis operon about fourfold higher than the transport operon. Both promoters showed increased activity during stationary-phase growth. In addition to the promoters, a 70-bp 5′ untranslated region (UTR) upstream ofsynA was found to have a direct repeat and an inverted repeat that overlapped three putative integration host factor binding sites. Mutation of this 70-bp UTR and of the direct repeat upregulated both syn and ctr transcription. Regulation through the synA UTR was absent in a K1 Escherichia coli strain that produces identical capsular polysaccharide, implicating species-specific regulation. Meningococcal sialic acid capsule expression is initiated by divergent promoters in a 134-bp intergenic region, is repressed at the transcriptional level by the 5′ UTR of synA, is increased during stationary-phase growth, and shows species-specific regulation. Transcriptional regulation is another important control point for sialic capsule expression inN. meningitidis.
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Cao, Min, Letal Salzberg, Ching Sung Tsai, Thorsten Mascher, Carla Bonilla, Tao Wang, Rick W. Ye, Leticia Márquez-Magaña, and John D. Helmann. "Regulation of the Bacillus subtilis Extracytoplasmic Function Protein σY and Its Target Promoters." Journal of Bacteriology 185, no. 16 (August 15, 2003): 4883–90. http://dx.doi.org/10.1128/jb.185.16.4883-4890.2003.
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ABSTRACT The Bacillus subtilis extracytoplasmic function sigma factor σY is of unknown function. We demonstrate that the sigY operon is expressed from an autoregulatory promoter site, PY. We selected for transposon-induced mutations that upregulate PY transcription in an attempt to identify genes involved in σY regulation. The resulting insertions disrupted yxlC, the gene immediately downstream of sigY. However, the phenotype of the yxlC::Tn10 insertion was due to polarity on the downstream genes of the sigY operon; a nonpolar insertion in yxlC did not lead to derepression of PY. Further analyses revealed that both yxlD and yxlE encoded proteins important for the negative regulation of σY activity. A comparison of the transcriptomes of wild-type and yxlC::Tn10 mutant strains revealed elevated expression of several operons. However, only one additional gene, ybgB, was unambiguously identified as a direct target for σY. This was supported by analysis of direct targets for σY transcription with whole-genome runoff transcription followed by macroarray analysis.
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Allen, Todd D., Tonya Watkins, Lasse Lindahl, and Janice M. Zengel. "Regulation of Ribosomal Protein Synthesis in Vibrio cholerae." Journal of Bacteriology 186, no. 17 (September 1, 2004): 5933–37. http://dx.doi.org/10.1128/jb.186.17.5933-5937.2004.
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ABSTRACT We have investigated the regulation of the S10 and spc ribosomal protein (r-protein) operons in Vibrio cholerae. Both operons are under autogenous control; they are mediated by r-proteins L4 and S8, respectively. Our results suggest that Escherichia coli-like strategies for regulating r-protein synthesis extend beyond the enteric members of the gamma subdivision of proteobacteria.
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Kanai, Yuki, Saburo Tsuru, and Chikara Furusawa. "Experimental demonstration of operon formation catalyzed by insertion sequence." Nucleic Acids Research 50, no. 3 (January 24, 2022): 1673–86. http://dx.doi.org/10.1093/nar/gkac004.
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Abstract Operons are a hallmark of the genomic and regulatory architecture of prokaryotes. However, the mechanism by which two genes placed far apart gradually come close and form operons remains to be elucidated. Here, we propose a new model of the origin of operons: Mobile genetic elements called insertion sequences can facilitate the formation of operons by consecutive insertion–deletion–excision reactions. This mechanism barely leaves traces of insertion sequences and thus difficult to detect in nature. In this study, as a proof-of-concept, we reproducibly demonstrated operon formation in the laboratory. The insertion sequence IS3 and the insertion sequence excision enhancer are genes found in a broad range of bacterial species. We introduced these genes into insertion sequence-less Escherichia coli and found that, supporting our hypothesis, the activity of the two genes altered the expression of genes surrounding IS3, closed a 2.7 kb gap between a pair of genes, and formed new operons. This study shows how insertion sequences can facilitate the rapid formation of operons through locally increasing the structural mutation rates and highlights how coevolution with mobile elements may shape the organization of prokaryotic genomes and gene regulation.
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Hirooka, Kazutake, Satoshi Kunikane, Hiroshi Matsuoka, Ken-Ichi Yoshida, Kanako Kumamoto, Shigeo Tojo, and Yasutaro Fujita. "Dual Regulation of the Bacillus subtilis Regulon Comprising the lmrAB and yxaGH Operons and yxaF Gene by Two Transcriptional Repressors, LmrA and YxaF, in Response to Flavonoids." Journal of Bacteriology 189, no. 14 (May 4, 2007): 5170–82. http://dx.doi.org/10.1128/jb.00079-07.
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ABSTRACT Bacillus subtilis LmrA is known to be a repressor that regulates the lmrAB and yxaGH operons; lmrB and yxaG encode a multidrug resistance pump and quercetin 2,3-dioxygenase, respectively. DNase I footprinting analysis revealed that LmrA and YxaF, which are paralogous to each other, bind specifically to almost the same cis sequences, LmrA/YxaF boxes, located in the promoter regions of the lmrAB operon, the yxaF gene, and the yxaGH operon for their repression and containing a consensus sequence of AWTATAtagaNYGgTCTA, where W, Y, and N stand for A or T, C or T, and any base, respectively (three-out-of-four match [in lowercase type]). Gel retardation analysis indicated that out of the eight flavonoids tested, quercetin, fisetin, and catechin are most inhibitory for LmrA to DNA binding, whereas quercetin, fisetin, tamarixetin, and galangin are most inhibitory for YxaF. Also, YxaF bound most tightly to the tandem LmrA/YxaF boxes in the yxaGH promoter region. The lacZ fusion experiments essentially supported the above-mentioned in vitro results, except that galangin did not activate the lmrAB and yxaGH promoters, probably due to its poor incorporation into cells. Thus, the LmrA/YxaF regulon presumably comprising the lmrAB operon, the yxaF gene, and the yxaGH operon is induced in response to certain flavonoids. The in vivo experiments to examine the regulation of the synthesis of the reporter β-galactosidase and quercetin 2,3-dioxgenase as well as that of multidrug resistance suggested that LmrA represses the lmrAB and yxaGH operons but that YxaF represses yxaGH more preferentially.
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Patel, Kevin, and Dasantila Golemi-Kotra. "Signaling mechanism by the Staphylococcus aureus two-component system LytSR: role of acetyl phosphate in bypassing the cell membrane electrical potential sensor LytS." F1000Research 4 (March 22, 2016): 79. http://dx.doi.org/10.12688/f1000research.6213.2.
Full textAbstract:
The two-component system LytSR has been linked to the signal transduction of cell membrane electrical potential perturbation and is involved in the adaptation of Staphylococcus aureus to cationic antimicrobial peptides. It consists of a membrane-bound histidine kinase, LytS, which belongs to the family of multiple transmembrane-spanning domains receptors, and a response regulator, LytR, which belongs to the novel family of non-helix-turn-helix DNA-binding domain proteins. LytR regulates the expression of cidABC and lrgAB operons, the gene products of which are involved in programmed cell death and lysis. In vivo studies have demonstrated involvement of two overlapping regulatory networks in regulating the lrgAB operon, both depending on LytR. One regulatory network responds to glucose metabolism and the other responds to changes in the cell membrane potential. Herein, we show that LytS has autokinase activity and can catalyze a fast phosphotransfer reaction, with 50% of its phosphoryl group lost within 1 minute of incubation with LytR. LytS has also phosphatase activity. Notably, LytR undergoes phosphorylation by acetyl phosphate at a rate that is 2-fold faster than the phosphorylation by LytS. This observation is significant in lieu of the in vivo observations that regulation of the lrgAB operon is LytR-dependent in the presence of excess glucose in the medium. The latter condition does not lead to perturbation of the cell membrane potential but rather to the accumulation of acetate in the cell. Our study provides insights into the molecular basis for regulation of lrgAB in a LytR-dependent manner under conditions that do not involve sensing by LytS.
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Overton, T. W., L. Griffiths, M. D. Patel, J. L. Hobman, C. W. Penn, J. A. Cole, and C. Constantinidou. "Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: new insights into microbial physiology." Biochemical Society Transactions 34, no. 1 (January 20, 2006): 104–7. http://dx.doi.org/10.1042/bst0340104.
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RNA was isolated from cultures of Escherichia coli strain MG1655 and derivatives defective in fnr, narXL, or narXL with narP, during aerobic growth, or anaerobic growth in the presence or absence of nitrate or nitrite, in non-repressing media in which both strain MG1655 and an fnr deletion mutant grew at similar rates. Glycerol was used as the non-repressing carbon source and both trimethylamine-N-oxide and fumarate were added as terminal electron acceptors. Microarray data supplemented with bioinformatic data revealed that the FNR (fumarate and nitrate reductase regulator) regulon includes at least 104, and possibly as many as 115, operons, 68 of which are activated and 36 are repressed during anaerobic growth. A total of 51 operons were directly or indirectly activated by NarL in response to nitrate; a further 41 operons were repressed. Four subgroups of genes implicated in management of reactive nitrogen compounds, NO and products of NO metabolism, were identified; they included proteins of previously unknown function. Global repression by the nitrate- and nitrite-responsive two-component system, NarQ-NarP, was shown for the first time. In contrast with the frdABCD, aspA and ansB operons that are repressed only by NarL, the dcuB-fumB operon was among 37 operons that are repressed by NarP.
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Gliese, Nicole, Viola Khodaverdi, Max Schobert, and Helmut Görisch. "AgmR controls transcription of a regulon with several operons essential for ethanol oxidation in Pseudomonas aeruginosa ATCC 17933." Microbiology 150, no. 6 (June 1, 2004): 1851–57. http://dx.doi.org/10.1099/mic.0.26882-0.
Full textAbstract:
The response regulator AgmR was identified to be involved in the regulation of the quinoprotein ethanol oxidation system of Pseudomonas aeruginosa ATCC 17933. Interruption of the agmR gene by insertion of a kanamycin-resistance cassette resulted in mutant NG3, unable to grow on ethanol. After complementation with the intact agmR gene, growth on ethanol was restored. Transcriptional lacZ fusions were used to identify four operons which are regulated by the AgmR protein: the exaA operon encodes the pyrroloquinoline quinone (PQQ)-dependent ethanol dehydrogenase, the exaBC operon encodes a soluble cytochrome c 550 and an aldehyde dehydrogenase, the pqqABCDE operon carries the PQQ biosynthetic genes, and operon exaDE encodes a two-component regulatory system which controls transcription of the exaA operon. Transcription of exaA was restored by transformation of NG3 with a pUCP20T derivative carrying the exaDE genes under lac-promoter control. These data indicate that the AgmR response regulator and the exaDE two-component regulatory system are organized in a hierarchical manner. Gene PA1977, which appears to form an operon with the agmR gene, was found to be non-essential for growth on ethanol.
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Fields, Christopher J., and Robert L. Switzer. "Regulation of pyr Gene Expression in Mycobacterium smegmatis by PyrR-Dependent Translational Repression." Journal of Bacteriology 189, no. 17 (June 29, 2007): 6236–45. http://dx.doi.org/10.1128/jb.00803-07.
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ABSTRACT Regulation of pyrimidine biosynthetic (pyr) genes by a transcription attenuation mechanism that is mediated by the PyrR mRNA-binding regulatory protein has been demonstrated for numerous gram-positive bacteria. Mycobacterial genomes specify pyrR genes and contain obvious PyrR-binding sequences in the initially transcribed regions of their pyr operons, but transcription antiterminator and attenuation terminator sequences are absent from their pyr 5′ leader regions. This work demonstrates that repression of pyr operon expression in Mycobacterium smegmatis by exogenous uracil requires the pyrR gene and the pyr leader RNA sequence for binding of PyrR. Plasmids containing the M. smegmatis pyr promoter-leader region translationally fused to lacZ also displayed pyrR-dependent repression, but transcriptional fusions of the same sequences to a lacZ gene that retained the lacZ ribosome-binding site were not regulated by PyrR plus uracil. We propose that PyrR regulates pyr expression in M. smegmatis, other mycobacteria, and probably in numerous other bacteria by a translational repression mechanism in which nucleotide-regulated binding of PyrR occludes the first ribosome-binding site of the pyr operon.
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Barragan, Carlos Eduardo, Andrés Julián Gutiérrez-Escobar, and Dolly Montoya Castaño. "Computational analysis of 1,3-propanediol operon transcriptional regulators: Insights into Clostridium sp. glycerol metabolism regulation." Universitas Scientiarum 20, no. 1 (October 2, 2014): 129. http://dx.doi.org/10.11144/javeriana.sc20-1.capo.
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We designed a strategy for the sequencing and bioinformatical characterization of the 1,3-propanediol operon regulator genes from the Colombian Clostridium sp. strain IBUN13A, which is taxonomically related to Clostridium butyricum;. Three genes are proposed to be involved in the operon’s transcriptional activity, the S and A genes through a two-component system and the third gene named Y, which encodes a putative transcriptional regulator similar to the domains of the S/A system. Phylogenetic analyses indicated that the predicted proteins had a modular structure consisting of domains homologous to different signal transduction systems, but had significant differences concerning their conserved residues, pointing to the possibility that they constitute ancestral domains. In accordance with the prediction of functions, we propose a mechanism of regulation of the proteins studied of the 1,3-propanediol operon of the native strain, as a response to the presence of glycerol in the medium, which provides valuable information on the overall regulation of the glycerol metabolism in Clostridium</em> sp.</p>
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Vallejo-García, Luz Cristina, María del Carmen Sánchez-Olmos, Rosa María Gutiérrez-Ríos, and Agustín López Munguía. "Glycosyltransferases Expression Changes in Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 Grown on Different Carbon Sources." Foods 12, no. 9 (May 4, 2023): 1893. http://dx.doi.org/10.3390/foods12091893.
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Leuconostoc mesenteroides strains are common contributors in fermented foods producing a wide variety of polysaccharides from sucrose through glycosyltransferases (GTFs). These polymers have been proposed as protective barriers against acidity, dehydration, heat, and oxidative stress. Despite its presence in many traditional fermented products and their association with food functional properties, regulation of GTFs expression in Ln. mesenteroides is still poorly understood. The strain Ln. mesenteroides ATCC 8293 contains three glucansucrases genes not found in operons, and three fructansucrases genes arranged in two operons, levLX and levC-scrB, a Glycoside-hydrolase. We described the first differential gene expression analysis of this strain when cultivated in different carbon sources. We observed that while GTFs are expressed in the presence of most sugars, they are down-regulated in xylose. We ruled out the regulatory effect of CcpA over GTFs and did not find regulatory elements with a direct effect on glucansucrases in the condition assayed. Our findings suggest that only operon levLX is repressed in xylose by LexA and that both fructansucrases operons can be regulated by the VicK/VicR system and PerR. It is essential to further explore the effect of environmental conditions in Ln. mesenteroides bacteria to better understand GTFs regulation and polymer function.
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McPhee, Joseph B., Manjeet Bains, Geoff Winsor, Shawn Lewenza, Agnieszka Kwasnicka, Michelle D. Brazas, Fiona S. L. Brinkman, and R. E. W. Hancock. "Contribution of the PhoP-PhoQ and PmrA-PmrB Two-Component Regulatory Systems to Mg2+-Induced Gene Regulation in Pseudomonas aeruginosa." Journal of Bacteriology 188, no. 11 (June 1, 2006): 3995–4006. http://dx.doi.org/10.1128/jb.00053-06.
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ABSTRACT When grown in divalent cation-limited medium, Pseudomonas aeruginosa becomes resistant to cationic antimicrobial peptides and polymyxin B. This resistance is regulated by the PhoP-PhoQ and PmrA-PmrB two-component regulatory systems. To further characterize Mg2+ regulation in P. aeruginosa, microarray transcriptional profiling was conducted to compare wild-type P. aeruginosa grown under Mg2+-limited and Mg2+-replete conditions to isogenic phoP and pmrA mutants grown under Mg2+-limited conditions. Under Mg2+-limited conditions (0.02 mM Mg2+), approximately 3% of the P. aeruginosa genes were differentially expressed compared to the expression in bacteria grown under Mg2+-replete conditions (2 mM Mg2+). Only a modest subset of the Mg2+-regulated genes were regulated through either PhoP or PmrA. To determine which genes were directly regulated, a bioinformatic search for conserved binding motifs was combined with confirmatory reverse transcriptase PCR and gel shift promoter binding assays, and the results indicated that very few genes were directly regulated by these response regulators. It was found that in addition to the previously known oprH-phoP-phoQ operon and the pmrHFIJKLM-ugd operon, the PA0921 and PA1343 genes, encoding small basic proteins, were regulated by Mg2+ in a PhoP-dependent manner. The number of known PmrA-regulated genes was expanded to include the PA1559-PA1560, PA4782-PA4781, and feoAB operons, in addition to the previously known PA4773-PA4775-pmrAB and pmrHFIJKLM-ugd operons.
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Yang, Soo-Jin, Kelly C. Rice, Raquel J. Brown, Toni G. Patton, Linda E. Liou, Yong Ho Park, and Kenneth W. Bayles. "A LysR-Type Regulator, CidR, Is Required for Induction of the Staphylococcus aureus cidABC Operon." Journal of Bacteriology 187, no. 17 (September 1, 2005): 5893–900. http://dx.doi.org/10.1128/jb.187.17.5893-5900.2005.
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ABSTRACT The Staphylococcus aureus cidABC and lrgAB operons have been shown to regulate murein hydrolase activity and affect antibiotic tolerance. The cid operon enhances murein hydrolase activity and antibiotic sensitivity, whereas the lrg operon inhibits these processes. Based on these findings and the structural similarities of the cidA and lrgA gene products to the bacteriophage holin family of proteins, we have proposed that the cid and lrg operons encode holin- and antiholin-like proteins, respectively, that function to control the murein hydrolase activity produced by the bacteria. Analysis of cid operon transcription revealed the presence of two transcripts, one spanning all three cid genes and whose expression is induced by growth in the presence of acetic acid and the other spanning cidB and cidC only that is produced in a sigma B-dependent manner. The cidABC operon lies immediately downstream from the cidR gene, encoding a potential LysR-type transcriptional regulator. In this study, we demonstrate that cidR is involved in the regulation of cidABC expression. Northern blot analyses revealed that the cidR gene product positively regulates cidABC expression by increasing transcription in the presence of acetic acid produced as a result of the metabolism of glucose. As expected for an operon that encodes a positive effector of murein hydrolase activity, the upregulation of cidABC expression resulted in increased murein hydrolase activity produced by these cells. Furthermore, it was demonstrated that antibiotic tolerance and stationary-phase survival of S. aureus are affected by the cidR gene. Taken together, these results demonstrate that the cidR gene product functions as a transcriptional activator of cidABC transcription in response to acetic acid accumulation in the growth medium.
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Omata, Tatsuo, Yukari Takahashi, Osamu Yamaguchi, and Takashi Nishimura. "Structure, function and regulation of the cyanobacterial high-affinity bicarbonate transporter, BCT1." Functional Plant Biology 29, no. 3 (2002): 151. http://dx.doi.org/10.1071/pp01215.
Full textAbstract:
The cmpABCD operon of the cyanobacterium Synechococcus sp. strain PCC7942, which is transcribed specifically under CO2-limited growth conditions, encodes an ATP-binding cassette (ABC) transporter involved in HCO3–uptake (designated BCT1). The product of the cmpA gene is a 42-kDa protein anchored to the plasma membrane, which binds HCO3– with high affinity (Kd= 5 µM) and acts as the substrate-binding protein of the transporter. The apparent Km(HCO3–) of BCT1 is 15 µM. BCT1 has the highest affinity for HCO3– among the HCO3– transporters of the Synechococcus strain and is essential for competitive utilization of HCO3– under CO2-limited conditions. BCT1 is closely related to the cyanobacterial nitrate/nitrite transporter (NRT) encoded by the nrtABCD genes. The BCT1 and NRT transporters, together with the putative cyanate transporter of cyanobacteria, comprise a monoanion transporter subfamily in the family of ABC importers. BCT1 and NRT are present in most fresh-water strains of cyanobacteria but seem to be absent in marine cyanobacterial strains. The low CO2-responsive induction of thecmp operon requires a LysR family protein CmpR, which is similar to CbbR (RbcR), the activator of the CO2 fixation operons of chemoautotrophic and purple photosynthetic bacteria.
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Veit, Katharina, Claudia Ehlers, and Ruth A. Schmitz. "Effects of Nitrogen and Carbon Sources on Transcription of Soluble Methyltransferases in Methanosarcina mazei Strain Gö1." Journal of Bacteriology 187, no. 17 (September 1, 2005): 6147–54. http://dx.doi.org/10.1128/jb.187.17.6147-6154.2005.
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ABSTRACT The methanogenic archaeon Methanosarcina mazei strain Gö1 uses versatile carbon sources and is able to fix molecular nitrogen with methanol as carbon and energy sources. Here, we demonstrate that when growing on trimethylamine (TMA), nitrogen fixation does not occur, indicating that ammonium released during TMA degradation is sufficient to serve as a nitrogen source and represses nif gene induction. We further report on the transcriptional regulation of soluble methyltransferases, which catalyze the initial step of methylamine consumption by methanogenesis, in response to different carbon and nitrogen sources. Unexpectedly, we obtained conclusive evidence that transcription of the mtmB2C2 operon, encoding a monomethylamine (MMA) methyltransferase and its corresponding corrinoid protein, is highly increased under nitrogen limitation when methanol serves as a carbon source. In contrast, transcription of the homologous mtmB1C1 operon is not affected by the nitrogen source but appears to be increased when TMA is the sole carbon and energy source. In general, transcription of operons encoding dimethylamine (DMA) and TMA methyltransferases and methylcobalamine:coenzyme M methyltransferases is not regulated in response to the nitrogen source. However, in all cases transcription of one of the homologous operons or genes is increased by TMA or its degradation products DMA and MMA.