scholarly journals Creatine utilization as a sole nitrogen source in Pseudomonas putida KT2440 is transcriptionally regulated by CahR

2021 ◽  
Author(s):  
Lauren A Hinkel ◽  
Graham G Willsey ◽  
Sean M Lenahan ◽  
Korin Eckstrom ◽  
Kristin C Schutz ◽  
...  
Keyword(s):  
Strain Distribution ◽  
Regulatory Networks ◽  
Transcriptional Regulators ◽  
Sole Source ◽  
Nitrogen Compounds ◽  
Ciliated Cells ◽  
Mobility Shift ◽  
Gene Encoding ◽  
Pseudomonas Putida Kt2440 ◽  
Evolution Of Metabolism

Glutamine amidotransferase-1 domain-containing AraC-family transcriptional regulators (GATRs) are present in the genomes of many bacteria, including all Pseudomonas species. The involvement of several characterized GATRs in amine-containing compound metabolism has been determined, but the full scope of GATR ligands and regulatory networks are still unknown. Here, we characterize Pseudomonas putida's detection of the animal-derived amine compound, creatine, a compound particularly enriched in muscle and ciliated cells by a creatine-specific GATR, PP_3665, here named CahR (Creatine amidohydrolase Regulator). cahR is necessary for transcription of the gene encoding creatinase (PP_3667/creA) in the presence of creatine and is critical for P. putida's ability to utilize creatine as a sole source of nitrogen. The CahR/creatine regulon is small and electrophoretic mobility shift demonstrates strong and specific CahR binding only at the creA promoter, supporting the conclusion that much of the regulon is dependent on downstream metabolites. Phylogenetic analysis of creA orthologs associated with cahR orthologs highlights a strain distribution and organization supporting likely horizontal gene transfer, particularly evident within the genus Acinetobacter. This study identifies and characterizes the GATR that transcriptionally controls P. putida metabolism of creatine, broadening the scope of known GATR ligands and suggesting GATR diversification during evolution of metabolism for aliphatic nitrogen compounds.

scholarly journals The HrpG/HrpX Regulon of Xanthomonads—An Insight to the Complexity of Regulation of Virulence Traits in Phytopathogenic Bacteria

2021 ◽  
Vol 9 (1) ◽  
pp. 187
Author(s):  
Doron Teper ◽  
Sheo Shankar Pandey ◽  
Nian Wang
Keyword(s):  
Regulatory Network ◽  
Regulatory Networks ◽  
Focal Point ◽  
Genetic Regulation ◽  
Transcriptional Regulators ◽  
Secretion System ◽  
In Planta ◽  
Type 3 Secretion System ◽  
Type 3 ◽  
Made In

Bacteria of the genus Xanthomonas cause a wide variety of economically important diseases in most crops. The virulence of the majority of Xanthomonas spp. is dependent on secretion and translocation of effectors by the type 3 secretion system (T3SS) that is controlled by two master transcriptional regulators HrpG and HrpX. Since their discovery in the 1990s, the two regulators were the focal point of many studies aiming to decipher the regulatory network that controls pathogenicity in Xanthomonas bacteria. HrpG controls the expression of HrpX, which subsequently controls the expression of T3SS apparatus genes and effectors. The HrpG/HrpX regulon is activated in planta and subjected to tight metabolic and genetic regulation. In this review, we cover the advances made in understanding the regulatory networks that control and are controlled by the HrpG/HrpX regulon and their conservation between different Xanthomonas spp.

The orphan nuclear receptor NGFI-B regulates expression of the gene encoding steroid 21-hydroxylase

1993 ◽  
Vol 13 (2) ◽  
pp. 861-868
Author(s):  
T E Wilson ◽  
A R Mouw ◽  
C A Weaver ◽  
J Milbrandt ◽  
K L Parker
Keyword(s):  
Nuclear Receptor ◽  
Transcriptional Activation ◽  
Core Promoter ◽  
Orphan Nuclear Receptor ◽  
Recognition Sequence ◽  
Mobility Shift ◽  
Adrenocortical Cells ◽  
Gene Encoding ◽  
Adult Rat ◽  
Gel Mobility Shift

As part of its trophic action to maintain the steroidogenic capacity of adrenocortical cells, corticotropin (ACTH) increases the transcription of the cytochrome P-450 steroid hydroxylase genes, including the gene encoding steroid 21-hydroxylase (21-OHase). We previously identified several promoter elements that regulate 21-OHase gene expression in mouse Y1 adrenocortical tumor cells. One of these elements, located at nucleotide -65, closely resembles the recognition sequence of the orphan nuclear receptor NGFI-B, suggesting that NGFI-B regulates this essential steroidogenic enzyme. To explore this possibility, we first used in situ hybridization to demonstrate high levels of NGFI-B transcripts in the adrenal cortex of the adult rat. In cultured mouse Y1 adrenocortical cells, treatment with ACTH, the major regulator of 21-OHase transcription, rapidly increased NGFI-B expression. Gel mobility shift and DNase I footprinting experiments showed that recombinantly expressed NGFI-B interacts specifically with the 21-OHase -65 element and identified one complex formed by Y1 extracts and the 21-OHase -65 element that contains NGFI-B. Expression of NGFI-B significantly augmented the activity of the intact 21-OHase promoter, while mutations of the -65 element that abolish NGFI-B binding markedly diminished NGFI-B-mediated transcriptional activation. Specific mutations of NGFI-B shown previously to impair either DNA binding or transcriptional activation diminished the effect of NGFI-B coexpression on 21-OHase expression. Finally, an oligonucleotide containing the NGFI-B response element conferred ACTH response to a core promoter from the prolactin gene, showing that this element is sufficient for ACTH induction. Collectively, these results identify a cellular promoter element that is regulated by NGFI-B and implicate NGFI-B in the transcriptional induction of 21-OHase by ACTH.

scholarly journals Amino Acid-Mediated Induction of the Basic Amino Acid-Specific Outer Membrane Porin OprD from Pseudomonas aeruginosa

1999 ◽  
Vol 181 (17) ◽  
pp. 5426-5432 ◽  
Author(s):  
Martina M. Ochs ◽  
Chung-Dar Lu ◽  
Robert E. W. Hancock ◽  
Ahmed T. Abdelal
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Regulatory Protein ◽  
Basic Amino Acid ◽  
Sole Source ◽  
Activation Mechanism ◽  
Beta Lactam ◽  
Mobility Shift ◽  
Carbon And Nitrogen

ABSTRACT Pseudomonas aeruginosa can utilize arginine and other amino acids as both carbon and nitrogen sources. Earlier studies have shown that the specific porin OprD facilitates the diffusion of basic amino acids as well as the structurally analogous beta-lactam antibiotic imipenem. The studies reported here showed that the expression of OprD was strongly induced when arginine, histidine, glutamate, or alanine served as the sole source of carbon. The addition of succinate exerted a negative effect on induction ofoprD, likely due to catabolite repression. The arginine-mediated induction was dependent on the regulatory protein ArgR, and binding of purified ArgR to its operator upstream of theoprD gene was demonstrated by gel mobility shift and DNase assays. The expression of OprD induced by glutamate as the carbon source, however, was independent of ArgR, indicating the presence of more than a single activation mechanism. In addition, it was observed that the levels of OprD responded strongly to glutamate and alanine as the sole sources of nitrogen. Thus, that the expression ofoprD is linked to both carbon and nitrogen metabolism ofPseudomonas aeruginosa.

Developing roles for Hox proteins in hindbrain gene regulatory networks

2018 ◽  
Vol 62 (11-12) ◽  
pp. 767-774 ◽  
Author(s):  
Priyanjali Ghosh ◽  
Charles G. Sagerström
Keyword(s):  
Functional Analysis ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Transcriptional Regulators ◽  
Hox Proteins ◽  
Recent Advances ◽  
Specific Focus ◽  
Gene Regulatory

Hox proteins have long been known to function as transcriptional regulators during development of the vertebrate hindbrain. In particular, these factors are thought to play key roles in assigning distinct fates to the rhombomere segments arising in the embryonic hindbrain. However, it remains uncertain exactly how the Hox proteins fit into the regulatory networks controlling hindbrain formation. For instance, it is unclear if Hox proteins fulfill similar roles in different rhombomeres and if they are absolutely required for all aspects of each rhombomere fate. Recent advances in the discovery, characterization and functional analysis of hindbrain gene regulatory networks is now allowing us to revisit these types of questions. In this review we focus on recent data on the formation of caudal rhombomeres in vertebrates, with a specific focus on zebrafish, to derive an up-to-date view of the role for Hox proteins in the regulation of hindbrain development.

scholarly journals CidR and CcpA Synergistically Regulate Staphylococcus aureus cidABC Expression

2019 ◽  
Vol 201 (23) ◽  
Author(s):  
Marat R. Sadykov ◽  
Ian H. Windham ◽  
Todd J. Widhelm ◽  
Vijaya Kumar Yajjala ◽  
Sean M. Watson ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Carbon Metabolism ◽  
Protein A ◽  
Transcriptional Regulators ◽  
Extracellular Dna ◽  
Regulatory Control ◽  
Pcr Analysis ◽  
Mobility Shift ◽  
Content Type ◽  
Biofilm Development

ABSTRACT The death and lysis of a subpopulation of Staphylococcus aureus cells during biofilm development benefit the whole bacterial population through the release of an important component of the biofilm matrix, extracellular DNA. Previously, we have demonstrated that these processes are affected by the gene products of the cidABC operon, the expression of which is controlled by the LysR-type transcriptional regulator, CidR. In this study, we characterized cis- and trans-acting elements essential for the induction of the cidABC operon. In addition to a CidR-binding site located within the cidABC promoter region, sequence analysis revealed the presence of a putative catabolite responsive element (cre box), suggestive of the involvement of the catabolite control protein A (CcpA) in the regulation of cidABC expression. This was confirmed using electrophoretic mobility shift assays and real-time reverse transcriptase PCR analysis demonstrating the direct positive control of cidABC transcription by the master regulator of carbon metabolism. Furthermore, the importance of CcpA and the identified cre site for the induction of the cidABC operon was demonstrated by examining the expression of PcidABC-lacZ reporter fusions in various mutant strains in which the genes involved in carbon metabolism and carbon catabolite repression were disrupted. Together the results of this study demonstrate the necessity of both transcriptional regulators, CidR and CcpA, for the induction of the cidABC operon and reveal the complexity of molecular interactions controlling its expression. IMPORTANCE This work focuses on the characterization of cis- and trans-acting elements essential for the induction of the cidABC operon in S. aureus. The results of this study are the first to demonstrate the synergistic control of cidABC expression by transcriptional regulators CidR and CcpA during carbohydrate metabolism. We established that the full induction of cidABC expression depends on the metabolic state of bacteria and requires both CidR and CcpA. Together, these findings delineate regulatory control of cidABC expression under different metabolic conditions and provide important new insights into our understanding of cell death mechanisms during biofilm development in S. aureus.

scholarly journals Identification of a Novel Streptococcal Gene Cassette Mediating SOS Mutagenesis in Streptococcus uberis

2007 ◽  
Vol 189 (14) ◽  
pp. 5210-5222 ◽  
Author(s):  
Emilia Varhimo ◽  
Kirsi Savijoki ◽  
Jari Jalava ◽  
Oscar P. Kuipers ◽  
Pekka Varmanen
Keyword(s):  
Uv Light ◽  
Streptococcus Thermophilus ◽  
Gene Cassette ◽  
Repeat Sequence ◽  
Mobile Dna ◽  
Mobility Shift ◽  
Gene Encoding ◽  
Sos Mutagenesis ◽  
Streptococcus Uberis ◽  
Y Family

ABSTRACT Streptococci have been considered to lack the classical SOS response, defined by increased mutation after UV exposure and regulation by LexA. Here we report the identification of a potential self-regulated SOS mutagenesis gene cassette in the Streptococcaceae family. Exposure to UV light was found to increase mutations to antibiotic resistance in Streptococcus uberis cultures. The mutational spectra revealed mainly G:C→A:T transitions, and Northern analyses demonstrated increased expression of a Y-family DNA polymerase resembling UmuC under DNA-damaging conditions. In the absence of the Y-family polymerase, S. uberis cells were sensitive to UV light and to mitomycin C. Furthermore, the UV-induced mutagenesis was almost completely abolished in cells deficient in the Y-family polymerase. The gene encoding the Y-family polymerase was localized in a four-gene operon including two hypothetical genes and a gene encoding a HdiR homolog. Electrophoretic mobility shift assays demonstrated that S. uberis HdiR binds specifically to an inverted repeat sequence in the promoter region of the four-gene operon. Database searches revealed conservation of the gene cassette in several Streptococcus species, including at least one genome each of Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus mitis, Streptococcus sanguinis, and Streptococcus thermophilus strains. In addition, the umuC operon was localized in several mobile DNA elements of Streptococcus and Lactococcus species. We conclude that the hdiR-umuC-ORF3-ORF4 operon represents a novel gene cassette capable of mediating SOS mutagenesis among members of the Streptococcaceae.

scholarly journals The Novel Streptococcal Transcriptional Regulator XtgS Negatively Regulates Bacterial Virulence and Directly Represses PseP Transcription

2020 ◽  
Vol 88 (10) ◽  
Author(s):  
Guangjin Liu ◽  
Tingting Gao ◽  
Xiaojun Zhong ◽  
Jiale Ma ◽  
Yumin Zhang ◽  
...  
Keyword(s):  
Strong Association ◽  
Challenge Test ◽  
Transcriptional Regulator ◽  
Transcriptional Regulators ◽  
Negative Regulator ◽  
Broad Host Range ◽  
Bacterial Survival ◽  
Mobility Shift ◽  
Upstream Gene ◽  
Content Type

ABSTRACT Streptococcus agalactiae (group B streptococcus [GBS]) has received continuous attention for its involvement in invasive infections and its broad host range. Transcriptional regulators have an important impact on bacterial adaptation to various environments. Research on transcriptional regulators will shed new light on GBS pathogenesis. In this study, we identified a novel XRE-family transcriptional regulator encoded on the GBS genome, designated XtgS. Our data demonstrate that XtgS inactivation significantly increases bacterial survival in host blood and animal challenge test, suggesting that it is a negative regulator of GBS pathogenicity. Further transcriptomic analysis and quantitative reverse transcription-PCR (qRT-PCR) mainly indicated that XtgS significantly repressed transcription of its upstream gene pseP. Based on electrophoretic mobility shift and lacZ fusion assays, we found that an XtgS homodimer directly binds a palindromic sequence in the pseP promoter region. Meanwhile, the PseP and XtgS combination naturally coexists in diverse Streptococcus genomes and has a strong association with sequence type, serotype diversification and host adaptation of GBS. Therefore, this study reveals that XtgS functions as a transcriptional regulator that negatively affects GBS virulence and directly represses PseP expression, and it provides new insights into the relationships between transcriptional regulator and genome evolution.

scholarly journals Genetic Manipulation of Transcriptional Regulators Alters Nicotine Biosynthesis in Tobacco

2020 ◽  
Vol 61 (6) ◽  
pp. 1041-1053 ◽  
Author(s):  
Shunya Hayashi ◽  
Mutsumi Watanabe ◽  
Makoto Kobayashi ◽  
Takayuki Tohge ◽  
Takashi Hashimoto ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Genetic Manipulation ◽  
Transcriptional Regulators ◽  
Knockout Mutant ◽  
Gene Encoding ◽  
Helix Loop Helix ◽  
Wide Range ◽  
Nicotine Biosynthesis ◽  
Transient Overexpression ◽  
The Impact

Abstract The toxic alkaloid nicotine is produced in the roots of Nicotiana species and primarily accumulates in leaves as a specialized metabolite. A series of metabolic and transport genes involved in the nicotine pathway are coordinately upregulated by a pair of jasmonate-responsive AP2/ERF-family transcription factors, NtERF189 and NtERF199, in the roots of Nicotiana tabacum (tobacco). In this study, we explored the potential of manipulating the expression of these transcriptional regulators to alter nicotine biosynthesis in tobacco. The transient overexpression of NtERF189 led to alkaloid production in the leaves of Nicotiana benthamiana and Nicotiana alata. This ectopic production was further enhanced by co-overexpressing a gene encoding a basic helix-loop-helix-family MYC2 transcription factor. Constitutive and leaf-specific overexpression of NtERF189 increased the accumulation of foliar alkaloids in transgenic tobacco plants but negatively affected plant growth. By contrast, in a knockout mutant of NtERF189 and NtERF199 obtained through CRISPR/Cas9-based genome editing, alkaloid levels were drastically reduced without causing major growth defects. Metabolite profiling revealed the impact of manipulating the nicotine pathway on a wide range of nitrogen- and carbon-containing metabolites. Our findings provide insights into the biotechnological applications of engineering metabolic pathways by targeting transcription factors.

scholarly journals Identification of an Acetoacetyl Coenzyme A Synthetase-Dependent Pathway for Utilization of l-(+)-3-Hydroxybutyrate in Sinorhizobium meliloti

2002 ◽  
Vol 184 (6) ◽  
pp. 1571-1577 ◽  
Author(s):  
Punita Aneja ◽  
Renata Dziak ◽  
Guo-Qin Cai ◽  
Trevor C. Charles
Keyword(s):  
Sinorhizobium Meliloti ◽  
Direct Evidence ◽  
Coenzyme A ◽  
Sole Source ◽  
Degradation Pathway ◽  
Synthetase Activity ◽  
Gene Encoding ◽  
Carbon Store ◽  
Utilization Pathway ◽  
Dependent Pathway

ABSTRACT d-(−)-3-Hydroxybutyrate (DHB), the immediate depolymerization product of the intracellular carbon store poly-3-hydroxybutyrate (PHB), is oxidized by the enzyme 3-hydroxybutyrate dehydrogenase to acetoacetate (AA) in the PHB degradation pathway. Externally supplied DHB can serve as a sole source of carbon and energy to support the growth of Sinorhizobium meliloti. In contrast, wild-type S. meliloti is not able to utilize the l-(+) isomer of 3-hydroxybutyrate (LHB) as a sole source of carbon and energy. In this study, we show that overexpression of the S. meliloti acsA2 gene, encoding acetoacetyl coenzyme A (acetoacetyl-CoA) synthetase, confers LHB utilization ability, and this is accompanied by novel LHB-CoA synthetase activity. Kinetics studies with the purified AcsA2 protein confirmed its ability to utilize both AA and LHB as substrates and showed that the affinity of the enzyme for LHB was clearly lower than that for AA. These results thus provide direct evidence for the LHB-CoA synthetase activity of the AcsA2 protein and demonstrate that the LHB utilization pathway in S. meliloti is AcsA2 dependent.

scholarly journals An essential E box in the promoter of the gene encoding the mRNA cap-binding protein (eukaryotic initiation factor 4E) is a target for activation by c-myc.

1996 ◽  
Vol 16 (9) ◽  
pp. 4754-4764 ◽  
Author(s):  
R M Jones ◽  
J Branda ◽  
K A Johnston ◽  
M Polymenis ◽  
M Gadd ◽  
...  
Keyword(s):  
Electrophoretic Mobility ◽  
Promoter Region ◽  
Binding Protein ◽  
Dominant Negative ◽  
Initiation Factor ◽  
Eukaryotic Initiation Factor ◽  
Mobility Shift ◽  
Gene Encoding ◽  
Eukaryotic Initiation Factor 4E ◽  
E Box

The mRNA cap-binding protein (eukaryotic initiation factor 4E [eIF4E]) binds the m7 GpppN cap on mRNA, thereby initiating translation. eIF4E is essential and rate limiting for protein synthesis. Overexpression of eIF4E transforms cells, and mutations in eIF4E arrest cells in G, in cdc33 mutants. In this work, we identified the promoter region of the gene encoding eIF4E, because we previously identified eIF4E as a potential myc-regulated gene. In support of our previous data, a minimal, functional, 403-nucleotide promoter region of eIF4E was found to contain CACGTG E box repeats, and this core eIF4E promoter was myc responsive in cotransfections with c-myc. A direct role for myc in activating the eIF4E promoter was demonstrated by cotransfections with two dominant negative mutants of c-myc (MycdeltaTAD and MycdeltaBR) which equally suppressed promoter function. Furthermore, electrophoretic mobility shift assays demonstrated quantitative binding to the E box motifs that correlated with myc levels in the electrophoretic mobility shift assay extracts; supershift assays demonstrated max and USF binding to the same motif. cis mutations in the core or flank of the eIF4E E box simultaneously altered myc-max and USF binding and inactivated the promoter. Indeed, mutations of this E box inactivated the promoter in all cells tested, suggesting it is essential for expression of eIF4E. Furthermore, the GGCCACGTG(A/T)C(C/G) sequence is shared with other in vivo targets for c-myc, but unlike other targets, it is located in the immediate promoter region. Its critical function in the eIF4E promoter coupled with the known functional significance of eIF4E in growth regulation makes it a particularly interesting target for c-myc regulation.

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