scholarly journals Integrated Temporal Regulation of the Photorespiratory Pathway. Circadian Regulation of Two Arabidopsis Genes Encoding Serine Hydroxymethyltransferase

2000 ◽  
Vol 123 (1) ◽  
pp. 381-392 ◽  
Author(s):  
C. Robertson McClung ◽  
Meier Hsu ◽  
Janet E. Painter ◽  
Jennifer M. Gagne ◽  
Sharon D. Karlsberg ◽  
...  
Keyword(s):  
Serine Hydroxymethyltransferase ◽  
Circadian Regulation ◽  
Temporal Regulation ◽  
Genes Encoding

scholarly journals PecS Is a Global Regulator of the Symptomatic Phase in the Phytopathogenic Bacterium Erwinia chrysanthemi 3937

2008 ◽  
Vol 190 (22) ◽  
pp. 7508-7522 ◽  
Author(s):  
Florence Hommais ◽  
Christine Oger-Desfeux ◽  
Frédérique Van Gijsegem ◽  
Sandra Castang ◽  
Sandrine Ligori ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Stress Response ◽  
Oxidative Stress Response ◽  
Erwinia Chrysanthemi ◽  
Secretion Systems ◽  
Phytopathogenic Bacterium ◽  
Temporal Regulation ◽  
Wide Range ◽  
Genes Encoding ◽  
Asymptomatic Phase

ABSTRACT Pathogenicity of the enterobacterium Erwinia chrysanthemi (Dickeya dadantii), the causative agent of soft-rot disease in many plants, is a complex process involving several factors whose production is subject to temporal regulation during infection. PecS is a transcriptional regulator that controls production of various virulence factors. Here, we used microarray analysis to define the PecS regulon and demonstrated that PecS notably regulates a wide range of genes that could be linked to pathogenicity and to a group of genes concerned with evading host defenses. Among the targets are the genes encoding plant cell wall-degrading enzymes and secretion systems and the genes involved in flagellar biosynthesis, biosurfactant production, and the oxidative stress response, as well as genes encoding toxin-like factors such as NipE and hemolysin-coregulated proteins. In vitro experiments demonstrated that PecS interacts with the regulatory regions of five new targets: an oxidative stress response gene (ahpC), a biosurfactant synthesis gene (rhlA), and genes encoding exported proteins related to other plant-associated bacterial proteins (nipE, virK, and avrL). The pecS mutant provokes symptoms more rapidly and with more efficiency than the wild-type strain, indicating that PecS plays a critical role in the switch from the asymptomatic phase to the symptomatic phase. Based on this, we propose that the temporal regulation of the different groups of genes required for the asymptomatic phase and the symptomatic phase is, in part, the result of a gradual modulation of PecS activity triggered during infection in response to changes in environmental conditions emerging from the interaction between both partners.

scholarly journals Expression of Genes Related to Carrageenan Synthesis during Carposporogenesis of the Red Seaweed Grateloupia imbricata

Marine Drugs ◽  
2020 ◽  
Vol 18 (9) ◽  
pp. 432
Author(s):  
Pilar Garcia-Jimenez ◽  
Sara R. Mantesa ◽  
Rafael R. Robaina
Keyword(s):  
Cytochrome P450 ◽  
Stress Proteins ◽  
Life Cycles ◽  
Raw Material ◽  
Red Seaweed ◽  
Red Seaweeds ◽  
Temporal Regulation ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Two Stages

Carrageenan, the foremost constituent of extracellular matrix of some rhodophyta, is a galactan backbone with a different number of sulphate groups attached. Variations of degree of sulphation are associated with different types of carrageenans, which vary according to seaweed life cycles, and have consequences for the exploitation of this raw material. In this work, we used three well-recognised stages of development thalli and two stages of cystocarp maturation to analyse genes that encode addition and elimination of sulphate groups to cell-wall galactan of the red seaweed Grateloupia imbricata. Expressions of carbohydrate sulfotransferase and galactose-6 sulfurylase and genes encoding stress proteins such as cytochrome P450 and WD40, were examined. Results showed that transcript expression of carbohydrate sulfotransferase occurs at all stage of thalli development. Meanwhile galactose-6 sulfurylase expressions displayed different roles, which could be related to a temporal regulation of cystocarp maturation. Cytochrome P450 and WD40 are related to the disclosure and maturation of cystocarps of G. imbricata. Our conclusion is that differential expression of genes encoding proteins involved in the sulphation and desulphation of galactan backbone is associated with alterations in thalli development and cystocarp maturation in the red seaweed Grateloupia imbricata. Exploitation of industry-valued carrageenan will depend on insight into gene mechanisms of red seaweeds.

scholarly journals Evidence for Temporal Regulation of the Two Pseudomonas cellulosa Xylanases Belonging to Glycoside Hydrolase Family 11

2002 ◽  
Vol 184 (15) ◽  
pp. 4124-4133 ◽  
Author(s):  
Kaveh Emami ◽  
Tibor Nagy ◽  
Carlos M. G. A. Fontes ◽  
Luis M. A. Ferreira ◽  
Harry J. Gilbert
Keyword(s):  
Glycoside Hydrolase ◽  
Catalytic Domain ◽  
Xylanase Activity ◽  
Glycoside Hydrolase Family ◽  
Side Chains ◽  
Temporal Regulation ◽  
Degrading Bacterium ◽  
Genes Encoding ◽  
Combined Action ◽  
Hydrolase Family

ABSTRACT Pseudomonas cellulosa is a highly efficient xylan-degrading bacterium. Genes encoding five xylanases, and several accessory enzymes, which remove the various side chains that decorate the xylan backbone, have been isolated from the pseudomonad and characterized. The xylanase genes consist of xyn10A, xyn10B, xyn10C, xyn10D, and xyn11A, which encode Xyn10A, Xyn10B, Xyn10C, Xyn10D, and Xyn11A, respectively. In this study a sixth xylanase gene, xyn11B, was isolated which encodes a 357-residue modular enzyme, designated Xyn11B, comprising a glycoside hydrolase family 11 catalytic domain appended to a C-terminal X-14 module, a homologue of which binds to xylan. Localization studies showed that the two xylanases with glycoside hydrolase family (GH) 11 catalytic modules, Xyn11A and Xyn11B, are secreted into the culture medium, whereas Xyn10C is membrane bound. xyn10C, xyn10D, xyn11A, and xyn11B were all abundantly expressed when the bacterium was cultured on xylan or β-glucan but not on medium containing mannan, whereas glucose repressed transcription of these genes. Although all of the xylanase genes were induced by the same polysaccharides, temporal regulation of xyn11A and xyn11B was apparent on xylan-containing media. Transcription of xyn11A occurred earlier than transcription of xyn11B, which is consistent with the predicted mode of action of the encoded enzymes. Xyn11A, but not Xyn11B, exhibits xylan esterase activity, and the removal of acetate side chains is required for xylanases to hydrolyze the xylan backbone. A transposon mutant of P. cellulosa in which xyn11A and xyn11B were inactive displayed greatly reduced extracellular but normal cell-associated xylanase activity, and its growth rate on medium containing xylan was indistinguishable from wild-type P. cellulosa. Based on the data presented here, we propose a model for xylan degradation by P. cellulosa in which the GH11 enzymes convert decorated xylans into substituted xylooligosaccharides, which are then hydrolyzed to their constituent sugars by the combined action of cell-associated GH10 xylanases and side chain-cleaving enzymes.

scholarly journals Genomic, transcriptomic, and structural analysis ofPseudomonasvirus PA5oct highlights the molecular complexity among Jumbo phages

2018 ◽  
Author(s):  
Katarzyna Danis-Wlodarczyk ◽  
Bob G. Blasdel ◽  
Ho Bin Jang ◽  
Dieter Vandenheuvel ◽  
Jean-Paul Noben ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Temporal Regulation ◽  
Automated Annotation ◽  
Genomic Complexity ◽  
Genome Expression ◽  
Double Stranded Dna ◽  
Genes Encoding ◽  
Molecular Complexity ◽  
Conserved Core ◽  
Core Genes

AbstractPseudomonasvirus PA5oct has a large, linear, double-stranded DNA genome (287,182 bp) and is related toEscherichiaphages 121Q/PBECO 4,Klebsiellaphage vB_KleM-RaK2,Klebsiellaphage K64-1, andCronobacterphage vB_CsaM_GAP32. A protein-sharing network analysis highlights the conserved core genes within this clade. Combining genome, RNAseq and mass spectrometry analyses of its virion proteins allowed us to accurately identify genes and elucidate regulatory elements for this phage (ncRNAs, tRNAs and promoter elements). In total PA5oct encodes 462 CDS (compared to 345in silicopredicted genes using automated annotation pipelines), of which 25.32%, have been identified as virion-associated based on ESI-MS/MS. The RNAseq-based temporal genome organization suggests a gradual take-over by viral transcripts from 21%, 69%, and 92% at 5, 15 and 25 min after infection, respectively. Like many large phages, PA5oct is not organized into contiguous regions of temporal transcription. However, although the temporal regulation of the PA5oct genome expression reveals specific genome clusters expressed in early and late infection, many genes encoding experimentally observed structural proteins surprisingly appear to remain almost untranscribed throughout the infection cycle. Within the host, operons associated with elements of a cryptic Pf1-like prophage are upregulated, as are operons responsible for Psl exopolysaccharide (pslE-J) and periplasmic nitrate reductase (napA-F) production. The characterization described here represents a crucial step towards understanding the genomic complexity as well as molecular diversity of jumbo viruses.

Circadian regulation of electrolyte absorption in the rat colon

2011 ◽  
Vol 301 (6) ◽  
pp. G1066-G1074 ◽  
Author(s):  
M. Soták ◽  
L. Polidarová ◽  
J. Musílková ◽  
M. Hock ◽  
A. Sumová ◽  
...  
Keyword(s):  
Clock Genes ◽  
Circadian Variation ◽  
Intestinal Transport ◽  
Rat Colon ◽  
Mrna Levels ◽  
Ion Transporters ◽  
Temporal Regulation ◽  
Nacl Absorption ◽  
Subjective Night ◽  
Genes Encoding

The intestinal transport of nutrients exhibits distinct diurnal rhythmicity, and the enterocytes harbor a circadian clock. However, temporal regulation of the genes involved in colonic ion transport, i.e., ion transporters and channels operating in absorption and secretion, remains poorly understood. To address this issue, we assessed the 24-h profiles of expression of genes encoding the sodium pump (subunits Atp1a1 and Atp1b1), channels (α-, β-, and γ-subunits of Enac and Cftr), transporters ( Dra, Ae1, Nkcc1, Kcc1, and Nhe3), and the Na+/H+ exchanger (NHE) regulatory factor ( Nherf1) in rat colonic mucosa. Furthermore, we investigated temporal changes in the spatial localization of the clock genes Per1, Per2, and Bmal1 and the genes encoding ion transporters and channels along the crypt axis. In rats fed ad libitum, the expression of Atp1a1, γ Enac, Dra, Ae1, Nhe3, and Nherf1 showed circadian variation with maximal expression at circadian time 12, i.e., at the beginning of the subjective night. The peak γ Enac expression coincided with the rise in plasma aldosterone. Restricted feeding phase advanced the expression of Dra, Ae1, Nherf, and γ Enac and decreased expression of Atp1a1. The genes Atp1b1, Cftr, α Enac, β Enac, Nkcc1, and Kcc1 did not show any diurnal variations in mRNA levels. A low-salt diet upregulated the expression of β Enac and γ Enac during the subjective night but did not affect expression of α Enac. Similarly, colonic electrogenic Na+ transport was much higher during the subjective night than the subjective day. These findings indicate that the transporters and channels operating in NaCl absorption undergo diurnal regulation and suggest a role of an intestinal clock in the coordination of colonic NaCl absorption.

scholarly journals New Roles for the Heterochronic Transcription Factor LIN-29 in Cuticle Maintenance and Lipid Metabolism at the Larval-to-Adult Transition in Caenorhabditis elegans

Genetics ◽  
2020 ◽  
Vol 214 (3) ◽  
pp. 669-690 ◽  
Author(s):  
Patricia Abete-Luzi ◽  
Tetsunari Fukushige ◽  
Sijung Yun ◽  
Michael W. Krause ◽  
David M. Eisenmann
Keyword(s):  
Transcription Factor ◽  
Caenorhabditis Elegans ◽  
Regulation Of Gene Expression ◽  
Early Time ◽  
Temporal Regulation ◽  
Adult Transition ◽  
Link Type ◽  
Offspring Production ◽  
Genes Encoding ◽  
Time Specific

Temporal regulation of gene expression is a crucial aspect of metazoan development. In the roundworm Caenorhabditis elegans, the heterochronic pathway controls multiple developmental events in a time-specific manner. The most downstream effector of this pathway, the zinc-finger transcription factor LIN-29, acts in the last larval stage (L4) to regulate elements of the larval-to-adult switch. Here, we explore new LIN-29 targets and their implications for this developmental transition. We used RNA-sequencing to identify genes differentially expressed between animals misexpressing LIN-29 at an early time point and control animals. Among 230 LIN-29-activated genes, we found that genes encoding cuticle collagens were overrepresented. Interestingly, expression of lin-29 and some of these collagens was increased in adults with cuticle damage, suggesting a previously unknown function for LIN-29 in adult cuticle maintenance. On the other hand, genes involved in fat metabolism were enriched among 350 LIN-29-downregulated targets. We used mass spectrometry to assay lipid content in animals overexpressing LIN-29 and observed reduced fatty acid levels. Many LIN-29-repressed genes are normally expressed in the intestine, suggesting cell-nonautonomous regulation. We identified several LIN-29 upregulated genes encoding signaling molecules that may act as mediators in the regulation of intestinally expressed genes encoding fat metabolic enzymes and vitellogenins. Overall, our results support the model of LIN-29 as a major regulator of adult cuticle synthesis and integrity, and as the trigger for metabolic changes that take place at the important transition from rapid growth during larval life to slower growth and offspring production during adulthood.

scholarly journals Midkine expression is regulated by the circadian clock in the retina of the zebrafish

2009 ◽  
Vol 26 (5-6) ◽  
pp. 495-501 ◽  
Author(s):  
ANDA-ALEXANDRA CALINESCU ◽  
PAMELA A. RAYMOND ◽  
PETER F. HITCHCOCK
Keyword(s):  
Circadian Clock ◽  
Direct Action ◽  
Horizontal Cells ◽  
Circadian Regulation ◽  
Heparin Binding ◽  
Qualitative And Quantitative ◽  
Subjective Night ◽  
Genes Encoding ◽  
Heparin Binding Growth Factors ◽  
Paracrine Actions

AbstractThe retina displays numerous processes that follow a circadian rhythm. These processes are coordinated through the direct action of light on photoreceptive molecules and, in the absence of light, through autocrine/paracrine actions of extracellular neuromodulators. We previously described the expression of the genes encoding the secreted heparin-binding growth factors, midkine-a (mdka) and midkine-b (mdkb), in the retina of the zebrafish. Here, we provide evidence that the expression of mdka and mdkb follows a daily rhythm, which is independent of the presence or absence of light, and we propose that the expression of mdka is regulated by the circadian clock. Both qualitative and quantitative measures show that for mdka, the levels of mRNA and protein decrease during the night and increase during the subjective day. Qualitative measures show that the expression of mdkb increases during the second half of the subjective night and decreases during the second half of the subjective day. Within horizontal cells, the two midkine paralogs show asynchronous circadian regulation. Though intensely studied in the contexts of physiology and disease, this is the first study to provide evidence for the circadian regulation of midkines in the vertebrate nervous system.

Characterization of three genes encoding enzymes of the folate biosynthetic pathway in Plasmodium falciparum

Parasitology ◽  
2001 ◽  
Vol 122 (1) ◽  
pp. 1-13 ◽  
Author(s):  
C.-S. LEE ◽  
E. SALCEDO ◽  
Q. WANG ◽  
P. WANG ◽  
P.F.G. SIMS ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Serine Hydroxymethyltransferase ◽  
Gtp Cyclohydrolase I ◽  
Gene Encoding ◽  
New Genes ◽  
Isolation And Characterization ◽  
Genes Encoding ◽  
Antifolate Drugs ◽  
Dihydroneopterin Aldolase

Although the folate metabolic pathway in malaria parasites is a major chemotherapeutic target, resistance to currently available antifolate drugs is an increasing problem. This pathway, however, includes a number of enzymes that, to date, have not been characterized despite their potential for clinical exploitation. As a step towards evaluation of additional targets in this pathway, we report the isolation and characterization of 3 new genes that encode homologues of GTP cyclohydrolase I (GTP-CH), dihydrofolate synthase/folylpolyglutamate synthase (DHFS/FPGS) and serine hydroxymethyltransferase (SHMT). The genes encoding GTP-CH and SHMT are unambiguously assigned to chromosome 12, while that for DHFS/FPGS is tentatively assigned to chromosome 13. All 3 genes are expressed in blood-stage parasites, yielding transcripts of which only ca 60–70% is accounted for by coding sequence. All 3 of the proteins predicted to be encoded by these genes display sequence differences compared to the human host homologues that may be of functional significance. These data bring the complement of cloned genes that encode activities in the pathway to seven, leaving only the gene encoding dihydroneopterin aldolase (DHNA) to be identified in the route from GTP to folate synthesis and folate turnover in the thymidylate cycle.

scholarly journals 2-Aminoacrylate Stress Induces a Context-Dependent Glycine Requirement inridAStrains of Salmonella enterica

2015 ◽  
Vol 198 (3) ◽  
pp. 536-543 ◽  
Author(s):  
Dustin C. Ernst ◽  
Diana M. Downs
Keyword(s):  
Salmonella Enterica ◽  
Serine Hydroxymethyltransferase ◽  
Content Type ◽  
Growth Defects ◽  
Genes Encoding ◽  
Glycine Cleavage ◽  
One Carbon Metabolism ◽  
Living Organisms ◽  
Cellular Components

ABSTRACTThe reactive enamine 2-aminoacrylate (2AA) is a metabolic stressor capable of damaging cellular components. Members of the broadly conserved Rid (RidA/YER057c/UK114) protein family mitigate 2AA stressin vivoby facilitating enamine and/or imine hydrolysis. Previous work showed that 2AA accumulation inridAstrains ofSalmonella entericaled to the inactivation of multiple target enzymes, including serine hydroxymethyltransferase (GlyA). However, the specific cause of aridAstrain's inability to grow during periods of 2AA stress had yet to be determined. Work presented here shows that glycine supplementation suppressed all 2AA-dependentridAstrain growth defects described to date. Depending on the metabolic context, glycine appeared to suppressridAstrain growth defects by eliciting a GcvB small RNA-dependent regulatory response or by serving as a precursor to one-carbon units produced by the glycine cleavage complex (GCV). In either case, the data suggest that GlyA is the most physiologically sensitive target of 2AA inactivation inS. enterica. The universally conserved nature of GlyA among free-living organisms highlights the importance of RidA in mitigating 2AA stress.IMPORTANCEThe RidA stress response prevents 2-aminoacrylate (2AA) damage from occurring in prokaryotes and eukaryotes alike. 2AA inactivation of serine hydroxymethyltransferase (GlyA) fromSalmonella entericarestricts glycine and one-carbon production, ultimately reducing fitness of the organism. The cooccurrence of genes encoding 2AA production enzymes and serine hydroxy-methyltransferase (SHMT) in many genomes may in part underlie the evolutionary selection for Rid proteins to maintain appropriate glycine and one-carbon metabolism throughout life.

Sign in / Sign up

Export Citation Format

Share Document