scholarly journals Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT

2020 ◽  
Vol 48 (14) ◽  
pp. 7786-7800
Author(s):  
Magda Dudek ◽  
Anissa Dieudonné ◽  
Diane Jouanneau ◽  
Tatiana Rochat ◽  
Gurvan Michel ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Regulatory Mechanisms ◽  
Dna Complexes ◽  
Extracellular Medium ◽  
Metabolic Intermediates ◽  
Family Protein ◽  
Algal Polysaccharides ◽  
Polysaccharide Utilization Loci ◽  
Secreted Enzymes ◽  
Gntr Family

Abstract Marine flavobacteria possess dedicated Polysaccharide Utilization Loci (PULs) enabling efficient degradation of a variety of algal polysaccharides. The expression of these PULs is tightly controlled by the presence of the substrate, yet details on the regulatory mechanisms are still lacking. The marine flavobacterium Zobellia galactanivorans DsijT digests many algal polysaccharides, including alginate from brown algae. Its complex Alginate Utilization System (AUS) comprises a PUL and several other loci. Here, we showed that the expression of the AUS is strongly and rapidly (<30 min) induced upon addition of alginate, leading to biphasic substrate utilization. Polymeric alginate is first degraded into smaller oligosaccharides that accumulate in the extracellular medium before being assimilated. We found that AusR, a GntR family protein encoded within the PUL, regulates alginate catabolism by repressing the transcription of most AUS genes. Based on our genetic, genomic, transcriptomic and biochemical results, we propose the first model of regulation for a PUL in marine bacteria. AusR binds to promoters of AUS genes via single, double or triple copies of operator. Upon addition of alginate, secreted enzymes expressed at a basal level catalyze the initial breakdown of the polymer. Metabolic intermediates produced during degradation act as effectors of AusR and inhibit the formation of AusR/DNA complexes, thus lifting transcriptional repression.

scholarly journals Emerging multifaceted roles of BAP1 complexes in biological processes

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Aileen Patricia Szczepanski ◽  
Lu Wang
Keyword(s):  
Transcriptional Repression ◽  
Target Genes ◽  
Regulatory Mechanisms ◽  
Biological Processes ◽  
Multiprotein Complex ◽  
Downstream Target ◽  
Evolutionarily Conserved ◽  
Complex Forms ◽  
Polycomb Repressive Complex 1

AbstractHistone H2AK119 mono-ubiquitination (H2AK119Ub) is a relatively abundant histone modification, mainly catalyzed by the Polycomb Repressive Complex 1 (PRC1) to regulate Polycomb-mediated transcriptional repression of downstream target genes. Consequently, H2AK119Ub can also be dynamically reversed by the BAP1 complex, an evolutionarily conserved multiprotein complex that functions as a general transcriptional activator. In previous studies, it has been reported that the BAP1 complex consists of important biological roles in development, metabolism, and cancer. However, identifying the BAP1 complex’s regulatory mechanisms remains to be elucidated due to its various complex forms and its ability to target non-histone substrates. In this review, we will summarize recent findings that have contributed to the diverse functional role of the BAP1 complex and further discuss the potential in targeting BAP1 for therapeutic use.

scholarly journals Transcriptional Repression Mediated by a TetR Family Protein, PfmR, from Thermus thermophilus HB8

2012 ◽  
Vol 194 (17) ◽  
pp. 4630-4641 ◽  
Author(s):  
Y. Agari ◽  
K. Sakamoto ◽  
S. Kuramitsu ◽  
A. Shinkai
Keyword(s):  
Transcriptional Repression ◽  
Thermus Thermophilus ◽  
Thermus Thermophilus Hb8 ◽  
Family Protein

scholarly journals Different Substrate Preferences Help Closely Related Bacteria To Coexist in the Gut

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Petra Louis
Keyword(s):  
Regulatory Mechanisms ◽  
Human Gut ◽  
Substrate Preferences ◽  
Pure Cultures ◽  
Bacteroides Ovatus ◽  
The Individual ◽  
Nutrient Profiles ◽  
Polysaccharide Utilization Loci ◽  
Complex Glycan ◽  
Over Time

ABSTRACT Many factors shape the ability of different microbes to coexist in microbial communities. In the human gut, dietary and host-derived nutrients largely drive microbial community structure. How gut microbes with very similar nutrient profiles are able to coexist over time within the same host is not fully understood. Tuncil et al. (mBio 8:e01068-17, 2017, https://doi.org/10.1128/mBio.01068-17 !) explored glycan prioritization in two closely related human gut bacteria, Bacteroides ovatus and Bacteroides thetaiotaomicron, on complex glycan mixtures that both organisms can degrade. Determining depletion of the individual glycans over time in pure cultures and cocultures revealed that the bacteria seem to have hardwired differences in their preferences for different glycans which likely contribute to their stable coexistence. The researchers also established that gene expression changes of the corresponding polysaccharide utilization loci did not always mirror glycan depletion, which highlights that additional regulatory mechanisms must be present.

scholarly journals BIOMARKER POTENTIAL OF IQ-DOMAIN GTPASE-ACTIVATING PROTEINS FAMILY PROTEIN IN PANCREATIC CANCER: A MINI REVIEW

2018 ◽  
Vol 11 (15) ◽  
pp. 24
Author(s):  
Anton Sumarpo ◽  
Agnes Anania Triavika Sahamastuti ◽  
Gisella Edny Tjugianto ◽  
Kenny Yonathan ◽  
David Agustriawan
Keyword(s):  
Pancreatic Cancer ◽  
Prognostic Biomarker ◽  
Regulatory Mechanisms ◽  
Human Pancreatic Cancer ◽  
Gtpase Activating Proteins ◽  
Pubmed Database ◽  
Family Protein ◽  
Predictive And Prognostic Biomarker ◽  
Molecular Regulatory Mechanisms

Objectives: Our present study was done to understand molecular regulatory mechanisms of IQGAP proteins and their potentials as biomarker in pancreatic cancer.Methods: In this review, relevant studies were obtained by assessing the PubMed database using the combination of words that included “IQGAP” and “pancreatic cancer”.Results: There is an increasing evidence showing that the expression of IQGAP1 and IQGAP3 is positively correlated with tumorigenesis; however, IQGAP2 might play a role to suppress tumor progression.Conclusion: IQGAP proteins might have potentials as predictive and prognostic biomarker for human pancreatic cancer.

scholarly journals Systematic Review of Calcium Channels and Intracellular Calcium Signaling: Relevance to Pesticide Neurotoxicity

2021 ◽  
Vol 22 (24) ◽  
pp. 13376
Author(s):  
Carmen Costas-Ferreira ◽  
Lilian R. F. Faro
Keyword(s):  
Oxidative Stress ◽  
Systematic Review ◽  
Nervous System ◽  
Neuronal Death ◽  
Regulatory Mechanisms ◽  
Extracellular Medium ◽  
Intracellular Calcium Signaling ◽  
Different Types ◽  
Ca2 Channels ◽  
Over Time

Pesticides of different chemical classes exert their toxic effects on the nervous system by acting on the different regulatory mechanisms of calcium (Ca2+) homeostasis. Pesticides have been shown to alter Ca2+ homeostasis, mainly by increasing its intracellular concentration above physiological levels. The pesticide-induced Ca2+ overload occurs through two main mechanisms: the entry of Ca2+ from the extracellular medium through the different types of Ca2+ channels present in the plasma membrane or its release into the cytoplasm from intracellular stocks, mainly from the endoplasmic reticulum. It has also been observed that intracellular increases in the Ca2+ concentrations are maintained over time, because pesticides inhibit the enzymes involved in reducing its levels. Thus, the alteration of Ca2+ levels can lead to the activation of various signaling pathways that generate oxidative stress, neuroinflammation and, finally, neuronal death. In this review, we also discuss some proposed strategies to counteract the detrimental effects of pesticides on Ca2+ homeostasis.

scholarly journals Map7D2 and Map7D1 facilitate MT stabilization through distinct mechanisms to control cell motility and neurite outgrowth

2021 ◽  
Author(s):  
Koji Kikuchi ◽  
Yasuhisa Sakamoto ◽  
Akiyoshi Uezu ◽  
Hideyuki Yamamoto ◽  
Kei-ichiro Ishiguro ◽  
...  
Keyword(s):  
Cell Motility ◽  
Neurite Outgrowth ◽  
Control Cell ◽  
Regulatory Mechanisms ◽  
Acetylated Tubulin ◽  
Family Protein ◽  
Associated Proteins ◽  
Direct Binding ◽  
The Brain

Microtubule (MT) dynamics are modulated through the coordinated action of various MT-associated proteins (MAPs). However, the regulatory mechanisms underlying MT dynamics remain unclear. Herein, we show that MAP7 family protein Map7D2 facilitates MT stabilization to control cell motility and neurite outgrowth. Map7D2, was highly expressed in the brain and testis, directly bound to MTs through its N-terminal half similarly to Map7, and promoted MT stabilization in vitro. Map7D2 localized prominently to the centrosome and partially on MTs in N1-E115 mouse glioblastoma cells, which expresses two of the four MAP7 family members, Map7D2 and Map7D1. Map7D2 loss decreased the intensity of MTs without affecting stable MT markers acetylated and detyrosinated tubulin, suggesting that Map7D2 stabilizes MTs via direct binding. In addition, Map7D2 loss increased the rate of random cell migration and neurite outgrowth, presumably by disturbing the balance between MT stabilization and destabilization. The other MAP7 family protein expressed in N1-E115, Map7D1, exhibited similar subcellular localization and gene knock-down phenotypes. However, in contrast to Map7D2, Map7D1 was required for the maintenance of acetylated tubulin levels. Taken together, our data suggest that Map7D2 and Map7D1 facilitate MT stabilization through distinct mechanisms for the control of cell motility and neurite outgrowth.

scholarly journals Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci

2016 ◽  
Vol 82 (10) ◽  
pp. 2975-2987 ◽  
Author(s):  
Cong Sun ◽  
Ge-yi Fu ◽  
Chong-ya Zhang ◽  
Jing Hu ◽  
Lin Xu ◽  
...  
Keyword(s):  
Brown Seaweed ◽  
Laminaria Japonica ◽  
Glycoside Hydrolases ◽  
Content Type ◽  
Polysaccharide Lyases ◽  
Good Potential ◽  
Alginate Lyases ◽  
Genotypic Characteristics ◽  
Algal Polysaccharides ◽  
Polysaccharide Utilization Loci

ABSTRACTThe members of the phylumBacteroidetesare recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research onBacteroidetesin the human gut, research on polysaccharide degradation by marineBacteroidetesis still rare. The genusAlgibacterbelongs to theFlavobacteriaceaefamily of theBacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (Laminaria japonica). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genusAlgibacterwith the proposed nameAlgibacter alginolyticasp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the classFlavobacteria. Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22Tcan completely degrade alginate. This work reveals that strain HZ22Thas good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22Tare worth further research.

scholarly journals PRC2 and EHMT1 regulate H3K27me2 and H3K27me3 establishment across the zygote genome

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Tie-Gang Meng ◽  
Qian Zhou ◽  
Xue-Shan Ma ◽  
Xiao-Yu Liu ◽  
Qing-Ren Meng ◽  
...  
Keyword(s):  
Early Development ◽  
Transcriptional Repression ◽  
Normal Development ◽  
De Novo ◽  
Micrococcal Nuclease ◽  
Regulatory Mechanisms ◽  
Facultative Heterochromatin ◽  
Mouse Zygotes ◽  
Essential Prerequisite

AbstractThe formation of zygote is the beginning of mammalian life, and dynamic epigenetic modifications are essential for mammalian normal development. H3K27 di-methylation (H3K27me2) and H3K27 tri-methylation (H3K27me3) are marks of facultative heterochromatin which maintains transcriptional repression established during early development in many eukaryotes. However, the mechanism underlying establishment and regulation of epigenetic asymmetry in the zygote remains obscure. Here we show that maternal EZH2 is required for the establishment of H3K27me3 in mouse zygotes. However, combined immunostaining with ULI-NChIP-seq (ultra-low-input micrococcal nuclease-based native ChIP-seq) shows that EZH1 could partially safeguard the role of EZH2 in the formation of H3K27me2. Meanwhile, we identify that EHMT1 is involved in the establishment of H3K27me2, and that H3K27me2 might be an essential prerequisite for the following de novo H3K27me3 modification on the male pronucleus. In this work, we clarify the establishment and regulatory mechanisms of H3K27me2 and H3K27me3 in mouse zygotes.

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