Biological Formation of Pyrroles: Nature′s Logic and Enzymatic Machinery

ChemInform ◽  
2006 ◽  
Vol 37 (42) ◽  
Author(s):  
Christopher T. Walsh ◽  
Sylvie Garneau-Tsodikova ◽  
Annaleise R. Howard-Jones
Keyword(s):  
Enzymatic Machinery

scholarly journals Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Plinio S. Vieira ◽  
Isabela M. Bonfim ◽  
Evandro A. Araujo ◽  
Ricardo R. Melo ◽  
Augusto R. Lima ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Transcriptional Activation ◽  
Molecular Mechanisms ◽  
Model Organism ◽  
Citrus Canker ◽  
Effector Proteins ◽  
Glycoside Hydrolases ◽  
Host Cells ◽  
System A ◽  
Enzymatic Machinery

AbstractXyloglucans are highly substituted and recalcitrant polysaccharides found in the primary cell walls of vascular plants, acting as a barrier against pathogens. Here, we reveal that the diverse and economically relevant Xanthomonas bacteria are endowed with a xyloglucan depolymerization machinery that is linked to pathogenesis. Using the citrus canker pathogen as a model organism, we show that this system encompasses distinctive glycoside hydrolases, a modular xyloglucan acetylesterase and specific membrane transporters, demonstrating that plant-associated bacteria employ distinct molecular strategies from commensal gut bacteria to cope with xyloglucans. Notably, the sugars released by this system elicit the expression of several key virulence factors, including the type III secretion system, a membrane-embedded apparatus to deliver effector proteins into the host cells. Together, these findings shed light on the molecular mechanisms underpinning the intricate enzymatic machinery of Xanthomonas to depolymerize xyloglucans and uncover a role for this system in signaling pathways driving pathogenesis.

scholarly journals Novel B-cell precursors blocked at the stage of DJH recombination.

1988 ◽  
Vol 8 (12) ◽  
pp. 5216-5223 ◽  
Author(s):  
L Ramakrishnan ◽  
N Rosenberg
Keyword(s):  
B Cell ◽  
Cell Lines ◽  
Leukemia Virus ◽  
Variable Region ◽  
Immunoglobulin Gene ◽  
Recombination System ◽  
Rearrangement Process ◽  
B Cell Precursors ◽  
Enzymatic Machinery

Abelson murine leukemia virus-transformed cells have provided the principal model for study of the early events in immunoglobulin gene rearrangements. In this communication, we describe a new type of Abelson virus-transformed pre-B-cell line that is arrested at the DJH stage of the recombination process. These cells differ from other pre-B transformants with respect to two properties associated with the immunoglobulin rearrangement process. First, in contrast to cell lines undergoing VH-to-DJH joining in vitro, none of these cell lines contained detectable levels of RNAs transcribed from their unrearranged VH genes. Second, only some of the cell lines recombined exogenous heptamer-nonamer sequences, indicating that many of them have lost at least a portion of the enzymatic machinery that mediates recombination. The correlation between the absence of unrearranged VH RNAs and the inability to rearrange endogenous immunoglobulin gene segments suggests that VH gene transcription is required both to maintain an active recombination system and for the final step in variable-region formation.

Novel B-cell precursors blocked at the stage of DJH recombination

1988 ◽  
Vol 8 (12) ◽  
pp. 5216-5223
Author(s):  
L Ramakrishnan ◽  
N Rosenberg
Keyword(s):  
B Cell ◽  
Cell Lines ◽  
Leukemia Virus ◽  
Variable Region ◽  
Immunoglobulin Gene ◽  
Recombination System ◽  
Rearrangement Process ◽  
B Cell Precursors ◽  
Enzymatic Machinery

Abelson murine leukemia virus-transformed cells have provided the principal model for study of the early events in immunoglobulin gene rearrangements. In this communication, we describe a new type of Abelson virus-transformed pre-B-cell line that is arrested at the DJH stage of the recombination process. These cells differ from other pre-B transformants with respect to two properties associated with the immunoglobulin rearrangement process. First, in contrast to cell lines undergoing VH-to-DJH joining in vitro, none of these cell lines contained detectable levels of RNAs transcribed from their unrearranged VH genes. Second, only some of the cell lines recombined exogenous heptamer-nonamer sequences, indicating that many of them have lost at least a portion of the enzymatic machinery that mediates recombination. The correlation between the absence of unrearranged VH RNAs and the inability to rearrange endogenous immunoglobulin gene segments suggests that VH gene transcription is required both to maintain an active recombination system and for the final step in variable-region formation.

scholarly journals Butyrivibrio hungateiMB2003 Competes Effectively for Soluble Sugars Released byButyrivibrio proteoclasticusB316Tduring Growth on Xylan or Pectin

2018 ◽  
Vol 85 (3) ◽  
Author(s):  
Nikola Palevich ◽  
William J. Kelly ◽  
Siva Ganesh ◽  
Jasna Rakonjac ◽  
Graeme T. Attwood
Keyword(s):  
Bacterial Species ◽  
Soluble Sugars ◽  
Plant Fiber ◽  
Content Type ◽  
Plant Polysaccharide ◽  
Rumen Microbes ◽  
Carbohydrate Degradation ◽  
Wide Range ◽  
Genes Encoding ◽  
Enzymatic Machinery

ABSTRACTRumen bacterial species belonging to the genusButyrivibrioare important degraders of plant polysaccharides, particularly hemicelluloses (arabinoxylans) and pectin. Currently, four species are recognized; they have very similar substrate utilization profiles, but little is known about how these microorganisms are able to coexist in the rumen. To investigate this question,Butyrivibrio hungateiMB2003 andButyrivibrio proteoclasticusB316Twere grown alone or in coculture on xylan or pectin, and their growth, release of sugars, fermentation end products, and transcriptomes were examined. In monocultures, B316Twas able to grow well on xylan and pectin, while MB2003 was unable to utilize either of these insoluble substrates to support significant growth. Cocultures of B316Tgrown with MB2003 revealed that MB2003 showed growth almost equivalent to that of B316Twhen either xylan or pectin was supplied as the substrate. The effect of coculture on the transcriptomes of B316Tand MB2003 was assessed; B316Ttranscription was largely unaffected by the presence of MB2003, but MB2003 expressed a wide range of genes encoding proteins for carbohydrate degradation, central metabolism, oligosaccharide transport, and substrate assimilation, in order to compete with B316Tfor the released sugars. These results suggest that B316Thas a role as an initiator of primary solubilization of xylan and pectin, while MB2003 competes effectively for the released soluble sugars to enable its growth and maintenance in the rumen.IMPORTANCEFeeding a future global population of 9 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation.Butyrivibriospecies are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings suggest that closely related species ofButyrivibriohave developed unique strategies for the degradation of plant fiber and the subsequent assimilation of carbohydrates in order to coexist in the competitive rumen environment. The identification of genes expressed during these competitive interactions gives further insight into the enzymatic machinery used by these bacteria as they degrade the xylan and pectin components of plant fiber.

Ageing in embryos from wheat grains stored at different temperatures: oxidative stress and antioxidant response

2011 ◽  
Vol 38 (7) ◽  
pp. 624 ◽  
Author(s):  
Carmelina Spanò ◽  
Stefania Bottega ◽  
Roberto Lorenzi ◽  
Isa Grilli
Keyword(s):  
Oxidative Stress ◽  
Low Temperature ◽  
Seed Viability ◽  
Storage Period ◽  
Antioxidant Response ◽  
Protective Role ◽  
Native Page ◽  
Wheat Grains ◽  
Different Temperatures ◽  
Enzymatic Machinery

In the present work we studied oxidative stress as an important cause of seed deterioration during ageing in embryos from durum wheat grains stored at room temperature and at low temperature (10°C). The protective role of low temperature on seed viability was confirmed. The increase of hydrogen peroxide content during dry storage was strongly correlated with the decrease of germinability. Ascorbate and glutathione showed a good correlation with grain germinability and significantly increased upon imbibition, in particular in embryos from viable grains. Ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), glutathione reductase (GR), glutathione peroxidase (GPX) and catalase (CAT) were studied quantitatively (enzymatic assays). APX, GR, and GPX were also studied qualitatively by native PAGE. The enzymes were active in dry, still viable, embryos whereas no activity was detected in non-viable embryos. With the exception of APX, all enzymatic activities decreased upon imbibition. The study of grains stored in different conditions indicated a negative correlation between the efficiency of the antioxidant enzymatic machinery and the age of the grain. The differences detected in differently stored materials confirmed that both germination parameters and the length of storage period are important in determining grain condition.

scholarly journals Linking the Salmonella enterica 1,2-propanediol utilization bacterial microcompartment shell to the enzymatic core via the shell protein PduB

2021 ◽  
Author(s):  
Nolan W Kennedy ◽  
Carolyn E Mills ◽  
Charlotte H Abrahamson ◽  
Andre Archer ◽  
Michael C Jewett ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Carbon Sources ◽  
Enzyme Concentration ◽  
Fluorescent Reporters ◽  
Shell Protein ◽  
Bacterial Microcompartment ◽  
Enzyme Encapsulation ◽  
Transmission Electron ◽  
Serovar Typhimurium ◽  
Enzymatic Machinery

Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is the sole protein responsible for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies also reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and systems-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis.

scholarly journals Application of immobilized mycelium-based pellets for the removal of organochlorine compounds: a review

2021 ◽  
Author(s):  
J. C. V. Pereira ◽  
M. P. Serbent ◽  
E. Skoronski
Keyword(s):  
Wastewater Treatment Plants ◽  
Cost Effective ◽  
Field Studies ◽  
Organochlorine Compounds ◽  
Environmental Persistence ◽  
Factors Affecting ◽  
Materials Used ◽  
Immobilization Techniques ◽  
Enzymatic Machinery

Abstract Organochlorines have diverse structures and applications and are included in the list of persistent organic pollutants (POPs) due to their toxicity and environmental persistence. The reduced capacity of conventional wastewater treatment plants to remove these compounds encourages the development of cost-effective and efficient remediation approaches. Fungal biotechnology can contribute to the development of these technologies through their enzymatic machinery but faces several drawbacks related to the use of dispersed mycelium. In this sense, investigations concerning the degradation of organochlorines using immobilized fungi demonstrated an increase in contaminants removal efficiency compared with degradation by free cells. Despite this interest, the mechanisms of immobilized fungi have not been comprehensively reviewed. In this paper, recent advances of laboratory and field studies in organochlorine compounds removal by fungi were reviewed, focusing on the role of immobilization techniques. Firstly, the mechanisms of organochlorines bioconversion by fungi and the factors affecting enzyme activity are elucidated and discussed in detail. Then, the main targeted compounds, fungi, technics, and materials used for immobilization are discussed, as well as their advantages and limitations. Furthermore, critical points for future studies of the fungi immobilization for organochlorines removal are proposed.

scholarly journals The Role of epigenetic modifications of DNA and histones in the treatment of oncohematological diseases

2021 ◽  
Vol 66 (2) ◽  
pp. 263-279
Author(s):  
D. V. Karpenko ◽  
N. A. Petinati ◽  
N. J. Drize ◽  
A. E. Bigildeev
Keyword(s):  
Clinical Trial ◽  
Cytosine Methylation ◽  
Current Knowledge ◽  
Hypomethylating Agents ◽  
Epigenetic Change ◽  
Therapeutic Approaches ◽  
Enzymatic Machinery ◽  
Key Pathways ◽  
Dna Cytosine Methylation

Introduction. Current knowledge of tumour biology attests a dual genetic and epigenetic nature of cancer cell abnormalities. Tumour epigenetics research provided insights into the key pathways mediating oncogenesis and facilitated novel epigenetic therapies.Aim — an overview of intricate involvement of epigenetic change in haematological morbidity and current therapeutic approaches to target the related mechanisms.Main findings. We review the best known epigenetic marks in tumour cells, e.g. DNA cytosine methylation, methylation and acetylation of histone proteins, the underlying enzymatic machinery and its role in oncogenesis. The epigenetic profile-changing drugs are described, including DNA hypomethylating agents, histone deacetylase and methylase inhibitors. A particular focus is made on substances currently approved in haematological therapy or undergoing clinical trial phases for future clinical availability.

scholarly journals Brain cell somatic gene recombination and its phylogenetic foundations

2020 ◽  
Vol 295 (36) ◽  
pp. 12786-12795 ◽  
Author(s):  
Gwendolyn Kaeser ◽  
Jerold Chun
Keyword(s):  
Brain Cell ◽  
Gene Recombination ◽  
Evolutionary Origins ◽  
Gene Optimization ◽  
Somatic Gene ◽  
Multiple Copies ◽  
Processed Pseudogenes ◽  
Near Term ◽  
Rt Inhibitors ◽  
Enzymatic Machinery

A new form of somatic gene recombination (SGR) has been identified in the human brain that affects the Alzheimer's disease gene, amyloid precursor protein (APP). SGR occurs when a gene sequence is cut and recombined within a single cell's genomic DNA, generally independent of DNA replication and the cell cycle. The newly identified brain SGR produces genomic complementary DNAs (gencDNAs) lacking introns, which integrate into locations distinct from germline loci. This brief review will present an overview of likely related recombination mechanisms and genomic cDNA-like sequences that implicate evolutionary origins for brain SGR. Similarities and differences exist between brain SGR and VDJ recombination in the immune system, the first identified SGR form that now has a well-defined enzymatic machinery. Both require gene transcription, but brain SGR uses an RNA intermediate and reverse transcriptase (RT) activity, which are characteristics shared with endogenous retrotransposons. The identified gencDNAs have similarities to other cDNA-like sequences existing throughout phylogeny, including intron-less genes and inactive germline processed pseudogenes, with likely overlapping biosynthetic processes. gencDNAs arise somatically in an individual to produce multiple copies; can be functional; appear most frequently within postmitotic cells; have diverse sequences; change with age; and can change with disease state. Normally occurring brain SGR may represent a mechanism for gene optimization and long-term cellular memory, whereas its dysregulation could underlie multiple brain disorders and, potentially, other diseases like cancer. The involvement of RT activity implicates already Food and Drug Administration–approved RT inhibitors as possible near-term interventions for managing SGR-associated diseases and suggest next-generation therapeutics targeting SGR elements.

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