LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 78

Search options

  1. Article ; Online: Microbiota and the plant immune system work together to defend against pathogens.

    Chakraborty, Joydeep

    Archives of microbiology

    2023  Volume 205, Issue 10, Page(s) 347

    Abstract: Plants are exposed to a myriad of microorganisms, which can range from helpful bacteria to deadly disease-causing pathogens. The ability of plants to distinguish between helpful bacteria and dangerous pathogens allows them to continuously survive under ... ...

    Abstract Plants are exposed to a myriad of microorganisms, which can range from helpful bacteria to deadly disease-causing pathogens. The ability of plants to distinguish between helpful bacteria and dangerous pathogens allows them to continuously survive under challenging environments. The investigation of the modulation of plant immunity by beneficial microbes is critical to understand how they impact plant growth improvement and defense against invasive pathogens. Beneficial bacterial populations can produce significant impact on plant immune responses, including regulation of immune receptors activity, MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) activation, transcription factors, and reactive oxygen species (ROS) signaling. To establish themselves, beneficial bacterial populations likely reduce plant immunity. These bacteria help plants to recover from various stresses and resume a regular growth pattern after they have been established. Contrarily, pathogens prevent their colonization by releasing toxins into plant cells, which have the ability to control the local microbiota via as-yet-unidentified processes. Intense competition among microbial communities has been found to be advantageous for plant development, nutrient requirements, and activation of immune signaling. Therefore, to protect themselves from pathogens, plants may rely on the beneficial microbiota in their environment and intercommunity competition amongst microbial communities.
    MeSH term(s) Plant Immunity ; Plants/microbiology ; Bacteria ; Signal Transduction ; Microbiota/physiology
    Language English
    Publishing date 2023-10-01
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 124824-8
    ISSN 1432-072X ; 0302-8933
    ISSN (online) 1432-072X
    ISSN 0302-8933
    DOI 10.1007/s00203-023-03684-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: In-silico structural analysis of Pseudomonas syringae effector HopZ3 reveals ligand binding activity and virulence function.

    Chakraborty, Joydeep

    Journal of plant research

    2021  Volume 134, Issue 3, Page(s) 599–611

    Abstract: Bacterial acetyltransferase effectors belonging to the Yersinia outer protein J (YopJ) group inhibit multiple immune signaling pathways in human and plants. The present study determines in-silico acetyl-coenzyme A (AcCoA) binding and Arabidopsis immune ... ...

    Abstract Bacterial acetyltransferase effectors belonging to the Yersinia outer protein J (YopJ) group inhibit multiple immune signaling pathways in human and plants. The present study determines in-silico acetyl-coenzyme A (AcCoA) binding and Arabidopsis immune regulator RPM1-interacting protein4 (RIN4) peptide interactions to YopJ effector hypersensitivity and pathogenesis-dependent outer proteinZ3 (HopZ3) from Pseudomonas syringae. Phylogenetic analysis revealed that HopZ3 was clustered by acetyltransferase effectors from plant bacterial pathogens. Structural juxtaposition shows HopZ3 comprises topology matched closer with HopZ1a than PopP2 effectors, respectively. AcCoA binds HopZ3 at two sites i.e., substrate binding pocket and catalytic site. AcCoA interactions to substrate binding pocket was transient and dissipated upon in-silico mutation of Ser 279 residue whereas, attachment to catalytic site was found to be stable in the presence of inositol hexaphosphate (IP6) as a co-factor. Interface atoms used for measuring hydrogen bond distances, bound or accessible surface area, and root-mean-square fluctuation (RMSF) values, suggests that the HopZ3 complex stabilizes after binding to AcCoA ligand and RIN4 peptide. The few non-conserved polymorphic residues that have been displayed on HopZ3 surface presumably confer intracellular recognitions within hosts. Collectively, homology modeling and interactive docking experiments were used to substantiate Arabidopsis immune 'guardee' interactions to HopZ3.
    MeSH term(s) Arabidopsis Proteins/genetics ; Bacterial Outer Membrane Proteins ; Bacterial Proteins/genetics ; Ligands ; Phylogeny ; Plant Diseases ; Pseudomonas syringae ; Virulence
    Chemical Substances Arabidopsis Proteins ; Bacterial Outer Membrane Proteins ; Bacterial Proteins ; Ligands
    Language English
    Publishing date 2021-03-17
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 2077362-6
    ISSN 1618-0860 ; 0918-9440
    ISSN (online) 1618-0860
    ISSN 0918-9440
    DOI 10.1007/s10265-021-01274-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Exploring the role of symbiotic modifier peptidases in the legume - rhizobium symbiosis.

    Ghosh, Prithwi / Chakraborty, Joydeep

    Archives of microbiology

    2024  Volume 206, Issue 4, Page(s) 147

    Abstract: Legumes can establish a mutual association with soil-derived nitrogen-fixing bacteria called 'rhizobia' forming lateral root organs called root nodules. Rhizobia inside the root nodules get transformed into 'bacteroids' that can fix atmospheric nitrogen ... ...

    Abstract Legumes can establish a mutual association with soil-derived nitrogen-fixing bacteria called 'rhizobia' forming lateral root organs called root nodules. Rhizobia inside the root nodules get transformed into 'bacteroids' that can fix atmospheric nitrogen to ammonia for host plants in return for nutrients and shelter. A substantial 200 million tons of nitrogen is fixed annually through biological nitrogen fixation. Consequently, the symbiotic mechanism of nitrogen fixation is utilized worldwide for sustainable agriculture and plays a crucial role in the Earth's ecosystem. The development of effective nitrogen-fixing symbiosis between legumes and rhizobia is very specialized and requires coordinated signaling. A plethora of plant-derived nodule-specific cysteine-rich (NCR or NCR-like) peptides get actively involved in this complex and tightly regulated signaling process of symbiosis between some legumes of the IRLC (Inverted Repeat-Lacking Clade) and Dalbergioid clades and nitrogen-fixing rhizobia. Recent progress has been made in identifying two such peptidases that actively prevent bacterial differentiation, leading to symbiotic incompatibility. In this review, we outlined the functions of NCRs and two nitrogen-fixing blocking peptidases: HrrP (host range restriction peptidase) and SapA (symbiosis-associated peptidase A). SapA was identified through an overexpression screen from the Sinorhizobium meliloti 1021 core genome, whereas HrrP is inherited extra-chromosomally. Interestingly, both peptidases affect the symbiotic outcome by degrading the NCR peptides generated from the host plants. These NCR-degrading peptidases can shed light on symbiotic incompatibility, helping to elucidate the reasons behind the inefficiency of nitrogen fixation observed in certain groups of rhizobia with specific legumes.
    MeSH term(s) Peptide Hydrolases/genetics ; Rhizobium/genetics ; Rhizobium/metabolism ; Symbiosis ; Medicago truncatula/genetics ; Medicago truncatula/metabolism ; Medicago truncatula/microbiology ; Ecosystem ; Peptides/metabolism ; Vegetables ; Nitrogen ; Nitrogen Fixation ; Root Nodules, Plant/microbiology
    Chemical Substances Peptide Hydrolases (EC 3.4.-) ; Peptides ; Nitrogen (N762921K75)
    Language English
    Publishing date 2024-03-11
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 124824-8
    ISSN 1432-072X ; 0302-8933
    ISSN (online) 1432-072X
    ISSN 0302-8933
    DOI 10.1007/s00203-024-03920-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article: In-silico structural analysis of Pseudomonas syringae effector HopZ3 reveals ligand binding activity and virulence function

    Chakraborty, Joydeep

    Journal of plant research. 2021 May, v. 134, no. 3

    2021  

    Abstract: Bacterial acetyltransferase effectors belonging to the Yersinia outer protein J (YopJ) group inhibit multiple immune signaling pathways in human and plants. The present study determines in-silico acetyl-coenzyme A (AcCoA) binding and Arabidopsis immune ... ...

    Abstract Bacterial acetyltransferase effectors belonging to the Yersinia outer protein J (YopJ) group inhibit multiple immune signaling pathways in human and plants. The present study determines in-silico acetyl-coenzyme A (AcCoA) binding and Arabidopsis immune regulator RPM1-interacting protein4 (RIN4) peptide interactions to YopJ effector hypersensitivity and pathogenesis-dependent outer proteinZ3 (HopZ3) from Pseudomonas syringae. Phylogenetic analysis revealed that HopZ3 was clustered by acetyltransferase effectors from plant bacterial pathogens. Structural juxtaposition shows HopZ3 comprises topology matched closer with HopZ1a than PopP2 effectors, respectively. AcCoA binds HopZ3 at two sites i.e., substrate binding pocket and catalytic site. AcCoA interactions to substrate binding pocket was transient and dissipated upon in-silico mutation of Ser 279 residue whereas, attachment to catalytic site was found to be stable in the presence of inositol hexaphosphate (IP6) as a co-factor. Interface atoms used for measuring hydrogen bond distances, bound or accessible surface area, and root-mean-square fluctuation (RMSF) values, suggests that the HopZ3 complex stabilizes after binding to AcCoA ligand and RIN4 peptide. The few non-conserved polymorphic residues that have been displayed on HopZ3 surface presumably confer intracellular recognitions within hosts. Collectively, homology modeling and interactive docking experiments were used to substantiate Arabidopsis immune ‘guardee’ interactions to HopZ3.
    Keywords Arabidopsis ; Pseudomonas syringae ; acetyl coenzyme A ; acetyltransferases ; active sites ; computer simulation ; humans ; hydrogen bonding ; hypersensitivity ; inositols ; ligands ; mutation ; peptides ; phylogeny ; research ; surface area ; topology ; virulence
    Language English
    Dates of publication 2021-05
    Size p. 599-611.
    Publishing place Springer Singapore
    Document type Article
    ZDB-ID 2077362-6
    ISSN 1618-0860 ; 0918-9440
    ISSN (online) 1618-0860
    ISSN 0918-9440
    DOI 10.1007/s10265-021-01274-8
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  5. Article ; Online: Entanglement of MAPK pathways with gene expression and its omnipresence in the etiology for cancer and neurodegenerative disorders.

    Chakraborty, Joydeep / Chakraborty, Sayan / Chakraborty, Sohag / Narayan, Mahesh N

    Biochimica et biophysica acta. Gene regulatory mechanisms

    2023  Volume 1866, Issue 4, Page(s) 194988

    Abstract: Mitogen Activated Protein Kinase (MAPK) is one of the most well characterized cellular signaling pathways that controls fundamental cellular processes including proliferation, differentiation, and apoptosis. These cellular functions are consequences of ... ...

    Abstract Mitogen Activated Protein Kinase (MAPK) is one of the most well characterized cellular signaling pathways that controls fundamental cellular processes including proliferation, differentiation, and apoptosis. These cellular functions are consequences of transcription of regulatory genes that are influenced and regulated by the MAP-Kinase signaling cascade. MAP kinase components such as Receptor Tyrosine Kinases (RTKs) sense external cues or ligands and transmit these signals via multiple protein complexes such as RAS-RAF, MEK, and ERKs and eventually modulate the transcription factors inside the nucleus to induce transcription and other regulatory functions. Aberrant activation, dysregulation of this signaling pathway, and genetic alterations in any of these components results in the developmental disorders, cancer, and neurodegenerative disorders. Over the years, the MAPK pathway has been a prime pharmacological target, to treat complex human disorders that are genetically linked such as cancer, Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. The current review re-visits the mechanism of MAPK pathways in gene expression regulation. Further, a current update on the progress of the mechanistic understanding of MAPK components is discussed from a disease perspective.
    MeSH term(s) Humans ; Mitogen-Activated Protein Kinases ; MAP Kinase Signaling System/genetics ; Neoplasms/genetics ; Neoplasms/drug therapy ; Neurodegenerative Diseases/genetics ; Gene Expression
    Chemical Substances Mitogen-Activated Protein Kinases (EC 2.7.11.24)
    Language English
    Publishing date 2023-09-21
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2918786-2
    ISSN 1876-4320 ; 1874-9399
    ISSN (online) 1876-4320
    ISSN 1874-9399
    DOI 10.1016/j.bbagrm.2023.194988
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Advancement of research on plant NLRs evolution, biochemical activity, structural association, and engineering.

    Chakraborty, Joydeep / Ghosh, Prithwi

    Planta

    2020  Volume 252, Issue 6, Page(s) 101

    Abstract: Main conclusion: In this review, we have included evolution of plant intracellular immune receptors, oligomeric complex formation, enzymatic action, engineering, and mechanisms of immune inspection for appropriate defense outcomes. NLR (Nucleotide ... ...

    Abstract Main conclusion: In this review, we have included evolution of plant intracellular immune receptors, oligomeric complex formation, enzymatic action, engineering, and mechanisms of immune inspection for appropriate defense outcomes. NLR (Nucleotide binding oligomerization domain containing leucine-rich repeat) proteins are the intracellular immune receptors that recognize pathogen-derived virulence factors to confer effector-triggered immunity (ETI). Activation of plant defense by the NLRs are often conveyed through N-terminal Toll-like/ IL-1 receptor (TIR) or non-TIR (coiled-coils or CC) domains. Homodimerization or self-association property of CC/ TIR domains of plant NLRs contribute to their auto-activity and induction of in planta ectopic cell death. High resolution crystal structures of Arabidopsis thaliana RPS4
    MeSH term(s) Animals ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis Proteins/chemistry ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Cell Death/genetics ; NLR Proteins/chemistry ; NLR Proteins/genetics ; NLR Proteins/metabolism ; Plant Immunity/genetics ; Structure-Activity Relationship
    Chemical Substances Arabidopsis Proteins ; NLR Proteins
    Language English
    Publishing date 2020-11-12
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 208909-9
    ISSN 1432-2048 ; 0032-0935 ; 1866-2749
    ISSN (online) 1432-2048
    ISSN 0032-0935 ; 1866-2749
    DOI 10.1007/s00425-020-03512-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Deoxyuracil in DNA in health and disease.

    Chakraborty, Joydeep / Stover, Patrick J

    Current opinion in clinical nutrition and metabolic care

    2020  Volume 23, Issue 4, Page(s) 247–252

    Abstract: Purpose of review: Genome instability has long been implicated as a primary causal factor in cancer and diseases of aging. The genome is constantly under attack from extrinsic and intrinsic damaging agents. Uracil misincorporation in DNA and its repair ... ...

    Abstract Purpose of review: Genome instability has long been implicated as a primary causal factor in cancer and diseases of aging. The genome is constantly under attack from extrinsic and intrinsic damaging agents. Uracil misincorporation in DNA and its repair is an intrinsic factor resulting in genomic instability and DNA mutations. Additionally, the presence of uracil in DNA can modify gene expression by interfering with promoter binding and transcription inhibition or upregulation of apoptotic proteins. In immune cells, uracil in DNA drives beneficial genomic diversity for antigen-driven immunity. This review addresses diseases that are linked to uracil accumulation in DNA, its causes, consequences, and the associated biomarkers of risk factors.
    Recent findings: Elevated genomic uracil is associated with megaloblastic anemia, neural tube defects, and retroviral immunity. Current evidence supporting causal mechanisms and nutritional interventions that rescue impaired pathways associated with uracil accumulation in DNA are summarized in this review.
    Summary: Nutritional deficiencies in B vitamins can cause uracil misincorporation into DNA leading to genome instability and associated diseases. Nutritional approaches to preventing uracil accumulation in DNA show some promise to address its associated diseases, but additional randomized controlled trials are needed.
    MeSH term(s) DNA/metabolism ; DNA Repair ; Deoxyuracil Nucleotides/metabolism ; Genetic Markers/genetics ; Genomic Instability/genetics ; Humans ; Nutritional Physiological Phenomena/genetics ; Risk Factors ; Uracil/metabolism ; Vitamin B Deficiency/genetics
    Chemical Substances Deoxyuracil Nucleotides ; Genetic Markers ; Uracil (56HH86ZVCT) ; DNA (9007-49-2)
    Language English
    Publishing date 2020-06-10
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1460178-3
    ISSN 1473-6519 ; 1363-1950
    ISSN (online) 1473-6519
    ISSN 1363-1950
    DOI 10.1097/MCO.0000000000000660
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article: The Emerging Role of PP2C Phosphatases in Tomato Immunity.

    Sobol, Guy / Chakraborty, Joydeep / Martin, Gregory B / Sessa, Guido

    Molecular plant-microbe interactions : MPMI

    2022  Volume 35, Issue 9, Page(s) 737–747

    Abstract: The antagonistic effect of plant immunity on growth likely drove evolution of molecular mechanisms that prevent accidental initiation and prolonged activation of plant immune responses. Signaling networks of pattern-triggered and effector-triggered ... ...

    Abstract The antagonistic effect of plant immunity on growth likely drove evolution of molecular mechanisms that prevent accidental initiation and prolonged activation of plant immune responses. Signaling networks of pattern-triggered and effector-triggered immunity, the two main layers of plant immunity, are tightly regulated by the activity of protein phosphatases that dephosphorylate their protein substrates and reverse the action of protein kinases. Members of the PP2C class of protein phosphatases have emerged as key negative regulators of plant immunity, primarily from research in the model plant
    MeSH term(s) Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis Proteins ; Disease Resistance/genetics ; Lycopersicon esculentum/genetics ; Lycopersicon esculentum/metabolism ; Pathogen-Associated Molecular Pattern Molecules ; Phosphoprotein Phosphatases/chemistry ; Phosphoprotein Phosphatases/genetics ; Phosphoprotein Phosphatases/metabolism ; Plant Immunity ; Plants/genetics ; Protein Kinases/genetics
    Chemical Substances Arabidopsis Proteins ; Pathogen-Associated Molecular Pattern Molecules ; Protein Kinases (EC 2.7.-) ; Phosphoprotein Phosphatases (EC 3.1.3.16)
    Language English
    Publishing date 2022-09-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 743331-1
    ISSN 1943-7706 ; 0894-0282
    ISSN (online) 1943-7706
    ISSN 0894-0282
    DOI 10.1094/MPMI-02-22-0037-CR
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: A systematic drug repurposing approach to identify promising inhibitors from FDA-approved drugs against Nsp4 protein of SARS-CoV-2.

    Chakraborty, Joydeep / Maity, Atanu / Sarkar, Hironmoy

    Journal of biomolecular structure & dynamics

    2021  Volume 41, Issue 2, Page(s) 550–559

    Abstract: COVID-19 is caused by SARS-CoV-2 and responsible for the ongoing global pandemic in the world. After more than a year, we are still in lurch to combat and control the situation. Therefore, new therapeutic options to control the ongoing COVID-19 are ... ...

    Abstract COVID-19 is caused by SARS-CoV-2 and responsible for the ongoing global pandemic in the world. After more than a year, we are still in lurch to combat and control the situation. Therefore, new therapeutic options to control the ongoing COVID-19 are urgently in need. In our study, we found that nonstructural protein 4 (Nsp4) of SARS-CoV-2 could be a potential target for drug repurposing. Due to availability of only the crystal structure of C-terminal domain of Nsp4 (Ct-Nsp4) and its crucial participation in viral RNA synthesis, we have chosen Ct-Nsp4 as a target for screening the 1600 FDA-approved drugs using molecular docking. Top 102 drugs were found to have the binding energy equal or less than -7.0 kcal/mol. Eribulin and Suvorexant were identified as the two most promising drug molecules based on the docking score. The dynamics of Ct-Nsp4-drug binding was monitored using 100 ns molecular dynamics simulations. From binding free energy calculation over the simulation, both the drugs were found to have considerable binding energy. The present study has identified Eribulin and Suvorexant as promising drug candidates. This finding will be helpful to accelerate the drug discovery process against COVID-19 disease.Communicated by Ramaswamy H. Sarma.
    MeSH term(s) Humans ; SARS-CoV-2 ; COVID-19 ; Drug Repositioning ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors
    Chemical Substances eribulin (LR24G6354G) ; Protease Inhibitors
    Language English
    Publishing date 2021-11-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2021.2009033
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article: The Emerging Role of PP2C Phosphatases in Tomato Immunity

    Sobol, Guy / Chakraborty, Joydeep / Martin, Gregory B. / Sessa, Guido

    Molecular plant-microbe interactions. 2022 Sept., v. 35, no. 9

    2022  

    Abstract: The antagonistic effect of plant immunity on growth likely drove evolution of molecular mechanisms that prevent accidental initiation and prolonged activation of plant immune responses. Signaling networks of pattern-triggered and effector-triggered ... ...

    Abstract The antagonistic effect of plant immunity on growth likely drove evolution of molecular mechanisms that prevent accidental initiation and prolonged activation of plant immune responses. Signaling networks of pattern-triggered and effector-triggered immunity, the two main layers of plant immunity, are tightly regulated by the activity of protein phosphatases that dephosphorylate their protein substrates and reverse the action of protein kinases. Members of the PP2C class of protein phosphatases have emerged as key negative regulators of plant immunity, primarily from research in the model plant Arabidopsis thaliana, revealing the potential to employ PP2C proteins to enhance plant disease resistance. As a first step towards focusing on the PP2C family for both basic and translational research, we analyzed the tomato genome sequence to ascertain the complement of the tomato PP2C family, identify conserved protein domains and signals in PP2C amino acid sequences, and examine domain combinations in individual proteins. We then identified tomato PP2Cs that are candidate regulators of single or multiple layers of the immune signaling network by in-depth analysis of publicly available RNA-seq datasets. These included expression profiles of plants treated with fungal or bacterial pathogen-associated molecular patterns, with pathogenic, nonpathogenic, and disarmed bacteria, as well as pathogenic fungi and oomycetes. Finally, we discuss the possible use of immunity-associated PP2Cs to better understand the signaling networks of plant immunity and to engineer durable and broad disease resistance in crop plants. Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
    Keywords Arabidopsis thaliana ; amino acids ; complement ; data collection ; evolution ; fungi ; immunity ; nucleotide sequences ; plant disease resistance ; protein kinases ; sequence analysis ; tomatoes
    Language English
    Dates of publication 2022-09
    Size p. 737-747.
    Publishing place The American Phytopathological Society
    Document type Article
    ZDB-ID 743331-1
    ISSN 1943-7706 ; 0894-0282
    ISSN (online) 1943-7706
    ISSN 0894-0282
    DOI 10.1094/MPMI-02-22-0037-CR
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

To top