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Article ; Online: Recent advances in the mass spectrometric profiling of bacterial lipids.

Jaisinghani, Neetika / Seeliger, Jessica C

2021 Volume 65, Page(s) 145–153

Abstract: Exploring the lipids of bacteria presents a predicament that may not be broadly recognized in a field dominated by the biology and biochemistry of eukaryotic - and especially, mammalian - lipids. Bacteria make multifarious metabolites that contain fatty ... ...

Abstract	Exploring the lipids of bacteria presents a predicament that may not be broadly recognized in a field dominated by the biology and biochemistry of eukaryotic - and especially, mammalian - lipids. Bacteria make multifarious metabolites that contain fatty acyl chains of unusual length and unsaturation attached to assorted headgroups, including sugars and fatty alcohols. Lipid profiling approaches developed for eukaryotic lipids often fail to detect, resolve, or identify bacterial lipids due to their wide range of polarities (including very hydrophobic species) and diverse positional and stereochemical variations. Global lipid profiling, or lipidomics, of bacteria has thus developed as a separate mission with methodological and scientific considerations tailored to the biology of these organisms. In this review, we summarize findings primarily from the last three years that exemplify recent advances and continuing challenges to learning about bacterial lipids.
MeSH term(s)	Bacteria/chemistry ; Lipidomics ; Lipids/analysis ; Lipids/chemistry ; Mass Spectrometry/methods
Chemical Substances	Lipids
Language	English
Publishing date	2021-09-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1439176-4
ISSN	1879-0402 ; 1367-5931
ISSN (online)	1879-0402
ISSN	1367-5931
DOI	10.1016/j.cbpa.2021.08.003
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Article: Cell wall proteomics in live

Jaisinghani, Neetika / Previti, Mary L / Andrade, Joshua / Askenazi, Manor / Ueberheide, Beatrix / Seeliger, Jessica C

bioRxiv : the preprint server for biology

2023

Abstract: The cell wall of mycobacteria plays a key role in interactions with the environment and its ability to act as a selective filter is crucial to bacterial survival. Proteins in the cell wall enable this function by mediating the import and export of ... ...

Abstract	The cell wall of mycobacteria plays a key role in interactions with the environment and its ability to act as a selective filter is crucial to bacterial survival. Proteins in the cell wall enable this function by mediating the import and export of diverse metabolites from ions to lipids to proteins. Accurately identifying cell wall proteins is an important step in assigning function, especially as many mycobacterial proteins lack functionally characterized homologues. Current methods for protein localization have inherent limitations that reduce accuracy. Here we showed that protein tagging by the engineered peroxidase APEX2 within live
Language	English
Publishing date	2023-03-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.29.534792
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Article ; Online: Proteomics from compartment-specific APEX2 labeling in Mycobacterium tuberculosis reveals Type VII secretion substrates in the cell wall.

Jaisinghani, Neetika / Previti, Mary L / Andrade, Joshua / Askenazi, Manor / Ueberheide, Beatrix / Seeliger, Jessica C

Cell chemical biology

2023 Volume 31, Issue 3, Page(s) 523–533.e4

Abstract: The cell wall of mycobacteria plays a key role in interactions with the environment. Its ability to act as a selective filter is crucial to bacterial survival. Proteins in the cell wall enable this function by mediating the import and export of diverse ... ...

Abstract	The cell wall of mycobacteria plays a key role in interactions with the environment. Its ability to act as a selective filter is crucial to bacterial survival. Proteins in the cell wall enable this function by mediating the import and export of diverse metabolites, from ions to lipids to proteins. Identifying cell wall proteins is an important step in assigning function, especially as many mycobacterial proteins lack functionally characterized homologues. Current methods for protein localization have inherent limitations that reduce accuracy. Here we showed that although chemical labeling of live cells did not exclusively label surface proteins, protein tagging by the engineered peroxidase APEX2 within live Mycobacterium tuberculosis accurately identified the cytosolic and cell wall proteomes. Our data indicate that substrates of the virulence-associated Type VII ESX secretion system are exposed to the periplasm, providing insight into the currently unknown mechanism by which these proteins cross the mycobacterial cell envelope.
MeSH term(s)	Mycobacterium tuberculosis/metabolism ; Bacterial Proteins/metabolism ; Proteomics ; Antigens, Bacterial ; Cell Wall/metabolism ; Type VII Secretion Systems/metabolism
Chemical Substances	Bacterial Proteins ; Antigens, Bacterial ; Type VII Secretion Systems
Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Journal Article
ISSN	2451-9448
ISSN (online)	2451-9448
DOI	10.1016/j.chembiol.2023.10.013
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Article ; Online: Optimized APEX2 peroxidase-mediated proximity labeling in fast- and slow-growing mycobacteria.

Ahamed, Mukshud / Jaisinghani, Neetika / Li, Michael / Winkeler, Ian / Silva, Shalika / Previti, Mary L / Seeliger, Jessica C

Methods in enzymology

2021 Volume 664, Page(s) 267–289

Abstract: Proximity labeling is a technology for tagging proteins and other biomolecules in living cells. These methods use enzymes that generate reactive species whose properties afford high spatial resolution for the localization of proteins to subcellular ... ...

Abstract	Proximity labeling is a technology for tagging proteins and other biomolecules in living cells. These methods use enzymes that generate reactive species whose properties afford high spatial resolution for the localization of proteins to subcellular compartments and the identification of endogenous interaction partners. Here we present the adaptation of the engineered peroxidase APEX2 to proximity labeling in mycobacteria, including the human pathogen Mycobacterium tuberculosis. APEX2 is uniquely suited for general use in bacteria because unlike other proximity labeling enzymes, it does not depend on metabolites like ATP that are found in the cytoplasm, but are absent from the bacterial periplasm. Importantly, we found that in slow-growing mycobacteria like M. tuberculosis, codon usage optimization is required for APEX2 export into the periplasm via fusion to an N-terminal secretion signal. APEX2 expressed from codon-optimized genes affords robust, compartment-specific protein labeling in the cytoplasm and the periplasm of both fast- and slow-growing species. Here we detail these updated constructs and provide an optimized protocol for APEX2-mediated protein labeling in mycobacteria. We expect this approach to be broadly useful for determining the localization of specific proteins, cataloging subcellular proteomes, and identifying interaction partners of 'bait' proteins expressed as fusions to APEX2.
MeSH term(s)	Coloring Agents ; Cytoplasm/metabolism ; DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; Endonucleases/metabolism ; Multifunctional Enzymes/metabolism ; Mycobacterium/genetics ; Mycobacterium/metabolism ; Peroxidase ; Proteome/metabolism
Chemical Substances	Coloring Agents ; Multifunctional Enzymes ; Proteome ; Peroxidase (EC 1.11.1.7) ; Endonucleases (EC 3.1.-) ; APEX2 protein, human (EC 4.2.99.18) ; DNA-(Apurinic or Apyrimidinic Site) Lyase (EC 4.2.99.18)
Language	English
Publishing date	2021-12-30
Publishing country	United States
Document type	Journal Article
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/bs.mie.2021.11.021
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Article ; Online: Adipocyte Model of Mycobacterium tuberculosis Infection Reveals Differential Availability of Iron to Bacilli in the Lipid-Rich Caseous Environment.

Nandy, Ananya / Mondal, Anupam Kumar / Pandey, Rajesh / Arumugam, Prabhakar / Dawa, Stanzin / Jaisinghani, Neetika / Rao, Vivek / Dash, Debasis / Gandotra, Sheetal

Infection and immunity

2018 Volume 86, Issue 6

Abstract: Mycobacterium ... ...

Abstract	Mycobacterium tuberculosis
MeSH term(s)	3T3-L1 Cells ; Adipocytes/metabolism ; Adipocytes/microbiology ; Animals ; Humans ; Iron/metabolism ; Lipid Metabolism ; Mice ; Mycobacterium tuberculosis/physiology ; RAW 264.7 Cells
Chemical Substances	Iron (E1UOL152H7)
Language	English
Publishing date	2018-05-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218698-6
ISSN	1098-5522 ; 0019-9567
ISSN (online)	1098-5522
ISSN	0019-9567
DOI	10.1128/IAI.00041-18
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Article ; Online: Quantitative Lipid Droplet Proteomics Reveals Mycobacterium tuberculosis Induced Alterations in Macrophage Response to Infection.

Menon, Dilip / Singh, Kaurab / Pinto, Sneha M / Nandy, Ananya / Jaisinghani, Neetika / Kutum, Rintu / Dash, Debasis / Prasad, T S Keshava / Gandotra, Sheetal

ACS infectious diseases

2019 Volume 5, Issue 4, Page(s) 559–569

Abstract: Growing evidence suggests the importance of lipid metabolism in pathogenesis of tuberculosis. Neutral lipids form the majority of lipids in a caseous granuloma, a pathology characteristic of tuberculosis. Cytosolic lipid droplets (LDs) of macrophages ... ...

Abstract	Growing evidence suggests the importance of lipid metabolism in pathogenesis of tuberculosis. Neutral lipids form the majority of lipids in a caseous granuloma, a pathology characteristic of tuberculosis. Cytosolic lipid droplets (LDs) of macrophages form the store house of these lipids and have been demonstrated to contribute to the inflammatory response to infection. The proteome of lipid droplets reflects the mechanisms of lipid metabolism active under a condition. However, infection induced changes in the proteome of these dynamic organelles remains elusive. Here, we employed quantitative proteomics to identify alterations induced upon infection with live Mycobacterium tuberculosis (Mtb) in comparison with heat killed bacilli or uninfected macrophages. We found increased abundance of proteins coupled with lipid metabolism, protein synthesis, and vesicular transport function in LDs upon infection with live Mtb. Using biochemical methods and microscopy, we validated ADP-ribosyltransferase (Arf)-like 8 (ARL8B) to be increased on the lipid droplet surface of live Mtb infected macrophages and that ARL8B is a bonafide LD protein. This study provides the first proteomic evidence that the dynamic responses to infection also encompass changes at the level of LDs. This information will be important in understanding how Mtb manipulates lipid metabolism and defense mechanisms of the host macrophage.
MeSH term(s)	Cell Line ; Humans ; Lipid Droplets/chemistry ; Lipid Droplets/metabolism ; Macrophages/chemistry ; Macrophages/immunology ; Macrophages/metabolism ; Macrophages/microbiology ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/physiology ; Proteome/chemistry ; Proteome/genetics ; Proteome/metabolism ; Proteomics ; Tuberculosis/immunology ; Tuberculosis/metabolism ; Tuberculosis/microbiology
Chemical Substances	Proteome
Language	English
Publishing date	2019-02-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2373-8227
ISSN (online)	2373-8227
DOI	10.1021/acsinfecdis.8b00301
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Article ; Online: Genome analysis identifies a spontaneous nonsense mutation in ppsD leading to attenuation of virulence in laboratory-manipulated Mycobacterium tuberculosis.

De Majumdar, Shyamasree / Sikri, Kriti / Ghosh, Payel / Jaisinghani, Neetika / Nandi, Malobi / Gandotra, Sheetal / Mande, Shekhar / Tyagi, Jaya Sivaswami

BMC genomics

2019 Volume 20, Issue 1, Page(s) 129

Abstract: Background: A previous laboratory study involving wild type, mutant and devR/dosR complemented strains of Mycobacterium tuberculosis reported the attenuation phenotype of complemented strain, Comp1. This phenotype was intriguing since the parental ... ...

Abstract	Background: A previous laboratory study involving wild type, mutant and devR/dosR complemented strains of Mycobacterium tuberculosis reported the attenuation phenotype of complemented strain, Comp1. This phenotype was intriguing since the parental strain H37Rv, devR mutant (Mut1) and additional complemented strains, Comp9 and Comp11, were virulent in the guinea pig model. Results: Towards deciphering the mechanism underlying the attenuation of Comp1, a whole genome sequencing approach was undertaken. Eight Single Nucleotide Polymorphisms (SNPs) unique to the Comp1 strain were identified. Of these, 5 SNPs were non-synonymous and included a G➞A mutation resulting in a W1591Stop mutation in ppsD gene of the phthiocerol dimycocerosate (PDIM) biosynthetic cluster. Targeted sequence analysis confirmed this mutation in only Comp1 strain and not in wild type (H37Rv), devR knockout (Mut1) or other complemented (Comp9 and Comp11) bacteria. Differential expression of the PDIM locus in Comp1 bacteria was observed which was associated with a partial deficiency of PDIM, an increased sensitivity to detergent and a compromised ability to infect human THP-1 cells. Conclusions: It is proposed that a spontaneous mutation in the ppsD gene of Comp1 underlies down-modulation of the PDIM locus which is associated with defects in permeability and infectivity as well as virulence attenuation in guinea pigs. Our study demonstrates the value of whole genome sequencing for resolving unexplainable bacterial phenotypes and recommends the assessment of PDIM status while assessing virulence properties of laboratory-manipulated strains of M. tuberculosis.
MeSH term(s)	Animals ; Bacterial Proteins/genetics ; Cell Wall/chemistry ; Codon, Nonsense ; Disease Models, Animal ; Gene Expression Regulation, Bacterial ; Guinea Pigs ; Humans ; Lipids/biosynthesis ; Lipids/genetics ; Mycobacterium tuberculosis/classification ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/pathogenicity ; Polyketide Synthases/genetics ; Polymorphism, Single Nucleotide ; THP-1 Cells ; Tuberculosis/microbiology ; Virulence/genetics ; Whole Genome Sequencing
Chemical Substances	Bacterial Proteins ; Codon, Nonsense ; Lipids ; phthiocerol dimycocerosate (63642-22-8) ; Polyketide Synthases (79956-01-7)
Language	English
Publishing date	2019-02-12
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-019-5482-y
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Article: Necrosis Driven Triglyceride Synthesis Primes Macrophages for Inflammation During

Jaisinghani, Neetika / Dawa, Stanzin / Singh, Kaurab / Nandy, Ananya / Menon, Dilip / Bhandari, Purva Deepak / Khare, Garima / Tyagi, Anil / Gandotra, Sheetal

Frontiers in immunology

2018 Volume 9, Page(s) 1490

Abstract: Pulmonary tuberculosis (TB) exhibits granulomatous inflammation, a site of controlling bacterial dissemination at the cost of host tissue damage. Intrigued by the granuloma type-dependent expression of inflammatory markers in TB, we sought to investigate ...

Abstract	Pulmonary tuberculosis (TB) exhibits granulomatous inflammation, a site of controlling bacterial dissemination at the cost of host tissue damage. Intrigued by the granuloma type-dependent expression of inflammatory markers in TB, we sought to investigate underlying metabolic changes that drive amplification of inflammation in TB. Here, we show an association of higher inflammation in necrotic granulomas with the presence of triglyceride (TG)-rich foamy macrophages. The conspicuous absence of these macrophages in solid granulomas identified a link between the ensuing pathology and the metabolic programming of foamy macrophages. Consistent with
Language	English
Publishing date	2018-07-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606827-8
ISSN	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2018.01490
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Article ; Online: Tuning the

Misra, Richa / Menon, Dilip / Arora, Gunjan / Virmani, Richa / Gaur, Mohita / Naz, Saba / Jaisinghani, Neetika / Bhaduri, Asani / Bothra, Ankur / Maji, Abhijit / Singhal, Anshika / Karwal, Preeti / Hentschker, Christian / Becher, Dörte / Rao, Vivek / Nandicoori, Vinay K / Gandotra, Sheetal / Singh, Yogendra

Journal of bacteriology

2019 Volume 201, Issue 7

Abstract: Bacterial alternative sigma factors are mostly regulated by a partner-switching mechanism. Regulation of the virulence-associated alternative sigma factor SigF ... ...

Abstract	Bacterial alternative sigma factors are mostly regulated by a partner-switching mechanism. Regulation of the virulence-associated alternative sigma factor SigF of
MeSH term(s)	Bacterial Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Mycobacterium tuberculosis/enzymology ; Mycobacterium tuberculosis/metabolism ; Phosphorylation ; Protein Binding ; Protein Kinase C/metabolism ; Protein Processing, Post-Translational ; Sigma Factor/metabolism
Chemical Substances	Bacterial Proteins ; FliA protein, Bacteria ; Sigma Factor ; protein kinase D (EC 2.7.10.-) ; Protein Kinase C (EC 2.7.11.13)
Language	English
Publishing date	2019-03-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00725-18
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Article ; Online: Phospholipid homeostasis, membrane tenacity and survival of Mtb in lipid rich conditions is determined by MmpL11 function.

Bothra, Ankur / Arumugam, Prabhakar / Panchal, Vipul / Menon, Dilip / Srivastava, Sonali / Shankaran, Deepthi / Nandy, Ananya / Jaisinghani, Neetika / Singh, Archana / Gokhale, Rajesh S / Gandotra, Sheetal / Rao, Vivek

Scientific reports

2018 Volume 8, Issue 1, Page(s) 8317

Abstract: The mycobacterial cell wall is a chemically complex array of molecular entities that dictate the pathogenesis of Mycobacterium tuberculosis. Biosynthesis and maintenance of this dynamic entity in mycobacterial physiology is still poorly understood. Here ... ...

Abstract	The mycobacterial cell wall is a chemically complex array of molecular entities that dictate the pathogenesis of Mycobacterium tuberculosis. Biosynthesis and maintenance of this dynamic entity in mycobacterial physiology is still poorly understood. Here we demonstrate a requirement for M. tuberculosis MmpL11 in the maintenance of the cell wall architecture and stability in response to surface stress. In the presence of a detergent like Tyloxapol, a mmpL11 deletion mutant suffered from a severe growth attenuation as a result of altered membrane polarity, permeability and severe architectural damages. This mutant failed to tolerate permissible concentrations of cis-fatty acids suggesting its increased sensitivity to surface stress, evident as smaller colonies of the mutant outgrown from lipid rich macrophage cultures. Additionally, loss of MmpL11 led to an altered cellular fatty acid flux in the mutant: reduced incorporation into membrane cardiolipin was associated with an increased flux into the cellular triglyceride pool. This increase in storage lipids like triacyl glycerol (TAG) was associated with the altered metabolic state of higher dormancy-associated gene expression and decreased sensitivity to frontline TB drugs. This study provides a detailed mechanistic insight into the function of mmpL11 in stress adaptation of mycobacteria.
MeSH term(s)	Bacterial Proteins/metabolism ; Cell Membrane/metabolism ; Fatty Acids/metabolism ; Homeostasis ; Mycobacterium tuberculosis/metabolism ; Phospholipids/metabolism
Chemical Substances	Bacterial Proteins ; Fatty Acids ; Phospholipids
Language	English
Publishing date	2018-05-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-26710-z
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