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  1. Article ; Online: Precision Targeting of Endogenous Epidermal Growth Factor Receptor (EGFR) by Structurally Aligned Dual-Modifier Labeling.

    de Jesus Salazar-Estrada, Ivan / Kamath, Karthik Shantharam / Liu, Fei

    ACS pharmacology & translational science

    2022  Volume 5, Issue 10, Page(s) 859–871

    Abstract: Covalent modification of endogenous proteins by chemical probes is used for proteome-wide profiling of cellular protein function and drug discovery. However, probe selectivity in the complex cellular environment is a challenge, and new probes with better ...

    Abstract Covalent modification of endogenous proteins by chemical probes is used for proteome-wide profiling of cellular protein function and drug discovery. However, probe selectivity in the complex cellular environment is a challenge, and new probes with better target selectivity are continuously needed. On the basis of the success of monocovalent activity-based and reactivity-based probes, an approach of structurally aligned dual-modifier labeling (SADL) was investigated here on its potential in improving target precision. Two reactive groups, based on the acrylamide and NHS ester chemistry, were linked with structural alignment to be under the same anilinoquinazoline ligand-directive for targeting the epidermal growth factor receptor (EGFR) protein kinase as the model system for proteome-wide profiling. The SADL approach was compared with its monocovalent precursors in a label-free MaxLFQ workflow using MDA-MB-468 triple negative breast cancer cells. The dual-modifier probe consistently showed labeling of EGFR with improved precision over both monocovalent precursors under various controls. The workflow also labeled endogenous USP34 and PKMYT1 with high selectivity. Precision labeling with two covalent modifiers under a common ligand directive may broaden protein identification opportunities in the native environment to complement genetic and antibody-based approaches for elucidating biological or disease mechanisms, as well as accelerating drug target discovery.
    Language English
    Publishing date 2022-09-19
    Publishing country United States
    Document type Journal Article
    ISSN 2575-9108
    ISSN (online) 2575-9108
    DOI 10.1021/acsptsci.2c00155
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Genome survey sequencing of wild cotton (Gossypium robinsonii) reveals insights into proteomic responses of pollen to extreme heat

    Masoomi‐Aladizgeh, Farhad / Kamath, Karthik Shantharam / Haynes, Paul A. / Atwell, Brian J.

    Plant, cell and environment. 2022 Apr., v. 45, no. 4

    2022  

    Abstract: Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid‐zone cotton (Gossypium robinsonii) was exposed to heat events during pollen ... ...

    Abstract Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid‐zone cotton (Gossypium robinsonii) was exposed to heat events during pollen development then mature pollen was subjected to deep proteomic analysis using 57 023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads (TEs), uninucleate microspores (UNs) and binucleate microspores (BNs) were exposed to 36°C or 40°C for 5 days and the resulting mature pollen was collected at anthesis (p‐TE, p‐UN and p‐BN, respectively). Using the sequential windowed acquisition of all theoretical mass spectra proteomic analysis, 2704 proteins were identified and quantified across all pollen samples analysed. Proteins predominantly decreased in abundance at all stages in response to heat, particularly after exposure of TEs to 40°C. Functional enrichment analyses demonstrated that extreme heat increased the abundance of proteins that contributed to increased messenger RNA splicing via spliceosome, initiation of cytoplasmic translation and protein refolding in p‐TE40. However, other functional categories that contributed to intercellular transport were inhibited in p‐TE40, linked potentially to Rab proteins. We ascribe the resilience of reproductive processes in G. robinsonii at temperatures up to 40°C, relative to commercial cotton, to a targeted reduction in protein transport.
    Keywords Gossypium ; cotton ; databases ; environment ; flowering ; genomics ; heat ; heat stress ; messenger RNA ; pollen ; pollen viability ; protein transport ; proteomics ; spliceosomes ; surveys
    Language English
    Dates of publication 2022-04
    Size p. 1242-1256.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 391893-2
    ISSN 1365-3040 ; 0140-7791
    ISSN (online) 1365-3040
    ISSN 0140-7791
    DOI 10.1111/pce.14268
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Genome survey sequencing of wild cotton (Gossypium robinsonii) reveals insights into proteomic responses of pollen to extreme heat.

    Masoomi-Aladizgeh, Farhad / Kamath, Karthik Shantharam / Haynes, Paul A / Atwell, Brian J

    Plant, cell & environment

    2022  Volume 45, Issue 4, Page(s) 1242–1256

    Abstract: Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid-zone cotton (Gossypium robinsonii) was exposed to heat events during pollen ... ...

    Abstract Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid-zone cotton (Gossypium robinsonii) was exposed to heat events during pollen development then mature pollen was subjected to deep proteomic analysis using 57 023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads (TEs), uninucleate microspores (UNs) and binucleate microspores (BNs) were exposed to 36°C or 40°C for 5 days and the resulting mature pollen was collected at anthesis (p-TE, p-UN and p-BN, respectively). Using the sequential windowed acquisition of all theoretical mass spectra proteomic analysis, 2704 proteins were identified and quantified across all pollen samples analysed. Proteins predominantly decreased in abundance at all stages in response to heat, particularly after exposure of TEs to 40°C. Functional enrichment analyses demonstrated that extreme heat increased the abundance of proteins that contributed to increased messenger RNA splicing via spliceosome, initiation of cytoplasmic translation and protein refolding in p-TE40. However, other functional categories that contributed to intercellular transport were inhibited in p-TE40, linked potentially to Rab proteins. We ascribe the resilience of reproductive processes in G. robinsonii at temperatures up to 40°C, relative to commercial cotton, to a targeted reduction in protein transport.
    MeSH term(s) Australia ; Extreme Heat ; Gossypium ; Pollen ; Proteomics
    Language English
    Publishing date 2022-02-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 391893-2
    ISSN 1365-3040 ; 0140-7791
    ISSN (online) 1365-3040
    ISSN 0140-7791
    DOI 10.1111/pce.14268
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Proteomic analysis of the developing mammalian brain links PCDH19 to the Wnt/β-catenin signalling pathway.

    de Nys, Rebekah / Gardner, Alison / van Eyk, Clare / Mincheva-Tasheva, Stefka / Thomas, Paul / Bhattacharjee, Rudrarup / Jolly, Lachlan / Martinez-Garay, Isabel / Fox, Ian W J / Kamath, Karthik Shantharam / Kumar, Raman / Gecz, Jozef

    Molecular psychiatry

    2024  

    Abstract: Clustering Epilepsy (CE) is a neurological disorder caused by pathogenic variants of the Protocadherin 19 (PCDH19) gene. PCDH19 encodes a protein involved in cell adhesion and Estrogen Receptor α mediated-gene regulation. To gain further insights into ... ...

    Abstract Clustering Epilepsy (CE) is a neurological disorder caused by pathogenic variants of the Protocadherin 19 (PCDH19) gene. PCDH19 encodes a protein involved in cell adhesion and Estrogen Receptor α mediated-gene regulation. To gain further insights into the molecular role of PCDH19 in the brain, we investigated the PCDH19 interactome in the developing mouse hippocampus and cortex. Combined with a meta-analysis of all reported PCDH19 interacting proteins, our results show that PCDH19 interacts with proteins involved in actin, microtubule, and gene regulation. We report CAPZA1, αN-catenin and, importantly, β-catenin as novel PCDH19 interacting proteins. Furthermore, we show that PCDH19 is a regulator of β-catenin transcriptional activity, and that this pathway is disrupted in CE individuals. Overall, our results support the involvement of PCDH19 in the cytoskeletal network and point to signalling pathways where PCDH19 plays critical roles.
    Language English
    Publishing date 2024-03-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 1330655-8
    ISSN 1476-5578 ; 1359-4184
    ISSN (online) 1476-5578
    ISSN 1359-4184
    DOI 10.1038/s41380-024-02482-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei.

    Nogueira, Karoline Maria Vieira / Mendes, Vanessa / Kamath, Karthik Shantharam / Cheruku, Anusha / Oshiquiri, Letícia Harumi / de Paula, Renato Graciano / Carraro, Claudia / Pedersoli, Wellington Ramos / Pereira, Lucas Matheus Soares / Vieira, Luiz Carlos / Steindorff, Andrei Stecca / Amirkhani, Ardeshir / McKay, Matthew J / Nevalainen, Helena / Molloy, Mark P / Silva, Roberto N

    Microbial cell factories

    2024  Volume 23, Issue 1, Page(s) 22

    Abstract: Background: Trichoderma reesei is an organism extensively used in the bioethanol industry, owing to its capability to produce enzymes capable of breaking down holocellulose into simple sugars. The uptake of carbohydrates generated from cellulose ... ...

    Abstract Background: Trichoderma reesei is an organism extensively used in the bioethanol industry, owing to its capability to produce enzymes capable of breaking down holocellulose into simple sugars. The uptake of carbohydrates generated from cellulose breakdown is crucial to induce the signaling cascade that triggers cellulase production. However, the sugar transporters involved in this process in T. reesei remain poorly identified and characterized.
    Results: To address this gap, this study used temporal membrane proteomics analysis to identify five known and nine putative sugar transporters that may be involved in cellulose degradation by T. reesei. Docking analysis pointed out potential ligands for the putative sugar transporter Tr44175. Further functional validation of this transporter was carried out in Saccharomyces cerevisiae. The results showed that Tr44175 transports a variety of sugar molecules, including cellobiose, cellotriose, cellotetraose, and sophorose.
    Conclusion: This study has unveiled a transporter Tr44175 capable of transporting cellobiose, cellotriose, cellotetraose, and sophorose. Our study represents the first inventory of T. reesei sugar transportome once exposed to cellulose, offering promising potential targets for strain engineering in the context of bioethanol production.
    MeSH term(s) Cellobiose/metabolism ; Proteome/metabolism ; Membrane Proteins/metabolism ; Cellulose/metabolism ; Membrane Transport Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Cellulase/metabolism ; Sugars/metabolism ; Oligosaccharides/metabolism ; Trichoderma/metabolism ; Glucans ; Hypocreales
    Chemical Substances sophorose (ZHQ3C30OP1) ; Cellobiose (16462-44-5) ; Proteome ; Membrane Proteins ; Cellulose (9004-34-6) ; Membrane Transport Proteins ; Cellulase (EC 3.2.1.4) ; Sugars ; Oligosaccharides ; Glucans
    Language English
    Publishing date 2024-01-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2091377-1
    ISSN 1475-2859 ; 1475-2859
    ISSN (online) 1475-2859
    ISSN 1475-2859
    DOI 10.1186/s12934-023-02279-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The phosphoproteome of rice leaves responds to water and nitrogen supply.

    Hamzelou, Sara / Melino, Vanessa J / Plett, Darren C / Kamath, Karthik Shantharam / Nawrocki, Arkadiusz / Larsen, Martin R / Atwell, Brian J / Haynes, Paul A

    Molecular omics

    2021  Volume 17, Issue 5, Page(s) 706–718

    Abstract: The scarcity of freshwater is an increasing concern in flood-irrigated rice, whilst excessive use of nitrogen fertilizers is costly and contributes to environmental pollution. To co-ordinate growth adaptation under prolonged exposure to limited water or ... ...

    Abstract The scarcity of freshwater is an increasing concern in flood-irrigated rice, whilst excessive use of nitrogen fertilizers is costly and contributes to environmental pollution. To co-ordinate growth adaptation under prolonged exposure to limited water or excess nitrogen supply, plants employ complex systems for signalling and regulation of metabolic processes. There is limited information on the involvement of one of the most important post-translational modifications (PTMs), protein phosphorylation, in plant adaptation to long-term changes in resource supply.
    MeSH term(s) Nitrogen ; Oryza ; Plant Leaves ; Tandem Mass Spectrometry ; Water
    Chemical Substances Water (059QF0KO0R) ; Nitrogen (N762921K75)
    Language English
    Publishing date 2021-10-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2515-4184
    ISSN (online) 2515-4184
    DOI 10.1039/d1mo00137j
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Probing the Role of the Chloroplasts in Heavy Metal Tolerance and Accumulation in Euglena gracilis

    Khatiwada, Bishal / Hasan, Mafruha T. / Sun, Angela / Kamath, Karthik Shantharam / Mirzaei, Mehdi / Sunna, Anwar / Nevalainen, Helena

    Microorganisms. 2020 Jan. 14, v. 8, no. 1

    2020  

    Abstract: The E. gracilis Zm-strain lacking chloroplasts, characterized in this study, was compared with the earlier assessed wild type Z-strain to explore the role of chloroplasts in heavy metal accumulation and tolerance. Comparison of the minimum inhibitory ... ...

    Abstract The E. gracilis Zm-strain lacking chloroplasts, characterized in this study, was compared with the earlier assessed wild type Z-strain to explore the role of chloroplasts in heavy metal accumulation and tolerance. Comparison of the minimum inhibitory concentration (MIC) values indicated that both strains tolerated similar concentrations of mercury (Hg) and lead (Pb), but cadmium (Cd) tolerance of the Z-strain was twice that of the Zm-strain. The ability of the Zm-strain to accumulate Hg was higher compared to the Z-strain, indicating the existence of a Hg transportation and accumulation mechanism not depending on the presence of chloroplasts. Transmission electron microscopy (TEM) showed maximum accumulation of Hg in the cytosol of the Zm-strain and highest accumulation of Cd in the chloroplasts of the Z-strain indicating a difference in the ability of the two strains to deposit heavy metals in the cell. The highly abundant heavy metal transporter MTP2 in the Z-strain may have a role in Cd transportation to the chloroplasts. A multidrug resistance-associated protein highly increased in abundance in the Zm-strain could be a potential Hg transporter to either cytosol or mitochondria. Overall, the chloroplasts appear to have major role in the tolerance and accumulation of Cd in E. gracilis.
    Keywords Euglena gracilis ; cadmium ; chloroplasts ; cytosol ; heavy metals ; lead ; mercury ; metal tolerance ; minimum inhibitory concentration ; mitochondria ; transmission electron microscopy ; transportation
    Language English
    Dates of publication 2020-0114
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms8010115
    Database NAL-Catalogue (AGRICOLA)

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  8. Article: Proteomic response of Euglena gracilis to heavy metal exposure – Identification of key proteins involved in heavy metal tolerance and accumulation

    Khatiwada, Bishal / Hasan, Mafruha T / Sun, Angela / Kamath, Karthik Shantharam / Mirzaei, Mehdi / Sunna, Anwar / Nevalainen, Helena

    Algal research. 2020 Jan., v. 45

    2020  

    Abstract: Contamination of the environment by heavy metals is an increasing problem globally. While the mechanisms bacteria and yeasts have developed to tolerate these metals are well covered in the published literature, much less is known about algae. In this ... ...

    Abstract Contamination of the environment by heavy metals is an increasing problem globally. While the mechanisms bacteria and yeasts have developed to tolerate these metals are well covered in the published literature, much less is known about algae. In this study, the wild-type Euglena gracilis (Z-strain) and the sugar loving E. gracilis var. saccharophila (B-strain) were exposed to the heavy metals cadmium (Cd), lead (Pb) and mercury (Hg). Minimum inhibitory concentration (MIC) studies indicated that the heavy metal tolerance of both strains was in the order of Pb > Cd > Hg. Based on microwave plasma atomic emission spectroscopy (MP-AES), the maximum Cd accumulation by Z-strain was 8.1 mg Cd per gram of dry weight (DW), which makes it a Cd hyperaccumulator.A total of 4493 proteins were quantified by SWATH mass spectrometry to assess the effect of the heavy metals on E. gracilis at the proteome level. In response to Cd, 960 proteins in the Z-strain and 127 in the B-strain changed in relative abundance compared to the untreated control. Proteins of high abundance included the major facilitator superfamily (MFS) transporters, cadmium/zinc-transporting ATPase and heavy metal transporting P1B-ATPase. Also, there was a substantial increase in the abundance of thiol-rich proteins that are paramount in metal chelation and sequestration as well as proteins involved in cellular stress response. A potential mechanism schematic for heavy accumulation in the E. gracilis Z-strain is outlined based on the data collected. The proteomic data presented here contribute to a better understanding of the effects of the exposure of E. gracilis to heavy metals by identifying proteins and thereby genes involved in heavy metal tolerance and accumulation. The information obtained can eventually be utilized for generating highly heavy metal-tolerant Euglena strains for environmental applications.
    Keywords Euglena gracilis ; adenosinetriphosphatase ; algae ; bacteria ; cadmium ; chelation ; data collection ; genes ; heavy metals ; lead ; mass spectrometry ; mercury ; metal tolerance ; minimum inhibitory concentration ; proteome ; proteomics ; stress response ; sugars ; transporters ; yeasts
    Language English
    Dates of publication 2020-01
    Publishing place Elsevier B.V.
    Document type Article
    ISSN 2211-9264
    DOI 10.1016/j.algal.2019.101764
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Multiple Abiotic Stresses Applied Simultaneously Elicit Distinct Responses in Two Contrasting Rice Cultivars.

    Habibpourmehraban, Fatemeh / Wu, Yunqi / Wu, Jemma X / Hamzelou, Sara / Masoomi-Aladizgeh, Farhad / Kamath, Karthik Shantharam / Amirkhani, Ardeshir / Atwell, Brian J / Haynes, Paul A

    International journal of molecular sciences

    2022  Volume 23, Issue 3

    Abstract: Rice crops are often subject to multiple abiotic stresses simultaneously in both natural and cultivated environments, resulting in yield reductions beyond those expected from single stress. We report physiological changes after a 4 day exposure to ... ...

    Abstract Rice crops are often subject to multiple abiotic stresses simultaneously in both natural and cultivated environments, resulting in yield reductions beyond those expected from single stress. We report physiological changes after a 4 day exposure to combined drought, salt and extreme temperature treatments, following a 2 day salinity pre-treatment in two rice genotypes-Nipponbare (a paddy rice) and IAC1131 (an upland landrace). Stomata closed after two days of combined stresses, causing intercellular CO2 concentrations and assimilation rates to diminish rapidly. Abscisic acid (ABA) levels increased at least five-fold but did not differ significantly between the genotypes. Tandem Mass Tag isotopic labelling quantitative proteomics revealed 6215 reproducibly identified proteins in mature leaves across the two genotypes and three time points (0, 2 and 4 days of stress). Of these, 987 were differentially expressed due to stress (
    MeSH term(s) Abscisic Acid/metabolism ; Gases/metabolism ; Gene Expression Regulation, Plant ; Genotype ; Oryza/genetics ; Oryza/physiology ; Photosynthesis ; Plant Leaves/metabolism ; Plant Proteins/metabolism ; Proteome/metabolism ; Proteomics ; Stress, Physiological/genetics ; Stress, Physiological/physiology
    Chemical Substances Gases ; Plant Proteins ; Proteome ; Abscisic Acid (72S9A8J5GW)
    Language English
    Publishing date 2022-02-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23031739
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Wild and Cultivated Species of Rice Have Distinctive Proteomic Responses to Drought.

    Hamzelou, Sara / Kamath, Karthik Shantharam / Masoomi-Aladizgeh, Farhad / Johnsen, Matthew M / Atwell, Brian J / Haynes, Paul A

    International journal of molecular sciences

    2020  Volume 21, Issue 17

    Abstract: Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species ( ...

    Abstract Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (
    MeSH term(s) Droughts ; Oryza/genetics ; Oryza/metabolism ; Plant Breeding ; Proteome/genetics ; Proteome/metabolism ; Selective Breeding ; Stress, Physiological
    Chemical Substances Proteome
    Language English
    Publishing date 2020-08-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms21175980
    Database MEDical Literature Analysis and Retrieval System OnLINE

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