Shotgun proteomic profiling of five species of New Zealand <i>Pachycladon</i>

Mirzaei, Mehdi; Pascovici, Dana; Keighley, Tim; George, Iniga S.; Voelckel, Claudia; Heenan, P. B.; Haynes, Paul A.

doi:10.1002/pmic.200900816

Cited by 14 publications

(10 citation statements)

References 26 publications

(29 reference statements)

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“…We have used a similar strategy in a previous study of species differentiation in Pachycladon, an endemic New Zealand plant family. In that instance the biological conclusions based on protein quantitation using NSAF values were strongly supported by post hoc validation at the genomic and metabolomic levels [42].…”

Section: Protein Identification and Quantitation Using Sds-page And Gpfmentioning

confidence: 94%

Quantitative proteomics of heavy metal stress responses in Sydney rock oysters

et al. 2012

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Currently, there are few predictive biomarkers in key biomonitoring species, such as oysters, that can detect heavy metal pollution in coastal waterways. Several attributes make oysters superior to other organisms for positive biomonitoring of heavy metal pollution. In particular, they are filter feeders with a high capacity for bioaccumulation. In this study, we used two proteomics approaches, namely label-free shotgun proteomics based on SDS-PAGE gel separation and gas phase fractionation, to investigate the heavy metal stress responses of Sydney rock oysters. Protein samples were prepared from haemolymph of oysters exposed to 100 μg/L of PbCl(2), CuCl(2), or ZnCl(2) for 4 days in closed aquaria. Peptides were identified using a Bivalvia protein sequence database, due to the unavailability of a complete oyster genome sequence. Statistical analysis revealed 56 potential biomarker proteins, as well as several protein biosynthetic pathways to be greatly impacted by metal stress. These have the potential to be incorporated into bioassays for prevention and monitoring of heavy metal pollution in Australian oyster beds. The study confirms that proteomic analysis of biomonitoring species is a promising approach for assessing the effects of environmental pollution, and our experiments have provided insights into the molecular mechanisms underlying oyster stress responses.

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Section: Protein Identification and Quantitation Using Sds-page And Gpfmentioning

confidence: 94%

Quantitative proteomics of heavy metal stress responses in Sydney rock oysters

et al. 2012

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“…The three protein identification output files from each biological replicate of peptide samples were combined together to produce a single merged output file for each strains MV fraction. To ensure data quality, identified proteins were filtered based on two criteria: reproducible identification across three replicates and a total spectral count of >6, making the minimum number of peptides used to identify each protein an average value of 2 per replicate [ 61 ]. The subcellular location and functions for each of the identified MV proteins was predicted using PSORTb 3.0.2 [ 62 ] and their gene otology (GO) molecular function derived from The UniProt database [ 63 ].…”

Section: Methodsmentioning

confidence: 99%

Comparative Analysis of Membrane Vesicles from Three Piscirickettsia salmonis Isolates Reveals Differences in Vesicle Characteristics

et al. 2016

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Membrane vesicles (MVs) are spherical particles naturally released from the membrane of Gram-negative bacteria. Bacterial MV production is associated with a range of phenotypes including biofilm formation, horizontal gene transfer, toxin delivery, modulation of host immune responses and virulence. This study reports comparative profiling of MVs from bacterial strains isolated from three widely disperse geographical areas. Mass spectrometry identified 119, 159 and 142 proteins in MVs from three different strains of Piscirickettsia salmonis isolated from salmonids in Chile (LF-89), Norway (NVI 5692) and Canada (NVI 5892), respectively. MV comparison revealed several strain-specific differences related to higher virulence capability for LF-89 MVs, both in vivo and in vitro, and stronger similarities between the NVI 5692 and NVI 5892 MV proteome. The MVs were similar in size and appearance as analyzed by electron microscopy and dynamic light scattering. The MVs from all three strains were internalized by both commercial and primary immune cell cultures, which suggest a potential role of the MVs in the bacterium’s utilization of leukocytes. When MVs were injected into an adult zebrafish infection model, an upregulation of several pro-inflammatory genes were observed in spleen and kidney, indicating a modulating effect on the immune system. The present study is the first comparative analysis of P. salmonis derived MVs, highlighting strain-specific vesicle characteristics. The results further illustrate that the MV proteome from one bacterial strain is not representative of all bacterial strains within one species.

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“…Protein sequences extracted from the sequenced genome of each individual strain were used as the search database (Palenik et al, 2003;Dufresne et al, 2008). To ensure data quality, identified proteins were filtered based on two criteria: reproducible identification across three replicates and a total spectral count of 45 (Gammulla et al, 2010;Mirzaei et al, 2011). A database of reversed sequences was searched to determine the false discovery rate.…”

Section: Label-free Shotgun Proteomicsmentioning

confidence: 99%

Effects of low temperature on tropical and temperate isolates of marine Synechococcus

et al. 2015

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Temperature is an important factor influencing the distribution of marine picocyanobacteria. However, molecular responses contributing to temperature preferences are poorly understood in these important primary producers. We compared the temperature acclimation of a tropical Synechococcus strain WH8102 with temperate strain BL107 at 18°C relative to 22°C and examined their global protein expression, growth patterns, photosynthetic efficiency and lipid composition.Global protein expression profiles demonstrate the partitioning of the proteome into major categories: photosynthesis (440%), translation (10-15%) and membrane transport (2-8%) with distinct differences between and within strains grown at different temperatures. At low temperature, growth and photosynthesis of strain WH8102 was significantly decreased, while BL107 was largely unaffected. There was an increased abundance of proteins involved in protein biosynthesis at 18°C for BL107. Each strain showed distinct differences in lipid composition with higher unsaturation in strain BL107. We hypothesize that differences in membrane fluidity, abundance of protein biosynthesis machinery and the maintenance of photosynthesis efficiency contribute to the acclimation of strain BL107 to low temperature. Additional proteins unique to BL107 may also contribute to this strain's improved fitness at low temperature. Such adaptive capacities are likely important factors favoring growth of temperate strains over tropical strains in high latitude niches.

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Shotgun proteomic profiling of five species of New Zealand Pachycladon

Cited by 14 publications

References 26 publications

Quantitative proteomics of heavy metal stress responses in Sydney rock oysters

Quantitative proteomics of heavy metal stress responses in Sydney rock oysters

Comparative Analysis of Membrane Vesicles from Three Piscirickettsia salmonis Isolates Reveals Differences in Vesicle Characteristics

Effects of low temperature on tropical and temperate isolates of marine Synechococcus

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