Comparative proteomics in the wild: Accounting for intrapopulation variability improves describing proteome response in a Gammarus pulex field population exposed to cadmium

Cogne, Yannick; Almunia, Christine; Gouveia, Duarte; Pible, Olivier; François, Adeline; Esposti, Davide Degli; Geffard, Olivier; Armengaud, Jean; Chaumot, Arnaud

doi:10.1016/j.aquatox.2019.105244

Cited by 17 publications

(10 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Shared peptides were assigned with the most detected protein as assessed by specific peptides. Spectral counts, defined as the number of MS/MS spectra assigned per protein, were counted for all validated proteins using only non-ambiguous peptides as previously described [20]. Comparison of protein abundance between culture conditions was performed using the TFold test [21] and by defining four statistical groups: blue for a fold-change ≥ 1.5 and a p-value ≤ 0.05, orange for a p-value ≤ 0.05 and fold-change ≤ 1.5, green for a fold-change ≥ 1.5 and a p-value ≥ 0.05, and red for a fold-change ≤ 1.5 and a p-value ≥ 0.05.…”

Section: Mass Spectrometry and Data Interpretationmentioning

confidence: 99%

See 1 more Smart Citation

Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics

et al. 2020

Self Cite

View full text Add to dashboard Cite

Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using the conserved dehalogenase DcmA, the only system for DCM degradation characterised at the sequence level so far. Using differential proteomics, we rapidly identified key determinants of DCM degradation for Hyphomicrobium sp. MC8b, an unsequenced facultative methylotrophic DCM-degrading strain. For this, we designed a pan-proteomics database comprising the annotated genome sequences of 13 distinct Hyphomicrobium strains. Compared to growth with methanol, growth with DCM induces drastic changes in the proteome of strain MC8b. Dichloromethane dehalogenase DcmA was detected by differential pan-proteomics, but only with poor sequence coverage, suggesting atypical characteristics of the DCM dehalogenation system in this strain. More peptides were assigned to DcmA by error-tolerant search, warranting subsequent sequencing of the genome of strain MC8b, which revealed a highly divergent set of dcm genes in this strain. This suggests that the dcm enzymatic system is less strongly conserved than previously believed, and that substantial molecular evolution of dcm genes has occurred beyond their horizontal transfer in the bacterial domain. Our study showed the power of pan-proteomics for quick characterization of new strains belonging to branches of the Tree of Life that are densely genome-sequenced.

show abstract

Section: Mass Spectrometry and Data Interpretationmentioning

confidence: 99%

“…MC8b was done similarly, with proteins validated on the basis of at least two distinct peptide sequences. In this case, no parsimony rule was used, and spectral counts were evaluated by using only non-ambiguous peptides as previously described [20].…”

Section: Mass Spectrometry and Data Interpretationmentioning

confidence: 99%

Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…This work assumes that if two populations have a different quantity of protein it means that the proportion of individuals which express that protein differs between populations. Inter-individual differences are not only pronounced but directly influence the population-level outcome of environmental change 136,137 . Consequently, even in the absence of a significant population-level response to the environment, some individuals may still respond plastically to changing conditions.…”

Section: Variation Of Biomarker Proteins a Consequence Of The Relatimentioning

confidence: 99%

Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata

Ebner

Ritz

Fumetti

2020

Sci Rep

View full text Add to dashboard Cite

Deducing impacts of environmental change on species and the populations they form in nature is an important goal in contemporary ecology. Achieving this goal is hampered by our limited understanding of the influence of naturally occurring environmental variation on the molecular systems of ecologically relevant species, as the pathways underlying fitness-affecting plastic responses have primarily been studied in model organisms and under controlled laboratory conditions. Here, to test the hypothesis that proteome variation systematically relates to variation in abiotic conditions, we establish such relationships by profiling the proteomes of 24 natural populations of the spring-dwelling caddisfly Crunoecia irrorata. We identified protein networks whose abundances correlated with environmental (abiotic) gradients such as in situ pH, oxygen- and nitrate concentrations but also climatic data such as past thermal minima and temperature seasonality. Our analyses suggest that variations in abiotic conditions induce discrete proteome responses such as the differential abundance of proteins associated with cytoskeletal function, heat-shock proteins and proteins related to post-translational modification. Identifying these drivers of proteome divergence characterizes molecular “noise”, and positions it as a background against which molecular signatures of species’ adaptive responses to stressful conditions can be identified.

show abstract

“…The dataset allows studying the intrapopulation proteome variability of long-term exposed individuals (Brameloup population) in relation to non-contaminated individuals (Pollon population) as described in Ref. [2]. Table 1 shows the total number of peptide-spectrum matches, peptides, non-ambiguous peptides, and proteins obtained for the male and female datasets.…”

Section: Datamentioning

confidence: 99%

“…As discussed in Ref. [2], the continuous exposure to Cd in the Brameloup site may have induced a chronic Cd-based oxidative stress in these animals. Data were deposited in the PRIDE database and are available in ProteomeXchange under the identifiers PXD013656 and PXD013712, respectively.…”

Section: Datamentioning

confidence: 99%

Shotgun proteomics datasets acquired on Gammarus pulex animals sampled from the wild

et al. 2019

Self Cite

View full text Add to dashboard Cite

This data article associated with the manuscript “Comparative proteomics in the wild: accounting for intrapopulation variability improves describing proteome response in a Gammarus pulex field population exposed to cadmium” refers to the shotgun proteomics analysis performed on 40 Gammarus pulex animals sampled from the wild. Proteins were extracted, digested with trypsin, and the resulting peptides were identified by tandem mass spectrometry. Here, we present the list of proteins from males and the list of proteins from females that are differentially detected between the Brameloup and the Pollon populations. Data are available via ProteomeXchange with identifiers PXD013656 and PXD013712, respectively.

show abstract

Comparative proteomics in the wild: Accounting for intrapopulation variability improves describing proteome response in a Gammarus pulex field population exposed to cadmium

Cited by 17 publications

References 46 publications

Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics

Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics

Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata

Shotgun proteomics datasets acquired on Gammarus pulex animals sampled from the wild

Contact Info

Product

Resources

About