Dataset Information

Proteomic analysis of Rhizobium favelukesii LPU83 in response to acid stress.

ABSTRACT: Acid soils constitute a severe problem for leguminous crops mainly through a disturbance in rhizobia-legume interactions. Rhizobium favelukesii—an acid-tolerant rhizobium able to nodulate alfalfa—is highly competitive for nodule occupation under acid conditions, but inefficient in biologic nitrogen fixation. In this work, we obtained a general description of the acid-stress response of R. favelukesii LPU83 by means of proteomics by comparing the total proteome profiles in the presence or absence of acid stress by nanoflow ultrahigh-performance liquid chromatography coupled to mass spectrometry. Thus, a total of 336 proteins were identified with a significant differential expression, 136 of which species were significantly overexpressed and 200 underexpressed in acidity. An in-silico functional characterization with those respective proteins revealed a complex and pleiotropic response by these rhizobia involving components of oxidative phosphorylation, glutamate metabolism, and peptidoglycan biosynthesis, among other pathways. Furthermore, a lower permeability was evidenced in the acid-stressed cells along with several overexpressed proteins related to γ-aminobutyric-acid metabolism, such as the gene product of livK, which was mutated. This mutant exhibited an acid-sensitive phenotype in agreement with the proteomics results. We conclude that both γ-aminobutyric-acid metabolism and a modified cellular envelope could be relevant to acid tolerance in R. favelukesii.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Rhizobium Favelukesii

SUBMITTER: Juliet Nilsson

LAB HEAD: Mariano Pistorio

PROVIDER: PXD013642 | Pride | 2022-04-08

REPOSITORIES: Pride

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Proteomic Analysis of Rhizobium favelukesii LPU83 in Response to Acid Stress.

Nilsson Juliet F JF Castellani Lucas G LG Draghi Walter O WO Pérez-Giménez Julieta J Torres Tejerizo Gonzalo A GA Pistorio Mariano M

Journal of proteome research 20190905 10

Acid soils constitute a severe problem for leguminous crops mainly through a disturbance in rhizobium-legume interactions. Rhizobium favelukesii-an acid-tolerant rhizobium able to nodulate alfalfa-is highly competitive for nodule occupation under acid conditions but inefficient for biologic nitrogen fixation. In this work, we obtained a general description of the acid-stress response of R. favelukesii LPU83 by means of proteomics by comparing the total proteome profiles in the pres ...[more]

PMID: 31432679

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Project description:During pregnancy, the Zika virus (ZIKV) can be vertically transmitted, causing Congenital Zika Syndrome (CZS) in fetuses. ZIKV infection in early gestational trimesters increases the chances to develop CZS. This syndrome involves several pathologies with a difficult diagnosis, which usually occurs in the postnatal stage. In this work, we aim to identify biological processes and molecular pathways related to CZS development and propose a series of putative protein and metabolite biomarkers for CZS prognosis in early pregnancy trimesters. Twenty-five serum samples of pregnant women were analyzed. For biological analysis, samples were separated into 3 biological groups composed of a control group of healthy pregnant women and two groups of ZIKV-infected pregnant women bearing non- microcephalic and microcephalic fetuses. Control and ZIKV-infected groups - without microcephalic fetuses - were subdivided into healthy and Cognitive Developmental Delay (CDD) newborns for biomarker analysis. We detected over 1,000 proteins and 500 metabolites by bottom-up proteomics and untargeted metabolomics, respectively. Statistical approaches - (t-Student, Limma, ANOVA, and DIABLO) - were applied to find CZS differentially abundant proteins (DAP) and metabolites (DAM). Enrichment analysis (i.e., biological processes and molecular pathways) of the DAP and the DAM allowed us to identify the ECM organization and proteoglycans, amino acid metabolism, and arachidonic acid metabolism as signatures in the CZS development. Five proteins and four metabolites were selected as CZS biomarkers candidates. The protein-based model indicated superior performance values for the Vitamin K-dependent protein S, Selenoprotein P, Inter-alpha- trypsin inhibitor heavy chain H2, Kallistatin, and Protein Z-dependent protease inhibitor proteins. Furthermore, the metabolite-based model was able to predict CZS with a probability of 90%. Serum multi-omics analysis led us to propose for further studies nine potential biomarkers for CZS early prognosis with high sensitivity and specificity.

Project description:The experiment was carried out during two vegetation seasons from 25th of April to 10th of September. Two Polish potato cultivars, the drought-tolerant Gwiazda and drought-sensitive Oberon were used. Selected tubers with transverse diameters of 3 - 4 cm were pre-sprouted for 2 weeks before planting. Plants were grown in a vegetation hall in pots filled with a thin layer of gravel on the bottom and the universal vegetable soil substrate ‘Hollas’ (Agaris Polska Ltd., Poland) produced from peat with the addition of chalk at a pH range of 5.5-6.5. Additionally, in phase 20 of the BBCH-scale of plant development, MIS-3 (Intermag) fertilizer was applied. Water content (WC) in volumetric basis in soil pots was measured according Black (1965). Weather conditions during the years of study were monitored using a Weather Campbell Station (Campbell Scientific Inc.) located in close proximity, and a thermohygrograph placed between pots. Meteorological data of air temperature, the photosynthetically active radiation, and humidity were comparable in the years of study and favorable for potato development. Three weeks after the initiation of the tuberisation phase (56 DAP), plants were divided into 3 groups, each consisting of 6 plants. The first group of plants was subjected to soil drought (remained without irrigation, day/night temperature 22°C/18°C), the second one to high temperature (day/night temperature 38°C/25°C) and the third one was watered according to needs and at optimal temperature (control plants, day/night temperature 22°C/18°C). Stress application lasted 14 days and finished at 70 DAP. During this period, plants were placed in phytotron equipped with six Hortilux Schreder Lamps with Philips light bulbs of 1600 W each. Air humidity was in the range 65-70%. WC under 14 days of soil drought reached 30% (v/v), and remained 80% (v/v) in control and high temperature conditions. During the recovery period, after 14 days of stress treatment, WC reached control levels. Plant root material for proteomic research was collected on the 14th day of stress treatment (70 DAP).

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Dataset Information

Proteomic analysis of Rhizobium favelukesii LPU83 in response to acid stress.

Dataset's files

Publications

Proteomic Analysis of <i>Rhizobium favelukesii</i> LPU83 in Response to Acid Stress.

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