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A deep comparative metaproteomic study on the complex wastewater treatment microbiome

ABSTRACT: We performed a deep, comparative metaproteomics study on three aerobic granular sludge wastewater treatment communities to determine the core microbiome and the occurrence and relative abundance of the central nutrient-removing organisms. Our systematic study underscores the importance of metaproteomics when characterizing complex microbiomes, and the necessity of accurate reference sequence databases to improve the comparison between studies and omics approaches.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Wastewater Metagenome

SUBMITTER: Martin Pabst

LAB HEAD: Martin Pabst

PROVIDER: PXD030677 | Pride | 2023-11-19

REPOSITORIES: Pride

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Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis

Project description:Photosynthesis is the energetic basis for most life on Earth, and in plants it operates inside double-membrane-bound organelles called chloroplasts. The photosynthetic apparatus comprises numerous proteins encoded by the nuclear and organellar genomes. Maintenance of this apparatus requires the action of internal chloroplast proteases, but a role for the nucleocytosolic ubiquitin-proteasome system (UPS) was not expected owing to the barrier presented by the double-membrane envelope. Here, we show that photosynthesis proteins (including those encoded internally by chloroplast genes) are ubiquitinated, and processed via the CHLORAD pathway: they are degraded by the 26S proteasome following CDC48-dependent retrotranslocation to the cytosol. This demonstrates that the reach of the UPS extends to the interior of endosymbiotically-derived chloroplasts, where it acts to regulate one of the most fundamental processes of life.

2022-12-06 | PXD031388 | Pride

Changes in polysome association of mRNA throughout growth and development in Arabidopsis thaliana (Polysome association)

Project description:Translational control is a key regulatory step in the expression of genes as proteins. In plant cells, translational efficiency of mRNAs differs on different mRNA species, and the efficiency dynamically changes in various conditions. To gain a global view of translational control throughout growth and development, we performed genome-wide analysis of polysome association of mRNA over growth and leaf development in Arabidopsis thaliana by applying the mRNAs in polysome to DNA microarray. This analysis revealed that the degree of polysome association of mRNA had different levels depending on mRNA species, and the polysome association changed greatly throughout growth and development for each. In the growth stage, transcripts showed varying changes in polysome association from strongly depressed to unchanged degree, with the majority of transcripts showing dissociation from ribosomes. On the other hand, during leaf development, the polysome association of transcripts showed a normal distribution from repressed to activated mRNAs when comparing between expanding and expanded leaves. In addition, functional category analysis of the microarray data suggested that translational control has a physiological significance in plant growth and development process, especially in category of signaling and protein synthesis. Besides this, we compared changes in polysome association of mRNAs between various conditions and characterized translational controls in each. This result suggested that mRNAs translation might be controlled by complicated mechanisms for response to each condition. Our results highlight the importance of dynamic changes in mRNA translation in plant development and growth. Experiment using two-flactionated mRNA in 4 developmental stages, Polysomal mRNA vs. total mRNA. Biological replicates: 2. Compared 2DAG and 21DAG, or Young leaves and Mature leaves.

2015-09-01 | E-GEOD-69069 | biostudies-arrayexpress

Plasma membrane proteome of adhesion-competent endometrial epithelial cells and its modulation by Rab11a

Project description:Human endometrial epithelium (EE) is composed of a multitude of proteins, amongst which those localized on the plasma membrane (plasma membrane proteins-PMPs) are of critical relevance in early stages of implantation. Evidences support the key role of few PMPs in implantation. However, many remain unidentified, as efforts have not been made till date to generate the plasma membrane proteome of human EE cells, using a gel-free approach. This study presents a protein catalogue of the PMP enriched fraction of Ishikawa cell line; often used as an in vitro model for embryo-adhesive EE. Liquid Chromatography with tandem mass spectrometry identified 3598 proteins. Of these, 1963 proteins were annotated for their membrane localization. Of 1963 proteins, 1321 were found to have transmembrane domain and 43 proteins had GPI anchor. Extensive data mining revealed endometrial expression of 943 proteins reported in human and/or rodents. Further, quantitative alterations were observed in the plasma membrane proteome on perturbation of intracellular trafficking. Silencing of Rab11a (known for its role in plasma membrane organization) expression caused alteration in the abundance of 74 proteins. Caveolin-1 and EpCAM levels were reduced whereas Rab4a abundance increased in the PMP extracts of Rab11a-deficient cells, compared to control cells. Briefly, the study reports the identity of several novel plasma membrane-localized proteins. A major spin-off of the study is the identification of novel proteins trafficked by Rab11a to the plasma membrane. Targeted analysis of novel PMPs may reveal their specific roles in endometrial receptivity and implantation.

2019-11-08 | PXD015010 | Pride

Changes in polysome association of mRNA throughout growth and development in Arabidopsis thaliana

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-09-01 | E-GEOD-69070 | biostudies-arrayexpress

HiC-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

2022-06-24 | E-MTAB-10848 | biostudies-arrayexpress

Proteomic analysis of human follicular fluid in poor ovarian responders during in vitro fertilization

Project description:Poor ovarian response (POR) observed in controlled ovarian stimulation (COS) is often observed during in vitro fertilization and embryo transfer (IVF-ET) cycles and is a major problem. A POR has been found to be related to several factors, including advanced age, high body mass index, and history of ovarian or pelvic surgery. However, it is difficult to predict POR, as there are no specific biomarkers known. In this study, we used quantitative proteomic analyses to investigate potential biomarkers that can predict poor response during IVF based on follicular fluid samples. A total of 1,079 proteins were identified using a high-resolution orbitrap mass spectrometer coupled online to a nano flow liquid chromatography system. It is notable that 65 up-regulated and 66 down-regulated proteins were found to be functionally enriched in poor responders. We also validated these differentially expressed proteins (DEPs) using a triple-quadrupole (QQQ) mass spectrometer for quantification of targeted proteins. Of the DEPs, three proteins (pregnancy zone protein, renin, and sushi repeat-containing protein SRPX) were regarded as statistically significant (p < 0.05). These proteins (one known as an inhibitor of cell growth and another as a regulator of angiogenesis) are potential biomarkers candidates of POR in IVF.

2018-07-05 | PXD005436 | Pride

Proteome of Agave angustifolia Haw.: insights about metabolism of amino acids in albino plantlets

Project description:Amino acids (AA) are essential molecules for life because they are precursors for the synthesis of proteins and other organic compounds. Their metabolism in plants involves more than one cellular compartment, among which the chloroplast plays a key role. From the 20 essential AA, ten (Arg, Lys, Thr, Leu, Ile, Val, Trp, Phe, Tyr and His) are only synthesized in the plastids and seven (Asp, Cys, Gln, Glu, Gly, Ser and Met) can be synthesized in both chloroplast and other parts of the cell. Despite knowing the roles of AA in plant physiology, little has been assessed in plants with albino phenotypes, lacking chloroplasts. To assess the effect of chloroplast biogenesis disturbances on AA metabolism in albino and variegated somaclonal variations of Agave angustifolia Haw., a comparative proteomic based TMT- synchronous precursor selection (SPS)-MS3 strategy was used to determine the status of AA biosynthetic pathways. Besides the 20 essential AA was quantified to underpin proteomics finding. A total of 2,442 different proteins were identified in the proteome of the somaclonal variants, from which 82 correspond to enzymes participating in AA biosynthesis. From these 82, 32 proteins were differentially accumulated. On the other hand, the concentration of 16 and 12 of the AA synthesized by the chloroplast were over-accumulated in the variegated and albino somaclonal variant, respectively. In plantlets devoid of functional chloroplasts, there is a surprising increase of AA and key enzymes of the AA biosyntethic pathways, compared to green plantlets. This could suggest que la activation of AA biosynthesis is key to sustaining albino and variegated plantlets survival that lack chloroplasts.

2024-01-29 | PXD039512 | Pride

Global microRNA profiling of mouse hemopoietic stem cells (LSKs), promyelocytes, myelocytes and granulocytes.

Project description:This study sought to determine the dynamic changes of miRNA expression during mouse granulopoiesis. We not only performed analyses of miRNA expression levels in whole cells but also analyzed purified nuclear and cytoplasmic cell fractions to profile miRNA subcellular localization. qRT-PCR analysis of miRNAs was performed on whole cell, nuclear and cytoplasmic RNAs extracted from mouse hemopoietic stem cells (LSKs), promyelocytes, myelocytes and granulocytes. 100 ng of RNA was reversed transcribed using the Taqman miRNA Reverse Transcription Kit and Megaplex RT Primers rodent pool A and B (Life Technologies). Complementary DNA (cDNA) was amplified using a TaqMan rodent microRNA A and B Array v2.0 (Life Technologies) with TaqMan Universal PCR Master Mix on an ABI 7900HT Sequence Detection System.

2014-05-14 | E-GEOD-57623 | biostudies-arrayexpress

Identification of post-transcriptional regulatory networks during myeloblast-to-monocyte differentiation transition

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-07-01 | E-GEOD-67838 | biostudies-arrayexpress

A robust and universal metaproteomics workflow for research studies and routine diagnostics within 24 hours

Project description:A new workflow for metaproteomics is presented in this study and is shown to enable the analysis of a broad range of different samples in only 24 h. The standardized sample preparation includes the combined cell lysis and phenol extraction in a ball mill followed by FASP digestion. The bioinformatic workflow using the MetaProteomeAnalyzer software was expanded with new functionalities such as annotation of metaproteins via protein BLAST or an integrated compare tool. The new workflow was shown to produce at least two times the protein identifications than previous iterations. Through many individual improvements combined into a single standardized workflow, a drastic increase in the quantity and quality of generated results was achieved.

2019-09-04 | PXD010550 | Pride

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