Dataset Information

Systematic Proteogenomic Approach To Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins.

ABSTRACT: One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to fill the knowledge gaps between human genomic information and the corresponding proteomic information. These gaps are due to "missing" proteins (MPs)-predicted proteins with insufficient evidence from mass spectrometry (MS), biochemical, structural, or antibody analyses-that currently account for 2579 of the 19587 predicted human proteins (neXtProt, 2017-01). We address some of the lessons learned from the inconsistent annotations of missing proteins in databases (DB) and demonstrate a systematic proteogenomic approach designed to explore a potential new function of a known protein. To illustrate a cautious and strategic approach for characterization of novel function in vitro and in vivo, we present the case of Na(+)/H(+) exchange regulatory cofactor 1 (NHERF1/SLC9A3R1, located at chromosome 17q25.1; hereafter NHERF1), which was mistakenly labeled as an MP in one DB (Global Proteome Machine Database; GPMDB, 2011-09 release) but was well known in another public DB and in the literature. As a first step, NHERF1 was determined by MS and immunoblotting for its molecular identity. We next investigated the potential new function of NHERF1 by carrying out the quantitative MS profiling of placental trophoblasts (PXD004723) and functional study of cytotrophoblast JEG-3 cells. We found that NHERF1 was associated with trophoblast differentiation and motility. To validate this newly found cellular function of NHERF1, we used the Caenorhabditis elegans mutant of nrfl-1 (a nematode ortholog of NHERF1), which exhibits a protruding vulva (Pvl) and egg-laying-defective phenotype, and performed genetic complementation work. The nrfl-1 mutant was almost fully rescued by the transfection of the recombinant transgenic construct that contained human NHERF1. These results suggest that NHERF1 could have a previously unknown function in pregnancy and in the development of human embryos. Our study outlines a stepwise experimental platform to explore new functions of ambiguously denoted candidate proteins and scrutinizes the mandated DB search for the selection of MPs to study in the future.

SUBMITTER: Na K

PROVIDER: S-EPMC6610236 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Systematic Proteogenomic Approach To Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins.

Na Keun K Shin Heon H Cho Jin-Young JY Jung Sang Hee SH Lim Jaeseung J Lim Jong-Sun JS Kim Eun Ah EA Kim Hye Sun HS Kang Ah Reum AR Kim Ji Hye JH Shin Jeong Min JM Jeong Seul-Ki SK Kim Chae-Yeon CY Park Jun Young JY Chung Hyung-Min HM Omenn Gilbert S GS Hancock William S WS Paik Young-Ki YK

Journal of proteome research 20171101 12

One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to fill the knowledge gaps between human genomic information and the corresponding proteomic information. These gaps are due to "missing" proteins (MPs)-predicted proteins with insufficient evidence from mass spectrometry (MS), biochemical, structural, or antibody analyses-that currently account for 2579 of the 19587 predicted human proteins (neXtProt, 2017-01). We address some of the lessons learned from the inco ...[more]

PMID: 28960081

Similar Datasets

Project description:In this work, we explored the intrinsic disorder status of the three members of the synuclein family of proteins-α-, β-, and γ-synucleins-and showed that although all three human synucleins are highly disordered, the highest levels of disorder are observed in γ-synuclein. Our analysis of the peculiarities of the amino acid sequences and modeled 3D structures of the human synuclein family members revealed that the pathological mutations A30P, E46K, H50Q, A53T, and A53E associated with the early onset of Parkinson's disease caused some increase in the local disorder propensity of human α-synuclein. A comparative sequence-based analysis of the synuclein proteins from various evolutionary distant species and evaluation of their levels of intrinsic disorder using a set of commonly used bioinformatics tools revealed that, irrespective of their origin, all members of the synuclein family analyzed in this study were predicted to be highly disordered proteins, indicating that their intrinsically disordered nature represents an evolutionary conserved and therefore functionally important feature. A detailed functional disorder analysis of the proteins in the interactomes of the human synuclein family members utilizing a set of commonly used disorder analysis tools showed that the human α-synuclein interactome has relatively higher levels of intrinsic disorder as compared with the interactomes of human β- and γ- synucleins and revealed that, relative to the β- and γ-synuclein interactomes, α-synuclein interactors are involved in a much broader spectrum of highly diversified functional pathways. Although proteins interacting with three human synucleins were characterized by highly diversified functionalities, this analysis also revealed that the interactors of three human synucleins were involved in three common functional pathways, such as the synaptic vesicle cycle, serotonergic synapse, and retrograde endocannabinoid signaling. Taken together, these observations highlight the critical importance of the intrinsic disorder of human synucleins and their interactors in various neuronal processes.

Project description:In the context of continuous cultural, social, and economic changes happening around the globe, the predictable patterns of the life course of the past observed over successive birth cohorts will not remain stable across generations. In this study, three reproductive role indicators-first sexual encounter, first marriage, and first birth-for three synthetic birth cohorts were used to identify and characterize the reproductive trajectories of youths. In our analysis, for the sake of comparison with global literature, we considered youths to be between ages 15 and 24. The analysis was conducted using data extracted from the 2005, 2011, and 2016 Ethiopian Demographic Health Survey for Oromia National Regional State. Three synthetic birth cohorts of youths of birth years between 1975 and 1989 were constructed for the analysis. A sequence analysis based on dynamic hamming distance with partition around medoids technique was employed to extract the typologies of reproductive trajectories of youths. In addition, discrepancy analysis and a sequence regression tree analysis were employed to characterize the identified typologies of trajectories. Data management was done using STATA 14 and all analyses were carried out using R software. The study identified four different typologies of reproductive trajectories among the youth. The sex of respondents was the primary discriminating factor of the typologies of reproductive trajectories. The findings support the notion of changing norms in reproductive behavior among the less educated youth irrespective of sex. The discriminating power of education was stronger for female youth in urban areas than rural females. It implies that the postponement of reproductive role assumption was stronger among educated female youths residing in urban than their rural counterparts. Normative reproductive practices such as early marriage and adolescent fertility are still common practices that require efforts of communities and local government bodies to ameliorate these practices. Results of the study indicate that less educated youth should be targeted in programs that aim at improving youth empowerment (i.e., training and employment opportunities) as well as their sexual and reproductive health.

Dataset Information

Systematic Proteogenomic Approach To Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins.

Publications

Systematic Proteogenomic Approach To Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets