Abstract：
:Although the legume-rhizobium symbiosis is a most-important biological process, there is a limited knowledge about the protein interaction network between host and symbiont. Using interolog- and domain-based approaches, we constructed an interspecies protein interactome containing 5115 protein-protein interactions between 2291 Glycine max and 290 Bradyrhizobium diazoefficiens USDA 110 proteins. The interactome was further validated by the expression pattern analysis in nodules, gene ontology term semantic similarity, co-expression analysis, and luciferase complementation image assay. In the G. max-B. diazoefficiens interactome, bacterial proteins are mainly ion channel and transporters of carbohydrates and cations, while G. max proteins are mainly involved in the processes of metabolism, signal transduction, and transport. We also identified the top 10 highly interacting proteins (hubs) for each species. Kyoto Encyclopedia of Genes and Genomes pathway analysis for each hub showed that a pair of 14-3-3 proteins (SGF14g and SGF14k) and 5 heat shock proteins in G. max are possibly involved in symbiosis, and 10 hubs in B. diazoefficiens may be important symbiotic effectors. Subnetwork analysis showed that 18 symbiosis-related soluble N-ethylmaleimide sensitive factor attachment protein receptor proteins may play roles in regulating bacterial ion channels, and SGF14g and SGF14k possibly regulate the rhizobium dicarboxylate transport protein DctA. The predicted interactome provide a valuable basis for understanding the molecular mechanism of nodulation in soybean.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Zhang L,Liu JY,Gu H,Du Y,Zuo JF,Zhang Z,Zhang M,Li P,Dunwell JM,Cao Y,Zhang Z,Zhang YMdoi
10.1021/acs.jproteome.8b00209subject
Has Abstractpub_date
2018-09-07 00:00:00pages
3061-3074issue
9eissn
1535-3893issn
1535-3907journal_volume
17pub_type
杂志文章abstract：:Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, resear...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00894
更新日期：2018-04-06 00:00:00
abstract：:The SEQUEST program was the first and remains one of the most widely used tools for assigning a peptide sequence within a database to a tandem mass spectrum. The cross correlation score is the primary score function implemented within SEQUEST and it is this score that makes the tool particularly sensitive. Unfortunate...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800420s
更新日期：2008-10-01 00:00:00
abstract：:Shotgun proteomics produces collections of tandem mass spectra that contain all the data needed to identify mutated peptides from clinical samples. Identifying these sequence variations, however, has not been feasible with conventional database search strategies, which require exact matches between observed and expect...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900850m
更新日期：2010-04-05 00:00:00
abstract：:Malignant processes such as metastasis, invasion, or angiogenesis are tightly dependent on the composition of the extracellular medium, which is itself affected by the release of proteins by the tumor cells. p53, a major tumor suppressor protein very frequently mutated and/or inactivated in cancer cells, is known to m...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900383g
更新日期：2009-10-01 00:00:00
abstract：:We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (meta...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00385
更新日期：2020-11-06 00:00:00
abstract：:Gastric cancer (GC) is among the most common cancers worldwide. Gastric carcinogenesis is a multistep and multifactorial process beginning with chronic gastritis induced by Helicobacter pylori (H. pylori) infection. This process is often described via a sequence of events known as Correas's cascade, a stepwise progres...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00281
更新日期：2016-08-05 00:00:00
abstract：:The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify "missing" proteins in the neXtProt knowledgebase. We present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using protein extraction procedures and LC-MS/MS analysis, we detected 235 protei...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00400
更新日期：2016-11-04 00:00:00
abstract：:Campylobacter jejuni, an important foodborne microorganism, poses severe and emergent threats to human health as antibiotic resistance becomes increasingly prevalent. The mechanisms of drug resistance are hard to decipher, and little is known at the metabolic level. Here we apply metabolomic profiling to discover meta...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501061d
更新日期：2015-02-06 00:00:00
abstract：:There are new challenges for hazard and risk assessment in the chemical industry with regard to REACH legislation in Europe and related activities in the U.S. and Japan, which require the development of novel in vitro models for the molecular characterization of drug- or chemical-related effects replacing conventional...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100514e
更新日期：2010-11-05 00:00:00
abstract：:Over the past few years, awareness has risen that for mass-spectrometry-based proteomics methods to mature into everyday analytical and clinical practices, extensive quality assessment is mandatory. A currently overlooked source of qualitative information originates from the mass spectrometer itself. Apart from the ac...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00127
更新日期：2015-05-01 00:00:00
abstract：:A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragm...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00184
更新日期：2015-06-05 00:00:00
abstract：:This study demonstrates a direct role of venom protein expression alteration in the evolution of snake venom toxicity. Avian skeletal muscle contractile response to exogenously administered acetylcholine is completely inhibited upon exposure to South Australian and largely preserved following exposure to Queensland ea...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00764
更新日期：2015-11-06 00:00:00
abstract：:We compared the metabolomic profile of aqueous humor from patients with primary open-angle glaucoma (POAG; n = 26) with that of a group of age- and sex-matched non-POAG controls (n = 26), all participants undergoing cataract surgery. Supervised paired partial least-squares discriminant analysis showed good predictive ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00915
更新日期：2019-03-01 00:00:00
abstract：:Blood is an ideal window for viewing our health and disease status. Because blood circulates throughout the entire body and carries secreted, shed, and excreted signature proteins from every organ and tissue type, it is thus possible to use the blood proteome to achieve a comprehensive assessment of multiple-organ phy...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301178a
更新日期：2013-05-03 00:00:00
abstract：:Influenza viruses continue evolving and have the ability to cause a global pandemic, so it is very important to elucidate its pathogenesis and find new treatment methods. In recent years, proteomics has made important contributions to describing the dynamic interaction between influenza viruses and their hosts, especi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00778
更新日期：2021-01-01 00:00:00
abstract：:Outbreaks of porcine epidemic diarrhea virus (PEDV) have caused significant lethality rates in neonatal piglets, which pose a serious threat to the swine industry worldwide. Available commercial vaccines fail to protect against the emergence of high virulence of PEDV variants. Therefore, the endemic state of the PEDV ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00897
更新日期：2019-04-05 00:00:00
abstract：:The protein kinase AKT is a central kinase in the heart and has a major impact on growth/hypertrophy, survival/apoptosis, and metabolism. To gain more insight into AKT isoform-specific signaling at the molecular level, we investigated the phosphoproteome of HL-1 cardiomyocytes carrying AKT1 or AKT2 isoform-specific kn...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500131g
更新日期：2014-10-03 00:00:00
abstract：:Neuroblastoma (NB) is an infant tumor which frequently differentiates into neurons. We used two-dimensional differential in-gel electrophoresis (2D-DIGE) to analyze the cytosolic and nuclear protein expression patterns of LAN-5 cells following neuronal differentiating agent all-trans-retinoic acid treatment. We identi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060701g
更新日期：2007-07-01 00:00:00
abstract：:Numerous reports have predicted/hypothesized a role for probenazole-induced protein (PBZ1) as a molecular marker in rice self-defense mechanism. However, the precise function of PBZ1 remains unknown. In the present study, we examined PBZ1 as a putative cell death marker in rice. For this, we focused our attention on a...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr700878t
更新日期：2008-04-01 00:00:00
abstract：:The Mycobacterium tuberculosis membrane is rich in antigens that are potential targets for diagnostics and the development of new vaccines. To better understand the mechanisms underlying MTB virulence and identify new targets for therapeutic intervention, we investigated the differential composition of membrane proteo...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400334k
更新日期：2013-12-06 00:00:00
abstract：:Nicotinamide adenine dinucleotide (NAD) is a coenzyme found in all living cells and mediates multiple cellular signaling pathways. In the present study, a 35% decrease of cellular NAD level is achieved by stable expression of the N-terminal truncated CD38, a NAD hydrolase. CD38-expressing (CD38(+)) cells have the lowe...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4010597
更新日期：2014-02-07 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301039b
更新日期：2013-05-03 00:00:00
abstract：:Hypoxia inducible factor (HIF)-2α protein expression in solid tumors promotes stem-like phenotype in cancer stem cells and increases tumorigenic potential in nonstem cancer cells. Recently, we have shown that HIF-1/2α gene expression is correlated to neuroblastoma (NB) poor survival and to undifferentiated tumor state...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00457
更新日期：2016-10-07 00:00:00
abstract：:The Halobacterium salinarum gas vesicle (GV) is an extremely stable intracellular organelle with air trapped inside a proteinaceous membrane. Reported here is a comparative proteomics analysis of GV and GV depleted lysate (GVD) to reveal the membrane structural proteins. Ten proteins encoded by gvp-1 (gvpMLKJIHGFED-1 ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1009383
更新日期：2011-03-04 00:00:00
abstract：:Nanobacteria may cause peripheral neuropathy by adhesion to the perineurium. This hypothesis receives support from five independent observations: (1) identification of perineurial apatite in diabetic patients with peripheral neuropathy, (2) massive presence of nanobacteria in a diabetic patient, (3) beneficial effect ...
journal_title：Journal of proteome research
pub_type： 信件
doi：10.1021/pr049935v
更新日期：2004-09-01 00:00:00
abstract：:Nasopharyngeal carcinoma (NPC) is one of the most common malignant tumors in Southeast Asia. Unfortunately, most NPC victims have had metastasis when first diagnosed due to its deep location and vague symptoms. To date, discovery of sensitive and specific biomarkers for improving detection of NPC remains a challenge. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900454e
更新日期：2009-12-01 00:00:00
abstract：:Tandem mass spectrometry (MS/MS) combined with bioinformatics tools have enabled fast and systematic protein identification based on peptide-to-spectrum matches. However, it remains challenging to obtain accurate identification of endogenous peptides, such as neuropeptides, peptide hormones, peptide pheromones, venom ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400446z
更新日期：2013-12-06 00:00:00
abstract：:Histone post-translational modifications (PTMs) are fundamental players of chromatin regulation, as they contribute to editing histone chemical properties and recruiting proteins for gene transcription and DNA repair. Mass spectrometry (MS)-based proteomics is currently the most widely adopted strategy for high-throug...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00544
更新日期：2018-01-05 00:00:00
abstract：:Proteomics has been applied to study intracellular bacteria and phagocytic vacuoles in different host cell lines, especially macrophages (Mφs). For mycobacterial phagosomes, few studies have identified over several hundred proteins for systems assessment of the phagosome maturation and antigen presentation pathways. M...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101245u
更新日期：2011-05-06 00:00:00
abstract：:An important mechanism by which plants defend themselves against pathogens is the rapid execution of a hypersensitive response (HR). Tomato plants containing the Cf-4 resistance gene mount an HR that relies on the activation of phosphorylation cascades, when challenged with the Avr4 elicitor secreted by the pathogenic...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800619h
更新日期：2009-03-01 00:00:00
