Abstract：
:Geobacillus thermodenitrificans NG80-2 is a crude oil-degrading thermophilic bacterium isolated from an oil reservoir in China. In this study, the gene clusters and pathways for the degradation of benzoate (via benzoyl-CoA), phenylacetate (via phenylacetyl-CoA), 4-hydroxyphenylacetate (via 3,4-dihydroxyphenylacetate) and anthranilate (via 3-hydroxyanthranilate) were confirmed using combined in silico analysis and proteomics approaches. It was observed that synthesis of the enzymes catalyzing initial activation, ring oxidation and ring cleavage reactions were generally induced specifically by their respective substrates, while many of the enzymes catalyzing downstream reactions exhibited broader substrate specificities. Novel genes encoding benzoyl-CoA epoxidase and 3,4-dihydroxyphenylacetate 2,3-dioxygenase, and a paaX homologue that serves as a positive regulator of benzoate degradation were proposed. Downregulation of the glycolysis pathway, along with upregulation of the gluconeogenesis pathway and the glyoxylate bypass (phenylacetate) were detected in association with the utilization of the aromatics. This novel proteomics approach confirmed the presence of multiple metabolic pathways for aromatic compounds in NG80-2, which is highly advantageous to the survival of this thermophilic bacterium under reservoir conditions.
journal_name
J Proteomicsjournal_title
Journal of proteomicsauthors
Li Y,Wu J,Wang W,Ding P,Feng Ldoi
10.1016/j.jprot.2011.10.035subject
Has Abstractpub_date
2012-02-02 00:00:00pages
1201-10issue
4eissn
1874-3919issn
1876-7737pii
S1874-3919(11)00545-8journal_volume
75pub_type
杂志文章abstract：:Deciphering Plasmodium vivax biology has long been a challenge for groups working on this parasite, mainly due to the complications involved in propagating it in vitro. However, adapting P. vivax strains in non-human primates and the arrival of high-performance analysis methods has led to increased knowledge regarding...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2020.103719
更新日期：2020-04-30 00:00:00
abstract：:The application of proteomics to respiratory diseases, such as asthma and COPD, has been limited compared to other fields, like cancer. Both asthma and COPD are recognised to be multi-factorial and complex diseases, both consisting of clusters of multiple disease phenotypes. The complexity of these diseases combined w...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2011.10.008
更新日期：2011-12-10 00:00:00
abstract：UNLABELLED:Brevibacterium linens DSM 20158 is an industrially important actinobacterium which is well-known for the production of amino acids and enzymes. However, as this strain has an unsequenced genome, there is no detailed information regarding its proteome although another strain of this microbe, BL2, has a shotgu...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2013.02.029
更新日期：2013-05-27 00:00:00
abstract：:A large-scale proteomic approach was devised to advance the understanding of venom composition. Bothrops jararaca venom was fractionated by OFFGEL followed by chromatography, generating peptidic and proteic fractions. The latter was submitted to trypsin digestion. Both fractions were separately analyzed by reversed-ph...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.06.029
更新日期：2017-01-16 00:00:00
abstract：:Salinity is one of the major environmental constraints limiting yield of crop plants in many semi-arid and arid regions around the world. To understand responses in soybean seedling to salt stress at proteomic level, the extracted proteins from seedling leaves of salt-sensitive genotype Jackson and salt-tolerant genot...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.11.026
更新日期：2012-02-16 00:00:00
abstract：:Prediabetes is a risk factor for the development of diabetes. Early diagnosis of prediabetes may prevent the onset and progression of diabetes and its associated complications. Therefore, this study aimed at the identification of novel markers for efficient prediction of prediabetes. In this pursuit, we have evaluated...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103481
更新日期：2019-09-30 00:00:00
abstract：UNLABELLED:Mitral regurgitation (MR) is a common valvular lesion frequently caused by mitral valve prolapse (MVP). Surgical intervention in MVP patients with significant MR is predicated on symptoms and measures of left ventricular dysfunction. Because these indicators may be subjective or imprecise, serological biomar...
journal_title：Journal of proteomics
pub_type： 临床试验,杂志文章
doi：10.1016/j.jprot.2013.10.009
更新日期：2013-12-06 00:00:00
abstract：:Reactive nitrogen species are formed during a variety of disease states and have been shown to modify several amino acids on proteins. To date, the majority of research in this area has focused on the nitration of tyrosine residues to form 3-nitrotyrosine. However, emerging evidence suggests that another modification,...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2011.05.032
更新日期：2011-10-19 00:00:00
abstract：:Flooding negatively affects the growth of soybean, whereas the plant-derived smoke enhances seedling growth of crops. To clarify the mechanism underlying the recovery from flooding stress, proteomic analysis was performed based on morphological results. Growth of soybean seedlings was inhibited under flooding stress, ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.04.031
更新日期：2018-06-15 00:00:00
abstract：:Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2017.04.019
更新日期：2018-03-20 00:00:00
abstract：:Much attention has been paid to the broodiness of the Muscovy duck, but the molecular mechanism of broodiness remains largely unknown. In this study, the ovary tissues of Muscovy ducks during the broody and laying periods were used to investigate differentially expressed proteins (DEPs) by the iTRAQ-based proteomics a...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103401
更新日期：2019-07-30 00:00:00
abstract：:Combinatorial peptide ligand libraries (CPLLs) have been adopted for harvesting and identifying traces of casein (used as a fining agent) present in white wines. Although minute amounts (200 microL) of CPLL beads are added to the entire content of a wine bottle (750 mL), they are able to sequester with high efficiency...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2010.05.010
更新日期：2010-08-05 00:00:00
abstract：:Spontaneous isoaspartyl formation from aspartyl dehydration or asparaginyl deamidation is a major source of modifications in protein structures. In cells, these conformational changes could be reverted by the protein L-isoaspartyl methyltransferase (PIMT) repair enzyme that converts the isoaspartyl residues into aspar...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2011.04.026
更新日期：2011-08-12 00:00:00
abstract：:Sheep have a variable ability to resist gastrointestinal nematode infection, but the key factors mediating this response are poorly defined. Here we report the first large-scale application of quantitative proteomic technologies to define proteins that are differentially abundant between sheep selectively bred to have...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.01.016
更新日期：2012-04-03 00:00:00
abstract：UNLABELLED:Dietary fiber/starch imbalance can lead to diarrhea in rabbits. However, the underlying molecular mechanisms are largely unknown, and this is the first study on the proteome profile of the cecal tissue of diarrheic rabbits. In this study, one group of weanling rabbits was fed a high fiber/starch diet (contro...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.03.019
更新日期：2014-05-30 00:00:00
abstract：:Royal jelly (RJ) is a secretory protein from the hypopharyngeal glands of nurse honeybee workers, which contains a variety of proteins of which major royal jelly proteins (MRJPs) are some of the most important. It plays important roles both for honeybee and human. Each family of MRJP 1-5 displays a string of modified ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.06.008
更新日期：2012-09-18 00:00:00
abstract：:There is a wide range of pathological conditions proved to be associated with inflammation. The inflammatory process offers protection against harmful stimuli such as induced cell injury and tissues damage by means of specialized mediators and cells. Alarmins, also known as endogenous danger signals or damage-associat...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2016.11.006
更新日期：2017-02-05 00:00:00
abstract：:FGF8 specifies early tooth development by directing the migration of the early tooth founder cells to the site of tooth emergence. To date the effect of the FGF8 in adult dental pulp has not been studied. We have assessed the regenerative potential of FGF8 by evaluating changes in the proteome landscape of dental pulp...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.05.004
更新日期：2018-07-15 00:00:00
abstract：UNLABELLED:The venom proteome of the Malayan blue coral snake, Calliophis bivirgata flaviceps from west Malaysia was investigated by 1D-SDS-PAGE and shotgun-LCMS/MS. A total of 23 proteins belonging to 11 protein families were detected from the venom proteome. For the toxin proteins, the venom consists mainly of phosph...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.11.014
更新日期：2016-01-30 00:00:00
abstract：UNLABELLED:The sea cucumber Apostichopus japonicus is becoming an excellent model marine invertebrate for studies of environmentally-induced aestivation. Reversible protein phosphorylation as a regulatory mechanism in aestivation is known for some terrestrial aestivators but has never before been documented in sea cucu...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.09.016
更新日期：2016-03-01 00:00:00
abstract：:The development of type 2 diabetes (T2D) is strongly associated with obesity. In humans, T2D increases the risk for end organ complications. Among these, heart disease has been ranked as the leading cause of death. We used a proteomic methodology to test the hypothesis that a pre-diabetic state generated by high-fat d...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.02.018
更新日期：2011-05-01 00:00:00
abstract：UNLABELLED:The composition and toxicological profile of the venom of the rattlesnake Crotalus simus in Mexico was analyzed at the subspecies and individual levels. Venoms of the subspecies C. s. simus, C. s. culminatus and C. s. tzabcan greatly differ in the expression of the heterodimeric neurotoxin complex 'crotoxin'...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2013.05.024
更新日期：2013-07-11 00:00:00
abstract：:Spectral similarity calculation is widely used in protein identification tools and mass spectra clustering algorithms while comparing theoretical or experimental spectra. The performance of the spectral similarity calculation plays an important role in these tools and algorithms especially in the analysis of large-sca...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.104070
更新日期：2021-02-10 00:00:00
abstract：:Proteomics is becoming more widely used as a tool in fish physiology and toxicology and can offer mechanistic insight into organism responses to environmental signals and stressors. Using a LTQ Orbitrap Velos MS/MS, we detected 1075 proteins in the reproductive testis of fathead minnow. Proteins localized to the testi...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.11.023
更新日期：2013-02-21 00:00:00
abstract：:Compared to radiation-sensitive bacteria, the nucleoids of radiation-resistant Deinococcus species show a higher degree of compaction. Such a condensed nucleoid may contribute to the extreme radiation resistance of Deinococcus by limiting dispersion of radiation-induced DNA fragments. Architectural proteins may play a...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.03.002
更新日期：2012-05-17 00:00:00
abstract：:No effective screening method is available for oral squamous cell carcinoma (OSCC) that is recognized to influence by environmental factors as well as human papillomavirus (HPV) and Epstein-Barr virus (EBV). Therefore, we sought to identify salivary biomarkers for screening of OSCC with or without HPV and/or EBV infec...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2017.11.022
更新日期：2018-02-20 00:00:00
abstract：:Deposition of calcium oxalate (CaOx) crystals in renal interstitium is one of the key factors that cause progressive inflammation in kidney stone disease. Macrophages are responsible for elimination of these crystals but their roles to worsen inflammatory process remain under-investigated. This study thus aimed to def...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.06.015
更新日期：2018-08-15 00:00:00
abstract：:Increased life expectancy and broader restorative dental treatment alternatives for missing teeth have resulted in an increasing request of bone regeneration/augmentation procedures not only in healthy patients, but also in elderly and medically compromised ones. This is also combined with a growing demand for short i...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2018.01.017
更新日期：2018-09-30 00:00:00
abstract：:Post-weaning multi-systemic wasting syndrome (PMWS), which is primarily caused by porcine circovirus type 2 (PCV2), is an emerging swine immunosuppressive disease. To characterize the interaction between target immune cells and PCV2, the differential proteomes of porcine alveolar macrophages, with and without PCV2 inf...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.03.039
更新日期：2012-06-18 00:00:00
abstract：:Quantitative proteomic comparisons require a sufficient number of samples to reach an acceptable level of significance. But 2D gel electrophoresis commonly results in incomplete data sets due to spots with missing values reducing thereby the number of parallel measurements for individual proteins. Here we investigated...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.12.019
更新日期：2012-03-16 00:00:00
