scholarly journals Erratum: Corrigendum: Large-scale identification of encystment-related proteins and genes in Pseudourostyla cristata

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Xiuxia Gao ◽  
Fenfen Chen ◽  
Tao Niu ◽  
Ruidan Qu ◽  
Jiwu Chen
Keyword(s):  
Large Scale ◽  
Related Proteins ◽  
Pseudourostyla Cristata

scholarly journals Large-scale identification of encystment-related proteins and genes in Pseudourostyla cristata

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Xiuxia Gao ◽  
Fenfen Chen ◽  
Tao Niu ◽  
Ruidan Qu ◽  
Jiwu Chen
Keyword(s):  
Molecular Mechanism ◽  
Vegetative Cell ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Qrt Pcr ◽  
Resting Cyst ◽  
Specific Proteins ◽  
Resting Cysts ◽  
Related Proteins ◽  
Pseudourostyla Cristata

Abstract The transformation of a ciliate into cyst is an advance strategy against an adverse situation. However, the molecular mechanism for the encystation of free-living ciliates is poorly understood. A large-scale identification of the encystment-related proteins and genes in ciliate would provide us with deeper insights into the molecular mechanisms for the encystations of ciliate. We identified the encystment-related proteins and genes in Pseudourostyla cristata with shotgun LC-MS/MS and scale qRT-PCR, respectively, in this report. A total of 668 proteins were detected in the resting cysts, 102 of these proteins were high credible proteins, whereas 88 high credible proteins of the 724 total proteins were found in the vegetative cells. Compared with the vegetative cell, 6 specific proteins were found in the resting cyst. However, the majority of high credible proteins in the resting cyst and the vegetative cell were co-expressed. We compared 47 genes of the co-expressed proteins with known functions in both the cyst and the vegetative cell using scale qRT-PCR. Twenty-seven of 47 genes were differentially expressed in the cyst compared with the vegetative cell. In our identifications, many uncharacterized proteins were also found. These results will help reveal the molecular mechanism for the formation of cyst in ciliates.

scholarly journals Large-scale proteomic analysis of the grapevine leaf apoplastic fluid reveals mainly stress-related proteins and cell wall modifying enzymes

2013 ◽  
Vol 13 (1) ◽  
pp. 24 ◽  
Author(s):  
Bertrand Delaunois ◽  
Thomas Colby ◽  
Nicolas Belloy ◽  
Alexandra Conreux ◽  
Anne Harzen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Proteomic Analysis ◽  
Large Scale ◽  
Apoplastic Fluid ◽  
Related Proteins

scholarly journals The Prognostic Value of Autophagy-Related Markers Bclin-1 and LC-3 in Colorectal Cancers: A Systematic Review and Meta-analysis

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Jin-xiao Li ◽  
Qian Yan ◽  
Na Liu ◽  
Wen-jiang Zheng ◽  
Man Hu ◽  
...  
Keyword(s):  
Large Scale ◽  
Meta Analysis ◽  
Prognostic Significance ◽  
Beclin 1 ◽  
Cochrane Library ◽  
Comprehensive Treatment ◽  
Newcastle Ottawa Scale ◽  
Related Proteins ◽  
The Relationship

Objective. At present, the relationship between autophagosomes and the prognosis of various cancers has become a subject of active investigation. A series of studies have demonstrated the correlation between autophagy microtubule-associated protein light chain 3 (LC-3), Beclin-1, and colorectal cancer (CRC). Since autophagy has dual regulatory roles in tumors, the results of this correlation are also uncertain. Hence, we summarized the relationship between Beclin-1, LC-3, and CRC using systematic reviews and meta-analysis to clarify their prognostic significance in it. Methods. PubMed, EMBASE, Cochrane Library, and Web of Science databases were searched online up to April 1, 2019. The quality of the involving studies was assessed against the Newcastle-Ottawa Scale (NOS). Pooled hazard ratio (HR) and 95% confidence interval (CI) in a fixed or random effects model were used to assess the strength of correlation between Beclin-1, LC-3, and CRC. Results. A total of 9 articles were collected, involving 2,297 patients. Most literatures scored more than 6 points, suggesting that the quality of our including research was acceptable. Our finding suggested that the expression of Beclin-1 was not associated with overall survival (HR = 0.68, 95% CI (0.31–1.52), P=0.351). Nonetheless, LC-3 expression exerted significant impact on OS (HR = 0.51, 95% CI (0.35–0.74), P<0.05). Subgroup analysis exhibited that Beclin-1 expression was associated with OS at TNM stage III (HR = 0.04, 95% CI = 0.02–0.08, P<0.05), surgical treatment (HR = 1.53, 95% CI (1.15–2.02), P=0.003), and comprehensive treatment (HR = 0.27 95% CI (0.08–0.92), P=0.036), respectively. Similarly, the results showed the increased LC-3 expression in CRC was related to OS in multivariate analyses (HR = 0.44, 95% CI (0.34–0.57), P<0.05), stages (HR = 0.51, 95% CI (0.35–0.74), P<0.05), and comprehensive treatment (HR = 0.44, 95% CI (0.34–0.57), P<0.05). Conclusions. Autophagy-related proteins of LC-3 might be an important marker of CRC progression. However, since the number of the original studies was limited, more well-designed, large-scale, high-quality studies are warranted to provide more convincing and reliable information.

scholarly journals The Full-Length Protein Encoded by Human Cytomegalovirus Gene UL117 Is Required for the Proper Maturation of Viral Replication Compartments

2008 ◽  
Vol 82 (7) ◽  
pp. 3452-3465 ◽  
Author(s):  
Zhikang Qian ◽  
Baoqin Xuan ◽  
Te Tee Hong ◽  
Dong Yu
Keyword(s):  
Human Cytomegalovirus ◽  
Large Scale ◽  
Full Length ◽  
Wild Type ◽  
Virus Growth ◽  
Reading Frame ◽  
Early Proteins ◽  
Immediate Early Proteins ◽  
Novel Transcripts ◽  
Related Proteins

ABSTRACT Previously, two large-scale mutagenic analyses showed that mutations in the human cytomegalovirus (HCMV) gene UL117 resulted in a defect in virus growth in fibroblasts. Early transcriptional analyses have revealed several mRNAs from the UL119-UL115 region; however, specific transcripts encoding UL117-related proteins have not been identified. In this study, we identified two novel transcripts arising from the UL117 gene locus, and we reported that the UL117 open reading frame encoded the full-length protein pUL117 (45 kDa) and the shorter isoform pUL117.5 (35 kDa) as the result of translation initiation at alternative in-frame ATGs. Both proteins were expressed with early kinetics, but pUL117 accumulated at a lower abundance relative to that of pUL117.5. During HCMV infection, both proteins localized predominantly to the nucleus, and the major fraction of pUL117 localized in viral nuclear replication compartments. We constructed mutant HCMV viruses in which the entire UL117 coding sequence was deleted or the expression of pUL117 was specifically abrogated. The growth of mutant viruses was significantly attenuated, indicating that pUL117 was required for efficient virus infection in fibroblasts. Cells infected with the pUL117-deficient mutant virus accumulated representative viral immediate-early proteins and early proteins normally. In the absence of pUL117, the accumulation of replicating viral DNA was reduced by no more than twofold at early times and was indistinguishable from that of the wild type at 72 h postinfection. Strikingly, there was a 12- to 24-h delay in the development of nuclear replication compartments and a marked delay in the expression of late viral proteins. We conclude that pUL117 acts to promote the development of nuclear replication compartments to facilitate viral growth.

scholarly journals Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes

2016 ◽  
Author(s):  
Morgan N. Price ◽  
Kelly M. Wetmore ◽  
R. Jordan Waters ◽  
Mark Callaghan ◽  
Jayashree Ray ◽  
...  
Keyword(s):  
Protein Function ◽  
Large Scale ◽  
Hypothetical Proteins ◽  
Data Set ◽  
Protein Coding ◽  
Bacterial Proteins ◽  
Genome Wide ◽  
Protein Functions ◽  
Mutant Phenotypes ◽  
Related Proteins

SummaryThe function of nearly half of all protein-coding genes identified in bacterial genomes remains unknown. To systematically explore the functions of these proteins, we generated saturated transposon mutant libraries from 25 diverse bacteria and we assayed mutant phenotypes across hundreds of distinct conditions. From 3,903 genome-wide mutant fitness assays, we obtained 14.9 million gene phenotype measurements and we identified a mutant phenotype for 8,487 proteins with previously unknown functions. The majority of these hypothetical proteins (57%) had phenotypes that were either specific to a few conditions or were similar to that of another gene, thus enabling us to make informed predictions of protein function. For 1,914 of these hypothetical proteins, the functional associations are conserved across related proteins from different bacteria, which confirms that these associations are genuine. This comprehensive catalogue of experimentally-annotated protein functions also enables the targeted exploration of specific biological processes. For example, sensitivity to a DNA-damaging agent revealed 28 known families of DNA repair proteins and 11 putative novel families. Across all sequenced bacteria, 14% of proteins that lack detailed annotations have an ortholog with a functional association in our data set. Our study demonstrates the utility and scalability of high-throughput genetics for large-scale annotation of bacterial proteins and provides a vast compendium of experimentally-determined protein functions across diverse bacteria.

scholarly journals Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

2020 ◽  
Vol 117 (13) ◽  
pp. 7208-7215 ◽  
Author(s):  
Kathy Y. Wei ◽  
Danai Moschidi ◽  
Matthew J. Bick ◽  
Santrupti Nerli ◽  
Andrew C. McShan ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Conformational Transition ◽  
Protein Structures ◽  
Computational Design ◽  
Spectroscopic Characterization ◽  
De Novo Design ◽  
Viral Fusion ◽  
Naturally Occurring ◽  
Related Proteins

The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320–327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol. 13, 1280–1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149–21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations—one short (∼66 Å height) and the other long (∼100 Å height)—reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.

Characterisation of protein structure/function relationship by sequence analysis without previous alignment: Distinction between sub-groups of protein kinases

1995 ◽  
Vol 15 (3) ◽  
pp. 161-171 ◽  
Author(s):  
Marie-Anne Guerrucci ◽  
Robert Bellé
Keyword(s):  
Structure Function ◽  
Protein Kinases ◽  
Tyrosine Kinases ◽  
Large Scale ◽  
Data Bank ◽  
Structure Function Relationship ◽  
Protein Functions ◽  
Function Relationship ◽  
Related Proteins ◽  
Relationship Of

Using an approach for protein comparison by computer analysis based on signal treatment methods without previous alignment of the sequence, we have analysed the structure/function relationship of related proteins. The aim was to demonstrate that from a few members of related proteins, specific parameters can be obtained and used for the characterisation of newly sequenced proteins obtained by molecular biology techniques. The analysis was performed on protein kinases, which comprise the largest known family of proteins, and therefore allows valid estimations to be made. We show that using only a dozen defined proteins, the specific parameters extracted from their sequences classified the protein kinase family into two sub-groups: the protein serine/threonine kinases (PSKs) and the protein tyrosine kinases (PTKs). The analysis, largely involving computation, appears applicable to large scale data-bank analysis and prediction of protein functions.

scholarly journals Mycobacterium tuberculosisFunctional Network Analysis by Global Subcellular Protein Profiling

2005 ◽  
Vol 16 (1) ◽  
pp. 396-404 ◽  
Author(s):  
Kwasi G. Mawuenyega ◽  
Christian V. Forst ◽  
Karen M. Dobos ◽  
John T. Belisle ◽  
Jin Chen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Large Scale ◽  
Organizational Structures ◽  
Protein Profiling ◽  
Gene Products ◽  
Proteomics Data ◽  
Systematic Analysis ◽  
Its Gene ◽  
Proteome Profile ◽  
Related Proteins

Trends in increased tuberculosis infection and a fatality rate of ∼23% have necessitated the search for alternative biomarkers using newly developed postgenomic approaches. Here we provide a systematic analysis of Mycobacterium tuberculosis (Mtb) by directly profiling its gene products. This analysis combines high-throughput proteomics and computational approaches to elucidate the globally expressed complements of the three subcellular compartments (the cell wall, membrane, and cytosol) of Mtb. We report the identifications of 1044 proteins and their corresponding localizations in these compartments. Genome-based computational and metabolic pathways analyses were performed and integrated with proteomics data to reconstruct response networks. From the reconstructed response networks for fatty acid degradation and lipid biosynthesis pathways in Mtb, we identified proteins whose involvements in these pathways were not previously suspected. Furthermore, the subcellular localizations of these expressed proteins provide interesting insights into the compartmentalization of these pathways, which appear to traverse from cell wall to cytoplasm. Results of this large-scale subcellular proteome profile of Mtb have confirmed and validated the computational network hypothesis that functionally related proteins work together in larger organizational structures.

scholarly journals Glycolysis stimulation and storage protein accumulation are hallmarks of maize (Zea mays L.) grain filling

2020 ◽  
Vol 63 (1) ◽  
Author(s):  
Jung-Tae Kim ◽  
Gibum Yi ◽  
Mi-Jung Kim ◽  
Beom-Young Son ◽  
Hwan-Hee Bae ◽  
...  
Keyword(s):  
Zea Mays ◽  
Carbohydrate Metabolism ◽  
Large Scale ◽  
Storage Proteins ◽  
Caloric Intake ◽  
Grain Filling ◽  
Protein Accumulation ◽  
Proteome Changes ◽  
Related Proteins ◽  
And Storage

Abstract Maize (Zea mays L.) is a major dietary source of human caloric intake. Grain filling, the developmental stage of the seed during which starch and proteins accumulate, is of great interest in plant biology and agronomy. However, proteomic datasets covering maize seed development, especially during grain filling, are much scarcer than transcriptomic datasets, largely due to the labor-intensive and costly nature of the large-scale analysis required for proteomics. Here, we searched for proteins that showed changes in abundance during four time-points covering the middle stages of grain filling by two-dimensional electrophoresis, MALDI-TOF, and database searches. We detected 1384 protein spots, of which 48 exhibited differential accumulation during grain filling. Of those, we identified the underlying protein for 32 spots: they included enzymes of carbohydrate metabolism, stress-related proteins, and storage proteins, the latter of which represented 34% of all changing proteins during grain filling. Proteins related to carbohydrate metabolism reached their maximum accumulation around 15–20 days after pollination (DAP) and subsequently dropped until 30 DAP. The rise of stress-related proteins such as heat shock proteins demonstrated their involvement in grain filling and seed maturation. This study catalogues the proteome changes during grain filling and provides basic but critical information regarding the biological changes during maize kernel development.

TUNING THE PRECISION OF PREDICTORS TO REDUCE OVERESTIMATION OF PROTEIN DISORDER OVER LARGE DATASETS

2013 ◽  
Vol 11 (02) ◽  
pp. 1250023 ◽  
Author(s):  
ANTONIO DEIANA ◽  
ANDREA GIANSANTI
Keyword(s):  
Large Scale ◽  
Simple Procedure ◽  
A Priori ◽  
Disordered Proteins ◽  
Protein Disorder ◽  
The Past ◽  
Quantitative Estimates ◽  
Genome Wide ◽  
Human Proteins ◽  
Related Proteins

This is a study on the precision of four known protein disorder predictors, ranked among the best-performing ones: DISOPRED2, PONDR VSL2B, IUPred and ESpritz. We address here the problem of a systematic overestimation of the number of disordered proteins recognized through the use of these predictors, considered as a standard. Some of these predictors, used with their default setting, have a low precision, implying a tendency to overestimate the occurrence of disordered proteins in genome-wide surveys. Moreover, different predictors often disagree on the evaluation of individual proteins. To cope with this problem and in order to propose a simple procedure that enhances precision based on precision-recall curves, we re-tuned the discriminative thresholds of the predictors by training and cross-validating their performance on a cured dataset. After re-tuning, both the disagreement among predictors and the tendency to overestimate the occurrence of disordered proteins are reduced. This is shown in a dedicated study over the human proteome and a set of cancer-related human proteins, with no a priori disorder annotation. Simple quantitative estimates suggest that the occurrence of disorder among cancer-related proteins and other similar large-scale surveys has been overestimated in the past.

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